bluuebunny/crossref_metadata_2025_split huggingface dataset:
Potential of imputation for cost-efficient genomic selection for resistance toFlavobacterium columnarein rainbow trout (Oncorhynchus mykiss)
Authors: Fraslin C. , Robledo D. , Kause A. , Houston R.D. 
Published: January 2023

AbstractBackgroundFlavobacterium columnareis the pathogen agent of columnaris disease, a major emerging disease affecting rainbow trout aquaculture. Selective breeding using genomic selection has potential to achieve cumulative improvement of host resistance. However, genomic selection is expensive partly due to the cost of genotyping high numbers of animals using high-density SNP arrays. The objective of this study was to assess the efficiency of genomic selection for resistance toF. columnareusingin silicolow-density (LD) panels combined with imputation. After a natural outbreak of columnaris disease, 2,874 challenged fish and 469 fish from the parental generation (n=81 parents) were genotyped with 27,907 SNPs. The efficiency of genomic prediction using LD-panels was assessed for panels of 10 different densities, createdin silicousing two sampling methods, random and equally spaced. All LD-panels were also imputed to the full 28K HD-panel using the parental generation as the reference population, and genomic predictions were reevaluated. The potential of prioritizing SNPs showing association with resistance toF. columnarewas also tested for the six lower densities.ResultsSimilar results were obtained with random and equally spaced sampling of SNPs for accuracy of both imputation and genomic predictions. Using LD-panels of at least 3,000 makers or lower density panels (as low as 300 markers) combined with imputation resulted in comparable accuracy to the 28K HD-panel and 11% higher accuracy than pedigree-based predictions.ConclusionsCompared to using the commercial HD-panel, LD-panels with imputation may provide a more affordable route to genomic prediction of breeding values, supporting wider adoption of genomic selection in aquaculture breeding programmes.
Chondro/osteoclasts and mast cells are co-villains in the joint destruction of rheumatoid arthritis
Authors: McClure John , McClure Sheena F 
Published: January 2023

ABSTRACTChondro/osteoclasts and mast cells are cells of interest in the cartilage and bone destruction of joints affected by rheumatoid arthritis (RA). Both are major cellular components of the vascular synovial pannus proliferation characteristic of this disease. Chondroclasts degrade calcified cartilage and osteoclasts degrade bone tissue. Chondroclasts and osteoclasts are identical cell types and differentiate from monocyte precursors. Our studies show a close microanatomical relationship between these cells and new capillary formation (shown by the lectinPsophocarpus tetragonolobus– PTL-11) in the resorption sites of the mineralized tissues. Clast and mast cells express receptors for the lectin lPHA indicating beta1,6-acetylglucosaminal transferase V (GNTase V/MGAT5) activity providing a mechanism for neoangiogenesis. In addition to an angiogenetic function for mast cells it is probable that their products control monocyte differentiation and chondro/osteoclastogenesis.
Identification of novel myeloid-derived cell states with implication in cancer outcome
Authors: Guimarães Gabriela Rapozo , Maklouf Giovanna Resk , Teixeira Cristiane Esteves , de Oliveira Santos Leandro , Tessarollo Nayara Gusmão , Pretti Marco Antônio , Toledo Nayara Evelin , da Cruz Jéssica Gonçalves Vieira , Falchetti Marcelo , Dimas Mylla M. , Serain Alessandra Freitas , de Macedo Fabiane Carvalho , Rodrigues Fabiana Resende , Bastos Nina Carrossini , da Silva Jesse Lopes , da Rocha Edroaldo Lummertz , Chaves Cláudia Bessa Pereira , de Melo Andreia Cristina , Moraes-Vieira Pedro Manoel Mendes , Mori Marcelo A. , Boroni Mariana 
Published: January 2023

AbstractTumor-associated myeloid-derived cells (MDCs) significantly impact cancer prognosis and treatment response due to their remarkable plasticity and tumorigenic behaviors. We integrated single-cell RNA-Sequencing datasets from seven different cancers, resulting in a comprehensive collection of 29 MDC subpopulations in the tumor microenvironment (TME). Distinguishing resident-tissue from monocyte-derived macrophages, we discovered a resident-tissue-like subpopulation within monocyte-derived macrophages. Additionally, hypoxia-driven macrophages emerged as a prominent TME component. Deconvolution of these profiles revealed five subpopulations as independent prognostic markers across various cancer types. Validation in large cohorts confirmed the FOLR2-expressing macrophage association with poor clinical outcomes in ovarian and triple-negative breast cancer. Moreover, the marker TREM2, commonly used to define immunosuppressive tumor-associated macrophages, cannot solely predict cancer prognosis, as different polarization states of macrophages express this marker in a context-dependent manner. This comprehensive MDC atlas offers valuable insights and a foundation for novel analyses, advancing strategies for treating solid cancers.
Conserved folding landscape of monomeric initiator caspases
Authors: Nag Mithun , Clark A. Clay 
Published: January 2023

AbstractThe apoptotic caspase subfamily evolved into two subfamilies - monomeric initiators and dimeric effectors. Sequence variations in the conserved caspase-hemoglobinase fold resulted in changes in oligomerization, enzyme specificity, and regulation, making caspases an excellent model for examining the mechanisms of molecular evolution in fine-tuning structure, function, and allosteric regulation. We examined the urea-induced equilibrium folding/unfolding of two initiator caspases, monomeric caspase-8 and cFLIPL, over a broad pH range. Both proteins unfold by a three-state equilibrium mechanism that includes a partially folded intermediate. In addition, both proteins undergo a conserved pH-dependent conformational change that is controlled by an evolutionarily conserved mechanism. We show that the conformational free energy landscape of the caspase monomer is conserved in the monomeric and dimeric subfamilies. Molecular dynamics simulations in the presence or absence of urea, coupled with limited trypsin proteolysis and mass spectrometry, show that the small subunit is unstable in the protomer and unfolds prior to the large subunit. In addition, the unfolding of helix 2 in the large subunit results in disruption of a conserved allosteric site. Because the small subunit forms the interface for dimerization, our results highlight an important driving force for the evolution of the dimeric caspase subfamily through stabilizing the small subunit.
Microbial fingerprints reveal interaction between museum objects, curators and visitors
Authors: Simon Lukas M , Flocco Cecilia , Henke David , Rauer Luise , Müller Christian , Vogel Johannes , Quassier Christiane , Overmann Jörg , Simon Stefan 
Published: January 2023

AbstractMicrobiomes populate the border between humans and their environment. Whether the microbiome can be leveraged to gain information on human interaction with museum objects is unclear. To answer this question, museum objects varying in material and size from two museums, the Museum für Naturkunde and the Pergamonmuseum in Berlin, Germany, which forms part of UNESCO World Heritage since 1999, were defined. In total 126 samples of natural and cultural heritage objects were taken with sterile nylon flocked swabs and subsequently subjected to 16S rRNA amplicon sequencing. By comparing the microbial composition of touched and untouched mollusc and fossil natural heritage objects we derived a robust microbial touch signature characterized by increased abundance of microbes known to be present in human skin. Application of this touch signature to cultural heritage objects from the Pergamonmuseum revealed areas of differential exposure to human contact on the Ishtar gate and Sam’al gate lions. Moreover, we were able to distinguish museum objects and personal office items touched by two different individuals with high sensitivity. Our results demonstrate that the microbial composition of museum objects gives insight into the degree of exposure to human contact, which is an important parameter for conservation and heritage science, and possibly provenance research.
Targets and cross-reactivity of human T cell recognition of Common Cold Coronaviruses
Authors: Tarke Alison , Zhang Yun , Methot Nils , Narowski Tara M. , Phillips Elizabeth , Mallal Simon , Frazier April , Filaci Gilberto , Weiskopf Daniela , Dan Jennifer M. , Premkumar Lakshmanane , Scheuermann Richard H. , Sette Alessandro , Grifoni Alba 
Published: January 2023

SUMMARYThe Coronavirus (CoV) family includes a variety of viruses able to infect humans. Endemic CoVs that can cause common cold belong to the alphaCoV and betaCoV genera, with the betaCoV genus also containing subgenera with zoonotic and pandemic concern, including sarbecoCoV (SARS-CoV and SARS-CoV-2) and merbecoCoV (MERS-CoV). It is therefore warranted to explore pan-CoV vaccine concepts, to provide adaptive immune protection against new potential CoV outbreaks, particularly in the context of betaCoV sub lineages. To explore the feasibility of eliciting CD4+T cell responses widely cross-recognizing different CoVs, we utilized samples collected pre-pandemic to systematically analyze T cell reactivity against representative alpha (NL63) and beta (OC43) common cold CoVs (CCC). Similar to previous findings on SARS-CoV-2, the S, N, M, and nsp3 antigens were immunodominant for both viruses while nsp2 and nsp12 were immunodominant for NL63 and OC43, respectively. We next performed a comprehensive T cell epitope screen, identifying 78 OC43 and 87 NL63-specific epitopes. For a selected subset of 18 epitopes, we experimentally assessed the T cell capability to cross-recognize sequences from representative viruses belonging to alphaCoV, sarbecoCoV, and beta-non-sarbecoCoV groups. We found general conservation within the alpha and beta groups, with cross-reactivity experimentally detected in 89% of the instances associated with sequence conservation of >67%. However, despite sequence conservation, limited cross-reactivity was observed in the case of sarbecoCoV (50% of instances), indicating that previous CoV exposure to viruses phylogenetically closer to this subgenera is a contributing factor in determining cross-reactivity. Overall, these results provided critical insights in the development of future pan-CoV vaccines.
Preventing psychological symptoms among cancer survivors through a digital mindfulness psychoeducation program: Protocol of a randomized controlled trial
Authors: Klainin-Yobas Piyanee , Hounsri Kanokwan , Chng Wee Joo , Emily Ang Neo Kim , Shawn Goh Yong-Shian 
Published: January 2023

AbstractBackgroundCancer survivors experience challenges, that may affect their psychological well-being. Technology-based, mindfulness-based interventions have been offered to cancer survivors; however, contents do not sufficiently cover issues related to cancer and its treatments. This study protocol presents a three-arm randomized controlled trial (RCT) that aims to examine the effectiveness of a digital mindfulness psychoeducation programme (Digital-MindCAN programme) on psychological symptoms among cancer survivors. This program contains knowledge linking to cancer-related matters, mindfulness principles and mindfulness practice, which will be delivered real-time using a videotelephony software.MethodsEligible cancer survivors will include adults who completed curative treatments from two weeks to two years. They will be randomly assigned to one of the three groups: Digital-MindCAN programme with standard care, Palouse Mindfulness programme with standard care, and a wait-list control group. A convenience sample will be recruited from a tertiary hospital in Singapore. A target sample size will be 150 participants, with 50 participants in each group. Primary outcomes encompass objective stress and subjective stress. Secondary outcomes comprise psychological well-being, perceived relaxation, mindfulness, resilience, depression, and anxiety. Self-administered questionnaires and physiological measures will be used to collect participants’ responses. Focus group interviews will be conducted for intervention groups after the end of the eighth session. Quantitative data will be analyzed by descriptive statistics, analysis of covariance and repeated measures analysis of variance. Qualitative findings will be analyzed using a realist evaluation method.DiscussionThis RCT will be the first to test the effectiveness of the technology-based, mindfulness-based intervention on cancer survivors in Singapore. Positive findings will add knowledge and inform clinical practice. Specifically, the Digital-MindCAN intervention may be offered as part of standard care for cancer survivors. Future research can be implemented and further tested the program in other healthcare institutions.Trial registrationThis study has been registered with ISCTN Clinical Trial Registry (Trial NO.ISRCTN10756933).
Reflexivity and academic identity in accounting: intersubjective reflexive identity work as a feminist academic
Authors: Haynes Kathryn 
Published: January 2023

PurposeI provide an exploration and critique of reflexive research practice, which explores the nature of reflexivity, its relevance to and influence on accounting academic identity formation.Design/methodology/approachThe paper gives detailed explanations of three different approaches to reflexivity dependent on perspectives on reality and exemplifies the chosen approach – intersubjective reflexivity. It draws from three personal experiences to illustrate intersubjective reflexive practice in action and its impact on academic identity, including my own identity as a feminist accounting academic. The examples involve the process of reflexively “being struck” regarding voice and representation; addressing power, privilege and decolonisation in knowledge production; and negotiating insider/outsider academic identities.FindingsI reconceptualise and illustrate reflexivity as academic identity formation that enables transformative experience and more reflexive academic praxis within a turbulent academic context. Reflexive academic identity formation will resonate with accounting academics who are reflecting on the role and purpose of the accounting academy and their identity within it.Originality/valueThe paper provides a significant contribution into understanding intersubjective reflexivity, by reconceptualising intersubjective reflexivity beyond research and applying it to the identity formation of accounting academics. I identify the process of reflexive identity transformation through active engagement in identity work and emotion work, which transforms academic praxis. I argue for a broader more nuanced and power-laden perspective on reflexivity and academic praxis, which moves us to consider the responsibility of our academic identity and actions as accounting academics.
Explaining consumers' continuous purchase intention toward subscriber-based knowledge payment platforms: findings from PLS-SEM and fsQCA
Authors: Liu Xin , Zhang Chenghu , Wu Jiaqi 
Published: January 2023

PurposeThe purpose of this study is to investigate the influencing mechanism of consumers' continuous purchase intention toward the subscriber-based knowledge payment platforms (SBKPPs).Design/methodology/approachThis study obtained 226 valid samples through questionnaire surveys and used partial least square structural equation modeling (PLS-SEM) and fuzzy-set qualitative comparative analysis (fsQCA) methods to elucidate the complex causal patterns of consumers' continuous purchase intention toward the SBKPPs.FindingsThe findings revealed that perceived utilitarian value, perceived hedonic value and perceived social value directly affected consumers' continuous purchase intention, while content quality and service quality indirectly affected consumers' continuous purchase intention. In addition, this study also demonstrated that all factors must be combined to play a role, and there exist four configurations resulting in consumers' continuous purchase intention toward the SBKPPs.Research limitations/implicationsThe results can help researchers and practitioners better understand the causal patterns of consumers' continuous purchase intention toward the SBKPPs.Originality/valueThis study contributes to the knowledge payment literature by investigating consumers' continuous purchase intention toward the SBKPPs. This study also provides practical enlightenment for the SBKPPs' marketing.
A novel grey prediction model with structure variability and real domain fractional order and its performance comparisons
Authors: Mao Cuiwei , Gou Xiaoyi , Zeng Bo 
Published: January 2023

PurposeThis paper aims to overcome the problem that the single structure of the driving term of the grey prediction model is not adapted to the complexity and diversity of the actual modeling objects, which leads to poor modeling results.Design/methodology/approachFirstly, the nonlinear law between the raw data and time point is fully mined by expanding the nonlinear term and the range of order. Secondly, through the synchronous optimization of model structure and parameter, the dynamic adjustment of the model with the change of the modeled object is realized. Finally, the objective optimization of nonlinear driving term and cumulative order of the model is realized by particle swarm optimization PSO algorithm.FindingsThe model can achieve strong compatibility with multiple existing models through parameter transformation. The synchronous optimization of model structure and parameter has a significant improvement over the single optimization method. The new model has a wide range of applications and strong modeling capabilities.Originality/valueA novel grey prediction model with structure variability and optimizing parameter synchronization is proposed.HighlightsThe highlights of the paper are as follows:A new grey prediction model with a unified nonlinear structure is proposed.The new model can be fully compatible with multiple traditional grey models.The new model solves the defect of poor adaptability of the traditional grey models.The parameters of the new model are optimized by PSO algorithm.Cases verify that the new model outperforms other models significantly.
Broadening the field of information
Authors: Bosancic Boris 
Published: January 2023

PurposeThe paper discusses the notion of information with regard to its carriers, representatives (or structural carriers) and carried-related processes of transmission, accumulation and processing through the developmental periods of the inorganic and organic world. In the first period, information is contained in a representation of the outcome of physical, chemical and other processes in the physical, chemical and other structures of the non-living world and refers to environmental information. In the second period, information begins to be used to create the physical and chemical structures of the living world and is contained in instructions of the genetic code. In the third period, with the evolution of cognitive systems and intelligence of living beings, in addition to those listed, information is finally being used to build its own structures, which in this paper are called knowledge structures.Design/methodology/approachIn addition to the usual scientific methods in conceptual papers of this type (analysis, synthesis, etc.), the methodology of the paper also relies on the method of analogy, which was used to detect the carriers and representatives of information in the processes of transmission, accumulation and processing of information and the method of classification in order to propose a new taxonomy related to the concept of information.FindingsThe paper shows that information carriers and information representatives appear in each of the three mentioned processes - transmission, accumulation and processing of information - and that they need to be distinguished from the information itself. This insight opened a new perspective in observing this concept and led to the proposal of a new taxonomy related to the concept of information in a given context, eliminating seemingly incommensurable approaches to its study in different scientific fields.Originality/valueThe conducted synthesis results in information being recognized as a transmittable/transmissible documentation of reality inseparable from its carrier and its representative.
Comparing perspectives on organisational silence: an analysis of the Gosport inquiry
Authors: Powell Martin 
Published: January 2023

PurposeThis paper examines different perspectives on the broad umbrella term of organisational silence. It identifies ten perspectives on organisational silence from the previous literature on inquiries into failings of British National Health Service providers. The purpose of this paper is to address these issues.Design/methodology/approachUsing content analysis, it applies ten perspectives on organisational silence to the report of the inquiry into the Gosport Hospital.FindingsThere is some overlap between the perspectives in that they draw on the same authors, and stress similar issues. There is some evidence for most of the perspectives in the report, but some perspectives appear stronger than others. However, none of the perspectives seem to cover the full spectrum of behaviour and place differential emphasis on different processes. It is not clear whether all ten perspectives add independent analytical value. This suggests that some might be extended or combined with the umbrella term of organisational silence more fully opened.Originality/valueThis is the first study in healthcare to review perspectives on organisational silence and apply them to a case study.
Should I donate secondhand clothes? Cognitive, affective, and conative model during the COVID-19 pandemic
Authors: Amin Muslim , Herjanto Halimin 
Published: January 2023

PurposeThis study aims to investigate the secondhand clothes (SHC) donating behavior phenomenon using the cognitive-affective-conative model and examines the moderating role of COVID-19 knowledge on the relationship between the desire to donate and actual SHC donating behavior.Design/methodology/approachA total of 160 questionnaires were distributed to potential participants who donated their clothes to thrift shops during the COVID-19 pandemic in the USA.FindingsA total of 145 useable surveys were collected for analysis. The study found that the desire to donate SHC plays an essential role in enhancing actual SHC donating behavior. In addition, the study found that perceived responsibility and altruistic fear positively influence the desire to donate SHC. In contrast, individuals’ COVID-19 knowledge does not moderate the relationship between the desire to donate SHC and actual SHC donating behavior.Originality/valueA limited empirical study uses the cognitive–affective–conative approach to SHC donating behavior. The findings of this study enhance the body of SHC’s theoretical knowledge and enhance individuals’ participation in donation programs in support of their community and humanitarian programs.