bluuebunny/crossref_metadata_2025_split huggingface dataset:
A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data
Authors: Berihu Maria , Somera Tracey S. , Malik Assaf , Medina Shlomit , Piombo Edoardo , Tal Ofir , Cohen Matan , Ginatt Alon , Ofek-Lalzar Maya , Doron-Faigenboim Adi , Mazzola Mark , Freilich Shiri 
Published: January 2023

Abstract
Background
The design of ecologically sustainable and plant-beneficial soil systems is a key goal in actively manipulating root-associated microbiomes. Community engineering efforts commonly seek to harness the potential of the indigenous microbiome through substrate-mediated recruitment of beneficial members. In most sustainable practices, microbial recruitment mechanisms rely on the application of complex organic mixtures where the resources/metabolites that act as direct stimulants of beneficial groups are not characterized. Outcomes of such indirect amendments are unpredictable regarding engineering the microbiome and achieving a plant-beneficial environment.

Results
This study applied network analysis of metagenomics data to explore amendment-derived transformations in the soil microbiome, which lead to the suppression of pathogens affecting apple root systems. Shotgun metagenomic analysis was conducted with data from ‘sick’ vs ‘healthy/recovered’ rhizosphere soil microbiomes. The data was then converted into community-level metabolic networks. Simulations examined the functional contribution of treatment-associated taxonomic groups and linked them with specific amendment-induced metabolites. This analysis enabled the selection of specific metabolites that were predicted to amplify or diminish the abundance of targeted microbes functional in the healthy soil system. Many of these predictions were corroborated by experimental evidence from the literature. The potential of two of these metabolites (dopamine and vitamin B12) to either stimulate or suppress targeted microbial groups was evaluated in a follow-up set of soil microcosm experiments. The results corroborated the stimulant’s potential (but not the suppressor) to act as a modulator of plant beneficial bacteria, paving the way for future development of knowledge-based (rather than trial and error) metabolic-defined amendments. Our pipeline for generating predictions for the selective targeting of microbial groups based on processing assembled and annotated metagenomics data is available at https://github.com/ot483/NetCom2.

Conclusions
This research demonstrates how genomic-based algorithms can be used to formulate testable hypotheses for strategically engineering the rhizosphere microbiome by identifying specific compounds, which may act as selective modulators of microbial communities. Applying this framework to reduce unpredictable elements in amendment-based solutions promotes the development of ecologically-sound methods for re-establishing a functional microbiome in agro and other ecosystems.
Expanded catalogue of metagenome-assembled genomes reveals resistome characteristics and athletic performance-associated microbes in horse
Authors: Li Cunyuan , Li Xiaoyue , Guo Rongjun , Ni Wei , Liu Kaiping , Liu Zhuang , Dai Jihong , Xu Yueren , Abduriyim Shamshidin , Wu Zhuangyuan , Zeng Yaqi , Lei Bingbing , Zhang Yunfeng , Wang Yue , Zeng Weibin , Zhang Qiang , Chen Chuangfu , Qiao Jun , Liu Chen , Hu Shengwei 
Published: January 2023

AbstractBackgroundAs a domesticated species vital to humans, horses are raised worldwide as a source of mechanical energy for sports, leisure, food production, and transportation. The gut microbiota plays an important role in the health, diseases, athletic performance, and behaviour of horses.ResultsHere, using approximately 2.2 Tb of metagenomic sequencing data from gut samples from 242 horses, including 110 samples from the caecum and 132 samples from the rectum (faeces), we assembled 4142 microbial metagenome-assembled genomes (MAG), 4015 (96.93%) of which appear to correspond to new species. From long-read data, we successfully assembled 13 circular whole-chromosome bacterial genomes representing novel species. The MAG contained over 313,568 predicted carbohydrate-active enzymes (CAZy), over 59.77% of which had low similarity match in CAZy public databases. High abundance and diversity of antibiotic resistance genes (ARG) were identified in the MAG, likely showing the wide use of antibiotics in the management of horse. The abundances of at least 36 MAG (e.g. MAG belonging toLachnospiraceae,Oscillospiraceae, andRuminococcus) were higher in racehorses than in nonracehorses. These MAG enriched in racehorses contained every gene in a major pathway for producing acetate and butyrate by fibre fermentation, presenting potential for greater amount of short-chain fatty acids available to fuel athletic performance.ConclusionOverall, we assembled 4142 MAG from short- and long-read sequence data in the horse gut. Our dataset represents an exhaustive microbial genome catalogue for the horse gut microbiome and provides a valuable resource for discovery of performance-enhancing microbes and studies of horse gut microbiome.
A methodology for the public health surveillance and epidemiologic analysis of outdoor falls that require an emergency medical services response
Authors: Rundle Andrew G. , Crowe Remle P. , Wang Henry E. , Lo Alexander X. 
Published: January 2023

Abstract
Background
Falls are a common cause of injury with significantly associated medical costs yet public health surveillance of injuries from falls is underdeveloped. In addition, the epidemiologic understanding of outdoor falls, which have been reported to account for 47% of all injurious falls, is scant. Here we present methods to use emergency medical services (EMS) data as a public health surveillance tool for fall injuries, including those that occur secondary to syncope and heat illness, with a focus on the scope and epidemiology of outdoor fall injuries.

Methods
Using the 2019 National Emergency Medical Services Information System (NEMSIS) data, we developed an approach to identify EMS encounters for fall injuries, syncope and heat illness. NEMSIS variables used in our algorithm included the EMS respondent’s impression of the encounter, the reported major symptoms and the cause of injury. With these data we identified injuries from falls and, using the NEMSIS data on the location of the encounter, we identified fall injuries as occurring indoors or outdoors. We present the descriptive epidemiology of the identified patients.

Results
There were 1,854,909 injuries from falls that required an EMS response identified in the NEMSIS data, with 4% of those injuries secondary to episodes of syncope (n = 73,126) and heat illness. Sufficient data were available from 94% of injurious falls that they could be assigned to indoor or outdoor locations, with 9% of these fall injuries occurring outdoors. Among fall injuries identified as occurring outdoors, 85% occurred on streets and sidewalks. Patient age was the primary sociodemographic characteristic that varied by location of the injurious fall. Sixty-six percent of fall injuries that occurred indoors were among those age 65 years or older, while this figure was 34% for fall injuries occurring outdoors on a street or sidewalk.

Conclusion
The occurrence of outdoor fall injuries identified in the NEMSIS data were substantially lower than reported in other data sets. However, numerically fall injuries occurring outdoors represent a substantial public health burden. The strengths and weaknesses of using this approach for routine public health surveillance of injuries from falls, syncope and heat illness are discussed.
Spatial distribution of poverty in Pakistan: an asset-based approach
Authors: Ullah Kifayat , Chishti Muhammad Zubair 
Published: January 2023

Abstract
The main objective of this study is to construct a valid and reliable asset index at household level by using NSER-BISP data in order to compute asset poverty for provinces, districts, and tehsils of the Pakistan. An asset index may be better measure than current income or expenditure for gauging household’s long-term capacity for buying goods and services and its potential resilience to economic shocks. The study employs multiple correspondence analysis (MCA) to construct asset index contrary to principal component analysis (PCA), as MCA provides us weights and contributions of each dimension of binary variable separately. The average MCA score is showing the level of asset-based poverty wherein higher values of index are representing higher level of poverty. The findings indicate that incidence of asset-based poverty is differently observed across provinces and within provinces through disaggregation of the MCA score at district and tehsil levels. By and large, the poorest districts of Pakistan are belonging to Baluchistan (i.e., Sherani, Kohlu, Chaghi, and Dera Bugti) and Sindh (i.e., Badin, Umerkot, Tando Muhammad Khan, and Tharparker) provinces; however, districts of Punjab (i.e., Lahore, Rawalpindi, and Gujranwala) province are found relatively lower asset-based poverty. Further, the analysis highlights the prevalence of asset-based poverty at tehsils level as well where again the tehsils of Baluchistan and Sindh provinces are bearing the highest asset-based poverty. Furthermore, the study also contributes by visualizing the prevalence of geographical asset-based poverty at district level for all four provinces of Pakistan by GIS mapping.
Perinatal mental health in medical school curricula: a national scoping survey of British universities and student psychiatry societies
Authors: King Jacob D. , Crowley Grace , El-Maraghy Manal , Davis William , Jauhari Archana , Wilson-Jones Charlotte 
Published: January 2023

Aims and methodWith increasing recognition of the prevalence and impact of perinatal mental health (PMH) disorders comes a responsibility to ensure that tomorrow's doctors can support families during the perinatal period. Online surveys seeking information about the inclusion of PMH education in undergraduate curricula were sent to psychiatry curriculum leads and student psychiatry societies from each university medical school in the UK between April and September 2021.ResultsResponses were received from 32/35 (91.4%) medical schools. Two-thirds reported specific inclusion of PMH content in the core curriculum, typically integrated into general adult psychiatry or obstetric teaching. Students at the remaining schools were all likely to be examined on the topic or see perinatal cases during at least one clinical attachment.Clinical implicationsPMH education offers an opportunity for collaboration between psychiatry and other disciplines. Future work looking at educational case examples with objective outcomes would be valuable.
Intranasal Carbetocin Reduces Hyperphagia, Anxiousness, and Distress in Prader-Willi Syndrome: CARE-PWS Phase 3 Trial
Authors: Roof Elizabeth , Deal Cheri L , McCandless Shawn E , Cowan Ronald L , Miller Jennifer L , Hamilton Jill K , Roeder Elizabeth R , McCormack Shana E , Roshan Lal Tamanna R , Abdul-Latif Hussein D , Haqq Andrea M , Obrynba Kathryn S , Torchen Laura C , Vidmar Alaina P , Viskochil David H , Chanoine Jean-Pierre , Lam Carol K L , Pierce Melinda J , Williams Laurel L , Bird Lynne M , Butler Merlin G , Jensen Diane E , Myers Susan E , Oatman Oliver J , Baskaran Charumathi , Chalmers Laura J , Fu Cary , Alos Nathalie , McLean Scott D , Shah Ajay , Whitman Barbara Y , Blumenstein Brent A , Leonard Sarah F , Ernest Jessica P , Cormier Joseph W , Cotter Sara P , Ryman Davis C 
Published: January 2023

Abstract

Context
Prader-Willi syndrome (PWS) is a rare genetic disorder characterized by endocrine and neuropsychiatric problems including hyperphagia, anxiousness, and distress. Intranasal carbetocin, an oxytocin analog, was investigated as a selective oxytocin replacement therapy.

Objective
To evaluate safety and efficacy of intranasal carbetocin in PWS.

Design
Randomized, double-blind, placebo-controlled phase 3 trial with long-term follow-up.

Setting
Twenty-four ambulatory clinics at academic medical centers.

Participants
A total of 130 participants with PWS aged 7 to 18 years.

Interventions
Participants were randomized to 9.6 mg/dose carbetocin, 3.2 mg/dose carbetocin, or placebo 3 times daily during an 8-week placebo-controlled period (PCP). During a subsequent 56-week long-term follow-up period, placebo participants were randomly assigned to 9.6 mg or 3.2 mg carbetocin, with carbetocin participants continuing at their previous dose.

Main outcome measures
Primary endpoints assessed change in hyperphagia (Hyperphagia Questionnaire for Clinical Trials [HQ-CT]) and obsessive-compulsive symptoms (Children's Yale-Brown Obsessive-Compulsive Scale [CY-BOCS]) during the PCP for 9.6 mg vs placebo, and the first secondary endpoints assessed these same outcomes for 3.2 mg vs placebo. Additional secondary endpoints included assessments of anxiousness and distress behaviors (PWS Anxiousness and Distress Behaviors Questionnaire [PADQ]) and clinical global impression of change (CGI-C).

Results
Because of onset of the COVID-19 pandemic, enrollment was stopped prematurely. The primary endpoints showed numeric improvements in both HQ-CT and CY-BOCS which were not statistically significant; however, the 3.2-mg arm showed nominally significant improvements in HQ-CT, PADQ, and CGI-C scores vs placebo. Improvements were sustained in the long-term follow-up period. The most common adverse event during the PCP was mild to moderate flushing.

Conclusions
Carbetocin was well tolerated, and the 3.2-mg dose was associated with clinically meaningful improvements in hyperphagia and anxiousness and distress behaviors in participants with PWS.

Clinical Trials Registration Number
NCT03649477
Hydrozoan sperm-specific SPKK motif-containing histone H2B variants stabilise chromatin with limited compaction
Authors: Török Anna , Browne Martin J. G. , Vilar Jordina C. , Patwal Indu , DuBuc Timothy Q. , Febrimarsa  , Atcheson Erwan , Frank Uri , Gornik Sebastian G. , Flaus Andrew 
Published: January 2023

ABSTRACT
Many animals achieve sperm chromatin compaction and stabilisation by replacing canonical histones with sperm nuclear basic proteins (SNBPs) such as protamines during spermatogenesis. Hydrozoan cnidarians and echinoid sea urchins lack protamines and have evolved a distinctive family of sperm-specific histone H2Bs (spH2Bs) with extended N termini rich in SPK(K/R) motifs. Echinoid sperm packaging is regulated by spH2Bs. Their sperm is negatively buoyant and fertilises on the sea floor. Hydroid cnidarians undertake broadcast spawning but their sperm properties are poorly characterised. We show that Hydractinia echinata and H. symbiolongicarpus sperm chromatin possesses higher stability than somatic chromatin, with reduced accessibility to transposase Tn5 integration and to endonucleases in vitro. In contrast, nuclear dimensions are only moderately reduced in mature Hydractinia sperm. Ectopic expression of spH2B in the background of H2B.1 knockdown results in downregulation of global transcription and cell cycle arrest in embryos, without altering their nuclear density. Taken together, SPKK-containing spH2B variants act to stabilise chromatin and silence transcription in Hydractinia sperm with only limited chromatin compaction. We suggest that spH2Bs could contribute to sperm buoyancy as a reproductive adaptation.
Equating NHANES Monitor-Based Physical Activity to Self-Reported Methods to Enhance Ongoing Surveillance Efforts
Authors: WELK GREGORY J. , LAMOUREUX NICHOLAS R. , ZENG CHENGPENG , ZHU ZHENGYUAN , BERG EMILY , WOLFF-HUGHES DANA L. , TROIANO RICHARD P. 
Published: January 2023

ABSTRACT

Purpose
Harmonization of assessment methods represents an ongoing challenge in physical activity research. Previous research has demonstrated the utility of calibration approaches to enhance agreement between measures of physical activity. The present study utilizes a calibration methodology to add behavioral context from the Global Physical Activity Questionnaire (GPAQ), an established report-based measure, to enhance interpretations of monitor-based data scored using the novel Monitor Independent Movement Summary (MIMS) methodology.

Methods
Matching data from the GPAQ and MIMS were obtained from adults (20–80 yr of age) assessed in the 2011–2014 National Health and Nutrition Examination Survey. After developing percentile curves for self-reported activity, a zero-inflated quantile regression model was developed to link MIMS to estimates of moderate to vigorous physical activity (MVPA) from the GPAQ.

Results
Cross-validation of the model showed that it closely approximated the probability of reporting MVPA across age and activity-level segments, supporting the accuracy of the zero-inflated model component. Validation of the quantile regression component directly corresponded to the 25%, 50%, and 75% values for both men and women, further supporting the model fit.

Conclusions
This study offers a method of improving activity surveillance by translating accelerometer signals into interpretable behavioral measures using nationally representative data. The model provides accurate estimates of minutes of MVPA at a population level but, because of the bias and error inherent in report-based measures of physical activity, is not suitable for converting or interpreting individual-level data. This study provides an important preliminary step in utilizing information from both device- and report-based methods to triangulate activity related outcomes; however additional measurement error modeling is needed to improve precision.
Is individual perfusion dose-response different than ventilation dose-response for lung cancer patients treated with radiotherapy?
Authors: Forghani Farnoush , Castillo Richard , Castillo Edward , PhD Bernard Jones , Rusthoven Chad , Kwak Jennifer , Moiseenko Vitali , Grills Inga , Miften Moyed , Vinogradskiy Yevgeniy , Guerrero Thomas 
Published: January 2023

Objective: Current ventilation and perfusion dose–response studies focus on single-modalities (ventilation or perfusion) and perform pulmonary-toxicity assessment related to radiotherapy on a population-based basis. This study aims at quantitative and clinical evaluation of intrapatient differences between ventilation and perfusion dose–responses among lung cancer patients treated with radiotherapy. Methods: 20 patients enrolled on a prospective functional avoidance protocol underwent single photon emission computed tomography-CT ventilation and perfusion scans pre- and post-radiotherapy. Relative changes in pre- to post-treatment ventilation and perfusion in lung regions receiving ≥20 Gy were calculated. In addition, the slopes of the linear fit to the relative ventilation and perfusion changes in regions receiving 0–60 Gy were calculated. A radiologist read and assigned a functional defect score to pre- and post-treatment ventilation/perfusion scans. Results: 25% of patients had a difference >35% between ventilation and perfusion pre- to post-treatment changes and 20–30% of patients had opposite directions for ventilation and perfusion pre- to post-treatment changes. Using a semi-quantitative scale, radiologist assessment showed that 20% of patients had different pre- to post-treatment ventilation changes when compared to pre- to post-treatment perfusion changes. Conclusion: Our data showed that ventilation dose–response can differ from perfusion dose–response for 20–30% of patients. Therefore, when performing thoracic dose–response in cancer patients, it is insufficient to look at ventilation or perfusion alone; but rather both modes of functional imaging may be needed when predicting for clinical outcomes. Advances in knowledge: The significance of this study can be highlighted by the differences between the intrapatient dose–response assessments of this analysis compared to existing population-based dose–response analyses. Elucidating intrapatient ventilation and perfusion dose–response differences may be valuable in predicting pulmonary toxicity in lung cancer patients post-radiotherapy.
The conditional effect of family resilience on family quality of life during the Covid-19 pandemic
Authors: Setiawan Tery , Wardani Ria , Theresia Ellen 
Published: January 2023

Introduction: The Covid-19 pandemic has brought unprecedented challenges, both economically and psychologically, to most families across the world. Yet, little study has been done on this topic in Indonesia, even after the second year of the pandemic. This study examines how the Covid-19 economic impact and parental stress are related to the family quality of life (FQOL) and how the relation is moderated by family resilience. Methods: To this end, we employed previously tested measures to assess the level of parental stress, family resilience and FQOL. Especially for the latter, we modified the measure, developed by Beach Center on Disability, by including only four domains (i.e., family interaction, parenting, emotional well-being, and material well-being) to adjust to our research context. Results: Based on 169 participants, our confirmatory factor analysis (CFA) displays that all employed measures in the study are valid and reliable. Our regression analysis shows that there are significant direct relations of parental stress & family resilience with FQOL. However, we find that family resilience only positively moderates the relation between the Covid-19 economic impact and FQOL but not the relation between parental stress and FOQL; indicating that high family resilience can only buffer the effect of economic impact on FQOL. Discussion: This study presents a view on how the Covid-19 pandemic affects the way families live and hence, their quality of life. In addition, the findings suggest the importance of family relationship and support in times of crisis, not limited to the Covid-19 pandemic.