SjTPdb: integrated transcriptome and proteome database and analysis platform for Schistosoma japonicum

<p>Abstract</p> <p>Background</p> <p><it>Schistosoma japonicum </it>is one of the three major blood fluke species, the etiological agents of schistosomiasis which remains a serious public health problem with an estimated 200 million people infected in 76 countries. In recent years, enormous amounts of both transcriptomic and proteomic data of schistosomes have become available, providing information on gene expression profiles for developmental stages and tissues of <it>S. japonicum</it>. Here, we establish a public searchable database, termed SjTPdb, with integrated transcriptomic and proteomic data of <it>S. japonicum</it>, to enable more efficient access and utility of these data and to facilitate the study of schistosome biology, physiology and evolution.</p> <p>Description</p> <p>All the available ESTs, EST clusters, and the proteomic dataset of <it>S. japonicum </it>are deposited in SjTPdb. The core of the database is the 8,420 <it>S. japonicum </it>proteins translated from the EST clusters, which are well annotated for sequence similarity, structural features, functional ontology, genomic variations and expression patterns across developmental stages and tissues including the tegument and eggshell of this flatworm. The data can be queried by simple text search, BLAST search, search based on developmental stage of the life cycle, and an integrated search for more specific information. A PHP-based web interface allows users to browse and query SjTPdb, and moreover to switch to external databases by the following embedded links.</p> <p>Conclusion</p> <p>SjTPdb is the first schistosome database with detailed annotations for schistosome proteins. It is also the first integrated database of both transcriptome and proteome of <it>S. japonicum</it>, providing a comprehensive data resource and research platform to facilitate functional genomics of schistosome. SjTPdb is available from URL: <url>http://function.chgc.sh.cn/sj-proteome/index.htm</url>.</p

A Guaranteed Global Convergence Social Cognitive Optimizer

From the analysis of the traditional social cognitive optimization (SCO) in theory, we see that traditional SCO is not guaranteed to converge to the global optimization solution with probability one. So an improved social cognitive optimizer is proposed, which is guaranteed to converge to the global optimization solution. The global convergence of the improved SCO algorithm is guaranteed by the strategy of periodic restart in use under the conditions of participating in comparison, which helps to avoid the premature convergence. Then we give the convergence proof for the improved SCO based on Solis and Wets’ research results. Finally, simulation results on a set of benchmark problems show that the proposed algorithm has higher optimization efficiency, better global performance, and better stable optimization outcomes than the traditional SCO for nonlinear programming problems (NLPs)

Value of reduced glomerular filtration rate assessment with cardiometabolic index: insights from a population-based Chinese cohort

Abstract Background Recent studies have suggested that cardiometabolic index (CMI), a novel estimate of visceral adipose tissue, could be of use in the evaluation of cardiovascular risk factors. However, the potential utility and clinical significance of CMI in the detection of reduced estimated glomerular filtration rate (eGFR) remains uncertain. The purpose of this study was to investigate the usefulness of CMI in assessing reduced eGFR in the general Chinese population. Methods This cross-sectional analysis included 11,578 participants (mean age: 53.8 years, 53.7% females) from Northeast China Rural Cardiovascular Health Study (NCRCHS) of general Chinese population (data collected from January 2013 to August 2013). CMI was calculated by triglyceride to high density lipoprotein cholesterol ratio multiply waist-to-height ratio. Reduced eGFR was defined as eGFR< 60 ml/min per 1.73m2. Multivariate regressions were performed to determine CMI’s association with eGFR value and eGFR reduction, ROC analyses were employed to investigate CMI’s discriminating ability for decreased eGFR. Results The prevalence of reduced eGFR was 1.7% in males and 2.5% in females. CMI was notably more adverse in reduced eGFR groups, regardless of genders. In fully adjusted multivariate linear models, each 1 SD increment of CMI caused 3.150 ml/min per 1.73m2 and 2.411 ml/min per 1.73m2 loss of eGFR before CMI reached 1.210 and 1.520 in males and females, respectively. In logistic regression analyses, per 1 SD increase of CMI brought 51.6% additional risk of reduced eGFR in males while caused 1.347 times of risk in females. After divided into quartiles, people in the top quartile of CMI had higher adjusted ORs of having reduced eGFR, with ORs of 4.227 (1.681, 10.627) and 3.442 (1.685–7.031) for males and females respectively. AUC of CMI was revealed to be 0.633 (0.620–0.646) in males and 0.684 (0.672–0.695) in females. Conclusions Higher CMI was independently associated with greater burden of reduced eGFR, highlighting VAT distribution and dysfunction as a potential mechanism underlying the association of obesity with kidney damage and adverse cardiovascular outcomes. The findings from this study provided important insights regarding the potential usefulness and clinical relevance of CMI in the detection of reduced eGFR among general Chinese population.https://deepblue.lib.umich.edu/bitstream/2027.42/146138/1/12882_2018_Article_1098.pd

A Unified Geometric Model of Repeating and Non-Repeating Fast Radio Bursts

Fast radio bursts (FRBs) are millisecond-duration extragalactic radio transients. They apparently fall into repeaters and non-repeaters. However, such a classification has lacked a motivation on the physical picture. Here we propose a unified geometric model to distinguish between the repeaters and non-repeaters, in which the quasi-tangential (QT) propagation effect within the magnetospheric polar cap of a neutron star is considered. In this model, the non-repeaters arise from the sources whose emitting region has a smaller impact angle with respect to the magnetic axis, while the repeaters come from the sources whose emitting region has a larger impact angle. The observational discriminant polarization properties between the repeaters and non-repeaters are an important clue to verifying this unified geometric model since the polarization is sensitive to the QT propagation effect. Moreover, our model effectively explains all of the other discriminant properties, including bandwidth, duration, peak luminosity, energy, brightness temperature, time-frequency downward drifting, and repetition rate, providing compelling evidence for the magnetospheric origin of FRBs.Comment: 16 pages, 8 figure

Effects of gastrointestinal motility on obesity

Background: Changes of gastrointestinal motility, which are important related to the food digestion and absorption in the gastrointestinal tract, may be one of the factors in obesity-formation. Aims The changes of gastrointestinal motility were explored in the rats from diet-induced obesity (DIO), diet-induced obese resistant (DR) or control (CON) by diet intervention. Methods: After fed with a high fat diet (HFD), 100 male Sprague–Dawley rats were divided into DIO, DR and CON groups. The rats from DIO and DR groups were fed with HFD, and CON with a basic diet (BD) for 6 weeks. Body weight, energy intake, gastric emptying, intestinal transit, motility of isolated small intestine segments and colon’s function were measured in this study. Expression of interstitial cells of Cajal (ICCs) and enteric nervous system (ENS) - choline acetyltransferase (ChAT), vasoactive intestinal peptides (VIP), substance P (SP) and NADPH-d histochemistry of nitric oxide synthase (NOS) were determined by immunohistochemistry. Results: Body weight and intake energy in the DIO group were higher than those in the DR group (p < 0.05). Gastric emptying of DIO group rats (78.33 ± 4.95%) was significantly faster than that of DR group (51.79 ± 10.72%) (p < 0.01). The peak value of motility in rat’s duodenum from the DR group was significantly higher than that in the DIO group (p < 0.05). In addition, the expression of interstitial cells of Cajal (ICC), choline acetyltransferase (ChAT), substance P (SP), vasoactive intestinal peptides (VIP) and neuronal nicotinamide adenine dinucleotide phosphate-diaphorase (NADPH-d) in the intestine of rats were significantly increased in the DIO group when compared to the DR group (p < 0.05). Conclusion: A faster gastric emptying, a weaker contraction of duodenum movement, and a stronger contraction and relaxation of ileum movement were found in the rats from the DIO group. It indicated that there has effect of gastrointestinal motility on obesity induced by HFD

Potential biomarkers relating pathological proteins, neuroinflammatory factors and free radicals in PD patients with cognitive impairment: a cross-sectional study

BACKGROUND: Cognitive impairment strikingly reduces the quality of life of Parkinson’s disease (PD) patients. Studies find that pathological proteins, neuroinflammatory factors and free radicals may involve in the pathogenesis of cognitive impairment of PD, however, results are inconclusive. METHODS: We recruited 62 PD patients and 31 healthy controls. PD patients were identified with cognitive impairment, including PD with mild cognitive impairment (PD-MCI) and PD with dementia (PDD) according to the diagnostic criteria for PD-MCI and PDD issued by Movement Disorder Society Task Force. The levels of pathological proteins, including β-amyloid 1–42 (Aβ1-42),Total-tau (T-tau) and phosphorelated tau (P-tau), neuroinflammatory factors,including tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), interleukin-6 (IL-6), interferon-γ (INF-γ) and prostaglandin E(2) (PGE(2)), free radicals, including hydroxyl radical (·OH), hydrogen peroxide (H(2)O(2)) and nitric oxide (NO) in cerebrospinal fluid(CSF) were detected. The levels of above factors in CSF were compared among healthy controls and patients with and without cognitive impairment. Correlation analyses were performed between Montreal Cognitive Assessment (MoCA) score and the levels of above factors in CSF. RESULTS: T-tau level in CSF from PD-CI patients are significantly elevated comparing with those without cognitive impairment and controls (P = 0.016 and 0.004, respectively). The levels of P-tau (S396) and · OH in PD-CI patients are significantly higher than controls (P = 0.001 and 0.014, respectively). IL-6 levels in PD-CI patients are strikingly enhanced comparing with those without cognitive impairment (P = 0.005). MoCA score is negatively correlated with the levels of T-tau (r = -0.340), P-tau (S396) (r = -0.448), IL-6 (r = -0.489) and · OH (r = -0.504) in PD-CI patients. CONCLUSIONS: Elevated levels of T-tau, P-tau (S396), IL-6 and · OH in CSF are significantly correlated with cognitive impairment in PD patients. This investigation may suggest the potential biomarkers relating pathological proteins, neuroinflammatory factors and free radicals in PD patients with cognitive impairment