bluuebunny/crossref_metadata_2025_split huggingface dataset:
Copy number of the eukaryotic rRNA gene can be counted comprehensively
Authors: Yabuki Akinori , Hoshino Tatsuhiko , Nakamura Tamiko , Mizuno Keiko 
Published: August 2023

AbstractGene sequence has been widely used in molecular ecology. For instance, the ribosomal RNA (rRNA) gene has been widely used as a biological marker to understand microbial communities. The variety of the detected rRNA gene sequences reflects the diversity of the microorganisms existing in the analyzed sample. Their biomass also can be estimated by applying quantitative sequencing with the information of rRNA gene copy numbers in genomes, however, the information on rRNA gene copy number is still limited. Especially, the copy number in microbial eukaryotes is much less understood than that of prokaryotes, possibly because of the large and complex structure of eukaryotic genomes. In this communication, we report an alternative approach that is more appropriate from the existing method of quantitative sequencing and demonstrate that the copy number of eukaryotic rRNA can be measured efficiently and comprehensively. By applying this approach widely, information on the eukaryotic rRNA copy number can be determined, and their community structures can be depicted and compared more efficiently.
A conserved transcription factor controls gluconeogenesis via distinct targets in hypersaline-adapted archaea with diverse metabolic capabilities
Authors: Hackley Rylee K. , Vreugdenhil-Hayslette Angie , Darnell Cynthia L. , Schmid Amy K. 
Published: August 2023

AbstractTimely regulation of carbon metabolic pathways is essential for cellular processes and to prevent futile cycling of intracellular metabolites. InHalobacterium salinarum, a hypersaline adapted archaeon, a sugar-sensing TrmB family protein controls gluconeogenesis and other biosynthetic pathways. Notably,Hbt. salinarumdoes not utilize carbohydrates for energy, uncommon among Haloarchaea. We characterized a TrmB-family transcriptional regulator in a saccharolytic generalist,Haloarcula hispanica, to investigate whether the targets and function of TrmB, or its regulon, is conserved in related species with distinct metabolic capabilities. InHar. hispanica, TrmB binds to 15 sites across the genome and induces the expression of genes primarily involved in gluconeogenesis and tryptophan biosynthesis. An important regulatory control point inHbt. salinarum, activation ofppsAand repression ofpykA, is absent inHar. hispanica. Contrary to its role inHbt. salinarumand saccharolytic hyperthermophiles, TrmB does not act as a global regulator: it does not directly repress the expression of glycolytic enzymes, peripheral pathways such as cofactor biosynthesis, or catabolism of other carbon sources inHar. hispanica. Cumulatively, these findings suggest re-wiring of the TrmB regulon alongside metabolic network evolution in Haloarchaea.
Neuroendocrine control of synaptic transmission by PHAC-1 inC. elegans
Authors: Stratigi Aikaterini , Soler-García Miguel , Krout Mia , Shukla Shikha , Bono Mario De , Richmond Janet E. , Laurent Patrick 
Published: August 2023

AbstractA dynamic interplay between synaptic and neuromodulatory signalling guarantees flexible but robust neuronal circuits. Presynaptic modulation plays a crucial role in controlling the excitatory-inhibitory balance within networks. Here, we designed a genetic screen to identify genes involved in the neuromodulation of theC. elegansneuromuscular junctions (NMJ) and identified the orthologs of the Protein Phosphatase 1 regulatory subunit PHACTR1 (phac-1)and the presynaptic phosphoproteins Synapsin (snn-1). Fivede novovariants of human PHACTR1 are associated with severe early-onset epilepsies (DEE70). To understand the impact of these variants, we introduced the DEE70 mutations intophac-1. These mutations resulted in the formation of a constitutively active PP1-PHAC-1 holoenzyme that disrupts cholinergic signalling at the NMJ. By using quantitative fluorescence imaging, electron microscopy and electrophysiology, we found that the constitutive holoenzyme alters the synaptic vesicle cycle, reduces the synaptic vesicle reserve pool, and increases neuropeptide release by dense-core vesicles. Notably, while SNN-1 phosphoregulation contributes to NMJ signalling, genetic interactions suggest that SNN-1 is not the main effector of PP1-PHAC-1 holoenzyme signalling. Collectively, our results confirm the pathogenicity of DEE70 variants, clarify their dominant-positive effects, and provide evidence of a presynaptic mode of action for DEE70.
The Role of Decompressive Craniectomy following Microsurgical Repair of a Ruptured Aneurysm: Analysis of a South Australian Cerebrovascular Registry
Authors: O’Donohoe Tom J , Ovenden Christopher , Bouras George , Chidambaram Seevakan , Plummer Stephanie , Davidson Andrew S , Kleinig Timothy , Abou-Hamden Amal 
Published: August 2023

AbstractBackgroundDecompressive craniectomy (DC) remains a controversial intervention for established or anticipated intracranial hypertension among patients with aneurysmal subarachnoid haemorrhage (aSAH).MethodsWe identified aSAH patients who underwent DC following microsurgical aneurysm repair from a prospectively maintained cerebrovascular registry and compared their outcomes with a propensity-matched cohort who did not. Logistic regression was used to identify predictors of undergoing decompressive surgery and post-operative outcome. The outcomes of interest were inpatient mortality, unfavourable outcome at first and final follow-up, NIS-Subarachnoid Hemorrhage Outcome Measure and modified Rankin Score (mRS) at first and final follow-up.ResultsA total of 246 consecutive patients with aSAH underwent microsurgical clipping of the culprit aneurysm between 01/09/2011 and 20/07/2020. Of these, 46 patients underwent DC and were included in the final analysis. Unsurprisingly, patients treated with DC had a greater chance of unfavourable outcome (p<0.001) and higher median mRS (p<0.001) compared with those who did not at final follow-up. Despite this, almost two-thirds (64.1%) of patients undergoing a DC had a favourable outcome at this time-point. When compared with a propensity-matched cohort who did not, patients treated with DC fared worse at all endpoints. Multivariable logistic regression revealed that the presence of intracerebral haemorrhage (ICH) and increased pre-operative mid-line shift were predictive of undergoing DC, and WFNS grade ≥ 4 and a delayed ischaemic neurological deficit requiring endovascular angioplasty were associated with an unfavourable outcome.ConclusionsOur data suggest that DC can be performed with acceptable rates of morbidity and mortality, particularly among patients who present with lower grade aSAH. Further research is required to determine the superiority, or otherwise, of DC compared with structured medical management of intracranial hypertension in this context, and to identify predictors of requiring decompressive surgery and patient outcome.
An amortized approach to non-linear mixed-effects modeling based on neural posterior estimation
Authors: Arruda Jonas , Schälte Yannik , Peiter Clemens , Teplytska Olga , Jaehde Ulrich , Hasenauer Jan 
Published: August 2023

AbstractNon-linear mixed-effects models are a powerful tool for studying heterogeneous populations in various fields, including biology, medicine, economics, and engineering. Here, the aim is to find a distribution over the parameters that describe the whole population using a model that can generate simulations for an individual of that population. However, fitting these distributions to data is computationally challenging if the description of individuals is complex and the population is large. To address this issue, we propose a novel machine learning-based approach: We exploit neural density estimation based on conditional normalizing flows to approximate individual-specific posterior distributions in an amortized fashion, thereby allowing for efficient inference of population parameters. Applying this approach to problems from cell biology and pharmacology, we demonstrate its unseen flexibility and scalability to large data sets compared to established methods.
Structures of wild-type and a constitutively closed mutant of connexin26 shed light on channel regulation by CO2
Authors: Brotherton Deborah H. , Nijjar Sarbjit , Savva Christos G. , Dale Nicholas , Cameron Alexander D. 
Published: August 2023

AbstractConnexins allow intercellular communication by forming gap junction channels (GJCs) between juxtaposed cells. Connexin26 (Cx26) can be regulated directly by CO2. This is proposed to be mediated through carbamylation of K125. We show that mutating K125 to glutamate, mimicking the negative charge of carbamylation, causes Cx26 GJCs to be constitutively closed. Through cryo-EM we observe that the K125E mutation pushes a conformational equilibrium towards the channel having a constricted pore entrance, similar to effects seen on raising the partial pressure of CO2. In previous structures of connexins, the cytoplasmic loop, important in regulation and where K125 is located, is disordered. Through further cryo-EM studies we trap distinct states of Cx26 and observe density for the cytoplasmic loop. The interplay between the position of this loop, the conformations of the transmembrane helices and the position of the N-terminal helix, which controls the aperture to the pore, provides a mechanism for regulation.
Multi-scale characterisation of homologous recombination deficiency in breast cancer
Authors: Jacobson Daniel H. , Pan Shi , Fisher Jasmin , Secrier Maria 
Published: August 2023

ABSTRACTBackgroundHomologous recombination is a robust, broadly error-free mechanism of double strand break repair, and deficiencies cause reliance on alternative repair processes, leading to sensitivity to PARP inhibitors. Patients displaying homologous recombination deficiency can be identified using ‘mutational signatures’. However, these patterns are difficult to reliably infer from exome sequencing. Additionally, as mutational signatures are a historical record of mutagenic processes, this limits their utility in describing the current status of a tumour.ResultsHere, we apply two methods for classifying homologous recombination deficiency in breast cancer to explore the features and heterogeneity associated with this phenotype. Firstly, we apply a likelihood-based method which leverages small insertions and deletions to improve classification of homologous recombination deficiency in exome sequenced breast cancers. We find that whilst BRCA+ homologous recombination deficient samples display strong similarities to those harbouring BRCA defects, they deviate in microenvironmental features such as hypoxic signalling. Secondly, using this classification we develop a 228-gene transcriptional signature which simultaneously characterises homologous recombination deficiency and BRCA1/2-defect status, and is linked with PARP inhibitor response. Finally, we apply this signature to single-cell RNA-sequenced breast cancer cohorts to study homologous recombination deficiency at single cell resolution and demonstrate that these cells present a distinct milieu of interactions with immune cells in their microenvironment compared to their HR proficient counterparts, which could inform checkpoint blockade for HRD tumours.ConclusionsWe apply multi-scale approaches to characterise homologous recombination deficiency in breast cancer through the development of mutational and transcriptional signatures. We show that indels, even at low levels, can improve homologous recombination deficiency classification. Additionally, we demonstrate the heterogeneity of homologous recombination deficiency, especially in relation to BRCA status, and show that indications of this feature can be captured at a single-cell level, enabling further investigations into interactions between DNA repair deficient cells and their tumour microenvironment.
Navigating multiple accountabilities through managers’ boundary work in professional service firms
Authors: Azambuja Ricardo , Baudot Lisa , Malsch Bertrand 
Published: August 2023

PurposeThis study explores the professional work of managers in professional service firms (PSFs) by focusing on the relational position of managers as they interface between diverse groups of actors and navigate a multiplicity of accountabilities.Design/methodology/approachDrawing on an ethnographic study of managers in a Brazilian PSF, this study demonstrates through observations, interviews and shadowing how PSF managers address multiple accountabilities in the conduct of professional work.FindingsTo navigate multiple accountabilities, PSF managers perform several forms of boundary work, which the authors conceptualize as “revamping” and “remolding” operations and “translating” and “transforming” understandings. The form of boundary work performed depends on the configuration of two elements of accountability demands: knowledge orientation and extent of exposure. Although analytically distinct, these elements intertwine, suggesting the need for a dynamic perspective on accountability. The analysis shows that professional work extends beyond fixed or passive views of hierarchical and intrinsic accountability to emphasize that managers exude accountability of an adaptive nature.Research limitations/implicationsThis study illustrates and theorizes the role of boundary work in PSFs, develops its link to accountability, and identifies its scholarly and practical affordances and limitations for understanding managers’ professional work when navigating multiple accountabilities.Originality/valueThe findings reveal perspectives and behaviors of managers embedded in PSFs, illustrating their unstructured and agentic experiences of accountability and boundary work in practice. The insights can be extended to other contexts where managers face multiple accountabilities in conducting professional work.
Implications for multinational enterprises from emerging market subsidiaries’ reverse knowledge transfer
Authors: Fjellström Daniella , Chowdhury Ehsanul Huda , Ahmad Sohail , Batkhuu Bolortuya 
Published: August 2023

PurposeThis study aims to understand the role of drivers, underlying challenges and, consequently, the implications of the reverse knowledge transfer (RKT) process for the multinational enterprises (MNE)s.Design/methodology/approachA dyadic qualitative research design was used with a cross-country design covering perspectives from both the headquarters and subsidiaries from the USA, Denmark, Pakistan, India and Bangladesh. In-depth interviews were conducted with managers in multiple sectors such as information technology, telecommunications, project management and engineering.FindingsThe study reveals the constraints and drivers of the RKT process, and furthermore elaborates on the implications for MNEs. RKT can lead to the development of new processes, subsidiary independence and intra-organizational knowledge transfer. Besides, it can entail challenges such as position insecurity for subsidiaries and a blurring of the MNE market vision. The findings demonstrate several implications for the MNEs.Practical implicationsThe study highlights the direct implications of RKT for the multinational enterprises. The findings serve as a practical guide for global managers seeking to improve their competitive edge.Originality/valueThe study presents a framework of the RKT process from emerging market subsidiaries to parent companies, that demonstrates the role of drivers, underlying challenges and implications of the RKT process for the MNEs.
On the consequences of electronic performance monitoring in organizations: theory and evidence
Authors: Kalischko Thomas , Riedl René 
Published: August 2023

PurposeThe potential applications of information and communication technologies in the workplace are wide-ranging and, especially since the COVID-19 pandemic, have increasingly found their way into the field of electronic performance monitoring (EPM) of employees. This study aims to examine the influence of EPM on individual performance considering the aspects of privacy invasion, organizational trust and individual stress within an organization. Thus, important insights are generated for academia as well as business.Design/methodology/approachA theoretical framework was developed which conceptualizes perceived EPM as independent variable and individual performance as dependent variable. Moreover, the framework conceptualizes three mediator variables (privacy invasion, organizational trust and individual stress). Based on a large-scale survey (N = 1,119), nine hypotheses were tested that were derived from the developed framework.FindingsThe results indicate that perception of EPM significantly increases privacy invasion, reduces organizational trust, increases individual stress and ultimately reduces individual performance. Moreover, it was found that privacy invasion reduces organizational trust and that this lowered trust increases individual stress. Altogether, these findings suggest that the use of EPM by employers may be associated with significant negative consequences.Originality/valueThis research enriches the literature on digital transformation, as well as human–machine interaction, by adopting a multidimensional theoretical and empirical perspective regarding EPM in the workplace context, in which the influence of EPM perceptions on individual performance is examined under the influence of different aspects (privacy invasion, organizational trust and individual stress) not currently considered in this combination in the literature.
Student engagement through teamwork skills: the mediating role of psychological well-being
Authors: Bhargava Sheela , Sharma Renu 
Published: August 2023

PurposeThe study aims to examine the mediating effect of psychological well-being (PWB) on the relationship between teamwork skills and student engagement (SE) in higher education institutional setups.Design/methodology/approachThe study used a triangulation mixed-methods approach. Data were collected from final-year students pursuing post-graduation and graduation in private colleges in India. In the main study, quantitative data was gathered from 276 students through a survey. The relationship among the variables-teamwork skills, SE and PWB was empirically validated through path analysis; mediation was also conducted. In the auxiliary study, qualitative data was gathered through focus group sessions and was analyzed using thematic analysis.FindingsResults depicted that teamwork skills positively predict students' engagement with their academic program. Additionally, PWB partially mediates the relationship between teamwork skills and SE.Originality/valueThe study was conducted to expand understanding of aspects related to promoting students' engagement in HEIs in Delhi and Haryana through being attentive toward teamwork skills development and through taking care of students' PWB.
Justice in the workplace: Islamic principles for wage determination
Authors: Yasmeen Kausar 
Published: August 2023

PurposeThe objective of this study is to construct a theoretical framework concerning wage determination, grounded inprinciples and supplemented by conventional theories. It discusses the Islamic perspectives on minimum wage and examines contemporary challenges and intricacies in its application.Design/methodology/approachThis study uses thematic analysis to create the conceptual framework, drawing upon a review of pertinent literature such as academic papers, books and articles published up to 2023.FindingsThe framework encompasses various categories, namely, employee characteristics, job characteristics, market factors, compensation practices and Islamic principles. Each category consists of multiple variables. The resulting framework offers a holistic and ethically grounded methodology for wage determination, aligning with both Islamic and conventional perspectives. This study notes the absence of a universally agreed-upon minimum wage. Islamic economics faces challenges due to the unclear application of principles, limited awareness, legal constraints and a lack of empirical evidence on wage systems, along with complexities in their implementation.Research limitations/implicationsThe paper’s limited scope focuses solely on the Islamic perspective on wage determination, without comparing it to the conventional viewpoint. This may have implications for future research.Practical implicationsThe insights on Islamic principles and wage determination guide scholars and policymakers interested in promoting just and equitable wages.Originality/valueThis study is distinct in its integration of various factors to propose an all-encompassing framework for wage determination, rooted in the Quran andprinciples, while also reinforcing the framework with conventional theories. Additionally, it adds to the growing body of literature by investigating the Quran’s stance andprinciples on minimum wage, as well as discusses the challenges involved in implementing an Islamic approach to wage determination, which has received limited attention in Islamic literature.
Antecedents of women’s social entrepreneurship: values development and the perceived desirability and feasibility of social venture creation
Authors: de Magdalene Persephone 
Published: August 2023

PurposeThis paper aims to identify the values antecedents of women’s social entrepreneurship. It explores where and how these values emerge and how they underpin the perceived desirability and feasibility of social venture creation.Design/methodology/approachValues development across the life-course is interrogated through retrospective sense-making by thirty UK-based women social entrepreneurs.FindingsThe findings express values related to empathy, social justice and action-taking, developed, consolidated and challenged in a variety of experiential domains over time. The cumulative effects of these processes result in the perceived desirability and feasibility of social entrepreneurial venture creation as a means of effecting social change and achieving coherence between personal values and paid work, prompting social entrepreneurial action-taking.Originality/valueThis paper offers novel, contextualised insights into the role that personal values play as antecedents to social entrepreneurship. It contributes to the sparse literature focussed on both women’s experiences of social entrepreneurship generally, and on their personal values specifically.