bluuebunny/crossref_metadata_2025_split huggingface dataset:
A meta-analysis of immune-cell fractions at high resolution reveals novel associations with common phenotypes and health outcomes
Authors: Luo Qi , Dwaraka Varun B. , Chen Qingwen , Tong Huige , Zhu Tianyu , Seale Kirsten , Raffaele Joseph M. , Zheng Shijie C. , Mendez Tavis L. , Chen Yulu , Carreras Natalia , Begum Sofina , Mendez Kevin , Voisin Sarah , Eynon Nir , Lasky-Su Jessica A. , Smith Ryan , Teschendorff Andrew E. 
Published: July 2023

AbstractBackgroundChanges in cell-type composition of tissues are associated with a wide range of diseases and environmental risk factors and may be causally implicated in disease development and progression. However, these shifts in cell-type fractions are often of a low magnitude, or involve similar cell subtypes, making their reliable identification challenging. DNA methylation profiling in a tissue like blood is a promising approach to discover shifts in cell-type abundance, yet studies have only been performed at a relatively low cellular resolution and in isolation, limiting their power to detect shifts in tissue composition.MethodsHere we derive a DNA methylation reference matrix for 12 immune-cell types in human blood and extensively validate it with flow-cytometric count data and in whole-genome bisulfite sequencing data of sorted cells. Using this reference matrix, we perform a directional Stouffer and fixed effects meta-analysis comprising 23,053 blood samples from 22 different cohorts, to comprehensively map associations between the 12 immune-cell fractions and common phenotypes. In a separate cohort of 4386 blood samples, we assess associations between immune-cell fractions and health outcomes.ResultsOur meta-analysis reveals many associations of cell-type fractions with age, sex, smoking and obesity, many of which we validate with single-cell RNA sequencing. We discover that naïve and regulatory T-cell subsets are higher in women compared to men, while the reverse is true for monocyte, natural killer, basophil, and eosinophil fractions. Decreased natural killer counts associated with smoking, obesity, and stress levels, while an increased count correlates with exercise and sleep. Analysis of health outcomes revealed that increased naïve CD4 + T-cell and N-cell fractions associated with a reduced risk of all-cause mortality independently of all major epidemiological risk factors and baseline co-morbidity. A machine learning predictor built only with immune-cell fractions achieved a C-index value for all-cause mortality of 0.69 (95%CI 0.67–0.72), which increased to 0.83 (0.80–0.86) upon inclusion of epidemiological risk factors and baseline co-morbidity.ConclusionsThis work contributes an extensively validated high-resolution DNAm reference matrix for blood, which is made freely available, and uses it to generate a comprehensive map of associations between immune-cell fractions and common phenotypes, including health outcomes.
Targeted screening and identification of chlorhexidine as a pro-myogenic circadian clock activator
Authors: Kiperman Tali , Li Weini , Xiong Xuekai , Li Hongzhi , Horne David , Ma Ke 
Published: July 2023

Abstract
Background
The circadian clock is an evolutionarily conserved mechanism that exerts pervasive temporal control in stem cell behavior. This time-keeping machinery is required for orchestrating myogenic progenitor properties in regenerative myogenesis that ameliorates muscular dystrophy. Here we report a screening platform to discover circadian clock modulators that promote myogenesis and identify chlorhexidine (CHX) as a clock-activating molecule with pro-myogenic activities.

Methods
A high-throughput molecular docking pipeline was applied to identify compounds with a structural fit for a hydrophobic pocket within the key circadian transcription factor protein, Circadian Locomotor Output Cycles Kaput (CLOCK). These identified molecules were further screened for clock-modulatory activities and functional validations for pro-myogenic properties.

Results
CHX was identified as a clock activator that promotes distinct aspects of myogenesis. CHX activated circadian clock that reduced cycling period length and augmented amplitude. This action was mediated by the targeted CLOCK structure via augmented interaction with heterodimer partner Bmal1, leading to enhanced CLOCK/Bmal1-controlled transcription with upregulation of core clock genes. Consistent with its clock-activating function, CHX displayed robust effects on stimulating myogenic differentiation in a clock-dependent manner. In addition, CHX augmented the proliferative and migratory activities of myoblasts.

Conclusion
Our findings demonstrate the feasibility of a screening platform to discover clock modulators with myogenic regulatory activities. Discovery of CHX as a pro-myogenic molecule could be applicable to promote regenerative capacities in ameliorating dystrophic or degenerative muscle diseases.
Differential Salmonella Typhimurium intracellular replication and host cell responses in caecal and ileal organoids derived from chicken
Authors: Lacroix-Lamandé Sonia , Bernardi Ophélie , Pezier Tiffany , Barilleau Emilie , Burlaud-Gaillard Julien , Gagneux Anissa , Velge Philippe , Wiedemann Agnès 
Published: July 2023

AbstractChicken infection with Salmonella Typhimurium is an important source of foodborne human diseases. Salmonella colonizes the avian intestinal tract and more particularly the caecum, without causing symptoms. This thus poses a challenge for the prevention of foodborne transmission. Until now, studies on the interaction of Salmonella with the avian gut intestine have been limited by the absence of in vitro intestinal culture models. Here, we established intestinal crypt‐derived chicken organoids to better decipher the impact of Salmonella intracellular replication on avian intestinal epithelium. Using a 3D organoid model, we observed a significantly higher replication rate of the intracellular bacteria in caecal organoids than in ileal organoids. Our model thus recreates intracellular environment, allowing Salmonella replication of avian epithelium according to the intestinal segment. Moreover, an inhibition of the cellular proliferation was observed in infected ileal and caecal organoids compared to uninfected organoids. This appears with a higher effect in ileal organoids, as well as a higher cytokine and signaling molecule response in infected ileal organoids at 3 h post-infection (hpi) than in caecal organoids that could explain the lower replication rate of Salmonella observed later at 24 hpi. To conclude, this study demonstrates that the 3D organoid is a model allowing to decipher the intracellular impact of Salmonella on the intestinal epithelium cell response and illustrates the importance of the gut segment used to purify stem cells and derive organoids to specifically study epithelial cell -Salmonella interaction.
Decomposition and nutrient dynamics of stumps and coarse roots of Eucalyptus plantations in southern China
Authors: Deng Xiangsheng , Liang Xiang , Shen Lu , Liu Haiyu , Yang Mei , Zeng Min , Liang Mengqiang , Cheng Fei 
Published: July 2023

Abstract
Key message
Primary remains of Eucalyptus (E. urophylla × E. grandis) plantations following clear-cutting are the stumps and coarse roots. A chrono-sequence approach revealed that the biomass of coarse roots is higher than that of stumps, while they have a smaller rate of biomass loss than stumps. This implies that coarse roots serve as long-term stock for nutrients (carbon, nitrogen, and phosphorus).

Context
A significant quantity of stumps and coarse roots persist in the forest floor following the clear-cutting of Eucalyptus plantations in China. The decomposition of these stumps and coarse roots is a crucial aspect of the nutrient stocks in plantation ecosystems.

Aims
We described the stock and decomposition dynamics of stumps and coarse roots on Eucalyptus plantations, as well as the nutrient loss rate associated with them.

Methods
We used a chrono-sequence of 0–6-year-old clear-cutting stands of Eucalyptus plantations in southern China. The biomass and nutrient stocks of these samples were assessed at different times of decomposition.

Results
The highest biomass of stump-root system was 33.8 Mg·ha−1, with nutrient stocks were 16.3 Mg·ha−1, and 63.0 kg·ha−1, and 6710.9 g·ha−1, for C, N, and P. The coarse roots accounted for 81–96% of the biomass of the stump-root system. The loss rate of biomass and nutrients from stumps was higher than that of coarse roots. This suggests that the decomposition of coarse roots could serve as a long-term source of nutrients, thereby improving the nutrient status of the plantations.

Conclusion
Stumps and coarse roots serve as significant nutrient stocks that decay at varying rates. The loss of nutrients must be considered while analyzing the decomposition dynamics following clear-cutting in Eucalyptus plantations.
Aso volcano, Japan: assessing the 100-year probability of a new caldera-forming eruption based on expert judgements with Bayes Net and Importance Sampling uncertainty analysis
Authors: Aspinall Willy , Sparks R. Stephen J. , Hill Brittain E. , Costa Antonio , Connor Charles , Inakura Hirohito , Hasenaka Toshiaki , Miyoshi Masaya , Kiyosugi Koji , Tsuji Tomohiro , Ushioda Masashi 
Published: July 2023

AbstractThe Aso-4 explosive eruption on Kyushu, Japan, 89,500 years ago was one of the biggest eruptions in the last one hundred millennia, with a magnitude of approximately M8. Modern society requires the likelihood of natural events with potentially disastrous consequences to be evaluated, even if probabilities of occurrence are diminishingly small. For some situations, it is not satisfactory to assert an event scenario probability is “negligible” or can be “ignored”. Judicial hearings or litigation may require risk levels to be quantified, in which case, statements of scientific confidence could be decisive. Internationally, e.g., for nuclear site safety evaluations, event likelihoods on order of 10–7/year are often considered for quantitative assessment. At such hazard levels, this might include evaluating the proposition that a particular volcano can deliver a future super-eruption, a supposition that could be attached to Aso volcano. But, simplistically taking the average recurrence interval between past caldera-forming eruptions at a given volcano is an unreliable guide to the likelihood of a future repeat: each past event represented a unique set of tectonic and magmatic conditions within a continually evolving volcanic system. Such processes are not temporally stationary nor statistically uniform. To evaluate the probability of a new M8 event at Aso, within the next 100 years, we performed a comprehensive stochastic probability uncertainty analysis using a model implemented with advanced computational Bayes Net (BN) software. Our eruption process model is informed by multiple strands of evidence from volcanology, petrology, geochemistry and geophysics, together with estimates of epistemic (knowledge) uncertainty, adduced from reviews of published data, modelling and from expert judgement elicitation. Several lines of evidence characterise the likely structure, magmatic composition and eruptive state of the present-day Aso volcano, which has had numerous smaller eruptions since Aso-4. To calculate the probability of another M8 eruption of Aso, we implemented probabilistic ‘Importance Sampling’ in our model. With this approach, we find the chance of an Aso-4 scale eruption (characterised by mean volume 500 km3DRE and approximate 90% credible interval [210 ‥ 1200] km3DRE) is less than 1–in–1 billion in the next 100 years (i.e., < 10–9probability). Based on current volcanological understanding and evidence, we believe this probability estimate is robust to within an order of magnitude.
Horizon scanning: what next for bovine TB control in England?
Authors: McCormack James 
Published: July 2023

AbstractEngland is currently in year nine of its 25-year strategy to achieve TB freedom. This talk will speculate on what new tools and approaches could be introduced in the future to help us achieve our goal.Using Defra’s response to the independent review of its TB programme as a starting point and building on the plenary talk by the UK CVO, I will look at some opportunities that could arise under the different aspects of the response.Firstly, how best to help farmers reduce their herd TB risk through better informed purchasing decisions will be considered, including looking at the recent publication of the health ratings for every cattle herd in England.Cattle vaccination, and its associated DIVA test could be the biggest change in Tb control in England in many years while the related development of a molecularly defined tuberculin which could become the default testing reagent.Advances in whole genome sequencing will allow us to sequence the genome of M.bovis isolated from most infected herds in England and these data could unlock a variety of opportunities from tracing the spread of infection to ground-truthing the efficacy of testing and epidemiological assessment of breakdowns.Finally, the move to vaccination as the primary way of controlling TB in badgers with culling used very sparingly will be considered using a case study of how a targeted badger cull successfully removed infection from an area in Cumbria and enabled the switch to vaccination.
Exploring the contribution of case study research to the evidence base for occupational therapy: a scoping review
Authors: McQuaid Leona , Thomson Katie , Bannigan Katrina 
Published: July 2023

AbstractBackgroundCase study research is generating interest to evaluate complex interventions. However, it is not clear how this is being utilized by occupational therapists or how feasible it is to contribute to the evidence base. This scoping review explores case study research within occupational therapy in terms of how it is defined, the methodological characteristics adopted, such as data collection and analysis, and the range of practice contexts in which it is applied. We consider the viability of case study research for contributing to our evidence base.MethodsOpinion, text and empirical studies within an occupational therapy practice context were included. A three-step extensive search following Joanna Briggs Institute methodology was conducted in June 2020 and updated in July 2021 across ten databases, websites, peer-reviewed and grey literature from 2016 onwards. Study selection was completed by two independent reviewers. A data extraction table was developed and piloted and data charted to align with research questions. Data extraction was completed by one reviewer and a 10% sample cross checked by another.ResultsEighty-eight studies were included in the review consisting of (n = 84) empirical case study and (n = 4) non-empirical papers. Case study research has been conducted globally, with a range of populations across different settings. The majority were conducted in a community setting (n= 48/84; 57%) with populations experiencing neurodevelopmental disorder (n= 32/84; 38%), stroke (n= 14/84;17%) and non-diagnosis specific (n= 13/84; 15%). Methodologies adopted quantitative (n= 42/84; 50%), mixed methods (n= 22/84; 26%) and qualitative designs (n= 20/84; 24%). However, identifying the methodology and ‘case’ was a challenge due to methodological inconsistencies.ConclusionsCase study research is useful when large-scale inquiry is not appropriate; for cases of complexity, early intervention efficacy, theory testing or when small participant numbers are available. It appears a viable methodology to contribute to the evidence base for occupation and health as it has been used to evaluate interventions across a breadth of occupational therapy practice contexts. Viability could be enhanced through consistent conduct and reporting to allow pooling of case data. A conceptual model and description of case study research in occupational therapy is proposed to support this.Systematic review registrationOpen Science Framework 10.17605/OSF.IO/PCFJ6.
Inhibitory control towards angry stimuli in patients with binge eating disorder: a pilot study
Authors: Schag Kathrin , Sandler Lea , Zipfel Stephan , Derntl Birgit , Giel Katrin Elisabeth 
Published: July 2023

AbstractBackgroundEmotion regulation theories and the negative urgency concept assume that negative mood increases binge eating. Negative emotions are considered as a trigger for binge eating, while binge eating itself is regarded as an impulsive behavior and should thus be increased within the negative urgency concept. Anger might be a specific negative emotion triggering binge eating in patients with binge eating disorder (BED). We investigated how inhibitory control as one main factor of impulsivity is influenced by anger stimuli in patients with BED and two control groups.MethodsWe compared patients with BED (N = 20) with normal-weight healthy control participants (NW-CG, N = 20) and BMI-matched overweight and obese control participants (BMI-CG, N = 18). We used the emotional Stop Signal task (eSST) to investigate inhibitory control, where we presented angry facial expressions in comparison with neutral facial expressions as emotional stimuli.ResultsAll participants showed decreased inhibitory control in the angry versus neutral condition, i.e., a faster Stop Signal Reaction Time and a lower percentage of correct reactions. However, no significant group differences emerged in terms of performance. Performance in the eSST did not correlate with negative urgency, disorder- or emotion-related characteristics.ConclusionsThe current pilot study does not deliver evidence for decreased inhibitory control towards angry stimuli in patients with BED, as we detected a general and not disorder-related effect in all participants that might represent the conjunction of inhibitory control and anger. A direct mood induction technique might have led to different results. Further research in healthy and clinical groups is needed.
Children’s injury database: development of an injury surveillance system in a pediatric emergency department
Authors: McCain Jennifer E. , Bridgmon Ashley E. , King William D. , Monroe Kathy 
Published: July 2023

Abstract
Background
Injuries are the leading cause of death in children and are also a leading cause of all emergency department (ED) visits for children. Obtaining epidemiologic data to define the wide range of childhood injuries for individual communities is challenging. The Children’s Injury Database (CID) is an injury surveillance system developed to collect data from injury-related visits to our tertiary care pediatric emergency department.

Results
During 2021, a total of 15,168 injury visits were analyzed representing 22% of total ED visits (68,834). A total of 2053 injury visits (13.5%) resulted in hospital admission. The 10 leading injury types included: falls, poisonings, motor vehicle collision (MVC), assault, dog bite, burns, sports, pedestrian, bicycle, and all-terrain vehicle (ATV). Admission rates varied by age group with children ages 13 years and older having the highest rate of admission (18.4%). The median length of stay (LOS) for all injured children requiring admission was 2 days while the median LOS for preschoolers was 1 day, the median LOS for school-age children was 2 days, and the median LOS for teenagers was 3 days. While MVCs were the most common cause of vehicle-related injuries, ATV-related injuries had the highest rate of admission (51%).

Conclusions
In this study, teenagers had significantly higher admission rates, lengths of stay, and hospital charges. Black and Hispanic children were under-represented in the number of visits for injuries compared to all ED visits. Further research should focus on disparities in injury-related visits based on race as well as gender. CID has demonstrated that injury surveillance systems can assist with reporting new injury patterns while also acting as a stimulus for new research ideas, planning interventions targeting the most at-risk populations, and evaluating the effectiveness of injury prevention interventions.
Robotic‐assisted technology does not influence functional outcomes among obese and morbidly obese total knee arthroplasty patients
Authors: McCormick Brian P. , Trent Sarah , Geng Xue , Lee Ji Won , Boucher Henry R. 
Published: July 2023

AbstractPurposeDespite benefits of total knee arthroplasty (TKA) on function and quality of life, obese patients have less improved functional outcomes following TKA compared to their normal weight counterparts. Furthermore, obesity is a risk factor for aseptic loosening and revision surgery following TKA. With known benefits of robotic‐assisted TKA (RaTKA) in precision and patient satisfaction, we aimed to evaluate the differences in patient reported outcome and early complication rates for patients undergoing RaTKA versus conventional TKA among patients of varying BMI groups.MethodsThis study was a retrospective cohort study of patients who underwent conventional versus RaTKA. Patients were grouped by BMI range (< 30 kg/m2, 30–40 kg/m2, and > 40 kg/m2). Patient‐reported outcomes were measured by Oxford Knee Scores and 12‐Item Short Form Survey scores preoperatively, 6‐month, 1‐year, and 2‐year postoperatively. Mixed‐effects linear models were built for each patient‐reported outcome to assess the interaction between type of surgery and BMI while adjusting for known confounders such as demographic variables.ResultsA total of 350 patients (n = 186 RaTKA, n = 164 conventional TKA) met inclusion criteria. SF‐12 physical scores were significantly higher at 2‐year follow‐up among non‐obese patients compared to obese and morbidly obese patients (p = 0.047). There was no statistically significant interaction between the type of surgery performed (RaTKA versus conventional TKA) and obesity regarding their effects on patient reported outcomes.ConclusionsThis study demonstrates no differences in functional outcomes among patients undergoing RaTKA compared to conventional TKA. Furthermore, obesity had no significant effect on this association.Level of evidenceIII.