A Data Transformation System for Biological Data Sources

Scientific data of importance to biologists in the Human Genome Project resides not only in conventional databases, but in structured files maintained in a number of different formats (e.g. ASN.1 and ACE) as well a.s sequence analysis packages (e.g. BLAST and FASTA). These formats and packages contain a number of data types not found in conventional databases, such as lists and variants, and may be deeply nested. We present in this paper techniques for querying and transforming such data, and illustrate their use in a prototype system developed in conjunction with the Human Genome Center for Chromosome 22. We also describe optimizations performed by the system, a crucial issue for bulk data

The Interdisciplinary Ph.D. in Evaluation: Reflections on Its Development and First Seven Years

Background: The Interdisciplinary Ph.D. in Evaluation (IDPE) program at Western Michigan University (WMU) was designed and developed to address the increasing need and demand for highly trained and skilled evaluators. After only six and a half years, the program’s graduates are serving in important evaluation leadership positions throughout the world. Purpose: The purpose of this article is to provide readers with a historical overview and up-to-date description of the IDPE and is intended for those who are interested in evaluation curriculum and advances in the profession. Setting: Not applicable. Intervention: Not applicable. Research Design: Not applicable. Data Collection and Analysis: In this article each of the program’s current and previous leaders reflect on their role in the IDPE. Findings: The concept, design, and operations of this program should be of interest both to evaluation scholars and to those who administer graduate education programs in evaluation.  Keywords: evaluation training, doctoral programming, interdisciplinary programming, evaluation histor

Revised Status of Rare and Endangered Unionaea (Mollusca: Margaritiferidae, Unionidae) in Arkansas

Harris and Gordon (1987) reviewed the distribution and status of 18 rare and /or endangered unionacean bivalve species (commonly referred to as clams, mussels, freshwater mussels, naiads) that occur or have occurred in Arkansas. They discussed four species that were federally listed as endangered, four species that were considered endangered or extirpated within Arkansas, four species considered threatened within Arkansas, four species of special concern within Arkansas, and two species for which the conservation status was considered uncertain due to questions regarding taxonomic validity. Numerous unionacean field surveys have been performed during 1986 1996, and a substantial database of new distributional and relative abundance information has been accumulated. Two additional unionacean species have been listed as federally endangered, one additional species has been listed as federally threatened, and one endangered species has been newly discovered within Arkansas bringing the total number of federally protected unionacean species occurring within Arkansas to eight. The conservation status of 16 additional unionacean species occurring in Arkansas is discussed also

Growth Curves of Four Species of Commercially Valuable Freshwater Mussels (Bivalva: Unionidae)

North American freshwater mussels (Bivalvia: Unionidae) have been exploited commercially for over 100 years and have been regulated using shell size limits and/or harvest seasons. Presently, freshwater mussels are considered a threatened faunal group in North America due to the large numbers of endangered, threatened or special concern species. Therefore, management of this fauna should emphasize their long-term sustainability. The objectives of this study were 1) to construct von Bertalanffy growth curves for selected commercially-most-valuable species, Fusconaia ebena, Megalonaias nervosa, Amblema plicata and Quadrula quadrula, from five rivers and two reservoirs, 2) to compare species-specific von Bertalanffy growth curves from different rivers and reservoirs, and 3) to provide information on size at onset of sexual maturity in F. ebena and A. plicata. Von Bertalanffy growth curves of four commercially valuable Ambleminae species were used in this study to compare drainage-specific growth. Growth curves for all four species investigated were significantly different between pairs of drainages. Approximate size at onset of sexual maturity was determined for Arkansas F. ebena and A. plicata. Von Bertalanffy growth curves, coupled with life history and population dynamics information, could be useful in assessing and determining national/state harvest sizes and/or drainage specific harvest sizes once annual growth line formation is confirmed

A Mg(OH)2 coprecipitation method for determining chromium speciation and isotopic composition in seawater

Chromium (Cr) stable isotopes have emerged as a powerful tool for tracking environmental redox transfor- mations. This is because Cr isotopes are fractionated during redox reactions between Cr(III) and Cr(VI). In order to fully exploit the information recorded within Cr isotope compositions, we must be able to track changes in Cr speciation throughout the environment and, in particular, the changes in speciation between input to the ocean and eventual deposition in sediments. We must also be able to access the isotope compositions of each Cr species, rather than only total dissolved Cr. We have thus developed a magnesium hydroxide coprecipitation method that meets these objectives. This method achieves complete recovery and has a typical precision on concentration measurements of !8% (1σ). It was tested using seawater collected from Saanich Inlet, a persis- tently anoxic fjord on the Pacific coast of Canada. Chromium speciation profiles and proof-of-concept isotope ratio measurements on selected samples indicate that isotopically lighter Cr(III) can be isolated from coexisting isotopically heavier Cr(VI), effectively resolving species-specific Cr isotope compositions. While the oxygenated surface waters of Saanich Inlet follow the generally observed correlation between seawater Cr concentration and its isotopic composition, seawater from anoxic depths diverges from this array, indicating that different pro- cesses are responsible for setting the isotope composition of these deeper waters. Broader application of Mg(OH)2 coprecipitation has strong potential to yield new insights into the fractionation of Cr isotopes in the oceans and the pathways that ultimately set the Cr isotopic composition of marine sediments and sedimentary archives

Interactive computer-based interventions for weight loss or weight maintenance in overweight or obese people

BACKGROUND: The World Health Organization (WHO) estimates that the number of obese or overweight individuals worldwide will increase to 1.5 billion by 2015. Chronic diseases associated with overweight or obesity include diabetes, heart disease, hypertension and stroke. OBJECTIVES: To assess the effects of interactive computer-based interventions for weight loss or weight maintenance in overweight or obese people. SEARCH METHODS: We searched several electronic databases, including CENTRAL, MEDLINE, EMBASE, CINAHL, LILACS and PsycINFO, through 25 May 2011. We also searched clinical trials registries to identify studies. We scanned reference lists of included studies and relevant systematic reviews. SELECTION CRITERIA: Studies were included if they were randomized controlled trials or quasi-randomized controlled trials that evaluated interactive computer-based weight loss or weight maintenance programs in adults with overweight or obesity. We excluded trials if the duration of the intervention was less than four weeks or the loss to follow-up was greater than 20% overall. DATA COLLECTION AND ANALYSIS: Two authors independently extracted study data and assessed risk of bias. Where interventions, control conditions, outcomes and time frames were similar between studies, we combined study data using meta-analysis. MAIN RESULTS: We included 14 weight loss studies with a total of 2537 participants, and four weight maintenance studies with a total of 1603 participants. Treatment duration was between four weeks and 30 months. At six months, computer-based interventions led to greater weight loss than minimal interventions (mean difference (MD) -1.5 kg; 95% confidence interval (CI) -2.1 to -0.9; two trials) but less weight loss than in-person treatment (MD 2.1 kg; 95% CI 0.8 to 3.4; one trial). At six months, computer-based interventions were superior to a minimal control intervention in limiting weight regain (MD -0.7 kg; 95% CI -1.2 to -0.2; two trials), but not superior to infrequent in-person treatment (MD 0.5 kg; 95% -0.5 to 1.6; two trials). We did not observe consistent differences in dietary or physical activity behaviors between intervention and control groups in either weight loss or weight maintenance trials. Three weight loss studies estimated the costs of computer-based interventions compared to usual care, however two of the studies were 11 and 28 years old, and recent advances in technology render these estimates unlikely to be applicable to current or future interventions, while the third study was conducted in active duty military personnel, and it is unclear whether the costs are relevant to other settings. One weight loss study reported the cost-effectiveness ratio for a weekly in-person weight loss intervention relative to a computer-based intervention as USD 7177 (EUR 5678) per life year gained (80% CI USD 3055 to USD 60,291 (EUR 2417 to EUR 47,702)). It is unclear whether this could be extrapolated to other studies. No data were identified on adverse events, morbidity, complications or health-related quality of life. AUTHORS' CONCLUSIONS: Compared to no intervention or minimal interventions (pamphlets, usual care), interactive computer-based interventions are an effective intervention for weight loss and weight maintenance. Compared to in-person interventions, interactive computer-based interventions result in smaller weight losses and lower levels of weight maintenance. The amount of additional weight loss, however, is relatively small and of brief duration, making the clinical significance of these differences unclear

Association between canine leishmaniosis and Ehrlichia canis co-infection: a prospective case-control study

Abstract Background In the Mediterranean basin, Leishmania infantum is a major cause of disease in dogs, which are frequently co-infected with other vector-borne pathogens (VBP). However, the associations between dogs with clinical leishmaniosis (ClinL) and VBP co-infections have not been studied. We assessed the risk of VBP infections in dogs with ClinL and healthy controls. Methods We conducted a prospective case-control study of dogs with ClinL (positive qPCR and ELISA antibody for L. infantum on peripheral blood) and clinically healthy, ideally breed-, sex- and age-matched, control dogs (negative qPCR and ELISA antibody for L. infantum on peripheral blood) from Paphos, Cyprus. We obtained demographic data and all dogs underwent PCR on EDTA-blood extracted DNA for haemoplasma species, Ehrlichia/Anaplasma spp., Babesia spp., and Hepatozoon spp., with DNA sequencing to identify infecting species. We used logistic regression analysis and structural equation modelling (SEM) to evaluate the risk of VBP infections between ClinL cases and controls. Results From the 50 enrolled dogs with ClinL, DNA was detected in 24 (48%) for Hepatozoon spp., 14 (28%) for Mycoplasma haemocanis, 6 (12%) for Ehrlichia canis and 2 (4%) for Anaplasma platys. In the 92 enrolled control dogs, DNA was detected in 41 (45%) for Hepatozoon spp., 18 (20%) for M. haemocanis, 1 (1%) for E. canis and 3 (3%) for A. platys. No Babesia spp. or “Candidatus Mycoplasma haematoparvum” DNA was detected in any dog. No statistical differences were found between the ClinL and controls regarding age, sex, breed, lifestyle and use of ectoparasitic prevention. A significant association between ClinL and E. canis infection (OR = 12.4, 95% CI: 1.5–106.0, P = 0.022) was found compared to controls by multivariate logistic regression. This association was confirmed using SEM, which further identified that younger dogs were more likely to be infected with each of Hepatozoon spp. and M. haemocanis, and dogs with Hepatozoon spp. were more likely to be co-infected with M. haemocanis. Conclusions Dogs with ClinL are at a higher risk of co-infection with E. canis than clinically healthy dogs. We recommend that dogs diagnosed with ClinL should be tested for E. canis co-infection using PCR

Improving human effectiveness for extreme-scale problem solving : final report (assessing the effectiveness of electronic brainstorming in an industrial setting).

An experiment was conducted comparing the effectiveness of individual versus group electronic brainstorming in order to address difficult, real world challenges. While industrial reliance on electronic communications has become ubiquitous, empirical and theoretical understanding of the bounds of its effectiveness have been limited. Previous research using short-term, laboratory experiments have engaged small groups of students in answering questions irrelevant to an industrial setting. The current experiment extends current findings beyond the laboratory to larger groups of real-world employees addressing organization-relevant challenges over the course of four days. Findings are twofold. First, the data demonstrate that (for this design) individuals perform at least as well as groups in producing quantity of electronic ideas, regardless of brainstorming duration. However, when judged with respect to quality along three dimensions (originality, feasibility, and effectiveness), the individuals significantly (p<0.05) out performed the group working together. The theoretical and applied (e.g., cost effectiveness) implications of this finding are discussed. Second, the current experiment yielded several viable solutions to the wickedly difficult problem that was posed