Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa.

Background: Escherichia coli is considered a leading bacterial trigger of inflammatory bowel disease (IBD). E. coli isolates from IBD patients primarily belong to phylogroup B2.

Pilot of a mobile money school fee payment system in rural Benin.

We present a rationale for, and results from, the pilot of a direct individual-to-institution remittance system in the context of school fee payment in rural Benin. Data confirm that school fees act as an impediment to educational attainment, and in very rural poor settings such as northern Benin, students often depend on extended family and kinship networks to pay fees. But existing remittance options are costly, in terms of fees, time, and risk.

American Gut: an Open Platform for Citizen Science Microbiome Research.

Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging to integrate and the extent of microbial and molecular diversity in human stool remains unknown. Using standardized protocols from the Earth Microbiome Project and sample contributions from over 10,000 citizen-scientists, together with an open research network, we compare human microbiome specimens primarily from the United States, United Kingdom, and Australia to one another and to environmental samples. Our results show an unexpected range of beta-diversity in human stool microbiomes compared to environmental samples; demonstrate the utility of procedures for removing the effects of overgrowth during room-temperature shipping for revealing phenotype correlations; uncover new molecules and kinds of molecular communities in the human stool metabolome; and examine emergent associations among the microbiome, metabolome, and the diversity of plants that are consumed (rather than relying on reductive categorical variables such as veganism, which have little or no explanatory power).

Creating a 3D microbial and chemical snapshot of a human habitat.

One of the goals of forensic science is to identify individuals and their lifestyle by analyzing the trace signatures left behind in built environments. Here, microbiome and metabolomic methods were used to see how its occupants used an office and to also gain insights into the lifestyle characteristics such as diet, medications, and personal care products of the occupants. 3D molecular cartography, a molecular visualization technology, was used in combination with mass spectrometry and microbial inventories to highlight human-environmental interactions.

Automated placement of interfaces in conformational kinetics calculations using machine learning.

Several recent implementations of algorithms for sampling reaction pathways employ a strategy for placing interfaces or milestones across the reaction coordinate manifold. Interfaces can be introduced such that the full feature space describing the dynamics of a macromolecule is divided into Voronoi (or other) cells, and the global kinetics of the molecular motions can be calculated from the set of fluxes through the interfaces between the cells. Although some methods of this type are exact for an arbitrary set of cells, in practice, the calculations will converge fastest when the interfaces are placed in regions where they can best capture transitions between configurations corresponding to local minima.

Solid State Sensor for Simultaneous Measurement of Total Alkalinity and pH of Seawater.

A novel design is demonstrated for a solid state, reagent-less sensor capable of rapid and simultaneous measurement of pH and Total Alkalinity (A) using ion sensitive field effect transistor (ISFET) technology to provide a simplified means of characterization of the aqueous carbon dioxide system through measurement of two "master variables": pH and A. ISFET-based pH sensors that achieve 0.001 precision are widely used in various oceanographic applications.

Quantifying the development of user-generated art during 2001-2010.

One of the main questions in the humanities is how cultures and artistic expressions change over time. While a number of researchers have used quantitative computational methods to study historical changes in literature, music, and cinema, our paper offers the first quantitative analysis of historical changes in visual art created by users of a social online network. We propose a number of computational methods for the analysis of temporal development of art images.

Wayfinding and Glaucoma: A Virtual Reality Experiment.

Purpose: Wayfinding, the process of determining and following a route between an origin and a destination, is an integral part of everyday tasks. The purpose of this study was to investigate the impact of glaucomatous visual field loss on wayfinding behavior using an immersive virtual reality (VR) environment.

Methods: This cross-sectional study included 31 glaucomatous patients and 20 healthy subjects without evidence of overall cognitive impairment.

Feasibility Study of a Mobile Health Intervention for Older Adults on Oral Anticoagulation Therapy.

Oral anticoagulation treatment (OAT) such as warfarin therapy is recommended for older adults with atrial fibrillation, heart failure, or who are at risk for venous thromboembolism. Despite its proven benefits, older adults report both dissatisfaction with OAT and reduced quality of life that can potentially lead to low adherence to OAT and decreased treatment efficacy. To test the feasibility of Mobile Applications for Seniors to enhance Safe anticoagulation therapy (MASS), a mobile-based health technology intervention designed to promote independence and self-care.

Kernel Density Estimation as a Measure of Environmental Exposure Related to Insulin Resistance in Breast Cancer Survivors.

Environmental factors may influence breast cancer; however, most studies have measured environmental exposure in neighborhoods around home residences (static exposure). We hypothesize that tracking environmental exposures over time and space (dynamic exposure) is key to assessing total exposure. This study compares breast cancer survivors' exposure to walkable and recreation-promoting environments using dynamic Global Positioning System (GPS) and static home-based measures of exposure in relation to insulin resistance.

Bringing the Dynamic Microbiome to Life with Animations.

Our bodies and natural environment contain complex microbial communities, colloquially termed microbiomes. We previously created a web-based application, EMPeror, for visualizing ordinations derived from comparisons of these microbiome communities. We have now improved EMPeror to create interactive animations that connect successive samples to highlight patterns over time.

Age-Friendly Communities Initiative: Public Health Approach to Promoting Successful Aging.

Older adults consistently prefer aging in place, which requires a high level of community support and services that are currently lacking. With a rapidly aging population, the present infrastructure for healthcare will prove even more inadequate to meet seniors' physical and mental health needs. A paradigm shift away from the sole focus on delivery of interventions at an individual level to more prevention-focused, community-based approaches will become essential.

Grazing Incidence Cross-Sectioning of Thin-Film Solar Cells via Cryogenic Focused Ion Beam: A Case Study on CIGSe.

Cryogenic focused ion beam (Cryo-FIB) milling at near-grazing angles is employed to fabricate cross-sections on thin Cu(In,Ga)Se2 with >8x expansion in thickness. Kelvin probe force microscopy (KPFM) on sloped cross sections showed reduction in grain boundaries potential deeper into the film. Cryo Fib-KPFM enabled the first determination of the electronic structure of the Mo/CIGSe back contact, where a sub 100 nm thick MoSey assists hole extraction due to 45 meV higher work function.

A multi-site array for combined local electrochemistry and electrophysiology in the non-human primate brain.

Background: Currently, the primary technique employed in circuit-level study of the brain is electrophysiology, recording local field or action potentials (LFPs or APs). However most communication between neurons is chemical and the relationship between electrical activity within neurons and chemical signaling between them is not well understood in vivo, particularly for molecules that signal at least in part by non-synaptic transmission.

New Method: We describe a multi-contact array and accompanying head stage circuit that together enable concurrent electrophysiological and electrochemical recording.

Proper evaluation of alignment-free network comparison methods.

Motivation: Network comparison is a computationally intractable problem with important applications in systems biology and other domains. A key challenge is to properly quantify similarity between wiring patterns of two networks in an alignment-free fashion. Also, alignment-based methods exist that aim to identify an actual node mapping between networks and as such serve a different purpose.

Crowdsourcing the unknown: the satellite search for Genghis Khan.

Massively parallel collaboration and emergent knowledge generation is described through a large scale survey for archaeological anomalies within ultra-high resolution earth-sensing satellite imagery. Over 10K online volunteers contributed 30K hours (3.4 years), examined 6,000 km², and generated 2.

Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications.

Biological processes are fundamentally driven by complex interactions between biomolecules. Integrated high-throughput omics studies enable multifaceted views of cells, organisms, or their communities. With the advent of new post-genomics technologies, omics studies are becoming increasingly prevalent; yet the full impact of these studies can only be realized through data harmonization, sharing, meta-analysis, and integrated research.

CGLX: a scalable, high-performance visualization framework for networked display environments.

The Cross Platform Cluster Graphics Library (CGLX) is a flexible and transparent OpenGL-based graphics framework for distributed, high-performance visualization systems. CGLX allows OpenGL based applications to utilize massively scalable visualization clusters such as multiprojector or high-resolution tiled display environments and to maximize the achievable performance and resolution. The framework features a programming interface for hardware-accelerated rendering of OpenGL applications on visualization clusters, mimicking a GLUT-like (OpenGL-Utility-Toolkit) interface to enable smooth translation of single-node applications to distributed parallel rendering applications.

Artificial and natural duplicates in pyrosequencing reads of metagenomic data.

Background: Artificial duplicates from pyrosequencing reads may lead to incorrect interpretation of the abundance of species and genes in metagenomic studies. Duplicated reads were filtered out in many metagenomic projects. However, since the duplicated reads observed in a pyrosequencing run also include natural (non-artificial) duplicates, simply removing all duplicates may also cause underestimation of abundance associated with natural duplicates.

A primer on metagenomics.

Metagenomics is a discipline that enables the genomic study of uncultured microorganisms. Faster, cheaper sequencing technologies and the ability to sequence uncultured microbes sampled directly from their habitats are expanding and transforming our view of the microbial world. Distilling meaningful information from the millions of new genomic sequences presents a serious challenge to bioinformaticians.

CD-HIT Suite: a web server for clustering and comparing biological sequences.

Unlabelled: CD-HIT is a widely used program for clustering and comparing large biological sequence datasets. In order to further assist the CD-HIT users, we significantly improved this program with more functions and better accuracy, scalability and flexibility. Most importantly, we developed a new web server, CD-HIT Suite, for clustering a user-uploaded sequence dataset or comparing it to another dataset at different identity levels.

Analysis and comparison of very large metagenomes with fast clustering and functional annotation.

Background: The remarkable advance of metagenomics presents significant new challenges in data analysis. Metagenomic datasets (metagenomes) are large collections of sequencing reads from anonymous species within particular environments. Computational analyses for very large metagenomes are extremely time-consuming, and there are often many novel sequences in these metagenomes that are not fully utilized.

Identification of ribosomal RNA genes in metagenomic fragments.

Motivation: Identification of genes coding for ribosomal RNA (rRNA) is considered an important goal in the analysis of data from metagenomics projects. Here, we report the development of a software program designed for the identification of rRNA genes from metagenomic fragments based on hidden Markov models (HMMs). This program provides rRNA gene predictions with high sensitivity and specificity on artificially fragmented genomic DNAs.

High-precision radiocarbon dating and historical biblical archaeology in southern Jordan.

Recent excavations and high-precision radiocarbon dating from the largest Iron Age (IA, ca. 1200-500 BCE) copper production center in the southern Levant demonstrate major smelting activities in the region of biblical Edom (southern Jordan) during the 10th and 9th centuries BCE. Stratified radiocarbon samples and artifacts were recorded with precise digital surveying tools linked to a geographic information system developed to control on-site spatial analyses of archaeological finds and model data with innovative visualization tools.