616 research outputs found
Two-component regulation: modelling, predicting & identifying protein-protein interactions & assessing signalling networks of bacteria
Two-component signalling systems (TCSs) are found in most prokaryotic genomes. They typically comprise of two proteins, a histidine (or sensor) kinase (HK) and an associated response regulator (RR), containing transmitter and receiver domains respectively, which interact to achieve transfer of a phosphoryl group from a histidine residue (of the transmitter domain in the HK) to an aspartate residue (of the partner RR’s receiver domain). An automated analysis pipeline using the NCBI’s RPS-BLAST tool was developed to identify and classify all TCS genes from completed prokaryotic genomes using the PFAM and CDD protein domain databases. A large proportion of TCS genes were found to be simple hybrid kinases (HYs) containing both a transmitter domain and a receiver domain within a single protein, presumably the result of the fusion or combination of separate HK and RR genes. This propensity to consolidate functionality into a single protein was found to be limited in the presence of either a transmembrane sensory/input domain or a DNA binding domain – two spatially separated functions.
While HK and RR genes are usually found together in the genome, in some species a large proportion of TCS domains are found as part of complex hybrid kinases (genes containing multiple TCS domains), in isolated or orphaned genes, or in complex gene clusters. In such organisms the lack of paired HK and RR genes makes it difficult to define genome-encoded signalling networks.
Identifying paired transmitter and receiver domains from a pan-genomic survey of prokaryotes gives a database of amino acid sequences for thousands of interacting protein-protein
complexes. Covariation between columns of multiple sequence alignments (MSAs) identifies particular pairs of residues representing interactions within the docked complex. Using numerical scores, these amino acids pairs were successfully used as explanatory variables in a generalised linear model (GLM) to predict the probabilities of interaction between transmitter and receiver domains
Data-parallel intra decoding for block-based image and video coding on massively parallel architectures
Impact of sample preservation and manipulation on insect gut microbiome profiling : a test case with fruit flies (Diptera, Tephritidae)
High-throughput sequencing (HTS) techniques are of great value for the investigation of microbial communities, and have been extensively used to study the gut microbiome. While most studies focus on the human gut, many others have investigated insects. However, because of the rapid spread of HTS techniques, a lot of variation exists in the protocols for sample preparation. In the present study, we investigated the impact of two widely adopted sample-processing procedures preceding library preparation, i.e., preservation of insect tissue in 70% ethanol (EtOH) and sample dissection. We used the fruit fly Ceratitis capitata (Diptera: Tephritidae) as a model organism and set up two experiments, one comparing the effects of sample manipulation and preservation across life stages and the other across fruit samples from different sources. The results of this study showed no major effects of dissection on the outcome of HTS. However, EtOH preservation did have effects on the recovered gut microbiome, the main effect being a significant reduction of the dominant genus, Providencia, in EtOH-preserved samples. Less abundant bacterial groups were also affected resulting in altered microbial profiles obtained from samples preserved in 70% EtOH. These results have important implications for the planning of future studies and when comparing studies that used different sample preparation protocols
Ultra high definition video decoding with motion JPEG XR using the GPU
Many applications require real-time decoding of highresolution video pictures, for example, quick editing of video sequences in video editing applications. To increase decoding speed, parallelism can be exploited, yet, block-based image and video coding standards are difficult to decode in parallel because of the high number of dependencies between blocks. This paper investigates the parallel decoding capabilities of the new JPEG XR image coding standard for use on the massively-parallel architecture of the GPU. The potential of parallelism of the hierarchical frequency coding scheme used in the standard is addressed and a parallel decoding scheme is described suitable for real-time decoding of Ultra High Definition (4320p) Motion JPEG XR video sequences. Our results show a decoding speed of up to 46 frames per second for Ultra High Definition (4320p) sequences with high-dynamic range (32-bit/ 4: 2: 0) luma and chroma components
Reduced-complexity multiview prediction scheme with content-adaptive disparity vector estimation
Correlation modeling with decoder-side quantization distortion estimation for distributed video coding
Detectable HIV Viral Load in Kenya: Data from a Population-Based Survey.
IntroductionAt the individual level, there is clear evidence that Human Immunodeficiency Virus (HIV) transmission can be substantially reduced by lowering viral load. However there are few data describing population-level HIV viremia especially in high-burden settings with substantial under-diagnosis of HIV infection. The 2nd Kenya AIDS Indicator Survey (KAIS 2012) provided a unique opportunity to evaluate the impact of antiretroviral therapy (ART) coverage on viremia and to examine the risks for failure to suppress viral replication. We report population-level HIV viral load suppression using data from KAIS 2012.MethodsBetween October 2012 to February 2013, KAIS 2012 surveyed household members, administered questionnaires and drew serum samples to test for HIV and, for those found to be infected with HIV, plasma viral load (PVL) was measured. Our principal outcome was unsuppressed HIV viremia, defined as a PVL ≥ 550 copies/mL. The exposure variables included current treatment with ART, prior history of an HIV diagnosis, and engagement in HIV care. All point estimates were adjusted to account for the KAIS 2012 cluster sampling design and survey non-response.ResultsOverall, 61·2% (95% CI: 56·4-66·1) of HIV-infected Kenyans aged 15-64 years had not achieved virological suppression. The base10 median (interquartile range [IQR]) and mean (95% CI) VL was 4,633 copies/mL (0-51,596) and 81,750 copies/mL (59,366-104,134), respectively. Among 266 persons taking ART, 26.1% (95% CI: 20.0-32.1) had detectable viremia. Non-ART use, younger age, and lack of awareness of HIV status were independently associated with significantly higher odds of detectable viral load. In multivariate analysis for the sub-sample of patients on ART, detectable viremia was independently associated with younger age and sub-optimal adherence to ART.DiscussionThis report adds to the limited data of nationally-representative surveys to report population- level virological suppression. We established heterogeneity across the ten administrative and HIV programmatic regions on levels of detectable viral load. Timely initiation of ART and retention in care are crucial for the elimination of transmission of HIV through sex, needle and syringe use or from mother to child. Further refinement of geospatial mapping of populations with highest risk of transmission is necessary
Structural and magnetic characterization of very thin Co-Cr films
In this paper we describe the nucleation and growth of thin Co-Cr layers on different substrates and seedlayers. Especially the presence and formation of the initial layer is considered, and corresponding growth mechanisms are proposed. The magnetic properties of these layers have been analyzed by in-plane VSM and by anomalous Hall effect (AHE) measurements. Even layers as thin as 5 nm are shown to exhibit a perpendicular magnetic anisotropy. For a high coercive Co-Cr film the formation of dot-like domains is shown by the Bitter-colloid/SEM technique
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