Quantitative Comparison of Abundance Structures of Generalized Communities: From B-Cell Receptor Repertoires to Microbiomes

The \emph{community}, the assemblage of organisms co-existing in a given space and time, has the potential to become one of the unifying concepts of biology, especially with the advent of high-throughput sequencing experiments that reveal genetic diversity exhaustively. In this spirit we show that a tool from community ecology, the Rank Abundance Distribution (RAD), can be turned by the new MaxRank normalization method into a generic, expressive descriptor for quantitative comparison of communities in many areas of biology. To illustrate the versatility of the method, we analyze RADs from various \emph{generalized communities}, i.e.\ assemblages of genetically diverse cells or organisms, including human B cells, gut microbiomes under antibiotic treatment and of different ages and countries of origin, and other human and environmental microbial communities. We show that normalized RADs enable novel quantitative approaches that help to understand structures and dynamics of complex generalize communities

Oceanic heat advection to the Arctic in the last Millennium

EGU2011-8738 At present, the Arctic is responding faster to global warming than most other areas on earth, as indicated by rising air temperatures, melting glaciers and ice sheets and a decline of the sea ice cover. As part of the meridional overturning circulation which connects all ocean basins and influences global climate, northward flowing Atlantic Water is the major means of heat and salt advection towards the Arctic where it strongly affects the sea ice distribution. Records of its natural variability are critical for the understanding of feedback mechanisms and the future of the Arctic climate system, but continuous historical records reach back only ca. 150 years. To reconstruct the history of temperature variations in the Fram Strait Branch of the Atlantic Current we analyzed a marine sediment core from the western Svalbard margin. In multidecadal resolution the Atlantic Water temperature record derived from planktic foraminifer associations and Mg/Ca measurements shows variations corresponding to the well-known climatic periods of the last millennium (Medieval Climate Anomaly, Little Ice Age, Modern/Industrial Period). We find that prior to the beginning of atmospheric CO2 rise at ca. 1850 A.D. average summer temperatures in the uppermost Atlantic Water entering the Arctic Ocean were in the range of 3-4.5°C. Within the 20th century, however, temperatures rose by ca. 2°C and eventually reached the modern level of ca. 6°C. Such values are unprecedented in the 1000 years before and are presumably linked to the Arctic Amplification of global warming. Taking into account the ongoing rise of global temperatures, further warming of inflowing Atlantic Water is expected to have a profound influence on sea ice and air temperatures in the Arctic

Fine Particulate air Pollution is Associated with Higher Vulnerability to Atrial Fibrillation—The APACR Study

The acute effects and the time course of fine particulate pollution (PM2.5) on atrial fibrillation/flutter (AF) predictors, including P-wave duration, PR interval duration, and P-wave complexity, were investigated in a community-dwelling sample of 106 nonsmokers. Individual-level 24-h beat-to-beat electrocardiogram (ECG) data were visually examined. After identifying and removing artifacts and arrhythmic beats, the 30-min averages of the AF predictors were calculated. A personal PM2.5 monitor was used to measure individual-level, real-time PM2.5 exposures during the same 24-h period, and corresponding 30-min average PM2.5 concentration were calculated. Under a linear mixed-effects modeling framework, distributed lag models were used to estimate regression coefficients (βs) associating PM2.5 with AF predictors. Most of the adverse effects on AF predictors occurred within 1.5–2 h after PM2.5 exposure. The multivariable adjusted βs per 10-µg/m3 rise in PM2.5 at lag 1 and lag 2 were significantly associated with P-wave complexity. PM2.5 exposure was also significantly associated with prolonged PR duration at lag 3 and lag 4. Higher PM2.5 was found to be associated with increases in P-wave complexity and PR duration. Maximal effects were observed within 2 h. These findings suggest that PM2.5 adversely affects AF predictors; thus, PM2.5 may be indicative of greater susceptibility to AF

Amino acid substitutions within HLA-B*27- restricted T cell epitopes prevent recognition by hepatitis delta virus-specific CD8+ T cells

Virus-specific CD8 T cell response seems to play a significant role in the outcome of hepatitis delta virus (HDV) infection. However, the HDV-specific T cell epitope repertoire and mechanisms of CD8 T cell failure in HDV infection have been poorly characterized. We therefore aimed to characterize HDV-specific CD8 T cell epitopes and the impacts of viral mutations on immune escape. In this study, we predicted peptide epitopes binding the most frequent human leukocyte antigen (HLA) types and assessed their HLA binding capacities. These epitopes were characterized in HDV-infected patients by intracellular gamma interferon (IFN-γ) staining. Sequence analysis of large hepatitis delta antigen (L-HDAg) and HLA typing were performed in 104 patients. The impacts of substitutions within epitopes on the CD8 T cell response were evaluated experimentally and by in silico studies. We identified two HLA-B*27-restricted CD8 T cell epitopes within L-HDAg. These novel epitopes are located in a relatively conserved region of L-HDAg. However, we detected molecular footprints within the epitopes in HLA-B*27-positive patients with chronic HDV infections. The variant peptides were not cross-recognized in HLA-B*27-positive patients with resolved HDV infections, indicating that the substitutions represent viral escape mutations. Molecular modeling of HLA-B*27 complexes with the L-HDAg epitope and its potential viral escape mutations indicated that the structural and electrostatic properties of the bound peptides differ considerably at the T cell receptor interface, which provides a possible molecular explanation for the escape mechanism. This viral escape from the HLA-B*27-restricted CD8 T cell response correlates with a chronic outcome of hepatitis D infection. T cell failure resulting from immune escape may contribute to the high chronicity rate in HDV infection. © 2018 American Society for Microbiology

Modeling and Bioinformatics Identify Responders to G-CSF in Patients With Amyotrophic Lateral Sclerosis

Objective: Developing an integrative approach to early treatment response classification using survival modeling and bioinformatics with various biomarkers for early assessment of filgrastim (granulocyte colony stimulating factor) treatment effects in amyotrophic lateral sclerosis (ALS) patients. Filgrastim, a hematopoietic growth factor with excellent safety, routinely applied in oncology and stem cell mobilization, had shown preliminary efficacy in ALS. Methods: We conducted individualized long-term filgrastim treatment in 36 ALS patients. The PRO-ACT database, with outcome data from 23 international clinical ALS trials, served as historical control and mathematical reference for survival modeling. Imaging data as well as cytokine and cellular data from stem cell analysis were processed as biomarkers in a non-linear principal component analysis (NLPCA) to identify individual response. Results: Cox proportional hazard and matched-pair analyses revealed a significant survival benefit for filgrastim-treated patients over PRO-ACT comparators. We generated a model for survival estimation based on patients in the PRO-ACT database and then applied the model to filgrastim-treated patients. Model-identified filgrastim responders displayed less functional decline and impressively longer survival than non-responders. Multimodal biomarkers were then analyzed by PCA in the context of model-defined treatment response, allowing identification of subsequent treatment response as early as within 3 months of therapy. Strong treatment response with a median survival of 3.8 years after start of therapy was associated with younger age, increased hematopoietic stem cell mobilization, less aggressive inflammatory cytokine plasma profiles, and preserved pattern of fractional anisotropy as determined by magnetic resonance diffusion tensor imaging (DTI-MRI). Conclusion: Long-term filgrastim is safe, is well-tolerated, and has significant positive effects on disease progression and survival in a small cohort of ALS patients. Developing and applying a model-based biomarker response classification allows use of multimodal biomarker patterns in full potential. This can identify strong individual treatment responders (here: filgrastim) at a very early stage of therapy and may pave the way to an effective individualized treatment option

DNA methylation associated with persistent ADHD suggests TARBP1 as novel candidate

Contains fulltext : 231077.pdf (Publisher’s version ) (Open Access

Enhanced modern heat transfer to the Arctic by warm Atlantic water

The Arctic is responding more rapidly to global warming than most other areas on our planet. Northward-flowing Atlantic Water is the major means of heat advection toward the Arctic and strongly affects the sea ice distribution. Records of its natural variability are critical for the understanding of feedback mechanisms and the future of the Arctic climate system, but continuous historical records reach back only ~150 years. Here, we present a multidecadal-scale record of ocean temperature variations during the past 2000 years, derived from marine sediments off Western Svalbard (79°N). We find that early–21st-century temperatures of Atlantic Water entering the Arctic Ocean are unprecedented over the past 2000 years and are presumably linked to the Arctic amplification of global warming