bluuebunny/crossref_metadata_2025_split huggingface dataset:
Linguistic and Geographic Diversity in Research on Second Language Acquisition and Multilingualism: An Analysis of Selected Journals
Authors: Bylund Emanuel , Khafif Zainab , Berghoff Robyn 
Published: May 2023

Abstract
The present study assesses linguistic and geographic diversity in selected outlets of SLA and multilingualism research. Specifically, we examine over 2,000 articles published in specialized top-tier journals, recording the languages under study and their acquisition order, author affiliations, the country in which the research was conducted, and citations. In the sample, there were 183 unique languages and 174 unique pairings, corresponding to 3 per cent of the world’s 7,000 languages and less than 0.001 per cent of 24.5 million possible language combinations. English was overwhelmingly the most common language, followed by Spanish and Mandarin Chinese. North America and Western Europe were both the main producers of knowledge and the main sites for research on multilingualism in the sample. Crucially, the regions with the highest levels of linguistic diversity and societal multilingualism (typically the Global South) were only marginally represented. The findings also show that studies on English and northern Anglophone settings were likely to elicit more citations than studies on other languages and settings, and that less studied languages were included more frequently in article titles.
IEPAPI: a method for immune epitope prediction by incorporating antigen presentation and immunogenicity
Authors: Deng Juntao , Zhou Xiao , Zhang Pengyan , Cheng Weibin , Liu Min , Tian Junzhang 
Published: May 2023

Abstract
CD8+ T cells can recognize peptides presented by class I human leukocyte antigen (HLA-I) of nucleated cells. Exploring this immune mechanism is essential for identifying T-cell vaccine targets in cancer immunotherapy. Over the past decade, the wealth of data generated by experiments has spawned many computational approaches for predicting HLA-I binding, antigen presentation and T-cell immune responses. Nevertheless, existing HLA-I binding and antigen presentation prediction approaches suffer from low precision due to the absence of T-cell receptor (TCR) recognition. Direct modeling of T-cell immune responses is less effective as TCR recognition’s mechanism still remains underexplored. Therefore, directly applying these existing methods to screen cancer neoantigens is still challenging. Here, we propose a novel immune epitope prediction method termed IEPAPI by effectively incorporating antigen presentation and immunogenicity. First, IEPAPI employs a transformer-based feature extraction block to acquire representations of peptides and HLA-I proteins. Second, IEPAPI integrates the prediction of antigen presentation prediction into the input of immunogenicity prediction branch to simulate the connection between the biological processes in the T-cell immune response. Quantitative comparison results on an independent antigen presentation test dataset exhibit that IEPAPI outperformed the current state-of-the-art approaches NetMHCpan4.1 and mhcflurry2.0 on 100 (25/25) and 76% (19/25) of the HLA subtypes, respectively. Furthermore, IEPAPI demonstrates the best precision on two independent neoantigen datasets when compared with existing approaches, suggesting that IEPAPI provides a vital tool for T-cell vaccine design.
An interpretable single-cell RNA sequencing data clustering method based on latent Dirichlet allocation
Authors: Yang Qi , Xu Zhaochun , Zhou Wenyang , Wang Pingping , Jiang Qinghua , Juan Liran 
Published: May 2023

Abstract
Single-cell RNA sequencing (scRNA-seq) detects whole transcriptome signals for large amounts of individual cells and is powerful for determining cell-to-cell differences and investigating the functional characteristics of various cell types. scRNA-seq datasets are usually sparse and highly noisy. Many steps in the scRNA-seq analysis workflow, including reasonable gene selection, cell clustering and annotation, as well as discovering the underlying biological mechanisms from such datasets, are difficult. In this study, we proposed an scRNA-seq analysis method based on the latent Dirichlet allocation (LDA) model. The LDA model estimates a series of latent variables, i.e. putative functions (PFs), from the input raw cell–gene data. Thus, we incorporated the ‘cell-function-gene’ three-layer framework into scRNA-seq analysis, as this framework is capable of discovering latent and complex gene expression patterns via a built-in model approach and obtaining biologically meaningful results through a data-driven functional interpretation process. We compared our method with four classic methods on seven benchmark scRNA-seq datasets. The LDA-based method performed best in the cell clustering test in terms of both accuracy and purity. By analysing three complex public datasets, we demonstrated that our method could distinguish cell types with multiple levels of functional specialization, and precisely reconstruct cell development trajectories. Moreover, the LDA-based method accurately identified the representative PFs and the representative genes for the cell types/cell stages, enabling data-driven cell cluster annotation and functional interpretation. According to the literature, most of the previously reported marker/functionally relevant genes were recognized.
A novel mechanism regulating pyroptosis-induced fibrosis in endometriosis via lnc-MALAT1/miR-141-3p/NLRP3 pathway
Authors: Xu Ying , Liu Hengwei , Xiong Wenqian , Peng Yuan , Li Xiaoou , Long Xuefeng , Jin Jie , Liang Jiaxin , Weng Ruiwen , Liu Junjun , Zhang Ling , Liu Yi 
Published: May 2023

Abstract
Endometriosis is a chronic inflammatory disease distinguished by ectopic endometrium and fibrosis. NLRP3 inflammasome and pyroptosis are present in endometriosis. Aberrant increase of Long noncoding (Lnc)-metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) plays a vital role in endometriosis. However, the relationship between lnc-MALAT1, pyroptosis, and fibrosis is not completely known. In the present study, we found that the pyroptosis levels in ectopic endometrium of patients with endometriosis were significantly increased, consistent with fibrosis levels. Lipopolysaccharide (LPS) + ATP could induce pyroptosis of primary endometrial stromal cells (ESCs), thereby releasing interleukin (IL)-1β and stimulating transforming growth factor (TGF)-β1-mediated fibrosis. NLRP3 inhibitor MCC950 had the same effect as TGF-β1 inhibitor SB-431542 in suppressing the fibrosis-inducing effect of LPS + ATP in vivo and in vitro. The abnormal increase of lnc-MALAT1 in ectopic endometrium was connected with NLRP3-mediated pyroptosis and fibrosis. Leveraging bioinformatic prediction and luciferase assays combined with western blotting and quantitative reverse transcriptase-polymerase chain reaction, we validated that lnc-MALAT1 sponges miR-141-3p to promote NLRP3 expression. Silencing lnc-MALAT1 in HESCs ameliorated NLRP3-mediated pyroptosis and IL-1β release, thereby relieving TGF-β1-mediated fibrosis. Consequently, our findings suggest that lnc-MALAT1 is critical for NLRP3-induced pyroptosis and fibrosis in endometriosis through sponging miR-141-3p, which may indicate a new therapeutic target of endometriosis treatment.
A learning process to deliver virtual staff training involving patients in shared haemodialysis care
Authors: Barnes Tania , Wilkie Martin 
Published: May 2023

ABSTRACT
Shared haemodialysis (HD) care (SHC) is a person-centred approach delivering a flexible choice of options for centre-based HD patients to become more involved in their treatment. To support this, a 4-day course was developed to provide healthcare professionals with the confidence and skills to engage, involve, support and train patients in their care and has been accessed by &gt;700 UK staff over 9 years. The disruption caused by the coronavirus disease 2019 pandemic in 2020 prompted a revision of what was deliverable within the restrictions. In response to this, we designed, developed and tested a virtual training program that was shorter and more accessible while remaining effective in meeting its core objectives. This provides a greater geographical reach and enables a collaborative team approach with patients and staff learning from and with each other, thus supporting a partnership approach advocated in shared decision making. In this review we explore the learning that informed the virtual training program 2022 and provide qualitative evaluation to demonstrate evidence of understanding, behavioural change and organisational benefit. Using a validated evaluation, we present key themes that support the initiation, development and sustainability of SHC in the form of a roadmap to guide strategic planning.
Changes in thyroid function parameters 3 months after allogeneic and autologous hematopoietic stem cell transplantation in children
Authors: Lebbink Chantal A , Bresters Dorine , Tersteeg Joni P B , van den Bos Cor , Dierselhuis Miranda P , Lentjes Eef G W M , Verrijn Stuart Annemarie A , Fiocco Marta , Tissing Wim J E , van Santen Hanneke M 
Published: May 2023

Abstract

Background
Thyroid dysfunction (hypo- and hyperthyroidism) has been reported as a late effect after hematopoietic stem cell transplantation (HSCT) in children. Short-term effects of HSCT on thyroid function parameters are, however, unclear.

Methods
We prospectively evaluated thyroid function parameters before and 3 months after HSCT in all children (&lt;21 years) who underwent HSCT during a 2-year period in the Princess Máxima Center, the Netherlands.

Results
Among 72 children, none had thyroidal hypothyroidism or hyperthyroidism 3 months after HSCT. Changes in thyroid function parameters (either aberrant thyroid-stimulating hormone [TSH] or free thyroxine [FT4] concentrations) were found in 16% before and in 10% 3 months after HSCT. Reverse triiodothyronine (rT3) was found elevated in 9.3% before and in 37% 3 months after HSCT, which could be related to poor physical condition. An individual decline in FT4 concentration of ≥20% was found in 10.5% (6/57) 3 months after HSCT.

Conclusion
In conclusion, thyroidal hypo- and hyperthyroidism are very rare 3 months after HSCT. These results indicate that surveillance for hypo- and hyperthyroidism may start later in time. The changes in thyroid function parameters found 3 months after HSCT might reflect euthyroid sick syndrome.
COVID-19 vaccine hesitancy among first-generation immigrants living in Sweden
Authors: Svallfors Signe , Larsson Elin C , Puranen Bi , Ekström Anna Mia 
Published: May 2023

Abstract

Background
In many countries, immigrants face higher risks of contracting and dying from COVID-19 compared with the native-born population. Moreover, their COVID-19 vaccination uptake tends to be lower. This study aimed to investigate COVID-19 vaccine hesitancy in relation to sociodemographic characteristics, COVID-19-related exposures and social values, norms and perceptions among first-generation immigrants in Sweden. Vaccine hesitancy is an important public health issue to ensure protection against vaccine-preventable mortality and morbidity.

Methods
Nation-wide representative data were collected by the Migrant World Values Survey. Descriptive and multinomial multivariate analyses were performed to analyze vaccine hesitancy among 2612 men and women aged ≥16 years.

Results
One-quarter of the respondents expressed some degree of vaccine hesitancy; 5% said they would definitely not vaccinate, 7% probably not, 4% did not know and 7% did not want to answer. Young age, arriving to Sweden during the large migration wave in 2015, Eastern European origin, female gender, lower education and low trust in authorities, and less perceived benefits of vaccination were all significant determinants of vaccine hesitancy.

Conclusions
The results underscore the importance of trust in healthcare providers and government authorities. Additionally, the importance of providing adequate and targeted information about vaccination to groups who face the largest barriers to care, enabling informed decision-making about the benefits and risks of vaccination in relation to health risks. Given these health risks, it is crucial that government agencies and the health sector address the multiple social dimensions that shape the low vaccine uptake and, in turn, health equity.
Nothofagus pumilio regeneration failure following wildfire in the sub-Antarctic forests of Tierra del Fuego, Argentina
Authors: Ruggirello Matthew Joseph , Bustamante Gimena N , Soler Rosina M 
Published: May 2023

Abstract
Wildfires on the island of Tierra del Fuego in southern Argentina are not considered to have been a historic driver of forest dynamics. However, dramatic increases in the human population of the island over the last half-century have greatly increased fire ignition sources and thus the frequency of wildfires in the region. Lenga (Nothofagus pumilio (Poep. et Endl.) Krasser) forests support diverse ecosystem services by providing habitat for endemic flora and fauna and also represent a valuable timber resource for the forest industry of Tierra del Fuego. Evaluating the impact of forest fires on lenga regeneration is important not only because lenga is a native, slow-growing species that seems to lack adaptations that would allow it to recover rapidly after fire, but also because low tree species diversity on the island of Tierra del Fuego means lenga post-fire regeneration failure may lead to ecosystem state shifts. To determine how site characteristics and fire-impacted variables modulate post-fire regeneration densities and spatial patterns in lenga forests, we installed 192 plots (160 burned, 32 unburned) in which we measured site-characteristic (e.g. aspect, elevation) and fire-impacted (e.g. basal area, canopy cover) variables and tallied seedlings and saplings. Regeneration densities were significantly lower in burned than unburned plots. This was exacerbated with increasing distance from the unburned forest edge. Increasing distance to live trees that either survived fire or were outside the burned area negatively impacted regeneration as well. Time since fire negatively affected sapling, but not seedling counts. We concluded that lenga regeneration in the interior of burned areas is largely absent, delaying and potentially preventing forest recovery. These interior areas of burned lenga forests are unlikely to regenerate closed-canopy tree cover through passive restoration alone. Active restoration may be needed in these critical areas where live legacy trees are not present.
Self-contained Beta-with-Spikes approximation for inference under a Wright–Fisher model
Authors: Guerrero Montero Juan , Blythe Richard A 
Published: May 2023

AbstractWe construct a reliable estimation method for evolutionary parameters within the Wright–Fisher model, which describes changes in allele frequencies due to selection and genetic drift, from time-series data. Such data exist for biological populations, for example via artificial evolution experiments, and for the cultural evolution of behavior, such as linguistic corpora that document historical usage of different words with similar meanings. Our method of analysis builds on a Beta-with-Spikes approximation to the distribution of allele frequencies predicted by the Wright–Fisher model. We introduce a self-contained scheme for estimating parameters in the approximation, and demonstrate its robustness with synthetic data, especially in the strong-selection and near-extinction regimes where previous approaches fail. We further apply the method to allele frequency data for baker’s yeast (Saccharomyces cerevisiae), finding a significant signal of selection in cases where independent evidence supports such a conclusion. We further demonstrate the possibility of detecting time points at which evolutionary parameters change in the context of a historical spelling reform in the Spanish language.
Impact of pathogen genetics on clinical phenotypes in a population of Talaromyces marneffei from Vietnam
Authors: Sephton-Clark Poppy , Nguyen Thu , Hoa Ngo Thi , Ashton Philip , van Doorn H Rogier , Ly Vo Trieu , Le Thuy , Cuomo Christina A 
Published: May 2023

Abstract
Talaromycosis, a severe and invasive fungal infection caused by Talaromyces marneffei, is difficult to treat and impacts those living in endemic regions of Southeast Asia, India, and China. While 30% of infections result in mortality, our understanding of the genetic basis of pathogenesis for this fungus is limited. To address this, we apply population genomics and genome-wide association study approaches to a cohort of 336 T. marneffei isolates collected from patients who enrolled in the Itraconazole vs Amphotericin B for Talaromycosis trial in Vietnam. We find that isolates from northern and southern Vietnam form two distinct geographical clades, with isolates from southern Vietnam associated with increased disease severity. Leveraging longitudinal isolates, we identify multiple instances of disease relapse linked to unrelated strains, highlighting the potential for multistrain infections. In more frequent cases of persistent talaromycosis caused by the same strain, we identify variants arising over the course of patient infections that impact genes predicted to function in the regulation of gene expression and secondary metabolite production. By combining genetic variant data with patient metadata for all 336 isolates, we identify pathogen variants significantly associated with multiple clinical phenotypes. In addition, we identify genes and genomic regions under selection across both clades, highlighting loci undergoing rapid evolution, potentially in response to external pressures. With this combination of approaches, we identify links between pathogen genetics and patient outcomes and identify genomic regions that are altered during T. marneffei infection, providing an initial view of how pathogen genetics affects disease outcomes.
Control of cellularization, nuclear localization, and antipodal cell cluster development in maize embryo sacs
Authors: Chettoor Antony M , Yang Bing , Evans Matthew M S 
Published: May 2023

Abstract
The maize female gametophyte contains four cell types: two synergids, an egg cell, a central cell, and a variable number of antipodal cells. In maize, these cells are produced after three rounds of free-nuclear divisions followed by cellularization, differentiation, and proliferation of the antipodal cells. Cellularization of the eight-nucleate syncytium produces seven cells with two polar nuclei in the central cell. Nuclear localization is tightly controlled in the embryo sac. This leads to precise allocation of the nuclei into the cells upon cellularization. Nuclear positioning within the syncytium is highly correlated with their identity after cellularization. Two mutants are described with extra polar nuclei, abnormal antipodal cell morphology, and reduced antipodal cell number, as well as frequent loss of antipodal cell marker expression. Mutations in one of these genes, indeterminate gametophyte2 encoding a MICROTUBULE ASSOCIATED PROTEIN65-3 homolog, shows a requirement for MAP65-3 in cellularization of the syncytial embryo sac as well as for normal seed development. The timing of the effects of ig2 suggests that the identity of the nuclei in the syncytial female gametophyte can be changed very late before cellularization.
Daily Life of Ukrainian Jewish Children in the Zhmerinka Ghetto during the Holocaust in Transnistria
Authors: Tomchuk Lilia 
Published: May 2023

Abstract
Established at the end of August 1941 in the region then known as Transnistria, the Zhmerinka ghetto was exceptional for several reasons. Though historians have portrayed it as a “model ghetto” or “miniature state” given its organization, maintenance of Jewish community life, and higher survival rate, the individual experiences of the ghetto inmates, particularly those of children, have been largely excluded from historical scholarship. Drawing on survivor accounts, this article addresses the everyday lives of Ukrainian-Jewish children in Zhmerinka’s unique environment. By examining family dynamics and gender roles in various settings, this study explores how the artificial “normality” of the ghetto included for children new roles and responsibilities, forced labor and violence, and survival strategies that helped them cope with these distorted realities.
Outside In: challenges for evolutionary studies on entry
Authors: Capone Gianluca 
Published: May 2023

Abstract
This short note reviews the evolutionary modeling literature focusing on the specific topic of entry of new firms. A large variety of choices have been employed to model entry, often motivated by the need to keep the model simple and comprehensible. Entry is more subject to simplification pressures than other elements of industrial dynamics because a deeper treatment of the phenomenon requires the specification of details external to the focal industry. Starting from more recent and elaborate models of entry, some proposals for further advancement are put forth.
Unsexing citation: Closing the gender gap in global public law
Authors: Dixon Rosalind , Versteeg Mila 
Published: May 2023

Abstract
Gender equality matters in the global public law academy for at least three reasons: the production of diverse scholarship, and substantive equality of opportunity for, and the equal exercise of social power by, female-identifying scholars. And while the global public law academy is in many ways becoming more diverse and inclusive, a great deal of work remains to be done to achieve true gender equality, especially after COVID-19, given its impact on geographic and gender (in)equality. In this article, we examine one important dimension to gender equality in the global public law academy: the degree to which articles by female-identifying scholars are cited at rates comparable to those authored by male-identifying scholars. To do so, we construct a unique database of articles published and cited within I•CON itself and use a variety of empirical techniques to analyze this data. Doing so, we find a clear pattern of gendered citation in global public law: while 37% of I•CON articles are authored by at least one female, only 25% of citations include at least one female author. We explore a variety of gendered and non-gendered explanations for the pattern. Perhaps our most striking finding is that male-author teams cite female authors at lower rates than author teams that have at least one female author, an effect that persists even when we account for self-citation, time trends, and the reputation of the cited authors. Notably, female authors cite female scholars at about the same rate as which they are published; the gender citation gap appears to be driven by the citation practices of male scholars alone. This finding suggests that implicit bias in citation, especially by male authors, cannot be ruled out. We therefore explore potential gender-conscious responses to the phenomenon.
From hierarchical to panoptic control: The Chinese solution in monitoring judges
Authors: He Xin 
Published: May 2023

Abstract
In the wake of the 2014 judicial reforms, are Chinese judges in most circumstances free in their decision-making? Based primarily on interviews with judges, this article argues that although a truncated hierarchy has led to increased judicial autonomy, the state maintains its tight grip over judges. In its new form, the state’s control is more indirect, external, ex post, diffused, and ideological. It allows the state to closely monitor judges’ entire handling of cases (hence the designation “panoptic”). It has some similarities with, yet fundamentally differs from, existing patterns in authoritarian states. While judges’ accountability continues to be largely a bureaucratic matter, this Chinese form of control has nonetheless been effective at a time of soaring caseloads, a slimmed-down judiciary, and increasing insistence on legitimacy. This article seeks to deepen understanding of developments in Chinese courts and, more widely, judicial politics in authoritarian states.