The Biorepository and Integrative Genomics resource for inclusive genomics: insights from a diverse pediatric and admixed cohort.

The Biorepository and Integrative Genomics (BIG) Initiative in Tennessee has developed a pioneering resource to address gaps in genomic research by linking genomic, phenotypic, and environmental data from a diverse Mid-South population, including underrepresented groups. We analyzed 13,152 genomes from BIG and found significant genetic diversity, with 50% of participants inferred to have non-European or several types of admixed ancestry. Ancestry within the BIG cohort is stratified, with distinct geographic and demographic patterns, as African ancestry is more common in urban areas, while European ancestry is more common in suburban regions.

Piezosurgery in Third Molar Extractions: A Systematic Review.

: The aim of this systematic review was to evaluate the clinical efficacy, benefits, and limitations of piezosurgery in tooth extractions compared to conventional methods. Piezosurgery has emerged as a minimally invasive alternative, promoting better preservation of soft tissues and bone structures. Understanding its impact on postoperative outcomes such as pain, swelling, trismus, and bone healing is critical for its application in oral surgery; We restricted our search to English-language articles published between 1 January 2004 and 28 August 2024, in PubMed, Scopus, and Web of Science.

Creating a biomedical knowledge base by addressing GPT inaccurate responses and benchmarking context.

We created GNQA, a generative pre-trained transformer (GPT) knowledge base driven by a performant retrieval augmented generation (RAG) with a focus on aging, dementia, Alzheimer's and diabetes. We uploaded a corpus of three thousand peer reviewed publications on these topics into the RAG. To address concerns about inaccurate responses and GPT 'hallucinations', we implemented a context provenance tracking mechanism that enables researchers to validate responses against the original material and to get references to the original papers.

Focal Versus Combined Focal Plus Radial Extracorporeal Shockwave Therapy in Lateral Elbow Tendinopathy: A Retrospective Study.

Lateral epicondylitis of the elbow, commonly known as tennis elbow, is a musculoskeletal disorder characterized by pain and degeneration of the common extensor tendon. Despite various treatments, optimal management remains debated. This study aimed to compare the effectiveness of focal extracorporeal shockwave therapy (F-ESWT) alone versus a combination of focal and radial pressure waves (F-ESWT+R-PW) in treating chronic lateral epicondylitis.

Building pangenome graphs.

Pangenome graphs can represent all variation between multiple reference genomes, but current approaches to build them exclude complex sequences or are based upon a single reference. In response, we developed the PanGenome Graph Builder, a pipeline for constructing pangenome graphs without bias or exclusion. The PanGenome Graph Builder uses all-to-all alignments to build a variation graph in which we can identify variation, measure conservation, detect recombination events and infer phylogenetic relationships.

Osteonecrosis of the Jaws Associated with Herpes Zoster Infection: A Systematic Review and a Rare Case Report.

The investigation's goal was to obtain further knowledge about the connection between infection and dentistry therapy for the osteonecrosis of the jaws, combining the review with a case report relevant to the purpose. It is important to study this association because it is a possible additional factor to be considered in the causes of the osteonecrosis of the jaws. We limited our search to English-language papers published between 1 January 2004 and 7 June 2024 in PubMed, Scopus, and Web of Science that were relevant to our topic.

Three-dimensional environment sensitizes pancreatic cancer cells to the anti-proliferative effect of budesonide by reprogramming energy metabolism.

Background: Pancreatic ductal adenocarcinoma (PDAC) is the most lethal cancer with an aggressive metastatic phenotype and very poor clinical prognosis. Interestingly, a lower occurrence of PDAC has been described in individuals with severe and long-standing asthma. Here we explored the potential link between PDAC and the glucocorticoid (GC) budesonide, a first-line therapy to treat asthma.

A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats.

The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared with its predecessor. Gene annotations are now more complete, improving the mapping precision of genomic, transcriptomic, and proteomics datasets.

A comprehensive analysis of SARS-CoV-2 missense mutations indicates that all possible amino acid replacements in the viral proteins occurred within the first two-and-a-half years of the pandemic.

The surveillance of COVID-19 pandemic has led to the determination of millions of genome sequences of the SARS-CoV-2 virus, with the accumulation of a wealth of information never collected before for an infectious disease. Exploring the information retrieved from the GISAID database reporting at that time >13 million genome sequences, we classified the 141,639 unique missense mutations detected in the first two-and-a-half years (up to October 2022) of the pandemic. Notably, our analysis indicates that 98.

Pangenome reconstruction in rats enhances genotype-phenotype mapping and novel variant discovery.

The HXB/BXH family of recombinant inbred rat strains is a unique genetic resource that has been extensively phenotyped over 25 years, resulting in a vast dataset of quantitative molecular and physiological phenotypes. We built a pangenome graph from 10x Genomics Linked-Read data for 31 recombinant inbred rats to study genetic variation and association mapping. The pangenome includes 0.

Visualization of automatically combined disease maps and pathway diagrams for rare diseases.

Investigation of molecular mechanisms of human disorders, especially rare diseases, require exploration of various knowledge repositories for building precise hypotheses and complex data interpretation. Recently, increasingly more resources offer diagrammatic representation of such mechanisms, including disease-dedicated schematics in pathway databases and disease maps. However, collection of knowledge across them is challenging, especially for research projects with limited manpower.

A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats.

The seventh iteration of the reference genome assembly for -mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared to its predecessor. Gene annotations are now more complete, significantly improving the mapping precision of genomic, transcriptomic, and proteomics data sets.

Short-Term Outcomes of an ESDM Intervention in Italian Children with Autism Spectrum Disorder following the COVID-19 Lockdown.

The COVID-19 pandemic caused a temporary lockdown period in Italy, during which the delivery of in-person treatment for children with autism spectrum disorder (ASD) in public health services was discontinued. This occurrence represented a crucial challenge for both families and professionals. We assessed the short-term outcomes of a sample of 18 children who received an early intervention with the Early Start Denver Model (ESDM), delivered at low intensity over one year in the pre-pandemic period, after six months of interruption of in-presence treatment due to lockdown restrictions.

A draft human pangenome reference.

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels.

A novel quantitative trait locus implicates in the propensity for genome-wide short tandem repeat expansions in mice.

Short tandem repeats (STRs) are a class of rapidly mutating genetic elements typically characterized by repeated units of 1-6 bp. We leveraged whole-genome sequencing data for 152 recombinant inbred (RI) strains from the BXD family of mice to map loci that modulate genome-wide patterns of new mutations arising during parent-to-offspring transmission at STRs. We defined quantitative phenotypes describing the numbers and types of germline STR mutations in each strain and performed quantitative trait locus (QTL) analyses for each of these phenotypes.

Building pangenome graphs.

Pangenome graphs can represent all variation between multiple reference genomes, but current approaches to build them exclude complex sequences or are based upon a single reference. In response, we developed the PanGenome Graph Builder (PGGB), a pipeline for constructing pangenome graphs without bias or exclusion. PGGB uses all-to-all alignments to build a variation graph in which we can identify variation, measure conservation, detect recombination events, and infer phylogenetic relationships.

Ultrasound-based Neuropathy Diagnosis in COVID-19 Patients in Post-intensive Care Rehabilitation Settings: A Retrospective Observational Study.

Objectives: Using ultrasound (US) scanning to examine the correlation between increase of common fibular nerve's (CFN) cross sectional area (CSA) and functional impairment of foot dorsiflexor muscles as an early sign of peripheral neuropathy.

Design: Retrospective observational study.

Setting: In-patient rehabilitation unit between November 2020 and July 2021.

Gastrointestinal Disorders and Food Selectivity: Relationship with Sleep and Challenging Behavior in Children with Autism Spectrum Disorder.

The aim of this study was to evaluate the interaction between gastrointestinal (GI) disorders, sleep problems, and challenging behaviors in children with a diagnosis of Autism Spectrum Disorder (ASD) and their effect on parental stress. The secondary objective was to assess the frequency and type of GI and feeding disorders in a sample of children with ASD through a multidisciplinary assessment and, finally, to investigate families' perceptions and satisfaction with the proposed multidisciplinary approach. All children underwent a comprehensive gastroenterological and neuropsychiatric evaluation supported by standardized questionnaires.

LAMC2 marks a tumor-initiating cell population with an aggressive signature in pancreatic cancer.

Background: Tumor-initiating cells (TIC), also known as cancer stem cells, are considered a specific subpopulation of cells necessary for cancer initiation and metastasis; however, the mechanisms by which they acquire metastatic traits are not well understood.

Methods: LAMC2 transcriptional levels were evaluated using publicly available transcriptome data sets, and LAMC2 immunohistochemistry was performed using a tissue microarray composed of PDAC and normal pancreas tissues. Silencing and tracing of LAMC2 was performed using lentiviral shRNA constructs and CRISPR/Cas9-mediated homologous recombination, respectively.

Unexpected Vertical Transmission of SARS-CoV-2: Discordant Clinical Course and Transmission from Mother to Newborn.

Mother-to-newborn COVID-19 transmission is mainly postnatal, but single-case reports and small case series have also described SARS-CoV-2 transplacental transmission. Unfortunately, studies regarding vertical transmission of SARS-CoV-2 lack systematic approaches to diagnosis and classification. So far, scientific evidence seems to suggest that the severity of maternal infection increases the risk of vertical transmission.