Coding

MOTIVATION: Single cell profiling has become a common practice to investigate the complexity of tissues, organs and organisms. Recent technological advances are expanding our capabilities to profile various molecular layers beyond the transcriptome such as, but not limited to, the genome, the epigenome and the proteome. Depending on the experimental procedure, these data can be obtained from separate assays or from the very same cells. Despite development of computational methods for data integration is an active research field, most of the available strategies have been devised for the joint analysis of two modalities and cannot accommodate a high number of them...

SUMMARY: PlasCAT is an easy-to-use cloud-based bioinformatics tool that enables de novo plasmid sequence assembly from raw sequencing data. Non-technical users can now assemble sequences from long reads and short reads without ever touching a line of code. PlasCAT uses high-performance computing servers to reduce run times on assemblies and deliver results faster. AVAILABILITY AND IMPLEMENTATION: PlasCAT is freely available on the web at https://sequencing.genofab...

MOTIVATION: Peptides are promising agents for the treatment of a variety of diseases due to their specificity and efficacy. However, the development of peptide-based drugs is often hindered by the potential toxicity of peptides, which poses a significant barrier to their clinical application. Traditional experimental methods for evaluating peptide toxicity are time-consuming and costly, making the development process inefficient. Therefore, there is an urgent need for computational tools specifically designed to predict peptide toxicity accurately and rapidly, facilitating the identification of safe peptide candidates for drug development...

A. fumigatus is a deadly fungal pathogen, responsible for >400,000 infections/year and high mortality rates. A. fumigatus strains exhibit variation in infection-relevant traits, including in their virulence. However, most A. fumigatus protein-coding genes, including those that modulate its virulence, are shared between A. fumigatus strains and closely related non-pathogenic relatives. We hypothesized that A. fumigatus genes exhibit substantial genetic variation in the non-coding regions immediately upstream to the start codons of genes, which could reflect differences in gene regulation between strains...

OBJECTIVES: To study the prevalence of exocrine pancreas insufficiency (EPI) at a population level and the subsequent risk of pancreatic ductal adenocarcinoma (PDAC). METHODS: Using TriNetX (a database of over 79 million US residents), we included patients ≥18 years with EPI (identified via ICD-10 codes) and continuous follow-up from 2016-2022. Patients with prior pancreas resection and PDAC before an EPI diagnosis were excluded. The primary outcome was EPI prevalence...

The HIV-1 provirus mainly consists of internal coding region flanked by 1 long terminal repeats (LTRs) at each terminus. The LTRs play important roles in HIV-1 reverse transcription, integration, and transcription. However, despite of the significant study advances of the internal coding regions of HIV-1 by using definite reference classification, there are no systematic and phylogenetic classifications for HIV-1 5' LTRs, which hinders our elaboration on 5' LTR and a better understanding of the viral origin, spread and therapy...

In this study, an extensive analysis of microsatellite markers (Single Tandem Repeats-STRs) in Penaeus vannamei was conducted at an advanced level. The markers were thoroughly examined, characterized, and specific markers located within coding regions were identified. Out of a total of 306 STRs, 117 were classified as perfect markers based on their single repeat motif. Among these perfect markers, 62 were found to be associated with predicted coding genes (mRNA), which were involved in various functions such as binding, catalytic activity, ATP-dependent activity, transcription, structural and molecular regulation...

Long non-coding RNAs (lncRNAs) are involved significantly in the development of human cancers. lncRNA HOTAIR has been reported to play an oncogenic role in many human cancers. Its specific regulatory role is still elusive. And it might have enormous potential to interpret the malignant progression of tumors in a broader perspective, that is, in pan-cancer. We comprehensively investigated the effect of HOTAIR expression on tumor prognosis across human malignancies by analyzing multiple cancer-related databases like The Cancer Genome Atlas (TCGA) and Tumor Immune Estimation Resource (TIMER)...

Non-small cell lung cancer (NSCLC) is the most common histopathological type, and it is purposeful for screening potential prognostic biomarkers for NSCLC. This study aims to identify the lncRNAs and mRNAs related to survival of non-small cell lung cancer (NSCLC). The expression profile data of lung adenocarcinoma and lung squamous cell carcinoma were downloaded in The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) dataset. A total of eight survival related long non-coding RNAs (lncRNAs) and 262 survival related mRNAs were filtered...

The widely used Vermon 1024-element matrix array for three-dimensional (3D) ultrasound imaging has three blank rows in the elevational direction, which breaks the elevation periodicity, thus degrading volumetric image quality. To bypass the blank rows in elevation while maintaining the steering capability in azimuth, we proposed a row transmission (RT) scheme to improve 3D spatial resolution. Specifically, we divided the full array into four apertures, each with multiple rows along the elevation. Each multi-row aperture (MRA) was further divided into subapertures to transmit diverging waves sequentially...

In the task of multiview multilabel (MVML) classification, each instance is represented by several heterogeneous features and associated with multiple semantic labels. Existing MVML methods mainly focus on leveraging the shared subspace to comprehensively explore multiview consensus information across different views, while it is still an open problem whether such shared subspace representation is effective to characterize all relevant labels when formulating a desired MVML model. In this article, we propose a novel label-driven view-specific fusion MVML method named L-VSM, which bypasses seeking for a shared subspace representation and instead directly encodes the feature representation of each individual view to contribute to the final multilabel classifier induction...

Visualizing event timelines for collaborative text writing is an important application for navigating and understanding such data, as time passes and the size and complexity of both text and timeline increase. They are often employed by applications such as code repositories and collaborative text editors. In this paper, we present a visualization tool to explore historical records of writing of legislative texts, which were discussed and voted on by an assembly of representatives. Our visualization focuses on event timelines from text documents that involve multiple people and different topics, allowing for observation of different proposed versions of said text or tracking data provenance of given text sections, while highlighting the connections between all elements involved...

Event cameras respond to scene dynamics and provide signals naturally suitable for motion estimation with advantages, such as high dynamic range. The emerging field of event-based vision motivates a revisit of fundamental computer vision tasks related to motion, such as optical flow and depth estimation. However, state-of-the-art event-based optical flow methods tend to originate in frame-based deep-learning methods, which require several adaptations (data conversion, loss function, etc.) as they have very different properties...

Pre-trained visual-language (ViL) models have demonstrated good zero-shot capability in video understanding tasks, where they were usually adapted through fine-tuning or temporal modeling. However, in the task of open-vocabulary temporal action localization (OV-TAL), such adaption reduces the robustness of ViL models against different data distributions, leading to a misalignment between visual representations and text descriptions of unseen action categories. As a result, existing methods often strike a trade-off between action detection and classification...

BACKGROUND: To overcome knowledge gaps and optimize long-term follow-up (LTFU) care for childhood cancer survivors, the concept of the Survivorship Passport (SurPass) has been invented. Within the European PanCareSurPass project, the semiautomated and interoperable SurPass (version 2.0) will be optimized, implemented, and evaluated at 6 LTFU care centers representing 6 European countries and 3 distinct health system scenarios: (1) national electronic health information systems (EHISs) in Austria and Lithuania, (2) regional or local EHISs in Italy and Spain, and (3) cancer registries or hospital-based EHISs in Belgium and Germany...

IMPORTANCE: The National Cancer Institute comprehensive cancer centers (CCCs) lack spatial and temporal evaluation of their self-designated catchment areas. OBJECTIVE: To identify disparities in cancer stage at diagnosis within and outside a CCC's catchment area across a 10-year period using spatial and statistical analyses. DESIGN, SETTING, AND PARTICIPANTS: This cross-sectional, population-based study conducted between 2010 and 2019 utilized cancer registry data for the Johns Hopkins Sidney Kimmel CCC (SKCCC)...

INTRODUCTION: Information from published studies describing dental treatment of nonmilitary personnel in a military theater of operations is sparse. The primary objective of this study is to determine the number of dental emergencies (DEs) and the types of dental treatment rendered on non-U.S. military (civilian) personnel treated by Navy dentists in 2007-2008 in Iraq and 2009 in Afghanistan. The second objective is to compare the type of DE treatment procedures provided to civilian personnel to the type of DE treatment procedures performed on U...

Iron accumulation has been associated with the pathogenesis of neurodegenerative diseases and memory decline. As previously described by our research group, iron overload in the neonatal period induces persistent memory deficits and increases oxidative stress and apoptotic markers. The neuronal insult caused by iron excess generates an energetic imbalance that can alter glutamate concentrations and thus trigger excitotoxicity. Drugs that block glutamatergic receptor eligibly mitigate neurotoxicity; among them is perampanel (PER), a reversible AMPA receptor (AMPAR) antagonist...

This study determined natural and artificial radionuclide concentrations to evaluate natural radioactivity and health risk levels of nine travertines in the Yaprakhisar and Balkayası regions in Turkey. The samples coded B1-M, B2, B5, B7, B8, and B10 represent waste derived from the Yaprakhisar travertines, as well as samples T5-M, T12, and Z1 travertines derived from Balkayası. The levels of natural and artificial radionuclide concentrations (232 Th, 40 K, and 137 Cs) were measured using a high-purity germanium (HpGe) detector system...

PURPOSE: A computational method based on Monte-Carlo calculations is presented and used to calculate isodose curves for a new upright and tilting CT scanner useful for radiation protection purposes. METHODS: The TOPAS code platform with imported CAD files for key components was used to construct a calculation space for the scanner. A sphere of water acts as the patient would by creating scatter out of the bore. Maximum intensity dose maps are calculated for various possible tilt angles to make sure radiation protection for site planning uses the maximum possible dose everywhere...