bluuebunny/crossref_metadata_2025_split huggingface dataset:
A standard workflow for community-driven manual curation ofStrongyloidesgenome annotations
Authors: Bryant Astra S. , Akimori Damia , Stoltzfus Jonathan D. C. , Hallem Elissa A. 
Published: November 2023

Advances in the functional genomics and bioinformatics toolkits forStrongyloidesspecies have positioned these species as genetically tractable model systems for gastrointestinal parasitic nematodes. As community interest in mechanistic studies ofStrongyloidesspecies continues to grow, publicly accessible reference genomes and associated genome annotations are critical resources for researchers. Genome annotations for multipleStrongyloidesspecies are broadly available via the WormBase and WormBase ParaSite online repositories. However, a recent phylogenetic analysis of the receptor-type guanylate cyclase (rGC) gene family in twoStrongyloidesspecies highlights the potential for errors in a large percentage of currentStrongyloidesgene models. Here, we present three examples of gene annotation updates within theStrongyloidesrGC gene family; each example illustrates a type of error that may occur frequently within the annotation data forStrongyloidesgenomes. We also extend our analysis to 405 previously curatedStrongyloidesgenes to confirm that gene model errors are found at high rates across gene families. Finally, we introduce a standard manual curation workflow for assessing gene annotation quality and generating corrections, and we discuss how it may be used to facilitate community-driven curation of parasitic nematode biodata.This article is part of the Theo Murphy meeting issue ‘Strongyloides: omics to worm-free populations’.
GPT-4 Multimodal Analysis on Ophthalmology Clinical Cases Including Text and Images
Authors: Sorin Vera , Kapelushnik Noa , Hecht Idan , Zloto Ofira , Glicksberg Benjamin S. , Bufman Hila , Barash Yiftach , Nadkarni Girish N. , Klang Eyal 
Published: November 2023

AbstractObjectiveRecent advancements in GPT-4 have enabled analysis of text with visual data. Diagnosis in ophthalmology is often based on ocular examinations and imaging, alongside the clinical context. The aim of this study was to evaluate the performance of multimodal GPT-4 (GPT-4V) in an integrated analysis of ocular images and clinical text.MethodsThis retrospective study included 40 patients seen in our institution with ocular pathologies. Cases were selected by a board certified ophthalmologist, to represent various pathologies and match the level for ophthalmology residents. We provided the model with each image, without and then with the clinical context. We also asked two non-ophthalmology physicians to write diagnoses for each image, without and then with the clinical context. Answers for both GPT-4V and the non-ophthalmologists were evaluated by two board-certified ophthalmologists. Performance accuracies were calculated and compared.ResultsGPT-4V provided the correct diagnosis in 19/40 (47.5%) cases based on images without clinical context, and in 27/40 (67.5%) cases when clinical context was provided. Non-ophthalmologists physicians provided the correct diagnoses in 24/40 (60.0%), and 23/40 (57.5%) of cases without clinical context, and in 29/40 (72.5%) and 27/40 (67.5%) with clinical context.ConclusionGPT-4V at its current stage is not yet suitable for clinical application in ophthalmology. Nonetheless, its ability to simultaneously analyze and integrate visual and textual data, and arrive at accurate clinical diagnoses in the majority of cases, is impressive. Multimodal large language models like GPT-4V have significant potential to advance both patient care and research in ophthalmology.
Efficacy ofWolbachia-mediated sterility to suppress adultAedes aegyptipopulations
Authors: Bansal Somya , Chong Chee-Seng , Dickens Borame , Lim Jue Tao , Ng Youming , Deng Lu , Lee Caleb , Tan Li Yun , Kakani Evidoxia , Yu David Du , Chain Grace , Ma Pei , Sim Shuzhen , Ng Lee Ching , Tan Cheong Huat 
Published: November 2023

AbstractIncompatible insect technique coupled with sterile insect technique (IIT-SIT) via releases of sterile maleWolbachia-infected mosquitoes is a promising tool for dengue control. In a six-year trial from 2016 to 2022, comprising 10.35 km2of high-rise housing estates and 607,872 residents, we designed a synthetic control study methodology to assess the efficacy of IIT-SIT in reducing adult femaleAedes aegyptipopulations, using data from a large, routinely collected, nationwide surveillance system of 57,990 unique mosquito traps in public housing estates.We demonstrated thatWolbachia-based IIT-SIT dramatically reduces wildtypeAedes aegyptipopulations by an average of 60.64% (95% CI: 59.59%–61.44%) and 79.37% (95% CI: 78.85%–79.87%) in 3, 6 months of releases and eventually 90.17% (95% CI: 89.92%–90.42%) in 12 and more months of releases. We further found a smaller but non-negligible suppression effect which gradually increased over time (47.91%, 95% CI: 47.29%–48.52%) in adjacent, non-intervention sites. Our results demonstrate the potential of IIT-SIT for strengthening dengue control in tropical cities, where dengue burden is the greatest.
The use of intravascular ultrasound (IVUS) during percutaneous coronary intervention does not reduce all cause in-hospital mortality but doubles the cost with higher utilization in privately insured patients
Authors: Movahed Mohammad Reza , Nathan Allistair , Hashemzadeh Mehrtash 
Published: November 2023

AbstractBackgroundThe effect of using intravascular ultrasound (IVUS) during percutaneous coronary intervention (PCI) on short-term mortality is not well established. The goal of this study was to evaluate any association between the use of IVUS during PCI on mortality vs no ICUC in a large inpatient database.MethodWe used the National Inpatient Sample (NIS) database for available ICD-10 codes from 2016-2020 for IVUS and PCIs.ResultsA total of 10,059,56 PCIs were performed. 206,910 underwent IVUS-guided PCI vs 9,852,359 without IVUS use. Mortality did not differ between the two groups with 2.52% mortality in the IVUS arm vs 2.59% in no IVUS cohort, p=0.4. The mean age of patients with ICUS use was 65.5 vs 70.1 years without IVUS. Total in-hospital cost in the IVUS group was double that without IVUS (141,920$ vs 71,568$). Furthermore, IVUS utilization was significantly higher in patients with private HMO patients (28.3% vs 17.2%).ConclusionIn-patient all-cause mortality using IVUS during PCI was similar to those patients without IVUS utilization but doubled the cost with higher utilization in privately insured patients
HandMol: Coupling WebXR, AI and HCI technologies for Immersive, Natural, Collaborative and Inclusive Molecular Modeling
Authors: Cortes Rodriguez Fabio J. , Krapp Lucien F. , Dal Peraro Matteo , Abriata Luciano A. 
Published: November 2023

AbstractExcept for isolated developments and specific software extensions, molecular graphics and modeling have historically been stuck at flat screens for visualization, mouse operations for molecular manipulation, menus and command line interfaces for controls, and single-user interfaces that only allow collaboration by streaming video hence limited to just sharing the view of the user operating the software. We demonstrate here how various technologies are ripe enough to enable much more fluent, immersive and natural human-computer interactions that in turn facilitate collaboration between human users, using affordable hardware through the internet and without even installing any specialized programs. For this, we introduce HandMol, a web app that exploits (i) WebXR for molecular visualization and manipulation in virtual reality, (ii) speech recognition coupled to a large language model to pass commands orally, (iii) speech synthesis for auditory feedback, (iv) WebRTC to communicate multiple instances of the tool without even requiring a server, and (v) external APIs to flexibly account for molecular mechanics, exemplified here with an endpoint running an AMBER forcefield for protein and nucleic acids and another running a DFT-trained neural network, ANI-2x, to allow exploration of conformation and some simple reactivity at high speed and accuracy. We show example applications to situations from daily work and education in chemistry and structural biology where HandMol can provide an advantage over traditional software: exploring and explaining molecular conformations and reactivity, docking and undocking small molecules into/out of protein pockets, threading molecules through nanopores, preparing systems for molecular simulations and for protein design, etc. We also present a brief study showing how users, even with limited or even no experience in VR, can significantly benefit from these kinds of technologies. As a draft prototype for the moment, HandMol is made available free of charge and without registration athttps://go.epfl.ch/handmol, in (optional but greatly appreciated) exchange for feedback on usability and on features expected for this kind of tools.
New-onset prostate cancer in type 2 diabetes mellitus exposed to the SGLT2I, DPP4I and GLP1a: A population-based cohort study
Authors: Chou Oscar Hou In , Lu Lei , Chung Cheuk To , Chan Jeffrey Shi Kai , Chan Raymond Ngai Chiu , Hiu Athena Lee Yan , Dee Edward Christopher , Ng Kenrick , Pui Hugo Hok Him , Lee Sharen , Cheung Bernard Man Yung , Tse Gary , Zhou Jiandong 
Published: November 2023

AbstractBackgroundSodium-glucose cotransporter 2 inhibitors (SGLT2I) have been suggested to reduce new-onset cancer amongst type-2 diabetes mellitus (T2DM) patients.ObjectiveThis real-world study aims to compare the risks of prostate cancer between SGLT2I and dipeptidyl peptidase-4 inhibitors (DPP4I) amongst T2DM patients.Design, setting and participantsThis was a retrospective population-based cohort study of prospectively recorded data on type-2 diabetes mellitus (T2DM) male patients prescribed either SGLT2I or DPP4I between January 1st2015 and December 31st2020 from Hong Kong.MethodsThe primary outcome was new-onset prostate cancer. The secondary outcomes included cancer-related mortality and all-cause mortality. Propensity score matching (1:1 ratio) using the nearest neighbour search was performed and multivariable Cox regression was applied to compare the risk. A three-arm sensitivity analysis including the glucagon-like peptide-1 receptor agonist (GLP1a) cohort was conducted.ResultsThis study included 42129 male T2DM patients (median age: 61.0 years old [SD: 12.2]; SGLT2I: n=17120; DPP4I: n=25009). After matching, the number of prostate cancers was significantly lower in SGLT2I users (n = 60) than in DPP4I (n = 102). SGLT2I use was associated with lower prostate cancer risks (HR: 0.45; 95% CI: 0.30-0.70) after adjustments than DPP4I. The results remained consistent in the sensitivity analysis. SGLT2I reduced the risks of prostate cancer prominently amongst patients who were older (age >65), patients with 2ndand 3rdquartile of HbA1c, concurrent metformin uses, and concurrent sulphonylurea uses. SGLT2I was associated with higher risks of prostate cancer amongst sulphonylurea non-users.ConclusionThe real-world study demonstrated SGLT2I was associated with lower risks of new-onset prostate cancer after matching and adjustments compared to DPP4I. This result warrants further prospective studies.Graphical abstract
A deep generative model for estimating single-cell RNA splicing and degradation rates
Authors: Mizukoshi Chikara , Kojima Yasuhiro , Nomura Satoshi , Hayashi Shuto , Abe Ko , Shimamura Teppei 
Published: November 2023

AbstractMessenger RNA splicing and degradation are critical for gene expression regulation, the abnormality of which leads to diseases. Previous methods for estimating kinetic rates have limitations, assuming uniform rates across cells. We introduce DeepKINET, a deep generative model that estimates splicing and degradation rates at single-cell resolution from scRNA-seq data. DeepKINET outperformed existing methods on simulated and metabolic labeling datasets. Applied to forebrain and breast cancer data, it identified RNA-binding proteins responsible for kinetic rate diversity. DeepKINET also analyzed the effects of splicing factor mutations on target genes in erythroid lineage cells. DeepKINET effectively reveals cellular heterogeneity in post-transcriptional regulation.
HIHISIV: a database of gene expression in HIV and SIV host immune response
Authors: Costa Raquel Lopes , Gadelha Luiz , D’arc Mirela , Ribeiro-Alves Marcelo , Robertson David L , Schwartz Jean-Marc , Soares Marcelo A. , Porto Fábio 
Published: November 2023

AbstractIn the battle of the host against lentiviral pathogenesis, the immune response is crucial. However, several questions remain unanswered about the interaction with different viruses and their influence on disease progression. The simian immunodeficiency virus (SIV) infecting nonhuman primates (NHP) is widely used as a model for the study of the human immunodeficiency virus (HIV). Both because they are evolutionarily linked and because they share physiological and anatomical similarities that are largely explored to understand the disease progression. The HIHISIV database was developed to support researchers to integrate and evaluate the large number of transcriptional data associated with the presence/absence of the pathogen (SIV or HIV) and the host response (NHP and human). The datasets are composed of microarray and RNA-Seq gene expression data that were selected, curated, analyzed, enriched, and stored in a relational database. Six query templates comprise the main data analysis functions and the resulting information can be downloaded. The HIHISIV database provides accurate resources for browsing and visualizing results and for more robust analyses of pre-existing data in transcriptome repositories.Database URLhttps://hihisiv.github.io
FliH and FliI help FlhA bring strict order to flagellar protein export inSalmonella
Authors: Kinoshita Miki , Minamino Tohru , Uchihashi Takayuki , Namba Keiichi 
Published: November 2023

AbstractThe flagellar type III secretion system (fT3SS) switches substrate specificity from rod-hook-type to filament-type upon hook completion, terminating hook assembly and initiating filament assembly. The FlhA ring is directly involved in substrate recognition, allowing the fT3SS to coordinate flagellar protein export with assembly, but the mechanism remains a mystery. Here, we report that the highly conserved GYXLI motif of FlhA is important for ordered protein export by the fT3SS. The fT3SS with theflhA(Y369A/R370A/L371A/I372A)(AAAA) orflhA(Y369G/R370G/L371G/I372G)(GGGG) mutation did not switch the substrate specificity at an appropriate timing of hook assembly. The A372V/T and G372V substitutions recovered the export switching function of the AAAA and GGGG mutants, respectively, in the presence but not in the absence of FliH and FliI, components of the flagellar ATPase complex. Interestingly, a filament-type substrate, FlgL, was secreted via the fT3SS with the AAAA or GGGG mutation during hook assembly in the absence of FliH and FliI but not in their presence. These observations suggest that FlhA requires the flagellar ATPase complex not only to efficiently remodel its ring structure responsible for the substrate specificity switching of the fT3SS but also to correct substrate recognition errors that occur during flagellar assembly.
A genome-wide association study of neonatal metabolites
Authors: He Quanze , Liu Hankui , Lu Lu , Zhang Qin , Wang Qi , Wang Benjing , Wu Xiaojuan , Guan Liping , Mao Jun , Xue Ying , Zhang Chunhua , He Yuxing , Peng Xiangwen , Peng Huanhuan , Zhao Kangrong , Li Hong , Jin Xin , Zhao Lijian , Zhang Jianguo , wang Ting 
Published: November 2023

SummaryThe hereditary component significantly influences the concentration of metabolites in adults. Nevertheless, the precise influence of genetic factors on neonatal metabolites remains uncertain. To bridge this gap, we employed genotype imputation techniques on large-scale low-pass genome data obtained from non-invasive prenatal testing. Subsequently, we conducted association studies on a total of 75 metabolic components in neonates. The study identified a total 17 previous reported associations and 13 novel discovered associations between single nucleotide polymorphisms and metabolic components. These associations were initially found in the discovery cohort (8,744 participants) and subsequently confirmed in a replication cohort (19,041 participants). The average heritability of metabolic components was calculated to be 76.2%, with a range of 69-78.8%. The aforementioned findings offer valuable insights pertaining to the genetic architecture of neonatal metabolism.In BriefLarge-scale genomes of maternal non-invasive prenatal testing provide insights into the genetic contribution to neonatal metabolism.HighlightsGWAS of 27,785 low-pass genomes revealed 13 novel associations of neonatal metabolic components.Estimated an average of 76.2% heritability of neonatal metabolic components and showed the individual concentration can be accurately predicted from polygenic risk scores.A total of 17 established relationships have been observed, providing evidence that maternal genomes can be utilized in neonatal metabolite GWAS.
Ambulatory vEEG discontinued against medical advice among individuals with intellectual disabilities: a retrospective chart review
Authors: Nurse Ewan S. , Winterling Nicholas , Cook Mark J. 
Published: November 2023

AbstractObjectiveThis retrospective chart review aims to quantify the rate of patients with intellectual disability (ID) accessing an Australian ambulatory EEG service, and understand the implications of discontinuing studies against medical advice.MethodsElectronic records of referrals, patient monitoring notes, and EEG reports were accessed retrospectively. Each referral was assessed to determine whether the patient had an ID. For each study where patients were discharged against medical advice, the outcomes of their EEG report were assessed and compared between the ID and non-ID groups. Exploratory analysis was performed assessing the effects of age, the percentage of the requested monitoring undertaken, and outcome rates as a function of monitoring duration.ResultsThere were significantly more patients in the ID group with early disconnection than the non-ID group (Chi squared test,p=0.000). There was no significant difference in the rates of clinical outcomes between the ID and non-ID groups amongst patients who disconnected early.ConclusionsAlthough rates of early disconnection are higher in those with ID, study outcomes are largely similar between patients with and without ID in this retrospective analysis of an ambulatory EEG service.SignificanceAmbulatory EEG is a viable alternative to inpatient monitoring for patients with ID.Highlights three bullet points (one sentence each, with a maximum of 130 characters - including spacesRecording EEG remains a challenge for patients with epilepsy and IDThis study shows that patients with ID are more likely to disconnect early compared to those without IDStudy outcomes are not significantly different between those with and without ID, however some outcomes may be underpowered
The cytokine genes ofOncorhynchus masou formosanusinclude a defective interleukin-4A gene
Authors: Yen Ying-Hsuan , Zheng De Yu , Yang Shu Yuan , Gwo Jin-Chywan , Fugmann Sebastian D. 
Published: November 2023

AbstractOncorhynchus masou formosanus(Formosa land-locked salmon) is a critically endangered salmonid fish endemic to Taiwan. To begin to understand how its drastic change in lifestyle from anadromous to exclusively river-dwelling is reflected in its immune genes, we characterized the genes encoding six cytokines (IL-2A, IL-2B, IL-4A, IL-4B1, IL-4B2, and IL-17A/F2a) important for T cell responses as no genomic data is available for this fish. Interestingly, all genes appeared homozygous indicative of a genetic bottleneck. TheIL2andIL17A/F2agenes and their products are highly similar to their characterized homologs inOncorhynchus mykiss(rainbow trout) and other salmonid fish. Two notable differences were observed inIL4family important for type 2 immune responses. First,O. m. formosanuscarries not only one but two genes encoding IL-4B1 proteins and expansions of these genes are present in other salmonid fish. Second, theOmfoIL4Agene carries a 228 bp deletion that results in a premature stop codon and hence a non-functional IL-4A cytokine. This suggests a reduced ability for T cell responses against parasitic infections in this species.
Humans adapt rationally to approximate estimates of uncertainty
Authors: Pulcu Erdem , Browning Michael 
Published: November 2023

SummaryEfficient learning requires estimation of, and adaptation to, different forms of uncertainty. If uncertainty is caused by randomness in outcomes (noise), observed events should have less influence on beliefs, whereas if uncertainty is caused by a change in the process being estimated (volatility) the influence of events should increase. Previous work has demonstrated that humans respond appropriately to changes in volatility, but there is less evidence of a rational response to noise. Here, we test adaptation to variable levels of volatility and noise in human participants, using choice behaviour and pupillometry as a measure of the central arousal system. We find that participants adapt as expected to changes in volatility, but not to changes in noise. Using a Bayesian observer model, we demonstrate that participants are, in fact, adapting to estimated noise, but that their estimates are imprecise, leading them to misattribute it as volatility and thus to respond inappropriately.
hictk: blazing fast toolkit to work with .hic and .cool files
Authors: Rossini Roberto , Paulsen Jonas 
Published: November 2023

AbstractMotivationHi-C is gaining prominence as a method for mapping genome organization. With declining sequencing costs and a growing demand for higher-resolution data, efficient tools for processing Hi-C datasets at different resolutions are crucial. Over the past decade, the .hic and Cooler file formats have become the de-facto standard to store interaction matrices produced by Hi-C experiments in binary format. Interoperability issues make it unnecessarily difficult to convert between the two formats and to develop applications that can process each format natively.ResultsWe developed hictk, a toolkit that can transparently operate on .hic and .cool files with excellent performance. The toolkit is written in C++ and consists of a C++ library with Python and R bindings as well as CLI tools to perform common operations directly from the shell, including converting between .hic and .mcool formats. We benchmark the performance of hictk and compare it with other popular tools and libraries. We conclude that hictk significantly outperforms existing tools while providing the flexibility of natively working with both file formats without code duplication.AvailabilityThe hictk library, Python bindings and CLI tools are released under the MIT license as a multi-platform application available at github.com/paulsengroup/hictk. Pre-built binaries for Linux and macOS are available on bioconda. Python bindings for hictk are available on GitHub at github.com/paulsengroup/hictkpy, while R bindings are available on GitHub at github.com/paulsengroup/hictkR.Contactjonas.paulsen@ibv.uio.noSupplementary informationSupplementary data are available atBioinformaticsonline.