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  • Institute of Physics (IOP)  (23)
  • Public Library of Science  (13)
  • Oxford University Press  (11)
  • 2015-2019  (47)
  • 1
    Publication Date: 2015-08-27
    Description: The adaptor protein-2 sigma subunit (AP22) is pivotal for clathrin-mediated endocytosis of plasma membrane constituents such as the calcium-sensing receptor (CaSR). Mutations of the AP22 Arg15 residue result in familial hypocalciuric hypercalcaemia type 3 (FHH3), a disorder of extracellular calcium (Ca 2+ o ) homeostasis. To elucidate the role of AP22 in Ca 2+ o regulation, we investigated 65 FHH probands, without other FHH-associated mutations, for AP22 mutations, characterized their functional consequences and investigated the genetic mechanisms leading to FHH3. AP22 mutations were identified in 17 probands, comprising 5 Arg15Cys, 4 Arg15His and 8 Arg15Leu mutations. A genotype–phenotype correlation was observed with the Arg15Leu mutation leading to marked hypercalcaemia. FHH3 probands harboured additional phenotypes such as cognitive dysfunction. All three FHH3-causing AP22 mutations impaired CaSR signal transduction in a dominant-negative manner. Mutational bias was observed at the AP22 Arg15 residue as other predicted missense substitutions (Arg15Gly, Arg15Pro and Arg15Ser), which also caused CaSR loss-of-function, were not detected in FHH probands, and these mutations were found to reduce the numbers of CaSR-expressing cells. FHH3 probands had significantly greater serum calcium (sCa) and magnesium (sMg) concentrations with reduced urinary calcium to creatinine clearance ratios (CCCR) in comparison with FHH1 probands with CaSR mutations, and a calculated index of sCa x sMg/100 x CCCR, which was ≥ 5.0, had a diagnostic sensitivity and specificity of 83 and 86%, respectively, for FHH3. Thus, our studies demonstrate AP22 mutations to result in a more severe FHH phenotype with genotype–phenotype correlations, and a dominant-negative mechanism of action with mutational bias at the Arg15 residue.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 2
    Publication Date: 2015-05-27
    Description: Motivation: Although gene-expression signature-based biomarkers are often developed for clinical diagnosis, many promising signatures fail to replicate during validation. One major challenge is that biological samples used to generate and validate the signature are often from heterogeneous biological contexts—controlled or in vitro samples may be used to generate the signature, but patient samples may be used for validation. In addition, systematic technical biases from multiple genome-profiling platforms often mask true biological variation. Addressing such challenges will enable us to better elucidate disease mechanisms and provide improved guidance for personalized therapeutics. Results: Here, we present a pathway profiling toolkit, Adaptive Signature Selection and InteGratioN (ASSIGN), which enables robust and context-specific pathway analyses by efficiently capturing pathway activity in heterogeneous sets of samples and across profiling technologies. The ASSIGN framework is based on a flexible Bayesian factor analysis approach that allows for simultaneous profiling of multiple correlated pathways and for the adaptation of pathway signatures into specific disease. We demonstrate the robustness and versatility of ASSIGN in estimating pathway activity in simulated data, cell lines perturbed pathways and in primary tissues samples including The Cancer Genome Atlas breast carcinoma samples and liver samples exposed to genotoxic carcinogens. Availability and implementation: Software for our approach is available for download at: http://www.bioconductor.org/packages/release/bioc/html/ASSIGN.html and https://github.com/wevanjohnson/ASSIGN . Contact : andreab@genetics.utah.edu or wej@bu.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 3
    Publication Date: 2016-07-13
    Description: Many prokaryotes utilize type IV secretion systems (T4SSs) to translocate substrates (e.g. nucleoprotein, DNA, protein) across the cell envelope, and/or to elaborate surface structures (i.e. pili or adhesins). Among eight distinct T4SS classes, P-T4SSs are typified by the Agrobacterium tumefaciens vir T4SS, which is comprised of 12 scaffold components (VirB1–VirB11, VirD4). While most P-T4SSs include all 12 Vir proteins, some differ from the vir archetype by either containing additional scaffold components not analogous to Vir proteins or lacking one or more of the Vir proteins. In a special case, the Rickettsiales vir homolog ( rvh ) P-T4SS comprises unprecedented gene family expansion. rvh contains three families of gene duplications ( rvhB9 , rvhB8 , rvhB4 ): RvhB9,8,4-I are conserved relative to equivalents in other P-T4SSs, while RvhB9,8,4-II have evolved atypical features that deviate substantially from other homologs. Furthermore, rvh contains five VirB6-like genes ( rvhB6a – e ), which are tandemly arrayed and contain large N- and C-terminal extensions. Our work herein focuses on the complexity underpinned by rvh gene family expansion. Furthermore, we describe an RvhB10 insertion, which occurs in a region that forms the T4SS pore. The significance of these curious properties to rvh structure and function is evaluated, shedding light on a highly complex T4SS.
    Print ISSN: 0928-8244
    Topics: Biology , Medicine
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  • 4
    Publication Date: 2015-01-25
    Description: We investigate the potential and accuracy of clustering-based redshift estimation using the method proposed by Ménard et al. This technique enables the inference of redshift distributions from measurements of the spatial clustering of arbitrary sources, using a set of reference objects for which redshifts are known. We apply it to a sample of spectroscopic galaxies from the Sloan Digital Sky Survey (SDSS) and show that, after carefully controlling the sampling efficiency over the sky, we can estimate redshift distributions with high accuracy. Probing the full colour space of the SDSS galaxies, we show that we can recover the corresponding mean redshifts with an accuracy ranging from z  = 0.001 to 0.01. We indicate that this mapping can be used to infer the redshift probability distribution of a single galaxy. We show how the lack of information on the galaxy bias limits the accuracy of the inference and show comparisons between clustering redshifts and photometric redshifts for this data set. This analysis demonstrates, using real data, that clustering-based redshift inference provides a powerful data-driven technique to explore the redshift distribution of arbitrary data sets, without any prior knowledge of the spectral energy distribution of the sources.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 5
    Publication Date: 2015-12-23
    Description: The increasing number of high rise buildings may contribute to lack of natural ventilation in modern buildings. Generally, fans and air conditioning are used in the modern building for cooling and air ventilation. Most of the energy in tropical regions are consumed by heating, cooling and ventilation appliances. Therefore, solar power appliances for cooling, heating and ventilation will be a suitable option for saving energy from the household sector. A modified-structure building is designed and constructed with solar chimney to enhance ventilation rate that increases cooling performance and ensure thermal comfort. An evaporative cooler is introduced with a newly designed room to enhance the temperature reduction capacity. The room temperature is compared with a non-modified room as well as with ambient temperature. The results show that passive cooling system with evaporative cooler was able to reduce temperature by 5°C compared to the ambient temperature and about 2°C to 3°C b...
    Print ISSN: 1757-8981
    Electronic ISSN: 1757-899X
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 6
    Publication Date: 2016-02-28
    Description: The Two-Micron All-Sky Survey (2MASS) has mapped out the low-redshift Universe down to K S  ~ 14 mag. As its near-infrared photometry primarily probes the featureless Rayleigh–Jeans tail of galaxy spectral energy distributions, colour-based redshift estimation is rather uninformative. Until now, redshift estimates for this data set have relied on optical follow-up suffering from selection biases. Here, we use the newly developed technique of clustering-based redshift estimation to infer the redshift distribution of the 2MASS sources regardless of their optical properties. We characterize redshift distributions of objects from the Extended Source Catalogue as a function of near-infrared colours and brightness and report some observed trends. We also apply the clustering redshift technique to dropout populations, sources with non-detections in one or more near-infrared bands, and present their redshift distributions. Combining all extended sources, we confirm with clustering redshifts that the distribution of this sample extends up to z  ~ 0.35. We perform a similar analysis with the Point Source Catalogue and show that it can be separated into stellar and extragalactic contributions with galaxies reaching z  ~ 0.7. We estimate that the Point Source Catalogue contains 1.6 million extragalactic objects: as many as in the Extended Source Catalogue but probing a cosmic volume 10 times larger.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 7
    Publication Date: 2015-11-05
    Description: Motivation: The Cancer Genome Atlas (TCGA) RNA-Sequencing data are used widely for research. TCGA provides ‘Level 3’ data, which have been processed using a pipeline specific to that resource. However, we have found using experimentally derived data that this pipeline produces gene-expression values that vary considerably across biological replicates. In addition, some RNA-Sequencing analysis tools require integer-based read counts, which are not provided with the Level 3 data. As an alternative, we have reprocessed the data for 9264 tumor and 741 normal samples across 24 cancer types using the Rsubread package. We have also collated corresponding clinical data for these samples. We provide these data as a community resource. Results: We compared TCGA samples processed using either pipeline and found that the Rsubread pipeline produced fewer zero-expression genes and more consistent expression levels across replicate samples than the TCGA pipeline. Additionally, we used a genomic-signature approach to estimate HER2 (ERBB2) activation status for 662 breast-tumor samples and found that the Rsubread data resulted in stronger predictions of HER2 pathway activity. Finally, we used data from both pipelines to classify 575 lung cancer samples based on histological type. This analysis identified various non-coding RNA that may influence lung-cancer histology. Availability and implementation: The RNA-Sequencing and clinical data can be downloaded from Gene Expression Omnibus (accession number GSE62944). Scripts and code that were used to process and analyze the data are available from https://github.com/srp33/TCGA_RNASeq_Clinical . Contact: stephen_piccolo@byu.edu or andreab@genetics.utah.edu Supplementary information: Supplementary material is available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 8
    Publication Date: 2015-11-20
    Description: This paper presents an investigation on titanium dioxide (TiO 2 ) and zinc oxide (ZnO) bilayer film, which is used as sensing membrane for extended-gate field effect transistor (EGFET) for pH sensing application. TiO 2 /ZnO thin films were deposited using sol-gel spin coating method on indium tin oxide (ITO) substrates. After the deposition, the bilayer films were annealed at constant temperatures which is 400 °C for 15, 30, 40 and 60 minutes. The sensitivity of the TiO 2 thin film towards pH buffer solution was measured by dipping the sensing membrane in pH4, pH7 and pH10 buffer solution. By varying the annealing time, we found that the TiO 2 /ZnO thin film annealed at 400°C for 15 minutes gave the highest sensitivity compared to other annealing conditions, with the value of 64.87 mV/pH.
    Print ISSN: 1757-8981
    Electronic ISSN: 1757-899X
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 9
    Publication Date: 2018-12-04
    Description: Since hundreds year ago, the application of natural dyes on batik is unique procedure to obtain special fabrics and colour. Today, this technique is gaining popularity all over the world, because of the increased awareness on environmental, ecological aspects, and pollution control. In this research, extraction of dyes from wood of Morinda citrifolia using simple precipitation assisted brine solution has been investigated. The color components extracted and isolated from Morinda citrifolia plant were characterized by Thin Layer Chromatography (TLC), IR techniques and reflectance methods. The natural dye extract obtained from the Morinda citrifolia was used for the dyeing of cotton fabrics. The results indicated that the extracted dye increase significant improvement in fabrics colour. The treated fabrics showed excellent antibacterial activity Gram-positive bacteria Staphylococcus aureus (S. aureus).
    Print ISSN: 1757-8981
    Electronic ISSN: 1757-899X
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 10
    Publication Date: 2018-08-01
    Description: Spatio-temporal analysis of Kilim River using Very High-Resolution (VHR) satellite image between the years of 2005 and 2012 are vital to assess river morphological changes and erosion detection over the specific time duration. Therefore, this study utilizes remote sensing and Geographical Information System (GIS) capabilities to identify the channel migration and shifting as well as to calculate the rate of erosion and accretion. Classification of the river from Quickbird and WorldView-2 images is carry out using Maximum Likelihood Classification (MLC) technique whereas feature selection tool performs to extract river feature from the raw image. Subsequently, river feature been overlaid to identify the changes of riverbank pattern and to calculate the rate of riverbank erosion in terms of area. The result shows the total area of erosion is 27252.959 m 2 and the total area of accretion is 6079.999 m 2 . A maximum erosion of 6993.102 m 2 detected at Se...
    Print ISSN: 1755-1307
    Electronic ISSN: 1755-1315
    Topics: Geography , Geosciences , Physics
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