bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of diabetic kidney disease risk using machine learning models: a population-based cohort study of Asian adults
Authors: Sabanayagam Charumathi , He Feng , Nusinovici Simon , Li Jialiang , Lim Cynthia , Tan Gavin , Cheng Ching-Yu 
Published: August 2022

ABSTRACTBackgroundMachine learning (ML) techniques improve disease prediction by identifying the most relevant features in multi-dimensional data. We compared the accuracy of ML algorithms for predicting incident diabetic kidney disease (DKD).MethodsWe utilized longitudinal data from 1365 Chinese, Malay and Indian participants aged 40-80 years with diabetes but free of DKD who participated in the baseline and 6-year follow-up visit of the Singapore Epidemiology of Eye Diseases Study (2004-2017). Incident DKD (11.9%) was defined as an estimated glomerular filtration rate (eGFR) <60 mL/min/1.73m2 with at least 25% decrease in eGFR at follow-up from baseline. 339 features including participant characteristics, retinal imaging, genetic and blood metabolites were used as predictors. Performances of several ML models were compared to each other and to logic regression (LR) model based on established features of DKD (age, sex, ethnicity, duration of diabetes, systolic blood pressure, HbA1c, and body mass index) using area under the receiver operating characteristic curve (AUC).ResultsML model, Elastic Net (EN) had the best AUC (95% confidence interval) of 0.851 (0.847-0.856), which was 7.0% relatively higher than by LR 0.795 (0.790-0.801). Sensitivity and specificity of EN were 88.2% and 65.9% vs. 73.0% and 72.8% by LR. The top-15 predictors included age, ethnicity, antidiabetic medication, hypertension, diabetic retinopathy, systolic blood pressure, HbA1c, eGFR and metabolites related to lipids, lipoproteins, fatty acids and ketone bodies.ConclusionsOur results showed ML together with feature selection improves prediction accuracy of DKD risk in an asymptomatic stable population and identifies novel risk factors including metabolites.Funding SupportThis study was supported by the National Medical Research Council, NMRC/OFLCG/001/2017 and NMRC/HCSAINV/MOH-001019-00. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Conflicts of interestNone declared.
Non-invasive tumor probability maps developed using autopsy tissue identify novel areas of tumor beyond the imaging-defined margin
Authors: Bobholz Samuel A. , Lowman Allison K. , Connelly Jennifer M. , Duenweg Savannah R. , Kyereme Fitzgerald , Winiarz Aleksandra , Stebbins Margaret A. , Nath Biprojit , Brehler Michael , Bukowy John , Cochran Elizabeth J. , Coss Dylan , Lupo Janine M. , Phillips Joanna J. , Ellingson Benjamin M. , Krucoff Max , Mueller Wade M. , Agarwal Mohit , Banerjee Anjishnu , LaViolette Peter S. 
Published: August 2022

AbstractBackgroundThis study identified a clinically significant subset of glioma patients with tumor outside of contrast-enhancement present at autopsy, and subsequently developed a method for detecting non-enhancing tumor using radio-pathomic mapping. We tested the hypothesis that autopsy-based radio-pathomic tumor probability maps would be able to non-invasively identify areas of infiltrative tumor beyond traditional imaging signatures.MethodsA total of 159 tissue samples from 65 subjects were aligned to MRI acquired nearest to death for this study. Demographic and survival characteristics for patients with and without tumor beyond the contrast-enhancing margin were computed. An ensemble algorithm was used to predict pixelwise tumor presence from pathological annotations using segmented cellularity (Cell), extracellular fluid (ECF), and cytoplasm (Cyt) density as input (6 train/3 test subjects). A second level of ensemble algorithms were used to predict voxel-wise Cell, ECF, and Cyt on the full dataset (43 train/22 test subjects) using 5-by-5 voxel tiles from T1, T1+C, FLAIR, and ADC as input. The models were then combined to generate non-invasive whole brain maps of tumor probability.ResultsTumor outside of contrast was identified in 41.5 percent of patients, who showed worse survival outcomes (HR=3.90, p<0.001). Tumor probability maps reliably tracked non-enhancing tumor in the test set, external data collected pre-surgery, and longitudinal data to identify treatment-related changes and anticipate recurrence.ConclusionsThis study developed a multi-1 stage model for mapping gliomas using autopsy tissue samples as ground truth, which was able to identify regions of tumor beyond traditional imaging signatures.
Charge neutralization of the active site glutamates does not limit substrate binding and transport by EmrE
Authors: Spreacker Peyton J. , Brousseau Merissa , Hisao Grant S. , Soltani Mohammad , Davis James H. , Henzler-Wildman Katherine A. 
Published: August 2022

AbstractEmrE, a small multidrug resistance (SMR) transporter from E. coli, confers broad-spectrum resistance to polyaromatic cations and quaternary ammonium compounds. Previous transport assays demonstrate that EmrE transports a +1 and a +2 substrate with the same stoichiometry of 2 protons:1 cationic substrate. This suggests that EmrE substrate binding capacity is limited to neutralization of the two essential glutamates, E14A and E14B (one from each subunit in the antiparallel homodimer), in the primary binding site. Here we explicitly test this hypothesis, since EmrE has repeatedly broken expectations for membrane protein structure and transport mechanism. We previously showed that EmrE can bind a +1 cationic substrate and proton simultaneously, with cationic substrate strongly associated with one E14 residue while the other remains accessible to bind and transport a proton. Here we demonstrate that EmrE can bind a +2 cation substrate and a proton simultaneously using NMR pH titrations of EmrE saturated with divalent substrates, for a net +1 charge in the transport pore. Further, we find that EmrE can alternate access and transport a +2 substrate and proton at the same time. Together, these results lead us to conclude that E14 charge neutralization does not limit the binding and transport capacity of EmrE.
Insane in the vembrane: filtering and transforming VCF/BCF files
Authors: Hartmann Till , Schröder Christopher , Kuthe Elias , Lähnemann David , Köster Johannes 
Published: August 2022

SummaryData from sequencing of DNA or RNA samples is routinely scanned for variation. Such variation data is stored in the standardized VCF/BCF format with additional annotations. Analyses of variants usually involve steps where filters are applied to narrow down the list of candidates for further analysis. A number of tools for this task exist, differing in functionality, speed, syntax and supported annotations. Thus, users have to switch between tools depending on the filtering task, and have to adapt to the respective filtering syntax. We present vembrane as a command line VCF/BCF filtering tool that consolidates and extends the filtering functionality of previous software to meet any imaginable filtering use case. To this end, vembrane exposes the VCF/BCF file type specification and its inofficial extensions by the annotation tools VEP and SnpEff as Python data structures. vembrane filter enables filtration by arbitrary Python expressions over (combinations of) annotations, requiring only basic knowledge of the Python programming language. vembrane table allows users to generate tables from subsets of annotations or functions thereof. Finally, it is fast, thanks to pysam, a Python wrapper around htslib, and by relying on Python’s lazy evaluation.Availability and ImplementationSource code and installation instructions are available at github.com/vembrane/vembrane, DOI: 10.5281/zen-odo.7003981.
Clostridioides difficilePCR ribotype 151 is polyphyletic and includes pathogenic isolates from cryptic clade C-II with mono-toxin pathogenicity loci that can escape routine diagnostics
Authors: Ducarmon Quinten R. , van der Bruggen Tjomme , Harmanus Céline , Sanders Ingrid M.J.G. , Daenen Laura G.M. , Fluit Ad C. , Vossen Rolf H.A.M. , Kloet Susan L. , Kuijper Ed J. , Smits Wiep Klaas 
Published: August 2022

ABSTRACTWe report a patient case with pseudomembranous colitis associated with a mono-toxin producingClostridioides difficilebelonging to the very rarely diagnosed PCR ribotype (RT) 151. The infection was difficult to diagnose, since the isolate and the feces sample tested negative for toxin-encoding genes using a routine commercial test. This prompted us to sequence n = 11 RT151s from various geographical regions to study their genomic characteristics and relatedness. By including whole genome sequence data from other sources, we could further place these isolates into the phylogenetic tree ofC. difficileand assign them to their respective clades. These analyses revealed that 1) RT151s are polyphyletic with isolates falling into clades 1, and cryptic clades C-I and C-II 2) RT151 contains both non-toxigenic and toxigenic isolates and 3) RT151 C-II isolates contained mono-toxin pathogenicity loci (PaLoc). Additional analysis with PacBio circular consensus sequencing revealed that the isolate from our patient case report contains a novel PaLoc insertion site, lackedtcdAand a had significantly divergenttcdBsequence that might explain the failure of the diagnostic test. The study is noteworthy as 1) RT151 encompasses both typical and cryptic clades and 2) conclusive evidence for CDI due to clade C-II isolates was hitherto lacking.
CRISPR Screens Identify Novel Regulators of cFLIP Dependency and Ligand-Independent, TRAIL-R1-Mediated Cell Death
Authors: Kuehnle Neil , Osborne Scout Mask , Liang Ziyan , Manzano Mark , Gottwein Eva 
Published: August 2022

AbstractKaposi’s sarcoma-associated herpesvirus (KSHV) causes primary effusion lymphoma (PEL). PEL cell lines require expression of the cellular FLICE inhibitory protein (cFLIP) for survival, although KSHV encodes a viral homolog of this protein (vFLIP). Cellular and viral FLIP proteins have several functions, including, most importantly, the inhibition of pro-apoptotic caspase 8 and modulation of NF-κB signaling. To investigate the essential role of cFLIP and its potential redundancy with vFLIP in PEL cells, we first performed rescue experiments with human or viral FLIP proteins known to affect FLIP target pathways differently. The long and short isoforms of cFLIP and molluscum contagiosum virus MC159L, which are all strong caspase 8 inhibitors, efficiently rescued the loss of endogenous cFLIP activity in PEL cells. KSHV vFLIP was unable to fully rescue the loss of endogenous cFLIP and is therefore functionally distinct. Next, we employed genome-wide CRISPR/Cas9 synthetic rescue screens to identify loss of function perturbations that can compensate for cFLIP knockout. Results from these screens and our validation experiments implicate the canonical cFLIP target caspase 8 and TRAIL receptor 1 (TRAIL-R1 or TNFRSF10A) in promoting constitutive death signaling in PEL cells. However, this process was independent of TRAIL receptor 2 or TRAIL, the latter of which is not detectable in PEL cell cultures. The requirement for cFLIP is also overcome by inactivation of the ER/Golgi resident chondroitin sulfate proteoglycan synthesis and UFMylation pathways, Jagunal homolog 1 (JAGN1) or CXCR4. UFMylation and JAGN1, but not chondroitin sulfate proteoglycan synthesis or CXCR4, contribute to TRAIL-R1 expression. In sum, our work shows that cFLIP is required in PEL cells to inhibit ligand-independent TRAIL-R1 cell death signaling downstream of a complex set of ER/Golgi-associated processes that have not previously been implicated in cFLIP or TRAIL-R1 function.
ΔNp63 Regulates Homeostasis, Stemness, and Suppression of Inflammation in the Adult Epidermis
Authors: Eyermann Christopher E. , Chen Xi , Somuncu Ozge S. , Li Jinyu , Joukov Alexander N. , Chen Jiang , Alexandrova Evguenia M. 
Published: August 2022

ABSTRACTThe p63 transcription factor is critical for epidermis formation in embryonic development, but its role in the adult epidermis is poorly understood. Here we show that acute genetic ablation of ΔNp63, the main p63 isoform, in adult epidermis disrupts keratinocyte proliferation and self-maintenance and, unexpectedly, triggers an inflammatory psoriasis-like condition. Mechanistically, single-cell RNA sequencing revealed down-regulation of the cell cycle genes, up-regulation of differentiation markers, and induction of several pro-inflammatory pathways in ΔNp63-ablated keratinocytes. Intriguingly, ΔNp63-ablated cells disappear three weeks post-ablation, at the expense of the remaining non-ablated cells. This is not associated with active cell death mechanisms, but rather with reduced self-maintenance capacity. Indeed,in vivowound healing assay, a physiological readout of the epidermal stem cell function, is severely impaired in ΔNp63-ablated mice. We found that the Wnt signaling pathway (Wnt10a, Fzd6, Fzd10) and the AP1 factors (JunB, Fos, FosB) are the likely ΔNp63 effectors responsible for keratinocyte proliferation/stemness and suppression of differentiation, respectively, while interleukins IL-1a, IL-18, IL-24, and IL-36γ are the likely negative effectors responsible for the suppression of inflammation. These data establish ΔNp63 as a critical node that coordinates epidermal homeostasis, stemness, and suppression of inflammation in the adult epidermis, upstream of known regulatory pathways.
Loss of LRP1 in adult neural stem cells impairs migration to ischemic lesions
Authors: Dietert Kristi , Mahesula Swetha , Hegde Sheetal , Verschelde John , Reed Pamela , Sprague Shane , Kokovay Erzsebet , Sayre Naomi L. 
Published: August 2022

SummaryAfter ischemia, cells in the brain parenchyma upregulate stromal derived factor 1 (SDF1), driving chemokine receptor CXCR4-mediated migration of adult neural stem cells from the subventricular zone (SVZ) to the ischemic injury. We discovered a novel regulator of CXCR4 in neural stem cells, low-density lipoprotein receptor related protein 1 (LRP1). We employed a tamoxifen-inducible Nestin-Cre to drive expression of a tdTomato reporter and also knockout floxed LRP1 in adult mice and then subjected mice to middle-cerebral artery occlusion. Examination 2 weeks post-stroke reveals a loss of tdTomato positive cells localizing from the SVZ to the lesion. We show that loss of LRP1 disrupts CXCR4-mediated neural stem cell migration in vitro, which is likely driven by LRP1-mediated loss of CXCR4 expression in vivo. Altogether, our results suggest that LRP1 is a novel regulator of CXCR4 in neural stem cells.Highlights-LRP1 KO in adult neural stem cells disrupts migration to ischemic lesions in vivo.-LRP1 KO in adult neural stem cells disrupts migration towards SDF1 in vitro.-LRP1 positively regulates expression of CXCR4 in adult neural stem cells.eTOC blurbAdult neural stem cells can home to ischemic brain injury and are considered an important part of the repair process after stroke. However, little is known about what molecules help drive this response. The authors discovered that LRP1 is a novel regulator of CXCR4, which is essential for neural stem cell migration to ischemic injury.
Behavioral entrainment to rhythmic auditory stimulation can be modulated by tACS depending on the electrical stimulation field properties
Authors: Cabral-Calderin Yuranny , Hinsberg Daniela van , Thielscher Axel , Henry Molly J. 
Published: August 2022

AbstractSynchronization between auditory stimuli and brain rhythms is beneficial for perception. In principle, auditory perception could be improved by facilitating neural entrainment to sounds via brain stimulation. However, high inter-individual variability of brain stimulation effects questions the usefulness of this approach. Here we aimed to modulate auditory perception by modulating neural entrainment to frequency modulated (FM) sounds using transcranial alternating current stimulation (tACS). In addition, we evaluated the advantage of using tACS montages spatially optimized for each individual’s anatomy and functional data compared to a standard montage applied to all participants. Across two different sessions, 2-Hz tACS was applied targeting auditory brain regions. Concurrent with tACS, participants listened to FM stimuli with modulation rate matching the tACS frequency but with different phase lags relative to the tACS, and detected silent gaps embedded in the FM sound. We observed that tACS modulated the strength of behavioral entrainment to the FM sound in a phase-lag specific manner. Both the optimal tACS lag and the magnitude of the tACS effect were variable across participants and sessions. Inter-individual variability of tACS effects was best explained by the strength of the inward electric field, depending on the field focality and proximity to the target brain region. Although additional evidence is necessary, our results also provided suggestive insights that spatially optimizing the electrode montage could be a promising tool to reduce inter-individual variability of tACS effects. This work demonstrates that tACS effectively modulates entrainment to sounds depending on the optimality of the electric field. However, the lack of reliability on optimal tACS lags calls for caution when planning tACS experiments based on separate sessions.
Dimeric G-quadruplex motifs-induced NFRs determine strong replication origins in vertebrates
Authors: Poulet-Benedetti Jérémy , Tonnerre-Doncarli Caroline , Valton Anne-Laure , Laurent Marc , Gérard Marie , Barinova Natalja , Parisis Nikolaos , Massip Florian , Picard Franck , Prioleau Marie-Noëlle 
Published: August 2022

AbstractReplication of vertebrate genomes is tightly regulated to ensure accurate duplication, but our understanding of the interplay between genetic and epigenetic factors in this regulation remains incomplete. Here, we investigated the involvement of three elements enriched at gene promoters and replication origins: guanine-rich motifs potentially forming G-quadruplexes (pG4s), nucleosome-free regions (NFRs), and the histone variant H2A.Z, in the firing of origins of replication in vertebrates. We show that two pG4s on the same DNA strand (dimeric pG4s) are sufficient to induce assembly of an efficient minimal replication origin without inducing transcription. Dimeric pG4s in replication origins trigger formation of an NFR next to precisely-positioned nucleosomes enriched in H2A.Z on this minimal origin and genome-wide. Thus, our data suggest a crucial role for dimeric pG4s in the organization and duplication of vertebrate genomes. It supports the hypothesis that a nucleosome close to an NFR is a shared signal for the formation of replication origins in eukaryotes.
Assembling highly repetitive Xanthomonas TALomes using Oxford Nanopore sequencing
Authors: Erkes Annett , Grove René , Žarković Milena , Krautwurst Sebastian , Koebnik Ralf , Morgan Richard D. , Wilson Geoffrey G. , Hölzer Martin , Marz Manja , Boch Jens , Grau Jan 
Published: August 2022

AbstractMost plant-pathogenic Xanthomonas bacteria harbor transcription activator-like effector (TALE) genes, which function as transcriptional activators of host plant genes and support infection. The entire repertoire of up to 29 TALE genes of a Xanthomonas strain is also referred to as TALome. The DNA-binding domain of TALEs is comprised of highly conserved repeats and TALE genes often occur in gene clusters, which precludes the assembly of TALE-carrying Xanthomonas genomes based on standard sequencing approaches. Here, we report the successful assembly of the 5 Mbp genomes of five Xanthomonas strains from Oxford Nanopore Technologies (ONT) sequencing data. For one of these strains, Xanthomonas oryzae pv. oryzae (Xoo) PXO35, we illustrate why Illumina short reads and longer PacBio reads are insufficient to fully resolve the genome. While ONT reads are perfectly suited to yield highly contiguous genomes, they suffer from a specific error profile within homopolymers. To still yield complete and correct TALomes from ONT assemblies, we present a computational correction pipeline specifically tailored to TALE genes, which yields at least comparable accuracy as Illumina-based polishing. We further systematically assess the ONT-based pipeline for its multiplexing capacity and find that, combined with computational correction, the complete TALome of Xoo PXO35 could have been reconstructed from less than 20,000 ONT reads. Our results indicate that multiplexed ONT sequencing combined with a computational correction of TALE genes constitutes a highly capable tool for characterizing the TALomes of huge collections of Xanthomonas strains in the future.
Genetic and lipidomic identification of tuberculostearic acid as a controller of mycobacterial membrane compartmentalization
Authors: Prithviraj Malavika , Kado Takehiro , Mayfield Jacob A. , Young David C. , Huang Annie D. , Motooka Daisuke , Nakamura Shota , Siegrist M. Sloan , Moody D. Branch , Morita Yasu S. 
Published: August 2022

AbstractMycobacteria diverge in a basic way from other bacterial and eukaryotic cells based on their distinct membrane structures. Here we report genome-wide transposon sequencing to discover the controllers of membrane compartmentalization in Mycobacterium smegmatis. cfa, a gene that encodes a putative cyclopropane-fatty-acyl-phospholipid synthase, shows the most significant effect on recovery from a membrane destabilizer, dibucaine. Lipidomic analysis of cfa deletion mutants demonstrates an essential role of Cfa in the synthesis of specific membrane lipids containing a C19:0 monomethyl-branched stearic acid. This molecule, also known as tuberculostearic acid (TBSA), has been intensively studied for decades due to its high level and genus-specific expression in mycobacteria. The proposed Cfa-mediated conversion of an unsaturation to a methylation matched well with its proposed role in lateral membrane organization, so we used new tools to determine the non-redundant effects of Cfa and TBSA in mycobacterial cells. cfa expression regulated major classes of membrane lipids including phosphatidylinositols, phosphatidylethanolamines and phosphatidylinositol mannosides. Cfa localized within the intracellular membrane domain (IMD), where it controls both cellular growth and recovery from membrane fluidization by facilitating subpolar localization of the IMD. Overall, cfa controls lateral membrane partitioning but does not detectably alter orthogonal transmembrane permeability. More generally, these results support the proposed role of the subpolar IMD as a subcellular site of mycobacterial control of membrane function.SignificanceMycobacteria remain major causes of disease worldwide based in part on their unusual membrane structures, which interface with the host. Here we discover the long sought biosynthetic origin of tuberculostearic acid (TBSA), a major fatty acid found selectively in mycobacteria, as well as its role in mycobacterial cells. The lipid is produced by an enzyme called Cfa, whose loss causes a growth defect and slow reformation of a membrane domain near the pole of the rod-shaped cell. Thus, our study offers mechanistic insights to the intrinsic molecular factors critical for mycobacterial plasma membrane partitioning.