Controller Area Network Based Distributed Control for Autonomous Vehicles

The goal of this project was to evaluate the potential of a controller area network (CAN bus) to be used as the communication network for a distributed control system on an autonomous agricultural vehicle. The prototype system utilized microcontroller-driven nodes to act as control points along a CAN bus. Messages were transferred to the steering, transmission, and hitch control nodes via a task computer. The task computer utilized global positioning system data to generate appropriate control commands. Laboratory and field testing demonstrated that each of the control nodes could function simultaneously over the CAN bus. Results showed that the task computer adequately applied a feedback control model to the system and achieved guidance accuracy levels well within the desired range. Testing also demonstrated the system’s ability to complete normal field operations, such as headland turning and implement control

Boulder ALignment Editor (ALE): a web-based RNA alignment tool

Summary: The explosion of interest in non-coding RNAs, together with improvements in RNA X-ray crystallography, has led to a rapid increase in RNA structures at atomic resolution from 847 in 2005 to 1900 in 2010. The success of whole-genome sequencing has led to an explosive growth of unaligned homologous sequences. Consequently, there is a compelling and urgent need for user-friendly tools for producing structure-informed RNA alignments. Most alignment software considers the primary sequence alone; some specialized alignment software can also include Watson–Crick base pairs, but none adequately addresses the needs introduced by the rapid influx of both sequence and structural data. Therefore, we have developed the Boulder ALignment Editor (ALE), which is a web-based RNA alignment editor, designed for editing and assessing alignments using structural information. Some features of BoulderALE include the annotation and evaluation of an alignment based on isostericity of Watson–Crick and non-Watson–Crick base pairs, along with the collapsing (horizontally and vertically) of the alignment, while maintaining the ability to edit the alignment

The mind-body-microbial continuum

Our understanding of the vast collection of microbes that live on and inside us (microbiota) and their collective genes (microbiome) has been revolutionized by culture-independent “metagenomic” techniques and DNA sequencing technologies. Most of our microbes live in our gut, where they function as a metabolic organ and provide attributes not encoded in our human genome. Metagenomic studies are revealing shared and distinctive features of microbial communities inhabiting different humans. A central question in psychiatry is the relative role of genes and environment in shaping behavior. The human microbiome serves as the interface between our genes and our history of environmental exposures; explorations of our microbiomes thus offer the possibility of providing new insights into our neurodevelopment and our behavioral phenotypes by affecting complex processes such as inter- and intra personal variations in cognition, personality, mood, sleep, and eating behavior, and perhaps even a variety of neuropsychiatric diseases ranging from affective disorders to autism. Better understanding of microbiome-encoded pathways for xenobiotic metabolism also has important implications for improving the efficacy of pharmacologic interventions with neuromodulator agents

Rate Response Assessment from Various Granular VRT Applicators

Variable-rate technology (VRT) adds complexity to application equipment, thereby confounding the assessment of applicator performance. The intent of this investigation was to assess the rate response of various VRT granular applicators: two spinner spreaders (A and B), and two pneumatic applicators (C and D). Variable-rate (VR) tests were conducted to quantify the rate response characteristics (delay and transition times) for the applicators. A sigmoidal function was used to model the rate response for five of the six tests. Applicator A exhibited a linear response during decreasing rate changes. Results indicated that only applicator B demonstrated consistent delay and transition times, enabling the use of a single “look-ahead” time for rate response time correction. Contouring of prescription maps increased the transition times for applicator D by enlarging the adjustment area between management zones. Rate changes were quicker for the two newer VR control systems, signifying advancement in hydraulic control valve technology. This research illustrates the need for standard testing protocols for VRT systems to help guide VRT software developers, equipment manufacturers, and end users

TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata

Motivation: Microbial community profiling is a highly active area of research, but tools that facilitate visualization of phylogenetic trees and associated environmental data have not kept up with the increasing quantity of data generated in these studies

SitePainter: a tool for exploring biogeographical patterns

As microbial ecologists take advantage of high-throughput analytical techniques to describe microbial communities across ever-increasing numbers of samples, the need for new analysis tools that reveal the intrinsic spatial patterns and structures of these populations is crucial. Here we present SitePainter, an interactive graphical tool that allows investigators to create or upload pictures of their study site, load diversity analyses data and display both diversity and taxonomy results in a spatial context. Features of SitePainter include: visualizing α -diversity, using taxonomic summaries; visualizing β -diversity, using results from multidimensional scaling methods; and animating relationships among microbial taxa or pathways overtime. SitePainter thus increases the visual power and ability to explore spatially explicit studies

Air Exchange Rate in a Horse Trailer During Road Transport

Horses traveling by road commonly experience heat stress conditions and poor air quality, which may be caused by insufficient ventilation; however, there are few estimates of air exchange in a horse trailer during transport. Air exchange rate was measured at ten locations within a four-horse trailer (internal volume 18.5 m3) using tracer gas decay measurement to assess the adequacy of ventilation. Three vehicle speeds (13, 48, and 97 km h-1) and three window configurations (all windows and roof vents closed, all windows open, all windows open and roof vents open forward) were tested with and without animals present in the trailer. External air temperature ranged from 22.3°C to 28.3°C with an average of 25.3°C, and internal air temperature ranged from 29.9°C to 34.8°C with an average of 31.3°C with animals present. Air exchange rate increased with vehicle speed and open window and vent area. The average air exchange rate over all vehicle speeds and ventilation configurations was 0.52 min-1 with animals present and 0.76 min-1 without animals. Without animals present, the maximum mean exchange rate was 1.42 min-1 at 97 km h-1 at the rear left window with all windows and vents open; the lowest mean exchange rate was 0.12 min-1 at 13 km h-1 with all windows and vents closed at the lower position of the rearmost stall divider. With animals present, the maximum air exchange rate observed was 0.84 min-1 with all windows and vents open and traveling at 97 km h-1. Ventilation in the trailer was not adequate when compared to recommendations for stabled horses for any combination of vehicle speed or ventilation configuration. Increasing open vent area, either by increasing the number and size of roof vents or the size of windows in the sidewall, would be the most cost-effective means of increasing air exchange in a horse trailer

Moving pictures of the human microbiome

BackgroundUnderstanding the normal temporal variation in the human microbiome is critical to developing treatments for putative microbiome-related afflictions such as obesity, Crohn’s disease, inflammatory bowel disease and malnutrition. Sequencing and computational technologies, however, have been a limiting factor in performing dense time series analysis of the human microbiome. Here, we present the largest human microbiota time series analysis to date, covering two individuals at four body sites over 396 timepoints.ResultsWe find that despite stable differences between body sites and individuals, there is pronounced variability in an individual’s microbiota across months, weeks and even days. Additionally, only a small fraction of the total taxa found within a single body site appear to be present across all time points, suggesting that no core temporal microbiome exists at high abundance (although some microbes may be present but drop below the detection threshold). Many more taxa appear to be persistent but non-permanent community members.ConclusionsDNA sequencing and computational advances described here provide the ability to go beyond infrequent snapshots of our human-associated microbial ecology to high-resolution assessments of temporal variations over protracted periods, within and between body habitats and individuals. This capacity will allow us to define normal variation and pathologic states, and assess responses to therapeutic interventions

Sharing and archiving nucleic acid structure mapping data

Nucleic acids are particularly amenable to structural characterization using chemical and enzymatic probes. Each individual structure mapping experiment reveals specific information about the structure and/or dynamics of the nucleic acid. Currently, there is no simple approach for making these data publically available in a standardized format. We therefore developed a standard for reporting the results of single nucleotide resolution nucleic acid structure mapping experiments, or SNRNASMs. We propose a schema for sharing nucleic acid chemical probing data that uses generic public servers for storing, retrieving, and searching the data. We have also developed a consistent nomenclature (ontology) within the Ontology of Biomedical Investigations (OBI), which provides unique identifiers (termed persistent URLs, or PURLs) for classifying the data. Links to standardized data sets shared using our proposed format along with a tutorial and links to templates can be found at http://snrnasm.bio.unc.edu