bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in bowel sounds of inpatients undergoing general anesthesia
Authors: Wang Guojing , Wang Mingjun , Liu Hongyun , Zhao Suping , Liu Lu , Wang Weidong 
Published: July 2020

Abstract
Background: General anesthesia can affect intestinal function, but there is no objective, practical and effective indicator to evaluate the inhibition and recovery of intestinal function. The main objectives of this study were to assess whether bowel sounds (BSs) changed before, immediately after and 3 hours after general anesthesia, and whether these changes in BSs are an effective indicator of intestinal function and an accurate guide for post-operative feeding. Methods: We randomly selected 26 inpatients and collected three sets of 5-minute continuous BS data before the operation (Pre-op), immediately after the operation (Pro-op) and three hours after the operation (3h-Pro-op) for each patient. Then the linear and nonlinear characteristic values (CVs) of each effective bowel sound were extracted and paired t-tests and rank-sum tests were used to evaluate the changes in the BSs. Results: The differences in CVs, between Pre-op and Pro-op, as well as between Pro-op and 3h-Pro-op, were statistically significant (p <0.05). However, there is no statistically significant differences between all the CVs between Pre-op and 3h-Pro-op (p >0.05). Conclusion: BSs changes before and after general anesthesia. Furthermore, the BSs are weakened due to general anesthesia and recover to the pre-op state three hours later. Therefore, the BSs can be an indicator of intestinal function under general anesthesia, so as to provide guidance for postoperative feeding, which is of considerable clinical significance.
Inference about Time-dependent Prognostic Accuracy Measures in the Presence of Competing Risks
Authors: Dey Rajib , Sebastiani Giada , Saha-Chaudhuri Paramita 
Published: July 2020

Abstract
Background: Evaluating a candidate marker or developing a model for predicting risk of future conditions is one of the major goals in medicine. However, model development and assessment for a time-to-event outcome may be complicated in the presence of competing risks. In this manuscript, we propose local and global estimators of cause-specific AUC for right-censored survival times in the presence of competing risks. Methods: The local estimator - cause-specific weighted mean rank (cWMR) - is a local average of time-specific observed cause-specific AUCs within a neighborhood of given time t. The global estimator - cause-specific fractional polynomials (cFPL) - is based on modelling the cause-specific AUC as a function of t through fractional polynomials. Results: We investigated the performance of the proposed cWMR and cFPL estimators through simulation studies and real-life data analysis. The estimators perform well in small samples, have minimal bias and appropriate coverage. Conclusions: The local estimator cWMR and the global estimator cFPL will provide computationally efficient options for assessing the prognostic accuracy of markers for time-to-event outcome in the presence of competing risks in many practical settings.
Predictive values of ANGPTL8 on risk of all-cause mortality in diabetic patients: results from the REACTION Study
Authors: Zou Huajie , Xu Yongping , Chen Xi , Yin Ping , Li Danpei , Li Wenjun , Xie Junhui , Shao Shiying , Liu Liegang , Yu Xuefeng 
Published: July 2020

Abstract
Background: ANGPTL8, an important regulator of lipid metabolism, is increased in diabetes and is associated with insulin resistance. However, the role of ANGPTL8 in the outcomes of diabetic patients remains unclear. This study aimed to investigate circulating levels of ANGPTL8 in participants with and without diabetes and its potential associations with clinical outcomes in a 5-year cohort study.Methods: Propensity-matched cohorts of subjects with and without diabetes from the Risk Evaluation of Cancers in Chinese Diabetic Individuals: A longitudinal (REACTION) study were generated on the basis of age, sex and body mass index at baseline. The primary outcome was all-cause mortality. The secondary outcomes were a composite of new-onset major adverse cardiovascular events, hospitalization for heart failure, and renal dysfunction (eGFR <60/min/1.73 m2).Results: We identified 769 matched pairs of diabetic patients and control subjects. Serum ANGPTL8 levels were elevated in patients with diabetes compared to control subjects (618.82 318.08 vs 581.20 299.54 pg/mL, p =0.03). Binary logistic regression analysis showed that elevated ANGPTL8 levels were associated with greater risk ratios (RRs) of death (RR in quartile 4 vs quartile 1, 3.54; 95% CI 1.32 – 9.50) and renal dysfunction (RR in quartile 4 vs quartile 1, 12.43; 95% CI 1.48 – 104.81) only in diabetic patients. Multivariable-adjusted restricted cubic spline analyses revealed a significant, linear relationship between ANGPTL8 and all-cause mortality in diabetic patients (p for nonlinear trend =0.99, p for linear trend =0.01) but not in control subjects (p for nonlinear trend =0.26, p for linear trend =0.80). According to ROC curve analysis, the inclusion of ANGPTL8 in QFrailty score significantly improved its predictive performance for mortality in patients with diabetes. Conclusion: Serum ANGPTL8 levels were associated with an increased risk of all-cause mortality and could be used as a potential biomarker for the prediction of death in patients with diabetes.
Functional characterization of mungbean CONSTANS-LIKE genes reveals a key role for CONSTANS-LIKE 2 in the control of flowering time in A. thaliana under short-day conditions
Authors: Liu Chenyang , Zhang Qianqian , Zhu Hong , Cai Chunmei , Li Shuai 
Published: July 2020

Abstract
Background: CONSTANS-LIKE (COL) genes play important roles in the regulation of plant growth and development, and they have been analyzed in many plant species. However, few investigations have examined COL genes in mungbean (Vigna radiata).Results: In this study, we identified and characterized a total 14 of VrCOL genes from mungbean, which distributed on 7 of the 11 mungbean chromosomes. Based on their conserved domains, VrCOLs were clustered into three groups (I, II and III), which contained 4, 5 and 5 members, respectively. The gene structures and conserved motifs of the VrCOL genes were analyzed, and two duplicated gene pairs, VrCOL1/VrCOL2 and VrCOL8/VrCOL9, were identified. A total of 82 cis-acting elements were found in the VrCOL promoter regions, and the numbers and types of cis-acting elements in each VrCOL promoter region differed. As a result, the expression patterns of VrCOLs varied in different tissues, and under long day and short day conations throughout the day. Among these VrCOL genes, VrCOL2 showed a close phylogenetic relationship with Arabidopsis thaliana (A. thaliana) CO and displayed daily oscillations in expression under short day conditions but not long day conditions. In addition, overexpression of VrCOL2 accelerated flowering in A. thaliana under short day conditions by activating the expression of flowering time gene AtFT and AtTSF.Conclusion: Overall, we identified 14 VrCOL genes from mungbean using genome-wide identification. Characteristics and transcription pattern analysis of VrCOL genes revealed their important roles in plant growth and development, and our results suggested that VrCOL2 regulate flowering time under short day conditions in A. thaliana. Our study lays the foundation for further dissection of VrCOL gene functions.
Two Weeks Of Western Diet Disrupts Liver Molecular Markers Of Cholesterol Metabolism In Rat
Authors: St-Amand Roxane , Sock Emilienne T. Ngo , Quinn Samantha , Lavoie Jean-Marc , St-Pierre David H. 
Published: July 2020

Abstract
Background: The present study was designed to test the hypothesis that in the liver, excessive fat accumulation impairs cholesterol metabolism mainly by altering the low-density lipoprotein-receptor (LDL-R) pathway. Method: Young male Wistar rats were fed standard (SD), high fat (HFD; 60% kcal) or Western (WD; 40% fat + 35% sucrose (17.5% fructose)) diets for 2 or 6 weeks. Results: Weight gain (~ 40g) was observed only following 6 weeks of the obesogenic diets (P < 0.01). Compared to the 2-week treatment, obesogenic diets tripled fat pad weight (~ 20 vs 7 g) after 6 weeks. Hepatic triglyceride (TG) levels were greater in response to both the WD and HFD compared to the SD (P < 0.01) at 2 and 6 weeks and their concentrations were greater (P < 0.05) in WD than HFD at 2 weeks. Plasma total cholesterol levels were higher (P < 0.05) in animals submitted to WD. After 2 and 6 weeks, liver expression of LDL-R, proprotein convertase subtilisin/kexin 9 (PCSKk9) and sterol regulatory element binding protein 2 (SREBP2), involved in LDL-cholesterol uptake, was lower in animals submitted to WD than in others treated with HFD or SD (P < 0.01). Similarly, low-density lipoprotein-receptor-related protein 1 (LRP1) and acyl-CoA cholesterol acyltransferase-2 (ACAT-2) mRNA levels were lower (P < 0.01) among WD compared to SD-fed rats. Expression of the gene coding the main regulator of endogenous cholesterol synthesis, 3-hydroxy-3-methyl-glutaryl-CoA reductase (HMGCoAR) was reduced in response to WD compared to SD and HFD at 2 (P < 0.001) and 6 (P < 0.05) weeks. Being enriched in fructose, the WD strongly promoted the expression of carbohydrate-response element binding protein (ChREBP) and acetyl-CoA carboxylase (ACC), two key regulators of de novo lipogenesis. Conclusion: These results show that the WD promptly increased TG levels in the liver by potentiating fat storage. This impaired the pathway of hepatic cholesterol uptake via the LDL-R axis, promoting a rapid increase in plasma total cholesterol levels. These results indicate that liver fat content is a factor involved in the regulation of plasma cholesterol.
Metalloproteins and apolipoprotein C: candidate plasma biomarkers of T2DM screened by comparative proteomics and lipidomics in ZDF rats
Authors: Wang Shuai , Lu Zhiyuan , Wang Yuxin , Zhang Tianran , He Xiaodong 
Published: July 2020

Abstract
Background: Early diagnosis of type 2 diabetes mellitus (T2DM) is still difficult. Screening of plasma biomarkers has great significance of optimizing diagnosis and predicting the complications of T2DM.Methods: We used a special diet, Purina #5008, to induce diabetes in Zucker leptin receptor gene-deficient rats (fa/fa) to establish Zucker diabetic fatty (ZDF) rats, simulating the early stage of T2DM. The differentially expressed proteins (DEP) and lipids (DEL), as potential biomarkers, were screened to compare the plasma expression levels in ZDF rats and their basic diet-fed wild-type controls (fa/+) by Tandem Mass Tags (TMT) and liquid chromatography-tandem mass spectrometry.Results: These two groups had different plasma proteins and lipids profiles consisting of 84 DEPs and, 179 DELs identified in the positive ion mode and 178 DELs in the negative ion mode, respectively. Enrichment analysis of these different indicators showed that oxidative stress, insulin resistance and metabolic disorders of glycan and lipid played an important role in generating the difference. Some markers can be used as candidate biomarkers in prediction and treatments of T2DM, such as ceruloplasmin, apolipoprotein C-I, apolipoprotein C-II, apolipoprotein C-IV.Conclusion: These plasma differences help to optimize the diagnosis and predict the complications of T2DM, although this remains to be verified in the crowd. Trace elements related-metalloproteins, such as ceruloplasmin, and lipid metabolism and transport-related apolipoprotein C are expected to be candidate biomarkers of T2DM and should be given more attention.
Genome-wide association study and Mendelian randomization analysis provide insights for improving rice yield potential
Authors: Su Jing , Xu Kai , Wu Chao , Li Zirong , Hu Zhongli , Zheng Xingfei , Song Shufeng , Tang Wenbang , Tang Zhonghai , Li Lanzhi 
Published: July 2020

Abstract
Background: Rice yield has a complex genetic architecture, which mainly determined by its three component traits: the number of grains per panicle (GPP), kilo-grain weight (KGW) and tillers per plant (TP). Exploring ideotype breeding based on selection for genetically less complex component traits is an alternative route for further improving rice production. Thus, it is important that studying the genetic basis of relationship between rice yield and component traits and selecting the component traits to improve the rice production. Main text: In this study, we carried out meta-analyses of genome-wide association study (Meta-GWAS) with two populations (575 + 1495 F1) in different environments for yield and its three component traits in rice. 3589 significant loci for three components traits were detected, while only 3 significant loci for yield were detected. It indicated that rice yield is mainly controlled by minor-effect loci and hardly to be identified. Selecting quantitative trait locus (QTL)/gene affected component traits to further enhance yield is recommended. Mendelian randomization (MR) design was adopted to investigate the genetic effects of loci on yield through component traits and estimate the genetic relationship between rice yield and its component traits by these loci. The loci for GPP or TP mainly had a positive genetic effect on yield, but the loci for KGW with different direction of effects (positive effect or negative effect). Additionally, TP (Beta=1.865) has a greater effect on yield than KGW (Beta=1.016) and GPP (Beta=0.086). Five significant loci for component traits with indirect effect on yield were identified. Pyramiding superior alleles of the five loci revealed improved yield. A combination of direct and indirect effects may better contribute to the yield potential of rice.Conclusions: Our findings provided a rationale for using component traits as indirect indices to enhanced rice yield, which will be helpful for further understanding the genetic basis of yield, and provide valuable information for improving rice yield potential.
Transcriptomic profiling of germinating seeds under cold stress and characterization of the cold-tolerant gene LTG5 in rice
Authors: Pan Yinghua , Liang Haifu , Gao Lijun , Dai Gaoxing , Chen Weiwei , Yang Xinghai , Qing Dongjin , Gao Ju , Wu Hao , Huang Juan , Zhou Weiyong , Huang Chengcui , Liang Yuntao , Deng Guofu 
Published: July 2020

Abstract
Background: Low temperature is a limiting factor of rice productivity and geographical distribution. Wild rice (Oryza rufipogon Griff.) is an important germplasm resource for rice improvement. It has superior tolerance to many abiotic stresses, including cold stress, but little is known about the mechanism underlying its resistance to cold. Results: This study elucidated the molecular genetic mechanisms of wild rice in tolerating low temperature. Comprehensive transcriptome profiles of two rice genotypes (cold-sensitive ce 253 and cold-tolerant Y12-4) at the germinating stage under cold stress were comparatively analyzed. A total of 42.44–68.71 million readings were obtained, resulting in the alignment of 29 128 and 30 131 genes in genotypes 253 and Y12-4, respectively. Many common and differentially expressed genes (DEGs) were analyzed in the cold-sensitive and cold-tolerant genotypes. Results showed more upregulated DEGs in the cold-tolerant genotype than in the cold-sensitive genotype at four stages under cold stress. Gene ontology enrichment analyses based on cellular process, metabolic process, response stimulus, membrane part, and catalytic activity indicated more upregulated genes than downregulated ones in the cold-tolerant genotype than in the cold-sensitive genotype. Quantitative real-time polymerase chain reaction was performed on seven randomly selected DEGs to confirm the RNA Sequencing (RNA-seq) data. These genes showed similar expression patterns corresponding with the RNA-Seq method. Weighted gene co-expression network analysis（WGCNA）revealed Y12-4 showed more positive genes than 253 under cold stress. We also explored the cold tolerance gene LTG5 (Low Temperature Growth 5) encoding a UDP-glucosyltransferase. The overexpression of the LTG5 gene conferred cold tolerance to indica rice. Conclusion: Gene resources related to cold stress from wild rice can be valuable for improving the cold tolerance of crops.
Malaria outbreak in Riaba district, Bioko Island – Lessons learned
Authors: Guerra Carlos A , Fuseini Godwin , Donfack Oliver Tresor , Smith Jordan M , Mifumu Teresa Ayingono Ondo , Akadiri Gninoussa , Eyang Delicias Esono Mba , Eburi Consuelo Oki , Vaz Liberato Motobe , Micha Víctor Mba , Okenve Leonor Ada , Janes Christopher R , Andeme Ramona Mba , Rivas Matilde Riloha , Phiri Wonder P , Slotman Michel A , Smith Dave L , García Guillermo Alberto 
Published: July 2020

Abstract
At the beginning of 2019, a sudden surge of malaria cases was observed in the district of Riaba, Bioko Island. Between January and April, confirmed malaria cases increased 3.8-fold compared to the same period in 2018. Concurrently, anopheline human biting rate (HBR) increased 2.1-fold. During the outbreak, 82.2% of the district population was tested for malaria with a rapid diagnostic test; 37.2% of those tested had a detectable infection and were treated according to national guidelines. Vector control interventions, including indoor residual spraying and larval source management were scaled-up. After the interventions, the number of confirmed cases decreased by 70% and the overall parasite prevalence in the communities by 43.8%. Observed prevalence in a follow up malaria indicator survey, however, was significantly higher than elsewhere on the island, and higher than in previous years. There was no significant reduction in HBR, which remained high for the rest of the year. The surge was attributed to various factors, chiefly increased rainfall and a large number of anthropogenic anopheline breeding sites created by construction works. This case study highlights the need for sustained vector control interventions and multi-sector participation, particularly in malaria control and elimination settings with persistently high local malaria receptivity.
Hill-based dissimilarity indices and null models for analysis of microbial community assembly
Authors: Modin Oskar , Liébana Raquel , Saheb-Alam Soroush , Wilén Britt-Marie , Suarez Carolina , Hermansson Malte , Persson Frank 
Published: July 2020

Abstract
Background: High-throughput amplicon sequencing of marker genes, such as the 16S rRNA gene in Bacteria and Archaea, provides a wealth of information about the composition of microbial communities. To quantify differences between samples and draw conclusions about factors affecting community assembly, dissimilarity indices are typically used. However, results are subject to several biases and data interpretation can be challenging. The Jaccard and Bray-Curtis indices, which are often used to quantify taxonomic dissimilarity, are not necessarily the most logical choices. Instead, we argue that Hill-based indices, which make it possible to systematically investigate the impact of relative abundance on dissimilarity, should be used for robust analysis of data. In combination with a null model, mechanisms of microbial community assembly can be analyzed. Here, we also introduce a new software, qdiv, which enables rapid calculations of Hill-based dissimilarity indices in combination with null models.Results: Using amplicon sequencing data from two experimental systems, aerobic granular sludge (AGS) reactors and microbial fuel cells (MFC), we show that the choice of dissimilarity index can have considerable impact on results and conclusions. High dissimilarity between replicates because of random sampling effects make incidence-based indices less suited for identifying differences between groups of samples. Determining a consensus table based on count tables generated with different bioinformatic pipelines reduced the number of low-abundant, potentially spurious amplicon sequence variants (ASVs) in the data sets, which led to lower dissimilarity between replicates. Analysis with a combination of Hill-based indices and a null model allowed us to show that different ecological mechanisms acted on different fractions of the microbial communities in the experimental systems.Conclusions: Hill-based indices provide a rational framework for analysis of dissimilarity between microbial community samples. In combination with a null model, the effects of deterministic and stochastic community assembly factors on taxa of different relative abundances can be systematically investigated. Calculations of Hill-based dissimilarity indices in combination with a null model can be done in qdiv, which is freely available as a Python package (https://github.com/omvatten/qdiv). In qdiv, a consensus table can also be determined from several count tables generated with different bioinformatic pipelines.
Deciphering the archaeal communities in tree rhizosphere of the Qinghai-Tibetan Plateau
Authors: Zhang Mengjun , Chai Liwei , Huang Muke , Jia Weiqian , Guo Jiabao , Huang Yi 
Published: July 2020

Abstract
Background: The Qinghai-Tibetan Plateau represents one of the most important component of the terrestrial ecosystem and a particularly vulnerable region, which harbouring complex and diverse microbiota. The knowledge about their underground microorganisms have largely been studied, but the characteristics of rhizosphere microbiota, particularly archaeal communities remains unclear.Results: High-throughput Illumina sequencing was used to investigate the rhizosphere archaeal communities of two native alpine trees (Picea crassifolia and Populus szechuanica) living on the Qinghai-Tibetan Plateau. The archaeal community structure in rhizospheres significantly differed from that in bulk soil. Thaumarchaeota was the dominant archaeal phylum in all soils tested (92.46-98.01%), while its relative abundance in rhizospheres were significantly higher than that in bulk soil. Ammonium nitrogen, soil organic matter, available phosphorus and pH were significantly correlated with the archaeal community structure, and the deterministic processes dominated the assembly of archaeal communities across all soils. In addition, the network structures of the archaeal community in the rhizosphere were less complex than they were in the bulk soil, and an unclassified archaeal group (Unclassified_k_norank) was identified as the keystone species in all archaeal networks. Conclusions: Overall, the structure, assembly and co-occurrence patterns of archaeal communities are significantly affected by the presence of roots of alpine trees living on the Qinghai-Tibetan Plateau. This study provides new insights into our understanding of archaeal communities in vulnerable ecosystems.