bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dietary Trends and Dementia - A Multi-Country Ecological Analysis
Authors: Reed Robert 
Published: January 2023

AbstractBackgroundThis research evaluates the association between increased animal product consumption and population-level dementia incidence.Design/methodology/approachPublicly available data from 54 countries across a 10-year span was used to conduct a multivariate panel data regression to determine significant relationships between dietary changes and rates of dementia. Fixed effects analysis controls for the effect of omitted time-invariant differences between countries.FindingsExcess calorie consumption is associated with a significant increase in dementia whereas fish consumption appears protective. On a population-level basis, increases in milk and egg consumption were associated with an increase in dementia rates. Meat, as a broadly defined category, was found to have no significant effect.Practical ImplicationsThis study supports the well-documented benefits of calorie control and fish consumption to protect against dementia, but indicates that egg and milk consumption is associated with increased population-level dementia incidence.Originality/valueThis research expands current literature by using an updated data set, evaluating considerably more countries, and utilizing a regression model that controls for the effects of time-invariant sources of heterogeneity in the data.
Combined severe-to-profound hearing and vision impairment – experiences of daily life and need of support, an interview study
Authors: Turunen-Taheri Satu , Hagerman Sirelius Annica , Hellström Sten , Skjönsberg Åsa , Backenroth Gunnel 
Published: January 2023

AbstractObjectivesThe purpose of the present study was to describe experiences of disabilities and factors affecting daily life from the perspective of adult persons with severe-to-profound hearing impairment in combination with severe vision impairment. Furthermore, the study also investigated which kind of support individuals with dual sensory loss received, and their experiences as citizens in the society.MethodsSemi-structured qualitative interviews were performed, analyzed, and categorized using content analysis.ResultsFourteen interviews were performed, with equal number of both sexes. Mean age was 70.1 years (47-81 years). Analysis of the data resulted in 22 categories, six sub-themes and two main themes. Two main themes emerged asIsolationandThe Ability to control one’s own daily life. Surprisingly, most of the participants did not think of their vision and hearing impairment as a combined disability. The interviews showed various kind of strategies to handle daily life. The Deafblind-team unit was reported to offer excellent health care. Companion services for persons with disabilities proved to have become more difficult to get support from and created lack of independence and control over their own lives. However, it was also obvious that the participants felt a positive outlook on life and more solution-oriented in order to adjust their everyday life to their life-situation.ConclusionsThe combination of vision and hearing impairment demonstrated isolation, and the respondents in the study have a need of support in everyday lives. At the same time, they struggle to have the ability to control their own lives.
The effect of emotion regulation on emotional eating among undergraduate students in China: the chain mediating role of impulsivity and depressive symptoms
Authors: Yang Huimin , Zhou Xinyi , Xie Longjiao , Sun Jing 
Published: January 2023

AbstractThis study aimed to examine the relationship between difficulties in emotion regulation and emotional eating and the role of impulsivity and depressive symptoms in mediating this chain. Four hundred ninety-four undergraduate students participated in the study. A self-designed questionnaire was used in the survey from February 6 to 13, 2022, to finish our purpose, including the Emotional Eating Scale (EES-R), Depression Scale (CES-D), the Short Version of the Impulsivity Behavior Scale (UPPS-P) and Difficulties in Emotion Regulation Scale (DERS). Results showed that 1) There was a positive correlation between difficulties in emotion regulation, impulsivity, depressive symptoms, and emotional eating, respectively.2) Impulsivity and depressive symptoms mediated the relationship between emotion regulation and emotional eating separately. 3) Impulsivity and depressive symptoms played the mediating chain role between emotion regulation and emotional eating.
Research on the mental health status of frontline medical staff during the normalization of the COVID-19 pandemic
Authors: Sun Ning , Li Laiyou , Xu Jinmei , zhou Shuping , Fan Chaoyan , Li Hongyu , Yang Shuang 
Published: January 2023

AbstractObjectiveThis study aimed to investigate the relationship between personality characteristics and psychological health of hospitals’ frontline medical staff and provide a basis and reference for targeted psychological health education for frontline medical staff and for the staff of related departments to formulate relevant policies.MethodsThe self-evaluation scale of symptoms (SCL-90) was used to investigate the mental health status of 150 first-line medical staff in Zhejiang Province in response to the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pneumonia.ResultsThe average scores of SCL-90 and somatization, obsessive-compulsive, depression, anxiety, hostility, terror, and psychotic factors were significantly higher than those of the normal sample in the first-aid medical staff of Aihu Hubei. The degree of influence on the mental health status of the frontline medical staff in service in Hubei is as follows, from high to low: the degree of suspicion that they may have been infected when new coronavirus pneumonia-related symptoms occur, the degree of fear of being infected and thus bring the infection to their families, and whether they have received a medical check-up recently, as well as a high level of education (bothP<0.05).ConclusionThe psychological health level of the frontline medical staff is lower than the national norm. In the context of the increasing number of confirmed cases and the new type of coronavirus pneumonia in the absence of any specific curative treatments, the frontline medical staff is under great psychological pressure. It is necessary to institute targeted mental health promotion to relieve the psychological pressure endured by the frontline medical staff, promote their physical and mental health, and better respond to the pandemic in China.
Integration of chromatin accessibility and gene expression data with cisREAD reveals a switch from PU.1/SPIB-driven to AP-1-driven gene regulation during B cell activation
Authors: Emmett Amber M.L. , Saadi Amel , Care Matthew A. , Doody Gina M. , Tooze Reuben M. , Westhead David R. 
Published: January 2023

ABSTRACTHuman B cell differentiation into antibody secreting plasma cells is a critical process in the adaptive immune response, whose regulation at the genetic level remains incompletely understood. To reveal the temporal sequence of transcription factor driven cellular changes we generated chromatin accessibility (ATAC-seq) and gene expression (RNA-seq) data fromin vitrodifferentiation of human B cells into plasma cells using a published protocol for differentiation up to the plasma cell stage. Using a new computational method, cisREAD (cis-Regulatory Elements Across Differentiation), we defined a core set ofcis-regulatory elements that are confidently linked to dynamic transcription factor binding and changes in gene expression across the mature B lineage. Here we describe how cisREAD identifies regulatory element ‘communities’, based on chromatin accessibility and transcription factor co-occupancy, and prioritizes those whose accessibility predicts differential gene expression through regularized regression models. Through downstream analyses of cisREAD-predicted regulation, we show how transcription factors reshape B cell epigenomes and transcriptomes in response to differentiation stimuli. Our results confirm roles for OCT2, IRF4 and PRDM1 in plasma cell differentiation, and reveal that a shift from PU.1/SPIB-driven to AP-1-driven gene regulation is a key determinant of B cell activation.GRAPHICAL ABSTRACTIntegration of epigenomic and transcriptomic datasets with the cisREAD method, followed by clustering and network analysis, reveals that gene regulation shifts from PU.1/SPIB to AP-1 upon B cell activation.
Single Molecule Mechanics and Kinetics of Cardiac Myosin Interacting with Regulated Thin Filaments
Authors: Clippinger Schulte Sarah R. , Scott Brent , Barrick Samantha K. , Stump W. Tom , Blackwell Thomas , Greenberg Michael J. 
Published: January 2023

AbstractThe cardiac cycle is a tightly regulated process wherein the heart generates force to pump blood to the body during systole and then relaxes during diastole. Disruption of this finely tuned cycle can lead to a range of diseases including cardiomyopathies and heart failure. Cardiac contraction is driven by the molecular motor myosin, which pulls regulated thin filaments in a calcium-dependent manner. In some muscle and non-muscle myosins, regulatory proteins on actin tune the kinetics, mechanics, and load dependence of the myosin working stroke; however, it is not well understood whether or how thin filament regulatory proteins tune the mechanics of the cardiac myosin motor. To address this critical gap in knowledge, we used single-molecule techniques to measure the kinetics and mechanics of the substeps of the cardiac myosin working stroke in the presence and absence of thin filament regulatory proteins. We found that regulatory proteins gate the calcium-dependent interactions between myosin and the thin filament. At physiologically relevant ATP concentrations, cardiac myosin’s mechanics and unloaded kinetics are not affected by thin filament regulatory proteins. We also measured the load-dependent kinetics of cardiac myosin at physiologically relevant ATP concentrations using an isometric optical clamp, and we found that thin filament regulatory proteins do not affect either the identity or magnitude of myosin’s primary load-dependent transition. Interestingly, at low ATP concentrations, thin filament regulatory proteins have a small effect on actomyosin dissociation kinetics, suggesting a mechanism beyond simple steric blocking. These results have important implications for both disease modeling and computational models of muscle contraction.Significance StatementHuman heart contraction is powered by the molecular motor β-cardiac myosin, which pulls on thin filaments consisting of actin and the regulatory proteins troponin and tropomyosin. In some muscle and non-muscle systems, these regulatory proteins tune the kinetics, mechanics, and load dependence of the myosin working stroke. Despite having a central role in health and disease, it is not well understood whether the mechanics or kinetics of β-cardiac myosin are affected by regulatory proteins. We show that regulatory proteins do not affect the mechanics or load-dependent kinetics of the working stroke at physiologically relevant ATP concentrations; however, they can affect the kinetics at low ATP concentrations, suggesting a mechanism beyond simple steric blocking. This has important implications for modeling of cardiac physiology and diseases.
Thermal plasticity of wing spot size inDrosophila guttifera: investigating the relevance to Wingless morphogen
Authors: Fukutomi Yuichi , Takahashi Aya , Koshikawa Shigeyuki 
Published: January 2023

AbstractThermal plasticity of animal color patterns has been studied to investigate the molecular mechanisms of phenotypic plasticity. There are examples in which the formation of color patterns is controlled by a morphogen. The extracellular distribution of a morphogen can be plastic with temperature change. Whether alteration of morphogen distribution with temperature change produces thermal plasticity in color patterns has not been studied. To address this question, polka-dotted wing spots ofDrosophila guttifera, whose inducer iswinglessmorphogen, can be a suitable model system. In this study, we rearedD. guttiferaat different temperatures to test whether wing spots show thermal plasticity. We found that wing size becomes larger and spot size adjusted with wing size becomes smaller at lower temperatures. We also changed the rearing temperature in the middle of the pupal period and found that the most sensitive developmental period for wing size and spot size is different. The results suggest that developmental mechanisms for the thermal plasticity of wing size and spot size are different. We also found that the most sensitive stage for spot size was part of the pupal period including stages at whichwinglessis expressed in the polka-dotted pattern. Therefore, it is suggested that temperature change might affect the process of specifying spot areas by Wingless in the extracellular region.
A field-capable rapid plant DNA extraction protocol using microneedle patches for botanical survey and monitoring
Authors: Selz Jonathan , Adam Nicolas R. , Magrini Céline E. M. , Montandon Fulvia Malvido , Buerki Sven , Maerkl Sebastian J. 
Published: January 2023

ABSTRACTPremiseA novel protocol for rapid plant DNA extractions using microneedles is proposed, which supports botanic surveys, taxonomy and systematics. This protocol can be conducted in the field with limited laboratory skills and equipment. The protocol is validated by conducting sequencing and comparing results with Qiagen spin-column DNA extractions using BLAST analyses.Methods and ResultsTwo sets of DNA extractions were conducted on 13 species spanning various leaf anatomies and phylogenetic lineages: i) fresh leaves were punched with custom polymeric microneedle patches to recover genomic DNA ii) Qiagen DNA extractions. Three plastid (matK,rbcL,trnH-psbA) and one nuclear ribosomal (ITS) DNA regions were amplified, and Sanger or Nanopore sequenced. The proposed method reduced the extraction to 1 min and yielded the same DNA sequences as Qiagen.ConclusionsOur drastically faster and simpler method is compatible with Nanopore sequencing and suitable for multiple applications including high-throughput DNA-based species identification and monitoring.
Parental care shapes the evolution of molecular genetic variation
Authors: Mashoodh R , Trowsdale A , Manica A , Kilner RM 
Published: January 2023

AbstractCooperative social behaviours, such as parental care, have long been hypothesized to relax selection leading to the accumulation of genetic variation in populations. Although the idea has been discussed for decades, there has been relatively little experimental work to investigate how social behaviour contributes to genetic variation in populations. Here, we investigate how parental care can shape molecular genetic variation in the subsocial insectNicrophorus vespilloides. Using whole genome sequencing of populations that had evolved in the presence or absence of parental care for 30 generations, we show that parental care maintains levels of standing genetic variation. In contrast, under a harsh environment without care, strong directional selection caused a reduction in genetic variation. Furthermore, we show that adaptation to the loss of care is associated with genetic divergence between populations at loci related to stress, morphological development and transcriptional regulation. These data reveal how social behaviour is linked to the genetic processes that shape and maintain genetic diversity within populations, and provides rare empirical evidence for an old hypothesis.Lay SummarySocial behaviours, such as parental care, have long been hypothesized to result in the accumulation of genetic variation in populations. Here, we investigate how parental care can shape molecular genetic variation in a species that perform biparental care,Nicrophorus vespilloides. Using genome sequencing of populations that had evolved in the presence or absence of parental care for 30 generations, we show that parental care maintains levels of standing genetic variation. In contrast, under a harsh environment without care, populations lost genetic variation. Furthermore, we show that adaptation to the loss of care is associated with genetic divergence between populations at genes related to stress, morphological development and transcriptional regulation. These data reveal how social behaviour is linked to the genetic processes that shape and maintain genetic diversity within populations.
Missing data in amortized simulation-based neural posterior estimation
Authors: Wang Zijian , Hasenauer Jan , Schälte Yannik 
Published: January 2023

AbstractAmortized simulation-based neural posterior estimation provides a novel machine learning based approach for solving parameter estimation problems. It has been shown to be computationally efficient and able to handle complex models and data sets. Yet, the available approach cannot handle the in experimental studies ubiquitous case of missing data, and might provide incorrect posterior estimates. In this work, we discuss various ways of encoding missing data and integrate them into the training and inference process. We implement the approaches in the BayesFlow methodology, an amortized estimation framework based on invertible neural networks, and evaluate their performance on multiple test problems. We find that an approach in which the data vector is augmented with binary indicators of presence or absence of values performs the most robustly. Accordingly, we demonstrate that amortized simulation-based inference approaches are applicable even with missing data, and we provide a guideline for their handling, which is relevant for a broad spectrum of applications.
Odd-even disparity in the population of slipped hairpins in RNA repeat sequences with implications for phase separation
Authors: Maity Hiranmay , Nguyen Hung T. , Hori Naoto , Thirumalai D. 
Published: January 2023

AbstractLow complexity nucleotide repeat sequences, which are implicated in several neurological disorders, undergo liquid-liquid phase separation (LLPS) provided the number of repeat units,n, exceeds a critical value. Here, we establish a link between the folding landscapes of the monomers of trinucleotide repeats and their propensity to self-associate. Simulations using a coarse-grained Self-Organized Polymer (SOP) model for (CAG)nrepeats in monovalent salt solutions reproduce experimentally measured melting temperatures, which are available only for smalln. By extending the simulations to largen, we show that the free energy gap, ΔGS, between the ground state (GS) and slipped hairpin (SH) states is a predictor of aggregation propensity. The GS for evennis a perfect hairpin (PH) whereas it is a SH whennis odd. The value of ΔGS(zero for oddn) is larger for evennthan for oddn. As a result, the rate of dimer formation is slower in (CAG)30relative to (CAG)31, thus linking ΔGSto RNA-RNA association. The yield of the dimer decreases dramatically, compared to the wild type, in mutant sequences in which the population of the SH is decreases substantially. Association between RNA chains is preceded by a transition to the SH even if the GS is a PH. The finding that the excitation spectra, which depends on the exact sequence,n, and ionic conditions, is a predictor of self-association, should also hold for other RNAs (mRNA for example) that undergo LLPS.
Distinct Functional cerebral Hypersensitivity networks during incisional and inflammatory pain in rats
Authors: Kreitz S. , Pradier B. , Segelcke D. , Amirmohseni S. , Hess A. , Faber C. , Pogatzki-Zahn E. 
Published: January 2023

AbstractAlthough the pathophysiology of pain has been investigated tremendously, there are still many open questions, especially with regard to specific pain entities and their pain-related symptoms. To increase the translational impact of (preclinical) animal pain neuroimaging studies, the use of disease-specific pain models, as well as relevant stimulus modalities, are critical. Yet, the challenges of identifying neuroimaging signatures at a pain entity- and modality-specific level are manifold. Therefore, we developed a comprehensive framework for brain network analysis in disease-specific pain models combining functional MRI with graph-theory and data classification by linear discriminant analysis. This enabled us to expand our knowledge of stimulus (mechanical vs. electrical) modality processing under incisional (INC) and pathogen-induced inflammatory (CFA) pain entities compared to acute pain conditions. In short, graph-theoretical analyses revealed distinct Network Signatures of Pain Hypersensitivity (NSPH) for INC and CFA, resulting in impaired discrimination of stimulus modalities in both pain models compared to control conditions (CTR). Such specific neuroimaging signatures are an important step toward identifying novel pain biomarkers for certain diseases and relevant outcomes to evaluate target engagement of novel therapeutic options, which ultimately can be translated to the clinic.
Insights into the metabolic specificities of pathogenic strains from theRalstonia solanacearum species complex
Authors: Baroukh Caroline , Cottret Ludovic , Pires Emma , Peyraud Rémi , Guidot Alice , Genin Stéphane 
Published: January 2023

AbstractAll the strains grouped under the speciesRalstonia solanacearumrepresent a species complex which collectively constitute a devastating plant pathogen responsible of many diseases on agricultural crops throughout the world. The strains have different lifestyles and host range. Here we sought whether specific metabolic pathways contribute to strain diversification. To this end, we carried out systematic comparisons, followed by manual expertise on 11 strains representing the diversity of the species complex. We reconstructed the metabolic network of each strain from its genome sequence and looked for the metabolic pathways differentiating the different reconstructed networks and, by extension, the different strains. Finally, we conducted an experimental validation by determining the metabolic profile of each strain with the Biolog technology, also in a comparative approach. Results revealed that the metabolism is conserved between strains, with a core-metabolism composed of 82% of the pan-reactome. The 3 species composing the species complex could be distinguished according to the presence/absence of some metabolic pathways, in particular one implying salicylic acid degradation. Phenotypic assays revealed that the trophic preferences on organic acids and several amino acids such as glutamine, glutamate, aspartate and asparagine are conserved between strains. Finally, the generation and assessment of the transcription factorphcAregulating virulence in each specie showed that the faster growth compared to the WT strain was conserved acrossRalstonia solanacearumspecies complex.Author summaryRalstonia solanacearumis one of the most important threats to plant health worldwide, causing disease on a very large range of agricultural crops such as tomato or potato. Behind theRalstonia solanacearumname are hundreds of strains with different host range and lifestyle, classified into three species. Studying the differences between strain allows to better apprehend the biology of the pathogen and the specificity of some strains. None of the published genomic comparative studies have focused on the metabolism of the strains so far. We developed a new bioinformatic pipeline to build high-quality metabolic networks and used a combination of metabolic modeling and high-throughput phenotypic Biolog microplates to look for the metabolic differences between 11 strains across the three species. Our study revealed that genes encoding for enzymes are overall conserved, with few variations between strains. However, at the level of the phenotype, more variations were observed. These variations probably result from regulation rather than the presence or absence of enzymes in the genome.