De novo transcriptome analysis of Perna viridis highlights tissue-specific patterns for environmental studies

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Ultrasonic tomographic imaging of defects in industrial materials

Ultrasonic tomography has been fairly widely applied for imaging of inhomogeneities in isotropic materials, particularly in the medical field, however, little success has been made in its application to industrial materials. This is largely due to the complex nature of ultrasonic wave propagation in these anisotropic materials. The three dimensional characteristics of ultrasonic wave propagation in anisotropic materials have been thoroughly studied for single crystals and also studied recently for different composites [1,2,3]. Understanding these characteristics provides the theoretical background for developing appropriate ultrasonic tomographic imaging methods for industrial materials

Functional compensation of glutathione S-transferase M1 (GSTM1) null by another GST superfamily member,GSTM2

The gene for glutathione-S-transferase (GST) M1 (GSTM1), a member of the GST-superfamily, is widely studied in cancer risk with regard to the homozygous deletion of the gene (GSTM1 null), leading to a lack of corresponding enzymatic activity. Many of these studies have reported inconsistent findings regarding its association with cancer risk. Therefore, we employed in silico, in vitro, and in vivo approaches to investigate whether the absence of a functional GSTM1 enzyme in a null variant can be compensated for by other family members. Through the in silico approach, we identified maximum structural homology between GSTM1 and GSTM2. Total plasma GST enzymatic activity was similar in recruited individuals, irrespective of their GSTM1 genotype (positive/null). Furthermore, expression profiling using real-time PCR, western blotting, and GSTM2 overexpression following transient knockdown of GSTM1 in HeLa cells confirmed that the absence of GSTM1 activity can be compensated for by the overexpression of GSTM

A Reverse Transcriptase-PCR Assay for Detecting Filarial Infective Larvae in Mosquitoes

The Global Programme for the Elimination of Lymphatic Filariasis (GPELF) was launched in the year 1998 with the goal of eliminating lymphatic filariasis by 2020. As the success of mass drug administration (MDA) in the global program drives the rates of infection in endemic populations to very low levels, the development of new, highly sensitive methods are required for monitoring transmission by screening mosquitoes for the presence of L3 infective larvae. The current method of mosquito dissection to identify L3 larvae is laborious and insensitive and is not amenable to screening large numbers of mosquitoes. Existing molecular assays for the detection of filarial parasite DNA in mosquitoes are sensitive and can easily screen large numbers of vectors. However, current PCR-based methods cannot distinguish between infected mosquitoes that contain any stage of the parasite and infective mosquitoes that harbor third stage larvae (L3) capable of establishing new infections in humans. This paper reports the first development of a molecular L3-detection assay for a filarial parasite in mosquitoes based on RT-PCR detection of an L3-activated gene transcript. This strategy of detecting stage-specific messenger RNA from filarial parasites may also prove useful for detecting infective stages of other vector-borne pathogens

Simulating biosignatures from pre-oxygen photosynthesising life on TRAPPIST-1e

This is the author accepted manuscript. The final version is available on open access from Oxford University Press via the DOI in this recordData availability: The model output used for this study will be made available following this work’s acceptance for publicationIn order to assess observational evidence for potential atmospheric biosignatures on exoplanets, it will be essential to test whether spectral fingerprints from multiple gases can be explained by abiotic or biotic-only processes. Here, we develop and apply a coupled 1D atmosphere-ocean-ecosystem model to understand how primitive biospheres, which exploit abiotic sources of H2 , CO and O2 , could influence the atmospheric composition of rocky terrestrial exoplanets. We apply this to the Earth at 3.8 Ga and to TRAPPIST-1e. We focus on metabolisms that evolved before the evolution of oxygenic photosynthesis, which consume H2 and CO and produce potentially detectable levels of CH4 . O2 -consuming metabolisms are also considered for TRAPPIST-1e, as abiotic O2 production is predicted on M-dwarf orbiting planets. We show that these biospheres can lead to high levels of surface O2 (approximately 1–5 %) as a result of CO consumption, which could allow high O2 scenarios, by removing the main loss mechanisms of atomic oxygen. Increasing stratospheric temperatures, which increases atmospheric OH can reduce the likelihood of such a state forming. O2 -consuming metabolisms could also lower O2 levels to around 10 ppm and support a productive biosphere at low reductant inputs. Using predicted transmission spectral features from CH4 , CO, O2 /O3 and CO2 across the hypothesis space for tectonic reductant input, we show that biotically-produced CH4 may only be detectable at high reductant inputs. CO is also likely to be a dominant feature in transmission spectra for planets orbiting M-dwarfs, which could reduce the confidence in any potential biosignature observations linked to these biospheres.Science and Technology Facilities Council (STFC)UK Research and InnovationJohn Templeton FoundationLeverhulme TrustHill Family ScholarshipInstitute of Physic

FPGA acceleration of the phylogenetic likelihood function for Bayesian MCMC inference methods

Background Likelihood (ML)-based phylogenetic inference has become a popular method for estimating the evolutionary relationships among species based on genomic sequence data. This method is used in applications such as RAxML, GARLI, MrBayes, PAML, and PAUP. The Phylogenetic Likelihood Function (PLF) is an important kernel computation for this method. The PLF consists of a loop with no conditional behavior or dependencies between iterations. As such it contains a high potential for exploiting parallelism using micro-architectural techniques. In this paper, we describe a technique for mapping the PLF and supporting logic onto a Field Programmable Gate Array (FPGA)-based co-processor. By leveraging the FPGA\u27s on-chip DSP modules and the high-bandwidth local memory attached to the FPGA, the resultant co-processor can accelerate ML-based methods and outperform state-of-the-art multi-core processors. Results We use the MrBayes 3 tool as a framework for designing our co-processor. For large datasets, we estimate that our accelerated MrBayes, if run on a current-generation FPGA, achieves a 10× speedup relative to software running on a state-of-the-art server-class microprocessor. The FPGA-based implementation achieves its performance by deeply pipelining the likelihood computations, performing multiple floating-point operations in parallel, and through a natural log approximation that is chosen specifically to leverage a deeply pipelined custom architecture. Conclusions Heterogeneous computing, which combines general-purpose processors with special-purpose co-processors such as FPGAs and GPUs, is a promising approach for high-performance phylogeny inference as shown by the growing body of literature in this field. FPGAs in particular are well-suited for this task because of their low power consumption as compared to many-core processors and Graphics Processor Units (GPUs)

The Relationship Between Stigma and Health-Related Quality of Life in People Living with HIV Who Have Full Access to Antiretroviral Treatment: An Assessment of Earnshaw and Chaudoir's HIV Stigma Framework Using Empirical Data.

The aim was to empirically test the tenets of Earnshaw and Chaudoir's HIV stigma framework and its potential covariates for persons living with HIV in Sweden. Partial least squares structural equation modelling was used on survey data from 173 persons living with HIV in Sweden. Experiencing stigma was reported to a higher extent by younger persons and by women who had migrated to Sweden. As expected, anticipated stigma was related to lower Physical functioning, and internalized stigma to lower Emotional wellbeing. In contrast to that hypothesized by the HIV stigma framework, enacted stigma was not related to Physical functioning and no relationships were found between HIV-related stigma and antiretroviral adherence. These results indicate that the HIV stigma framework may need to be revised for contexts where a very high proportion of persons living with HIV are diagnosed and under efficient treatment

Midgut Barrier Imparts Selective Resistance to Filarial Worm Infection in Culex pipiens pipiens

Mosquitoes in the Culex pipiens complex thrive in temperate and tropical regions worldwide, and serve as efficient vectors of Bancroftian lymphatic filariasis (LF) caused by Wuchereria bancrofti in Asia, Africa, the West Indies, South America, and Micronesia. However, members of this mosquito complex do not act as natural vectors for Brugian LF caused by Brugia malayi, or for the cat parasite B. pahangi, despite their presence in South Asia where these parasites are endemic. Previous work with the Iowa strain of Culex pipiens pipiens demonstrates that it is equally susceptible to W. bancrofti as is the natural Cx. p. pipiens vector in the Nile Delta, however it is refractory to infection with Brugia spp. Here we report that the infectivity barrier for Brugia spp. in Cx. p. pipiens is the mosquito midgut, which inflicts internal and lethal damage to ingested microfilariae. Following per os Brugia exposures, the prevalence of infection is significantly lower in Cx. p. pipiens compared to susceptible mosquito controls, and differs between parasite species with <50% and <5% of Cx. p. pipiens becoming infected with B. pahangi and B. malayi, respectively. When Brugia spp. mf were inoculated intrathoracically to bypass the midgut, larvae developed equally well as in controls, indicating that, beyond the midgut, Cx. p. pipiens is physiologically compatible with Brugia spp. Mf isolated from Cx. p. pipiens midguts exhibited compromised motility, and unlike mf derived from blood or isolated from the midguts of Ae. aegypti, failed to develop when inoculated intrathoracically into susceptible mosquitoes. Together these data strongly support the role of the midgut as the primary infection barrier for Brugia spp. in Cx. p. pipiens. Examination of parasites recovered from the Cx. p. pipiens midgut by vital staining, and those exsheathed with papain, suggest that the damage inflicted by the midgut is subcuticular and disrupts internal tissues. Microscopic studies of these worms reveal compromised motility and sharp bends in the body; and ultrastructurally the presence of many fluid or carbohydrate-filled vacuoles in the hypodermis, body wall, and nuclear column. Incubation of Brugia mf with Cx. p. pipiens midgut extracts produces similar internal damage phenotypes; indicating that the Cx. p. pipiens midgut factor(s) that damage mf in vivo are soluble and stable in physiological buffer, and inflict damage on mf in vitro