Complete Genomic Sequences of Three Salmonella enterica subsp. enterica Serovar Muenchen Strains from an Orchard in San Joaquin County, California.

We present here the complete genome sequences of three Salmonella enterica subsp. enterica serovar Muenchen strains, LG24, LG25, and LG26. All three strains were isolated from almond drupes grown in an orchard in San Joaquin County, California, in 2016. These genomic sequences are nonidentical and will contribute to our understanding of S. enterica genomics

Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput “omics” Data

High-throughput “omics” technologies bring new opportunities for biological and biomedical researchers to ask complex questions and gain new scientific insights. However, the voluminous, complex, and context-dependent data being maintained in heterogeneous and distributed environments plus the lack of well-defined data standard and standardized nomenclature imposes a major challenge which requires advanced computational methods and bioinformatics infrastructures for integration, mining, visualization, and comparative analysis to facilitate data-driven hypothesis generation and biological knowledge discovery. In this paper, we present the challenges in high-throughput “omics” data integration and analysis, introduce a protein-centric approach for systems integration of large and heterogeneous high-throughput “omics” data including microarray, mass spectrometry, protein sequence, protein structure, and protein interaction data, and use scientific case study to illustrate how one can use varied “omics” data from different laboratories to make useful connections that could lead to new biological knowledge

Estimating and modeling the dynamics of the intensity of infection with Schistosoma japonicum in villagers of Leyte, Philippines. Part II: Intensity-specific transmission of S. japonicum. The schistosomiasis transmission and ecology project

A dynamic model of Schistosoma japonicum transmission is presented that incorporates effects of infection intensity, age, and sex. We use four infection intensity classes to investigate the impact of ecologic changes and public health interventions on the burden of infection within communities. Age- and sex-specific infection data from three disease-endemic villages in the Philippines are used to estimate the parameters of the model. The model gives good qualitative agreement with observed fecal egg counts adjusted for the accuracy of the Kato-Katz examination. Our results suggest that differences in infection burden between villages are caused by differences in both the infection process and the recovery process in humans. We describe the potential impact of mass treatment of all humans on the numbers with high infection. Furthermore, we show that a sudden reduction in snail population size would affect high prevalence and low prevalence communities in different ways. Copyright © 2005 by The American Society of Tropical Medicine and Hygiene.published_or_final_versio

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

Motivation: UniRef databases provide full-scale clustering of UniProtKB sequences and are utilized for a broad range of applications, particularly similarity-based functional annotation. Non-redundancy and intra-cluster homogeneity in UniRef were recently improved by adding a sequence length overlap threshold. Our hypothesis is that these improvements would enhance the speed and sensitivity of similarity searches and improve the consistency of annotation within clusters. Results: Intra-cluster molecular function consistency was examined by analysis of Gene Ontology terms. Results show that UniRef clusters bring together proteins of identical molecular function in more than 97% of the clusters, implying that clusters are useful for annotation and can also be used to detect annotation inconsistencies. To examine coverage in similarity results, BLASTP searches against UniRef50 followed by expansion of the hit lists with cluster members demonstrated advantages compared with searches against UniProtKB sequences; the searches are concise (∼7 times shorter hit list before expansion), faster (∼6 times) and more sensitive in detection of remote similarities (>96% recall at e-value <0.0001). Our results support the use of UniRef clusters as a comprehensive and scalable alternative to native sequence databases for similarity searches and reinforces its reliability for use in functional annotation. Availability and implementation: Web access and file download from UniProt website at http://www.uniprot.org/uniref and ftp://ftp.uniprot.org/pub/databases/uniprot/uniref. BLAST searches against UniRef are available at http://www.uniprot.org/blast/ Contact: [email protected]

Theobromine for the treatment of persistent cough: A randomised, multicentre, double-blind, placebo-controlled clinical trial

© Journal of Thoracic Disease. Background: To investigate the effect of BC1036 on health-related quality of life (QOL) in subjects with persistent cough. The secondary objective was to investigate the effect of BC1036 on subjective cough severity. Methods: This was a randomised, multicentre, double-blind, placebo-controlled, parallel-group study in 289 subjects with persistent cough. Subjects received BC1036 or placebo twice daily for 14 days. The primary endpoint comprised cough-related QOL assessed using the validated Leicester Cough Questionnaire (LCQ) at Day 14. Secondary endpoints comprised the LCQ scores at Day 7 and Day 28, cough severity VAS scores at each visit and pulmonary function tests. Results: At baseline, mean total LCQ score in the BC1036 group was lower (i.e., worse QOL) than placebo (P < 0.001), indicating significant between-group heterogeneity. Mean baseline-adjusted change in LCQ score at Day 14 was greater for BC1036 [mean (SD) 2.4±3.5] compared to placebo [mean (SD) score 2.2±3.0], but did not reach statistical significance (P=0.60). Mean cough severity VAS score decreased to a greater extent in the BC1036 group compared to placebo, but again the results were not statistically significant (-12.2±23.28 in BC1036 group and -11.0±21.34 in placebo group at Day 14, P=0.688). There was no significant change in pulmonary function measurements. The adverse event (AE) profile was similar in both groups. Conclusions: This study showed that BC1036 was well tolerated and, although the primary endpoint did not achieve statistical significance, the magnitude of improvement was greater with BC1036 compared to placebo with respect to improving QOL and reducing cough severity. Clinical trial registration: ClinicalTrials.gov: NCT01656668

The Stone-Campbell Movement: A Global History--Reviews and Comments

From the Stone-Campbell Journal website: Editors D. Newell Williams, Douglas A. Foster, and Paul M. Blowers offer their second substantial contribution to Stone-Campbell historiography with The Stone-Campbell Movement: A Global History (Chalice, 2013), an unprecedented global survey. (1) A core of thirteen scholars collaboratively wrote this unique narrative that highlights groups of people (women, African Americans, global Christians, and others) often neglected in traditional histories. In this review essay, three Stone-Campbell Movement historians each review roughly one-third of the volume