Promoting Biosecurity in the Equine Community: A New Resource for Extension Educators and the Equine Industry

For biosecurity practices to be effective in the equine industry, they must be tailored to the unique challenges faced by horse owners (e.g., close animal contact, manure handling, and reliance on heavy visitor traffic). The Tools For Promoting Biosecurity in Vermont\u27s Equine Industry CD-ROM will help Extension educators with limited equine background answer questions regarding horse housing, health, and management. The CD-ROM also enables horse owners to evaluate their facilities in terms of how much risk of infectious disease they face and helps them design preventative plans to make their facilities safer for both animals and clientele

Hyperemesis gravidarum: current perspectives.

Hyperemesis gravidarum is a complex condition with a multifactorial etiology characterized by severe intractable nausea and vomiting. Despite a high prevalence, studies exploring underlying etiology and treatments are limited. We performed a literature review, focusing on articles published over the last 10 years, to examine current perspectives and recent developments in hyperemesis gravidarum

Leveraging Global Gene Expression Patterns to Predict Expression of Unmeasured Genes

BackgroundLarge collections of paraffin-embedded tissue represent a rich resource to test hypotheses based on gene expression patterns; however, measurement of genome-wide expression is cost-prohibitive on a large scale. Using the known expression correlation structure within a given disease type (in this case, high grade serous ovarian cancer; HGSC), we sought to identify reduced sets of directly measured (DM) genes which could accurately predict the expression of a maximized number of unmeasured genes

Bottom habitat mapping using towed underwater videography: subtidal oyster reefs as an example application

Towed underwater video has become a widely used method for bottom habitat mapping in coastal waters, but very little has been published on this relatively new and effective approach. We use a case study on two oyster reefs to illustrate the pros and cons of towed video, visualization techniques, and future research topics. Towed video is deployed in similar fashion to single-beam sonars, yielding narrow swaths of video imagery that are recorded concurrently with global positioning system (GPS) data for georeferencing. The major advantages over acoustic (sonar) methods are that image processing and interpretation are relatively simple, and there is little or no need for subsequent ground-truthing. The system used in the present study consists of an underwater black and white camera mounted on a steel frame, differential GPS unit, and digital video camera for recording. It was assembled from off-the-shelf items, and total cost was approximately $3500 (2006 US$). The imagery from both study reefs was of sufficient quality to allow classification of the surveyed bottom into three categories: nonreef, low-density shell, and high-density shell. Some reef characteristics such as the amount of vertical relief were easily discernable and showed substantial differences between the two reefs. Reef bottom areal coverages determined from the video imagery compared well with recent previous studies on the two reefs using other methods. Water clarity limitations represent the major obstacle to widespread use of video for routine mapping of oyster reefs. Turbidity–image quality relations remain to be quantified

Effects of a Large Fishing Closure on Benthic Communitites in the Western Gulf of Maine: Recovery from the Effects of Gillnets and Otter Trawls

The recovery of benthic communities inside the western Gulf of Maine fishing closure area was evaluated by comparing invertebrate assemblages at sites inside and outside of the closure four to six years after the closure was established. The major restriction imposed by the closure was a year-round prohibition of bottom gillnets and otter trawls. A total of 163 seafloor sites (~half inside and half outside the closure) within a 515-km2 study area were sampled with some combination of Shipek grab, Wildco box corer, or underwater video. Bottom types ranged from mud (silt and clay) to boulders, and the effects of the closure on univariate measures (total density, biomass, taxonomic richness) of benthos varied widely among sediment types. For sites with predominantly mud sediments, there were mixed effects on inside and outside infauna and no effect on epifauna. For sites with mainly sand sediments, there were higher density, biomass, and taxonomic richness for infauna inside the closure, but no significant effects on epifauna. For sites dominated by gravel (which included boulders in some areas), there were no effects on infauna but strong effects on epifaunal density and taxonomic richness. For fishing gear, the data indicated that infauna recovered in sand from the impacts of otter trawls operated inside the closure but that they did not recover in mud, and that epifauna recovered on gravel bottoms from the impact of gillnets used inside the closure. The magnitudes of impact and recovery, however, cannot be inferred directly from our data because of a confounding factor of different fishing intensities outside the closure for a direct comparison of preclosure and postclosure data. The overall negative impact of trawls is likely underestimated by our data, whereas the negative impact of gillnets is likely overestimated

Discovery of chemically induced mutations in rice by TILLING

BACKGROUND: Rice is both a food source for a majority of the world's population and an important model system. Available functional genomics resources include targeted insertion mutagenesis and transgenic tools. While these can be powerful, a non-transgenic, unbiased targeted mutagenesis method that can generate a range of allele types would add considerably to the analysis of the rice genome. TILLING (Targeting Induced Local Lesions in Genomes), a general reverse genetic technique that combines traditional mutagenesis with high throughput methods for mutation discovery, is such a method. RESULTS: To apply TILLING to rice, we developed two mutagenized rice populations. One population was developed by treatment with the chemical mutagen ethyl methanesulphonate (EMS), and the other with a combination of sodium azide plus methyl-nitrosourea (Az-MNU). To find induced mutations, target regions of 0.7–1.5 kilobases were PCR amplified using gene specific primers labeled with fluorescent dyes. Heteroduplexes were formed through denaturation and annealing of PCR products, mismatches digested with a crude preparation of CEL I nuclease and cleaved fragments visualized using denaturing polyacrylamide gel electrophoresis. In 10 target genes screened, we identified 27 nucleotide changes in the EMS-treated population and 30 in the Az-MNU population. CONCLUSION: We estimate that the density of induced mutations is two- to threefold higher than previously reported rice populations (about 1/300 kb). By comparison to other plants used in public TILLING services, we conclude that the populations described here would be suitable for use in a large scale TILLING project

miQC : An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data

Single-cell RNA-sequencing (scRNA-seq) has made it possible to profile gene expression in tissues at high resolution. An important preprocessing step prior to performing downstream analyses is to identify and remove cells with poor or degraded sample quality using quality control (QC) metrics. Two widely used QC metrics to identify a 'low-quality' cell are (i) if the cell includes a high proportion of reads that map to mitochondrial DNA (mtDNA) encoded genes and (ii) if a small number of genes are detected. Current best practices use these QC metrics independently with either arbitrary, uniform thresholds (e.g. 5%) or biological context-dependent (e.g. species) thresholds, and fail to jointly model these metrics in a data-driven manner. Current practices are often overly stringent and especially untenable on certain types of tissues, such as archived tumor tissues, or tissues associated with mitochondrial function, such as kidney tissue [1]. We propose a data-driven QC metric (miQC) that jointly models both the proportion of reads mapping to mtDNA genes and the number of detected genes with mixture models in a probabilistic framework to predict the low-quality cells in a given dataset. We demonstrate how our QC metric easily adapts to different types of single-cell datasets to remove low-quality cells while preserving high-quality cells that can be used for downstream analyses. Our software package is available at https://bioconductor.org/packages/miQC. Author summary We developed the miQC package to predict the low-quality cells in a given scRNA-seq dataset by jointly modeling both the proportion of reads mapping to mitochondrial DNA (mtDNA) genes and the number of detected genes using mixture models in a probabilistic framework. We demonstrate how our QC metric easily adapts to different types of single-cell datasets to remove low-quality cells while preserving high-quality cells that can be used for downstream analyses.Peer reviewe

Informed choice about breast cancer prevention: randomized controlled trial of an online decision aid intervention

Abstract Introduction Tamoxifen and raloxifene are chemopreventive drugs that can reduce women's relative risk of primary breast cancer by 50%; however, most women eligible for these drugs have chosen not to take them. The reasons for low uptake may be related to women's knowledge or attitudes towards the drugs. We aimed to examine the impact of an online breast cancer chemoprevention decision aid (DA) on informed intentions and decisions of women at high risk of breast cancer. Methods We conducted a randomized clinical trial, assessing the effect of a DA about breast cancer chemoprevention on informed choices about chemoprevention. Women (n = 585), 46- to 74-years old old, completed online baseline, post-test, and three-month follow-up questionnaires. Participants were randomly assigned to either an intervention group, a standard control group that answered questions about chemoprevention at baseline, or a three-month control group that did not answer questions about chemoprevention at baseline. The main outcome measures were whether women's intentions and decisions regarding chemoprevention drugs were informed, and whether women who viewed the DA were more likely to make informed decisions than women who did not view the DA, using a dichotomous composite variable 'informed choice' (yes/no) to classify informed decisions as those reflecting sufficient knowledge and concordance between a woman's decision and relevant attitudes. Results Analyses showed that more intervention than standard control participants (52.7% versus 5.9%) made informed decisions at post-test, P <0.001. At the three-month follow-up, differences in rates of informed choice between intervention (16.9%) and both control groups (11.8% and 8.0%) were statistically non-significant, P = 0.067. Conclusions The DA increased informed decision making about breast cancer chemoprevention, although the impact on knowledge diminished over time. This study was not designed to determine how much knowledge decision makers must retain over time. Examining informed decisions increases understanding of the impact of DAs. A standard for defining and measuring sufficient knowledge for informed decisions is needed. Trial registration ClinicalTrials.gov: NCT00967824http://deepblue.lib.umich.edu/bitstream/2027.42/112557/1/13058_2013_Article_3282.pd

Informed choice about breast cancer prevention: randomized controlled trial of an online decision aid intervention

Abstract Introduction Tamoxifen and raloxifene are chemopreventive drugs that can reduce women's relative risk of primary breast cancer by 50%; however, most women eligible for these drugs have chosen not to take them. The reasons for low uptake may be related to women's knowledge or attitudes towards the drugs. We aimed to examine the impact of an online breast cancer chemoprevention decision aid (DA) on informed intentions and decisions of women at high risk of breast cancer. Methods We conducted a randomized clinical trial, assessing the effect of a DA about breast cancer chemoprevention on informed choices about chemoprevention. Women (n = 585), 46- to 74-years old old, completed online baseline, post-test, and three-month follow-up questionnaires. Participants were randomly assigned to either an intervention group, a standard control group that answered questions about chemoprevention at baseline, or a three-month control group that did not answer questions about chemoprevention at baseline . The main outcome measures were whether women's intentions and decisions regarding chemoprevention drugs were informed, and whether women who viewed the DA were more likely to make informed decisions than women who did not view the DA, using a dichotomous composite variable 'informed choice' (yes/no) to classify informed decisions as those reflecting sufficient knowledge and concordance between a woman's decision and relevant attitudes. Results Analyses showed that more intervention than standard control participants (52.7% versus 5.9%) made informed decisions at post-test, P <0.001. At the three-month follow-up, differences in rates of informed choice between intervention (16.9%) and both control groups (11.8% and 8.0%) were statistically non-significant, P = 0.067. Conclusions The DA increased informed decision making about breast cancer chemoprevention, although the impact on knowledge diminished over time. This study was not designed to determine how much knowledge decision makers must retain over time. Examining informed decisions increases understanding of the impact of DAs. A standard for defining and measuring sufficient knowledge for informed decisions is needed. Trial registration ClinicalTrials.gov: NCT00967824http://deepblue.lib.umich.edu/bitstream/2027.42/135728/1/13058_2013_Article_3282.pd

Human Impacts on Forest Biodiversity in Protected Walnut-Fruit Forests in Kyrgyzstan

We used a spatially explicit model of forest dynamics, supported by empirical field data and socioeconomic data, to examine the impacts of human disturbances on a protected forest landscape in Kyrgyzstan. Local use of 27 fruit and nut species was recorded and modeled. Results indicated that in the presence of fuelwood cutting with or without grazing, species of high socioeconomic impor- tance such as Juglans regia, Malus spp., and Armeniaca vulgaris were largely eliminated from the landscape after 50–150 yr. In the absence of disturbance or in the presence of grazing only, decline of these species occurred at a much lower rate, owing to competi- tive interactions between tree species. This suggests that the current intensity of fuelwood harvesting is not sustainable. Conversely, cur- rent grazing intensities were found to have relatively little impact on forest structure and composition, and could potentially play a positive role in supporting regeneration of tree species. These results indicate that both positive and negative impacts on biodiversity can arise from human populations living within a protected area. Potentially, these could be reconciled through the development of participatory approaches to conservation management within this reserve, to ensure the maintenance of its high conservation value while meeting human needs