bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel antibiotic resistance genes from the hospital effluent are disseminated into the marine environment in Norway
Authors: Radisic Vera , Victor Manish P. , Grevskott Didrik H. , Marathe Nachiket P. 
Published: September 2024

AbstractHospital effluent comprises feces of many individuals, including patients undergoing antibiotic treatment. Although, hospital effluent is an important source for contamination of the environment with antibiotic resistance genes (ARGs) and pathogens, how hospital effluent in a low resistance setting contributes to antimicrobial resistance (AMR) in the environment is largely understudied. The aim of our study was to understand the microbiota and resistome of hospital effluent, and its role in the spread of AMR in the marine environment in Norway. We further aimed at describing/characterizing novel resistance factors from hospital effluent and the receiving sewage treatment plant (STP). 24-hour composite samples of the hospital effluent and the influent and effluent of the receiving STP were collected at two sampling time-points (February and April 2023) in Bergen city, Norway. Isolation ofEscherichia coliandKlebsiellaspp. was performed, using ECC and SCAI plates with cefotaxime, tigecycline or meropenem, followed by antibiotic susceptibility testing, using EUVSEC3 plates. Whole-genome sequencing of selected strains (n=36) and shotgun metagenomics of sewage samples (n=6) were performed, using Illumina NovaSeq. ARGs were identified with USEARCH, and known and novel ARGs were assembled with fARGene. AllE. colistrains (n=66) were multidrug-resistant (MDR), while 92.3% of theKlebsiellaspp. strains (n=55) showed MDR phenotype. The sequenced strains carried multiple clinically important ARGs, including carbapenemases such as NDM-5 (n=3) and KPC-3 (n=3). We obtained 238 Gigabases of sequence data from which we identified 676 unique ARGs with >200 ARGs shared across samples. We assembled 1,205 ARGs using fARGene, 365 gene sequences represented novel ARGs (< 90% amino acid (aa) identity). Both known and novel ARGs (n=54) were shared between the hospital effluent and the treated effluent of the receiving STP. We show that hospital effluent in Norway has a high diversity of both known and novel ARGs. Our study demonstrates that hospital effluent is a source of clinically relevant pathogens, as well as known and novel ARGs, reaching the marine environment in Norway through treated sewage.
Implementing portable, real-time 16S rRNA sequencing in the healthcare sector enhances antimicrobial stewardship
Authors: Carlisle David , Cunningham-Oakes Edward , Booth June , Frankland Andrew , McDowell Michael , Pilgrim Jack , Rzeszutek Aleksandra , Evans Ceri , Larkin Susan , Li Ang , Loftus Christopher , Samuel Merna , Scott Nicola , Swithenbank Luke , Owen Victoria , Darby Alistair C , Smielewska Anna 
Published: September 2024

BackgroundAntimicrobial resistance (AMR) poses a significant global health challenge, resulting in over 1.27 million deaths in 2019 and projected to cause up to 10 million deaths annually in the future. To address this issue, the healthcare sector requires rapid and accurate bacterial identification, which is currently not readily available for effective antimicrobial stewardship. In a UK national first, we implemented 16S ribosomal RNA (rRNA) sequencing using Oxford Nanopore Technology (ONT) in an NHS setting to enhance diagnostic capabilities, aiming to reduce antibiotic misuse and improve patient outcomes.MethodsWe implemented 16S rRNA sequencing via ONT, running samples from seven NHS hospitals across Cheshire and Merseyside. We focused on samples from sterile sites, such as “pus”, “fluid”, and “tissue”, typically collected from critical care units. The assay was validated against traditional methods including Sanger sequencing and MALDI-TOF, with a turnaround time of 24-72 hours. Clinical impact was measured by analysing changes in antibiotic regimens and patient outcomes based on 16S assay results over a period of several months post-launch.FindingsONT 16S rRNA sequencing significantly impacted antibiotic treatment in 34.2% of cases, reducing patient stays and outperforming traditional methods by detecting additional bacterial organisms and identifying bacteria missed by reference labs. It provided species-level identification and confirmed non-infectious conditions in 5.4% of cases, aiding alternative treatment decisions. Its speed, cost-effectiveness, and minimal training requirements contributed to its successful integration into clinical practice.InterpretationThe integration of ONT 16S sequencing into routine NHS diagnostics has significantly improved antimicrobial stewardship by offering a faster, more sensitive, and accurate bacterial identification method. Earlier use of this assay in cases where routine cultures are likely to fail could enhance patient outcomes further by enabling timely, targeted antibiotic therapies, reducing hospital stays, and curbing unnecessary antibiotic use.
Medication adherence and hospitalizations in older patients with coronary heart disease in Vietnam
Authors: Van Nguyen Tan , Hang Nguyen Thi Thuy , Dung Truong Ngoc , Viet Nguyen Quoc , Huy Nguyen Quang , Huy Nguyen Quoc , Trinh Ngo Thi Kim , Amsalu Erkihun , Wong Wei Jin , Nguyen Tu Ngoc 
Published: September 2024

AbstractAimThis study aimed to assess medication adherence among older people with coronary heart disease and its relationship with hospitalizations.MethodsThis is a prospective cohort study conducted at the outpatient clinics of a major hospital in Vietnam from November 2022 to June 2023. Consecutive older patients with coronary heart disease were recruited and followed for 6 months. Medication adherence was defined using the five[item Medication Adherence Report Scale (MARS-5). Multivariable logistic regression models were applied to examine the impact of medication adherence on hospitalization due to cardiovascular disease (CVD) and all-cause hospitalization.ResultsThere were 643 participants. They had a mean age of 73 (SD 8), and 74.3% were male. Overall, 76.4% (491/643) were classified as “adherence”. Over 6 months follow-up, 23.3% of the participants admitted to hospital (9.2% were CVD-hospitalization). The CVD-hospitalization rate was significantly higher in the non-adherence group compared to the adherence group (13.8% versus 7.7%, p = 0.023, respectively). In logistic regression models, medication adherence was associated with a significant reduced odds of CVD hospitalization (adjusted OR 0.48, 95%CI 0.27 – 0.86). Medication adherence was also associated with a trend of reduced all-cause hospitalization (adjusted OR 0.75, 95%CI 0.49 – 1.15).ConclusionsThis study showed a positive relationship between medication adherence and reduced risk of CVD hospitalization in older people with coronary heart disease. Healthcare providers should consider incorporating adherence assessment into the long-term care for older patients with coronary heart disease.
Textual Triage: Assessing GPT4 for Classification of Free-Text Medication-Related Messages for Hypertension Management
Authors: Batugo Ashley , Hwang Sy , Davoudi Anahita , Luong Thaibinh , Lee Natalie , Mowery Danielle L 
Published: September 2024

AbstractPatient-generated free-text messages are a well-recognized source of clinical burden and burnout for clinicians. Machine learning approaches such as Large Language Models (LLMs) may be applied to alleviate this burden by automatically triaging and classifying messages, but their performance in this domain has not been fully characterized. In this study, we analyzed the effectiveness of GPT4 for classifying patient and provider messages for hypertension management through prompt engineering, comparing its performance to an alternative unsupervised generative statistical approach. The results of this study suggest GPT is promising for classification of medical-related messages even with very few guiding examples.
Digital phenotyping from wearables using AI characterizes psychiatric disorders and identifies genetic associations
Authors: Liu Jason , Borsari Beatrice , Li Yunyang , Liu Susanna , Gao Yuan , Xin Xin , Lou Shaoke , Jensen Matthew , Garrido-Martín Diego , Verplaetse Terril , Ash Garrett , Zhang Jing , Girgenti Matthew J. , Roberts Walter , Gerstein Mark 
Published: September 2024

AbstractPsychiatric disorders are complex and influenced by both genetic and environmental factors. However, studying the full spectrum of these disorders is hindered by practical limitations on measuring human behavior. This highlights the need for novel technologies that can measure behavioral changes at an intermediate level between diagnosis and genotype. Wearable devices are a promising tool in precision medicine, since they can record physiological measurements over time in response to environmental stimuli and do so at low cost and minimal invasiveness. Here we analyzed wearable and genetic data from a cohort of the Adolescent Brain Cognitive Development study. We generated >250 wearable-derived features and used them as intermediate phenotypes in an interpretable AI modeling framework to assign risk scores and classify adolescents with psychiatric disorders. Our model identifies key physiological processes and leverages their temporal patterns to achieve a higher performance than has been previously possible. To investigate how these physiological processes relate to the underlying genetic architecture of psychiatric disorders, we also utilized these intermediate phenotypes in univariate and multivariate GWAS. We identified a total of 29 significant genetic loci and 52 psychiatric-associated genes, including ELFN1 and ADORA3. These results show that wearable-derived continuous features enable a more precise representation of psychiatric disorders and exhibit greater detection power compared to categorical diagnostic labels. In summary, we demonstrate how consumer wearable technology can facilitate dimensional approaches in precision psychiatry and uncover etiological linkages between behavior and genetics.
Evaluating the Joint Effects of Recurrent Copy Number Variants and Polygenic Scores on the Risk of Psychiatric Disorders in the iPSYCH2015 Case-Cohort Sample
Authors: Vaez Morteza , Montalbano Simone , Waples Ryan , Krebs Morten Dybdahl , Hellberg Kajsa-Lotta Georgii , Gådin Jesper , Bybjerg-Grauholm Jonas , Mortensen Preben B. , Børglum Anders D. , Nordentoft Merete , Geschwind Daniel H. , Helenius Dorte , Werge Thomas , Schork Andrew J. , Ingason Andrés 
Published: September 2024

AbstractThe impact of rare recurrent copy number variants (rCNVs) and polygenic background attributed to common variants, on the risk of psychiatric disorders is well-established in separate studies. However, it remains unclear how polygenic background modulates the effect of rCNVs. Using the population-representative iPSYCH2015 case-cohort sample (N=96,599), we investigated the association between absolute risk of psychiatric disorders and carriage of rCNVs and polygenic scores (PGS), as well as the interaction effect between the two on disease risk. Carriers of rCNVs with higher gene constraint scores had an increased absolute risk for autism, ADHD, and schizophrenia, but not depression, whereas an increase in PGS for each respective disorder was associated with higher absolute risk across all four disorders. Similarly, elevated absolute risks were observed with the increase of both PGS and gene constraints of rCNVs except in the case of depression. In contrast to some previous case-control studies, our joint analysis of rCNV groups and PGS revealed no indication of significant interactive effect between these two factors on disease risk. Also, we found no significant interactions of PGS with any of the most common individual rCNVs, except in the case of 16p13.11 duplication, which was found to attenuate the effect of ADHD-PGS on the absolute risk of ADHD. This study advances our understanding of the interplay between rare and common important genetic risk factors for major psychiatric disorders and sheds light on the importance of population-based samples in implementing precision medicine.
A yeast-based reverse genetics system to generate HCoV-OC43 reporter viruses encoding an eighth sgRNA
Authors: Duguay Brett A. , Tooley Trinity H. , Pringle Eric S. , Rohde John R. , McCormick Craig 
Published: September 2024

ABSTRACTCoronaviruses have large, positive-sense single-stranded RNA genomes that challenge conventional strategies for mutagenesis. Here, we report the development of a new reverse genetics system for the endemic human coronavirus (HCoV) OC43 that utilizes transformation-associated recombination (TAR) to assemble complete viral genomes from dsDNA genome fragments via homologous recombination inSaccharomyces cerevisiae. Following cDNA synthesis from HCoV-OC43 viral RNA, we used TAR to capture fragments of the HCoV-OC43 genome to store as sequence-validated dsDNA parts. We performed combinatorial assembly in yeast to obtain an intact dsDNA copy of the HCoV-OC43 genome sufficient to launch viral replication upon introduction into human cells, yielding the yeast assembled OC43YAvirus. We also expanded the OC43YAgenome by inserting an eighth body transcription regulatory sequence (B-TRS) and an mClover3-H2B reporter gene between theMandNgenes, designed to allow the reporter protein to be translated from its own subgenomic mRNA. We thoroughly evaluated OC43YAand the OC43-mCloYAreporter virus, and demonstrated comparable viral gene expression, fitness in cell culture, and susceptibility to antivirals, compared to their natural progenitor. In summary, this new HCoV-OC43 reverse genetics system provides a modular platform for mutagenesis and combinatorial assembly of HCoV-OC43 genomes, and demonstrates the feasibility of expanding the genome while avoiding disruption of native coding sequences.IMPORTANCEHuman coronavirus OC43 (HCoV-OC43) is an endemic human coronavirus that typically causes relatively mild respiratory illnesses and displays seasonal patterns of infection. We developed a new system to assemble DNA copies of HCoV-OC43 genomes and generate recombinant viruses for research purposes. This system uses yeast, first to capture segments of DNA encompassing the entire RNA-based viral genome, and then to stitch them together into complete DNA genome copies that can be amplified in bacteria and introduced into human cells to initiate an infectious cycle, ultimately yielding recombinant viruses with comparable properties to their natural progenitors. We also devised a strategy to expand the viral genome, adding a gene for a reporter protein encoded by an additional eighth subgenomic mRNA. This yeast-based genome assembly system provides a modular platform for rapid mutagenesis and combinatorial assembly of HCoV-OC43 genomes and demonstrates the feasibility of expanding the genome.
Histone demethylase enzymes KDM5A and KDM5B modulate immune response by suppressing transcription of endogenous retroviral elements
Authors: Chen Huadong , Sarah Letitia , Pucciarelli Daniela , Mao Ying , Diolaiti Morgan E. , Galonić Fujimori Danica , Ashworth Alan 
Published: September 2024

AbstractEpigenetic factors, including lysine-specific demethylases such as the KDM5 paralogs KDM5A and KDM5B have been implicated in cancer and the regulation of immune responses. Here, we performed a comprehensive multiomic study in cells lacking KDM5A or KDM5B to map changes in transcriptional regulation and chromatin organization. RNA-seq analysis revealed a significant decrease in the expression of Krüppel-associated box containing zinc finger (KRAB-ZNF) genes in KDM5A or KDM5B knockout cell lines, which was accompanied by changes ATAC-seq and H3K4me3 ChIP-seq. Pharmacological inhibition of KDM5A and KDM5B catalytic activity with a pan-KDM5 inhibitor, CPI-455, did not significantly change KRAB-ZNF expression, raising the possibility that regulation of KRAB-ZNF expression does not require KDM5A and KDM5B demethylase activity. KRAB-ZNF are recognized suppressors of the transcription of endogenous retroviruses (ERVs) and HAP1 cells withKDM5AorKDM5Bgene inactivation showed elevated ERV expression, increased dsRNA levels and elevated levels of immune response genes. Acute degradation of KDM5A using a dTAG system in HAP1 cells led to increased ERV expression, demonstrating that de-repression of ERV genes occurs rapidly after loss of KDM5A. Co-immunoprecipitation of KDM5A revealed an interaction with the Nucleosome Remodeling and Deacetylase (NuRD) complex suggesting that KDM5A and NuRD may act together to regulate the expression of ERVs through KRAB-ZNFs. These findings reveal roles of KDM5A and KDM5B in modulating ERV expression and underscore the therapeutic potential of using degraders of KDM5A and KDM5B to modulate tumor immune responses.Author SummaryThe histone demethylases KDM5A and KDM5B are transcriptional repressors that play an important role in cancer and immune response, making them attractive drug targets. Unfortunately, small molecule inhibitors, including CPI-455, that block KDM5A and KDM5B enzymatic activity, have shown only limited effectiveness at suppressing cancer cell viability as single agents in vitro. In this study we undertook a multi-omics approach to map transcriptional and chromatin changes in KDM5A and KDM5B deficient cells compared to those treated with CPI-455. The datasets revealed that KDM5A and KDM5B modulate the expression of KRAB-ZNF genes and that loss of either gene was associated with increased expression of ERV genes and upregulation of immune response markers. Surprisingly, pharmacological inhibition of these enzymes did not phenocopy genetic ablation. In contrast, acute degradation of KDM5A using a dTAG system caused an increase in ERV expression, providing evidence that this immune modulation is independent of demethylase activity. Together with the limited success of small molecule inhibitors, our data provide strong rationale for the development of KDM5A and KDM5B degraders to modulate tumor immune responses.
Structural insights into the molecular recognition of integrin αVβ3 by RGD-containing ligands: The role of the specificity-determining loop (SDL)
Authors: Mariasoosai Charles , Bose Santanu , Natesan Senthil 
Published: September 2024

ABSTRACTIntegrin αVβ3 is a prominent member of the “RGD-recognizing” integrin family of cell surface receptors. αVβ3 binds to various extracellular matrix (ECM) proteins and oxysterols such as 25-hydroxycholesterol, is implicated in several diseases, including cancer metastasis, lung fibrosis, inflammation, and autoimmune diseases, and is pursued as a valuable therapeutic target. Despite enormous efforts to seek a pure antagonist, to date, no single drug candidate has successfully reached clinics due to associated partial agonism and toxicity issues. Developing effective and safe inhibitors require a thorough understanding of the molecular interactions and structural changes related to the receptor’s activation and inhibition mechanisms. This study offers a comprehensive residue-residue contact and network analyses of the ligand-binding β-propeller βI domains (headpiece) based on all available experimental structures of integrin αVβ3 in unliganded, agonist-, antagonist-, and antibody-bound states. The analyses reveal many critical interactions that were not reported before and show that specific orientation and interactions of residues from the specificity-determining loop (SDL) are critical in molecular recognition and regulation. Also, the network analysis reveals that residues from the nearby allosteric site (site II) connect to the primary RGD-binding site via SDL, which likely acts as an interface between the two sites. Our results provide valuable insights into molecular interactions, structural changes, distinct features of the active and inactive headpiece conformations, the role of SDL in ligand recognition, and SDL-mediated allostery. Thus, the insights from this study may facilitate the designing of pure antagonists or site II-mediated allosteric modulators to integrin αVβ3 to treat various diseases.
Inducible and reversible SOD2 knockdown in mouse skeletal muscle drives impaired pyruvate oxidation and reduced metabolic flexibility
Authors: Ostrom Ethan L. , Stuppard Rudy , Mattson-Hughes Aurora , Marcinek David J. 
Published: September 2024

AbstractAbstract FigureGraphical AbstractHighlightsSOD2 knockdown and recovery is achieved in skeletal muscle by using a shRNA targeted to SOD2 mRNA controlled by a tetracycline Response Element and reverse tetracycline transactivator proteinSOD2 KD is induced by administering doxycycline in the drinking waterMitochondrial functional decline and recovery follows the time course of SOD2 protein decline and recoverySustained SOD2 KD precipitates reduced metabolic flexibility in skeletal muscle mitochondria characterized by impaired pyruvate respiration in the presence of other substratesIntroductionSkeletal muscle mitochondrial dysfunction is a key characteristic of aging muscle and contributes to age related diseases such as sarcopenia, frailty, and type 2 diabetes. Mitochondrial oxidative distress has been implicated as a driving factor in these age-related diseases, however whether it is a cause, or a consequence of mitochondrial dysfunction remains to be determined. The development of more flexible genetic models is an important tool to test the mechanistic role of mitochondrial oxidative stress on skeletal muscle metabolic dysfunction. We characterize a new model of inducible and reversible mitochondrial redox stress using a tetracycline controlled skeletal muscle specific short hairpin RNA targeted to superoxide dismutase 2 (iSOD2).MethodsiSOD2 KD and control (CON) animals were administered doxycycline for 3-or 12-weeks and followed for up to 24 weeks and mitochondrial respiration and muscle contraction were measured to define the time course of SOD2 KD and muscle functional changes and recovery.ResultsMaximum knockdown of SOD2 protein occurred by 6 weeks and recovered by 24 weeks after DOX treatment. Mitochondrial aconitase activity and maximum mitochondrial respiration declined in KD muscle by 12 weeks and recovered by 24 weeks. There were minimal changes in gene expression between KD and CON muscle. Twelve-week KD showed a small, but significant decrease in muscle fatigue resistance. The primary phenotype was reduced metabolic flexibility characterized by impaired pyruvate driven respiration when other substrates are present. The pyruvate dehydrogenase kinase inhibitor dichloroacetate partially restored pyruvate driven respiration, while the thiol reductant DTT did not.ConclusionWe use a model of inducible and reversible skeletal muscle SOD2 knockdown to demonstrate that elevated matrix superoxide reversibly impairs mitochondrial substrate flexibility characterized by impaired pyruvate oxidation. Despite the bioenergetic effect, the limited change in gene expression suggests that the elevated redox stress in this model is confined to the mitochondrial matrix.
Criterion for assessing accumulated neurotoxicity of alpha-synuclein oligomers in Parkinson’s disease
Authors: Kuznetsov Andrey V. 
Published: September 2024

AbstractThe paper introduces a parameter called “accumulated neurotoxicity” of α-syn oligomers, which measures the cumulative damage these toxic species inflict on neurons over time, given the years it typically takes for such damage to manifest. A threshold value for accumulated neurotoxicity is estimated, beyond which neuron death is likely. Numerical results suggest that rapid deposition of α-syn oligomers into fibrils minimizes toxicity, indicating that the formation of Lewy bodies might play a neuroprotective role. Strategies such as reducing α-syn monomer production or enhancing degradation can decrease accumulated toxicity. In contrast, slower degradation (reflected by longer half-lives of monomers and free aggregates) increases toxicity, supporting the idea that impaired protein degradation may contribute to Parkinson’s disease progression. The study also examines the sensitivity of accumulated toxicity to different model parameters.