bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-throughput functional mapping of variants in an arrhythmia gene,KCNE1, reveals novel biology
Authors: Muhammad Ayesha , Calandranis Maria E. , Li Bian , Yang Tao , Blackwell Daniel J. , Harvey M. Lorena , Smith Jeremy E. , Chew Ashli E. , Capra John A. , Matreyek Kenneth A. , Fowler Douglas M. , Roden Dan M. , Glazer Andrew M. 
Published: April 2023

AbstractBackgroundKCNE1encodes a 129-residue cardiac potassium channel (IKs) subunit. KCNE1 variants are associated with long QT syndrome and atrial fibrillation. However, most variants have insufficient evidence of clinical consequences and thus limited clinical utility.ResultsHere, we demonstrate the power of variant effect mapping, which couples saturation mutagenesis with high-throughput sequencing, to ascertain the function of thousands of protein coding KCNE1 variants. We comprehensively assayed KCNE1 variant cell surface expression (2,554/2,709 possible single amino acid variants) and function (2,539 variants). We identified 470 loss-of-surface expression and 588 loss-of-function variants. Out of the 588 loss-of-function variants, only 155 had low cell surface expression. The latter half of the protein is dispensable for protein trafficking but essential for channel function. 22 of the 30 KCNE1 residues (73%) highly intolerant of variation were in predicted close contact with binding partners KCNQ1 or calmodulin. Our data were highly concordant with gold standard electrophysiological data (ρ = −0.65), population and patient cohorts (32/38 concordant variants), and computational metrics (ρ = −0.55). Our data provide moderate-strength evidence for the ACMG/AMP functional criteria for benign and pathogenic variants.ConclusionsComprehensive variant effect maps ofKCNE1can both provide insight into IKschannel biology and help reclassify variants of uncertain significance.
Genome-scale metabolic models consistently predictin vitrocharacteristics ofCorynebacterium striatum
Authors: Bäuerle Famke , Gusak Gwendolyn O. , Camus Laura , Heilbronner Simon , Dräger Andreas 
Published: April 2023

ABSTRACTGenome-scale metabolic models (GEMs) are organism specific knowledge bases which can be used to unravel pathogenicity or improve production of specific metabolites in biotechnology applications. The present work combinesin silicoandin vitroapproaches to create and curate strain-specific genome-scale metabolic models ofCorynebacterium striatum. Approaches towards modeling rarely studied organisms are scarce. We introduce a cost-effective and easy experimental protocol which can be adapted to other organisms as well. Furthermore, the comparability of growth kinetics andin silicogrowth rates is discussed. This work introduces five newly created strain-specific genome-scale metabolic models (GEMs) of high quality, satisfying all contemporary standards and requirements. All these models have been benchmarked using the community standard test suite Metabolic Model Testing (MEMOTE) and experimentally validated by laboratory experiments conducted specifically for this purpose. For the curation of those models, the software infrastructurerefineGEMswas developed to work on these models in parallel and to comply with the quality standards for GEMs. The model predictions were confirmed by experimental data and a new comparison metric based on the doubling time was developed to quantify bacterial growth. Future modeling projects can rely on the proposed software, which is independent of specific environmental conditions. The validation approach based on the growth rate calculation is now accessible and closely aligned with biological questions. The curated models are freely available via BioModels and a GitHub repository and can be used. The open-source software refineGEMs is available fromhttps://github.com/draeger-lab/refinegems.
A Novel Risk Assessment Model Predicts Major Bleeding Risk at Admission in Medical Inpatients
Authors: Mittman Benjamin G , Sheehan Megan , Kojima Lisa , Cassachia Nicholas , Lisheba Oleg , Hu Bo , Pappas Matthew , Rothberg Michael B. 
Published: May 2023

AbstractBackgroundVenous thromboembolism (VTE) is the leading cause of preventable hospital death in the US. Guidelines from the American College of Chest Physicians and American Society for Hematology recommend providing pharmacological VTE prophylaxis to acutely or critically ill medical patients at acceptable bleeding risk, but there is currently only one validated risk assessment model (RAM) for estimating bleeding risk. We developed a RAM using risk factors at admission and compared it with the International Medical Prevention Registry on Venous Thromboembolism (IMPROVE) model.MethodsA total of 46,314 medical patients admitted to a Cleveland Clinic Health System hospital from 2017-2020 were included. Data were split into training (70%) and validation (30%) sets with equivalent bleeding event rates in each set. Potential risk factors for major bleeding were identified from the IMPROVE model and literature review. Penalized logistic regression using LASSO was performed on the training set to select and regularize important risk factors for the final model. The validation set was used to assess model calibration and discrimination and compare performance with IMPROVE. Bleeding events and risk factors were confirmed through chart review.ResultsThe incidence of major in-hospital bleeding was 0.58%. Active peptic ulcer (OR = 5.90), prior bleeding (OR = 4.24), and history of sepsis (OR = 3.29) were the strongest independent risk factors. Other risk factors included age, male sex, decreased platelet count, increased INR, increased PTT, decreased GFR, ICU admission, CVC or PICC placement, active cancer, coagulopathy, and in-hospital antiplatelet drug, steroid, or SSRI use. In the validation set, the Cleveland Clinic Bleeding Model (CCBM) had better discrimination than IMPROVE (0.86 vs. 0.72, p < .001) and, at equivalent sensitivity (54%), categorized fewer patients as high-risk (6.8% vs. 12.1%, p < .001).ConclusionsFrom a large population of medical inpatients, we developed and validated a RAM to accurately predict bleeding risk at admission. The CCBM may be used in conjunction with VTE risk calculators to decide between mechanical and pharmacological prophylaxis for at-risk patients.
1,25-dihydroxyvitamin D3 potentiates the innate immune response of peripheral blood mononuclear cells from Japanese Black cattle
Authors: Oyamada Youki , Iizasa Ei’ichi , Usa Amane , Otomaru Konosuke 
Published: April 2023

Abstract1,25-dihydroxyvitamin D3(1,25(OH)2D3), a bioactive Vitamin D, is known to regulate immune responses in mammals. However, its impact on the innate immune responses of Japanese Black cattle, which are beef cattle endemic to Japan, remains unknown. Thus, in this study, we investigated the effect of 1,25(OH)2D3on the immune responses of PBMC from Japanese Black cattle. PBMC were cultured with or without 1,25(OH)2D3for measurement of cell viability, and stimulated with or without 1,25(OH)2D3and lipopolysaccharide (LPS) for measurement of the gene expressions. As the results, the treatment of 1,25(OH)2D3increased the cell viability. It also upregulated antibacterial peptides,DEFB10andLAPwith or without LPS stimulation. Moreover, 1,25(OH)2D3enhanced the inflammatory responses,CXCL8with LPS stimulation andNOS2with or without LPS stimulation, while reducing the expression of anti-inflammatory cytokineIL10 with or without LPS stimulation, leading to an inflammatory phenotype. However, in contrast to humans and mice, 1,25(OH)2D3did not alter the expression ofTNFand downregulatedTREM1with LPS treatment. These results suggest that 1,25(OH)2D3potentiates the innate immune responses of Japanese Black cattle, albeit with different effects and mechanisms as compared to humans and mice.
Building alternative splicing and evolution-aware sequence-structure maps for protein repeats
Authors: Szatkownik Antoine , Zea Diego Javier , Richard Hugues , Laine Elodie 
Published: April 2023

AbstractAlternative splicing of repeats in proteins provides a mechanism for rewiring and fine-tuning protein interaction networks. In this work, we developed a robust and versatile method, ASPRING, to identify alternatively spliced protein repeats from gene annotations. ASPRING leverages evolutionary meaningful alternative splicing-aware hierarchical graphs to provide maps between protein repeats sequences and 3D structures. We re-think the definition of repeats by explicitly accounting for transcript diversity across several genes/species. Using a stringent sequence-based similarity criterion, we detected over 5,000 evolutionary conserved repeats by screening virtually all human protein-coding genes and their orthologs across a dozen species. Through a joint analysis of their sequences and structures, we extracted specificity-determining sequence signatures and assessed their implication in experimentally resolved and modelled protein interactions. Our findings demonstrate the widespread alternative usage of protein repeats in modulating protein interactions and open avenues for targeting repeat-mediated interactions.HighlightsRobust detection of alternatively used repeated protein regions in evolutionThe approach relies on sequence similarity and identifies conserved signaturesMapping of the repeats onto protein isoform 3D models predicted by AlphaFold5 000 repeats detected over the human coding fraction, about one third disorderedAssessment of the structural coverage of their interactions with protein partners
Only Zn2+and Fe2+out of 12 cations can fold ALS-linked nascent hSOD1
Authors: Lim Liangzhong , Kang Jian , Song Jianxing 
Published: April 2023

Abstract153-residue copper-zinc superoxide dismutase 1 (hSOD1) is the first gene whose mutation was linked to FALS, while wild-type hSOD1 aggregation is associated with SALS. So far >180 ALS-causing mutations have been identified within hSOD1, but the underlying mechanism still remains enigmatic. Mature hSOD1 is extremely stable constrained by a disulfide bridge to adopt a Greek-key β-barrel fold that houses copper and zinc cofactors. Conversely, nascent hSOD1 is unfolded and prone to aggregation, requiring Zn2+to initiate folding to a coexistence of folded and unfolded states. Recent studies demonstrate mutations disrupting Zn2+-binding correlate with their capacity to form toxic aggregates. Therefore, to decode the role of cations in hSOD1 folding provide not only mechanistic insights, but also therapeutic prospects for hSOD1-linked ALS. Here by NMR, we visualized the effect of 12 cations, encompassing 8 essential for humans (Na+, K+, Ca2+, Zn2+, Mg2+, Mn2+,Cu2+,Fe2+), 3 mimicking zinc (Ni2+, Cd2+, Co2+), and environmentally abundant Al3+. Surprisingly, most cations, including Zn2+-mimics, exhibited negligible binding or induction for folding of nascent hSOD1. Cu2+displayed extensive binding to the unfolded state but induced severe aggregation. Unexpectedly, here for the first time Fe2+was deciphered to have Zn2+-like folding-inducing ability. Surprisingly, Zn2+failed to induce folding of H80S/D83S-hSOD1, while Fe2+could. By contrast, Zn2+could trigger folding of G93A-hSOD1, but Fe2+failed. Notably, pre-existing Fe2+disrupted the Zn2+-induced folding of G93A-hSOD1. Comparing with ATP-induced folded state, our results delineate that hSOD1 maturation requires: 1) intrinsic folding capacity encoded by the sequence; 2) specific Zn2+-coordination; 3) disulfide formation and Cu-load catalyzed by hCCS. This study decodes a previously-unknown interplay of cations in controlling the initial folding of hSOD1, thus not only underscoring the critical role of Zn2+in hSOD1-associated ALS, but also suggesting novel hSOD1-dependent mechanisms for Cu2+/Fe2+-induced cytotoxicity likely relevant to other diseases and aging.
Detection of Ghost Introgression from Phylogenomic Data Requires a Full-Likelihood Approach
Authors: Pang Xiao-Xu , Zhang Da-Yong 
Published: April 2023

AbstractIn recent years, the study of hybridization and introgression has made significant progress, with ghost introgression - the transfer of genetic material from extinct or unsampled lineages to extant species - emerging as a key area for research. Accurately identifying ghost introgression, however, presents a challenge. To address this issue, we focused on simple cases involving three species with a known phylogenetic tree. Using mathematical analyses and simulations, we evaluated the performance of popular phylogenetic methods, including HyDe and PhyloNet/MPL, and the full-likelihood method, Bayesian Phylogenetics and Phylogeography (BPP), in detecting ghost introgression. Our findings suggest that heuristic approaches relying on site patterns or gene tree topologies struggle to differentiate ghost introgression from introgression between sampled non-sister species, frequently leading to incorrect identification of donor and recipient species. The full-likelihood method BPP using multilocus sequence alignments, by contrast, is capable of detecting ghost introgression in phylogenomic datasets. We analyzed a real-world phylogenomic dataset of 14 species ofJaltomata(Solanaceae) to showcase the potential of full-likelihood methods for accurate inference of introgression.
The phospholipid biosynthesis enzyme PlsB contains three distinct domains for membrane association, lysophosphatidic acid synthesis and dimerization
Authors: Li Yumei , Li Anjie , Liu Zhenfeng 
Published: April 2023

AbstractBiosynthesis of phospholipids is fundamental for membrane biogenesis in all living organisms. As a member of the Glycerol-3-phosphate (G3P) Acyltransferase (GPAT) family, PlsB is a crucial enzyme catalyzing the first step of phospholipid synthesis by converting G3P and fatty acyl-coenzyme A (CoA)/acyl-carrier protein (ACP) into lysophosphatidic acid and free CoA (CoASH)/ACP. In bacterial cells, PlsB participates in the formation of persister cells related to multidrug tolerance, and is hence considered as a potential target for anti-persister therapy. By using the single-particle cryo-electron microscopy (cryo-EM) method, we have solved the structure of full-length PlsB fromThemomonas haemolytica(ThPlsB) at 2.79 Å resolution. TheThPlsB protein forms a homodimer withC2 symmetry and each monomer contains three distinct domains, namely the amino-terminal domain (NTD), the middle catalytic domain (MCD) and the carboxy-terminal domain (CTD). For the first time, we have unraveled the binding sites of a fatty acyl-CoA and a 1,2-dioleoyl-sn-glycero-3-phosphate (DOPA) molecule in the MCD of PlsB. The interactions betweenThPlsB and the membrane involve two surface-exposed amphipathic regions located in the NTD and MCD respectively. The results of structural and biochemical analyses suggest a membrane surface association-catalysis coupling model for the PlsB-mediated biosynthesis of lysophosphatidic acid occurring at the membrane-cytosol interface.
The relationship between hyperglycaemia on admission and patient outcome is modified by hyperlactatemia and diabetic status: a retrospective analysis of the eICU collaborative research database
Authors: Fitzgerald Oisin , Perez-Concha Oscar , Gallego-Luxan Blanca , Rudd Lachlan , Jorm Louisa 
Published: May 2023

AbstractBoth blood glucose and lactate are well-known predictors of organ dysfunction and mortality in critically ill patients. Previous research has shown that concurrent adjustment for glucose and lactate modifies the relationship between these variables and patient outcomes, including blunting of the association between blood glucose and patient outcome. We aim to investigate the relationship between ICU admission blood glucose and hospital mortality while accounting for lactate and diabetic status. Across 43,250 ICU admissions, weighted to account for missing data, we assessed the predictive ability of several logistic regression and generalised additive models that included blood glucose, blood lactate and diabetic status. We found that inclusion of blood glucose marginally improved predictive performance in all patients: AUC-ROC 0.665 vs 0.659, with a greater degree of improvement seen in non- diabetics: AUC-ROC 0.675 vs 0.663. Inspection of the estimated risk profiles revealed the standard U-shaped risk profile for blood glucose was only present in non-diabetic patients after controlling for blood lactate levels. Future research should aim to utilise observational data to estimate whether interventions such as insulin further modify this effect, with the goal of informing future RCTs of interventions targeting glycaemic control in the ICU.
No Laughing White Matter: Cortical Cholinergic Pathways and Cognitive Decline in Parkinson’s Disease
Authors: Crockett Rachel A. , Wilkins Kevin B. , Aditham Sudeep , Brontë-Stewart Helen M. 
Published: May 2023

AbstractBackgroundApproximately one third of recently diagnosed Parkinson’s disease (PD) patients experience cognitive decline. The nucleus basalis of Meynert (NBM) degenerates early in PD and is crucial for cognitive function. The two main NBM white matter pathways include a lateral and medial trajectory. However, research is needed to determine which pathway, if any, are associated with PD-related cognitive decline.MethodsThirty-seven PD patients with no mild cognitive impairment (MCI) were included in this study. Participants either developed MCI at 1-year follow up (PD MCI-Converters; n=16) or did not (PD no-MCI; n=21). Mean diffusivity (MD) of the medial and lateral NBM tracts were extracted using probabilistic tractography. Between-group differences in MD for each tract was compared using ANCOVA, controlling for age, sex, and disease duration. Control comparisons of the internal capsule MD were also performed. Associations between baseline MD and cognitive outcomes (working memory, psychomotor speed, delayed recall, and visuospatial function) were assessed using linear mixed models.ResultsPD MCI-Converters had significantly greater MD of both NBM tracts compared to PD no-MCI (p<.001). No difference was found in the control region (p=.06). Trends were identified between: 1) lateral tract MD, poorer visuospatial performance (p=.05) and working memory decline (p=.04); and 2) medial tract MD and reduced psychomotor speed (p=.03).ConclusionsReduced integrity of the NBM tracts is evident in PD patients up to one year prior to the development of MCI. Thus, deterioration of the NBM tracts in PD may be an early marker of those at risk of cognitive decline.
Disturbed laterality of non-rapid eye movement sleep oscillations in post-stroke human sleep: a pilot study
Authors: Simpson Benjamin K. , Rangwani Rohit , Abbasi Aamir , Chung Jeffrey M. , Reed Chrystal M. , Gulati Tanuj 
Published: May 2023

AbstractSleep is known to promote recovery post-stroke. However, there is a paucity of data profiling sleep oscillations post-stroke in the human brain. Recent rodent work showed that resurgence of physiologic spindles coupled to sleep slow oscillations(SOs) and concomitant decrease in pathological delta(δ) waves is associated with sustained motor performance gains during stroke recovery. The goal of this study was to evaluate bilaterality of non-rapid eye movement (NREM) sleep-oscillations (namely SOs,δ-waves, spindles and their nesting) in post-stroke patients versus healthy control subjects. We analyzed NREM-marked electroencephalography (EEG) data in hospitalized stroke-patients (n=5) and healthy subjects (n=3) from an open-sourced dataset. We used a laterality index to evaluate symmetry of NREM oscillations across hemispheres. We found that stroke subjects had pronounced asymmetry in the oscillations, with a predominance of SOs,δ-waves, spindles and nested spindles in one hemisphere, when compared to the healthy subjects. Recent preclinical work classified SO-nested spindles as restorative post-stroke andδ-wave-nested spindles as pathological. We found that the ratio of SO-nested spindles laterality index toδ-wave-nested spindles laterality index was lower in stroke subjects. Using linear mixed models (which included random effects of concurrent pharmacologic drugs), we found large and medium effect size forδ-wave nested spindle and SO-nested spindle, respectively. Our results indicate considering laterality index of NREM oscillations might be a useful metric for assessing recovery post-stroke and that factoring in pharmacologic drugs may be important when targeting sleep modulation for neurorehabilitation post-stroke.
Predicting Virus Fitness: Towards a structure-based computational model
Authors: Thakur Shivani , Kepp Kasper Planeta , Mehra Rukmankesh 
Published: May 2023

AbstractPredicting the impact of new emerging virus mutations is of major interest in surveillance and for understanding the evolutionary forces of the pathogen. The SARS-CoV-2 surface spike-protein (S-protein) binds to human ACE2 receptors as a critical step in host cell infection. At the same time, S-protein binding to human antibodies neutralizes the virus and prevents interaction with ACE2. Here we combine these two binding properties in a simple virus fitness model, using structure-based computation of all possible mutation effects averaged over 10 ACE2 complexes and 10 antibody complexes of the S-protein (∼3,80,000 computed mutations), and validated the approach against diverse experimental binding/escape data of ACE2 and antibodies. The ACE2-antibody selectivity change caused by mutation (i.e., the differential change in binding to ACE2 vs. immunity-inducing antibodies) is proposed to be a key metric of fitness model, enabling systematic error cancelation when evaluated. In this model, new mutations become fixated if they increase the selective binding to ACE2 relative to circulating antibodies, assuming that both are present in the host in a competitive binding situation. We use this model to categorize viral mutations that may best reach ACE2 before being captured by antibodies. Our model may aid the understanding of variant-specific vaccines and molecular mechanisms of viral evolution in the context of a human host.