Encoding of low-quality DNA profiles as genotype probability matrices for improved profile comparisons, relatedness evaluation and database searches

Many DNA profiles recovered from crime scene samples are of a quality that does not allow them to be searched against, nor entered into, databases. We propose a method for the comparison of profiles arising from two DNA samples, one or both of which can have multiple donors and be affected by low DNA template or degraded DNA. We compute likelihood ratios to evaluate the hypothesis that the two samples have a common DNA donor, and hypotheses specifying the relatedness of two donors. Our method uses a probability distribution for the genotype of the donor of interest in each sample. This distribution can be obtained from a statistical model, or we can exploit the ability of trained human experts to assess genotype probabilities, thus extracting much information that would be discarded by standard interpretation rules. Our method is compatible with established methods in simple settings, but is more widely applicable and can make better use of information than many current methods for the analysis of mixed-source, low-template DNA profiles. It can accommodate uncertainty arising from relatedness instead of or in addition to uncertainty arising from noisy genotyping. We describe a computer program GPMDNA, available under an open source license, to calculate LRs using the method presented in this paper.Comment: 28 pages. Accepted for publication 2-Sep-2016 - Forensic Science International: Genetic

Erratum Re: “Coping With Racism: Moderators of the Discrimination—Distress Link Among Mexican-Origin Adolescents”

The publisher's final edited version of this article is available at Child Dev This corrects the article "Coping With Racism: Moderators of the Discrimination—Adjustment Link Among Mexican-Origin Adolescents" in Child Dev, volume 89 on page e293

Efficacy of a crosslinked hyaluronic acid-based hydrogel as a tear film supplement: a masked controlled study.

This is the final publish manuscript distributed under a Creative Commons Attribution License 2.0 UK, which can also be found on the publisher's website at: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0099766Keratoconjunctivitis sicca (KCS), or dry eye, is a significant medical problem in both humans and dogs. Treating KCS often requires the daily application of more than one type of eye drop in order to both stimulate tear prodcution and provide a tear supplement to increase hydration and lubrication. A previous study demonstrated the potential for a crosslinked hyaluronic acid-based hydrogel (xCMHA-S) to reduce the clinical signs associated with KCS in dogs while using a reduced dosing regimen of only twice-daily administration. The present study extended those results by comparing the use of the xCMHA-S to a standard HA-containing tear supplement in a masked, randomized clinical study in dogs with a clinical diagnosis of KCS. The xCMHA-S was found to significantly improve ocular surface health (conjunctival hyperaemia, ocular irritation, and ocular discharge) to a greater degree than the alternative tear supplement (P = 0.0003). Further, owners reported the xCMHA-S treatment as being more highly effective than the alternative tear supplement (P = 0.0024). These results further demonstrate the efficacy of the xCMHA-S in reducing the clinical signs associated with KCS, thereby improving patient health and owner happiness

Bayesian classification with Gaussian processes

We consider the problem of assigning an input vector to one of m classes by predicting P(c|x) for c=1,...,m. For a two-class problem, the probability of class one given x is estimated by s(y(x)), where s(y)=1/(1+e-y). A Gaussian process prior is placed on y(x), and is combined with the training data to obtain predictions for new x points. We provide a Bayesian treatment, integrating over uncertainty in y and in the parameters that control the Gaussian process prior the necessary integration over y is carried out using Laplace's approximation. The method is generalized to multiclass problems (m>2) using the softmax function. We demonstrate the effectiveness of the method on a number of datasets

SWAS and Arecibo observations of H2O and OH in a diffuse cloud along the line-of-sight to W51

Observations of W51 with the Submillimeter Wave Astronomy Satellite (SWAS) have yielded the first detection of water vapor in a diffuse molecular cloud. The water vapor lies in a foreground cloud that gives rise to an absorption feature at an LSR velocity of 6 km/s. The inferred H2O column density is 2.5E+13 cm-2. Observations with the Arecibo radio telescope of hydroxyl molecules at ten positions in W51 imply an OH column density of 8E+13 cm-2 in the same diffuse cloud. The observed H2O/OH ratio of ~ 0.3 is significantly larger than an upper limit derived previously from ultraviolet observations of the similar diffuse molecular cloud lying in front of HD 154368. The observed variation in H2O/OH likely points to the presence in one or both of these clouds of a warm (T > 400) gas component in which neutral-neutral reactions are important sources of OH and/or H2O.Comment: 15 pages (AASTeX) including 4 (eps) figures. To appear in the Astrophysical Journa

Department of Homeland Security Science and Technology Directorate: Developing Technology to Protect America

In response to a congressional mandate and in consultation with Department of Homeland Security's (DHS) Science and Technology Directorate (S&T), the National Academy conducted a review of S&T's effectiveness and efficiency in addressing homeland security needs. This review included a particular focus that identified any unnecessary duplication of effort, and opportunity costs arising from an emphasis on homeland security-related research. Under the direction of the National Academy Panel, the study team reviewed a wide variety of documents related to S&T and homeland security-related research in general. The team also conducted interviews with more than 200 individuals, including S&T officials and staff, officials from other DHS component agencies, other federal agencies engaged in homeland security-related research, and experts from outside government in science policy, homeland security-related research and other scientific fields.Key FindingsThe results of this effort indicated that S&T faces a significant challenge in marshaling the resources of multiple federal agencies to work together to develop a homeland security-related strategic plan for all agencies. Yet the importance of this role should not be underestimated. The very process of working across agencies to develop and align the federal homeland security research enterprise around a forward-focused plan is critical to ensuring that future efforts support a common vision and goals, and that the metrics by which to measure national progress, and make changes as needed, are in place

Development and validation of the guideline for reporting evidence-based practice educational interventions and teaching (GREET)

Abstract Background The majority of reporting guidelines assist researchers to report consistent information concerning study design, however, they contain limited information for describing study interventions. Using a three-stage development process, the Guideline for Reporting Evidence-based practice Educational interventions and Teaching (GREET) checklist and accompanying explanatory paper were developed to provide guidance for the reporting of educational interventions for evidence-based practice (EBP). The aim of this study was to complete the final development for the GREET checklist, incorporating psychometric testing to determine inter-rater reliability and criterion validity. Methods The final development for the GREET checklist incorporated the results of a prior systematic review and Delphi survey. Thirty-nine items, including all items from the prior systematic review, were proposed for inclusion in the GREET checklist. These 39 items were considered over a series of consensus discussions to determine the inclusion of items in the GREET checklist. The GREET checklist and explanatory paper were then developed and underwent psychometric testing with tertiary health professional students who evaluated the completeness of the reporting in a published study using the GREET checklist. For each GREET checklist item, consistency (%) of agreement both between participants and the consensus criterion reference measure were calculated. Criterion validity and inter-rater reliability were analysed using intra-class correlation coefficients (ICC). Results Three consensus discussions were undertaken, with 14 items identified for inclusion in the GREET checklist. Following further expert review by the Delphi panelists, three items were added and minor wording changes were completed, resulting in 17 checklist items. Psychometric testing for the updated GREET checklist was completed by 31 participants (n = 11 undergraduate, n = 20 postgraduate). The consistency of agreement between the participant ratings for completeness of reporting with the consensus criterion ratings ranged from 19 % for item 4 Steps of EBP, to 94 % for item 16 Planned delivery. The overall consistency of agreement, for criterion validity (ICC 0.73) and inter-rater reliability (ICC 0.96), was good to almost perfect. Conclusion The final GREET checklist comprises 17 items which are recommended for reporting EBP educational interventions. Further validation of the GREET checklist with experts in EBP research and education is recommended