bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive analysis of NAC transcription factor family uncovers drought and salinity stress response in pearl millet (Pennisetum glaucum)&nbsp;
Authors: Dudhate Ambika , Shinde Harshraj , Yu Pei , Tsugama Daisuke , Gupta Shashi Kumar , Liu Shenkui , Takano Tetsuo 
Published: December 2020

Abstract
Background: Pearl millet (Pennisetum glaucum) is a cereal crop that possesses the ability to withstand drought, salinity and high temperature stresses. The NAC [NAM (No Apical Meristem), ATAF1 (Arabidopsis thaliana Activation Factor 1), and CUC2 (Cup-shaped Cotyledon)] transcription factor family is one of the largest transcription factor families in plants. NAC family members are known to regulate plant growth and abiotic stress response. Currently, no reports are available on the functions of the NAC family in pearl millet. Results: Our genome-wide analysis found 151 NAC transcription factor genes (PgNACs) in the pearl millet genome. Thirty-eight and 76 PgNACs were found to be segmental and dispersed duplicated respectively. Phylogenetic analysis divided these NAC transcription factors into 11 groups (A-K). Three PgNACs (-073, -29, and -151) were found to be membrane-associated transcription factors. Seventeen other conserved motifs were found in PgNACs. Based on the similarity of PgNACs to NAC proteins in other species, the functions of PgNACs were predicted. In total, 88 microRNA target sites were predicted in 59 PgNACs. A previously performed transcriptome analysis suggests that the expression of 30 and 42 PgNACs are affected by salinity stress and drought stress, respectively. The expression of 36 randomly selected PgNACs were examined by quantitative reverse transcription-PCR. Many of these genes showed diverse salt- and drought-responsive expression patterns in roots and leaves. These results confirm that PgNACs are potentially involved in regulating abiotic stress tolerance in pearl millet.Conclusion: The pearl millet genome contains 151 NAC transcription factor genes that can be classified into 11 groups. Many of these genes are either upregulated or downregulated by either salinity or drought stress and may therefore contribute to establishing stress tolerance in pearl millet.
Predicting Osteoporosis with Body Compositions in Postmenopausal Women: A Noninvasive Method
Authors: Hsu Wei-Hsiu , Hsu Wei-Bin , Fan Chun-Hao , Hsu Wen-Wei Robert 
Published: December 2020

Abstract
Background: The prevalence of osteoporosis is rising steadily as the aging population increases. Bone mineral density (BMD) assessment is an established test for osteoporosis. However, the accessibility and radiation exposure limited its role in community screening. A more convenient approach for screening is suggested.Methods: A total of 363 postmenopausal women over 50 age were included in this study and assessed with the body composition [including fat-free mass (FFM), fat mass (FM), and basal metabolic rate (BMR)] and BMD. Normal distributions and correlation coefficients among variables were calculated using the Shapiro-Wilk test and Pearson’s correlation analysis, respectively. A receiver operating characteristic (ROC) curve was plotted and the area under ROC curves (AUC) was determined the optimal cut-off values of the body composition variables for osteoporosis prediction.Results: The correlation coefficient of FFM, FM, FM ratio and BMR with femur neck T-score were 0.373, 0.266, 0.165, and 0.369, respectively while with spine T-score were 0.350, 0.251, 0.166, and 0.352, respectively (p<0.01 for all). FFM, FM, and BMR showed an optimal cut-off value of 37.9 kg, 18.6 kg, and 1187.5 kcal for detecting osteoporosis.Conclusions: The present study provided a model to predict osteoporosis in postmenopausal women and the optimal cut-off value of FFM, FM, and BMR could be calculated in Asian population. Among these factors, BMR seemed a better predictor than others. The BMR could be a target for exercise intervention in postmenopausal women for maintaining or improving BMD.Trial registration: ClinicalTrials.gov, NCT02936336. Registered 13 October 2016 -Retrospectively registered
Post-status epilepticus treatment with the Fyn inhibitor, saracatinib, improves cognitive function in mice
Authors: Luo Xinming , Zhao Jing , Wu Wenyue , Fu Jie , Li Zhengyu , Zhang Ming , Lu Jie 
Published: December 2020

Abstract
BackgroundStatus epilepticus (SE) is a life-threatening neurological disorder. The hippocampus, as an important area of the brain that regulates cognitive function, is usually damaged after SE, and cognitive deficits often result from hippocampal neurons lost after SE. Fyn, a non-receptor Src family of tyrosine kinases, is potentially associated with the onset of seizure. Saracatinib, a Fyn inhibitor, suppresses epileptogenesis and reduces epileptiform spikes. However, whether saracatinib inhibits cognitive deficits after SE is still unknown.MethodsIn the present study, a pilocarpine-induced SE mouse model was used to answer this question by using the Morris water maze and normal object recognition behavioral tests.ResultsWe found that saracatinib inhibited the loss in cognitive function following SE. Furthermore, we found that the number of hippocampal neurons in the saracatinib treatment group was increased, when compared to the SE group.ConclusionsThese results showed that saracatinib can improve cognitive functions by reducing the loss of hippocampal neurons after SE, suggesting that Fyn dysfunction is involved in cognitive deficits after SE, and that the inhibition of Fyn is a possible treatment to improve cognitive function in SE patients.
NMFNA: a non-negative matrix factorization network analysis method for identifying communities and characteristic genes from pancreatic cancer data
Authors: Ding Qian , Sun Yan , Shang Junliang , Li Feng , Zhang Yuanyuan , Liu Jin-Xing 
Published: December 2020

Abstract
Background: Pancreatic cancer (PC) is a common type of digestive system disease. Comprehensive analysis of different types of PC genetic data plays a crucial role in understanding its biological mechanisms. Currently, Non-negative Matrix Factorization (NMF) based methods are widely used for data analysis. Nevertheless, it is a challenge for them to integrate and decompose different types of data simultaneously.Results: In this paper, a Non-negative Matrix Factorization Network Analysis method, NMFNA, is proposed, which introduces a graph regularized constraint to NMF, for identifying communities and characteristic genes from two-type PC data. Firstly, three PC networks, i.e., methylation network (ME), copy number variation network (CNV), and the bipartite network between them, are constructed by both ME and CNV data of PC downloaded from the TCGA database, using the Pearson Correlation Coefficient. Then, the NMFNA is proposed to detect core communities and characteristic genes from these three PC networks effectively due to its introduced graph regularized constraint, which is the highlight of NMFNA. Finally, both gene ontology enrichment analysis and pathway enrichment analysis are performed to deeply understand the biological functions of detected core communities.Conclusions: Experimental results demonstrated that the NMFNA facilitates the integration and decomposition of two types of PC data simultaneously and can serve as an alternative method for detecting communities and characteristic genes from multiple genetic networks. The data and demo codes of NMFNA are available online at https://github.com/CDMB-lab/NMFNA.
Genomic outcomes from diverse SNP panels obtained with different de novo building-loci pipelines in a varied species context: Can pipelines be influencing biological interpretations?
Authors: Casanova Adrian , Maroso Francesco , Blanco Andrés , Hermida Miguel , Rios Nestor , Garcia Graciela , Manuzzi Alice , Zane Lorenzo , Verissimo Ana , Garcia-Marin Jose-Luis , Bouza Carmen , Vera Manuel , Martinez Paulino 
Published: December 2020

Abstract
Background: The irruption of Next-generation sequencing (NGS) and restriction site-associated DNA sequencing (RAD-seq) in the last decade has led to the identification of thousands of molecular markers and their genotyping for refined genomic screening. This approach has been especially useful for non-model organisms with limited genomic resources. Many building-loci pipelines have been developed to obtain robust single nucleotide polymorphism (SNPs) genotyping datasets using a de novo RAD-seq approach, i.e. without reference genomes. Here, the performances of two building-loci pipelines, STACKS 2 and Meyer’s 2b-RAD v2.1 pipeline, were compared using a diverse set of aquatic species representing different genomic and/or population structure scenarios. Two bivalve species (Manila clam and common edible cockle) and three fish species (brown trout, silver catfish and small-spotted catshark) were studied. Four SNP panels were evaluated in each species to test both different building-loci pipelines and criteria for SNP selection. Furthermore, for Manila clam and brown trout, a reference genome approach was used as control. Results: Despite different outcomes were observed between pipelines and species with the diverse SNP calling and filtering steps tested, no remarkable differences were found on genetic diversity and differentiation within species with the SNP panels obtained with a de novo approach. The main differences were found in brown trout between the de novo and reference genome approaches. Genotyped vs missing data mismatches were the main genotyping difference detected between the two building-loci pipelines or between the de novo and reference genome comparisons. Conclusions: Tested building-loci pipelines seem not to have a substantial influence on population genetics inference. Preliminary trials with bioinformatic pipelines are suggested to evaluate their influence in population parameters related to the specific goals of the study.
Electrochemical p erformance of La2NiO4+δ-Ce0.55La0.45O2-δ as a promising bifunctional oxygen electrode for reversible solid oxide cells
Authors: Li Pengzhang , Yang Wei , Tian Chuanjin , Zhao Wenyan , Lü Zhe , Xie Zhipeng , Wang Chang-An 
Published: December 2020

Abstract
In this work, La2NiO4+δ-xCe0.55La0.45O2-δ (denoted as LNO-xLDC) with various LDC contents (x = 0, 10, 20, 30 and 40, wt %) were prepared and evaluated as bifunctional oxygen electrodes for reversible solid oxide cells (RSOCs). Compared with the pure LNO, the optimum composition of LNO-30LDC exhibited the lowest polarization resistance (Rp) of 0.53 and 0.12 Ω·cm2 in air at 650 and 750 oC, respectively. The enhanced electrochemical performance of LNO-30LDC oxygen electrode was mainly attributed to the extended triple phase boundary and more oxygen ionic transfer channels. The hydrogen electrode supported single cell with LNO-30LDC oxygen electrode displayed peak power densities of 276, 401 and 521 mW·cm-2 at 700, 750 and 800 oC, respectively. Moreover, the electrolysis current density of the single cell demonstrated 526.39 mA·cm-2 under 1.5 V at 800 oC, and the corresponding hydrogen production rate was 220.03 ml·cm-2·h-1. The encouraging results indicated that LNO-30LDC was a promising bifunctional oxygen electrode material for RSOCs.
Maternal DHA supplementation influences sex-specific disruption of placental gene expression following early prenatal stress
Authors: Jašarević Eldin , Hecht Patrick M. , Fritsche Kevin L. , Geary David C. , Rivera Rocío M. , Beversdorf David 
Published: December 2020

Abstract
Early life adversity is widely recognized as a key risk factor for early developmental perturbations and contributes to the presentation of neuropsychiatric disorders in adulthood. Neurodevelopmental disorders exhibit a strong sex-bias in susceptibility, presentation, onset and severity, although the underlying mechanisms conferring vulnerability are not well understood. Environmental perturbations during pregnancy, such as malnutrition or stress, have been associated with sex-specific reprogramming that contribute to increased disease risk in adulthood, whereby stress and nutritional insufficiency may be additive and further exacerbate poor offspring outcomes. To determine whether maternal supplementation of docosahexanoic acid (DHA) exerts an effect on offspring outcome following exposure to early prenatal stress (EPS), dams were fed a purified 10:1 omega-6/omega-3 diet supplemented with either 1.0% preformed DHA/kg feed weight (DHA-enriched) or no additional DHA (denoted as the control diet, CTL). Dams were administered chronic variable stress during the first week of pregnancy (Embryonic day, E0.5 – 7.5) and developmental milestones were assessed at E 12.5. Exposure to early prenatal stress (EPS) decreased placenta and embryo weight in males, but not females, exposed to the CTL diet. DHA-enrichment reversed the sex-specific decrease in placenta and embryo weight following EPS. Early prenatal exposure upregulated expression of genes associated with oxygen and nutrient transport, including hypoxia inducible factor 3α (HIF3α), peroxisome proliferator-activated receptor alpha (PPARα), and insulin like growth binding factor 1 (IGFBP1), in placenta of CTL diet males exposed to EPS. DHA-enrichment in EPS-exposed animals abrogated the male-specific upregulation of PPARα, HIF3α, and IGFBP1. Taken together, these studies suggest that maternal dietary DHA enrichment may buffer against maternal stress programming of sex-specific outcomes during early development.
Genome-wide identification of GH3 genes in Brassica oleracea and identification of a promoter region for anther-specific expression of a GH3 gene
Authors: Jeong Jiseong , Park Sunhee , Im Jeong Hui , Yi Hankuil 
Published: December 2020

Abstract
Background: The Gretchen Hagen 3 ( GH3 ) genes encode acyl acid amido synthetases, many of which have been shown to modulate the amount of active plant hormones or their precursors. GH3 genes, especially Group Ⅲ subgroup 6 GH3 genes, and their expression patterns in economically important B. oleracea var. oleracea have not been systematically identified. Results: As a first step to understand regulation and molecular functions of Group Ⅲ subgroup 6 GH3 genes, 34 GH3 genes including four subgroup 6 genes were identified in B. oleracea var. oleracea . Synteny found around subgroup 6 GH3 genes in B. oleracea var. oleracea and Arabidopsis thaliana indicated that these genes are evolutionarily related. Although expression of four subgroup 6 GH3 genes in B. oleracea var. oleracea is not induced by auxin, gibberellic acid, or jasmonic acid, the genes show different organ-dependent expression patterns. Among subgroup 6 GH3 genes in B. oleracea var. oleracea , only BoGH3.13-1 is expressed in anthers when microspores, polarized microspores, and bicellular pollens are present, similar to two out of four syntenic A. thaliana subgroup 6 GH3 genes. Detailed analyses of promoter activities further showed that BoGH3.13-1 is expressed in tapetal cells and pollens in anther, and also expressed in leaf primordia and floral abscission zones. Conclusions: Sixty-two base pairs (bp) region (-340 ~ -279 bp upstream from start codon) and about 450 bp region (-1489 to -1017 bp) in BoGH3.13-1 promoter are important for expressions in anther and expressions in leaf primordia and floral abscission zones, respectively. The identified anther-specific promoter region can be used to develop male sterile transgenic Brassica plants.
Cloning, Characterization, and Expression Features of Chicken CDS2 Splicing Variants
Authors: Xu Yuanyuan , Zhang Shuping , Guo Yujun , Chen Wen , Huang Yanqun 
Published: December 2020

Abstract
Background: The CDS gene encodes the CDP-diacylglycerol synthase enzyme that catalyzes the formation of CDP-diacylglycerol (CDP-DAG) from phosphatidic acid. At present, there are no reports of CDS2 in birds. Here, we identified chicken CDS2 transcripts by combining conventional RT- PCR amplification, 5' RACE (Fig. 1A), and 3' RACE, explored the spatio-temporal expression profiles of total CDS2 and the longest transcript variant CDS2-4, and investigated the effect of exogenous insulin on total the mRNA level of CDS2 by quantitative real-time PCR. Results: Four transcripts of chicken CDS2 (CDS2-1, -2, -3, and -4) were identified, which were alternatively spliced at the 3′-untranslated region (UTR). CDS2 was widely expressed in all tissues examined and the longest variant CDS2-4 was the major transcript. Both total CDS2 and CDS2-4 were prominently expressed in adipose tissue and the heart, and exhibited low expression in the liver and pectoralis of 49 day-old chickens. Quantitative real-time PCR revealed that total CDS2 and CDS2-4 had different spatio-temporal expression patterns in chicken. Total CDS2 exhibited a similar temporal expression tendency with a high level in the later period of incubation (embryonic day 19 [E19] or 1-day-old) in the brain, liver, and pectoralis. While CDS2-4 presented a distinct temporal expression pattern in these tissues, CDS2-4 levels peaked at 21 days in the brain and pectoralis, while liver CDS2-4 mRNA levels were highest at the early stage of hatching (E10). Total CDS2 (P < 0.001) and CDS2-4 (P = 0.0090) mRNA levels in the liver were differentially regulated throughout development of the chicken. Exogenous insulin significantly downregulated the level of total CDS2 at 240 min in the pectoralis of Silky chickens (P < 0.01). Total CDS2 levels in the liver of Silky chickens were higher than that of the broiler in the basal state and after insulin stimulation. Conclusion: Chicken CDS2 has multiple transcripts with variation at the 3′-UTR, which was prominently expressed in adipose tissue. Total CDS2 and CDS2-4 presented distinct spatio-temporal expression patterns, and they were differentially regulated with age in liver. Insulin could regulate chicken CDS2 levels in a breed- and tissue-specific manner.
Disease Burden from Coronavirus Disease 2019 Symptoms Among Inpatients at the Temporary Military Hospitals in Wuhan: A Retrospective Multi-Center Cross-Sectional Study
Authors: He Mai-hong , Li Xiao-xiao , Tan Qing , Yong Chen , Yue Kong , You Jian-ping , Lin Xian , Lin Ying , Qing Zheng 
Published: December 2020

Abstract
Background: Since the advent of the coronavirus disease 2019 (COVID-19) pandemic, in most parts of the world, people are still at risk of the disease. We aimed to establish a set of disability weights (DWs) for COVID-19 symptoms, evaluate the disease burden of inpatients, analyze the characteristics, and influencing factors of the disease. Methods: The symptoms were identified by literature review and medical staff questionnaire. DWs of COVID-19 symptoms were determined by the person-trade-off approach proposed by the World Health Organization. The extracted medical records data of 2,702 randomly selected inpatients with COVID-19 at three temporary military hospitals in Wuhan, China, were analyzed and used to calculate the disability adjusted life years (DALY). Means DALY between gender and age groups were tested by analysis of variance. Multiple line regression models were used to determine the relationship between DALY and age, gender, body mass index, length of stay, symptom duration before admission, and native place. Results: For the DALY of each inpatient, severe expiratory dyspnea and mild cough and sore throat had the highest (0.399) and lowest (0.004) weights, respectively. The average synthetic DALY and daily DALY were 2.29±1.33 and 0.18±0.15 days, respectively. Fever and fatigue contributed the largest DALY at 31.36%; nausea and vomiting, and anxiety and depression contributed the least at 7.05%. There were significant differences between gender and age groups in both synthetic and daily DALY. Age, body mass index, length of stay, and symptom duration before admission were strongly related to both synthetic and daily DALY. Conclusions: COVID-19 and its symptoms could cause heavy disease burden. Although the disease burden was higher among females than in the males; however, their daily disease burdens were similar. Life value differs for different age groups; taking the changing life value with age into account; the disease burden in the younger population was higher than that in the older population. Besides, treatment at the hospitals relieved the disease burden efficiently, while delay in hospitalization could worsen it. Therefore, deployment of adequate medical resources for early hospitalization of patients with moderate or severe symptoms is needed by the public health authority.
Hydrolysis products from sockeye (Oncorhynchus nerka L.) heads from the Kamchatka Peninsula produced by different methods: biological value
Authors: Volkov Vladimir , Mezenova Olga , Moersel Joerg-Thomas , Kuehn Sascha , Grimm Thomas , Hoehling Axel , Barabanov Sergei , Volkov Kirill 
Published: December 2020

Introduction. Sockeye salmon (Oncorhynchus nerka L.) is a valuable Pacific salmon. Sockeye heads are a significant share in processing sockeye salmon. Traditionally, fish by-products are used to make fishmeal. However, due to the high content of collagen proteins and fat in sockeye salmon heads, it is difficult to produce fishmeal from this raw material. Controlled enzymatic or combined hydrolysis allows protein, fat, and minerals to be extracted to supply the market with higher value products with desirable features. This research was aimed to analyse the chemical composition and biological value of hydrolysis products obtained from sockeye heads.
Study objects and methods. We investigated hydrolysis products of sockeye salmon heads, namely protein hydrolysates, fat and sludge. Thermal hydrolysis and enzymatic-thermal hydrolysis were used for the tests. Thermal hydrolysis was realized in reactor. For enzymatic-thermal hydrolysis, the raw material was pre-treated by proteolytic enzyme Alcalase. The hydrolysates obtained were investigated. Chemical composition was determined in accordance with State Standard 7636-85. HPLC was used for molecular weight and amino acid analysis. Gas chromatography was used for fatty acid analysis. Biological value of proteins was determined by the balance of the amino acid composition comparing it with the “ideal protein model”.
Results and discussion. Thermal hydrolysis resulted in the production of protein hydrolysate powder with protein content of 92.0% dry matter and a protein recovery rate of 39.6%. Combined hydrolysis resulted in the production of protein hydrolysate powder with protein content of 92.6% and a protein recovery rate of 83%. All protein hydrolysates contained all essential amino acids. The biological value of protein hydrolysate obtained by thermal and combined hydrolysis was 80.1 and 82.8%, respectively.
Conclusion. Hydrolysed products obtained by thermal and enzymatic-thermal hydrolysis had a valuable chemical composition and could be recommended for food and feed use.