redbiom: a Rapid Sample Discovery and Feature Characterization System.

Meta-analyses at the whole-community level have been important in microbiome studies, revealing profound features that structure Earth's microbial communities, such as the unique differentiation of microbes from the mammalian gut relative to free-living microbial communities, the separation of microbiomes in saline and nonsaline environments, and the role of pH in driving soil microbial compositions. However, our ability to identify the specific features of a microbiome that differentiate these community-level patterns have lagged behind, especially as ever-cheaper DNA sequencing has yielded increasingly large data sets. One critical gap is the ability to search for samples that contain specific features (for example, sub-operational taxonomic units [sOTUs] identified by high-resolution statistical methods for removing amplicon sequencing errors). Here we introduce redbiom, a microbiome caching layer, which allows users to rapidly query samples that contain a given feature, retrieve sample data and metadata, and search for samples that match specified metadata values or ranges (e.g., all samples with a pH of >7), implemented using an in-memory NoSQL database called Redis. By default, redbiom allows public anonymous sample access for over 100,000 publicly available samples in the Qiita database. At over 100,000 samples, the caching server requires only 35 GB of resident memory. We highlight how redbiom enables a new type of characterization of microbiome samples and provide tutorials for using redbiom with QIIME 2. redbiom is open source under the BSD license, hosted on GitHub, and can be deployed independently of Qiita to enable search of proprietary or clinically restricted microbiome databases.IMPORTANCE Although analyses that combine many microbiomes at the whole-community level have become routine, searching rapidly for microbiomes that contain a particular sequence has remained difficult. The software we present here, redbiom, dramatically accelerates this process, allowing samples that contain microbiome features to be rapidly identified. This is especially useful when taxonomic annotation is limited, allowing users to identify environments in which unannotated microbes of interest were previously observed. This approach also allows environmental or clinical factors that correlate with specific features, or vice versa, to be identified rapidly, even at a scale of billions of sequences in hundreds of thousands of samples. The software is integrated with existing analysis tools to enable fast, large-scale microbiome searches and discovery of new microbiome relationships

Signaling Cascade Involved in Rapid Stimulation of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) by Dexamethasone

Impairment of mucociliary clearance with reduced airway fluid secretion leads to chronically inflamed airways. Cystic fibrosis transmembrane conductance regulator (CFTR) is crucially involved in airway fluid secretion and dexamethasone (dexa) has previously been shown to elevate CFTR activity in airway epithelial cells. However, the pathway by which dexa increases CFTR activity is largely unknown. We aimed to determine whether the increase of CFTR activity by dexa is achieved by non-genomic signaling and hypothesized that the phosphoinositide 3-kinase (PI3K) pathway is involved in CFTR stimulation. Primary rat airway epithelial cells and human bronchial submucosal gland-derived Calu-3 cells were analyzed in Ussing chambers and kinase activation was determined byWestern blots. Results demonstrated a critical involvement of PI3K and protein kinase B (AKT) signaling in the dexa-induced increase of CFTR activity, while serum and glucocorticoid dependent kinase 1 (SGK1) activity was not essential. We further demonstrated a reduced neural precursor cell expressed, developmentally downregulated 4-like (NEDD4L) ubiquitin E3 ligase activity induced by dexa, possibly responsible for the elevated CFTR activity. Finally, increases of CFTR activity by dexa were demonstrated within 30 min accompanied by rapid activation of AKT. In conclusion, dexa induces a rapid stimulation of CFTR activity which depends on PI3K/AKT signaling in airway epithelial cells. Glucocorticoids might thus represent, in addition to their immunomodulatory actions, a therapeutic strategy to rapidly increase airway fluid secretion

Glucocorticoids Equally Stimulate Epithelial Na+ Transport in Male and Female Fetal Alveolar Cells

Preterm infants frequently suffer from respiratory distress syndrome (RDS), possibly due to lower expression of epithelial Na+ channels (ENaC). RDS incidence is sex-specific, affecting males almost twice as often. Despite the use of antenatal glucocorticoids (GCs), the sex difference persists. It is still controversial whether both sexes benefit equally from GCs. We previously showed that Na+ transport is higher in female compared with male fetal distal lung epithelial (FDLE) cells. Since GCs increase Na+ transport, we hypothesized that their stimulating effect might be sex-specific. We analyzed FDLE cells with Ussing chambers and RT-qPCR in the presence or absence of fetal serum. In serum-free medium, GCs increased the ENaC activity and mRNA expression, independent of sex. In contrast, GCs did not increase the Na+ transport in serum-supplemented media and abolished the otherwise observed sex difference. Inhibition of the GC receptor in the presence of serum did not equalize Na+ transport between male and female cells. The GC-induced surfactant protein mRNA expression was concentration and sex-specific. In conclusion, female and male FDLE cells exhibit no sex difference in response to GCs with regard to Na+ transport, and GR activity does not contribute to the higher Na+ transport in females

First experiences with the implementation of the European standard EN 62304 on medical device software for the quality assurance of a radiotherapy unit

BACKGROUND: According to the latest amendment of the Medical Device Directive standalone software qualifies as a medical device when intended by the manufacturer to be used for medical purposes. In this context, the EN 62304 standard is applicable which defines the life-cycle requirements for the development and maintenance of medical device software. A pilot project was launched to acquire skills in implementing this standard in a hospital-based environment (in-house manufacture). METHODS: The EN 62304 standard outlines minimum requirements for each stage of the software life-cycle, defines the activities and tasks to be performed and scales documentation and testing according to its criticality. The required processes were established for the pre-existent decision-support software FlashDumpComparator (FDC) used during the quality assurance of treatment-relevant beam parameters. As the EN 62304 standard implicates compliance with the EN ISO 14971 standard on the application of risk management to medical devices, a risk analysis was carried out to identify potential hazards and reduce the associated risks to acceptable levels. RESULTS: The EN 62304 standard is difficult to implement without proper tools, thus open-source software was selected and integrated into a dedicated development platform. The control measures yielded by the risk analysis were independently implemented and verified, and a script-based test automation was retrofitted to reduce the associated test effort. After all documents facilitating the traceability of the specified requirements to the corresponding tests and of the control measures to the proof of execution were generated, the FDC was released as an accessory to the HIT facility. CONCLUSIONS: The implementation of the EN 62304 standard was time-consuming, and a learning curve had to be overcome during the first iterations of the associated processes, but many process descriptions and all software tools can be re-utilized in follow-up projects. It has been demonstrated that a standards-compliant development of small and medium-sized medical software can be carried out by a small team with limited resources in a clinical setting. This is of particular relevance as the upcoming revision of the Medical Device Directive is expected to harmonize and tighten the current legal requirements for all European in-house manufacturers

Characterization of the fecal microbiome in cats with inflammatory bowel disease or alimentary small cell lymphoma.

Feline chronic enteropathy (CE) is a common gastrointestinal disorder in cats and mainly comprises inflammatory bowel disease (IBD) and small cell lymphoma (SCL). Both IBD and SCL in cats share features with chronic enteropathies such as IBD and monomorphic epitheliotropic intestinal T-cell lymphoma in humans. The aim of this study was to characterize the fecal microbiome of 38 healthy cats and 27 cats with CE (13 cats with IBD and 14 cats with SCL). Alpha diversity indices were significantly decreased in cats with CE (OTU p = 0.003, Shannon Index p = 0.008, Phylogenetic Diversity p = 0.019). ANOSIM showed a significant difference in bacterial communities, albeit with a small effect size (P = 0.023, R = 0.073). Univariate analysis and LEfSE showed a lower abundance of facultative anaerobic taxa of the phyla Firmicutes (families Ruminococcaceae and Turicibacteraceae), Actinobacteria (genus Bifidobacterium) and Bacteroidetes (i.a. Bacteroides plebeius) in cats with CE. The facultative anaerobic taxa Enterobacteriaceae and Streptococcaceae were increased in cats with CE. No significant difference between the microbiome of cats with IBD and those with SCL was found. Cats with CE showed patterns of dysbiosis similar to those in found people with IBD

A quantitative study of particle size effects in the magnetorelaxometry of magnetic nanoparticles using atomic magnetometry

The discrimination of immobilised superparamagnetic iron oxide nanoparticles (SPIONs) against SPIONs in fluid environments via their magnetic relaxation behaviour is a powerful tool for bio-medical imaging. Here we demonstrate that a gradiometer of laser-pumped atomic magnetometers can be used to record accurate time series of the relaxing magnetic field produced by pre-polarised SPIONs. We have investigated dry in vitro maghemite nanoparticle samples with different size distributions (average radii ranging from 14 to 21 nm) and analysed their relaxation using the Néel–Brown formalism. Fitting our model function to the magnetorelaxation (MRX) data allows us to extract the anisotropy constant K and the saturation magnetisation MS of each sample. While the latter was found not to depend on the particle size, we observe that K is inversely proportional to the (time- and size-) averaged volume of the magnetised particle fraction. We have identified the range of SPION sizes that are best suited for MRX detection considering our specific experimental conditions and sample preparation technique

redbiom: a Rapid Sample Discovery and Feature Characterization System

Meta-analyses at the whole-community level have been important in microbiome studies, revealing profound features that structure Earth’s microbial communities, such as the unique differentiation of microbes from the mammalian gut relative to free-living microbial communities, the separation of microbiomes in saline and nonsaline environments, and the role of pH in driving soil microbial compositions. However, our ability to identify the specific features of a microbiome that differentiate these community-level patterns have lagged behind, especially as ever-cheaper DNA sequencing has yielded increasingly large data sets. One critical gap is the ability to search for samples that contain specific features (for example, sub-operational taxonomic units [sOTUs] identified by high-resolution statistical methods for removing amplicon sequencing errors). Here we introduce redbiom, a microbiome caching layer, which allows users to rapidly query samples that contain a given feature, retrieve sample data and metadata, and search for samples that match specified metadata values or ranges (e.g., all samples with a pH of >7), implemented using an in-memory NoSQL database called Redis. By default, redbiom allows public anonymous sample access for over 100,000 publicly available samples in the Qiita database. At over 100,000 samples, the caching server requires only 35 GB of resident memory. We highlight how redbiom enables a new type of characterization of microbiome samples and provide tutorials for using redbiom with QIIME 2. redbiom is open source under the BSD license, hosted on GitHub, and can be deployed independently of Qiita to enable search of proprietary or clinically restricted microbiome databases