bluuebunny/crossref_metadata_2025_split huggingface dataset:
MoBPSweb: A web-based framework to simulate and compare breeding programs
Authors: Pook Torsten , Büttgen Lisa , Ganesan Amudha , Ha Ngoc-Thuy , Simianer Henner 
Published: February 2021

AbstractIn this study, we introduce a new web-based simulation framework (“MoBPSweb”) that combines a unified language to describe breeding programs with the simulation software MoBPS, standing for “Modular Breeding Program Simulator.” Thereby, MoBPSweb provides a flexible environment to log, simulate, evaluate, and compare breeding programs. Inputs can be provided via modules ranging from a Vis.js-based environment for “drawing” the breeding program to a variety of modules to provide phenotype information, economic parameters, and other relevant information. Similarly, results of the simulation study can be extracted and compared to other scenarios via output modules (e.g., observed phenotypes, the accuracy of breeding value estimation, inbreeding rates), while all simulations and downstream analysis are executed in the highly efficient R-package MoBPS.
Heuristic hyperparameter optimization of deep learning models for genomic prediction
Authors: Han Junjie , Gondro Cedric , Reid Kenneth , Steibel Juan P 
Published: February 2021

AbstractThere is a growing interest among quantitative geneticists and animal breeders in the use of deep learning (DL) for genomic prediction. However, the performance of DL is affected by hyperparameters that are typically manually set by users. These hyperparameters do not simply specify the architecture of the model; they are also critical for the efficacy of the optimization and model-fitting process. To date, most DL approaches used for genomic prediction have concentrated on identifying suitable hyperparameters by exploring discrete options from a subset of the hyperparameter space. Enlarging the hyperparameter optimization search space with continuous hyperparameters is a daunting combinatorial problem. To deal with this problem, we propose using differential evolution (DE) to perform an efficient search of arbitrarily complex hyperparameter spaces in DL models, and we apply this to the specific case of genomic prediction of livestock phenotypes. This approach was evaluated on two pig and cattle datasets with real genotypes and simulated phenotypes (N = 7,539 animals and M = 48,541 markers) and one real dataset (N = 910 individuals and M = 28,916 markers). Hyperparameters were evaluated using cross-validation. We compared the predictive performance of DL models using hyperparameters optimized by DE against DL models with “best practice” hyperparameters selected from published studies and baseline DL models with randomly specified hyperparameters. Optimized models using DE showed a clear improvement in predictive performance across all three datasets. DE optimized hyperparameters also resulted in DL models with less overfitting and less variation in predictive performance over repeated retraining compared to non-optimized DL models.
Characterization of a pericentric inversion in plateau fence lizards (Sceloporus tristichus): evidence from chromosome-scale genomes
Authors: Bedoya Ana M , Leaché Adam D 
Published: February 2021

Abstract
Spiny lizards in the genus Sceloporus are a model system among squamate reptiles for studies of chromosomal evolution. While most pleurodont iguanians retain an ancestral karyotype formula of 2n = 36 chromosomes, Sceloporus exhibits substantial karyotype variation ranging from 2n =  22 to 46 chromosomes. We present two annotated chromosome-scale genome assemblies for the Plateau Fence Lizard (Sceloporus tristichus) to facilitate research on the role of pericentric inversion polymorphisms on adaptation and speciation. Based on previous karyotype work using conventional staining, the S. tristichus genome is characterized as 2n =  22 with six pairs of macrochromosomes and five pairs of microchromosomes and a pericentric inversion polymorphism on chromosome 7 that is geographically variable. We provide annotated, chromosome-scale genomes for two lizards located at opposite ends of a dynamic hybrid zone that are each fixed for different inversion polymorphisms. The assembled genomes are 1.84–1.87 Gb (1.72 Gb for scaffolds mapping to chromosomes) with a scaffold N50 of 267.5 Mb. Functional annotation of the genomes resulted in ∼15K predicted gene models. Our assemblies confirmed the presence of a 4.62-Mb pericentric inversion on chromosome 7, which contains 62 annotated coding genes with known functions. In addition, we collected population genomics data using double digest RAD-sequencing for 44 S. tristichus to estimate population structure and phylogeny across the Colorado Plateau. These new genomic resources provide opportunities to perform genomic scans and investigate the formation and spread of pericentric inversions in a naturally occurring hybrid zone.
EnvRtype: a software to interplay enviromics and quantitative genomics in agriculture
Authors: Costa-Neto Germano , Galli Giovanni , Carvalho Humberto Fanelli , Crossa José , Fritsche-Neto Roberto 
Published: February 2021

AbstractEnvirotyping is an essential technique used to unfold the nongenetic drivers associated with the phenotypic adaptation of living organisms. Here, we introduce the EnvRtype R package, a novel toolkit developed to interplay large-scale envirotyping data (enviromics) into quantitative genomics. To start a user-friendly envirotyping pipeline, this package offers: (1) remote sensing tools for collecting (get_weather and extract_GIS functions) and processing ecophysiological variables (processWTH function) from raw environmental data at single locations or worldwide; (2) environmental characterization by typing environments and profiling descriptors of environmental quality (env_typing function), in addition to gathering environmental covariables as quantitative descriptors for predictive purposes (W_matrix function); and (3) identification of environmental similarity that can be used as an enviromic-based kernel (env_typing function) in whole-genome prediction (GP), aimed at increasing ecophysiological knowledge in genomic best-unbiased predictions (GBLUP) and emulating reaction norm effects (get_kernel and kernel_model functions). We highlight literature mining concepts in fine-tuning envirotyping parameters for each plant species and target growing environments. We show that envirotyping for predictive breeding collects raw data and processes it in an eco-physiologically smart way. Examples of its use for creating global-scale envirotyping networks and integrating reaction-norm modeling in GP are also outlined. We conclude that EnvRtype provides a cost-effective envirotyping pipeline capable of providing high quality enviromic data for a diverse set of genomic-based studies, especially for increasing accuracy in GP across untested growing environments.
Why are rare variants hard to impute? Coalescent models reveal theoretical limits in existing algorithms
Authors: Si Yichen , Vanderwerff Brett , Zöllner Sebastian 
Published: February 2021

AbstractGenotype imputation is an indispensable step in human genetic studies. Large reference panels with deeply sequenced genomes now allow interrogating variants with minor allele frequency &lt; 1% without sequencing. Although it is critical to consider limits of this approach, imputation methods for rare variants have only done so empirically; the theoretical basis of their imputation accuracy has not been explored. To provide theoretical consideration of imputation accuracy under the current imputation framework, we develop a coalescent model of imputing rare variants, leveraging the joint genealogy of the sample to be imputed and reference individuals. We show that broadly used imputation algorithms include model misspecifications about this joint genealogy that limit the ability to correctly impute rare variants. We develop closed-form solutions for the probability distribution of this joint genealogy and quantify the inevitable error rate resulting from the model misspecification across a range of allele frequencies and reference sample sizes. We show that the probability of a falsely imputed minor allele decreases with reference sample size, but the proportion of falsely imputed minor alleles mostly depends on the allele count in the reference sample. We summarize the impact of this error on genotype imputation on association tests by calculating the r2 between imputed and true genotype and show that even when modeling other sources of error, the impact of the model misspecification has a significant impact on the r2 of rare variants. To evaluate these predictions in practice, we compare the imputation of the same dataset across imputation panels of different sizes. Although this empirical imputation accuracy is substantially lower than our theoretical prediction, modeling misspecification seems to further decrease imputation accuracy for variants with low allele counts in the reference. These results provide a framework for developing new imputation algorithms and for interpreting rare variant association analyses.
Maize centromeric chromatin scales with changes in genome size
Authors: Wang Na , Liu Jianing , Ricci William A , Gent Jonathan I , Dawe R Kelly 
Published: February 2021

Abstract
Centromeres are defined by the location of Centromeric Histone H3 (CENP-A/CENH3) which interacts with DNA to define the locations and sizes of functional centromeres. An analysis of 26 maize genomes including 110 fully assembled centromeric regions revealed positive relationships between centromere size and genome size. These effects are independent of variation in the amounts of the major centromeric satellite sequence CentC. We also backcrossed known centromeres into two different lines with larger genomes and observed consistent increases in functional centromere sizes for multiple centromeres. Although changes in centromere size involve changes in bound CENH3, we could not mimic the effect by overexpressing CENH3 by threefold. Literature from other fields demonstrate that changes in genome size affect protein levels, organelle size and cell size. Our data demonstrate that centromere size is among these scalable features, and that multiple limiting factors together contribute to a stable centromere size equilibrium.
Delirium in Older Patients With COVID-19: Prevalence, Risk Factors, and Clinical Relevance
Authors: Mendes Aline , Herrmann François R , Périvier Samuel , Gold Gabriel , Graf Christophe E , Zekry Dina 
Published: February 2021

Abstract

Background
Delirium prevalence increases with age and is associated with poor outcomes. We aimed to investigate the prevalence and risk factors for delirium in older patients hospitalized with COVID-19, as well as its association with length of stay and mortality.

Method
This was a retrospective study of patients aged 65 years and older hospitalized with COVID-19. Data were collected from computerized medical records and all patients had delirium assessment at admission. Risk factors for delirium as well as the outcomes mentioned above were studied by 2-group comparison, logistic regression, and Cox proportional hazard models.

Results
Of a total of 235 Caucasian patients, 48 (20.4%) presented with delirium, which was hypoactive in 41.6% of cases, and hyperactive and mixed in 35.4% and 23.0%, respectively. Patients with cognitive impairment had a nearly 4 times higher risk of developing delirium compared to patients who were cognitively normal before SARS-CoV-2 infection (odds ratio 3.7; 95% CI: 1.7–7.9, p = .001). The presence of delirium did not modify the time from symptoms’ onset to hospitalization or the length of stay in acute care, but it was associated with an increased risk of dying (hazard ratio 2.1; 95% CI: 1.2–3.7, p = .0113).

Conclusion
Delirium was a prevalent condition in older people admitted with COVID-19 and preexisting cognitive impairment was its main risk factor. Delirium was associated with higher in-hospital mortality. These results highlight the importance of early recognition of delirium especially when premorbid cognitive comorbidities are present.
Cocomposing an Aesthetic Self Through Play: Toward a Transformative Framework for Dementia Care
Authors: Li Bing Yu 
Published: February 2021

Abstract

Background and Objectives
Aging and deterioration mark a new phase in many older adults’ life, highlighting the importance of creativity and imagination. This article introduces the implementation of an innovative program, Play Intervention for Dementia, at a nursing home in Hong Kong, with emphasis on its contribution to the conceptual framework for understanding the selfhood of older adults with dementia.

Research Design and Methods
As a community-based participatory action research project, this study democratized knowledge production by integrating voices of practitioners with diverse backgrounds through video-based methods.

Results
Play, as an activity replete with free expressions and impulsive interactions, is an ideal realm for exploring and establishing selfhood with older adults with dementia. It has been found that “aesthetic self,” an alternative self emerging from immediate aesthetic experience and carrying transformative power within the caring relationship, is a necessary element of self-construction in life with dementia.

Discussion and Implications
Integrating theories and practice, this framework provides a new lens for understanding and responding to selfhood, disease, and life.
NEU1 is more abundant in uveitic retina with concomitant desialylation of retinal cells
Authors: Lorenz Lea , Amann Barbara , Hirmer Sieglinde , Degroote Roxane L , Hauck Stefanie M , Deeg Cornelia A 
Published: February 2021

Abstract
Desialylation of cell surface glycoproteins carried out by sialidases affects various immunological processes. However, the role of neuraminidase 1 (NEU1), one of the four mammalian sialidases, in inflammation and autoimmune disease is not completely unraveled to date. In this study, we analyzed the retinal expression of NEU1 in equine recurrent uveitis (ERU), a spontaneous animal model for autoimmune uveitis. Mass spectrometry revealed significantly higher abundance of NEU1 in retinal Müller glial cells (RMG) of ERU-diseased horses compared to healthy controls. Immunohistochemistry uncovered NEU1 expression along the whole Müller cell body in healthy and uveitic states and confirmed higher abundance in inflamed retina. Müller glial cells are the principal macroglial cells of the retina and play a crucial role in uveitis pathogenesis. To determine whether higher expression levels of NEU1 in uveitic RMG correlate with the desialylation of retinal cells, we performed lectin-binding assays with sialic acid-specific lectins. Through these experiments, we could demonstrate a profound loss of both α2-3- and α2-6-linked terminal sialic acids in uveitis. Hence, we hypothesize that the higher abundance of NEU1 in uveitic RMG plays an important role in the pathogenesis of uveitis by desialylation of retinal cells. As RMG become activated in the course of uveitis and actively promote inflammation, we propose that NEU1 might represent a novel activation marker for inflammatory RMG. Our data provide novel insights in the expression and implication of NEU1 in inflammation and autoimmune disease.
Come together to promote health: case study and theoretical perspectives from a Kenyan community-based program
Authors: Goodman Michael L , Elliott Aleisha J , Gitari Stanley , Keiser Philip , Raimer-Goodman Lauren , Seidel Sarah E 
Published: February 2021

Summary
Over the past four decades, group-based microfinance programs have spread rapidly throughout south Asia, sub-Saharan Africa and Latin America. Recent evaluations of the programs have identified social capital as a common byproduct of frequent association by members, increasing trust, belonging and normative influence. Concurrently, social capital is increasingly recognized as an important health determinant. We present an overview of a program intervention operating in Kenya that utilizes a microfinance approach to produce social capital, and seeks to leverage that social capital to promote health at three levels—the village, group, and individual. A theory of change is presented for each of these three levels, demonstrating conceptually and with program examples how social capital can be applied to promote health. Related social theories and approaches, further research and program directions are given for each of the three levels. We identify potential to improve a broad range of health outcomes through this innovative model, which requires engagement with health promotion researchers and planners in low- and middle-income countries for further refinement and validation.
Evaluation of soybean (Glycine max L.) adaptation to northern European regions under different agro-climatic scenarios
Authors: Boulch Guénolé , Elmerich Chloé , Djemel Amina , Lange Bastien 
Published: February 2021

Abstract
Soybean is a candidate crop to increase the independency of Europe in leguminous protein crops. However, its adaptation to northern European regions is not yet well defined due to the lack of long-term references. Herein, we simulated soybean yield potential in northern France and identified the main yield limiting factors under rainfed vs. irrigated conditions. Two cultivars representing maturity groups 000 and 00 were planted within three different trials. Leaf area index, shoot and pod biomass, main phenological stages and yield were recorded to evaluate CROPGRO-soybean model predictability. Adjustment of genetic coefficients was performed prior to simulate yield on 21-years weather database (1999–2018) at Beauvais (France, N 49.46°, E 2.07°) and Estrées-Mons (France, N 49.88°, E 3.01°) under different water regimes and planting dates. Predictions showed that adding irrigation at grain filling period would increase yield potential to the level of non-water limited scenarios. Although simulated yield variability is reduced with irrigation, the remaining variability suggests that water is not the only yield-limiting factor. A tentative explanation is proposed by deriving environmental covariates from the model. The analysis confirmed the importance of precipitation amount (optimum around 200 mm) and duration (optimum around 60 days) of the flowering to physiological maturity period under rainfed conditions. Under irrigated conditions, increasing evapotranspiration and average minimum temperature affected simulated yield positively while increasing the number of days below 10 °C had a negative impact. These results give insights for soybean crop management and bring indications to breeders for adapting the existing genetic material to northern Europe.
Effects of different defatted rice bran sources and processing technologies on nutrient digestibility in cannulated growing pigs
Authors: Huang Bingbing B , Sun Zhiqiang Q , Wang Li , Wang Lu , Shi Huangwei W , Hu Qile L , Lyu Zhiqian Q , Li Defa F , Zang Jianjun J , Lai Changhua H 
Published: February 2021

Abstract
The objective of this study was to evaluate the effects of different defatted rice bran (DFRB) sources and processing technologies on nutrient digestibility in different intestinal segments of pigs. Nine barrows with T-cannula in the distal ileum were randomly allotted to nine different sources in which oil was pressed extracted for seven sources and was solvent extracted for two sources. The experiment contained 6 periods of 12 d, including 8 d for diet adaptation, 2 d for fecal collection, and 2 d for digesta collection. The apparent ileal digestibility (AID) of dry matter (DM), ash, total dietary fiber (TDF), insoluble dietary fiber (IDF), neutral detergent fiber (NDF), acid detergent fiber (ADF), and hemicellulose in different sources of DFRB was quite variable. There were no differences in the AID of dietary gross energy (GE), organic matter (OM), ether extract (EE), crude protein (CP), and soluble dietary fiber (SDF) between different sources of DFRB. There were no differences in the AID of dietary EE, TDF, IDF, and hemicellulose between different processing technologies. Pressed DFRBs have greater (P &lt; 0.05) average AID of dietary GE, DM, ash, OM, CP, SDF, and NDF and lower (P &lt; 0.01) ADF compared with solvent-extracted DFRBs. The apparent total tract digestibility (ATTD) of most of the dietary nutrients, except for the ATTD of dietary EE, SDF, and hemicellulose, significantly varied in different sources of DFRB (P &lt; 0.05). In addition, pressed DFRB had greater (P &lt; 0.05) ATTD of dietary SDF, NDF, ADF, and hemicellulose compared with solvent-extracted DFRB. The apparent hindgut digestibility (AHD) of dietary DM, SDF, NDF, and ADF significantly varied (P &lt;0.05) in different sources of DFRB. Exception with DM, there are no differences in the AHD of nutrients digestibility between pressed DFRB and solvent-extracted DFRB. In conclusion, DFRB in different sources and processing technologies with different physicochemical properties had different effects on nutrient digestibility in the foregut and hindgut of pigs.
Home range, habitat selection, density, and diet of golden jackals in the Eastern Plains Landscape, Cambodia
Authors: Kamler Jan F , Minge Christin , Rostro-García Susana , Gharajehdaghipour Tazarve , Crouthers Rachel , In Visattha , Pay Chen , Pin Chanratana , Sovanna Prum , Macdonald David W 
Published: February 2021

AbstractWe used radiocollars and GPS collars to determine the movements and habitat selection of golden jackals (Canis aureus) in a seasonally dry deciduous forest with no human settlements in eastern Cambodia. We also collected and analyzed 147 scats from jackals to determine their seasonal diet and prey selection. The mean (± SE) annual size of home-range ranges (47.1 ± 2.5 km2; n = 4), which were mutually exclusive between mated pairs, was considerably larger than that previously reported for this species, resulting in an extremely low density (0.01 jackal/km2). The unusually large home ranges and low density probably were due to the harsh dry season when most understory vegetation is burned and nearly all waterholes dry up, thereby causing a large seasonal decline in the availability of small vertebrate prey. Resident groups consisted of an alpha pair, but no betas, and were situated only in areas not occupied by leopards (Panthera pardus) and dholes (Cuon alpinus). Jackals avoided dense forests and streams, and had a strong selection for dirt roads, possibly to avoid larger predators. Overall the jackal diet was diverse, with at least 16 prey items identified, and there was no significant difference in diet composition between the cool-dry and hot-dry seasons. Scat analysis showed that the main food items consumed by jackals were processional termites (Hospitalitermes spp.; 26% biomass consumed), followed by wild pig (Sus scrofa; 20%), muntjac (Muntiacus vaginalis; 20%), and civets (17%). Compared to available biomass, jackals were not random in their consumption of ungulates because muntjac were selectively consumed over larger ungulate species. Dietary overlap with dholes and leopards was relatively low, and consumption patterns indicated jackals were preying on ungulates rather than scavenging from kills of larger carnivores. Our results showed that the jackal is an extremely adaptable and opportunistic species that exhibits unique behaviors to survive in an extreme environment near the edge of its distribution.
Post-operative abscess in inguinal hernial sac—case report of an unusual complication of perforated acute appendicitis
Authors: Chan Chin Bruno M , Aakif Muhammad , Khan Ata U 
Published: February 2021

Abstract
Acute appendicitis is a common condition, with a lifetime risk of 7–8%. Common complications of surgical management include bleeding, bowel injury, residual abscess formation and post-operative ileus. This is a rare case of a 50-year-old male who underwent laparoscopic converted to open appendicectomy for perforated acute appendicitis, with a complication of post-operative fluid collection that extended into the right inguinal hernia sac.