bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of population structure inferred by principal component analysis or the admixture model
Authors: van Waaij Jan , Li Song , Garcia-Erill Genís , Albrechtsen Anders , Wiuf Carsten 
Published: June 2023

AbstractPrincipal component analysis (PCA) is commonly used in genetics to infer and visualize population structure and admixture between populations. PCA is often interpreted in a way similar to inferred admixture proportions, where it is assumed that individuals belong to one of several possible populations or are admixed between these populations. We propose a new method to assess the statistical fit of PCA (interpreted as a model spanned by the top principal components) and to show that violations of the PCA assumptions affect the fit. Our method uses the chosen top principal components to predict the genotypes. By assessing the covariance (and the correlation) of the residuals (the differences between observed and predicted genotypes), we are able to detect violation of the model assumptions. Based on simulations and genome wide human data we show that our assessment of fit can be used to guide the interpretation of the data and to pinpoint individuals that are not well represented by the chosen principal components. Our method works equally on other similar models, such as the admixture model, where the mean of the data is represented by linear matrix decomposition.
A CD24+CD271+Melanoma Cancer Stem Cell Possesses Hybrid Characteristics of its Single Marker Counterparts and Promotes Invasion and Therapeutic Resistance
Authors: Knowles Olivia , Doldan Patricio , Hillier-Richardson Isabella , Lunt Stephanie , Youssef Gehad , Gammon Luke , Mackenzie Ian C. , Philpott Michael P. , Rizvi Hasan , Bergamaschi Daniele , Harwood Catherine A. , Biddle Adrian 
Published: June 2023

AbstractAn important role for phenotype switching has been demonstrated in metastasis and therapeutic resistance of both melanoma and epithelial tumours. Phenotype switching in epithelial tumours is driven by a minority cancer stem cell sub-population with lineage plasticity, but such a sub-population has not been identified in melanoma. We investigated whether cell surface markers used to identify cancer stem cells in epithelial tumours could identify a cancer stem cell sub-population with lineage plasticity in melanoma. We identified a CD24+CD271+minority sub-population in melanoma that possesses the stem cell characteristics of lineage plasticity and self-renewal. This population displayed hybrid characteristics, combining the attributes of discrete CD24+and CD271+cellular sub-populations but with heightened sphere formation, lineage plasticity, migratory ability and drug resistance over its single-marker counterparts. CD24+and CD24+CD271+stem cell sub-populations were observed in 10% of human melanomas, mainly at the invasive front. The lack of CD24+and CD24+CD271+stem cells in the majority of human melanoma specimens led us to conclude that they may be dispensable for melanoma progression. Nevertheless, the enhanced sphere formation, lineage plasticity, migratory ability and drug resistance of the CD24+CD271+sub-population may signal a contextual requirement for these stem cells when melanomas face challenging environments both clinically and in experimental systems.
Prolonged viral shedding from noninfectious individuals confounds wastewater-based epidemiology
Authors: Phan Tin , Brozak Samantha , Pell Bruce , Ciupe Stanca M. , Ke Ruian , Ribeiro Ruy M. , Gitter Anna , Mena Kristina D. , Perelson Alan S. , Kuang Yang , Wu Fuqing 
Published: June 2023

AbstractWastewater surveillance has been widely used to track and estimate SARS-CoV-2 incidence. While both infectious and recovered individuals shed virus into wastewater, epidemiological inferences using wastewater often only consider the viral contribution from the former group. Yet, the persistent shedding in the latter group could confound wastewater-based epidemiological inference, especially during the late stage of an outbreak when the recovered population outnumbers the infectious population. To determine the impact of recovered individuals’ viral shedding on the utility of wastewater surveillance, we develop a quantitative framework that incorporates population-level viral shedding dynamics, measured viral RNA in wastewater, and an epidemic dynamic model. We find that the viral shedding from the recovered population can become higher than the infectious population after the transmission peak, which leads to a decrease in the correlation between wastewater viral RNA and case report data. Furthermore, the inclusion of recovered individuals’ viral shedding into the model predicts earlier transmission dynamics and slower decreasing trends in wastewater viral RNA. The prolonged viral shedding also induces a potential delay in the detection of new variants due to the time needed to generate enough new cases for a significant viral signal in an environment dominated by virus shed by the recovered population. This effect is most prominent toward the end of an outbreak and is greatly affected by both the recovered individuals’ shedding rate and shedding duration. Our results suggest that the inclusion of viral shedding from non-infectious recovered individuals into wastewater surveillance research is important for precision epidemiology.
A multi-organ map of the human immune system across age, sex and ethnicity
Authors: Mangiola S , Milton M , Ranathunga N , Li-Wai-Suen CSN , Odainic A , Yang E , Hutchison W , Garnham A , Iskander J , Pal B , Yadav V , Rossello JFJ , Carey VJ , Morgan M , Bedoui S , Kallies A , Papenfuss AT 
Published: June 2023

SummaryUnderstanding tissue biology’s heterogeneity is crucial for advancing precision medicine. Despite the centrality of the immune system in tissue homeostasis, a detailed and comprehensive map of immune cell distribution and interactions across human tissues and demographics remains elusive. To fill this gap, we harmonised data from 12,981 single-cell RNA sequencing samples and curated 29 million cells from 45 anatomical sites to create a comprehensive compositional and transcriptional healthy map of the healthy immune system. We used this resource and a novel multilevel modelling approach to track immune ageing and test differences across sex and ethnicity. We uncovered conserved and tissue-specific immune-ageing programs, resolved sex-dependent differential ageing and identified ethnic diversity in clinically critical immune checkpoints. This study provides a quantitative baseline of the immune system, facilitating advances in precision medicine. By sharing our immune map, we hope to catalyse further breakthroughs in cancer, infectious disease, immunology and precision medicine.
OMA1 protease eliminates arrested protein import intermediates upon depolarization of the inner mitochondrial membrane
Authors: Krakowczyk Magda , Lenkiewicz Anna M. , Sitarz Tomasz , Marins Mussulini Ben Hur , Linke Vanessa , Malinska Dominika , Szczepankiewicz Andrzej , Wydrych Agata , Nieznanska Hanna , Serwa Remigiusz A. , Chacinska Agnieszka , Bragoszewski Piotr 
Published: June 2023

AbstractMost mitochondrial proteins originate from the cytosol and require active transport into the organelle. Such precursor proteins must be largely unfolded to pass through translocation channels in mitochondrial membranes. Misfolding of transported proteins can result in their arrest and translocation failure. Arrested proteins block further import, disturbing mitochondrial functions and cellular proteostasis. Cellular responses to translocation failure have been defined in yeast. To discover molecular mechanisms that resolve failed import events in human cells, we developed the translocase clogging model using a fusion protein with a rigid domain. The mechanism we uncover differs significantly from these described in fungi, where ATPase-driven extraction of blocked protein is directly coupled with proteasomal processing. We found human cells to rely primarily on mitochondrial factors to clear translocation channel blockage. The mitochondrial membrane depolarization triggered proteolytic cleavage of the stalled protein, which involved mitochondrial protease OMA1. The cleavage allowed releasing the protein fragment that blocked the translocase. The released fragment was further cleared in the cytosol by the valosin containing protein (VCP)/p97 and proteasome.
Molecular basis of VEGFR1 autoinhibition at the plasma membrane
Authors: Chakraborty Manas Pratim , Das Diptatanu , Mondal Purav , Kaul Pragya , Bhattacharyya Soumi , Das Prosad Kumar , Das Rahul 
Published: June 2023

AbstractLigand-independent activation of VEGFR is a hallmark in diabetes and several cancers. Like most RTKs, the VEGFR2, the primary VEGF receptor, is activated spontaneously at higher receptor concentrations. An exception is VEGFR1, which remains constitutively inactive in the basal state. Ligand stimulation transiently phosphorylates VEGFR1 and induces weak kinase activation in endothelial cells. Recent studies, however, suggest that VEGFR1 signaling is indispensable in regulating various physiological or pathological events, which is puzzling. Why VEGFR1 is differentially regulated is an open question. Here we elucidate a mechanism of juxtamembrane inhibition that shifts the equilibrium more to the inactive state, rendering VEGFR1 an inefficient kinase. Our data suggest that a combination of tyrosine phosphatase activity and JM inhibition suppress the basal phosphorylation of VEGFR1. We conclude that a subtle imbalance in phosphatase activation or removing juxtamembrane inhibition is sufficient to induce basal activation of VEGFR1 and remodel tyrosine phosphorylation to be sustained.
Setdb1 safeguards genome integrity in muscle stem cells to allow for regenerative myogenesis and inflammation
Authors: Garcia Pauline , Jarassier William , Brun Caroline , Giordani Lorenzo , Agostini Fany , Kung Wai Hing , Peccate Cécile , Ravent Jade , Fall Sidy , Petit Valentin , Cheung Tom H , Ait-Si-Ali Slimane , Le Grand Fabien 
Published: June 2023

ABSTRACTModulations in chromatin structure orchestrate gene expression and direct stem cell fate. More specifically, the histone 3 lysine 9 Methyltransferase Setdb1 controls transcriptional repression to regulate pluripotency and self-renewal. While Setdb1 functions have been extensively studied in embryonic stem cells and in cancer cells, less is known on its role in adult stem cellsin vivo. Here, we show that Setdb1 expression by adult muscle stem cells (MuSCs) is required for muscle tissue regeneration following acute injury. We find that SETDB1 represses the expression of the endogenous retroviruses (ERVs) family of transposable elements in MuSCs. ERV de-expression inSetdb1-nullMuSCs prevents their amplification following exit from quiescence and promotes cell death. Multi-omics profiling further shows that the absence of SETDB1 in MuSCs leads to the activation of the DNA-sensing cGAS-STING pathway, entailing increased cytokine expression.In vivo, conditional disruption ofSetdb1in MuSCs provokes aberrant infiltration of inflammatory cells including the appearance of a pathological macrophage lineage. The ensuing histiocytosis is accompanied by necrosis of the newly formed muscle fibers which, in addition with the progressive loss of MuSCs, completely abolish skeletal muscle tissue repair. In contrast, disruption ofSetdb1gene in another muscle-resident cell type, the fibro-adipogenic progenitors (FAPs), does not impact regenerative inflammation. In conclusion, the control of genome stability by SETDB1 in an adult somatic stem cell is necessary for both its regenerative potential and an adequate inflammation regulating tissue repair.
Nutrient enrichment alters gene expression in ‘Ca.’Aquarickettsia rohweri, promoting parasite expansion and horizontal transmission
Authors: Speare Lauren , Klinges J Grace , Duke William C , Muller Erinn M , Thurber Rebecca L Vega 
Published: June 2023

AbstractOcean warming, disease, and pollution contributed to global declines in coral abundances and diversity. In the Caribbean, corals previously dominated reefs, providing an architectural framework for diverse ecological habitats, but have significantly declined due to infectious microbial disease. Key species like coralAcropora cervicornis, are now considered critically endangered, prompting researchers to focus on scientific endeavors to identify factors that influence coral disease resistance and resilience. We previously showed that disease susceptibility, growth rates, and bleaching risk were all associated with the abundance of a single bacterial parasite, ‘Ca.’Aquarickettsia rohweri which proliferatesin vivounder nutrient enrichment. Yet how nutrients influence parasite physiology and life history strategies within its host are unknown. We performed microscopy and transcriptomic analyses of ‘Ca.’A. rohweri populations during a 6-week nutrient exposure experiment. Microscopy showed that this parasite was abundant in coral tissue and densely packed in mucocytes prior to nutrient enrichment. ‘Ca.’A. rohweri energy scavenging genes and those potentially involved in this habitat transition are significantly upregulated during enrichment. Specifically, transcripts involved in signaling, virulence, two-component systems, and nutrient import genes are elevated under higher nutrients. These data support the predicted role of ‘Ca.’A. rohweri as a highly active nutrient-responsiveA. cervicornisparasite, and provide a glimpse at the mechanism of induced disease susceptibility while implicating nutrient exposure in its horizontal transmission.SignificanceThe coral disease crisis has contributed to global declines in coral abundance and diversity and is exacerbated by environmental stressors like eutrophication. Thus, identifying factors that influence coral disease resistance and resilience is a top priority. The Rickettsiales-like bacterium,‘Candidatus’Aquarickettsia rohweri is ubiquitous coral symbiont that is strongly linked to coral disease susceptibility in staghorn coral, and is undergoing positive selection across the Caribbean. Although‘Ca.’A. rohweri is a putative parasite, little is known about the activity of this bacterium in coral tissue. This work supports the role of‘Ca.’A. rohweri as a highly active, nutrient-responsive parasite and proposes a mechanism for how‘Ca.’A. rohweri contributes to coral disease susceptibility, parasite expansion, and horizontal transmission.
Developing a guiding framework based on sustainable development to alleviate poverty, hunger and disease
Authors: Abusaada Hisham , Elshater Abeer 
Published: June 2023

PurposeSustainable development (SD) is vital in alleviating poverty, hunger and disease (PHD). The purpose of this study is to present a guiding framework with pathways targeting the sustainability challenges concerning PHD based on urban planning and design literature.Design/methodology/approachA narrative review and content analysis of 27 articles published by 11 journals indexed in Scopus were conducted using bibliometrics analysis.FindingsThe study’s findings discuss contemporary normative planning and design ideas and their ability to alleviate PHD. Considering these findings, the authors recommend that urban planning and design implementation processes carefully pursue the United Nations Sustainable Development Goals (SDGs) and Vision 2030 by tracking qualitative metrics that consider social, cultural and spiritual well-being.Originality/valueThe contribution is to propose a conceptual framework for alleviating hunger, poverty and disease through Vision 2030. Practitioners and policymakers can use this framework to assess the impact of their actions. Hunger, poverty and disease research could be guided by this framework to identify and prioritize best practices in cities of the Global South.
Public governance, corporate governance and excessive ESG
Authors: Kuzey Cemil , Al-Shaer Habiba , Karaman Abdullah S. , Uyar Ali 
Published: June 2023

Purpose
Growing social concerns and ecological issues accelerate firms’ environmental, social and governance (ESG) engagement. Hence, this study aims to advance the existing literature by focusing on the interplay between institutional and firm governance mechanisms for greater ESG engagement. More specifically, the authors investigate whether public governance stimulates excessive ESG engagement and whether corporate governance moderates this relationship.

Design/methodology/approach
Using a sample of 43,803 firm-year observations affiliated with 41 countries and 9 industries, the authors adopt a country, industry and year fixed-effects regression analysis.

Findings
The authors find that public governance strength via its six dimensions stimulates excessive ESG engagement. This implies that firms in countries with strong voice and accountability, political stability, government effectiveness, regulatory quality, rule of law and control of corruption are more motivated for ESG engagement. Furthermore, corporate governance negatively moderates the relationship between all public governance dimensions (except political stability) and excessive ESG engagement. This implies that public governance and corporate governance are substitutes for encouraging firms to commit to ESG. Further tests reveal that whereas these results in the baseline analyses are valid for developed countries, they are not valid in emerging markets.

Research limitations/implications
The findings support the interplay between institutional and agency theories. In countries with strong (weak) institutional mechanisms, corporate governance becomes weak (strong) in inciting greater stakeholder engagement. This implies that the public governance mechanism alleviates agency costs, rendering internal mechanisms of corporate governance noncompulsory for ESG engagement.

Practical implications
The findings suggest that emerging countries need to reinforce their institutions for greater accountability, regulatory quality and control of corruption, which will have a domino effect on firms in addressing stakeholder expectations. The results also advise emerging country firms to augment their internal monitoring mechanisms for greater stakeholder engagement, such as structuring boards and establishing corporate social responsibility mechanisms, committees and policies.

Originality/value
This study contributes to the recent literature investigating the role of corporate governance mechanisms in excessive ESG engagement. The study also explores whether public governance is associated with greater ESG involvement and provides a comprehensive analysis of the association between six indicators of public governance quality and excessive ESG practices in developed and emerging economies.
The changing landscape of digital transformation in supply chains: impacts of industry 4.0 in Vietnam
Authors: Akbari Mohammadreza , Kok Seng Kiat , Hopkins John , Frederico Guilherme F. , Nguyen Hung , Alonso Abel Duarte 
Published: June 2023

PurposeThe purpose of the article is to contribute to the body of research on digital transformation among members of the supply chain operating in an emerging economy. This paper researches the digital transformation trends happening across Vietnamese supply chains, by investigating the current adoption rates, predicted impact levels and financial investments being made in key Industry 4.0 technologies.Design/methodology/approachBy using a semi-structured online survey, the experiences of 281 supply chain professionals in Vietnam were captured. Subsequently, statistical techniques examining variances in means, regression analysis and Monte Carlo simulation were applied.FindingsThe findings of this study offer a comprehensive understanding of Industry 4.0 technology in Vietnam, highlighting the prevalent technologies being prioritized. Big data analytics and the Internet of things are expected to have the most substantial impact on businesses over the next 5–10 years and have received the most financial investment. Conversely, Blockchain is perceived as having less potential for future investment. The study further identifies several technological synergies, such as combining advanced robotics, artificial intelligence and the Internet of things to build effective and flexible factories, that can lead to more comprehensive solutions. It also extends diffusion of innovation theory, encompassing investment and impact considerations.Originality/valueThis study offers valuable insights into the impact and financial investment in Industry 4.0 technologies by Vietnamese supply chain firms. It provides a theoretical contribution via an extension of the diffusion of innovation theory and contributes toward a better understanding of the current Industry 4.0 landscape in developing economies. The findings have significant implications for future managerial decision-making, on the impact, viability and resourcing needs when undertaking digital transformation.
Influence of employees’ beliefs and values on shaping green work culture for boosting firm’s environmental performance
Authors: Qasim Samina , Ahmed Waqar , Frooghi Reema 
Published: June 2023

Purpose
Environmental performance (EnPerf) needs to be critically studied so organizations can understand enhancing it. The purpose of this study is mainly to examine and explain the influence of beliefs and values of the human resources regarding religiosity (REL) and workplace spirituality (WS) on shaping an environmentally friendly work culture comprising environmental ethics (EE) and environmental passion (EP), to enhance EnPerf.

Design/methodology/approach
A survey methodology was used, and 316 responses were collected from the employees working in industries on the top list of polluting the environment using purposive sampling. Structural equation modeling was deployed to test the hypotheses.

Findings
This research is conducted to identify specific relationships of variables with the environment. It was discovered that WS affected EP and EE, positively affecting EnPerf.

Research limitations/implications
This study guides organizations and their management to adopt WS, EE and EP, as these all increase EnPerf in the organization.

Originality/value
Not much work has been conducted on the environmental culture based on REL and WS, using the ability-motivation-opportunity theory. This research analyzes employees’ intrinsic factors, such as REL and WS, to develop EP and EE. Thus helping to comprehend how they can use to enhance EnPerf, which is the current priority for the organizations.