bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sox11 is enriched in myogenic progenitors but dispensable for development and regeneration of skeletal muscle
Authors: Oprescu Stephanie N. , Baumann Nick , Chen Xiyue , Sun Qiang , Zhao Yu , Yue Feng , Wang Huating , Kuang Shihuan 
Published: April 2023

AbstractTranscription factors (TFs) play key roles in regulating the differentiation and function of stem cells, including muscle satellite cells (MuSCs), a resident stem cell population responsible for postnatal regeneration of the skeletal muscle. Sox11 belongs to the Sry-related HMG-box (SOX) family of TFs that play diverse roles in stem cell behavior and tissue specification. Analysis of single-cell RNA-sequencing (scRNA-seq) datasets identify a specific enrichment ofSox11mRNA in differentiating but not quiescent MuSCs. Consistent with the scRNA-seq data,Sox11levels increase during differentiation of murine primary myoblasts in vitro. scRNA-seq data comparing muscle regeneration in young and old mice further demonstrate thatSox11expression is reduced in aged MuSCs. Age-related decline ofSox11expression is associated with reduced chromatin contacts within the topologically associated domains. Unexpectedly, Myod1Cre-driven deletion ofSox11in embryonic myoblasts has no effects on muscle development and growth, resulting in apparently healthy muscles that regenerate normally. Pax7CreERor Rosa26CreERdriven (MuSC-specific or global) deletion ofSox11in adult mice similarly has no effects on MuSC differentiation or muscle regeneration. These results identify Sox11 as a novel myogenic differentiation marker with reduced expression in quiescent and aged MuSCs, but the specific function of Sox11 in myogenesis remain to be elucidated.
Matrin3 mediates differentiation through stabilizing chromatin accessibility and chromatin loop-domain interactions, and YY1 mediated enhancer-promoter interactions
Authors: Liu Tianxin , Zhu Qian , Yan Kai , Bingham Trevor , Cha Hye Ji , Mehta Stuti , Schlaeger Thorsten M , Yuan Guo-Cheng , Orkin Stuart H 
Published: April 2023

AbstractAlthough emerging evidence indicates that alterations in proteins within nuclear compartments elicit changes in chromosomal architecture and differentiation, the underlying mechanisms are not well understood. Here we investigate the direct role of the abundant nuclear complex protein Matrin3 (Matr3) in chromatin architecture and development in the context of myogenesis. Using an acute targeted protein degradation platform (dTAG-Matr3), we reveal the dynamics of development-related chromatin reorganization. Upon acute depletion of Matr3, gains in chromatin accessibility and MyoD binding were observed, prior to widespread loss in the steady-state Matr3-knockout. These initial changes correlated with gene expression changes later in development. High-throughput chromosome conformation capture (Hi-C) experiments revealed substantial chromatin loop rearrangements soon after Matr3 depletion. Notably, YY1 binding was detected in close proximity to enhancer and promoter regions, accompanied by the emergence of novel YY1-mediated enhancer-promoter loops, which occurred concurrently with changes in histone modifications and chromatin-level binding patterns. Overall, our results suggest that Matr3 mediates differentiation through stabilizing chromatin accessibility and chromatin loop-domain interactions, and highlight a conserved and direct role for Matr3 in maintenance of chromosomal architecture.
The bioactive dietary polyphenol preparation alleviates depression and anxiety-like behaviors by modulating the regional heterogeneity of microglia morphology
Authors: Yang Eun-Jeong , Frolinger Tal , Westfall Susan , Iqbal Umar Haris , Murrough James , Pasinetti Giulio M. 
Published: April 2023

ABSTRACTScopeThe goal of this study is to investigate the effects of a bioactive dietary polyphenol preparation (BDPP), which is made up of grape-derived polyphenols, on microglial responses, as well as the underlying molecular mechanisms in depression and anxiety-like behaviors.Methods and resultsWe find that treatment with BDPP significantly decreased depression-like and anxiety-like behaviors induced by chronic stress in mice, while leaving their locomotor activity unaffected. We also find that BDPP treatment reversed microglia activation in the amygdala and hippocampal formation, regions of the brain involved in emotional regulation, from an amoeboid shape to ramified shape. Additionally, BDPP treatment modulates the release of pro-inflammatory cytokines such as interleukin-6 via high mobility box 1 protein and the receptor for advanced glycation end products (HMGB1-RAGE) signaling pathway in activated microglia induced by chronic stress.ConclusionOur findings suggest regional heterogeneity in microglial responses following chronic stress in subregions of the corticolimbic circuit. Specifically, activation of the immune-inflammatory HMGB1-RAGE pathway might provide a new avenue for therapeutic intervention in stress-induced anxiety- and depression-like behavior, using bioactive and bioavailable polyphenols.
Early microbial intervention reduces diarrhea while improves later milk production in newborn calves
Authors: Shen Yizhao , Li Yan , Wu Tingting , Dong Quanbin , Deng Qiufeng , Liu Lu , Guo Yanfei , Cao Yufeng , Li Qiufeng , Shi Jing , Zou Huayiyang , Jiao Yuwen , Ding Luoyang , Li Jianguo , Gao Yanxia , Hu Shixian , Wang Yifeng , Chen Lianmin 
Published: April 2023

ABSTRACTThe rumen of neonatal calves is not well-developed and exhibits limited functionality. Therefore, the establishment of intestinal microbiota may play an instrumental role in their health and performance, but it has been rarely explored. Thus, we aim to explore the temporal colonization of the gut microbiome and the potential benefits of early microbial intervention in newborn calves. We followed up on the temporal dynamics of the gut microbiome and plasma metabolome in 36 newborn calves during the first two months of life and established their relationships with their health status and performance. We also evaluated whether microbiota transplantation (MT) could influence their phenotypes by modulating metabolism and its impact on later milk production performance.We showed that the composition and ecological interactions of the gut microbiome are likely to reach maturity one month after birth. Temporal changes in the gut microbiome of newborn calves are widely associated with changes in their physiological statuses, such as growth and fiber digestion. Importantly, we observed that MT reshapes the gut microbiome of newborns by altering the abundance and interaction ofBacteroidesspecies, as well as amino acid pathways, such as arginine biosynthesis. Two-year follow-up of those calves further showed that MT improves their later milk production. Notably, MT improves fiber digestion, antioxidant capacity of newborns while reducing diarrhea. MT also contributes to significant changes in the metabolomic landscape, and with putative causal mediation analysis, we suggest that altered gut microbial composition in newborns may influence physiological status through microbial-derived metabolites. The data from the study may help develop strategies to manipulate the gut microbiota during early life, which may be significantly relevant to the health and production of newborn calves.HIGHLIGHTSThe gut microbial composition and ecological interaction in newborn calves reach maturity one month after birthTemporal shifts in the gut microbiome of newborn calves are associated with phenotypic changes, including growth, digestion, and antioxidative capacityEarly microbial intervention in newborn calves reduces diarrhea while improving later milk productionThe gut microbial impact on newborn calves is mediated by plasma metabolites
Rhytidome- and cork-type barks of holm oak, cork oak and their hybrids highlight processes leading to cork formation
Authors: Armendariz Iker , López de Heredia Unai , Soler Marçal , Puigdemont Adrià , Mercè Ruiz Maria , Jové Patricia , Soto Álvaro , Serra Olga , Figueras Mercè 
Published: April 2023

ABSTRACTThe periderm is basic for land plants due to its protective role during radial growth, which is achieved by the polymers deposited in the cell walls. In most trees, like holm oak, the periderm is frequently replaced by subsequent internal periderms yielding a heterogeneous outer bark made of a mixture of periderms and phloem tissues, known as rhytidome. Exceptionally, cork oak forms a persistent or long-lived periderm which results in a homogeneous outer bark of thick phellem cell layers known as cork. Here we use the outer bark of cork oak, holm oak, and their natural hybrids’ to analyse the chemical composition, the anatomy and the transcriptome, and further understand the mechanisms underlying periderm development. The inclusion of hybrid samples showing rhytidome-type and cork-type barks is valuable to approach to cork and rhytidome development, allowing an accurate identification of candidate genes and processes. The present study underscores that biotic stress and cell death signalling are enhanced in rhytidome-type barks whereas lipid metabolism and cell cycle are enriched in cork-type barks. Development-related DEGs, showing the highest expression, highlight cell division, cell expansion, and cell differentiation as key processes leading to cork or rhytidome-type barks.
Optimizing expression of Nanobody®molecules in Pichia pastoris through co-expression of auxiliary proteins under methanol and methanol-free conditions
Authors: De Groeve Manu , Laukens Bram , Schotte Peter 
Published: April 2023

AbstractBackgroundAblynx NV, a subsidiary of Sanofi, has a long-standing focus on the development of Nanobody®molecules as biopharmaceuticals (Nanobody®is a registered trademark of Ablynx NV). Nanobody molecules are single variable domains, and they have been met with great success part due to their favorable expression properties in several microbial systems. Nevertheless, the search for the host of the future is an ongoing and challenging process.Komagataella phaffi(Pichia pastoris) is one of the most suitable organisms to produce Nanobody molecules. In addition, genetic engineering of Pichia is easy and an effective approach to improve titers.ResultsHere we report thatP. pastorisengineered to co-express genes encoding four auxiliary proteins (HAC1, KAR2, PDI and RPP0), leads to a marked improvement in the expression of Nanobody molecules using the AOX1 methanol induction system. Titer improvement is mainly attributed to HAC1, and its beneficial effect was also observed in a methanol-free expression system.ConclusionOur findings are based on over a thousand fed-batch fermentations and offer a valuable guide to produce Nanobody molecules inP. pastoris. The presented differences in expressability between types of Nanobody molecules will be helpful for researchers to select both the type of Nanobody molecule and Pichia strain and may stimulate further the development of a more ecological methanol-free expression platform.
Considerations on brain age predictions from repeatedly sampled data across time
Authors: Korbmacher Max , Wang Meng-Yun , Eikeland Rune , Buchert Ralph , Andreassen Ole A. , Espeseth Thomas , Leonardsen Esten , Westlye Lars T. , Maximov Ivan I. , Specht Karsten 
Published: April 2023

AbstractIntroductionBrain age, the estimation of a person’s age from magnetic resonance imaging (MRI) parameters, has been used as a general indicator of health. The marker requires however further validation for application in clinical contexts. Here, we show how brain age predictions perform for for the same individual at various time points and validate our findings with age-matched healthy controls.MethodsWe used densly sampled T1-weighted MRI data from four individuals (from two datasets) to observe how brain age corresponds to age and is influenced by acquision and quality parameters. For validation, we used two cross-sectional datasets. Brain age was predicted by a pre-trained deep learning model.ResultsWe find small within-subject correlations between age and brain age. We also find evidence for the influence of field strength on brain age which replicated in the cross-sectional validation data, and inconclusive effects of scan quality.ConclusionThe absence of maturation effects for the age range in the presented sample, brain age model-bias (including training age distribution and field strength) and model error are potential reasons for small relationships between age and brain age in longitudinal data. Future brain age models should account for differences in field strength and intra-individual differences.
Spatiotemporal coordination of Rac1 and Cdc42 at the whole cell level during cell ruffling
Authors: Hladyshau Siarhei , Stoop Jorik P , Kamada Kosei , Nie Shuyi , Tsygankov Denis V 
Published: April 2023

AbstractRho-GTPases are central regulators within a complex signaling network that controls the cytoskeletal organization and cell movement. This network includes multiple GTPases, such as the most studied Rac1, Cdc42, and RhoA, and their numerous effectors that provide mutual regulation and feedback loops. Here we investigate the temporal and spatial relationship between Rac1 and Cdc42 during membrane ruffling using a simulation model which couples GTPase signaling with cell morphodynamics to capture the GTPase behavior observed with FRET-based biosensors. We show that membrane velocity is regulated by the kinetic rate of GTPase activation rather than the concentration of active GTPase. Our model captures both uniform and polarized ruffling. We also show that cell-type specific time delays between Rac1 and Cdc42 activation can be reproduced with a single signaling motif, in which the delay is controlled by feedback from Cdc42 to Rac1. The resolution of our simulation output matches those of the time-lapsed recordings of cell dynamics and GTPase activity. This approach allows us to validate simulation results with quantitative precision using the same pipeline for the analysis of simulated and experimental data.
A multi-actor ICT platform for increasing sustainability and resilience of small-scale farmers after pandemic crisis
Authors: Cimino Antonio , Longo Francesco , Solina Vittorio , Verteramo Saverino 
Published: April 2023

PurposeThis paper proposes an Information and Communication Technology (ICT) platform to increase the sustainability and resilience of smallholders to face supply chain disruptions in the event of COVID-like crises. The platform facilitates interactions between smallholders and buyers, workers and freight transport companies in agri-food ecosystems. Furthermore, this research work presents the implementation of the freight transport companies’ platform module.Design/methodology/approachThe research work begins with a literature review aiming at analyzing current available ICT solutions supporting smallholders and other actors in the agri-food supply chain. This analysis identifies the research gaps which have to be filled by the platform. Then, the authors proceed with the analysis of the operational scenarios of each platform actor by interacting with experts and operators working in the agri-food sector. The results of such analysis resulted in a comprehensive, unambiguous and consistent set of specification being used to define the platform structure and modules architecture. The platform modules have been developed by using the web-application framework Laravel.FindingsPreliminary tests show that the proposed platform is usable and promises to improve the resilience and economic, social and environmental sustainability of agri-food supply chains, with a focus on smallholders.Originality/valueThe research work allows players in the agri-food supply chain and in particular small local producers to react and mitigate the impact of COVID-like crises through development of a platform in which smallholders, citizens (buyers and workers) and freight transport companies are simultaneously present.
The mediating role of workplace spirituality between personal attributes and job performances of Indian bus drivers
Authors: Jayakumar V. , Vinodkumar M.N. 
Published: April 2023

PurposeTransport industry is one of the leading accident causing industries all around the world. Personal attributes like educational qualification, work experience, marital status, consumption of alcohol, hours of work of bus drivers are known to influence such accidents. In the present study, the mediating effects of Workplace spirituality (WS) among bus drivers between the personal attributes and job performance variables like self-reported accidents, punishments and appraisals are carried out.Design/methodology/approachA mediation analysis of WS between personal attributes and job performances of bus drivers is conducted in the present study. Since there is scarcity of studies measuring the effects of WS of bus drivers, new scale to measure WS was developed. The study was carried out in the government-owned road transport corporation in the state of Kerala, India. Responses were obtained from 617 male drivers.FindingsUsing exploratory factor analysis, four factors were identified, namely Meaningful work, Sense of Community, Mindfulness and Compassion. Confirmatory factory analysis provided good fit. The intercorrelations of personal attributes of drivers (independent variables) between WS factors (mediating variables) and job performance variables (dependent variables) were found out. Mediation analysis showed complete mediation of WS factors between marital status, alcohol consumption, hours of work and job performances like number of self-reported accidents, punishments and appraisals. The WS levels of drivers decrease significantly as working hours per goes beyond the legally allowed working hours.Originality/valuePsychological attributes like Mindfulness, Sense of community, compassion etc. which are collectively known as WS influence the job performances of employees in other industries. Yet it is not studied in the transport industry. Hence, in the present study, the levels of WS are studied among bus drivers of government-owned road transport corporation in the State of Kerala, India.
Spatiotemporal patterns of research on Southern Hemisphere amphidromous galaxiids: A semi–quantitative review
Authors: Lee Finnbar , Boddy Nixie C. , Bloxham Matthew , McIntosh Angus R. , Perry George L. W. , Simon Kevin S. 
Published: April 2023

AbstractAmphidromy is a distinctive life‐history strategy of some fish species that involves spawning in fresh or brackish water followed by dispersal to sea by newly hatched larvae, where they develop for a short period. Individuals then return to freshwater as juveniles, where they feed and grow, before maturing and spawning. Six amphidromous species from the Southern Hemisphere genus Galaxias (G. truttaceus, G. fasciatus, G. argenteus, G. postvectis, G. brevipinnis, G. maculatus) are recreationally, culturally, and economically important as the juveniles are harvested. Due to ongoing population declines and a lack of critical demographic information, there is growing concern about the management of the species. Here, we used semi‐quantitative review, culturomics, and bibliometric tools to analyse peer‐reviewed research conducted on the six amphidromous species of Galaxias to: (i) understand how spatiotemporal patterns of research have shifted over the last five decades, and (ii) identify critical research gaps. Forty percent of studies (n = 295) covered a spatial extent of 10 km or less and 87% of studies lasted less than 2 years – studies were largely small and short relative to the species' ranges and their longevity. Additionally, we found important research gaps; for example, studies on the effects of climate change and the associated effects of disturbance, and the marine phase are scarce in the peer‐reviewed literature. Finally, we suggest that quantitative models have been underutilized as tools for studying amphidromous galaxiids and should be embraced to answer questions not readily addressed with field and laboratory‐based techniques. If these species are to be effectively managed, their population dynamics across spatiotemporal scales must be understood and critical and long‐standing gaps in research knowledge addressed.
A comparison of endodontic referrals and treatment in the public and private sectors in Western Australia
Authors: Thanissorn Charn , Ye Johnson , Girgis Daniel , van Dort Nathan , Abbott Paul V. 
Published: April 2023

AbstractThe aim was to compare referral patterns and treatment provided by specialist Endodontists and Endodontic Registrars. A retrospective review was conducted of the clinical records of the first 25 patients seen by seven private endodontic clinicians and the equivalent number (175) of patients seen by five public sector endodontic clinicians from 1 January 2017. The average age and range of medical co‐morbidities of patients in the public sector were statistically greater. Referred patients and referrers mainly worked in metropolitan Perth. The most frequent reasons for referral in both public and private sectors were to assess and manage non‐painful endodontic pathosis, to manage pain, and to manage calcified canals. There was a wide range of cases referred to both sectors but with similar patterns suggesting that the training of specialists adequately prepares them for private practice. The results also indicate that Endodontists must be proficient in all aspects of the speciality.
Febrile ulceronecrotic Mucha–Habermann disease during pregnancy: A case report
Authors: Avcı Ceylan , Gürbüz Özlem , Özbağçıvan Özlem , Lebe Banu 
Published: April 2023

AbstractFebrile ulceronecrotic Mucha–Habermann disease (FUMHD) is a rare and severe form of ‘pityriasis lichenoides et varioliformis acuta’, with a progressive and potentially fatal course. To the best of our knowledge, there has been no reported case of FUMDH during pregnancy before. Due to life‐threatening nature of the disease and the lack of evidence‐based treatment, management of FUMHD in pregnancy is a therapeutic challenge. Additionally, some of the drugs that are effective in the treatment are contraindicated in pregnancy. Herein, we report a 27‐year‐old woman diagnosed with FUMHD in her 19th week of pregnancy and treated with ceftriaxone and erythromycin.
Keyword‐Assisted Topic Models
Authors: Eshima Shusei , Imai Kosuke , Sasaki Tomoya 
Published: April 2023

AbstractIn recent years, fully automated content analysis based on probabilistic topic models has become popular among social scientists because of their scalability. However, researchers find that these models often fail to measure specific concepts of substantive interest by inadvertently creating multiple topics with similar content and combining distinct themes into a single topic. In this article, we empirically demonstrate that providing a small number of keywords can substantially enhance the measurement performance of topic models. An important advantage of the proposed keyword‐assisted topic model (keyATM) is that the specification of keywords requires researchers to label topics prior to fitting a model to the data. This contrasts with a widespread practice of post hoc topic interpretation and adjustments that compromises the objectivity of empirical findings. In our application, we find that keyATM provides more interpretable results, has better document classification performance, and is less sensitive to the number of topics.