Transitioning to clean cooking fuels is not only part of achieving SDG7, but also makes a significant contribution to mitigating climate change by reducing carbon emissions. The paper contradicts the conventional wisdom that electricity is too expensive to cook with. The paper explores the energy required to cook dishes using different technologies and fuels by analysing data from Cooking Diaries and Controlled Cooking tests conducted under the MECS programme. Electric pressure cookers (EPCs) use least energy when compared with electric hotplates, and a detailed description of how the EPC works explains why this should be. The paper draws out distinctions between African and Asian dishes, notably the impact of energy intensive dishes prepared mostly in Africa. Standard efficiency based approaches to comparing the performance of stoves are not appropriate to modern electric cooking devices so an alternative approach based on specific energy consumptions is proposed e.g. charcoal stoves use 15 times as much energy as EPCs to cook African dishes. Energy ratios provide a basis for estimating carbon emission reductions associated with transitioning to modern cooking fuels. Historical costs show that the cost of cooking with an EPC can be only 20% of the cost of cooking with charcoal, which highlights the potential for modern, energy efficient electric cooking devices to defy the conventional wisdom of the energy ladder.

Oxidative stress (OS) is reported in several chronic diseases. Extra-cellular superoxide dismutase (ec-SOD) catalyzes the dismutation of superoxide anion with a protective role on endothelial cells. In chronic kidney diseases (CKD), OS and thyroid dysfunction (low T3 syndrome) are fre-quently present, but their relationship has not been investigated. This cohort study evaluated ec-SOD activity in CKD patients during haemodialysis, divided into: “acute hemodialytic pa-tients” (AH, 1-3 months of treatment) and “chronic hemodialytic patients” (CH, treated for a longer period). We also evaluated plasmatic total antioxidant capacity (TAC) and the relation-ships with thyroid hormones. Two basal samples (“basal 1”, 3 days after the last dialysis and “basal 2”, 2 days after the last dialysis) were collected. On the same day of basal 2, a sample was collected 5 and 10 min after the standard heparin dose and at the end of the procedure. The ec-SOD values were significantly higher in CH vs AH in all determinations. Moreover, they pre-sented lower TAC values. Dividing CH patients into two subgroups according to fT3 levels (nor-mal or low) we found significantly lower ec-SOD values in the group with low fT3 at basal, 5 and 10 min samples. Finally, a significant correlation was observed between fT3 and ec-SOD in the basal 1 samples. These data, confirming OS and low T3 syndrome in CKD, suggest that low fT3 concentrations can influence ec-SOD activity and therefore contribute to possible endothelial oxi-dative damage in such a situation.

A reduced ability to work with information contained in a text is usually registered in low-achieving students. One important internal factor influencing reading comprehension concerns the child’s executive functioning. The current study investigated whether the domain-specific intervention ExeFun-READ targeting language abilities related to reading comprehension and executive functioning in primary school children would be effective in improving their scholastic performance in their reading domain and executive functioning. ExeFun-READ is designed to address the relations between domain-specific versus thinking-skill-oriented (domain-general) instruction. A child’s active learning is focused on semantic, phonetic, morphological and syntactical comprehension of linguistic material. In total, 151 students attending grade four from seven elementary schools took part in the project. The study concerned a pretest-intervention-posttest experimental design with three conditions: the experimental condition, an active, and a passive control group. To assess the children’s level of EF, the Delis–Kaplan Executive Function System test battery was used; to assess children’s language ability in reading domain, the Cognitive Abilities Test (the verbal battery, Thorndike & Hagan, 1986 [1]), was used. In the current study, the intervention led to improved language abilities related to reading comprehension, but in terms of executive functioning the improvement only extended to switching fluency. Regarding the effects of the ExeFun-READ intervention on children’s reading abilities, specified as language abilities related to reading comprehension, significant improvements were found in vocabulary, completion of sentences, and classification of terms in the group of children that received the ExeFun-READ intervention.

Methicillin-resistant Staphylococcus aureus (MRSA) constitutes a serious public health concern with a considerable impact on patients' health and substantial healthcare costs. In this study, patients, and healthcare workers (HCWs)from six public hospitals in Benin were screened for MRSA. Strains were identified as MRSA using conventional microbiological methods in Benin and confirmed using Matrix-Assisted Laser Desorption/Ionization Time of Flight (MALDI-TOF) mass spectrometry in Belgium. Whole genome sequencing (WGS) was used on confirmed MRSA isolates to characterize their genomic content and study their relatedness. In total,304 and 61 samples were collected from patients and HCWs, respectively. The mecA gene was detected in all isolates. The isolates were assigned to five sequence types (STs), with ST8 (55.6%, n=15), ST152 (18.52%, n=5), and ST121 (18.52%, n=5) being the most common. All isolates carried multiple virulence genes, including genes encoding the Panton-Valentine leukocidin toxin (48.15%, n=13) and the test gene (29.63%, n=8) associated with toxic shock syndrome. The presence of strains carrying numerous genomic features associated with antibiotic resistance and virulence in HCWs is a major public health concern. This study highlights the need to implement a multimodal strategy for reducing the risk of cross-transmission of MRSA in hospitals.

Climate change complies firms to introduce various measures to enhance both their competitiveness and sustainability, particularly energy efficiency measures (EEMs). Energy efficiency is particularly important in energy-intensive sectors such as the industrial sector. However, EEMs within the industrial firms are hindered by several internal barriers such as competing interests within firms, the lack of information regarding energy efficiency opportunities, and the low technical competence. In this regard, energy audit aims to improve energy efficiency in facilities and to tackle internal barriers to energy efficiency. We construct a model which aims to explore the importance of energy audit in implementing EEMs and reducing the intensity of internal barriers to energy efficiency. Our research model was empirically tested through survey data gathered from 193 industrial firms in Morocco. Results show that competing interests, the lack of information and the low technical competence hinder the adoption of EEMs within industrial firms. In addition, energy audits enhance EEMs, and mitigate the negative effect of the lack of information and the low technical competence on the adoption of EEMs. However, energy audits do not attenuate the negative effect of competing interests on EEMs. This study reinforces previous studies with additional confirmation regarding the importance of energy audits for tackling the lack of information, and the low technical competence within firms. Furthermore, our study extends prior research as we found that energy audits do not reduce the intensity of competing interests within firms regarding EMMs’ implementation.

Deep-Brain Stimulation (DBS) is a a highly effective and safe medical treatment that improves the lives of patients with a wide range of neurological and psychiatric deceases, and has been consolidated as a first-line tool in the treatment of these conditionsin the last two decades. Closed Loop Deep-Brain Stimulation (CLDBS) pushes this tool further by automatically adjusting the stimulation parameters to the brain response in real time. In this context, this paper presents a Low-Noise Amplifier (LNA) and a Neurostimulator circuits fabricated in the low-power/low-voltage 65 nm CMOS process from the TSMC, which were designed targeting implantable applications. To achieve the best trade-off between input-referred noise and power consuption, metaheuristic algorithms were employed to determine and optimizes the dimentions of the LNA devices during the design phase. The measurement results showed that the LNA had a gain of 40.6 dB, a 3 dB bandwidth spanning over three decades from 10 Hz to 8.6 kHz, and a power consumption of 6.19 uW. Simulations results indicated an input-referred noise of 4.86 uVrms for the LNA. The circuit of the Neurostimulator is a programmable Howland Current-Pump, whose measurements showed its ability to generate currents with arbitrary shapes ranging from between 325 uA to +318 uA. The simulations showed a quiescent power consumption of 0.13 W with a zero neurostimulation current. The LNA and the Neurostimulator circuits are supplied with 1.2 V voltage and occupy a microdevice area of 145 um x 311 um and 88 um x 89 um, respectively, making them suitable for implantation in applications involving Closed Loop Deep-Brain Stimulation.

Low-cost particulate matter (PM) sensors offer an excellent opportunity to improve our knowledge about this type of pollution. Their size and their cost, which support multi-node network deployment, along with their temporal resolution, enable them to report fine spatio-temporal resolution for a given area. These sensors have known issues across performance metrics. Generally, the literature focuses on the PM mass concentration reported by these sensors but some models of sensors also report particle number concentrations (PNC) segregated into different PM size bins. In this study, 8 units of each Alphasense OPC-R1, Plantower PMS5003 and Sensirion SPS30 have been exposed, under controlled conditions, to short-lived peaks of PM generated using two different combustion sources of PM, exposing the sensors to different particle size distributions to quantify and better understand the low cost sensors performance across a range of relevant environmental ranges. The PNC reported by the sensors were analysed. This study showed that there is added value in directly using the PNC reported by the sensors instead of the mass concentrations, which could aid the efforts to calibrate these sensors to a known accuracy. It demonstrated that all sensors tested here could track the fine temporal variation of PNC, that the Alphasense OPC-R1 could closely follow the variations of size distribution between the two sources of PM, and it showed that particle size distribution and composition are more impactful on the sensors measurement than relative humidity.

A low-resource emotional speech synthesis system for empathetic speech synthesis based on modelling prosody features is presented here. Secondary emotions, identified to be needed for empathetic speech, are modelled and synthesised in this paper. As secondary emotions are subtle in nature, they are difficult to model compared to primary emotions. They are also less explored, and this is one of the few studies that model secondary emotions in speech. Current speech synthesis research uses large databases and deep learning techniques to develop emotion models. There are many secondary emotions, and hence, developing large databases for each of the secondary emotions is expensive. This research presents a proof-of-concept using hand-crafted feature extraction and modelling of these features using a low resource-intensive machine learning approach, thus creating synthetic speech with secondary emotions. Here, a quantitative model-based transformation is used to shape the emotional speech fundamental frequency contour. Speech rate and mean intensity are modelled via rule-based approaches. Using these models, an emotional text-to-speech synthesis system to synthesise five secondary emotions - anxious, apologetic, confident, enthusiastic and worried is developed. A perception test to evaluate the synthesised emotional speech is also conducted.

The increasing regulatory pressure to monitor and reduce GHG emissions and air pollutants requires cost-effective methods for their surveillance. The most common technique used for scientific investigations on gas concentration monitoring in barns are accurate but expensive and with a complex maintenance. This research study analysed the potential use of a low-cost portable measurement devices for the measurement of ammonia (NH3) and carbon dioxide (CO2) concentrations in an open dairy barn. A comparison between gas concentrations acquired at different heights from the floor by using portable devices and those acquired by a photoacoustic infrared multigas spectroscope (i.e., reference measurement) in the same sampling locations was carried out to determine the precision of the low-cost portable devices. The performance of low-cost portable devices was statistically analysed by the application of the one-way analysis of variance, correlation analysis and regression analysis. The results showed a significant difference between gas concentration values at various heights from the floor for both NH3 and CO2. The correlations between concentrations acquired by the low-cost portable device and the INNOVA were statistically significant (r=0.83; P<0.001) for gas concentrations monitored at 0.4 m from the floor. Compared with the reference measurement device, the low-cost devices were effective in the monitoring of NH3 concentrations at 0.40 m from the floor though it underestimated them in the barn at increasing of the height from the floor, whereas the device was not adequate for CO2 concentrations. In detail, the relative measurement error of the low-cost devices compared to INNOVA was reduced close to the floor during NH3 concentration measurements. Within these limitations, this device could be useful for monitoring NH3 concentration in the barn and to assess variation in NH3 concentrations mainly related to the animal occupied zone. Further efforts are needed in this field of research to identify low-cost device that could simplify emission estimation from open dairy barns.

Introduction. Self-sampling has the potential to increase cervical cancer screening (CCS) among women living with HIV (WLWH) in low and middle-income countries (LMICs). However, our understanding of how HPV self-collection studies have been conducted in WLWH is limited. The purpose of this scoping review was to examine the extent to which the HPV self-sampling has been applied among WLWH in LMICs. Method: We conducted multiple searches in several databases for articles published between 2000 and January 2022. With the combination of keywords relating to HPV self-sampling, LMICs, and WLWH, we retrieved over 9,000 articles. We used pre-defined inclusion and exclusion criteria to select relevant studies for this review. Once a study met the inclusion criteria, we created a table to extract each study’s characteristics and classified them under common themes. We used a qualitative descriptive approach to summarize the scoping results. Results: A total of 12 articles were included in the final review. Overall, 3,178 women were enrolled in those studies and 2,105 (66%) of them were WLWH. The self-sampling participation rate was 92.6%. The findings of our study show that 43% of the WLWH in 8 of the studies reviewed tested positive for high-risk HPV (hr-HPV) genotypes, indicating 4 out of 10 WLWH in the studies are at risk of cervical cancer. The prevalence of the hr-HPV in WLWH was 18% higher than that of HIV-negative women. Most women in the study found the self-sampling experience acceptable, easy to use, convenient, and comfortable. Self-sampling performance in detecting hr HPV genotypes is comparable to clinician-performed sampling. However, limited access (i.e., affordability, availability, transportation), limited knowledge about self-screening, doubts about the credibility of self-sampling results, and stigma remain barriers to wide acceptance and implementation of self-sampling. In conclusion, the findings of this review highlight that (a) cervical cancer is a threat to every sexually active woman but for WLWH the threat increases, (b) self-sampling laboratory performance is similar to clinician performed sampling, (c) self-sampling is associated with an increase in cervical cancer screening uptake and (d) WLWH reported a positive experience with self-sampling. However, personal, environmental, and structural barriers challenge the application of self-sampling in LMICs, and these need to be addressed. Keywords: keyword 1; keyword 2; keyword 3 (List three to ten pertinent keywords specific to the article yet reasonably common within the subject discipline.)

Large quantities of real-time particle data are becoming available from low-cost particle monitors. However, it is crucial to determine the quality of these measurements. The largest network of monitors in the United States is maintained by the PurpleAir company, which offers two monitors: PA-I and PA-II. PA-I monitors have a single sensor (PMS1003) and PA-II monitors employ two independent PMS5003 sensors. We determine a new calibration factor for the PA-I monitor and revise a previously published calibration algorithm for PA-II monitors (ALT-CF3). From the PurpleAir API site, we downloaded 83 million hourly average PM2.5 values in the PurpleAir database from Washington, Oregon, and California between January 1, 2017 and September 8, 2021. Daily outdoor PM2.5 means from 194 PA-II monitors were compared to daily means from 47 nearby Federal regulatory sites using gravimetric Federal Reference Methods (FRM). We find a revised calibration factor of 3.4 for the PA-II monitors. For the PA-I monitors, we determined a new calibration factor (also 3.4) by comparing 26 outdoor PA-I sites to 117 nearby outdoor PA-II sites. These results show that PurpleAir PM2.5 measurements can agree well with regulatory monitors when an optimum calibration factor is found.

A right frontoparietal neoplastic lesion was found in a young-aged patient with analgesic refractory headache. Surgical resection was performed, and the pathologist analysis turned out a cellular ependymoma with signs of anaplasia. In the follow-up, a MRI showed a suspicious lesion, so a [18F]Fluorocholine PET/CT was performed. An increased uptake was described in the right parietal region on the margin of residual cystic lesion. The patient got a complete resection which was confirmed later by MR. In the pathology analysis, a focally congestive cerebral parenchyma with a central histiocytic reaction to foreign body area was described. Foreign body reaction in brain tissue is a very rare immune response that has not been well studied. Haemostatic material has been reported as a possible trigger of this response in other organs and could be detected by [18F]FDG PET/CT. Following the experience of the current case report, [18F]Fluorocholine PET/CT could also show a false positive related to foreign body reaction.

The instability of traveling pulses in nonlinear diffusion problems is inspected on the example of Gunn domains in semiconductors. Mathematically the problem is reduced to the calculation of the "energy" of the ground state in Schrödinger equation with a complicated potential. A general method to obtain the bottom-part spectrum of such equations based on the approximation of the potential by square wells is proposed and applied. Possible generalization of the approach to other types of nonlinear diffusion equations is discussed.

High-strength low-alloy steels (HSLAs) are widely used in the structural body components of many domestic motor vehicles owing to their better mechanical properties and greater resistance. The real production process of HSLA steelmaking can be regarded as a model that builds on the relationship between process parameters and product quality attributes. A surrogate modeling method is used, and the resulting production process model can be applied to predict the optimal manufacturing process parameters. We used different methods in this paper to build such a surrogate model, including linear regression, random forests, support vector regression, multilayer perception, and a simplified VGG model. We then applied three bio-inspired search algorithms, namely particle swarm optimization, the artificial bee colony algorithm, and the firefly algorithm, to search for the optimal controllable manufacturing process parameters. Through experiments on 9,000 test samples used for building the surrogate model, and 299 test samples for making the optimal process parameter selection, we found that the combination of a simplified VGG model and the firefly algorithm was the most successful at reaching a success rate of 100%—in other words, when the product quality attributes of all test samples satisfy the mechanical requirements of the end products.

In this paper we perform numerous numerical studies for the problem of low-rank matrix completion. We compare the Bayesian approaches and a recently introduced de-biased estimator which provides a useful way to build confidence intervals of interest. From a theoretical viewpoint, the de-biased estimator comes with a sharp minimax-optimal rate of estimation error whereas the Bayesian approach reaches this rate with an additional logarithmic factor. Our simulation studies show originally interesting results that the de-biased estimator is just as good as the Bayesian estimators. Moreover, Bayesian approaches are much more stable and can outperform the de-biased estimator in the case of small samples. However, we also find that the length of the confidence intervals revealed by the de-biased estimator for an entry is absolutely shorter than the length of the considered credible interval. These suggest further theoretical studies on the estimation error and the concentration for Bayesian methods as they are being quite limited up to present.

The log interpretation and evaluation of Chang 8 tight sandstone reservoir in Longdong West area, Ordos Basin, is facing great challenges due to the existence of low resistivity contrast oil pays. To better guide the exploration of oil resources in this area, the characteristics and control mechanism of low resistivity contrast oil pays were studied in this research. Firstly, according to the relative value of apparent resistivity increase rate of the target formation, the reservoir was divided into two types: low resistivity contrast oil pay (LRCP) and high resistivity oil pay (HRP). Then, the reservoir characteristics were studied by comparing and analyzing the experimental data, formation water data and logging data collected from the two reservoir types. On this basis, the control mechanism of LRCP was studied and summarized into reservoir micro factors and regional macro factors, respectively. It is found that the reservoir rock composition between LRCP and HRP is basically the same. Compared with HRP reservoir, the average porosity and permeability of LRCP reservoir are relatively better, but the pore structure is relatively poorer because of the high content of micro pores. When the filling pressure of crude oil is sufficient enough, the high oil saturation can be formed in LRCP reservoir. The high irreducible water saturation and high formation water salinity are the main micro factors reduced the reservoir resistivity. Besides, the difference of hydrocarbon expulsion capacity of source rock and the regional difference of formation water salinity are the macro factors influenced the distribution of LRCP and HRP from vertical and horizontal of the region. The formation of LRCP is controlled by the comprehensive influence of reservoir micro factors and regional macro factors. And the comprehensive consideration of the influence of micro factors and macro factors on LRCP is suggested during the log interpretation and evaluation.

We propose a novel transfer learning method for speech emotion recognition allowing us to obtain promising results when only few training data is available. With as low as 125 examples per emotion class, we were able to reach a higher accuracy than a strong baseline trained on 8 times more data. Our method leverages knowledge contained in pre-trained speech representations extracted from models trained on a more general self-supervised task which doesn’t require human annotations, such as the wav2vec model. We provide detailed insights on the benefits of our approach by varying the training data size, which can help labeling teams to work more efficiently. We compare performance with other popular methods on the IEMOCAP dataset, a well-benchmarked dataset among the Speech Emotion Recognition (SER) research community. Furthermore, we demonstrate that results can be greatly improved by combining acoustic and linguistic knowledge from transfer learning. We align acoustic pre-trained representations with semantic representations from the BERT model through an attention-based recurrent neural network. Performance improves significantly when combining both modalities and scales with the amount of data. When trained on the full IEMOCAP dataset, we reach a new state-of-the-art of 73.9% unweighted accuracy (UA).

Emerging pollutants as pharmaceuticals have been focusing international attention for few decades. Ciprofloxacin (CIP) is a common drug widely found in effluents from hospitals, industrial and different wastewater treatment plants, as well as rivers. In this work, the lab-scale 3D-BER system was established, and more than 90% of the antibiotic CIP removal from the Low C/N wastewater. Best results were obtained with current intensity, and different C/N ratio significantly improve the removal of CIP and nitrates, when the ideal conditions were; C/N = 1.5-3.5, pH =7.0-7.5, and I = 60 mA. The highest removal efficiency of CIP = 94.20 %, NO3--N= 95.53 % and total nitrogen (TN) = 84.27 %, respectively. In this novel system, the autotrophic-heterotrophic denitrifying bacteria played vital role for the removal of CIP and enhanced denitrification process. Thus, autotrophic denitrifying bacteria uses CO2 and H2 as carbon sources to reduce nitrates to N2. This system has the assortment and prosperous community revealed at the current intensity of 60 mA, and the analysis of bacterial community structure in effluent samples fluctuates under different condition of C/N ratios. According to the results of LC-MS/MS analysis, the intermediate products were proposed after efficient biodegradation of CIP. Microbial community on biodegrading was mostly found at phylum, and class level was dominantly responsible for the NO3--N and biodegradation of CIP. This work can provide some new insights towards the biodegradation of CIP and the efficient removal of nitrates from low C/N wastewater treatment by the novel 3D-BER system.

Abstract The COVID-19 pandemic is thought to began in Wuhan, China in December 2019. Mobility analysis identified East-Asia and Oceania countries to be highly-exposed to COVID-19 spread, consistent with the earliest spread occurring in these regions. However, here we show that while a strong positive correlation between case-numbers and exposure level could be seen early-on as expected, at later times the infection-level is found to be negatively correlated with exposure-level. Moreover, the infection level is positively correlated with the population size, which is puzzling since it has not reached the level necessary for population-size to affect infection-level through herd immunity. These issues are resolved if a low-virulence Corona-strain (LVS) began spreading earlier in China outside of Wuhan, and later globally, providing immunity from the later appearing high-virulence strain (HVS). Following its spread into Wuhan, cumulative mutations gave rise to the emergence of an HVS, known as SARS-CoV-2, starting the COVID-19 pandemic. We model the co-infection by an LVS and an HVS, and show that it can explain the evolution of the COVID-19 pandemic and the non-trivial dependence on the exposure level to China and the population-size in each country. We find that the LVS began its spread a few months before the onset of the HVS, and that its spread doubling-time is $\sim 1.59\pm 0.17$ times slower than the HVS. Although more slowly spreading, its earlier onset allowed the LVS to spread globally before the emergence of the HVS. In particular, in countries exposed earlier to the LVS and/or having smaller population-size, the LVS could achieve herd-immunity earlier, and quench the later-spread HVS at earlier stages. We find our two-parameter (the spread-rate and the initial onset time of the LVS) can accurately explain the current infection levels (R^2$\mathrm{=0.74}$; correlation p-value (p) of 5x10^-13$$). Furthermore, countries exposed early should have already achieved herd-immunity. We predict that in those countries cumulative infection levels could rise by no more than 2-3 times the current level through local-outbreaks, even in the absence of any containment measures. We suggest several tests and predictions to further verify the double-strain co-infection model and discuss the implications of identifying the LVS.

Uniform illumination is a key requirement in different research fields. However, this requirement is often difficult to achieve when high intensity is required at the same time. Recent advancements in LED lamps allow nowadays for compact and economical solutions. In this work we present a suitable solution for various laboratory purposes requiring stable, uniform and high intensity illumination. The system is composed of four identical high power white LED arrays of 30 mm diameter each, placed on a supporting and cooling structure having a minimum volume of 26 cm x 26 cm x 8 cm. A numerical model has been developed, based on a ray tracing software, in order to simulate the performances. These have then been experimentally validated with measurements of the power density map, carried out with a 1% uncertainty pyranometer. Data show that the built system is very stable over time and provides an illumination uniformity higher than 98%, on a surface of 50 mm radius, which reduces to 95% on a surface of 75 mm radius. The power density can be adjusted in the 390-1360 W m-2 range, not affecting uniformity.

In this paper, we draw on recent experiences from the Young Lives study to discuss some of the ethical and practical challenges facing longitudinal cohort studies in low- and middle-income countries in the time of coronavirus. We argue that COVID-19 has instigated an ‘ethics of disruption’ for social researchers across the world, and for longitudinal cohort studies like Young Lives, this requires navigating three core considerations: first, managing research relationships and reciprocity within an observational study design; second, maintaining methodological continuity and consistency across time; and third, balancing an immediate short-term response to COVID-19 against the longer-term perspective. We refer to the study’s plan to implement a new COVID-19 phone survey to illustrate how the team are navigating this altered ethical terrain.

Chronic kidney disease (CKD) affects >10% of the adult population. Each year approximately 120,000 Americans develop end-stage kideny disease and initiate dialysis, which is costly and associated with functional impairments, worse health-related quality of life, and high early-mortality rates exceeding 20% in the first year. Recent declarations by the World Kidney Day and the U.S. Government Executive Order seek to implement strategies that reduce the burden of kidney failure by slowing CKD progression and controlling uremia without dialysis. Pragmatic dietary interventions may have a role in improving CKD outcomes and preventing or delaying dialysis initiation. Evidence suggests that a patient-centered plant-dominant low-protein diet (PLADO) of 0.6-0.8 g/kg/day comprised of >50% plant-based sources, administered by dietitians trained in non-dialysis CKD care, can be promising. The scientific premise of the PLADO is based on the observations that high protein diets with high meat intake are not only associated with higher cardiovascular disease risk but also higher CKD incidence and faster CKD progression due to increased intraglomerular pressure and glomerular hyperfiltration. Meat intake increases production of nitrogenous end-products, worsens uremia, and may increase the risk of hyperkalemia, given constipation from the typical low fiber intake. Plant-dominant, fiber-rich, low-protein diet may lead to favorable alterations in the gut microbiome, which can modulate uremic toxin generation and slow CKD progression, along with reducing cardiovascular risk in CKD patients. PLADO is a heart-healthy, safe, flexible, and feasible diet that could be the centerpiece of a conservative and preservative CKD-management strategy that challenges the prevailing dialysis-centered paradigm.

In order to solve the problem of the poor oil displacement effect of high molecular weight alkali/surfactant/polymer (ASP) solution in low permeability reservoirs, Daqing Oilfield uses a partial quality tool to improve the oil displacement effect in low permeability reservoirs. Without changing the oil displacement capability of high molecular weight ASP solution in high permeability oil layers, the ASP solution is actively sheared in low permeability oil layers by using a partial quality tool to increase the injection capability of the solution and improve the overall oil recovery. In order to study the ability of the partial quality tool to improve the oil displacement effect, firstly, the matching degree of high molecular weight ASP solution to low permeability cores is studied, and the ability of quality control tools to change the molecular weight is studied. Then, experimental research on the pressure and oil displacement effect of high molecular weight ASP solution before and after the actions of the partial quality tool is carried out. The results show that ASP solutions with molecular weights of 1900 × 104 and 2500 × 104 have a poor oil displacement effect in low permeability reservoirs. After the action of the partial quality tool, the injection pressure is reduced by 5.22 MPa, and the oil recovery is increased by 7.79%. The injection pressure of the ASP solution after shearing by the partial quality tool is lower than that of the ASP solution with the same molecular weight and concentration without shearing, but the oil recovery is lower. On the whole, the use of the partial quality tool can obviously improve the oil displacement effect in low permeability reservoirs.

In our previous study, a novel barrier processing on a porous low-dielectric constant (low-k) film was developed: an ultrathin Mn oxide on a nitrogen-stuffed porous carbon-doped organosilica film (p-SiOCH(N)) as a barrier of the Cu film was fabricated. To form a better barrier Mn₂O_3-xN film, an additional annealing at 450°C was implemented. In this study, the electrical characteristics and reliability of this integrated Cu/Mn₂O_3-xN/p-SiOCH(N)/Si structure is investigated. The proposed Cu/Mn₂O_3-xN/p-SiOCH(N)/Si capacitors exhibited poor dielectric breakdown characteristics in the as-fabricted stage, although, less degradation was found after thermal stress. Moreover, its time-dependence-dielectric-breakdown electric-field acceleration factor slightly increased after thermal stress, leading to a larger dielectric lifetime in a low electric-field as compared to other MIS capacitors. Furthermore, its Cu barrier ability under electrical or thermal stress was improved. As a consequent, the proposed Cu/Mn₂O_3-xN/p-SiCOH(N) scheme is a promising integrity for back-end-of-line interconnects.

In the environments of all kinds open coal storage sites , mining-affected coalbeds, and goafs, parts of coal body at low moisture content (≤8%) are prone to spontaneous combustion under the influence of some external environmental factors. In order to examine the influence effect of low moisture content on the spontaneous combustion tendency of coals with different metamorphic grade, we conducted temperature programmed oxidation (TPO) experiment and differential scanning calorimetry (DSC) experiment to study the spontaneous combustion characteristics of coals with different metamorphic grade at four different low moisture content, and comparatively analyzed the change laws of the characteristic parameters of four different metamorphic grade coals at four different low moisture content. The experimental results indicate that: 1) Compared other low moisture content, anthracite and fat coal at low moisture content of 1.2% show stronger tendency to undergo spontaneous combustion, long flame coal and lignite at low moisture content of 3.4% and 5.6% are more prone to spontaneous combustion. 2) Four different metamorphic grade coals at low moisture content of 7.8% are less prone to spontaneous combustion; 3) Coals with different metamorphic grade have different tendency to undergo spontaneous combustion.

In the paper, an improved smart meter data-based three-stage algorithm to calculate the power/energy losses in the three-phase networks with the voltage level below 0.4 kV (low voltage - LV) is presented. In the first stage, a loading function of input data was built having as main feature the working at the same time with files from the database of smart metering system (SMS) containing the hourly electricity records, and files including the characteristic load profiles established by the Distribution Network Operator (DNO) for the consumers with standard energy meters depending the following factors: consumption class, day and season. In the second stage, a function which is based on the work with the structure vectors was implemented to identify easy the configuration of analysed networks. In the third stage, an improved version of forward/backward sweep-based algorithm was proposed to calculate fast the power/energy losses to three-phase LV distribution networks in balanced and unbalanced regime. A real LV rural distribution network from a pilot zone belonging to a Distribution Network Operator (DNO) from Romania was used to confirm the accuracy of the proposed approach. The comparison with the results obtained using the DigSilent PowerFactory Simulation Package certified the performance of the algorithm, the mean absolute percentage error (MAPE) being 0.94%.

CASBEE-City tool determines the city’s Built Environment Efficiency (BEE) by calculating the improvement of Quality of Life (Q) over human activities’ Environmental Load (L) within the city’s hypothetical boundary. A total of 58 variables (57 Q indicators and one variable for L) are used in the worldwide version of CASBEE-City which were grounded using ISO 37120:2014 Sustainable Development of Communities and 17 Sustainable Development Goals (SDGs) by the United Nations (UN). This paper examines the application of CASBEE-City for Malaysian cities using the case of Johor Bahru City and identifies assessment indicators which are customised based on the data availability, reliability and suitability through focus group discussions (FGDs) which involved 36 respondents (researchers, urban planners and stakeholders). This paper reveals Johor Bahru with moderate score B+ in 2010 and 2025. Consensus were also achieved from the 36 FGD respondents for the practicability and future potential of CASBEE-City and BEE framework in Johor Bahru.

This paper analyses and evaluate the precision and the accuracy the capability of low-cost terrestrial photogrammetry by using many digital cameras to construct a 3D model of an object. To obtain the goal, a building façade has imaged by two inexpensive digital cameras such as Canon and Pentax camera. Bundle adjustment and image processing calculated by using Agisoft PhotScan software. Several factors will be included during this study, different cameras, and control points. Many photogrammetric point clouds will be generated. Their accuracy will be compared with some natural control points which collected by the laser total station of the same building. The cloud to cloud distance will be computed for different comparison 3D models to investigate different variables. The practical field experiment showed a spatial positioning reported by the investigated technique was between 2-4cm in the 3D coordinates of a façade. This accuracy is optimistic since the captured images were processed without any control points.

LoRa and its upper layers definition LoRaWAN is one of the most promising LPWAN technologies for implementing the Internet of Things (IoT). Although being a popular technology, several works in the literature have revealed various weaknesses regarding the security of LoRaWAN v1.0 (the official 1st draft). By using all these recommendations from the academia and industry, the LoRa-Alliance has worked on the v1.0 to develop an enhanced version and provide more secure and trustable architecture. The result of these efforts ended-up with LoRaWAN v1.1, which was released on Oct 11, 2017. This manuscript aims at demystifying the security aspects and provide a comprehensive Security Risk Analysis related to latest version of LoRaWAN. Besides, it provides several remedies to the recognized vulnerabilities. To the best of authors’ knowledge, this work is one of its first kind by providing a detailed security analysis related to latest version of LoRaWAN. According to our analysis, end-device physical capture, rogue gateway and replay attacks are found to be threating for safety operation of the network. Eventually, v1.1 of LoRaWAN is found to be less vulnerable to attacks compared to v1.0, yet possesses several security implications that need to be addressed and fixed for the upcoming releases.

This paper focuses on the non-destructive dielectric measurement for low-loss planar materials with a thickness of less than 3 mm using a large coaxial probe with an outer diameter of 48 mm. The aperture probe calibration procedure required only to make a measurement of the half-space air and three offset shorts. The reflection coefficient for the thin material is measured using a Keysight E5071C network analyzer from 0.3 MHz to 650 MHz and then converted to a relative dielectric constant and tangent loss via closed form capacitance model and lift-off calibration process. Measurement error of dielectric constant, Δε_r is less than 2.5 % from 1 MHz to 400 MHz and the resolution of loss tangent, tan δ measurement is capable of achieving 3×10^-3.

This study evaluated the effect of low-level laser irradiation induces by diode laser on the speed of orthodontic tooth movement of canines submitted to initial retraction. Twenty-four mandibular canines were retracted by using NiTi spring (force of 150 g/side). Thirteen of those were irradiated with a diode laser 980-nm diode laser (Wiser Laser Doctor Smile, Lambda) operating at an 810-nm wavelength (1 W of output power, continuous wave of 66.7 J/cm2) that was equipped with a 0.6-mm optical fiber in continuous-wave mode. The canine retraction was accomplished by using prefabricated coil springs. The right of the mandible was chosen to be irradiated with the laser, whereas the left side was considered the control without laser irradiation. The laser was applied with 0-, 3-, 7-, and 14-day intervals. The amount of canine retraction was measured with a digital electronic caliper while the pain level was prompted by a patient questionnaire. The speed of tooth movement was significantly greater in the laser group than in the control group. The pain intensity was also at a lower level in the laser group. Our findings suggest that diode laser therapy can highly accelerate tooth movement during orthodontic treatment and can also effectively reduce pain level.

The effect of filling velocity on positive macrosegregations in large size steel ingots was studied. Macrosegregation and macro-/micro-structure were characterized on the hot-tops and a portion of the upper section of two ingots. The measurements revealed that segregation features in the two ingots varied as a function of the alloying elements, and that the severity of positive macrosegregation in the casting body was reduced when the filling rate was increased. It was also found that at the higher filling rate, grain morphologies in the first solidified zones of the ingot changed from columnar to equiaxe, and secondary dendrite arm spacing (SDAS) became slightly smaller in the intermediate and final solidified zones. The experimental findings were analyzed in the framework of diffusion and convection controlled solidification, as well as liquid metal flow theories. The solute dependence of segregation features was related to the difference in solid-liquid partition coefficient and diffusion capability of each element in the liquid iron. Calculation of Reynolds numbers (Re) during the filling process, for both ingots, showed that higher filling velocity caused more instable movement of the liquid metal in the initial solidification stage, resulting in the modification of grain morphology, as well as accelerated solidification rate.

Integrated ultra-low-loss waveguides are highly desired for integrated photonics to enable applications that require long delay lines, high-Q resonators, narrow filters, etc. Here we present an ultra-low-loss silicon waveguide on 500 nm thick SOI platform. Meter-scale delay lines, million-Q resonators and tens of picometer bandwidth grating filters are experimentally demonstrated. We design a low-loss low-reflection taper to seamlessly integrate the ultra-low-loss waveguide with standard heterogeneous Si/III-V integrated photonics platform to allow realization of high-performance photonic devices such as ultra-low-noise lasers and optical gyroscopes.

Infertility affects approximately 15% of couples worldwide, an estimated 30% of which is related to male factor infertility. Application of low level laser therapy (LLLT) to improve fertility status is a rapidly growing discipline in medicine. Laser therapy triggers a variety of biological processes through interaction with primary cellular photoacceptors. The present review aims at evaluating the literature available in the MEDLINE/ PubMed on cellular and molecular mechanisms of photobiomodulation in the domains of reproductive and veterinary medicine. We primarily focused on the clinical application of laser treatment on seminal quality, in particular its role in promoting spermatozoa motility, as well as the role of phototherapy in modulating assisted reproduction (ART). Additionally, we investigated the strength of evidence in support of the positive impact of photobiomodulation on facilitating ART.

Containing hundreds of spectral bands (features), hyperspectral images (HSIs) have high ability in discrimination of land cover classes. Traditional HSIs data processing methods consider the same importance for all bands in the original feature space (OFS), while different spectral bands play different roles in identification of samples of different classes. In order to explore the relative importance of each feature, we learn a weighting matrix and obtain the relative weighted feature space (RWFS) as an enriched feature space for HSIs data analysis in this paper. To overcome the difficulty of limited labeled samples which is common case in HSIs data analysis, we extend our method to semisupervised framework. To transfer available knowledge to unlabeled samples, we employ graph based clustering where low rank representation (LRR) is used to define the similarity function for graph. After construction the RWFS, any arbitrary dimension reduction method and classification algorithm can be employed in RWFS. The experimental results on two well-known HSIs data set show that some dimension reduction algorithms have better performance in the new weighted feature space.

Detecting IgE sensitizations in the serum of allergic dogs is commonly done using allergen extracts, but these are difficult to standardize. This article details the development and validation of the Pet Allergy Xplorer (PAX; Nextmune, Stockholm, Sweden), the first multiplex macroarray for the detection of IgE sensitization in dogs using allergen extracts and molecular components; the PAX is derived from the Allergy Xplorer (ALEX2; MacroArray Diagnostics, Vienna, Austria). The selection of allergens, cartridge processing, strategy for identifying and blocking IgE directed against cross-reactive carbohydrate determinants (CCD), and the method used for determining the positivity threshold are described. The validation of the PAX included evaluations of the specificity of its anti-IgE monoclonal antibody, specificity of IgE binding to target allergens, assay precision, and internal consistency. Additionally, the influence of possible confounding factors, such as sample type, the influence of hemolysis, lipemia, bilirubinemia, and elevated CCD-IgE, was tested. Finally, the sensitization rates of 23,858 European dogs to 145 environmental and Hymenoptera venom allergens were summarized. The PAX is accurate and reproducible and has a unique CCD-detection and blocking strategy; its molecular allergens offer a unique window on allergen cross-reactivity.

Dengue (DENV) and Zika (ZIKV) virus continue to pose significant challenges globally due to their widespread prevalence and severe health implications. Given the absence of effective vaccines and specific therapeutics, targeting of the highly conserved NS5 RNA-dependent RNA polymerase (RdRp) domain has emerged as a promising strategy. However, limited efforts have been made to develop inhibitors for this crucial target. In this study, we employed an integrated in silico approach utilizing combinatorial chemistry, docking, molecular dynamics simulations, MM/GBSA, and ADMET studies to target the allosteric N-pocket of DENV3-RdRp and ZIKV-RdRp. Using this methodology, we designed lycorine analogs with natural S-enantiomers (LYCS) and R-enantiomers (LYCR) as potential inhibitors of non-structural protein 5 (NS5) in DENV3 and ZIKV. Notably, 12 lycorine analogs displayed a robust binding free energy (<-9.00 kcal/mol), surpassing that of RdRp-Ribavirin (<-7.00 kcal/mol) along with promising ADMET score predictions (<4.00), of which (LYCR728-210, LYCS728-210, LYCR728-212, LYCS505-214) displayed binding properties to both DENV3 and ZIKV targets. This study highlights the potential of non-nucleoside lycorine-based analogs with different enantiomers that may present different or even completely opposite metabolic, toxicological, and pharmacological profiles as promising candidates for inhibiting NS5-RdRp in ZIKV and DENV3, paving the way for further exploration for the development of effective antiviral agents.

A better understanding of high temperature processes in slags contributes to facilitate knowledge based design of the solidified product. Here, a slag analogue with a nominal composition of 17 wt% LiMnO2 and 83 wt% Ca2SiO4 was synthesized encountering fairly high cooling rates. The Mn species from 1223 K to 1773 K was simulated using a thermodynamic model assuming a homogeneous melt. The micro-composition including the Mn species of the solidified slag was determined experimentally and was used as basis for molecular dynamics (MD) simulation. The MD simulation provides information on structure and viscosity at high temperatures, otherwise difficult to access. These parameters significantly influence oxidation state of redox-active elements and the solidified product. The micro-composition analyzed by electron probe micro analysis (EPMA) and synchrotron based micro-X-ray fluorescence (micro-XRF) showed that Mn-rich and Ca-Si-rich phases are separated. While the Mn-O phases did not contain noticeable Ca, the Ca2SiO4 phase had incorporated 0.6 wt% of Mn. The slag solidified into round shaped and droplet shaped grains of a Li-Mn-oxide, some Mn3O4 and Ca2SiO4. The powder X-ray diffraction (PXRD) confirmed the formation of larnite, the identity of the Li-Mn-oxide however remained inconclusive. The Mn oxidation state (OS) was identified using synchrotron based micro-X-ray absorption near edge spectroscopy (micro-XANES). The Mn-O grains, matched well with Li-Mn-oxides and a Mn OS: +3 e.g. LiMn3+O2. Small areas matching Hausmannite (Mn2+Mn23+O4) were also identified. The OS of Mn in the silicate phase could not be identified. For comparison a slowly cooled slag analogue with similar composition however higher Si content, was also subjected to micro-XANES. The slowly cooled slag formed long Mn-rich needles in a matrix of large calcium silicate crystals. The Mn-rich crystals matched well with the XANES spectrum of a Mn3+ Li-oxide like LiMn3+O2. At the rim of the needles the Mn-spectra matched well the Hausmannite (Mn2+Mn23+O4) reference. In the silicate phases Mn had a OS: +2, unambiguously. The melt structure at different temperatures of two compositions i.e. LiMn3+O2 and Ca2SiO4 was simulated using molecular dynamics (MD). They serve as model compositions assuming a heterogeneous melt. The results show significant different degrees of polymerization and viscosity. Information from MD simulations can support the identification of potentially different oxygen permeability and with that prediction of oxidation states. The bulk composition was identified by inductively coupled plasma optical emission spectrometry (ICP-OES), bulk structure by PXRD and bulk species by lab-XANES. The synchrotron micro analysis including micro-XRD were performed at the microfocus beamline I18 at the Diamond Light Source. Pure reference compounds were prepared and characterized with the same multi-modal approach.

The efficacy and cost-effectivness of Multigene Panel Next-Generation Sequencing (NGS) in directing patients towards genomically matched therapies remains uncertain. This study investigated metastatic colorectal cancer (mCRC) patients who underwent NGS analysis on formalin-fixed paraffin-embedded tumor samples. Data from 179 patients were analyzed, revealing no mutations in 39 patients (21.8%), one mutation in 83 patients (46.4%), and two or more mutations in 57 patients (31.8%). KRAS mutations were found in 87 patients (48.6%), including KRAS G12C mutations in 5 patients (2.8%), PIK3CA mutations in 40 patients (22.4%), BRAF mutations in 26 patients (14.5%). Less common mutations were identified: ERBB2 in 5 patients (2.8%) and SMO in 4 patients (2.2%). Additionally, MAP2K1, CTNNB1, and MYC were mutated in 3 patients (2.4%). Two mutations (1.1%) were observed in ERBB3, RAF1, MTOR, JAK1, and FGFR2. No significant survival differences were observed based on mutation numbers. 40% of patients had druggable molecular alterations, but only 1.1% received genomically guided treatment, suggesting limited application in standard practice. Despite this, expanded gene panel testing can identify actionable mutations, aiding personalized treatment strategies in metastatic CRC, although current eligibility for biomarker-guided trials remains limited.

Asymmetric lithium salts, such as Lithium (difluoromethanesulfonyl)(trifluoromethanesulfonyl)imide (LiDFTFSI), have been demonstrated to surpass traditional symmetric lithium salts with improved Li+ conductivity and the capacity to generate stable solid electrolyte interphase (SEI) while maintaining compatibility with aluminum (Al0) current collector. However, the intrinsic reductive mechanism through which LiDFTFSI influences battery performance remains unclear and under debate. Herein, the detailed SEI reactions of LiDFTFSI-based electrolytes were investigated by combining density functional theory and molecular dynamics, aiming to clarify the formation process and atomic structure of SEI. Our results show that asymmetric DFTFSI– weakens the interaction between carbonate solvents and Li+, and substantially alter the solvation structure, exhibiting a well-balanced coordination capacity to bis(trifluoromethanesulfonyl)imide (TFSI–). Nanoseconds hybrid molecular dynamics simulation further reveals that the preferential decomposition of LiDFTFSI produces sufficient LiF and Li2O to facilitate a robust SEI. Moreover, the abundant F– generated from LiDFTFSI decomposition accumulates on the Al surface and subsequently combines with Al3+ from the current collector to form AlF3, potentially inhibiting corrosion of the current collector. Overall, these findings elucidate how LiDFTFSI regulates the solvation sheath and SEI structure, advancing the development of high-performance electrolytes compatible with current collector.

Morphological and phylogenetic (45S nrDNA+RPB1 gene) analyses of three glomoid spore-producing arbuscular mycorrhizal fungi revealed the presence of two new species be-longing to the genus Glomus in the family Glomeraceae. In the field, Glomus highlandensis sp. nov. was found in a saltmarsh of the Scottish Highlands and in maritime sand dunes of the Baltic Sea in Poland, both saline environments, while G. mongioie sp. nov. originates from the Italian Alps. Phylogenetic placement analysis using environmental sequences indicated that G. highlandensis could have likely worldwide distribution while G. mongioie seems to be a rare species in the world. The molecular and phylogenetic analysis provided important insights about the presence of ribosomal variants in Glomus, with potential negative implication in phylogeny and species recognition.

Based on screening in computational biology and biological in vitro assays, five natural products isolated from extracts of the herbal medicine toad skin, such as cinobufagin (CBFi), bufalin (BFi), arenobufagin (ABFi), telocinobufagin (TBFi), bufotalin (BFTi), were subjected to molecular docking calculations with the use of SARS-CoV-2 main protease (PDB 6LU7 and 7BTF) and top-scoring ligand-receptor complexes were obtained. The results showed that the binding energy of ABFi to the 3CL protein was -17.044kcal/mol, which was higher than CBFi and TBFi. However, the binding energy of ABFi to the RdRp protease was -23.250 kcal/mol, which was much lower than that of CBFi and TBFi, EVEN lower than that of ABFi to the 3CL protein. ABFi also has polar interactions with amino acids such as Glu811, Ser814, Ser681 and Thr680 of RdRp enzyme. The results revealed that ABFi had a moderate inhibitory effect on the cell proliferation of SARS-CoV-2 in vitro, with an inhibition rate of 61.12%, even weaker than Remdesivir. This new discovery provides us with new ideas for in-depth studies on the development of natural products with this class of structural generalizations as inhibitors of SARS-CoV-2, and provides an experimental basis for the next step of mechanistic studies.

Entamoeba histolytica, throughout its lifecycle, encounters a variety of stressful conditions. This parasite possesses Heat Shock Response Elements (HSEs) which are crucial for regulating the ex-pression of various genes, aiding in its adaptation and survival. These HSEs are regulated by Heat Shock Transcription Factors (EhHSTFs). Our research has identified seven such factors in this parasite, designated as EhHSTF1 through EhHSTF7. Significantly, under heat shock condi-tions and in the presence of the antiamoebic compound emetine, EhHSTF5, EhHSTF6, and EhHSTF7 show overexpression, highlighting their essential role in gene response to these stressors. Currently, only EhHSTF7 has been confirmed to recognize the HSE in the promoter of the EhPgp5 gene (HSE_EhPgp5), leaving the binding potential of the other EhHSTFs to HSE yet to be explored. Consequently, our study aimed to examine both in vitro and in silico the oligomeri-zation and binding capabilities of the recombinant EhHSTF5 protein (rEhHSTF5) to HSE_EhPgp5. The in vitro results indicate that the oligomerization of rEhHSTF5 is concentration-dependent, with its dimeric conformation showing a higher affinity for HSE_EhPgp5 than its monomeric state. In silico analysis suggests that the alpha 3 α-helix (α3-helix) of the DNA-binding domain (DBD5) of EhHSTF5 is crucial in binding to the major groove of HSE, primarily through hydro-gen bonding and salt-bridge interactions. In summary, our results highlight the importance of oligomerization in enhancing the affinity of rEhHSTF5 for HSE_EhPgp5 and demonstrate its abil-ity to specifically recognize structural motifs within HSE_EhPgp5. These insights significantly contribute to our understanding of one of the potential molecular mechanisms employed by the parasite to efficiently respond to various stressors, thereby enabling successful adaptation and survival within its host environment.

DNA barcoding has emerged as a powerful tool in the field of taxonomy, transforming the way we identify and classify species. This review article aims to provide an up-to-date overview of the advancements in DNA barcoding techniques, their applications, and their impact on taxonomy and biodiversity studies. We will explore the evolution of DNA barcoding, the development of standardized barcode regions, and the challenges and limitations associated with this methodology. Additionally, we will delve into the diverse range of taxonomic groups for which DNA barcoding has been applied, highlighting key case studies and their contributions to our understanding of biodiversity. Furthermore, we will discuss the integration of DNA barcoding with other molecular and bioinformatic approaches, such as metabarcoding and machine learning, to enhance species identification and biodiversity assessment. This review aims to provide a comprehensive perspective on how DNA barcoding is reshaping the field of taxonomy and its implications for conservation, ecology, and evolutionary biology.

Proteolysis Targeting Chimeras (PROTACs) describe compounds that bind to and induce degradation of a target by simultaneously binding to a ubiquitin ligase. More generally referred to as bifunctional degraders, PROTACs have led the way in the field of targeted protein degradation (TPD) with several compounds currently undergoing clinical testing. Alongside bifunctional degraders, single-moiety compounds, or molecular glue degraders (MGDs), are increasingly being considered as a viable approach for development of therapeutics, driven by advances in rational discovery approaches. This review focusses on drug discovery with respect to bifunctional and molecular glue degraders within the ubiquitin proteasome system, including analysis of mechanistic concepts and discovery approaches, with an overview of current clinical and pre-clinical degrader status in oncology, neurodegenerative and inflammatory disease.

Background: The aim was to diagnose Candida in the oral cavity of subjects with type 2 diabetes mellitus (T2DM) using a genotyping technique and to compare the results with those from con-ventional diagnosis by Papanicolau (Pap) staining. Methods: Palatal mucosa smears were per-formed in 18 dental care patients diagnosed with T2DM and grade I, II, and III prosthetic stomatitis who met the inclusion criteria; 18 healthy control subjects were also included in the study. He-moglobin A1c (HbA1c) levels were determined from total blood. Using exfoliative cytology, the Pap staining technique was used to diagnose candidiasis. Exfoliative cytology was also used for molecular diagnosis; DNA was obtained for Candida genotyping and RNA was used for gene ex-pression studies. Results: Clinical patterns indicated that all subjects were positive for Candida; however, Pap analysis revealed only three positive subjects, whereas end-point polymerase chain reaction (PCR) analysis revealed fifteen subjects with some type of Candida. The most common Candida species found were Candida guilliermondii (38.8%), Candida krusei (33.3%), Candida tropicalis, and Candida lusitaniae (22.2%). Interestingly, the coexpression of different species of Candida was found in various patients. In all patients, HbA1c levels were increased. Gene expression analysis showed a significant decrease (p ≤ 0.05) in TLR2 expression in positive subjects, whereas TLR4 expression did not differ significantly among patients. Conclusions: The end-point PCR technique showed better sensitivity for diagnosis of Candida when compared with diagnosis by Pap staining. T2DM subjects showed an increased presence of C. guilliermondii that was correlated with decreased TLR2 expression

The high prevalence of thyroid nodules and increased availability of neck ultrasound have led to an increased incidence of diagnostic thyroid fine needle aspirations, with approximately 20% yielding indeterminate results. The recent availability of molecular tests has helped guide the clinical management of these cases. This paper aims to review and compare three main commercially available molecular cytology platforms in the U.S. – Afirma GSC, Thyroseq GC, and ThyGeNEXT+ThyraMIR. Sequential improvements of the Afirma GSC and Thyroseq GC tests have led to higher positive and negative predictive values, sensitivity, and specificity. Comparative studies revealed similar diagnostic performance between these tests, with considerations for factors such as cost and processing time. Thyroseq GC provides detailed genomic information and specific management recommendations. ThyGeNEXT+ThyraMIR, though less studied, presents promising results, particularly in miRNA analysis for weak driver mutations. Challenges in interpreting results include variations in reporting and the evolving nature of testing platforms. Questions persist regarding cost-effectiveness and the utility of ultrasound characteristics in selecting candidates for molecular testing. While molecular testing has primarily served diagnostic purposes, advancements in understanding genetic alterations now offer therapeutic implications. FDA-approved options target specific genetic alterations, signaling a promising future for tailored treatments.

Coarse-grained molecular dynamics simulations are employed to investigate spatiotemporal evolution of vesicles (polymersomes) via self-assembly of randomly distributed amphiphilic diblock copolymers in water. Vesiculation pathway consists of several intermediate structures such as spherical/rodlike aggregates, wormlike micelles, lamellae, and cavities. Lamella to vesicle transition occurs at a constant aggregation number and is accompanied by a reduction in the solvent accessible surface area. Simulation predictions are in qualitative agreement with the mechanism of vesicle formation in which the unfavorable hydrophobic interactions between water molecules and polymer segments along the edge of the lamella are eliminated at the expense of gaining curvature energy. However, rod-lamella-vesicle transition is accompanied by an increase in copolymer packing density. Hence, the change in the surface area accompanying vesiculation predicted by the simulations is significantly lower than theoretical estimates. Changes in information entropy, quantified by the expectation of the logarithm of the probability distribution function of the segmental stretch parameter s, defined as the difference between the maximum and instantaneous segmental extension, are statistically insignificant along the vesiculation pathway. For rods, lamellae and polymersomes, s follows a log normal distribution. This is explained based on the configurational dynamics of a single diblock chain in water.

BACE1 is involved in the production of beta-amyloid peptides, and inhibiting its activity is a potential therapeutic strategy for managing Alzheimer's disease, as excessive beta-amyloid accumulation is a characteristic feature of the disease.Computational results suggest that hypericin has the potential to act as an inhibitor of BACE1. The Molecular Docking results indicate a high binding affinity between hypericin and BACE1, with a notable binding energy score of -10.3 kcal/mol. Additionally, the formation of various chemical bonds, including hydrogen bonds and hydrophobic bonds, further supports the idea that hypericin may effectively interact with the active site of BACE1. It's important to note that while the in silico Molecular Docking results are promising, further in vitro and in vivo studies would be necessary to validate and better understand the inhibitory potential of hypericin against BACE1. Additionally, the practical application of hypericin as a BACE1 inhibitor in a therapeutic context would require careful consideration of factors such as bioavailability, safety, and efficacy.

Docking results suggest that Amentoflavone has a higher affinity for investigated Serine/threonine-protein kinases, indicating potential interactions that may influence the activities of these kinases. The negative values of the binding energies signify strong and stable interactions, suggesting that Amentoflavone could be a key molecule in modulating the functions of these kinases, which play crucial roles in cellular processes such as cell cycle regulation and apoptosis.

In its prefusion state, the SARS-CoV-2 Spike protein (similarly to other class I viral fusion proteins) is metastable, which is considered to be an important feature for optimizing or regulating their functions. After the binding process of its S1 subunit (S1) with the ACE2, the Spike protein (S) suffers a dramatic conformational change where S1 splits from the S2 subunit, which then penetrates the membrane of the host cell, promoting the fusion of the viral and cell membranes. This results in the infection of the host cell. In a previous work, we showed -using large scale molecular dynamics simulations- that the application of external electric fields (EF) induces drastic changes and damage in the receptor-binding domain (RBD) of the wild type Spike protein, as well of the Alpha, Beta and Gamma variants, leaving a structure which cannot be recognized any more by ACE2. In this work, we first extend the study to the Delta and Omicron variants and confirm the high sensitivity and extreme vulnerability of S to moderate EF (as weak as 104 V m-1), but, more importantly, we also show that, in contrast, the postfusion state of the spike protein does not suffer structural damage even if electric field intensities four orders of magnitude higher are applied. These results provide a solid scientific basis to confirm the prefusion state metastability roots of the SARS-CoV-2 Spike protein susceptibility to be damaged by EF. After the virus docks to the ACE2 receptor, the stable and robust postfusion conformation develops, which exhibits a similar resistance to EF (damage threshold higher than 108 V m-1) like most globular proteins.

SARS-CoV-2 attachment and entry inside mammalian cells is mainly mediated by human angiotensin-converting enzyme 2 (ACE2) and its interaction with spike protein. However, it is well known that spike protein also interacts with other molecules like glycosaminoglycans (GAG), e.g., heparan sulfate (HS) or Enoxaparin (EX), which are linear, anionically charged polysaccharides known for their biological activities. The mode of action of these two polysaccharides is to bind spike protein to block the interaction with ACE2 receptors. This study aimed to assess a model capable of confirming the activity of these GAGs in both the wild-type strain of SARS-CoV-2 and its variants, such as the highly variable BA.2.86. This was achieved by combining in silico modeling with in vitro determination using BacMam technology. The results showed the antiviral activity of HS and EX both in vitro and through the in-silico analysis, reconciling conflicting findings from recent studies on the cellular entry of SARS-CoV-2. In conclusion, it is possible to highlight the ability of these molecules to circumvent the high variability of SARS-CoV-2, providing valuable insights into intervention strategies targeting cell entry mechanisms and establishing a safe in vitro model.

In this study, cotton fabric reinforced phenolic resin (CPF) composites were modified by adding four two-dimensional fillers: graphitic carbon nitride (g-C3N4), graphite (Gr), molybdenum disulfide (MoS2), and hexagonal boron nitride (h-BN). The tribological properties of these modified materials were investigated under dry friction and water lubrication conditions. CPF/ Gr composite exhibits significantly better tribological performance than the other three fillers modified CPF composites under dry friction, with a 24% reduction in friction coefficient and a 78% reduction in wear rate compared to unmodified CPF composite. Under water lubrication conditions, all four fillers did not significantly alter the friction coefficient of the CPF composite. However, except for an excessive amount of Gr, the other three fillers can reduce the wear rate. Particularly, in the case of 10% MoS2 content, the wear rate decreased by 56%. Scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS) were employed for the analysis of the morphology and composition of the transfer films. Additionally, molecular dynamics (MD) simulations were conducted to investigate the adsorption effects of Gr, MoS2, and PF on the counterpart surface under both dry friction and water lubrication conditions. The difference in the adsorption capacity of Gr and MoS2 on the counterpart, as well as the resulting formation of transfer films, accounts for the variation in tribological behavior between CPF/Gr and CPF/MoS2 composites. By combining the lubrication properties of MoS2 and Gr under dry friction and water lubrication conditions, using them as co-fillers can achieve a synergistic lubrication effect.

The mechanical properties of α-chitin and chitosan biocomposite are investigated due to their broad range of potential applications in bioengineering, materials science, and environmental technology. Employing molecular dynamics (MD), and stress-strain analyses, this study comprehensively investigates biopolymers mechanical response and anisotropic mechanical behavior under uniaxial tensile loading conditions in an aqueous environment. Our computational models were validated against existing experimental data, showing high degrees of correspondence. Uniaxial tensile tests revealed that α-chitin exhibits a remarkable ultimate tensile strength (UTS) of 10.07 GPa in the crystalline chain direction (y-axis) at a high strain rate of 0.636, compared to a significantly lower UTS of 2.78 GPa in the perpendicular direction (x-axis) at a lower strain rate of 0.066. The biocomposite nanostructure, encompassing randomly distributed chitosan, reduced stiffness, maintaining remarkable flexibility as α-chitin, with a UTS of 5.03 GPa in the y-axis and 2.34 GPa in the x-axis. Further, the directional elastic modules for α-chitin were calculated as 51.76 GPa and 39.76 GPa in the x and y directions, respectively. In contrast, these values for the α-chitin-chitosan biocomposite were estimated as 31.66 GPa and 26.00 GPa, respectively. The findings provide valuable insights into the distinct mechanical properties of α-chitin and chitosan biocomposite, making a substantial contribution to optimizing these materials for specialized applications.

(1) Background: Type-2 Diabetes (T2DM) is a long-term medical disorder characterized by Insulin deficiency and high blood glucose levels. Among other medication to cure T2DM, the review of the literature found that various Pyrimidine derivative act as an agonist for G-protein-coupled receptor 119 (GPR119) was proposed to control blood glucose levels by enhancing the function of pancreatic beta-cells and its mechanism of action with fewer adverse effects.; (2) Methods: In the present research work, in-silico investigations were carried out to investigate the potential of Pyrimidine analogue as an agonists to the protein target GPR119 receptor. We performed exhaustive molecular modelling and protein modelling methodologies such as homology mod-elling, molecular docking along with various drug designing tools such as 3D-QSAR and pharmacophore mapping to ascertain the design of better GPR119 agonists.; (3) Results: On the basis of in-depth computa-tional studies, we designed new pyrimidine moiety and analyzed them for GPR-119 receptor agonist and fur-ther explored the ADME properties. Designed compounds found to exhibit better predicted activities as com-pared to reference compound; (4) Conclusions: The current research on pyrimidine derivatives, using molec-ular docking, 3D-QSAR and Pharmacophore mapping demonstrated that the obtained computational model has significant properties and the designed molecules and Dataset from this model, produced antidiabetic compound against the target GPR119 i.e., compound 1S, 1Z and 1D with the docking score of −11.696, -9.314 and -8.721 respectively. The pharmacokinetics and drug-likeness studies revealed that these compounds may be the future candidate for the treatment of diabetes acting via GPR119 agonist mechanism.

The combination of wet-lab experimental data on multi-site combinatorial mutations and machine learning is an innovative method in protein engineering. In this study, we present an improved innovative sequence–activity relationship (innov'SAR) methodology based on novel descriptors and digital signal processing (DSP) to construct a predictive model. In this improved approach, 21 experimental (R)-selective amine transaminases from Aspergillus terreus (AT-ATA) were used as an input to predict higher thermostability than that predicted using the existing data. We successfully improved the determination coefficient (R2) of the model from 0.66 to 0.92. In addition, root mean square deviation (RMSD) and root mean square fluctuation (RMSF) were estimated and conformation analysis based on molecular dynamics simulations was performed to verify the enhanced thermal stability of the screened mutants. The improved innov'SAR algorithm enhanced the predictive accuracy, suggesting a method for modifying the stability of AT-ATA, which may help in directed evolutionary screening and open up new avenues for protein engineering.

GaN nanowires grown on metal substrates attract an increasing interest for a wide range of applications. Herein, we report GaN nanowires grown by plasma-assisted molecular beam epitaxy on thin polycrystalline ZrN buffer layers, sputtered onto Si(111) substrates. The nanowire orientation is studied experimentally and described within a model as a function of the Ga beam angle, nanowire tilt angle and substrate rotation. We show that vertically aligned nanowires grow faster than inclined nanowires, which leads to an interesting effect of geometrical selection of the nanowire orientation in the directional molecular beam epitaxy technique. After a given growth time, this effect depends on the nanowire surface density. At low density, the nanowires continue to grow with random orientations as nucleated. At high density, the effect of preferential growth induced by unidirectional supply of material in MBE starts to dominate. Faster growing nanowires with smaller tilt angles shadow more inclined nanowires that grow slower. This helps to obtain more regular ensembles of vertically oriented GaN nanowires despite their random position induced by the metallic grains at nucleation. The obtained dense ensembles of vertically aligned GaN nanowires on ZrN/Si(111) surfaces are highly relevant for device applications. These results are not specific for GaN nanowires and should be relevant for any nanowires which are epitaxially linked to the randomly oriented surface grains in the directional molecular beam epitaxy.

The effect of graphene (GR) on Ni surface relaxation and reconstruction in three different substrate orientations: {111}, {001}, {011}, at two different temperatures: 300K and 400K was studied using Molecular Dynamics simulation. The change of the interplanar distances of the substrate and redistribution of Ni and C atoms in direction perpendicular to the surface were compared with the equilibrium state of GR and bulk Ni, in the absence of the counterpart. The surface reconstruction for GR/Ni system was analyzed base on the calculated radial pair distribution function of Ni and C atoms. The surface roughness was visualized using 2D atomic distribution maps. For the studied substrate orientations and temperatures, it was found that the most densely packed orientation of the Ni base {111} provides minimal changes of the structural parameters of both counterparts at 400 K.

The incorporation of polycarboxylate ether superplasticizer (PCE) type polymer and silica fume (SF) in high-performance concretes (HPC) leads to the achievement of remarkable rheological and mechanical improvements. In the fresh state, PCEs are adsorbed on cement particles and dispersants, in turn promoting the workability of the concrete. Silica fume enables a very well compacted concrete to be obtained, which is characterized by high mechanical parameters in its hardened state. Some PCEs are incompatible with silica fume, which can result in the loss of slump and in poor rheological behavior. The main objective of the research is the study of the influence of three types of PCEs, which all have a different molecular architecture, on the rheological and mechanical behavior of high-performance concretes containing 10% of SF as a partial replacement of cement. The results show that the carboxylic density of PCE has an influence on its compatibility with SF.

Gastric cancer (GC) is a highly heterogeneous, complex disease and the fifth most common cancer worldwide (about one million cases and 784 000 deaths worldwide in 2018). CG is lately diagnosed and guarantees a poor prognosis for GC (the 5-year survival rate is less than 20%, but in early detection can reach 90%). This study evaluated the transcriptional profile in tumor gastric samples to find genes highly expressed during tumor establishment and use the related proteins as targets to find new anticancer molecules. Data was collected at Gene Expression Omnibus (GEO) bank to obtain 3 dataset matrices that analyze gastric tumor tissue versus normal gastric tissue, performed microarray using GPL570 platform, and from different sources. The genes found in silico analysis were confirmed in several lines of GC cells by RT-qPCR. The protein data bank was used to find the correspondent proteins. Then a structural-based virtual screening was done to find molecules, and docking analysis was done using the DockThor server. Our results of transcriptomic analysis, together with RT-qPCR, confirm the high expression of the genes AJUBA, FBXL13, CCDC69, CD80 and NOLC1 in GC lines. Based on that, the correspondent proteins were used in SBVS analysis. Five molecules, one each target, MCULE-2386589557-0-6, MCULE-7343047040-0-1, MCULE-5230409338-0-3, MCULE-9178344200-0-1 and MCULE -5881513100-0-29. All molecules have favorable pharmacokinetic, pharmacodynamic and toxicological properties. Molecular docking analysis revealed that the molecules interact with proteins in critical sites for their activity. Using a virtual screening approach, a molecular docking study was performed for proteins encoded by genes that play important roles in cellular functions for carcinogenesis. Combining a systematic collection of public microarray data with a comparative meta-profiling, RT-qPCR, SBVS, and molecular docking analysis provided a suitable approach to find genes involved in GC and work the correspondent protein to strive for new molecules with anticancer properties.

Tamanu oil has traditionally been used to treat various skin problems. The oil has wound-healing and skin-regenerating capabilities, and encourages the growth of new skin cells, all of which are helpful for fading scars and hyperpigmentation, as well as promoting an all-around glow. The strong nutty odor and high viscosity are the major disadvantages associated with their application. The aim of this study was to create bigels using tamanu oil for its anti-scarring properties. Bigels were prepared with Tamanu oil ranging from 5 to 20% along with micronized xanthan gum and evaluated for their pH, viscosity, and spreadability. In silico studies were performed to analyze the binding affinity of the protein with the drug, and the anti-scarring activity was established using a full-thickness excision wound model. In silico studies have reported that the components Calanolide A, Inophyllum C, and 4-Norlanosta-17(20),24-diene-11,16-diol-21-oic acid, and 3-oxo-16,21-lactone had docking scores of -9.8, -11.3, and -11.1, respectively with the cytokine TGF- β1 receptor. An acute dermal irritation study in rabbits showed no irritation, erythema, eschar, or edema. In vivo excisional wound healing studies performed on wistar rats and subsequent histopathological studies showed that bigels had better healing properties when compared to the commercial formulation (Murivenna oil). This study substantiates the wound healing and scar reduction potential of Tamanu oil bigels.

Lysophosphatidic acid (LPA) is a promising biomarker candidate to screen for ovarian cancer (OC) and potentially stratify and treat patients according to disease stage. LPA is known to target actin-binding protein gelsolin that is a key regulator of actin filament assembly. Previous studies have shown that the phosphate headgroup of LPA alone is inadequate to bind to the short chain of amino acids in gelsolin known as the PIP2-binding domain. Thus, the molecular-level detail of the mechanism of LPA binding is poorly understood. Here, we model LPA binding to the PIP2-binding domain of gelsolin in the gelsolin-actin complex through extensive ten microsecond atomistic molecular dynamics (MD) simulations. We predict that LPA binding causes a local conformational rearrangement due to LPA interactions with both gelsolin and actin residues. These conformational changes are a result of the amphipathic nature of LPA, where the anionic phosphate, polar glycerol and ester groups, and lipophilic aliphatic tail mediate LPA binding via charged electrostatic, hydrogen bonding, and van der Waals interactions. The negatively-charged LPA headgroup binds to the PIP2-binding domain of gelsolin-actin while its hydrophobic tail is inserted into actin, creating a strong LPA-insertion pocket that weakens the gelsolin–actin interface. The computed structure, dynamics, and energetics of the ternary gelsolin–LPA–actin complex confirms that a quantitative OC assay is possible based on LPA-triggered actin release from the gelsolin-actin complex.

N'-(5-bromofuran-2-carbonyl)isonicotinohydrazide (1) was obtained as a white solid in 83% yield by 2-methyl-6-nitrobenzoic anhydride (MNBA)/4-dimethylaminopyridine (DMAP)-catalyzed reaction of 5-bromofuran-2-carboxylic acid and isoniazid in dichloromethane at room temperature. The structure of N'-(5-bromofuran-2-carbonyl)isonicotinohydrazide (1) was elucidated by 1H NMR, 13C NMR, FTIR, and the high resolution mass spectrometers. Molecular docking screening of the title compound (1) on the cyclooxygenase-2 (COX-2) protein (PDB ID: 5IKR) exhibited that compound (1) has a good binding affinity, suggesting that it is very interesting for further structure optimization and in-depth research as a potential COX-2 inhibitor.

Galectins have been shown to have roles in cancer progression via contributions to angiogenesis, metastasis, cell division, and evasion of immune destruction. This study analyses galectin-1, -3, and -9 serum concentrations in breast cancer patients by enzyme-linked immunosorbent assay (ELISA) against the characteristics of the patient and tumor such as stage, molecular subtype, and receptor expression. Galectin-9 was found to be statistically significantly increased in HER2 enriched tumors as well as being reduced in patients with hormone receptor positive tumors and increased in patients with HER2 amplified tissues. Galectin-1 was found to be statistically significantly increased in the serum of patients who had undergone hormonal, immunotherapy, or chemotherapy. These findings provide insight as to the changes in galectin levels during cancer progress, response to treatment and molecular phenotype. These findings are valuable in the further understanding of the relationships of galectin and tumor biology and can inform future research on therapeutic targets for galectin inhibitors and the utility of galectin biomarkers.

Mechanochemical technology is developing rapidly, judging by the scientific information in both basic and applied studies. However, many issues and points of view remain to be discussed. This review presents some new key issues for the optimization of mechanochemical processes in theoretical and practical aspects. Emphasis is placed on powder technology aspects, which are not always discussed compared to functional or microscopic viewpoints. The transfer of chemical species across the interparticle interface between organic and inorganic species during the mechanosynthesis of nanocomposite oxides offers many new possibilities, which are discussed here in detail. Since all material transport is preceded by charge transfer, its driving force has been searched for using terminology beyond the well-established electrochemical ones. The role of organic compounds during the whole process is emphasized, regardless of their survival in the final product. The similarity with the pharmaceutical phenomena is pointed out, although its mentality is very different from that of the synthesis of nanocomposites. Not only for the rational amorphization of the active pharmaceutical ingredient, but also for the stabilization of molecular dispersion states with the participation of excipients are discussed. The effects of liquids, either added or formed by mechanochemical auto-liquefaction, are presented with reference to the comparison between wet and dry grinding. Finally, mechanisms of apparent stabilization of mechanically activated states of products are elucidated to investigate the practical applicability of mechanochemically synthesized products

Cancer is a devastating disease, causing tremendous morbidity and mortality each year. Cancer can be considered as a genetic disease in the sense that instabilities in protooncogenes and tumor suppressor genes are among the hallmarks of cancer progression and metastasis. However, a particular cancer can express different proteins in different patients, making cancer a heterogeneous disease. This heterogeneity in part influences treatment resistance and failure. Therefore, it is crucial to understand the mechanism by which cancer cells develop and enhance resistance to different agents. This review aims to present the general paradigm and recent updates on cancer cell resistance to different antitumor agents. It demonstrates that tumor resistance results from a myriad of factors, including tumor microenvironment, supporting immune cells, and cancer stem cells. This interaction contributes to cancer cells overcoming the therapeutic effects of different classes of antitumor agents, such as cytotoxic chemotherapeutics, targeted agents, and immunotherapies. With the development of advanced molecular analysis, specialized genomic assessment has assisted clinicians and researchers in choosing selected agents combating cancer cells. Together, this approach can potentially reduce treatment toxicity, health system burden, and financial costs while improving patient quality of life. Understanding the exact mechanism of drug resistance in cancer cells can open the way to new effective and less toxic therapeutics.

Background: Currently, limited number of therapeutic options are available to treat Diabetes mellitus, and to find a potential candidate, laboratory work takes time and also needs animal studies. So, the aim of this study was to determine the efficacy of some natural phytocompounds with the aid of molecular docking, bioinformatics and in silico drug design approaches. Method: Two proteins (Human CYP3A4 linked to metformin and Human dipeptidyl peptidase-IV) were selected and molecular docking studies were conducted using Pymol, AutoDock Vina, PyRx, and Discovery Studio. Different important pharmacokinetic parameters like ADME and toxicity data were obtained from online databases SwissADME and pkCSM program. Results: It was found that human dipeptidyl peptidase-IV (PDB ID: 4A5S) has exhibited a maximal affinity of -9.7 Kcal/mol for bryonolic acid and hesperidin, but only -6.7 kcal/mol for metformin hydrochloride. Similarly, the highest affinity of hesperidin for human CYP3A4 bound to metformin (PDB ID: 5G5J) is -10.7 Kcal/mol compared to metformin hydrochlor (-6.3 Kcal/mol). Besides, all the compounds have been documented outstanding ADMET profile, and accepted by drug-likeness or Lipinski rule. Conclusions: The present study suggested that these compounds can be further investigated in vitro and in vivo to establish them as lead compounds against Diabetes mellitus..

Accumulation of extra fats in the body results in disturbance in homeostasis causing obesity. The pathophysiology of obesity has been associated with various genetic, epigenetic factors and the disturbed lifestyles of an individual. One of the outcomes is disturbance in the sleep cycle which leads to sleep disorders. The evolutionary significance of sleep lies in the fact that it saves energy and is crucial for adjustment of an individual to ecological and environmental factors, and thus maintains homeostasis. Sleep has an anabolic function and replenishes the wakefulness-associated loss of glycogen stores. However, the modern lifestyle is well known to disrupt sleep behavior and patterns affecting human health negatively. Alteration in homeostasis leads to several acute and chronic pathophysiological conditions like obesity and related metabolic morbidities being one amongst them. Shorter sleep duration and poor sleep quality are important risk factors associated with the development of obesity and have more adverse effects on energy homeostasis. Consequently, it is crucial to comprehend the obesity and sleep relationship and its therapeutic strategies, given that strong crosstalk exists between energy balance that favors obesity and sleep apnea. It is therefore highly recommended to the people with a high risk of obesity to maintain sleep discipline and good sleep hygiene in our daily life. Interventions are required to improve both sleep quality and quantity, and associated obesity. More focused research is needed for uncovering the pieces of evidence that determine whether such interventions can improve obesity-related health consequences. The present review discusses the important findings on the therapeutic and neuroendocrine mechanisms regulating sleep and obesity.

Four previously undescribed highly oxygenated diterpenoids (1–4), zeylleucapenoids A–D, characterized by halimane and labdane skeletons, were isolated from the aerial parts of Leucas zeylanica. Their structures were elucidated primarily by NMR experiments. The absolute configuration of 1 was established by theoretical ECD calculations and X-ray crystallographic analysis, whereas those for 2−4 were assigned by theoretical ORD calculations. Zeylleucapenoid D (4), with an IC₅₀ value of 38.45 μM in RAW264.7 macrophages and nontoxic activity for zebrafish embryo, and obviously inhibited pro-inflammatory cytokines TNF-α and IL-6 in a dose-dependent manner. Compound 4 inhibited of the expression of inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2). Furthermore, molecular docking analysis indicated the possible mechanism of action for 4 may be bind to targets by hydrogen- and hydrophobic- bond interactions.

Oil-tea (Camellia oleifera) is a woody oil crop whose nectar includes galactose derivatives that are toxic to honey bees. Interestingly, some mining bees of the genus Andrena can entirely live on nectar (and pollen) of oil tea and are able to metabolize these galactose derivatives. We present the first next-generation genomes for five and one Andrena species that are respectively specialized and non-specialized oil-tea pollinators, and combining with published genomes of six other Andrena species which did not visit oil-tea, we performed molecular evolution analyses on genes involved in metabolism of galactose derivatives. Six genes (NAGA, NAGA-like, galM, galK, galT, and galE) involved in galactose derivatives metabolism were identified in the five oil-tea specialized species, but only five (with the exception of NAGA-like) were discovered in the other Andrena species. Molecular evolution analyses revealed that NAGA-like, galK and galT in oil-tea specialized species appeared under positive selection. RNASeq analyses showed that NAGA-like, galK, and galT were significantly up-regulated in the specialized pollinator A. camellia compared to the non-specialized pollinator A. chekiangensis. Our study demonstrated that the genes NAGA-like, galK, and galT had played an important role in the evolutionary adaptation of the oil-tea specialized Andrena species.

The JC polyomavirus virus (JCPyV) affects more than 80% of the human population in their early life stage. It mainly affects immunocompromised individuals where virus replication in oligodendrocytes and astrocytes may lead to fatal progressive multifocal encephalopathy (PML). Virus protein 1 (VP1) is one of the major structural proteins of the viral capsid, responsible for keeping the virus alive in the gastrointestinal and urinary tracts. VP1 is often targeted for antiviral drug and vaccine development. Similarly, this study implied immunoinformatics and molecular dynamics simulation-based approaches to design a multi-epitope subunit vaccine targeting JCPyV. The VP1 protein epitopic sequences, which are highly conserved, were used to build the vaccine. This designed vaccine includes two adjuvants, five HTL epitopes, six CTL epitopes, and two linear BCL epitopes to stimulate cellular, humoral, and innate immune responses against JCPyV. Furthermore, molecular docking and molecular dynamics simulation (100ns) studies were used to examine the interaction and stability of the vaccine protein with TLR4. Trajectory analysis showed that the vaccine and TLR4 receptor form a stable complex with the vaccine protein. Overall, this study contributed to the path of vaccine development against JCPyV and may prevent PML from happening. However, this study needs experimental validation to conclude our findings.

Curcuma longa is only a rich source of curcumin (1) and its major analogues demethoxycurcumin (2) and bisdemethoxycurcumin (3) among the Curcuma species. The content ratio of these three curcumins in turmeric is depended on the varieties and growing environment. Recently, curcumin (1) has been reported as potential inhibitor of hepatic and enzymatic protein tyrosine phosphatase 1B (PTP1B) and its related disorders such as hypertriglyceridemia, hyperlipidemia and liver steatosis. Thus, we further purified curcumins (1–3) from C. longa and investigated their inhibitory effects against PTP1B and α-glucosidase enzymes. As the result, curcumins (1–3) exhibited potential PTP1B inhibition with IC50 values of 37.8 ± 1.4, 45.3 ± 0.7, and 72.6 ± 1.1 μM, respectively, and α-glucosidase inhibition with similar manner (IC50 values of 78.2 ± 0.2, 82.4 ± 0.6, and 90.6 ± 1.0 μM, respectively). These results reveal a key role of methoxylation in the variation of PTP1B and α-glucosidase inhibitory activity for these curcumins. In addition, density functional theory (DFT) was used accompanying with molecular docking (MD) to analyze the ligand stability and the interaction of curcumins (1–3) with PTP1B and glucoside hydrolase proteins. Assay-based results and the MD data obtained are highly correlation suggesting that the deterioration of the enzyme activity caused by the distortion of structural conformation of PTP1B and glucoside hydrolase may be related to the arrangement of amino acids in protein structure. This reported for the first time that inhibitory effects of curcumins (1–3) against PTP1B and glucoside hydrolase have been examined in vitro and in silico as well.

The genetic code conceals a ‘code within the codons’, which hints at biophysical interactions between amino acids and their cognate nucleotides. But research over decades has failed to corroborate systematic biophysical interactions across the code. Using molecular dynamics simulations and NMR, we have analysed interactions between the 20 standard proteinogenic amino acids and four RNA mononucleotides in three charge states. Our simulations show that 50% of amino acids bind best with their anticodonic middle base in the -1 charge state common to the backbone of RNA, while 95% of amino acids interact most strongly with at least one of their codonic or anticodonic bases. Preference for the cognate anticodonic middle base was greater than 99% of randomized assignments. We verify a selection of our results using NMR, and highlight challenges with both techniques for interrogating large numbers of weak interactions. Finally, we extend our simulations to a range of amino acids and dinucleotides, and corroborate similar preferences for cognate nucleotides. Despite some discrepancies between the predicted patterns and those observed in biology, the existence of weak stereochemical interactions means that random RNA sequences could template non-random peptides. This offers a compelling explanation for the emergence of genetic information in biology.

Human metapneumovirus is one of major causes of common cold among children, especially infants. Its key enzyme is RNA-dependent RNA-polymerase, which performs both replication and transcription, including capping and cap methylation. The goal of the work is to find possible inhibitors of RNA-dependent RNA-polymerase across the active compounds of Rosaceae plants. The candidates were selected by molecular docking to cap-transferring domain of RNA-polymerase (PDB ID: 4UCZ) in Autodock VINA. Among all the substances tested by docking, ellagic acid derivatives showed the most promising results (affinity values below -10 kcal/mol). Hence, they could be treated as possible candidate drugs against metapneumoviral infection after experimental examination. The main advantage of using these substances should be their low toxicity, which is quite uncommon for selective RNA polymerase inhibitors used in clinical practice. Occurrence of ellagic acid derivatives among the plants from Rosaceae family like raspberry could explain their effect during common cold.

This joint experimental-theoretical work focuses on molecular and photophysical properties of the spiropyran-containing amphiphilic molecule in organic and aqueous solutions. Being dissolved in tested organic solvents, the system demonstrates positive photochromism, i.e. upon UV stimulus the colorless spiropyran form is transformed into colorful merocyanine isomer. However, aqueous solution of the amphiphile possesses a negative photochromism: the orange-red merocyanine form turns to be thermodynamically more stable in water, and both UV and vis stimuli lead to the partial or complete photobleaching of the solution. The explanation of this phenomenon is given on the basis of density functional theory calculations and classical modeling including thermodynamic integration. The simulations reveal that stabilization of merocyanine in water proceeds with the energy of ca. 70 kJ mol−1, and that the Helmholtz free energy of hydration of merocyanine form is 100 kJ mol−1 lower as compared to the behavior of SP isomer in water. The explanation of such a difference lies in the molecular properties of the merocyanine: after ring-opening reaction this molecule transforms into a zwitterionic form, as evidenced by the electrostatic potential plotted around the opened form. The presence of three charged groups on the periphery of a flat conjugated backbone stimulates the self-assembly of merocyanine molecules in water, ending up with the formation of elongated associates with stack-like building blocks, as shown in molecular dynamics simulations of the aqueous solution with the concentration above critical micelle concentration. Our quantitative evaluation of the hydrophilicity switching in spiropyran/merocyanine containing surfactants may prompt the search for new systems, including colloidal and polymeric ones, aiming at remote tuning of their morphology, which could give new promising shapes and patterns for the needs of modern nanotechnology.

Documenting prehistoric and historical hemp retting for fiber extraction is important in the study of human uses of this iconic plant and its cultural implications. In paleoecology, hemp retting is usually inferred from indirect proxies, notably anomalously high percentages of Cannabis pollen in lake sediments, but some recent studies have also used specific molecular biomarkers (cannabinol, Cannabis DNA) as a more straightforward evidence. Here we provide direct evidence of hemp retting by identifying phylogenetic signatures (16S rRNA genes) from pectinolytic bacteria actually responsible for the fermentation process that separates the fiber from the stalk, namely Bacillus, Clostridium, Escherichia, Massilia, Methylobacterium, Pseusomonas, Rhizobium and Rhodobacter. These analyses have been performed in the sediments from an Iberian lake previously considered as an important hemp retting site during the last five centuries, on the basis of Cannabis pollen abundances. The good match between biomarker and pollen evidence, in the context of the recent historical development of hemp industry in Spain, can be useful to interpret paleoecological records from other similar lakes in the way toward a more regional view on the introduction, spreading, uses and associated cultural connotations of Cannabis in the Iberian Peninsula within European and Mediterranean contexts.

The effect of the communication channel size on the transport and subsequent detection of chemical messengers is investigated on millimetric and micrometric channels. The transport of the information carriers, being characterized by an advective and a diffusive contribution, was simulated by varying the flow velocity and the diffusion coefficient. Then, to evaluate the information quality, the Intersymbol Interference (ISI) between two consecutive signals at a specific release delay was estimated. This allowed us to verify that operating under micrometric channel conditions has a larger flow velocity range to obtain completely separated successive signals and smaller release delays can be used between signals. The theoretical results were confirmed by developing a prototype molecular communication platform operating under microfluidic conditions, which enables communication through fluorescent nanoparticles, namely Carbon Quantum Dots (CQDs).

Globally 390 millions of people are at risk of dengue infection; over the past 50 years the virus incidence increased thirty-fold. In Senegal, an unprecedented occurrence of outbreaks and sporadic cases was noticed since 2017. In October 2018 an outbreak of DENV-2 was reported in Rosso area in the north of Senegal at the border with Mauritania. Out of the 187 blood specimen samples collected, 27 were positives by qRT-PCR and 8 were serologically positive for DENV IgM. Serotyping using qRT-PCR reveals that isolates were positive for DENV-2. A subset of DENV-2 positives samples was selected and subjected to full genome sequencing followed by phylogenetic analysis. Analysis of 06 nearly completed genome sequences (n= 6) revealed that isolates belong to the cosmopolitan genotype and are closely related to the Mauritanian strains detected between 2017 and 2018 and those detected in many West African countries such as Burkina Faso or Cote d’Ivoire. Our results suggest a transboundary circulation of the DENV-2 cosmopolitan genotype between Senegal and Mauritania and call for a need of coordinated surveillance of arboviruses between these two countries. Interestingly, high level of homology between West African isolates highlights endemicity and call for a set-up of sub-regional viral genomic surveillance which will lead to a better understanding of viral dynamic, transmission and spread across Africa.

Ralstonia solanacearum is the causative agent of bacterial wilt, one of the most destructive plant diseases. While chemical control has an environmental impact, biological control strategies can allow sustainable agrosystems. Three lytic bacteriophages (phages) of R. solanacearum with biocontrol capacity in environmental water and plant were isolated from river water in Europe but not fully characterized, their genomic characterization being fundamental to understand their biology. In this work, the phage genomes were sequenced and subjected to bioinformatic analysis. The morphology was also observed by electron microscopy. Phylogenetic analyses were performed with a selection of phages able to infect R. solanacearum and the closely related phytopathogenic species R. pseudosolanacearum. The results indicated that the genomes of vRsoP-WF2, vRsoP-WM2 and vRsoP-WR2 range from 40,688 to 41,158 bp with almost 59% GC-contents, 52 ORFs in vRsoP-WF2 and vRsoP-WM2, and 53 in vRsoP-WR2 but, with only 22 or 23 predicted proteins with functional homologs in databases. Among them, two lysins and one exopolysaccharide (EPS) depolymerase, this type of depolymerase being identified in R. solanacearum phages for the first time. These three European phages belong to the same novel species within the Gyeongsanvirus, Autographiviridae family (formerly Podoviridae). These genomic data will contribute to a better understanding of the abilities of these phages to damage host cells and, consequently, to an improvement in the biological control of R. solanacearum.

The report introduces hybrid polyelectrolyte-stabilized colloids combining blue and green emitting building blocks, that are citrate carbon dots (CDs) and [TbL]+ chelate complexes with 1,3-diketonate derivatives of calix[4]arene. The joint incorporation of green and blue emitting blocks into the polysodium polystyrenesulfonate (PSS) aggregates is carried out through the solvent-exchange synthetic technique. The coordinative binding between Tb3+ centers and CD surface groups in initial DMF solutions both facilitates joint incorporation of [TbL]+ complexes and the CDs into the PSS-based nanobeads and affects fluorescence properties of [TbL]+ complexes and CDs, as well as their ability to temperature sensing. The variation of the synthetic conditions is represented herein as a tool for tuning the fluorescent response of the blue and green emitting blocks upon heating and cooling. The revealed regularities enable developing either dual band luminescent colloids for monitoring temperature changes within 25-50 C through double color emission, or to transform the colloids into ratiometric temperature sensors via simple concentration variation of [TbL]+ and CDs in initial DMF solution. Novel hybrid carbon dots-terbium chelate PSS-based nanoplatform opens an avenue for new generation of sensitive and customizable single excited dual band nanothermometers.

Gene expression data is key for the functional annotation of single nucleotide polymorphisms (SNPs) identified in genome-wide association studies (GWAS). Expression and splicing quantitative trait loci (e/sQTLs) in normal colon tissue, such as those from the University of Barcelona and University of Virginia RNA sequencing project (BarcUVa-Seq) and the Genotype-Tissue Expression project (GTEx), are required to gain biological insight of colon-related diseases risk loci. Moreover, transcriptome-wide association studies (TWAS) rely on reference gene expression imputation panels in the tissue of interest to nominate susceptibility genes. Also, it is of high interest to study the relationships between genes in a network framework. For facilitating these analyses, we have updated and expanded the scope of the Colon Transcriptome Explorer (CoTrEx) to the version 2.0. This web-based resource provides exhaustive visualization and analysis of transcriptome-wide gene expression profiles of normal colon tissue from BarcUVa-Seq and GTEx. In addition to the integration of new datasets, CoTrEx 2.0 provides additional e/sQTLs sets, as well as gene expression prediction models and regulatory and co-expression networks. It is freely available at https://barcuvaseq.org/cotrex/. Overall, it is of high interest for researchers aiming to investigate the genetic susceptibility to colon-related complex traits and diseases.

Background: Left ventricular noncompaction (LVNC) is a genetically determined cardiomyopathy, that occurs following a disruption of endomyocardial morphogenesis. The purpose of this study was to identify the clinical characteristics and genetic profile of children with LVNC. Methods: From February 2008 to July 2020, a total of 32 children (median 11.5 years) with LVNC were prospectively enrolled and followed up for the median of 4.02 years. Diagnosis was made based on characteristic features of LVNC in echocardiography and cardiovascular magnetic resonance (CMR). Patients’ clinical symptoms, family history, ECG, Holter ECG and genetic tests were also evaluated. Results: The most common presenting symptom was heart failure (31% of children). ECG abnormalities were noted in 56% of patients. The most prominent features were ventricular arrhythmias, sinus bradycardia and paroxysmal third-degree atrioventricular block. Most of the patients (94%) met the criteria for LVNC and CMR confirmed this diagnosis in 82% of cases. The molecular etiology was found in 53% of children. Conclusion: Although heart failure and arrhythmias were very frequent in our study group, thromboembolic events and genetic syndromes were rare. For accurate and reliable assessment of children with LVNC, it is necessary to get to know their family history and detailed clinical profile.

It has been more than a year since the first case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was found. This coronavirus has infected more than 110 million people worldwide by the end of February, 2021, and several virulent as well as more spreadable mutant forms of SARS-CoV-2 have emerged subsequently. In the latter group, three variants B.1.1.7, B.1.351, and P1 lineages, have been reported. Using computer simulation, the present paper investigates the structural differences between the wild type SARS-CoV-2 spike protein and its Asn501Tyr (N501Y) mutant variant. Time-based structural changes between the receptor binding domains of these two species are also examined. The N501Y mutation is common to all the three aforesaid mutant variants.

Phenotypes are driven by regulated gene expression, which in turn are mediated by complex interactions between diverse biological molecules. Protein-DNA interactions such as histone and transcription factor binding are well studied, along with RNA-RNA interactions in short RNA silencing of genes. In contrast, lncRNA-protein interaction (LPI) mechanisms are comparatively unknown, likely driven by the difficulties in studying LPI. However, LPI are emerging as key interactions in epigenetic mechanism, playing a role in development and disease. Their importance is further highlighted by their conservation across kingdoms. Hence, interest in LPI research is increasing. We therefore review the current state of the art in lncRNA-protein interactions. We specifically surveyed recent computational methods and databases which researchers can exploit for LPI investigation. We discovered that algorithm development is heavily reliant on a few generic databases containing curated LPI information. We show that early methods predict LPI using molecular docking, have limited scope and are slow, creating a data processing bottleneck. Recently, machine learning has become the strategy of choice in LPI prediction, likely due to the rapid growth in machine learning infrastructure and expertise. While many of these methods have notable limitations, machine learning is expected to be the basis of modern LPI prediction algorithms.

The growing population meet the challenge for agricultural production. CRISPR/Cas9 technology is based on plant research for the development of the new varieties as well as disease resistance crops. In addition the deletion of significant characters makes the new alleles from the CRISPR/Cas9. Recent and reliable molecular scissor for genetic engineering. The review is focused on the various application of the CRISPR/Cas9 technology in plant enhancement of plant disease resistance, stress burden in plant, nutritional improvement, and quality of crops from the CRISPR/Cas9 system. The clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein9 (cas9) is adopted from the prokaryotic type II system. CRISPR/Cas9 is simplicity and efficiency than ZENs and TALENs for the genome engineering. Due to rapid growing of the CRISPR/Cas9 system has been formulate the adaptation of many plant species. The current advancement of plants and future schemes of improve of CRISPR technology has been presented in contest of multiplex editing, knowledge on induced mutation whether the factor effect in CRISPR/Cas9 technology in plant. Remarkable perspective and challenges of CRISPR/Cas9 technology in significance of plant genetic modification.

In December 2019, the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in the province of Wuhan, China. Since then, it has spread worldwide with new mutations being reported. We performed genomic analysis to identify the changes in genetic diversity of SARS-CoV-2 between December 2019 and November 2020, and through molecular surveillance, we monitored the mutations that could be involved in viral fitness. We analyzed 2,213 complete genomes from 6 geographical regions worldwide, which were downloaded from GenBank and GISAID databases. Although SARS-CoV-2 presented low genetic diversity, there has been an increase over time, with the presence of several hotspot mutations throughout its genome. We identified 7 frequent mutations that resulted in non-synonymous substitutions (dN). Two of them, C14408T>P323L and A23403G>D614G, located in the nsp12 and Spike protein, respectively, emerged early in the pandemic and showed a considerable increase in frequency over time. Two other mutations, A1163T>I120F in nsp2 and G22992A>S477N in the Spike protein emerged recently and have spread in Oceania and Europe. Continuous molecular surveillance of SARS-CoV-2 will be necessary to detect and describe the transmission dynamics of new variants of the virus with clinical relevance. This information is important to improve programs to control the virus.

Arterial hypertension is a health problem that affects millions of people around the world. Particularly in Chile, according to the last health survey in 2019, 28.7% of the population had this condition, and arterial hypertension complications cause one in three deaths per year. In this work, we have used molecular simulation tools to evaluate new compounds designed in silico by our group as possible anti-hypertensive agents, taking Neutral Endopeptidase (NEP) as a target, a key enzyme in the arterial hypertension regulation at the level kidney. We use docking experiments, molecular dynamics simulation, free energy decomposition calculations (by MM-PBSA method), and ligand efficiency analysis to identify the best anti-hypertensive agent pharmacokinetic and toxicological predictions (ADME-Tox). The energetic components that contribute to the complexes stability are the electrostatic and Van der Waals components; however, when the ADME-Tox properties were analyzed, we conclude that the best anti-hypertensive candidate agents are Lig783 and Lig3444, taking Neutra Endopeptidase as a target.

Aims: Angiotensin-converting enzyme 2 (ACE2) plays an important role in the entry of coronaviruses into host cells. This paper described how carnosine, a naturally occurring supplement, can be an effective drug candidate for coronavirus disease (COVID-19) on the basis of molecular docking and modeling to host ACE2 co-crystallized with COVID-19 spike protein. Methods: First, the starting point was ACE2 inhibitors and their structure-activity relationship (SAR). Next, chemical similarity (or diversity) and PubMed searches made it possible to repurpose and assess approved or experimental drugs for COVID-19. In parallel, at all stages, authors performed bioactivity scoring to assess potential repurposed inhibitors at ACE2. Finally, investigators performed molecular docking and modeling of the identified drug candidate to host ACE2 co-crystallized with COVID-19 spike protein. Results: Carnosine emerged as the best known drug candidate to match ACE2 inhibitor structure. Preliminary docking was more optimal to ACE2 than the known typical angiotensin-converting enzyme 1 (ACE1) inhibitor (enalapril) and quite comparable to known or presumed ACE2 inhibitors. Viral spike protein elements binding to ACE2 were retained in the best carnosine pose in SwissDock at 1.75 Angstroms. Out of the three main areas of attachment expected to the co-crystallized protein structure, carnosine bind with higher affinity to two compared to the known ACE2 active site. LibDock score was 92.40 for site 3, 90.88 for site 1, and inside the active site 85.49. Conclusion: Carnosine has promising inhibitory interactions with host ACE2 co-crystallized with COVID-19 spike protein and hence could offer potential mitigating effect against current COVID-19 pandemic.

The regioselectivity in non-polar [3+2] cycloaddition (32CA) reactions has been studied within the Molecular Electron Density Theory (MEDT) at the B3LYP/6-311G(d,p) level. To this end, the 32CA reactions of nine simplest three-atom-components (TACs) with 2-methylpropane were selected. The electronic structure of the reagents has been characterised through the Electron Localisation Function (ELF) and the Conceptual DFT. The energy profiles of the two regioisomeric reaction paths and ELF of the transition state structures are studied to understand the origin of the regioselectivity in these 32CA reactions. This MEDT study permits to conclude that the least electronegative ends X1 atom of these TACs controls the asynchronicity in the C-X (X = C,N,O) single bond formation, and consequently, the regioselectivity. This behaviour is a consequence of the fact that the creation of the non-bonding electron density required for the formation of the new CX single bonds has a lesser energetic cost at the least electronegative X1 atom than that at the Z3 one.

We prepared heterogeneous alumina-silicate glasses by consolidating nanoparticles using molecular dynamics simulations. Consolidated glasses from either low alumina content alumina-silicate glasses or high alumina content alumina-silicate glasses show significantly improved ductility around consolidation pressure of ~3 GPa. The introduced structural heterogeneities, namely over-coordinated network formers and their neighboring oxygen atoms, are identified as plasticity carriers due to their high rearrangement propensity. In addition, consolidated oxide glass from both 23.4Al₂O₃76.6SiO₂ and 73.1Al₂O₃26.9SiO₂ nanoparticles show improved flow strength (up to 1 GPa) due to the introduction of chemical heterogeneities. Last but not least, apparent hardening behavior appears upon cold work in consolidated glasses, with an increase of yield strength from ~3.3 GPa to ~6.4 GPa. This method is a big advancement toward ultra-strong and ultra-tough glasses by breaking the structure, composition and size limitations in traditional melt-quench process.

The tumour-associated isoenzymes, hCA IX and hCA XII catalyze the hydration of carbon dioxide to bicarbonate and protons. These isoforms are highly overexpressed in many types of cancer, where they contribute for the acidification of the tumor environment promoting the tumor cell invasion and metastasis. In this work, in order to identify novel dual hCA IX and XII inhibitors, virtual screening techniques and biological assays were combined. A structure based virtual screening towards hCA IX and XII was performed using a database of approximately 26000 natural compounds. The best shared hits were submitted to a thermodynamic analysis and 3 promising best hits were identified and evaluated in terms of their hCA IX and XII inhibitor activity. In vitro biological assays are in line with the theoretical studies and revealed that Syringin, Lithospermic acid, and (-)- Dehydrodiconiferyl alcohol behave as good hCA IX and hCA XII dual inhibitors.

Chemical versatility of organic semiconductors provides nearly unlimited opportunities for tuning their electronic properties. However, despite decades of research, relationship between molecular structure, molecular packing and charge mobility in these materials remains poorly understood. This reduces the search for high-mobility organic semiconductors to the inefficient trial-and-error approach. For clarifying the abovementioned relationship, investigations of the effect of small changes in the chemical structure on OSs properties are particularly important. In this study, we address computationally the impact of substitution of C-H atom pairs by nitrogen atoms (N-substitution) on molecular properties, molecular packing and charge mobility of crystalline oligoacenes. Besides of decreasing frontier molecular orbital levels, N-substitution dramatically alters molecular electrostatic potential yielding pronounced electron-rich and electron-deficient areas. These changes in the molecular electrostatic potential strengthen face-to-face and edge-to-edge interactions in the corresponding crystals and result in the crossover from the herringbone packing motif to π-stacking. When the electron-rich and electron-deficient areas are large, sharply defined and, probably, have certain symmetry, charge mobility increases up to 3-4 cm2V-1s-1. The results obtained highlight the potential of azaacenes for application in organic electronic devices and are expected to facilitate rational design of organic semiconductors for steady improvement of organic electronics.

The aim of this study is the characterization and genomic tracing by phylogenetic analyses of 59 new SARS-CoV-2 Italian isolates obtained from patients attending clinical centres in North and Central Italy until the end of April 2020. All but one of the newly characterized genomes belonged to the lineage B.1, the most frequently identified in European countries, including Italy. Only a single sequence was found to belong to lineage B. A mean of 6 nucleotide substitutions per viral genome was observed, without significant differences between synonymous and non-synonymous mutations, indicating genetic drift as a major source for virus evolution. tMRCA estimation confirmed the probable origin of the epidemic between the end of January and the beginning of February with a rapid increase in the number of infections between the end of February and mid-March. Since early February, an effective reproduction number (Re) greater than 1 was estimated, which then increased reaching the peak of 2.3 in early March, confirming the circulation of the virus before the first COVID-19 cases were documented. Continuous use of state-of-the-art methods for molecular surveillance is warranted to trace virus circulation and evolution and inform effective prevention and containment of future SARS-CoV-2 outbreaks.

A large variety of molecular interactions occurs between biomolecular components in cells. When one or a cascade of molecular interactions results in a regulatory effect, by one component onto a downstream component, a so-called ‘causal interaction’ takes place. Causal interactions constitute the building blocks in our understanding of larger regulatory networks in cells. These causal interactions and the biological processes they enable (e.g., gene regulation) need to be described with a careful appreciation of molecular interactions that occur between entities. A proper description of this information enables archiving, sharing, and reuse by humans and for computational science. Various representations of causal relationships between biological components are currently used in a variety of resources. Here, we propose a checklist that accommodates current representations, and call it the Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). This checklist defines both the required core information, as well as a comprehensive set of other contextual details valuable to the end user and relevant for reusing and reproducing causal molecular interaction information. The MI2CAST checklist can be used as reporting guidelines when annotating and curating causal statements, while assuring uniformity and interoperability of the data across resources.

Recent emergence of novel coronavirus (SARS-CoV-2) all over the world has resulted more than 33,106 global deaths. To date well-established therapeutics modules for infected patients are unknown. In this present initiative, molecular interactions between FDA-approved antiviral drugs against the Hepatitis-C virus (HCV) have been investigated theoretically against the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2. HCV and SARS-CoV-2 are both +ssRNA viruses. At 25^o C beclabuvir, a non-nucleoside inhibitor of the RdRp_HCV can efficiently bind to RdRp _SARS-CoV-2 (ΔG_AutoDock = -9.95 kcal mol^-1) with an inhibition constant of 51.03 nM. Both the ΔG_London and ΔG_{GBVI / WSA} values were - 9.06 and - 6.67 kcal mol^-1, respectively for binding of beclabuvir to RdRp_SARS-CoV-2. In addition, beclabuvir has also shown better binding free energy with RdRp_SARS-CoV-2 (ΔG_vina = -8.0 kcal mol^-1) than that observed with the Thumb 1 domain of RdRp_HCV (ΔG_vina = -7.1 kcal mol^-1). InterProScan has suggested the RNA-directed 5'-3' polymerase activity exists within 549^th to 776^th amino acid residues of RdRp_SARS-CoV, where the major amino acid residues interacting being I591, Y621, C624, D625, A690, N693, L760, D762, D763, and E813-N817. Molecular interaction suggests occupancy of beclabuvir inside the active site environment of the RdRp_SARS-CoV-2, the enzyme essential for viral RNA synthesis. In conclusion, results suggest beclabuvir may serve as an anti-SARS-CoV-2 drug.

Coronavirus disease 2019 (COVID-19) is an emerging infectious disease that was first reported in Wuhan, China and has subsequently spread worldwide. In the absence of any antiviral or immunomodulatory therapies, the disease is spreading at an alarming rate. 5 to 10% of recovered patients in Wuhan test positive again; this suggest that for controlling COVID-19, vaccines may be better option than drugs. A clinical trial to evaluate an anti-COVID-19 vaccine has started recently. However, its efficacy and potency have to be evaluated and validated. As an alternative, we are presenting a first-of-its-kind, designed multi-peptide subunit based epitope vaccine against COVID-19. The vaccine construct comprise an adjuvant, CTL, HTL, and B-cell epitopes joined by linkers. The vaccine is non-toxic, non-allergenic, thermostable and immunogenic with the capability to elicit a humoral and cell-mediated immune response. The findings are validated with high-end computation-based methods. This unique vaccine is made up of 33 highly antigenic epitopes from three proteins that have a prominent role in host receptor recognition, viral entry, and pathogenicity. We advocate this vaccine must be synthesized and tested urgently as public health priority.

The Novel Coronavirus (COVID-19) is a positive-sense single-stranded RNA ((+)ssRNA) virus. The COVID-19 Main Proteases play very important role in the propagation of the Novel Coronavirus (COVID-19). It has already killed more than 8000 people around the world and thousands of people are getting infected every day. Therefore, it is very important to identify a potential inhibitor against COVID-19 Main Proteases to inhibit the propagation of the Novel Coronavirus (COVID-19). We have applied a drug repurposing approach of computational methodology, depending on the synergy of molecular docking and virtual screening techniques, aimed to identify possible potent inhibitors against Novel Coronavirus (COVID-19) from FDA approved antiviral compounds and from the library of active phytochemicals. On the basis of recently resolved COVID-19 Main Protease crystal structure (PDB:6LU7), the library of 100 FDA approved antiviral compounds and 1000 active components of Indian Medicinal Plants extracted for screening against COVID-19 Main Protease. The compounds were further screened using Pyrex virtual screening tool and then best inhibitors, top 19 compounds optimally docked to the COVID-19 Main Protease structure to understand the participation of specific amino acids with inhibitors at active sites. Total 19 best compounds were identified after screening based on their highest binding affinity with respect to the other screened compounds. Out of 19, 6 best compounds were further screened based on their binding affinity and best ADME properties. Nelfinavir exhibited highest binding energy -8.4 kcal/mol and strong stability with the TRP207, ILE281, LEU282, PHE3, PHE291, GLN127, ARG4, GLY283, GLU288, LYS5, LYS137, TYR126, GLY138, TYR126, SER139 and VAL135 amino acid residues of COVID-19 Main Protease participating in the interaction at the binding pocket. In addition to Nelfinavir (-8.4), Rhein (-8.1), Withanolide D (-7.8), Withaferin A (-7.7), Enoxacin (-7.4), and Aloe-emodin (-7.4) also showed good binding affinity and best ADME properties. Our findings suggest that these compounds can be used as potential inhibitors against COVID-19 Main Protease, which could be helpful in inhibiting the propagation of the Novel Coronavirus (COVID-19). Moreover, further in vitro and in vivo validation of these findings would be very helpful to bring these inhibitors to next level study.

The immunomodulatory behaviour of the CCR6/CCL20 axis in multi -system pathophysiology and molecular signalling was investigated at two clinically significant time points, using a Ccr6 - deficient mouse model of spontaneous colitis. Four groups of mice, (C57BL/6J, Ccr6^-/- of C57BL/6J, Winnie x Ccr6 ^-/- and Winnie) were utilized and (I) colonic clinical parameters (2) histology of colon, spleen, kidney and liver (3) T and B lymphocyte distribution in the spleen and MLN by flowcytometry (5) colonic CCL20, phosphorylated PI3K and phosphorylated Akt expression by immunohistochemistry and (6) colonic cytokine expression by RT-PCR were evaluated. CCR6 deficiency was shown to attenuate inflammation in the spleen, liver and gut while renal histology remained unaffected. Marked focal lobular inflammation with reactive nuclear features were observed in hepatocytes and a significant neutrophil infiltration in red pulp with extra medullary hemopoiesis in the spleen existed in Winnie. These changes were considerably reduced in Winnie x Ccr6^-/- with elevated goblet cell numbers and mucus production in the colonic epithelium. Results indicate that Ccr6- deficiency in the colitis model contributes towards resolution of disease. Our findings demonstrate an intricate networking role for CCR6 in immune activation, which is downregulated by Ccr6 deficiency, and could provide newer clinical therapies in colitis.

Curcumin is one of the bioactive metabolites of turmeric (Curcuma longa), known for its pleiotropic pharmacological actions, including antioxidant and anti-inflammation, anticholinesterase, immunomodulation, and neuroprotection. Substantial evidence suggests the therapeutic benefits of curcumin against neurodegenerative disorders, including Alzheimer’s disease (AD), acting on a diverse array of brain targets that make the molecular mechanisms complicated. System biology level-investigation could potentially present a comprehensive molecular mechanism to delineate the neuropharmacological action of curcumin. In this study, we used integrated system pharmacology and molecular simulation analysis to gain insights into the underlying mechanism of curcumin action against AD. Network pharmacology study identified curcumin-targeted potential cellular pathways such as phosphatidylinositol 3-kinase/protein kinase B (PI3K/Akt) signaling, neurotrophin signaling, toll-like receptor (TLR) signaling, and autophagy, and proteins such as tropomyosin receptor kinase B (TrkB), liver X-receptor-beta (LXR-β), estrogen receptor-β (ER-β), mammalian target of rapamycin (mTOR), TLR-2, N-methyl-D-acetate receptor subunit 2B (GluN2B), β-secretase and glycogen synthase kinase-3β (GSK-3β), which are intimately associated with neuronal growth and survival, immune response, and inflammation. Moreover, the molecular modeling further verified that curcumin showed a significant binding affinity to mTOR, TrkB, LXR-β, TLR-2, ER-β, GluN2B, β-secretase, and GSK-3β, which are the crucial regulators of molecular and cellular processes associated with AD. Together, the present system pharmacology and in silico findings demonstrate that curcumin might play a significant role in modulating AD-pathobiology, supporting its therapeutic application for the prevention and treatment of AD.

Matrix Metaloproteinase-2 (MMP-2) is an extracellular Zn²⁺ protease specific to type I and IV collagens. Its expression is associated with several inflammatory, degenerative, and malignant diseases. Conformational properties, domain movements, and interactions between MMP-2 and its associated metal ions were characterized using a 1.0 µs molecular dynamics simulation. Dihedral principle component analysis revealed 10 families of conformations with the greatest degree of variability occurring in the link region connecting the catalytic and hemopexin domains. Dynamics cross correlation analysis indicated domain movements corresponding to opening and closing of the hemopexin domain in relation to the fibronectin and catalytic domains facilitated by the link region. Interaction energies were calculated using the MMPBSA-interaction entropy analysis method and revealed strong binding energies for the catalytic Zn²⁺ ion 1, Ca²⁺ ion 1, and Ca²⁺ ion 3 with significant conformational stability at the binding sites of Zn²⁺ ion 1 and Ca²⁺ ion 1. Ca²⁺ ion 2 diffuses freely away from its crystallographically defined binding site. Zn²⁺ ion 2 plays a minor role in conformational stability of the catalytic domain while Ca²⁺ ion 3 is strongly attracted to the highly electronegative sidechains of the Asp residues around the central β-sheet core of the hemopexin domain.