bluuebunny/crossref_metadata_2025_split huggingface dataset:
A global barley panel revealing genomic signatures of breeding in modern Australian cultivars
Authors: Hill Camilla Beate , Angessa Tefera Tolera , Zhang Xiao‐Qi , Chen Kefei , Zhou Gaofeng , Tan Cong , Wang Penghao , Westcott Sharon , Li Chengdao 
Published: January 2021

SUMMARYThe future of plant cultivar improvement lies in the evaluation of genetic resources from currently available germplasm. Today’s gene pool of crop genetic diversity has been shaped during domestication and more recently by breeding. Recent efforts in plant breeding have been aimed at developing new and improved varieties from poorly adapted crops to suit local environments. However, the impact of these breeding efforts is poorly understood. Here, we assess the contributions of both historical and recent breeding efforts to local adaptation and crop improvement in a global barley panel by analysing the distribution of genetic variants with respect to geographic region or historical breeding category. By tracing the impact that breeding had on the genetic diversity of Hordeum vulgare (barley) released in Australia, where the history of barley production is relatively young, we identify 69 candidate regions within 922 genes that were under selection pressure. We also show that modern Australian barley varieties exhibit 12% higher genetic diversity than historical cultivars. Finally, field‐trialling and phenotyping for agriculturally relevant traits across a diverse range of Australian environments suggests that genomic regions under strong breeding selection and their candidate genes are closely associated with key agronomic traits. In conclusion, our combined data set and germplasm collection provide a rich source of genetic diversity that can be applied to understanding and improving environmental adaptation and enhanced yields.
1,135 ionomes reveal the global pattern of leaf and seed mineral nutrient and trace element diversity in Arabidopsis thaliana
Authors: Campos Ana Carolina A. L. , van Dijk William F. A. , Ramakrishna Priya , Giles Tom , Korte Pamela , Douglas Alex , Smith Pete , Salt David E. 
Published: January 2021

SUMMARYSoil is a heterogeneous reservoir of essential elements needed for plant growth and development. Plants have evolved mechanisms to balance their nutritional needs based on availability of nutrients. This has led to genetically based variation in the elemental composition, the ‘ionome’, of plants, both within and between species. We explore this natural variation using a panel of wild‐collected, geographically widespread Arabidopsis thaliana accessions from the 1001 Genomes Project including over 1,135 accessions, and the 19 parental accessions of the Multi‐parent Advanced Generation Inter‐Cross (MAGIC) panel, all with full‐genome sequences available. We present an experimental design pipeline for high‐throughput ionomic screenings and analyses with improved normalisation procedures to account for errors and variability in conditions often encountered in large‐scale, high‐throughput data collection. We report quantification of the complete leaf and seed ionome of the entire collection using this pipeline and a digital tool, Ion Explorer, to interact with the dataset. We describe the pattern of natural ionomic variation across the A. thaliana species and identify several accessions with extreme ionomic profiles. It forms a valuable resource for exploratory genetic mapping studies to identify genes underlying natural variation in leaf and seed ionome and genetic adaptation of plants to soil conditions.
Medical chart validation of inpatient diagnosis codes for transfusion‐related acute lung injury 2013‐2015
Authors: Fuller Candace C. , Nambudiri Vinod E. , Spencer‐Smith Caren , Curtis Lesley H. , Shinde Mayura , Cosgrove Austin , Johnson Margaret , Hickok Jason , Honda Stacey , Ismail Heba , Kaufman Richard Max , Kennedy Adee , Miller Karla M. , Mohlman David J. , Poland Russell E. , Rosofsky Robert , Smith Kimberly , Surani Salim R. , Baker Meghan A. 
Published: January 2021

AbstractIntroductionTransfusion‐related acute lung injury (TRALI), an adverse event occurring during or within 6 hours of transfusion, is a leading cause of transfusion‐associated fatalities reported to the US Food and Drug Administration. There is limited information on the validity of diagnosis codes for TRALI recorded in inpatient electronic medical records (EMRs).Study Designs and MethodsWe conducted a validation study to establish the positive predictive value (PPV) of TRALI International Classification of Diseases, Ninth Revision, Clinical Modification (ICD‐9‐CM) diagnosis codes recorded within a large hospital system between 2013 and 2015. A physician with critical care expertise confirmed the TRALI diagnosis. As TRALI is likely underdiagnosed, we used the specific code (518.7), and codes for respiratory failure (518.82) in combination with transfusion reaction (999.80, 999.89, E934.7).ResultsAmong almost four million inpatient stays, we identified 208 potential TRALI cases with ICD‐9‐CM codes and reviewed 195 medical records; 68 (35%) met clinical definitions for TRALI (26 [38%] definitive, 15 [22%] possible, 27 [40%] delayed). Overall, the PPV for all inpatient TRALI diagnoses was 35% (95% confidence interval (CI), 28‐42). The PPV for the TRALI‐specific code was 44% (95% CI, 35‐54).ConclusionWe observed low PPVs (<50%) for TRALI ICD‐9‐CM diagnosis codes as validated by medical charts, which may relate to inconsistent code use, incomplete medical records, or other factors. Future studies using TRALI diagnosis codes in EMR databases may consider confirming diagnoses with medical records, assessing TRALI ICD, Tenth Revision, Clinical Modification codes, or exploring alternative ways for of accurately identifying TRALI in EMR databases.Key Points
In 169 hospitals, we identified 208 potential TRALI cases, reviewed 195 charts, and confirmed 68 (35%) cases met TRALI clinical definitions.
As many potential TRALI cases identified with diagnosis codes did not meet clinical definitions, medical record confirmation may be prudent.
Weed seedbank diversity and sustainability indicators for simple and more diverse cropping systems
Authors: Liebman Matt , Nguyen Huong T. X. , Woods Matthew M. , Hunt Natalie D. , Hill Jason D. 
Published: January 2021

AbstractStorkey and Neve (2018) hypothesised that weed seedbank diversity could be used as an indicator of agroecosystem sustainability, with cropping systems associated with higher weed seedbank diversity being more agronomically and environmentally sustainable than those with lower weed diversity. We evaluated their hypothesis using multiple years of empirical data collected from a long‐term field experiment in Iowa, USA, and life cycle assessment models parameterised with data from that experiment. We found that diversifying a 2‐year maize–soyabean rotation with two additional crop phases, oat and lucerne, to form a 4‐year rotation (a) increased Simpson's diversity index for weed species in the soil seedbank, while (b) increasing maize and soyabean productivity, (c) maintaining total crop energy production and profitability, and (d) reducing herbicide‐related aquatic toxicity, fossil energy consumption, greenhouse gas emissions, damage to human health due to fine particulate matter, and discharge of soil sediment, nitrogen, and phosphorus. Increased weed biomass production and greater weed species diversity that occurred within oat and lucerne phases of the 4‐year rotation sequence did not result in a loss of weed control within maize and soyabean phases of the rotation. We suggest that while there was no cause‐and‐effect relationship between greater weed seedbank diversity and improved agroecosystem sustainability in agronomic, economic and environmental dimensions, all of these responses were driven in a parallel manner by cropping system diversification. Consequently, weed seedbank diversity may indeed be a useful agroecosystem sustainability indicator. Further evaluation of this hypothesis in more systems is warranted.
Experimental increase of blood glucose alters resting state EEG measures of excitation–inhibition balance
Authors: Walker Christopher P. , Buse John B. , Frohlich Flavio 
Published: January 2021

New Findings

What is the central question of this study?
Glucose is the dominant energy source for the brain. However, little is known about how glucose metabolism impacts the coordination of network activity in the brain in healthy adults.

What is the main finding and its importance?
We demonstrate that both α oscillations and the aperiodic signal components of the resting EEG are modulated by experimentally elevated blood glucose concentrations. Our findings suggest that glucose increases measures associated with excitation–inhibition (E:I) balance, but that the effect on α oscillations might plateau. Understanding the relationship between glucose consumption and E:I balance is crucial to developing our understanding of how metabolism shapes human brain activity.

AbstractBrain network oscillations can be divided broadly into periodic and aperiodic signal components, which are sensitive to state‐dependent changes in network coordination and excitation–inhibition (E:I) balance. We sought to address whether the dominant energy source of the brain, glucose, is implicated in the regulation of network activity and excitability. We conducted an experimenter‐blind, crossover study of the effect of blood glucose level (BGL) on the resting EEG frequency spectrum. Participants consumed a glucose drink (75 g glucose) or an equivalent volume of water on two separate visits. EEG data were sampled before and ≤3 h after the drink. We found that the experimentally induced changes in BGL exhibited an inverted U‐shaped relationship, with changes in the individual α frequency peak, whereas the slope of the aperiodic signal component of the frequency spectrum showed a positive linear association suggestive of greater excitation. In contrast, peak α power, which is typically associated with top‐down inhibitory processes, was negatively associated with changes in BGL. Collectively, these results suggest that high BGL alters brain network coordination in the form of α oscillations and measures associated with E:I balance.
Influence of a Coach Development Curriculum on Preservice Coaches’ Habitus
Authors: Kuklick Clayton , Harvey Stephen , King Roch 
Published: January 2021

The purpose of this cross-sectional study was to analyze the influences of a 4-year university-based coach development curriculum on coaching-students’ habitus. The occupational socialization framework and Bourdieu’s theory of practice were used to capture the socialization factors that influence how coaching habitus remain continuous or are modified across the temporal phases of coaching-students’ socialization (i.e., acculturation and preservice professionalization). Data were collected through interviews, interview reflections, and coaching philosophies, which were analyzed and compared across entering (ENCS;n = 23) and exiting (XCS;n = 10) cohorts.Habitus formation,enacting coaching habitus, andinfluences on coaching habituswere the main themes. XCS differed from ENCS by utilizingindividualized instructional coaching,planning and programming, variousmethods of coaching,andreflection and lifelong learningas key strategies toenact their habitus, which showed the influence of preservice professionalization on gaining cultural capital in the coaching field. The findings provide support for howpracticum cites,course content, andcoach developerswithin the curriculum influenced coaching-students’ habitus. This research offers novel insights in regard to the approaches used in the curriculum, the integration of occupational socialization and Bourdieu’s theory of practice frameworks, and the cross-comparative design for analyzing programmatic effectiveness.
Organic biomorphs may be better preserved than microorganisms in early Earth sediments
Authors: Nims Christine , Lafond Julia , Alleon Julien , Templeton Alexis S. , Cosmidis Julie 
Published: January 2021

Abstract
The Precambrian rock record contains numerous examples of microscopic organic filaments and spheres, commonly interpreted as fossil microorganisms. Microfossils are among the oldest traces of life on Earth, making their correct identification crucial to our understanding of early evolution. Yet, spherical and filamentous microscopic objects composed of organic carbon and sulfur can form in the abiogenic reaction of sulfide with organic compounds. Termed organic biomorphs, these objects form under geochemical conditions relevant to the sulfidic environments of early Earth. Furthermore, they adopt a diversity of morphologies that closely mimic a number of microfossil examples from the Precambrian record. Here, we tested the potential for organic biomorphs to be preserved in cherts; i.e., siliceous rocks hosting abundant microbial fossils. We performed experimental silicification of the biomorphs along with the sulfur bacterium Thiothrix. We show that the original morphologies of the biomorphs are well preserved through encrustation by nano-colloidal silica, while the shapes of Thiothrix cells degrade. Sulfur diffuses from the interior of both biomorphs and Thiothrix during silicification, leaving behind empty organic envelopes. Although the organic composition of the biomorphs differs from that of Thiothrix cells, both types of objects present similar nitrogen/carbon ratios after silicification. During silicification, sulfur accumulates along the organic envelopes of the biomorphs, which may promote sulfurization and preservation through diagenesis. Organic biomorphs possessing morphological and chemical characteristics of microfossils may thus be an important component in Precambrian cherts, challenging our understanding of the early life record.
Association between county level cannabis dispensary counts and opioid related mortality rates in the United States: panel data study
Authors: Hsu Greta , Kovács Balázs 
Published: January 2021

AbstractObjectiveTo examine county level associations between the prevalence of medical and recreational cannabis stores (referred to as dispensaries) and opioid related mortality rates.DesignPanel regression methods.Setting812 counties in the United States in the 23 states that allowed legal forms of cannabis dispensaries to operate by the end of 2017.ParticipantsThe study used US mortality data from the Centers for Disease Control and Prevention combined with US census data and data from Weedmaps.com on storefront dispensary operations. Data were analyzed at the county level by using panel regression methods.Main outcome measureThe main outcome measures were the log transformed, age adjusted mortality rates associated with all opioid types combined, and with subcategories of prescription opioids, heroin, and synthetic opioids other than methadone. The associations of medical dispensary and recreational dispensary counts with age adjusted mortality rates were also analyzed.ResultsCounty level dispensary count (natural logarithm) is negatively related to the log transformed, age adjusted mortality rate associated with all opioid types (β=−0.17, 95% confidence interval −0.23 to −0.11). According to this estimate, an increase from one to two storefront dispensaries in a county is associated with an estimated 17% reduction in all opioid related mortality rates. Dispensary count has a particularly strong negative association with deaths caused by synthetic opioids other than methadone (β=−0.21, 95% confidence interval −0.27 to −0.14), with an estimated 21% reduction in mortality rates associated with an increase from one to two dispensaries. Similar associations were found for medical versus recreational storefront dispensary counts on synthetic (non-methadone) opioid related mortality rates.ConclusionsHigher medical and recreational storefront dispensary counts are associated with reduced opioid related death rates, particularly deaths associated with synthetic opioids such as fentanyl. While the associations documented cannot be assumed to be causal, they suggest a potential association between increased prevalence of medical and recreational cannabis dispensaries and reduced opioid related mortality rates. This study highlights the importance of considering the complex supply side of related drug markets and how this shapes opioid use and misuse.
Geographical disparities in access to hospital care in Ontario, Canada: a spatial coverage modelling approach
Authors: Ge Erjia , Su Min , Zhao Ruiling , Huang Zhiyong , Shan Yina , Wei Xiaolin 
Published: January 2021

ObjectivesPrevious studies on geographical disparities in healthcare access have been limited by not accounting for the healthcare provider’s capacity, a key determinant of supply and demand relationships.DesignThis study proposed a spatial coverage modelling approach to evaluate disparities in hospital care access using Canadian Institute for Health Information data in 2007.SettingThis study focusses on accessibility of inpatient and emergency cares at both levels of individual hospital and the administrative regions of Local Health Integration Network (LHIN) levels.MeasuresWe integrated a set of traffic and geographical data to precisely estimate travel time as a measure of the level of accessibility to the nearest hospital by three scenarios: walking, driving and a combination of the both. We estimated population coverage rates, using hospital capacities and population in the catchments, as a measure of the level of the healthcare availability. Hospital capacities were calculated based on numbers of medical staff and beds, occupation rates and annual working hours of healthcare providers.ResultsWe observed significant disparities in hospital capacity, travel time and population coverage rate across the LHINs. This study included 25 teaching and 148 community hospitals. The teaching hospitals had stronger capacities with 489 209 inpatient and 130 773 emergency patients served in the year, while the population served in community hospitals were 2.64 times higher. Compared with north Ontario, more locations in the south could reach to hospitals within 30 min irrespective of the travel mode. Additionally, Northern Ontario has higher population coverage rates, for example, with 42.6~46.9% for inpatient and 15.7~44% for emergency cares, compared with 2.4~34.7% and 0.35~14.6% in Southern Ontario, within a 30 min catchment by driving.ConclusionCreating a comprehensive, flexible and integrated healthcare system should be considered as an effective approach to improve equity in access to care.
Effectiveness and safety of brain-computer interface technology in the treatment of poststroke motor disorders: a protocol for systematic review and meta-analysis
Authors: Zhang Xiaolin , Cao Di , Liu Junnan , Zhang Qi , Liu Mingjun 
Published: January 2021

IntroductionAbout 85% of stroke survivors have upper extremity dysfunction, and more than 60% have continuing hand dysfunction and cannot live independently after treatment. Numerous recent publications have explored brain-computer interfaces technology as rehabilitation tools to help subacute and chronic stroke patients recover upper extremity movement. Our study aims to synthesise results from randomised controlled trials to assess the effectiveness and safety of brain-computer interface technology in the treatment of poststroke motor disorders（PSMD）.Methods and analysisEnglish and Chinese search strategies will be conducted in eight databases: the China National Knowledge Infrastructure, Chinese Scientific Journal Database, Wanfang Database, China Doctoral Dissertations Full-Text Database, China Master’s Theses Full-Text Database, Cochrane Central Register of Controlled Trials, PubMed and Embase. In addition, manual retrieval of research papers, conference papers, ongoing experiments and internal reports, among others, will supplement electronic retrieval. The searches will select all eligible studies published on or before 8 June 2020. To enhance the effectiveness of the study, only randomised controlled trials related to brain-computer interface technology for poststroke motor disorders will be included. The Fugl-Meyer Motor Function score will be the primary outcome measure; the Modified Barthel Index, Modified Ashworth Score and the upper extremity freehand muscle strength assessment will be secondary outcomes. Side effects and adverse events will be included as safety evaluations. To ensure the quality of the systematic evaluation, study selection, data extraction and quality assessment will be independently performed by two authors, and a third author will handle any disagreement. Review Manager V.5.3.3 and STATA V.15.1 will be used to perform the data synthesis and subgroup analysis.Ethics and disseminationThis systemic review will evaluate the efficacy and safety of brain-computer interface technology combined with routine rehabilitation treatment for treatment of poststroke motor disorders. Since all included data will be obtained from published articles,the review does not require ethical approval. The review will be published in a peer-reviewed journal.PROSPERO registration numberCRD42020190868.
Postneoadjuvant surveillance and surgery as needed compared with postneoadjuvant surgery on principle in multimodal treatment for oesophageal cancer: a scoping review protocol
Authors: Schmucker Christine , Nagavci Blin , Hipp Julian , Schmoor Claudia , Meerpohl Joerg , Hoeppner Jens 
Published: January 2021

IntroductionIn current medical practice of curative treatment for non-metastatic oesophageal cancer, surgery on principle is carried out by oesophagectomy after neoadjuvant treatment. However, oesophagectomy is often associated with postoperative morbidity and mortality. Taking into account that modern neoadjuvant therapy is effective and many of patients show no vital tumour cells in the operative specimens, we aim to perform a scoping review as part of the development phase for a prospectively planned multicentre randomised controlled trial investigating ‘surgery as needed vs surgery on principle in patients with postneoadjuvant complete response of oesophageal cancer’ (Prospective trial registration number DRKS00022801). This scoping approach will allow us to finally define and/or adapt the research question including the design and methodology of the randomised controlled trial taking into account the findings for example, research gaps and/or pitfalls in the currently available study pool addressing this or very similar questions.Methods and analysisTo identify relevant research, we will conduct searches in the electronic databases Medline, Web of Science Core Collection, Cochrane Library and Science Direct. We will also check references of relevant studies and perform a cited reference research (forward citation tracking). Titles and abstracts of the records identified by the searches will be screened and full texts of all potentially relevant articles will be obtained. We will consider randomised trials and non-randomised controlled studies. Data extraction tables will be set up, including study and patients’ characteristics, aim of study and reported outcomes. We will summarise the data using tables and figures (eg, bubble plots) to present the research landscape and to describe potential clusters and/or gaps to support the planning of a randomised trial in this patient population.Ethics and disseminationEthical approval is not required for this scoping review. Study findings will be shared by publication in a peer-reviewed journal and by presentation to key stakeholders on scientific meetings.