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Interferons (IFN) constitute a primary line of protection against mucosal infection, with IFN research spanning over 60 years and encompassing a vast everexpanding amount of literature. Most of what is currently understood has been derived from extensive research defining the roles of "classical" type I IFNs, IFNα and IFNβ. However, little is known regarding responses elicited by less wellcharacterized IFN subtypes such as IFNε. In this paper, we combined a deductive text mining analysis of IFNε literature characterizing literature-derived knowledge with a comparative analysis of other type I and type III IFNs. Utilizing these approaches, three clusters of terms were extracted from the literature covering different aspects of IFNε research and a set of 47 genes uniquely cited in the context of IFNε. The use of these "in silico" approaches support the expansion of current understanding and the creation of new knowledge surrounding IFNε. [ABSTRACT FROM AUTHOR]

Due to their importance for computational biology, the methods and algorithms for multiple alignment of biological sequences have been the subject of continuous intensive research and innovation in the last 30 years. Within a PRACE research project we have designed and implemented metaheuristic algorithm for massively parallel MSA and based on it parallel software tool MSA_BG that has been ported on the European supercomputer Juqueen. In this paper we have investigated the Quality of Solution (QoS) of the parallel algorithm MSA_BG for multiple alignment of biological sequences on GPU-accelerated computing infrastructure based on 3 synthesized benchmarks of genetic sequences comprising the 8 segments of the swine virus AH1N1, the 9 genes of the severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human as well as the human genes BRCA1 and BRCA2 associated with the breast cancer issue. The analysis of the experimental results show that the QoS of the individual runs fall in the range of+10%, except for the case study of BRCA1 and BRCA2 where the range is within ∓1%. [ABSTRACT FROM AUTHOR]

This paper investigates an unexplored concept in Cyber Forensics, namely, a Programming Blunder. Programming Blunder is identified as a variable or a code segment or a field in a database table, which is hardly used or executed in the context of the application or the user's functionality. Blunder genes can be found in many parts of any program. It is the contention of this paper that this phenomenon of blunders needs to be studied systematically from its very genetic origins to their surface realizations in contrast to bugs and flaws, especially in view of their importance in software copyright infringement forensics. Some suggestions as to their applicability and functional importance for cyber forensics are also given including the vital need and a way to incorporate programming blunders into Abstraction- Filtration-Comparison test, the official software copyright infringement investigation procedure of US judiciary. [ABSTRACT FROM AUTHOR]

In this study, bioinformatics methods were used to screen key genes related to gastric cancer and the involved signaling pathways, and to explore relevant indicators of the occurrence and development of gastric cancer. The source data was downloaded from the Gene Expression Omnibus (GEO) of the National Center for Biotechnology Information (NCBI), and the differentially expressed genes were obtained using the GEO2R platform. These genes were then subjected to gene ontology (GO) biological process analysis and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Finally, KM-Plotter was used to analyze the effect of key genes on the survivorship curve of patients with gastric cancer. As a result, 744 differentially expressed genes were obtained, and genes related to the development and progression of gastric cancer were newly discovered: CELA3B and KCNJ16. Gastric cancer is one of the most common malignant tumors in the world, which is a serious threat to human health. According to the article of the China Anti-cancer Association The past and present life of Helicobacter pylori, there are 1,034,000 new cases of global cancer and 783,000 deaths in 2018. China is a country with high incidence of gastric cancer, and nearly half of the world’s new cases of gastric cancer and deaths occur in China. There are many factors affecting the occurrence of gastric cancer, but this paper argues that in addition to life and work habits, the incidence of gastric cancer depends on the patient’s genes. Under the combined effects of differential expression and special structure of many genes, it eventually leads to the occurrence of gastric cancer. The author of this essay will use the rich gene resources in the gene expression Omnibus (GEO) of the National Center for Biotechnology Information (NCBI) to screen, analyze, process and summarize the genes related to gastric cancer, explore its characteristics and significance and propose a new perspective on gastric cancer. [ABSTRACT FROM AUTHOR]

Wastes from livestock farms contain significant amounts of antibacterial drugs and antibiotic-resistant genes. Due to weak adsorption in the animal's body, antibiotics are released into the environment in an unchanged form or as metabolites in the composition of manure. In addition to the antibacterial agents, the manure of treated animals contains antibiotic-resistant bacteria. The use of manure in untreated form as a soil fertilizer can lead to the spread of antibiotic resistance among soil microorganisms. Composting is an effective way to reduce the content of antibiotic-resistant genes in manure. In this paper, the effect of the composting of cow manure contaminated with different concentrations of oxytetracycline on the temporal change in the number of two tetracycline-resistant genes tet(M) and tet(X) was evaluated. The initial concentrations of oxytetracycline in the cow manure were 50 mg kg -1, 150 mg kg -1 and 300 mg kg -1. Composts mixtures were incubated for 4 months. The number of copies of tet(M) and tet(X) genes was evaluated by the real-time PCR method using specific primers. It was found that the introduction of oxytetracycline in manure leads to an increase in the level of resistant genes tet(M) and tet(X). The higher the dose of antibiotic, the more genes were found. With the passage of time of the composting process, the content of resistant genes decreases. On the 75th day, resistant genes were not found in all samples of compost mixtures. [ABSTRACT FROM AUTHOR]

The rapid developments in the genetics field have generated a huge amount of biological data. Micro array gene expression data is an important instance of biological data. It has high dimensionality with a small number of samples accompanied with large number of genes. Therefore, using machine learning techniques for knowledge discovery in such data become a rich area for researchers. Classification taskdragged a high attention during the analysis ofsuch data, which objective classifying new unseen gene expression data sets into predefined classes. Therefore, implementing an effective gene selection technique and then adjusting a powerful classifier to achieve accurate classification accuracy is a challenge. This paper discusses some of recent research on machine learning approaches for gene expression selection and classification tasks. The paper also, presented a comparative study of these approaches as a first phase of our research motivated by building a newly, promising system for gene expression analysis. The results of the analysis showed that the support vector machine is the most often used classifier of higher classification accuracy. [ABSTRACT FROM AUTHOR]

Intraoperative papillary biopsies from kidneys of idiopathic-calcium oxalate stone formers (ICSF) have revealed a distinct pattern of mineral deposition in the interstitium of the renal papilla. The earliest sites of these deposits, termed Randall’s plaque, are found in the basement membrane of thin loops of Henle and appear to spread into the surrounding interstitium down to the papillary epithelium. Recent studies show kidney stones of ICSF patients grow attached to the renal papilla and at sites of Randall’s plaque. Together these observations suggest that plaque formation may be the critical step in stone formation. In order to control plaque formation and thereby reduce future kidney stone development, the mechanism of plaque deposition must be understood. Because the renal papilla has unique anatomical features similar to bone and the fact that the interstitial deposits of ICSF patients are formed of biological apatite, this paper tests the hypothesis that sites of interstitial plaque form as a result of cell-mediated osteoblast-like activity. [ABSTRACT FROM AUTHOR]

Many cellular processes exhibit periodic behaviors. Hence, one of the important tasks in gene expression data analysis is to detect subset of genes that exhibit cyclicity or periodicity in their gene expression time series profiles. Unfortunately, gene expression time series profiles are usually of very short length and highly contaminated with noise. This makes detection of periodic profiles a very difficult problem. Recently, a hypothesis testing method based on the Fisher g-statistic with correction for multiple testing has been proposed to detect periodic gene expression profiles. However, it was observed that the test is not reliable if the signal length is too short. In this paper, we performed extensive simulation study to investigate the statistical power of the test as a function of signal length, SNR, and the false discovery rate. We found that the number of periodic profiles can be severely underestimated for short length signal. The findings indicated that caution needs to be exercised when interpreting the test result for very short length signals. [ABSTRACT FROM AUTHOR]

The theory of gene assembly in ciliates has much in common with the theory of sorting by reversal. Both model processes that are based on splicing, and have a fixed begin and end product. The main difference is the type of splicing operations used to obtain the end product from the begin product. In this overview paper we show that the concept of breakpoint graph, known from the theory of sorting by reversal, has many uses in the theory of gene assembly. Our aim is to present the material in an intuitive and informal manner to allow for an efficient introduction into the subject. [ABSTRACT FROM AUTHOR]

Polycyclic aromatic hydrocarbons (PAHs) in the environment are highly genotoxic and carcinogenic, teratogenic and mutagenic, and their biodegradation genes and enzymes have attracted much attention. PAHs dioxygenase is one of the key enzymes for PAHs degradation, which is mainly produced by bacteria. It can open the rings of PAHs to form small molecule intermediate products through oxidation reaction, and finally oxidize to CO2 and water. At present, researches on the physicochemical properties, structural characteristics and functions of these enzymes have been carried out one after another. In this paper, the research status and development trend of PAHs degradation genes and enzymes were reviewed. [ABSTRACT FROM AUTHOR]

Dead code, which is not uncommon in software engineering, is an unexplored area in software piracy forensics. This paper primarily investigates the forensic importance of all programming blunders, including dead codes. Programming Blunder is identified as a variable or a code segment (including dead code) or a field in a database table, which is hardly used or executed in the context of the application or the user's functionality. Blunder genes can be found in many parts of any program. It is the contention of this paper that this phenomenon of blunders needs to be studied systematically from its very genetic origins to their surface realizations in contrast to bugs and flaws, especially in view of their importance in software copyright infringement forensics. The article discusses the idea -- expression merger aspects of programming blunders and finally, proposes the need and a way to incorporate programming blunders into Abstraction-Filtration- Comparison test, the official software copyright infringement investigation procedure of US judiciary. [ABSTRACT FROM PUBLISHER]

In this paper we extend the 2-D directed graphical representation for DNA sequences. The main purpose is to making a directed graph corresponding to a DNA sequence which hasn't any complete coincidence of the edges. To prevent repetition of the edge evector we define e→1 by using the outer product of two vectors and some mathematical concepts. Moreover, we have applied this method for some DNA sequences to show the advantage of this method over the some other methods. [ABSTRACT FROM AUTHOR]

Current DNA compression algorithms rely on finding repetitions within the DNA sequence so that similar subsequences can be encoded by referencing to each other. In this paper, we explore similarities between different chromosomes of the sequence “Saccharomyces cerevisiae”. These similarities are characterized by the existence of similar subsequences among different chromosomes. The longer the similar subsequences are, the higher the cross-similarities are. Our study indicates that these cross-sequence similarities are often significant as compared to self-sequence similarities. This implies that it would be advantageous to compress two or more sequences together so that similar subsequences found between multiple sequences can be encoded together. [ABSTRACT FROM AUTHOR]

The method of evaluating the physical traits of living creatures by generating essential proteins is known as gene expression. Translation and transcription are the two processes in gene expression. Gene Expression can be captured from DNA or RNA using a variety of approaches. High-throughput gene expression (NGS) data is having multiple advantages over the traditional gene expression dataset. Still one of the major disadvantages of NGS data is it is complex, comprising a large number of genes with few samples; among these thousands of significant genes, disease-causing genes must be identified. This issue should be solved by lowering the data source's dimension to a manageable level. Machine learning (ML) has proven its potential in the research areas of disease identification, and genomics in recent years. Many Machine Learning-based Gene Selection techniques have been described in the literature, to improve dimensionality reduction precision. In this work, a unique clinical support system based on the Relief-Cuckoo Search (CS)-Random Forest (RF) hybrid multi-stage significant gene identification technique is proposed for significant gene selection from the next-generation sequencing (NGS) dataset. This work can be helpful for the accurate identification of sepsis and the relevant genes associated with it, which helps early detection of the disease. This hybrid feature selection technique could be beneficial in later stages of disease treatment, such as disease diagnosis and drug development. The accuracy of the proposed model is 95.23 % which can be helpful for further analysis of various infectious diseases and thus helps the diagnosis procedure more convenient. [ABSTRACT FROM AUTHOR]

This study involves the prediction of the function and structure of putative genes in the genome of Clostridium acetobutylicum for the better elucidation of cellular metabolism. One bacterial strain was used in this study. About 50 hypothetical genes were retrieved from the whole-genome of C. acetobutylicum. KEGG, Pfam, UniProt, InterPro, ScanProsite, SMART, ProtParam, SignalP 4.0, TargetP 2.0, NCBI blast, HHpred, CPH modeling, PSIpred were the bioinformatic tools used in this study. Out of the 50 hypothetical genes, 3 genes were predicted. The function was analyzed for CA_C0024, CA_C0082, and CA_C00412 and they showed e value of 7.7e-16, 9.9e-81, and 7.6e-34 Conclusion: Based on the bioinformatics online tools tentative function and structure for CA_C0024, CA_C0082, and CA_C00412 were predicted. The functions were found to be transmembrane protein, transferase, and virulence-associated functions for CA_C0024, CA_C0082, and CA_C00412 respectively. The prediction for the gene CA_C0024 by HHpred and CPH modeler showed similarity to transferase from gram-positive bacteria. [ABSTRACT FROM AUTHOR]

The main objective of this study involves tentative function prediction of putative genes in the whole genome of the cellulolytic bacteria Bacillus methylotrophicus. This helps to get a clear idea about the organism's genetic makeup and thereby its metabolic pathways. for the better elucidation of cellular metabolism. Materials and methods: In this study, B. methylotrophicus strain was used. About 31 hypothetical genes were collected from the whole genome of B.methylotrophicus. The sequences were collected from the KEGG database. Some of the bioinformatics tools like, Pfam, Uniport, Interpro, SCANprosite, SMART, PROTparam, SignalP 4.0 server, TargetP 2.0 server, NCBI blast, HHpred, CPH modeling, and PSIpred were the tools used in this study. Results: Among these 31 hypothetical genes, the function and structure of 2 genes were predicted. The main function that was analyzed for RBAU_0404 and RBAU_0721 and showed e values 84 and 120 respectively. Conclusion: Based on the bioinformatics online tools, the tentative function and structure of RBAU_0404 and RBAU_0721 were predicted. For these genes, the function was similar to putative hydrolyze and RNA binding protein function for RBAU_0404 and RBAU_0721 respectively. CPH modeling was used to confirm the predicted function for the gene RBAU_0404 and it showed similarity to putative hydrolyze. [ABSTRACT FROM AUTHOR]

The aim of this study was to predict the structure and function of the putative gene in the whole genome of gut bacteria Ruminococcus albus for better elucidation of metabolic pathways. About 50 hypothetical genes were collected from R. albus to predict hypothetical proteins with various bioinformatics tools like Pfam, SMART, scanprosite, ProtParam, InterPro, UniProt, NCBI-blast, HHpred, CHP modeling, PSI pred. Function of Rumal_0123 was predicted based on the E value (0.53) and was similar to cell division functions. Based on bioinformatics tools, tentative function and structure for Rumal_0025 and Rumal_0123 were predicted. The function was found to be identical to the cell division function for Rumal_0123. [ABSTRACT FROM AUTHOR]

This study involves the prediction of the structure and function of putative genes in the genome of pathogenic and ligninolytic bacteria Brevibacillus agri, for better elucidation of its cellular metabolism. A total number of 50 hypothetical genes were collected from the genome of the bacteria B. agri. Bioinformatics online tools were used in this study to analyze the protein sequence and domains. The tools used include KEGG, PDB, SMART, ScanProsite, InterPro, ProtParam, NCBI-BLAST, HHpred, CPH(Copenhagen) modeling, and PSIpred. Out of 50 Hypothetical genes 4 genes were predicted. The function was analyzed for BA6348_03080, BA6348_03335, BA6348_03780, BA6348_01995 and they showed E-values of 7e-9,0, 0058, 6.5e-15, 0.000081 respectively. Based on the bioinformatics online tools tentative function and structure were predicted for BA6348_03080, BA6348_03335, BA6348_03780, BA6348_01995, and the functions were found to be similar to antimicrobial activity, isomerase, structural and motor proteins respectively, and the validation was done for the gene BA6348_01995 which showed similarity to motor protein from gram-negative bacteria Myxococcus xanthus. [ABSTRACT FROM AUTHOR]

A high genetic similarity in allelic frequency of CAPN1, TG5, GH and LEP genes was established between the III and IV generations of Hereford bull-calves (0.903 units) and heifers (0.973 units). The greatest values of similarity in bull-calves and heifers were found for CAPN1 gene: 0.514 units and 0.536 units, distance for GH gene 0.929 units and 0.802 units. The analysis of population structure showed that homozygous genotypes prevailed over heterozygous genotypes by 2.7-3.1 times for CAPN1 gene, 2.0-2.1 times for GH gene, 2.4-4.0 times for TG gene and 2, 3-4.0 times for LEP gene in heifers of the 3rd and 4th generations. The same superiority in bull-calves were by 1.3-6.0 times for CAPN1, GH И LEP genes. The observed heterozygosity (Hobs) varied from 0.154 units in GH and LEP genes up to 0.385 in.TG5 gene in III generation of bull-calves, and from 0.143 units in CAPN1 gene up to 0.571 units in TG5 gene in IV generation. The variety of heifers of IV generation was greater compared with III generation for CAPN1 and GH genes, the Hobs index in these genes were higher by 10.3% and by 4.7%. Heterozygosity test (HT) varied from negative values (–0.043... –0.272) in III generation of bull-calves to positive values in CAPN1, GH and LEP genes (+0.011... +0.093) in IV generation. High negative values of HT (-0.014... -0.140) were revealed in CAPN1, TG5, GH and LEP genes in heifers of III generation, and this indicator slightly increased for all genes (-0.011...+0.020) in IV generation. The presence of the desired alleles were found in 46.1% and 29.0% in bull-calves of 3rd and 4th generation, and 50% and 20% in heifers, respectively. [ABSTRACT FROM AUTHOR]

Characterization and identification of eukaryotic promoter is important for the gene prediction and genome annotation. In this paper, we study the structural characteristics of the core promoters in several eukaryotes through a series of DNA physicochemical properties and adopt a method that combines the alignment and average of multiple promoters and the nonlinear dimensionality reduction technique. The result shows that the eukaryotic core promoters have very special structural characteristics that are coherent between different species and independent of their sequence compositions. [ABSTRACT FROM AUTHOR]

Abstract. Dapsone Hypersensitive Syndrome (DHS) is the rare case of immunogenic disease that cause physiological damages even death case. However, in Papua Ethnic group this disease was frequently reported among leprosy patients since Dapsone is one of the main drugs in Multi Drugs Therapy standardized by WHO. Previous study in China found that HLA-B 13:01 is strongly associated to DHS in China population. Aim of this study was to detect HLA- B 13:01 gene among DHS leprosy patients in Papua using Sequence Based Typing Methods and qPCR method. This was cross sectional study among 34 leprosy patients that presented with DHS from Papua and West Papua Province. As the negative control we screened 52 leprosy patients that confirmed non-DHS patients. DNA was extracted from 3 mL blood specimens. HLA-B alleles were detected using Sequence Based Typing method by TBG kit and qPCR rapid detection kit using Nalagenetic. The results of HLA-sequence based typing among the 34 leprosy with DHS patients showed that 91,17 % were positively HLA-B:13:01 HLA-B 13:01 carrier consist of 82,35% Heterozygous and 8.82% Homozygous. In negative control 96,15% were non carrier of HLA-B 13:01 gene and 3,85% were heterozygous. Using qPCR procedure, HLA-B 13:01 was positively detected in DHS-leprosy patients and 96.15% negatively detected in Non-DHS leprosy patients but positive in 3.85% of heterozygote non-DHS. The concordances between SBT and qPCR methods were 100%. Conclusion of this study was HLA-B 13:01 gene can be detected in most of DHS leprosy patients in Papua Ethnics Group using SBT as well as qPCR rapid detection kit. [ABSTRACT FROM AUTHOR]

Although considerable knowledge has been accumulated on shifts in racial and ethnic boundary drawings, these shifts are usually analyzed over time - for instance, by contrasting historical boundaries between racial and ethnic groups to contemporary ones or by focusing on generational changes in individuals' group identification. The literature on boundaries speaks less to the social psychological processes of subjective shifts in racial and ethnic boundaries, as well as what drives these processes, and what barriers prevent particular boundary movements. One way that ethnic and racial boundaries are re-drawn at the micro-level is when individuals' ethnic and racial categorizations are challenged through the results genetic ancestry testing. Drawing on 57 in-depth interviews with individuals who have taken DNA ancestry tests, this paper examines how the results of DNA ancestry tests affect the way people draw ethnic and racial boundaries and what motivates these delimitations. We identify three main forms of boundary activity: boundary exapnsion, boundary maintenance, and boundary crossings. These patterns reveal how boundaries can be drawn and negotiated at the micro-level within significantly shorter periods of time than existing frameworks acknowledge. [ABSTRACT FROM AUTHOR]

Basal stem rot (BSR) disease is a devastating threat to Malaysia oil palm plantation, which is caused by Ganoderma boninense fungi. Dikaryon is the dominant stage of G. boninense and the pathogenic form of the fungus as compared to the monokaryon. Mating signalling response lead by mitogen-activated pathway (MAPK) responsible in the transformation of sterile monokaryon to pathogenic dikaryon. Expression of the STE3 gene involved in the autocrine activation of mating pathway. Mutations of STE3 gene in some pathogenic yeast resulted in inhibition of pheromone responses and blocked the signalling in the cell fusion. Identification of pheromone receptor, STE3 gene involved in mating signalling pathway is important to understand the mating response towards pathogenesis of G. boninense. Genome walking and polymerase chain reaction (PCR) were carried out to amplify isolate the full length of STE3 gene. Several in silico sequence analysis were conducted to characterise the STE3 gene. The full-length gene sequence including the upstream and downstream regions obtained could be used in future studies to understand pathogenesis of G. boninense. [ABSTRACT FROM AUTHOR]

Schmidtea mediterranea has a high regeneration ability. Previous studies have discovered genes contributing to this species’ regeneration ability, including genes with orthologs in human. However, no previous comparative studies have investigated these orthologs across a diversity of species. Understanding how the regeneration-related genes evolved in a diverse range of extant species is helpful to both the biological and medical field. Here I reported conservation measurements, pairwise dN/dS, of regeneration-related genes generated from 12 species against human. I then compared them to the pairwise dN/dS of housekeeping under the same criteria and found that the evolution process of genes related to regeneration varies across species and was less conserved than the housekeeping genes, indicating a less evolutionary constraint over regeneration-related genes. [ABSTRACT FROM AUTHOR]

DNA microarray has the characteristics of the higher dimension and redundancy, they bring into a series of the difficulties for the gene feature clasiffication. Pertaining to the two classical microarray datasets (cancer of colon set and leukemia set), firstly, the preprocess has been taken by the normalizing and the redundant data have been withdrawn; secondly, Principal Component Analysis method has been adopted to reduce the dimension of datasets and the information gene sets have been obtained; Finally, multiple classifiers have been utilized for the simulating tests, such as LS-SVM, SVM, BP, RBF, etc. They demonstrate that LS-SVM classifier has the higher accuracy for classification and show the approached method can make the correct judgment for classifying the feature of gene dataset, and provide the verifying reliance for clinical therapy further. [ABSTRACT FROM AUTHOR]

Since the emergence of SARS-CoV-2 in November 2019, there has been an exponential production of literature due to worldwide efforts to understand the interactions between the virus and the human body. Using an "in-house" developed script we retrieved gene annotations and identified phenotype enrichments. Human Phenotype Ontology terms were retrieved from the literature using the Onassis R package. This produced both disease-gene and disease-phenotype data as well as data for gene-phenotype interactions. Overall, we retrieved 181 human phenotypes that were identified by both approaches. Further indepth analysis of these relationships could provide further insights in the molecular mechanisms related with the observed phenotypes, answers and hypotheses for key concepts within COVID-19 research. [ABSTRACT FROM AUTHOR]