United States Department of Agriculture
Government•Washington D.C., District of Columbia, United States•
About: United States Department of Agriculture is a(n) government organization based out in Washington D.C., District of Columbia, United States. It is known for research contribution in the topic(s): Population & Virus. The organization has 50600 authors who have published 90831 publication(s) receiving 3496586 citation(s). The organization is also known as: USDA & Agriculture Department.
Topics: Population, Virus, Soil water, Gene, Salmonella
Papers published on a yearly basis
TL;DR: In order to make experimental studies comparable and statistically meaningful, the article recommends the following formula: per cent control = 100(X - Y)/X, which eliminates errors due to deaths in the control sample which were not due to the insecticide.
Abstract: There are several statistical methods used in biology (entomology) for computing the effectiveness of an insecticide, based on relating the number of dead insects in the treated plat to the number of live ones in the untreated plat. In order to make experimental studies comparable and statistically meaningful, the article recommends the following formula: per cent control = 100(X - Y)/X, where X = % living in the untreated check sample and Y = % living in the treated sample. Calculation using this method eliminates errors due to deaths in the control sample which were not due to the insecticide. An example based on treatments of San Jose scale includes computation of probable errors for X and Y, and the significance of the difference between the two counts. Common biometric convention holds that when the difference between the results of two experiments is greater than three times its probable error, the results are significant and due to the treatment applied.
01 Jan 2007-Transactions of the ASABE
TL;DR: In this paper, the authors present guidelines for watershed model evaluation based on the review results and project-specific considerations, including single-event simulation, quality and quantity of measured data, model calibration procedure, evaluation time step, and project scope and magnitude.
Abstract: Watershed models are powerful tools for simulating the effect of watershed processes and management on soil and water resources. However, no comprehensive guidance is available to facilitate model evaluation in terms of the accuracy of simulated data compared to measured flow and constituent values. Thus, the objectives of this research were to: (1) determine recommended model evaluation techniques (statistical and graphical), (2) review reported ranges of values and corresponding performance ratings for the recommended statistics, and (3) establish guidelines for model evaluation based on the review results and project-specific considerations; all of these objectives focus on simulation of streamflow and transport of sediment and nutrients. These objectives were achieved with a thorough review of relevant literature on model application and recommended model evaluation methods. Based on this analysis, we recommend that three quantitative statistics, Nash-Sutcliffe efficiency (NSE), percent bias (PBIAS), and ratio of the root mean square error to the standard deviation of measured data (RSR), in addition to the graphical techniques, be used in model evaluation. The following model evaluation performance ratings were established for each recommended statistic. In general, model simulation can be judged as satisfactory if NSE > 0.50 and RSR < 0.70, and if PBIAS + 25% for streamflow, PBIAS + 55% for sediment, and PBIAS + 70% for N and P. For PBIAS, constituent-specific performance ratings were determined based on uncertainty of measured data. Additional considerations related to model evaluation guidelines are also discussed. These considerations include: single-event simulation, quality and quantity of measured data, model calibration procedure, evaluation time step, and project scope and magnitude. A case study illustrating the application of the model evaluation guidelines is also provided.
01 Nov 1993-Journal of Nutrition
TL;DR: Two new diets may prove to be a better choice than AIN-76A for long-term as well as short-term studies with laboratory rodents because of a better balance of essential nutrients.
Abstract: For sixteen years, the American Institute of Nutrition Rodent Diets, AIN-76 and AIN-76A, have been used extensively around the world. Because of numerous nutritional and technical problems encountered with the diet during this period, it was revised. Two new formulations were derived: AIN-93G for growth, pregnancy and lactation, and AIN-93M for adult maintenance. Some major differences in the new formulation of AIN-93G compared with AIN-76A are as follows: 7 g soybean oil/100 g diet was substituted for 5 g corn oil/100 g diet to increase the amount of linolenic acid; cornstarch was substituted for sucrose; the amount of phosphorus was reduced to help eliminate the problem of kidney calcification in female rats; L-cystine was substituted for DL-methionine as the amino acid supplement for casein, known to be deficient in the sulfur amino acids; manganese concentration was lowered to one-fifth the amount in the old diet; the amounts of vitamin E, vitamin K and vitamin B-12 were increased; and molybdenum, silicon, fluoride, nickel, boron, lithium and vanadium were added to the mineral mix. For the AIN-93M maintenance diet, the amount of fat was lowered to 40 g/kg diet from 70 g/kg diet, and the amount of casein to 140 g/kg from 200 g/kg in the AIN-93G diet. Because of a better balance of essential nutrients, the AIN-93 diets may prove to be a better choice than AIN-76A for long-term as well as short-term studies with laboratory rodents.
Broad Institute1, Commonwealth Scientific and Industrial Research Organisation2, Massachusetts Institute of Technology3, Hebrew University of Jerusalem4, Science for Life Laboratory5, Pittsburgh Supercomputing Center6, Oklahoma State University–Stillwater7, Griffith University8, University of Wisconsin-Madison9, Dresden University of Technology10, California Institute for Quantitative Biosciences11, Flanders Institute for Biotechnology12, Parco Tecnologico Padano13, United States Department of Agriculture14, Purdue University15, Indiana University16
01 Aug 2013-Nature Protocols
TL;DR: This protocol provides a workflow for genome-independent transcriptome analysis leveraging the Trinity platform and presents Trinity-supported companion utilities for downstream applications, including RSEM for transcript abundance estimation, R/Bioconductor packages for identifying differentially expressed transcripts across samples and approaches to identify protein-coding genes.
Abstract: De novo assembly of RNA-seq data enables researchers to study transcriptomes without the need for a genome sequence; this approach can be usefully applied, for instance, in research on 'non-model organisms' of ecological and evolutionary importance, cancer samples or the microbiome. In this protocol we describe the use of the Trinity platform for de novo transcriptome assembly from RNA-seq data in non-model organisms. We also present Trinity-supported companion utilities for downstream applications, including RSEM for transcript abundance estimation, R/Bioconductor packages for identifying differentially expressed transcripts across samples and approaches to identify protein-coding genes. In the procedure, we provide a workflow for genome-independent transcriptome analysis leveraging the Trinity platform. The software, documentation and demonstrations are freely available from http://trinityrnaseq.sourceforge.net. The run time of this protocol is highly dependent on the size and complexity of data to be analyzed. The example data set analyzed in the procedure detailed herein can be processed in less than 5 h.
TL;DR: In this paper, the effects of dietary patterns on blood pressure were assessed in a clinical trial, Dietary Approaches to Stop Hypertension, where the subjects were fed a control diet that was low in fruits, vegetables, and dairy products, with a fat content typical of the average diet in the United States.
Abstract: Background It is known that obesity, sodium intake, and alcohol consumption influence blood pressure. In this clinical trial, Dietary Approaches to Stop Hypertension, we assessed the effects of dietary patterns on blood pressure. Methods We enrolled 459 adults with systolic blood pressures of less than 160 mm Hg and diastolic blood pressures of 80 to 95 mm Hg. For three weeks, the subjects were fed a control diet that was low in fruits, vegetables, and dairy products, with a fat content typical of the average diet in the United States. They were then randomly assigned to receive for eight weeks the control diet, a diet rich in fruits and vegetables, or a “combination” diet rich in fruits, vegetables, and low-fat dairy products and with reduced saturated and total fat. Sodium intake and body weight were maintained at constant levels. Results At base line, the mean (±SD) systolic and diastolic blood pressures were 131.3±10.8 mm Hg and 84.7±4.7 mm Hg, respectively. The combination diet reduced systolic and d...
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|Walter C. Willett||334||2399||413322|
|Eric S. Lander||301||826||525976|
|Patrick O. Brown||183||755||200985|
|Peter W.F. Wilson||181||680||139852|
|Roderick T. Bronson||169||679||107702|
|Stanley B. Prusiner||168||745||97528|
|Donald G. Truhlar||165||1518||157965|
|Robert G. Webster||158||843||90776|
|Joseph R. Ecker||148||381||94860|
|James B. Meigs||147||574||115899|
|Peter B. Jones||145||1857||94641|
|Michael F. Holick||145||767||107937|
|David A. Jackson||136||1095||68352|
|John F. Thompson||132||1420||95894|
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