bluuebunny/crossref_metadata_2025_split huggingface dataset:
PASTE2: Partial Alignment of Multi-slice Spatially Resolved Transcriptomics Data
Authors: Liu Xinhao , Zeira Ron , Raphael Benjamin J. 
Published: January 2023

AbstractSpatially resolved transcriptomics (SRT) technologies measure mRNA expression at thousands of locations in a tissue slice. However, nearly all SRT technologies measure expression in two dimensional slices extracted from a three-dimensional tissue, thus losing information that is shared across multiple slices from the same tissue. Integrating SRT data across multiple slices can help recover this information and improve downstream expression analyses, but multi-slice alignment and integration remains a challenging task. Existing methods for integrating SRT data either do not use spatial information or assume that the morphology of the tissue is largely preserved across slices, an assumption that is often violated due to biological or technical reasons. We introduce PASTE2, a method forpartialalignment and 3D reconstruction of multi-slice SRT datasets, allowing only partial overlap between aligned slices and/or slice-specific cell types. PASTE2 formulates a novelpartialFused Gromov-Wasserstein Optimal Transport problem, which we solve using a conditional gradient algorithm. PASTE2 includes a model selection procedure to estimate the fraction of overlap between slices, and optionally uses information from histological images that accompany some SRT experiments. We show on both simulated and real data that PASTE2 obtains more accurate alignments than existing methods. We further use PASTE2 to reconstruct a 3D map of gene expression in a Drosophila embryo from a 16 slice Stereo-seq dataset. PASTE2 produces accurate alignments of multi-slice datasets from multiple SRT technologies, enabling detailed studies of spatial gene expression across a wide range of biological applications.Code availabilitySoftware is available athttps://github.com/raphael-group/paste2
DiPRO1 dependent transcriptional and epigenetic regulation distinctly controls the fate of muscle and mesenchymal cancer cells
Authors: Rich Jeremy , Bennaroch Melanie , Notel Laura , Patalakh Polina , Alberola Julien , Opolon Paule , Bawa Olivia , Rondof Windy , Marchais Antonin , Dessen Philippe , Meurice Guillaume , Porlot Melanie , Roux Karine Ser-Le , Droin Nathalie , Raslova Hana , Geoerger Birgit , Pirozhkova Iryna 
Published: January 2023

ABSTRACTWe have recently identified the uncharacterized ZNF555 protein as a component of a productive complex, which is involved in the morbid function of the 4qA locus in facioscapulohumeral dystrophy. As a result of our current findings, ZNF555 is hereinafter referred to as DiPRO1 (Death, Differentiation and PROliferation related PROtein 1). In this study, we provide substantial evidence that DiPRO1 plays a role in human myoblast differentiation. It acts on regulatory binding regions of SIX1, which is a master regulator of myogenesis. We further describe the relevance of DiPRO1 in mesenchymal tumors, such as rhabdomyosarcoma (RMS) and Ewing sarcoma. DiPRO1 plays a repressor role in these tumors via the epigenetic regulators TIF1B and UHRF1 in order to maintain methylation of regulatory cis-elements and promoters. Loss of DiPRO1 eradicates cancer cells, by switching on a distinct transcriptional and epigenetic program. It consists of mimicking the host defense against the virus response by awakening the retrotransposable repeats (RE) and the ZNP/KZFP gene family. DiPRO1 also contributes to the balance of cellular decisions toward inflammation and/or apoptosis by controlling TNF-α via NF-kappaB signaling. Finally, we demonstrate that mesenchymal cancer tumors are vulnerable in response to si/shDiPRO1-based nanomedicines, positioning DiPRO1 as a potential new target for therapeutic intervention.Summary
Defective phagocytosis leads to neurodegeneration through systemic increased innate immune signaling
Authors: Elguero Johnny E. , Liu Guangmei , Tiemeyer Katherine , Gandevia Heena , Duro Lauren , McCall Kimberly 
Published: January 2023

SummaryIn nervous system development, disease and injury, neurons undergo programmed cell death, leaving behind cell corpses that are removed by phagocytic glia. Altered glial phagocytosis has been implicated in several neurological diseases including Alzheimer’s disease, Parkinson’s disease, and traumatic brain injury. To untangle the links between glial phagocytosis and neurodegeneration, we investigatedDrosophilamutants lacking the phagocytic receptor Draper. Loss of Draper leads to persistent neuronal cell corpses and age-dependent neurodegeneration. Here we investigate whether the phagocytic defects observed indrapermutants lead to chronic increased immune activation that promotes neurodegeneration. A major immune response inDrosophilais the activation of two NFκB signaling pathways that produce antimicrobial peptides, primarily in the fat body. We found that the antimicrobial peptide Attacin-A is highly upregulated in the fat body of ageddrapermutants and that inhibition of the Immune deficiency (Imd) pathway in the glia and fat body ofdrapermutants led to reduced neurodegeneration, indicating that immune activation promotes neurodegeneration indrapermutants. Taken together, these findings indicate that phagocytic defects lead to neurodegeneration via increased immune signaling, both systemically and locally in the brain.
An oviduct glycan increases sperm lifespan by diminishing ubiquinone and production of reactive oxygen species
Authors: Hughes Jennifer R. , McMorrow Katie J. , Bovin Nicolai , Miller David. J. 
Published: January 2023

AbstractSperm storage by females after mating for species-dependent periods is used widely among animals with internal fertilization to allow asynchrony between mating and ovulation. Many mammals store sperm in the lower oviduct where specific glycans on epithelial cells retain sperm to form a reservoir. Binding to oviduct cells suppresses sperm intracellular Ca2+and increases sperm longevity. We investigated the mechanisms by which a specific oviduct glycan, 3-O-sulfated Lewis X trisaccharide (suLeX), prolongs the lifespan of porcine sperm. Using targeted metabolomics, we report that binding to suLeXdiminishes the abundance of the precursor to ubiquinone and suppresses formation of fumarate, a specific citric acid cycle component, diminishing the activity of the electron transport chain and reducing the production of harmful reactive oxygen species (ROS). The enhanced sperm lifespan in the oviduct may be due to suppressed ROS production as many reports have demonstrated toxic effects of high ROS concentrations on sperm.
Chemical inhibition of bromodomain proteins in insect stage African trypanosomes perturbs silencing of the Variant Surface Glycoprotein repertoire and results in widespread changes in the transcriptome
Authors: Ashby Ethan C. , Havens Jennifer L. , Hardin Johanna , Schulz Danae 
Published: January 2023

AbstractThe eukaryotic protozoan parasiteTrypanosoma brucei, spp. is transmitted by the tsetse fly to both humans and animals, where it causes a fatal disease called African trypanosomiasis. While the parasite lacks canonical DNA sequence specific transcription factors, it does possess histones, histone modifications, and proteins that write, erase, and read histone marks. Chemical inhibition of chromatin interacting bromodomain proteins has previously been shown to perturb bloodstream specific trypanosome processes, including silencing of the Variant Surface Glycoprotein genes (VSGs) and immune evasion. Transcriptomic changes that occur in bromodomain inhibited bloodstream parasites mirror many of the changes that occur as parasites developmentally progress from the bloodstream to the insect stage. We performed RNA-seq timecourses to determine the effects of chemical bromodomain inhibition in insect stage parasites using the compound I-BET151. We found that treatment with I-BET151 causes large changes in the transcriptome of insect stage parasites, and also perturbs silencing ofVSGgenes. The transcriptomes of bromodomain inhibited parasites share some features with early metacyclic stage parasites in the fly salivary gland, implicating bromodomain proteins as important for regulating transcript levels for developmentally relevant genes. However, the downregulation of surface procyclin protein that typically accompanies developmental progression is absent in bromodomain inhibited insect stage parasites. We conclude that chemical modulation of bromodomain proteins causes widespread transcriptomic changes in multiple trypanosome life cycle stages. Understanding the gene regulatory processes that facilitate transcriptome remodeling in this highly diverged eukaryote may shed light on how these mechanisms evolved.
Single-cell transcriptomic profiling redefines the origin and specification of early adrenogonadal progenitors
Authors: Neirijnck Yasmine , Sararols Pauline , Kühne Françoise , Mayère Chloé , Nef Serge , Schedl Andreas 
Published: January 2023

SummaryAdrenal cortex and gonads represent the two major steroidogenic organs in mammals. Both tissues are considered to share a common developmental origin characterized by the expression ofNr5a1/Sf1. The precise origin of adrenogonadal progenitors and the processes driving differentiation toward the adrenal or gonadal fate remain, however, elusive. Here we provide a comprehensive single-cell transcriptomic atlas of early mouse adrenogonadal development including 52 cell types belonging to twelve major cell lineages. Trajectory reconstruction reveals that adrenogonadal cells emerge from the lateral plate rather than the intermediate mesoderm. Surprisingly, gonadal and adrenal fates show distinct molecular signatures uponNr5a1induction indicating the two tissues are specified independently. Finally, lineage separation into gonadal and adrenal fate involves canonical versus non-canonical Wnt signaling and differential expression ofHoxpatterning genes. Thus our study provides important insights into the molecular programs of adrenal and gonadal fate choice and will be a valuable resource for further research into early adrenogonadal ontogenesis.
The genomic diversity of Taiwanese Austronesian groups: implications for the ‘Into and Out of Taiwan’ models
Authors: Liu Dang , Ko Albert Min-Shan , Stoneking Mark 
Published: January 2023

AbstractThe origin and dispersal of the Austronesian language family, one of the largest and most widespread in the world, have long attracted the attention of linguists, archaeologists, and geneticists. Even though there is a growing consensus that Taiwan is the source of the spread of Austronesian languages, little is known about the migration patterns of the early Austronesians who settled in and left Taiwan, i.e., the “Into-Taiwan” and “Out-of-Taiwan” events. In particular, the genetic diversity/structure within Taiwan and how this relates to the Into/Out-of-Taiwan events is largely unexplored, because most genomic studies have largely utilized data from just two of the 16 recognized highland Austronesian groups in Taiwan. In this study, we generated the largest genome-wide dataset for Taiwanese Austronesians to date, including six highland groups and one lowland group from across the island, and two Taiwanese Han groups. We identified fine scale genomic structure in Taiwan, inferred the ancestry profile of the ancestors of Austronesians, and found that the southern Taiwanese Austronesians show excess genetic affinities toward the Austronesians outside of Taiwan. Our findings thus shed new light on the Into and Out-of-Taiwan dispersals.
Unionization and employee welfare: a theoretical investigation using earnings management
Authors: Lin Guoyu , Brown Anna Bergman , Lin Eric , Xu Chunhao 
Published: January 2023

PurposeUnionization is generally thought to improve employee welfare through higher compensation and benefits. However, managers of unionized firms have incentives to manage earnings downward to avoid sharing rents with unionized workers, which may explain why empirical findings on the association between unionization and employee compensation are mixed. This paper develops an analytical model incorporating earnings management into the relationship between newly unionized firms and employee compensation.Design/methodology/approachThe authors develop an analytical model that relies on Nash bargaining theory and signal jamming (Stein, 1989; Fischer and Verrecchia, 2000; Dye and Sridhar, 2004) and model a setting where newly unionized workers' collective bargaining power increases substantially. The authors' model analyzes the relationship between newly unionized firms and employee wages and benefits while incorporating firms' incentives to engage in earnings management.FindingsThe authors find that newly unionized firms are more likely to engage in income-decreasing earnings management to avoid paying higher salaries and wages to workers. Further, the authors find that this association is more pronounced when (1) the correlation of firms' earnings across periods is higher, (2) the cost of earnings management is lower and (3) firms' earnings are more volatile.Originality/valueThis is the first paper to analytically model the effect of new unionization on firms' earnings management and workers' welfare. The authors' model offers new cross-sectional predictions that have not been tested in the prior literature. Specifically, the authors show that newly unionized firms are more likely to engage in income-decreasing earnings management; when earnings are more highly correlated, the cost of earnings management is lower and earnings are more volatile. The authors' findings may be relevant to regulators and policymakers.
Bank competition and SMEs access to finance in India: evidence from World Bank Enterprise Survey
Authors: Rakshit Bijoy , Bardhan Samaresh 
Published: January 2023

PurposeThe primary purpose of this study is to investigate the effects of bank competition on SMEs' access to finance in selected Indian states. Using 9,281 firm-level observations from World Bank Enterprises Survey (WBES), this study tests the market power hypothesis versus the information hypothesis to determine whether bank competition promotes access to finance for financially constrained firms.Design/methodology/approachThe authors measure state-level bank competition using two structural indicators: the Herfindahl Hirschman Index (HHI) and three bank concentration ratios (CR3). The authors apply simple probit regression, probit model with sample selection (PSS) and two-stage least squares (2SLS) to examine the effects of bank competition on firms' financing constraints.FindingsThe results obtained through PSS and 2SLS indicate that bank competition alleviates firm's financing constraints and positively impacts its need for a bank loan and the decision to apply for bank credit. However, the prevalence of bank competition in promoting access to finance is more pronounced for small and medium-sized firms than for large firms. Higher bank competition also alleviates the credit constraints faced by female entrepreneurs.Practical implicationsReserve Bank of India (RBI) and other government stakeholders should ensure bank competition without hampering the agenda of bank consolidation to facilitate access to credit for SMEs. Regulators should also identify and monitor the financial institutions that make an insignificant contribution to promoting competitiveness in the financial system.Originality/valuePrevious studies primarily investigate the effect of bank competition on a firm's access to finance from advanced and cross-country perspectives. This study contributes to the literature on bank competition by examining its role in promoting access to finance from an emerging economy standpoint. Measurement of bank competition indicators at the state level is an additional contribution.
Exploring tourists’ experiences when visiting Petra archaeological heritage site: voices from TripAdvisor
Authors: Olorunsola Victor Oluwafemi , Saydam Mehmet Bahri , Lasisi Taiwo Temitope , Ozturen Ali 
Published: January 2023

Purpose
Archaeological heritage tourism has great potential for development in numerous destinations. However, literature on archaeological heritage tourism is scarce and empirical data are minimal. This paper aims to identify the main themes shared in online reviews by tourists, as well as identify factors known as satisfiers and dissatisfiers based on Herzberg’s two-factor theory among tourists who visited Petra UNESCO heritage site.

Design/methodology/approach
The research used content analyses to analyse 1,419 tourist’s online reviews on TripAdvisor. Leximancer software provided computer-assisted qualitative data analysis that pinpoint the dominant themes, after which further qualitative analysis found the main narratives associated with different satisfaction groups.

Findings
Successively, seven themes were revealed: entrance, trip, monastery, buildings, animal, carriage and safe. Furthermore, a four-dimensional model was postulated to help understand the components and flow of visitors’ experiences in an archaeological heritage site. In addition, the findings of the study revealed that tourists who scored their experience as 4 (very good) or 5 (excellent) (satisfiers) commonly shared perceptions about architecture, buildings, safe, temples, monasteries, tours, tombs and helpful. Contrarily, reviewers that rated their experience as 1 (terrible) or 2 (poor) (dissatisfiers) shared narratives around concepts such as expensive, animals, carriages, locals and shops.

Originality/value
The results offer valuable understandings of cultural heritage tourists’ overall experiences based on TripAdvisor reviews and facilitate the identification of the dominant themes associated with drivers of tourists’ satisfaction/dissatisfaction.
Investigating the mechanism of developers' willingness to adopt prefabricated housing using an integrated DEMATEL-SD framework
Authors: Wu Zezhou , Yang Kaijie , Wu Zhangmin , Xue Hong , Li Shenghan , Antwi-Afari Maxwell Fordjour 
Published: January 2023

PurposePrefabricated construction is an innovative technique for decreasing carbon emissions in the construction industry. However, as the investors of housing projects, a majority of developers are unwilling to adopt prefabricated housing in practice. To promote prefabricated housing, this study aims to develop an integrated framework of fuzzy-decision making trial and evaluation laboratory (fuzzy-DEMATEL) and system dynamics (SD) to understand the underlying influencing mechanism of developers' willingness.Design/methodology/approachThrough literature review, a total of 17 influencing factors were identified. Then, the interrelationships among the factors were evaluated by 10 experienced professionals, and the impacts given and received by each factor were further analyzed through fuzzy-DEMATEL. Based on the technology acceptance model (TAM), a SD model was developed to explore the influencing mechanism.FindingsThe major cause factors were identified, including mandatory implementation policies, economic incentive policies, environmental protection policies, component standardization and developers' economic strength. This group of factors was expected to be given priority attention in the case of limited resources. On the other hand, the results indicated that economic incentive policies and mandatory implementation policies could affect the developers' willingness via perceived usefulness, while the others mainly influenced perceived ease of use.Originality/valueLittle research has focused on the interrelationships among the influencing factors of developers' willingness to adopt prefabricated housing. This study contributed to understanding the mechanism of developers' willingness from a systematic view and providing the priority of influencing factors. Several strategies were proposed to improve the practical implementation of prefabricated housing development.
Towards an integrative analysis of underground environment and human health: a survey and field measurement approach
Authors: Chan Isabelle Y.S. , Chen Hao 
Published: January 2023

PurposeDue to land resource scarcity, sustainable urban development in high-density cities has long been challenging. As such, many cities are formulating plans to “dig deep”, resulting in more citizens working and/or staying underground for longer periods of time. However, owing to the particularities of underground space, the factors involved in the creation of a healthy environment are different from those involved in aboveground developments. This study thus aims to investigate the influences of various underground environment factors on users' health through a holistic approach.Design/methodology/approachTo achieve this aim, 12 underground sites and 12 corresponding aboveground sites are selected for a large-scale questionnaire survey, resulting in 651 survey samples. The survey covers post-occupancy evaluation of health (physical and psychosocial), underground environmental quality (visual, thermal, acoustic comfort, indoor air quality and ventilation), space design and greenery. Independent-sample T-test, Pearson correlation, multiple regression modelling and structural equation modelling are used to investigate whether significant differences exist between health of underground and aboveground users, and to develop an underground environment-health model for unveiling the significant associations between underground environment factors and users' health. To cross validate the results, an objective field measurement study is further conducted on six underground sites. The objective measurement results are used to cross validate the survey results.FindingsThe questionnaire results provide the following evidence: (1) health of underground users is significantly poorer than that of their aboveground counterparts; (2) underground development users' health is significantly affected by space design, greenery and environmental quality in terms of thermal comfort, indoor air quality, ventilation and acoustic comfort but not visual comfort; and (3) amongst the various identified factors, space design has the strongest predicting effects on human health. The field study echoes the survey findings and further unveils the relationships between different environmental factors and human health.Originality/valueThe results shed light on the importance of distinguishing between underground developments and aboveground ones in various guidelines and standards, especially those related to space management.
Does loadshedding affect the housing market in South Africa? Some empirical evidence
Authors: Marope Amogelang , Phiri Andrew 
Published: January 2023

Purpose
The purpose of this study is to quantify the impact of electricity power outages on the local housing market in South Africa.

Design/methodology/approach
This study uses the autoregressive distributive lag (ARDL) and quantile autoregressive distributive lag (QARDL) models on annual time series data, for the period 1971–2014. The interest rate, real income and inflation were used as control variables to enable a multivariate framework.

Findings
The results from the ARDL model show that real income is the only factor influencing housing price over the long run, whereas other variables only have short-run effects. The estimates from the QARDL further reveal hidden cointegration relationship over the long run with higher quantile levels of distribution and transmission losses raising the residential price growth.

Research limitations/implications
Overall, the findings of this study imply that the South African housing market is more vulnerable to property devaluation caused by power outages over the short run and yet remains resilient to loadshedding over the long run. Other macro-economic factors, such as real income and inflation, are more influential factors towards long-run developments in the residential market.

Originality/value
To the best of the authors’ knowledge, this is the first study to examine the empirical relationship between power outages and housing price growth.