bluuebunny/crossref_metadata_2025_split huggingface dataset:
A meta-analysis of genome-wide association studies for average daily gain and lean meat percentage in two Duroc pig populations
Authors: Zhou Shenping , Ding Rongrong , Meng Fanming , Wang Xingwang , Zhuang Zhanwei , Quan Jianping , Geng Qian , Wu Jie , Zheng Enqin , Wu Zhenfang , Yang Jianhui , Yang Jie 
Published: January 2021

Abstract
Background
Average daily gain (ADG) and lean meat percentage (LMP) are the main production performance indicators of pigs. Nevertheless, the genetic architecture of ADG and LMP is still elusive. Here, we conducted genome-wide association studies (GWAS) and meta-analysis for ADG and LMP in 3770 American and 2090 Canadian Duroc pigs.

Results
In the American Duroc pigs, one novel pleiotropic quantitative trait locus (QTL) on Sus scrofa chromosome 1 (SSC1) was identified to be associated with ADG and LMP, which spans 2.53 Mb (from 159.66 to 162.19 Mb). In the Canadian Duroc pigs, two novel QTLs on SSC1 were detected for LMP, which were situated in 3.86 Mb (from 157.99 to 161.85 Mb) and 555 kb (from 37.63 to 38.19 Mb) regions. The meta-analysis identified ten and 20 additional SNPs for ADG and LMP, respectively. Finally, four genes (PHLPP1, STC1, DYRK1B, and PIK3C2A) were detected to be associated with ADG and/or LMP. Further bioinformatics analysis showed that the candidate genes for ADG are mainly involved in bone growth and development, whereas the candidate genes for LMP mainly participated in adipose tissue and muscle tissue growth and development.

Conclusions
We performed GWAS and meta-analysis for ADG and LMP based on a large sample size consisting of two Duroc pig populations. One pleiotropic QTL that shared a 2.19 Mb haplotype block from 159.66 to 161.85 Mb on SSC1 was found to affect ADG and LMP in the two Duroc pig populations. Furthermore, the combination of single-population and meta-analysis of GWAS improved the efficiency of detecting additional SNPs for the analyzed traits. Our results provide new insights into the genetic architecture of ADG and LMP traits in pigs. Moreover, some significant SNPs associated with ADG and/or LMP in this study may be useful for marker-assisted selection in pig breeding.
A review of deep learning applications for genomic selection
Authors: Montesinos-López Osval Antonio , Montesinos-López Abelardo , Pérez-Rodríguez Paulino , Barrón-López José Alberto , Martini Johannes W. R. , Fajardo-Flores Silvia Berenice , Gaytan-Lugo Laura S. , Santana-Mancilla Pedro C. , Crossa José 
Published: January 2021

AbstractBackgroundSeveral conventional genomic Bayesian (or no Bayesian) prediction methods have been proposed including the standard additive genetic effect model for which the variance components are estimated with mixed model equations. In recent years, deep learning (DL) methods have been considered in the context of genomic prediction. The DL methods are nonparametric models providing flexibility to adapt to complicated associations between data and output with the ability to adapt to very complex patterns.Main bodyWe review the applications of deep learning (DL) methods in genomic selection (GS) to obtain a meta-picture of GS performance and highlight how these tools can help solve challenging plant breeding problems. We also provide general guidance for the effective use of DL methods including the fundamentals of DL and the requirements for its appropriate use. We discuss the pros and cons of this technique compared to traditional genomic prediction approaches as well as the current trends in DL applications.ConclusionsThe main requirement for using DL is the quality and sufficiently large training data. Although, based on current literature GS in plant and animal breeding we did not find clear superiority of DL in terms of prediction power compared to conventional genome based prediction models. Nevertheless, there are clear evidences that DL algorithms capture nonlinear patterns more efficiently than conventional genome based. Deep learning algorithms are able to integrate data from different sources as is usually needed in GS assisted breeding and it shows the ability for improving prediction accuracy for large plant breeding data. It is important to apply DL to large training-testing data sets.
Lifestyle modifications result in alterations in the gut microbiota in obese children
Authors: Cho Ky Young 
Published: January 2021

Abstract
Background
The association between the gut microbiota and pediatric obesity was analyzed in a cross-sectional study. A prospective study of obese children was conducted to assess the gut microbial alterations after a weight change. We collected fecal samples from obese children before and after a 2-month weight reduction program that consisted of individual counseling for nutritional education and physical activity, and we performed 16S rRNA gene amplicon sequencing using an Illumina MiSeq platform.

Results
Thirty-six participants, aged 7 to 18 years, were classified into the fat loss (n = 17) and the fat gain (n = 19) groups according to the change in total body fat (%) after the intervention. The baseline analysis of the gut microbiota in the preintervention stages showed dysbiotic features of both groups compared with those of normal-weight children. In the fat loss group, significantly decreased proportions of Bacteroidetes phylum, Bacteroidia class, Bacteroidales order, Bacteroidaceae family, and Bacteroides genus, along with increased proportions of Firmicutes phylum, Clostridia class, and Clostridiales order, were observed after intervention. The microbial richness was significantly reduced, without a change in beta diversity in the fat loss group. The fat gain group showed significantly deceased proportions of Firmicutes phylum, Clostridia class, Clostridiales order, Lachnospiraceae family, and Eubacterium hallii group genus, without a change in diversity after the intervention. According to the functional metabolic analysis by the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2, the “Nitrate Reduction VI” and “Aspartate Superpathway” pathways were predicted to increase significantly in the fat loss group. The cooccurring networks of genera were constructed and showed the different microbes that drove the changes between the pre- and postintervention stages in the fat loss and fat gain groups.

Conclusions
This study demonstrated that lifestyle modifications can impact the composition, richness, and predicted functional profiles of the gut microbiota in obese children after weight changes.

Trial registration
ClinicalTrials.govNCT03812497, registration date January 23, 2019, retrospectively registered.
Candidate genes and SNPs associated with stomatal conductance under drought stress in Vitis
Authors: Trenti Massimiliano , Lorenzi Silvia , Bianchedi Pier Luigi , Grossi Daniele , Failla Osvaldo , Grando Maria Stella , Emanuelli Francesco 
Published: January 2021

AbstractBackgroundUnderstanding the complexity of the vine plant’s response to water deficit represents a major challenge for sustainable winegrowing. Regulation of water use requires a coordinated action between scions and rootstocks on which cultivars are generally grafted to cope with phylloxera infestations. In this regard, a genome-wide association study (GWAS) approach was applied on an ‘ad hoc’ association mapping panel including differentVitisspecies, in order to dissect the genetic basis of transpiration-related traits and to identify genomic regions of grape rootstocks associated with drought tolerance mechanisms.The panel was genotyped with the GrapeReSeq Illumina 20 K SNP array and SSR markers, and infrared thermography was applied to estimate stomatal conductance values during progressive water deficit.ResultsIn the association panel the level of genetic diversity was substantially lower for SNPs loci (0.32) than for SSR (0.87). GWAS detected 24 significant marker-trait associations along the various stages of drought-stress experiment and 13 candidate genes with a feasible role in drought response were identified.Gene expression analysis proved that three of these genes (VIT_13s0019g03040, VIT_17s0000g08960,VIT_18s0001g15390) were actually induced by drought stress.Genetic variation of VIT_17s0000g08960 coding for a raffinose synthase was further investigated by resequencing the gene of 85 individuals since a SNP located in the region (chr17_10,497,222_C_T) was significantly associated with stomatal conductance.ConclusionsOur results represent a step forward towards the dissection of genetic basis that modulate the response to water deprivation in grape rootstocks. The knowledge derived from this study may be useful to exploit genotypic and phenotypic diversity in practical applications and to assist further investigations.
Prognostic nomogram for 30-day mortality of deep vein thrombosis patients in intensive care unit
Authors: Shen Runnan , Gao Ming , Tao Yangu , Chen Qinchang , Wu Guitao , Guo Xushun , Xia Zuqi , You Guochang , Hong Zilin , Huang Kai 
Published: January 2021

Abstract
Background
We aimed to use the Medical Information Mart for Intensive Care III database to build a nomogram to identify 30-day mortality risk of deep vein thrombosis (DVT) patients in intensive care unit (ICU).

Methods
Stepwise logistic regression and logistic regression with least absolute shrinkage and selection operator (LASSO) were used to fit two prediction models. Bootstrap method was used to perform internal validation.

Results
We obtained baseline data of 535 DVT patients, 91 (17%) of whom died within 30 days. The discriminations of two new models were better than traditional scores. Compared with simplified acute physiology score II (SAPSII), the predictive abilities of two new models were improved (Net reclassification improvement [NRI] > 0; Integrated discrimination improvement [IDI] > 0; P < 0.05). The Brier scores of two new models in training set were 0.091 and 0.108. After internal validation, corrected area under the curves for two models were 0.850 and 0.830, while corrected Brier scores were 0.108 and 0.114. The more concise model was chosen to make the nomogram.

Conclusions
The nomogram developed by logistic regression with LASSO model can provide an accurate prognosis for DVT patients in ICU.
Time-varying discrimination accuracy of longitudinal biomarkers for the prediction of mortality compared to assessment at fixed time point in severe burns patients
Authors: Yoon Jaechul , Kym Dohern , Hur Jun , Won Jae Hee , Yim Haejun , Cho Yong Suk , Chun Wook 
Published: January 2021

Abstract
Background
The progression of biomarkers over time is considered an indicator of disease progression and helps in the early detection of disease, thereby reducing disease-related mortality. Their ability to predict outcomes has been evaluated using conventional cross-sectional methods. This study investigated the prognostic performance of biomarkers over time.

Methods
Patients aged > 18 years admitted to the burn intensive care unit within 24 h of a burn incident were enrolled. Information regarding longitudinal biomarkers, including white blood cells; platelet count; lactate, creatinine, and total bilirubin levels; and prothrombin time (PT), were retrieved from a clinical database. Time-dependent receiver operating characteristic curves using cumulative/dynamic and incident/dynamic (ID) approaches were used to evaluate prognostic performance.

Results
Overall, 2259 patients were included and divided into survival and non-survival groups. By determining the area under the curve using the ID approach, platelets showed the highest c-index [0.930 (0.919–0.941)] across all time points. Conversely, the c-index of PT and creatinine levels were 0.862 (0.843–0.881) and 0.828 (0.809–0.848), respectively.

Conclusions
Platelet count was the best prognostic marker, followed by PT. Total bilirubin and creatinine levels also showed good prognostic ability. Although lactate was a strong predictor, it showed relatively poor prognostic performance in burns patients.
Total cholesterol concentration predicts the effect of plasmapheresis on hypertriglyceridemic acute pancreatitis: a retrospective case–control study
Authors: Chen Zhu , Huang Xiaolong , Han Na , Guo Yanxia , Chen Jing , Ning Yaogui , Zhang Minwei 
Published: January 2021

AbstractBackgroundWhat kind of patients with hypertriglyceridemic acute pancreatitis (HLAP) might benefit from plasmapheresis (PP) remains unknown. The objective of this study is to determine the predict function of total cholesterol (TC) on the Triglyceride (TG)-lowing effect in patients on either non-PP or PP therapy.MethodsPatients were categorized into high total cholesterol (HTC)/low total cholesterol (LTC) groups based on TC level of 12.4 mmol/L. The primary outcome was TG reduction to below 500 mg/dL within 48 h. Linear mixed-effect model and logistic regression analyses were used to assess the association of TC level and TG-lowing efficacy in different therapy groups.ResultsCompared with LTC group, patients with HTC showed more severe imaging manifestations (p < 0.001) and higher APACH II scores (p = 0.036). Deaths occurred only in HTC groups. Significant interaction of time sequence with the 2 TGs-lowing therapy groups on TG level was only found in HTC group (p < 0.001). In patients with elevated TC level, primary outcome occurred in 66.67% of patients in the PP group, and 27.91% in the non-PP group. After adjustment for age, gender, CT grade and APACH II score, the odd ratio remain significant (OR 5.47, 95% confidence interval [CI] 1.84–16.25,p = 0.002). Furthermore, in patients with lower TC level, no significant difference was found in primary outcome between PP group and non-PP group (81.25% versus 62.30%, adjusted OR 2.05; 95% CI 0.45–9.40;p = 0.353).ConclusionsTC could be a potential biomarker to predict the effects of TG-lowing therapy in patients with HLAP.
Metabolic syndrome components and acute pancreatitis: a case–control study in China
Authors: Shen Zhemin , Wang Xueqiao , Zhen Zili , Wang Yao , Sun Peilong 
Published: January 2021

Abstract
Background
Acute pancreatitis (AP) is a common inflammatory disorder of the pancreas. Recent evidence has shown that metabolic syndrome is positively correlated with the severity of AP. However, only a few studies have revealed the relationship between metabolic syndrome and the occurrence of AP. We therefore elucidated the association between metabolic syndrome and the occurrence of AP.

Methods
A hospital-based case–control study was conducted. A total of 705 patients admitted to our hospital from January 2016 to December 2018 were included in the study. Subjects were divided into case and control groups according to their diagnosis: (1) According to the revised Atlanta classification from 2012, patients diagnosed with AP were enrolled in the case group. (2) Patients without a history of AP or any disease related to metabolic syndrome were allocated into the control group. Controls were matched to cases individually by sex and age (control/case ratio = 1).

Results
The incidence rate of metabolic syndrome in AP patients was 30.9%, which was more frequent than that in controls (13.2%) (OR 2.837; 95% CI 1.873–4.298, p < 0.001). In the multivariate regression analysis, a history of smoking or alcohol consumption and biliary stones were significantly associated with AP (OR 2.441; 95% CI 1.865–5.172, p < 0.001; OR 1.777; 95% CI 1.060–2.977, p = 0.029; OR 28.995; 95% CI 13.253–63.435, p < 0.001). In addition, the occurrence of AP was significantly associated with total cholesterol (TC) (OR 1.992; 95% CI 1.246–3.183, p = 0.004), triglyceride (TG) (OR 2.134; 95% CI 1.403–3.245, p < 0.001), hyperglycaemia (OR 2.261; 95% CI 1.367–3.742, p = 0.001), and apolipoprotein A (Apo A) (OR 0.270; 95% CI 0.163–0.447, p < 0.001).

Conclusions
Metabolic syndrome and its components were associated with AP occurrence.
Chronic active EBV infection in refractory enteritis with longitudinal ulcers with a cobblestone appearance: an autopsied case report
Authors: Aihara Yosuke , Moriya Kei , Shimozato Naotaka , Nagamatsu Shinsaku , Kobayashi Shinya , Uejima Masakazu , Matsuo Hideki , Ishida Eiwa , Yagi Hideo , Nakatani Toshiya , Yoshiji Hitoshi , Kikuchi Eiryo 
Published: January 2021

Abstract
Background
Chronic active Epstein–Barr virus infection (CAEBV) is defined as Epstein–Barr virus (EBV)-positive T/NK cell-related neoplasia, and its major clinical symptom is systemic inflammation presenting as infectious mononucleocytosis, whereas enteritis and diarrhea are minor clinical symptoms. The complex mixture of tumorigenic processes of EBV-positive cells and physical symptoms of systemic inflammatory disease constitutes the varied phenotypes of CAEBV. Herein, we describe a case of CAEBV that was initially diagnosed as Crohn’s disease (CD) based on ileal ulcers and clinical symptoms of enteritis.

Case presentation
A 19-year-old woman complained of abdominal pain and fever. Blood examination showed normal blood cell counts without atypical lymphocyte but detected modest inflammation, hypoalbuminemia, slight liver dysfunction, and evidence of past EBV infection. The esophagogastroduodenoscopic findings were normal. However, colonoscopy revealed a few small ulcers in the terminal ileum. The jejunum and ileum also exhibited various forms of ulcers, exhibiting a cobblestone appearance, on capsule endoscopy. Based on these clinical findings, she was strongly suspected with CD. In the course of treatment by steroid and biologics for refractory enteritis, skin ulcers appeared about 50 months after her initial hospital visit. Immunohistology of her skin biopsy revealed proliferation of EBV-encoded small RNA (EBER)-positive atypical lymphocytes. We retrospectively assessed her previous ileal ulcer biopsy before treatment and found many EBER-positive lymphocytes. Blood EBV DNA was also positive. Therefore, she was diagnosed with extranodal NK/T-cell lymphoma with CAEBV-related enteritis rather than CD. She was treated with cyclosporine and prednisolone combination therapy for CAEBV-related systemic inflammation and chemotherapy for malignant lymphoma. Unfortunately, her disease continued to progress, leading to multiple organ failure and death at the age of 23 years.

Conclusion
Clinicians need to remember the possibility of CAEBV as a differential diagnosis of refractory enteritis. Enteritis with intestinal ulcer is a rare symptom of CAEBV, and it is impossible to acquire a definitive diagnosis by ulcer morphology only. In cases where the possibility of CAEBV remains, tissue EBVR expression should be checked by in situ hybridization and blood EBV DNA.
Is acute kidney injury age-dependent in older adults: an observational study in two centers from North China
Authors:   on behalf of China collaborative study on AKI (CCS-AKI), Xu Libin , Wu Yanhua , Chen Yuanhan , Li Ruiying , Wang Zhiqiang , Li Zhilian , Liu Guoping , Yu Lei , Shi Wei , Liang Xinling 
Published: January 2021

Abstract
Background
Although aging increases susceptibility to acute kidney injury (AKI), whether the AKI risk and the association between AKI and adverse outcomes are age-dependent remain unclear in older adults. The current study aimed to identify whether AKI risk was age-dependent in older adults and to investigate whether the association between AKI and mortality increased with increasing age.

Methods
Medical records from 47,012 adult hospital admissions, including 30,194 older adults aged 60 or older, in two tertiary general hospitals were studied retrospectively. AKI was identified based on changes in blood creatinine levels according to the Kidney Disease: Improving Global Outcomes criteria.

Results
Among the total population and 30,194 older adult patients, the raw incidences of AKI were 8.2 and 8.3%, respectively. The curve of the age-grouped AKI incidence was “U-shaped”, which revealed a positive relationship between the AKI incidence and age among the older adults aged 75 years or older. This trend of the age-AKI relationship was supported by further multivariable analysis. After adjusting for the Charlson Comorbidity Index score, the AKI was associated with in-hospital mortality; however, the associations did not increase with increasing age.

Conclusion
The AKI risk does not increase with age in older adults, except for those aged 75 and above. The association between AKI and in-hospital death did not increase in an age-dependent manner in older adults.

Trial registration
This study was retrospectively registered at clinicaltrials.gov (NCT03054142) on February 13, 2017.
Age-related changes in postural control in older women: transitional tasks in step initiation
Authors: Michalska Justyna , Kamieniarz Anna , Sobota Grzegorz , Stania Magdalena , Juras Grzegorz , Słomka Kajetan J. 
Published: January 2021

Abstract
Background
Aging, being a natural process, involves many functional and structural changes within the body. Identifying the age-related postural changes will provide insight into the role of aging on postural control during locomotion. The aim of this study was to identify age-related postural changes during a transitional task under different conditions.

Methods
Sixty healthy females divided into three age groups: A (50-60 y/o), B (60-70 y/o), and C (70-80 y/o). The transitional task was measured by two force platforms. The procedure consisted of three phases: quiet standing, transfer onto a second platform, and quiet standing on the second platform. Four different conditions were applied: unperturbed transfer, obstacle crossing, step-up, and step-down. Double-support time, transit time, and stability time before and after the step task were analyzed.

Results
The transit time was longer by 30% for subjects over 70 y/o. The double-support time was longer by 11% among adults 60-70 y/o, while in people over 70 y/o it was longer by almost 50% compared to the 50-60 y/o subjects. The stability time before the transitional task was longer by 17% among adults over 60 y/o compared to middle-age subjects. The stability times before and after the transitional task were longer for adults in the 50-60 y/o category.

Conclusion
The proposed procedure is adequate for assessing age-related changes in postural control while undergoing a transitional task. An analysis of the double-support time and stability time before and after the step task enabled the detection of early signs of balance changes in middle-age adults. Independent of age, the transitional task parameters changed with the increasing difficulty of the tasks.