γ-glutamyltransferase is linked to proteomic adaptions important for colonization.

γ-glutamyltransferase (gGT) is a virulence factor that promotes bacterial colonization and immune tolerance. Although some studies addressed potential functional mechanisms, the supportive role of gGT for colonization remains unclear. Additionally, it is unknown how different gGT expression levels may lead to compensatory mechanisms ensuring infection and persistence.

Gut microbiome alterations precede graft rejection in kidney transplantation patients.

Kidney transplantation (KT) is the best treatment for end-stage kidney disease, with graft survival critically affected by the recipient's immune response. The role of the gut microbiome in modulating this immune response remains underexplored. Our study investigates how microbiome alterations might be associated with allograft rejection by analyzing the gut microbiome using 16S rRNA gene amplicon sequencing of a multicenter prospective study involving 562 samples from 245 individuals of whom 217 received KT.

Comprehensive assessment of imaging quality of artificial intelligence-assisted compressed sensing-based MR images in routine clinical settings.

Background: Conventional MR acceleration techniques, such as compressed sensing, parallel imaging, and half Fourier often face limitations, including noise amplification, reduced signal-to-noise ratio (SNR) and increased susceptibility to artifacts, which can compromise image quality, especially in high-speed acquisitions. Artificial intelligence (AI)-assisted compressed sensing (ACS) has emerged as a novel approach that combines the conventional techniques with advanced AI algorithms. The objective of this study was to examine the imaging quality of the ACS approach by qualitative and quantitative analysis for brain, spine, kidney, liver, and knee MR imaging, as well as compare the performance of this method with conventional (non-ACS) MR imaging.

Machine learning-based analysis of a semi-automated PI-RADS v2.1 scoring for prostate cancer.

Background: Prostate Imaging-Reporting and Data System version 2.1 (PI-RADS v2.1) was developed to standardize the interpretation of multiparametric MRI (mpMRI) for prostate cancer (PCa) detection.

Unboxing the black box-one step forward to understand the soil microbiome: A systematic review.

Soil is one of the most important assets of the planet Earth, responsible for maintaining the biodiversity and managing the ecosystem services for both managed and natural ecosystems. It encompasses large proportion of microscopic biodiversity, including prokaryotes and the microscopic eukaryotes. Soil microbiome is critical in managing the soil functions, but their activities have diminutive recognition in few systems like desert land and forest ecosystems.

Assessment of regional water demand for coal-based power plants in India: exploring its regional impact on other cross-sectoral water stress.

Water use in coal power generation is one of the key points to highlight for the countries like India because country electricity demand increases rapidly which led to increase in water demand. The coal power sector in India will remain to be the dominant source of electricity generation until 2040 and will require a regular water supply, which is already in a stressful condition. This work focuses on the regional assessment of water withdrawal and consumption of the coal power sector at three broad stages includes fuel extraction, fuel preparation, and power generation.

Characterisation of prostate cancer using texture analysis for diagnostic and prognostic monitoring.

Automated classification of significant prostate cancer (PCa) using MRI plays a potential role in assisting in clinical decision-making. Multiparametric MRI using a machine-aided approach is a better step to improve the overall accuracy of diagnosis of PCa. The objective of this study was to develop and validate a framework for differentiating Prostate Imaging-Reporting and Data System version 2 (PI-RADS v2) grades (grade 2 to grade 5) of PCa using texture features and machine learning (ML) methods with diffusion-weighted imaging (DWI) and apparent diffusion coefficient (ADC).

Segmentation of prostate zones using probabilistic atlas-based method with diffusion-weighted MR images.

Background And Objective: Accurate segmentation of prostate and its zones constitute an essential preprocessing step for computer-aided diagnosis and detection system for prostate cancer (PCa) using diffusion-weighted imaging (DWI). However, low signal-to-noise ratio and high variability of prostate anatomic structures are challenging for its segmentation using DWI. We propose a semi-automated framework that segments the prostate gland and its zones simultaneously using DWI.

Tropical forest conversion to rubber plantation in southwest China results in lower fungal beta diversity and reduced network complexity.

Despite the extensive, ongoing conversion of tropical forests to rubber plantation, the effects of this land-use change on soil fungal community diversity and composition are still poorly known. We compared a network of sites of tropical forest in southern Yunnan, China, with a network of rubber plantation sites originally derived from this forest. Soil DNA was amplified for ITS2 and sequenced using Illumina MiSeq.

Tropical forest conversion to rubber plantation affects soil micro- & mesofaunal community & diversity.

Tropical rainforests play important roles in carbon sequestration and are hot spots for biodiversity. Tropical forests are being replaced by rubber (Hevea brasiliensis) plantations, causing widespread concern of a crash in biodiversity. Such changes in aboveground vegetation might have stronger impacts on belowground biodiversity.

Diversity and Distribution of Thermophilic Bacteria in Hot Springs of Pakistan.

Chilas and Hunza areas, located in the Main Mantle Thrust and Main Karakoram Thrust of the Himalayas, host a range of geochemically diverse hot springs. This Himalayan geothermal region encompassed hot springs ranging in temperature from 60 to 95 °C, in pH from 6.2 to 9.

Similarities and Contrasts in the Archaeal Community of Two Japanese Mountains: Mt. Norikura Compared to Mt. Fuji.

The community ecology, abundance, and diversity patterns of soil archaea are poorly understood-despite the fact that they are a major branch of life that is ubiquitous and important in nitrogen cycling in terrestrial ecosystems. We set out to investigate the elevational patterns of archaeal ecology, and how these compare with other groups of organisms. Many studies of different groups of organisms (plants, birds, etc.

Duplicate analysis method: a cheaper alternative to commercial IQC materials in limited resource settings for monitoring CD4 testing.

Background: India has a large number of HIV infected patients being followed up at anti-retroviral therapy (ART) centers. The patients are regularly offered CD4 count estimation for deciding their eligibility for ART initiation as well as for monitoring response to ART, making CD4 count estimation a very critical test. Hence, quality control of CD4 testing is utmost important for ultimate success of ART program.

Effects of functionalized and raw multi-walled carbon nanotubes on soil bacterial community composition.

Carbon nanotubes (CNTs) are widely used in industry, but their environmental impacts on soil microbial communities are poorly known. In this paper, we compare the effect of both raw and acid treated or functionalized (fCNTs) multi-walled carbon nanotubes (MWCNTs) on soil bacterial communities, applying different concentrations of MWCNTs (0 µg/g, 50 µg/g, 500 µg/g and 5000 µg/g) to a soil microcosm system. Soil DNA was extracted at 0, 2 and 8 weeks and the V3 region of the 16S rRNA gene was PCR-amplified and sequenced using paired-end Illumina bar-coded sequencing.

Spatial scaling effects on soil bacterial communities in Malaysian tropical forests.

Spatial scaling to some extent determines biodiversity patterns in larger organisms, but its role in microbial diversity patterns is much less understood. Some studies have shown that bacterial community similarity decreases with distance, whereas others do not support this. Here, we studied soil bacterial communities of tropical rainforest in Malaysia at two spatial scales: a local scale with samples spaced every 5 mover a 150-m transect, and a regional scale with samples 1 to 1,800 km apart.

Bacterial diversity in the mountains of South-West China: climate dominates over soil parameters.

Certain patterns in soil bacterial diversity and community composition have become evident from metagenomics studies on a range of scales, from various parts of the world. For example, soil pH has generally been seen as dominating variation in bacterial diversity, above all other soil and climate parameters. It is important however to test the generality of these relationships by studying previously un-sampled areas.

Differential modulation of phenotypic composition of HIV-infected and -uninfected PBMCs during cryopreservation.

This article was designed to determine variations in phenotypic composition of fresh and frozen PBMCs for assessing utility of cryopreserved PBMCs for phenotypic assays. Relative percentages of effector memory cells increased significantly as against percentages of naïve cells which showed significant decrease after cryopreservation in HIV-uninfected samples. These differences were not significant in HIV-infected individuals.

Elevational patterns in archaeal diversity on Mt. Fuji.

Little is known of how archaeal diversity and community ecology behaves along elevational gradients. We chose to study Mount Fuji of Japan as a geologically and topographically uniform mountain system, with a wide range of elevational zones. PCR-amplified soil DNA for the archaeal 16 S rRNA gene was pyrosequenced and taxonomically classified against EzTaxon-e archaeal database.

Tropical soil bacterial communities in Malaysia: pH dominates in the equatorial tropics too.

The dominant factors controlling soil bacterial community variation within the tropics are poorly known. We sampled soils across a range of land use types--primary (unlogged) and logged forests and crop and pasture lands in Malaysia. PCR-amplified soil DNA for the bacterial 16S rRNA gene targeting the V1-V3 region was pyrosequenced using the 454 Roche machine.

Distinctive phyllosphere bacterial communities in tropical trees.

Recent work has suggested that in temperate and subtropical trees, leaf surface bacterial communities are distinctive to each individual tree species and dominated by Alpha- and Gammaproteobacteria. In order to understand how general this pattern is, we studied the phyllosphere bacterial community on leaves of six species of tropical trees at a rainforest arboretum in Malaysia. This represents the first detailed study of 'true' tropical lowland tree phyllosphere communities.

Short communication: HIV antigen-specific reactivation of HIV infection from cellular reservoirs: implications in the settings of therapeutic vaccinations.

Therapeutic vaccinations using human immunodeficiency virus (HIV) antigens in HIV-infected patients on antiretroviral therapy (ART) have so far been attempted with the purpose of inducing CTL response. However, they can also be useful as a strategy for activation of latent HIV reservoir, which is thought to be mainly comprised of latently infected HIV-specific memory CD4 cells, eventually leading to elimination of the virus. The present study was carried out to explore the ability of different HIV antigens to activate HIV replication as assessed by intracellular P24 detection as well as to induce T cell responses in terms of cytokine expression by flow cytometry after stimulation of PBMCs from HIV-infected patients.

A hump-backed trend in bacterial diversity with elevation on Mount Fuji, Japan.

Little is known of how bacterial diversity in soils varies with elevation. One previous study found a decline with elevation, whereas another found no trend. We chose Mount Fuji of Japan as a geologically and topographically simple mountain system.