A study of the variation in the salivary peptide profiles of young healthy adults acquired using MALDI-TOF MS

A cross-sectional observational study was conducted to evaluate the inter-individual variation in the MALDI-TOF MS peptide profiles of unstimulated whole saliva in a population of 268 systemically healthy adults aged 18-30 yr (150 males and 118 females) with no apparent caries lesions or periodontal disease. Using Spectral Clustering, four...

Interindividual variation, correlations, and sex-related differences in the salivary biochemistry of young healthy adults

A cross-sectional observational study was conducted to evaluate interindividual biochemical variation in unstimulated whole saliva in a population of 268 systemically healthy young students, 18-30 yr of age, with no apparent caries lesions or periodontal disease. Salivary flow rate, protein content, pH, buffering capacity, mucins MUC5B and MUC7,...

The impact of hormonal contraception and pregnancy on sexually transmitted infections and on cervicovaginal microbiota in african sex workers

Background The observed association between Depo-Provera injectable use and increased HIV acquisition may be caused by hormone-induced increased susceptibility to other sexually transmitted infections (STIs) or changes in the cervicovaginal microbiota (VMB), accompanied by genital immune activation and/or mucosal remodeling. Methods Rwandan...

Correlates of the molecular vaginal microbiota composition of African women

Background: Sociodemographic, behavioral and clinical correlates of the vaginal microbiome (VMB) as characterized by molecular methods have not been adequately studied. VMB dominated by bacteria other than lactobacilli may cause inflammation, which may facilitate HIV acquisition and other adverse reproductive health outcomes. Methods: We...

Lactobacillus-dominated cervicovaginal microbiota associated with reduced HIV/STI prevalence and genital HIV viral load in african women

Cervicovaginal microbiota not dominated by lactobacilli may facilitate transmission of HIV and other sexually transmitted infections (STIs), as well as miscarriages, preterm births and sepsis in pregnant women. However, little is known about the exact nature of the microbiological changes that cause these adverse outcomes. In this study,...

Personalized microbial network inference via co-regularized spectral clustering

We use Human Microbiome Project (HMP) cohort [1] to infer personalized oral microbial networks of healthy individuals. To determine clustering of individuals with similar microbial profiles, co-regularized spectral clustering algorithm is applied to the dataset. For each cluster we discovered, we compute co-occurrence relationships among the...

Early respiratory microbiota composition determines bacterial succession patterns and respiratory health in children

Rationale: Many bacterial pathogens causing respiratory infections in children are common residents of the respiratory tract. Insight into bacterial colonization patterns and microbiota stability at a young age might elucidate healthy or susceptible conditions for development of respiratory disease. Objectives: To study bacterial succession of...

Lipoprotein metabolism indicators improve cardiovascular risk prediction

Background: Cardiovascular disease risk increases when lipoprotein metabolism is dysfunctional. We have developed a computational model able to derive indicators of lipoprotein production, lipolysis, and uptake processes from a single lipoprotein profile measurement. This is the first study to investigate whether lipoprotein metabolism...

OmpU as a biomarker for rapid discrimination between toxigenic and epidemic Vibrio cholerae O1/O139 and non-epidemic Vibrio cholerae in a modified MALDI-TOF MS assay

Background Cholera is an acute diarrheal disease caused by Vibrio cholerae. Outbreaks are caused by a genetically homogenous group of strains from serogroup O1 or O139 that are able to produce the cholera toxin. Rapid detection and identification of these epidemic strains is essential for an effective response to cholera outbreaks. Results The...

Identification of a new biomarker for fast discrimination between epidemic and non-epidemic Vibrio cholerae in a modified MALDI-TOF MS assay

Online Semi-Supervised Learning: Algorithm and Application in Metagenomics

As the amount of metagenomic data grows rapidly, online statistical learning algorithms are poised to play key rolein metagenome analysis tasks. Frequently, data are only partially labeled, namely dataset contains partial information about the problem of interest. This work presents an algorithm and a learning framework that is naturally...

Neighborhood co-regularized multi-view spectral clustering of microbiome data

In many unsupervised learning problems data can be available in different representations, often referred to as views. By leveraging information from multiple views we can obtain clustering that is more robust and accurate compared to the one obtained via the individual views. We propose a novel algorithm that is based on neighborhood co...

Multi-view multi-class classification for identification of pathogenic bacterial strains

In various learning problems data can be available in different representations, often referred to as views. We propose multi-class classification method that is particularly suitable for multi-view learning setting. The algorithm uses co-regularization and error-correcting techniques to leverage information from multiple views and in our...

Online co-regularized algorithms

We propose an online co-regularized learning algorithm for classification and regression tasks. We demonstrate that by sequentially co-regularizing prediction functions on unlabeled data points, our algorithm provides improved performance in comparison to supervised methods on several UCI benchmarks and a real world natural language processing...

Molecular machines in the synapse: Overlapping protein sets control distinct steps in neurosecretion

Activity regulated neurotransmission shapes the computational properties of a neuron and involves the concerted action of many proteins. Classical, intuitive working models often assign specific proteins to specific steps in such complex cellular processes, whereas modern systems theories emphasize more integrated functions of proteins. To test...