bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selection-driven trait loss in independently evolved cavefish populations
Authors: Moran Rachel L. , Richards Emilie J. , Ornelas-García Claudia Patricia , Gross Joshua B. , Donny Alexandra , Wiese Jonathan , Keene Alex C. , Kowalko Johanna E. , Rohner Nicolas , McGaugh Suzanne E. 
Published: November 2022

AbstractPredicting the outcome of evolution is a central goal of modern biology, yet, determining the relative contributions of deterministic events (i.e., selection) and stochastic events (i.e., drift and mutation) to the evolutionary process remains a major challenge. Systems where the same traits have evolved repeatedly provide natural replication that can be leveraged to study the predictability of molecular evolution and the genetic basis of adaptation. Although mutational screens in the laboratory have demonstrated that a diversity of genetic mutations can produce phenocopies of one another, in natural systems, similar genetic changes frequently underly the evolution of phenotypes across independent lineages. This suggests a substantial role for constraint and determinism in evolution and supports the notion that there may be characteristics which make certain mutations more likely to contribute to phenotypic evolution. Here we use large-scale whole genome resequencing in the Mexican tetra,Astyanax mexicanus, to demonstrate that selection has played a primary role in repeated evolution of both trait loss and trait enhancement across independent cave lineages. We identify candidate genes underlying repeated adaptation to caves and infer the mode of repeated evolution, revealing that selection on standing genetic variation andde novomutations both contribute substantially to repeated adaptation. Finally, we show that genes with evidence of repeated evolution have significantly longer coding regions compared to the rest of the genome, and this effect is most pronounced in genes evolving convergently via independent mutations. Importantly, our findings provide the first empirical support for the hypothesis that genes with larger mutational targets are more likely to be the substrate of repeated evolution and indicate that features of the novel cave environment may impact the rate at which mutations occur.
ViCloD, an interactive web tool for visualizing B cell repertoires and analyzing intraclonal diversities: application to human B-cell tumors
Authors: Jeusset Lucile , Abdollahi Nika , Verny Thibaud , Armand Marine , De Septenville Anne Langlois , Davi Frédéric , Bernardes Juliana S. 
Published: November 2022

AbstractHigh throughput sequencing of adaptive immune receptor repertoire (AIRR-seq) has provided numerous human immunoglobulin (IG) sequences allowing specific B cell receptor (BCR) studies such as the antigen-driven evolution of antibodies (soluble forms of the membrane-bound IG part of the BCR). AIRR-seq data allows researchers to examine intraclonal differences caused primarily by somatic hypermutations in IG genes and affinity maturation. Exploring this essential adaptive immunity process could help elucidate the generation of antibodies with high affinity or broadly neutralizing activities. Retracing their evolutionary history could also help to clarify how vaccines or pathogen exposition drive the humoral immune response. Computational methods are necessary for large-scale analysis of AIRR-seq properties. However, there is no efficient and interactive tool for analyzing intraclonal diversity, permitting users to explore adaptive immune receptor repertoires in biological and clinical applications. Here we developed ViCloD, a web server for large-scale visual analysis of repertoire clonality and intraclonal diversity. ViCloD uses data preprocessed by IMGT/HighV-QUEST and performs clonal grouping and evolutionary analyses, producing a collection of useful plots. The web server presents diverse functionalities, including repertoire navigation, clonal abundance analysis, and intraclonal evolutionary tree reconstruction. Users can download the analyzed data in different table formats and save the generated plots as images. ViCloD is a simple, versatile, and user-friendly tool that can help researchers and clinicians to analyze B cell intraclonal diversity. Moreover, its pipeline is optimized to process hundreds of thousands of sequences within a few minutes, allowing an efficient investigation of large and complex repertoires.Availability and implementationThe web server is available athttp://www.lcqb.upmc.fr/viclod/. The pipeline is available at github and allows users to run analyses locallyhttps://github.com/julibinho/ViCLoD
From primordial clocks to circadian oscillators
Authors: Pitsawong Warintra , Pádua Ricardo A. P. , Grant Timothy , Hoemberger Marc , Otten Renee , Bradshaw Niels , Grigorieff Nikolaus , Kern Dorothee 
Published: November 2022

AbstractCircadian rhythms play an essential role in many biological processes and surprisingly only three prokaryotic proteins are required to constitute a true post-translational circadian oscillator. The evolutionary history of the three Kai proteins indicates that KaiC is the oldest member and central component of the clock, with subsequent additions of KaiB and KaiA to regulate its phosphorylation state for time synchronization. The canonical KaiABC system in cyanobacteria is well understood, but little is known about more ancient systems that possess just KaiBC, except for reports that they might exhibit a basic, hourglass-like timekeeping mechanism. Here, we investigate the primordial circadian clock inRhodobacter sphaeroides(RS) that contains only KaiBC to elucidate its inner workings despite the missing KaiA. Using a combination X-ray crystallography and cryo-EM we find a novel dodecameric fold for KaiCRSwhere two hexamers are held together by a coiled-coil bundle of 12 helices. This interaction is formed by the C-terminal extension of KaiCRSand serves as an ancient regulatory moiety later superseded by KaiA. A coiled-coil register shift between daytime- and nighttime-conformations is connected to the phosphorylation sites through a long-range allosteric network that spans over 160 Å. Our kinetic data identify the difference in ATP-to-ADP ratio between day and night as the environmental cue that drives the clock and further unravels mechanistic details that shed light on the evolution of self-sustained oscillators.
The influence of social isolation and loneliness on the intention to travel for tourism
Authors: Añaña Edar da Silva , Borges Gustavo da Rosa , Petry Jonas Fernando 
Published: November 2022

Purpose
This study aims to evaluate the factors influencing certain negative feelings, such as social isolation disorder and loneliness, on consumers’ intentions to travel for tourism.

Design/methodology/approach
This quantitative research used a survey questionnaire composed of eight interval evaluation questions and six demographic variables for the data collection. A total of 290 usable responses were gathered from social networks. The evaluation of the Measurement Model adjustment and the verification of the research hypothesis was done by a structural equations modeling.

Findings
The results reveal that social isolation is not a monolithic construction; instead of that, it is a construct formed by two interrelated factors, the social isolation itself, involving the individual and her/his personality, and the social integration, a factor of situational order, referring to the relations of the individual with his reference group. Factors are influenced by the ease/difficulty of the individual, in cultivating relationships with other people and significantly influence the intention to travel for tourism.

Practical implications
The study contributes to tourism management by breaking the phenomenon down into two dimensions and evaluating the impact of each of them on consumer attitudes, which should be very useful for the segmentation and positioning of tourism products.

Originality/value
Results support the evidence reported by Murphy, who found that people tend to want to make friends, but that this tendency did not appear to be evident about travel and supported Hawthorne’s findings, that the more socially isolated people are, the less they will want to interact with others, demonstrating that social isolation is indeed an inhibitor of social interaction.
Challenges associated with sustainability accounting and reporting practices: a legitimacy perspective
Authors: Juusola Katariina , Srouji Reem 
Published: November 2022

Purpose
The purpose of this study was to use legitimacy theory to discuss three important aspects of sustainability accounting and reporting practices: the historical building of legitimacy for such practices, how organizations have adhered to them when building organizational legitimacy in a new legitimacy context (the Middle East and North Africa [MENA] region) and how sustainability professionals assess the legitimacy of them in this context.

Design/methodology/approach
The study applied an exploratory qualitative design and a paradigm-type approach to organizational discourse analysis. It used a document analysis and eight expert interviews as data sources.

Findings
The findings revealed that sustainability accounting and reporting face considerable challenges in the MENA region. Four discourses on organizational sustainability in the region were identified, namely, the normative/pragmatic, compliance, restrictive and performative discourses.

Practical implications
Awareness of the challenges and mechanics of sustainability accounting and reporting practices is important for managers, policymakers and consumers, who typically lack in-depth understanding of such practices and so would benefit from being better able to assess companies’ sustainability performance. The four identified discourses facilitate stakeholders’ understanding of sustainability practices in the MENA region.

Originality/value
The legitimacy of sustainability accounting and reporting has not previously been comprehensively investigated in non-Western contexts. This study discusses three important aspects of legitimacy: legitimacy of an object, legitimacy of a subject and legitimacy from an evaluator’s perspective. In doing so, it identifies the paradoxical nature of organizations’ attempts to comply with sustainability reporting practices.
Performance analysis of Pythagorean fuzzy entropy and distance measures in selecting software reliability growth models using TOPSIS framework
Authors: Arora H.D. , Naithani Anjali 
Published: November 2022

PurposeThe purpose of this paper is to create a numerical technique to tackle the challenge of selecting software reliability growth models (SRGMs).Design/methodology/approachA real-time case study with five SRGMs tested against a set of four selection indexes were utilised to show the functionality of TOPSIS approach. As a result of the current research, rating of the different SRGMs is generated based on their comparative closeness.FindingsAn innovative approach has been developed to generate the current SRGMs selection under TOPSIS environment by blending the entropy technique and the distance-based approach.Originality/valueIn any multi-criteria decision-making process, ambiguity is a crucial issue. To deal with the uncertain environment of decision-making, various devices and methodologies have been explained. Pythagorean fuzzy sets (PFSs) are perhaps the most contemporary device for dealing with ambiguity. This article addresses novel tangent distance-entropy measures under PFSs. Additionally, numerical illustration is utilized to ascertain the strength and authenticity of the suggested measures.
Examining purchase intention for luxury fashion: integrating theory of reasoned action, with affect-behavior-cognition (ABC) model, identity and social identity theories
Authors: Lau Mei Mei , Ng Peggy Mei Lan , Chan Elaine Ah Heung , Cheung Cherry Tin Yan 
Published: November 2022

PurposeThis study aims to study the attitude toward purchasing luxury fashion of young consumers based on an extended model that integrates the constructs of the theory of reasoned action (TRA), identity theory, social identity theory, affect–behavior–cognition (ABC) model of attitude and brand attractiveness.Design/methodology/approachA purposive sampling approach was used to collect data from 237 young luxury fashion consumers in Hong Kong. Results were analyzed using partial least square.FindingsThe findings revealed that self-identity predicts affect-based attitudes (i.e. passive engagement and active engagement), and social identity predicts cognition-based attitude (i.e. attitude toward celebrity endorsement). Moreover, both affect- and cognition-based attitudes were found to be antecedents that enhanced brand attractiveness, which in turn positively affected purchase intention.Research limitations/implicationsThis study collected data from Generation Z. Although this generation is the world’s most influential consumer group and is highly engaged in social media, the findings may not be representative of the entire population in Hong Kong. Therefore, the findings should be used cautiously in the whole luxury fashion industry.Originality/valueThis study extends the understanding of luxury fashion purchase intention from TRA to the connection among identity, social identity theories and ABC model of attitude and brand attractiveness. The findings of this study also contribute to practical insights on developing suitable marketing strategies for the Asian luxury fashion market.
Business model–dynamic capabilities and open innovation initiatives in research‐intensive organisations: A case of Australia's national science agency
Authors: Kriz Alexandra , Tresidder Julia , Dowd Anne‐Maree , Weerawardena Jay , Witell Lars , Snyder Hannah , de Pallant Rohan 
Published: November 2022

AbstractPublicly funded national science agencies create value as innovation catalysts and through their scientific and research missions, they tackle wicked problems. Understanding how dynamic capabilities and business model innovation enable research‐intensive organisations to seize the market in the mission is key to translating bold new science that has impact. We qualitatively explore how Australia's national science agency—the Commonwealth Scientific Industrial Research Organisation (CSIRO)—has pursued open innovation to support business model–dynamic capabilities in an evolving publicly funded landscape. We reflect on the value of open innovation initiatives that have allowed the CSIRO to ambidextrously pursue world‐class science while achieving impact.Points for practitionersDynamic capabilities and business model innovation are strategic tools for publicly funded national science agencies seeking to seize the market in the mission.We examine a case of business model–dynamic capabilities in CSIRO.Open innovation has been important for CSIRO as part of an ambidextrous approach.
Effect of processing treatments on the allergenicity of nuts and legumes: A meta‐analysis
Authors: Astuti Rizki Maryam , Palupi Nurheni Sri , Suhartono Maggy Thenawidjaja , Kusumaningtyas Eni , Lioe Hanifah Nuryani 
Published: November 2022

AbstractThe effective food processing to reduce nuts and legumes allergenicity could not be easily and directly concluded from reading a few published reports. Therefore, we conducted a meta‐analysis to investigate this issue. A literature search was conducted in eight electronic databases from January 2000 to June 11, 2021. The primary outcome of interest was the allergenicity of processed nuts or legumes determined by enzyme‐linked immunosorbent assay from in vitro studies. Data with the standardized mean difference (SMD) of 95% confidence interval (CI) were pooled using a random‐effect model by RevMan 5.4 software. Heterogeneity was assessed using Cochran's Q (PQ) and I2 tests. The search strategy identified 18,793 articles. However, only 61 studies met the inclusion criteria and were included in this meta‐analysis. There were 21 and 15 types of respective single and combined food processing treatments analyzed for their effects on reducing allergenicity. In single processing treatment, the extrusion and fermentation had the largest reduction in allergenicity, considering their SMD value, that is, −20.19 (95% CI: −22.22 to −18.17; the certainty of evidence: moderate) and −20.8 (95% CI: −24.10 to −17.50; the certainty of evidence: moderate), respectively. Whereas in the combination, the treatment of fermentation followed by proteolytic hydrolysis showed the most significant reduction (SMD: −53.34; 95% CI: −70.18 to −36.5) and the evidence quality of this treatment was considered moderate. In conclusion, these three food processing methods showed a desirable impact in reducing nuts or legumes allergenicity.Practical ApplicationNuts and legumes play an essential role as protein sources in food consumption worldwide, but they usually contain allergens. Our study has investigated the food processing methods that effectively reduce their allergenicity by meta‐analysis. The result gives valuable information for further laboratory investigation on allergens and can be used by food industries in providing foods from nuts and legumes with lower allergenicity.
Orbital inflammatory pseudotumor revealing multi‐organ immunoglobulin G4‐related disease
Authors: Ben Salah Raida , Kammoun Sonda , Mefteh Ansar , Frikha Faten , Rekik Mona , Trigui Amira , Bahloul Zouhir 
Published: November 2022

AbstractRelatively recently, the concept that immunoglobulin G4 (IgG4)‐related disease is a distinct chronic inflammatory disorder rather than a subset of Sjögren's syndrome has been accepted. IgG4‐related disease (IgG4‐RD) is a fibro‐inflammatory systemic immune‐mediated condition that can affect the pancreas, salivary glands, and lymph nodes. Almost every organ may be impacted synchronously or metachronously by this illness, which causes the development of sclerotic masses of varying sizes. Numerous other rheumatic diseases can present with characteristics of IgG4‐RD, making it difficult to distinguish between them. However, cases of IgG4‐RD involving the bilateral orbits, and pancreas with biological abnormalities are rare. We present a case of an 18‐year‐old female with vitiligo since the age of 3 years who presented with acute pancreatitis and acalculous cholecystitis, bilateral orbital masses, palpebral edema, and eosinophilia. The patient was diagnosed with IgG4‐RD in keeping with clinical presentation and the elevated serum IgG4 level and after elimination of other differential diagnoses. The patient's symptoms gradually relieved after glucocorticoid therapy. This case presents an uncommon combination of clinical features infrequently reported in the literature. Multi‐organ IgG4‐RD is a multisystemic mass, commonly creating diagnostic challenges for clinicians. Furthermore, and more importantly, it highlights the need to keep a differential of IgG4‐RD in mind, to aid in the early and correct treatment of the disease.
Enhancing the quality of allied health clinical supervision in a regional setting: An action research study
Authors: Gardner Marcus J. , McKinstry Carol , Perrin Byron M. 
Published: November 2022

AbstractObjectiveTo explore and describe strategies to enhance the implementation of an organisational clinical supervision framework and subsequently inform the development of a model of implementation of clinical supervision for allied health professionals in a regional health care setting.SettingA large regional health service in Victoria, providing hospital, rehabilitation, community, mental health and aged care services.ParticipantsAllied health managers employed at the health service were members of an action research group.DesignThis longitudinal study used an action research approach. The action research group informed the repeated cycles of planning, action and reflection. Data from recorded action research meetings were analysed using content analysis.ResultsThe action research group met 11 times over a 5‐year period informing four action research cycles. Six main themes relating to factors that enhanced the quality of clinical supervision emerged from the analysis of the action research group data: purpose and value of clinical supervision; clinical supervision characteristics; differences between disciplines; framework development; training and support and implementation of clinical supervision.ConclusionThe findings from this comprehensive longitudinal study provide evidence‐based approaches to the implementation of allied health clinical supervision. The action research approach used ensures that the strategies described are realistic and sustainable. A model has been developed to inform the implementation of clinical supervision for allied health.
IgG memory B cells expressing IL4R and FCER2 are associated with atopic diseases
Authors: Aranda Carlos J. , Gonzalez‐Kozlova Edgar , Saunders Sean P. , Fernandes‐Braga Weslley , Ota Miyo , Narayanan Sriram , He Jin‐Shu , Del Duca Ester , Swaroop Bose , Gnjatic Sacha , Shattner Gail , Reibman Joan , Soter Nicholas A. , Guttman‐Yassky Emma , Curotto de Lafaille Maria A. 
Published: November 2022

AbstractBackgroundAtopic diseases are characterized by IgE antibody responses that are dependent on cognate CD4 T cell help and T cell‐produced IL‐4 and IL‐13. Current models of IgE cell differentiation point to the role of IgG memory B cells as precursors of pathogenic IgE plasma cells. The goal of this work was to identify intrinsic features of memory B cells that are associated with IgE production in atopic diseases.MethodsPeripheral blood B lymphocytes were collected from individuals with physician diagnosed asthma or atopic dermatitis (AD) and from non‐atopic individuals. These samples were analyzed by spectral flow cytometry, single cell RNA sequencing (scRNAseq), and in vitro activation assays.ResultsWe identified a novel population of IgG memory B cells characterized by the expression of IL‐4/IL‐13 regulated genes FCER2/CD23, IL4R, IL13RA1, and IGHE, denoting a history of differentiation during type 2 immune responses. CD23+IL4R+IgG+ memory B cells had increased occurrence in individuals with atopic disease. Importantly, the frequency of CD23+IL4R+IgG+ memory B cells correlated with levels of circulating IgE. Consistently, in vitro stimulated B cells from atopic individuals generated more IgE+ cells than B cells from non‐atopic subjects.ConclusionsThese findings suggest that CD23+IL4R+ IgG+ memory B cells transcribing IGHE are potential precursors of IgE plasma cells and are linked to pathogenic IgE production.
Intramuscular adipogenesis in cattle: Effects of body fat distribution and macrophage infiltration
Authors: Yamada Tomoya 
Published: November 2022

AbstractEctopic fat is defined by the deposition of adipose tissue within non‐adipose tissue such as skeletal muscle. Japanese Black cattle (Wagyu) are characterized by the ability to accumulate high amounts of intramuscular adipose tissue. Obese conditions enhance the accumulation of ectopic fat. This review shows the effects of subcutaneous and visceral fat distribution on Wagyu intramuscular adipogenesis. Obese conditions also stimulate the macrophage infiltration into adipose tissues. Adipose tissue macrophages have reported to regulate adipose tissue growth and ectopic fat accumulation in humans and rodents. Wagyu is characterized by the higher capacity for intramuscular adipogenesis than Holsteins. This review discusses the depot‐specific effects of macrophage infiltration among subcutaneous, visceral, and intramuscular adipose tissue on intramuscular adipogenesis in Wagyu and Holstein cattle. Recently, metabolome analysis has been used to identify obesity‐related biomarkers by comparing the biological samples between lean and obese patients. This review introduces the metabolomic profiles of plasma and intramuscular adipose tissue between Wagyu and Holsteins.