bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-molecule analysis reveals cooperative stimulation of Rad51 filament nucleation and growth by mediator proteins
Authors: Belan Ondrej , Barroso Consuelo , Kaczmarczyk Artur , Anand Roopesh , Federico Stefania , O’Reilly Nicola , Newton Matthew D. , Maeots Erik , Enchev Radoslav I. , Martinez-Perez Enrique , Rueda David S. , Boulton Simon J. 
Published: November 2020

ABSTRACTHomologous recombination (HR) is an essential DNA double-strand break (DSBs) repair mechanism frequently inactivated in cancer. During HR, RAD51 forms nucleoprotein filaments on RPA-coated resected DNA and catalyses strand invasion into homologous duplex DNA. How RAD51 displaces RPA and assembles into long HR-proficient filaments remains uncertain. Here, we employ single-molecule imaging to investigate the mechanism of nematode RAD-51 filament growth in the presence of BRC-2 (BRCA2) and RAD-51 paralogs, RFS-1/RIP-1. BRC-2 nucleates RAD-51 on RPA-coated DNA, while RFS-1/RIP-1 acts as a ‘chaperone’ to promote 3’ to 5’ filament growth via highly dynamic engagement with 5’ filament ends. Inhibiting ATPase or mutation in RFS-1 Walker box leads to RFS-1/RIP-1 retention on RAD-51 filaments and hinders growth.rfs-1Walker box mutants display sensitivity to DNA damage and accumulate RAD-51 complexes non-functional for HRin vivo. Our work reveals the mechanism of RAD-51 nucleation and filament growth in the presence of recombination mediators.
A Minimal, Adaptive Binning Scheme for Weighted Ensemble Simulations
Authors: Torrillo Paul A. , Bogetti Anthony T. , Chong Lillian T. 
Published: November 2020

AbstractA promising approach for simulating rare events with rigorous kinetics is the weighted ensemble path sampling strategy. One challenge of this strategy is the division of configurational space into bins for sampling. Here we present a minimal adaptive binning (MAB) scheme for the automated, adaptive placement of bins along a progress coordinate within the framework of the weighted ensemble strategy. Results reveal that the MAB binning scheme, despite its simplicity, is more efficient than a manual, fixed binning scheme in generating transitions over large free energy barriers, generating a diversity of pathways, estimating rate constants, and sampling conformations. The scheme is general and extensible to any rare-events sampling strategy that employs progress coordinates.
GR chaperone cycle mechanism revealed by cryo-EM: inactivation of GR by GR:Hsp90:Hsp70:Hop client-loading complex
Authors: Wang Ray Yu-Ruei , Noddings Chari M. , Kirschke Elaine , Myasnikov Alexander G. , Johnson Jill L. , Agard David A. 
Published: November 2020

AbstractMaintaining a healthy proteome is fundamental for organism survival1,2. Integral to this are Hsp90 and Hsp70 molecular chaperones that together facilitate the folding, remodeling and maturation of Hsp90’s many “client” proteins3–7. The glucocorticoid receptor (GR) is a model client strictly dependent upon Hsp90/Hsp70 for activity8–13. Chaperoning GR involves a cycle of inactivation by Hsp70, formation of an inactive GR:Hsp90:Hsp70:Hop “loading” complex, conversion to an active GR:Hsp90:p23 “maturation” complex, and subsequent GR release14. Unfortunately, a molecular understanding of this intricate chaperone cycle is lacking for any client. Here, we report the cryo-EM structure of the GR loading complex, in which Hsp70 loads GR onto Hsp90, revealing the molecular basis of direct Hsp90/Hsp70 coordination. The structure reveals two Hsp70s—one delivering GR and the other scaffolding Hop. Unexpectedly, the Hop cochaperone interacts with all components of the complex including GR, poising Hsp90 for subsequent ATP hydrolysis. GR is partially unfolded and recognized via an extended binding pocket composed of Hsp90, Hsp70 and Hop, revealing the mechanism of GR loading and inactivation. Together with the GR maturation complex (Noddings et al., 2020), we present the first complete molecular mechanism of chaperone-dependent client remodeling, establishing general principles of client recognition, inhibition, transfer and activation.
SwarmTCR: a computational approach to predict the specificity of T Cell Receptors
Authors: Ehrlich Ryan , Kamga Larisa , Gil Anna , Luzuriaga Katherine , Selin Liisa , Ghersi Dario 
Published: November 2020

AbstractMotivationComputationally predicting the specificity of T cell receptors can be a powerful tool to shed light on the immune response against infectious diseases and cancers, autoimmunity, cancer immunotherapy, and immunopathology. With more T cell receptor sequence data becoming available, the need for bioinformatics approaches to tackle this problem is even more pressing. Here we present SwarmTCR, a method that uses labeled sequence data to predict the specificity of T cell receptors using a nearest-neighbor approach. SwarmTCR works by optimizing the weights of the individual CDR regions to maximize classification performance.ResultsWe compared the performance of SwarmTCR against a state-of-the-art method (TCRdist) and showed that SwarmTCR performed significantly better on epitopes EBV-BRLF1300, EBV-BRLF1109, NS4B214–222with single cell data and epitopes EBV-BRLF1300, EBV-BRLF1109, IAV-M158with bulk sequencing data (α and β chains). In addition, we show that the weights returned by SwarmTCR are biologically interpretable.AvailabilitySwarmTCR is distributed freely under the terms of the GPL-3 license. The source code and all sequencing data are available at GitHub (https://github.com/thecodingdoc/SwarmTCR)Contactdghersi@unomaha.edu
“Green washing” or “authentic effort”? An empirical investigation of the quality of sustainability reporting by banks
Authors: Khan Habib Zaman , Bose Sudipta , Mollik Abu Taher , Harun Harun 
Published: November 2020

PurposeThis study explores the quality of sustainability reporting (QSR) and the impact of regulatory guidelines, social performance and a standardised reporting framework (using the Global Reporting Initiative [GRI] guidelines) on QSR in the context of banks in Bangladesh.Design/methodology/approachUsing a sample of 315 banking firm-year observations over 13 years (2002–2014), a content analysis technique is used to develop the 11-item QSR index. Regression analysis is used to test the research hypotheses.FindingsInitially, QSR evolved symbolically in Bangladesh's banks but, over our investigation period, with QSR indicators gradually improving, the trends became substantive. The influences on QSR were sustainable banking practice regulatory guidelines, social performance and use of the GRI guidelines. However, until banks improve reporting information, such as external verification and trends over time, QSR cannot be regarded as fully substantive.Research limitations/implicationsThis study advances QSR research and debate among academic researchers. With regulatory agencies and stakeholders increasingly using sustainability reporting information for decision making, the information's quality is vital.Originality/valueThis study is the first on QSR in the banking industry context, with previous research mostly investigating the quantity of sustainability reporting. The current study also synthesises QSR with sustainability regulation and social performance factors which have rarely been used in the sustainability literature. To gain a holistic understanding of QSR, existing QSR measures are advanced by combining external reporting efforts with banks' internalisation initiatives.
The Asian region and COVID-19: approaches and gaps in controlling the virus
Authors: Mehta Poonam 
Published: November 2020

PurposeThe world is facing an unprecedented transformation in its social, economic and financial environments due to the emergence of a new pandemic called coronavirus disease 2019 (COVID-19). The norms on social distancing, lockdowns and sealing of international boundaries are the common measures taken by almost all regions of the world. However, the Asian region is found to have a relatively lesser number of infected cases and deaths due to COVID-19 in comparison to the other regions of the world. The present study has been aimed to review the roles of various factors as approaches, such as technology, business–government collaborations, financial bailouts and policies from government side and geographical and demographical factors of the countries in slowing down the transmission of virus in the Asian region including East Asia, South Asia and South East Asia for controlling COVID-19. Besides, the present study has also emphasised the gaps which have disabled the Asian region in controlling the transmission of virus.Design/methodology/approachFor framing the paper, various articles, national and international reports and academic papers have been reviewed, which are published in the period 2000–2020. The studies are shortlisted on the basis of keywords, such as COVID-19, coronavirus, severe acute respiratory syndrome-like coronavirus ( SARS-CoV-2), pandemic, virus, quarantine, Asia, etc.FindingsThe study has emphasised the roles of government, technology, business–government collaborations and geographical and demographical factors of countries as relevant factors in controlling COVID-19. Also, the study has highlighted inefficient health infrastructure, fear of social stigma and misinformation amongst citizens as those gaps where Asian regions are simultaneously found to be unprepared and inefficient to control the pandemic.Research limitations/implicationsThe present review would aid researchers in explaining the relevance of macro-level factors such as technology, business–government collaborations, government policies and financial bailouts and geographical and demographical factors of the region in controlling the transmission of pandemics and epidemics.Practical implicationsThe study would assist decision makers, governments and individuals in framing of the various strategies and interventions to control pandemics and epidemics.Social implicationsThe present study has explained the relevance of various behavioural and social factors as gaps which are responsible for speeding up the transmission of COVID-19. Here, the study would guide the society in taking various right steps during the phase of pandemic and lockdowns.Originality/valuePreviously, rarely any study has been found which has reviewed the roles of macro-level factors as approaches and gaps in the context of the Asian region to slow down the transmission of COVID-19.
Female CEOs and investment efficiency: evidence from an emerging economy
Authors: Ullah Irfan , Majeed Muhammad Ansar , Fang Hong-Xing , Khan Muhammad Arif 
Published: November 2020

Purpose
This study aims to investigate how the presence of female CEOs (FCEOs) affects investment efficiency in emerging economy, where female participation in business activities is limited.

Design/methodology/approach
This paper investigates the impact of CEO gender on investment efficiency by using investment efficiency measures proposed by Biddle et al. (2009), Chen et al. (2011) and Chen et al. (2013).

Findings
The findings suggest that FCEOs are associated with high level of investment efficiency. FCEOs improve corporate governance, streamline management and reduce inefficient investment decisions. In addition, FCEOs focus more on curbing underinvestment than overinvestment when making investment decisions. Furthermore, high financial reporting quality (FRQ) strengthens the effect of FCEOs on investment efficiency. The results suggest that FCEOs do not ameliorate the investment efficiency of state-owned enterprises.

Originality/value
This study enhances our understanding of the effects of FCEOs on corporate investment decisions in a male-dominated society. Efficient use of resources is vital from corporate and societal perspectives. Emerging economies are characterized by the unstable political and economic environment and low participation of females in decision-making. Hence, these economies require efficient utilization of resources. This study also sheds light on the role of FCEOs in curtailing underinvestment in emerging economies. It proves that FRQ is important in emerging economies because it strengthens the governance role of FCEOs.
Influences of climatic and social environment on variable maternal allocation among offspring in Alpine marmots
Authors: Plard Floriane , Chamiot‐clerc Benoit , Cohas Aurélie 
Published: November 2020

Abstract

In an environment with limited resources, parents may trade‐off the number of offspring produced against offspring mass. To maximize fitness under unpredictable environments, females must not only maximize mean annual reproductive success but also minimize between‐year variation in reproductive success. Thus, preferred strategies of maternal allocation might be to maximize the mass of their offspring or to produce a number of offspring of variable body masses.

Many social species have evolved in variable and unpredictable environments where only the social environment can be predicted. If mothers seem to alter their total reproductive allocation to offspring depending on their social environment, how the total expenditure is allocated between the different offspring is still unknown.

Here, we analysed how climatic and social environments influence strategies of maternal allocation and how these strategies impact pup first‐year survival in a wild population of Alpine marmots monitored between 1990 and 2016.

We found that females acted as income breeders using resources immediately available for reproduction. Our results showed that the proportion of maternal mass allocated to offspring varied mainly with litter size. However, how maternal allocation is shared between pups depended on climatic and social environments. In general, mothers tended to have litters of greater average mass and small variability in favourable social environments or when resources are abundant and lighter average pup mass but high variability in unfavourable social environments or when resources are scarce.

This variable allocation could correspond to dynamic bet‐hedging such that mothers influence the variance of pup mass within the litter in response to poor current environmental conditions. Our analysis of first‐year survival showed that females should maximize the body mass of their young whatever the conditions will be because pups of higher mass have higher survival, regardless of environmental conditions. When resources are scarce, this strategy might not be achievable for all pups so that mothers produced variable pups. In large litters, this strategy increased first‐year survival.

Because pup variability affects parental fitness, differential allocation between pups of the same litter could have large consequences on fitness and thus on reproductive strategies of social species.
Labor Market Effects of Spatial Licensing Requirements: Evidence from CPA Mobility
Authors: CASCINO STEFANO , TAMAYO ANE , VETTER FELIX 
Published: November 2020

ABSTRACTWe exploit the staggered introduction of CPA Mobility provisions in the United States to study the effects of spatial licensing requirements on the labor market for accounting professionals. Specifically, we examine whether the removal of licensing‐induced geographic barriers affects CPA wages and employment levels, as well as the pricing and quality of professional services. We find that, subsequent to the adoption of CPA Mobility provisions, wages of accounting professionals decrease, whereas employment levels are unaffected. The documented wage effect stems from smaller CPA firms, is more pronounced for CPAs holding senior positions, and persists over time. We also find that service prices decline and that this effect is concentrated in local CPA firms. Moreover, we document that the increased wage and price pressure is not associated with deteriorating service quality. Collectively, our results suggest that the removal of occupational licensing barriers has sizable effects on labor supply and service prices. Our findings inform the current regulatory debate on occupational licensing.
Team‐level human resource attributions and performance
Authors: Fan Di , Huang Yufang , Timming Andrew R. 
Published: November 2020

AbstractDrawing on attribution theory, this study explores the relationship between team‐level human resource attributions (HRAs) and team performance, and explains how transformational leadership moderates this relationship. The data were collected from leaders and subordinates across 77 work teams, for a total of 708 participants employed in seven manufacturing and service organizations in China. The study finds that the relationship between commitment‐focused team‐level HRAs and team performance is mediated by team engagement, and that self‐awareness of transformational leadership significantly strengthens the positive relationship between these variables. However, parallel moderated mediation relationships are not evident between control‐focused team‐level HRAs and team performance. The study is among the first to explore team‐level HRAs and contributes to the scholarly debates on the role of attributions in explaining the so‐called ‘black box’ between HRM and performance.
Patterns and preferences for accessing health and aged care services in older Aboriginal and Torres Strait Islander Australians
Authors: Larke Benjamin M. , Broe Gerald A. , Daylight Gail , Draper Brian , Cumming Robert G. , Allan Wendy , Donovan Terrence , Costa Daniel , Lah Suncica , Radford Kylie 
Published: November 2020

ObjectivesTo determine preferences for health and aged care services in Aboriginal and Torres Strait Islander Australians and explore related factors.MethodsMixed‐method, cross‐sectional study including 336 Aboriginal and Torres Strait Islander people aged 60 years and older from regional and urban areas.ResultsExclusive preference for Aboriginal Community Controlled services was most common. This preference significantly increased when preferences for, and use of, aged care and disability services were considered. The likelihood of holding an exclusive preference for Aboriginal Community Controlled services was higher in regional settings compared to urban and in those reporting lower engagement in traditional activities during childhood.ConclusionsThese findings suggest that the majority of older Australian Aboriginal and Torres Strait Islander people prefer aged and disability care provided by Aboriginal services. Given the anticipated increase in service demand in this population, there is a growing need for culturally safe services, particularly in regional settings.
Neoantigen prediction in human breast cancer using RNA sequencing data
Authors: Hashimoto Sachie , Noguchi Emiko , Bando Hiroko , Miyadera Hiroko , Morii Wataru , Nakamura Takako , Hara Hisato 
Published: November 2020

AbstractNeoantigens have attracted attention as biomarkers or therapeutic targets. However, accurate prediction of neoantigens is still challenging, especially in terms of its accuracy and cost. Variant detection using RNA sequencing (RNA‐seq) data has been reported to be a low‐accuracy but cost‐effective tool, but the feasibility of RNA‐seq data for neoantigen prediction has not been fully examined. In the present study, we used whole‐exome sequencing (WES) and RNA‐seq data of tumor and matched normal samples from six breast cancer patients to evaluate the utility of RNA‐seq data instead of WES data in variant calling to detect neoantigen candidates. Somatic variants were called in three protocols using: (i) tumor and normal WES data (DNA method, Dm); (ii) tumor and normal RNA‐seq data (RNA method, Rm); and (iii) combination of tumor RNA‐seq and normal WES data (Combination method, Cm). We found that the Rm had both high false‐positive and high false‐negative rates because this method depended greatly on the expression status of normal transcripts. When we compared the results of Dm with those of Cm, only 14% of the neoantigen candidates detected in Dm were identified in Cm, but the majority of the missed candidates lacked coverage or variant allele reads in the tumor RNA. In contrast, about 70% of the neoepitope candidates with higher expression and rich mutant transcripts could be detected in Cm. Our results showed that Cm could be an efficient and a cost‐effective approach to predict highly expressed neoantigens in tumor samples.
Sublethal irradiation promotes the metastatic potential of hepatocellular carcinoma cells
Authors: Cao Yulin , Yin Yuan , Wang Xue , Wu Zhifeng , Liu Yuhang , Zhang Fuzheng , Lin Junhua , Huang Zhaohui , Zhou Leyuan 
Published: November 2020

AbstractRadiotherapy (RT) represents one of the major treatment methods for cancers. However, many studies have observed that in descendant surviving tumor cells, sublethal irradiation can promote metastatic ability, which is closely related to the tumor microenvironment. We therefore investigated the functions and mechanisms of sublethal irradiated liver nonparenchymal cells (NPCs) in hepatocellular carcinoma (HCC). In this study, primary rat NPCs and McA‐RH7777 hepatoma cells were irradiated with 6 Gy X‐ray. Conditioned media (CM) from nonirradiated (SnonR), irradiated (SR), or irradiated plus radiosensitizer celecoxib‐treated (S[R + D]) NPCs were collected and added to sublethal irradiated McA‐RH7777 cells. We showed that CM from sublethal irradiated NPCs significantly promoted the migration and invasion ability of sublethal irradiated McA‐RH7777 cells, which was reversed by celecoxib. The differentially expressed genes in differently treated McA‐RH7777 cells were enriched mostly in the AMP‐activated protein kinase/mammalian target of rapamycin (AMPK/mTOR) signaling pathway. SR increased the migration and invasion ability of HCC cells by inhibiting AMPK/mTOR signaling, which was enhanced by the AMPK inhibitor compound C and blocked by the AMPK activator GSK‐621. Analyses of HCC tissues after neoadjuvant radiotherapy confirmed the effects of radiation on the AMPK/mTOR pathway. Cytokine antibody arrays and further functional investigations showed that matrix metalloproteinase‐8 (MMP‐8) partly mediates the promotion effects of SR on the migration and invasion ability of HCC cells by regulating AMPK/mTOR signaling. In summary, our data indicate that MMP‐8 secreted by irradiated NPCs enhanced the migration and invasion of HCC by regulating AMPK/mTOR signaling, revealing a novel mechanism mediating sublethal irradiation–induced HCC metastasis at the level of the tumor microenvironment.
Prognostic impact of ventilation‐perfusion defects and pulmonary diffusing capacity after single lung transplantation
Authors: Mohammad Milan , Kristensen Anna Warncke , Hedsund Caroline , Greve Anders M. , Perch Michael , Mortensen Jann , Berg Ronan M. G. 
Published: November 2020

AbstractBackgroundVentilation‐perfusion (VQ) scintigraphy and lung function testing are often used to assess allograft function after single lung transplantation (SLTX). However, it is unknown whether allograft defects on VQ scintigraphy presage all‐cause mortality after SLTX.ObjectiveTo investigate whether allograft defects on VQ scintigraphy portend poorer lung function and increased mortality after SLTX.MethodsWe retrospectively identified 45 consecutive patients in which a VQ scintigraphy was performed as part of the routine workup 12 weeks after SLTX. VQ scintigraphies were scored for matched and mismatched perfusion defects in the allograft. Lung function testing was performed according to established guidelines six months after SLTX. Time to all‐cause mortality was the endpoint.Results19 (42%) patients had matched VQ defects. After a median follow‐up of 4.1 (IQR 1.5–7.9) years since SLTX, 35 (78%) had died. Those with matched defects in the allograft had lower diffusing capacity (mean 42 [SD 14] versus mean 54 [SD 18] % of predicted, p < .05) and increased mortality (univariable HR 2.06, 95% CI: 1.05–4.06, p = .04). However, in multivariate analysis, only lower post‐transplantation diffusing capacity remained associated with mortality (HR 1.08, 95% CI: 1.02–1.30 per % lower diffusing capacity of predicted, p = .003).ConclusionIn SLTX patients, a lower diffusing capacity appeared to explain the increased mortality among those with matched VQ defects in the allograft.