3,773 Results Found

The efficient development of antiviral drugs, including efficient antiviral small interfering RNAs (siRNAs), requires continuous monitoring of the strict correspondence between a drug and the related highly variable viral DNA/RNA target(s). Deep sequ...

Analysis of RNA by deep-sequencing approaches has found widespread application in modern biology. In addition to measurements of RNA abundance under various physiological conditions, such techniques are now widely used for mapping and quantification...

Viroids are circular, highly structured, single-stranded, non-coding RNA pathogens known to infect and cause disease in several plant species. They are known to trigger the host plant’s RNA silencing machinery. The detection of viroid-derived small R...

Naturally occurring resistance-associated substitutions (RASs) can negatively impact the response to direct-acting antivirals (DAAs) agents-based therapies for hepatitis C virus (HCV) infection. Herein, we set out to characterize the RASs in the HCV1...

Using deep sequencing technologies such as Illumina’s platform, it is possible to obtain reads from the viral RNA population revealing the viral genome diversity within a single host. A range of software tools and pipelines can transform raw de...

Tissue-culture adaptation of viruses can modulate infection. Laboratory passage and bacterial artificial chromosome (BAC)mid cloning of human cytomegalovirus, HCMV, resulted in genomic deletions and rearrangements altering genes encoding the virus en...

This study aimed to determine shifts in microbial populations regarding richness and diversity from the daily use of a popular over-the-counter nasal spray. In addition, the finding of nasal commensal bacterial species that overlap with the oral micr...

Next-generation sequencing (NGS) technologies have revolutionized cancer genomics due to their high throughput sequencing capacity. Reports of the gene mutation profiles of various cancers by many researchers, including international cancer genome re...

The sheaf cohomology techniques are newly used to include Morse simplicial complexes in a rectangular-matrix chain, whose singular values are compatible with those of a square matrix, which can be used for multiple sequencing. The equivalence with th...

In the deep-sea environment, the volume available for an in-situ gene sequencer is severely limited. In addition, optical imaging systems are subject to real-time, large-scale defocusing problems caused by ambient temperature fluctuations and vibrati...

The precise mapping and quantification of the numerous RNA modifications that are present in tRNAs, rRNAs, ncRNAs/miRNAs, and mRNAs remain a major challenge and a top priority of the epitranscriptomics field. After the keystone discoveries of massive...

African swine fever virus (ASFV) is the causative agent of African swine fever, an economically important disease of pigs, often with a high case fatality rate. ASFV has demonstrated low genetic diversity among isolates collected within Eurasia. To e...

The adaptation tipping point and adaptation pathway approach developed to make decisions under deep uncertainty do not shed light on which among the multiple available pathways should be chosen as the preferred pathway. This creates the need to exten...

Here, we report the genome sequence and evidence for transcriptional activity of a virus-like element in the native Chilean berry tree Aristotelia chilensis. We propose to name the endogenous sequence as Aristotelia chilensis Virus 1 (AcV1). High-thr...

The robot task sequencing problem and trajectory planning problem are two important issues in the robotic optimization domain and are solved sequentially in two separate levels in traditional studies. This paradigm disregards the potential synergisti...

Multiple-type human papillomaviruses (HPV) infection presents a greater risk for persistence in asymptomatic individuals and may accelerate cancer development. To extend the scope of HPV types defined by probe-based assays, multiplexing deep sequenci...

Different human papillomavirus (HPV) types are characterized by differences in tissue tropism and ability to promote cell proliferation and transformation. In addition, clinical and experimental studies have shown that some genetic variants/lineages...

Across sub-Saharan Africa, key populations with elevated HIV-1 incidence and/or prevalence have been identified, but their contribution to disease spread remains unclear. We performed viral deep-sequence phylogenetic analyses to quantify transmission...

Cancer is one of the most deadly diseases, costing millions of lives and billions of USD every year. There are different ways to identify the biomarkers that can be used to detect cancer types and subtypes. RNA sequencing is steadily taking the lead...

Patients with hematuria are commonly given an invasive cystoscopy test to detect bladder cancer (BC). To avoid the risks associated with cystoscopy, several urine-based methods for BC detection have been developed, the most prominent of which is the...

Inherited retinal diseases (IRDs) are a clinically and genetically heterogeneous group of diseases which cause visual loss due to Mendelian mutations in over 250 genes, making genetic diagnosis challenging and time-consuming. Here, we developed a new...

Background: Exercise is one of the best nonpharmacologic therapies to treat hypertension. The blood pressure (BP) response to exercise is heritable. Yet, the genetic basis for the antihypertensive effects of exercise remains elusive. Methods: To asse...

Genomic prediction using whole-genome sequencing (WGS) data is challenged by the imbalance between a limited sample size (n) and an extensive number of single-nucleotide polymorphisms (SNPs) (p), where n $\ll$p. The high dimensionality of WGS...

PAX6 haploinsufficiency causes aniridia, a congenital eye disorder that involves the iris, and foveal hypoplasia. Comprehensive screening of the PAX6 locus, including the non-coding regions, by next-generation sequencing revealed four deep-intronic v...

Synergetic elongation of mesocotyl and coleoptile are crucial in governing maize seedlings emergence, especially for the maize sown in deep soil. Studying the genomic regions controlling maize deep-sowing tolerance would aid the development of new va...

Spodoptera litura is an emerging pest insect in cotton and arable crops in Central Asia. To explore the possibility of using baculoviruses as biological control agents instead of chemical pesticides, in a previous study we characterized a number of S...

Japanese encephalitis virus (JEV), a mosquito-borne Flavivirus, causes acute viral encephalitis with high morbidity and mortality in humans and animals. MicroRNAs (miRNAs) are small noncoding RNAs that are important modulators of the intricate host-...

Background: Reactivation of JC and BK polyomaviruses during immunosuppression can lead to adverse clinical outcomes. In renal transplant recipients, BKV-associated nephropathy can result in graft loss, while in patients with autoimmune disorders, pro...

Bacteria in rumen play pivotal roles in the digestion of nutrients to support energy for the host. In this study, metagenomic deep sequencing of bacterial metagenome extracted from the goats’ rumen generated 48.66 GB of data with 3,411,867 contigs an...

Seed germination is a key step in the new life cycle of plants. In agriculture, we regard the rapid and consistent process of seed germination as one of the necessary conditions to measure the high quality and yield of crops. ENO2 is a key enzyme in...

MicroRNAs (miRNAs) regulate gene expression and thereby influence cell fate and function. Recent studies suggest that an abundant class of miRNAs play important roles in immune cells, such as T cells, natural killer (NK) cells, B cells, and dendritic...

Circulating cell-free DNA (cfDNA) is emerging as a potential tumor biomarker. CfDNA-based biomarkers may be applicable in tumors without an available non-invasive screening method among at-risk populations. Esophageal squamous cell carcinoma (ESCC) a...

Mesocotyl length (MES) is an important trait that affects the emergence of maize seedlings after deep-seeding and is closely associated with abiotic stress. The elucidation of constitutive-QTLs (cQTLs) and candidate genes for MES and tightly molecula...

Background: Detecting Helicobacter pylori in fecal samples is easier and more comfortable than invasive techniques, especially in children. Thus, the objective of the present work was to detect H. pylori in feces from children by molecular methods as...

Many living organisms have DNA in their cells that is responsible for their biological features. DNA is an organic molecule of two complementary strands of four different nucleotides wound up in a double helix. These nucleotides are adenine (A), thym...

Human Activity Recognition (HAR) has gained significant attention due to its broad range of applications, such as healthcare, industrial work safety, activity assistance, and driver monitoring. Most prior HAR systems are based on recorded sensor data...

Accurate runoff prediction is one of the important tasks in various fields such as agriculture, hydrology, and environmental studies. Recently, with massive improvements of computational system and hardware, the deep learning-based approach has recen...

Background: COVID-19 genetic sequence research is crucial despite immunizations and pandemic control. COVID-19-causing SARS-CoV-2 must be understood genomically for several reasons. New viral strains may resist vaccines. Categorizing genetic sequence...

Routine surveillance in live poultry markets in the northern regions of Vietnam from 2016 to 2017 resulted in the isolation of 27 highly pathogenic avian H5N1 and H5N6 viruses of 3 different clades (2.3.2.1c, 2.3.4.4f, and 2.3.4.4g). Sequence and phy...

New analytics of post-transcriptional RNA modifications have paved the way for a tremendous upswing of the biological and biomedical research in this field. This especially applies to methods that included RNA-Seq techniques, and which typically resu...

In integrated circuit (IC) design, floorplanning is an important stage in obtaining the floorplan of the circuit to be designed. Floorplanning determines the performance, size, yield, and reliability of very large-scale integration circuit (VLSI) ICs...

This study addresses the performance of deep learning models for predicting human DNA sequence classification through an exploration of ideal feature representation, model architecture, and hyperparameter tuning. It contrasts traditional machine lear...

The solidifying steel follows highly nonlinear thermo-mechanical behavior depending on the loading history, temperature, and metallurgical phase fraction calculations (liquid, ferrite, and austenite). Numerical modeling with a computationally challen...

Recently proposed recommendation systems based on embedding vector technology allow us to utilize a wide range of information such as user side and item side information to predict user preferences. Since there is a lack of ability to use the sequent...

Driving risk prediction is crucial for advanced driving technologies, with deep learning approaches leading the way in driving safety analysis. Current driving risk prediction methods typically establish a mapping between driving features and risk st...

The green peach aphid (Myzus persicae) is a generalist pest damaging crops and transmitting viral pathogens. Using Illumina sequencing of small (s)RNAs and poly(A)-enriched long RNAs, we analyzed aphid virome components, viral gene expression and ant...

Commercial e-learning platforms have to overcome the challenge of resource overload and find the most suitable material for educators using a recommendation system (RS) when an exponential increase occurs in the amount of available online educational...

Human noroviruses (NoV) cause epidemics of acute gastroenteritis (AGE) worldwide and can be transmitted through consumption of contaminated foods. Fresh products such as shellfish can be contaminated by human sewage during production, which results i...

Current technologies that are used for genome-wide microRNA (miRNA) prediction are mainly based on BLAST tool. They often produce a large number of false positives. Here, we describe an effective approach for identifying orthologous pre-miRNAs in sev...

MicroRNAs (miRNAs) are 20- to 24-nucleotide endogenous small RNA molecules emerging as an important class of sequence-specific, trans-acting regulators for modulating gene expression at the post-transcription level. There has been a surge of interest...