Continuous noninvasive arterial pressure measurement using the volume clamp method: an evaluation of the CNAP device in intensive care unit patients.

The CNAP system allows continuous noninvasive arterial pressure measurement based on the volume clamp method using a finger cuff. We aimed to evaluate the agreement between arterial pressure measurements noninvasively obtained using the CNAP device and arterial catheter-derived arterial pressure measurements in intensive care unit patients. In 55 intensive care unit patients, we simultaneously recorded arterial pressure values obtained by an arterial catheter placed in the abdominal aorta through the femoral artery (criterion standard) and arterial pressure values determined noninvasively using CNAP.

Real-time monitoring of binding events on a thermostabilized human A2A receptor embedded in a lipid bilayer by surface plasmon resonance.

Membrane proteins (MPs) are prevalent drug discovery targets involved in many cell processes. Despite their high potential as drug targets, the study of MPs has been hindered by limitations in expression, purification and stabilization in order to acquire thermodynamic and kinetic parameters of small molecules binding. These bottlenecks are grounded on the mandatory use of detergents to isolate and extract MPs from the cell plasma membrane and the coexistence of multiple conformations, which reflects biochemical versatility and intrinsic instability of MPs.

Therapy-induced brain reorganization patterns in aphasia.

Both hemispheres are engaged in recovery from word production deficits in aphasia. Lexical therapy has been shown to induce brain reorganization even in patients with chronic aphasia. However, the interplay of factors influencing reorganization patterns still remains unresolved.

Orchestrating high-throughput genomic analysis with Bioconductor.

Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology. The project aims to enable interdisciplinary research, collaboration and rapid development of scientific software. Based on the statistical programming language R, Bioconductor comprises 934 interoperable packages contributed by a large, diverse community of scientists.

A discrete transition zone organizes the topological and regulatory autonomy of the adjacent tfap2c and bmp7 genes.

Despite the well-documented role of remote enhancers in controlling developmental gene expression, the mechanisms that allocate enhancers to genes are poorly characterized. Here, we investigate the cis-regulatory organization of the locus containing the Tfap2c and Bmp7 genes in vivo, using a series of engineered chromosomal rearrangements. While these genes lie adjacent to one another, we demonstrate that they are independently regulated by distinct sets of enhancers, which in turn define non-overlapping regulatory domains.

The Bioconductor channel in F1000Research.

Bioconductor ( bioconductor.org) is a rich source of software and know-how for the integrative analysis of genomic data. The Bioconductor channel in F1000Research provides a forum for task-oriented workflows that cover a solution to a current, important problem in genome-scale data analysis.

Protein quality control at the inner nuclear membrane.

The nuclear envelope is a double membrane that separates the nucleus from the cytoplasm. The inner nuclear membrane (INM) functions in essential nuclear processes including chromatin organization and regulation of gene expression. The outer nuclear membrane is continuous with the endoplasmic reticulum and is the site of membrane protein synthesis.

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.

In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates.

Transcriptome-wide profiling and posttranscriptional analysis of hematopoietic stem/progenitor cell differentiation toward myeloid commitment.

Hematopoietic stem cells possess lifelong self-renewal activity and generate multipotent progenitors that differentiate into lineage-committed and subsequently mature cells. We present a comparative transcriptome analysis of ex vivo isolated mouse multipotent hematopoietic stem/progenitor cells (Lin(neg)SCA-1(+)c-KIT(+)) and myeloid committed precursors (Lin(neg)SCA-1(neg)c-KIT(+)). Our data display dynamic transcriptional networks and identify a stem/progenitor gene expression pattern that is characterized by cell adhesion and immune response components including kallikrein-related proteases.

Fungal "colonisation" is associated with increased mortality in medical intensive care unit patients with liver cirrhosis.

Objectives: Patients with liver cirrhosis are at increased risk for fungal infections. However, distinction of fungal colonisation (FC) and invasive mycoses is difficult. Aim of this study was to analyse the impact of FC on mortality of cirrhotic ICU-patients.

HTSeq--a Python framework to work with high-throughput sequencing data.

Motivation: A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from standard workflows, custom scripts are needed.

Results: We present HTSeq, a Python library to facilitate the rapid development of such scripts.

Room-temperature vs iced saline indicator injection for transpulmonary thermodilution.

Purpose: Ice-cold injectate is assumed to provide best accuracy for transpulmonary thermodilution (TPTD)-derived cardiac index (CI), global end-diastolic volume index (GEDVI), and extravascular lung-water index (EVLWI). Room-temperature injectate might facilitate TPTD. Therefore, this study compares TPTD-results derived from iced injectate with room-temperature injectate TPTDs (TPTDRoom).

The effects of transjugular intrahepatic portosystemic stent shunt on systemic cardiocirculatory parameters.

Purpose: We aimed to evaluate the effects of transjugular intrahepatic portosystemic stent shunt (TIPS) on systemic cardiocirculatory parameters in patients treated with TIPS for portal hypertension-associated complications.

Materials And Methods: This prospective study was conducted in an intensive care unit of a German university hospital (October 2010-July 2013). We assessed hemodynamic parameters before and after TIPS placement using single-indicator transpulmonary thermodilution and pulse contour analysis.

Measuring genetic interactions in human cells by RNAi and imaging.

Observation of how genetic interactions modulate phenotypes is a powerful method for dissecting their underlying molecular and functional networks. Whereas in model organisms genetic interaction studies are well established, systematic analysis of genetic interactions in human cells has remained challenging. Here we provide a detailed protocol for large-scale mapping of genetic interactions in human cells using a high-throughput phenotyping approach.

Identification of regulatory networks in HSCs and their immediate progeny via integrated proteome, transcriptome, and DNA methylome analysis.

In this study, we present integrated quantitative proteome, transcriptome, and methylome analyses of hematopoietic stem cells (HSCs) and four multipotent progenitor (MPP) populations. From the characterization of more than 6,000 proteins, 27,000 transcripts, and 15,000 differentially methylated regions (DMRs), we identified coordinated changes associated with early differentiation steps. DMRs show continuous gain or loss of methylation during differentiation, and the overall change in DNA methylation correlates inversely with gene expression at key loci.

Association between different indexations of extravascular lung water (EVLW) and PaO2/FiO2: a two-center study in 231 patients.

Background: Variability of body weight (BW) and height calls for indexation of volumetric hemodynamic parameters. Extravascular lung water (EVLW) has formerly been indexed to actual BW (BW(act)) termed EVLW-index (EVLWI). In overweight patients indexation to BW(act) might inappropriately lower indexed EVLWI(act).

Enhancer loops appear stable during development and are associated with paused polymerase.

Developmental enhancers initiate transcription and are fundamental to our understanding of developmental networks, evolution and disease. Despite their importance, the properties governing enhancer-promoter interactions and their dynamics during embryogenesis remain unclear. At the β-globin locus, enhancer-promoter interactions appear dynamic and cell-type specific, whereas at the HoxD locus they are stable and ubiquitous, being present in tissues where the target genes are not expressed.

The processing of lexical ambiguity in healthy ageing and Parkinson׳s disease: role of cortico-subcortical networks.

Previous neuroimaging studies showed that correct resolution of lexical ambiguity relies on the integrity of prefrontal and inferior parietal cortices. Whereas prefrontal brain areas were associated with executive control over semantic selection, inferior parietal areas were linked with access to modality-independent representations of semantic memory. Yet insufficiently understood is the contribution of subcortical structures in ambiguity processing.

Dose-intensified granulocyte-monocyte apheresis in therapy refractory ulcerative colitis.

Granulocyte-monocyte apheresis (GMA) is an emerging therapeutic option in active course of ulcerative colitis (UC). Appropriate GMA dose, including total number, frequency, and duration of the individual GMA session, is a matter of debate. It was the aim of the present study to evaluate the efficacy of a dose-intensified GMA regimen in patients with moderately to severely active UC.

Paving the way for speech: voice-training-induced plasticity in chronic aphasia and apraxia of speech--three single cases.

Difficulties with temporal coordination or sequencing of speech movements are frequently reported in aphasia patients with concomitant apraxia of speech (AOS). Our major objective was to investigate the effects of specific rhythmic-melodic voice training on brain activation of those patients. Three patients with severe chronic nonfluent aphasia and AOS were included in this study.