bluuebunny/crossref_metadata_2025_split huggingface dataset:
A peptide-centric local stability assay to unveil protein targets of diverse ligands
Authors: Li Kejia , Chen Shijie , Wang Keyun , Wang Yan , Fang Zheng , Lyu Jiawen , Zhu Haiyang , Li Yanan , Yu Ting , Yang Feng , Zhang Xiaolei , Guo Siqi , Ruan Chengfei , Zhou Jiahua , Wang Qi , Luo Cheng , Ye Mingliang 
Published: October 2023

ABSTRACTWhile tremendous progress has been made in chemical proteomics for identifying protein-ligand interactions, it remains challenging for proteome-wide identification of ligand-binding regions without modifying the ligands. Here, we discovered that “disruptive trypsinization” amplifies the readout of ligand-induced protein local stability shifts, and explored this notion in developing “peptide-centric local stability assay” (PELSA), a modification-free approach which achieves unprecedented sensitivity in proteome-wide target identification and binding-region determination. We demonstrate the versatility of PELSA by investigating the interactions across various biological contexts including drug-target interactions, metabolism, epitope mapping, metal proteomics, and post-translational modification recognition. A PELSA study of the oncometabolite R2HG revealed functional insights about its targets and pathogenic processes in both cancer and immune cells. Thus, beyond offering users unprecedented sensitivity for characterizing diverse target-ligand interactions, PELSA supports informative screening and hypothesis generation studies throughout life science.
Three Conserved Immune Dysfunction and Exclusion Subtypes in Bladder and Pan-cancers: Prognostic and Immunotherapeutic Significance
Authors: Zheng Kun , Hai Youlong , Chen Hongqi , Hu Xiaoyong , Ni Kai 
Published: October 2023

AbstractMolecular subtyping is expected to enable bladder cancer (BC) precise treatment. However, its clinical application remains defective and controversial. Given the significance of tumor immune dysfunction and exclusion (TIDE) in tumor immune escape and immunotherapy, we aimed to develop a novel TIDE-based subtyping method to facilitate personalized management. Transcriptome data of BC was used to evaluate the heterogeneity and the status of TIDE patterns. We identified 69 TIDE biomarker genes and classified BC samples into three subtypes. Subtype I showed the lowest TIDE status and malignancy with the best prognosis and highest sensitivity to immune checkpoint blockade (ICB) treatment, which was enriched of metabolic related signaling pathways. Subtype III represented the highest TIDE status and malignancy with the poorest prognosis and resistance to ICB treatment, resulting from its inhibitory immune microenvironment and T cell terminal exhaustion. Subtype II was in a transitional state with intermediate TIDE level, malignancy, and prognosis. We further confirmed the existence and characteristics of our novel TIDE subtypes using real-world BC samples. This subtyping method was proved to be more efficient than known methods in identifying non-responders to immunotherapy. We also found that combining our TIDE subtypes with known biomarkers can improve the sensitivity and specificity in predicting ICB response. Moreover, besides guiding ICB treatment, this classification approach can assist in selecting the frontline or recommended drugs. Finally, the TIDE subtypes are conserved across pan-tumors. In conclusion, our novel TIDE-based strategy is a powerful clinical tool for BC and pan-cancer patients, and potentially guiding personalized immunotherapy.
Decoupling of the Onset of Anharmonicity between a Protein and Its Surface Water around 200 K
Authors: Zheng Lirong , Zhou Bingxin , Wu Banghao , Tan Yang , Huang Juan , Tyagi Madhusudan , Sakai Victoria García , Yamada Takeshi , O’Neill Hugh , Zhang Qiu , Hong Liang 
Published: October 2023

AbstractThe protein dynamical transition at ∼ 200 K, where the biomolecule transforms from a harmonic, non-functional form to an anharmonic, functional state, has been thought to be slaved to the thermal activation of dynamics in its surface hydration water. Here, by selectively probing the dynamics of protein and hydration water using elastic neutron scattering and isotopic labelling, we found that the onset of anharmonicity in the two components around 200 K are decoupled. The one in protein is an intrinsic transition, whose characteristic temperature is independent of the instrumental resolution time, but varies with the biomolecular structure and the amount of hydration, while the one of water is merely a resolution effect.
Balanced cell division is secured by two different regulatory sites in OxyS RNA
Authors: Elgrably-Weiss Maya , Hussain Fayyaz , Georg Jens , Shraiteh Bushra , Altuvia Shoshy 
Published: October 2023

ABSTRACTBy interfering with cell division, theEscherichia colioxidative stress-induced OxyS small RNA brings about cell cycle arrest thus allowing DNA damage repair. Cell division and cell elongation are opposing functions to the extent that inhibition of cell division requires a parallel inhibition of cell elongation for the cells to survive. In this study, we report that in addition to cell division OxyS inhibitsmepSencoding an essential peptidoglycan endopeptidase responsible for cell elongation. Furthermore, a phylogenetic evolutionary target conservation analysis of OxyS homologs to identify OxyS most common function revealed that the majority of OxyS targets belong to the category of “cell cycle” followed by “peptidoglycan metabolism”, especially cell elongation.mepSis the most frequent target of this category, predicted to be regulated by OxyS in 64 % of the 146 organisms studied. We suggest that cell cycle arrest and balancing between cell division and cell elongation are important and conserved functions of the oxidative stress induced sRNA OxyS.
Role of Cardiac Rehabilitation in Improving Outcomes after Myocardial Infarction
Authors: Nemani Raghu Ram Shanmukh , Gade Bala Sushritha , Panchumarthi Dedeepya , Bathula Bhargava Venkata Sasidhar Reddy , Panjiyar Binay Kumar 
Published: October 2023

AbstractMyocardial Infarction (MI) an integral part of Acute Coronary Syndrome (ACS) occurs due to Atherosclerotic narrowing of the Coronary blood vessels. ACS being one of the major cardiovascular diseases (CVDs) has led to a significant amount of mortality & morbidity. The post-myocardial infarction period greatly impacted the physical; psychological; social; emotional; and occupational well-being. Cardiac rehabilitation (CR) helps by addressing these immediate effects & also improves long-term well-being and overall quality of life. The benefits of CR include enhanced exercise capacity, risk factor reduction, improved quality of life (QOL), and reduced mortality and hospital readmission. We used a systematic literature review (SLR) approach in his article to provide a global overview of the cutting edge offered by CR in the post-MI phase. We reviewed 33 articles from journals of good repute published between 2013 and August 15, 2023, focusing on six selected papers for in-depth analysis. The analysis was focused on factors such as positive outcomes of CR, and the effects of CR in post-myocardial infarction. Even though there is a lack of statistically significant evidence for the benefits of CR; Meta-analyses confirm its positive impact on cardiovascular outcomes, such as decreased mortality, cardiac events, and hospital Readmissions. There is still a need for ongoing research to enhance the understanding of its mechanisms and statistically prove its effectiveness. As CR continues to evolve, referral and participation in CR should be increased as it improves overall health and well-being.
Understanding knowledge leadership in improving team outcomes in the health sector: a Covid-19 study
Authors: Khan Muhammad Aamir , Latif Khawaja Fawad , Shahid Sehrish , Shah Syed Asim 
Published: October 2023

PurposeThis study seeks to examine the role of knowledge-oriented leadership in the health sector to achieve team outcomes in the Covid-19 context. Drawing from the leader–member exchange (LMX), social cognitive and social identity theory, the present study develops a model linking knowledge-oriented leadership and team performance through the underlying psychological mechanisms of team efficacy, team cohesion, team commitment and team collaboration.Design/methodology/approachUtilizing quantitative data methodology, data were obtained from the pharmaceutical employees (health sector) of Pakistan during the pandemic. The partial least squares structural equation modeling was used to test the hypotheses.FindingsThe findings support the hypothesis that knowledge-oriented leadership significantly influences team outcomes. The study also verified that team collaboration effectively mediates the relationship between knowledge-oriented leadership and team performance.Originality/valueThe study is unique in the sense that it explores the newly established leader behavior (knowledge-oriented leadership) in understanding team outcomes in the health sector. The study concludes by making significant implications to overcome the challenges raised by Covid-19 pandemic.
Strategy creation behaviour and “last gasp” digitalization as predictors of sales performance and cash flow
Authors: Onjewu Adah-Kole Emmanuel , Nyuur Richard B. , Paul Salima , Wang Yong 
Published: October 2023

PurposeAlthough recent literature has examined diverse measures adopted by SMEs to navigate the COVID-19 turbulence, there is a shortage of evidence on how crisis-time strategy creation behaviour and digitalization activities increase (1) sales and (2) cash flow. Thus, predicated on a novel strategy creation perspective, this inquiry aims to investigate the crisis behaviour, sales and cash flow performance of 528 SMEs in Morocco.Design/methodology/approachNovel links between (1) aggregate wage cuts, (2) variable operating hours, (3) deferred payment to suppliers, (4) deferred payment to tax authorities and (5) sales performance are developed and tested. A further link between sales performance and cash flow is also examined and the analysis is conducted using a non-linear structural equation modelling technique.FindingsWhile there is a significant association between strategy creation behaviours and sales performance, only variable operating hours have a positive effect. Also, sales performance increases cash flow and this relationship is substantially strengthened by e-commerce digitalization and innovation.Originality/valueTheoretically, to the best of the authors’ knowledge, this is one of the first inquiries to espouse the strategy creation view to explain SMEs' crisis-time behaviour and digitalization. For practical purposes, to supplement Moroccan SMEs' propensity to seek tax deferrals, it is argued that debt and equity support measures are also needed to boost sales performance and cash flow.
Does Weisburd's law of crime concentration apply to traffic crashes? Implications for policing and traffic law enforcement
Authors: Park Sangjun , Lum Cynthia 
Published: October 2023

PurposeA considerable amount of police evaluation research focuses on innovative approaches to reduce crime at places. This is hardly coincidental; policing and place-based scholars have found crime is highly concentrated, and when police focus on these places, they can prevent and reduce crime. The regularity of such findings led Weisburd (2015) to assert the existence of a “law of crime concentration.” Given that bold assertion, the authors test whether the law of crime concentration is generalizable to one of the most common public safety concerns that police handle—traffic crashes.Design/methodology/approachTo determine whether the law of crime concentration applies to traffic crashes, the authors examined crash locations and times in all counties in Utah across four years. Following and expanding on Weisburd's methods, the authors calculate the bandwidth of concentration for these crashes and analyze various types by severity and possible explanations for variations in crash concentrations across the state.FindingsA small proportion of street segments and intersections experience a disproportionately high number of crashes, and the degree of concentration of crashes may be even higher than that of crime. Further, there are variations in the levels of crash concentration across counties and in the severity of injuries resulting from the crashes.Practical implicationsPlace-based criminologists and policing scholars have not often explored traffic crashes in their analyses. Yet, traffic problems take up a significant amount of law enforcement time and resources and are often priorities for most law enforcement agencies. Given what the authors know from traffic, policing and crime and place research, targeted approaches at micro traffic crash hot spots can be beneficial for public safety prevention.Originality/valueThis study is the first to explore the application of Weisburd's Law of Crime Concentration to traffic crashes. Given that police spend a significant amount of time and resources on traffic-related problems in their jurisdiction, finding more effective, evidence-based approaches to address this public safety concern should be a high priority for police and researchers alike.
Non-financial information assurance: a review of the literature and directions for future research
Authors: Farooq Muhammad Bilal , Azantouti Asem Saad Ali , Zaman Rashid 
Published: October 2023

Purpose
This study aims to review the literature on non-financial information (NFI) assurance including external assurance of sustainability reports (SRA) and integrated reports (IRA). The objectives are as follows: provide an overview of academic research; understand the nature of NFI assurance engagements by organising the literature around the five key elements of an assurance engagement; develop a framework for understanding NFI assurance; and provide directions for future research.

Design/methodology/approach
The study undertakes a structured literature review of 179 articles published from 1999 to 2023.

Findings
The review identified 324 researchers located in 35 different countries who published 179 articles on SRA and IRA. The researchers, their locations, journals, methods, theories and themes are examined. The literature is structured around the definition of an assurance engagement including a tripartite arrangement, subject matter, a suitable criterion, sufficient appropriate evidence and a written assurance report. A framework for understanding NFI assurance is offered. Avenues for future research, structured around the five elements of an assurance engagement, are presented.

Practical implications
Researchers will benefit from an overview of the literature and guidance on areas for future research. Lecturers can use the findings to develop content for their auditing courses. Reporting managers will benefit from a better understanding of this new form of assurance. Regulators can use this study’s insights to better inform the development of laws and corporate governance codes mandating NFI assurance. Standard setters can use these findings to guide the emergence of the new assurance standards. Assurance practitioners may use this research to inform practice.

Social implications
The findings may prove useful in addressing capture, which deters NFI assurance from enhancing disclosure credibility and fulfilling its transparency and accountability role. This is to the detriment of the wider society.

Originality/value
The consolidation of the literature around the five key elements of an assurance engagement is unique. The framework devised offers useful insights into the dynamics of assurance generally and NFI assurance more specifically. The study is timely given the new European Union regulations on NFI reporting and assurance and the work of the International Audit and Assurance Standards Board in developing a specialist NFI assurance standard.
Design and implementation of a measuring system used to evaluate the mechanical performance of the bone fixators
Authors: Guo Zhanshe , Liang Xiangdang , Wang Sen 
Published: October 2023

Purpose
This measuring system is designed to effectively simulate the mechanical reliability of the operated bone fixators. It can be used to pre-evaluate the mechanical performance of the operated fixator on the patients, including the static mechanical properties and fatigue properties when the patient walks after the operation.

Design/methodology/approach
It is mainly composed of a one-dimensional platform, a force sensor, a high measuring precision displacement sensor and a servo motor. Loading (which is used to simulate the loading status of the fixators after the operation) of the system is realized by the rotation of the servo motor. It can be read by a high precision force sensor. The relative displacement of the broken bone is obtained by a high precision laser displacement sensor. Corresponding theoretical analysis is also carried out.

Findings
Calibrated results of the system indicate that the output voltage and the measured force of the force sensors possess an excellent linear relationship, and the calculated nonlinear error is just 0.0002%. The maximum relative displacement between the operated broken bone under 700 N axial force is about 1 mm. Fatigue test under 550 N loading for 85,000 cycles also indicates the feasibility of the design.

Originality/value
This device is successfully designed and fabricated to pre-evaluate the mechanical performance of the bone fixators. High precision force sensor and displacement sensor are used to successfully increase the measuring ability of the system. This will offer some help to pertinent researchers.
Genomic characterization of New Delhi metallo‐beta‐lactamase–producing species of Morganellaceae, Yersiniaceae, and Enterobacteriaceae (other than Klebsiella) from Brazil over 2013–2022
Authors: Camargo Carlos Henrique , Yamada Amanda Yaeko , de Souza Andreia Rodrigues , Sacchi Claudio Tavares , Reis Alex Domingos , Santos Marlon Benedito Nascimento , de Assis Denise Brandão , de Carvalho Eneas , Takagi Elizabeth Harummyy , Cunha Marcos Paulo Vieira , Tiba‐Casas Monique Ribeiro 
Published: October 2023

AbstractOver the last decade, New Delhi metallo‐beta‐lactamase (NDM) carbapenemase has silently spread in Brazil. In this study, we analyzed a large collection of Enterobacterales other than Klebsiella spp. received in our reference laboratory between 2013 and 2022. A total of 32 clinical isolates displaying different pulsed‐field gel electrophoresis profiles, and represented by 11 species in the families Enterobacteriaceae (Citrobacter freundii, Citrobacter portucalensis, Enterobacter hormaechei, and Escherichia coli), Morganellaceae (Morganella morganii, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, and Raoultella ornithinolytica), and Yersiniaceae (Serratia marcescens) had their whole genomes sequenced and further analyzed. Antimicrobial susceptibility was determined by disk diffusion, except for polymyxin B, assessed by broth microdilution. The blaNDM‐1 allele was predominant (n = 29), but blaNDM‐5 was identified in an E. coli specimen with a novel ST, and the blaNDM‐7 allele was found in E. hormaechei ST45 and E. coli ST1049. Polymyxin was active against all but one Enterobacteriaceae isolate: an mcr‐1–producing E. coli presenting minimal inhibitory concentration (4 mg/L). Isolates producing extended‐spectrum β‐lactamases were common: cefotaximase from Munich (CTX‐M)‐15 (n = 10), CTX‐M‐2 (n = 4), and CTX‐M‐8 (n = 3) were detected, and the mcr‐1–producing E. coli was found to co‐produce both CTX‐M‐8 and CTX‐M‐55 β‐lactamases. The mcr‐9 gene was found in 5/8 E. hormaechei isolates, distributed in four different sequence types, all of them presenting susceptibility to polymyxin. This study showed that NDM‐producing Enterobacterales other than Klebsiella are already spread in Brazil, in diversified species, and cocarrying important resistance genes. Prompt detection and effective implementation of measures to prevent further spread are mandatory for mitigating the dissemination of NDM carbapenemase in hospital settings and preserving the already limited antimicrobial therapy options.
Temperature‐dependent scaling of fitness traits with body size in hydra
Authors: Tökölyi Jácint 
Published: October 2023

Abstract

Body size strongly depends on developmental temperature. In more than 80% of the ectotherm species investigated, including bacteria, protists, invertebrates and vertebrates, individuals developing at lower temperatures exhibit protracted growth and achieve larger sizes than individuals developing at higher temperatures (referred to as the ‘temperature‐size rule’, TSR). One hypothesis to explain the TSR posits that reproduction and/or survival change more steeply with size in cold environments, resulting in larger optimal body sizes and consequently increased selection for growth. However, clearly ascertaining whether size directly affects fitness traits in a temperature‐dependent way is challenging due to the interdependence of size, reproduction and survival.

To address this problem, experimental body size manipulation was performed in two male and two female strains of Hydra oligactis, a cold‐adapted temperate freshwater invertebrate. Experimentally enlarged and reduced individuals were followed at two distinct temperatures (8 and 12°C) in the laboratory to record sexual investment and postreproductive senescence. To gain insight into the underlying physiological processes, phenotypic observations were complemented with a large transcriptomic data set obtained from enlarged and reduced individuals from different temperatures.

Within male hydra strains, fecundity increased, while survival decreased more steeply with size in cold, compared with warmer temperature. Females showed similar, though less emphasized, trends. Reduced animals in the cold had slower sexual development and were less able to undergo compensatory growth, suggesting temperature‐dependent constraints on physiological performance.

Reduced and enlarged males differed dramatically in the expression of reproductive genes at low, but not at higher temperature, while in females, a complex transcriptomic restructuring was seen. In particular, metabolic genes were strongly affected by size manipulation, suggesting resource acquisition and allocation as a central mechanism driving allometric patterns.

These results suggest that being large is more beneficial in cold environments, at least in terms of reproduction, while at higher temperature even small individuals can maintain reproductive output. Lower reproduction, however, can be compensated by improved survival in small individuals facing colder environments. The reproductive advantage of large size can provide selection for increased growth at low temperature, thereby explaining the TSR in hydra.

Read the free Plain Language Summary for this article on the Journal blog.
Treatment of Accounting Changes and Covenant Violation Errors
Authors: ZHU CHUNMEI 
Published: October 2023

ABSTRACTGAAP provisions in loan contracts specify how to address the effect of accounting changes on financial covenants. I document a pronounced upward trend in and the dominance of frozen‐on‐request (FOR) GAAP provisions, which incorporate accounting changes unless either the borrower or the lender requests a freeze. FOR GAAP streamlines the process of incorporating accounting changes into covenant calculations by obviating the need for renegotiations and prevents opportunistic GAAP freezes by requiring good faith renegotiations. Therefore, FOR GAAP is more likely to incorporate accounting changes beneficial to covenant informativeness, leading to lower false positives (i.e., Type I errors of financial covenant violations) and false negatives (i.e., Type II errors of financial covenant violations). Based on a large sample of loan contracts, I find that FOR GAAP decreases false positives and false negatives after controlling for self‐selection bias and that the decrease is more pronounced when accounting changes relevant to financial covenants are more significant. My study provides new evidence of the role accounting standards and GAAP provisions play in debt contracting efficiency.