Informational rescaling of PCA maps with application to genetic distance.

Principal Component Analysis (PCA) is a powerful multivariate tool allowing the projection of data in low-dimensional representations. Nevertheless, datapoint distances on these low-dimensional projections are challenging to interpret. Here, we propose a computationally simple heuristic to transform a map based on standard PCA (when the variables are asymptotically Gaussian) into an entropy-based map where distances are based on mutual information (MI).

Human migration from the Levant and Arabia into Yemen since Last Glacial Maximum.

While a broad consensus about the first successful migration modern humans out of Africa seems established, the peopling of Arabia remains somewhat enigmatic. Identifying the ancestral populations that contributed to the gene pool of the current populations inhabiting Arabia and the impact of their contributions remains a challenging task. We investigate the genetic makeup of the current Yemeni population using 46 whole genomes and 169 genotype arrays derived from Yemeni individuals from all geographic regions across Yemen and 351 genotype arrays derived from neighboring populations providing regional context.

Anatolian genetic ancestry in North Lebanese populations.

Lebanon's rich history as a cultural crossroad spanning millennia has significantly impacted the genetic composition of its population through successive waves of migration and conquests from surrounding regions. Within modern-day Lebanon, the Koura district stands out with its unique cultural foundations, primarily characterized by a notably high concentration of Greek Orthodox Christians compared to the rest of the country. This study investigates whether the prevalence of Greek Orthodoxy in Koura can be attributed to modern Greek heritage or continuous blending resulting from the ongoing influx of refugees and trade interactions with Greece and Anatolia.

Assessment of genetic and clinical factors in T2D susceptibility among patients with hypertension.

Aims: Hypertension (HTN) and Type 2 Diabetes (T2D) often coexist, therefore understanding the relationship between both diseases is imperative to guide targeted prevention/therapy. This study aims to explore the relationship between HTN and T2D using genome-wide association study (GWAS) analysis and biochemical data to understand the implication of both clinical and genetic factors in these pathologies.

Methods: A total of 2,876 patients were enrolled.

Analysis of Cancer-Associated Mutations of POLB Using Machine Learning and Bioinformatics.

DNA damage is a critical factor in the onset and progression of cancer. When DNA is damaged, the number of genetic mutations increases, making it necessary to activate DNA repair mechanisms. A crucial factor in the base excision repair process, which helps maintain the stability of the genome, is an enzyme called DNA polymerase β (Pol β) encoded by the POLB gene.

Comparison of qPCR and metagenomic sequencing methods for quantifying antibiotic resistance genes in wastewater.

Surveillance methods of circulating antibiotic resistance genes (ARGs) are of utmost importance in order to tackle what has been described as one of the greatest threats to humanity in the 21st century. In order to be effective, these methods have to be accurate, quickly deployable, and scalable. In this study, we compare metagenomic shotgun sequencing (TruSeq DNA sequencing) of wastewater samples with a state-of-the-art PCR-based method (Resistomap HT-qPCR) on four wastewater samples that were taken from hospital, industrial, urban and rural areas.

HDL levels modulate the impact of type 2 diabetes susceptibility alleles in older adults.

Background: Type 2 Diabetes (T2D) is influenced by genetic, environmental, and ageing factors. Ageing pathways exacerbate metabolic diseases. This study aimed to examine both clinical and genetic factors of T2D in older adults.

Coronary artery disease patients with rs7904519 (TCF7L2) are at a persistent risk of type 2 diabetes.

Aims: Type 2 diabetes (T2D) and coronary artery disease (CAD) often coexist and share genetic factors.This study aimed to investigate the common genetic factors underlying T2D and CAD in patients with CAD.

Methods: A three-step association approach was conducted: a) a discovery step involving 943 CAD patients with T2D and 1,149 CAD patients without T2D; b) an eliminating step to exclude CAD or T2D specific variants; and c) a replication step using the UK Biobank data.

Evaluating skills for psychological recovery with gunshot injury survivors in a hospital-based early intervention program.

Gun violence is a serious public health problem that places surviving victims at increased risk for a variety of mental health problems, including posttraumatic stress disorder (PTSD) and depression. Recognizing that many gunshot injury survivors lack access to mental health care in the early aftermath of a shooting, there has been growing interest in the use of early, preventive mental health interventions to help prevent long-term mental health complications like PTSD as part of routine care for survivors in acute medical settings, where initial outreach to survivors may be more successful. This study evaluates clinical outcomes associated with one such early intervention-Skills for Psychological Recovery (SPR)-provided to gunshot injury survivors as part of a hospital-based early intervention program embedded in a Level 1 trauma center in the Midwestern United States.

Evaluating Drivers of the Patient Experience Triangle: Stress, Anxiety, and Frustration.

Patient experience is a widely used indicator for assessing the quality-of-care process during a patient's journey in hospital. However, the literature rarely discusses three components: patient stress, anxiety, and frustration. Furthermore, little is known about what drives each component during hospital visits.

Elevated Lp(a) Levels Correlate with Severe and Multiple Coronary Artery Stenotic Lesions.

Backgrounds And Aims: The role of Lipoprotein(a) (Lp(a)) in increasing the risk of cardiovascular diseases is reported in several populations. The aim of this study is to investigate the correlation of high Lp(a) levels with the degree of coronary artery stenosis.

Methods: Two hundred and sixty-eight patients were enrolled for this study.

Transfer learning for genotype-phenotype prediction using deep learning models.

Background: For some understudied populations, genotype data is minimal for genotype-phenotype prediction. However, we can use the data of some other large populations to learn about the disease-causing SNPs and use that knowledge for the genotype-phenotype prediction of small populations. This manuscript illustrated that transfer learning is applicable for genotype data and genotype-phenotype prediction.

Can We Convert Genotype Sequences Into Images for Cases/Controls Classification?

Converting genotype sequences into images offers advantages, such as genotype data visualization, classification, and comparison of genotype sequences. This study converted genotype sequences into images, applied two-dimensional convolutional neural networks for case/control classification, and compared the results with the one-dimensional convolutional neural network. Surprisingly, the average accuracy of multiple runs of 2DCNN was 0.

Genomic epidemiology and emergence of SARS-CoV-2 variants of concern in the United Arab Emirates.

Since the declaration of SARS-CoV-2 outbreak as a pandemic, the United Arab Emirates (UAE) public health authorities have adopted strict measures to reduce transmission as early as March 2020. As a result of these measures, flight suspension, nationwide RT-PCR and surveillance of viral sequences were extensively implemented. This study aims to characterize the epidemiology, transmission pattern, and emergence of variants of concerns (VOCs) and variants of interests (VOIs) of SARS-CoV-2 in the UAE, followed by the investigation of mutations associated with hospitalized cases.

Microbiome-based disease prediction with multimodal variational information bottlenecks.

Scientific research is shedding light on the interaction of the gut microbiome with the human host and on its role in human health. Existing machine learning methods have shown great potential in discriminating healthy from diseased microbiome states. Most of them leverage shotgun metagenomic sequencing to extract gut microbial species-relative abundances or strain-level markers.

Travel ban effects on SARS-CoV-2 transmission lineages in the UAE as inferred by genomic epidemiology.

Global and local whole genome sequencing of SARS-CoV-2 enables the tracing of domestic and international transmissions. We sequenced Viral RNA from 37 sampled Covid-19 patients with RT-PCR-confirmed infections across the UAE and developed time-resolved phylogenies with 69 local and 3,894 global genome sequences. Furthermore, we investigated specific clades associated with the UAE cohort and, their global diversity, introduction events and inferred domestic and international virus transmissions between January and June 2020.

What Makes a Robot Social? A Review of Social Robots from Science Fiction to a Home or Hospital Near You.

Purpose Of Review: We provide an outlook on the definitions, laboratory research, and applications of social robots, with an aim to understand what makes a robot social-in the eyes of science and the general public.

Recent Findings: Social robots demonstrate their potential when deployed within contexts appropriate to their form and functions. Some examples include companions for the elderly and cognitively impaired individuals, robots within educational settings, and as tools to support cognitive and behavioural change interventions.

Gut Microbiota Interplay With COVID-19 Reveals Links to Host Lipid Metabolism Among Middle Eastern Populations.

The interplay between the compositional changes in the gastrointestinal microbiome, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) susceptibility and severity, and host functions is complex and yet to be fully understood. This study performed 16S rRNA gene-based microbial profiling of 143 subjects. We observed structural and compositional alterations in the gut microbiota of the SARS-CoV-2-infected group in comparison to non-infected controls.

Motives for prescription opioid use: The role of alexithymia and distress tolerance.

Background And Objectives: Prescription opioid (PO) use disorder is a national public health crisis. Distress tolerance and alexithymia are two separate but related components of emotion regulation that are known to impact substance use disorders. No studies to date, however, have examined the role of distress tolerance and alexithymia in PO use disorder.

Deep Learning Improves Pancreatic Cancer Diagnosis Using RNA-Based Variants.

For optimal pancreatic cancer treatment, early and accurate diagnosis is vital. Blood-derived biomarkers and genetic predispositions can contribute to early diagnosis, but they often have limited accuracy or applicability. Here, we seek to exploit the synergy between them by combining the biomarker CA19-9 with RNA-based variants.

A Population-Specific Major Allele Reference Genome From The United Arab Emirates Population.

The ethnic composition of the population of a country contributes to the uniqueness of each national DNA sequencing project and, ideally, individual reference genomes are required to reduce the confounding nature of ethnic bias. This work represents a representative Whole Genome Sequencing effort of an understudied population. Specifically, high coverage consensus sequences from 120 whole genomes and 33 whole exomes were used to construct the first ever population specific major allele reference genome for the United Arab Emirates (UAE).