Association of single nucleotide polymorphisms of IL-6 gene with frailty in the Chinese Bai nationality.

To investigate the impact of 3 single nucleotide polymorphisms (SNPs) in the interleukin-6 (IL-6) gene and their interaction on susceptibility to frailty in the elderly in rural areas of China Bai nationality. Taking the Bai people in Dali, China as the research object, and according to the frailty phenotype scale, there were 2 groups: frail and non-frail. Basic information about the study participants was gathered using a questionnaire. Clinical biochemical indices were also evaluated and the Sanger method was used to identify the sequences of the IL-6 gene loci at rs1524107, rs1800796, and rs10499563. SHEsis online software was used to analyze the linkage disequilibrium of IL-6 gene sites and the relationship between haploids and frailty. The MDR software was used to analyze the 3 sites and their interactions. Among 231 rural Bai elderly people, 63 (27.3%) were frail and 168 (72.7%) were non-frail. The SNPs of rs1524107, rs1800796, and rs10499563 in the IL-6 gene were not associated with the occurrence of frailty, nor were they associated with clinical indicators such as grip strength and gait speed. After adjusting for age and gender, there was no significant difference in the distribution of the 3 genetic models composed of the 3 SNPs between frail and non-frail populations (all P > .05). The 3 haplotypes were not associated with the occurrence of frailty, and the interaction between the 3 loci was not associated with the susceptibility to frailty. The SNP of rs1524107, rs1800796, and rs10499563 sites of IL-6 gene may not be related to frailty susceptibility in Dali Bai people. Differences in frailty mechanisms among other populations at the gene level, which are of enormous significance for the prevention and treatment of frailty, require further research with larger samples and more gene loci.

Highly Efficient Active Learning With Tracklet-Aware Co-Cooperative Annotators for Person Re-Identification.

Supervised person re-identification (ReID) has attracted widespread attentions in the computer vision community due to its great potential in real-world applications. However, the demand of human annotation heavily limits the application as it is costly to annotate identical pedestrians appearing from different cameras. Thus, how to reduce the annotation cost while preserving the performance remains challenging and has been studied extensively. In this article, we propose a tracklet-aware co-cooperative annotators' framework to reduce the demand of human annotation. Specifically, we partition the training samples into different clusters and associate adjacent images in each cluster to produce the robust tracklet which decreases the annotation requirements significantly. Besides, to further reduce the cost, we introduce a powerful teacher model in our framework to implement the active learning strategy and select the most informative tracklets for human annotator, the teacher model itself, in our setting, also acts as an annotator to label the relatively certain tracklets. Thus, our final model could be well-trained with both confident pseudo-labels and human-given annotations. Extensive experiments on three popular person ReID datasets demonstrate that our approach could achieve competitive performance compared with state-of-the-art methods in both active learning and unsupervised learning (USL) settings.

Lactobacillus plantarum SHY130 isolated from yak yogurt attenuates hyperglycemia in C57BL/6J mice by regulating the enteroinsular axis.

Diabetes, one of the most serious and common chronic metabolic diseases affecting people worldwide in the 21st century, has become a major problem that needs to be addressed urgently. This study was designed to elucidate the anti-diabetic effect of yak yogurt-derived Lactobacillus (L.) plantarum SHY130 on C57BL/6J mice fed high-fat diet and streptozotocin (HFD/STZ), and the potential regulatory mechanisms involved. Mice were divided into 3 groups: normal control, diabetes, and diabetes treated with L. plantarum SHY130 (SHY130). Treatment with L. plantarum SHY130 had a regulatory effect on blood glucose and clearly ameliorated insulin resistance in T2DM mice. L. plantarum SHY130 inhibited the reduction in ß-cell mass and α-cell proliferation in the pancreas and increased the expression of the short-chain fatty acid (SCFA) receptors GPR43 and GPR41 in the colon of T2DM mice. Furthermore, L. plantarum SHY130 treatment readjusted intestinal flora structure, enhanced the abundance of SCFA-producing bacteria, such as Faecalibaculum, Odoribacter, Alistipes, and increased the levels of SCFAs in diabetic mice. In summary, L. plantarum SHY130 ameliorated hyperglycemia in HFD/STZ-induced diabetic mice by regulating the enteroinsular axis.

Effects of Preoperative HbA1c Levels on the Postoperative Outcomes of Coronary Artery Disease Surgical Treatment in Patients with Diabetes Mellitus and Nondiabetic Patients: A Systematic Review and Meta-Analysis.

AIMS: To investigate the effect of preoperative HbA1c levels on the postoperative outcomes of coronary artery disease surgery in diabetic and nondiabetic patients. METHODS AND RESULTS: The MEDLINE (via PubMed), Cochrane Library, Web of Science, Embase, Wanfang Data, China National Knowledge Infrastructure (CNKI), and Chinese Biology Medicine (CBM) databases were used to search the effects of different preoperative HbA1c levels on the postoperative outcomes of coronary artery disease surgical treatment in diabetic and nondiabetic patients from inception to December 2018. Two review authors worked in an independent and duplicate manner to select eligible studies, extract data, and assess the risk of bias of the included studies. We used a meta-analysis to synthesize data and analyze subgroups, sensitivity, and publication bias as well as the GRADE methodology if appropriate. The literature search retrieved 886 records initially, and 23 cohort studies were included in the meta-analysis. In this meta-analysis, we found that there was a reduced incidence of surgical site infections (OR = 2.94, 95% CI 2.18-3.98), renal failure events (OR = 1.63, 95% CI 1.13-2.33), and myocardial infarction events (OR = 1.69, 95% CI 1.16-2.47), as well as a shortened hospital stay (MD = 1.08, 95% CI 0.46-1.71), in diabetic patients after coronary artery disease surgical treatment with lower preoperative HbA1c levels. For nondiabetic patients, a higher preoperative HbA1c level resulted in an increase in the incidence of mortality (OR = 2.23, 95% CI 1.01-4.90) and renal failure (OR = 2.33, 95% CI 1.32-4.12). No significant difference was found between higher and lower preoperative HbA1c levels in the incidence of mortality (OR = 1.06, 95% CI 0.88-1.26), stroke (OR = 1.49, 95% CI 0.94-2.37), or atrial fibrillation (OR = 0.94, 95% CI 0.67-1.33); the length of ICU stay (MD = 0.20, 95% CI -0.14-0.55); or sepsis incidence (OR = 2.49, 95% CI 0.99-6.25) for diabetic patients or for myocardial infarction events (OR = 1.32, 95% CI 0.27-6.31) or atrial fibrillation events (OR = 0.99, 95% CI 0.74-1.33) for nondiabetic patients. The certainty of evidence was judged to be moderate or low. CONCLUSION: This meta-analysis showed that higher preoperative HbA1c levels may potentially increase the risk of surgical site infections, renal failure, and myocardial infarction and reduce the length of hospital stay in diabetic subjects after coronary artery disease surgical treatment and increase the risk of mortality and renal failure in nondiabetic patients. However, there was great inconsistency in defining higher preoperative HbA1c levels in the studies included; we still need high-quality RCTs with a sufficiently large sample size to further investigate this issue in the future. This trial is registered with CRD42019121531.

Association Between Perioperative Glycemic Control Strategy and Mortality in Patients With Diabetes Undergoing Cardiac Surgery: A Systematic Review and Meta-Analysis.

Objective: To analyze association between different perioperative glycemic control strategies and postoperative outcomes in patients with diabetes undergoing cardiac surgery. Methods: MEDLINE, Cochrane Library, Web of Science, EMBASE, Wanfang Data, China National Knowledge Infrastructure (CNKI) and China Biology Medicine (CBM) databases were searched from inception to January 31, 2019. Two researchers independently screened the literature, extracted data, and evaluated the risk of bias of included studies, and consensus was reached by discussion with a third researcher. Results: Six RCTs were included in the meta-analysis. We analyzed the effect of liberal (>180 mg/dl or 10.0 mmol/L), moderate (140-180 mg/dl or 7.8-10.0 mmol/L) and strict (<140 mg/dl or 7.8 mmol/L) glycemic control strategies in patients with diabetes undergoing cardiac surgery. The pooled results showed that strict glycemic control strategy was associated with a significant reduction in the risk of atrial fibrillation [OR = 0.48, 95%CI (0.32, 0.72), P < 0.001] and sternal wound infection [OR = 0.28, 95%CI (0.14, 0.54), P < 0.001], while there was no significant differences in postoperative mortality, stroke, and hypoglycemic episodes when compared with moderate control. In addition, there is no significant difference between moderate and liberal glycemic control strategies in postoperative mortality. However, moderate control was beneficial in reducing atrial fibrillation [OR = 0.28, 95%CI (0.13, 0.60), P = 0.001] compared with the liberal glycemic control strategy. Conclusions: This meta-analysis showed when compared with moderate glycemic control strategy in patients with diabetes undergoing cardiac surgery, maintained strict glycemic control was associated with lower risk of atrial fibrillation and sternal wound infection. No benefit was found with liberal glycemic control strategy, so it could be a poor glycemic control strategy.

Quality Assessment of Systematic Review of the Bariatric Surgery for Diabetes Mellitus.

OBJECTIVE: Using the AMSTAR tool, this study evaluated the quality of systematic reviews (SRs) that assessed the efficacy of bariatric surgery in diabetic patients. We aimed to identify studies that can be used as clinical references. METHODS: Medline (via PubMed), EMBASE, Epistemonikos, Web of Science, Cochrane Library, CBM, CNKI, and Wanfang Data were systematically searched from inception to December 31, 2017. Two reviewers independently selected SRs and extracted data. Disagreements were solved by discussions or through consultation with a third reviewer. Reviewers extracted data (characteristics of included SRs, e.g., publication year, language, and number of authors) into the predefined tables in the Microsoft Excel 2013 sheet. Data were visualized using the forest plot in RevMan 5.3 software. RESULTS: A total of 64 SRs were included. The average AMSTAR score was 7.4 ± 1.7. AMSTAR scores of 7 (n = 21, 32.8%) and 8 (n = 14, 28.1%) were most common. The AMSTAR scores of SRs published before 2016 (n = 46, 71.9%) were compared with SRs published after 2016 (n = 18, 28.1%), and no significant differences were observed (MD = -0.79, 95% confidence interval (CI) -1.65-0.07, P = 0.07). For SRs published in Chinese (n = 17, 26.6%) compared to those published in English (n = 47, 73.4%), the AMSTAR scores significantly differed (MD = 0.21, 95% CI (-0.55, 0.97), P = 0.59). For SRs published in China (n = 33, 51.6%) compared to those published outside of China (n = 31, 48.4%), significant differences in the AMSTAR scores were observed (MD = 1.10, 95% CI (0.29, 1.91), P = 0.008). For SRs with an author number ≤ 6 (n = 31, 48.4%) compared to SRs with authors ≥ 6 (n = 33, 51.6%), no significant differences were observed (MD = -0.36, 95% CI (-1.22, 0.50), P = 0.41). For high-quality SRs published after 2016 (n = 11, 17.2%) compared to other SRs (n = 53, 82.8%), statistically significant differences were noted (MD = 1.75, 95% CI (1.01, 2.49), P < 0.00001). CONCLUSIONS: The number of SRs assessing the efficacy of bariatric surgery in diabetic patients is increasing by year, but only a small number meet the criteria to support guideline recommendations. Study protocols not being registered, grey literature not retrieved, incorporation of grey literature as exclusion criteria, and failure to evaluate publication bias and report a conflict of interest were the main causes of low AMSTAR scores.

Prognostic factors for cesarean section outcome of pregnant women with gestational diabetes mellitus: a systematic review and meta-analysis.

Objective: To evaluate the prognostic factors for cesarean section outcome of pregnant women with diabetes mellitus. Methods: MEDLINE, EMBASE, Cochrane Library, CBM, CNKI and Wanfang database were searched. Two researchers independently screened the literature, extracted data, and evaluated the risk of bias of included studies. For pooled data with factors of perioperative outcome, the RevMan software was used for data translation and meta-analysis. The result is shown intuitively with the bubble diagram of evidence mapping by Excel 2016. Results: We included 12 randomized controlled trials (RCTs) in the meta-analysis. Twelve RCTs with 1,390 patients were included in the systematic review. The results show that the perioperative blood glucose management regimens, preoperative fasting and water deprivation, anesthesia regimens, postoperative fluid regimens, postoperative analgesia regimens, postoperative wound care regimens, psychological interventions, different dosing regimens for antibiotics, and obesity may affect the cesarean section outcome of diabetic mothers and newborns. The evidence for all the outcomes was low quality. Conclusion: Many prognostic factors have shown significant association with postoperative outcomes of cesarean section. More clinical research evidence with high-quality is needed.

A Blind Spectrum Sensing Method Based on Deep Learning.

Spectrum sensing is one of the technologies that is used to solve the current problem of low utilization of spectrum resources. However, when the signal-to-noise ratio is low, current spectrum sensing methods cannot well-handle a situation in which the prior information of the licensed user signal is lacking. In this paper, a blind spectrum sensing method based on deep learning is proposed that uses three kinds of neural networks together, namely convolutional neural networks, long short-term memory, and fully connected neural networks. Experiments show that the proposed method has better performance than an energy detector, especially when the signal-to-noise ratio is low. At the same time, this paper also analyzes the effect of different long short-term memory layers on detection performance, and explores why the deep-learning-based detector can achieve better performance.

Postoperative adverse events in patients with diabetes undergoing orthopedic and general surgery.

Factors that may result in the occurrence of adverse clinical events in diabetic patients during the postoperative period are not entirely clear. This study evaluated factors that may cause adverse events following elective orthopedic or general surgery.Patients with diabetes who underwent orthopedic or general surgery between January 2010 and October 2015 were retrospectively selected from the General Hospital of People's Liberation Army database. Factors associated with postoperative adverse events were analyzed using multivariable logistic regression.Among 1525 patients included, mean age was 63.5 ±â€Š10.8 years and mean duration of diabetes was 8.8 ±â€Š6.6 years. Among them, 49.9% underwent orthopedic surgery and 50.1% underwent general surgery. Postoperatively, 118 (7.7%) patients had adverse events, including delayed extubation (n = 43, 36.4%), circulatory disorder (n = 15, 12.7%), respiratory and circulatory abnormalities (n = 23, 19.5%), nonhealing of the incision (n = 11, 9.3%), infections at other sites (n = 15, 12.7%), other complications (n = 8, 6.8%), and death (n = 3, 2.5%). Multivariable regression analysis showed that age >65 years old [odds ratio (OR) = 2.23, 95% confidence interval (CI): 1.25-3.98], male sex (OR = 2.14, 95% CI: 1.24-3.38), postoperative peripheral blood glucose (OR = 1.13, 95% CI: 1.13-1.82), diabetic complications (OR = 2.41, 95% CI: 1.36-4.28), abnormal kidney function (OR = 2.73, 95% CI: 1.13-6.58) and general surgery (OR = 1.48, 95% CI: 1.11-5.26) were associated with the occurrence of postoperative adverse events.In patients with diabetes undergoing intermediate or major elective surgery, older age, male sex, high postoperative peripheral blood glucose, diabetic complications, abnormal kidney function, and general surgery type were associated with the occurrence of postoperative adverse events.

Orphan Genes Shared by Pathogenic Genomes Are More Associated with Bacterial Pathogenicity.

Orphan genes (also known as ORFans [i.e., orphan open reading frames]) are new genes that enable an organism to adapt to its specific living environment. Our focus in this study is to compare ORFans between pathogens (P) and nonpathogens (NP) of the same genus. Using the pangenome idea, we have identified 130,169 ORFans in nine bacterial genera (505 genomes) and classified these ORFans into four groups: (i) SS-ORFans (P), which are only found in a single pathogenic genome; (ii) SS-ORFans (NP), which are only found in a single nonpathogenic genome; (iii) PS-ORFans (P), which are found in multiple pathogenic genomes; and (iv) NS-ORFans (NP), which are found in multiple nonpathogenic genomes. Within the same genus, pathogens do not always have more genes, more ORFans, or more pathogenicity-related genes (PRGs)-including prophages, pathogenicity islands (PAIs), virulence factors (VFs), and horizontal gene transfers (HGTs)-than nonpathogens. Interestingly, in pathogens of the nine genera, the percentages of PS-ORFans are consistently higher than those of SS-ORFans, which is not true in nonpathogens. Similarly, in pathogens of the nine genera, the percentages of PS-ORFans matching the four types of PRGs are also always higher than those of SS-ORFans, but this is not true in nonpathogens. All of these findings suggest the greater importance of PS-ORFans for bacterial pathogenicity. IMPORTANCE Recent pangenome analyses of numerous bacterial species have suggested that each genome of a single species may have a significant fraction of its gene content unique or shared by a very few genomes (i.e., ORFans). We selected nine bacterial genera, each containing at least five pathogenic and five nonpathogenic genomes, to compare their ORFans in relation to pathogenicity-related genes. Pathogens in these genera are known to cause a number of common and devastating human diseases such as pneumonia, diphtheria, melioidosis, and tuberculosis. Thus, they are worthy of in-depth systems microbiology investigations, including the comparative study of ORFans between pathogens and nonpathogens. We provide direct evidence to suggest that ORFans shared by more pathogens are more associated with pathogenicity-related genes and thus are more important targets for development of new diagnostic markers or therapeutic drugs for bacterial infectious diseases.

Whole-genome sequencing of 175 Mongolians uncovers population-specific genetic architecture and gene flow throughout North and East Asia.

The genetic variation in Northern Asian populations is currently undersampled. To address this, we generated a new genetic variation reference panel by whole-genome sequencing of 175 ethnic Mongolians, representing six tribes. The cataloged variation in the panel shows strong population stratification among these tribes, which correlates with the diverse demographic histories in the region. Incorporating our results with the 1000 Genomes Project panel identifies derived alleles shared between Finns and Mongolians/Siberians, suggesting that substantial gene flow between northern Eurasian populations has occurred in the past. Furthermore, we highlight that North, East, and Southeast Asian populations are more aligned with each other than these groups are with South Asian and Oceanian populations.

dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation.

Carbohydrate-active enzyme (CAZymes) are not only the most important enzymes for bioenergy and agricultural industries, but also very important for human health, in that human gut microbiota encode hundreds of CAZyme genes in their genomes for degrading various dietary and host carbohydrates. We have built an online database dbCAN-seq (http://cys.bios.niu.edu/dbCAN_seq) to provide pre-computed CAZyme sequence and annotation data for 5,349 bacterial genomes. Compared to the other CAZyme resources, dbCAN-seq has the following new features: (i) a convenient download page to allow batch download of all the sequence and annotation data; (ii) an annotation page for every CAZyme to provide the most comprehensive annotation data; (iii) a metadata page to organize the bacterial genomes according to species metadata such as disease, habitat, oxygen requirement, temperature, metabolism; (iv) a very fast tool to identify physically linked CAZyme gene clusters (CGCs) and (v) a powerful search function to allow fast and efficient data query. With these unique utilities, dbCAN-seq will become a valuable web resource for CAZyme research, with a focus complementary to dbCAN (automated CAZyme annotation server) and CAZy (CAZyme family classification and reference database).

Effect of different types of anesthesia on intraoperative blood glucose of diabetic patients: A PRISMA-compliant systematic review and meta-analysis.

BACKGROUND: Systematic review which analyzes the impact of different anesthesia on intraoperative blood glucose levels of diabetes patients. METHODS: We searched Medline (via PubMed), Embase, Cochrane Library, Web of Science, Wangfang, CNKI, and CBM database through June 2016, included in randomized controlled trial (RCT), about different anesthesia on intraoperative blood glucose levels in patients with diabetes. Two researchers in 1 group independently screened literatures with eligibility criteria, extracted information, and used RevMan5.3 software to perform meta-analysis. RESULTS: We included 11 trials and performed the meta-analysis with 10 trials. The meta-analysis results suggested that compared with general anesthesia, the combined general-epidural anesthesia has a better glycemic control in intraoperative blood glucose levels (WMD -1.26, 95% confidence interval [CI] -1.77 to 0.76), the epidural anesthesia had no significant effects compared with general anesthesia (WMD -0.74, 95% CI 4.41-2.92), and the combined spinal-epidural anesthesia had no significant effects compared with epidural anesthesia (WMD -0.28, 95% CI -1.02 to 0.46). One study suggested that compared with epidural anesthesia, the combined general-epidural anesthesia can lower blood glucose levels CONCLUSION:: Existing evidence showed that compared with general anesthesia, the combined general-epidural anesthesia has a better glycemic control in intraoperative blood glucose levels.

pHMM-tree: phylogeny of profile hidden Markov models.

Protein families are often represented by profile hidden Markov models (pHMMs). Homology between two distant protein families can be determined by comparing the pHMMs. Here we explored the idea of building a phylogeny of protein families using the distance matrix of their pHMMs. We developed a new software and web server (pHMM-tree) to allow four major types of inputs: (i) multiple pHMM files, (ii) multiple aligned protein sequence files, (iii) mixture of pHMM and aligned sequence files and (iv) unaligned protein sequences in a single file. The output will be a pHMM phylogeny of different protein families delineating their relationships. We have applied pHMM-tree to build phylogenies for CAZyme (carbohydrate active enzyme) classes and Pfam clans, which attested its usefulness in the phylogenetic representation of the evolutionary relationship among distant protein families. Availability and Implementation: This software is implemented in C/C ++ and is available at http://cys.bios.niu.edu/pHMM-Tree/source/. Contact: zhanghan@nankai.edu.cn or yyin@niu.edu. Supplementary information: Supplementary data are available at Bioinformatics online.

HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomes.

Horizontal gene transfer (HGT) is a fast-track mechanism that allows genetically unrelated organisms to exchange genes for rapid environmental adaptation. We developed a new phyletic distribution-based software, HGT-Finder, which implements a novel bioinformatics algorithm to calculate a horizontal transfer index and a probability value for each query gene. Applying this new tool to the Aspergillus fumigatus, Aspergillus flavus, and Aspergillus nidulans genomes, we found 273, 542, and 715 transferred genes (HTGs), respectively. HTGs have shorter length, higher guanine-cytosine (GC) content, and relaxed selection pressure. Metabolic process and secondary metabolism functions are significantly enriched in HTGs. Gene clustering analysis showed that 61%, 41% and 74% of HTGs in the three genomes form physically linked gene clusters (HTGCs). Overlapping manually curated, secondary metabolite gene clusters (SMGCs) with HTGCs found that 9 of the 33 A. fumigatus SMGCs and 31 of the 65 A. nidulans SMGCs share genes with HTGCs, and that HTGs are significantly enriched in SMGCs. Our genome-wide analysis thus presented very strong evidence to support the hypothesis that HGT has played a very critical role in the evolution of SMGCs. The program is freely available at http://cys.bios.niu.edu/HGTFinder/ HGTFinder.tar.gz.

Camelid genomes reveal evolution and adaptation to desert environments.

Bactrian camel (Camelus bactrianus), dromedary (Camelus dromedarius) and alpaca (Vicugna pacos) are economically important livestock. Although the Bactrian camel and dromedary are large, typically arid-desert-adapted mammals, alpacas are adapted to plateaus. Here we present high-quality genome sequences of these three species. Our analysis reveals the demographic history of these species since the Tortonian Stage of the Miocene and uncovers a striking correlation between large fluctuations in population size and geological time boundaries. Comparative genomic analysis reveals complex features related to desert adaptations, including fat and water metabolism, stress responses to heat, aridity, intense ultraviolet radiation and choking dust. Transcriptomic analysis of Bactrian camels further reveals unique osmoregulation, osmoprotection and compensatory mechanisms for water reservation underpinned by high blood glucose levels. We hypothesize that these physiological mechanisms represent kidney evolutionary adaptations to the desert environment. This study advances our understanding of camelid evolution and the adaptation of camels to arid-desert environments.