Focus on 14 sewage treatment plants in the Mpumalanga Province, South Africa in order to gauge the efficiency of wastewater treatment

PKIn order to identify the treatment methods used in different sewage treatment plants (STPs) in the Mpumalanga Province and to determine the efficiency of wastewater treatment by these plants, municipal STPs were surveyed, and raw and treated wastewater samples collected. A total of 14 STPs were visited and the collected samples were analysed for physicochemical and microbiological parameters using standard methods. The treatment methods identified included ponds, activated sludge and trickling filters. The reduction of turbidity by the plants varied between 6.2 and 99.6% while conductivity, pH and temperature varied slightly between the influent and the effluent wastewater. Thirteen (92.8%) of the plants used chlorine for disinfection of the final effluent, however only 2 (14.2%) of the plants managed to produce effluent with 0 (zero) faecal conforms per 100 m€. Common pathogenic bacteria isolated from the final effluent included Salmonella, Shigella, Escherichia coli, Vibrio spp. and Enterococcus spp. The final effluent was used for irrigation and recycling purposes in 4 plants, all the other treatment plants discharged the effluent into the river or to the environment. The present study indicated that there is a move toward the renovation of wastewater treatment by the municipalities in the Mpumalanga Province with the adoption of biological treatment. All the STPs reduced the turbidity of wastewater as well as the different microbial indicators counts; however, several pathogenic bacterial organisms could still be detected in the final effluent. Further studies are needed to confirm the role of the treatment procedures on nutrient reduction and elimination of other viral and parasitic pathogens by the sewage treatment plants

Anti-N-methyl-d-aspartate receptor encephalitis triggered by emotional stress

© 2019, Copyright © 2019 Baylor University Medical Center. A 22-year-old woman presented with disorganized behaviors, restlessness, and subacute decline in mental status in the setting of stress. Extensive workup for autoimmune diseases disclosed positive anti-N-methyl-d-aspartate (NMDA) receptor antibodies. We recommend that fertility preservation should be discussed and stress management should be considered in patients with a history of anti-NMDA autoimmune encephalitis because this can help in preventing relapse

Informatics for RNA sequencing: A web resource for analysis on the cloud

Massively parallel RNA sequencing (RNA-seq) has rapidly become the assay of choice for interrogating RNA transcript abundance and diversity. This article provides a detailed introduction to fundamental RNA-seq molecular biology and informatics concepts. We make available open-access RNA-seq tutorials that cover cloud computing, tool installation, relevant file formats, reference genomes, transcriptome annotations, quality-control strategies, expression, differential expression, and alternative splicing analysis methods. These tutorials and additional training resources are accompanied by complete analysis pipelines and test datasets made available without encumbrance at www.rnaseq.wiki

ORegAnno 3.0: A community-driven resource for curated regulatory annotation

The Open Regulatory Annotation database (ORegAnno) is a resource for curated regulatory annotation. It contains information about regulatory regions, transcription factor binding sites, RNA binding sites, regulatory variants, haplotypes, and other regulatory elements. ORegAnno differentiates itself from other regulatory resources by facilitating crowd-sourced interpretation and annotation of regulatory observations from the literature and highly curated resources. It contains a comprehensive annotation scheme that aims to describe both the elements and outcomes of regulatory events. Moreover, ORegAnno assembles these disparate data sources and annotations into a single, high quality catalogue of curated regulatory information. The current release is an update of the database previously featured in the NAR Database Issue, and now contains 1 948 307 records, across 18 species, with a combined coverage of 334 215 080 bp. Complete records, annotation, and other associated data are available for browsing and download at http://www.oreganno.org/

Theory of proximity effect in superconductor/ferromagnet heterostructures

We present a microscopic theory of proximity effect in the ferromagnet/superconductor/ferromagnet (F/S/F) nanostructures where S is s-wave low-T_c superconductor and F's are layers of 3d transition ferromagnetic metal. Our approach is based on the solution of Gor'kov equations for the normal and anomalous Green's functions together with a self-consistent evaluation of the superconducting order parameter. We take into account the elastic spin-conserving scattering of the electrons assuming s-wave scattering in the S layer and s-d scattering in the F layers. In accordance with the previous quasiclassical theories, we found that due to exchange field in the ferromagnet the anomalous Green's function F(z) exhibits the damping oscillations in the F-layer as a function of distance z from the S/F interface. In the given model a half of period of oscillations is determined by the length \xi_m^0 = \pi v_F/E_ex, where v_F is the Fermi velocity and E_ex is the exchange field, while damping is governed by the length l_0 = (1/l_{\uparrow} + 1/l_{\downarrow})^{-1} with l_{\uparrow} and l_{\downarrow} being spin-dependent mean free paths in the ferromagnet. The superconducting transition temperature T_c(d_F) of the F/S/F trilayer shows the damping oscillations as a function of the F-layer thickness d_F with period \xi_F = \pi/\sqrt{m E_ex}, where m is the effective electron mass. We show that strong spin-conserving scattering either in the superconductor or in the ferromagnet significantly suppresses these oscillations. The calculated T_c(d_F) dependences are compared with existing experimental data for Fe/Nb/Fe trilayers and Nb/Co multilayers.Comment: 13 pages, REVTeX4, 8 PS-figures; improved version, submitted to PR

Integrative genomic analysis reveals low T-cell infiltration as the primary feature of tobacco use in HPV-positive oropharyngeal cancer

Although tobacco use is an independent adverse prognostic feature in HPV(+) oropharyngeal squamous cell carcinoma (OPSCC), the biologic features associated with tobacco use have not been systematically investigated. We characterized genomic and immunologic features associated with tobacco use through whole exome sequencing, mRNA hybridization, and immunohistochemical staining in 47 HPV(+) OPSCC tumors. Low expression of transcripts in a T cell-inflamed gene expression profile (TGEP) was associated with tobacco use at diagnosis and lower overall and disease-free survival. Tobacco use was associated with an increased proportion of T \u3e C substitutions and a lower proportion of expected mutational signatures, but not with increases in mutational burden or recurrent oncogenic mutations. Our findings suggest that rather than increased mutational burden, tobacco\u27s primary and clinically relevant association in HPV(+) OPSCC is immunosuppression of the tumor immune microenvironment. Quantitative assays of T cell infiltration merit further study as prognostic markers in HPV(+) OPSCC

CIViCpy: A Python software evelopment and analysis toolkit for the CIViC knowledgebase

PURPOSE: Precision oncology depends on the matching of tumor variants to relevant knowledge describing the clinical significance of those variants. We recently developed the Clinical Interpretations for Variants in Cancer (CIViC; civicdb.org) crowd-sourced, expert-moderated, and open-access knowledgebase. CIViC provides a structured framework for evaluating genomic variants of various types (eg, fusions, single-nucleotide variants) for their therapeutic, prognostic, predisposing, diagnostic, or functional utility. CIViC has a documented application programming interface for accessing CIViC records: assertions, evidence, variants, and genes. Third-party tools that analyze or access the contents of this knowledgebase programmatically must leverage this application programming interface, often reimplementing redundant functionality in the pursuit of common analysis tasks that are beyond the scope of the CIViC Web application. METHODS: To address this limitation, we developed CIViCpy (civicpy.org), a software development kit for extracting and analyzing the contents of the CIViC knowledgebase. CIViCpy enables users to query CIViC content as dynamic objects in Python. We assess the viability of CIViCpy as a tool for advancing individualized patient care by using it to systematically match CIViC evidence to observed variants in patient cancer samples. RESULTS: We used CIViCpy to evaluate variants from 59,437 sequenced tumors of the American Association for Cancer Research Project GENIE data set. We demonstrate that CIViCpy enables annotation of \u3e 1,200 variants per second, resulting in precise variant matches to CIViC level A (professional guideline) or B (clinical trial) evidence for 38.6% of tumors. CONCLUSION: The clinical interpretation of genomic variants in cancers requires high-throughput tools for interoperability and analysis of variant interpretation knowledge. These needs are met by CIViCpy, a software development kit for downstream applications and rapid analysis. CIViCpy is fully documented, open-source, and available free online

Metagenomic analysis of DNA viruses with targeted sequence capture of canine lobular orbital adenomas and normal conjunctiva

Our study aims are: (1) to evaluate phenotypically normal canine conjunctival and orbital tissue and tissue from canine lobular orbital adenomas (CLOAs) for the presence of viral genomic material and (2) phylogenetically classify detected DNA viruses to determine if a DNA virus is associated with CLOAs. A total of 31 formalin fixed paraffin embedded CLOA tissue samples, 4 papillomas or sarcoid, and 10 fresh clinically normal conjunctival tissues were included in this study. Genomic DNA was isolated from all samples and sequencing libraries were prepared. The libraries were molecularly indexed and pooled and viral DNA was enriched via targeted sequence capture utilizing ViroCap. The libraries were sequenced on the Illumina HiSeq platform and compared to known viral DNA reference genomes to identify viral DNA. Carnivore parvovirus was identified in 6.4% and 20% of CLOA tissue and normal conjunctival samples, respectively. This study showed that conjunctival tissue from healthy dogs and CLOAs uncommonly harbor DNA viruses, and no DNA virus was associated with these tumors. Further studies are needed to evaluate the etiologic cause of CLOAs