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View article: A nextflow pipeline for molecular quantitative trait loci mapping in small sample size datasets with an application in Atlantic salmon
A nextflow pipeline for molecular quantitative trait loci mapping in small sample size datasets with an application in Atlantic salmon Open
View article: Sequence-based chromatin activity modeling and regulatory impact prediction of genetic variants in farmed animals using deep learning
Sequence-based chromatin activity modeling and regulatory impact prediction of genetic variants in farmed animals using deep learning Open
Noncoding genomic variations are crucial for the genetic regulation of traits; however, their functional impact in farmed animals remains underexplored due to limited genomic resources and the absence of tailored computational tools. Here,…
View article: Hybrid Quantum Convolutional Neural Network-Aided Pilot Assignment in Cell-Free Massive MIMO Systems
Hybrid Quantum Convolutional Neural Network-Aided Pilot Assignment in Cell-Free Massive MIMO Systems Open
A sophisticated hybrid quantum convolutional neural network (HQCNN) is conceived for handling the pilot assignment task in cell-free massive MIMO systems, while maximizing the total ergodic sum throughput. The existing model-based solution…
View article: A Nextflow pipeline for molecular quantitative trait loci mapping in small sample size datasets with an application in Atlantic salmon
A Nextflow pipeline for molecular quantitative trait loci mapping in small sample size datasets with an application in Atlantic salmon Open
Background Molecular quantitative trait loci (molQTL) mapping, particularly for gene expression and chromatin accessibility, provides crucial insights into the regulatory and functional potential of genetic variation. While significant pro…
View article: VN1K: a genome graph-based and function-driven multi-omics and phenomics resource for the Vietnamese population
VN1K: a genome graph-based and function-driven multi-omics and phenomics resource for the Vietnamese population Open
Vietnam, the 16th most populated nation, remains profoundly underrepresented in global genomic databases. Here, we present VN1K, a first-ever comprehensive and well-curated resource of multi-omics data with a wide-range of phenotypic infor…
View article: Sequence-based chromatin activity modeling and regulatory impact prediction of genetic variants in farmed animals using deep learning
Sequence-based chromatin activity modeling and regulatory impact prediction of genetic variants in farmed animals using deep learning Open
Non-coding genomic variations are crucial for the genetic regulation of traits; how-ever, their functional impact in farmed animals remains underexplored due to lim-ited genomic resources and the absence of tailored computational tools. He…
View article: Investigation on multi-corners crash-box structure subjected to axial crushing
Investigation on multi-corners crash-box structure subjected to axial crushing Open
This paper investigated the crushing behavior of multi-corner crash-box subjected to quasi-static axial impact loading via FEM numerical simulation and experiments. The effects of the number of welded lines on the welded area and the heat-…
View article: Vulnerability-Aware Spatio-Temporal Learning for Generalizable and Interpretable Deepfake Video Detection
Vulnerability-Aware Spatio-Temporal Learning for Generalizable and Interpretable Deepfake Video Detection Open
Detecting deepfake videos is highly challenging due to the complex intertwined spatial and temporal artifacts in forged sequences. Most recent approaches rely on binary classifiers trained on both real and fake data. However, such methods …
View article: A combined AI and cell biology approach surfaces targets and mechanistically distinct Inflammasome inhibitors
A combined AI and cell biology approach surfaces targets and mechanistically distinct Inflammasome inhibitors Open
Inflammasomes are protein complexes that mediate innate immune responses whose dysregulation has been linked to a spectrum of acute and chronic human conditions, which dictates therapeutic development that is aligned with disease variabili…
View article: FakeFormer: Efficient Vulnerability-Driven Transformers for Generalisable Deepfake Detection
FakeFormer: Efficient Vulnerability-Driven Transformers for Generalisable Deepfake Detection Open
Recently, Vision Transformers (ViTs) have achieved unprecedented effectiveness in the general domain of image classification. Nonetheless, these models remain underexplored in the field of deepfake detection, given their lower performance …
View article: Abstract 1486 Development of Activity-Based Protein Profiling Assays for the Human Rhomboid Proteases
Abstract 1486 Development of Activity-Based Protein Profiling Assays for the Human Rhomboid Proteases Open
Rhomboid intramembrane proteases (RIPs) are a family of serine hydrolases distinguished by their membrane-embedded active sites and proposed involvement in metabolic and neurodegenerative diseases as well as cancer. Despite the ubiquity of…
View article: LAA-Net: Localized Artifact Attention Network for Quality-Agnostic and Generalizable Deepfake Detection
LAA-Net: Localized Artifact Attention Network for Quality-Agnostic and Generalizable Deepfake Detection Open
This paper introduces a novel approach for high-quality deepfake detection called Localized Artifact Attention Network (LAA-Net). Existing methods for high-quality deepfake detection are mainly based on a supervised binary classifier coupl…
View article: Alteration in the gut microbiome is associated with changes in bone metabolism after laparoscopic sleeve gastrectomy
Alteration in the gut microbiome is associated with changes in bone metabolism after laparoscopic sleeve gastrectomy Open
Laparoscopic sleeve gastrectomy (LSG), the most common bariatric surgical procedure, leads to durable weight loss and improves obesity-related comorbidities. However, it induces abnormalities in bone metabolism. One unexplored potential co…
View article: A Combinatorial AI and Cell Biology Approach Identifies Mechanistically Distinct Inflammasome Inhibitors and Implicates the Raf Pathway in Inflammasome Signaling
A Combinatorial AI and Cell Biology Approach Identifies Mechanistically Distinct Inflammasome Inhibitors and Implicates the Raf Pathway in Inflammasome Signaling Open
View article: Precocious infant fecal microbiome promotes enterocyte barrier dysfuction, altered neuroendocrine signaling and associates with increased childhood obesity risk
Precocious infant fecal microbiome promotes enterocyte barrier dysfuction, altered neuroendocrine signaling and associates with increased childhood obesity risk Open
Early life gut microbiome composition has been correlated with childhood obesity, though microbial functional contributions to disease origins remain unclear. Here, using an infant birth cohort (n = 349) we identify a distinct fecal…
View article: Dissecting vocabulary biases datasets through statistical testing and automated data augmentation for artifact mitigation in Natural Language Inference
Dissecting vocabulary biases datasets through statistical testing and automated data augmentation for artifact mitigation in Natural Language Inference Open
In recent years, the availability of large-scale annotated datasets, such as the Stanford Natural Language Inference and the Multi-Genre Natural Language Inference, coupled with the advent of pre-trained language models, has significantly …
View article: An integrative pipeline for circular RNA quantitative trait locus discovery with application in human T cells
An integrative pipeline for circular RNA quantitative trait locus discovery with application in human T cells Open
Motivation Molecular quantitative trait locus (QTL) mapping has proven to be a powerful approach for prioritizing genetic regulatory variants and causal genes identified by genome-wide association studies. Recently, this success has been e…
View article: An integrative framework for circular RNA quantitative trait locus discovery with application in human T cells
An integrative framework for circular RNA quantitative trait locus discovery with application in human T cells Open
Molecular quantitative trait locus (QTL) mapping of genetic variants with intermediate molecular phenotypes has proven to be a powerful approach for prioritizing genetic regulatory variants and causal genes identified by Genome-wide associ…
View article: Deep probabilistic model for lossless scalable point cloud attribute compression
Deep probabilistic model for lossless scalable point cloud attribute compression Open
In recent years, several point cloud geometry compression methods that utilize advanced deep learning techniques have been proposed, but there are limited works on attribute compression, especially lossless compression. In this work, we bu…
View article: Assessing polygenic risk score models for applications in populations with under-represented genomics data: an example of Vietnam
Assessing polygenic risk score models for applications in populations with under-represented genomics data: an example of Vietnam Open
Most polygenic risk score (PRS)models have been based on data from populations of European origins (accounting for the majority of the large genomics datasets, e.g. >78% in the UK Biobank and >85% in the GTEx project). Although sever…
View article: A comprehensive evaluation of polygenic score and genotype imputation performances of human SNP arrays in diverse populations
A comprehensive evaluation of polygenic score and genotype imputation performances of human SNP arrays in diverse populations Open
View article: HA and M2 sequences alter the replication of 2013–16 H1 live attenuated influenza vaccine infection in human nasal epithelial cell cultures
HA and M2 sequences alter the replication of 2013–16 H1 live attenuated influenza vaccine infection in human nasal epithelial cell cultures Open
From 2013 to 2016, the H1N1 component of live, attenuated influenza vaccine (LAIV) performed very poorly in contrast to the inactivated influenza vaccine. We utilized a primary, differentiated human nasal epithelial cell (hNEC) culture sys…
View article: Imputation and polygenic score performances of human genotyping arrays in diverse populations
Imputation and polygenic score performances of human genotyping arrays in diverse populations Open
Regardless of the overwhelming use of next-generation sequencing technologies, microarray-based genotyping combined with the imputation of untyped variants remains a cost-effective means to interrogate genetic variations across the human g…
View article: LmTag: functional-enrichment and imputation-aware tag SNP selection for population-specific genotyping arrays
LmTag: functional-enrichment and imputation-aware tag SNP selection for population-specific genotyping arrays Open
Despite the rapid development of sequencing technology, single-nucleotide polymorphism (SNP) array is still the most cost-effective genotyping solutions for large-scale genomic research and applications. Recent years have witnessed the rap…
View article: HA and M2 sequences alter the replication of 2013-16 H1 Live Attenuated Influenza Vaccine Infection in Human Nasal Epithelial Cell cultures
HA and M2 sequences alter the replication of 2013-16 H1 Live Attenuated Influenza Vaccine Infection in Human Nasal Epithelial Cell cultures Open
From 2013-2016, the H1N1 component of live, attenuated influenza vaccine (LAIV) performed very poorly in contrast to the inactivated influenza vaccine. We utilized a primary, differentiated human nasal epithelial (hNEC) culture system to a…
View article: Circall: fast and accurate methodology for discovery of circular RNAs from paired-end RNA-sequencing data
Circall: fast and accurate methodology for discovery of circular RNAs from paired-end RNA-sequencing data Open
Background Circular RNA (circRNA) is an emerging class of RNA molecules attracting researchers due to its potential for serving as markers for diagnosis, prognosis, or therapeutic targets of cancer, cardiovascular, and autoimmune diseases.…
View article: Liquid biopsy uncovers distinct patterns of DNA methylation and copy number changes in NSCLC patients with different EGFR-TKI resistant mutations
Liquid biopsy uncovers distinct patterns of DNA methylation and copy number changes in NSCLC patients with different EGFR-TKI resistant mutations Open
Targeted therapy with tyrosine kinase inhibitors (TKI) provides survival benefits to a majority of patients with non-small cell lung cancer (NSCLC). However, resistance to TKI almost always develops after treatment. Although genetic and ep…
View article: End-to-End Information Extraction by Character-Level Embedding and Multi-Stage Attentional U-Net
End-to-End Information Extraction by Character-Level Embedding and Multi-Stage Attentional U-Net Open
Information extraction from document images has received a lot of attention recently, due to the need for digitizing a large volume of unstructured documents such as invoices, receipts, bank transfers, etc. In this paper, we propose a nove…
View article: Multiscale deep context modeling for lossless point cloud geometry\n compression
Multiscale deep context modeling for lossless point cloud geometry\n compression Open
We propose a practical deep generative approach for lossless point cloud\ngeometry compression, called MSVoxelDNN, and show that it significantly reduces\nthe rate compared to the MPEG G-PCC codec. Our previous work based on\nautoregressiv…
View article: Genetic analysis of Vietnamese patients with early-onset Alzheimer's disease
Genetic analysis of Vietnamese patients with early-onset Alzheimer's disease Open
Purpose of the study: Alzheimer's disease (AD) is the most common type of dementia and its prevalence is rapidly increasing worldwide. Early-onset Alzheimer's disease (EOAD) constitutes of patients with age of onset earlier than 65 …