bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of the genetic diversity in RNA-directed RNA polymerase sequences: implications for an automated RNA virus classification system
Authors: Tian Zhongshuai , Hu Tao , Holmes Edward C , Ji Jingkai , Shi Weifeng 
Published: July 2024

Abstract
RNA viruses are characterized by a broad host range and high levels of genetic diversity. Despite a recent expansion in the known virosphere following metagenomic sequencing, our knowledge of the species rank genetic diversity of RNA viruses, and how often they are misassigned and misclassified, is limited. We performed a clustering analysis of 7801 RNA-directed RNA polymerase (RdRp) sequences representing 1897 established RNA virus species. From this, we identified substantial genetic divergence within some virus species and inconsistency in RNA virus assignment between the GenBank database and The International Committee on Taxonomy of Viruses (ICTV). In particular, 27.57% virus species comprised multiple virus operational taxonomic units (vOTUs), including Alphainfluenzavirus influenzae, Mammarenavirus lassaense, Apple stem pitting virus, and Rotavirus A, with each having over 100 vOTUs. In addition, the distribution of average amino acid identity between vOTUs within single assigned species showed a relatively low threshold: &lt;90% and sometimes &lt;50%. However, when only exemplar sequences from virus species were analyzed, 1889 of the ICTV-designated RNA virus species (99.58%) were clustered into a single vOTU. Clustering of the RdRp sequences from different virus species also revealed that 17 vOTUs contained two distinct virus species. These potential misassignments were confirmed by phylogenetic analysis. A further analysis of average nucleotide identity (ANI) values ranging from 70% to 97.5% revealed that at an ANI of 82.5%, 1559 (82.18%) of the 1897 virus species could be correctly clustered into one single vOTU. However, at ANI values &gt;82.5%, an increasing number of species were clustered into two or more vOTUs. In sum, we have identified some inconsistency and misassignment of the RNA virus species based on the analysis of RdRp sequences alone, which has important implications for the development of an automated RNA virus classification system.
Video-Based Coaching for Laparoscopic Salpingectomy
Authors: Muir Teale M. , Pruszynski Jessica , Kho Kimberly A. , Ramirez Christina I. , Donnellan Nicole M. , Chao Lisa 
Published: July 2024

OBJECTIVE:
To evaluate the effect of video-based coaching on the gynecology resident performance of laparoscopic salpingectomy.

METHODS:
PGY-1 and PGY-2 residents were randomized before their gynecology rotations to standard gynecology curriculum (control group) or standard curriculum plus two video-coaching sessions by a fellowship-trained minimally invasive gynecologic surgeon (VBC group). Residents were video recorded intraoperatively performing three unilateral laparoscopic salpingectomies. Participants in the VBC group were coached between the procedures. The primary outcome was the improvement in modified GOALS (Global Operative Assessment of Laparoscopic Skills) and OSA-LS (Objective Structured Assessment of Laparoscopic Salpingectomy) scores, compared with baseline, in the VBC and control groups, with videos independently graded by three blinded minimally invasive gynecologic surgeons. A minimum sample size of 18 participants (nine per group) was needed to achieve 90% power to detect a difference of 5.0 points.

RESULTS:
From October 2021 to December 2022, 28 PGY-1 and PGY-2 residents completed the study with 14 participants per group. Baseline characteristics were similar between groups. In the VBC group, modified GOALS scores significantly improved by 3.0 points from video 1 to video 2 (P=.04) and by 3.2 points from video 1 to video 3 (P=.02). Modified OSA-LS scores also increased significantly in the VBC group, by 6.1 points from video 1 to video 3 (P=.02). In the control group, modified GOALS and OSA-LS scores improved from baseline but were not significant (P=.2, P=.5). Video-based coaching also enhanced resident comfort and confidence in performing laparoscopic surgery.

CONCLUSION:
Video-based coaching improves resident performance of laparoscopic salpingectomy and can be used as an adjunct to resident surgical training.

CLINICAL TRIAL REGISTRATION:

ClinicalTrials.gov, NCT05103449.
Positional End-Point Nystagmus in Patients with Diagnosis of Acute Unilateral Vestibulopathy
Authors: Domínguez-Durán Emilio , Prieto-Sánchez-de-Puerta Lucía , Tena-García Beatriz , Acosta-Mosquera María Eugenia , Sánchez-Gómez Serafín 
Published: July 2024

Introduction
Recently, end-point nystagmus, traditionally observed in an upright position, has been identified in the Dix–Hallpike position among healthy subjects, suggesting a physiological origin.
However, its characteristics in individuals with vestibular hypofunction remain unexplored.

Objective
To elucidate the impact of vestibular hypofunction on the characteristics of positional end-point nystagmus.

Methods
Thirty-one patients diagnosed with acute unilateral vestibulopathy according to Bárány Society criteria were selected. A video head impulse test was conducted in all participants, followed by McClure and Dix–Hallpike maneuvers with and without gaze fixation, and with the initial position of the eye in the straight-ahead position or in the horizontal end-point position. Nystagmus direction, sense, latency, slow-phase velocity, and duration were recorded. The relationship between these characteristics and video head impulse test values was analyzed.

Results
Positional end-point nystagmus was observed in 92.6% of subjects with vestibular hypofunction, significantly more than in healthy individuals. Nystagmus direction varied depending on the performed positional test and on the vestibulo-ocular reflex gains. Gaze occlusion and the initial horizontal end-point position increased its frequency.

Conclusion
Vestibular hypofunction influences the manifestation of positional end-point nystagmus. Recognizing this nystagmus can aid in resolving diagnostic uncertainties and preventing the misdiagnosis of benign paroxysmal positional vertigo in subjects with acute unilateral vestibulopathy.
Urethral Bulking
Authors: Fleischmann Nicole , Chughtai Bilal , Plair Andre , Hurtado Eric , Jacobson Nina , Segal Saya , Panza Joseph , Cichowski Sara B. 
Published: July 2024

Objective
This Clinical Practice Statement aims to provide clinicians with evidence-based guidance for the use of urethral bulking agents (UBAs) in the treatment of stress urinary incontinence (SUI).

Methods
We conducted a structured search of the English literature published from January 1960 to November 2022. Search terms identified studies of both current and historic UBAs. Data extracted at the time of full-text review included type of study, research setting, number of participants, age group, bulking agent, primary outcome, secondary outcome, efficacy, and complications.

Results
One thousand five hundred ninety-four nonduplicate articles were identified using the search criteria. After limiting the article types to randomized control led trials, prospective studies, guideline documents, reviews, meta-analyses, and case reports of complications, 395 studies were screened.

Conclusions
Based on our findings, we propose the following recommendations for clinicians when considering UBA: First, UBA is indicated in cases of demonstrable SUI. Intrinsic sphincter deficiency is not predictive of patient outcomes. Second, patients should be counseled on the risks, lack of long-term efficacy data, potential need for repeat injections, possible need for surgery for recurrent SUI, implications for future procedures, and pelvic imaging findings that may be observed after UBA. Third, UBA may be considered for initial management of SUI. Fourth, UBA is an option for patients with persistent or recurrent SUI after a sling procedure. Fifth, clinicians may prioritize UBA over surgery in specific patient populations. Sixth, polyacrylamide hydrogel demonstrates marginally improved safety and durability data over other available agents.
Impact of Donor Warm Ischemia Time on Graft Survival for Donation After Circulatory Death Kidney Transplantation
Authors: Chumdermpadetsuk Ritah R. , Alvino Donna Marie L. , Kaul Sumedh , Fleishman Aaron , Eckhoff Devin E. , Pavlakis Martha , Lee David D. 
Published: July 2024

Background.
The utilization of kidneys donated after circulatory death (DCD) is an important strategy to address the ongoing shortage of organs suitable for transplantation in the United States. However, the nonuse rate of DCD kidneys remains high compared with kidneys donated after brain death (DBD) because of concerns regarding the injury incurred during donor warm ischemia time (DWIT). Therefore, we investigated the impact of DWIT on the risk of death-censored graft failure after DCD kidney transplantation (KT).

Methods.
Retrospective analysis was conducted on DCD KTs using the Standard Transplant Analysis and Research data set. The association of DWIT with death-censored graft failure was evaluated using multivariable Cox proportional hazard regression, with reference to DCD KTs with Kidney Donor Risk Index (KDRI) of ≤0.78 and the median DWIT of 26 min.

Results.
A total of 28 032 DCD kidney-alone transplants between January 2010 and December 2021 were studied. When stratified by KDRI, increasing DWIT was associated with a clinically significant increased risk for death-censored graft failure only in the subset of kidneys with KDRI >1.14 but not in those with KDRI >0.78–≤0.94 and >0.94–≤1.14, compared with the reference group.

Conclusions.
We suggest that clinicians should not decline kidneys on the basis of DWIT in favor of potential offers of DBD or other DCD kidneys with shorter DWIT, provided that their KDRI scores are within an acceptable limit. Our study highlights opportunities for more efficient usage of DCD kidneys and improving the shortage of transplantable organs.
PairK: Pairwise k-mer alignment for quantifying protein motif conservation in disordered regions
Authors: Halpin Jackson C. , Keating Amy E. 
Published: July 2024

ABSTRACTProtein-protein interactions are often mediated by a modular peptide recognition domain binding to a short linear motif (SLiM) in the disordered region of another protein. The ability to predict domain-SLiM interactions would allow researchers to map protein interaction networks, predict the effects of perturbations to those networks, and develop biologically meaningful hypotheses. Unfortunately, sequence database searches for SLiMs generally yield mostly biologically irrelevant motif matches or false positives. To improve the prediction of novel SLiM interactions, researchers employ filters to discriminate between biologically relevant and improbable motif matches. One promising criterion for identifying biologically relevant SLiMs is the sequence conservation of the motif, exploiting the fact that functional motifs are more likely to be conserved than spurious motif matches. However, the difficulty of aligning disordered regions has significantly hampered the utility of this approach. We present PairK (pairwise k-mer alignment), an MSA-free method to quantify motif conservation in disordered regions. PairK outperforms both standard MSA-based conservation scores and a modern LLM-based conservation score predictor on the task of identifying biologically important motif instances. PairK can quantify conservation over wider phylogenetic distances than MSAs, indicating that SLiMs may be more conserved than is implied by MSA-based metrics. PairK is available as open-source code athttps://github.com/jacksonh1/pairk.
Polygenic Risk Score predicts QTc-prolongation and Short-Term Mortality in Patients using QT-prolonging Psychoactive Medications
Authors: Altaraihi Mays 
Published: July 2024

AbstractBackgroundThere is a genetic component to the QT-interval. This study investigated whether a polygenic risk score for QTc (PRSQTc) could predict ΔQTc and short-term mortality in first-time users of QT-prolonging medications (QTPM) with a known risk of Torsade de Pointes.MethodsFirst-time users of psychoactive QTPM in the Copenhagen Hospital Biobank and the Danish Blood Donor Study from 2009-2021 were included. ΔQTc was calculated and all-cause 30-day mortality following initiation of treatment was explored. All models were adjusted for conventional QT-prolonging risk factors, and models investigating death were additionally adjusted for potential comorbidity confounders.ResultsThe PRSQTccould predict ΔQTc (2.88 milliseconds (ms) for every increase of standard deviation in PRSQTc(P <0.001)) following treatment initiation. Individuals in the top ≥ 80 % of PRSQTchad a higher risk of ΔQTc of ≥60 ms compared to individuals in <80 % PRSQTc(OR = 4.88 P = 0.019). Furthermore, the study has also shown that the shorter QTc before initiation of QTPM, the higher the risk of greater ΔQTc.A high PRSQTccould also predict short-term mortality following treatment initiation: Individuals in the top PRSQTc≥90 % had an odds ratio of 1.84 (P-value = 0.002) for short-term mortality compared to individuals with PRSQTc<90 %. Individuals in the top PRSQTc≥99 % had an odds ratio of 4.95 (P-value = 0.009) for short-term mortality compared to individuals in the <99 % PRSQTcIt could be replicated that PRSQTc≥90 % was a predictor of short-term mortality with OR 1.52 (P-value = 0.002) compared to PRSQTc<90 % in a bigger cohort (N=15.249).ConclusionPRSQTcseems to be predictive of ΔQTc following initiation of treatment. PRSQTcproves to be a sufficient predictor of 30-day mortality after initiation of QT-prolonging psychoactive drugs with a known risk of Torsade de Pointes.If used in a clinical setting, PRSQTmay help prevent sudden cardiac deaths associated with QTPM.
Size control and oscillations of active droplets in synthetic cells
Authors: Sastre Judit , Thatte Advait , Bergmann Alexander M. , Stasi Michele , Tena-Solsona Marta , Weber Christoph A. , Boekhoven Job 
Published: July 2024

AbstractOscillations in the formation and dissolution of molecular assemblies inside living cells are pivotal in orchestrating various cellular functions and processes. However, designing such rhythmic patterns in synthetic cells remains a challenge. Here, we demonstrate the spontaneous emergence of spatio-temporal oscillations in the number of droplets, size, and position within a synthetic cell. The coacervate-based droplets in these synthetic cells sediment and fuse at the cell’s bottom. Through a newly discovered size control mechanism, the sedimented, large droplets shrink by expelling droplet material. The expelled molecules nucleate new droplets at the top of the synthetic cell, which grow and sediment again. These oscillations are sustained by converting chemical fuel into waste and can continue for hundreds of periods without evidence of fatigue. Strikingly, the period of the oscillation is in the minute’s regime and tunable. The design of oscillating organelles in synthetic cells brings us closer to creating more life-like materials andde novolife.
Refinement of theBrassica napusNLRome using RenSeq
Authors: Wu Jiaxu , Mukhopadhyay Soham , Pérez-López Edel 
Published: July 2024

ABSTRACTCanola (Brassica napusL.), a valuable oilseed crop, faces significant challenges from diseases such as clubroot and blackleg, threatening global yields. To improve disease resistance, it’s crucial to accurately annotate nucleotide-binding leucine-rich repeat receptors (NLRs), which are key components of plant immune systems. This study focuses on refining the NLR repertoire (NLRome) of the Westar cultivar using Resistance gene enrichment sequencing (RenSeq). Initially, only 345 NLR genes were identified in the Westar genome annotation, a figure significantly lower than other canola cultivars. By employing RenSeq, we expanded the annotated NLR genes to 715, including 287 full NLRs and 428 partial NLRs, thus providing a more comprehensive understanding of the NLR diversity in this cultivar. Our findings reveal crucial genomic regions with previously misannotated NLR genes and identify key integrated domains that may contribute to enhanced disease resistance. This refined NLRome not only advances the fundamental understanding ofB. napusgenetics but also offers valuable insights for breeding programs and biotechnological applications aimed at improving crop resilience. The data generated in this study is available in public repositories for further research and application.
Cerebellar systems consolidation driven by the temporal dynamics of Purkinje cell excitability
Authors: Seo Jewoo , Kim Yong Gyu , Lee Yong-Seok , Kim Sang Jeong 
Published: July 2024

AbstractSystems consolidation, essential for long-term memory formation, orchestrates the reorganization of newly encoded memories from the cortex into subsequent neural circuitry. While the role of synaptic mechanism in consolidation is well understood, the contribution of neuronal intrinsic excitability (IE) remains relatively unexplored. Herein, we adopted the optokinetic reflex, a cerebellum-dependent learning model, and manipulated IE of the sole output of the cerebellar cortex, Purkinje cells (PCs), to corroborate the direct causality between neuronal IE and memory consolidation. Optogenetic modulation of PC-IE post-learning uncovered a critical temporal window for its role in systems consolidation. Specifically, increasing PC-IE within 90 minutes after learning disrupted memory consolidation, while outside this window, memory retention remained unaffected. Under physiological conditions, PC-IE naturally decreased during this time frame and returned to baseline thereafter. Moreover, abnormally heightened PC-IE eliminated intrinsic plasticity in flocculus-targeting neurons (FTNs) within the medial vestibular nucleus (MVN), a key downstream circuit involved in long-term memory storage. These findings highlight the precise temporal dynamics of IE as a pivotal mechanism in systems consolidation, emphasizing its vulnerability to disruptions.
Broad substrate scope C-C oxidation in cyclodipeptides catalysed by a flavin-dependent filament
Authors: Sutherland Emmajay , Harding Christopher J. , De Bergendal Tancrede Martin Y Du Monceau , Florence Gordon J. , Ackermann Katrin , Bode Bela E. , Synowksy Silvia , Sundaramoorthy Ramasubramanian , Czekster Clarissa Melo 
Published: July 2024

ABSTRACTCyclic dipeptides are produced by organisms in all domains of life. Many possess biological activities as anticancer and antimicrobial compounds. Oxidations are frequently present in these biologically active peptides. C-C bond oxidation is catalysed by tailoring enzymes, including cyclodipeptide oxidases. These flavin-dependent enzymes are underexplored due to their complex three-dimensional arrangement involving multiple copies of two distinct small subunits and unclear mechanistic features underlying substrate selection and catalysis. Here, we determined the structure and mechanism of the cyclodipeptide oxidase from the halophileNocardiopsis dassonvillei(NdasCDO), part of the biosynthetic pathway for nocazine natural products. We showNdasCDO forms filaments in solution with a covalently bound FMN cofactor in the interface between three distinct subunits. The enzyme is promiscuous, using many cyclic dipeptides as substrates in a distributive manner. The reaction is optimal at high pH, involving the formation of a radical intermediate. Pre-steady state kinetics, a sizeable solvent kinetic isotope effect and lack of viscosity effects support that a step coupled to FMN regeneration determines the rate of the reaction. Our work dissects the complex mechanistic and structural features of this dehydrogenation reaction. This sets the stage to utilizingNdasCDO as a biocatalyst and expands the FMN-dependent oxidase family to include enzyme filaments.
MYC and p53 alterations cooperate through VEGF signaling to repress cytotoxic T cell and immunotherapy responses in prostate cancer
Authors: Murphy Katherine C. , DeMarco Kelly D. , Zhou Lin , Lopez-Diaz Yvette , Ho Yu-jui , Li Junhui , Bai Shi , Simin Karl , Zhu Lihua Julie , Mercurio Arthur M. , Ruscetti Marcus 
Published: July 2024

AbstractPatients with castration-resistant prostate cancer (CRPC) are generally unresponsive to tumor targeted and immunotherapies. Whether genetic alterations acquired during the evolution of CRPC impact immune and immunotherapy responses is largely unknown. Using our innovative electroporation-based mouse models, we generated distinct genetic subtypes of CRPC found in patients and uncovered unique immune microenvironments. Specifically, mouse and human prostate tumors withMYCamplification andp53disruption had weak cytotoxic lymphocyte infiltration and an overall dismal prognosis. MYC and p53 cooperated to induce tumor intrinsic secretion of VEGF, which by signaling through VEGFR2 expressed on CD8+T cells, could directly inhibit T cell activity. Targeting VEGF-VEGFR2 signalingin vivoled to CD8+T cell-mediated tumor and metastasis growth suppression and significantly increased overall survival inMYCandp53altered CPRC. VEGFR2 blockade also led to induction of PD-L1, and in combination with PD-L1 immune checkpoint blockade produced anti-tumor efficacy in multiple preclinical CRPC mouse models. Thus, our results identify a genetic mechanism of immune suppression through VEGF signaling in prostate cancer that can be targeted to reactivate immune and immunotherapy responses in an aggressive subtype of CRPC.SignificanceThough immune checkpoint blockade (ICB) therapies can achieve curative responses in many treatment-refractory cancers, they have limited efficacy in CRPC. Here we identify a genetic mechanism by which VEGF contributes to T cell suppression, and demonstrate that VEGFR2 blockade can potentiate the effects of PD-L1 ICB to immunologically treat CRPC.
ETV4 and ETV5 Orchestrate FGF-Mediated Lineage Specification and Epiblast Maturation during Early Mouse Development
Authors: Simon Claire S. , Garg Vidur , Kuo Ying-Yi , Niakan Kathy K. , Hadjantonakis Anna-Katerina 
Published: July 2024

AbstractCell fate decisions in early mammalian embryos are tightly regulated processes crucial for proper development. While FGF signaling plays key roles in early embryo patterning, its downstream effectors remain poorly understood. Our study demonstrates that the transcription factorsEtv4andEtv5are critical mediators of FGF signaling in cell lineage specification and maturation in mouse embryos. We show that loss ofEtv5compromises primitive endoderm formation at pre-implantation stages. Furthermore,Etv4/5deficiency delays naïve pluripotency exit and epiblast maturation, leading to elevated NANOG and reduced OTX2 expression within the blastocyst epiblast. As a consequence of delayed pluripotency progression,Etv4/5deficient embryos exhibit anterior visceral endoderm migration defects post-implantation, a process essential for coordinated embryonic patterning and gastrulation initiation. Our results demonstrate the successive roles of these FGF signaling effectors in early lineage specification and embryonic body plan establishment, providing new insights into the molecular control of mammalian development.Summary statementFGF signaling effectors ETV4/5 regulate lineage specification and embryo patterning in mice, affecting primitive endoderm formation and pluripotency exit.