bluuebunny/crossref_metadata_2025_split huggingface dataset:
Japanese sake making using wild yeasts isolated from natural environments
Authors: Nakagawa Tomoyuki , Yoshimura Akihiro , Sawai Yoshinori , Hisamatsu Kentaro , Akao Takeshi , Masaki Kazuo 
Published: February 2024

ABSTRACT
Saccharomyces cerevisiae is one of the most important microorganisms for the food industry, including Japanese sake, beer, wine, bread, and other products. For sake making, Kyokai sake yeast strains are considered one of the best sake yeast strains because these strains possess fermentation properties that are suitable for the quality of sake required. In recent years, the momentum for the development of unique sake, which is distinct from conventional sake, has grown, and there is now a demand to develop unique sake yeasts that have different sake making properties than Kyokai sake yeast strains. In this minireview, we focus on “wild yeasts,” which inhabit natural environments, and introduce basic research on the wild yeasts for sake making, such as their genetic and sake fermentation aspects. Finally, we also discuss the molecular breeding of wild yeast strains for sake fermentation and the possibility for sake making using wild yeasts.
Homogeneity pursuit and variable selection in regression models for multivariate abundance data
Authors: Hui Francis K C , Maestrini Luca , Welsh Alan H 
Published: February 2024

ABSTRACT
When building regression models for multivariate abundance data in ecology, it is important to allow for the fact that the species are correlated with each other. Moreover, there is often evidence species exhibit some degree of homogeneity in their responses to each environmental predictor, and that most species are informed by only a subset of predictors. We propose a generalized estimating equation (GEE) approach for simultaneous homogeneity pursuit (ie, grouping species with similar coefficient values while allowing differing groups for different covariates) and variable selection in regression models for multivariate abundance data. Using GEEs allows us to straightforwardly account for between-response correlations through a (reduced-rank) working correlation matrix. We augment the GEE with both adaptive fused lasso- and adaptive lasso-type penalties, which aim to cluster the species-specific coefficients within each covariate and encourage differing levels of sparsity across the covariates, respectively. Numerical studies demonstrate the strong finite sample performance of the proposed method relative to several existing approaches for modeling multivariate abundance data. Applying the proposed method to presence–absence records collected along the Great Barrier Reef in Australia reveals both a substantial degree of homogeneity and sparsity in species-environmental relationships. We show this leads to a more parsimonious model for understanding the environmental drivers of seabed biodiversity, and results in stronger out-of-sample predictive performance relative to methods that do not accommodate such features.
Incorporating participants’ welfare into sequential multiple assignment randomized trials
Authors: Wang Xinru , Deliu Nina , Narita Yusuke , Chakraborty Bibhas 
Published: February 2024

ABSTRACT
Dynamic treatment regimes (DTRs) are sequences of decision rules that recommend treatments based on patients’ time-varying clinical conditions. The sequential, multiple assignment, randomized trial (SMART) is an experimental design that can provide high-quality evidence for constructing optimal DTRs. In a conventional SMART, participants are randomized to available treatments at multiple stages with balanced randomization probabilities. Despite its relative simplicity of implementation and desirable performance in comparing embedded DTRs, the conventional SMART faces inevitable ethical issues, including assigning many participants to the empirically inferior treatment or the treatment they dislike, which might slow down the recruitment procedure and lead to higher attrition rates, ultimately leading to poor internal and external validities of the trial results. In this context, we propose a SMART under the Experiment-as-Market framework (SMART-EXAM), a novel SMART design that holds the potential to improve participants’ welfare by incorporating their preferences and predicted treatment effects into the randomization procedure. We describe the steps of conducting a SMART-EXAM and evaluate its performance compared to the conventional SMART. The results indicate that the SMART-EXAM can improve the welfare of the participants enrolled in the trial, while also achieving a desirable ability to construct an optimal DTR when the experimental parameters are suitably specified. We finally illustrate the practical potential of the SMART-EXAM design using data from a SMART for children with attention-deficit/hyperactivity disorder.
Perceptions of Safe Staffing, Self-Reported Mental Well-being and Intentions to Leave the Profession among UK Social Workers: A Mixed Methods Study
Authors: McFadden Paula , Maclochlainn Justin , Manthorpe Jill , Naylor Rachel , Schroder Heike , McGrory Susan , Ravalier Jermaine , Nicholl Patricia , Currie Denise , Kirby Karen , Davies Hannah , Mullineux Judith , McColgan Mary , Mallett John 
Published: February 2024

Abstract
The purpose of this study was to examine social workers’ perceptions of safe staffing levels and correlate these perceptions with standardised measurements of well-being in the UK. This cross-sectional mixed-methods study analysed data from 406 social workers from November 2022 until late January 2023. Data were collected using anonymous online surveys including both qualitative and quantitative methods examining mental well-being, burnout and intentions to leave the profession post-coronavirus disease 2019. Findings revealed that only one-third of social workers responding perceived that they work in an environment of safe staffing. There were also significant differences in well-being and an increase in personal, work-related and client-related burnout in social workers who believed their service did not operate a safe staff-to-service user ratio. Likewise, compared to those who perceived their service to operate within a safe staff-to-service-user ratio, those who perceived unsafe ratios were more likely to communicate their intention to leave the profession. Qualitative findings helped contextualise the quantitative results. These findings suggest that increased demand for social work services, shortage of qualified social workers, high workloads, inadequate resources and retention problems, contribute to additional pressure on existing staff and have implications for policy, practice and research in social work.
Splenectomy at early stage of autoimmune arthritis delayed inflammatory response and reduced joint deterioration in mice
Authors: Khanfar Esam , Olasz Katalin , Gál Szonja , Gajdócsi Erzsébet , Kajtár Béla , Kiss Tamás , Balogh Péter , Berki Timea , Boldizsár Ferenc 
Published: February 2024

Abstract
The spleen plays a role in innate and adaptive immunity, and autoimmune diseases like rheumatoid arthritis (RA). We investigated the effect of splenectomy in early and moderate stages of autoimmune arthritis in a mouse model. To induce recombinant human G1-induced arthritis (GIA), BALB/c mice were immunized intraperitoneally three times in 4-week intervals with the rhG1 antigen. Mice were splenectomized on day 7 (SPE1) or day 35 (SPE2) after the initiation of immunization; tested for clinical severity, joint radiological and histological changes, serum levels of inflammatory cytokines and autoantibodies, and rhG1-specific immune responses; and compared to those in control mice with spleen left intact. Circulating Tregs and T-helper subset ratios in the spleen and inguinal lymph nodes (LNs) were also examined using flow cytometry. The onset of severe inflammatory response was significantly delayed in SPE1 and SPE2 groups compared to control mice at early stages of GIA, which was associated with increased circulating Tregs. After the third immunization, as disease progressed, the severity scores were robustly increased in all mice. Nevertheless, in splenectomized mice, we observed reduced joint deterioration and cartilage damage, more Th2 cells in LNs, and reduced levels of pro-inflammatory cytokines and autoantibodies in their sera. Mesenteric LN cells of splenectomized mice exhibited weaker response in vitro against the rhG1 antigen compared to control mice spleen. In conclusion, splenectomy in the early stages of GIA delayed the inflammatory response, suggesting a protective effect against the development and progression of severe destructive arthritis.
Neural correlates of an illusionary sense of agency caused by virtual reality
Authors: Cai Yiyang , Yang Huichao , Wang Xiaosha , Xiong Ziyi , Kühn Simone , Bi Yanchao , Wei Kunlin 
Published: February 2024

Abstract
Sense of agency (SoA) is the sensation that self-actions lead to ensuing perceptual consequences. The prospective mechanism emphasizes that SoA arises from motor prediction and its comparison with actual action outcomes, while the reconstructive mechanism stresses that SoA emerges from retrospective causal processing about the action outcomes. Consistent with the prospective mechanism, motor planning regions were identified by neuroimaging studies using the temporal binding (TB) effect, a behavioral measure often linked to implicit SoA. Yet, TB also occurs during passive observation of another’s action, lending support to the reconstructive mechanism, but its neural correlates remain unexplored. Here, we employed virtual reality (VR) to modulate such observation-based SoA and examined it with functional magnetic resonance imaging (fMRI). After manipulating an avatar hand in VR, participants passively observed an avatar’s “action” and showed a significant increase in TB. The binding effect was associated with the right angular gyrus and inferior parietal lobule, which are critical nodes for inferential and agency processing. These results suggest that the experience of controlling an avatar may potentiate inferential processing within the right inferior parietal cortex and give rise to the illusionary SoA without voluntary action.
Divergent growth of the transient brain compartments in fetuses with nonsyndromic isolated clefts involving the primary and secondary palate
Authors: Masse Olivia , Brumfield Olivia , Ahmad Esha , Velasco-Annis Clemente , Zhang Jennings , Rollins Caitlin K , Connolly Susan , Barnewolt Carol , Shamshirsaz Alireza A , Qaderi Shohra , Javinani Ali , Warfield Simon K , Yang Edward , Gholipour Ali , Feldman Henry A , Grant Patricia E , Mulliken John B , Pierotich Lana , Estroff Judy 
Published: February 2024

Abstract
Cleft lip/palate is a common orofacial malformation that often leads to speech/language difficulties as well as developmental delays in affected children, despite surgical repair. Our understanding of brain development in these children is limited. This study aimed to analyze prenatal brain development in fetuses with cleft lip/palate and controls. We examined in utero MRIs of 30 controls and 42 cleft lip/palate fetal cases and measured regional brain volumes. Cleft lip/palate was categorized into groups A (cleft lip or alveolus) and B (any combination of clefts involving the primary and secondary palates). Using a repeated-measures regression model with relative brain hemisphere volumes (%), and after adjusting for multiple comparisons, we did not identify significant differences in regional brain growth between group A and controls. Group B clefts had significantly slower weekly cerebellar growth compared with controls. We also observed divergent brain growth in transient brain structures (cortical plate, subplate, ganglionic eminence) within group B clefts, depending on severity (unilateral or bilateral) and defect location (hemisphere ipsilateral or contralateral to the defect). Further research is needed to explore the association between regional fetal brain growth and cleft lip/palate severity, with the potential to inform early neurodevelopmental biomarkers and personalized diagnostics.
Mapping individual aspects of bilingual experience to adaptations in brain structure
Authors: DeLuca Vincent , Voits Toms , Ni Jianzhang , Carter Felix , Rahman Foyzul , Mazaheri Ali , Krott Andrea , Segaert Katrien 
Published: February 2024

Abstract
Individual differences in using multiple languages are thought to differentially affect brain structure and function. The present study assessed the neuroanatomical predictions of an emerging theory, the Unifying the Bilingual Experience Trajectories framework, which provides the most comprehensive set of predictions of how individual differences in bilingual experiences lead to specific neural and cognitive adaptations. A total of 140 young adults with variable language experiences were scanned using magnetic resonance imaging and completed demographic questionnaires. Brain structure measures implicated in predictions of the Unifying the Bilingual Experience Trajectories model were extracted and regressed against the model’s experiential factors. Consistent with the model’s predictions, greater intensity and diversity of bilingual language use resulted in changes in gray matter volume in cortical regions involved in executive control (including inferior frontal gyrus, middle temporal gyrus, angular gyrus, and medial frontal gyrus), indicating adaptations toward handling increased executive control demands. Conversely, duration of bilingual engagement resulted in changes within white matter microstructure (bilateral superior longitudinal fasciculus) and increases in subcortical gray matter (left caudate), indicative of adaptations toward increased efficiency of control. Overall, this research enhances our understanding of how bilingual experiences influence brain structure and provides the first direct empirical evidence for the predictions made by the Unifying the Bilingual Experience Trajectories framework.
Denise Levertov’s “Histrionics”
Authors: Parrish Melissa 
Published: February 2024

Abstract
This essay argues that Denise Levertov’s antiwar poetry challenges contemporary assumptions about the limits of bearing witness to war. Contrary to George Oppen’s intimation that she should limit her writing to “authentic” accounts of her own domestic experience, Levertov wrote about her uneven relationship with the “here” of the Cold War homefront and the “there” of the Vietnam War’s violence. In grappling with these two seemingly disparate domains, she exposes the Cold War security state’s reliance on gendered household motifs to justify state-sponsored violence across geographic and temporal divides. Levertov treats wartime witnessing as an imaginative and critical encounter with racial and gendered violence—one that relies less on narrating discrete and directly observed events and more on challenging the permissibility of perpetual war itself.
Pragmatic Trial Design to Compare Real-world Effectiveness of Different Treatments for Inflammatory Bowel Diseases: The PRACTICE-IBD European Consensus
Authors: Fantini Massimo Claudio , Fiorino Gionata , Colli Agostino , Laharie David , Armuzzi Alessandro , Caprioli Flavio Andrea , Gisbert Javier P , Kirchgesner Julien , Macaluso Fabio Salvatore , Magro Fernando , Ghosh Subrata ,   PRACTICE-IBD study group, Allez Matthieu , Amiot Aurelien , Atreya Raja , Barreiro-de Acosta Manuel , Biancone Livia , Castiglione Fabiana , Chaparro María , Dignass Axel , Doherty Glen , Domènech Eugeni , Fries Walter , Halfvarson Jonas , Kopylov Uri , Onali Sara , Pugliese Daniela , Ribaldone Davide Giuseppe , Saibeni Simone , Savarino Edoardo Vincenzo 
Published: February 2024

Abstract

Background and Aims
Pragmatic studies designed to test interventions in everyday clinical settings can successfully complement the evidence from registration and explanatory clinical trials. The European consensus project PRACTICE-IBD was developed to identify essential criteria and address key methodological issues needed to design valid, comparative, pragmatic studies in inflammatory bowel diseases [BDs].

Methods
Statements were issued by a panel of 11 European experts in IBD management and trial methodology, on four main topics: [I] study design; [II] eligibility, recruitment and organisation, flexibility; [III] outcomes; [IV] analysis. The consensus process followed a modified Delphi approach, involving two rounds of assessment and rating of the level of agreement [1 to 9; cut-off ≥7 for approval] with the statements by 18 additional European experts in IBD.

Results
At the first voting round, 25 out of the 26 statements reached a mean score ≥7. Following the discussion that preceded the second round of voting, it was decided to eliminate two statements and to split one into two. At the second voting round, 25 final statements were approved: seven for study design; six for eligibility, recruitment and organisation, flexibility; eight for outcomes; and four for analysis.

Conclusions
Pragmatic, randomised, clinical trials can address important questions in IBD clinical practice, and may provide complementary, high-level evidence, as long as they follow a methodologically rigorous approach. These 25 statements intend to offer practical guidance in the design of high-quality, pragmatic, clinical trials that can aid decision making in choosing a management strategy for IBDs.
Unilateral nasal obstruction mediates reversible morphological and phenotypic changes in masticatory muscles of growing rats
Authors: Iwaki Shuntaro , Yonemitsu Ikuo , Tabata Makoto , Keitoku Mirei , Guan Hao , Ono Takashi 
Published: February 2024

Abstract

Objective
Mouth breathing as a result of nasal obstruction affects craniofacial growth and development. This study aimed to investigate the effects of unilateral nasal obstruction and its recovery, along with the role of nitric oxide (NO) in masticatory muscle physiology.

Materials and Methods
Forty-eight 4-week-old male rats were divided into control and experimental groups. The five experimental groups were subjected to left-sided nasal obstruction by suturing the external nostril, and the sutures were removed after 1, 3, 5, 7, or 9 weeks to allow for varying recovery periods. We assessed morphological changes in masseter, temporalis, and digastric muscle, by examining cross-sectional area (CSA) and myosin heavy chain (MHC) isoform composition of muscle fibers. Reverse transcription-quantitative real-time polymerase chain reaction to measure messenger RNA (mRNA) levels for tumor necrosis factor-α (TNF-α), glucose transporter 4 (GLUT4), and neuronal nitric oxide synthase (nNOS) were conducted.

Results
The SpO2, CSA, and fibers showing MHC-2b isoforms were significantly lower, while RT-PCR showed higher mRNA levels in TNF-α and nNOS, and a decrease in GLUT4 mRNA in the jaw-closing muscles in the long-term nasal obstruction groups than that in the control group.

Limitations
The study findings should be interpreted cautiously because of the functional differences between rodents and humans in terms of respiratory mechanisms.

Conclusions
Unilateral nasal obstruction affects the morphology and contractile characteristics of the rat masticatory muscles during development, with possible involvement of NO in muscle hypofunction. These changes may revert to baseline levels if the nasal obstruction is eliminated before puberty in rats.
A bootstrap-based approach to combine individual-based forest growth models and remotely sensed data
Authors: Fortin Mathieu , van Lier Olivier , Côté Jean-François , Erdle Heidi , White Joanne 
Published: February 2024

Abstract
Combining forest growth models with remotely sensed data is possible under a generalized hierarchical model-based (GHMB) inferential framework. This implies the existence of two submodels: the growth model itself ($\mathcal{M}_{1}$) and a second submodel that links the growth predictions to some remotely sensed variables ($\mathcal{M}_{2}$). Analytical GHMB estimators are available to fit submodel $\mathcal{M}_{2}$ and account for the uncertainty stemming from submodel $\mathcal{M}_{1}$, i.e. the growth model. However, when the growth model is individual based, it is usually too complex to be differentiated with respect to its parameters. As a result, the analytical GHMB estimators cannot be used. In this study, we developed a bootstrap approach for the GHMB inferential framework in order to combine individual-based forest growth models with remotely sensed data. Through simulation studies, we showed that the bootstrap estimators were nearly unbiased when both submodels were linear. The estimator of the parameter estimates remained nearly unbiased when submodel $\mathcal{M}_{1}$ became complex, i.e. non-differentiable, and submodel $\mathcal{M}_{2}$ was nonlinear with heterogeneous variances and correlated error terms. The variance estimator showed some biases but these were relatively small. We further demonstrated through a real-world case study that the predictions of a complex individual-based model could be linked to a Landsat-8 near-infrared spectral band in the boreal forest zone of Quebec, Canada.
Skeletal muscle ageing: lessons from teleosts
Authors: Quach Tuyen K , Taylor Megan F , Currie Peter D , Eynon Nir , Ruparelia Avnika A 
Published: February 2024

Abstract
Ageing is the greatest risk factor for a multitude of age-related diseases including sarcopenia -the loss of skeletal muscle mass and strength - which occurs at remarkable rates each year. There is an unmet need not only to understand the mechanisms that drive sarcopenia, but also to identify novel therapeutic strategies. Given the ease and affordability of husbandry, along with advances in genomics, genome editing technologies and imaging capabilities, teleost models are increasingly used for ageing and sarcopenia research. Here, we explain how teleost species such as zebrafish, African turquoise killifish and medaka recapitulate many of the classical hallmarks of sarcopenia, and discuss the various dietary, pharmacological and genetic approaches that have been used in teleosts to understand the mechanistic basis of sarcopenia.
Words of Chinese Origin in the OED: Misinformation and Attestation
Authors: Zhong Ai 
Published: February 2024

Abstract
Recent decades have seen small batches of Chinese loanwords and words from Chinese English entering the Oxford English Dictionary (OED). Meanwhile, a muddle of misinformation on the dictionary’s inclusion of certain Chinese-origin words has occurred again and again in various Chinese media forms. The present study examines the extent to which these uninformed news stories are associated with prominent features of the OED. In order to assess the possibility of including the words mentioned in the pieces of misinformation, the study explores the current treatment of Chinese-origin words in the OED and adopts Diamond’s (2016) four criteria for entry, namely evidence of usage, longevity, naturalization, and lexicographical significance. Although the words examined are inadequate in meeting all criteria for inclusion, the misinformed new stories attest to an awareness of Chinese influence on the English lexicon and evidence the reception and reputation of the OED in Chinese media and culture. Moreover, the bits of false news reports expose lexicographers to new knowledge of some prospective candidates for lexicographical inclusion.