Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets.

BackgroundBioinformatics software often requires human-generated tabular text files as input and has specific requirements for how those data are formatted. Users frequently manage these data in spreadsheet programs, which is convenient for researchers who are compiling the requisite information because the spreadsheet programs can easily be used on different platforms including laptops and tablets, and because they provide a familiar interface. It is increasingly common for many different researchers to be involved in compiling these data, including study coordinators, clinicians, lab technicians and bioinformaticians. As a result, many research groups are shifting toward using cloud-based spreadsheet programs, such as Google Sheets, which support the concurrent editing of a single spreadsheet by different users working on different platforms. Most of the researchers who enter data are not familiar with the formatting requirements of the bioinformatics programs that will be used, so validating and correcting file formats is often a bottleneck prior to beginning bioinformatics analysis.Main textWe present Keemei, a Google Sheets Add-on, for validating tabular files used in bioinformatics analyses. Keemei is available free of charge from Google's Chrome Web Store. Keemei can be installed and run on any web browser supported by Google Sheets. Keemei currently supports the validation of two widely used tabular bioinformatics formats, the Quantitative Insights into Microbial Ecology (QIIME) sample metadata mapping file format and the Spatially Referenced Genetic Data (SRGD) format, but is designed to easily support the addition of others.ConclusionsKeemei will save researchers time and frustration by providing a convenient interface for tabular bioinformatics file format validation. By allowing everyone involved with data entry for a project to easily validate their data, it will reduce the validation and formatting bottlenecks that are commonly encountered when human-generated data files are first used with a bioinformatics system. Simplifying the validation of essential tabular data files, such as sample metadata, will reduce common errors and thereby improve the quality and reliability of research outcomes

Examination and implementation of a proposal for a Ph.D. program in Administrative Sciences

The purpose of this thesis is to conduct a feasibility study for establishing a Ph.D. program for the Administrative Sciences department and to prepare a Ph.D. proposal to submit to the Academic Council for program approval. According to the Academic Council requirements regarding the Ph.D. program, the following questions are addressed: (1) does the department have an active masters program; (2) does the department offer adequate physical facilities to support Ph.D. research; (3) is the faculty diverse enough; (4) is the faculty currently active in research; (5) does the faculty have sufficient doctoral program experience; and (6) does the department have sufficient faculty members in the subfield where it is proposed to award the doctorate. The results of this study indicate that the Department of Administrative Sciences meets all the criteria set forth by the Academic Council Policy Manual (Section 259). A strong Administrative Sciences doctoral program would strengthen the Naval Postgraduate School's mission to serve DON/DOD advanced educational needs.http://archive.org/details/examinationndimp1094538554Lieutenant, United States NavyApproved for public release; distribution is unlimited

Relative occurrence of the family Kalotermitidae (Isoptera) under different termite sampling methods

The termite family Kalotermitidae constitutes a wood-nesting termite family that accounts for about 15% of all extant termite species. In recent decades, field studies have been carried out to assess termite diversity in various wooded habitats and geographic locations. Three sampling methods have been favored expert, transect, and alate light-trap surveys. Expert collecting is not spatially quantifiable but relies on field personnel to recognize and sample termite niches. The transect method aims to standardize and quantify termite abundance and diversity. Light trapping is a passive method for sampling nocturnal alate flights. We compared our expert survey results and results of published sampling methods for their proportional yields of kalotermitid versus non-kalotermitid encounters. Using an odds ratio statistic, we found that worldwide, there is about a 50.6-fold greater likelihood of encountering a kalotermitid sample versus a non-kalotermitid using the expert survey method and a 15.3-fold greater likelihood using alate trapping than using the transect method. There is about a 3.3 -fold greater likelihood of collecting a kalotermitid specimen versus a non-kalotermitid sample using the expert survey method than using the alate trap method. Transect studies in which only termite species diversity was reported gave similar low Kalotermitidae yields. We propose that multiple biases in sampling methodology include tools, time constraints, habitat type, geographical location, topographical conditions, and human traits account for the divergent outcomes in sampling the abundance and diversity of Kalotermitidae compared to other termite families

Gravitationally Collapsing Shells in (2+1) Dimensions

We study gravitationally collapsing models of pressureless dust, fluids with pressure, and the generalized Chaplygin gas (GCG) shell in (2+1)-dimensional spacetimes. Various collapse scenarios are investigated under a variety of the background configurations such as anti-de Sitter(AdS) black hole, de Sitter (dS) space, flat and AdS space with a conical deficit. As with the case of a disk of dust, we find that the collapse of a dust shell coincides with the Oppenheimer-Snyder type collapse to a black hole provided the initial density is sufficiently large. We also find -- for all types of shell -- that collapse to a naked singularity is possible under a broad variety of initial conditions. For shells with pressure this singularity can occur for a finite radius of the shell. We also find that GCG shells exhibit diverse collapse scenarios, which can be easily demonstrated by an effective potential analysis.Comment: 27 pages, Latex, 11 figures, typos corrected, references added, minor amendments in introduction and conclusion introd

Predicting cannabis cultivation on national forests using a rational choice framework

Government agencies in the United States eradicated 10.3 million cannabis plants in 2010. Most (94%) of these plants were outdoor-grown, and 46% of those were discovered on federal lands, primarily on national forests in California, Oregon, and Washington. We developed models that reveal how drug markets, policies, and environmental conditions affect grow siting decisions. The models were built on a rational choice theoretical structure, and utilized data describing 2322 cannabis grow locations (2004–2012) and 9324 absence locations in the states\u27 national forests. Predictor variables included cannabis market prices, law enforcement density, and socioeconomic, demographic, and environmental variables.We also used the models to construct regional maps of grow site likelihood. Significant predictors included marijuana street price and variables associated with grow site productivity (e.g., elevation and proximity to water), production costs, and risk of discovery. Overall, the pattern of grow site establishment on national forests is consistent with rational choice theory. In particular, growers consider cannabis prices and law enforcement when selecting sites. Ongoing adjustments in state cannabis laws could affect cultivation decisions on national forests. Any changes in cannabis policies can be reflected in our models to allow agencies to redirect interdiction resources and potentially increase discovery success

Predicting cannabis cultivation on national forests using a rational choice framework

Government agencies in the United States eradicated 10.3 million cannabis plants in 2010. Most (94%) of these plants were outdoor-grown, and 46% of those were discovered on federal lands, primarily on national forests in California, Oregon, and Washington. We developed models that reveal how drug markets, policies, and environmental conditions affect grow siting decisions. The models were built on a rational choice theoretical structure, and utilized data describing 2322 cannabis grow locations (2004–2012) and 9324 absence locations in the states\u27 national forests. Predictor variables included cannabis market prices, law enforcement density, and socioeconomic, demographic, and environmental variables.We also used the models to construct regional maps of grow site likelihood. Significant predictors included marijuana street price and variables associated with grow site productivity (e.g., elevation and proximity to water), production costs, and risk of discovery. Overall, the pattern of grow site establishment on national forests is consistent with rational choice theory. In particular, growers consider cannabis prices and law enforcement when selecting sites. Ongoing adjustments in state cannabis laws could affect cultivation decisions on national forests. Any changes in cannabis policies can be reflected in our models to allow agencies to redirect interdiction resources and potentially increase discovery success

Pathogen transmission from vaccinated hosts can cause dose-dependent reduction in virulence

Many livestock and human vaccines are leaky because they block symptoms but do not prevent infection or onward transmission. This leakiness is concerning because it increases vaccination coverage required to prevent disease spread and can promote evolution of increased pathogen virulence. Despite leakiness, vaccination may reduce pathogen load, affecting disease transmission dynamics. However, the impacts on post-transmission disease development and infectiousness in contact individuals are unknown. Here, we use transmission experiments involving Marek disease virus (MDV) in chickens to show that vaccination with a leaky vaccine substantially reduces viral load in both vaccinated individuals and unvaccinated contact individuals they infect. Consequently, contact birds are less likely to develop disease symptoms or die, show less severe symptoms, and shed less infectious virus themselves, when infected by vaccinated birds. These results highlight that even partial vaccination with a leaky vaccine can have unforeseen positive consequences in controlling the spread and symptoms of disease

Low Temperature Opacities

Previous computations of low temperature Rosseland and Planck mean opacities from Alexander & Ferguson (1994) are updated and expanded. The new computations include a more complete equation of state with more grain species and updated optical constants. Grains are now explicitly included in thermal equilibrium in the equation of state calculation, which allows for a much wider range of grain compositions to be accurately included than was previously the case. The inclusion of high temperature condensates such as Al$_2$O$_3$ and CaTiO$_3$ significantly affects the total opacity over a narrow range of temperatures before the appearance of the first silicate grains. The new opacity tables are tabulated for temperatures ranging from 30000 K to 500 K with gas densities from 10$^{-4}$ g cm$^{-3}$ to 10$^{-19}$ g cm$^{-3}$. Comparisons with previous Rosseland mean opacity calculations are discussed. At high temperatures, the agreement with OPAL and Opacity Project is quite good. Comparisons at lower temperatures are more divergent as a result of differences in molecular and grain physics included in different calculations. The computation of Planck mean opacities performed with the opacity sampling method are shown to require a very large number of opacity sampling wavelength points; previously published results obtained with fewer wavelength points are shown to be significantly in error. Methods for requesting or obtaining the new tables are provided.Comment: 39 pages with 12 figures. To be published in ApJ, April 200