bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring Pathogenic Mutation in Allosteric Proteins: the Prediction and Beyond
Authors: Zhang Huiling , Ju Zhen , Zhang Jingjing , Li Xijian , Xiao Hanyang , Chen Xiaochuan , li Yuetong , Wang Xinran , Wei Yanjie 
Published: March 2024

AbstractAllosteric regulation that triggers the functional activity of a protein through conformational changes is an inherent function of the protein in numerous physiological and pathological scenarios. In the post-genomic era, a central challenge for disease genomes is the identification of the biological effects of specific somatic variants on allosteric proteins and the phenotypes they influence during the initiation and progression of diseases. Here, we analyzed more than 38539 mutations observed in 90 human genes with 740 allosteric protein chains. We found that existing allosteric protein mutations are associated with many diseases, but the clinical significance of the majority of mutations in allosteric proteins remains unclear. Next, we developed a machine-learning-based model for pathogenic mutation prediction of allosteric proteins based on the intrinsic characteristics of proteins and the prediction results from existed methods. When tested on the benchmark allosteric protein dataset, the proposed method achieves AUCs of 0.868 and AUPR of 0.894 on allosteric proteins. Furthermore, we explored the performance of existing methods in predicting the pathogenicity of mutations at allosteric sites and identified potential significant pathogenic mutations at allosteric sites using the proposed method. In summary, these findings illuminate the significance of allosteric mutation in disease processes, and contribute a valuable tool for the identification of pathogenic mutations as well as previously unknown disease-causing allosteric-protein-encoded genes.
Edinger-Westphal ghrelin receptor signalling regulates binge alcohol consumption in a sex specific manner
Authors: Pearl Amy , Pinares-Garcia Paulo , Shesham Arnav , Maddern Xavier , Anversa Roberta G , Brown Robyn M , Reed Felicia M , Giardino William J , Lawrence Andrew J , Walker Leigh C 
Published: March 2024

AbstractBackgroundRates of risky drinking are continuing to rise, particularly in women, yet sex as a biological variable has been largely ignored. An emerging yet understudied potential component of this circuitry is the central projecting Edinger-Westphal (EWcp), which is made up of two prominent, but distinct cell populations expressing either an array of neuropeptides (including cocaine and amphetamine regulated transcript; CART) or vGlut2 (glutamatergic).MethodsHere, we use a combination of approaches including genetic, molecular biology, behavioural testing, and electrophysiology to understand how the EWcp contributes to alcohol consumption in female versus male mice.ResultsChemogenetic inhibition of EWcpCARTcells reduced binge drinking specifically in female, but not male mice. Further, inhibition of EWcpCARTcells prevented ghrelin induced drinking, and viral–mediated ghrelin receptor (Ghsr) knockdown in the EWcp reduced binge drinking in female, but not male mice. RNAscope revealedGhsrexpression across peptidergic (marked by CART) and glutamatergic populations in the EWcp, with neurons from female mice more sensitive to bath application of ghrelin than male mice. Targeted knockdown ofGhsrfrom distinct EWcp populations revealed GHSR signalling on peptidergic, but not glutamatergic cells mediate binge drinking in female mice. Finally, both a GHSR inverse agonist and antagonist delivered directly within the EWcp reduced binge drinking in female mice.ConclusionsThese findings suggest the EWcp is a region mediating excessive alcohol bingeing through GHSR actions on peptidergic cells (CART-expressing) in female mice and expand our understanding of the neural mechanism(s) underpinning how the ghrelin system mediates alcohol consumption.
Expansion of pneumococcal serotype 23F and 14 lineages with genotypic changes in capsule polysaccharide locus and virulence gene profiles post introduction of pneumococcal conjugate vaccine in Blantyre, Malawi
Authors: Cave Rory , Kalizang’oma Akuzike , Chaguza Chrispin , Mwalukomo Thandie S. , Kamng’ona Arox , Brown Comfort , Msefula Jacquline , Bonomali Farouck , Nyirenda Roseline , Swarthout Todd D. , Kwambana-Adams Brenda , French Neil , Heyderman Robert S. 
Published: March 2024

AbstractSince the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) in Malawi in 2011, there has been persistent carriage of vaccine serotype (VT)Streptococcus pneumoniae, despite high vaccine coverage. To determine if there has been a genetic change within the VT capsule polysaccharide (cps) loci since the vaccine’s introduction, we compared 1,022 whole-genome-sequenced VT isolates from 1998 to 2019. We identified the clonal expansion of a multidrug-resistant, penicillin non-susceptible serotype 23F GPSC14-ST2059 lineage, a serotype 14 GPSC9-ST782 lineage and a novel serotype 14 sequence type GPSC9-ST18728 lineage. Serotype 23F GPSC14-ST2059 had an I253T mutation within the capsule oligosaccharide repeat unit polymerase Wzy protein, which is predictedin silicoto alter the protein pocket cavity. Moreover, serotype 23F GPSC14-ST2059 had SNPs in the DNA binding sites for the cps transcriptional repressors CspR and SpxR. Serotype 14 GPSC9-ST782 harbour a non-truncated version of the large repetitive protein (Lrp), containing a Cna protein B-type domain which is also present in proteins associated with infection and colonisation. These emergent lineages also harboured genes associated with antibiotic resistance, and the promotion of colonisation and infection which were absent in other lineages of the same serotype. Together these data suggest that in addition to serotype replacement, modifications of the capsule locus associated with changes in virulence factor expression and antibiotic resistance may promote vaccine escape. In summary, the study highlights that the persistence of vaccine serotype carriage despite high vaccine coverage in Malawi may be partly caused by expansion of VT lineages post PCV13 rollout.Impact StatementOur findings highlight the potential for clonal expansion of multidrug-resistant, penicillin-non-susceptible vaccine serotype lineages with capsule locus modifications, within a high carriage and disease burden population. This shift has occurred among young children where there has been high vaccine coverage, posing challenges for effective vaccine scheduling and design. Furthermore, this study emphasises the importance of ongoingStreptococcus pneumoniaegenomic surveillance as new or modified pneumococcal vaccines are implemented.2. Data summaryWhole genome sequencing assemblies for the PCVPA survey have been deposited in the BioProject PRJNA1011974.
Somatic polyploidy supports biosynthesis and tissue function by increasing transcriptional output
Authors: Lessenger Alexander T. , Swaffer Mathew P. , Skotheim Jan M. , Feldman Jessica L. 
Published: March 2024

AbstractCell size and biosynthetic capacity generally increase with increased DNA content. Polyploidy has therefore been proposed to be an adaptive strategy to increase cell size in specialized tissues with high biosynthetic demands. However, if and how DNA concentration limits cellular biosynthesisin vivois not well understood, and the impacts of polyploidy in non-disease states is not well studied. Here, we show that polyploidy in theC. elegansintestine is critical for cell growth and yolk biosynthesis, a central role of this organ. Artificially lowering the DNA/cytoplasm ratio by reducing polyploidization in the intestine gave rise to smaller cells with more dilute mRNA. Highly-expressed transcripts were more sensitive to this mRNA dilution, whereas lowly-expressed genes were partially compensated – in part by loading more RNA Polymerase II on the remaining genomes. DNA-dilute cells had normal total protein concentration, which we propose is achieved by increasing production of translational machinery at the expense of specialized, cell-type specific proteins.
Whitham approach to Generalized Hydrodynamics
Authors: Møller Frederik , Schüttelkopf Philipp , Schmiedmayer Jörg , Erne Sebastian 
Published: March 2024

The formation of dispersive shock waves in one-dimensional Bose gas represents a limitation of Generalized Hydrodynamics (GHD) due to the coarse-grained nature of the theory. Nevertheless, GHD accurately captures long-wavelength behavior, thus indicating an implicit knowledge of the underlying microscopic physics. Such representations are already known through the Whitham modulation theory, where dispersionless equations describe the evolution of the slowly varying shock wave parameters. Here we study the correspondence between Whitham's approach to the Gross-Pitaevskii equation and GHD in the semiclassical limit and beyond. Our findings enable the recovery of the shock wave solution directly from GHD simulations, which we demonstrate for both zero and finite temperature. Additionally, we study how free expansion protocols affect the shock wave density and their implications for experimental detection. The combined picture of Whitham and GHD lends itself to additional physical interpretation regarding the formation of shock waves.

Published by the American Physical Society
2024
Improved multiple-Toeplitz matrices reconstruction method using quadratic spatial smoothing for coherent signals DOA estimation
Authors: Qi Bingbing , Xu Lijun , Liu Xiaogang 
Published: March 2024

PurposeThe purpose of this paper is to exploit the multiple-Toeplitz matrices reconstruction method combined with quadratic spatial smoothing processing to improve the direction-of-arrival (DOA) estimation performance of coherent signals at low signal-to-noise ratio (SNRs).Design/methodology/approachAn improved multiple-Toeplitz matrices reconstruction method is proposed via quadratic spatial smoothing processing. Our proposed method takes advantage of the available information contained in the auto-covariance matrices of individual Toeplitz matrices and the cross-covariance matrices of different Toeplitz matrices, which results in a higher noise suppression ability.FindingsTheoretical analysis and simulation results show that, compared with the existing Toeplitz matrix processing methods, the proposed method improves the DOA estimation performance in cases with a low SNR. Especially for the cases with a low SNR and small snapshot number as well as with closely spaced sources, the proposed method can achieve much better performance on estimation accuracy and resolution probability.Research limitations/implicationsThe study investigates the possibility of reusing pre-existing designs for the DOA estimation of the coherent signals. The proposed technique enables achieve good estimation performance at low SNRs.Practical implicationsThe paper includes implications for the DOA problem at low SNRs in communication systems.Originality/valueThe proposed method proved to be useful for the DOA estimation at low SNR.
Role of brand heritage and nostalgia in developing perceived brand authenticity
Authors: Kumar Vikas , Kaushal Vikrant 
Published: March 2024

Purpose
With the increasing competition and rise in the number of brands in almost every product category, consumers need help to figure out authentic brands. Thus, it becomes imperative for marketers to examine the factors that influence the perceptions of brand authenticity (PBA) and its favorable outcomes for the brand. This paper aims to explore the critical antecedents (i.e. “brand heritage” and “brand nostalgia”) and consequences [i.e. “consumer brand engagement” (CBE) and “perceived brand ownership” (PBO)] of PBA in this study.

Design/methodology/approach
In total, 368 responses were collected online through a self-administered survey method and were analyzed using structural equation modeling in AMOS v 25.

Findings
The findings reveal that both brand heritage and brand nostalgia can affect PBA. In addition, PBA engenders CBE and PBO among consumers toward the brand.

Practical implications
The study findings help the marketers to find ways to induce authenticity perceptions among consumers about their brands, which can further translate into PBO and CBE.

Originality/value
This study empirically verifies a model to enhance PBA through brand heritage and nostalgia. Further, it explores CBE and PBO as the potential outcomes of PBA.
Contested imaginaries: workfinding information practices of STEM-trained immigrant women in Canada
Authors: Caidi Nadia , Muzaffar Saadia , Kalbfleisch Elizabeth 
Published: March 2024

PurposeThis pan-Canadian study examines the information practices of STEM-trained immigrant women to Canada as they navigate workfinding and workplace integration. Our study focuses on a population of highly skilled immigrant women from across Canada and uses an information practice lens to examine their lived experiences of migration and labour market integration. As highly trained STEM professionals in pursuit of employment, our participants have specific needs and challenges, and as we explore these, we consider the intersection of their information practices with government policies, settlement services and the hiring practices of STEM employers.Design/methodology/approachWe conducted a qualitative study using in-depth interviews with 74 immigrant women across 13 Canadian provinces and territories to understand the nature of their engagement with employment-seeking in STEM sectors. This article reports the findings related to the settlement and information experiences of the immigrant women as they navigate new information landscapes.FindingsAs immigrants, as women and as STEM professionals, the experiences of the 74 participants reflect both marginality and privilege. The reality of their intersectional identities is that these women may not be well-served by broader settlement resources targeting newcomers, but neither are the specific conventions of networking and job-seeking in the STEM sectors in Canada fully apparent or accessible to them. The findings also point to the broader systemic and contextual factors that participants have to navigate and that shape in a major way their workfinding journeys.Originality/valueThe findings of this pan-Canadian study have theoretical and practical implications for policy and research. Through interviews with these STEM professionals, we highlight the barriers and challenges of an under-studied category of migrants (the highly skilled and “desirable” type of immigrants). We provide a critical discussion of their settlement experiences and expose the idiosyncrasies of a system that claims to value skilled talent while structurally making it very difficult to deliver on its promises to recruit and retain highly qualified personnel. Our findings point to specific aspects of these skilled professionals’ experiences, as well as the broader systemic and contextual factors that shape their workfinding journey.
The impact of Islamic of corporate social responsibility on social welfare with financial fraud as moderating: study in Indonesia
Authors: Tarjo Tarjo , Anggono Alexander , Zakik Zakik , Nordin Shahrina Md , Priyadi Unggul 
Published: March 2024

Purpose
This study aims to empirically examine the influence of Islamic corporate social responsibility (ICSR) on social welfare moderated by financial fraud.

Design/methodology/approach
The method used was the mix method. The number of respondents was 410. They combined the moderate regression analysis with PROCESS Andrew F Hayes to test the research hypothesis. After conducting the survey, it was continued by conducting interviews with the village community and the head of the village.

Findings
The first finding of this study is that ICSR has a significant positive effect on social welfare. The second finding is that financial fraud weakens the influence of ICSR on social welfare. The results of the interviews also confirmed the two findings of this study.

Research limitations/implications
The high level of bias in answering the questions is due to the low public knowledge of ICSR. In addition, the interviews still needed to involve the oil and gas companies and government.

Practical implications
The main implication is improving social welfare, especially for those affected by offshore oil drilling. Furthermore, stakeholders are more sensitive to the adverse effects of financial fraud. Finally, to make drilling companies more transparent and on target in implementing ICSR.

Originality/value
The main novelty in this research is using of the mixed method. In addition, applying financial fraud as a moderating variable is rarely studied empirically.
Challenges and sustainability of Indian mental health: evaluating volunteer-based community mental health clinics with a complex adaptive system framework
Authors: Kumar Manoj , Bos Rekha , de Wit Emma Emily , Bunders-Aelen J.G.F. 
Published: March 2024

Purpose
This study aims to evaluate how a community psychiatry model, referred to as the Mental Health Action Trust (MHAT) in India, provides decentralized care and comprehensive services to people with severe mental illness living in poverty. Using the complex adaptive system (CAS) framework, the authors aim to understand the factors that contribute to the diverse outcomes of the MHAT community mental health programme as observed in four different locations.

Design/methodology/approach
Four MHAT clinics were purposively chosen from two districts in Kerala. A comparative case study methodology was used to document each clinic’s MHAT services and activities, as found during field visits and interviews with staff members and volunteers.

Findings
The study shows that all four clinics met the basic aim of providing free, quality mental health care to the poorest populations, although not all aspects of the comprehensive model could be equally provided. Alignment with the MHAT vision, appropriate leadership, the relationship with partners and their level of community engagement determined the varied success between clinics.

Originality/value
The current study evaluation stresses that community ownership is crucial. Careful attention must be paid to the characteristics of selected partners, including their leadership styles and ability to garner resources.
Unraveling the effects of COVID-19 on the textile industry in South Asia region: a comparative study of major players
Authors: Zahra Zainab , Elahi Ali Raza , Khan Waqas , Mehmood Bilal , Sohail Muhammad 
Published: March 2024

PurposeThe COVID-19 pandemic has caused widespread disruptions to global industries, with the textile sector in South Asia being particularly hard hit. While previous studies have focused on the performance of textile sectors in individual countries, there is a gap in the literature on the comparative impact of the pandemic on the textile industry in South Asian nations. This study aims to fill this gap by investigating the performance of the textile sector in South Asian countries and identifying best practices for overcoming the pandemic’s adverse effects.Design/methodology/approachUsing a comparative approach, this study analyzes the impact of COVID-19 on the performance of the textile sector in Pakistan, India and Bangladesh.FindingsOur findings reveal that COVID-19 significantly negatively impacts the textile industry in Pakistan and India. However, Bangladesh has shown effective practices to support the textile industry and mitigate the pandemic’s adverse effects.Practical implicationsThe findings of this study hold considerable implications for legislators, leaders, investors and supply chain management professionals operating within the South Asian textile sector. This research has the potential to inform policymakers in formulating strategies to facilitate the textile sector’s resilience during emergencies like the COVID-19 pandemic.Originality/valueThis paper provides significant theoretical additions to the current body of literature regarding the impact of COVID-19 on the textile sector in South Asia. The research uses the global value chain (GVC) theory as a theoretical framework to enhance understanding of the impact of global supply chains and interdependencies on the textile sector in the region.
Ship coping strategies for hurricane-induced port disruptions
Authors: Zhou Yan , Wang Chuanxu 
Published: March 2024

PurposeDisruptions at ports may destroy the planned ship schedules profoundly, which is an imperative operation problem that shipping companies need to overcome. This paper attempts to help shipping companies cope with port disruptions through recovery scheduling.Design/methodology/approachThis paper studies the ship coping strategies for the port disruptions caused by severe weather. A novel mixed-integer nonlinear programming model is proposed to solve the ship schedule recovery problem (SSRP). A distributionally robust mean conditional value-at-risk (CVaR) optimization model was constructed to handle the SSRP with port disruption uncertainties, for which we derive tractable counterparts under the polyhedral ambiguity sets.FindingsThe results show that the size of ambiguity set, confidence level and risk-aversion parameter can significantly affect the optimal values, decision-makers should choose a reasonable parameter combination. Besides, sailing speed adjustment and handling rate adjustment are effective strategies in SSRP but may not be sufficient to recover the schedule; therefore, port skipping and swapping are necessary when multiple or longer disruptions occur at ports.Originality/valueSince the port disruption is difficult to forecast, we attempt to take the uncertainties into account to achieve more meaningful results. To the best of our knowledge, there is barely a research study focusing on the uncertain port disruptions in the SSRP. Moreover, this is the first paper that applies distributionally robust optimization (DRO) to deal with uncertain port disruptions through the equivalent counterpart of DRO with polyhedral ambiguity set, in which a robust mean-CVaR optimization formulation is adopted as the objective function for a trade-off between the expected total costs and the risk.