bluuebunny/crossref_metadata_2025_split huggingface dataset:
MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database
Authors: Shao Xinhao , Gomez Clarissa D , Kapoor Nandini , Considine James M , Grams Christopher , Gao Yu (Tom) , Naba Alexandra 
Published: November 2022

Abstract
The extracellular matrix (ECM) is a complex assembly of proteins that constitutes the scaffold organizing cells, tissues, and organs. Over the past decade, mass-spectrometry-based proteomics has become the method of choice to profile the composition of the ECM, or the matrisome, of tissues. To assist non-specialists with the reuse of ECM proteomic datasets, we released MatrisomeDB (https://matrisomedb.org) in 2020. Here, we report the expansion of the database to include 25 new curated studies on the ECM of 24 new tissues in addition to datasets on tissues previously included, more than doubling the size of the original database and achieving near-complete coverage of the in-silico predicted matrisome. We further enhanced data visualization by maps of peptides and post-translational-modifications detected onto domain-based representations and 3D structures of ECM proteins. We also referenced external resources to facilitate the design of targeted mass spectrometry assays. Last, we implemented an abstract-mining tool that generates an enrichment word cloud from abstracts of studies in which a queried protein is found with higher confidence and higher abundance relative to other studies in MatrisomeDB.
The European Nucleotide Archive in 2022
Authors: Burgin Josephine , Ahamed Alisha , Cummins Carla , Devraj Rajkumar , Gueye Khadim , Gupta Dipayan , Gupta Vikas , Haseeb Muhammad , Ihsan Maira , Ivanov Eugene , Jayathilaka Suran , Balavenkataraman Kadhirvelu Vishnukumar , Kumar Manish , Lathi Ankur , Leinonen Rasko , Mansurova Milena , McKinnon Jasmine , O’Cathail Colman , Paupério Joana , Pesant Stéphane , Rahman Nadim , Rinck Gabriele , Selvakumar Sandeep , Suman Swati , Vijayaraja Senthilnathan , Waheed Zahra , Woollard Peter , Yuan David , Zyoud Ahmad , Burdett Tony , Cochrane Guy 
Published: November 2022

Abstract
The European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena), maintained by the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI), offers those producing data an open and supported platform for the management, archiving, publication, and dissemination of data; and to the scientific community as a whole, it offers a globally comprehensive data set through a host of data discovery and retrieval tools. Here, we describe recent updates to the ENA’s submission and retrieval services as well as focused efforts to improve connectivity, reusability, and interoperability of ENA data and metadata.
The initiation factor 3 (IF3) residues interacting with initiator tRNA elbow modulate the fidelity of translation initiation and growth fitness in Escherichia coli
Authors: Singh Jitendra , Mishra Rishi Kumar , Ayyub Shreya Ahana , Hussain Tanweer , Varshney Umesh 
Published: November 2022

Abstract
Initiation factor 3 (IF3) regulates the fidelity of bacterial translation initiation by debarring the use of non-canonical start codons or non-initiator tRNAs and prevents premature docking of the 50S ribosomal subunit to the 30S pre-initiation complex (PIC). The C-terminal domain (CTD) of IF3 can carry out most of the known functions of IF3 and sustain Escherichia coli growth. However, the roles of the N-terminal domain (NTD) have remained unclear. We hypothesized that the interaction between NTD and initiator tRNAfMet (i-tRNA) is essential to coordinate the movement of the two domains during the initiation pathway to ensure fidelity of the process. Here, using atomistic molecular dynamics (MD) simulation, we show that R25A/Q33A/R66A mutations do not impact NTD structure but disrupt its interaction with i-tRNA. These NTD residues modulate the fidelity of translation initiation and are crucial for bacterial growth. Our observations also implicate the role of these interactions in the subunit dissociation activity of CTD of IF3. Overall, the study shows that the interactions between NTD of IF3 and i-tRNA are crucial for coupling the movements of NTD and CTD of IF3 during the initiation pathway and in imparting growth fitness to E. coli.
Enteroviral 2C protein is an RNA-stimulated ATPase and uses a two-step mechanism for binding to RNA and ATP
Authors: Yeager Calvin , Carter Griffin , Gohara David W , Yennawar Neela H , Enemark Eric J , Arnold Jamie J , Cameron Craig E 
Published: November 2022

Abstract
The enteroviral 2C protein is a therapeutic target, but the absence of a mechanistic framework for this enzyme limits our understanding of inhibitor mechanisms. Here, we use poliovirus 2C and a derivative thereof to elucidate the first biochemical mechanism for this enzyme and confirm the applicability of this mechanism to other members of the enterovirus genus. Our biochemical data are consistent with a dimer forming in solution, binding to RNA, which stimulates ATPase activity by increasing the rate of hydrolysis without impacting affinity for ATP substantially. Both RNA and DNA bind to the same or overlapping site on 2C, driven by the phosphodiester backbone, but only RNA stimulates ATP hydrolysis. We propose that RNA binds to 2C driven by the backbone, with reorientation of the ribose hydroxyls occurring in a second step to form the catalytically competent state. 2C also uses a two-step mechanism for binding to ATP. Initial binding is driven by the α and β phosphates of ATP. In the second step, the adenine base and other substituents of ATP are used to organize the active site for catalysis. These studies provide the first biochemical description of determinants driving specificity and catalytic efficiency of a picornaviral 2C ATPase.
New constraints on exotic spin-dependent interactions with an ensemble-NV-diamond magnetometer
Authors: Liang Hang , Jiao Man , Huang Yue , Yu Pei , Ye Xiangyu , Wang Ya , Xie Yijin , Cai Yi-Fu , Rong Xing , Du Jiangfeng 
Published: November 2022

ABSTRACT
Laboratory search of exotic interactions is crucial for exploring physics beyond the standard model. We report new experimental constraints on two exotic spin-dependent interactions at the micrometer scale based on ensembles of nitrogen-vacancy (NV) centers in diamond. A thin layer of NV electronic spin ensembles is synthesized as the solid-state spin quantum sensor, and a lead sphere is taken as the interacting nucleon source. Our result establishes new bounds for two types of exotic spin interactions at the micrometer scale. For an exotic parity-odd spin- and velocity-dependent interaction, improved bounds are set within the force range from 5 to 500 μm. The upper limit of the corresponding coupling constant $g_A^eg_V^N$ at 330 μm is more than 1000-fold more stringent than the previous constraint. For the P, T-violating scalar-pseudoscalar nucleon-electron interaction, improved constraints are established within the force range from 6 to 45 μm. The limit of the corresponding coupling constant $g_S^Ng_P^e$ is improved by more than one order of magnitude at 30 μm. This work demonstrates that a solid-state NV ensemble can be a powerful platform for probing exotic spin-dependent interactions.
Learning physics-consistent particle interactions
Authors: Han Zhichao , Kammer David S , Fink Olga 
Published: November 2022

Abstract
Interacting particle systems play a key role in science and engineering. Access to the governing particle interaction law is fundamental for a complete understanding of such systems. However, the inherent system complexity keeps the particle interaction hidden in many cases. Machine learning methods have the potential to learn the behavior of interacting particle systems by combining experiments with data analysis methods. However, most existing algorithms focus on learning the kinetics at the particle level. Learning pairwise interaction, e.g., pairwise force or pairwise potential energy, remains an open challenge. Here, we propose an algorithm that adapts the Graph Networks framework, which contains an edge part to learn the pairwise interaction and a node part to model the dynamics at particle level. Different from existing approaches that use neural networks in both parts, we design a deterministic operator in the node part that allows to precisely infer the pairwise interactions that are consistent with underlying physical laws by only being trained to predict the particle acceleration. We test the proposed methodology on multiple datasets and demonstrate that it achieves superior performance in inferring correctly the pairwise interactions while also being consistent with the underlying physics on all the datasets. While the previously proposed approaches are able to be applied as simulators, they fail to infer physically consistent particle interactions that satisfy Newton’s laws. Moreover, the proposed physics-induced graph network for particle interaction also outperforms the other baseline models in terms of generalization ability to larger systems and robustness to significant levels of noise. The developed methodology can support a better understanding and discovery of the underlying particle interaction laws, and hence, guide the design of materials with targeted properties.
HOXA5 is a key regulator of class 3 semaphorins expression in the synovium of rheumatoid arthritis patients
Authors: Martínez-Ramos Sara , Rafael-Vidal Carlos , Malvar-Fernández Beatriz , Rodriguez-Trillo Angela , Veale Douglas , Fearon Ursula , Conde Carmen , Conde-Aranda Javier , Radstake Timothy R D J , Pego-Reigosa Jose María , Reedquist Kris A , García Samuel 
Published: November 2022

Abstract

Objective
Class 3 semaphorins are reduced in the synovial tissue of RA patients and these proteins are involved in the pathogenesis of the disease. The aim of this study was to identify the transcription factors involved in the expression of class 3 semaphorins in the synovium of RA patients.

Methods
Protein and mRNA expression in synovial tissue from RA and individuals at risk (IAR) patients, human umbilical vein endothelial cells (HUVEC) and RA fibroblast-like synoviocytes (FLS) was determined by ELISA, immunoblotting and quantitative PCR. TCF-3, EBF-1 and HOXA5 expression was knocked down using siRNA. Cell viability, migration and invasion were determined using MTT, calcein, wound closure and invasion assays, respectively.

Results
mRNA expression of all class 3 semaphorins was significantly lower in the synovium of RA compared with IAR patients. In silico analysis suggested TCF-3, EBF-1 and HOXA5 as transcription factors involved in the expression of these semaphorins. TCF-3, EBF-1 and HOXA5 silencing significantly reduced the expression of several class 3 semaphorin members in FLS and HUVEC. Importantly, HOXA5 expression was significantly reduced in the synovium of RA compared with IAR patients and was negatively correlated with clinical disease parameters. Additionally, TNF-α down-regulated the HOXA5 expression in FLS and HUVEC. Finally, HOXA5 silencing enhanced the migratory and invasive capacities of FLS and the viability of HUVEC.

Conclusion
HOXA5 expression is reduced during the progression of RA and could be a novel therapeutic strategy for modulating the hyperplasia of the synovium, through the regulation of class 3 semaphorins expression.
Serial changes in renal indices in chronic HCV patients with and without HIV co-infection receiving sofosbuvir and tenofovir-based therapies
Authors: Abdel Alem Shereen , El Garhy Naeema , El Khateeb Engy , Khalil Mahmoud , Cordie Ahmed , Elsharkawy Aisha , Fouad Rabab , Esmat Gamal , Abdelbary Mohammad Salah 
Published: November 2022

AbstractBackgroundSofosbuvir (SOF) is authorized for hepatitis C virus (HCV) patients. The nephrotoxicity of SOF on HCV mono-infected and HCV–human immunodeficiency virus (HIV) individuals receiving antiretroviral therapy (ART) remains controversial.MethodsA prospective study including 159 HCV mono-infected and 124 HCV–HIV individuals (47 were ART naïve and 77 were tenofovir [TDF]-based ART) who presented with an estimated glomerular filtration rate (eGFR) ≥30 ml/min/1.73 m2 at baseline and were treated with SOF–daclatasvir for 12 weeks. The eGFR was estimated using the Chronic Kidney Disease Epidemiology Collaboration equation over the study period.ResultsHCV patients had a progressive decline in median levels of eGFR compared with HCV–HIV patients who were ART naïve and those receiving TDF-based ART during and after discontinuing SOF–DAC treatment (96, 109 and 114 at baseline vs 94, 117 and 108 at the end of treatment [EOT]) vs 95, 114 and 115 ml/min/1.73 m2 at 12 weeks after treatment [SVR12], respectively). Moreover, the rate of eGFR stage worsening was more pronounced in HCV mono-infected compared with HCV–HIV individuals who were ART naïve and those receiving TDF-based ART (21.4% vs 8.5% and 14.3% at EOT; 21.4% vs 2.1% and 6.5% at SVR12, respectively). Multivariable regression analysis showed that baseline variables were not independent predictors of eGFR stage worsening either at EOT or SVR12.ConclusionsBecause the changes in eGFR were minimal and not of clinical significance, and TDF was not associated with an increase in renal dysfunction, SOF-based direct-acting antivirals could be safely used in HCV mono-infected and HCV–HIV individuals, even in those on TDF-based ART.
Cochlear Implantation in Children with Enlarged Vestibular Aqueduct: A Systematic Review of Surgical Implications and Outcomes
Authors: Hansen Marie-Louise Uhre , Rye Rasmussen Eva , Cayé-Thomasen Per , Mey Kristianna 
Published: November 2022

Objectives:
This study investigated age at implantation, improvement in hearing and speech perception outcomes, as well as surgical complications in pediatric cochlear implant recipients with Pendred Syndrome (PS) or non-syndromic enlarged vestibular aqueduct (NSEVA).

Design:
A systematic review of the literature between 1984 and 2021 was performed. Two independent reviewers performed abstract and full-text screening using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines. The inclusion criteria were: English language, cochlear implant, age at implantation available, age <18 years, PS, Mondini malformation, and enlarged vestibular aqueduct. Full-text analysis was completed using the National Institute of Health assessment tool for case series and case-control studies. Studies were also graded according to the Oxford Centre for Evidence-Based Medicine grading system.

Results:
In total, 198 studies were identified and screened, and 55 studies were included for analysis. Audiological outcomes were available in 46 studies, and the four-frequency pure-tone audiogram average improved by 60 to 78 dB HL due to cochlear implantation. Auditory performance and speech intelligibility scores increased by 44%. The overall average implantation age was 60 months. The implantation age was 21 months lower in the studies where individuals were implanted after the year 2000 compared with those implanted before the year 2000. Perilymph gusher/oozing was the most common surgical incident reported, occurring in 187 of 1572 implantations.

Conclusions:
In children with PS/NSEVA, cochlear implantation improves pure-tone average by 60 to 78 dB HL and capacity of auditory performance/speech intelligibility by 44%. The implantation age for these children has decreased during the last two decades but is still somewhat higher than reported for unselected pediatric cochlear implantation. Perilymph gusher/oozing is the most common surgical complication.
Predictors of National Physical Therapy Examination Failure in Graduates of a Blended Doctor of Physical Therapy Program
Authors: Lazinski Melissa J. , Rockefeller Kathleen , Cheng M. Samuel 
Published: November 2022

Introduction:
Passing the National Physical Therapy Examination (NPTE) is a necessary step in progressing into a professional career. The purpose of this study was to identify student factors that predicted failure on the first attempt of the NPTE in graduates of a blended Doctor of Physical Therapy (DPT) program.

Review of Literature:
Student factors that may affect NPTE outcomes have been studied in traditional physical therapist education programs but have not been studied in blended programs. Blended instruction is a delivery format that combines distance asynchronous learning and face-to-face synchronous learning in a complementary way.

Subjects:
Two hundred ten graduates from 6 consecutive cohorts of a DPT program taught in a blended format.

Methods.
Retrospective observational cohort design. Demographic, preadmission, and in-program academic data and NPTE pass/fail status were collected. Variables were analyzed with forward stepwise logistic regression for their ability to predict first-time NPTE failure. Receiver operating characteristic curves were plotted to determine cut points of predictive variables.

Results.
Two regression analyses were conducted. First, an analysis of all variables identified 3 significant predictors: comprehensive examination score, cumulative third-year grade point average, and Graduate Record Examination Verbal Reasoning (GRE-V) score, which explained 43.2% of the variance. The second analysis excluded variables occurring late in matriculation to identify early occurring predictors. This yielded 2 early predictive variables, GRE-V score and academic difficulty, which explained 29.5% of the variance.

Discussion and Conclusion.
To our knowledge, this is the first study of predictors of NPTE outcomes in blended DPT program graduates. Like previous studies, a mix of preadmission and in-program factors predicted first-time NPTE failure. These findings may help inform admissions policies, academic advising processes, and academic warning policies in blended programs. Future research is needed to explore factors unique to blended educational settings and the qualities of the students they attract.
End-of-Life in Pediatric Patients Supported by Ventricular Assist Devices: A Network Database Cohort Study
Authors: Hollander Seth A. , Pyke-Grimm Kimberly A. , Shezad Muhammad F. , Zafar Farhan , Cousino Melissa K. , Feudtner Chris , Char Danton S. 
Published: November 2022

OBJECTIVES:
Most pediatric patients on ventricular assist device (VAD) survive to transplantation. Approximately 15% will die on VAD support, and the circumstances at the end-of-life are not well understood. We, therefore, sought to characterize patient location and invasive interventions used at the time of death.

DESIGN:
Retrospective database study of a cohort meeting inclusion criteria.

SETTING:
Thirty-six centers participating in the Advanced Cardiac Therapies Improving Outcomes Network (ACTION) Registry.

PATIENTS:
Children who died on VAD therapy in the period March 2012 to September 2021.

INTERVENTIONS:
None.

MEASUREMENTS AND MAIN RESULTS:
Of the 117 of 721 patients (16%) who died on VAD, the median (interquartile range) age was 5 years (1–16 yr) at 43 days (17–91 d) postimplant. Initial goals of therapy were bridge to consideration for candidacy for transplantation in 60 of 117 (51%), bridge to transplantation in 44 of 117 (38%), bridge to recovery 11 of 117 (9%), or destination therapy (i.e., VAD as the endpoint) in two of 117 (2%). The most common cause of death was multiple organ failure in 35 of 117 (30%), followed by infection in 12 of 117 (10%). Eighty-five of 92 (92%) died with a functioning device in place. Most patients were receiving invasive interventions (mechanical ventilation, vasoactive infusions, etc.) at the end of life. Twelve patients (10%) died at home.

CONCLUSIONS:
One-in-six pediatric VAD patients die while receiving device support, with death occurring soon after implant and usually from noncardiac causes. Aggressive interventions are common at the end-of-life. The ACTION Registry data should inform future practices to promote informed patient/family and clinician decision-making to hopefully reduce suffering at the end-of-life.
Evaluation of Inferior Intercavernous Sinus in Patients With Pituitary Microadenoma by Contrast-Enhanced SPACE Imaging
Authors: Zhao Xianjing , Wu Yue , Rui Wenting , Wang Jing , Wu Shiman , Zhang Qi , Hao Xiaozhu , Tang Ying , Ren Yan , Sun Huaping , Yao Zhenwei 
Published: November 2022

Objective
Inferior intercavernous sinus (iICS) is a venous channel below the pituitary gland. Inferior intercavernous sinus injury is predisposed to cause venous bleeding during dura incision in transsphenoidal surgery for pituitary adenomas. Therefore, this study aimed to perform a radiological assessment of iICS before transsphenoidal surgery for pituitary microadenoma.

Methods
A retrospective evaluation was performed on 156 patients who underwent magnetic resonance imaging examinations in our hospital before endoscopic transsphenoidal surgery for pituitary microadenoma. Both sagittal reformatted and coronal contrast-enhanced (CE) sampling perfection with application optimized contrast using different flip angle evolutions (SPACE) images were interpreted for the presence, shape, and size of the iICS.

Results
In CE SPACE, the iICS was identified in 72 patients (46.15%) with pituitary microadenoma. The iICS was appeared as a filiform-shaped hyperintense structure below the pituitary gland on coronal CE SPACE planes and a crescent-shaped hyperintense structure on sagittal CE SPACE planes. The mean ± SD width, depth, and height of iICS were 11.15 ± 3.47 mm, 5.29 ± 1.24 mm, and 1.41 ± 0.19 mm, respectively.

Conclusions
Contrast-enhanced SPACE may serve as a promising technique in evaluating iICS and individualized preoperative planning before transsphenoidal surgery for pituitary microadenoma.
Unusual Extramedullary Manifestation in Multiple Myeloma
Authors: Strauss Dimitrios , Sachpekidis Christos , Dapunt Ulrike , Goldschmidt Hartmut , Dimitrakopoulou-Strauss Antonia 
Published: November 2022

Abstract
A 73-year-old man with multiple myeloma (initial diagnosis 21 months earlier) was referred to our center for a whole-body 18F-FDG PET/CT. We detected a bilateral synchronous testicular manifestation, which was confirmed by histopathology after orchiectomy. Besides hypermetabolic lesions in the spine and ribs (most likely old fractures), known osteolysis showed no uptake. Extramedullary manifestation occurs in 13% to 20% of cases, among these 4% demonstrate testicular manifestation, which is associated with poor survival rates. Optimal therapy management is still unclear, due to limited data. To the authors’ knowledge, so far only 3 comparable cases have been described.