bluuebunny/crossref_metadata_2025_split huggingface dataset:
WGVD: an integrated web-database for wheat genome variation and selective signatures
Authors: Wang Jierong , Fu Weiwei , Wang Rui , Hu Dexiang , Cheng Hong , Zhao Jing , Jiang Yu , Kang Zhensheng 
Published: September 2020

Abstract

Bread wheat is one of the most important crops worldwide. With the release of the complete wheat reference genome and the development of next-generation sequencing technology, a mass of genomic data from bread wheat and its progenitors has been yield and has provided genomic resources for wheat genetics research. To conveniently and effectively access and use these data, we established Wheat Genome Variation Database, an integrated web-database including genomic variations from whole-genome resequencing and exome-capture data for bread wheat and its progenitors, as well as selective signatures during the process of wheat domestication and improvement. In this version, WGVD contains 7 346 814 single nucleotide polymorphisms (SNPs) and 1 044 400 indels focusing on genic regions and upstream or downstream regions. We provide allele frequency distribution patterns of these variations for 5 ploidy wheat groups or 17 worldwide bread wheat groups, the annotation of the variant types and the genotypes of all individuals for 2 versions of bread wheat reference genome (IWGSC RefSeq v1.0 and IWGSC RefSeq v2.0). Selective footprints for Aegilops tauschii, wild emmer, domesticated emmer, bread wheat landrace and bread wheat variety are evaluated with two statistical tests (FST and Pi) based on SNPs from whole-genome resequencing data. In addition, we provide the Genome Browser to visualize the genomic variations, the selective footprints, the genotype patterns and the read coverage depth, and the alignment tool Blast to search the homologous regions between sequences. All of these features of WGVD will promote wheat functional studies and wheat breeding.

Database URL
http://animal.nwsuaf.edu.cn/code/index.php/Wheat
A climate-sensitive transition matrix growth model for uneven-aged mixed-species oak forests in North China
Authors: Du Xue , Chen Xinyun , Zeng Weisheng , Meng Jinghui 
Published: September 2020

AbstractOak-dominated forests, economically and ecologically valuable ecosystems, are widely distributed in China. These oak-dominated forests are now generally degraded coppice forests, and are of relatively low quality. Climate change has been shown to affect forest growth, tree mortality, and recruitment, but available forest growth models are lacking to study climate effects. In this study, a climate-sensitive, transition-matrix growth model (CM) was developed for uneven-aged, mixed-species oak forests using data collected from 253 sample plots from the 8th (2010) and 9th (2015) Chinese National Forest Inventory in Shanxi Province, China. To investigate robustness of the model, we also produced a variable transition model that did not consider climate change (NCM), and fixed parameter transition matrix model (FM), using the same data. Short-term and long-term predictive performance of CM, NCM, and FM were compared. Results indicated that for short-term prediction (5 years), there was almost no significant difference among the three predictive models, though CM exhibited slightly better performance. In contrast, for long-term prediction (100 years), CM, under the three representative concentration pathways (RCPs), i.e. RCP2.6, RCP4.5 and RCP8.5, indicated rather different dynamics that were more reliable because climate factors were considered which could significantly influence forest dynamics, especially in long-term prediction intervals. The CM model provides a framework for the management of mixed-species oak forests in the context of climate change.
Engaging Māori with qualitative healthcare research using an animated comic
Authors: Kearns Ciléin , Baggott Christina , Harwood Matire , Reid Alice , Fingleton James , Levack William , Beasley Richard 
Published: September 2020

Abstract
This article reports an effective strategy for recruiting patients with asthma to a qualitative study using an animated comic advertised on social media. An ad spend of NZ$432 on Facebook resulted in 101 study enquiries, and 27 participants taking part in the focus groups, of which 16 (56%) were Māori, the Indigenous Peoples of New Zealand. Representation of Māori amongst participants was over five times higher than their proportion in the local population (9.7%), resulting in data fulfilling the principle of equal explanatory power, an approach to research which can help advance Māori health development and address inequity. The success of this campaign is of particular interest for health researchers in New Zealand where Māori continue to be disproportionately affected by poorer health outcomes compared with non-Māori, particularly those with asthma. Approaches that better engage and support participation of under-represented communities in clinical research are of wider global interest. We reflect on the recruitment strategy and outcomes within a Kaupapa Māori framework, explore how this can be applied more widely in healthcare, and suggest direction for future study and implementation.
Lay summary
We designed an animated comic to advertise a study for patients with asthma. This was shared locally with a Facebook ad. The approach was highly engaging with the public, and resulted in rapid recruitment. Interestingly, participation of Māori (the Indigenous People of New Zealand) was over five times higher than their proportion in the local population. Māori have poorer health outcomes and increased barriers to healthcare access compared with non-Māori, particularly those with asthma. Approaches which can engage and support under-represented communities to participate in clinical research are of wider global interest. In this article, we reflect on the recruitment strategy and outcomes, and suggest direction for future study and implementation.
The Evolutionary Continuum of Functional Homodonty to Heterodonty in the Dentition of Halichoeres Wrasses
Authors: Cohen Karly E , Weller Hannah I , Westneat Mark W , Summers Adam P 
Published: September 2020

Synopsis
Vertebrate dentitions are often collapsed into a few discrete categories, obscuring both potentially important functional differences between them and insight into their evolution. The terms homodonty and heterodonty typically conflate tooth morphology with tooth function, and require context-dependent subcategories to take on any specific meaning. Qualifiers like incipient, transient, or phylogenetic homodonty attempt to provide a more rigorous definition but instead highlight the difficulties in categorizing dentitions. To address these issues, we recently proposed a method for quantifying the function of dental batteries based on the estimated stress of each tooth (inferred using surface area) standardized for jaw out-lever (inferred using tooth position). This method reveals a homodonty–heterodonty functional continuum where small and large teeth work together to transmit forces to a prey item. Morphological homodonty or heterodonty refers to morphology, whereas functional homodonty or heterodonty refers to transmission of stress. In this study, we use Halichoeres wrasses to explore how a functional continuum can be used in phylogenetic analyses by generating two continuous metrics from the functional homodonty–heterodonty continuum. Here we show that functionally heterodont teeth have evolved at least 3 times in Halichoeres wrasses. There are more functionally heterodont teeth on upper jaws than on lower jaws, but functionally heterodont teeth on the lower jaws bear significantly more stress. These nuances, which have functional consequences, would be missed by binning entire dentitions into discrete categories. This analysis points out areas worth taking a closer look at from a mechanical and developmental point of view with respect to the distribution and type of heterodonty seen in different jaws and different areas of jaws. These data, on a small group of wrasses, suggest continuous dental variables can be a rich source of insight into the evolution of fish feeding mechanisms across a wider variety of species.
Stock dynamics and predator–prey effects of Atlantic bonito and bluefish as top predators in the Black Sea
Authors: Daskalov Georgi M , Demirel Nazli , Ulman Aylin , Georgieva Yoana , Zengin Mustafa 
Published: September 2020

AbstractThis study uses surplus production model-based methods to assess data-poor stocks and estimate key reference points for Atlantic bonito (Sarda sarda) and bluefish (Pomatomus saltatrix) in the Black Sea. Our results demonstrate that the catch maximum sustainable yield (CMSY) method, using catch data only, yields similar results to the more accurate Bayesian Schaefer model (BSM) method, fitted with commercial catch-per-unit-of-effort data, and therefore is suitable in assessing data-poor stocks. We explore the ecological impacts of the two stocks on other commercial species and compare impacts of predation and fishing. Prior to 1995, the consumption of bonito and bluefish on anchovy, horse mackerel, and sprat exceeded the removal of those prey species by the fisheries. Later on, the trends reversed, with catches of prey species becoming more than three times higher than their predation by bonito and bluefish. Horse mackerel, the main prey of bluefish, has declined to critical levels since 1995, which is likely contributing to the general decline in bluefish, along with overfishing. Heavy fishing of bonito and bluefish has caused their current depleted states and combined with their significant impact on prey fish contributed to the ecosystem regime shift in the Black Sea. Due to the present steady positioning of low stock regimes, the recovery of the two stocks need decisive and possibly prolonged rebuilding measures, including a reduction in fishing pressure, efficient control of under-sized catch, and ensuring sufficient prey biomass availability.
Rose vs. Rho: a comparison of two approaches to address retrospective patterns in stock assessments
Authors: Legault Christopher M 
Published: September 2020

AbstractTwo approaches to address retrospective patterns in stock assessments are compared. The Rose approach is an ensemble of models that all remove the retrospective pattern through changes in data, parameter values, or model assumptions. It is time intensive and can result in a wide range of historical abundance trends. The Rho approach modifies the terminal year estimates of a single model that exhibits a retrospective pattern. It is fast and easy to apply but results in a discontinuous time series. Neither approach identifies the source of the retrospective pattern. The pros and cons of these two approaches are compared in terms of catch advice and stock status using four examples with varying strength and direction of retrospective patterns. The choice of which approach to use could be based on time and expertise available to conduct and maintain an assessment, with Rose preferred if a lot of both are available while Rho preferred otherwise. If the Rho approach is used, managers should consider adjusting their control rule or risk buffer to account for the difference between Rose and Rho results shown here.
Translational and Sliding Stability for Two-Dimensional Minimal Cones in Euclidean Spaces
Authors: Liang Xiangyu 
Published: September 2020

Abstract
In this article, we prove the translational stability for all two-dimensional Almgren minimal cones in ${\mathbb{R}}^n$ and the Almgren (resp. topological) sliding stability for the two-dimensional Almgren (resp. topological) minimal cones in ${\mathbb{R}}^3$. As proved in [ 19], when several two-dimensional Almgren (resp. topological) minimal cones are translational, Almgren (resp. topological) sliding stable, and Almgren (resp. topological) unique, their almost orthogonal union stays minimal. As a consequence, the results of this article, together with the uniqueness properties proved in [ 14], permit us to use all two-dimensional minimal cones in ${\mathbb{R}}^3$ to generate new families of minimal cones by taking their almost orthogonal unions.
The emerging role of clinical informatics fellows in service learning during the COVID-19 pandemic
Authors: Subash Meera , Sakumoto Matthew , Bass Jeremy , Hong Peter , Muniyappa Anoop , Pierce Logan , Purmal Colin , Ramaswamy Priya , Sono Reiri , Uptegraft Colby , Feinstein David , Khanna Raman 
Published: September 2020

Abstract

Objective
The study sought to describe the contributions of clinical informatics (CI) fellows to their institutions’ coronavirus disease 2019 (COVID-19) response.

Materials and Methods
We designed a survey to capture key domains of health informatics and perceptions regarding fellows’ application of their CI skills. We also conducted detailed interviews with select fellows and described their specific projects in a brief case series.

Results
Forty-one of the 99 CI fellows responded to our survey. Seventy-five percent agreed that they were “able to apply clinical informatics training and interest to the COVID-19 response.” The most common project types were telemedicine (63%), reporting and analytics (49%), and electronic health record builds and governance (32%). Telehealth projects included training providers on existing telehealth tools, building entirely new virtual clinics for video triage of COVID-19 patients, and pioneering workflows and implementation of brand-new emergency department and inpatient video visit types. Analytics projects included reports and dashboards for institutional leadership, as well as developing digital contact tracing tools. For electronic health record builds, fellows directly contributed to note templates with embedded screening and testing guidance, adding COVID-19 tests to order sets, and validating clinical triage workflows.

Discussion
Fellows were engaged in projects that span the breadth of the CI specialty and were able to make system-wide contributions in line with their educational milestones.

Conclusions
CI fellows contributed meaningfully and rapidly to their institutions’ response to the COVID-19 pandemic.
Optimum roughage proportion in barley-based feedlot cattle diets: growth performance, feeding behavior, and carcass traits
Authors: Koenig Karen M , Chibisa Gwinyai E , Penner Gregory B , Beauchemin Karen A 
Published: September 2020

Abstract
High grain diets are fed to finishing beef cattle to maximize animal performance in a cost-effective manner. However, a small amount of roughage is incorporated in finishing diets to help prevent ruminal acidosis, although few studies have examined optimum roughage inclusion level in barley-based diets. The objective of the study was to evaluate the effects of roughage proportion in barley-based finishing diets on growth performance, feeding behavior, and carcass traits of feedlot cattle. Crossbred beef steers (n = 160; mean body weight ± SD, 349.7 ± 21.4 kg) were allocated to 20 pens that were assigned randomly to four dietary treatments (five pens of eight steers per treatment). The treatment diets contained barley silage at 0%, 4%, 8%, and 12% of dietary dry matter (DM). The remainder of the diets (DM basis) consisted of 80%, 76%, 72%, and 68% barley grain, respectively, 15% corn dried distiller’s grains, 5% mineral and vitamin supplement, and 32 mg monensin/kg diet DM. The diets were fed as total mixed rations for ad libitum intake (minimum of 5% refusal) once per day. Cattle were weighed on 2 consecutive days at the start and end of the experiment and on 1 d every 3 wk throughout the experiment (124 d). Two pens for each treatment group were equipped with an electronic feeding system (GrowSafe Systems Ltd., Calgary, Alberta) to monitor feed intake and feeding behavior of individual cattle. The data for dry matter intake (DMI), average daily gain (ADG), gain:feed (G:F) ratio, and carcass traits were analyzed as a completely randomized design with fixed effect of barley silage proportion and pen replicate as experimental unit. Feeding behavior data were analyzed similarly, but with animal as experimental unit. Averaged over the study, DMI increased linearly (11.1, 11.3, 11.7, 11.8 kg/d; P = 0.001) as barley silage proportion increased from 0%, 4%, 8%, and 12% of DM, but ADG was not affected (carcass-adjusted,1.90, 1.85, 1.87, 1.89 kg/d; P ≥ 0.30). Consequently, G:F ratio decreased linearly (carcass-adjusted, 168.9, 163.8, 158.5, 160.6 g/kg DMI; P = 0.023). When averaged over the study, proportion of barley silage in the diet had no linear or quadratic effects (P &gt; 0.10) on meal frequency, duration of meals, intermeal duration, or meal size, but eating rate decreased linearly with increasing silage proportion (P = 0.008). There was no diet effect on liver abscesses (P ≥ 0.92), and effects on carcass characteristics were minor or nonexistent. We conclude that increasing the proportion of barley silage in a feedlot finishing diet at the expense of barley grain to minimize the incidence of ruminal acidosis may decrease feed conversion efficiency.
Effects of zinc oxide nanoparticles on regulatory appetite and heat stress protein genes in broiler chickens subjected to heat stress
Authors: Ramiah Suriya Kumari , Atta Awad Elmutaz , Hemly Nur Izzah Mohd , Ebrahimi Mahdi , Joshua Olubodun , Jamshed Muhammad , Saminathan Mookiah , Soleimani Abdoreza Farjam , Idrus Zulkifli 
Published: September 2020

Abstract
This study was conducted to explore the effect of the zinc oxide nanoparticles (ZnONPs) supplement on the regulatory appetite and heat stress (HS) genes in broiler chickens raised under high or normal ambient temperatures. In this study, 240 one-day-old male broiler chicks (Cobb 500) were randomly assigned to 48 battery cages. From day 1, these 48 cages were randomly subjected to four different treatment strategies: Control (wherein, their basal diet included 60 mg/kg of ZnO), ZNONPs 40 (wherein basal diet included 40 mg/kg of ZnONPs), ZnONPs 60 (basal diet included 60 mg/kg of ZnONPs), and ZnONPs 100 (basal diet included 100 mg/kg of ZnONPs). Thereafter, from day 22 to 42, the chickens from each dietary treatment group were subjected to different temperature stresses either normal (23 ± 1 °C constant) or HS (34 ± 1 °C for 6 h/d), which divided them into eight different treatment groups. Our findings revealed that dietary ZnONPs altered the gene expression of cholecystokinin (ileum), heat stress proteins (HSP) 70 (jejunum and ileum), and HSP 90 (duodenum, jejunum, and ileum). The gene expression of ghrelin was affected by the interaction between the ZnONPs concentration and temperature in the duodenum and stomach. More studies are required to elucidate its complex physiological and biochemical functions of the regulation of gene expression within the intestine in heat-stressed broiler chickens.
Brexit and the discursive construction of the corporation
Authors: Fuller Crispian 
Published: September 2020

AbstractThe UK decision to exit the EU in 2016 has led to economic uncertainty. Foreign corporations with UK subsidiaries have sought to mediate these uncertainties while a final agreement is negotiated. Critical to this is the relationship between headquarter-subsidiary relations (HQs) and these subsidiaries. Discourse analysis has increasingly been used to examine corporate relations, with the corporation viewed as socially constructed through discourses and perpetual deliberations. Deploying a discourse approach, and recognising the importance of topological spatial relations, this article examines the relationship between HQs and UK-based subsidiaries during the Brexit negotiation period. In conclusion, HQs have generally devolved responsibility to subsidiaries for responding to Brexit, involving ‘consensual’ relations with subsidiaries and less intrusive ‘stretched’ topological power relations.
Prion Protein Gene (PRNP) Sequences Suggest Differing Vulnerability to Chronic Wasting Disease for Florida Key Deer (Odocoileus virginianus clavium) and Columbian White-Tailed Deer (O. v. leucurus)
Authors: Perrin-Stowe Tolulope I N , Ishida Yasuko , Terrill Emily E , Hamlin Brian C , Penfold Linda , Cusack Lara M , Novakofski Jan , Mateus-Pinilla Nohra E , Roca Alfred L 
Published: September 2020

Abstract
Chronic wasting disease (CWD) is a fatal, highly transmissible spongiform encephalopathy caused by an infectious prion protein. CWD is spreading across North American cervids. Studies of the prion protein gene (PRNP) in white-tailed deer (WTD; Odocoileus virginianus) have identified non-synonymous substitutions associated with reduced CWD frequency. Because CWD is spreading rapidly geographically, it may impact cervids of conservation concern. Here, we examined the genetic vulnerability to CWD of 2 subspecies of WTD: the endangered Florida Key deer (O. v. clavium) and the threatened Columbian WTD (O. v. leucurus). In Key deer (n = 48), we identified 3 haplotypes formed by 5 polymorphisms, of which 2 were non-synonymous. The polymorphism c.574G&gt;A, unique to Key deer (29 of 96 chromosomes), encodes a non-synonymous substitution from valine to isoleucine at codon 192. In 91 of 96 chromosomes, Key deer carried c.286G&gt;A (G96S), previously associated with substantially reduced susceptibility to CWD. Key deer may be less genetically susceptible to CWD than many mainland WTD populations. In Columbian WTD (n = 13), 2 haplotypes separated by one synonymous substitution (c.438C&gt;T) were identified. All of the Columbian WTD carried alleles that in other mainland populations are associated with relatively high susceptibility to CWD. While larger sampling is needed, future management plans should consider that Columbian WTD are likely to be genetically more vulnerable to CWD than many other WTD populations. Finally, we suggest that genetic vulnerability to CWD be assessed by sequencing PRNP across other endangered cervids, both wild and in captive breeding facilities.
Labour Migration and the Gulf Arab States: Some Observations on the Potential of the GCR
Authors: Bastaki Jinan 
Published: September 2020

Abstract
Recently, there has been some exploration of labour mobility policies in the context of refugees as a way of local country integration that can help with refugee self-reliance, with some examples from Africa and Latin America. Building on these examples, this paper explores the opportunities the Global Compact for Refugees presents in the countries making up the Gulf Cooperation Council, specifically the United Arab Emirates (UAE), as related to expanding access to third-country solutions, refugee self-reliance, and responsibility-sharing. Many of the countries making up the Gulf Cooperation Council rely in large part on expatriate labour and are indeed made up of majority non-citizens. Many Syrians who have been able to obtain work visas have preferred to go to the UAE rather than seek refuge in other neighbouring countries. Some positive initiatives, such as a 2018 Amnesty Law in the UAE, which created a specific category of residency permits for those from countries suffering war and natural disasters, have ensured that de facto refugees are protected against refoulement in the event that they lose their residency. However, in order for labour migration in this context to work, there need to be better guarantees and minimum protections, such as schooling for children and healthcare.