Impacts of urban emissions and air quality in São Paulo State, Brazil.

Daily violations of air quality have an impact on urban populations and cause damage to the environment. Thus, the study evaluated the violations of the daily concentrations of SO, NO, and PM, in regions of the State of São Paulo (SSP), based on the National Environment Council (CONAMA) resolution no 491/2018 and the World Health Organization (WHO - World Health Organization. (2016).

The Hows of Resident-Driven Community Empowerment toward Health Equity.

Background: This article details community engagement, design, and implementation strategies for the Raices-Xidid-Roots (RXR) Academy. RXR provided a linguistically accessible and culturally relevant curriculum to residents of Spanish and Somali-speaking immigrant, asylee, and refugee backgrounds.

Objectives: This study examined the implementation of the RXR program, including participation and adjustments needed to foster participant engagement and active voice, and explored participant actions to address self-identified aspirations as part of participation.

"It depends:" a qualitative study on digital health academic-industry collaboration.

Background: Academic-industry collaborations (AICs) are endorsed to alleviate challenges in digital health, but partnership experiences remain understudied. The qualitative study's objective investigated collaboration experiences between academic institutions and digital health companies.

Methods: A phenomenology methodology captured experiences of AICs, eliciting perspectives from academic researchers and industry affiliates (e.

Fire foci dynamics and their relationship with socioenvironmental factors and meteorological systems in the state of Alagoas, Northeast Brazil.

The objective is to evaluate the fire foci dynamics via environmental satellites and their relationship with socioenvironmental factors and meteorological systems in the state of Alagoas, Brazil. Data considered the period between 2000 and 2017 and was obtained from CPTEC/INPE. Annual and monthly analyzes were performed based on descriptive, exploratory (boxplot) and multivariate statistics analyzes (cluster analysis (CA), principal component analysis (PCA)) and Poisson regression models (based on 2000 and 2010 census data).

Amazonian deforestation and soil biodiversity.

Clearance and perturbation of Amazonian forests are one of the greatest threats to tropical biodiversity conservation of our times. A better understanding of how soil communities respond to Amazonian deforestation is crucially needed to inform policy interventions that effectively protect biodiversity and the essential ecosystem services it provides. We assessed the impact of deforestation and ecosystem conversion to arable land on Amazonian soil biodiversity through a meta-analysis.

RNA-Rocket: an RNA-Seq analysis resource for infectious disease research.

Motivation: RNA-Seq is a method for profiling transcription using high-throughput sequencing and is an important component of many research projects that wish to study transcript isoforms, condition specific expression and transcriptional structure. The methods, tools and technologies used to perform RNA-Seq analysis continue to change, creating a bioinformatics challenge for researchers who wish to exploit these data. Resources that bring together genomic data, analysis tools, educational material and computational infrastructure can minimize the overhead required of life science researchers.

Curation, integration and visualization of bacterial virulence factors in PATRIC.

Motivation: We've developed a highly curated bacterial virulence factor (VF) library in PATRIC (Pathosystems Resource Integration Center, www.patricbrc.org) to support infectious disease research.

Comparative genomic analysis at the PATRIC, a bioinformatic resource center.

The Pathosystems Resource Integration Center (PATRIC) is a genomics-centric relational database and bioinformatics resource designed to assist scientists in infectious-disease research. This method paper provides detailed instructions on using this resource to finding data specific to genomes, saving it in a personalized workspace and using a variety of interactive tools to analyze that data. While PATRIC contains many diverse tools and functionalities to explore both genome-scale and gene expression data, the main focus of this chapter is on comparative analysis of bacterial genomes.

Comparative nutritional and chemical phenome of Clostridium difficile isolates determined using phenotype microarrays.

Objectives: Clostridium difficile infection (CDI) is the leading cause of infectious diarrhea in North America and Europe. The risk of CDI increases significantly in the case where antimicrobial treatment reduces the number of competing bacteria in the gut, thus leading to the increased availability of nutrients and loss of colonization resistance. The objective of this study was to determine comprehensive nutritional utilization and the chemical sensitivity profile of historic and newer C.

Standardized metadata for human pathogen/vector genomic sequences.

High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenetic studies to track the origin and spread of disease outbreaks. To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and consistent formats.

Consensus statement understanding health and malnutrition through a systems approach: the ENOUGH program for early life.

Nutrition research, like most biomedical disciplines, adopted and often uses experimental approaches based on Beadle and Tatum's one gene-one polypeptide hypothesis, thereby reducing biological processes to single reactions or pathways. Systems thinking is needed to understand the complexity of health and disease processes requiring measurements of physiological processes, as well as environmental and social factors, which may alter the expression of genetic information. Analysis of physiological processes with omics technologies to assess systems' responses has only become available over the past decade and remains costly.

Comparative phylogenomics and evolution of the Brucellae reveal a path to virulence.

Brucella species include important zoonotic pathogens that have a substantial impact on both agriculture and human health throughout the world. Brucellae are thought of as "stealth pathogens" that escape recognition by the host innate immune response, modulate the acquired immune response, and evade intracellular destruction. We analyzed the genome sequences of members of the family Brucellaceae to assess its evolutionary history from likely free-living soil-based progenitors into highly successful intracellular pathogens.

Differential stress transcriptome landscape of historic and recently emerged hypervirulent strains of Clostridium difficile strains determined using RNA-seq.

C. difficile is the most common cause of nosocomial diarrhea in North America and Europe. Genomes of individual strains of C.

PATRIC, the bacterial bioinformatics database and analysis resource.

The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org).

The condition-dependent transcriptional landscape of Burkholderia pseudomallei.

Burkholderia pseudomallei (Bp), the causative agent of the often-deadly infectious disease melioidosis, contains one of the largest prokaryotic genomes sequenced to date, at 7.2 Mb with two large circular chromosomes (1 and 2). To comprehensively delineate the Bp transcriptome, we integrated whole-genome tiling array expression data of Bp exposed to >80 diverse physical, chemical, and biological conditions.

Bacterial DNA sifted from the Trichoplax adhaerens (Animalia: Placozoa) genome project reveals a putative rickettsial endosymbiont.

Eukaryotic genome sequencing projects often yield bacterial DNA sequences, data typically considered as microbial contamination. However, these sequences may also indicate either symbiont genes or lateral gene transfer (LGT) to host genomes. These bacterial sequences can provide clues about eukaryote-microbe interactions.

Database resources for the tuberculosis community.

Access to online repositories for genomic and associated "-omics" datasets is now an essential part of everyday research activity. It is important therefore that the Tuberculosis community is aware of the databases and tools available to them online, as well as for the database hosts to know what the needs of the research community are. One of the goals of the Tuberculosis Annotation Jamboree, held in Washington DC on March 7th-8th 2012, was therefore to provide an overview of the current status of three key Tuberculosis resources, TubercuList (tuberculist.

Proteomic comparison of historic and recently emerged hypervirulent Clostridium difficile strains.

Clostridium difficile in recent years has undergone rapid evolution and has emerged as a serious human pathogen. Proteomic approaches can improve the understanding of the diversity of this important pathogen, especially in comparing the adaptive ability of different C. difficile strains.

Functional assignment of Mycobacterium tuberculosis proteome revealed by genome-scale fold-recognition.

Hundreds of putative enzymes from Mycobacterium tuberculosis as well as other mycobacteria remain categorized as "conserved hypothetical proteins" or "hypothetical proteins", offering little or no information on their functional role in pathogenic and non-pathogenic processes. In this study we have predicted the fold and 3-D structure of more than 99% of all proteins encoded in the genome of M. tuberculosis H37Rv.

Helicobacter pylori colonization ameliorates glucose homeostasis in mice through a PPAR γ-dependent mechanism.

Background: There is an inverse secular trend between the incidence of obesity and gastric colonization with Helicobacter pylori, a bacterium that can affect the secretion of gastric hormones that relate to energy homeostasis. H. pylori strains that carry the cag pathogenicity island (PAI) interact more intimately with gastric epithelial cells and trigger more extensive host responses than cag(-) strains.

Comparative genomics of early-diverging Brucella strains reveals a novel lipopolysaccharide biosynthesis pathway.

Unlabelled: Brucella species are Gram-negative bacteria that infect mammals. Recently, two unusual strains (Brucella inopinata BO1T and B. inopinata-like BO2) have been isolated from human patients, and their similarity to some atypical brucellae isolated from Australian native rodent species was noted.

Comparative genomics of early-diverging Brucella strains reveals a novel lipopolysaccharide biosynthesis pathway.

Unlabelled: Brucella species are Gram-negative bacteria that infect mammals. Recently, two unusual strains (Brucella inopinata BO1(T) and B. inopinata-like BO2) have been isolated from human patients, and their similarity to some atypical brucellae isolated from Australian native rodent species was noted.

Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011.

We present the preparation, resources, results and analysis of three tasks of the BioNLP Shared Task 2011: the main tasks on Infectious Diseases (ID) and Epigenetics and Post-translational Modifications (EPI), and the supporting task on Entity Relations (REL). The two main tasks represent extensions of the event extraction model introduced in the BioNLP Shared Task 2009 (ST'09) to two new areas of biomedical scientific literature, each motivated by the needs of specific biocuration tasks. The ID task concerns the molecular mechanisms of infection, virulence and resistance, focusing in particular on the functions of a class of signaling systems that are ubiquitous in bacteria.