Comparative analysis of 3D-culture system for murine neonatal heart regeneration: a systematic approach for big gene expression data

[[abstract]]Cardiovascular diseases are the leading cause of death worldwide. Loss or dysfunction of cardiomyocytes is associated with many forms of heart disease. The adult mammalian heart has a limited regenerative ability after damage, leading to the formation of fibrotic scar tissues, hypertrophy, contractile dysfunction and ul-timately, organ failure. In contrast, neonatal mammalian cardiomyocytes retain a significant replenishing potential briefly after birth. There is increasing enthusiasm to grow neonatal cardiomyocytes in 3D culture systems to artificially restore heart function. Various scaffolds and matrices are available, but the molecular and cellu-lar mechanisms underlying proliferation and differentiation of neonatal mammalian cardiomyocytes are not very well understood. Here, we utilize a systematic strategy to analyze the extensive genome-scale gene expression profiles of two different 3D constructs. We present a comprehensive comparison that may help improve the protocols for growing cardiomyocytes in a 3D culture system.[[notice]]補正完畢[[incitationindex]]EI[[conferencetype]]國際[[conferencedate]]20140513~20140516[[booktype]]電子版[[iscallforpapers]]Y[[conferencelocation]]Tainan, Taiwa

Myocardial Infarction Classification by Morphological Feature Extraction from Big 12-Lead ECG Data

[[abstract]]Rapid and accurate diagnosis of patients with acute myocardial infarction is vital. The ST segment in Electrocardiography (ECG) represents the change of electric potential during the period from the end of ventricular depolarization to the beginning of repolarization and plays an important role in the detection of myocardial infarction. However, ECG monitoring generates big volumes of data and the underlying complexity must be extracted by a combination of methods. This study combines the advantages of polynomial approximation and principal component analysis. The proposed approach is stable for the 12-lead ECG data collected from the PTB database and achieves an accuracy of 98.07%.[[notice]]補正完畢[[incitationindex]]EI[[conferencetype]]國際[[conferencedate]]20140513~20140516[[booktype]]電子版[[iscallforpapers]]Y[[conferencelocation]]Tainan, Taiwa

Cluster-based Classification of Diabetic Nephropathy among Type 2

[[abstract]]The prevalence of type 2 diabetes is increasing at an alarming rate. Various complications are associated with type 2 diabetes, with diabetic nephropathy being the leading cause of renal failure among diabetics. Often, when patients are diagnosed with diabetic nephropathy, their renal functions have already been significantly damaged, speeding up the progression towards end stage renal disease. Therefore, a risk prediction tool may be beneficial for the implementation of early treatment and prevention. In the present study, we propose to develop a prediction model integrating clustering and classification approaches for the identification of diabetic nephropathy among type 2 diabetes patients. Clinical and genotyping data are obtained from 345 type 2 diabetic patients(160 with non-diabetic nephropathy and 185 with diabetic nephropathy). The performance of using clinical features alone for cluster-based classification is compared with that of utilizing a combination of clinical and genetic attributes. We find that the inclusion of genetic features yield better prediction results. Further refinement of the proposed approach has the potential to facilitate the accurate identification of diabetic nephropathy and the development of better treatment in a clinical setting.[[incitationindex]]EI[[conferencetype]]國際[[conferencedate]]20140507~2014009[[booktype]]電子版[[iscallforpapers]]Y[[conferencelocation]]Kyoto, Japa

SOHSite: incorporating evolutionary information and physicochemical properties to identify protein S-sulfenylation sites

Distribution of KEGG pathway annotations for S-sulfenylated proteins. (DOCX 15 kb

The GMRT EoR Experiment: Limits on Polarized Sky Brightness at 150 MHz

The GMRT reionization effort aims to map out the large scale structure of the Universe during the epoch of reionization (EoR). Removal of polarized Galactic emission is a difficult part of any 21 cm EoR program, and we present new upper limits to diffuse polarized foregrounds at 150 MHz. We find no high significance evidence of polarized emission in our observed field at mid galactic latitude (J2000 08h26m+26). We find an upper limit on the 2-dimensional angular power spectrum of diffuse polarized foregrounds of [l^2 C_l/(2 PI)]^{1/2}< 3K in frequency bins of width 1 MHz at 300<l<1000. The 3-dimensional power spectrum of polarized emission, which is most directly relevant to EoR observations, is [k^3 P_p(k)/(2 PI^2)]^{1/2} 0.03 h/Mpc, k < 0.1 h/Mpc. This can be compared to the expected EoR signal in total intensity of [k^3 P(k)/ (2 PI^2) ]^{1/2} ~ 10 mK. We find polarized structure is substantially weaker than suggested by extrapolation from higher frequency observations, so the new low upper limits reported here reduce the anticipated impact of these foregrounds on EoR experiments. We discuss Faraday beam and depth depolarization models and compare predictions of these models to our data. We report on a new technique for polarization calibration using pulsars, as well as a new technique to remove broadband radio frequency interference. Our data indicate that, on the edges of the main beam at GMRT, polarization squint creates ~ 3% leakage of unpolarized power into polarized maps at zero rotation measure. Ionospheric rotation was largely stable during these solar minimum night time observations.Comment: 17 pages, 6 figures, 2 tables; changed figures, added appendices. To appear in MNRA

Gene Expression Profiling of Biological Pathway Alterations by Radiation Exposure

[[abstract]]Though damage caused by radiation has been the focus of rigorous research, the mechanisms through which radiation exerts harmful effects on cells are complex and not well-understood. In particular, the influence of low dose radiation exposure on the regulation of genes and pathways remains unclear. In an attempt to investigate the molecular alterations induced by varying doses of radiation, a genome-wide expression analysis was conducted. Peripheral blood mononuclear cells were collected from five participants and each sample was subjected to 0.5 Gy, 1 Gy, 2.5 Gy, and 5 Gy of cobalt 60 radiation, followed by array-based expression profiling. Gene set enrichment analysis indicated that the immune system and cancer development pathways appeared to be the major affected targets by radiation exposure. Therefore, 1 Gy radioactive exposure seemed to be a critical threshold dosage. In fact, after 1 Gy radiation exposure, expression levels of several genes including FADD, TNFRSF10B, TNFRSF8, TNFRSF10A, TNFSF10, TNFSF8, CASP1, and CASP4 that are associated with carcinogenesis and metabolic disorders showed significant alterations. Our results suggest that exposure to low-dose radiation may elicit changes in metabolic and immune pathways, potentially increasing the risk of immune dysfunctions and metabolic disorders.[[notice]]補正完畢[[incitationindex]]SCI[[incitationindex]]EI[[booktype]]電子

A simulation-calibrated limit on the H i power spectrum from the GMRT Epoch of Reionization experiment

The Giant Metrewave Radio Telescope Epoch of Reionization experiment is an ongoing effort to measure the power spectrum from neutral hydrogen at high redshift. We have previously reported an upper limit of (70 mK)^2 at wavenumbers of k ≈ 0.65 h Mpc^(−1) using a basic piecewise-linear foreground subtraction. In this paper, we explore the use of a singular value decomposition to remove foregrounds with fewer assumptions about the foreground structure. Using this method, we also quantify, for the first time, the signal loss due to the foreground filter and present new power spectra adjusted for this loss, providing a revised measurement of a 2σ upper limit at (248 mK)^2 for k = 0.50 h Mpc^(−1). While this revised limit is larger than previously reported, we believe it to be more robust and still represents the best current constraint on reionization at z ≈ 8.6

Pathway using WUDAPT's Digital Synthetic City tool towards generating urban canopy parameters for multi-scale urban atmospheric modeling

The WUDAPT (World Urban Database and Access Portal Tools project goal is to capture consistent information on urban form and function for cities worldwide that can support urban weather, climate, hydrology and air quality modeling. These data are provided as urban canopy parameters (UCPs) as used by weather, climate and air quality models to simulate the effects of urban surfaces on the overlying atmosphere. Information is stored with different levels of detail (LOD). With higher LOD greater spatial precision is provided. At the lowest LOD, Local Climate Zones(LCZ) with nominal UCP ranges is provided (order 100 m or more). To describe the spatial heterogeneity present in cities with great specificity at different urban scales we introduce the Digital Synthetic City (DSC) tool to generate UCPs at any desired scale meeting the fit-for-purpose goal of WUDAPT. 3D building and road elements of entire city landscapes are simulated based on readily available data. Comparisons with real-world urban data are very encouraging. It is customized (C-DSC) to incorporate each city's unique building morphologies based on unique types, variations and spatial distribution of building typologies, architecture features, construction materials and distribution of green and pervious surfaces. The C-DSC uses crowdsourcing methods and sampling within city Testbeds from around the world. UCP data can be computed from synthetic images at selected grid sizes and stored such that the coded string provides UCP values for individual grid cells

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London