The explosive emergence of wireless technologies and standards, covering licensed and unlicensed spectrum bands has triggered the appearance of a huge amount of wireless technologies, with many of them coexisting in the same band. Unfortunately, the wireless spectrum is a scarce resource, and the available frequency bands will not scale with the foreseen demand for new capacity. Certain parts of the spectrum, in particular the license-free ISM bands, are overcrowded, while other parts, mostly licensed bands, may be significantly underutilized. As such, there is a need to introduce more advanced techniques to access and share the wireless medium, either to improve the coordination within a given band, or to explore the possibilities of intelligently using unused spectrum in underutilized (e.g., licensed) bands. Therefore, in this paper, we present an open source SDR-based framework that can be employed to devise disruptive techniques to optimize the sub-optimal use of radio spectrum that exists today. Additionally, we describe three use cases where the proposed framework can be employed along with intelligent algorithms to achieve improved spectrum utilization.

With the inclusion of snakebite envenoming on the World Health Organisation’s list of Neglected Tropical Diseases, an incentive has been established to promote research and development effort in novel snakebite antivenom therapies. Different technological approaches are being pursued by different research groups, including the use of small molecule inhibitors against enzymatic toxins, as well as peptide and oligonucleotide-based aptamers and antibody-based biotherapeutics against both enzymatic and non-enzymatic toxins. In this article, the most recent advances in these fields are presented, and the advantages, disadvantages, and feasibility of using different toxin-neutralizing molecules are reviewed. Particular focus within small molecules is directed towards the inhibitors, varespladib, batimastat, and marimastat, while in the field of antibody-based therapies, novel recombinant polyclonal plantivenom technology is discussed.

In order to provide high capacity and universal access of telecommunication networks, this paper reviews and prospects the advanced multiplexing technology, physical layer digital signal processing technology, infrastructure sharing technology, security protection technology, intelligent control management and other key technologies for beyond 100G next generation passive optical network (NG-PON).

High molecular weight glutenin subunits (HMW-GS) and Low molecular weight glutenin subunits (LMW-GS) in mature grains play important roles in the formation of glutenin macropolymer and gluten quality. To characterize the expressed glutenin genes of the bread wheat variety Xinmai 26 during seed development, in this study, we measured the dough rheological properties of mature grains through farinograph and gluten testing system, and revealed its strong gluten quality. The compositions of HMW-GS and LMW-GS were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Further, a total of 18 full-length transcripts were obtained by third-generation RNA sequencing, including 5 transcripts of HMW-GS genes and 13 transcripts of LMW-GS genes (8 intact genes and 5 pseudogenes). The deduced protein structures of transcript sequences exhibit the typical HMW-GS and LMW-GS structural characteristics. Moreover, a specific functional marker was developed to make better use of the extra cysteine residue of 1Dx5 subunit. This study provides an efficient method to accurately identify glutenin genes in bread wheat through matching full-length transcripts to their spectrum of glutenin, which will be helpful to understand the contributions of glutenin genes to wheat quality.

This paper represents a groundbreaking paradigm shift in network optimization. Departing from traditional static methodologies, this innovative approach harnesses the power of Generative Artificial Intelligence (AI) and Large Language Models (LLMs) to optimize cloud networks dynamically. By integrating advanced AI algorithms, this framework continuously adapts and evolves, ensuring optimal real-time performance. This dynamic optimization enhances efficiency and resilience, allowing cloud networks to adjust seamlessly to changing demands and conditions. Through the fusion of cutting-edge technology and adaptive intelligence, this approach heralds a new era in network optimization, empowering organizations to achieve unprecedent-ed levels of agility and scalability in their cloud infrastructures.

The global COVID-19 pandemic claiming global spread continues to evolve, now to the verge of a third wave of outbreak possibly caused by the novel variants of concern of severe acute respiratory syndrome corona virus-2 (SARS-CoV-2). The test positivity rate (TPR) and case fatal-ity rate (CFR) have increased steeply in the second wave of COVID-19 compared to the first. From the example of Kerala, a state in southern India, positivity increased from 1.33% at the peak of wave one in 10th June 2020 to 13.45% during 10th June 2021 in the second wave of pandemic. SARS-CoV-2 is an enveloped single-stranded RNA virus. Angiotensin-Converting Enzyme-2 (ACE-2) is a trans membrane surface protein present on multiple types of cells in the human body to which the viral spike protein attaches. Genetic variations in the SARS-CoV-2 and ACE2 receptor can affect the transmission, clinical manifestations, mortality and the efficacy of drugs and vaccines for COVID-19. Mutations are the primary cause of genetic variations. Given the high TPR and CFR, it is necessary to understand the variations of SARS-CoV-2 and cellular receptors of SARS-CoV-2 at the molecular level. In this review, we summarize the impact of genetic and ep-igenetic variations in determining COVID-19 pathogenesis and disease outcome.

The world has now entered into a replacement era of genomics due to the continued advancements within the next generation high throughput sequencing technologies, which incorporates sequencing by synthesis-fluorescent in place sequencing (FISSEQ), pyrosequencing, sequencing by ligation using polony amplification, supported oligonucleotide detection (SOLiD), sequencing by hybridization alongside sequencing by ligation, and nanopore technology. Great impacts of those methods are often seen for solving the genome related problems of plant and Animalia which will open the door of a replacement era of genomics. This might ultimately overcome the Sanger sequencing that ruled for 30 years. NGS is predicted to advance and make the drug discovery process more rapid.

DNA sequencing methods were first developed more than 20 years ago with the publication of two approaches to sequencing methodology that became known as Sanger sequencing (1), based on enzymatic synthesis from a single-stranded DNA template with chain termination using dideoxynucleotides (ddNTPs) and Maxim-Gilbert sequencing (2),which involved chemical degradation ofend-radio-labeled DNA fragments. Both methods relied on four-lane,high resolution polyacrylamide gel electrophoresis to separate the labeled fragment and allow the base sequence to be read in a staggered ladder-like fashion. Sanger sequencing was technically easier and faster, and thus became the main DNA sequencing method for the vast majority of applications.

Background. Gene rearrangements affecting KMT2A are frequent in acute myeloid leukemia (AML) and are often associated with a poor prognosis. KMT2A gene fusions are often detected by chromosome banding analysis and confirmed by fluorescence in-situ hybridization. However, small intragenic insertions, termed KMT2A partial tandem duplication (PTD), are particularly challenging to detect using standard molecular and cytogenetic approaches. Methods. We have validated the use of a custom hybrid capture based next-generation sequencing (NGS) panel for comprehensive profiling of AML patients seen at our institution. This NGS panel targets the entire consensus coding DNA sequence of KMT2A; to deduce the presence of a PTD we used the relative ratio of KMT2A exons coverage. We sought to corroborate the KMT2A-PTD NGS results using (1) multiplex-ligation probe amplification (MLPA) and (2) optical genome mapping (OGM). Results. We analyzed 932 AML cases and identified 41 individuals harboring a KMT2A-PTD. MLPA, NGS and OGM confirmed the presence of a KMT2A-PTD in 22 of the cases analyzed where orthogonal testing was possible. Two false positive PTD calls by NGS could be explained by the presence of cryptic structural variants impacting KMT2A and interfering with PTD analysis. OGM revealed the nature of these previously undetected gene rearrangements in KMT2A, while MLPA yielded in-conclusive results. MLPA analysis for KMT2A-PTD is limited to exon 4, whereas NGS and OGM resolved KMT2A-PTD sizes and copy number levels. Conclusion. KMT2A-PTDs are complex gene rearrangements that cannot be fully ascertained using a single genomic platform. MLPA, NGS panels and OGM are complementary technologies applied in standard of care testing for AML patients. MLPA and NGS panels are designed for targeted copy number analysis; however, our results show that integration of concurrent genomic alterations is needed for accurate KMT2A-PTD identification. Unbalanced chromosomal rearrangements overlapping with KMT2A can interfere with the diagnostic sensitivity and specificity of copy number based KMT2A-PTD detection methodologies.

In this study, a structural profiling of equid alphaherpesvirus 1 (EHV-1) transcriptome was carried out using next-generation (Illumina) and third-generation (Oxford Nanopore Technologies) sequencing platforms. We annotated the canonical mRNA molecules and their isoforms, including transcript start and end site isoforms, and splice variants. Additionally, a number of putative 5′-truncated mRNAs containing shorter in-frame ORFs were detected. We also demonstrated that EHV-1 produces a high number of non-coding transcripts, including antisense and intergenic RNAs. One of the most remarkable features of the EHV-1 is the generation of abundant fusion transcripts some of which encoding chimeric polypeptides. We observed a higher number of splicing and transcriptional overlaps than in related viruses. Additionally, we found that many upstream genes of tandem gene clusters have their own transcript end sites (TESs) besides the co-terminal TESs, which is rare in other alphaherpesviruses. We show here that the replication origins (OriS and OriL) of the virus are co-localized with promoter sequences and overlap with specific RNA molecules. Furthermore, we discovered a novel non-coding RNA (designated as NOIR) that overlaps the 5′-ends of the longer transcript variants encoded by the two main transactivator genes ORF64 and 65 bracketing the OriL. These all suggest the existence of a central regulatory system which controls the genome-wide transcription and the replication through a mechanism based on the interference between the machineries carrying out the synthesis of DNA and RNA.

The rising importance of Big Data in modern information analysis is supported by vast quantities of user data, but it is only possible to collect sufficient data for all tasks within certain data-gathering contexts. There are many cases where a domain is too novel, too niche, or too sparsely collected to adequately support Big Data tasks. To remedy this, we have created ADG Engine that allows for the generation of additional data that follows the trends and patterns of the data that’s already been collected. Using a database structure that tracks users across different activity types, ADG Engine can use all available information to maximize the authenticity of the generated data. Our efforts are particularly geared towards data analytics by identifying abnormalities in the data and allowing the user to generate normal and abnormal data at custom ratios. In situations where it would be impractical or impossible to expand the available dataset by collecting more data, it can still be possible to move forward with algorithmically expanded data datasets.

Flammability was evaluated and the results showed the values of critical flux at extinguishment (CFE) as 49.5kW/㎡ on average, total heat release (Qt) as 0.21MJ on average, and peak heat release rate (Qp) as 0.66kW on average, which satisfied all of the thresholds presented by the IMO. Therefore, flame-retardant plywood, of which the flame-retardant performance was evaluated, was determined to be an applicable finishing material that satisfies fire safety standards.

Recently concluded, large-scale cancer genomics studies involving multiregion sequencing of primary tumors and paired metastases appear to indicate that many or most cancer patients have one or more “clonal" mutations in their tumors. Clonal mutations are those that are present in all of a patient’s cancer cells. Clonally mutated proteins can potentially be targeted by inhibitors or E3 ligase small molecule glues, but developing new small molecule drugs for each patient is not feasible currently. Achilles Therapeutics is currently the only company specifically targeting clonal mutations. However, they are doing so with tumor-derived T cells. To address the potential limitations of immunotherapy, I have devised another approach for exploiting clonal mutations, which I call “Oncolytic Vector Efficient Replication Contingent on Omnipresent Mutation Engagement” (OVERCOME). The ideal version of OVERCOME would likely employ a bioengineered facultative intracellular bacterium. The bacterium would initially be attenuated, but (transiently) reverse its attenuation upon clonal mutation detection.

Indiana Vesiculovirus (IVV; formerly as Vesicular stomatitis virus and Vesicular stomatitis Indiana virus) causes a disease in livestock that is very similar to the foot and mouth disease thereby an outbreak may lead to significant economic loss. Long-read sequencing (LRS) -based approaches revealed a hidden complexity of the transcriptomes in several viruses already. This technique was utilized already for the sequencing of the IVV genome, but our study is the first for the application of this technique for the profiling of IVV transcriptome. Since LRS is able to sequence full-length RNA molecules, and thereby providing more accurate annotation of the transcriptomes than the traditional short-read sequencing methods. The objectives of this study were to assemble the complete transcriptome of using nanopore sequencing, to ascertain cell-type specificity and dynamics of viral gene expression and to evaluate host gene expression changes induced by the viral infection. We carried out a time-course analysis of IVV gene expression in human glioblastoma and primate fibroblast cell lines using a nanopore-based LRS approach and applied both amplified and direct cDNA sequencing, as well as cap-selection for a fraction of samples. Our investigations revealed that, although the IVV genome is simple, it generates a relative complex transcriptomic architecture. In this study, we also demonstrated that IVV transcripts vary in structure and exhibit differential gene expression patterns in the two examined cell types.

Non-coding RNAs (ncRNAs) comprise a diverse class of non-protein coding transcripts that regulate critical cellular processes associated with cancer. Advances in RNA-sequencing (RNA-Seq) have led to the characterization of non-coding RNA expression across different types of human cancers. Through comprehensive RNA-Seq profiling, a growing number of studies demonstrate that ncRNAs, including long non-coding RNA (lncRNAs) and microRNAs (miRNA), play central roles in progenitor B-cell Acute Lymphoblastic Leukemia (B-ALL) pathogenesis. Furthermore, due to their central roles in cellular homeostasis and their potential as biomarkers, the study of ncRNAs continues to provide new insight into the molecular mechanisms of B-ALL. This article reviews the ncRNA signatures reported for all B-ALL subtypes, focusing on technological developments in transcriptome profiling and recently discovered examples of ncRNAs with biologic and therapeutic relevance in B-ALL.

In the last couple of years, the implementation of long-read sequencing (LRS) technologies for transcriptome profiling has uncovered an extreme complexity of viral gene expression. In this study, we carried out a systematic analysis on the pseudorabies virus transcriptome by combining our current data obtained by using Pacific Biosciences Sequel and Oxford Nanopore Technologies MinION sequencings with our earlier data generated by other LRS and short-read sequencing techniques. As a result, we identified a number of novel genes, transcripts, and transcript isoforms, including splice and length variants, and also confirmed earlier annotated RNA molecules. One of the major findings of this study is the discovery of a large number of 5’-truncated putative mRNAs embedded into larger host mRNAs. A large fraction of these RNA molecules contain in-frame ORFs, which may encode N-terminally truncated polypeptides. These study demonstrates that the PRV transcriptome is much more complex than previously appreciated.

RaTG13 (a bat derived SARS-like CoV) is the closest relative sequence of SARS-CoV-2 reported till date. The sample from which RaTG13 was sequenced was a bat fecal swab collected in 2013 from Tongguan, Mojiang, Yunnan province, China. The Illumina based sequence of RaTG13, MN996532.1, was deposited on 27^th Jan 2020 and the raw data (Illumina), https://www.ncbi.nlm.nih.gov/sra/SRX7724752[accn]. There are discrepancies in dates about when the metagenome sequencing of RaTG13 sample was done (2018 or 2020), both stated by the same corresponding author. Comparison of the RNA Seq data of RaTG13 fecal swab to the corresponding data from the bat fecal swabs deposited by the same working group using the same methods indicated that the RaTG13 raw data seemed to be different in various aspects. The fecal swab sample showed abnormally less read of bacterial reads in the swab was exceptionally low, i.e. 0.7%, compared to the 20-90% abundance in other fecal swabs from bats processed by similar methods. Also, another raw data in the form of amplicon sequences was deposited in May 2020; however, the dates mentioned on the files of the sequenced amplicons were older (2017, 2018). The genome assembly of RaTG13 could not be done de-novo and the average coverage of the genome ~8%. Also, literature indicates that RaTG13 RBD cannot bind to Rhinolophus ACE-2 receptors. Collectively, the anomalies in the raw data of RaTG13 and other issues pose an important question about the overall authenticity of the RaTG13 genome sequence.

To fully appreciate genetics, one must understand the link between genotype (DNA sequence) and phenotype (observable characteristics). Advances in high-throughput genomic sequencing technologies and applications, so-called “-omics”, have made genetic sequencing readily available across fields in biology from applications in non-traditional study organisms to precision medicine. Thus, understanding these tools is critical for any biologist, especially those early in their career. This comprehensive review discusses the chronological development of different sequencing methods, the bioinformatics steps to analyzing this data, and social and ethical issues raised by these techniques that must be discussed and evaluated.

Klebsiella pneumoniae, a major cause of both hospital and community-acquired infections, is listed by the World Health Organization as a critical priority antibiotic- resistant bacterial pathogen. With the appearance of sequencing techniques such as Next-generation Sequencing (NGS), there is the possibility to obtain the whole genome of the bacteria, getting to know all antimicrobial resistance determinants. The purpose of this study has been to apply this new technology to clinical microbiology, in order to characterize the resistome present in carbapenem-resistant K.pneumoniae strains isolated in a tertiary hospital in Valencia, Spain. A total of 234 isolates were prepared for whole-genome sequencing with Ilumina MiSeq, and sequences were later studied for antimicrobial resistance genes, sequence-typing and plasmids. Sequence-typing showed four major circulating clones in our hospital settings: ST11, ST307, ST101 and ST147, carrying different plasmids and different resistance determinants such as OXA-48 and NDM-1 carbapenemase. Application of new technologies such as whole-genome sequencing in clinical microbiology gives advantages when it comes to rapid therapy adjustment, consequently improving the patient’s clinical outcomes.

The decomposition of straw is a dynamic process, which is reflected in the decomposing microbial consortia, however, this process is poorly understood. Here we performed an experiment on the gradual colonization of oat straw by the soil microbial community. The results showed that soil respiration and bacterial diversity were negatively correlated – while the first decreased, the latter increased. In accordance with the dynamics of diversity and respiration, succession was divided into early, middle, and late decomposition phases. Analysis of 16S rRNA and ITS2 amplicon sequencing data revealed three jointly changing groups of phylotypes, corresponding with distinguished phases of decomposition. The presence of cellulolytic members of Proteobacteria, Bacteroidota, Firmicutes, and Actinobacteriota for bacteria and Ascomycota for fungi had been detected since the early phase, but most of the initial phylotypes were gone by the end of the phase. The second phase marked the functional core with a constant set of other phylotypes from these phyla, persisting in the community. Full metagenome sequencing of the microbial community from the end of the middle phase confirmed that major members of this consortium had GH genes, connected to cellulose and chitin degradation. The appearance of non-cellulolytic members from Bdellovibrio, Myxococcota, Chloroflexi, and Crenarchaeota characterized the last phase of the mature community.

Among all economically important plant species in the world, grapevine (Vitis vinifera L.) is the most cultivated fruit plant. It has a significant impact on the economies of many countries through wine and fresh and dried fruit production. In recent years, the grape and wine industry has been facing outbreaks of known and emerging viral diseases across the world. Although high-throughput sequencing (HTS) has been used extensively in grapevine virology, the application and potential of third-generation sequencing have not been explored in understanding grapevine viruses and their impact on the grapevine. Nanopore sequencing, a third-generation technology, can be used for direct sequencing of both RNA and DNA with minimal infrastructure. Compared to other HTS methods, the MinION nanopore platform is faster and more cost-effective and allows for long-read sequencing. Due to the size of the MinION device, it can be easily carried for field viral disease surveillance. This review article discusses grapevine viruses and their diagnostic methods, the principle of nanopore sequencing technology and its application in grapevine virus detection, virus–plant interactions, as well as the characterization of viral RNA modifications.

Illumina and nanopore sequencing technologies are powerful tools that can be used to determine the bacterial composition of complex microbial communities. In this study, we compared nasal microbiota results at genus level using both Illumina and nanopore 16S rRNA gene sequencing. We also monitored the progression of nanopore sequencing in the accurate identification of species, using pure, single species cultures, and evaluated the performance of the nanopore EPI2ME 16S data analysis pipeline. Fifty-nine nasal swabs were sequenced using Illumina MiSeq and Oxford Nanopore 16S rRNA gene sequencing technologies. In addition, five pure cultures of relevant bacterial species were sequenced with the nanopore sequencing technology. The Illumina MiSeq sequence data were processed using bioinformatics modules present in the Mothur software package. Albacore and Guppy base calling, a workflow in nanopore EPI2ME and an in house developed bioinformatics script were used to analyze the nanopore data. At genus level, similar bacterial diversity profiles were found, and five main and established genera were identified by both platforms. However, probably due to mismatching of the nanopore sequence primers, the nanopore sequencing platform identified Corynebacterium in much lower abundance compared to Illumina sequencing. Further, when using default settings in the EPI2ME workflow, almost all sequence reads that seem to belong to the bacterial genus Dolosigranulum and a considerable part to the genus Haemophilus were only identified at family level. Nanopore sequencing of single species cultures demonstrated at least 88% accurate identification of the species at genus and species level for 4/5 strains tested, including improvements in accurate sequence read identification when the basecaller Guppy and Albacore, and when flowcell versions R9.4 and R9.2 were compared.

this paper we present approaches for generating random numbers along with potential applications. Rather than trying to provide extensive coverage of several techniques or algorithms that have appeared in the scientific literature, we focus on some representative approaches presenting their workings and properties in detail. Our goal is to delineate their strengths and weaknesses as well as their potential application domains so as the reader can judge what would be the best approach for the application in hand, possibly a combination of the available approaches. For instance, a physical source of randomness can be used for the initial seed, then suitable preprocessing can enhance its randomness and then the output of the preprocessing can feed different types of generators, e.g. a linear congruential generator, a cryptographically secure one and one based on the combination of one way hash functions and shared key cryptoalgorithms in various modes of operation. Then, if desired, the outputs of the different generators can be combined giving the final random sequence. Moreover, we present a set of practical randomness tests which can be applied on the outputs of random number generators in order to assess their randomness characteristics. In order to demonstrate the importance of unpredictable random sequences, we present an application of cryptographically secure generators in domains where unpredictability is one of the major requirements, i.e. eLotteries and cryptographic key generation.

Background : The current corruption case in Indonesia are severely problematic since it is normalized by society. As a response, the current agenda of the Indonesian government to tackle it is by raising awareness of youth towards Indonesia’s corruption case. Aim : This study aims to knowing the importance of anti-corruption education and its applications among students. Method : The methodology of this study is the use of a qualitative survey on Faculty of Pharmacy students and interviews with representatives of students of the Faculty of Pharmacy. The population of this study is students of Airlangga University. The sample of this study is 52 students of class C the Faculty of Pharmacy Result : Students have awareness about corruption and even proposed that the current anti-corruption education is not enough to tackle corruption. Recommendation : The researcher suggests that students can be brave to campaign about the importance of anti-corruption education to the public. Limitation : The limitation of this study is that it is difficult to conduct research because in the online pandemic era, this results in delays in the research process.

Pancasila is the identity of the Indonesian nation, which means that Pancasila is a national characteristic that cannot be found in any country. Pancasila points are taken from the noble values of the Indonesian state. These principles contain culture, customs, and national character known as manners, cooperation, and high nationalism. As the successor to Indonesian culture, the young generation must be able to preserve and develop Pancasila. In this era of globalization, there are many challenges for the younger generation in preserving Pancasila. This study aims to provide an overview of the decline of Pancasila identity among the younger generation due to the impact of globalization. The research question that has been determined is how the practice behaviour of the younger generation towards the implementation of Pancasila, the solutions and efforts that all Indonesian people can make regarding the crisis of Pancasila identity in the era of globalization. This research method uses a literature review. The research sources were conducted from the latest journals and books published in 2019 until 2021 related to the theme of Pancasila and the millennial generation. The results showed that globalization has greatly facilitated foreign cultures to enter Indonesia. The younger generations use this foreign culture as a lifestyle without filtering it, whether it contains Pancasila values or not. This causes Pancasila has been forgotten and no longer applied in their everyday life. Young people can make various efforts to preserve the national identity, namely Pancasila. Apart from the role of the young generation itself, Indonesian society can also play an essential role in supporting the younger generation to continue implementing Pancasila in their lives. By conducting this research, it is hoped that Indonesia's young generation can understand, select, and stay away from the negative impacts of globalization that enter Indonesia freely. The solution that can be given from this research is that the younger generation must love their own culture more and practice every principle in Pancasila. Parents, educational institutions, and the government must also support the younger generation to maintain national identity, Pancasila values. The limitation of this research is that the researcher did not conduct any primary data, which means the data were not directly from the source. This causes the accuracy of this study to be less guaranteed. The recommendation that the researchers can give for further research is to obtain primary data to ensure accuracy and explore research topics regarding the fading of Pancasila identity in the younger generation in this era of globalization.

Technological developments, as a result of globalization, indirectly affect human lifestyles, one of which is the Indonesian people. In a situation of change towards the Industrial Revolution 4.0, Pancasila has a role as a guide for the Indonesian people to be what by the noble values ​​of the nation. However, the role of the millennial generation in maintaining these noble values ​​is important considering that they are the spearhead of the country's development. From this statement, this study aims to identify and formulate steps to maintain the noble values ​​of Pancasila among the millennial generation so that it does not eliminate national identity and understand the urgency of implementing the Pancasila lifestyle in the era of globalization. By using the literature review method, it can be seen that "grounding" and strengthening the essence of Pancasila values ​​can be a solution so that the existence of Pancasila continues to shine. The Pancasila lifestyle deserves to be implemented because it regulates all behaviors of speech, thought, behavior, action, and good manners so that it must be expressed in the life of the nation and state as well as our everyday life.

As the international community attaches importance to environmental and climate issues, carbon dioxide emissions in various countries have been subject to constraints and limits. Carbon trading market, as a market tool to reduce greenhouse gas emissions, has gone through a development process from a pilot carbon market to a national carbon market in China. At present, the industries included in the national carbon market are mainly the electric power industry, and the carbon emissions of the electric power industry account for about 40% of the national carbon emissions. According to the construction history of foreign carbon markets, China's future carbon quota allocation will gradually transition from free allocation to auction allocation,the auction mechanism will bring a heavy economic burden to the electric power industry, especially the thermal power generation industry. Therefore, this study takes Guangdong Province as an example to optimize the power generation mix with the objective of minimizing the total economic cost after the innovative introduction of the carbon quota auction mechanism and constructs an optimization model of the power generation mix based on the auction ratio by comprehensively applying the system dynamics model and the multi-objective linear programming model and systematically researches the power generation structure under different auction ratios with the time scale of months and quantitatively evaluates the economic inputs needed to reduce the greenhouse gas emissions.The results of the study show that after comprehensively comparing the total economic cost, renewable energy development and carbon emissions, it is the most scientific and reasonable to set the auction ratio of carbon allowances at 20%, which achieves the best level of economic and environmental benefits.

Paraphrase Generation is one of the most important and challenging tasks in the field of Natural Language Generation. The paraphrasing techniques help to identify or to extract/generate phrases/sentences conveying the similar meaning. The paraphrasing task can be bifurcated into two sub-tasks namely, Paraphrase Identification (PI) and Paraphrase Generation (PG). Most of the existing proposed state-of-the-art systems have the potential to solve only one problem at a time. This paper proposes a light-weight unified model that can simultaneously classify whether given pair of sentences are paraphrases of each other and the model can also generate multiple paraphrases given an input sentence. Paraphrase Generation module aims to generate fluent and semantically similar paraphrases and the Paraphrase Identification systemaims to classify whether sentences pair are paraphrases of each other or not. The proposed approach uses an amalgamation of data sampling or data variety with a granular fine-tuned Text-To-Text Transfer Transformer (T5) model. This paper proposes a unified approach which aims to solve the problems of Paraphrase Identification and generation by using carefully selected data-points and a fine-tuned T5 model. The highlight of this study is that the same light-weight model trained by keeping the objective of Paraphrase Generation can also be used for solving the Paraphrase Identification task. Hence, the proposed system is light-weight in terms of the model’s size along with the data used to train the model which facilitates the quick learning of the model without having to compromise with the results. The proposed system is then evaluated against the popular evaluation metrics like BLEU (BiLingual Evaluation Understudy):, ROUGE (Recall-Oriented Understudy for Gisting Evaluation), METEOR, WER (Word Error Rate), and GLEU (Google-BLEU) for Paraphrase Generation and classification metrics like accuracy, precision, recall and F1-score for Paraphrase Identification system. The proposed model achieves state-of-the-art results on both the tasks of Paraphrase Identification and paraphrase Generation.

Precision metagenomic approaches using Oxford Nanopore Technology (ONT) sequencing has been shown to allow recovery of complete genomes of Escherichia coli O157:H7 from overnight enrichments of agricultural waters. This study tests the applicability of a similar approach for Cronobacter genome recovery from powdered infant formula (PIF) overnight enrichments, where Cronobacter typically dominates the overall microbiome (>90%). In this study, we aimed to test whether using ONT sequencing of overnight PIF enrichments could recover a completely closed Cronobacter genome for further genomic characterization. Ten PIF samples, each inoculated with different Cronobacter strains, covering Cronobacter sakazakii, C. muytjensii, C. dublinensis, C. turicensis, and C. universalis, were processed according to the Bacteriological Analytical Manual (BAM) protocol. qPCR was used for initial screening (detection and quantification) of the overnight enrichments and confirmed that the spiked PIF samples after the overnight enrichment have high levels of Cronobacter (107 to 109 CFU/mL). DNA from overnight PIF enrichments was extracted from the enrichment broth and sequenced using ONT. Results showed that ONT sequencing could accurately identify, characterize, and close the genomes of Cronobacter strains from overnight PIF enrichments in 3 days, much faster than the nearly two weeks required by the current BAM method. Complete genome recovery and species differentiation were achieved. This suggests that combining qPCR with ONT sequencing provides a rapid, cost-effective alternative for detecting and characterizing Cronobacter in PIF, enabling timely corrective actions during outbreaks.

Dinoflagellates are one of the largest groups of marine microalgae and exhibit diverse trophic strategies. Within these niches, dinoflagellates can produce secondary metabolites that are known to be toxic, which can lead to ecologically harmful blooms. Amphidinium carterae is one species of dinoflagellate that produces toxic compounds and is used as a model for dinoflagellate studies. The extent to which the microbiome surrounding A. carterae affects its growth and secondary metabolite synthesis is still being assessed, as well as the impact of bacterial data on sequencing and assembly. An antibiotic cocktail was previously shown to eliminate 16S amplification from the dinoflagellate culture. Even with drastically reduced bacterial numbers, bacterial populations are likely to be present. In this experiment we used novel Nanopore long-read sequencing techniques on A. carterae cultures to assemble 15 full bacterial genomes ranging from 2.9-6.0 Mb and found that the use of antibiotics decreased the percentage of reads mapping back to bacteria. We also identified shifts in the microbiome composition and identified a potentially deleterious bacterial species arising in the absence of the antibiotic-treatment. Multiple antibiotic-resistance genes were identified, as well as evidence that the bacterial population do not contribute to toxic secondary metabolite synthesis.

Neurofibromatosis type1 (NF1) is an autosomal dominant disorder caused by mutations in the NF1gene. Although congenital pseudarthrosis of the tibia (CPT) has frequently been associated with NF1, the underlying molecular mechanism of CPT in these NF1 patients is yet ill-understood. The aim of the present study was to detect NF1 mutations from genomic DNA and to harbor variants associated with CPT in NF1 patients. Whole-exome sequencing was first carried out with samples from two patients with CPT in one NF1 family, and a novel mutation c.2324A>G (p.E775G) in NF1 gene was identified. Additionally, a missense variant c.455C>T (p.P152L) in BCOR gene completely co-segregated with the CPT phenotype within this family. Subsequently, NF1 and NF2 genes in four other unrelated patients with both NF1 and CPT were screened using targeted sequencing. Four mutations in NF1 gene, including two known mutations (c.2288T>C/p.L763P, c.574 C>T/p.R192*) and two novel mutations (c.768delT/p.F256Lfs*25, c.2229_2230delTG/ p.V744Qfs*23) were detected. Further study confirmed that CPT was present in NF1 families, and NF1 mutations were closely associated with these complex phenotypes. Moreover, the data from the current study indicated that male gender might be a susceptibility factor for CPT in NF1. Therefore, we speculated that BCOR variants might be related to CPT phenotype among male NF1 patients.

The raw material purchasing (RMP) problem is to determine the purchasing quantities of raw materials in given periods or cycles. Raw material purchasing optimization is crucial for large-scale steel plants because it is closely related to the supply of raw materials and cost savings. The raw material purchasing of large-scale steel enterprises is characterized by many varieties, large quantities, and high costs. The RMP objective is to minimize the total purchasing cost consisting of the price of raw materials, purchasing set-up costs, and inventory costs and meet product demand. We present a mixed integer linear programming (MILP) model and a column generation (CG) solution for the resulting optimization problem. The column generation algorithm is the generalization of the branch & bound algorithm with solving the linear programming (LP) relaxation of MILP using column generation (CG), and its advantage is to handle large-sized MILPs. Experimental results show the effectiveness and efficiency of the solution.

We discuss a formalism which allows for the calculation of a higher harmonic current response to an applied electric field for disordered superconducting systems described on the basis of tight-binding models. The theory is based on an expansion of the density matrix in powers of the field amplitudes where we solve the equation of motion for the individual components. This allows the evaluation of higher order response functions on significantly larger lattices than one can achieve with a previously used approach, which is based on a direct temporal integration of the equation of motion for the complete density matrix. In case of small lattices, where both methods can be applied by including also the contribution of collective modes, we demonstrate the agreement of the corresponding results.

Asphaltene is a component of crude oil that, if mishandled, may create substantial transportation and industrial concerns. It is a solid by nature, with a diverse set of molecular compositions. Furthermore, the oil industry has identified emulsion generation and clogging precipitate as key concerns. The emulsified water droplets in the process are just what give the raw oil its increased viscosity; hence, power is squandered to transport the oil around. The information has been separated into sections based on simulation, solubilization, agglomeration, precipitation, and evidence of model chemicals in the literature. We have included research that investigates the bulk rheology and interfacial rheology of asphaltene to describe its interfacial activity more clearly.

Introduction: Industrial revolution 4.0 in the current era of globalization plays an active role in the modern era in Indonesia. The influence of increasingly advanced technology affects the millennial generation as the nation's next generation to make Pancasila the basis of the State or the foundation of a State. In addition, the millennial generation has begun to shift the guidelines of life from Pancasila so that the appreciation of Pancasila values is starting to disappear along with the development of the times and in line with the progress of Science and Technology (IPTEK). If this continues, then the values of Pancasila will be replaced by a new ideology that will cause behavioural changes in society. Purpose: this study aims to provide the proper application to millennial life using Pancasila values, knowing the behaviour of the millennial generation towards the implementation of Pancasila values, and making Pancasila a way of life. Methods: the method used in this research is Literature Review and takes sources from journals published in 2019 to 2021 related to the Pancasila theme and the millennial generation. Results: the study results show that with the existence of Pancasila as the ideology and principle of the State, it is expected to strengthen the attitude and nature of the community in accepting things outside the norms that exist in Indonesia. In addition, the younger generation is expected to be able to apply Pancasila values along with the development of science and technology in the modern era and current globalization. The research question is how to make the millennial generation implement Pancasila in life in the contemporary period and what solutions can continue to instil Pancasila values ​​in the 4.0 industrial revolution. Recommendation: the conclusion drawn is that Pancasila can become a unifying tool for the nation if the current generation or millennial generation still desires to maintain its values ​​, even though they are in a modern era and many influences from its outside cultures. Limitation: the limitation of this research is not getting all the data directly from the source. The researcher recommends using primary data for the following study to ensure its truth and accuracy better because the researcher directly obtains it.

Vaginitis is a widespread issue for women worldwide, yet current diagnostic tools are lacking. Bacterial vaginosis (BV) is the most prevalent type of vaginitis, found in 10-50% of reproductive aged women. Current diagnostic methods for BV rely on clinical criteria, microscopy, or detection of a few microbes by qPCR. However, many vaginal infections lack a single etiological agent and are characterized by changes in the vaginal microbiome community structure (e.g. BV is defined as a loss of protective lactobacilli resulting in an overgrowth of anaerobic bacteria). Shotgun metagenomic sequencing provides a comprehensive view of all the organisms present in the vaginal microbiome (VMB) allowing for a better understanding of all potential etiologies. Here, we describe a robust VMB metagenomics sequencing test with a sensitivity of 88.5%, specificity of 96.2%, and a positive predictive value of 95.8% certified by Clinical Laboratory Improvement Amendments (CLIA), the College of American Pathologist (CAP) and the Clinical Laboratory Evaluation Program (CLEP). We sequenced over 7,000 human vaginal samples with this pipeline and described general findings and comparison to US census data.

It has been widely established that the characterization of extracellular vesicles (EVs), particularly small EVs (sEVs), shed by different cell types into biofluids, helps identify biomarkers and therapeutic targets in neurological and neurodegenerative diseases. Recent studies are also exploring the efficacy of mesenchymal stem cell-derived extracellular vesicles naturally enriched with therapeutic microRNAs and proteins for treating various diseases. Besides, EVs released by various neural cells play a crucial function in the modulation of signal transmission in the brain in physiological conditions. However, in pathological conditions, such EVs can facilitate the spread of pathological proteins from one brain region to the other. On the other hand, analysis of EVs in biofluids can identify sensitive biomarkers for diagnosis, prognosis, and disease progression. This review discusses the potential therapeutic use of stem cell-derived EVs in several central nervous system diseases. It lists their differences and similarities and confers various studies exploring EVs as biomarkers. Further advances in EV research in the coming years will likely lead to the routine use of EVs in therapeutic settings.

Legume plants enter symbiosis with soil nitrogen-fixing bacteria (rhizobia), thereby gaining access to the assimilable atmospheric nitrogen. This symbiosis is important for agriculture, thus, biofertilizers with effective strains of rhizobia are created for crop legumes to increase their yield and minimize the amounts of mineral fertilizers used. In this work, we sequenced and characterized the genome of Rhizobium leguminosarum bv. viciae strain RCAM1022, a component of the ‘Rhizotorfin’ biofertilizer produced in Russia and used for pea (Pisum sativum L.).

Objective Our objective was to observe the benefits and limitations of WES (Whole Exome Sequencing) in the prenatal setting, in the Romanian population. The scope was to observe the diagnostic yield in comparison to molecular karyotyping testing, which had negative results, as well as a case of consanguinity. Methods The first criteria was selecting pregnancies with abnormal ultrasound findings. These findings would not lead the medical team to a certain known syndrome. Second, we performed SNP-array, which tested negative in all cases, except for Case number 9 which had an abnormal result. The ulterior testing method was WES, using Massive Parallel Sequencing of the whole coding region of the human genome on Next Generation Sequencing Platform, NovaSeq 6000 (average coverage >100X, read length: 2x100bp). The Twist Human Core Exome kit RefSeq & Mitochondrial panel (Twist Bioscience) was used for the library preparation. Bioinformatic analysis was performed by direct comparison of the genome of the test sample with the human reference sequence (hg38). Results Our small cohort of 10 patients, resulted in a 50% diagnostic yield. After receiving the results whether a diagnose or a negative result, 2 couples chose to terminate the pregnancy, 5 were born affirmatively without symptoms, and are still monitored up to date. One of the pregnancies led to a stillbirth. We have also found 3 incidental findings that helped the multidisciplinary team better manage the patient as well as the members at risk. Conclusion In this article we present 10 cases which were tested through prenatal WES, showing the great diagnostic yield in comparison to SNP-array in our selected cases. As a closing remark, we wish to highlight the benefits of WES testing in prenatal cases. Further testing is needed to get a clearer picture of the prenatal diagnostic yield in the Romanian population.

The Arbas cashmere goat is a unique biological resource that plays a vital role in livestock husbandry in China. LCDM is a medium with special small molecules (consisting of human LIF, CHIR99021, (S)-(+)-dimethindene maleate, and minocycline hydrochloride) for generation pluripotent stem cells (PSCs) with bidirectional developmental potential in mice, humans, pigs, and bovines. However, there is no report on whether LCDM can support for generation of PSCs with the same ability in Arbas cashmere goats. In this study, we applied LCDM to generation goat induced PSCs (giPSCs) from goat fetal fibroblasts (GFFs) by reprogramming. The derived giPSCs exhibited stem cell morphology, expressing pluripotent markers, and could differentiate into three germ layers. Moreover, the giPSCs differentiated into the trophectoderm lineage by spontaneous and directed differentiation in vitro. The giPSCs contributed to embryonic and extraembryonic tissue in preimplantation blastocysts and postimplantation chimeric embryos. RNA-sequencing analysis showed that the giPSCs were very close to goat embryos at the blastocyst stage and giPSCs have similar properties to typical extended PSCs (EPSCs). The establishment of giPSCs with LCDM provides a new way to generate high quality of PSCs from domestic animals and lays the foundation for basic and applied research in biology and agriculture.

Emerging infectious disease threats require rapid response tools to inform diagnostics, treatment, and outbreak control. RNA-based metagenomics offers this; however, most approaches are time-consuming and laborious. Here, we present a simple and fast protocol – the RAPIDprep assay – with the aim to provide cause agnostic laboratory diagnosis of infection within 24 hours of sample collection by sequencing ribosomal RNA-depleted total RNA. The method is based on the synthesis and amplification of double-stranded cDNA followed by short-read sequencing with minimal handling and clean-up steps to improve processing time. The approach was optimized and applied to a range of clinical respiratory samples to demonstrate diagnostic and quantitative performance. Our results showed robust depletion of both human and microbial rRNA, and library amplification across different sample types, qualities and extraction kits using a single protocol without input nucleic acid quantification or quality assessment. Furthermore, we demonstrate the genomic yield of both known and undiagnosed pathogens with complete genomes recovered in most cases to inform molecular epidemiological investigations and vaccine design. The RAPIDprep assay is a simple and effective tool, and representative of an important shift towards integration of modern genomic techniques to infectious disease investigations.

Non-vertebrate species represent about ~95% of known metazoan (animal) diversity. They remain to this day relatively unexplored genetically, but understanding their genome structure and function is pivotal for expanding our current knowledge of evolution, ecology and biodiversity. Following the continuous improvements and decreasing costs of sequencing technologies, many genome assembly tools have been released, leading to a significant amount of genome projects being completed in recent years. In this review, we examine the current state of genome projects of non-vertebrate animal species. We present an overview of available sequencing technologies, assembly approaches, as well as pre and post-processing steps, genome assembly evaluation methods, and their application to non-vertebrate animal genomes.

Wildfires have continued to increase in frequency and severity in Southern California due in part to climate change. To gain a further understanding of microbial soil communities’ response to fire and functions that may enhance post-wildfire resilience, soil fungal and bacterial microbiomes were studied from different wildfire areas in the Gold Creek Preserve within the Angeles National Forest using 16S, FITS, 18S, 12S, PITS, and CO1 amplicon sequencing. Sequencing datasets from December 2020 and June 2021 samplings were analyzed using DNA Subway, ranacapa, stats, vcd, EZBioCloud, and mixomics. Significant differences were found among bacterial and fungal taxa associated with different fire areas in the Gold Creek Preserve. There was evidence of seasonal shifts in the alpha diversity of the bacterial communities. In the sparse partial least squares analysis, there were strong associations (r>0.8) between longitude, elevation, and a defined cluster of Amplicon Sequence Variants (ASVs). The Chi-square test revealed differences in fungi:bacteria (F:B) proportions between different trails (p=2*10^-16). sPLS results focused on a cluster of Green Trail samples with high elevation and longitude. Analysis revealed the cluster included the post-fire pioneer fungi Pyronema, and Tremella. Chlorellales algae, and pathogenic Fusarium sequences were elevated. Bacterivorous Corallococcus, which secretes antimicrobials, and bacterivorous flagellate Spumella, were associated with the cluster. There was functional redundancy in clusters that were differently composed, but shared similar ecological functions. These results implied a set of traits for post fire resiliency. These included photo-autotrophy, mineralization of pyrolyzed organic matter and aromatic/oily compounds, pathogenicity and parasitism, antimicrobials, and N-metabolism.

High-quality chromosome-scale haplotype sequences— of diploid genomes, polyploid genomes and metagenomes — provide important insights into genetic variation associated with disease and biodiversity. However, whole-genome short read sequencing does not yield haplotype information that spans whole chromosomes directly. Computational assembly of shorter haplotype fragments is required for haplotype reconstruction, which can be challenging owing to limited fragment lengths and high haplotype and repeat variability across genomes. Recent advancements in long-read and chromosome-scale sequencing technologies, alongside computational innovations, are improving the reconstruction of haplotypes at the level of whole chromosomes. Here, we review recent methodological progress in these areas and discuss perspectives that could enable routine high-quality haplotype reconstruction in clinical and evolutionary studies.

Long-read single-molecule sequencing has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. It also has been widely used to study structural variants, phase haplotypes and more. Here, we introduce the assembler— SMARTdenovo, which is an SMS assembler that follows the overlap-layout-consensus (OLC) paradigm. SMARTdenovo (RRID: SCR_017622) was designed to be a fast assembler that did not require highly accurate raw reads for error correction, unlike other, contemporaneous SMS assemblers. It has performed well for evaluating congeneric assemblers and has been successful for a variety of assembly projects. It is compatible with Canu for assembling high-quality genomes, and several of the assembly strategies in this program have been incorporated into subsequent popular assemblers. The assembler has been in use since 2015, and here we provide information on the development of SMARTdenovo and how to implement its algorithms into current projects.

Kiwifruit vines are generally sensitive to waterlogging stress. So far, molecular responses of different kiwifruit genotypes for waterlogging stress are less well-explored. In this study, using RNA-sequencing, we examined transcriptional regulation in the roots of a waterlogging-tolerant genotype KR5 (Actinidia valvata), and a sensitive genotype ‘Hayward’ (Actinidia deliciosa) subjected to 0, 12, 24, and 72 h of waterlogging. Compared with 0 h, transcriptional adjustments of these two genotypes occurred as early as 12 h and became notably pronounced 72 h after waterlogging. Waterlogging stress for 72 h promoted the expression of genes involved in ethylene biosynthesis, sucrose and hexose transport, anaerobic fermentation, nitrate reduction, alanine accumulation, and reactive oxygen scavenging in both genotypes. The differential regulation of genes encoding 9-cis-epoxycarotenoid dioxygenase, phosphoglucomutase, alanine-glyoxylate transaminase, and other enzymes pointed to their diverse strategies upon waterlogging in these two genotypes. In addition, more sucrose and trehalose contents, as well as a higher activity of alcohol dehydrogenase and manganese superoxide dismutases were stimulated in KR5 roots after 72h of waterlogging than that in ‘Hayward’. Overall, our results provided more insights into the molecular basis of the waterlogging response in kiwifruit.

Abstract Objective: Endometriosis is a chronic disease characterized by the growth of endometrial cells outside the uterine cavity. The dysfunction of the immune system is strongly associated with the progression of endometriosis, and is also correlated to the diversity of microbiota in the genital tract. According to previous studies, the microbiota significantly contributes to multi-systemic function, but the evidence of endometriosis and adenomyosis remains insufficient. Thus, the present study attempted to identify the characteristics of microbiota in endometriosis patients, and the connection between microbiota and immunological dysfunction. Methods: In order to compare and explore the potential microbiota correlated to endometriosis and adenomyosis in the genital tract, 134 samples obtained from the cervical canal, posterior fornix and uterine cavity were analyzed by 16s-rRNA sequencing. The raw data was filtered, analyzed and visualized, and bio-information methods were used to identify the different and distinctive characteristics of microbiota. Results: Two different locations near the cervix, cervical canal and posterior fornix, exhibited no differences in alpha diversity. Among the different disease groups, five microbiota were distinctive in the genus level, and Atopobium presented with the greatest significance in adenomyoisis-endometriosis patients. The LEfSe analysis failed to identify the special biomarkers, while several characteristic functions were identified through PICRUSt. Conclusion: Lactobacillus is dominant in the female lower genital tract, and Atopobium is distinctively higher in patients with endometriosis combined with adenomyosis. Several different functions of microbiota were explored, and these are found to be associated with endometriosis and adenomyosis. These findings may provide a new concept of microbiota/immune system/endometriosis system. There is an urgent need to investigate the potential microbial biomarkers of endometriosis in the future.

Data on the KIT mutation rate in skin melanoma in the central European region is missing. Accordingly, in a cohort of 79 double wild type (BRAF/NRAS) skin melanoma KIT mutation was assessed by Sanger sequencing of exons 9,11,13,17 and 18. In this skin melanoma cohort KIT mutation frequency was found to be 34/79 (43%) with a significantly higher rate in acrolentiginous melanoma (ALM) as compared to UV-induced common variants (20/34, 58.8% versus 14/45, 31.1%, p=0.014). Exon 11 was the most frequent mutation site (44.7%) followed by exon 9 (21.1%) equally characterizing UV-induced common histotypes and ALM tumors. KIT mutation hotspots were identified in exon 9 (c491/492), in exon 11 (c559,c572, c570), in exon 13 (c642), in exon 17 (c822) and in exon 18 (c853). The relatively high KIT mutation rate in skin melanoma in this central-European cohort justifies regular testing of this molecular target.

Sutherlandia frutescens (S. frutescens) has been traditionally used as an herbal medicine to ameliorate symptoms associated with cancer, infectious diseases, as well as inflammation. The objective of this investigation was to explore the impact of S. frutescens on the expression of genes in a murine macrophage cell line (i.e., RAW 264.7). We found that treatment with an ethanolic-extract of S. frutescens (SFE) 1 h prior to the stimulation with LPS and IFNγ for 24 h significantly affected the expression of 715 genes in RAW 264.7 cells. When the post-stimulation period was shortened to 8 h, the number of genes that were significantly impacted by SFE diminished to 50. Pathway analysis revealed that inflammatory signaling pathways, such as NF-κB, MAPK, and TNF, as well as signaling pathways associated with immune-related responses, were inhibited by SFE treatment. These findings are consistent with previously reported anti-inflammatory activity of SFE and enable better understanding of the immune-modulating properties of this botanical. To our knowledge, this represents the first report on the impact of S. frutescens on global gene expression in an immune cell population.

While digital libraries offer essential benefits for the digital age such as constant availability and accessibility, they often fail in providing a similarly enjoyable browsing experience that benefits engagement and serendipitous exploration inherent to traditional library experiences. In this paper, we propose a virtual reality (VR) library environment that emulates a traditional library promoting an engaging browsing experience that benefits browsing enjoyment and serendipity. The implemented system uses procedural content generation to dynamically generate a library-like environment, wherein each room corresponds to a specific category of the digital library. To assess the usability of the implemented system, we conducted an A/B study comparing the VR environment with the web interface of Project Gutenberg. The results of the study suggest that while the physical demand for using the VR environment is higher, the system can significantly benefit the browsing experience and entice users’ curiosity. Furthermore, the study suggests that the system can increase user engagement and users generally felt that using the system was rewarding.

Advanced lithography requires highly sensitive photoresists to improve lithographic efficiency, and it is critical yet challenging to develop high-sensitivity photoresists and imaging strategies. Here, we report a novel strategy for ultra-high sensitivity using hexafluoroisopropanol (HFIP)-containing fluoropolymer photoresists. The incorporation of HFIP, with its strong electrophilic property and electron-withdrawing effect of the fluorine atoms, significantly increases the acidity of the photoresist after exposure, enabling imaging without conventional photoacid generators (PAGs). The HFIP-containing photoresist has been evaluated by electron beam lithography to achieve a trench of ~40 nm at an extremely low dose of 3 μC/cm2, which shows sensitivity enhancement by ~10 times to the commercial PAGs involved system, revealing its high-sensitivity and high-resolution features. Our results demonstrate a new type of PAGs and a novel approach to higher-performance imaging beyond conventional photoresist performance tuning.

Given the imperative of security, sustainability of supply, strategic considerations, and energy independence, there is a widely acknowledged need to persist in utilizing coal as the primary fuel for electricity generation in power plants. However, in order to combat the rising levels of CO2 in the atmosphere, it is crucial to advance the development of carbon capture and storage (CCS) technologies that enable fossil fuel power plants to achieve zero emissions. These technologies play a pivotal role in capturing and effectively storing CO2, thus ensuring that coal-based power generation can continue while significantly reducing its environmental impact. By implementing CCS solutions, fossil fuel power plants can transition towards a more sustainable and environmentally friendly energy future.The utilization of chemical solvents for CO2 absorption, coupled with long-term storage, presents an intriguing and commercially viable technology for CO2 capture. However, the significant energy demands of the solvent regeneration process necessitate optimization, particularly in large-scale power plants. While the current cost of CO2 capture stands at approximately #55,000.00(Naira) per ton of CO2, the objective is to reduce this cost to below #25,000.00(Naira) per ton of CO2. This reduction in cost is essential to ensure the economic feasibility and widespread adoption of CO2 capture technologies in power generation.This research paper explores various approaches to address the energy demands associated with amine scrubbing integration in a commercial power plant. It provides a comprehensive analysis, both technically and economically, of the performance of these different approaches. While some of the proposed schemes may result in minor efficiency reductions, the key objective is to calculate the specific cost per ton of CO2 captured. The primary focus is on identifying the most suitable configuration to implement large-scale, cost-effective schemes that can serve as a foundation for CO2 capture demonstration projects. By determining the optimal configuration, this research aims to pave the way for the successful implementation of efficient and economically viable CO2 capture technologies in the power generation sector.

This study investigates the impact of narrow-band terahertz pulses on the ferroelectric order parameter in Ba0.8Sr0.2TiO3 films on various substrates. The 375 nm thick BST film on an MgO (001) substrate exhibits enhanced THz-induced second harmonic generation when excited by THz pulses with a central frequency of 1.6 THz, due to the resonant excitation of the soft phonon mode. Conversely, the BST film on a Si (001) substrate shows no enhancement, due to its polycrystalline state. The 800 nm thick BST film on an MgO (111) substrate demonstrates maximum of second harmonic generation signal when excited by THz pulses at 1.8 THz, that is also very close to it`s soft mode frequency (1.9 THz). Notably, the frequency spectrum of the BST/MgO (111) film reveals peaks at both the fundamental and doubled frequencies, highlighting the quadratic dependence of SHG intensity on the THz pulse's electric field strength.

Metal halide perovskites (MHPs), in particular lead-based halide perovskites have earned a recognized fame in several fields for their outstanding optoelectronics properties including direct generation of free charge carriers, optimal ambipolar charge carrier transport properties, high absorption coefficient, point-defect tolerance, and compositional versatility. Nowadays, this class of materials represents a real and promising alternative of silica for the photovoltaic technologies. This worthy success led to a growing interest in the exploration of MHP materials in other hot research fields such as the solar-driven photocatalytic water splitting towards hydrogen production, CO2 reduction to CO and CH4, useful organic reactions such as organic synthesis (formation of C-C, C-N, and C-O bonds), and pollutants and dye degradation. Nevertheless, many of these perovskite materials showed air and moisture instability problems that considerably hinder their practical application for photocatalytic water splitting and photodegradation of CO2. Moreover, if the chemical instability is a problem that can be in part mitigated by the optimization of the lattice structure, the presence of lead represents a real problem for the practical application of these type of materials in commercial devices. To successfully overcome this problem, lead-free metal halide perovskites (LFMHPs) have gained increasing interest thanks to their promising optoelectronic properties, comparable to lead-based materials, and their eco-friendly nature. Among all the lead-free perovskite alternatives, this mini review will focus the attention on the bismuth-based perovskites and perovskite derivatives with specific focus on solar-driven photocatalysis application for H2 evolution.

The conversion of methane into chemicals is of interest to achieve a decarbonized future. Fuel cells are electrochemical devices commonly used to obtain electrical energy, but can be utilized either for chemicals production or both energy and chemicals cogeneration. In this work, the partial oxidation of methane in fuel cells for electricity generation and valuable chemicals production at the same time is reviewed. For this purpose, different types of methane-fed fuel cells, both low temperature fuel cells, such as PEMFCs and AAEMFCs, and high temperature fuel cells, such as SOFCs, have been used. Also if few works have been devoted to this topic, the promising results drive the development of fuel cells using methane as the source for the cogeneration of power and valuable chemicals.

Background: In the current era of globalization, the Indonesian government's problem today is the weakening of nationalism and patriotism among the millennial generation. The large number of foreign cultures that have entered Indonesia has caused a sense of nationalism and patriotism. In addition, Indonesia is also facing the problem of spreading the Covid-19 virus. During the pandemic, various policies set by the government received protests from some circles because they felt their freedom was restricted. Therefore, the awareness of millennial generation nationalism is needed, especially during the Covid-19 pandemic like today. This research aims to make millennials aware of nationalism sense, which mainly to prevent the spread of Covid-19. This research is used to answer the questions of what the problems that arise due to the waning of the spirit of nationalism during the pandemic are? and what efforts should be made to maintain the spirit of nationalism? Methods: This research is a qualitative study using the literature review method. The articles used are research published in 2019 to 2021 in Google Scholar, with keywords that match the topic of millennial generation nationalism in the Covid-19 pandemic. Results and Discussion: The results of the study found that the spirit of Indonesian nationalism during the Covid-19 pandemic was decreasing. The decline in the sense of nationalism is due to several government policies that impact the psychology of society and the Indonesian economy. As a result, society, particularly the millennial generation, must play a role in breaking the chain of the Covid-19 virus's propagation by following the government's health standards. Conclusion: The government and society need to work together to understand nationalism in the millennial generation, especially in dealing with problems caused by the Covid-19 pandemic. Based on this, various efforts need to be made to foster the spirit of nationalism and overcome the Covid-19 pandemic. So that later, it can produce a generation that upholds the value of nationalism in everyday life.

Introduction: Indonesia consists of a plural society with different ethnic, religious, racial, skin color, and other cultures. The difference must be understood by everyone, especially the younger generation in the digital age. If the younger generation does not have a sufficient understanding of multicultural education values, it will impact the moral crisis of the Indonesian nation. This research emphasizes the importance of multicultural education to the younger generation to understand the differences (pluralism) in society and respect them. Method: The method uses a qualitative method with the literature review method by collecting data on ten journals published in 2019, 2020, 2021. Results: The rise of socio-cultural conflicts in Indonesia is why applying multicultural values to the younger generation. Multiculturalism is needed to establish morals and sensitivity for a young person in the face of various social problems and symptoms at a growing age. Conclusion: Multicultural education is vital to the younger generation considering Indonesia has diverse nations and cultures. The efforts that can make to improve the morale of the nation's children, namely by learning citizenship education and religious education and utilizing information technology to spread things related to the values of multicultural education to the broader community

Introduction: Pancasila was born as the ideology of the Indonesian nation, which reflects the values cultural values, ethics, morals, and the spirit of the nation. Pancasila was born as a form of national character, which reflects divinity, nationality, unity, togetherness, and justice. The purpose of this research is to know the practice of Pancasila values ​​in the life of the nation and the state. Especially, the implementation of the life of the younger generation in the 21st century today. Methods: This study is literature research where data is collected using keywords in the database. Literature source search carried out with the help of Boolean operators and using the PICOS format. The results of selecting articles, using PRISMA Flow Diagrams. The search results found 125 articles that match the research theme. After checking for duplication, 82 articles were excluded because of the similarity in the results of the discussion. In the end, there were 43 articles used as a literature source. Results: Based on the analysis of research findings, which are supported by literature sources, it shows that the current values ​​of Pancasila are worrying. This can be seen, where people's behavior has been contaminated by external cultures due to technological sophistication. At present, it can be said that the ethics and morals of society do not reflect the values ​​of Pancasila. Conclusion: In order to re-install the values ​​of Pancasila in people's lives, the participation of all parties is necessary. This is especially so, for today's younger generation. Therefore, it is necessary to develop a model for teaching Pancasila to be carried out by schools and colleges. So that later, it can produce a generation of ethics and morals who love the country.

Three computer algorithms are presented. One reduces a network $\CALN$ to its interior, $\CALI$. Another counts all the triangles in the network, and the last randomly generates networks similar to $\CALN$ given just its interior $\CALI$. But these algorithms are not the usual numeric programs that manipulate a matrix representation of the network; they are set-based. Union and meet are essential binary operators; contained_in is the basic relational comparator. The interior $\CALI$ is shown to have desirable formal properties and to provide an effective way of revealing ``communities'' in social networks.

In this paper, we revisit the hydrodynamics supporting the design and development of the RiverCat class of catamaran ferries operating in Sydney Harbor since 1991. More advanced software is used here. This software accounts for the hydrodynamics of the transom demisterns which experience partial or full ventilation, depending on the vessel speed. This ventilation gives rise to the hydrostatic drag, which adds to the total drag of the vessel. The presence of the transom also creates a hollow in the water. This hollow causes an effective hydrodynamic lengthening of the vessel, which leads to a reduction in the wave resistance. Hence a detailed analysis is required in order to optimize the size of the transom. It is demonstrated that the drag of the vessel and the wave generation can be predicted with good accuracy. Finally, the software is also used to optimize the vessel further by means of affine transformations of the hull geometry.

In present work, the effects of bioflavonoids (ginkgetin and sciadopitysin) on stimulus-induced superoxide generation, tyrosyl and serine/threonine phosphorylation of proteins in human neutrophils, and the translocation of cytosolic compounds (p47phox, p67phox and Rac) to cell membrane were studied, which were isolated from the needles of Taxus media var. Hicksii. Meanwhile, three normal flavonoids (apigenin, quercetin and isoquercetin) were involved as contrasts. The results indicated that ginkgetin and sciadopitysin were capable of concentration-dependently inhibitory effects on the superoxide generation induced by N-formyl-methionyl-leucyl-phenylalanine (fMLP), arachidonic acid (AA) and phorbol-12-myristate 13-acetate (PMA). And they also suppressed fMLP- and AA- induced tyrosyl or PMA-induced serine/threonine phosphorylation and the translocation of cytosolic compounds (p47phox, p67phox and Rac) to cell membrane, which were in parallel with the suppression of the stimulus-induced superoxide generation. The effect of these compounds on the radical-scavenging was also investigated. Ginkgetin and sciadopitysin did not show remarkable effect on DPPH radical-scavenging activity, and they didn’t display the radical-scavenging activity on superoxide anion generated by phenagine methoxysulfate (PMS)-NADH system. Apparently, ginkgetin and sciadopitysin had great performance in pharmacological value and they are worthy of in-depth study.

When a microgrid is grid-tied to a distribution system, it can provide surplus power generation to the distribution system, if any abnormality or interruption occurs in the distribution system, the microgrid can operate in standalone mode to isolate the impact of the abnormality or interruption. However, if the microgrid can not collect enough information from the distribution system, it may cause the failure of generation transferring of distribution feeders, or even further influence the stability of the distribution system. In this paper, a strategy for the resilient control of a microgrid is proposed. It can solve the above-mentioned problem, reduce the duration of the outage of loads. This strategy is experimented in the microgrid in the Institute of Nuclear Energy Research (INER), the reliability is also analyzed to evaluate the unavailability of the microgrid in INER, and it is verified that the proposed strategy can reduce the duration of the outage of loads, and hence the reliability of a microgrid can be upgraded.

Modern electrical power systems integrate renewable generation, with solar generation being one of the pioneers worldwide. In Latin America, the greatest potential and development of solar generation is found in Chile through the National Electric System. However, its energy matrix faces a crisis of drought and reduction of emissions that limits hydroelectric generation and involves the definitive withdrawal of coal generation. The dispatch of these plants is carried out by the system operator, who uses a simplified mechanism, called “economic merit list” and which does not reflect the real costs of the plants to the damage of the operating and marginal cost of the system. This inefficient dispatch scheme fails to optimize the availability of stored gas and its use over time. Therefore, a real-time redispatch model is proposed that minimizes the operation cost function of the power plants, integrating the variable generation cost as a polynomial function of the net specific fuel consumption, adding gas volume stock restrictions and water reservoirs. In addition, the redispatch model uses an innovative "maximum dispatch power" restriction, which depends on the demand associated with the automatic load disconnection scheme due to low frequency. Finally, by testing real simulation cases, the redispatch model manages to optimize the operation and dispatch costs of power plants, allowing the technical barriers of the market to be broken down with the aim of integrating ancillary services in the short term, using the power reserves in primary (PFC), secondary (SCF), and tertiary (TCF) frequency control.

Large language models (LLMs) excel in providing natural language responses that sound authoritative, reflect knowledge of the context area, and can present from a range of varied perspectives. Agent Based Models and Simulation consist of simulated agents that interact within a simulated environment to explore societal, social, and ethical, among other, problems. Agents generate large volumes of data over time and discerning useful and relevant content is an onerous task. LLMs can help in communicating agents’ perspectives on key events by providing natural language narratives. However, these narratives need to be factual, transparent, and reproducible. To this end, we present a structured narrative prompt for sending queries to LLMs. Chi-square tests and Fisher’s Exact tests are applied to assess statistically significant difference in sentiment scores of the narrative messages between simulation generated narratives, ChatGPT-generated narratives, and real tweets. The narrative prompt structure effectively yields narratives with the desired components from ChatGPT. This structure is expected to be extensible across LLMs. In 14 out of 44 categories, ChatGPT generated narratives which has sentiment scores that were not discernibly different, in terms of statistical significance (alpha level of 0.05), from the sentiment expressed in real tweets. Three outcomes are provided: (1) a list of benefits and challenges for LLMs in narrative generation; (2) a structured prompt for requesting narratives of a LLM based on simulated agents’ information; and (3) an assessment of statistical significance in the sentiment prevalence of the generated narratives compared to real tweets. This indicates significant promise in the utilization of LLMs for helping to connect simulated agent’s experiences with real people.

Progesterone receptor (PGR) expression level determines biological characteristics of the serous ovarian carcinoma, and low PGR expression appears to be associated with chemoresistance and worse outcome. In this study, we aimed to find relationships between tumor progesterone receptor level and RNA-profile (miRNAs, piwiRNAs, and mRNAs), determining its biological characteristics and behavior. For this purpose, we applied next generation sequencing of small noncoding RNAs, quantitative RT-PCR, and immunohistochemistry to analyze FFPE and frozen tumor samples as well as blood plasma from patients with benign cystadenoma (BSC), serous borderline tumour (SBT), low-grade and high-grade serous ovarian carcinoma (LGSOC and HGSOC, respectively). We found significant upregulation of MMP7 and MUC16 and downregulation of PGR in LGSOC and HGSOC in comparison with BSC. The tissue content of miR-199a-5p, miR-214-3p, miR-424-3p, miR-424-5p, miR-125b-5p significantly inversely correlated with the expression level of MUC16 and blood serum CA125 concentration, and significantly directly correlated with the PGR expression level in tumor tissue. On the contrary, the tissue content of miR-16-5p, miR-17-5p, miR-20a-5p, miR-93-5p, responsible for epithelial-mesenchymal transition (EMT) of the cell, significantly directly correlated with the blood serum CA125 concentration and significantly inversely correlated with the PGR expression level in the tumor tissue. Levels of the EMT-associated miRNAs significantly directly correlated with the content of hsa_piR_022437, hsa_piR_009295, hsa_piR_020813, hsa_piR_004307, hsa_piR_019914 in tumor tissues. Among them, expression level of hsa_piR_004307 significantly inversly correlated with the PGR expression level in the tumor. Two optimal logistic regression models were developed based on the quantitation of hsa_piR_020813, miR-16-5p, hsa_piR_022437 or hsa_piR_004307, hsa_piR_019914, miR-93-5p in the tumor tissue, both of which significantly diagnose PGR-negative tumor phenotype with 93% sensitivity. According to FunRich3.1.3 functional enrichment analysis tool, 72 gene-targets of miRNA and piRNA identified here as markers of PGR-negative ovarian tumor phenotype were proven to be mutated in different cancers such as ovarian, breast, colorectal, liver, stomach, lung, endometrial, thyroid cancer. Among them, the blood plasma levels of miR-16-5p and hsa_piR_022437 can be used to diagnose PGR-negative tumor phenotype with 86% sensitivity before surgery and chemotherapy to choose the treatment strategy for this most aggressive type of ovarian cancer (for instance, neoadjuvant chemotherapy followed by cytoreduction in combination with hyperthermic intraperitoneal chemotherapy) to increase the effectiveness of treatment and longevity of the patient.

Head and neck squamous cell carcinoma (HNSCC) is a highly heterogeneous and the most common form of head and neck cancer, posing significant challenges for disease management. Single-cell RNA sequencing (sc-RNAseq) has emerged as a valuable tool for addressing these challenges by enabling detailed characterization of the tumor microenvironment (TME) at the cellular level. This review assesses the utility of sc-RNAseq in HNSCC research, compiling current strategies employing single-cell technologies. For HNSCC etiology, sc-RNAseq allows for the construction of cellular atlases, characterization of different cell types, and investigation of key genes and processes involved in cancer initiation, development, and progression within the TME. In terms of HNSCC diagnosis and prognosis, the high resolution offered by sc-RNAseq enables the identification of cell type-specific signatures, enhancing prognostic models and disease stratifiers for more accurate patient outcome assessments. Regarding HNSCC treatment, sc-RNAseq provides insights into cellular responses to various treatments, including radiotherapy, chemotherapy, and immunotherapy, contributing to improved patient stratification and personalized treatment strategies. This review highlights the unique contributions of sc-RNAseq to HNSCC research, addressing its cellular and biological complexity, and emphasizes its potential for advancing research and clinical practice in other cancer types.

Autism spectrum disorder (ASD) is a common condition with lifelong implications. The last decade has seen dramatic improvements in DNA sequencing and related bioinformatics and databases. We analyzed the raw DNA sequencing files on the Variantyx® bioinformatics platform for the last 50 ASD patients evaluated with trio whole genome sequencing (trio-WGS). “Qualified” variants were defined as coding, rare, and evolutionarily conserved. Primary Diagnostic Variants (PDV) additionally were in genes directly linked to ASD and matched clinical correlation. A PDV was identified in 34/50 (68%) of cases, including 25 (50%) cases with heterozygous de novo and 10 (20%) with inherited variants. De novo variants in genes directly associated with ASD were far more likely to be Qualifying than non-Qualifying versus a control group of genes (P=0.0002), validating that most are indeed disease related. Sequence reanalysis increased diagnostic yield from 28% to 68%, mostly by inclusion of de novo PDVs in genes not yet reported as ASD associated. Thirty-three subjects (66%) had treatment recommendation(s) based on DNA analyses. Our results demonstrate high yield of trio-WGS for revealing molecular diagnoses in ASD that is greatly enhanced by re-analyzing DNA sequencing files. In contrast to previous reports, de novo variants dominate the findings, mostly representing novel conditions. This has implications to the cause and rising prevalence of autism.

Autism spectrum disorder (ASD) is a common condition with lifelong implications and a strong hereditary component suggesting genetic underpinnings. The last decade has seen dramatic improvements in DNA sequencing and related bioinformatics and databases. We analyzed the raw DNA sequencing files on the Variantyx® bioinformatics platform for the last 50 ASD patients evaluated with trio whole genome sequencing (trio-WGS). “Qualified” variants were defined as coding, rare, and evolutionarily conserved. Primary Diagnostic Variants (PDV) additionally were in genes directly linked to ASD and matched clinical correlation. A PDV was identified in 34/50 (68%) of cases, including 25 (50%) cases with heterozygous de novo and 10 (20%) with inherited variants. De novo variants in genes directly associated with ASD were far more likely to be Qualifying than non-Qualifying versus a control group of genes not associated with ASD (P = 0.0002, odds ratio 29), validating that most are indeed disease related. Only 14/34 (41%) of PDV cases had the variant listed on the laboratory report, and reanalysis increased diagnostic yield from 28% to 68%. Variants that we assigned as PDVs yet not on the report were predominately de novo in genes not yet reported as ASD associated. Many subjects both with and without a PDV had inherited Qualifying variants in known ASD-associated genes, suggesting polygenic inheritance. Thirty-three subjects (66%) had treatment recommendation(s) based on DNA analyses. Our results demonstrate high yield of trio-WGS for revealing molecular diagnoses in ASD that is greatly enhanced by re-analyzing DNA sequencing files. In contrast to previous reports, de novo variants dominate the findings, mostly representing novel conditions. This has implications to the cause and rising prevalence of autism.

The etiology of autism spectrum disorder (ASD) has not yet been completely elucidated. Through time, multiple attempts have been made to uncover the causes of ASD. Different theories have been proposed, such as that it is caused by “Gods Wrath,” alternations in the gut–brain axis with an emphasis on gut dysbiosis, post vaccine complications, and genetic or even autoimmune causes. In this review we present data covering over 170 000 participants at age ranging from 2 to 14 years focusing on human cell changes rather than using animal models found in previous studies. The male/female ratio was 4:1. Data collection occurred in many countries covering ethnically diversified subjects. Moreover, we aim to show how the progress in genetic techniques influence the explanation found in medical White Papers based on the human genetic samples we have observed from our studies

Atypical hemolytic uremic syndrome (aHUS) is a rare and life-threatening disease characterized by microangiopathic hemolytic anemia, thrombocytopenia, and acute kidney injury, necessitating differentiation from other thrombotic microangiopathy disorders. Definitive biomarkers for disease diagnosis and activity are currently lacking, and identifying molecular markers is essential. We conducted single-cell sequencing on peripheral blood mononuclear cells from 13 aHUS patients, 3 aHUS family members, and 4 healthy controls. Analysis included clustering, cell type annotation, pseudotime estimation, and cell-cell communication. Immune cell populations differ among aHUS, aHUS families, and healthy controls. Disease activity and treatment influence T, NK, B, and monocyte subpopulations, with increased intermediate monocyte levels distinguishing aHUS from controls and aHUS groups with varying disease activity. Subclustering revealed differential gene expression in patients compared to controls; higher expression of mitochondria-related genes suggests cell metabolism may influence clinical course. Pseudotime trajectory analysis demonstrated unique immune cell differentiation, and cell-cell interaction analysis identified distinct signaling pathways among patients, family members, and controls. This single-cell sequencing study is the first to confirm immune cell dysregulation in aHUS pathogenesis, offering valuable insights into molecular mechanisms and potential new diagnostic and disease activity markers.

Desmin is a class III intermediate filament highly expressed in cardiac, smooth and striated muscle Autosomal dominant or recessive mutations in the desmin gene (DES) result in a variety of diseases, including cardiomyopathies and myofibrillar myopathy, collectively called desminopathies. Here we describe the clinical, histological and radiological features of a Greek patient with a myofibrillar myopathy and cardiomyopathy linked to the c.734A>G,p.(Glu245Gly) heterozygous variant in the DES gene. Moreover, through ribonucleic acid sequencing analysis in skeletal muscle we show that this variant provokes a defect in exon 3 splicing and thus should be considered clearly pathogenic

PIK3CA is a gene usually mutated in breast cancer and has an important role in tumor progression and treatment. Therefore, there is required a technique to detect low-rate PIK3CA mutations improving the clinical conduct. This study aimed to compare chip-based dPCR and Sanger sequencing to detect PIK3CA mutations in breast cancer patients. Fifty-seven tumor samples from breast cancer patients were collected and analyzed by Sanger sequencing and dPCR for PIK3CA mutations (E545K, H1047R, and H1047L). Digital PCR sensitivity, specificity, and overall performance were estimated by contingency tables, receptor operator characteristic (ROC), and area under the curve (AUC). Sanger sequencing identified PIK3CA mutations in six patients (10.5%), two with H1047R, and four with E545K. Digital PCR confirmed those mutations and identified 19 additional patients with at least one mutation. Comparison between dPCR and Sanger sequencing showed a sensitivity of 100% (95% CI 53-100%), and a specificity of 84.2% (95% CI 83 - 84.2%). Besides, H1047R mutation showed a significant association with breast cancer phenotype (p =0.019) and lymphatic node infiltration (p =0.046). Digital PCR showed a high sensitivity to detect mutations in tumor samples and it might be capable to detect low-rate mutations and tumor subpopulations not detected by Sanger sequencing.

Human metapneumovirus (HMPV) is an important cause of upper and lower respiratory tract disease in individuals of all ages. It is estimated that most individuals will be infected by HMPV by the age of 5 years old. Despite this burden of disease, there remains caveats in our knowledge of virus global genetic diversity due to a lack of HMPV sequencing, particularly at whole genome scale. The purpose of this study was to create a simple and robust approach for HMPV whole genome sequencing to be used for genomic epidemiological studies. To design our assay, all available HMPV full length genome sequences were downloaded from the NCBI GenBank database and used to design four primer sets to amplify long, overlapping amplicons spanning the viral genome and, importantly, specific to all known HMPV subtypes. These amplicons were then pooled and sequenced on an Illumina iSeq; however the approach is suitable to other common NGS platforms. We demonstrate the utility of this method using a representative subset of clinical samples and examine these sequences using a phylogenetic approach. Here we present an amplicon-based method for the whole genome sequencing of HMPV from clinical extracts that can be used to better inform genomic studies of HMPV epidemiology and evolution.

Recombinant laboratory plasmids (RLPs) are common in biological research and freely shared among academic research laboratories (ARLs), a practice required by many research funding agencies. However, the generation of accurate, reproducible results in experiments utilizing RLPs can be hampered by a lack of accompanying sequence information and metadata. This culture of RLP sharing without knowledge of sequence or etiology is accepted by publishers, not regulated by governments, and outside the realm of bio-industry. In addition, no centralized infrastructure currently exists to collate such data, which at the moment is fragmented across companies, non-profits, and governments and thus is not easily accessed or enacted toward threat assessment. The ubiquity, free exchange, and dual-use risk of RLPs exemplifies a biosecurity threat and elevates the need to characterize their composition to facilitate improved biorisk management by the academic community. A number of common sense solutions are available to create a culture that addresses the biosecurity gap posed by RLP sharing. Culture shift in RLP management will require new norms, effective data management for collation of RLP sequences and metadata, and an incentive structure that encourages sequencing by stakeholders. The next generation of researchers must initiate and champion this shift with support from funding agencies and endorsement from governments and international organizations. Coordination of efforts and stakeholders will require international public/private collaboration, a structure that will be critical to ensure widespread utility as well as the ability of lower-resourced partners to participate, contribute, and benefit.

The use of circulating cell-free (cf) DNA to monitor cancer progression and response to therapy has significant potential but there is only limited data on whether this technique can detect the presence of low frequency subclones that may ultimately confer therapy resistance. In this study, we sought to evaluate whether whole-exome sequencing of cfDNA can accurately profile the mutation landscape of metastatic melanoma. We used whole-exome sequencing (WES) to identify variants in matched tumor-derived genomic (g) DNA and plasma-derived cfDNA isolated from a cohort of 10 metastatic cutaneous melanoma patients. WES parameters such as sequencing coverage and total sequencing reads were comparable between gDNA and cfDNA. There was significant concordance between gDNA and cfDNA based on the total number of variants identified and the degree of overlap in variants which was independent of the site of tumor biopsy. The mutant allele frequency of common single nucleotide variants was lower in cfDNA reflecting lower read depth and dilution of circulating tumor DNA in the circulation by other cfDNA species. In addition to known melanoma driver mutations, several other melanoma-associated mutations were found to be concordant between matched gDNA and cfDNA. This study highlights that WES of cfDNA can capture clinically-relevant mutations present in melanoma metastases, but does not appear to provide any additional unique information on tumor heterogeneity. Targeted deep sequencing may be required to detect low frequency genomic aberrations known for predicting therapy resistance.

Here we describe ARSA-16S, a tool and accompanying reference database for the analysis of bacterial 16S amplicons. Among other features, ARSA-16S is based on a new model, approach, and algorithm for sequence-level assignment of reads understood as probability distributions, assigns reads individually, and is designed with non-overlapping amplicons covering two non-contiguous regions. A new set of primers for the amplification and sequencing of the V4 and V6 regions is also provided.

The whole genome sequencing (WGS) has become a crucial tool to understand genome structure and genetic variation. The MinION sequencing of Oxford Nanopore Technologies (ONT) is an excellent approach for performing WGS and has advantages in comparison with other Next-Generation Sequencing (NGS): It is relatively inexpensive, portable, has simple library preparation, can be monitored in real-time, and has no theoretical limits on read length. Sorghum bicolor (L.) Moench is diploid (2n = 2x = 20) with a genome size of about 730 Mb, and its genome sequence information is released in the Phytozome database. Therefore, sorghum can be be used as a good reference. However, plant species have complex and large genomes compared to animals or microorganisms. As a result, complete genome sequencing is difficult for plant species. MinION sequencing that produces long-reads can be an excellent tool to overcome the weak assembly of short-reads generated from NGS by minimizing the generation of gaps or covering the repetitive sequence that appears on the plant genome. Here, we conducted the genome sequencing for S. bicolor cv. BTx623 using the MinION platform and obtained 895,678 reads and 17.9 gigabytes(Gb) (ca. 25X coverage of reference) from long-read sequence data. Through a de novo assembly using two different tools and mapped assembled contigs against the sorghum reference genome, a total of 6,124 contigs (covering 45.9%) were generated from Canu, and a total of 2,661 contigs (covering 50%) were generated from Minimap and Miniasm with a Racon pipeline. Our results provide a pipeline of long-read sequencing analysis for plant species using the MinION platform and a clue to determine the total sequencing scale for optimal coverage based on various genome sizes.

In this work we demonstrate the proof-of-concept of real-time discrimination between patches of serine or isoleucine monomers in the primary structure of custom-engineered, macro-dipole-like peptides, at uni-molecular level. We employed single-molecule recordings to examine the ionic current through the α-hemolysin (α-HL) nanopore, when hydrophilic serine or hydrophobic isoleucine residues, flanked by segments of oppositely charged arginine and glutamic amino acids functioning as a voltage-dependent ‘molecular brake’ on the peptide, were driven at controllable rates across the nanopore. The observed differences in the ionic currents blockades through the nanopore, visible at time resolutions corresponding to peptide threading through the α-HL’s constriction region, was explained by a simple model of the volumes of electrolyte excluded by either amino acid species, as groups of three serine or isoleucine monomers transiently occupy the α-HL. To provide insights into the conditions ensuring optimal throughput of peptide readout through the nanopore, we probed the sidedness-dependence of peptide association to and dissociation from the electrically and geometrically asymmetric α-HL.

One consequence of the global technological advancement in conventional metallurgy is the fast depletion rate of valuable minerals, which are also becoming increasingly difficult to find in pure and economically viable forms. This has spurred more interest in technologies that investigate ability of different microorganisms to mobilize valuable metals from their ores via diverse metabolic processes. This study was carried out therefore to isolate, identify and characterize iron solubilizing bacteria from Iron stones of Agbaja iron ore mining site of Kogi State, Nigeria. Crushed samples in the range of 0.25µm and 0.75µm particle sizes were cultured in a modified 9k media to facilitate bacterial growth and pure cultures were then isolated and sub-cultured for further bioleaching studies. Morphological and biochemical analysis suggests that some of the bacteria identified are members of Acidithiobacillus spp, Pseudomonas spp, and Leptospirillum spp. Studies conducted on pure cultures and mixed consortium of the identified organisms shows that a mixture of the three organisms leached iron ore to about 96.16%. Also results of growth pattern due to bacteria countafter 24-72hours of incubation ranged between 0.1×10³ cfu/ml and 12.3 ×10³ cfu/ml for Acidithiobacillus spp. The need to explore the molecular characteristics of these organisms with a view to generating more information on the quality/quantity of their DNA for future cloning activities was also investigated in this work. DNA was extracted using zymo fungal/bacterial extraction mini prep kit ^TM (cat #6001) and subsequently subjected to 1% agarose gel electrophoresis. Visible bands were obtained with Alpha Innotech Gel Documentation Machine. DNA amplification was carried out using a pettier based thermo cycler PCR machine and electrophoresed on 1.5% agarose gel. Results of the PCR shows a visible band corresponding to 1.5kbp using this primer 27F (5¹-GAGTTTGATCCTGGCTCAG-3¹) and 1492R (5^1-GGTTACCTTGTTACGACT-3¹). DNA purity check shows two of the bacteria possess very good qualities for sequencing for further molecular analysis.

As one of the world's most populous countries, Indonesia is struggling with the composition of its people, the majority of whom are unemployed productive-age individuals with low education levels. Another issue is the high poverty rate, which is followed by issues of gender inequality. The government cannot solve these social issues on its own. There is a need for community support to solve these problems through sustainable social entrepreneurship activities. Using the Theory of Planned Behavior and Outcome Expectation, this study will determine the factors that influence the interest of individuals known as the Z and Millennial generation, aged 18 to 34 years old, in becoming social entrepreneurs. This study applied a quantitative approach with a judgmental sampling technique to a sample of Generation Z and Millennials who have ever participated in social activities but have not yet started their own business. The study gathered 210 respondents, who were then analyzed using the PLS-SEM method with multiple group analysis generation-based comparison. According to the findings, the Millennial Generation's Attitude Toward Behavior, Subjective Norms, and Outcome Expectation all had a positive impact on Social Entrepreneurial Intention. Meanwhile, Subjective Norms had no effect on Social Entrepreneurial Intention in the Z Generation. Only attitude toward behavior, perceived behavioral control, and outcome expectation have a positive effect on the development of social entrepreneurial intentions. Furthermore, the findings of this study confirm that subjective norms influence attitude toward behavior and Perceived Behavioral Control in both Generation Z and millennials.

Trio-based exome sequencing and high-resolution HLA typing were employed to analyze three patients with autoimmune adrenal insufficiency (AAI), including those with autoimmune polyglandular syndrome (APS) type 2, as well as their parents. Benign or likely benign variants of the AIRE gene were identified in all participants of the study. These variants, coupled with clinical data and the results of antibody studies to type I interferons, helped to exclude APS-1. Patients with APS-2, in contrast to patient with AAI, inherited distinct variants of unknown significance in the CLEC16A gene, which is associated with autoimmune diseases including AAI. Various risk alleles in other genes associated with autoimmunity were identified in all patients. HLA typing of second class loci revealed alleles related to APS types 2, 3, and 4. Nevertheless, the frequencies of the haplotypes identified are substantial in the healthy Russian population, precluding from regarding these alleles as genetic determinants linked to APS development. Immunological examination can detect antibody carriers and predict the risk of autoimmune disease development. In the future, to identify genetic predictors of autoimmune endocrinopathies, it is recommended to analyze the whole genome of patients and their relatives, examining clinically relevant variants in non-coding regions.

The objective of this research was to analyze the evolution and trend of the generation gap and nursing education from 1968 to 2021 through bibliometric indicators. The method used is a bibliometric, descriptive and retrospective study of documents in Scopus, with descriptors “Nursing educat*”, “generation* and the Boolean operator “AND”, N= 653 web documents from 1968 to 2021, and filters of the type bib, csv. The search was carried out on October 9, 2021, using the Bibliometrix R Package software and the Biblioshiny tool. The Results indicate high scientific production in 2020 (54 articles disclosed). This study demonstrates patterns and lines of research in nursing education, such as educational models, interpersonal relationships, and organizational innovation.

Boutique hotels emerged in the late 1970s since then the product has become more mainstream. The draw of boutique hotels is more personalized services. When marketing and providing services to a niche market it is smart to be able to differentiate potential guests to best meet their needs. The generational cohort theory states that a population may be divided into segments based on their generation. This research focuses on Generation X to find out what they are seeking in a boutique hotel product. Based upon how they chose their travel destination there were significant differences between culinary experience, attractions/activities, and cost/budget.

Pairs of potential and flow variables have long been established for interfacing object-oriented component models of physical systems. Recently, however, the use of triplets has been discovered for the purpose of robust modeling. New and powerful Modelica libraries have been developed such as the DLR ThermoFluid Stream library or the introduction of the Dialectic Mechanics library. Their use of triplets is entangled with a special modeling approach that uses Linear Implicit Equilibrium Dynamics. In this paper, we study the basic motivation of this approach, its benefits and drawbacks before we finally demonstrate how it beneficially impacts the generation of corresponding simulation code.

This paper aims to explore how climate change affects electricity generation (fossil-fueled power plants, hydroelectric stations, wind systems and photovoltaics) and energy demand in residential buildings in Greece for the period up to 2050. In both cases RCP scenarios results are considered in the appropriate spatial and temporal dimension. Energy supply technologies were examined through statistical regression models and/or mathematical equations correlating climatic parameters with energy productivity. With respect to energy demand, bottom-up models were developed that integrate behavioral and policy aspects. The analysis showed that climate change is expected to mainly affect electricity generation from hydro and thermal power plants, while the impacts on solar and wind energy are significantly lower. The range of impacts on hydro potential and electricity generation depends on the geographical location of the power plants and shows significant uncertainty due to the corresponding uncertainty in climate models estimates regarding precipitation and runoff changes while showing significant geographical variations. With respect to energy demand, climate change is expected to affect energy consumption, but the expected range of effects depends on both the implementation and the characteristics (deep vs. shallow renovation) of measures for upgrading the thermal performance of the building stock and the intensity of climate change.

This paper aims to study and analyze a new Peltier cell layout using a PCM in biphasic mode, with the liquid phase encapsulating the p-n junctions and the solid one playing the role of heat sink. The selected PCM is an organic compound that operates within a temperature range corresponding to the melting process. The phase change zone encompasses the working temperature of the Peltier cell, avoiding thermal gradient variation across the cell section and maintaining the operating conditions and the cell efficiency. PCM encapsulates the Peltier cell thermocouples, creating a layer that increases the power generation as the thickness reduces. We simulated the performance of the new configuration for different temperature gaps between both sides of the cell, obtaining an improvement in power generation from 1.65 to 7.93. This power increase ratio depends on the temperature gap and transient time to reach the steady working temperature. The control of the layer thickness, transient time, and working temperatures resides in the external heating power source, which varies the operating conditions regulating the heat power and the airflow. Maximum output power from the cell prototype is 36.5 W, while conventional Peltier cells operating in similar conditions produce 7.3 W, which represents a power gain of 500%.

This paper performs a comprehensive analysis of the wind energy potential of onshore regions in Greece with emphasis on quantifying the volume risk and the spatial covariance structure. Optimization techniques are employed to derive efficient wind capacity allocation plans (also known as generation portfolios) incorporating different yield aspirations. The generation profile of minimum variance and other optimal portfolios along the efficient frontier are subject to rigorous evaluation using a fusion of descriptive and statistical methods. In particular, principal component analysis is employed to estimate factor models and investigate the spatiotemporal properties of wind power generation, providing valuable insights into the persistence of volume risk. The overarching goal of the study is to employ a set of statistical and mathematical programming tools guiding investors, aggregators and policy makers in their selection of wind energy generating assets. The findings of this research challenge the effectiveness of current policies and industry practices, offering a new perspective on wind energy harvesting with a focus on the management of volume risk.

The sandwich generation caregivers provide simultaneous care for multiple generations. Caregiving is a dynamic process, and each generation has its unique set of needs. Moreover, studies have indicated a growing population within this group. However, despite extensive research efforts, the caregiving practices employed by the sandwich generation remain inadequately explained. Therefore, the objective of this study was to shed light on the caregiving practices offered by the sandwich generation. The grounded theory approach was selected as the conceptual framework for investigating the research objective. Purposive and snowball sampling methods were utilized to recruit 18 participants from the sandwich generation. The data collected through interviews and observations were analyzed using the 2015 version of Corbin and Strauss methodology. The findings revealed that sandwich generation caregivers are influenced by prominent personality traits, issues related to the elderly, and dependencies and interdependencies within the caregiving process. Sandwich caregivers employ a range of strategies influenced by intervening and background factors. Throughout this process, caregivers encounter both positive and negative consequences. Consequently, policymakers and planners should prioritize the establishment and expansion of support systems for caregiving.

It is currently unknown whether thrombin generation is associated with venous thromboembolism (VTE) recurrence, major bleeding, and mortality in the elderly. Therefore, our aim was to prospectively study the association between thrombin generation and VTE recurrence, major bleeding and mortality in elderly patients with acute VTE. Consecutive patients aged ≥65years with acute VTE were followed for 2 years starting from 1 year after the index VTE. Primary outcomes were VTE recurrence, major bleeding and mortality. Thrombin generation was assessed in 565 patients 1 year after the index VTE. At this time, 59% of patients were still anticoagulated. Thrombin generation was discriminatory for VTE recurrence, but not for major bleeding and mortality in non-anticoagulated patients. Moreover, peak ratio (adjusted subhazard ratio 4.09, 95% CI, 1.12-14.92) and normalized peak ratio (adjusted subhazard ratio 2.18, 95% CI, 1.28-3.73) in presence/absence of thrombomodulin were associated with VTE recurrence, but not with major bleeding and mortality after adjustment for potential confounding factors. In elderly patients, thrombin generation was associated with VTE recurrence, but not with major bleeding and/or mortality. Therefore, our study suggests the potential usefulness of thrombin generation measurement after anticoagulation completion for VTE to help identifying among elderly patients those at higher risk of VTE recurrence.

The paper investigates experimentally the influence of the Fused Filament Fabrication (FFF) pre-processing strategy on the tribological properties of parts made of PEI (polyetherimide), investigating the difference in the weight loss of the samples caused by abrasive wear before and after the test. The samples were tested for abrasive wear resistance on a tribometer constructed according to ASTM G65/16 (dry sand). Two types of specimen printing orientation along X-axis (lengthwise) and along Z-axis (heightwise) were tested in the study. Three types of path generation strategies were used for manufacturing "X" and "Z" specimens and totally 18 samples were made and tested. Path deposition strategy was carried out with path deposition width of 0.5mm and parallel paths in all slicing layers. In order to reduce the voids in volume, deposition path axes in subsequent layers were shifted by 0.25mm offset. Garnet abrasive Fe3Al2(SiO4)3 was used for this test. The analysis of the experimental data shows the relationship between the samples building direction (X, Z), applied deposition strategies (1X - 3X and 1Z - 3Z) on the resulting resistance to abrasive wear.Keywords: PEI, FFF, path generation strategy, abrasive wear

This survey proposed an evaluation model to analyze and examine different approaches to generativity. In addition to problem domain concepts, the following concepts were used to define this model: Complexity and complexity management, and Systematics view to achieve unified and integrated insight into disparate evaluation criteria. The research's approach to the said concepts is first introduced. Then, the evaluation model is presented.

Character education is essential for the current millennial generation and must be applied in everyday life in the surrounding community. The character of the millennial generation is different from the previous generation, which requires us to pay more attention to character education which is starting to erode along with the times. The Millennial generation is a generation that in everyday life can never be separated from science and technology. In this digital era, the millennial generation has a social function of strength in technology. In this study, there are research questions that will be discussed in this article, namely the first regarding what problems occur in the millennial generation who occupy the digital era?. Second, what is the important role and influence of the digital era on character education for the millennial generation in Indonesia?. Writing this article uses a qualitative research method, namely a literature review study, where researchers use or look for references from journals or books. Samples of respondents were taken randomly from each region, and there were ten respondents. From this research, it is found that the millennial generation in the digital era chooses to use social media to access the latest news and information rather than reading print media that contains education. This article aims to find out the importance of character education for the millennial generation, which is starting to erode with the times in the digital era. Many people underestimate character education, especially for the current millennial generation. Therefore, we must implement educational programs at any level, especially in Indonesia, because the character shows the national identity. This article will discuss the vital role and influence of character education for millennials who live in the digital era to be aware of the importance of character education in citizenship.

The increasingly used approach of combining different simulation software in testing of automated driving systems (ADS) increases the need for potential and convenient software designs. Recently developed co-simulation platforms (CSP) provide the possibility to cover the high demand on testing kilometers for ADS by combining vehicle simulation software (VSS) with traffic flow simulation software (TFSS) environments. The emphasis on the demand of testing kilometers is not enough to choose a suitable CSP. The complexity level of the used vehicle, object, sensors and environment models is essential for valid and representative simulation results. Choosing a suitable CSP raises the question of how the test procedures should be defined and constructed and what the relevant test scenarios are. Parameters of the ADS, the environments, objects, sensors in VSS as well as traffic parameters in TFSS can be used to define and generate test scenarios. In order to generate a large number of scenarios in a systematic and automated way, suitable and appropriate software designs are required. In this paper we present a software design for CSP based on the Model-View-Controller (MVC) design pattern and implementation of a complex CSP for virtual testing of ADS. Based on this design, an implementation of a CSP is presented using the VSS from IPG Automotive called CarMaker and the TFSS from PTV Group called Vissim. The results have shown that the presented CSP design and the implementation of the co-simulation can be used to generate relevant scenarios for testing of ADS.

The Convective Rainfall Rate from Cloud Physical Properties (CRPh) for Meteosat Second Generation Satellites is a day-only precipitation algorithm developed at the Spanish Meteorological Agency (AEMET) for EUMETSAT’ Satellite Application Facility in support to Nowcasting and Very Short Range Forecasting (NWC SAF). It is therefore mainly intended to provide input for monitoring and near-real-time forecasts for the next few hours. This paper critically discusses the theoretical basis of the algorithm with special emphasis in the empirical values and assumptions in the microphysics of precipitation and compares the performances of the CRPh with its antecessor, the Convective Rainfall Rate algorithm (CRR), using an object-based method. The analyses show that AEMET’s CRPh is physically consistent and that outperforms the CRR. The applicability of the algorithm for nowcasting and the challenges to evolve the product to an all-day algorithm are also presented.

An understanding of the cultural conditions that determine the factors affecting nurses’ intention to leave is important for countries suffering from nurse shortage. Aim: to examine factors influencing intention to leave among female hospital nurses in a large Japanese sample, classified into four generations by age considering economic conditions. Methods: a cross-sectional survey with convenience sampling was conducted. Anonymous self-administered questionnaires were distributed to all nurses in 30 hospitals. To assess intention to leave, basic attributes, life conditions, work characteristics, and factors of psychosocial work environment were addressed. After classifying data into four generations based on age cohorts, we conducted multivariate logistic regression analysis using the completed data (N = 5,074, mean age = 36.24). Results: regardless of generational characteristics influenced by economic conditions, effort and monetary reward were generation-common factors. Over-commitment, social support, and the presence of a role model were generation-common factors in three generations. While having children increased intention to leave in the generation born 1965–1979, having family members in need of caregiving other than children decreased the risk in the generation born in the 1980s. Conclusion: generational countermeasures considering factors of psychosocial work environment and life conditions are needed to avert female nurse turnover.

Analysis of complex DNA mixtures is limited by the selected genetic markers characterized and assay technology. Small panels of short tandem repeats (STRs) are the current standards in most countries. Extension of STRs with hundreds of single nucleotide polymorphisms (SNPs) is now commercially available. The current set of extension SNPs focus on phenotypic and biogeographic ancestry informative SNPs. Larger panels with thousands of SNPs have been developed that can identify up to 10 contributors to forensic DNA samples. Herein, multiple sets of SNPs were selected with the focus of increasing the upper limit of detectable contributors. Larger SNP panel sets with lower minor allele frequency (MAF) alleles can detect large numbers of contributors to in silico mixtures of randomly selected profiles from the 1,000 Genomes project. These results provide a path to enable characterization of complex DNA mixtures that are currently impossible to analyse.

Leishmania major is the main causative agent of cutaneous leishmaniasis in humans. The Friedlin strain of this species (LmjF) was chosen when a multi-laboratory consortium undertook the objective of deciphering the first genome sequence for a parasite of the genus Leishmania. The objective was successfully attained in 2005, and this represented a milestone for Leishmania molecular biology studies around the world. Although the LmjF genome sequence was done following a shotgun strategy and using classical Sanger sequencing, the results were excellent and this genome assembly served as the reference for subsequent genome assemblies in other Leishmania species. Here, we present a new assembly for the genome of this strain (named LMJFC for clarity), generated by the combination of two high throughput sequencing platforms, Illumina short-read sequencing and PacBio Single Molecular Real-Time (SMRT) sequencing, which provides long-read sequences. Apart from resolving uncertain nucleotide positions, several genomic regions have been reorganized and a more precise composition of tandemly repeated gene loci was attained. Additionally, the genome annotation has been improved by adding 542 genes and more accurate coding-sequences defined for around two hundred genes, based on the transcriptome delimitation also carried out in this work. As a result, we are providing gene models (including untranslated regions and introns) for 11,238 genes. Genomic information ultimately determines the biology of every organism; therefore, our understanding of molecular mechanisms will depend on the availability of precise genome sequences and accurate gene annotations. In this regards, this work is providing an improved genome sequence and updated transcriptome annotations for the reference L. major Friedlin strain.

Transfer RNA (tRNA) modifications are essential for the temperature adaptation of thermophilic and psychrophilic organisms, as they control the rigidity and flexibility of transcripts. To further understand how specific tRNA modifications are adjusted to maintain functionality in response to temperature fluctuations, we investigated whether tRNA modifications represent an adaptation of bacteria to different growth temperatures (minimal, optimal, and maximal), focusing on closely related psychrophilic (P. halocryophilus and E. sibiricum), mesophilic (B. subtilis), and thermophilic (G. stearothermophilus) Bacillales. Utilizing an RNA sequencing approach combined with chemical pre-treatment of tRNA samples, we systematically profiled dihydrouridine (D), 4-thiouridine (s4U), 7-methyl-guanosine (m7G), and pseudouridine (Ψ) modifications at single-nucleotide resolution. Despite their close relation, each bacterium exhibited a unique tRNA modification profile. Our findings revealed increased tRNA modifications in the thermophilic bacteria at higher temperatures, particularly showing elevated levels of s4U8 and Ψ55 modifications compared to non-thermophilic bacteria, indicating a temperature-dependent regulation that may contribute to thermotolerance. Furthermore, we observed higher levels of D modifications in psychrophilic and mesophilic bacteria indicating an adaptive strategy for cold environments by enhancing local flexibility in tRNAs. Our method demonstrated high effectiveness in identifying tRNA modifications compared to an established tool, highlighting its potential for precise tRNA profiling studies.

The purpose of this study was to identify candidate novel species performing beneficial ecological functions from soil. The hypothesis was that novel culturable species with antibiotic production potential could be readily found from soil in the Nature Canyon at Los Angeles Pierce College. 137 bacterial isolates from soil were grown on nutrient agar, ISP-6 medium, or LB agar and partial 16S was ascertained using the Sanger platform for regions V1-V4. One of the potentially novel isolates, Pseudomonas sp. 21-C3-ER, was isolated on nutrient agar from fallow soil in an agricultural nature preserve in Los Angeles. The soil conditions were 3.7% moisture, clay texture by touch, 13.37% organic matter, pH=6.63, TDS=638, 150 ppm nitrogen, 114 ppm phosphate, and 42 ppm potash. Whole genome sequencing was performed on the DNBseq platform and species identification was performed with TRUEBacID; the closest relative was Pseudomonas brassicacearum subsp. neoaurantiaca which was 92.05% similar by genomic evidence. 197 virulence factors were identified including flagellar biosynthesis, motor proteins, Beta-lactamase, Fosfomycin, copper, and sulfur drug resistance. Gram stain of strain 21-C3-ER revealed gram negative rods. Rods were visualized with scanning electron microscopy, revealing individuals approximately 1 µm in length. Secondary metabolite analysis using antiSMASH showed a variety of post-translationally modified proteins and a promysalin analog. The qualitative test for pyoverdine siderophore production using UV light was positive. Metabolic analysis using RAST indicated genes were present for pyoverdine production, antimicrobial resistance, and ammonification. The nitrate reduction test was positive. Denitrifying bacteria may prevent leaching of nitrates from soil, since ammonia has a higher affinity to soil and organic matter than nitrate. We propose Pseudomonas fernandeno as a novel species. The type stain is 21-C3-ER.

Barcoding of DNA is a species identification technique that utilizes a small DNA fragment from a specific gene or genes known as "sequencing." The idea behind DNA barcoding is that a single sequence can be used to specifically identify an organism to species by comparison with a reference library of these DNA sections. Herbal adulteration can be monitored using DNA barcodes that utilize medicinal plants such as Atropa belladonna. Because it is challenging to distinguish between species solely based on morphology, other plants belonging to the same genus are replacing it in trade. Such replacement with plants not utilized for medical purposes could have negative side effects. Also, Atropa belladonna's positive effects can be completely lost. Taxonomists also have trouble distinguishing the genuine Atropa belladonna plant from cultivated items. As a result, DNA barcoding can now be used to overcome this challenge. The development of DNA barcodes may help with trade control, which protects and conserves endangered species from export outside of the country due to their economic and biological significance. In this review, we discuss the DNA barcoding of Atropa belladonna plant in the medicinal plants field.