bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved access to diabetic retinopathy screening through primary care-based teleophthalmology during the COVID-19 pandemic
Authors: Dow Eliot R. , Chen Karen M. , Basina Marina , Dang Jimmy , Khan Nergis C. , Kim Michael , Levine Marcie , Mishra Kapil , Perera Chandrashan , Phadke Anuradha , Tan Marilyn , Weng Kirsti , Do Diana V. , Mahajan Vinit B. , Mruthyunjaya Prithvi , Leng Theodore , Myung David 
Published: May 2023

ABSTRACTBackgroundPrimary care practices play a critical role in ensuring that patients with diabetes undergo an annual eye examination, the importance of which is underscored by the Healthcare Effectiveness Data and Information Set (HEDIS) quality measures. Store-and-forward teleophthalmology, where ocular images are read remotely by an ophthalmologist, has the potential to facilitate this role.MethodsIn this report, we aim to measure if using a primary care-based teleophthalmology program improves access to eye examinations for diabetic patients as reflected in HEDIS measures. Over a 20-month period, non-mydriatic fundus photographs were obtained at five primary care sites in the San Francisco Bay Area from patients with a new or existing diagnosis of diabetes mellitus type 1 or 2 who needed an annual eye examination. Collected photographs were evaluated remotely by vitreoretinal specialists for diabetic retinopathy. Our primary measures were the proportion and number of annual eye exams of diabetic patients in primary care clinics that participated in the teleophthalmology program compared to clinics that did not participate. Additional measures included the number of patients with DR who were identified through the program, gradeability of fundus photographs, and characteristics of the study population.ResultsThe program screened 760 unique patients, 84 of whom were found to have DR (11.1%). The rate of ungradable photos was 9.7%, which was greater for patients who self-reported as racially non-White. For the duration of the study, including during the COVID-19 pandemic, both the proportion and number of diabetic patients receiving annual eye examination increased (17.1% increase in proportion, 14.8% increase in number). In comparison, primary care sites that did not offer the teleophthalmology service declined in these measures (2.3% decrease in proportion, 17.0% decrease in number).ConclusionsPrimary care-based teleophthalmology improves access to eye exam for diabetic patients and identifies patients with diabetic retinopathy across diverse communities.
Deep Learning-based Workflow for Automatic Extraction of Atria and Epicardial Adipose Tissue on cardiac Computed Tomography in Atrial Fibrillation
Authors: Wang Guan-Jie , Kuo Ling , Chang Shih-Lin , Lin Yenn-Jiang , Chung Fa-Po , Lo Li-Wei , Hu Yu-Feng , Chao Tze-Fan , Tuan Ta-Chuan , Liao Jo-Nan , Chang Ting-Yung , Lin Chin-Yu , Liu Chih-Min , Liu Shin-Huei , Kuo Ming-Ren , Lee Guan-Yi , Huang Yu-Shan , Wu Cheng-I , Chen Shih-Ann , Lu Chia-Feng 
Published: May 2023

AbstractBackgroundPreoperative measurements of left atrium (LA) and epicardial adipose tissue (EAT) volumes in computed tomography (CT) images have been reported to be associated with an increased risk of atrial fibrillation (AF) recurrence. We aimed to design a deep learning-based workflow to provide a reliable automatic segmentation of atria, pericardium and EAT, which can facilitate future applications in AF.MethodsA total of 157 patients with AF who underwent radiofrequency catheter ablation were enrolled in this study. The 3D U-Net models of LA, right atrium (RA) and pericardium were used to develop the pipeline of total, LA-and RA-EAT automatic segmentation. We defined the attenuation range between -190 to -30 HU as fat within the pericardium to obtain total EAT. Regions between the dilated endocardial boundaries and endocardial walls of LA or RA within the pericardium were used to detect the voxels attributed to fat, resulting in LA-EAT and RA-EAT.ResultsThe LA, RA and pericardium segmentation models achieved Dice coefficients of 0.960 ± 0.010, 0.945 ± 0.013 and 0.967 ± 0.006, respectively. The 3D segmentation models correlated well with ground truth for LA, RA and pericardium (r=0.99 and p < 0.001 for all). For the results of EAT, LA-EAT and RA-EAT segmentation, Dice coefficients of our proposed method were 0.870 ± 0.027, 0.846 ± 0.057 and 0.841 ± 0.071, respectively.ConclusionsOur proposed workflow for automatic LA/RA and EAT segmentation applying 3D U-Nets on CT images was reliable in patients with AF.
Clinically validated metatranscriptomic analysis of human and microbial components of FFPE tissue biopsies
Authors: Toma Ryan , Hu Lan , Demusaj Diana , Mehrtash Mory , Wohlman Robert , Banavar Guru , Vuyisich Momchilo 
Published: May 2023

AbstractRecent studies have identified microbial components in most tumors and invoked microorganisms in cancer onset and progression. The microbial functions responsible for these effects likely include production of genotoxins, modification of human gene expression, and protection of cancer cells from immune surveillance. Metatranscriptomics (MT) is a powerful tool for the development of potential cancer diagnostics and therapeutics, as well as investigating cancer initiation and progression. This is because MT data can quantify human and microbial gene expression, as well as provide strain level taxonomic classification of the microorganisms in the tumor microenvironment (TME). In addition, the microbial data derived from the MT method can easily be normalized across different samples, since many human transcripts can act as internal standards. When collecting tissue samples for clinical studies, researchers have the option of using fresh or Formalin-Fixed Paraffin-Embedded (FFPE) samples. FFPE samples are much easier to study, due to their widespread availability and ease of collection, storage, and handling. Little research exists comparing FFPE samples and fresh tissues, and there is no literature examining the differences in microbial signatures between these two sample preservation methods. In this study, we analyzed matched FFPE samples and fresh tissue samples from colon polyps of 13 participants for microbial and human components. We found that our clinically validated MT method generated equivalent data from FFPE samples and fresh tissue samples with high concordance for human gene expression (Pearson 0.70), microbial species (Pearson 0.94), and KEGG Orthologs (Pearson 0.97). These data indicate that FFPE samples are suitable for use in metatranscriptomic analyses, which will enable more diverse and larger oncology studies, as well as any other studies that benefit from MT analysis of tissue samples.
ST-segment depression on resting electrocardiogram in patients with out prior cardiac disease — a comparison with stress electrocardiogram and echocardiography —
Authors: Morita Masaki 
Published: May 2023

AbstractBackgroundThe clinical significance of ST-segment depression (STD) on electrocardiogram (ECG) in resting patients without prior cardiac disease and symptoms of angina pectoris in unclear. This study was aimed to elucidate this problem.MethodsPatients with non-anginal chest pain or those who underwent ECG screening were enrolled. Echocardiography (Echo) and resting and stress ECG were performed.; stress ECG was recorded during exercise and recovery period. For stress ECG, ST-segment/heart-rate loop was adopted. The clinical results in patients with and without STD on resting ECG were compared.ResultsEighty-two patients were included; a mean age of 61.4 ± 14.1 years old. ECG revealed that 13 (15.9%) patients had left ventricular hypertrophy (LVH; Sokolow-Lyon’s voltage > 3.5 mV), whereas 34 (41.5%) patients had STD (ST-segment voltage at the J point < –0.05 mV). Echo revealed a mean left ventricular mass (LVM) of 182 ± 74 g. The stress ECG revealed the mean recovery index was –1.2° ± 19.1°. A correlation of STD voltage with Romhilt-Estes score on resting ECG (r = –0.34, p = 0.0015) and LVM on Echo (r = –0.26, p = 0.018) were observed. From ROC curves, STD tended to diagnose more accurately than other ECG parameters. From multiple logistic analysis, age, Romhilt-Estes score and peak STD on stress ECG were independently correlated with STD on resting ECG.ConclusionIn the patients without prior cardiac disease and anginal chest pain, STD on resting ECG was suggestive of older age, LVH on ECG (independent) and LVH on Echo (not independent).RegistrationURL:https://www.umin.ac.jp/ctr/index.htm; Unique identifier: UMIN000050291WHAT IS KNOWNST-segment depression (STD) on resting electrocardiogram (ECG) among the subjects without prior cardiac disease and symptoms of angina is suggested to imply left ventricular hypertrophy.WHAT THE STUDY ADDSIn order to investigate the significance of STD on resting ECG among the subjects without history of cardiac disease or anginal chest pain, especially to rule out the incidence of silent myocardial ischemia, echocardiogram and stress ECG were contemporarily performed for them.
Protein phosphorylation and oxidative protein modification mediate plant photosystem II disassembly and repair
Authors: McKenzie Steven D. , Puthiyaveetil Sujith 
Published: May 2023

AbstractThe light-driven water-splitting reaction of photosystem II exposes its key reaction center core protein subunits to irreversible oxidative photodamage. A rapid repair cycle replaces photodamaged core subunits in plants, but how the large antenna-core supercomplex structures of plant photosystem II disassemble for repair is not currently understood. Phosphorylation of reaction center core protein subunits has been suggested as a mechanism of disassembly. Consistent with this, we find specific involvement of phosphorylation in removing peripheral antenna from the core and monomerization of the dimeric cores inArabidopsis. However, photosystem disassembly occurred to some degree even in the absence of phosphorylation as suggestive of other unknown mechanisms of disassembly. Here we show that the oxidative modifications of amino acid residues in core protein subunits of photosystem II are active mediators of disassembly. Exogenously-applied hydrogen peroxide induces photosystem disassembly, especially the conversion of the monomeric cores into two reaction center subcomplexes. We further show that the extent of monomer disassembly is proportional to the oxidative protein damage, with the fully disassembled reaction center subcomplexes containing more modifications. In the monomeric core, some amino acid oxidative modifications map at the D1-CP43 interface as consistent with a dissociation of the core along these subunits. Oxidative modifications thus likely disassemble only the damaged monomeric cores, ensuring an economical photosystem disassembly process. Our results suggest oxidative protein modification represents an ancient mechanism of photosystem disassembly, and that phosphorylation originated later in evolution to impart explicit control over the repair process.
Extreme mitochondrial reduction in a novel group of free-living metamonads
Authors: Williams Shelby K. , Jerlström Hultqvist Jon , Eglit Yana , Salas-Leiva Dayana E. , Curtis Bruce , Orr Russell J. S. , Stairs Courtney W. , Atalay Tuğba N. , MacMillan Naomi , Simpson Alastair G. B. , Roger Andrew J. 
Published: May 2023

SummaryMetamonads are a diverse group of heterotrophic microbial eukaryotes adapted to living in hypoxic environments. All metamonads but one harbour metabolically altered ‘mitochondrion-related organelles’ (MROs) with reduced functions relative to aerobic mitochondria, however the degree of reduction varies markedly over the metamonad tree. To further investigate metamonad MRO diversity, we generated high quality draft genomes, transcriptomes, and predicted proteomes for five recently discovered free-living metamonads. Phylogenomic analyses placed these organisms in a group we informally named the ‘BaSk’ (Barthelonids+Skoliomonads) clade, which emerges as a deeply branching sister group to the Fornicata, a metamonad phylum that includes parasitic and free-living flagellates. Extensive bioinformatic analyses of the manually curated gene models showed that these organisms are predicted to have extremely reduced MRO proteomes in comparison to other free-living metamonads. Loss of the mitochondrial iron-sulfur cluster (ISC) assembly system in some organisms in this group appears to be linked to the acquisition in their common ancestral lineage of a SUF-like minimal system (SMS) Fe/S cluster pathway through lateral gene transfer (LGT). One of the isolates,Skoliomonas litria, appears to have undergone further mitochondrial reduction having lost all other known MRO pathways. No proteins were confidently assigned to the predicted MRO proteome of this organism suggesting that the organelle has been lost. The extreme mitochondrial reduction observed within this free-living anaerobic protistan clade is unprecedented and demonstrates that mitochondrial functions, under some conditions, may be completely lost even in free-living organisms.
cellsnake: a user-friendly tool for single-cell RNA sequencing analysis
Authors: Umu Sinan U. , Vander-Elst Karoline Rapp , Karlsen Victoria T. , Chouliara Manto , Bækkevold Espen Sønderaal , Jahnsen Frode Lars , Domanska Diana 
Published: May 2023

AbstractBackgroundSingle-cell RNA sequencing (scRNA-seq) provides high-resolution transcriptome data to understand the heterogeneity of cell populations at the single-cell level. The analysis of scRNA-seq data requires the utilization of numerous computational tools. However, non-expert users usually experience installation issues, a lack of critical functionality or batch analysis modes, and the steep learning curves of existing pipelines.ResultsWe have developed cellsnake, a comprehensive, reproducible, and accessible single-cell data analysis workflow, to overcome these problems. Cellsnake offers advanced features for standard users and facilitates downstream analyses in both R and Python environments. It is also designed for easy integration into existing workflows, allowing for rapid analyses of multiple samples.ConclusionAs an open-source tool, cellsnake is accessible through Bioconda, PyPi, Docker, and GitHub, making it a cost-effective and user-friendly option for researchers. By using cellsnake, researchers can streamline the analysis of scRNA-seq data and gain insights into the complex biology of single cells.
Dynamics of a Lipid Vesicle across a Microfluidic Constriction: How does the Fluidity of the Encapsulation and its Micro-Environment Matter?
Authors: Kahali Tanoy , Panigrahi Devi Prasad , Chakraborty Suman 
Published: May 2023

AbstractConstriction in the flow passage in the physiological circulatory system is central to the occurrence of several diseased conditions such as thrombosis and is also pivotal towards the understanding of several regulatory processes in the human microvasculature. It is, therefore, imperative to advance a mechanistic insight on the dynamics of the transiting cellular encapsulations in a physiologically-mimicking micro-confinement, with particular focus on deciphering the role of its mechano-physical properties. Here we bring out a quantitative depiction on the role of the membrane fluidity and the initial deflation (shape deviation from sphericity) of a lipid vesicle during its morphological transition from stretching to tumbling via rolling as it migrates across a microfluidic constriction. Based on our experimental observations as well as theoretical insights, we construct a regime map to elucidate the range of the key dimensionless parameters orchestrating the dynamic transition. Our results further bring out the role of the initial position of the lipid vesicle on its subsequent stretching dynamics, exhibiting characteristic nonlinearities and non-monotonic trends. In addition, our observations on the vesicle’s stretching dynamics emerge from mapping selectively with the viscosity contrast between the encapsulated and the suspending fluid medium, offering potential physiologically relevant cues on the impact of the aging of a cellular moiety on its deformability as it transits through a constricted path. Such mechanistic insights may potentially enable establishing quantitative correlations between the dynamical transition of a cellular encapsulation and its mechano-physical properties, which may in turn, have decisive implications in various states of health and disease while circulating across microvascular fluidic pathways.Impact StatementThis study brings out a quantitative mechanistic insight into the dynamics of migrating lipid vesicles as they migrate through a constricted microfluidic passage. Having a direct similitude with the movement of red blood cells in human microvascular pathways, the resulting mapping between the initial shape and bending properties of the vesicle membrane with three distinct morphological transitions (stretching, rolling, and tumbling) provides cues for understanding the healthy and diseased states of the cells based on their morpho-dynamic features and establish exclusive connectivity of the same with the cell membrane as well as the cytoplasm properties, a paradigm that is currently non-existant. This, in turn, may lead to a novel mechanistic approach of label-free disease detection based on cellular imaging, for which the current understanding is mostly empirical rather than fundamental.
An operational methodology to identify Critical Ecosystem Areas to help nations achieve the Kunming-Montreal Global Biodiversity Framework
Authors: Venegas-Li Ruben , Grantham Hedley S. , Rainey Hugo , Diment Alex , Tizard Robert , Watson James E.M. 
Published: May 2023

AbstractThe Kunming-Montreal Global Biodiversity Framework (GBF) will become the most important multilateral agreement to guide biodiversity conservation actions globally over the coming decades. An ecosystem goal and various targets for maintaining integrity, restoring degraded ecosystems, and achieving representation in conservation areas feature throughout the GBF. Here, we propose an operational framework that combines disparate information on ecosystem type, extent, integrity, levels of protection, and risk of collapse to support the identification of irreplaceable ‘Critical Ecosystem Areas’ (CEAs), to help advance these ecosystem targets. The framework classifies each component ecosystem based on its integrity, importance in ensuring no ecosystem collapse and its relative value to achieving representation if protected. These CEAs are immediate conservation opportunities, given that they achieve multiple ecosystem goals and targets in the GBF. We showcase its application using Myanmar’s forested ecosystems as a case study and argue that it could be immediately used across all terrestrial ecosystems.
Enhancing drug repurposing on graphs by integrating drug molecular structure as feature
Authors: Ayuso-Muñoz Adrián , Prieto-Santamaría Lucía , Álverez-Pérez Andrea , Otero-Carrasco Belén , Serrano Emilio , Rodríguez-González Alejandro 
Published: May 2023

AbstractDrug repurposing has become increasingly important, particularly in light of the COVID-19 pandemic. This process involves identifying new therapeutic uses for existing drugs, which can significantly reduce the cost, risk, and time associated with developing new drugs,de novodevelopment. A previous conducted study proved that Deep Learning can be used to streamline this process by identifying drug repurposing hypotheses. The study presented a model called REDIRECTION, which utilized the rich biomedical information available in graph form and combined it with Geometric Deep Learning to find new indications for existing drugs. The reported metrics for this model were 0.87 for AUROC and 0.83 for AUPRC. In this current study, the importance of node features in GNNs is explored. Specifically, the study used GNNs to embed two-dimensional drug molecular structures and obtain corresponding features. These features were incorporated into the drug repurposing graph, along with some other enhancements, resulting in an improved model called DMSR. Performance score for the reported metrics values raised by 0.0448 in AUROC and 0.0919 in AUPRC. Based on these findings, we believe that the method used for embedding drug molecular structures is interesting and captures valuable information about drugs. Its incorporation in the graph for drug repurposing can significantly benefit the process, leading to improved performance evaluation metrics.
Polyphosphate uses mTOR, pyrophosphate, and Rho GTPase components to potentiate bacterial survival inDictyostelium
Authors: Rahman Ryan J. , Rijal Ramesh , Jing Shiyu , Chen Te-An , Ismail Issam , Gomer Richard H. 
Published: May 2023

AbstractHuman macrophages and the eukaryotic microbeDictyostelium discoideumingest bacteria by phagocytosis, and then kill the ingested bacteria. Some pathogenic bacteria secrete linear chains of phosphate residues (polyphosphate; polyP), and the polyP causes the phagocytes to not kill the ingested bacteria. InD. discoideum, the effect of polyP requires the G protein-coupled receptor GrlD, suggesting that polyP uses a signal transduction pathway to inhibit killing of ingested bacteria. Here we show that in addition to GrlD, theD. discoideumpolyP signaling pathway requires the GPCR interacting arrestin-like protein AdcB, inositol hexakisphosphate kinase A (I6kA), the Rho GTPase RacE, and the TOR component Lst8.D. discoideumalso secretes polyP, and at high concentrations polyP inhibitsD. discoideumcytokinesis. The polyP inhibition of bacterial killing pathway does not appear to involve many of the polyP inhibition of cytokinesis pathway components. These data suggest the intriguing possibility that if there is a similar polyP inhibition of bacterial killing pathway in macrophages, pharmacologically blocking this pathway could potentiate macrophage killing of pathogenic bacteria.ImportanceAlthough most bacteria are quickly killed after phagocytosis by a eukaryotic cell, some pathogenic bacteria prevent their killing after phagocytosis. PathogenicMycobacteriumspecies secrete polyP, and the polyP is necessary for the bacteria to prevent their killing after phagocytosis. Conversely, exogenous polyP prevents the killing of ingested bacteria that are normally killed after phagocytosis by human macrophages and the eukaryotic microbeDictyostelium discoideum. This suggests the possibility that in these cells, a signal transduction pathway is used to sense polyP and prevent killing of ingested bacteria. In this report, we identify key components of the polyP signal transduction pathway inD. discoideum. In cells lacking these components, polyP is unable to inhibit killing of ingested bacteria. The pathway components have orthologues in human cells, and an exciting possibility is that pharmacologically blocking this pathway in human macrophages would cause them to kill ingested pathogens such asM. tuberculosis.