Assessment of Food Intake, Obesity, and Health Risk among the Homeless in Rhode Island.

PubMed

Martins, Diane C; Gorman, Kathleen S; Miller, Robin J; Murphy, Leah; Sor, Sekboppa; Martins, Jonah C; Vecchiarelli, Maria L

2015-01-01

The objective of this study was to examine the relationship between the nutritional status, incidence of food insecurity, and health risk among the homeless population in Rhode Island. This correlational study utilized a convenience sample of 319 homeless adults from Rhode Island's largest service agency for the homeless. Information on use of services such as access to emergency foods, shelters, and the Supplemental Nutrition Assistance Program (SNAP) was requested. Food security was measured by the six-item subset of the USDA Food Security Core Module. Anthropometric measures included height, weight, and waist circumference. A 24-hr dietary recall was collected to determine the food intake for a subset of participants who agreed to supply this information (n = 197). Average dietary recall data indicated insufficient intake of vegetables, fruit, dairy, and meats/beans. It also indicated excessive intake of fats. Of the 313 participants, 29.4% were overweight and 39% were obese. Over 94% of the participants were food insecure, with 64% of this subset experiencing hunger. Fifty-five percent of the participants were currently receiving SNAP benefits. The majority of the sample was found to be food insecure with hunger. © 2015 Wiley Periodicals, Inc.

The National Inventory of Down Woody Materials: Methods, Outputs, and Future Directions

Treesearch

Christopher W. Woodall

2003-01-01

The Forest Inventory and Analysis Program (FIA) of the USDA Forest Service conducts a national inventory of forests of the United States. A subset of FIA permanent inventory plots are sampled every year for numerous forest health indicators ranging fiom soils to understory vegetation. Down woody material (DWM) is an FIA indicator that refines estimation of forest...

76 FR 33703 - Endangered Species; Permit No. 16439

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-09

... unmarked individuals with passive integrated transponder tags, and dart tags; and genetic tissue sampling. A first subset of fish would be anesthetized and tagged with acoustic transmitters; a second subset would have fin rays sampled for ageing; and a third subset of fish would be gastrically lavaged for diet...

Aircrew Sizing Survey 2011

DTIC Science & Technology

2014-10-01

Resource JSF Joint Strike Fighter JPATS Joint Primary Aircraft Training System USMC United States Marine Corps USAF United States Air Force LIST...Surface Anthropometry Resource (CAESAR) was developed for the Joint Strike Fighter (JSF) program. The ACSS was intended to replace the JSF-CAESAR...an aircrew sample was made in 2003 by Hudson et al. They extracted a subset, named JSF CAESAR (Joint Strike Fighter), from the Civilian American and

Quality assessment program for EuroFlow protocols: summary results of four-year (2010-2013) quality assurance rounds.

PubMed

Kalina, Tomas; Flores-Montero, Juan; Lecrevisse, Quentin; Pedreira, Carlos E; van der Velden, Vincent H J; Novakova, Michaela; Mejstrikova, Ester; Hrusak, Ondrej; Böttcher, Sebastian; Karsch, Dennis; Sędek, Łukasz; Trinquand, Amelie; Boeckx, Nancy; Caetano, Joana; Asnafi, Vahid; Lucio, Paulo; Lima, Margarida; Helena Santos, Ana; Bonaccorso, Paola; van der Sluijs-Gelling, Alita J; Langerak, Anton W; Martin-Ayuso, Marta; Szczepański, Tomasz; van Dongen, Jacques J M; Orfao, Alberto

2015-02-01

Flow cytometric immunophenotyping has become essential for accurate diagnosis, classification, and disease monitoring in hemato-oncology. The EuroFlow Consortium has established a fully standardized "all-in-one" pipeline consisting of standardized instrument settings, reagent panels, and sample preparation protocols and software for data analysis and disease classification. For its reproducible implementation, parallel development of a quality assurance (QA) program was required. Here, we report on the results of four consecutive annual rounds of the novel external QA EuroFlow program. The novel QA scheme aimed at monitoring the whole flow cytometric analysis process (cytometer setting, sample preparation, acquisition and analysis) by reading the median fluorescence intensities (MedFI) of defined lymphocytes' subsets. Each QA participant applied the predefined reagents' panel on blood cells of local healthy donors. A uniform gating strategy was applied to define lymphocyte subsets and to read MedFI values per marker. The MedFI values were compared with reference data and deviations from reference values were quantified using performance score metrics. In four annual QA rounds, we analyzed 123 blood samples from local healthy donors on 14 different instruments in 11 laboratories from nine European countries. The immunophenotype of defined cellular subsets appeared sufficiently standardized to permit unified (software) data analysis. The coefficient of variation of MedFI for 7 of 11 markers performed repeatedly below 30%, average MedFI in each QA round ranged from 86 to 125% from overall median. Calculation of performance scores was instrumental to pinpoint standardization failures and their causes. Overall, the new EuroFlow QA system for the first time allowed to quantify the technical variation that is introduced in the measurement of fluorescence intensities in a multicentric setting over an extended period of time. EuroFlow QA is a proficiency test specific for laboratories that use standardized EuroFlow protocols. It may be used to complement, but not replace, established proficiency tests. © 2014 International Society for Advancement of Cytometry. © 2014 International Society for Advancement of Cytometry.

A Preliminary Analysis of LANDSAT-4 Thematic Mapper Radiometric Performance

NASA Technical Reports Server (NTRS)

Justice, C.; Fusco, L.; Mehl, W.

1984-01-01

Analysis was performed to characterize the radiometry of three Thematic Mapper (TM) digital products of a scene of Arkansas. The three digital products examined were the NASA raw (BT) product, the radiometrically corrected (AT) product and the radiometrically and geometrically corrected (PT) product. The frequency distribution of the digital data; the statistical correlation between the bands; and the variability between the detectors within a band were examined on a series of image subsets from the full scene. The results are presented from one 1024 x 1024 pixel subset of Realfoot Lake, Tennessee which displayed a representative range of ground conditions and cover types occurring within the full frame image. Bands 1, 2 and 5 of the sample area are presented. The subsets were extracted from the three digital data products to cover the same geographic area. This analysis provides the first step towards a full appraisal of the TM radiometry being performed as part of the ESA/CEC contribution to the NASA/LIDQA program.

Changing Social Networks Among Homeless Individuals: A Prospective Evaluation of a Job- and Life-Skills Training Program.

PubMed

Gray, Heather M; Shaffer, Paige M; Nelson, Sarah E; Shaffer, Howard J

2016-10-01

Social networks play important roles in mental and physical health among the general population. Building healthier social networks might contribute to the development of self-sufficiency among people struggling to overcome homelessness and substance use disorders. In this study of homeless adults completing a job- and life-skills program (i.e., the Moving Ahead Program at St. Francis House, Boston), we prospectively examined changes in social network quality, size, and composition. Among the sample of participants (n = 150), we observed positive changes in social network quality over time. However, social network size and composition did not change among the full sample. The subset of participants who reported abstaining from alcohol during the months before starting the program reported healthy changes in their social networks; specifically, while completing the program, they re-structured their social networks such that fewer members of their network used alcohol to intoxication. We discuss practical implications of these findings.

Promoting Resiliency in Children of Mothers with Co-Occurring Disorders and Histories of Trauma: Impact of a Skills-Based Intervention Program on Child Outcomes

ERIC Educational Resources Information Center

Noether, Chanson D.; Brown, Vivian; Finkelstein, Norma; Russell, Lisa A.; VanDeMark, Nancy R.; Morris, Laura S.; Graeber, Carla

2007-01-01

Using a quasi-experimental design, this study examined the effectiveness of a standardized intervention model designed to build resiliency in children of women with co-occurring mental health and substance use disorders and histories of interpersonal abuse. The children and mothers who participated in this study were a subset of the sample used…

Architectural design of an Algol interpreter

NASA Technical Reports Server (NTRS)

Jackson, C. K.

1971-01-01

The design of a syntax-directed interpreter for a subset of Algol is described. It is a conceptual design with sufficient details and completeness but as much independence of implementation as possible. The design includes a detailed description of a scanner, an analyzer described in the Floyd-Evans productions, a hash-coded symbol table, and an executor. Interpretation of sample programs is also provided to show how the interpreter functions.

Mid-infrared spectroscopy predictions as indicator traits in breeding programs for enhanced coagulation properties of milk.

PubMed

Cecchinato, A; De Marchi, M; Gallo, L; Bittante, G; Carnier, P

2009-10-01

The aims of this study were to investigate variation of milk coagulation property (MCP) measures and their predictions obtained by mid-infrared spectroscopy (MIR), to investigate the genetic relationship between measures of MCP and MIR predictions, and to estimate the expected response from a breeding program focusing on the enhancement of MCP using MIR predictions as indicator traits. Individual milk samples were collected from 1,200 Brown Swiss cows (progeny of 50 artificial insemination sires) reared in 30 herds located in northern Italy. Rennet coagulation time (RCT, min) and curd firmness (a(30), mm) were measured using a computerized renneting meter. The MIR data were recorded over the spectral range of 4,000 to 900 cm(-1). Prediction models for RCT and a(30) based on MIR spectra were developed using partial least squares regression. A cross-validation procedure was carried out. The procedure involved the partition of available data into 2 subsets: a calibration subset and a test subset. The calibration subset was used to develop a calibration equation able to predict individual MCP phenotypes using MIR spectra. The test subset was used to validate the calibration equation and to estimate heritabilities and genetic correlations for measured MCP and their predictions obtained from MIR spectra and the calibration equation. Point estimates of heritability ranged from 0.30 to 0.34 and from 0.22 to 0.24 for RCT and a(30), respectively. Heritability estimates for MCP predictions were larger than those obtained for measured MCP. Estimated genetic correlations between measures and predictions of RCT were very high and ranged from 0.91 to 0.96. Estimates of the genetic correlation between measures and predictions of a(30) were large and ranged from 0.71 to 0.87. Predictions of MCP provided by MIR techniques can be proposed as indicator traits for the genetic enhancement of MCP. The expected response of RCT and a(30) ensured by the selection using MIR predictions as indicator traits was equal to or slightly less than the response achievable through a single measurement of these traits. Breeding strategies for the enhancement of MCP based on MIR predictions as indicator traits could be easily and immediately implemented for dairy cattle populations where routine acquisition of spectra from individual milk samples is already performed.

An Analysis of a Biometric Screening and Premium Incentive-Based Employee Wellness Program: Enrollment Patterns, Cost, and Outcome.

PubMed

Maeng, Daniel D; Geng, Zhi; Marshall, Wendy M; Hess, Allison L; Tomcavage, Janet F

2017-11-14

Since 2012, a large health care system has offered an employee wellness program providing premium discounts for those who voluntarily undergo biometric screenings and meet goals. This study evaluates the program impact on care utilization and total cost of care, taking into account employee self-selection into the program. A retrospective claims data analysis of 6453 employees between 2011 and 2015 was conducted, categorizing the sample into 3 mutually exclusive subgroups: Subgroup 1 enrolled and met goals in all years, Subgroup 2 enrolled or met goals in some years but not all, and Subgroup 3 never enrolled. Each subgroup was compared to a cohort of employees in other employer groups (N = 24,061). Using a difference-in-difference method, significant reductions in total medical cost (14.2%; P = 0.014) and emergency department (ED) visits (11.2%; P = 0.058) were observed only among Subgroup 2 in 2015. No significant impact was detected among those in Subgroup 1. Those in Subgroup 1 were less likely to have chronic conditions at baseline. The results indicate that the wellness program enrollment was characterized by self-selection of healthier employees, among whom the program appeared to have no significant impact. Yet, cost savings and reductions in ED visits were observed among the subset of employees who enrolled or met goal in some years but not all, suggesting a potential link between the wellness program and positive behavior changes among certain subsets of the employee population.

Design of a verifiable subset for HAL/S

NASA Technical Reports Server (NTRS)

Browne, J. C.; Good, D. I.; Tripathi, A. R.; Young, W. D.

1979-01-01

An attempt to evaluate the applicability of program verification techniques to the existing programming language, HAL/S is discussed. HAL/S is a general purpose high level language designed to accommodate the software needs of the NASA Space Shuttle project. A diversity of features for scientific computing, concurrent and real-time programming, and error handling are discussed. The criteria by which features were evaluated for inclusion into the verifiable subset are described. Individual features of HAL/S with respect to these criteria are examined and justification for the omission of various features from the subset is provided. Conclusions drawn from the research are presented along with recommendations made for the use of HAL/S with respect to the area of program verification.

PyCCF: Python Cross Correlation Function for reverberation mapping studies

NASA Astrophysics Data System (ADS)

Sun, Mouyuan; Grier, C. J.; Peterson, B. M.

2018-05-01

PyCCF emulates a Fortran program written by B. Peterson for use with reverberation mapping. The code cross correlates two light curves that are unevenly sampled using linear interpolation and measures the peak and centroid of the cross-correlation function. In addition, it is possible to run Monto Carlo iterations using flux randomization and random subset selection (RSS) to produce cross-correlation centroid distributions to estimate the uncertainties in the cross correlation results.

The Carnegie Supernova Project I. Photometry data release of low-redshift stripped-envelope supernovae

NASA Astrophysics Data System (ADS)

Stritzinger, M. D.; Anderson, J. P.; Contreras, C.; Heinrich-Josties, E.; Morrell, N.; Phillips, M. M.; Anais, J.; Boldt, L.; Busta, L.; Burns, C. R.; Campillay, A.; Corco, C.; Castellon, S.; Folatelli, G.; González, C.; Holmbo, S.; Hsiao, E. Y.; Krzeminski, W.; Salgado, F.; Serón, J.; Torres-Robledo, S.; Freedman, W. L.; Hamuy, M.; Krisciunas, K.; Madore, B. F.; Persson, S. E.; Roth, M.; Suntzeff, N. B.; Taddia, F.; Li, W.; Filippenko, A. V.

2018-02-01

The first phase of the Carnegie Supernova Project (CSP-I) was a dedicated supernova follow-up program based at the Las Campanas Observatory that collected science data of young, low-redshift supernovae between 2004 and 2009. Presented in this paper is the CSP-I photometric data release of low-redshift stripped-envelope core-collapse supernovae. The data consist of optical (uBgVri) photometry of 34 objects, with a subset of 26 having near-infrared (YJH) photometry. Twenty objects have optical pre-maximum coverage with a subset of 12 beginning at least five days prior to the epoch of B-band maximum brightness. In the near-infrared, 17 objects have pre-maximum observations with a subset of 14 beginning at least five days prior to the epoch of J-band maximum brightness. Analysis of this photometric data release is presented in companion papers focusing on techniques to estimate host-galaxy extinction and the light-curve and progenitor star properties of the sample. The analysis of an accompanying visual-wavelength spectroscopy sample of 150 spectra will be the subject of a future paper. Based on observations collected at Las Campanas Observatory.Tables 2-8 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/609/A134

Birds of a feather stay active together: a case study of an all-male older adult exercise program.

PubMed

Dunlop, William L; Beauchamp, Mark R

2013-04-01

In this article, the authors report the results of a case study examining a group-based exercise program for older adult men. The purpose of the investigation was to identify the elements of this program responsible for its appeal. Interviews, conducted with a purposely sampled subset of program members, were subject to content-analytic procedures. Participants identified social connectedness (reflected by themes of demographic homogeneity, support and care, customs and traditions, and interpersonal comparisons) and supportive leadership behaviors (constituted by communication, the provision of choice, and individualized attention) as major attractions in the program. A few participants also noted the challenge that exists when a program is seen by some as being a social program that provides opportunities for exercise and by others as an exercise program that provides opportunities for socializing. Findings are discussed in relation to contextual factors associated with older adult men's involvement in physical activity programs.

Classification of urine sediment based on convolution neural network

NASA Astrophysics Data System (ADS)

Pan, Jingjing; Jiang, Cunbo; Zhu, Tiantian

2018-04-01

By designing a new convolution neural network framework, this paper breaks the constraints of the original convolution neural network framework requiring large training samples and samples of the same size. Move and cropping the input images, generate the same size of the sub-graph. And then, the generated sub-graph uses the method of dropout, increasing the diversity of samples and preventing the fitting generation. Randomly select some proper subset in the sub-graphic set and ensure that the number of elements in the proper subset is same and the proper subset is not the same. The proper subsets are used as input layers for the convolution neural network. Through the convolution layer, the pooling, the full connection layer and output layer, we can obtained the classification loss rate of test set and training set. In the red blood cells, white blood cells, calcium oxalate crystallization classification experiment, the classification accuracy rate of 97% or more.

Selection of reliable reference genes for quantitative real-time PCR gene expression analysis in Jute (Corchorus capsularis) under stress treatments

PubMed Central

Niu, Xiaoping; Qi, Jianmin; Zhang, Gaoyang; Xu, Jiantang; Tao, Aifen; Fang, Pingping; Su, Jianguang

2015-01-01

To accurately measure gene expression using quantitative reverse transcription PCR (qRT-PCR), reliable reference gene(s) are required for data normalization. Corchorus capsularis, an annual herbaceous fiber crop with predominant biodegradability and renewability, has not been investigated for the stability of reference genes with qRT-PCR. In this study, 11 candidate reference genes were selected and their expression levels were assessed using qRT-PCR. To account for the influence of experimental approach and tissue type, 22 different jute samples were selected from abiotic and biotic stress conditions as well as three different tissue types. The stability of the candidate reference genes was evaluated using geNorm, NormFinder, and BestKeeper programs, and the comprehensive rankings of gene stability were generated by aggregate analysis. For the biotic stress and NaCl stress subsets, ACT7 and RAN were suitable as stable reference genes for gene expression normalization. For the PEG stress subset, UBC, and DnaJ were sufficient for accurate normalization. For the tissues subset, four reference genes TUBβ, UBI, EF1α, and RAN were sufficient for accurate normalization. The selected genes were further validated by comparing expression profiles of WRKY15 in various samples, and two stable reference genes were recommended for accurate normalization of qRT-PCR data. Our results provide researchers with appropriate reference genes for qRT-PCR in C. capsularis, and will facilitate gene expression study under these conditions. PMID:26528312

Potential for false positive HIV test results with the serial rapid HIV testing algorithm.

PubMed

Baveewo, Steven; Kamya, Moses R; Mayanja-Kizza, Harriet; Fatch, Robin; Bangsberg, David R; Coates, Thomas; Hahn, Judith A; Wanyenze, Rhoda K

2012-03-19

Rapid HIV tests provide same-day results and are widely used in HIV testing programs in areas with limited personnel and laboratory infrastructure. The Uganda Ministry of Health currently recommends the serial rapid testing algorithm with Determine, STAT-PAK, and Uni-Gold for diagnosis of HIV infection. Using this algorithm, individuals who test positive on Determine, negative to STAT-PAK and positive to Uni-Gold are reported as HIV positive. We conducted further testing on this subgroup of samples using qualitative DNA PCR to assess the potential for false positive tests in this situation. Of the 3388 individuals who were tested, 984 were HIV positive on two consecutive tests, and 29 were considered positive by a tiebreaker (positive on Determine, negative on STAT-PAK, and positive on Uni-Gold). However, when the 29 samples were further tested using qualitative DNA PCR, 14 (48.2%) were HIV negative. Although this study was not primarily designed to assess the validity of rapid HIV tests and thus only a subset of the samples were retested, the findings show a potential for false positive HIV results in the subset of individuals who test positive when a tiebreaker test is used in serial testing. These findings highlight a need for confirmatory testing for this category of individuals.

Potential for false positive HIV test results with the serial rapid HIV testing algorithm

PubMed Central

2012-01-01

Background Rapid HIV tests provide same-day results and are widely used in HIV testing programs in areas with limited personnel and laboratory infrastructure. The Uganda Ministry of Health currently recommends the serial rapid testing algorithm with Determine, STAT-PAK, and Uni-Gold for diagnosis of HIV infection. Using this algorithm, individuals who test positive on Determine, negative to STAT-PAK and positive to Uni-Gold are reported as HIV positive. We conducted further testing on this subgroup of samples using qualitative DNA PCR to assess the potential for false positive tests in this situation. Results Of the 3388 individuals who were tested, 984 were HIV positive on two consecutive tests, and 29 were considered positive by a tiebreaker (positive on Determine, negative on STAT-PAK, and positive on Uni-Gold). However, when the 29 samples were further tested using qualitative DNA PCR, 14 (48.2%) were HIV negative. Conclusion Although this study was not primarily designed to assess the validity of rapid HIV tests and thus only a subset of the samples were retested, the findings show a potential for false positive HIV results in the subset of individuals who test positive when a tiebreaker test is used in serial testing. These findings highlight a need for confirmatory testing for this category of individuals. PMID:22429706

Effects of Sample Selection on Estimates of Economic Impacts of Outdoor Recreation

Treesearch

Donald B.K. English

1997-01-01

Estimates of the economic impacts of recreation often come from spending data provided by a self-selected subset of a random sample of site visitors. The subset is frequently less than half the onsite sample. Biased vectors of per trip spending and impact estimates can result if self-selection is related to spending pattctns, and proper corrective procedures arc not...

A Survey of Object Oriented Languages in Programming Environments.

DTIC Science & Technology

1987-06-01

subset of natural languages might be more effective , and make the human-computer interface more friendly. 19 .. .. . . -.. -, " ,. o...and complexty of Ada. He meant that the language contained too many features that made it complicated to use effectively . Much of the complexity comes...by sending messages to a class instance. A small subset of the methods in Smalltalk-80 are not expressed in the !-’ Smalhalk-80 programming language

Deconvoluting Post-Transplant Immunity: Cell Subset-Specific Mapping Reveals Pathways for Activation and Expansion of Memory T, Monocytes and B Cells

PubMed Central

Grigoryev, Yevgeniy A.; Kurian, Sunil M.; Avnur, Zafi; Borie, Dominic; Deng, Jun; Campbell, Daniel; Sung, Joanna; Nikolcheva, Tania; Quinn, Anthony; Schulman, Howard; Peng, Stanford L.; Schaffer, Randolph; Fisher, Jonathan; Mondala, Tony; Head, Steven; Flechner, Stuart M.; Kantor, Aaron B.; Marsh, Christopher; Salomon, Daniel R.

2010-01-01

A major challenge for the field of transplantation is the lack of understanding of genomic and molecular drivers of early post-transplant immunity. The early immune response creates a complex milieu that determines the course of ensuing immune events and the ultimate outcome of the transplant. The objective of the current study was to mechanistically deconvolute the early immune response by purifying and profiling the constituent cell subsets of the peripheral blood. We employed genome-wide profiling of whole blood and purified CD4, CD8, B cells and monocytes in tandem with high-throughput laser-scanning cytometry in 10 kidney transplants sampled serially pre-transplant, 1, 2, 4, 8 and 12 weeks. Cytometry confirmed early cell subset depletion by antibody induction and immunosuppression. Multiple markers revealed the activation and proliferative expansion of CD45RO+CD62L− effector memory CD4/CD8 T cells as well as progressive activation of monocytes and B cells. Next, we mechanistically deconvoluted early post-transplant immunity by serial monitoring of whole blood using DNA microarrays. Parallel analysis of cell subset-specific gene expression revealed a unique spectrum of time-dependent changes and functional pathways. Gene expression profiling results were validated with 157 different probesets matching all 65 antigens detected by cytometry. Thus, serial blood cell monitoring reflects the profound changes in blood cell composition and immune activation early post-transplant. Each cell subset reveals distinct pathways and functional programs. These changes illuminate a complex, early phase of immunity and inflammation that includes activation and proliferative expansion of the memory effector and regulatory cells that may determine the phenotype and outcome of the kidney transplant. PMID:20976225

Deconvoluting post-transplant immunity: cell subset-specific mapping reveals pathways for activation and expansion of memory T, monocytes and B cells.

PubMed

Grigoryev, Yevgeniy A; Kurian, Sunil M; Avnur, Zafi; Borie, Dominic; Deng, Jun; Campbell, Daniel; Sung, Joanna; Nikolcheva, Tania; Quinn, Anthony; Schulman, Howard; Peng, Stanford L; Schaffer, Randolph; Fisher, Jonathan; Mondala, Tony; Head, Steven; Flechner, Stuart M; Kantor, Aaron B; Marsh, Christopher; Salomon, Daniel R

2010-10-14

A major challenge for the field of transplantation is the lack of understanding of genomic and molecular drivers of early post-transplant immunity. The early immune response creates a complex milieu that determines the course of ensuing immune events and the ultimate outcome of the transplant. The objective of the current study was to mechanistically deconvolute the early immune response by purifying and profiling the constituent cell subsets of the peripheral blood. We employed genome-wide profiling of whole blood and purified CD4, CD8, B cells and monocytes in tandem with high-throughput laser-scanning cytometry in 10 kidney transplants sampled serially pre-transplant, 1, 2, 4, 8 and 12 weeks. Cytometry confirmed early cell subset depletion by antibody induction and immunosuppression. Multiple markers revealed the activation and proliferative expansion of CD45RO(+)CD62L(-) effector memory CD4/CD8 T cells as well as progressive activation of monocytes and B cells. Next, we mechanistically deconvoluted early post-transplant immunity by serial monitoring of whole blood using DNA microarrays. Parallel analysis of cell subset-specific gene expression revealed a unique spectrum of time-dependent changes and functional pathways. Gene expression profiling results were validated with 157 different probesets matching all 65 antigens detected by cytometry. Thus, serial blood cell monitoring reflects the profound changes in blood cell composition and immune activation early post-transplant. Each cell subset reveals distinct pathways and functional programs. These changes illuminate a complex, early phase of immunity and inflammation that includes activation and proliferative expansion of the memory effector and regulatory cells that may determine the phenotype and outcome of the kidney transplant.

Evaluation of volatile organic compounds in two Mojave Desert basins-Mojave River and Antelope Valley-in San Bernardino, Los Angeles, and Kern Counties, California, June-October 2002

USGS Publications Warehouse

Densmore, Jill N.; Belitz, Kenneth; Wright, Michael T.; Dawson, Barbara J.; Johnson, Tyler D.

2005-01-01

The California Aquifer Susceptibility Assessment of the Ground-Water Ambient Monitoring and Assessment Program was developed to assess water quality and susceptibility of ground-water resources to contamination from surficial sources. This study focuses on the Mojave River and the Antelope Valley ground-water basins in southern California. Volatile organic compound (VOC) data were evaluated in conjunction with tritium data to determine a potential correlation with aquifer type, depth to top of perforations, and land use to VOC distribution and occurrence in the Mojave River and the Antelope Valley Basins. Detection frequencies for VOCs were compiled and compared to assess the distribution in each area. Explanatory variables were evaluated by comparing detection frequencies for VOCs and tritium and the number of compounds detected. Thirty-three wells were sampled in the Mojave River Basin (9 in the floodplain aquifer, 15 in the regional aquifer, and 9 in the sewered subset of the regional aquifer). Thirty-two wells were sampled in the Antelope Valley Basin. Quality-control samples also were collected to identify, quantify, and document bias and variability in the data. Results show that VOCs generally were detected slightly more often in the Antelope Valley Basin samples than in the Mojave River Basin samples. VOCs were detected more frequently in the floodplain aquifer than in the regional aquifer and the sewered subset. Tritium was detected more frequently in the Mojave River Basin samples than in the Antelope Valley Basin samples, and it was detected more frequently in the floodplain aquifer than in the regional aquifer and the sewered subset. Most of the samples collected in both basins for this study contained old water (water recharged prior to 1952). In general, in these desert basins, tritium need not be present for VOCs to be present. When VOCs were detected, young water (water recharge after 1952) was slightly more likely to be contaminated than old water. Trihalomethanes (THMs) were detected less frequently in the Mojave River Basin samples than in the Antelope Valley Basin samples. The THMs that were detected in the Mojave River Basin were detected more frequently in the floodplain aquifer than in the regional aquifer and sewered subset. Solvents were detected more frequently in the Mojave River samples than in the Antelope Valley samples. In the Mojave River Basin samples, solvents were detected less frequently in the floodplain aquifer than in the regional aquifer and the sewered subset. Benzene, toluene, ethylbenzene and xylene (BTEX) were not detected in either study area. Methyl tert-butyl ether (MTBE) was detected in one sample from both the Mojave River and Antelope Valley Basins. The most frequently detected compound (detected in more than 10 percent of the wells) in the Mojave River Basin was chloroform. The two most frequently detected compounds in the Antelope Valley Basin were chloroform and tetrachloroethylene (PCE). In the Mojave River Basin, aquifer type and land use within 1,640 ft (500 m) of the well head were not statistically correlated with the number of VOCs detected, although VOCs were detected more frequently in the floodplain aquifer than in the regional aquifer and the sewered subset. Depth to the top of the perforations was an explanatory factor for the number of VOCs detected in the Mojave River Basin; the detection frequency was greater for shallow wells than for deep wells. In the Antelope Valley Basin, neither aquifer type, depth to the top of the perforations, nor land use within 1,640 ft of the well head were explanatory factors for the number of VOCs detected. Although aquifer type and depth to top of the perforations did explain the presence of tritium in the Mojave River Basin, land use within 1,640 ft of the well head was not a statistically significant explanatory factor for the presence of tritium in this basin. Aquifer type, depth to the top of the perfora

Sample size determination for bibliographic retrieval studies

PubMed Central

Yao, Xiaomei; Wilczynski, Nancy L; Walter, Stephen D; Haynes, R Brian

2008-01-01

Background Research for developing search strategies to retrieve high-quality clinical journal articles from MEDLINE is expensive and time-consuming. The objective of this study was to determine the minimal number of high-quality articles in a journal subset that would need to be hand-searched to update or create new MEDLINE search strategies for treatment, diagnosis, and prognosis studies. Methods The desired width of the 95% confidence intervals (W) for the lowest sensitivity among existing search strategies was used to calculate the number of high-quality articles needed to reliably update search strategies. New search strategies were derived in journal subsets formed by 2 approaches: random sampling of journals and top journals (having the most high-quality articles). The new strategies were tested in both the original large journal database and in a low-yielding journal (having few high-quality articles) subset. Results For treatment studies, if W was 10% or less for the lowest sensitivity among our existing search strategies, a subset of 15 randomly selected journals or 2 top journals were adequate for updating search strategies, based on each approach having at least 99 high-quality articles. The new strategies derived in 15 randomly selected journals or 2 top journals performed well in the original large journal database. Nevertheless, the new search strategies developed using the random sampling approach performed better than those developed using the top journal approach in a low-yielding journal subset. For studies of diagnosis and prognosis, no journal subset had enough high-quality articles to achieve the expected W (10%). Conclusion The approach of randomly sampling a small subset of journals that includes sufficient high-quality articles is an efficient way to update or create search strategies for high-quality articles on therapy in MEDLINE. The concentrations of diagnosis and prognosis articles are too low for this approach. PMID:18823538

Using Parental Profiles to Predict Membership in a Subset of College Students Experiencing Excessive Alcohol Consequences: Findings From a Longitudinal Study

PubMed Central

Varvil-Weld, Lindsey; Mallett, Kimberly A.; Turrisi, Rob; Abar, Caitlin C.

2012-01-01

Objective: Previous research identified a high-risk subset of college students experiencing a disproportionate number of alcohol-related consequences at the end of their first year. With the goal of identifying pre-college predictors of membership in this high-risk subset, the present study used a prospective design to identify latent profiles of student-reported maternal and paternal parenting styles and alcohol-specific behaviors and to determine whether these profiles were associated with membership in the high-risk consequences subset. Method: A sample of randomly selected 370 incoming first-year students at a large public university reported on their mothers’ and fathers’ communication quality, monitoring, approval of alcohol use, and modeling of drinking behaviors and on consequences experienced across the first year of college. Results: Students in the high-risk subset comprised 15.5% of the sample but accounted for almost half (46.6%) of the total consequences reported by the entire sample. Latent profile analyses identified four parental profiles: positive pro-alcohol, positive anti-alcohol, negative mother, and negative father. Logistic regression analyses revealed that students in the negative-father profile were at greatest odds of being in the high-risk consequences subset at a follow-up assessment 1 year later, even after drinking at baseline was controlled for. Students in the positive pro-alcohol profile also were at increased odds of being in the high-risk subset, although this association was attenuated after baseline drinking was controlled for. Conclusions: These findings have important implications for the improvement of existing parent- and individual-based college student drinking interventions designed to reduce alcohol-related consequences. PMID:22456248

Using parental profiles to predict membership in a subset of college students experiencing excessive alcohol consequences: findings from a longitudinal study.

PubMed

Varvil-Weld, Lindsey; Mallett, Kimberly A; Turrisi, Rob; Abar, Caitlin C

2012-05-01

Previous research identified a high-risk subset of college students experiencing a disproportionate number of alcohol-related consequences at the end of their first year. With the goal of identifying pre-college predictors of membership in this high-risk subset, the present study used a prospective design to identify latent profiles of student-reported maternal and paternal parenting styles and alcohol-specific behaviors and to determine whether these profiles were associated with membership in the high-risk consequences subset. A sample of randomly selected 370 incoming first-year students at a large public university reported on their mothers' and fathers' communication quality, monitoring, approval of alcohol use, and modeling of drinking behaviors and on consequences experienced across the first year of college. Students in the high-risk subset comprised 15.5% of the sample but accounted for almost half (46.6%) of the total consequences reported by the entire sample. Latent profile analyses identified four parental profiles: positive pro-alcohol, positive anti-alcohol, negative mother, and negative father. Logistic regression analyses revealed that students in the negative-father profile were at greatest odds of being in the high-risk consequences subset at a follow-up assessment 1 year later, even after drinking at baseline was controlled for. Students in the positive pro-alcohol profile also were at increased odds of being in the high-risk subset, although this association was attenuated after baseline drinking was controlled for. These findings have important implications for the improvement of existing parent- and individual-based college student drinking interventions designed to reduce alcohol-related consequences.

Parsing the genetic heterogeneity of chromosome 12q susceptibility genes for Alzheimer disease by family-based association analysis.

PubMed

Lin, Ping-I; Martin, Eden R; Browning-Large, Carrie A; Schmechel, Donald E; Welsh-Bohmer, Kathleen A; Doraiswamy, P Murali; Gilbert, John R; Haines, Jonathan L; Pericak-Vance, Margaret A

2006-07-01

Previous linkage studies have suggested that chromosome 12 may harbor susceptibility genes for late-onset Alzheimer disease (LOAD). No risk genes on chromosome 12 have been conclusively identified yet. We have reported that the linkage evidence for LOAD in a 12q region was significantly increased in autopsy-confirmed families particularly for those showing no linkage to alpha-T catenin gene, a LOAD candidate gene on chromosome 10 [LOD score increased from 0.1 in the autopsy-confirmed subset to 4.19 in the unlinked subset (optimal subset); p<0.0001 for the increase in LOD score], indicating a one-LOD support interval spanning 6 Mb. To further investigate this finding and to identify potential candidate LOAD risk genes for follow-up analysis, we analyzed 99 single nucleotide polymorphisms in this region, for the overall sample, the autopsy-confirmed subset, and the optimal subset, respectively, for comparison. We saw no significant association (p<0.01) in the overall sample. In the autopsy-confirmed subset, the best finding was obtained in the activation transcription factor 7 (ATF7) gene (single-locus association, p=0.002; haplotype association global, p=0.007). In the optimal subset, the best finding was obtained in the hypothetical protein FLJ20436 (FLJ20436) gene (single-locus association, p=0.0026). These results suggest that subset and covariate analyses may be one approach to help identify novel susceptibility genes on chromosome 12q for LOAD.

"Effects of a Web-Based Intervention on Family Functioning Following Pediatric Traumatic Brain Injury"

PubMed Central

Minich, Nori; Taylor, H. Gerry; Kirkwood, Michael; Brown, Tanya Maines; Stancin, Terry; Wade, Shari L

2015-01-01

Objective Investigate effectiveness of an online Counselor-Assisted Problem-Solving (CAPS) intervention on family functioning after traumatic brain injury (TBI). Methods Participants were randomized to CAPS (n = 65) or internet resource comparison (IRC; n = 67). CAPS is a counselor-assisted web-based program. IRC was given access to online resources. Outcomes were examined 6 months, 12 months, and 18 months after baseline. Injury severity, age, and SES were examined as moderators. Results A main effect of time was noted for teen-reported conflict and parent-reported problem solving. CAPS had decreased parent-reported conflict and a reduction in parental effective communication. Effects were specific to subsets of the sample. Conclusions CAPS, a family-based problem-solving intervention designed to address problem behaviors, had modest effects on some aspects of family functioning, when compared to IRC. Effects were generally limited to subsets of the families and were not evident across all follow-up assessments. PMID:26461100

When self-reliance is not safe: associations between reduced help-seeking and subsequent mental health symptoms in suicidal adolescents.

PubMed

Labouliere, Christa D; Kleinman, Marjorie; Gould, Madelyn S

2015-04-01

The majority of suicidal adolescents have no contact with mental health services, and reduced help-seeking in this population further lessens the likelihood of accessing treatment. A commonly-reported reason for not seeking help is youths' perception that they should solve problems on their own. In this study, we explore associations between extreme self-reliance behavior (i.e., solving problems on your own all of the time), help-seeking behavior, and mental health symptoms in a community sample of adolescents. Approximately 2150 adolescents, across six schools, participated in a school-based suicide prevention screening program, and a subset of at-risk youth completed a follow-up interview two years later. Extreme self-reliance was associated with reduced help-seeking, clinically-significant depressive symptoms, and serious suicidal ideation at the baseline screening. Furthermore, in a subset of youth identified as at-risk at the baseline screening, extreme self-reliance predicted level of suicidal ideation and depressive symptoms two years later even after controlling for baseline symptoms. Given these findings, attitudes that reinforce extreme self-reliance behavior may be an important target for youth suicide prevention programs. Reducing extreme self-reliance in youth with suicidality may increase their likelihood of appropriate help-seeking and concomitant reductions in symptoms.

When Self-Reliance Is Not Safe: Associations between Reduced Help-Seeking and Subsequent Mental Health Symptoms in Suicidal Adolescents

PubMed Central

Labouliere, Christa D.; Kleinman, Marjorie; Gould, Madelyn S.

2015-01-01

The majority of suicidal adolescents have no contact with mental health services, and reduced help-seeking in this population further lessens the likelihood of accessing treatment. A commonly-reported reason for not seeking help is youths’ perception that they should solve problems on their own. In this study, we explore associations between extreme self-reliance behavior (i.e., solving problems on your own all of the time), help-seeking behavior, and mental health symptoms in a community sample of adolescents. Approximately 2150 adolescents, across six schools, participated in a school-based suicide prevention screening program, and a subset of at-risk youth completed a follow-up interview two years later. Extreme self-reliance was associated with reduced help-seeking, clinically-significant depressive symptoms, and serious suicidal ideation at the baseline screening. Furthermore, in a subset of youth identified as at-risk at the baseline screening, extreme self-reliance predicted level of suicidal ideation and depressive symptoms two years later even after controlling for baseline symptoms. Given these findings, attitudes that reinforce extreme self-reliance behavior may be an important target for youth suicide prevention programs. Reducing extreme self-reliance in youth with suicidality may increase their likelihood of appropriate help-seeking and concomitant reductions in symptoms. PMID:25837350

A genomic scan for age at onset of Alzheimer's disease in 437 families from the NIMH Genetic Initiative.

PubMed

Dickson, M Ryan; Li, Jian; Wiener, Howard W; Perry, Rodney T; Blacker, Deborah; Bassett, Susan S; Go, Rodney C P

2008-09-05

We performed linkage analysis for age at onset (AAO) in the total Alzheimer's disease (AD) NIMH sample (N = 437 families). Families were subset as late-onset (320 families, AAO > or = 65) and early/mixed (117 families, at least 1 member with 50 < AAO < 65). Treating AAO as a censored trait, we obtained the gender and APOE adjusted residuals in a parametric survival model and analyzed the residuals as the quantitative trait (QT) in variance-component linkage analysis. For comparison, AAO-age at exam (AAE) was analyzed as the QT adjusting for affection status, gender, and APOE. Heritabilities for residual and AAO-AAE outcomes were 66.3% and 74.0%, respectively for the total sample, 56.0% and 57.0% in the late-onset sample, and 33.0% for both models in the early/mixed sample. The residual model yielded the largest peaks on chromosome 1 with LOD = 2.0 at 190 cM in the total set, LOD = 1.7 at 116 cM on chromosome 3 in the early/mixed subset, and LOD = 1.4 at 71 and 86 cM, respectively, on chromosome 6 in the late-onset subset. For the AAO-AAE outcome model the largest peaks were identified on chromosome 1 at 137 cM (LOD = 2.8) and chromosome 6 at 69 cM (LOD = 2.3) and 86 cM (LOD = 2.2) all in the late-onset subset. Additional peaks with LOD > or = 1 were identified on chromosomes 1, 2, 3, 6, 8, 9, 10, and 12 for the total sample and each subset. Results replicate previous findings, but identify additional suggestive peaks indicating the genetics of AAO in AD is complex with many chromosomal regions potentially containing modifying genes. 2008 Wiley-Liss, Inc.

A genetic programming approach to oral cancer prognosis.

PubMed

Tan, Mei Sze; Tan, Jing Wei; Chang, Siow-Wee; Yap, Hwa Jen; Abdul Kareem, Sameem; Zain, Rosnah Binti

2016-01-01

The potential of genetic programming (GP) on various fields has been attained in recent years. In bio-medical field, many researches in GP are focused on the recognition of cancerous cells and also on gene expression profiling data. In this research, the aim is to study the performance of GP on the survival prediction of a small sample size of oral cancer prognosis dataset, which is the first study in the field of oral cancer prognosis. GP is applied on an oral cancer dataset that contains 31 cases collected from the Malaysia Oral Cancer Database and Tissue Bank System (MOCDTBS). The feature subsets that is automatically selected through GP were noted and the influences of this subset on the results of GP were recorded. In addition, a comparison between the GP performance and that of the Support Vector Machine (SVM) and logistic regression (LR) are also done in order to verify the predictive capabilities of the GP. The result shows that GP performed the best (average accuracy of 83.87% and average AUROC of 0.8341) when the features selected are smoking, drinking, chewing, histological differentiation of SCC, and oncogene p63. In addition, based on the comparison results, we found that the GP outperformed the SVM and LR in oral cancer prognosis. Some of the features in the dataset are found to be statistically co-related. This is because the accuracy of the GP prediction drops when one of the feature in the best feature subset is excluded. Thus, GP provides an automatic feature selection function, which chooses features that are highly correlated to the prognosis of oral cancer. This makes GP an ideal prediction model for cancer clinical and genomic data that can be used to aid physicians in their decision making stage of diagnosis or prognosis.

Species undersampling in tropical bat surveys: effects on emerging biodiversity patterns.

PubMed

Meyer, Christoph F J; Aguiar, Ludmilla M S; Aguirre, Luis F; Baumgarten, Julio; Clarke, Frank M; Cosson, Jean-François; Estrada Villegas, Sergio; Fahr, Jakob; Faria, Deborah; Furey, Neil; Henry, Mickaël; Jenkins, Richard K B; Kunz, Thomas H; Cristina MacSwiney González, M; Moya, Isabel; Pons, Jean-Marc; Racey, Paul A; Rex, Katja; Sampaio, Erica M; Stoner, Kathryn E; Voigt, Christian C; von Staden, Dietrich; Weise, Christa D; Kalko, Elisabeth K V

2015-01-01

Undersampling is commonplace in biodiversity surveys of species-rich tropical assemblages in which rare taxa abound, with possible repercussions for our ability to implement surveys and monitoring programmes in a cost-effective way. We investigated the consequences of information loss due to species undersampling (missing subsets of species from the full species pool) in tropical bat surveys for the emerging patterns of species richness (SR) and compositional variation across sites. For 27 bat assemblage data sets from across the tropics, we used correlations between original data sets and subsets with different numbers of species deleted either at random, or according to their rarity in the assemblage, to assess to what extent patterns in SR and composition in data subsets are congruent with those in the initial data set. We then examined to what degree high sample representativeness (r ≥ 0·8) was influenced by biogeographic region, sampling method, sampling effort or structural assemblage characteristics. For SR, correlations between random subsets and original data sets were strong (r ≥ 0·8) with moderate (ca. 20%) species loss. Bias associated with information loss was greater for species composition; on average ca. 90% of species in random subsets had to be retained to adequately capture among-site variation. For nonrandom subsets, removing only the rarest species (on average c. 10% of the full data set) yielded strong correlations (r > 0·95) for both SR and composition. Eliminating greater proportions of rare species resulted in weaker correlations and large variation in the magnitude of observed correlations among data sets. Species subsets that comprised ca. 85% of the original set can be considered reliable surrogates, capable of adequately revealing patterns of SR and temporal or spatial turnover in many tropical bat assemblages. Our analyses thus demonstrate the potential as well as limitations for reducing survey effort and streamlining sampling protocols, and consequently for increasing the cost-effectiveness in tropical bat surveys or monitoring programmes. The dependence of the performance of species subsets on structural assemblage characteristics (total assemblage abundance, proportion of rare species), however, underscores the importance of adaptive monitoring schemes and of establishing surrogate performance on a site by site basis based on pilot surveys. © 2014 The Authors. Journal of Animal Ecology © 2014 British Ecological Society.

On sample size and different interpretations of snow stability datasets

NASA Astrophysics Data System (ADS)

Schirmer, M.; Mitterer, C.; Schweizer, J.

2009-04-01

Interpretations of snow stability variations need an assessment of the stability itself, independent of the scale investigated in the study. Studies on stability variations at a regional scale have often chosen stability tests such as the Rutschblock test or combinations of various tests in order to detect differences in aspect and elevation. The question arose: ‘how capable are such stability interpretations in drawing conclusions'. There are at least three possible errors sources: (i) the variance of the stability test itself; (ii) the stability variance at an underlying slope scale, and (iii) that the stability interpretation might not be directly related to the probability of skier triggering. Various stability interpretations have been proposed in the past that provide partly different results. We compared a subjective one based on expert knowledge with a more objective one based on a measure derived from comparing skier-triggered slopes vs. slopes that have been skied but not triggered. In this study, the uncertainties are discussed and their effects on regional scale stability variations will be quantified in a pragmatic way. An existing dataset with very large sample sizes was revisited. This dataset contained the variance of stability at a regional scale for several situations. The stability in this dataset was determined using the subjective interpretation scheme based on expert knowledge. The question to be answered was how many measurements were needed to obtain similar results (mainly stability differences in aspect or elevation) as with the complete dataset. The optimal sample size was obtained in several ways: (i) assuming a nominal data scale the sample size was determined with a given test, significance level and power, and by calculating the mean and standard deviation of the complete dataset. With this method it can also be determined if the complete dataset consists of an appropriate sample size. (ii) Smaller subsets were created with similar aspect distributions to the large dataset. We used 100 different subsets for each sample size. Statistical variations obtained in the complete dataset were also tested on the smaller subsets using the Mann-Whitney or the Kruskal-Wallis test. For each subset size, the number of subsets were counted in which the significance level was reached. For these tests no nominal data scale was assumed. (iii) For the same subsets described above, the distribution of the aspect median was determined. A count of how often this distribution was substantially different from the distribution obtained with the complete dataset was made. Since two valid stability interpretations were available (an objective and a subjective interpretation as described above), the effect of the arbitrary choice of the interpretation on spatial variability results was tested. In over one third of the cases the two interpretations came to different results. The effect of these differences were studied in a similar method as described in (iii): the distribution of the aspect median was determined for subsets of the complete dataset using both interpretations, compared against each other as well as to the results of the complete dataset. For the complete dataset the two interpretations showed mainly identical results. Therefore the subset size was determined from the point at which the results of the two interpretations converged. A universal result for the optimal subset size cannot be presented since results differed between different situations contained in the dataset. The optimal subset size is thus dependent on stability variation in a given situation, which is unknown initially. There are indications that for some situations even the complete dataset might be not large enough. At a subset size of approximately 25, the significant differences between aspect groups (as determined using the whole dataset) were only obtained in one out of five situations. In some situations, up to 20% of the subsets showed a substantially different distribution of the aspect median. Thus, in most cases, 25 measurements (which can be achieved by six two-person teams in one day) did not allow to draw reliable conclusions.

A Simple Joint Estimation Method of Residual Frequency Offset and Sampling Frequency Offset for DVB Systems

NASA Astrophysics Data System (ADS)

Kwon, Ki-Won; Cho, Yongsoo

This letter presents a simple joint estimation method for residual frequency offset (RFO) and sampling frequency offset (STO) in OFDM-based digital video broadcasting (DVB) systems. The proposed method selects a continual pilot (CP) subset from an unsymmetrically and non-uniformly distributed CP set to obtain an unbiased estimator. Simulation results show that the proposed method using a properly selected CP subset is unbiased and performs robustly.

How to Select a Good Training-data Subset for Transcription: Submodular Active Selection for Sequences

DTIC Science & Technology

2009-01-01

selection and uncertainty sampling signif- icantly. Index Terms: Transcription, labeling, submodularity, submod- ular selection, active learning , sequence...name of batch active learning , where a subset of data that is most informative and represen- tative of the whole is selected for labeling. Often...representative subset. Note that our Fisher ker- nel is over an unsupervised generative model, which enables us to bootstrap our active learning approach

Selecting the optimum plot size for a California design-based stream and wetland mapping program.

PubMed

Lackey, Leila G; Stein, Eric D

2014-04-01

Accurate estimates of the extent and distribution of wetlands and streams are the foundation of wetland monitoring, management, restoration, and regulatory programs. Traditionally, these estimates have relied on comprehensive mapping. However, this approach is prohibitively resource-intensive over large areas, making it both impractical and statistically unreliable. Probabilistic (design-based) approaches to evaluating status and trends provide a more cost-effective alternative because, compared with comprehensive mapping, overall extent is inferred from mapping a statistically representative, randomly selected subset of the target area. In this type of design, the size of sample plots has a significant impact on program costs and on statistical precision and accuracy; however, no consensus exists on the appropriate plot size for remote monitoring of stream and wetland extent. This study utilized simulated sampling to assess the performance of four plot sizes (1, 4, 9, and 16 km(2)) for three geographic regions of California. Simulation results showed smaller plot sizes (1 and 4 km(2)) were most efficient for achieving desired levels of statistical accuracy and precision. However, larger plot sizes were more likely to contain rare and spatially limited wetland subtypes. Balancing these considerations led to selection of 4 km(2) for the California status and trends program.

SEMIPARAMETRIC ADDITIVE RISKS REGRESSION FOR TWO-STAGE DESIGN SURVIVAL STUDIES

PubMed Central

Li, Gang; Wu, Tong Tong

2011-01-01

In this article we study a semiparametric additive risks model (McKeague and Sasieni (1994)) for two-stage design survival data where accurate information is available only on second stage subjects, a subset of the first stage study. We derive two-stage estimators by combining data from both stages. Large sample inferences are developed. As a by-product, we also obtain asymptotic properties of the single stage estimators of McKeague and Sasieni (1994) when the semiparametric additive risks model is misspecified. The proposed two-stage estimators are shown to be asymptotically more efficient than the second stage estimators. They also demonstrate smaller bias and variance for finite samples. The developed methods are illustrated using small intestine cancer data from the SEER (Surveillance, Epidemiology, and End Results) Program. PMID:21931467

Computerized stratified random site-selection approaches for design of a ground-water-quality sampling network

USGS Publications Warehouse

Scott, J.C.

1990-01-01

Computer software was written to randomly select sites for a ground-water-quality sampling network. The software uses digital cartographic techniques and subroutines from a proprietary geographic information system. The report presents the approaches, computer software, and sample applications. It is often desirable to collect ground-water-quality samples from various areas in a study region that have different values of a spatial characteristic, such as land-use or hydrogeologic setting. A stratified network can be used for testing hypotheses about relations between spatial characteristics and water quality, or for calculating statistical descriptions of water-quality data that account for variations that correspond to the spatial characteristic. In the software described, a study region is subdivided into areal subsets that have a common spatial characteristic to stratify the population into several categories from which sampling sites are selected. Different numbers of sites may be selected from each category of areal subsets. A population of potential sampling sites may be defined by either specifying a fixed population of existing sites, or by preparing an equally spaced population of potential sites. In either case, each site is identified with a single category, depending on the value of the spatial characteristic of the areal subset in which the site is located. Sites are selected from one category at a time. One of two approaches may be used to select sites. Sites may be selected randomly, or the areal subsets in the category can be grouped into cells and sites selected randomly from each cell.

An evaluation of exact methods for the multiple subset maximum cardinality selection problem.

PubMed

Brusco, Michael J; Köhn, Hans-Friedrich; Steinley, Douglas

2016-05-01

The maximum cardinality subset selection problem requires finding the largest possible subset from a set of objects, such that one or more conditions are satisfied. An important extension of this problem is to extract multiple subsets, where the addition of one more object to a larger subset would always be preferred to increases in the size of one or more smaller subsets. We refer to this as the multiple subset maximum cardinality selection problem (MSMCSP). A recently published branch-and-bound algorithm solves the MSMCSP as a partitioning problem. Unfortunately, the computational requirement associated with the algorithm is often enormous, thus rendering the method infeasible from a practical standpoint. In this paper, we present an alternative approach that successively solves a series of binary integer linear programs to obtain a globally optimal solution to the MSMCSP. Computational comparisons of the methods using published similarity data for 45 food items reveal that the proposed sequential method is computationally far more efficient than the branch-and-bound approach. © 2016 The British Psychological Society.

Delineation of soil temperature regimes from HCMM data

NASA Technical Reports Server (NTRS)

Day, R. L.; Petersen, G. W. (Principal Investigator)

1982-01-01

The subsetting of HCMM data into ORSER format was completed for four dates using a modified SUBSET program. Large areas (approximately 2500 scan lines, 1680 elements) were selected to increase the occurrence of suitable control points for registration. Average daily temperatures (ADT) were calculated for each date. The MERGE program combined registered daytime temperature (DAY-IR) with nighttime temperature (NIGHT-IR) to form a separate two-channel data set. The SUBTRAN program averaged the DAY-IR and NIGHT-IR creating a third ADT channel. Registration equations for the four ADT data sets were generated. A one dimensional soil heat flow equation was modified to allow for mean annual soil temperature predictions using merged ADT data sets.

Program Enhances Drawings Of Three-Dimensional Objects

NASA Technical Reports Server (NTRS)

Hedgley, David R., Jr.

1992-01-01

SILHOUETTE is program for line drawings rendering any subset of polygons as silhouette. Program is improvement on, and replacement for, HIDDEN LINE COMPUTER CODE (ARC-11446). Offers combinations of silhouette and nonsilhouette specifications for arbitrary solid. Written in FORTRAN 77.

Compressive passive millimeter wave imager

DOEpatents

Gopalsami, Nachappa; Liao, Shaolin; Elmer, Thomas W; Koehl, Eugene R; Heifetz, Alexander; Raptis, Apostolos C

2015-01-27

A compressive scanning approach for millimeter wave imaging and sensing. A Hadamard mask is positioned to receive millimeter waves from an object to be imaged. A subset of the full set of Hadamard acquisitions is sampled. The subset is used to reconstruct an image representing the object.

A structural model of treatment program and individual counselor leadership in innovation transfer.

PubMed

Joe, George W; Becan, Jennifer E; Knight, Danica K; Flynn, Patrick M

2017-03-23

A number of program-level and counselor-level factors are known to impact the adoption of treatment innovations. While program leadership is considered a primary factor, the importance of leadership among clinical staff to innovation transfer is less known. Objectives included explore (1) the influence of two leadership roles, program director and individual counselor, on recent training activity and (2) the relationship of counselor attributes on training endorsement. The sample included 301 clinical staff in 49 treatment programs. A structural equation model was evaluated for key hypothesized relationships between exogenous and endogenous variables related to the two leadership roles. The importance of organizational leadership, climate, and counselor attributes (particularly counseling innovation interest and influence) to recent training activity was supported. In a subset of 68 counselors who attended a developer-led training on a new intervention, it was found that training endorsement was higher among those with high innovation interest and influence. The findings suggest that each leadership level impacts the organization in different ways, yet both can promote or impede technology transfer.

Monocyte Subset Dynamics in Human Atherosclerosis Can Be Profiled with Magnetic Nano-Sensors

PubMed Central

Wildgruber, Moritz; Lee, Hakho; Chudnovskiy, Aleksey; Yoon, Tae-Jong; Etzrodt, Martin; Pittet, Mikael J.; Nahrendorf, Matthias; Croce, Kevin; Libby, Peter; Weissleder, Ralph; Swirski, Filip K.

2009-01-01

Monocytes are circulating macrophage and dendritic cell precursors that populate healthy and diseased tissue. In humans, monocytes consist of at least two subsets whose proportions in the blood fluctuate in response to coronary artery disease, sepsis, and viral infection. Animal studies have shown that specific shifts in the monocyte subset repertoire either exacerbate or attenuate disease, suggesting a role for monocyte subsets as biomarkers and therapeutic targets. Assays are therefore needed that can selectively and rapidly enumerate monocytes and their subsets. This study shows that two major human monocyte subsets express similar levels of the receptor for macrophage colony stimulating factor (MCSFR) but differ in their phagocytic capacity. We exploit these properties and custom-engineer magnetic nanoparticles for ex vivo sensing of monocytes and their subsets. We present a two-dimensional enumerative mathematical model that simultaneously reports number and proportion of monocyte subsets in a small volume of human blood. Using a recently described diagnostic magnetic resonance (DMR) chip with 1 µl sample size and high throughput capabilities, we then show that application of the model accurately quantifies subset fluctuations that occur in patients with atherosclerosis. PMID:19461894

Mass loss from hot, luminous stars

NASA Astrophysics Data System (ADS)

Burnley, Adam Warwick

A general enquiry into the physics of mass loss from hot, luminous stars is presented. Ha spectroscopy of 64 Galactic early-type stars has been obtained using the telescopes of the Isaac Newton Group (ING) and the Anglo-Australian Observatory (AAO). The sample was selected to include objects with published radio and/or mm fluxes. The Halpha observations are quantitatively modelled using a modified version of the FORSOL code developed by Puls et al. (1996). FORSOL has been coupled with the PIKAIA subroutine (Charbonneau and Knapp, 1996) to create PHALTEE (Program for Halpha Line Transfer with Eugenic Estimation), in order to search a specified parameter space for the 'best' (quasi- least-squares) model fit to the data, using a genetic algorithm. This renders Ha modelling both more objective and automated. Where possible, both mass-loss rates and velocity field beta-exponents are determined for the sample. New mm-wave observations of nineteen Galactic early-type stars, including a subset of the Halpha sample, have been obtained using the Sub-millimetre Common User Bolometer Array (SCUBA). Where possible, mean fluxes are calculated, and these data used with the results of a literature survey of mm and cm fluxes to determine mass-loss rates for a larger sample, of 53 Galactic early-type stars. The incidence of nonthermal emission is examined, with 23% of the sample exhibiting strong evidence for nonthermal flux. The occurrence of binarity and excess X-ray emission amongst the nonthermal emitters is also investigated. For the subset of 36 stars common to both the Halpha and mm/radio samples, the results permit a comparison of mass-loss rates derived using diagnostics that probe the wind conditions at different radial depths. A mean value of log (Mradio/MHalpha) = 0.02 +/- 0.05 is obtained for the thermal radio emitters. The wind-momentum-luminosity relationship (WLR) for the sample is also investigated.

Local Feature Selection for Data Classification.

PubMed

Armanfard, Narges; Reilly, James P; Komeili, Majid

2016-06-01

Typical feature selection methods choose an optimal global feature subset that is applied over all regions of the sample space. In contrast, in this paper we propose a novel localized feature selection (LFS) approach whereby each region of the sample space is associated with its own distinct optimized feature set, which may vary both in membership and size across the sample space. This allows the feature set to optimally adapt to local variations in the sample space. An associated method for measuring the similarities of a query datum to each of the respective classes is also proposed. The proposed method makes no assumptions about the underlying structure of the samples; hence the method is insensitive to the distribution of the data over the sample space. The method is efficiently formulated as a linear programming optimization problem. Furthermore, we demonstrate the method is robust against the over-fitting problem. Experimental results on eleven synthetic and real-world data sets demonstrate the viability of the formulation and the effectiveness of the proposed algorithm. In addition we show several examples where localized feature selection produces better results than a global feature selection method.

Characteristics of CD8+ T cell subsets in Chinese patients with chronic HIV infection during initial ART.

PubMed

Jiao, Yanmei; Hua, Wei; Zhang, Tong; Zhang, Yonghong; Ji, Yunxia; Zhang, Hongwei; Wu, Hao

2011-03-25

CD8+ T cells may play an important role in protecting against HIV. However, the changes of CD8+ T cell subsets during early period of ART have not been fully studied. Twenty-one asymptomatic treatment-naive HIV-infected patients with CD4 T+ cells less than 350 cells/μl were enrolled in the study. Naïve, central memory(CM), effective memory(EM) and terminally differentiated effector (EMRA) CD8+ cell subsets and their activation and proliferation subsets were evaluated in blood samples collected at base line, and week 2, 4, 8 and 12 of ART. The total CD8+ T cells declined and the Naïve and CM subsets had a tendency of increase. Activation levels of all CD8+ T cell subsets except EMRA subset decreased after ART. However, proliferation levels of total CD8+ T cells, EMRA, EM and CM subsets increased at the first 4 weeks of ART, then decreased. Proliferation level of the naïve cells decreased after ART. The changes of CD8+ T cell subsets during initial ART are complex. Our results display a complete phenotypical picture of CD8+ cell subsets during initial ART and provide insights for understanding of immune status during ART.

Characteristics of CD8+ T cell subsets in Chinese patients with chronic HIV infection during initial ART

PubMed Central

2011-01-01

Background CD8+ T cells may play an important role in protecting against HIV. However, the changes of CD8+ T cell subsets during early period of ART have not been fully studied. Methods Twenty-one asymptomatic treatment-naive HIV-infected patients with CD4 T+ cells less than 350 cells/μl were enrolled in the study. Naïve, central memory(CM), effective memory(EM) and terminally differentiated effector (EMRA) CD8+ cell subsets and their activation and proliferation subsets were evaluated in blood samples collected at base line, and week 2, 4, 8 and 12 of ART. Results The total CD8+ T cells declined and the Naïve and CM subsets had a tendency of increase. Activation levels of all CD8+ T cell subsets except EMRA subset decreased after ART. However, proliferation levels of total CD8+ T cells, EMRA, EM and CM subsets increased at the first 4 weeks of ART, then decreased. Proliferation level of the naïve cells decreased after ART. Conclusion The changes of CD8+ T cell subsets during initial ART are complex. Our results display a complete phenotypical picture of CD8+ cell subsets during initial ART and provide insights for understanding of immune status during ART. PMID:21435275

2015 Long-Term Hydrologic Monitoring Program Sampling and Analysis Results at Rio Blanco, Colorado

DOE Office of Scientific and Technical Information (OSTI.GOV)

Findlay, Rick; Kautsky, Mark

2015-12-01

The U.S. Department of Energy (DOE) Office of Legacy Management conducted annual sampling at the Rio Blanco, Colorado, Site for the Long-Term Hydrologic Monitoring Program (LTHMP) on May 20–21, 2015. This report documents the analytical results of the Rio Blanco annual monitoring event, the trip report, and the data validation package. The groundwater and surface water monitoring samples were shipped to the GEL Group Inc. laboratories for conventional analysis of tritium and analysis of gamma-emitting radionuclides by high-resolution gamma spectrometry. A subset of water samples collected from wells near the Rio Blanco site was also sent to GEL Group Inc.more » for enriched tritium analysis. All requested analyses were successfully completed. Samples were collected from a total of four onsite wells, including two that are privately owned. Samples were also collected from two additional private wells at nearby locations and from nine surface water locations. Samples were analyzed for gamma-emitting radionuclides by high-resolution gamma spectrometry, and they were analyzed for tritium using the conventional method with a detection limit on the order of 400 picocuries per liter (pCi/L). Four locations (one well and three surface locations) were analyzed using the enriched tritium method, which has a detection limit on the order of 3 pCi/L. The enriched locations included the well at the Brennan Windmill and surface locations at CER-1, CER-4, and Fawn Creek 500 feet upstream.« less

Optimizing tertiary storage organization and access for spatio-temporal datasets

NASA Technical Reports Server (NTRS)

Chen, Ling Tony; Rotem, Doron; Shoshani, Arie; Drach, Bob; Louis, Steve; Keating, Meridith

1994-01-01

We address in this paper data management techniques for efficiently retrieving requested subsets of large datasets stored on mass storage devices. This problem represents a major bottleneck that can negate the benefits of fast networks, because the time to access a subset from a large dataset stored on a mass storage system is much greater that the time to transmit that subset over a network. This paper focuses on very large spatial and temporal datasets generated by simulation programs in the area of climate modeling, but the techniques developed can be applied to other applications that deal with large multidimensional datasets. The main requirement we have addressed is the efficient access of subsets of information contained within much larger datasets, for the purpose of analysis and interactive visualization. We have developed data partitioning techniques that partition datasets into 'clusters' based on analysis of data access patterns and storage device characteristics. The goal is to minimize the number of clusters read from mass storage systems when subsets are requested. We emphasize in this paper proposed enhancements to current storage server protocols to permit control over physical placement of data on storage devices. We also discuss in some detail the aspects of the interface between the application programs and the mass storage system, as well as a workbench to help scientists to design the best reorganization of a dataset for anticipated access patterns.

Unbiased feature selection in learning random forests for high-dimensional data.

PubMed

Nguyen, Thanh-Tung; Huang, Joshua Zhexue; Nguyen, Thuy Thi

2015-01-01

Random forests (RFs) have been widely used as a powerful classification method. However, with the randomization in both bagging samples and feature selection, the trees in the forest tend to select uninformative features for node splitting. This makes RFs have poor accuracy when working with high-dimensional data. Besides that, RFs have bias in the feature selection process where multivalued features are favored. Aiming at debiasing feature selection in RFs, we propose a new RF algorithm, called xRF, to select good features in learning RFs for high-dimensional data. We first remove the uninformative features using p-value assessment, and the subset of unbiased features is then selected based on some statistical measures. This feature subset is then partitioned into two subsets. A feature weighting sampling technique is used to sample features from these two subsets for building trees. This approach enables one to generate more accurate trees, while allowing one to reduce dimensionality and the amount of data needed for learning RFs. An extensive set of experiments has been conducted on 47 high-dimensional real-world datasets including image datasets. The experimental results have shown that RFs with the proposed approach outperformed the existing random forests in increasing the accuracy and the AUC measures.

PhOD - The Global Drifter Program

Science.gov Websites

February 2018. (As of May 2018). Download all data Subsets of database are also available through February 2018. Download subsets of data Many historical drogue off dates have been reevaluated. As of November buoydata_15001_feb18.dat-gz, dirfl_15001_feb18.dat May 1, 2018: Milestone reached On Tuesday, May 1, 2018, NOAA's

Intervening to Improve Compassion Fatigue Resiliency in Forensic Nurses.

PubMed

Flarity, Kathleen; Nash, Kim; Jones, Whitney; Steinbruner, Dave

2016-01-01

Evidence suggests that forensic nurses (FNs) may be predisposed to compassion fatigue (CF) as a result of the challenges of the profession including high caseloads, role ambiguity, prosecution goals, vicarious traumatization, attending to survivors' emotional needs, and empowering victims. The purpose of this exploratory study was to determine the prevalence of CF in a convenience sample of 55 FNs and examine the treatment effectiveness of a multifaceted education program in an intervention subset. The intervention was intended to increase compassion satisfaction (CS) and decrease CF symptoms in FNs in one organization who participated in the training. The hypothesis was that the FNs will have moderate to high CF and moderate to high CS and the CF intervention will add in CF prevention and resiliency as measured with an improvement in the Professional Quality of Life test scores (B. H. ). In the prevalence sample, 69% of the FNs had moderate to low CS, 73% had moderate to high burnout, and 73% had moderate to high levels of secondary traumatic stress (STS). In the intervention group, the education program resulted in a statistically significant increase in CS and decreases in STS symptoms.

Retention of court-referred youths in residential treatment programs: client characteristics and treatment process effects.

PubMed

Orlando, Maria; Chan, Kitty S; Morral, Andrew R

2003-05-01

The juvenile justice system relies heavily on residential treatment services for adolescents. Because treatment dropout limits the likely effectiveness of these services, in this study we examine the client and program characteristics associated with program retention among a sample of adolescent probationers referred to residential rehabilitation by the Juvenile Court in Los Angeles. Participants in the present study (n = 291) are a subset of those in the Adolescent Outcomes Project, conducted within RAND's Drug Policy Research Center, to examine the outcomes of youths entering treatment at seven residential treatment programs. Three months after a preadmission interview, youths were asked about their perceptions of counselors at the program, other residents, and their feelings of safety in the program. In addition, they were asked whether they needed and had received various services (e.g., job training, legal advice, family counseling). Results of a multivariate survival analysis revealed that pretreatment characteristics including motivation and substance use severity, as well as treatment program factors including safety, and perceived over- and underprovision of services, contribute significantly to the prediction of retention. Pretreatment environmental risk factors and ratings of program counselor and resident support were marginally significant. These results imply that changes in adolescent residential program delivery may serve to increase retention rates, thus improving long-term outcomes.

Psychological Treatment as Part of Dropout Prevention: An Israeli Program

ERIC Educational Resources Information Center

Schwartz, Hava; Hain, Rebecca

2014-01-01

This article reports on the integration of psychotherapy in a comprehensive dropout prevention program developed at the Dean of Students' office of Ben-Gurion University of the Negev in Israel. The program's psychologists conducted psychotherapy with a subset of dropout prevention program participants who had reacted with emotional turmoil to the…

Academic Executive Programs in Public Administration and Management: Some Variety across Europe

ERIC Educational Resources Information Center

Reichard, Christoph

2017-01-01

Universities and other higher education institutions in Europe offer a vast and increasing number of academic degree programs in the broad field of Public Administration. A subset of these programs is those offering postgraduate degrees to experienced students being already employed by public or private organisations. These executive programs are…

Progressive Sampling Technique for Efficient and Robust Uncertainty and Sensitivity Analysis of Environmental Systems Models: Stability and Convergence

NASA Astrophysics Data System (ADS)

Sheikholeslami, R.; Hosseini, N.; Razavi, S.

2016-12-01

Modern earth and environmental models are usually characterized by a large parameter space and high computational cost. These two features prevent effective implementation of sampling-based analysis such as sensitivity and uncertainty analysis, which require running these computationally expensive models several times to adequately explore the parameter/problem space. Therefore, developing efficient sampling techniques that scale with the size of the problem, computational budget, and users' needs is essential. In this presentation, we propose an efficient sequential sampling strategy, called Progressive Latin Hypercube Sampling (PLHS), which provides an increasingly improved coverage of the parameter space, while satisfying pre-defined requirements. The original Latin hypercube sampling (LHS) approach generates the entire sample set in one stage; on the contrary, PLHS generates a series of smaller sub-sets (also called `slices') while: (1) each sub-set is Latin hypercube and achieves maximum stratification in any one dimensional projection; (2) the progressive addition of sub-sets remains Latin hypercube; and thus (3) the entire sample set is Latin hypercube. Therefore, it has the capability to preserve the intended sampling properties throughout the sampling procedure. PLHS is deemed advantageous over the existing methods, particularly because it nearly avoids over- or under-sampling. Through different case studies, we show that PHLS has multiple advantages over the one-stage sampling approaches, including improved convergence and stability of the analysis results with fewer model runs. In addition, PLHS can help to minimize the total simulation time by only running the simulations necessary to achieve the desired level of quality (e.g., accuracy, and convergence rate).

Data-driven confounder selection via Markov and Bayesian networks.

PubMed

Häggström, Jenny

2018-06-01

To unbiasedly estimate a causal effect on an outcome unconfoundedness is often assumed. If there is sufficient knowledge on the underlying causal structure then existing confounder selection criteria can be used to select subsets of the observed pretreatment covariates, X, sufficient for unconfoundedness, if such subsets exist. Here, estimation of these target subsets is considered when the underlying causal structure is unknown. The proposed method is to model the causal structure by a probabilistic graphical model, for example, a Markov or Bayesian network, estimate this graph from observed data and select the target subsets given the estimated graph. The approach is evaluated by simulation both in a high-dimensional setting where unconfoundedness holds given X and in a setting where unconfoundedness only holds given subsets of X. Several common target subsets are investigated and the selected subsets are compared with respect to accuracy in estimating the average causal effect. The proposed method is implemented with existing software that can easily handle high-dimensional data, in terms of large samples and large number of covariates. The results from the simulation study show that, if unconfoundedness holds given X, this approach is very successful in selecting the target subsets, outperforming alternative approaches based on random forests and LASSO, and that the subset estimating the target subset containing all causes of outcome yields smallest MSE in the average causal effect estimation. © 2017, The International Biometric Society.

Effect of freezing of sputum samples on flow cytometric analysis of lymphocyte subsets.

PubMed

Jaksztat, E; Holz, O; Paasch, K; Kelly, M M; Hargreave, F E; Cox, G; Magnussen, H; Jörres, R A

2004-08-01

Sputum samples should be processed shortly after induction to prevent cell degradation. For intermediate storage, freezing of homogenised samples or immediate fixation have been shown to be suitable for cytospins. The aim of this study was to investigate whether freezing or immediate fixation of sputum affect the analysis of lymphocyte subsets by flow cytometry. Selected plugs from 24 sputum samples were homogenised. One aliquot was processed immediately and analysed by flow cytometry. A second aliquot was homogenised, frozen at -20 C after addition of dimethylsulfoxide and stored for a median time of 6 days. In six samples a third aliquot was fixed in formalin after induction and stored for up to 72 h before further processing. Compared to immediate processing, percentages of total lymphocytes and T-suppressor cells were elevated after being frozen, with a minor decrease in the T4/T8 ratio. Proportions of total lymphocytes, T-helper and T-suppressor cells correlated between native and frozen samples, intra-class correlation coefficients being 0.74, 0.85 and 0.70, respectively. The formalin-fixed aliquots could not be analysed with the antibodies used. In conclusion, freezing seems to be a suitable technique to store sputum samples for flow cytometry of CD3, CD4 and CD8 lymphocyte subsets. Its effects were minor compared to the variation between subjects.

A brief measure of attitudes toward mixed methods research in psychology.

PubMed

Roberts, Lynne D; Povee, Kate

2014-01-01

The adoption of mixed methods research in psychology has trailed behind other social science disciplines. Teaching psychology students, academics, and practitioners about mixed methodologies may increase the use of mixed methods within the discipline. However, tailoring and evaluating education and training in mixed methodologies requires an understanding of, and way of measuring, attitudes toward mixed methods research in psychology. To date, no such measure exists. In this article we present the development and initial validation of a new measure: Attitudes toward Mixed Methods Research in Psychology. A pool of 42 items developed from previous qualitative research on attitudes toward mixed methods research along with validation measures was administered via an online survey to a convenience sample of 274 psychology students, academics and psychologists. Principal axis factoring with varimax rotation on a subset of the sample produced a four-factor, 12-item solution. Confirmatory factor analysis on a separate subset of the sample indicated that a higher order four factor model provided the best fit to the data. The four factors; 'Limited Exposure,' '(in)Compatibility,' 'Validity,' and 'Tokenistic Qualitative Component'; each have acceptable internal reliability. Known groups validity analyses based on preferred research orientation and self-rated mixed methods research skills, and convergent and divergent validity analyses based on measures of attitudes toward psychology as a science and scientist and practitioner orientation, provide initial validation of the measure. This brief, internally reliable measure can be used in assessing attitudes toward mixed methods research in psychology, measuring change in attitudes as part of the evaluation of mixed methods education, and in larger research programs.

Comparison of Genetic Algorithm, Particle Swarm Optimization and Biogeography-based Optimization for Feature Selection to Classify Clusters of Microcalcifications

NASA Astrophysics Data System (ADS)

Khehra, Baljit Singh; Pharwaha, Amar Partap Singh

2017-04-01

Ductal carcinoma in situ (DCIS) is one type of breast cancer. Clusters of microcalcifications (MCCs) are symptoms of DCIS that are recognized by mammography. Selection of robust features vector is the process of selecting an optimal subset of features from a large number of available features in a given problem domain after the feature extraction and before any classification scheme. Feature selection reduces the feature space that improves the performance of classifier and decreases the computational burden imposed by using many features on classifier. Selection of an optimal subset of features from a large number of available features in a given problem domain is a difficult search problem. For n features, the total numbers of possible subsets of features are 2n. Thus, selection of an optimal subset of features problem belongs to the category of NP-hard problems. In this paper, an attempt is made to find the optimal subset of MCCs features from all possible subsets of features using genetic algorithm (GA), particle swarm optimization (PSO) and biogeography-based optimization (BBO). For simulation, a total of 380 benign and malignant MCCs samples have been selected from mammogram images of DDSM database. A total of 50 features extracted from benign and malignant MCCs samples are used in this study. In these algorithms, fitness function is correct classification rate of classifier. Support vector machine is used as a classifier. From experimental results, it is also observed that the performance of PSO-based and BBO-based algorithms to select an optimal subset of features for classifying MCCs as benign or malignant is better as compared to GA-based algorithm.

A genetic programming approach to oral cancer prognosis

PubMed Central

Tan, Mei Sze; Tan, Jing Wei; Yap, Hwa Jen; Abdul Kareem, Sameem; Zain, Rosnah Binti

2016-01-01

Background The potential of genetic programming (GP) on various fields has been attained in recent years. In bio-medical field, many researches in GP are focused on the recognition of cancerous cells and also on gene expression profiling data. In this research, the aim is to study the performance of GP on the survival prediction of a small sample size of oral cancer prognosis dataset, which is the first study in the field of oral cancer prognosis. Method GP is applied on an oral cancer dataset that contains 31 cases collected from the Malaysia Oral Cancer Database and Tissue Bank System (MOCDTBS). The feature subsets that is automatically selected through GP were noted and the influences of this subset on the results of GP were recorded. In addition, a comparison between the GP performance and that of the Support Vector Machine (SVM) and logistic regression (LR) are also done in order to verify the predictive capabilities of the GP. Result The result shows that GP performed the best (average accuracy of 83.87% and average AUROC of 0.8341) when the features selected are smoking, drinking, chewing, histological differentiation of SCC, and oncogene p63. In addition, based on the comparison results, we found that the GP outperformed the SVM and LR in oral cancer prognosis. Discussion Some of the features in the dataset are found to be statistically co-related. This is because the accuracy of the GP prediction drops when one of the feature in the best feature subset is excluded. Thus, GP provides an automatic feature selection function, which chooses features that are highly correlated to the prognosis of oral cancer. This makes GP an ideal prediction model for cancer clinical and genomic data that can be used to aid physicians in their decision making stage of diagnosis or prognosis. PMID:27688975

Chemical library subset selection algorithms: a unified derivation using spatial statistics.

PubMed

Hamprecht, Fred A; Thiel, Walter; van Gunsteren, Wilfred F

2002-01-01

If similar compounds have similar activity, rational subset selection becomes superior to random selection in screening for pharmacological lead discovery programs. Traditional approaches to this experimental design problem fall into two classes: (i) a linear or quadratic response function is assumed (ii) some space filling criterion is optimized. The assumptions underlying the first approach are clear but not always defendable; the second approach yields more intuitive designs but lacks a clear theoretical foundation. We model activity in a bioassay as realization of a stochastic process and use the best linear unbiased estimator to construct spatial sampling designs that optimize the integrated mean square prediction error, the maximum mean square prediction error, or the entropy. We argue that our approach constitutes a unifying framework encompassing most proposed techniques as limiting cases and sheds light on their underlying assumptions. In particular, vector quantization is obtained, in dimensions up to eight, in the limiting case of very smooth response surfaces for the integrated mean square error criterion. Closest packing is obtained for very rough surfaces under the integrated mean square error and entropy criteria. We suggest to use either the integrated mean square prediction error or the entropy as optimization criteria rather than approximations thereof and propose a scheme for direct iterative minimization of the integrated mean square prediction error. Finally, we discuss how the quality of chemical descriptors manifests itself and clarify the assumptions underlying the selection of diverse or representative subsets.

Artifacts in time-resolved NUS: A case study of NOE build-up curves from 2D NOESY.

PubMed

Dass, Rupashree; Kasprzak, Paweł; Koźmiński, Wiktor; Kazimierczuk, Krzysztof

2016-04-01

Multidimensional NMR spectroscopy requires time-consuming sampling of indirect dimensions and so is usually used to study stable samples. However, dynamically changing compounds or their mixtures commonly occur in problems of natural science. Monitoring them requires the use multidimensional NMR in a time-resolved manner - in other words, a series of quick spectra must be acquired at different points in time. Among the many solutions that have been proposed to achieve this goal, time-resolved non-uniform sampling (TR-NUS) is one of the simplest. In a TR-NUS experiment, the signal is sampled using a shuffled random schedule and then divided into overlapping subsets. These subsets are then processed using one of the NUS reconstruction methods, for example compressed sensing (CS). The resulting stack of spectra forms a temporal "pseudo-dimension" that shows the changes caused by the process occurring in the sample. CS enables the use of small subsets of data, which minimizes the averaging of the effects studied. Yet, even within these limited timeframes, the sample undergoes certain changes. In this paper we discuss the effect of varying signal amplitude in a TR-NUS experiment. Our theoretical calculations show that the variations within the subsets lead to t1-noise, which is dependent on the rate of change of the signal amplitude. We verify these predictions experimentally. As a model case we choose a novel 2D TR-NOESY experiment in which mixing time is varied in parallel with shuffled NUS in the indirect dimension. The experiment, performed on a sample of strychnine, provides a near-continuous NOE build-up curve, whose shape closely reflects the t1-noise level. 2D TR-NOESY reduces the measurement time compared to the conventional approach and makes it possible to verify the theoretical predictions about signal variations during TR-NUS. Copyright © 2016 Elsevier Inc. All rights reserved.

The Midwest Stream Quality Assessment

USGS Publications Warehouse

,

2012-01-01

In 2013, the U.S. Geological Survey (USGS) National Water-Quality Assessment Program (NAWQA) and USGS Columbia Environmental Research Center (CERC) will be collaborating with the U.S. Environmental Protection Agency (EPA) National Rivers and Streams Assessment (NRSA) to assess stream quality across the Midwestern United States. The sites selected for this study are a subset of the larger NRSA, implemented by the EPA, States and Tribes to sample flowing waters across the United States (http://water.epa.gov/type/rsl/monitoring/riverssurvey/index.cfm). The goals are to characterize water-quality stressors—contaminants, nutrients, and sediment—and ecological conditions in streams throughout the Midwest and to determine the relative effects of these stressors on aquatic organisms in the streams. Findings will contribute useful information for communities and policymakers by identifying which human and environmental factors are the most critical in controlling stream quality. This collaborative study enhances information provided to the public and policymakers and minimizes costs by leveraging and sharing data gathered under existing programs. In the spring and early summer, NAWQA will sample streams weekly for contaminants, nutrients, and sediment. During the same time period, CERC will test sediment and water samples for toxicity, deploy time-integrating samplers, and measure reproductive effects and biomarkers of contaminant exposure in fish or amphibians. NRSA will sample sites once during the summer to assess ecological and habitat conditions in the streams by collecting data on algal, macroinvertebrate, and fish communities and collecting detailed physical-habitat measurements. Study-team members from all three programs will work in collaboration with USGS Water Science Centers and State agencies on study design, execution of sampling and analysis, and reporting.

Altered cytokine production by specific human peripheral blood cell subsets immediately following space flight

NASA Technical Reports Server (NTRS)

Crucian, B. E.; Cubbage, M. L.; Sams, C. F.

2000-01-01

In this study, flow cytometry was used to positively identify the specific lymphocyte subsets exhibiting space flight-induced alterations in cytokine production. Whole blood samples were collected from 27 astronauts at three points (one preflight, two postflight) surrounding four space shuttle missions. Assays performed included serum/urine stress hormones, white blood cell (WBC) phenotyping, and intracellular cytokine production following mitogenic stimulation. Absolute levels of peripheral granulocytes were significantly elevated following space flight, but the levels of circulating lymphocytes and monocytes were unchanged. Lymphocyte subset analysis demonstrated a decreased percentage of T cells, whereas percentages of B cells and natural killer (NK) cells remained unchanged after flight. Nearly all the astronauts exhibited an increased CD4/CD8 T cell ratio. Assessment of naive (CD45RA+) vs. memory (CD45RO+) CD4+ T cell subsets was ambiguous, and subjects tended to group within specific missions. Although no significant trend was seen in absolute monocyte levels, a significant decrease in the percentage of the CD14+ CD16+ monocytes was seen following space flight in all subjects tested. T cell (CD3+) production of interleukin-2 (IL-2) was significantly decreased after space flight, as was IL-2 production by both CD4+ and CD8+ T cell subsets. Production of interferon-gamma (IFN-gamma) was not altered by space flight for the CD8+ cell subset, but there was a significant decrease in IFN-gamma production for the CD4+ T cell subset. Serum and urine stress hormone analysis indicated significant physiologic stresses in astronauts following space flight. Altered peripheral leukocyte subsets, altered serum and urine stress hormone levels, and altered T cell cytokine secretion profiles were all observed postflight. In addition, there appeared to be differential susceptibility to space flight regarding cytokine secretion by T cell subsets. These alterations may be the result of either microgravity exposure or the physiologic stresses of landing and readaptation to unit gravity. Future studies, including in-flight analysis or sampling, will be necessary to determine the cause of these alterations.

Uranium hydrogeochemical and stream sediment reconnaissance of the Philip Smith Mountains NTMS quadrangle, Alaska

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1981-09-01

Results of a hydrogeochemical and stream sediment reconnaissance of the Philip Smith Mountains NTMS quadrangle, Alaska are presented. In addition to this abbreviated data release, more complete data are available to the public in machine-readable form. In this data release are location data, field analyses, and laboratory analyses of several different sample media. For the sake of brevity, many field site observations have not been included in this volume. These data are, however, available on the magnetic tape. Appendices A and B describe the sample media and summarize the analytical results for each medium. The data were subsetted by onemore » of the Los Alamos National Laboratory (LANL) sorting programs into groups of stream sediment and lake sediment samples. For each group which contains a sufficient number of observations, statistical tables, tables of raw data, and 1:1000000 scale maps of pertinent elements have been included in this report.« less

Approximate error conjugation gradient minimization methods

DOEpatents

Kallman, Jeffrey S

2013-05-21

In one embodiment, a method includes selecting a subset of rays from a set of all rays to use in an error calculation for a constrained conjugate gradient minimization problem, calculating an approximate error using the subset of rays, and calculating a minimum in a conjugate gradient direction based on the approximate error. In another embodiment, a system includes a processor for executing logic, logic for selecting a subset of rays from a set of all rays to use in an error calculation for a constrained conjugate gradient minimization problem, logic for calculating an approximate error using the subset of rays, and logic for calculating a minimum in a conjugate gradient direction based on the approximate error. In other embodiments, computer program products, methods, and systems are described capable of using approximate error in constrained conjugate gradient minimization problems.

Effects of sample size and sampling frequency on studies of brown bear home ranges and habitat use

USGS Publications Warehouse

Arthur, Steve M.; Schwartz, Charles C.

1999-01-01

We equipped 9 brown bears (Ursus arctos) on the Kenai Peninsula, Alaska, with collars containing both conventional very-high-frequency (VHF) transmitters and global positioning system (GPS) receivers programmed to determine an animal's position at 5.75-hr intervals. We calculated minimum convex polygon (MCP) and fixed and adaptive kernel home ranges for randomly-selected subsets of the GPS data to examine the effects of sample size on accuracy and precision of home range estimates. We also compared results obtained by weekly aerial radiotracking versus more frequent GPS locations to test for biases in conventional radiotracking data. Home ranges based on the MCP were 20-606 km2 (x = 201) for aerial radiotracking data (n = 12-16 locations/bear) and 116-1,505 km2 (x = 522) for the complete GPS data sets (n = 245-466 locations/bear). Fixed kernel home ranges were 34-955 km2 (x = 224) for radiotracking data and 16-130 km2 (x = 60) for the GPS data. Differences between means for radiotracking and GPS data were due primarily to the larger samples provided by the GPS data. Means did not differ between radiotracking data and equivalent-sized subsets of GPS data (P > 0.10). For the MCP, home range area increased and variability decreased asymptotically with number of locations. For the kernel models, both area and variability decreased with increasing sample size. Simulations suggested that the MCP and kernel models required >60 and >80 locations, respectively, for estimates to be both accurate (change in area <1%/additional location) and precise (CV < 50%). Although the radiotracking data appeared unbiased, except for the relationship between area and sample size, these data failed to indicate some areas that likely were important to bears. Our results suggest that the usefulness of conventional radiotracking data may be limited by potential biases and variability due to small samples. Investigators that use home range estimates in statistical tests should consider the effects of variability of those estimates. Use of GPS-equipped collars can facilitate obtaining larger samples of unbiased data and improve accuracy and precision of home range estimates.

Column Subset Selection, Matrix Factorization, and Eigenvalue Optimization

DTIC Science & Technology

2008-07-01

Pietsch and Grothendieck, which are regarded as basic instruments in modern functional analysis [Pis86]. • The methods for computing these... Pietsch factorization and the maxcut semi- definite program [GW95]. 1.2. Overview. We focus on the algorithmic version of the Kashin–Tzafriri theorem...will see that the desired subset is exposed by factoring the random submatrix. This factorization, which was invented by Pietsch , is regarded as a basic

Moderate physical activity of music aerobic exercise increases lymphocyte counts, specific subsets, and differentiation.

PubMed

Yeh, Shu-Hui; Lai, Hsiu-Ling; Hsiao, Chiu-Yueh; Lin, Li-Wei; Chuang, Yu-Kuan; Yang, Yu-Yeng; Yang, Kuender D

2014-09-01

Moderate physical activity has been shown to promote immunity. Different moderate physical activities may have different effects on immunity. This study investigated the impacts of a 12-week regular music aerobic exercise (MAE) program on leukocyte distribution, lymphocyte subsets, and lymphocyte polarization. The study used a case-control design with pretest and posttest. Forty-seven middle-age women were recruited for this study. Three participants dropped out, 22 completed the 12-week MAE program, and the other 22 participants who had heat-intolerance or limited schedule eligibility were enrolled as the control group without the MAE exercise. Results showed that the MAE exercise for 12 weeks didn't change red blood cells or total leukocytes but increased lymphocyte counts. The women in MAE group revealed significant increases (P ≤ 0.01) of CD3CD4, CD3CD8, and CD4CD25 cells, associated with Treg polarization showing enhanced FoxP3 but not T-bet, Gata-3, or RORγT expression (P < .01). The control group without exercise revealed insignificant change of lymphocyte subsets or lymphocyte polarization. This study shows that MAE increases specific lymphocyte subsets and enhances Treg cell differentiation. It is suggested to encourage moderate physical activity of music aerobic exercise to enhance lymphocyte function of middle-aged women.

Pupal habitat productivity of Anopheles gambiae complex mosquitoes in a rural village in western Kenya.

PubMed

Mutuku, Francis M; Bayoh, M Nabie; Gimnig, John E; Vulule, John M; Kamau, Luna; Walker, Edward D; Kabiru, Ephantus; Hawley, William A

2006-01-01

The productivity of larval habitats of the malaria vector Anopheles gambiae for pupae (the stage preceding adult metamorphosis) is poorly known, yet adult emergence from habitats is the primary determinant of vector density. To assess it, we used absolute sampling methods in four studies involving daily sampling for 25 days in 6 habitat types in a village in western Kenya. Anopheles gambiae s.s. comprised 82.5% of emergent adults and Anopheles arabiensis the remainder. Pupal production occurred from a subset of habitats, primarily soil burrow pits, and was discontinuous in time, even when larvae occupied all habitats continuously. Habitat stability was positively associated with pupal productivity. In a dry season, pupal productivity was distributed between burrow pits and pools in streambeds. Overall, these data support the notion that source reduction measures against recognizably productive habitats would be a useful component of an integrated management program for An. gambiae in villages.

Body burdens of heavy metals in Lake Michigan wetland turtles.

PubMed

Smith, Dayna L; Cooper, Matthew J; Kosiara, Jessica M; Lamberti, Gary A

2016-02-01

Tissue heavy metal concentrations in painted (Chrysemys picta) and snapping (Chelydra serpentina) turtles from Lake Michigan coastal wetlands were analyzed to determine (1) whether turtles accumulated heavy metals, (2) if tissue metal concentrations were related to environmental metal concentrations, and (3) the potential for non-lethal sampling techniques to be used for monitoring heavy metal body burdens in freshwater turtles. Muscle, liver, shell, and claw samples were collected from painted and snapping turtles and analyzed for cadmium, chromium, copper, iron, lead, magnesium, manganese, and zinc. Turtle tissues had measurable quantities of all eight metals analyzed. Statistically significant correlations between tissue metal concentrations and sediment metal concentrations were found for a subset of metals. Metals were generally found in higher concentrations in the larger snapping turtles than in painted turtles. In addition, non-lethal samples of shell and claw were found to be possible alternatives to lethal liver and muscle samples for some metals. Human consumption of snapping turtles presents potential health risks if turtles are harvested from contaminated areas. Overall, our results suggest that turtles could be a valuable component of contaminant monitoring programs for wetland ecosystems.

Symptomatic and Subclinical Infection with Rotavirus P[8]G9, Rural Ecuador

PubMed Central

Endara, Pablo; Trueba, Gabriel; Solberg, Owen D.; Bates, Sarah J.; Ponce, Karina; Cevallos, William; Matthijnssens, Jelle

2007-01-01

During the past decade, rotavirus genotype G9 has spread throughout the world, adding to and sometimes supplanting the common genotypes G1–G4. We report evidence of this spread in a population sample within rural Ecuador. A total of 1,656 stool samples were collected from both patients with diarrhea and asymptomatic residents in 22 remote communities in northwestern Ecuador from August 2003 through February 2006. Rotavirus was detected in 23.4% of case-patients and 3.2% of controls. From these 136 rotavirus-positive samples, a subset of 47 were genotyped; 72% were of genotype G9, and 62% were genotype P[8]G9. As a comparison, 29 rotavirus-positive stool samples were collected from a hospital in Quito during March 2006 and genotyped; 86% were of genotype P[8]G9. Few countries have reported P[8]G9 rotavirus detection rates as high as those of the current study. This growing prevalence may require changes to current vaccination programs to include coverage for this genotype. PMID:17553272

Electron donor concentrations in sediments and sediment properties at the agricultural chemicals team research site near New Providence, Iowa, 2006-07

USGS Publications Warehouse

Maharjan, Bijesh; Korom, Scott F.; Smith, Erik A.

2013-01-01

The concentrations of electron donors in aquifer sediments are important to the understanding of the fate and transport of redox-sensitive constituents in groundwater, such as nitrate. For a study by the U.S. Geological Survey National Water-Quality Assessment Program, 50 sediment samples were collected from below the water table from 11 boreholes at the U.S. Geological Survey Agricultural Chemicals Team research site near New Providence, Iowa, during 2006-07. All samples were analyzed for gravel, sand (coarse, medium, and fine), silt, clay, Munsell soil color, inorganic carbon content, and for the following electron donors: organic carbon, ferrous iron, and inorganic sulfide. A subset of 14 sediment samples also was analyzed for organic sulfur, but all of these samples had concentrations less than the method detection limit; therefore, the presence of this potential electron donor was not considered further. X-ray diffraction analyses provided important semi-quantitative information of well-crystallized dominant minerals within the sediments that might be contributing electron donors.

The NASA Electronic Parts and Packaging (NEPP) Program: Overview and Update FY15 and Beyond

NASA Technical Reports Server (NTRS)

LaBel, Kenneth A.; Sampson, Michael J.

2016-01-01

The NASA Electronic Parts and Packaging (NEPP) program, and its subset the NASA Electronic Parts Assurance Group (NEPAG), are NASA's point-of-contacts for reliability and radiation tolerance of electrical, electronic, and electromechanical (EEE) parts and their packages. This presentation includes a Fiscal Year 2015 program overview.

Participatory Equity and Student Outcomes in Living-Learning Programs of Differing Thematic Types

ERIC Educational Resources Information Center

Soldner, Matthew Edward

2011-01-01

This study evaluated participatory equity in varying thematic types of living-learning programs and, for a subset of student group x program type combinations found to be below equity, used latent mean modeling to determine whether statistically significant mean differences existed between the outcome scores of living-learning participants and…

Reducing seed dependent variability of non-uniformly sampled multidimensional NMR data

NASA Astrophysics Data System (ADS)

Mobli, Mehdi

2015-07-01

The application of NMR spectroscopy to study the structure, dynamics and function of macromolecules requires the acquisition of several multidimensional spectra. The one-dimensional NMR time-response from the spectrometer is extended to additional dimensions by introducing incremented delays in the experiment that cause oscillation of the signal along "indirect" dimensions. For a given dimension the delay is incremented at twice the rate of the maximum frequency (Nyquist rate). To achieve high-resolution requires acquisition of long data records sampled at the Nyquist rate. This is typically a prohibitive step due to time constraints, resulting in sub-optimal data records to the detriment of subsequent analyses. The multidimensional NMR spectrum itself is typically sparse, and it has been shown that in such cases it is possible to use non-Fourier methods to reconstruct a high-resolution multidimensional spectrum from a random subset of non-uniformly sampled (NUS) data. For a given acquisition time, NUS has the potential to improve the sensitivity and resolution of a multidimensional spectrum, compared to traditional uniform sampling. The improvements in sensitivity and/or resolution achieved by NUS are heavily dependent on the distribution of points in the random subset acquired. Typically, random points are selected from a probability density function (PDF) weighted according to the NMR signal envelope. In extreme cases as little as 1% of the data is subsampled. The heavy under-sampling can result in poor reproducibility, i.e. when two experiments are carried out where the same number of random samples is selected from the same PDF but using different random seeds. Here, a jittered sampling approach is introduced that is shown to improve random seed dependent reproducibility of multidimensional spectra generated from NUS data, compared to commonly applied NUS methods. It is shown that this is achieved due to the low variability of the inherent sensitivity of the random subset chosen from a given PDF. Finally, it is demonstrated that metrics used to find optimal NUS distributions are heavily dependent on the inherent sensitivity of the random subset, and such optimisation is therefore less critical when using the proposed sampling scheme.

Discovery of Remote Globular Cluster Satellites of M87

NASA Astrophysics Data System (ADS)

Sparkman, Lea; Guo, Rachel; Toloba, Elisa; Guhathakurta, Puragra; Peng, Eric W.; Ferrarese, Laura; Cote, Patrick; NGVS Collaboration

2016-01-01

We present the discovery of several tens of globular clusters (GCs) in the outer regions of the giant elliptical M87, the brightest galaxy in the Virgo Cluster. These M87 GC satellites were discovered in the course of Keck/DEIMOS spectroscopic follow up of GC candidates that were identified in the Next Generation Virgo cluster Survey (NGVS). Specifically, the primary targets of this Keck spectroscopic campaign were GC satellites of early-type dwarf (dE) galaxies. However, we found that our sample contained a subset of GCs for which M87 is the most likely host. This subset is consistent with having an r^-1 power-law surface density distribution and a radial velocity distribution both centered on M87. The remote M87 GC satellites span the radial range 140 to 900 kpc, out to about a third of the Virgo Cluster's virial radius (for comparison, M87's effective radius is only 8 kpc). These M87 GC satellites are probably former satellites of other Virgo Cluster galaxies that have subsequently been cannibalized by M87.This research was supported by the National Science Foundation and the UC Santa Cruz Science Internship Program.

The Influence of Host Galaxies in Type Ia Supernova Cosmology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Uddin, Syed A.; Mould, Jeremy; Lidman, Chris

We use a sample of 1338 spectroscopically confirmed and photometrically classified Type Ia supernovae (SNe Ia) sourced from Carnegie Supernova Project, Center for Astrophysics Supernova Survey, Sloan Digital Sky Survey-II, and SuperNova Legacy Survey SN samples to examine the relationships between SNe Ia and the galaxies that host them. Our results provide confirmation with improved statistical significance that SNe Ia, after standardization, are on average more luminous in massive hosts (significance >5 σ ), and decline more rapidly in massive hosts (significance >9 σ ) and in hosts with low specific star formation rates (significance >8 σ ). We studymore » the variation of these relationships with redshift and detect no evolution. We split SNe Ia into pairs of subsets that are based on the properties of the hosts and fit cosmological models to each subset. Including both systematic and statistical uncertainties, we do not find any significant shift in the best-fit cosmological parameters between the subsets. Among different SN Ia subsets, we find that SNe Ia in hosts with high specific star formation rates have the least intrinsic scatter ( σ {sub int} = 0.08 ± 0.01) in luminosity after standardization.« less

The Influence of Host Galaxies in Type Ia Supernova Cosmology

NASA Astrophysics Data System (ADS)

Uddin, Syed A.; Mould, Jeremy; Lidman, Chris; Ruhlmann-Kleider, Vanina; Zhang, Bonnie R.

2017-10-01

We use a sample of 1338 spectroscopically confirmed and photometrically classified Type Ia supernovae (SNe Ia) sourced from Carnegie Supernova Project, Center for Astrophysics Supernova Survey, Sloan Digital Sky Survey-II, and SuperNova Legacy Survey SN samples to examine the relationships between SNe Ia and the galaxies that host them. Our results provide confirmation with improved statistical significance that SNe Ia, after standardization, are on average more luminous in massive hosts (significance >5σ), and decline more rapidly in massive hosts (significance >9σ) and in hosts with low specific star formation rates (significance >8σ). We study the variation of these relationships with redshift and detect no evolution. We split SNe Ia into pairs of subsets that are based on the properties of the hosts and fit cosmological models to each subset. Including both systematic and statistical uncertainties, we do not find any significant shift in the best-fit cosmological parameters between the subsets. Among different SN Ia subsets, we find that SNe Ia in hosts with high specific star formation rates have the least intrinsic scatter (σ int = 0.08 ± 0.01) in luminosity after standardization.

User's Manual for the National Water-Quality Assessment Program Invertebrate Data Analysis System (IDAS) Software: Version 3

USGS Publications Warehouse

Cuffney, Thomas F.

2003-01-01

The Invertebrate Data Analysis System (IDAS) software provides an accurate, consistent, and efficient mechanism for analyzing invertebrate data collected as part of the National Water-Quality Assessment Program and stored in the Biological Transactional Database (Bio-TDB). The IDAS software is a stand-alone program for personal computers that run Microsoft (MS) Windows?. It allows users to read data downloaded from Bio-TDB and stored either as MS Excel? or MS Access? files. The program consists of five modules. The Edit Data module allows the user to subset, combine, delete, and summarize community data. The Data Preparation module allows the user to select the type(s) of sample(s) to process, calculate densities, delete taxa based on laboratory processing notes, combine lifestages or keep them separate, select a lowest taxonomic level for analysis, delete rare taxa, and resolve taxonomic ambiguities. The Calculate Community Metrics module allows the user to calculate over 130 community metrics, including metrics based on organism tolerances and functional feeding groups. The Calculate Diversities and Similarities module allows the user to calculate nine diversity and eight similarity indices. The Data export module allows the user to export data to other software packages and produce tables of community data that can be imported into spreadsheet and word-processing programs. Though the IDAS program was developed to process invertebrate data downloaded from USGS databases, it will work with other data sets that are converted to the USGS (Bio-TDB) format. Consequently, the data manipulation, analysis, and export procedures provided by the IDAS program can be used by anyone involved in using benthic macroinvertebrates in applied or basic research.

A brief measure of attitudes toward mixed methods research in psychology

PubMed Central

Roberts, Lynne D.; Povee, Kate

2014-01-01

The adoption of mixed methods research in psychology has trailed behind other social science disciplines. Teaching psychology students, academics, and practitioners about mixed methodologies may increase the use of mixed methods within the discipline. However, tailoring and evaluating education and training in mixed methodologies requires an understanding of, and way of measuring, attitudes toward mixed methods research in psychology. To date, no such measure exists. In this article we present the development and initial validation of a new measure: Attitudes toward Mixed Methods Research in Psychology. A pool of 42 items developed from previous qualitative research on attitudes toward mixed methods research along with validation measures was administered via an online survey to a convenience sample of 274 psychology students, academics and psychologists. Principal axis factoring with varimax rotation on a subset of the sample produced a four-factor, 12-item solution. Confirmatory factor analysis on a separate subset of the sample indicated that a higher order four factor model provided the best fit to the data. The four factors; ‘Limited Exposure,’ ‘(in)Compatibility,’ ‘Validity,’ and ‘Tokenistic Qualitative Component’; each have acceptable internal reliability. Known groups validity analyses based on preferred research orientation and self-rated mixed methods research skills, and convergent and divergent validity analyses based on measures of attitudes toward psychology as a science and scientist and practitioner orientation, provide initial validation of the measure. This brief, internally reliable measure can be used in assessing attitudes toward mixed methods research in psychology, measuring change in attitudes as part of the evaluation of mixed methods education, and in larger research programs. PMID:25429281

xMSanalyzer: automated pipeline for improved feature detection and downstream analysis of large-scale, non-targeted metabolomics data.

PubMed

Uppal, Karan; Soltow, Quinlyn A; Strobel, Frederick H; Pittard, W Stephen; Gernert, Kim M; Yu, Tianwei; Jones, Dean P

2013-01-16

Detection of low abundance metabolites is important for de novo mapping of metabolic pathways related to diet, microbiome or environmental exposures. Multiple algorithms are available to extract m/z features from liquid chromatography-mass spectral data in a conservative manner, which tends to preclude detection of low abundance chemicals and chemicals found in small subsets of samples. The present study provides software to enhance such algorithms for feature detection, quality assessment, and annotation. xMSanalyzer is a set of utilities for automated processing of metabolomics data. The utilites can be classified into four main modules to: 1) improve feature detection for replicate analyses by systematic re-extraction with multiple parameter settings and data merger to optimize the balance between sensitivity and reliability, 2) evaluate sample quality and feature consistency, 3) detect feature overlap between datasets, and 4) characterize high-resolution m/z matches to small molecule metabolites and biological pathways using multiple chemical databases. The package was tested with plasma samples and shown to more than double the number of features extracted while improving quantitative reliability of detection. MS/MS analysis of a random subset of peaks that were exclusively detected using xMSanalyzer confirmed that the optimization scheme improves detection of real metabolites. xMSanalyzer is a package of utilities for data extraction, quality control assessment, detection of overlapping and unique metabolites in multiple datasets, and batch annotation of metabolites. The program was designed to integrate with existing packages such as apLCMS and XCMS, but the framework can also be used to enhance data extraction for other LC/MS data software.

EPA Facility Registry Service (FRS): CAMDBS

EPA Pesticide Factsheets

This web feature service contains location and facility identification information from EPA's Facility Registry Service (FRS) for the subset of facilities that link to the Clean Air Markets Division Business System (CAMDBS). Administered by the EPA Clean Air Markets Division, within the Office of Air and Radiation, CAMDBS supports the implementation of market-based air pollution control programs, including the Acid Rain Program and regional programs designed to reduce the transport of ozone. FRS identifies and geospatially locates facilities, sites or places subject to environmental regulations or of environmental interest. Using vigorous verification and data management procedures, FRS integrates facility data from EPA's national program systems, other federal agencies, and State and tribal master facility records and provides EPA with a centrally managed, single source of comprehensive and authoritative information on facilities. This data set contains the subset of FRS integrated facilities that link to CAMDBS facilities once the CAMDBS data has been integrated into the FRS database. Additional information on FRS is available at the EPA website https://www.epa.gov/enviro/facility-registry-service-frs.

The First SeaWiFS HPLC Analysis Round-Robin Experiment (SeaHARRE-1)

NASA Technical Reports Server (NTRS)

Hooker, Stanford B. (Editor); Firestone, Elaine R. (Editor); Claustre, Herve; Ras, Josephine; VanHeukelem, Laurie; Berthon, Jean-Francois; Targa, Cristina; vanderLinde, Dirk; Barlow, Ray; Sessions, Heather

2001-01-01

Four laboratories, which had contributed to various aspects of SeaWiFS calibration and validation activities, participated in the first SeaWiFS HPLC Analysis Round-Robin Experiment (SeaHARRE-1): Horn Point Laboratory (USA), the Joint Research Centre (Italy), the Laboratoire de Physique et Chimie Marines (France), and the Marine and Coastal Management group (South Africa). The analyses of the data are presented in Chapter 1 and the individual methods of the four groups are presented in Chapters 2-5. The average (or overall) conclusions of the round-robin are derived from 12 in situ stations occupied during a cruise in the Mediterranean Sea, although, only 11 stations are used in the analyses. The data set is composed of 12 replicates taken during each sampling opportunity with 3 replicates going to each of the 4 laboratories. The average (or overall) results from the intercomparison of 15 pigments or pigment associations are as follows (in some cases, data subsets that exclude pigments which were not analyzed by all the laboratories, or that had unusually large variances, are used to exclude a variety of problematic pigments): a) the accuracy of the four methods in determining the concentration of total chlorophyll a is 7.9%, (one method did not separate mono- and divinyl chlorophyll a, and if the samples containing significant divinyl chlorophyll a concentrations are ignored, the four methods have an accuracy of 6.7%); b) the accuracy in determining the full set of pigments is 19.1%; c) there is a reduction in accuracy of approximately - 12.2% for every decade (factor of 10) decrease in concentration (based on a data subset); d) the precision of the four methods using a subset data is 8.617( 6.2% for an edited subset); e) the repeatability of the four methods using the subset data is 9.2% (7.2%; for an edited subset, and f) the reproducibility of the four methods using the subset data is 21.31% (15.0% for an edited subset).

Automatic identification of variables in epidemiological datasets using logic regression.

PubMed

Lorenz, Matthias W; Abdi, Negin Ashtiani; Scheckenbach, Frank; Pflug, Anja; Bülbül, Alpaslan; Catapano, Alberico L; Agewall, Stefan; Ezhov, Marat; Bots, Michiel L; Kiechl, Stefan; Orth, Andreas

2017-04-13

For an individual participant data (IPD) meta-analysis, multiple datasets must be transformed in a consistent format, e.g. using uniform variable names. When large numbers of datasets have to be processed, this can be a time-consuming and error-prone task. Automated or semi-automated identification of variables can help to reduce the workload and improve the data quality. For semi-automation high sensitivity in the recognition of matching variables is particularly important, because it allows creating software which for a target variable presents a choice of source variables, from which a user can choose the matching one, with only low risk of having missed a correct source variable. For each variable in a set of target variables, a number of simple rules were manually created. With logic regression, an optimal Boolean combination of these rules was searched for every target variable, using a random subset of a large database of epidemiological and clinical cohort data (construction subset). In a second subset of this database (validation subset), this optimal combination rules were validated. In the construction sample, 41 target variables were allocated on average with a positive predictive value (PPV) of 34%, and a negative predictive value (NPV) of 95%. In the validation sample, PPV was 33%, whereas NPV remained at 94%. In the construction sample, PPV was 50% or less in 63% of all variables, in the validation sample in 71% of all variables. We demonstrated that the application of logic regression in a complex data management task in large epidemiological IPD meta-analyses is feasible. However, the performance of the algorithm is poor, which may require backup strategies.

OPTIMAL NETWORK TOPOLOGY DESIGN

NASA Technical Reports Server (NTRS)

Yuen, J. H.

1994-01-01

This program was developed as part of a research study on the topology design and performance analysis for the Space Station Information System (SSIS) network. It uses an efficient algorithm to generate candidate network designs (consisting of subsets of the set of all network components) in increasing order of their total costs, and checks each design to see if it forms an acceptable network. This technique gives the true cost-optimal network, and is particularly useful when the network has many constraints and not too many components. It is intended that this new design technique consider all important performance measures explicitly and take into account the constraints due to various technical feasibilities. In the current program, technical constraints are taken care of by the user properly forming the starting set of candidate components (e.g. nonfeasible links are not included). As subsets are generated, they are tested to see if they form an acceptable network by checking that all requirements are satisfied. Thus the first acceptable subset encountered gives the cost-optimal topology satisfying all given constraints. The user must sort the set of "feasible" link elements in increasing order of their costs. The program prompts the user for the following information for each link: 1) cost, 2) connectivity (number of stations connected by the link), and 3) the stations connected by that link. Unless instructed to stop, the program generates all possible acceptable networks in increasing order of their total costs. The program is written only to generate topologies that are simply connected. Tests on reliability, delay, and other performance measures are discussed in the documentation, but have not been incorporated into the program. This program is written in PASCAL for interactive execution and has been implemented on an IBM PC series computer operating under PC DOS. The disk contains source code only. This program was developed in 1985.

On the Viability of PTSD Checklist (PCL) Short Form Use: Analyses from Mississippi Gulf Coast Hurricane Katrina Survivors

ERIC Educational Resources Information Center

Hirschel, Michael J.; Schulenberg, Stefan E.

2010-01-01

One measure commonly used to assess posttraumatic stress disorder is the PTSD Checklist (PCL). Lang and Stein (2005) extracted 4 subsets of PCL items, validating 2 of them for possible use in screening in primary care settings. The viability of the 4 item subsets was evaluated psychometrically in the present study with a sample of Hurricane…

Brief Report: Checklist for Autism Spectrum Disorder--Most Discriminating Items for Diagnosing Autism

ERIC Educational Resources Information Center

Mayes, Susan D.

2018-01-01

The smallest subset of items from the 30-item Checklist for Autism Spectrum Disorder (CASD) that differentiated 607 referred children (3-17 years) with and without autism with 100% accuracy was identified. This 6-item subset (CASD-Short Form) was cross-validated on an independent sample of 397 referred children (1-18 years) with and without autism…

Minimizing the average distance to a closest leaf in a phylogenetic tree.

PubMed

Matsen, Frederick A; Gallagher, Aaron; McCoy, Connor O

2013-11-01

When performing an analysis on a collection of molecular sequences, it can be convenient to reduce the number of sequences under consideration while maintaining some characteristic of a larger collection of sequences. For example, one may wish to select a subset of high-quality sequences that represent the diversity of a larger collection of sequences. One may also wish to specialize a large database of characterized "reference sequences" to a smaller subset that is as close as possible on average to a collection of "query sequences" of interest. Such a representative subset can be useful whenever one wishes to find a set of reference sequences that is appropriate to use for comparative analysis of environmentally derived sequences, such as for selecting "reference tree" sequences for phylogenetic placement of metagenomic reads. In this article, we formalize these problems in terms of the minimization of the Average Distance to the Closest Leaf (ADCL) and investigate algorithms to perform the relevant minimization. We show that the greedy algorithm is not effective, show that a variant of the Partitioning Around Medoids (PAM) heuristic gets stuck in local minima, and develop an exact dynamic programming approach. Using this exact program we note that the performance of PAM appears to be good for simulated trees, and is faster than the exact algorithm for small trees. On the other hand, the exact program gives solutions for all numbers of leaves less than or equal to the given desired number of leaves, whereas PAM only gives a solution for the prespecified number of leaves. Via application to real data, we show that the ADCL criterion chooses chimeric sequences less often than random subsets, whereas the maximization of phylogenetic diversity chooses them more often than random. These algorithms have been implemented in publicly available software.

Cellular and Molecular Dynamics of Th17 Differentiation and its Developmental Plasticity in the Intestinal Immune Response

PubMed Central

Bhaumik, Suniti; Basu, Rajatava

2017-01-01

After emerging from the thymus, naive CD4 T cells circulate through secondary lymphoid tissues, including gut-associated lymphoid tissue of the intestine. The activation of naïve CD4 T cells by antigen-presenting cells offering cognate antigen initiate differentiation programs that lead to the development of highly specialized T helper (Th) cell lineages. Although initially believed that developmental programing of effector T cells such as T helper 1 (Th1) or T helper 2 (Th2) resulted in irreversible commitment to a fixed fate, subsequent studies have demonstrated greater flexibility, or plasticity, in effector T cell stability than originally conceived. This is particularly so for the Th17 subset, differentiation of which is a highly dynamic process with overlapping developmental axes with inducible regulatory T (iTreg), T helper 22 (Th22), and Th1 cells. Accordingly, intermediary stages of Th17 cells are found in various tissues, which co-express lineage-specific transcription factor(s) or cytokine(s) of developmentally related CD4 T cell subsets. A highly specialized tissue like that of the intestine, which harbors the largest immune compartment of the body, adds several layers of complexity to the intricate process of Th differentiation. Due to constant exposure to millions of commensal microbes and periodic exposure to pathogens, the intestinal mucosa maintains a delicate balance between regulatory and effector T cells. It is becoming increasingly clear that equilibrium between tolerogenic and inflammatory axes is maintained in the intestine by shuttling the flexible genetic programming of a developing CD4 T cell along the developmental axis of iTreg, Th17, Th22, and Th1 subsets. Currently, Th17 plasticity remains an unresolved concern in the field of clinical research as targeting Th17 cells to cure immune-mediated disease might also target its related subsets. In this review, we discuss the expanding sphere of Th17 plasticity through its shared developmental axes with related cellular subsets such as Th22, Th1, and iTreg in the context of intestinal inflammation and also examine the molecular and epigenetic features of Th17 cells that mediate these overlapping developmental programs. PMID:28408906

Cleaning and Cleanliness Verification Techniques for Mars Returned Sample Handling

NASA Technical Reports Server (NTRS)

Mickelson, E. T.; Lindstrom, D. J.; Allton, J. H.; Hittle, J. D.

2002-01-01

Precision cleaning and cleanliness verification techniques are examined as a subset of a comprehensive contamination control strategy for a Mars sample return mission. Additional information is contained in the original extended abstract.

An Integrated Cell Purification and Genomics Strategy Reveals Multiple Regulators of Pancreas Development

PubMed Central

Benitez, Cecil M.; Qu, Kun; Sugiyama, Takuya; Pauerstein, Philip T.; Liu, Yinghua; Tsai, Jennifer; Gu, Xueying; Ghodasara, Amar; Arda, H. Efsun; Zhang, Jiajing; Dekker, Joseph D.; Tucker, Haley O.; Chang, Howard Y.; Kim, Seung K.

2014-01-01

The regulatory logic underlying global transcriptional programs controlling development of visceral organs like the pancreas remains undiscovered. Here, we profiled gene expression in 12 purified populations of fetal and adult pancreatic epithelial cells representing crucial progenitor cell subsets, and their endocrine or exocrine progeny. Using probabilistic models to decode the general programs organizing gene expression, we identified co-expressed gene sets in cell subsets that revealed patterns and processes governing progenitor cell development, lineage specification, and endocrine cell maturation. Purification of Neurog3 mutant cells and module network analysis linked established regulators such as Neurog3 to unrecognized gene targets and roles in pancreas development. Iterative module network analysis nominated and prioritized transcriptional regulators, including diabetes risk genes. Functional validation of a subset of candidate regulators with corresponding mutant mice revealed that the transcription factors Etv1, Prdm16, Runx1t1 and Bcl11a are essential for pancreas development. Our integrated approach provides a unique framework for identifying regulatory genes and functional gene sets underlying pancreas development and associated diseases such as diabetes mellitus. PMID:25330008

Evaluating the effect of spatial subsetting on subpixel unmixing methodology applied to ASTER over a hydrothermally altered terrain

NASA Astrophysics Data System (ADS)

Ayoobi, Iman; Tangestani, Majid H.

2017-10-01

This study investigates the effect of spatial subsets of Advanced Spaceborne Thermal Emission and Reflection radiometer (ASTER) L1B visible-near infrared and short wave-infrared (VNIR-SWIR) data on matched filtering results at the central part of Kerman magmatic arc, where abundant porphyry copper deposits exist. The matched filtering (MF) procedure was run separately at sites containing hydrothermal minerals such as sericite, kaolinite, chlorite, and jarosite to map the abundances of these minerals on spatial subsets containing 100, 75, 50, and 25 percent of the original scene. Results were evaluated by comparing the matched filtering scores with the mineral abundances obtained by semi-quantitative XRD analysis of corresponding field samples. It was concluded that MF method should be applied to the whole scene prior to any data subsetting.

Adenovirus-specific T-cell Subsets in Human Peripheral Blood and After IFN-γ Immunomagnetic Selection.

PubMed

Qian, Chongsheng; Wang, Yingying; Cai, Huili; Laroye, Caroline; De Carvalho Bittencourt, Marcelo; Clement, Laurence; Stoltz, Jean-François; Decot, Véronique; Reppel, Loïc; Bensoussan, Danièle

2016-01-01

Adoptive antiviral cellular immunotherapy by infusion of virus-specific T cells (VSTs) is becoming an alternative treatment for viral infection after hematopoietic stem cell transplantation. The T memory stem cell (TSCM) subset was recently described as exhibiting self-renewal and multipotency properties which are required for sustained efficacy in vivo. We wondered if such a crucial subset for immunotherapy was present in VSTs. We identified, by flow cytometry, TSCM in adenovirus (ADV)-specific interferon (IFN)-γ+ T cells before and after IFN-γ-based immunomagnetic selection, and analyzed the distribution of the main T-cell subsets in VSTs: naive T cells (TN), TSCM, T central memory cells (TCM), T effector memory cell (TEM), and effector T cells (TEFF). In this study all of the different T-cell subsets were observed in the blood sample from healthy donor ADV-VSTs, both before and after IFN-γ-based immunomagnetic selection. As the IFN-γ-based immunomagnetic selection system sorts mainly the most differentiated T-cell subsets, we observed that TEM was always the major T-cell subset of ADV-specific T cells after immunomagnetic isolation and especially after expansion in vitro. Comparing T-cell subpopulation profiles before and after in vitro expansion, we observed that in vitro cell culture with interleukin-2 resulted in a significant expansion of TN-like, TCM, TEM, and TEFF subsets in CD4IFN-γ T cells and of TCM and TEM subsets only in CD8IFN-γ T cells. We demonstrated the presence of all T-cell subsets in IFN-γ VSTs including the TSCM subpopulation, although this was weakly selected by the IFN-γ-based immunomagnetic selection system.

Subsetting and Formatting Landsat-7 LOR ETM+ and Data Products

NASA Technical Reports Server (NTRS)

Reid, Michael R.

2000-01-01

The Landsat-7 Processing System (LPS) processes Landsat-7 Enhanced Thematic Mapper (ETM+) instrument data into large, contiguous segments called "subintervals" and stores them in Level OR (LOR) data files. The LPS processed subinterval products must be subsetted and reformatted before the Level I processing systems can ingest them. The initial full subintervals produced by the LPS are stored mainly in HDF Earth Observing System (HDF-EOS) format which is an extension to the Hierarchical Data Format (HDF). The final LOR products are stored in native HDF format. Primarily the EOS Core System (ECS) and alternately the DAAC Emergency System (DES) subset the subinterval data for the operational Landsat-7 data processing systems. The HDF and HDF-EOS application programming interfaces (APIs) can be used for extensive data subsetting and data reorganization. A stand-alone subsetter tool has been developed which is based on some of the DES code. This tool makes use of the HDF and HDFEOS APIs to perform Landsat-7 LOR product subsetting and demonstrates how HDF and HDFEOS can be used for creating various configurations of full LOR products. How these APIs can be used to efficiently subset, format, and organize Landsat-7 LOR data as demonstrated by the subsetter tool and the DES is discussed.

Environmental Asbestos Assessment Manual: Superfund Method for the Determination of Asbestos in Ambient Air, Part 1: Method

EPA Science Inventory

This is a sampling and analysis method for the determination of asbestos in air. Samples are analyzed by transmission electron microscopy (TEM). Although a small subset of samples are to be prepared using a direct procedure, the majority of samples analyzed using this method wil...

Sub-sampling genetic data to estimate black bear population size: A case study

USGS Publications Warehouse

Tredick, C.A.; Vaughan, M.R.; Stauffer, D.F.; Simek, S.L.; Eason, T.

2007-01-01

Costs for genetic analysis of hair samples collected for individual identification of bears average approximately US$50 [2004] per sample. This can easily exceed budgetary allowances for large-scale studies or studies of high-density bear populations. We used 2 genetic datasets from 2 areas in the southeastern United States to explore how reducing costs of analysis by sub-sampling affected precision and accuracy of resulting population estimates. We used several sub-sampling scenarios to create subsets of the full datasets and compared summary statistics, population estimates, and precision of estimates generated from these subsets to estimates generated from the complete datasets. Our results suggested that bias and precision of estimates improved as the proportion of total samples used increased, and heterogeneity models (e.g., Mh[CHAO]) were more robust to reduced sample sizes than other models (e.g., behavior models). We recommend that only high-quality samples (>5 hair follicles) be used when budgets are constrained, and efforts should be made to maximize capture and recapture rates in the field.

Dimethyl fumarate–induced lymphopenia in MS due to differential T-cell subset apoptosis

PubMed Central

Ghadiri, Mahtab; Rezk, Ayman; Li, Rui; Evans, Ashley; Luessi, Felix; Zipp, Frauke; Giacomini, Paul S.; Antel, Jack

2017-01-01

Objective: To examine the mechanism underlying the preferential CD8+ vs CD4+ T-cell lymphopenia induced by dimethyl fumarate (DMF) treatment of MS. Methods: Total lymphocyte counts and comprehensive T-cell subset analyses were performed in high-quality samples obtained from patients with MS prior to and serially following DMF treatment initiation. Random coefficient mixed-effects analysis was used to model the trajectory of T-cell subset losses in vivo. Survival and apoptosis of distinct T-cell subsets were assessed following in vitro exposure to DMF. Results: Best-fit modeling indicated that the DMF-induced preferential reductions in CD8+ vs CD4+ T-cell counts nonetheless followed similar depletion kinetics, suggesting a similar rather than distinct mechanism involved in losses of both the CD8+ and CD4+ T cells. In vitro, DMF exposure resulted in dose-dependent reductions in T-cell survival, which were found to reflect apoptotic cell death. This DMF-induced apoptosis was greater for CD8+ vs CD4+, as well as for memory vs naive, and conventional vs regulatory T-cell subsets, a pattern which mirrored preferential T-cell subset losses that we observed during in vivo treatment of patients. Conclusions: Differential apoptosis mediated by DMF may underlie the preferential lymphopenia of distinct T-cell subsets, including CD8+ and memory T-cell subsets, seen in treated patients with MS. This differential susceptibility of distinct T-cell subsets to DMF-induced apoptosis may contribute to both the safety and efficacy profiles of DMF in patients with MS. PMID:28377940

Search for anomalous kinematics in tt dilepton events at CDF II.

PubMed

Acosta, D; Adelman, J; Affolder, T; Akimoto, T; Albrow, M G; Ambrose, D; Amerio, S; Amidei, D; Anastassov, A; Anikeev, K; Annovi, A; Antos, J; Aoki, M; Apollinari, G; Arisawa, T; Arguin, J-F; Artikov, A; Ashmanskas, W; Attal, A; Azfar, F; Azzi-Bacchetta, P; Bacchetta, N; Bachacou, H; Badgett, W; Barbaro-Galtieri, A; Barker, G J; Barnes, V E; Barnett, B A; Baroiant, S; Barone, M; Bauer, G; Bedeschi, F; Behari, S; Belforte, S; Bellettini, G; Bellinger, J; Ben-Haim, E; Benjamin, D; Beretvas, A; Bhatti, A; Binkley, M; Bisello, D; Bishai, M; Blair, R E; Blocker, C; Bloom, K; Blumenfeld, B; Bocci, A; Bodek, A; Bolla, G; Bolshov, A; Booth, P S L; Bortoletto, D; Boudreau, J; Bourov, S; Brau, B; Bromberg, C; Brubaker, E; Budagov, J; Budd, H S; Burkett, K; Busetto, G; Bussey, P; Byrum, K L; Cabrera, S; Campanelli, M; Campbell, M; Canepa, A; Casarsa, M; Carlsmith, D; Carron, S; Carosi, R; Cavalli-Sforza, M; Castro, A; Catastini, P; Cauz, D; Cerri, A; Cerrito, L; Chapman, J; Chen, C; Chen, Y C; Chertok, M; Chiarelli, G; Chlachidze, G; Chlebana, F; Cho, I; Cho, K; Chokheli, D; Chou, J P; Chu, M L; Chuang, S; Chung, J Y; Chung, W-H; Chung, Y S; Ciobanu, C I; Ciocci, M A; Clark, A G; Clark, D; Coca, M; Connolly, A; Convery, M; Conway, J; Cooper, B; Cordelli, M; Cortiana, G; Cranshaw, J; Cuevas, J; Culbertson, R; Currat, C; Cyr, D; Dagenhart, D; Da Ronco, S; D'Auria, S; de Barbaro, P; De Cecco, S; De Lentdecker, G; Dell'Agnello, S; Dell'Orso, M; Demers, S; Demortier, L; Deninno, M; De Pedis, D; Derwent, P F; Dionisi, C; Dittmann, J R; Dörr, C; Doksus, P; Dominguez, A; Donati, S; Donega, M; Donini, J; D'Onofrio, M; Dorigo, T; Drollinger, V; Ebina, K; Eddy, N; Ehlers, J; Ely, R; Erbacher, R; Erdmann, M; Errede, D; Errede, S; Eusebi, R; Fang, H-C; Farrington, S; Fedorko, I; Fedorko, W T; Feild, R G; Feindt, M; Fernandez, J P; Ferretti, C; Field, R D; Flanagan, G; Flaugher, B; Flores-Castillo, L R; Foland, A; Forrester, S; Foster, G W; Franklin, M; Freeman, J C; Fujii, Y; Furic, I; Gajjar, A; Gallas, A; Galyardt, J; Gallinaro, M; Garcia-Sciveres, M; Garfinkel, A F; Gay, C; Gerberich, H; Gerdes, D W; Gerchtein, E; Giagu, S; Giannetti, P; Gibson, A; Gibson, K; Ginsburg, C; Giolo, K; Giordani, M; Giunta, M; Giurgiu, G; Glagolev, V; Glenzinski, D; Gold, M; Goldschmidt, N; Goldstein, D; Goldstein, J; Gomez, G; Gomez-Ceballos, G; Goncharov, M; González, O; Gorelov, I; Goshaw, A T; Gotra, Y; Goulianos, K; Gresele, A; Griffiths, M; Grosso-Pilcher, C; Grundler, U; Guenther, M; Guimaraes da Costa, J; Haber, C; Hahn, K; Hahn, S R; Halkiadakis, E; Hamilton, A; Han, B-Y; Handler, R; Happacher, F; Hara, K; Hare, M; Harr, R F; Harris, R M; Hartmann, F; Hatakeyama, K; Hauser, J; Hays, C; Hayward, H; Heider, E; Heinemann, B; Heinrich, J; Hennecke, M; Herndon, M; Hill, C; Hirschhbuehl, D; Hocker, A; Hoffman, K D; Holloway, A; Hou, S; Houlden, M A; Huffman, B T; Huang, Y; Hughes, R E; Huston, J; Ikado, K; Incandela, J; Introzzi, G; Iori, M; Ishizawa, Y; Issever, C; Ivanov, A; Iwata, Y; Iyutin, B; James, E; Jang, D; Jarrell, J; Jeans, D; Jensen, H; Jeon, E J; Jones, M; Joo, K K; Jun, S Y; Junk, T; Kamon, T; Kang, J; Karagoz Unel, M; Karchin, P E; Kartal, S; Kato, Y; Kemp, Y; Kephart, R; Kerzel, U; Khotilovich, V; Kilminster, B; Kim, D H; Kim, H S; Kim, J E; Kim, M J; Kim, M S; Kim, S B; Kim, S H; Kim, T H; Kim, Y K; King, B T; Kirby, M; Kirsch, L; Klimenko, S; Knuteson, B; Ko, B R; Kobayashi, H; Koehn, P; Kong, D J; Kondo, K; Konigsberg, J; Kordas, K; Korn, A; Korytov, A; Kotelnikov, K; Kotwal, A V; Kovalev, A; Kraus, J; Kravchenko, I; Kreymer, A; Kroll, J; Kruse, M; Krutelyov, V; Kuhlmann, S E; Kwang, S; Laasanen, A T; Lai, S; Lami, S; Lammel, S; Lancaster, J; Lancaster, M; Lander, R; Lannon, K; Lath, A; Latino, G; Lauhakangas, R; Lazzizzera, I; Le, Y; Lecci, C; LeCompte, T; Lee, J; Lee, J; Lee, S W; Lefèvre, R; Leonardo, N; Leone, S; Levy, S; Lewis, J D; Li, K; Lin, C; Lin, C S; Lindgren, M; Liss, T M; Lister, A; Litvintsev, D O; Liu, T; Liu, Y; Lockyer, N S; Loginov, A; Loreti, M; Loverre, P; Lu, R-S; Lucchesi, D; Lujan, P; Lukens, P; Lungu, G; Lyons, L; Lys, J; Lysak, R; MacQueen, D; Madrak, R; Maeshima, K; Maksimovic, P; Malferrari, L; Manca, G; Marginean, R; Marino, C; Martin, A; Martin, M; Martin, V; Martínez, M; Maruyama, T; Matsunaga, H; Mattson, M; Mazzanti, P; McFarland, K S; McGivern, D; McIntyre, P M; McNamara, P; NcNulty, R; Mehta, A; Menzemer, S; Menzione, A; Merkel, P; Mesropian, C; Messina, A; Miao, T; Miladinovic, N; Miller, L; Miller, R; Miller, J S; Miquel, R; Miscetti, S; Mitselmakher, G; Miyamoto, A; Miyazaki, Y; Moggi, N; Mohr, B; Moore, R; Morello, M; Movilla Fernandez, P A; Mukherjee, A; Mulhearn, M; Muller, T; Mumford, R; Munar, A; Murat, P; Nachtman, J; Nahn, S; Nakamura, I; Nakano, I; Napier, A; Napora, R; Naumov, D; Necula, V; Niell, F; Nielsen, J; Nelson, C; Nelson, T; Neu, C; Neubauer, M S; Newman-Holmes, C; Nigmanov, T; Nodulman, L; Norniella, O; Oesterberg, K; Ogawa, T; Oh, S H; Oh, Y D; Ohsugi, T; Okusawa, T; Oldeman, R; Orava, R; Orejudos, W; Pagliarone, C; Palencia, E; Paoletti, R; Papadimitriou, V; Pashapour, S; Patrick, J; Pauletta, G; Paulini, M; Pauly, T; Paus, C; Pellett, D; Penzo, A; Phillips, T J; Piacentino, G; Piedra, J; Pitts, K T; Plager, C; Pompos, A; Pondrom, L; Pope, G; Portell, X; Poukhov, O; Prakoshyn, F; Pratt, T; Pronko, A; Proudfoot, J; Ptohos, F; Punzi, G; Rademachker, J; Rahaman, M A; Rakitine, A; Rappoccio, S; Ratnikov, F; Ray, H; Reisert, B; Rekovic, V; Renton, P; Rescigno, M; Rimondi, F; Rinnert, K; Ristori, L; Robertson, W J; Robson, A; Rodrigo, T; Rolli, S; Rosenson, L; Roser, R; Rossin, R; Rott, C; Russ, J; Rusu, V; Ruiz, A; Ryan, D; Saarikko, H; Sabik, S; Safonov, A; St Denis, R; Sakumoto, W K; Salamanna, G; Saltzberg, D; Sanchez, C; Sansoni, A; Santi, L; Sarkar, S; Sato, K; Savard, P; Savoy-Navarro, A; Schlabach, P; Schmidt, E E; Schmidt, M P; Schmitt, M; Scodellaro, L; Scribano, A; Scuri, F; Sedov, A; Seidel, S; Seiya, Y; Semeria, F; Sexton-Kennedy, L; Sfiligoi, I; Shapiro, M D; Shears, T; Shepard, P F; Sherman, D; Shimojima, M; Shochet, M; Shon, Y; Shreyber, I; Sidoti, A; Siegrist, J; Siket, M; Sill, A; Sinervo, P; Sisakyan, A; Skiba, A; Slaughter, A J; Sliwa, K; Smirnov, D; Smith, J R; Snider, F D; Snihur, R; Soha, A; Somalwar, S V; Spalding, J; Spezziga, M; Spiegel, L; Spinella, F; Spiropulu, M; Squillacioti, P; Stadie, H; Stelzer, B; Stelzer-Chilton, O; Strologas, J; Stuart, D; Sukhanov, A; Sumorok, K; Sun, H; Suzuki, T; Taffard, A; Tafirout, R; Takach, S F; Takano, H; Takashima, R; Takeuchi, Y; Takikawa, K; Tanaka, M; Tanaka, R; Tanimoto, N; Tapprogge, S; Tecchio, M; Teng, P K; Terashi, K; Tesarek, R J; Tether, S; Thom, J; Thompson, A S; Thomson, E; Tipton, P; Tiwari, V; Trkaczyk, S; Toback, D; Tollefson, K; Tomura, T; Tonelli, D; Tönnesmann, M; Torre, S; Torretta, D; Tourneur, S; Trischuk, W; Tseng, J; Tsuchiya, R; Tsuno, S; Tsybychev, D; Turini, N; Turner, M; Ukegawa, F; Unverhau, T; Uozumi, S; Usynin, D; Vacavant, L; Vaiciulis, A; Varganov, A; Vataga, E; Vejcik, S; Velev, G; Veszpremi, V; Veramendi, G; Vickey, T; Vidal, R; Vila, I; Vilar, R; Vollrath, I; Volobouev, I; von der Mey, M; Wagner, P; Wagner, R G; Wagner, R L; Wagner, W; Wallny, R; Walter, T; Yamashita, T; Yamamoto, K; Wan, Z; Wang, M J; Wang, S M; Warburton, A; Ward, B; Waschke, S; Waters, D; Watts, T; Weber, M; Wester, W C; Whitehouse, B; Wicklund, A B; Wicklund, E; Williams, H H; Wilson, P; Winer, B L; Wittich, P; Wolbers, S; Wolter, M; Worcester, M; Worm, S; Wright, T; Wu, X; Würthwein, F; Wyatt, A; Yagil, A; Yang, C; Yang, U K; Yao, W; Yeh, G P; Yi, K; Yoh, J; Yoon, P; Yorita, K; Yoshida, T; Yu, I; Yu, S; Yu, Z; Yun, J C; Zanello, L; Zanetti, A; Zaw, I; Zetti, F; Zhou, J; Zsenei, A; Zucchelli, S

2005-07-08

We report on a search for anomalous kinematics of tt dilepton events in pp collisions at square root of s=1.96 TeV using 193 pb(-1) of data collected with the CDF II detector. We developed a new a priori technique designed to isolate the subset in a data sample revealing the largest deviation from standard model (SM) expectations and to quantify the significance of this departure. In the four-variable space considered, no particular subset shows a significant discrepancy, and we find that the probability of obtaining a data sample less consistent with the SM than what is observed is 1.0%-4.5%.

User's manual for the National Water-Quality Assessment Program Invertebrate Data Analysis System (IDAS) software, version 5

USGS Publications Warehouse

Cuffney, Thomas F.; Brightbill, Robin A.

2011-01-01

The Invertebrate Data Analysis System (IDAS) software was developed to provide an accurate, consistent, and efficient mechanism for analyzing invertebrate data collected as part of the U.S. Geological Survey National Water-Quality Assessment (NAWQA) Program. The IDAS software is a stand-alone program for personal computers that run Microsoft Windows(Registered). It allows users to read data downloaded from the NAWQA Program Biological Transactional Database (Bio-TDB) or to import data from other sources either as Microsoft Excel(Registered) or Microsoft Access(Registered) files. The program consists of five modules: Edit Data, Data Preparation, Calculate Community Metrics, Calculate Diversities and Similarities, and Data Export. The Edit Data module allows the user to subset data on the basis of taxonomy or sample type, extract a random subsample of data, combine or delete data, summarize distributions, resolve ambiguous taxa (see glossary) and conditional/provisional taxa, import non-NAWQA data, and maintain and create files of invertebrate attributes that are used in the calculation of invertebrate metrics. The Data Preparation module allows the user to select the type(s) of sample(s) to process, calculate densities, delete taxa on the basis of laboratory processing notes, delete pupae or terrestrial adults, combine lifestages or keep them separate, select a lowest taxonomic level for analysis, delete rare taxa on the basis of the number of sites where a taxon occurs and (or) the abundance of a taxon in a sample, and resolve taxonomic ambiguities by one of four methods. The Calculate Community Metrics module allows the user to calculate 184 community metrics, including metrics based on organism tolerances, functional feeding groups, and behavior. The Calculate Diversities and Similarities module allows the user to calculate nine diversity and eight similarity indices. The Data Export module allows the user to export data to other software packages (CANOCO, Primer, PC-ORD, MVSP) and produce tables of community data that can be imported into spreadsheet, database, graphics, statistics, and word-processing programs. The IDAS program facilitates the documentation of analyses by keeping a log of the data that are processed, the files that are generated, and the program settings used to process the data. Though the IDAS program was developed to process NAWQA Program invertebrate data downloaded from Bio-TDB, the Edit Data module includes tools that can be used to convert non-NAWQA data into Bio-TDB format. Consequently, the data manipulation, analysis, and export procedures provided by the IDAS program can be used to process data generated outside of the NAWQA Program.

Characterization of tumor-associated T-lymphocyte subsets and immune checkpoint molecules in head and neck squamous cell carcinoma

PubMed Central

Thelen, Martin; Reuter, Sabrina; Zentis, Peter; Shimabukuro-Vornhagen, Alexander; Theurich, Sebastian; Wennhold, Kerstin; Garcia-Marquez, Maria; Tharun, Lars; Quaas, Alexander; Schauss, Astrid; Isensee, Jörg; Hucho, Tim; Huebbers, Christian

2017-01-01

The composition of tumor-infiltrating lymphocytes (TIL) reflects biology and immunogenicity of cancer. Here, we characterize T-cell subsets and expression of immune checkpoint molecules in head and neck squamous cell carcinoma (HNSCC). We analyzed TIL subsets in primary tumors (n = 34), blood (peripheral blood mononuclear cells (PBMC); n = 34) and non-cancerous mucosa (n = 7) of 34 treatment-naïve HNSCC patients and PBMC of 15 healthy controls. Flow cytometry analyses revealed a highly variable T-cell infiltration mainly of an effector memory phenotype (CD45RA−/CCR7−). Naïve T cells (CD45RA+/CCR7+) were decreased in the microenvironment compared to PBMC of patients, while regulatory T cells (CD4+/CD25+/CD127low and CD4+/CD39+) were elevated. Furthermore, we performed digital image analyses of entire cross sections of HNSCC to define the ‘Immunoscore’ (CD3+ and CD8+ cell infiltration in tumor core and invasive margin) and quantified MHC class I expression on tumor cells by immunohistochemistry. Immune checkpoint molecules cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4), programmed cell death 1 (PD-1) and programmed cell death 1 ligand 1 (PD-L1) were increased in TILs compared to peripheral T cells in flow-cytometric analysis. Human papillomavirus (HPV) positive tumors showed higher numbers of TILs, but a similar composition of T-cell subsets and checkpoint molecule expression compared to HPV negative tumors. Taken together, the tumor microenvironment of HNSCC is characterized by a strong infiltration of regulatory T cells and high checkpoint molecule expression on T-cell subsets. In view of increasingly used immunotherapies, a detailed knowledge of TILs and checkpoint molecule expression on TILs is of high translational relevance. PMID:28574843

The Cross-Entropy Based Multi-Filter Ensemble Method for Gene Selection.

PubMed

Sun, Yingqiang; Lu, Chengbo; Li, Xiaobo

2018-05-17

The gene expression profile has the characteristics of a high dimension, low sample, and continuous type, and it is a great challenge to use gene expression profile data for the classification of tumor samples. This paper proposes a cross-entropy based multi-filter ensemble (CEMFE) method for microarray data classification. Firstly, multiple filters are used to select the microarray data in order to obtain a plurality of the pre-selected feature subsets with a different classification ability. The top N genes with the highest rank of each subset are integrated so as to form a new data set. Secondly, the cross-entropy algorithm is used to remove the redundant data in the data set. Finally, the wrapper method, which is based on forward feature selection, is used to select the best feature subset. The experimental results show that the proposed method is more efficient than other gene selection methods and that it can achieve a higher classification accuracy under fewer characteristic genes.

Selection-Fusion Approach for Classification of Datasets with Missing Values

PubMed Central

Ghannad-Rezaie, Mostafa; Soltanian-Zadeh, Hamid; Ying, Hao; Dong, Ming

2010-01-01

This paper proposes a new approach based on missing value pattern discovery for classifying incomplete data. This approach is particularly designed for classification of datasets with a small number of samples and a high percentage of missing values where available missing value treatment approaches do not usually work well. Based on the pattern of the missing values, the proposed approach finds subsets of samples for which most of the features are available and trains a classifier for each subset. Then, it combines the outputs of the classifiers. Subset selection is translated into a clustering problem, allowing derivation of a mathematical framework for it. A trade off is established between the computational complexity (number of subsets) and the accuracy of the overall classifier. To deal with this trade off, a numerical criterion is proposed for the prediction of the overall performance. The proposed method is applied to seven datasets from the popular University of California, Irvine data mining archive and an epilepsy dataset from Henry Ford Hospital, Detroit, Michigan (total of eight datasets). Experimental results show that classification accuracy of the proposed method is superior to those of the widely used multiple imputations method and four other methods. They also show that the level of superiority depends on the pattern and percentage of missing values. PMID:20212921

Colonization and effector functions of innate lymphoid cells in mucosal tissues

PubMed Central

Kim, Myunghoo; Kim, Chang H.

2016-01-01

Innate lymphoid cells (ILCs) protect mucosal barrier tissues to fight infection and maintain tissue integrity. ILCs and their progenitors are developmentally programmed to migrate, differentiate and populate various mucosal tissues and associated lymphoid tissues. Functionally mature ILC subsets respond to diverse pathogens such as bacteria, viruses, fungi and parasites in subset-specific manners. In this review, we will discuss how ILCs populate mucosal tissues and regulate immune responses to distinct pathogens to protect the host and maintain tissue integrity. PMID:27365193

Accuracy of national key performance indicator reporting from two Aboriginal medical services: potential to underestimate the performance of primary health care.

PubMed

2017-05-09

Objective The aim of the present study was to assess the accuracy of extracting national key performance indicator (nKPI) data for the Online Community Health Reporting Environment for Health Services (OCHREStreams) program using the Pen Computer Systems (Leichhardt, NSW, Australia) Clinical Audit Tool (CAT) from Communicare (Telstra Health Communicare Systems, Perth, WA, Australia), a commonly used patient information management system (PIMS) in Aboriginal primary care. Methods Two Aboriginal Community-Controlled Health Services (ACCHSs) were recruited to the present study. A sample of regular clients aged ≥55 years from each ACCHS was selected and a subset of 13 nKPIs was examined. A manual case note audit of the nKPI subset within Communicare was undertaken by a clinician at each participating ACCHS and acted as a 'gold standard' comparator for three query methods: (1) internal Communicare nKPI reports; (2) PenCS CAT nKPI manual filtering (a third-party data-extraction tool); and (3) nKPI data submitted to the Improvement Foundation qiConnect portal. Results No errors were found in nKPI data extraction from Communicare using the CAT and subsequent submission to the qiConnect portal. However, the Communicare internal nKPI report included deceased clients and past patients, and we can be very confident that deceased clients and past patients are also included in the qiConnect portal data. This resulted in inflation of client denominators and an underestimation of health service performance, particularly for nKPIs recording activity in the past 6 months. Several minor errors were also detected in Communicare internal nKPI reports. Conclusions CAT accurately extracts a subset of nKPI data from Communicare. However, given the widespread use of Communicare in ACCHSs, the inclusion of deceased clients and past patients in the OCHREStreams nKPI data program is likely to have resulted in systematic under-reporting of health service performance nationally. What is known about the topic? There has been limited validation of health data exported via data-extraction tools in Australia. More specifically, there are no current published data describing the accuracy of the CAT in mapping health data extracted from Communicare or the accuracy of internal nKPI reports generated by Communicare. Further, no systematic review has been undertaken to assess the accuracy of the nKPI data submission pathway from PIMSs at the health service level to the OCHREStreams qiConnect portal using the CAT. What does this paper add? The CAT accurately extracts a subset of nKPI data from Communicare and accurately submits this to the qiConnect portal. Minor errors exist in some Communicare internal nKPI reports. The inclusion of deceased clients and past patients in the nKPI reporting system for ACCHSs is likely to have resulted in systematic under-reporting of health service performance nationally through this program. What are the implications for practitioners? The inclusion of deceased clients and past patients in the OCHREStreams nKPI program limits the usefulness of these data for local quality improvement activities and national monitoring of health service performance for participating ACCHSs. The use of the CAT by ACCHSs independently from the OCHREStreams program can enable deceased clients and past patients to be excluded from reports that can provide more accurate nKPI data from Communicare for local quality improvement and planning purposes.

Effector CD8 T cells dedifferentiate into long-lived memory cells.

PubMed

Youngblood, Ben; Hale, J Scott; Kissick, Haydn T; Ahn, Eunseon; Xu, Xiaojin; Wieland, Andreas; Araki, Koichi; West, Erin E; Ghoneim, Hazem E; Fan, Yiping; Dogra, Pranay; Davis, Carl W; Konieczny, Bogumila T; Antia, Rustom; Cheng, Xiaodong; Ahmed, Rafi

2017-12-21

Memory CD8 T cells that circulate in the blood and are present in lymphoid organs are an essential component of long-lived T cell immunity. These memory CD8 T cells remain poised to rapidly elaborate effector functions upon re-exposure to pathogens, but also have many properties in common with naive cells, including pluripotency and the ability to migrate to the lymph nodes and spleen. Thus, memory cells embody features of both naive and effector cells, fuelling a long-standing debate centred on whether memory T cells develop from effector cells or directly from naive cells. Here we show that long-lived memory CD8 T cells are derived from a subset of effector T cells through a process of dedifferentiation. To assess the developmental origin of memory CD8 T cells, we investigated changes in DNA methylation programming at naive and effector cell-associated genes in virus-specific CD8 T cells during acute lymphocytic choriomeningitis virus infection in mice. Methylation profiling of terminal effector versus memory-precursor CD8 T cell subsets showed that, rather than retaining a naive epigenetic state, the subset of cells that gives rise to memory cells acquired de novo DNA methylation programs at naive-associated genes and became demethylated at the loci of classically defined effector molecules. Conditional deletion of the de novo methyltransferase Dnmt3a at an early stage of effector differentiation resulted in reduced methylation and faster re-expression of naive-associated genes, thereby accelerating the development of memory cells. Longitudinal phenotypic and epigenetic characterization of the memory-precursor effector subset of virus-specific CD8 T cells transferred into antigen-free mice revealed that differentiation to memory cells was coupled to erasure of de novo methylation programs and re-expression of naive-associated genes. Thus, epigenetic repression of naive-associated genes in effector CD8 T cells can be reversed in cells that develop into long-lived memory CD8 T cells while key effector genes remain demethylated, demonstrating that memory T cells arise from a subset of fate-permissive effector T cells.

Integrated Task and Data Parallel Programming

NASA Technical Reports Server (NTRS)

Grimshaw, A. S.

1998-01-01

This research investigates the combination of task and data parallel language constructs within a single programming language. There are an number of applications that exhibit properties which would be well served by such an integrated language. Examples include global climate models, aircraft design problems, and multidisciplinary design optimization problems. Our approach incorporates data parallel language constructs into an existing, object oriented, task parallel language. The language will support creation and manipulation of parallel classes and objects of both types (task parallel and data parallel). Ultimately, the language will allow data parallel and task parallel classes to be used either as building blocks or managers of parallel objects of either type, thus allowing the development of single and multi-paradigm parallel applications. 1995 Research Accomplishments In February I presented a paper at Frontiers 1995 describing the design of the data parallel language subset. During the spring I wrote and defended my dissertation proposal. Since that time I have developed a runtime model for the language subset. I have begun implementing the model and hand-coding simple examples which demonstrate the language subset. I have identified an astrophysical fluid flow application which will validate the data parallel language subset. 1996 Research Agenda Milestones for the coming year include implementing a significant portion of the data parallel language subset over the Legion system. Using simple hand-coded methods, I plan to demonstrate (1) concurrent task and data parallel objects and (2) task parallel objects managing both task and data parallel objects. My next steps will focus on constructing a compiler and implementing the fluid flow application with the language. Concurrently, I will conduct a search for a real-world application exhibiting both task and data parallelism within the same program. Additional 1995 Activities During the fall I collaborated with Andrew Grimshaw and Adam Ferrari to write a book chapter which will be included in Parallel Processing in C++ edited by Gregory Wilson. I also finished two courses, Compilers and Advanced Compilers, in 1995. These courses complete my class requirements at the University of Virginia. I have only my dissertation research and defense to complete.

Integrated Task And Data Parallel Programming: Language Design

NASA Technical Reports Server (NTRS)

Grimshaw, Andrew S.; West, Emily A.

1998-01-01

his research investigates the combination of task and data parallel language constructs within a single programming language. There are an number of applications that exhibit properties which would be well served by such an integrated language. Examples include global climate models, aircraft design problems, and multidisciplinary design optimization problems. Our approach incorporates data parallel language constructs into an existing, object oriented, task parallel language. The language will support creation and manipulation of parallel classes and objects of both types (task parallel and data parallel). Ultimately, the language will allow data parallel and task parallel classes to be used either as building blocks or managers of parallel objects of either type, thus allowing the development of single and multi-paradigm parallel applications. 1995 Research Accomplishments In February I presented a paper at Frontiers '95 describing the design of the data parallel language subset. During the spring I wrote and defended my dissertation proposal. Since that time I have developed a runtime model for the language subset. I have begun implementing the model and hand-coding simple examples which demonstrate the language subset. I have identified an astrophysical fluid flow application which will validate the data parallel language subset. 1996 Research Agenda Milestones for the coming year include implementing a significant portion of the data parallel language subset over the Legion system. Using simple hand-coded methods, I plan to demonstrate (1) concurrent task and data parallel objects and (2) task parallel objects managing both task and data parallel objects. My next steps will focus on constructing a compiler and implementing the fluid flow application with the language. Concurrently, I will conduct a search for a real-world application exhibiting both task and data parallelism within the same program m. Additional 1995 Activities During the fall I collaborated with Andrew Grimshaw and Adam Ferrari to write a book chapter which will be included in Parallel Processing in C++ edited by Gregory Wilson. I also finished two courses, Compilers and Advanced Compilers, in 1995. These courses complete my class requirements at the University of Virginia. I have only my dissertation research and defense to complete.

The Efficacy of Machine Learning Programs for Navy Manpower Analysis

DTIC Science & Technology

1993-03-01

This thesis investigated the efficacy of two machine learning programs for Navy manpower analysis. Two machine learning programs, AIM and IXL, were...to generate models from the two commercial machine learning programs. Using a held out sub-set of the data the capabilities of the three models were...partial effects. The author recommended further investigation of AIM’s capabilities, and testing in an operational environment.... Machine learning , AIM, IXL.

Lessons learned: a pilot study on occupational therapy effectiveness for children with sensory modulation disorder.

PubMed

Miller, Lucy Jane; Schoen, Sarah A; James, Katherine; Schaaf, Roseann C

2007-01-01

The purpose of this pilot study was to prepare for a randomized controlled study of the effectiveness of occupational therapy using a sensory integration approach (OT-SI) with children who have sensory processing disorders (SPD). A one-group pretest, posttest design with 30 children was completed with a subset of children with SPD, those with sensory modulation disorder. Lessons learned relate to (a) identifying a homogeneous sample with quantifiable inclusion criteria, (b) developing an intervention manual for study replication and a fidelity to treatment measure, (c) determining which outcomes are sensitive to change and relate to parents' priorities, and (d) clarifying rigorous methodologies (e.g., blinded examiners, randomization, power). A comprehensive program of research is needed, including multiple pilot studies to develop enough knowledge that high-quality effectiveness research in occupational therapy can be completed. Previous effectiveness studies in OT-SI have been single projects not based on a unified long-term program of research.

DOE Office of Scientific and Technical Information (OSTI.GOV)

SEDLACEK,III, A.J.FINFROCK,C.

As a member of the science-support part of the ITT-lead LISA development program, BNL is tasked with the acquisition of UV Raman spectral fingerprints and associated scattering cross-sections for those chemicals-of-interest to the program's sponsor. In support of this role, the present report contains the first installment of UV Raman spectral fingerprint data on the initial subset of chemicals. Because of the unique nature associated with the acquisition of spectral fingerprints for use in spectral pattern matching algorithms (i.e., CLS, PLS, ANN) great care has been undertaken to maximize the signal-to-noise and to minimize unnecessary spectral subtractions, in an effortmore » to provide the highest quality spectral fingerprints. This report is divided into 4 sections. The first is an Experimental section that outlines how the Raman spectra are performed. This is then followed by a section on Sample Handling. Following this, the spectral fingerprints are presented in the Results section where the data reduction process is outlined. Finally, a Photographs section is included.« less

Biogeography and Metabolic Potential of Soil Microbial Communities Across Local Environmental Gradients Illuminated Through Metagenomics

NASA Astrophysics Data System (ADS)

Sharrar, A.; Diamond, S.; Butterfield, C.; Starr, E.; Thomas, B. C.; Banfield, J. F.

2016-12-01

Soils are extremely heterogeneous and diverse microbial habitats. The distribution of microbes and their metabolic functions in soil is important for carbon and nitrogen cycling and overall ecosystem functioning. Little is known about biogeographical patterns of microbes in soil and how they relate to different environmental gradients. To address this topic, we have obtained metagenomes from 86 soil samples taken at the Eel River Critical Zone Observatory and a nearby meadow in the northern California Angelo Coast Range Reserve over a period of two years. These samples span a variety of environmental parameters, including depth, relief, time since last rainfall, and proximity to root carbon inputs. Phylogenetic diversity and community overlap between these samples was analyzed using ribosomal protein sequence identity and scaffold coverage. Independent of genomic bins, de-replicated ribosomal protein sequences were used to identify thousands of unique organisms between datasets. Despite environmental differences, a subset of these organisms were found in every sample. The dominant phyla in this cosmopolitan subset were Proteobacteria, Actinobacteria, Gemmatimonadetes, Verrucomicrobia, Acidobacteria, and Rokubacteria. Archaea and Nitrospirae were particularly prevalent at depths below 30cm. Patterns of ribosomal protein scaffold coverage across samples was used to compare the similarity of the microbial communities. We found that location was the greatest predictor of community similarity, followed by depth. In a subset of 60 samples taken in the same meadow, sampling plot was a greater predictor of community similarity than time since last rainfall in the same year. In addition, genome-independent analyses revealed differences in the metabolic potential for functions involved in nitrogen and carbon metabolism across environmental gradients. This study will further our understanding of soil biogeography and its relationship to overall biogeochemical cycling.

Design of focused and restrained subsets from extremely large virtual libraries.

PubMed

Jamois, Eric A; Lin, Chien T; Waldman, Marvin

2003-11-01

With the current and ever-growing offering of reagents along with the vast palette of organic reactions, virtual libraries accessible to combinatorial chemists can reach sizes of billions of compounds or more. Extracting practical size subsets for experimentation has remained an essential step in the design of combinatorial libraries. A typical approach to computational library design involves enumeration of structures and properties for the entire virtual library, which may be unpractical for such large libraries. This study describes a new approach termed as on the fly optimization (OTFO) where descriptors are computed as needed within the subset optimization cycle and without intermediate enumeration of structures. Results reported herein highlight the advantages of coupling an ultra-fast descriptor calculation engine to subset optimization capabilities. We also show that enumeration of properties for the entire virtual library may not only be unpractical but also wasteful. Successful design of focused and restrained subsets can be achieved while sampling only a small fraction of the virtual library. We also investigate the stability of the method and compare results obtained from simulated annealing (SA) and genetic algorithms (GA).

Impact of Maltreatment on Children Served in Community Mental Health Programs

ERIC Educational Resources Information Center

Walrath, Christine M.; Ybarra, Michele L.; Sheehan, Angela K.; Holden, E. Wayne; Burns, Barbara J.

2006-01-01

Despite a decline in the incidence of child abuse over the last decade, victimization rates remain troubling. This study used a subset of data from the national evaluation of the Comprehensive Community Mental Health Services for Children and Their Families Program to investigate and compare the demographic, psychosocial, and service use…

Clinical Psychology Ph.D. Program Rankings: Evaluating Eminence on Faculty Publications and Citations

ERIC Educational Resources Information Center

Matson, Johnny L.; Malone, Carrie J.; Gonzalez, Melissa L.; McClure, David R.; Laud, Rinita B.; Minshawi, Noha F.

2005-01-01

Program rankings and their visibility have taken on greater and greater significance. Rarely is the accuracy of these rankings, which are typically based on a small subset of university faculty impressions, questioned. This paper presents a more comprehensive survey method based on quantifiable measures of faculty publications and citations. The…

Training for International Development: A Summary of Faculty and Foreign Student Interviews.

ERIC Educational Resources Information Center

Wallace, George; And Others

To determine a basic design for training Colorado State University (CSU) faculty for assignment to international development programs, a written questionnaire and oral interview were administered to faculty with experience in international programs in Africa, the Middle East, and Latin America. A subset of 10 selected from each geographical…

Seismic Characterizations of Fractures: Dynamic Diagnostics

NASA Astrophysics Data System (ADS)

Pyrak-Nolte, L. J.

2017-12-01

Fracture geometry controls fluid flow in a fracture, affects mechanical stability and influences energy partitioning that affects wave scattering. Our ability to detect and monitor fracture evolution is controlled by the frequency of the signal used to probe a fracture system, i.e. frequency selects the scales. No matter the frequency chosen, some set of discontinuities will be optimal for detection because different wavelengths sample different subsets of fractures. The select subset of fractures is based on the stiffness of the fractures which in turn is linked to fluid flow. A goal is obtaining information from scales outside the optimal detection regime. Fracture geometry trajectories are a potential approach to drive a fracture system across observation scales, i.e. moving systems between effective medium and scattering regimes. Dynamic trajectories (such as perturbing stress, fluid pressure, chemical alteration, etc.) can be used to perturb fracture geometry to enhance scattering or give rise to discrete modes that are intimately related to the micro-structural evolution of a fracture. However, identification of these signal features will require methods for identifying these micro-structural signatures in complicated scattered fields. Acknowledgment: This material is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Geosciences Research Program under Award Number (DE-FG02-09ER16022).

Feature Sampling in Detection: Implications for the Measurement of Perceptual Independence

ERIC Educational Resources Information Center

Macho, Siegfried

2007-01-01

The article presents the feature sampling signal detection (FS-SDT) model, an extension of the multivariate signal detection (SDT) model. The FS-SDT model assumes that, because of attentional shifts, different subsets of features are sampled for different presentations of the same multidimensional stimulus. Contrary to the SDT model, the FS-SDT…

Beach seine data from near Britannia mines and in Howe Sound, British Columbia, during 1997. Canadian data report of fisheries and aquatic sciences number 1044

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grout, J.A.

As part of a study to explore the impacts of acid mine drainage from the Britannia Mine, a beach seine sampling program was initiated on Howe Sound to assess the species composition, abundance, and distribution of the near-shore fish community. Sampling was carried out in April 1997 at 23 sites on the east and west shores of the sound to attempt to differentiate between the fish communities using foreshore areas near Britannia Beach, which may be impacted by acid mine drainage, and fish communities in more distant areas thought to be less affected by mine pollution. Data are presented formore » the 13,882 individuals from 18 families and 39 species of fish, and stomach content data are also presented for a subset of the juvenile salmonids caught at Britannia Beach and Furry Creek. In addition, physical oceanographic data for each site are included.« less

There is a need for new systemic sclerosis subset criteria. A content analytic approach.

PubMed

Johnson, S R; Soowamber, M L; Fransen, J; Khanna, D; Van Den Hoogen, F; Baron, M; Matucci-Cerinic, M; Denton, C P; Medsger, T A; Carreira, P E; Riemekasten, G; Distler, J; Gabrielli, A; Steen, V; Chung, L; Silver, R; Varga, J; Müller-Ladner, U; Vonk, M C; Walker, U A; Wollheim, F A; Herrick, A; Furst, D E; Czirjak, L; Kowal-Bielecka, O; Del Galdo, F; Cutolo, M; Hunzelmann, N; Murray, C D; Foeldvari, I; Mouthon, L; Damjanov, N; Kahaleh, B; Frech, T; Assassi, S; Saketkoo, L A; Pope, J E

2018-01-01

Systemic sclerosis (SSc) is heterogenous. The objectives of this study were to evaluate the purpose, strengths and limitations of existing SSc subset criteria, and identify ideas among experts about subsets. We conducted semi-structured interviews with randomly sampled international SSc experts. The interview transcripts underwent an iterative process with text deconstructed to single thought units until a saturated conceptual framework with coding was achieved and respondent occurrence tabulated. Serial cross-referential analyses of clusters were developed. Thirty experts from 13 countries were included; 67% were male, 63% were from Europe and 37% from North America; median experience of 22.5 years, with a median of 55 new SSc patients annually. Three thematic clusters regarding subsetting were identified: research and communication; management; and prognosis (prediction of internal organ involvement, survival). The strength of the limited/diffuse system was its ease of use, however 10% stated this system had marginal value. Shortcomings of the diffuse/limited classification were the risk of misclassification, predictions/generalizations did not always hold true, and that the elbow or knee threshold was arbitrary. Eighty-seven percent use more than 2 subsets including: SSc sine scleroderma, overlap conditions, antibody-determined subsets, speed of progression, and age of onset (juvenile, elderly). We have synthesized an international view of the construct of SSc subsets in the modern era. We found a number of factors underlying the construct of SSc subsets. Considerations for the next phase include rate of change and hierarchal clustering (e.g. limited/diffuse, then by antibodies).

Use of internal control T-cell populations in the flow cytometric evaluation for T-cell neoplasms.

PubMed

Hunt, Alicia M; Shallenberger, Wendy; Ten Eyck, Stephen P; Craig, Fiona E

2016-09-01

Flow cytometry is an important tool for identification of neoplastic T-cells, but immunophenotypic abnormalities are often subtle and must be distinguished from nonneoplastic subsets. Use of internal control (IC) T-cells in the evaluation for T-cell neoplasms was explored, both as a quality measure and as a reference for evaluating abnormal antigen expression. All peripheral blood specimens (3-month period), or those containing abnormal T-cells (29-month period), stained with CD45 V500, CD2 V450, CD3 PE-Cy7, CD7 PE, CD4 Per-CP-Cy5.5, CD8 APC-H7, CD56 APC, CD16&57 FITC, were evaluated. IC T-cells were identified (DIVA, BD Biosciences) and median fluorescence intensity (MFI) recorded. Selected files were merged and reference templates generated (Infinicyt, Cytognos). IC T-cells were present in all specimens, including those with abnormal T-cells, but subsets were less well-represented. IC T-cell CD3 MFI differed between instruments (p = 0.0007) and subsets (p < 0.001), but not specimen categories, and served as a longitudinal process control. Merged files highlighted small unusual IC-T subsets: CD2+(dim) (0.25% total), CD2- (0.03% total). An IC reference template highlighted neoplastic T-cells, but was limited by staining variability (IC CD3 MFI reference samples different from test (p = 0.003)). IC T-cells present in the majority of specimens can serve as positive and longitudinal process controls. Use of IC T-cells as an internal reference is limited by variable representation of subsets. Analysis of merged IC T-cells from previously analyzed patient samples can alert the interpreter to less-well-recognized non-neoplastic subsets. However, application of a merged file IC reference template was limited by staining variability. © 2016 Clinical Cytometry Society. © 2016 International Clinical Cytometry Society.

Ordered-subsets linkage analysis detects novel Alzheimer disease loci on chromosomes 2q34 and 15q22.

PubMed

Scott, William K; Hauser, Elizabeth R; Schmechel, Donald E; Welsh-Bohmer, Kathleen A; Small, Gary W; Roses, Allen D; Saunders, Ann M; Gilbert, John R; Vance, Jeffery M; Haines, Jonathan L; Pericak-Vance, Margaret A

2003-11-01

Alzheimer disease (AD) is a complex disorder characterized by a wide range, within and between families, of ages at onset of symptoms. Consideration of age at onset as a covariate in genetic-linkage studies may reduce genetic heterogeneity and increase statistical power. Ordered-subsets analysis includes continuous covariates in linkage analysis by rank ordering families by a covariate and summing LOD scores to find a subset giving a significantly increased LOD score relative to the overall sample. We have analyzed data from 336 markers in 437 multiplex (>/=2 sampled individuals with AD) families included in a recent genomic screen for AD loci. To identify genetic heterogeneity by age at onset, families were ordered by increasing and decreasing mean and minimum ages at onset. Chromosomewide significance of increases in the LOD score in subsets relative to the overall sample was assessed by permutation. A statistically significant increase in the nonparametric multipoint LOD score was observed on chromosome 2q34, with a peak LOD score of 3.2 at D2S2944 (P=.008) in 31 families with a minimum age at onset between 50 and 60 years. The LOD score in the chromosome 9p region previously linked to AD increased to 4.6 at D9S741 (P=.01) in 334 families with minimum age at onset between 60 and 75 years. LOD scores were also significantly increased on chromosome 15q22: a peak LOD score of 2.8 (P=.0004) was detected at D15S1507 (60 cM) in 38 families with minimum age at onset >/=79 years, and a peak LOD score of 3.1 (P=.0006) was obtained at D15S153 (62 cM) in 43 families with mean age at onset >80 years. Thirty-one families were contained in both 15q22 subsets, indicating that these results are likely detecting the same locus. There is little overlap in these subsets, underscoring the utility of age at onset as a marker of genetic heterogeneity. These results indicate that linkage to chromosome 9p is strongest in late-onset AD and that regions on chromosome 2q34 and 15q22 are linked to early-onset AD and very-late-onset AD, respectively.

Promoter classifier: software package for promoter database analysis.

PubMed

Gershenzon, Naum I; Ioshikhes, Ilya P

2005-01-01

Promoter Classifier is a package of seven stand-alone Windows-based C++ programs allowing the following basic manipulations with a set of promoter sequences: (i) calculation of positional distributions of nucleotides averaged over all promoters of the dataset; (ii) calculation of the averaged occurrence frequencies of the transcription factor binding sites and their combinations; (iii) division of the dataset into subsets of sequences containing or lacking certain promoter elements or combinations; (iv) extraction of the promoter subsets containing or lacking CpG islands around the transcription start site; and (v) calculation of spatial distributions of the promoter DNA stacking energy and bending stiffness. All programs have a user-friendly interface and provide the results in a convenient graphical form. The Promoter Classifier package is an effective tool for various basic manipulations with eukaryotic promoter sequences that usually are necessary for analysis of large promoter datasets. The program Promoter Divider is described in more detail as a representative component of the package.

Characterizing the bioactivity of complex environmental ...

EPA Pesticide Factsheets

Bioassays can be employed to evaluate the integrated effects of complex mixtures of both known and unidentified contaminants present in environmental samples. However, such methods have typically focused on one or a few bioactivities despite the fact that the chemicals in a mixture may exhibit a wide range of activities. High throughput toxicology approaches that can rapidly screen samples for a broad diversity of biological activities offer a means to provide a more comprehensive characterization. To test this concept, twenty-four ambient water samples were collected, extracted, and screened for their ability to interact with or modulate over 80 different transcription factors using the Attagene subset of assays utilized by the US EPA’s ToxCast Program. Samples evaluated included water collected at five sites along a spatial gradient centered around a wastewater discharge into the Maumee River, Ohio, USA; 10 samples were collected in varying proximity to a wastewater discharge within the St. Louis River Area of Concern (AOC), MN; and eight samples were associated with a nation-wide US Geological Survey Mixture Study. Samples collected along the Maumee River showed a gradient response in the number of observed activities, ranging from three positive assay responses observed far upstream of discharge to seven positive responses in water from the mixing zone. TGFb signaling and the aryl hydrocarbon receptor (AhR) activation were the biological activities obser

SERDP and ESTCP Expert Panel Workshop on Research and Development Needs for the Environmental Remediation Application of Molecular Biological Tools

DTIC Science & Technology

2005-10-01

used to infer metabolic rates in marine systems. For example, there is evidence from both pure cultures and environmental samples that rbcL...It includes many useful bioinformatics features such as constructing a neighbor-joining tree for a subset of sequences, downloading a subset of...further provide software that allow users to extract useful information from sequences. The most commonly used feature is probe/primer design

Developing an Assessment Process for a Master's of Science Degree in a Pharmaceutical Sciences Program.

PubMed

Bloom, Timothy J; Hall, Julie M; Liu, Qinfeng; Stagner, William C; Adams, Michael L

2016-09-25

Objective. To develop a program-level assessment process for a master's of science degree in a pharmaceutical sciences (MSPS) program. Design. Program-level goals were created and mapped to course learning objectives. Embedded assessment tools were created by each course director and used to gather information related to program-level goals. Initial assessment iterations involved a subset of offered courses, and course directors met with the department assessment committee to review the quality of the assessment tools as well as the data collected with them. Insights from these discussions were used to improve the process. When all courses were used for collecting program-level assessment data, a modified system of guided reflection was used to reduce demands on committee members. Assessment. The first two iterations of collecting program-level assessment revealed problems with both the assessment tools and the program goals themselves. Course directors were inconsistent in the Bloom's Taxonomy level at which they assessed student achievement of program goals. Moreover, inappropriate mapping of program goals to course learning objectives were identified. These issues led to unreliable measures of how well students were doing with regard to program-level goals. Peer discussions between course directors and the assessment committee led to modification of program goals as well as improved assessment data collection tools. Conclusion. By starting with a subset of courses and using course-embedded assessment tools, a program-level assessment process was created with little difficulty. Involving all faculty members and avoiding comparisons between courses made obtaining faculty buy-in easier. Peer discussion often resulted in consensus on how to improve assessment tools.

A Simple Application of Compressed Sensing to Further Accelerate Partially Parallel Imaging

PubMed Central

Miao, Jun; Guo, Weihong; Narayan, Sreenath; Wilson, David L.

2012-01-01

Compressed Sensing (CS) and partially parallel imaging (PPI) enable fast MR imaging by reducing the amount of k-space data required for reconstruction. Past attempts to combine these two have been limited by the incoherent sampling requirement of CS, since PPI routines typically sample on a regular (coherent) grid. Here, we developed a new method, “CS+GRAPPA,” to overcome this limitation. We decomposed sets of equidistant samples into multiple random subsets. Then, we reconstructed each subset using CS, and averaging the results to get a final CS k-space reconstruction. We used both a standard CS, and an edge and joint-sparsity guided CS reconstruction. We tested these intermediate results on both synthetic and real MR phantom data, and performed a human observer experiment to determine the effectiveness of decomposition, and to optimize the number of subsets. We then used these CS reconstructions to calibrate the GRAPPA complex coil weights. In vivo parallel MR brain and heart data sets were used. An objective image quality evaluation metric, Case-PDM, was used to quantify image quality. Coherent aliasing and noise artifacts were significantly reduced using two decompositions. More decompositions further reduced coherent aliasing and noise artifacts but introduced blurring. However, the blurring was effectively minimized using our new edge and joint-sparsity guided CS using two decompositions. Numerical results on parallel data demonstrated that the combined method greatly improved image quality as compared to standard GRAPPA, on average halving Case-PDM scores across a range of sampling rates. The proposed technique allowed the same Case-PDM scores as standard GRAPPA, using about half the number of samples. We conclude that the new method augments GRAPPA by combining it with CS, allowing CS to work even when the k-space sampling pattern is equidistant. PMID:22902065

Evaluating physical habitat and water chemistry data from statewide stream monitoring programs to establish least-impacted conditions in Washington State

USGS Publications Warehouse

Wilmoth, Siri K.; Irvine, Kathryn M.; Larson, Chad

2015-01-01

Various GIS-generated land-use predictor variables, physical habitat metrics, and water chemistry variables from 75 reference streams and 351 randomly sampled sites throughout Washington State were evaluated for effectiveness at discriminating reference from random sites within level III ecoregions. A combination of multivariate clustering and ordination techniques were used. We describe average observed conditions for a subset of predictor variables as well as proposing statistical criteria for establishing reference conditions for stream habitat in Washington. Using these criteria, we determined whether any of the random sites met expectations for reference condition and whether any of the established reference sites failed to meet expectations for reference condition. Establishing these criteria will set a benchmark from which future data will be compared.

Colonization and effector functions of innate lymphoid cells in mucosal tissues.

PubMed

Kim, Myunghoo; Kim, Chang H

2016-10-01

Innate lymphoid cells (ILCs) protect mucosal barrier tissues to fight infection and maintain tissue integrity. ILCs and their progenitors are developmentally programmed to migrate, differentiate and populate various mucosal tissues and associated lymphoid tissues. Functionally mature ILC subsets respond to diverse pathogens such as bacteria, viruses, fungi and parasites in subset-specific manners. In this review, we will discuss how ILCs populate mucosal tissues and regulate immune responses to distinct pathogens to protect the host and maintain tissue integrity. Copyright © 2016 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Inferences about nested subsets structure when not all species are detected

USGS Publications Warehouse

Cam, E.; Nichols, J.D.; Hines, J.E.; Sauer, J.R.

2000-01-01

Comparisons of species composition among ecological communities of different size have often provided evidence that the species in communities with lower species richness form nested subsets of the species in larger communities. In the vast majority of studies, the question of nested subsets has been addressed using information on presence-absence, where a '0' is interpreted as the absence of a given species from a given location. Most of the methodological discussion in earlier studies investigating nestedness concerns the approach to generation of model-based matrices. However, it is most likely that in many situations investigators cannot detect all the species present in the location sampled. The possibility that zeros in incidence matrices reflect nondetection rather than absence of species has not been considered in studies addressing nested subsets, even though the position of zeros in these matrices forms the basis of earlier inference methods. These sampling artifacts are likely to lead to erroneous conclusions about both variation over space in species richness and the degree of similarity of the various locations. Here we propose an approach to investigation of nestedness, based on statistical inference methods explicitly incorporating species detection probability, that take into account the probabilistic nature of the sampling process. We use presence-absence data collected under Pollock?s robust capture-recapture design, and resort to an estimator of species richness originally developed for closed populations to assess the proportion of species shared by different locations. We develop testable predictions corresponding to the null hypothesis of a nonnested pattern, and an alternative hypothesis of perfect nestedness. We also present an index for assessing the degree of nestedness of a system of ecological communities. We illustrate our approach using avian data from the North American Breeding Bird Survey collected in Florida Keys.

Innate lymphoid cells: a paradigm for low SSI in cleft lip repair.

PubMed

Simmerman, Erika; Qin, Xu; Marshall, Brendan; Perry, Libby; Cai, Lei; Wang, Tailing; Yu, Jack; Akbari, Omid; Baban, Babak

2016-10-01

Cleft lip and palate reconstructions demonstrate significantly lower surgical site infection rates compared with clean-contaminated cases, prompting investigation into the pathophysiology causing this discrepancy. Recent studies have identified a new group of innate lymphocytes called innate lymphoid cells (ILCs), located in barrier surfaces of the skin, airways, and intestine. Our objectives were to explore for the first time the presence of ILCs in the vermillion of neonates and young children undergoing cleft lip reconstruction and characterize their composition by measuring the three classes of ILCs. Lip tissue samples were collected from 13 subjects undergoing vermillion resection during cleft lip reconstructive surgery. Preparative, transmission electron microscopy, and analytical flow cytometry were performed. The functionality of ILCs was tested in terms of their capacity to produce type 1 (IFN-γ/TNF-α), type 2 (IL-5/IL-13), and type 3 (IL-17/IL-22) cytokines. Data were analyzed using Student t test or the analysis of variance to establish significance (P < 0.05) among groups for all other data. All three classes of ILCs were detected and visualized in the tissue samples. In all samples, the level of ILC2 subset was significantly higher than the other two ILC subsets (P < 0.01), followed by the ILC1 subset, which was present in significantly higher levels than the ILC3 subset (P < 0.05). Our data place ILCs for the first time in the interface of oral mucosal immunity, tissue microenvironment, and homeostasis during and after tissue development, possibly explaining lower infection rates in cleft lip or palate reconstructions. Copyright © 2016 Elsevier Inc. All rights reserved.

Fiscal Year 2011 Afghanistan Infrastructure Fund Projects Are Behind Schedule and Lack Adequate Sustainment Plans

DTIC Science & Technology

2012-07-30

interconnected subset ofUSATD Economic Support Fund ( ESl -") projects, which arc essential to meet program ol~jcctives. Under the program, DOS and US AID...with conunent: The congressional reporting requirements in the KDAA cover AIF funded projects, whether executed hy DoD or DOS. ESl ’-tunded projects

Heterogeneity in Neutrophil Microparticles Reveals Distinct Proteome and Functional Properties*

PubMed Central

Dalli, Jesmond; Montero-Melendez, Trinidad; Norling, Lucy V; Yin, Xiaoke; Hinds, Charles; Haskard, Dorian; Mayr, Manuel; Perretti, Mauro

2013-01-01

Altered plasma neutrophil microparticle levels have recently been implicated in a number of vascular and inflammatory diseases, yet our understanding of their actions is very limited. Herein, we investigate the proteome of neutrophil microparticles in order to shed light on their biological actions. Stimulation of human neutrophils, either in suspension or adherent to an endothelial monolayer, led to the production of microparticles containing >400 distinct proteins with only 223 being shared by the two subsets. For instance, postadherent microparticles were enriched in alpha-2 macroglobulin and ceruloplasmin, whereas microparticles produced by neutrophils in suspension were abundant in heat shock 70 kDa protein 1. Annexin A1 and lactotransferrin were expressed in both microparticle subsets. We next determined relative abundance of these proteins in three types of human microparticle samples: healthy volunteer plasma, plasma of septic patients and skin blister exudates finding that these proteins were differentially expressed on neutrophil microparticles from these samples reflecting in part the expression profiles we found in vitro. Functional assessment of the neutrophil microparticles subsets demonstrated that in response to direct stimulation neutrophil microparticles produced reactive oxygen species and leukotriene B4 as well as locomoted toward a chemotactic gradient. Finally, we investigated the actions of the two neutrophil microparticles subsets described herein on target cell responses. Microarray analysis with human primary endothelial cells incubated with either microparticle subset revealed a discrete modulation of endothelial cell gene expression profile. These findings demonstrate that neutrophil microparticles are heterogenous and can deliver packaged information propagating the activation status of the parent cell, potentially exerting novel and fundamental roles both under homeostatic and disease conditions. PMID:23660474

Efficient bootstrap estimates for tail statistics

NASA Astrophysics Data System (ADS)

Breivik, Øyvind; Aarnes, Ole Johan

2017-03-01

Bootstrap resamples can be used to investigate the tail of empirical distributions as well as return value estimates from the extremal behaviour of the sample. Specifically, the confidence intervals on return value estimates or bounds on in-sample tail statistics can be obtained using bootstrap techniques. However, non-parametric bootstrapping from the entire sample is expensive. It is shown here that it suffices to bootstrap from a small subset consisting of the highest entries in the sequence to make estimates that are essentially identical to bootstraps from the entire sample. Similarly, bootstrap estimates of confidence intervals of threshold return estimates are found to be well approximated by using a subset consisting of the highest entries. This has practical consequences in fields such as meteorology, oceanography and hydrology where return values are calculated from very large gridded model integrations spanning decades at high temporal resolution or from large ensembles of independent and identically distributed model fields. In such cases the computational savings are substantial.

Optimized probability sampling of study sites to improve generalizability in a multisite intervention trial.

PubMed

Kraschnewski, Jennifer L; Keyserling, Thomas C; Bangdiwala, Shrikant I; Gizlice, Ziya; Garcia, Beverly A; Johnston, Larry F; Gustafson, Alison; Petrovic, Lindsay; Glasgow, Russell E; Samuel-Hodge, Carmen D

2010-01-01

Studies of type 2 translation, the adaption of evidence-based interventions to real-world settings, should include representative study sites and staff to improve external validity. Sites for such studies are, however, often selected by convenience sampling, which limits generalizability. We used an optimized probability sampling protocol to select an unbiased, representative sample of study sites to prepare for a randomized trial of a weight loss intervention. We invited North Carolina health departments within 200 miles of the research center to participate (N = 81). Of the 43 health departments that were eligible, 30 were interested in participating. To select a representative and feasible sample of 6 health departments that met inclusion criteria, we generated all combinations of 6 from the 30 health departments that were eligible and interested. From the subset of combinations that met inclusion criteria, we selected 1 at random. Of 593,775 possible combinations of 6 counties, 15,177 (3%) met inclusion criteria. Sites in the selected subset were similar to all eligible sites in terms of health department characteristics and county demographics. Optimized probability sampling improved generalizability by ensuring an unbiased and representative sample of study sites.

The NSO FTS database program and archive (FTSDBM)

NASA Technical Reports Server (NTRS)

Lytle, D. M.

1992-01-01

Data from the NSO Fourier transform spectrometer is being re-archived from half inch tape onto write-once compact disk. In the process, information about each spectrum and a low resolution copy of each spectrum is being saved into an on-line database. FTSDBM is a simple database management program in the NSO external package for IRAF. A command language allows the FTSDBM user to add entries to the database, delete entries, select subsets from the database based on keyword values including ranges of values, create new database files based on these subsets, make keyword lists, examine low resolution spectra graphically, and make disk number/file number lists. Once the archive is complete, FTSDBM will allow the database to be efficiently searched for data of interest to the user and the compact disk format will allow random access to that data.

Evaluation of Cooper 12-minute walk/run test as a marker of cardiorespiratory fitness in young urban children with persistent asthma.

PubMed

Weisgerber, Michael; Danduran, Michael; Meurer, John; Hartmann, Kathryn; Berger, Stuart; Flores, Glenn

2009-07-01

To evaluate Cooper 12-minute run/walk test (CT12) as a one-time estimate of cardiorespiratory fitness and marker of fitness change compared with treadmill fitness testing in young children with persistent asthma. A cohort of urban children with asthma participated in the asthma and exercise program and a subset completed pre- and postintervention fitness testing. Treadmill fitness testing was conducted by an exercise physiologist in the fitness laboratory at an academic children's hospital. CT12 was conducted in a college recreation center gymnasium. Forty-five urban children with persistent asthma aged 7 to 14 years participated in exercise interventions. A subset of 19 children completed pre- and postintervention exercise testing. Participants completed a 9-week exercise program where they participated in either swimming or golf 3 days a week for 1 hour. A subset of participants completed fitness testing by 2 methods before and after program completion. CT12 results (meters), maximal oxygen consumption ((.)Vo2max) (mL x kg(-1) x min(-1)), and treadmill exercise time (minutes). CT12 and maximal oxygen consumption were moderately correlated (preintervention: 0.55, P = 0.003; postintervention: 0.48, P = 0.04) as one-time measures of fitness. Correlations of the tests as markers of change over time were poor and nonsignificant. In children with asthma, CT12 is a reasonable one-time estimate of fitness but a poor marker of fitness change over time.

Non-suppressive regulatory T cell subset expansion in pulmonary arterial hypertension.

PubMed

Sada, Yoshiharu; Dohi, Yoshihiro; Uga, Sayuri; Higashi, Akifumi; Kinoshita, Hiroki; Kihara, Yasuki

2016-08-01

Regulatory T cells (Tregs) have been reported to play a pivotal role in the vascular remodeling of pulmonary arterial hypertension (PAH). Recent studies have revealed that Tregs are heterogeneous and can be characterized by three phenotypically and functionally different subsets. In this study, we investigated the roles of Treg subsets in the pathogenesis of PAH in eight patients with PAH and 14 healthy controls. Tregs and their subsets in peripheral blood samples were analyzed by flow cytometry. Treg subsets were defined as CD4(+)CD45RA(+)FoxP3(low) resting Tregs (rTregs), CD4(+)CD45RA(-)FoxP3(high) activated Tregs (aTregs), and CD4(+)CD45RA(-)FoxP3(low) non-suppressive Tregs (non-Tregs). The proportion of Tregs among CD4(+) T cells was significantly higher in PAH patients than in controls (6.54 ± 1.10 vs. 3.81 ± 0.28 %, p < 0.05). Of the three subsets, the proportion of non-Tregs was significantly elevated in PAH patients compared with controls (4.06 ± 0.40 vs. 2.79 ± 0.14 %, p < 0.01), whereas those of rTregs and aTregs were not different between the two groups. Moreover, the expression levels of cytotoxic T lymphocyte antigen 4, a functional cell surface molecule, in aTregs (p < 0.05) and non-Tregs (p < 0.05) were significantly higher in PAH patients compared with controls. These results suggested the non-Treg subset was expanded and functionally activated in peripheral lymphocytes obtained from IPAH patients. We hypothesize that immunoreactions involving the specific activation of the non-Treg subset might play a role in the vascular remodeling of PAH.

Systematic wavelength selection for improved multivariate spectral analysis

DOEpatents

Thomas, Edward V.; Robinson, Mark R.; Haaland, David M.

1995-01-01

Methods and apparatus for determining in a biological material one or more unknown values of at least one known characteristic (e.g. the concentration of an analyte such as glucose in blood or the concentration of one or more blood gas parameters) with a model based on a set of samples with known values of the known characteristics and a multivariate algorithm using several wavelength subsets. The method includes selecting multiple wavelength subsets, from the electromagnetic spectral region appropriate for determining the known characteristic, for use by an algorithm wherein the selection of wavelength subsets improves the model's fitness of the determination for the unknown values of the known characteristic. The selection process utilizes multivariate search methods that select both predictive and synergistic wavelengths within the range of wavelengths utilized. The fitness of the wavelength subsets is determined by the fitness function F=.function.(cost, performance). The method includes the steps of: (1) using one or more applications of a genetic algorithm to produce one or more count spectra, with multiple count spectra then combined to produce a combined count spectrum; (2) smoothing the count spectrum; (3) selecting a threshold count from a count spectrum to select these wavelength subsets which optimize the fitness function; and (4) eliminating a portion of the selected wavelength subsets. The determination of the unknown values can be made: (1) noninvasively and in vivo; (2) invasively and in vivo; or (3) in vitro.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kautsky, Mark; Nguyen, Jason; Darr, Paul S.

The Long-Term Surveillance and Maintenance Plan (LTSMP) for Amchitka details how the U.S. Department of Energy (DOE) intends to fulfill its mission to maintain protection of human health and the environment at and around the sites on Amchitka Island. The LTSMP calls for monitoring to be performed every 5 years, at least in the initial phase of the project. The purpose of the monitoring is to develop a baseline of activity concentrations for selected radionuclides in biota, water, and soil, both on Amchitka and at the reference location on Adak Island, approximately 322 km (200 miles) northeast of Amchitka. Datamore » compiled by the Consortium for Risk Evaluation with Stakeholder Participation (CRESP, 2006) are being included as part of the baseline data set. The specific biological, water, and sediment samples collected during the 2011 sampling event were developed through close coordination with the primary stakeholders, including the Alaska Department of Environmental Conservation, the Aleutian Pribilof Island Association, and the U.S. Fish and Wildlife Service (USFWS). Amchitka is managed by the USFWS as part of the Alaska Maritime National Wildlife Refuge. Two plans were developed to address specific needs of the biological- and the terrestrial-monitoring programs. Results from these monitoring programs will help determine whether the environment is being impacted by radionuclide migration and uptake, and if subsistence and commercial-catch seafood is safe for human consumption. The RESRAD-BIOTA code is being used to evaluate ecological health relative to the radionuclide levels determined from this sampling event. The samples were sent to three laboratories for analysis. With the exception of the seawater samples, most of the samples were sent to the Center for Accelerator Mass Spectrometry at the Lawrence Livermore National Laboratory. A smaller subset of rock-weed samples, Star reindeer lichen samples, and soil samples collected from beneath the lichen were sent to UAF for cesium-137 analysis. Marine sediment samples were also collected and sent to UAF for testing. The seawater samples were sent to the University of Miami Tritium Laboratory for enriched tritium analysis. Results from the seawater samples for tritium were received in September 2011. Results from the 2011 sampling are expected to be available on the LM web site in 2012. (authors)« less

Altered Cytokine Production By Specific Human Peripheral Blood Cell Subsets Immediately Following Spaceflight

NASA Technical Reports Server (NTRS)

Crucian, Brian E.; Cubbage, Michael L.; Sams, Clarence F.

1999-01-01

In this study, we have attempted to combine standard immunological assays with the cellular resolving power of the flow cytometer to positively identify the specific cell types involved in spaceflight-induced immune alterations. We have obtained whole blood samples from 27 astronauts collected at three timepoints (L-10, R+0 and R+3) surrounding four recent space shuttle missions. The duration of these missions ranged from 10 to 18 days. Assays performed included serum/urine cortisol, comprehensive subset phenotyping, assessment of cellular activation markers and intracellular cytokine production following mitogenic stimulation. Absolute levels of peripheral granulocytes were significantly elevated following spaceflight, but the levels of circulating lymphocytes and monocytes were unchanged. Lymphocyte subset analysis demonstrated trends towards a decreased percentage of T cells and an increased percentage of B cells. Nearly all of the astronauts exhibited an increased CD4:CD8 ratio, which was dramatic in some individuals. Assessment of memory (CD45RA+) vs. naive (CD45RO+) CD4+ T cell subsets was more ambiguous, with subjects tending to group more as a flight crew. All subjects from one mission demonstrated an increased CD45RA:CD45RO ratio, while all subjects from another Mission demonstrated a decreased ratio. While no significant trend was seen in the monocyte population as defined by scatter, a decreased percentage of the CD14+ CD16+ monocyte subset was seen following spaceflight in all subjects tested. In general, most of the cellular changes described above which were assessed at R+O and compared to L-10 trended to pre-flight levels by R+3. Although no significant differences were seen in the expression of the cellular activation markers CD69 and CD25 following exposure to microgravity, significant alterations were seen in cytokine production in response to mitogenic activation for specific subsets. T cell (CD3+) production of IL-2 was significantly decreased after at R+O as was IL-2 production by both CD4+ and CD8+ T cell subsets for most subjects. Production of IFN(sub gamma) did not appear to be affected by microgravity exposure in either T cells in general or in the CD8+ T cell subset. There was a spaceflight-induced decrease in IFN(sub gamma) production in the CD4+ T cell subset, however it did not reach statistical significance. Serum and urine stress-hormone analysis indicated significant physiologic stresses in astronauts following spaceflight. In summary, these results demonstrate alterations in the peripheral immune system of astronauts immediately after spaceflight of 10 to 18 days duration and support continued research regarding microgravity and immunology (including in-flight sampling) prior to routine long-term spaceflight for astronauts.

Analysis of variograms with various sample sizes from a multispectral image

USDA-ARS?s Scientific Manuscript database

Variogram plays a crucial role in remote sensing application and geostatistics. It is very important to estimate variogram reliably from sufficient data. In this study, the analysis of variograms with various sample sizes of remotely sensed data was conducted. A 100x100-pixel subset was chosen from ...

Analysis of variograms with various sample sizes from a multispectral image

USDA-ARS?s Scientific Manuscript database

Variograms play a crucial role in remote sensing application and geostatistics. In this study, the analysis of variograms with various sample sizes of remotely sensed data was conducted. A 100 X 100 pixel subset was chosen from an aerial multispectral image which contained three wavebands, green, ...

Multiple-Matrix Sampling: A Technique for Maximizing the Effectiveness of Lengthy Survey Instruments.

ERIC Educational Resources Information Center

Shemick, John M.

1983-01-01

In a project to identify and verify professional competencies for beginning industrial education teachers, researchers found a 173-item questionnaire unwieldy. Using multiple-matrix sampling, they distributed subsets of items to respondents, resulting in adequate returns as well as duplication, postage, and time savings. (SK)

Evaluation of a Chlamydia trachomatis-specific, commercial, real-time PCR for use with ocular swabs.

PubMed

Pickering, Harry; Holland, Martin J; Last, Anna R; Burton, Matthew J; Burr, Sarah E

2018-02-20

Trachoma, the leading infectious cause of blindness worldwide, is caused by conjunctival Chlamydia trachomatis infection. Trachoma is diagnosed clinically by observation of conjunctival inflammation and/or scarring; however, there is evidence that monitoring C. trachomatis infection may be required for elimination programmes. There are many commercial and 'in-house' nucleic acid amplification tests for the detection of C. trachomatis DNA, but the majority have not been validated for use with ocular swabs. This study evaluated a commercial assay, the Fast-Track Vaginal swab kit, using conjunctival samples from trachoma-endemic areas. An objective, biostatistical-based method for binary classification of continuous PCR data was developed, to limit potential user-bias in diagnostic settings. The Fast-Track Vaginal swab assay was run on 210 ocular swab samples from Guinea-Bissau and Tanzania. Fit of individual amplification curves to exponential or sigmoid models, derivative and second derivative of the curves and final fluorescence value were examined for utility in thresholding for determining positivity. The results from the Fast-Track Vaginal swab assay were evaluated against a commercial test (Amplicor CT/NG) and a non-commercial test (in-house droplet digital PCR), both of whose performance has previously been evaluated. Significant evidence of exponential amplification (R 2  > 0.99) and final fluorescence > 0.15 were combined for thresholding. This objective approach identified a population of positive samples, however there were a subset of samples that amplified towards the end of the cycling protocol (at or later than 35 cycles), which were less clearly defined. The Fast-Track Vaginal swab assay showed good sensitivity against the commercial (95.71) and non-commercial (97.18) tests. Specificity was lower against both (90.00 and 96.55, respectively). This study defined a simple, automated protocol for binary classification of continuous, real-time qPCR data, for use in an end-point diagnostic test. This method identified a population of positive samples, however, as with manual thresholding, a subset of samples that amplified towards the end of the cycling program were less easily classified. When used with ocular swabs, the Fast-Track Vaginal swab assay had good sensitivity for C. trachomatis detection, but lower specificity than the commercial and non-commercial assays it was evaluated against, possibly leading to false positives.

The effects of land use on fluvial sediment chemistry for the conterminous U.S. - Results from the first cycle of the NAWQA Program: Trace and major elements, phosphorus, carbon, and sulfur

USGS Publications Warehouse

Horowitz, A.J.; Stephens, V.C.

2008-01-01

In 1991, the U.S. Geological Survey (USGS) began the first cycle of its National Water Quality Assessment (NAWQA) Program. The Program encompassed 51 river basins that collectively accounted for more than 70% of the total water use (excluding power generation), and 50% of the drinking water supply in the U.S. The basins represented a variety of hydrologic settings, rock types (geology), land-use categories, and population densities. One aspect of the first cycle included bed sediment sampling; sites were chosen to represent baseline and important land-use categories (e.g., agriculture, urban) in each basin. In total, over 1200 bed sediment samples were collected. All samples were size-limited (< 63????m) to facilitate spatial and/or temporal comparisons, and subsequently analyzed for a variety of chemical constituents including major (e.g., Fe, Al,) and trace elements (e.g., Cu, Zn, Cd), nutrients (e.g., P), and carbon. The analyses yielded total (??? 95% of the concentrations present), rather than total-recoverable chemical data. Land-use percentages, upstream underlying geology, and population density were determined for each site and evaluated to asses their relative influence on sediment chemistry. Baseline concentrations for the entire U.S. also were generated from a subset of all the samples, and are based on material collected from low population (??? 27??p km- 2) density, low percent urban (??? 5%), agricultural or undeveloped areas. The NAWQA baseline values are similar to those found in other national and global datasets. Further, it appears that upstream/underlying rock type has only a limited effect (mostly major elements) on sediment chemistry. The only land-use category that appears to substantially affect sediment chemistry is percent urban, and this result is mirrored by population density; in fact, the latter appears more consistent than the former.

Mimosa: Mixture Model of Co-expression to Detect Modulators of Regulatory Interaction

NASA Astrophysics Data System (ADS)

Hansen, Matthew; Everett, Logan; Singh, Larry; Hannenhalli, Sridhar

Functionally related genes tend to be correlated in their expression patterns across multiple conditions and/or tissue-types. Thus co-expression networks are often used to investigate functional groups of genes. In particular, when one of the genes is a transcription factor (TF), the co-expression-based interaction is interpreted, with caution, as a direct regulatory interaction. However, any particular TF, and more importantly, any particular regulatory interaction, is likely to be active only in a subset of experimental conditions. Moreover, the subset of expression samples where the regulatory interaction holds may be marked by presence or absence of a modifier gene, such as an enzyme that post-translationally modifies the TF. Such subtlety of regulatory interactions is overlooked when one computes an overall expression correlation. Here we present a novel mixture modeling approach where a TF-Gene pair is presumed to be significantly correlated (with unknown coefficient) in a (unknown) subset of expression samples. The parameters of the model are estimated using a Maximum Likelihood approach. The estimated mixture of expression samples is then mined to identify genes potentially modulating the TF-Gene interaction. We have validated our approach using synthetic data and on three biological cases in cow and in yeast. While limited in some ways, as discussed, the work represents a novel approach to mine expression data and detect potential modulators of regulatory interactions.

Proteome Characterization Centers - TCGA

Cancer.gov

The centers, a component of NCI’s Clinical Proteomic Tumor Analysis Consortium, will analyze a subset of TCGA samples to define proteins translated from cancer genomes and their related biological processes.

The Self-Adapting Focused Review System. Probability sampling of medical records to monitor utilization and quality of care.

PubMed

Ash, A; Schwartz, M; Payne, S M; Restuccia, J D

1990-11-01

Medical record review is increasing in importance as the need to identify and monitor utilization and quality of care problems grow. To conserve resources, reviews are usually performed on a subset of cases. If judgment is used to identify subgroups for review, this raises the following questions: How should subgroups be determined, particularly since the locus of problems can change over time? What standard of comparison should be used in interpreting rates of problems found in subgroups? How can population problem rates be estimated from observed subgroup rates? How can the bias be avoided that arises because reviewers know that selected cases are suspected of having problems? How can changes in problem rates over time be interpreted when evaluating intervention programs? Simple random sampling, an alternative to subgroup review, overcomes the problems implied by these questions but is inefficient. The Self-Adapting Focused Review System (SAFRS), introduced and described here, provides an adaptive approach to record selection that is based upon model-weighted probability sampling. It retains the desirable inferential properties of random sampling while allowing reviews to be concentrated on cases currently thought most likely to be problematic. Model development and evaluation are illustrated using hospital data to predict inappropriate admissions.

Identifying Depressed Older Adults in Primary Care: A Secondary Analysis of a Multisite Randomized Controlled Trial

PubMed Central

Voils, Corrine I.; Olsen, Maren K.; Williams, John W.; for the IMPACT Study Investigators

2008-01-01

Objective: To determine whether a subset of depressive symptoms could be identified to facilitate diagnosis of depression in older adults in primary care. Method: Secondary analysis was conducted on 898 participants aged 60 years or older with major depressive disorder and/or dysthymic disorder (according to DSM-IV criteria) who participated in the Improving Mood–Promoting Access to Collaborative Treatment (IMPACT) study, a multisite, randomized trial of collaborative care for depression (recruitment from July 1999 to August 2001). Linear regression was used to identify a core subset of depressive symptoms associated with decreased social, physical, and mental functioning. The sensitivity and specificity, adjusting for selection bias, were evaluated for these symptoms. The sensitivity and specificity of a second subset of 4 depressive symptoms previously validated in a midlife sample was also evaluated. Results: Psychomotor changes, fatigue, and suicidal ideation were associated with decreased functioning and served as the core set of symptoms. Adjusting for selection bias, the sensitivity of these 3 symptoms was 0.012 and specificity 0.994. The sensitivity of the 4 symptoms previously validated in a midlife sample was 0.019 and specificity was 0.997. Conclusion: We identified 3 depression symptoms that were highly specific for major depressive disorder in older adults. However, these symptoms and a previously identified subset were too insensitive for accurate diagnosis. Therefore, we recommend a full assessment of DSM-IV depression criteria for accurate diagnosis. PMID:18311416

Delineation of soil temperature regimes from HCMM data

NASA Technical Reports Server (NTRS)

Day, R. L.; Petersen, G. W. (Principal Investigator)

1981-01-01

Supplementary data including photographs as well as topographic, geologic, and soil maps were obtained and evaluated for ground truth purposes and control point selection. A study area (approximately 450 by 450 pixels) was subset from LANDSAT scene No. 2477-17142. Geometric corrections and scaling were performed. Initial enhancement techniques were initiated to aid control point selection and soils interpretation. The SUBSET program was modified to read HCMM tapes and HCMM data were reformated so that they are compatible with the ORSER system. Initial NMAP products of geometrically corrected and scaled raw data tapes (unregistered) of the study were produced.

Neural networks for vertical microcode compaction

NASA Astrophysics Data System (ADS)

Chu, Pong P.

1992-09-01

Neural networks provide an alternative way to solve complex optimization problems. Instead of performing a program of instructions sequentially as in a traditional computer, neural network model explores many competing hypotheses simultaneously using its massively parallel net. The paper shows how to use the neural network approach to perform vertical micro-code compaction for a micro-programmed control unit. The compaction procedure includes two basic steps. The first step determines the compatibility classes and the second step selects a minimal subset to cover the control signals. Since the selection process is an NP- complete problem, to find an optimal solution is impractical. In this study, we employ a customized neural network to obtain the minimal subset. We first formalize this problem, and then define an `energy function' and map it to a two-layer fully connected neural network. The modified network has two types of neurons and can always obtain a valid solution.

Transcriptional specialization of human dendritic cell subsets in response to microbial vaccines

PubMed Central

Banchereau, Romain; Baldwin, Nicole; Cepika, Alma-Martina; Athale, Shruti; Xue, Yaming; Yu, Chun I; Metang, Patrick; Cheruku, Abhilasha; Berthier, Isabelle; Gayet, Ingrid; Wang, Yuanyuan; Ohouo, Marina; Snipes, LuAnn; Xu, Hui; Obermoser, Gerlinde; Blankenship, Derek; Oh, Sangkon; Ramilo, Octavio; Chaussabel, Damien; Banchereau, Jacques; Palucka, Karolina; Pascual, Virginia

2014-01-01

The mechanisms by which microbial vaccines interact with human APCs remain elusive. Herein, we describe the transcriptional programs induced in human DCs by pathogens, innate receptor ligands and vaccines. Exposure of DCs to influenza, Salmonella enterica and Staphylococcus aureus allows us to build a modular framework containing 204 transcript clusters. We use this framework to characterize the responses of human monocytes, monocyte-derived DCs and blood DC subsets to 13 vaccines. Different vaccines induce distinct transcriptional programs based on pathogen type, adjuvant formulation and APC targeted. Fluzone, Pneumovax and Gardasil, respectively, activate monocyte-derived DCs, monocytes and CD1c+ blood DCs, highlighting APC specialization in response to vaccines. Finally, the blood signatures from individuals vaccinated with Fluzone or infected with influenza reveal a signature of adaptive immunity activation following vaccination and symptomatic infections, but not asymptomatic infections. These data, offered with a web interface, may guide the development of improved vaccines. PMID:25335753

Uncertainty Analysis via Failure Domain Characterization: Polynomial Requirement Functions

NASA Technical Reports Server (NTRS)

Crespo, Luis G.; Munoz, Cesar A.; Narkawicz, Anthony J.; Kenny, Sean P.; Giesy, Daniel P.

2011-01-01

This paper proposes an uncertainty analysis framework based on the characterization of the uncertain parameter space. This characterization enables the identification of worst-case uncertainty combinations and the approximation of the failure and safe domains with a high level of accuracy. Because these approximations are comprised of subsets of readily computable probability, they enable the calculation of arbitrarily tight upper and lower bounds to the failure probability. A Bernstein expansion approach is used to size hyper-rectangular subsets while a sum of squares programming approach is used to size quasi-ellipsoidal subsets. These methods are applicable to requirement functions whose functional dependency on the uncertainty is a known polynomial. Some of the most prominent features of the methodology are the substantial desensitization of the calculations from the uncertainty model assumed (i.e., the probability distribution describing the uncertainty) as well as the accommodation for changes in such a model with a practically insignificant amount of computational effort.

Protection by and maintenance of CD4 effector memory and effector T cell subsets in persistent malaria infection.

PubMed

Opata, Michael M; Ibitokou, Samad A; Carpio, Victor H; Marshall, Karis M; Dillon, Brian E; Carl, Jordan C; Wilson, Kyle D; Arcari, Christine M; Stephens, Robin

2018-04-01

Protection at the peak of Plasmodium chabaudi blood-stage malaria infection is provided by CD4 T cells. We have shown that an increase in Th1 cells also correlates with protection during the persistent phase of malaria; however, it is unclear how these T cells are maintained. Persistent malaria infection promotes protection and generates both effector T cells (Teff), and effector memory T cells (Tem). We have previously defined new CD4 Teff (IL-7Rα-) subsets from Early (TeffEarly, CD62LhiCD27+) to Late (TeffLate, CD62LloCD27-) activation states. Here, we tested these effector and memory T cell subsets for their ability to survive and protect in vivo. We found that both polyclonal and P. chabaudi Merozoite Surface Protein-1 (MSP-1)-specific B5 TCR transgenic Tem survive better than Teff. Surprisingly, as Tem are associated with antigen persistence, Tem survive well even after clearance of infection. As previously shown during T cell contraction, TeffEarly, which can generate Tem, also survive better than other Teff subsets in uninfected recipients. Two other Tem survival mechanisms identified here are that low-level chronic infection promotes Tem both by driving their proliferation, and by programming production of Tem from Tcm. Protective CD4 T cell phenotypes have not been precisely determined in malaria, or other persistent infections. Therefore, we tested purified memory (Tmem) and Teff subsets in protection from peak pathology and parasitemia in immunocompromised recipient mice. Strikingly, among Tmem (IL-7Rαhi) subsets, only TemLate (CD62LloCD27-) reduced peak parasitemia (19%), though the dominant memory subset is TemEarly, which is not protective. In contrast, all Teff subsets reduced peak parasitemia by more than half, and mature Teff can generate Tem, though less. In summary, we have elucidated four mechanisms of Tem maintenance, and identified two long-lived T cell subsets (TemLate, TeffEarly) that may represent correlates of protection or a target for longer-lived vaccine-induced protection against malaria blood-stages.

Dense mesh sampling for video-based facial animation

NASA Astrophysics Data System (ADS)

Peszor, Damian; Wojciechowska, Marzena

2016-06-01

The paper describes an approach for selection of feature points on three-dimensional, triangle mesh obtained using various techniques from several video footages. This approach has a dual purpose. First, it allows to minimize the data stored for the purpose of facial animation, so that instead of storing position of each vertex in each frame, one could store only a small subset of vertices for each frame and calculate positions of others based on the subset. Second purpose is to select feature points that could be used for anthropometry-based retargeting of recorded mimicry to another model, with sampling density beyond that which can be achieved using marker-based performance capture techniques. Developed approach was successfully tested on artificial models, models constructed using structured light scanner, and models constructed from video footages using stereophotogrammetry.

Rotary engine performance computer program (RCEMAP and RCEMAPPC): User's guide

NASA Technical Reports Server (NTRS)

Bartrand, Timothy A.; Willis, Edward A.

1993-01-01

This report is a user's guide for a computer code that simulates the performance of several rotary combustion engine configurations. It is intended to assist prospective users in getting started with RCEMAP and/or RCEMAPPC. RCEMAP (Rotary Combustion Engine performance MAP generating code) is the mainframe version, while RCEMAPPC is a simplified subset designed for the personal computer, or PC, environment. Both versions are based on an open, zero-dimensional combustion system model for the prediction of instantaneous pressures, temperature, chemical composition and other in-chamber thermodynamic properties. Both versions predict overall engine performance and thermal characteristics, including bmep, bsfc, exhaust gas temperature, average material temperatures, and turbocharger operating conditions. Required inputs include engine geometry, materials, constants for use in the combustion heat release model, and turbomachinery maps. Illustrative examples and sample input files for both versions are included.

Legal and definitional issues affecting the identification and education of adults with specific learning disabilities in adult education programs.

PubMed

Taymans, Juliana M

2012-01-01

Although the exact prevalence is not determined, a noticeable subset of individuals who enroll in adult education and training programs have either diagnosed or undiagnosed specific learning disabilities (SLD). Understanding SLD is important basic information for adult educators to inform program policies as well as determine effective instructional practices. This article discusses the development of definitions of SLD and current agreement on the nature of SLD relevant to working with adults. It concludes with implications for adult education programs.

Practical aspects of modeling aircraft dynamics from flight data

NASA Technical Reports Server (NTRS)

Iliff, K. W.; Maine, R. E.

1984-01-01

The purpose of parameter estimation, a subset of system identification, is to estimate the coefficients (such as stability and control derivatives) of the aircraft differential equations of motion from sampled measured dynamic responses. In the past, the primary reason for estimating stability and control derivatives from flight tests was to make comparisons with wind tunnel estimates. As aircraft became more complex, and as flight envelopes were expanded to include flight regimes that were not well understood, new requirements for the derivative estimates evolved. For many years, the flight determined derivatives were used in simulations to aid in flight planning and in pilot training. The simulations were particularly important in research flight test programs in which an envelope expansion into new flight regimes was required. Parameter estimation techniques for estimating stability and control derivatives from flight data became more sophisticated to support the flight test programs. As knowledge of these new flight regimes increased, more complex aircraft were flown. Much of this increased complexity was in sophisticated flight control systems. The design and refinement of the control system required higher fidelity simulations than were previously required.

Development of a Renewable Hydrogen Production and Fuel Cell Education Program

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mann, Michael D.

2011-11-20

This report presents the results of a program designed to develop an education program to 1) Provide exposure to the basics of hydrogen-based technologies to a large number of students. This exposure will provide a level of training that will allow students to converse and work with other scientists and engineers in this field. It will also serve to spark a level of interest in a subset of students who will then continue with more advanced coursework and/or research; 2) Provide a “mid-level” training to a moderate level of students. More detailed and directed education will provide students with themore » ability to work to support industry and government development of hydrogen technologies. This level of training would be sufficient to work in the industry, but not be a leader in research and development; and 3) Provide detailed training to a smaller subset of students with a strong interest and propensity to make significant contributions to the technology development. These individuals will have extensive hands-on experience through internships that will play a major role in industry, government, and academia.« less

Tissue-specific programming of memory CD8 T cell subsets impacts protection against lethal respiratory virus infection

PubMed Central

Tahiliani, Vikas

2016-01-01

How tissue-specific anatomical distribution and phenotypic specialization are linked to protective efficacy of memory T cells against reinfection is unclear. Here, we show that lung environmental cues program recently recruited central-like memory cells with migratory potentials for their tissue-specific functions during lethal respiratory virus infection. After entering the lung, some central-like cells retain their original CD27hiCXCR3hi phenotype, enabling them to localize near the infected bronchiolar epithelium and airway lumen to function as the first line of defense against pathogen encounter. Others, in response to local cytokine triggers, undergo a secondary program of differentiation that leads to the loss of CXCR3, migration arrest, and clustering within peribronchoarterial areas and in interalveolar septa. Here, the immune system adapts its response to prevent systemic viral dissemination and mortality. These results reveal the striking and unexpected spatial organization of central- versus effector-like memory cells within the lung and how cooperation between these two subsets contributes to host defense. PMID:27879287

Exploratory subsetting of autism families based on savant skills improves evidence of genetic linkage to 15q11-q13.

PubMed

Nurmi, Erika L; Dowd, Michael; Tadevosyan-Leyfer, Ovsanna; Haines, Jonathan L; Folstein, Susan E; Sutcliffe, James S

2003-07-01

Autism displays a remarkably high heritability but a complex genetic etiology. One approach to identifying susceptibility loci under these conditions is to define more homogeneous subsets of families on the basis of genetically relevant phenotypic or biological characteristics that vary from case to case. The authors performed a principal components analysis, using items from the Autism Diagnostic Interview, which resulted in six clusters of variables, five of which showed significant sib-sib correlation. The utility of these phenotypic subsets was tested in an exploratory genetic analysis of the autism candidate region on chromosome 15q11-q13. When the Collaborative Linkage Study of Autism sample was divided, on the basis of mean proband score for the "savant skills" cluster, the heterogeneity logarithm of the odds under a recessive model at D15S511, within the GABRB3 gene, increased from 0.6 to 2.6 in the subset of families in which probands had greater savant skills. These data are consistent with the genetic contribution of a 15q locus to autism susceptibility in a subset of affected individuals exhibiting savant skills. Similar types of skills have been noted in individuals with Prader-Willi syndrome, which results from deletions of this chromosomal region.

Measuring diversity in Gossypium hirsutum using the CottonSNP63K Array

USDA-ARS?s Scientific Manuscript database

A CottonSNP63K array and accompanying cluster file has been developed and includes 45,104 intra-specific SNPs and 17,954 inter-specific SNPs for automated genotyping of cotton (Gossypium spp.) samples. Development of the cluster file included genotyping of 1,156 samples, a subset of which were iden...

Household Behavior with Respect to Meat Consumption: Differences between Households with and without Children.

PubMed

Maria, Merlino Valentina; Danielle, Borra; Tibor, Verduna; Stefano, Massaglia

2017-10-31

Meat consumers around the world are increasingly paying attention to product quality and safety, and are starting to reduce their meat consumption, especially with regard to red meat. This trend is prevalent in households with children who prefer health-certified meat products. Our study compares meat consumption habits in households with and without children or adolescences (0-18 years). A structured questionnaire was distributed to 401 retail purchasers at 12 different points of sales of meat in the Piedmont region in northwest Italy. Socio-demographic variables and quantitative-qualitative meat consumption habits of retail purchasers were investigated. One part of the questionnaire analyzed the relative importance of 12 meat choice purchasing attributes by employing the Best-Worst scaling methodology, a type of choice experiment. Our research found that households without children (subset B) have higher weekly meat consumption habits than those with children (subset A). Alternatively, the households with children (subset A) have a diet characterized by a greater variety of protein sources, such as legumes and fish. Both of the considered subsets preferred trusted butchers for meat buying, with supermarkets as a second choice. However, only consumers of subset A bought meat from farm butchers. Our team performed a consumer analysis to identify meat consumption patterns in the two considered subsets. Simultaneously, a Best-Worst analysis evidenced several choice attributes with different relevance for the two investigated samples segmentation in three clusters of purchase.

Household Behavior with Respect to Meat Consumption: Differences between Households with and without Children

PubMed Central

Danielle, Borra; Tibor, Verduna; Stefano, Massaglia

2017-01-01

Meat consumers around the world are increasingly paying attention to product quality and safety, and are starting to reduce their meat consumption, especially with regard to red meat. This trend is prevalent in households with children who prefer health-certified meat products. Our study compares meat consumption habits in households with and without children or adolescences (0–18 years). A structured questionnaire was distributed to 401 retail purchasers at 12 different points of sales of meat in the Piedmont region in northwest Italy. Socio-demographic variables and quantitative-qualitative meat consumption habits of retail purchasers were investigated. One part of the questionnaire analyzed the relative importance of 12 meat choice purchasing attributes by employing the Best-Worst scaling methodology, a type of choice experiment. Our research found that households without children (subset B) have higher weekly meat consumption habits than those with children (subset A). Alternatively, the households with children (subset A) have a diet characterized by a greater variety of protein sources, such as legumes and fish. Both of the considered subsets preferred trusted butchers for meat buying, with supermarkets as a second choice. However, only consumers of subset A bought meat from farm butchers. Our team performed a consumer analysis to identify meat consumption patterns in the two considered subsets. Simultaneously, a Best-Worst analysis evidenced several choice attributes with different relevance for the two investigated samples segmentation in three clusters of purchase. PMID:29088120

Selective extraction of halogenated compounds from data measured by comprehensive multidimensional gas chromatography/high resolution time-of-flight mass spectrometry for non-target analysis of environmental and biological samples.

PubMed

Hashimoto, Shunji; Zushi, Yasuyuki; Fushimi, Akihiro; Takazawa, Yoshikatsu; Tanabe, Kiyoshi; Shibata, Yasuyuki

2013-03-22

We developed a method that selectively extracts a subset from comprehensive 2D gas chromatography (GC×GC) and high-resolution time-of-flight mass spectrometry (HRTOFMS) data to detect and identify trace levels of organohalogens. The data were obtained by measuring several environmental and biological samples, namely fly ash, soil, sediment, the atmosphere, and human urine. For global analysis, some samples were measured without purification. By using our novel software, the mass spectra of organochlorines or organobromines were then extracted into a data subset under high mass accuracy conditions that were approximately equivalent to a mass resolution of 6000 for some samples. Mass defect filtering as pre-screening for the data extraction was very effective in removing the mass spectra of hydrocarbons. Those results showed that data obtained with HRTOFMS are valuable for global analysis of organohalogens, and probably of other compounds if specific data extraction methods can be devised. Copyright © 2013 Elsevier B.V. All rights reserved.

NASA Curation Preparation for Ryugu Sample Returned by JAXA's Hayabusa2 Mission

NASA Technical Reports Server (NTRS)

Nakamura-Messenger, Keiko; Righter, Kevin; Snead, Christopher J.; McCubbin, Francis M.; Pace, Lisa F.; Zeigler, Ryan A.; Evans, Cindy

2017-01-01

The NASA OSIRIS-REx and JAXA Hayabusa2 missions to near-Earth asteroids Bennu and Ryugu share similar mission goals of understanding the origins of primitive, organic-rich asteroids. Under an agreement between JAXA and NASA, there is an on-going and productive collaboration between science teams of Hayabusa2 and OSIRIS-REx missions. Under this agreement, a portion of each of the returned sample masses will be exchanged between the agencies and the scientific results of their study will be shared. NASA’s portion of the returned Hayabusa2 sample, consisting of 10% of the returned mass, will be jointly separated by NASA and JAXA. The sample will be legally and physically transferred to NASA’s dedicated Hayabusa2 curation facility at Johnson Space Center (JSC) no later than one year after the return of the Hayabusa2 sample to Earth (December 2020). The JSC Hayabusa2 curation cleanroom facility design has now been completed. In the same manner, JAXA will receive 0.5% of the total returned OSIRIS-REx sample (minimum required sample to return 60 g, maximum sample return capacity of 2 kg) from the rest of the specimen. No later than one year after the return of the OSIRIS-REx sample to Earth (September 2023), legal, physical, and permanent custody of this sample subset will be transferred to JAXA, and the sample subset will be brought to JAXA’s Extraterrestrial Sample Curation Center (ESCuC) at Institute of Space and Astronautical Science, Sagamihara City Japan.

F-35 Joint Strike Fighter (JSF) Program: Background and Issues for Congress

DTIC Science & Technology

2011-04-26

bulkheads on the F-22.”28 Third, the driveshaft, lift-fan clutch, and actuator for the F-35B’s roll-post nozzles will be redesigned following...levels of participation in the program. International partners are also assisting with Initial Operational Test and Evaluation ( IOT &E), a subset of...Week/Ares blog, March 15, 2010. 59 Currently, the UK, Italy, and the Netherlands have agreed to participate in the IOT &E program. UK, the senior F

The predictive information obtained by testing multiple software versions

NASA Technical Reports Server (NTRS)

Lee, Larry D.

1987-01-01

Multiversion programming is a redundancy approach to developing highly reliable software. In applications of this method, two or more versions of a program are developed independently by different programmers and the versions are combined to form a redundant system. One variation of this approach consists of developing a set of n program versions and testing the versions to predict the failure probability of a particular program or a system formed from a subset of the programs. The precision that might be obtained, and also the effect of programmer variability if predictions are made over repetitions of the process of generating different program versions, are examined.

Egg laying sequence influences egg mercury concentrations and egg size in three bird species: Implications for contaminant monitoring programs

USGS Publications Warehouse

Ackerman, Joshua T.; Eagles-Smith, Collin A.; Herzog, Mark P.; Yee, Julie L.; Hartman, C. Alex

2016-01-01

Bird eggs are commonly used in contaminant monitoring programs and toxicological risk assessments, but intra-clutch variation and sampling methodology could influence interpretability. We examined the influence of egg laying sequence on egg mercury concentrations and burdens in American avocets, black-necked stilts, and Forster's terns. The average decline in mercury concentrations between the first and last egg laid was 33% for stilts, 22% for terns, and 11% for avocets, and most of this decline occurred between the first and second eggs laid (24% for stilts, 18% for terns, and 9% for avocets). Trends in egg size with egg laying order were inconsistent among species and overall differences in egg volume, mass, length, and width were <3%. We summarized the literature and, among 17 species studied, mercury concentrations generally declined by 16% between the first and second eggs laid. Despite the strong effect of egg laying sequence, most of the variance in egg mercury concentrations still occurred among clutches (75%-91%) rather than within clutches (9%-25%). Using simulations, we determined that to accurately estimate a population's mean egg mercury concentration using only a single random egg from a subset of nests, it would require sampling >60 nests to represent a large population (10% accuracy) or ≥14 nests to represent a small colony that contained <100 nests (20% accuracy).

Impact of exercise programs among helicopter pilots with transient LBP.

PubMed

Andersen, Knut; Baardsen, Roald; Dalen, Ingvild; Larsen, Jan Petter

2017-06-20

Flight related low back pain (LBP) among helicopter pilots is frequent and may influence flight performance. Prolonged confined sitting during flights seems to weaken lumbar trunk (LT) muscles with associated secondary transient pain. Aim of the study was to investigate if structured training could improve muscular function and thus improve LBP related to flying. 39 helicopter pilots (35 men and 4 women), who reported flying related LBP on at least 1 of 3 missions last month, were allocated to two training programs over a 3-month period. Program A consisted of 10 exercises recommended for general LBP. Program B consisted of 4 exercises designed specifically to improve LT muscular endurance. The pilots were examined before and after the training using questionnaires for pain, function, quality of health and tests of LT muscular endurance as well as ultrasound measurements of the contractility of the lumbar multifidus muscle (LMM). Approximately half of the participants performed the training per-protocol. Participants in this subset group had comparable baseline characteristics as the total study sample. Pre and post analysis of all pilots included, showed participants had marked improvement in endurance and contractility of the LMM following training. Similarly, participants had improvement in function and quality of health. Participants in program B had significant improvement in pain, function and quality of health. This study indicates that participants who performed a three months exercise program had improved muscle endurance at the end of the program. The helicopter pilots also experienced improved function and quality of health. Identifier: NCT01788111 Registration date; February 5th, 2013, verified April 2016.

Dissecting the genetic heterogeneity of myopia susceptibility in an Ashkenazi Jewish population using ordered subset analysis

PubMed Central

Simpson, Claire L.; Wojciechowski, Robert; Ibay, Grace; Stambolian, Dwight

2011-01-01

Purpose Despite many years of research, most of the genetic factors contributing to myopia development remain unknown. Genetic studies have pointed to a strong inherited component, but although many candidate regions have been implicated, few genes have been positively identified. Methods We have previously reported 2 genomewide linkage scans in a population of 63 highly aggregated Ashkenazi Jewish families that identified a locus on chromosome 22. Here we used ordered subset analysis (OSA), conditioned on non-parametric linkage to chromosome 22 to detect other chromosomal regions which had evidence of linkage to myopia in subsets of the families, but not the overall sample. Results Strong evidence of linkage to a 19-cM linkage interval with a peak OSA nonparametric allele-sharing logarithm-of-odds (LOD) score of 3.14 on 20p12-q11.1 (ΔLOD=2.39, empirical p=0.029) was identified in a subset of 20 families that also exhibited strong evidence of linkage to chromosome 22. One other locus also presented with suggestive LOD scores >2.0 on chromosome 11p14-q14 and one locus on chromosome 6q22-q24 had an OSA LOD score=1.76 (ΔLOD=1.65, empirical p=0.02). Conclusions The chromosome 6 and 20 loci are entirely novel and appear linked in a subset of families whose myopia is known to be linked to chromosome 22. The chromosome 11 locus overlaps with the known Myopia-7 (MYP7, OMIM 609256) locus. Using ordered subset analysis allows us to find additional loci linked to myopia in subsets of families, and underlines the complex genetic heterogeneity of myopia even in highly aggregated families and genetically isolated populations such as the Ashkenazi Jews. PMID:21738393

Auditing Complex Concepts in Overlapping Subsets of SNOMED

PubMed Central

Wang, Yue; Wei, Duo; Xu, Junchuan; Elhanan, Gai; Perl, Yehoshua; Halper, Michael; Chen, Yan; Spackman, Kent A.; Hripcsak, George

2008-01-01

Limited resources and the sheer volume of concepts make auditing a large terminology, such as SNOMED CT, a daunting task. It is essential to devise techniques that can aid an auditor by automatically identifying concepts that deserve attention. A methodology for this purpose based on a previously introduced abstraction network (called the p-area taxonomy) for a SNOMED CT hierarchy is presented. The methodology algorithmically gathers concepts appearing in certain overlapping subsets, defined exclusively with respect to the p-area taxonomy, for review. The results of applying the methodology to SNOMED’s Specimen hierarchy are presented. These results are compared against a control sample composed of concepts residing in subsets without the overlaps. With the use of the double bootstrap, the concept group produced by our methodology is shown to yield a statistically significant higher proportion of error discoveries. PMID:18998838

Auditing complex concepts in overlapping subsets of SNOMED.

PubMed

Wang, Yue; Wei, Duo; Xu, Junchuan; Elhanan, Gai; Perl, Yehoshua; Halper, Michael; Chen, Yan; Spackman, Kent A; Hripcsak, George

2008-11-06

Limited resources and the sheer volume of concepts make auditing a large terminology, such as SNOMED CT, a daunting task. It is essential to devise techniques that can aid an auditor by automatically identifying concepts that deserve attention. A methodology for this purpose based on a previously introduced abstraction network (called the p-area taxonomy) for a SNOMED CT hierarchy is presented. The methodology algorithmically gathers concepts appearing in certain overlapping subsets, defined exclusively with respect to the p-area taxonomy, for review. The results of applying the methodology to SNOMED's Specimen hierarchy are presented. These results are compared against a control sample composed of concepts residing in subsets without the overlaps. With the use of the double bootstrap, the concept group produced by our methodology is shown to yield a statistically significant higher proportion of error discoveries.

Applications of fluorescence spectroscopy for predicting percent wastewater in an urban stream

USGS Publications Warehouse

Goldman, Jami H.; Rounds, Stewart A.; Needoba, Joseph A.

2012-01-01

Dissolved organic carbon (DOC) is a significant organic carbon reservoir in many ecosystems, and its characteristics and sources determine many aspects of ecosystem health and water quality. Fluorescence spectroscopy methods can quantify and characterize the subset of the DOC pool that can absorb and re-emit electromagnetic energy as fluorescence and thus provide a rapid technique for environmental monitoring of DOC in lakes and rivers. Using high resolution fluorescence techniques, we characterized DOC in the Tualatin River watershed near Portland, Oregon, and identified fluorescence parameters associated with effluent from two wastewater treatment plants and samples from sites within and outside the urban region. Using a variety of statistical approaches, we developed and validated a multivariate linear regression model to predict the amount of wastewater in the river as a function of the relative abundance of specific fluorescence excitation/emission pairs. The model was tested with independent data and predicts the percentage of wastewater in a sample within 80% confidence. Model results can be used to develop in situ instrumentation, inform monitoring programs, and develop additional water quality indicators for aquatic systems.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parker, D.; Sutherland, K.; Chasar, D.

The U.S. Department of Energy (DOE) Building America program, in collaboration with Florida Power and Light (FPL), conducted a phased residential energy-efficiency retrofit program. This research sought to establish impacts on annual energy and peak energy reductions from the technologies applied at two levels of retrofit - shallow and deep, with savings levels approaching the Building America program goals of reducing whole-house energy use by 40%. Under the Phased Deep Retrofit (PDR) project, we have installed phased, energy-efficiency retrofits in a sample of 56 existing, all-electric homes. End-use savings and economic evaluation results from the phased measure packages and singlemore » measures are summarized in this report. Project results will be of interest to utility program designers, weatherization evaluators, and the housing remodel industry. Shallow retrofits were conducted in all homes from March to June 2013. The measures for this phase were chosen based on ease of installation, targeting lighting (CFLs and LED lamps), domestic hot water (wraps and showerheads), refrigeration (cleaning of coils), pool pump (reduction of operating hours), and the home entertainment center (smart plugs). Deep retrofits were conducted on a subset of ten PDR homes from May 2013 through March 2014. Measures included new air source heat pumps, duct repair, ceiling insulation, heat pump water heaters, variable speed pool pumps and learning thermostats. Major appliances such as refrigerators and dishwashers were replaced where they were old and inefficient.« less

Analysis of the Factors Affecting the Interval between Blood Donations Using Log-Normal Hazard Model with Gamma Correlated Frailties.

PubMed

Tavakol, Najmeh; Kheiri, Soleiman; Sedehi, Morteza

2016-01-01

Time to donating blood plays a major role in a regular donor to becoming continues one. The aim of this study was to determine the effective factors on the interval between the blood donations. In a longitudinal study in 2008, 864 samples of first-time donors in Shahrekord Blood Transfusion Center,  capital city of Chaharmahal and Bakhtiari Province, Iran were selected by a systematic sampling and were followed up for five years. Among these samples, a subset of 424 donors who had at least two successful blood donations were chosen for this study and the time intervals between their donations were measured as response variable. Sex, body weight, age, marital status, education, stay and job were recorded as independent variables. Data analysis was performed based on log-normal hazard model with gamma correlated frailty. In this model, the frailties are sum of two independent components assumed a gamma distribution. The analysis was done via Bayesian approach using Markov Chain Monte Carlo algorithm by OpenBUGS. Convergence was checked via Gelman-Rubin criteria using BOA program in R. Age, job and education were significant on chance to donate blood (P<0.05). The chances of blood donation for the higher-aged donors, clericals, workers, free job, students and educated donors were higher and in return, time intervals between their blood donations were shorter. Due to the significance effect of some variables in the log-normal correlated frailty model, it is necessary to plan educational and cultural program to encourage the people with longer inter-donation intervals to donate more frequently.

SSR_pipeline: a bioinformatic infrastructure for identifying microsatellites from paired-end Illumina high-throughput DNA sequencing data

USGS Publications Warehouse

Miller, Mark P.; Knaus, Brian J.; Mullins, Thomas D.; Haig, Susan M.

2013-01-01

SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (e.g., microsatellites) from paired-end high-throughput Illumina DNA sequencing data. The program suite contains 3 analysis modules along with a fourth control module that can automate analyses of large volumes of data. The modules are used to 1) identify the subset of paired-end sequences that pass Illumina quality standards, 2) align paired-end reads into a single composite DNA sequence, and 3) identify sequences that possess microsatellites (both simple and compound) conforming to user-specified parameters. The microsatellite search algorithm is extremely efficient, and we have used it to identify repeats with motifs from 2 to 25bp in length. Each of the 3 analysis modules can also be used independently to provide greater flexibility or to work with FASTQ or FASTA files generated from other sequencing platforms (Roche 454, Ion Torrent, etc.). We demonstrate use of the program with data from the brine fly Ephydra packardi (Diptera: Ephydridae) and provide empirical timing benchmarks to illustrate program performance on a common desktop computer environment. We further show that the Illumina platform is capable of identifying large numbers of microsatellites, even when using unenriched sample libraries and a very small percentage of the sequencing capacity from a single DNA sequencing run. All modules from SSR_pipeline are implemented in the Python programming language and can therefore be used from nearly any computer operating system (Linux, Macintosh, and Windows).

SSR_pipeline: a bioinformatic infrastructure for identifying microsatellites from paired-end Illumina high-throughput DNA sequencing data.

PubMed

Miller, Mark P; Knaus, Brian J; Mullins, Thomas D; Haig, Susan M

2013-01-01

SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (e.g., microsatellites) from paired-end high-throughput Illumina DNA sequencing data. The program suite contains 3 analysis modules along with a fourth control module that can automate analyses of large volumes of data. The modules are used to 1) identify the subset of paired-end sequences that pass Illumina quality standards, 2) align paired-end reads into a single composite DNA sequence, and 3) identify sequences that possess microsatellites (both simple and compound) conforming to user-specified parameters. The microsatellite search algorithm is extremely efficient, and we have used it to identify repeats with motifs from 2 to 25 bp in length. Each of the 3 analysis modules can also be used independently to provide greater flexibility or to work with FASTQ or FASTA files generated from other sequencing platforms (Roche 454, Ion Torrent, etc.). We demonstrate use of the program with data from the brine fly Ephydra packardi (Diptera: Ephydridae) and provide empirical timing benchmarks to illustrate program performance on a common desktop computer environment. We further show that the Illumina platform is capable of identifying large numbers of microsatellites, even when using unenriched sample libraries and a very small percentage of the sequencing capacity from a single DNA sequencing run. All modules from SSR_pipeline are implemented in the Python programming language and can therefore be used from nearly any computer operating system (Linux, Macintosh, and Windows).

The Sampling and Analysis Plan, Galena Airport and Kalakaket Creek Radio Relay Station, Alaska. Addendum

DTIC Science & Technology

1994-09-08

information deactivated during 1993. Currently, approximately 30 required in a QAPP per the U.S. Environmental caretakers are present at the facility...the total analytical cost. A subset of those Galena Airport-The current environmental samples collected and screened will be sent to an investigative...sampling report United States Environmental Protection Agency (US preparation. EPA), USAF, state, and local requirements. Ms. Sandy Smith is

Evaluation of subset matching methods and forms of covariate balance.

PubMed

de Los Angeles Resa, María; Zubizarreta, José R

2016-11-30

This paper conducts a Monte Carlo simulation study to evaluate the performance of multivariate matching methods that select a subset of treatment and control observations. The matching methods studied are the widely used nearest neighbor matching with propensity score calipers and the more recently proposed methods, optimal matching of an optimally chosen subset and optimal cardinality matching. The main findings are: (i) covariate balance, as measured by differences in means, variance ratios, Kolmogorov-Smirnov distances, and cross-match test statistics, is better with cardinality matching because by construction it satisfies balance requirements; (ii) for given levels of covariate balance, the matched samples are larger with cardinality matching than with the other methods; (iii) in terms of covariate distances, optimal subset matching performs best; (iv) treatment effect estimates from cardinality matching have lower root-mean-square errors, provided strong requirements for balance, specifically, fine balance, or strength-k balance, plus close mean balance. In standard practice, a matched sample is considered to be balanced if the absolute differences in means of the covariates across treatment groups are smaller than 0.1 standard deviations. However, the simulation results suggest that stronger forms of balance should be pursued in order to remove systematic biases due to observed covariates when a difference in means treatment effect estimator is used. In particular, if the true outcome model is additive, then marginal distributions should be balanced, and if the true outcome model is additive with interactions, then low-dimensional joints should be balanced. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

G-STRATEGY: Optimal Selection of Individuals for Sequencing in Genetic Association Studies

PubMed Central

Wang, Miaoyan; Jakobsdottir, Johanna; Smith, Albert V.; McPeek, Mary Sara

2017-01-01

In a large-scale genetic association study, the number of phenotyped individuals available for sequencing may, in some cases, be greater than the study’s sequencing budget will allow. In that case, it can be important to prioritize individuals for sequencing in a way that optimizes power for association with the trait. Suppose a cohort of phenotyped individuals is available, with some subset of them possibly already sequenced, and one wants to choose an additional fixed-size subset of individuals to sequence in such a way that the power to detect association is maximized. When the phenotyped sample includes related individuals, power for association can be gained by including partial information, such as phenotype data of ungenotyped relatives, in the analysis, and this should be taken into account when assessing whom to sequence. We propose G-STRATEGY, which uses simulated annealing to choose a subset of individuals for sequencing that maximizes the expected power for association. In simulations, G-STRATEGY performs extremely well for a range of complex disease models and outperforms other strategies with, in many cases, relative power increases of 20–40% over the next best strategy, while maintaining correct type 1 error. G-STRATEGY is computationally feasible even for large datasets and complex pedigrees. We apply G-STRATEGY to data on HDL and LDL from the AGES-Reykjavik and REFINE-Reykjavik studies, in which G-STRATEGY is able to closely-approximate the power of sequencing the full sample by selecting for sequencing a only small subset of the individuals. PMID:27256766

CryoEM and image sorting for flexible protein/DNA complexes.

PubMed

Villarreal, Seth A; Stewart, Phoebe L

2014-07-01

Intrinsically disordered regions of proteins and conformational flexibility within complexes can be critical for biological function. However, disorder, flexibility, and heterogeneity often hinder structural analyses. CryoEM and single particle image processing techniques offer the possibility of imaging samples with significant flexibility. Division of particle images into more homogenous subsets after data acquisition can help compensate for heterogeneity within the sample. We present the utility of an eigenimage sorting analysis for examining two protein/DNA complexes with significant conformational flexibility and heterogeneity. These complexes are integral to the non-homologous end joining pathway, and are involved in the repair of double strand breaks of DNA. Both complexes include the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) and biotinylated DNA with bound streptavidin, with one complex containing the Ku heterodimer. Initial 3D reconstructions of the two DNA-PKcs complexes resembled a cryoEM structure of uncomplexed DNA-PKcs without additional density clearly attributable to the remaining components. Application of eigenimage sorting allowed division of the DNA-PKcs complex datasets into more homogeneous subsets. This led to visualization of density near the base of the DNA-PKcs that can be attributed to DNA, streptavidin, and Ku. However, comparison of projections of the subset structures with 2D class averages indicated that a significant level of heterogeneity remained within each subset. In summary, image sorting methods allowed visualization of extra density near the base of DNA-PKcs, suggesting that DNA binds in the vicinity of the base of the molecule and potentially to a flexible region of DNA-PKcs. Copyright © 2013 Elsevier Inc. All rights reserved.

Toward Lower Organic Environments in Astromaterial Sample Curation for Diverse Collections

NASA Technical Reports Server (NTRS)

Allton, J. H.; Allen, C. C.; Burkett, P. J.; Calaway, M. J.; Oehler, D. Z.

2012-01-01

Great interest was taken during the frenzied pace of the Apollo lunar sample return to achieve and monitor organic cleanliness. Yet, the first mission resulted in higher organic contamination to samples than desired. But improvements were accomplished by Apollo 12 [1]. Quarantine complicated the goal of achieving organic cleanliness by requiring negative pressure glovebox containment environments, proximity of animal, plant and microbial organic sources, and use of organic sterilants in protocols. A special low organic laboratory was set up at University of California Berkeley (UCB) to cleanly subdivide a subset of samples [2, 3, 4]. Nevertheless, the basic approach of handling rocks and regolith inside of a positive pressure stainless steel glovebox and restrict-ing the tool and container materials allowed in the gloveboxes was established by the last Apollo sample re-turn. In the last 40 years, the collections have grown to encompass Antarctic meteorites, Cosmic Dust, Genesis solar wind, Stardust comet grains and Hayabusa asteroid grains. Each of these collections have unique curation requirements for organic contamination monitor-ing and control. Here is described some changes allowed by improved technology or driven by changes in environmental regulations and economy, concluding with comments on organic witness wafers. Future sample return missions (OSIRIS-Rex; Mars; comets) will require extremely low levels of organic contamination in spacecraft collection and thus similarly low levels in curation. JSC Curation is undertaking a program to document organic baseline levels in current operations and devise ways to reduce those levels.

History and evaluation of national-scale geochemical data sets for the United States

USGS Publications Warehouse

Smith, David B.; Smith, Steven M.; Horton, John D.

2013-01-01

Six national-scale, or near national-scale, geochemical data sets for soils or stream sediments exist for the United States. The earliest of these, here termed the ‘Shacklette’ data set, was generated by a U.S. Geological Survey (USGS) project conducted from 1961 to 1975. This project used soil collected from a depth of about 20 cm as the sampling medium at 1323 sites throughout the conterminous U.S. The National Uranium Resource Evaluation Hydrogeochemical and Stream Sediment Reconnaissance (NURE-HSSR) Program of the U.S. Department of Energy was conducted from 1975 to 1984 and collected either stream sediments, lake sediments, or soils at more than 378,000 sites in both the conterminous U.S. and Alaska. The sampled area represented about 65% of the nation. The Natural Resources Conservation Service (NRCS), from 1978 to 1982, collected samples from multiple soil horizons at sites within the major crop-growing regions of the conterminous U.S. This data set contains analyses of more than 3000 samples. The National Geochemical Survey, a USGS project conducted from 1997 to 2009, used a subset of the NURE-HSSR archival samples as its starting point and then collected primarily stream sediments, with occasional soils, in the parts of the U.S. not covered by the NURE-HSSR Program. This data set contains chemical analyses for more than 70,000 samples. The USGS, in collaboration with the Mexican Geological Survey and the Geological Survey of Canada, initiated soil sampling for the North American Soil Geochemical Landscapes Project in 2007. Sampling of three horizons or depths at more than 4800 sites in the U.S. was completed in 2010, and chemical analyses are currently ongoing. The NRCS initiated a project in the 1990s to analyze the various soil horizons from selected pedons throughout the U.S. This data set currently contains data from more than 1400 sites. This paper (1) discusses each data set in terms of its purpose, sample collection protocols, and analytical methods; and (2) evaluates each data set in terms of its appropriateness as a national-scale geochemical database and its usefulness for national-scale geochemical mapping.

Patch testing with uranyl acetate in veterans exposed to depleted uranium during the 1991 Gulf war and the Iraqi conflict.

PubMed

Shvartsbeyn, Marianna; Tuchinda, Papapit; Gaitens, Joanna; Squibb, Katherine S; McDiarmid, Melissa A; Gaspari, Anthony A

2011-01-01

The Depleted Uranium Follow-Up Program is a clinical surveillance program run by the Baltimore Veterans Affairs Medical Center since 1993 for veterans of the Gulf and Iraqi wars who were exposed to depleted uranium (DU) as a result of "friendly-fire" incidents. In 2009, 40 veterans from this cohort were screened for skin reactivity to metals by patch-testing with extended metal series and uranyl acetate (0.25%, 2.5%, and 25%). A control arm comprised 46 patients without any known occupational exposures to DU who were seen at the University of Maryland Dermatology Clinic for evaluation of allergic contact dermatitis. Excluding irritant reactions, no patch-test reactions to uranyl acetate were observed in the participants. Irritant reactions to DU were more common in the clinic cohort, likely reflective of the demographic differences between the two arms of the study. Biologic monitoring of urine uranium concentrations in the DU program participants with 24-hour urine samples showed evidence of percutaneous uranium absorption from the skin patches. We conclude that dermatitis observed in a subset of the veterans was unrelated to their military DU exposure. Our data suggest that future studies of skin testing with uranyl acetate should utilize 0.25%, the least irritating concentration.

Evaluation of a Faith-Based Culturally Relevant Program for African American Substance Users at Risk for HIV in the Southern United States

ERIC Educational Resources Information Center

MacMaster, Samuel A.; Jones, Jenny L.; Rasch, Randolph F. R.; Crawford, Sharon L.; Thompson, Stephanie; Sanders, Edwin C., II

2007-01-01

Objective: This article provides an evaluation of a federally funded faith-based program that serves African Americans who use heroin and cocaine and are at risk for HIV/AIDS in Nashville, Tennessee. Methods: Data were collected from 163 individuals at baseline and 6- and 12-month follow-up interviews. A subset of participants (n = 51) completed…

Comparison of Antemortem and Environmental Samples for Zebrafish Health Monitoring and Quarantine.

PubMed

Crim, Marcus J; Lawrence, Christian; Livingston, Robert S; Rakitin, Andrei; Hurley, Shane J; Riley, Lela K

2017-07-01

Molecular diagnostic assays offer both exquisite sensitivity and the ability to test a wide variety of sample types. Various types of environmental sample, such as detritus and concentrated water, might provide a useful adjunct to sentinels in routine zebrafish health monitoring. Similarly, antemortem sampling would be advantageous for expediting zebrafish quarantine, without euthanasia of valuable fish. We evaluated the detection of Mycobacterium chelonae, M. fortuitum, M. peregrinum, Pseudocapillaria tomentosa, and Pseudoloma neurophilia in zebrafish, detritus, pooled feces, and filter membranes after filtration of 1000-, 500-, and 150-mL water samples by real-time PCR analysis. Sensitivity varied according to sample type and pathogen, and environmental sampling was significantly more sensitive than zebrafish sampling for detecting Mycobacterium spp. but not for Pseudocapillaria neurophilia or Pseudoloma tomentosa. The results of these experiments provide strong evidence of the utility of multiple sample types for detecting pathogens according to each pathogen's life cycle and ecological niche within zebrafish systems. In a separate experiment, zebrafish subclinically infected with M. chelonae, M. marinum, Pleistophora hyphessobryconis, Pseudocapillaria tomentosa, or Pseudoloma neurophilia were pair-spawned and individually tested with subsets of embryos from each clutch that received no rinse, a fluidizing rinse, or were surface-disinfected with sodium hypochlorite. Frequently, one or both parents were subclinically infected with pathogen(s) that were not detected in any embryo subset. Therefore, negative results from embryo samples may not reflect the health status of the parent zebrafish.

Comparison of Antemortem and Environmental Samples for Zebrafish Health Monitoring and Quarantine

PubMed Central

Crim, Marcus J; Lawrence, Christian; Livingston, Robert S; Rakitin, Andrei; Hurley, Shane J; Riley, Lela K

2017-01-01

Molecular diagnostic assays offer both exquisite sensitivity and the ability to test a wide variety of sample types. Various types of environmental sample, such as detritus and concentrated water, might provide a useful adjunct to sentinels in routine zebrafish health monitoring. Similarly, antemortem sampling would be advantageous for expediting zebrafish quarantine, without euthanasia of valuable fish. We evaluated the detection of Mycobacterium chelonae, M. fortuitum, M. peregrinum, Pseudocapillaria tomentosa, and Pseudoloma neurophilia in zebrafish, detritus, pooled feces, and filter membranes after filtration of 1000-, 500-, and 150-mL water samples by real-time PCR analysis. Sensitivity varied according to sample type and pathogen, and environmental sampling was significantly more sensitive than zebrafish sampling for detecting Mycobacterium spp. but not for Pseudocapillaria neurophilia or Pseudoloma tomentosa. The results of these experiments provide strong evidence of the utility of multiple sample types for detecting pathogens according to each pathogen's life cycle and ecological niche within zebrafish systems. In a separate experiment, zebrafish subclinically infected with M. chelonae, M. marinum, Pleistophora hyphessobryconis, Pseudocapillaria tomentosa, or Pseudoloma neurophilia were pair-spawned and individually tested with subsets of embryos from each clutch that received no rinse, a fluidizing rinse, or were surface-disinfected with sodium hypochlorite. Frequently, one or both parents were subclinically infected with pathogen(s) that were not detected in any embryo subset. Therefore, negative results from embryo samples may not reflect the health status of the parent zebrafish. PMID:28724491

When Remembering Causes Forgetting: Retrieval-Induced Forgetting as Recovery Failure

ERIC Educational Resources Information Center

Bauml, Karl-Heinz; Zellner, Martina; Vilimek, Roman

2005-01-01

Retrieval practice on a subset of previously learned material can cause forgetting of the unpracticed material and make it inaccessible to consciousness. Such inaccessibility may arise because the material is no longer sampled from the set of to-be-recalled items, or, though sampled, its representation is not complete enough to be recovered into…

Response Latency as a Function of Hypothesis-Testing Strategies in Concept Identification

ERIC Educational Resources Information Center

Fink, Richard T.

1972-01-01

The ability of M. Levine's subset-sampling assumptions to account for the decrease in response latency following the trial of the last error was investigated by employing a distributed stimulus set composed of four binary dimensions and a procedure which required Ss to make an overt response in order to sample each dimension. (Author)

Methodological considerations for implementation of lymphocyte subset analysis in a clinical reference laboratory.

PubMed

Muirhead, K A; Wallace, P K; Schmitt, T C; Frescatore, R L; Franco, J A; Horan, P K

1986-01-01

As the diagnostic utility of lymphocyte subset analysis has been recognized in the clinical research laboratory, a wide variety of reagents and cell preparation, staining and analysis methods have also been described. Methods that are perfectly suitable for analysis of smaller sample numbers in the biological or clinical research setting are not always appropriate and/or applicable in the setting of a high volume clinical reference laboratory. We describe here some of the specific considerations involved in choosing a method for flow cytometric analysis which minimizes sample preparation and data analysis time while maximizing sample stability, viability, and reproducibility. Monoclonal T- and B-cell reagents from three manufacturers were found to give equivalent results for a reference population of healthy individuals. This was true whether direct or indirect immunofluorescence staining was used and whether cells were prepared by Ficoll-Hypaque fractionation (FH) or by lysis of whole blood. When B cells were enumerated using a polyclonal anti-immunoglobulin reagent, less cytophilic immunoglobulin staining was present after lysis than after FH preparation. However, both preparation methods required additional incubation at 37 degrees C to obtain results concordant with monoclonal B-cell reagents. Standard reagents were chosen on the basis of maximum positive/negative separation and the availability of appropriate negative controls. The effects of collection medium and storage conditions on sample stability and reproducibility of subset analysis were also assessed. Specimens collected in heparin and stored at room temperature in buffered medium gave reproducible results for 3 days after specimen collection, using either FH or lysis as the preparation method. General strategies for instrument optimization, quality control, and biohazard containment are also discussed.

Designing single- and multiple-shell sampling schemes for diffusion MRI using spherical code.

PubMed

Cheng, Jian; Shen, Dinggang; Yap, Pew-Thian

2014-01-01

In diffusion MRI (dMRI), determining an appropriate sampling scheme is crucial for acquiring the maximal amount of information for data reconstruction and analysis using the minimal amount of time. For single-shell acquisition, uniform sampling without directional preference is usually favored. To achieve this, a commonly used approach is the Electrostatic Energy Minimization (EEM) method introduced in dMRI by Jones et al. However, the electrostatic energy formulation in EEM is not directly related to the goal of optimal sampling-scheme design, i.e., achieving large angular separation between sampling points. A mathematically more natural approach is to consider the Spherical Code (SC) formulation, which aims to achieve uniform sampling by maximizing the minimal angular difference between sampling points on the unit sphere. Although SC is well studied in the mathematical literature, its current formulation is limited to a single shell and is not applicable to multiple shells. Moreover, SC, or more precisely continuous SC (CSC), currently can only be applied on the continuous unit sphere and hence cannot be used in situations where one or several subsets of sampling points need to be determined from an existing sampling scheme. In this case, discrete SC (DSC) is required. In this paper, we propose novel DSC and CSC methods for designing uniform single-/multi-shell sampling schemes. The DSC and CSC formulations are solved respectively by Mixed Integer Linear Programming (MILP) and a gradient descent approach. A fast greedy incremental solution is also provided for both DSC and CSC. To our knowledge, this is the first work to use SC formulation for designing sampling schemes in dMRI. Experimental results indicate that our methods obtain larger angular separation and better rotational invariance than the generalized EEM (gEEM) method currently used in the Human Connectome Project (HCP).

Kraken: ultrafast metagenomic sequence classification using exact alignments

PubMed Central

2014-01-01

Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster abundance estimation programs, which only classify small subsets of metagenomic data. Using exact alignment of k-mers, Kraken achieves classification accuracy comparable to the fastest BLAST program. In its fastest mode, Kraken classifies 100 base pair reads at a rate of over 4.1 million reads per minute, 909 times faster than Megablast and 11 times faster than the abundance estimation program MetaPhlAn. Kraken is available at http://ccb.jhu.edu/software/kraken/. PMID:24580807

Data splitting for artificial neural networks using SOM-based stratified sampling.

PubMed

May, R J; Maier, H R; Dandy, G C

2010-03-01

Data splitting is an important consideration during artificial neural network (ANN) development where hold-out cross-validation is commonly employed to ensure generalization. Even for a moderate sample size, the sampling methodology used for data splitting can have a significant effect on the quality of the subsets used for training, testing and validating an ANN. Poor data splitting can result in inaccurate and highly variable model performance; however, the choice of sampling methodology is rarely given due consideration by ANN modellers. Increased confidence in the sampling is of paramount importance, since the hold-out sampling is generally performed only once during ANN development. This paper considers the variability in the quality of subsets that are obtained using different data splitting approaches. A novel approach to stratified sampling, based on Neyman sampling of the self-organizing map (SOM), is developed, with several guidelines identified for setting the SOM size and sample allocation in order to minimize the bias and variance in the datasets. Using an example ANN function approximation task, the SOM-based approach is evaluated in comparison to random sampling, DUPLEX, systematic stratified sampling, and trial-and-error sampling to minimize the statistical differences between data sets. Of these approaches, DUPLEX is found to provide benchmark performance with good model performance, with no variability. The results show that the SOM-based approach also reliably generates high-quality samples and can therefore be used with greater confidence than other approaches, especially in the case of non-uniform datasets, with the benefit of scalability to perform data splitting on large datasets. Copyright 2009 Elsevier Ltd. All rights reserved.

Evaluation and characterization of a genetically diverse Musa germplasm core subset.

USDA-ARS?s Scientific Manuscript database

The USDA-ARS, Tropical Agriculture Research Station is responsible for curating germplasm of several regionally and internationally important agricultural crops. Evaluation and characterization of Musa (bananas) genetic resources are an important component of programmed research. In a global coll...

Characterization of αβ and γδ T cell subsets expressing IL-17A in ruminants and swine.

PubMed

Elnaggar, Mahmoud M; Abdellrazeq, Gaber S; Dassanayake, Rohana P; Fry, Lindsay M; Hulubei, Victoria; Davis, William C

2018-08-01

As part of our ongoing program to expand immunological reagents available for research in cattle, we developed a monoclonal antibody (mAb) to bovine interleukin-17A (IL-17A), a multifunctional cytokine centrally involved in regulating innate and adaptive immune responses. Initial comparative studies demonstrated the mAb recognizes a conserved epitope expressed on orthologues of IL-17A in sheep, goats and pigs. Comparative flow cytometric analyses of lymphocyte subsets stimulated with phorbol 12-myristate 13-acetate (PMA) and ionomycin revealed differences in expression of IL-17A by CD4, CD8, and γδ T cells across ruminants and swine species. Results in cattle showed the largest proportion of IL-17A + cells were CD4 + followed by γδ and CD8 + T cells. Further analysis revealed the IL-17A + γδ T cell subset was comprised of WC1.1 + , WC1.2 + , and WC1 - subsets. Analysis of the IL-17A + CD8 + T cell subset revealed it was comprised of αβ and γδ T cell subsets. Results in sheep and goats revealed IL-17A is expressed mainly by CD4 + and CD8 + T cells, with little expression by γδ T cells. Analysis of IL-17A + CD8 + T cells showed the majority were CD8 + αβ in sheep, whereas they were CD8 + γδ in goats. The majority of the sheep and goat IL-17A + γδ T cells were WC1 + . Results obtained in swine showed expression of IL-17A by CD4, CD8, and γδ T cell subsets were similar to results reported in other studies. Comparison of expression of IL-17A with IFN-γ revealed subsets co-expressed IL-17A and IFN-γ in cattle, sheep, and goats. The new mAb expands opportunities for immunology research in ruminants and swine. Copyright © 2018 Elsevier Ltd. All rights reserved.

Survival of porcine reproductive and respiratory syndrome virus in houseflies.

PubMed

Otake, Satoshi; Dee, Scott A; Moon, Roger D; Rossow, Kurt D; Trincado, Carlos; Farnham, MacDonald; Pijoan, Carlos

2003-07-01

The objectives of the study were to determine the duration of porcine reproductive and respiratory syndrome virus (PRRSV) survival in houseflies (Musca domestica Linnaeus) following feeding on an infected pig, and to determine whether the virus was present on the exterior surface or within the internal viscera of the fly. A total of 210 laboratory-colonized houseflies were allowed to feed to repletion on a pig, experimentally infected with PRRSV on day 7 postinoculation, and then maintained alive under laboratory conditions (27 degrees C). Two subsets (A and B) of 30 flies were collected at each of the following sampling points; 0, 6, and 12 hours post feeding (pf). Subset A contained an extra group of 30 flies collected at 24 hours pf due to the availability of extra flies. Flies in subset A were processed as whole fly homogenates, while the exterior surface washes and digestive organs were collected from flies in subset B. Whole fly homogenates, collected at 0, 6, and 12 hours pf, were positive by both polymerase chain reaction (PCR) and swine bioassay. Digestive organs, collected at 0 and 12 hours pf, were positive by PCR and swine bioassay. The PRRSV RNA was detected by PCR from the exterior surface wash of subset B flies collected at 0, 6, and 12 hours pf; however, only the subset collected at 0 hour pf was swine bioassay-positive. This study indicates that infectious PRRSV can survive within the intestinal tract of houseflies for up to 12 hours following feeding on an infected pig, but only for a short period on the exterior surface of the flies.

High-grading bias: subtle problems with assessing power of selected subsets of loci for population assignment.

PubMed

Waples, Robin S

2010-07-01

Recognition of the importance of cross-validation ('any technique or instance of assessing how the results of a statistical analysis will generalize to an independent dataset'; Wiktionary, en.wiktionary.org) is one reason that the U.S. Securities and Exchange Commission requires all investment products to carry some variation of the disclaimer, 'Past performance is no guarantee of future results.' Even a cursory examination of financial behaviour, however, demonstrates that this warning is regularly ignored, even by those who understand what an independent dataset is. In the natural sciences, an analogue to predicting future returns for an investment strategy is predicting power of a particular algorithm to perform with new data. Once again, the key to developing an unbiased assessment of future performance is through testing with independent data--that is, data that were in no way involved in developing the method in the first place. A 'gold-standard' approach to cross-validation is to divide the data into two parts, one used to develop the algorithm, the other used to test its performance. Because this approach substantially reduces the sample size that can be used in constructing the algorithm, researchers often try other variations of cross-validation to accomplish the same ends. As illustrated by Anderson in this issue of Molecular Ecology Resources, however, not all attempts at cross-validation produce the desired result. Anderson used simulated data to evaluate performance of several software programs designed to identify subsets of loci that can be effective for assigning individuals to population of origin based on multilocus genetic data. Such programs are likely to become increasingly popular as researchers seek ways to streamline routine analyses by focusing on small sets of loci that contain most of the desired signal. Anderson found that although some of the programs made an attempt at cross-validation, all failed to meet the 'gold standard' of using truly independent data and therefore produced overly optimistic assessments of power of the selected set of loci--a phenomenon known as 'high grading bias.'

Linkage studies in primary open angle glaucoma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Avramopoulos, D.; Grigoriadu, M.; Kitsos, G.

1994-09-01

Glaucoma is a leading cause of blindness worldwide. The majority of glaucoma is associated with an open, normal appearing anterior chamber angle and is termed primary open angle glaucoma (POAG, MIM 137760). It is characterized by elevated intraocular pressure and onset in middle age or later. A subset of POAG with juvenile onset has recently been linked to chromosome 1q in two families with autosomal dominant inheritance. Eleven pedigrees with autosomal dominant POG (non-juvenile-onset) have been identified in Epirus, Greece. In the present study DNA samples have been collected from 50 individuals from one large pedigree, including 12 affected individuals.more » Preliminary results of linkage analysis with chromosome 1 microsatellites using the computer program package LINKAGE Version 5.1 showed no linkage with the markers previously linked to juvenile-onset POAG. Further linkage analysis is being pursued, and the results will be presented.« less

On and Off the Mat: Yoga Experiences of Middle-Aged and Older Adults.

PubMed

Wertman, Annette; Wister, Andrew V; Mitchell, Barbara A

2016-06-01

This article explores potential differences in yoga practice between middle-and older-aged adults. A health belief - life course model frames this research, and a mixed-methods analytic strategy is employed to examine life course pathways into yoga and motivations to practice, as well as perceived barriers and health benefits. For the quantitative analyses, a convenience sample of 452 participants was collected using an online questionnaire. For the qualitative analyses, face-to-face interviews were conducted with a sub-set of 20 participants. Unique differences between the age groups (both current age and age when started yoga) as well as by gender were found for selected pathways, reasons/motivations, and barriers to engage in yoga as well as for perceived health benefits. In addition, results underscore the importance of informational cues and social linkages that affect how individuals adopt and experience yoga. Implications for health promotion programs that target older adults are discussed.

Subclinical Influenza Virus A Infections in Pigs Exhibited at Agricultural Fairs, Ohio, USA, 2009–2011

PubMed Central

Nolting, Jacqueline M.; Nelson, Sarah W.; Slemons, Richard D.

2012-01-01

Agricultural fairs are associated with bidirectional, interspecies transmission of influenza virus A between humans and pigs. We examined pigs exhibited at agricultural fairs in Ohio during 2009–2011 for signs of influenza-like illness and collected nasal swab specimens from a representative subset of these animals. Influenza virus A was recovered from pigs at 12/53 (22.6%) fairs during the 3-year sampling period. Pigs at 10/12 (83.3%) fairs from which influenza virus A was recovered did not show signs of influenza-like illness. Hemagglutinin, neuraminidase, and matrix gene combinations of the isolates were consistent with influenza virus A concurrently circulating among swine herds in the United States. Subclinical influenza virus A infections in pigs at agricultural fairs may pose a risk to human health and create challenges for passive surveillance programs for influenza virus A in swine herds. PMID:23171654

Clinical significance of Tim3-positive T cell subsets in patients with multiple sclerosis.

PubMed

Feng, Xuemei; Feng, Juan

2016-12-01

The present study evaluated associations between the percentages of T cell immunoglobulin and mucin domain 3 (Tim3)-positive T cells and related cytokines and multiple sclerosis (MS). We collected peripheral blood samples from 30 MS patients and 30 healthy controls. Flow cytometry was used to determine the proportions of CD3 + Tim3 + , CD4 + Tim3 + , and CD4 + CD25 + Tim3 + in peripheral blood mononuclear cells (PBMCs) and related cell subsets. The serum concentrations of galectin-9, IL-17, and IFN-γ also were determined using enzyme-linked immunosorbent assays (ELISA). The percentages of Tim3-positive T cells in CD4 + and CD4 + CD25 + T cell subsets were significantly lower among MS patients than among controls. This difference was particularly evident in the CD4 + CD25(high) T cell subset. The proportions of CD4 + Tim3 + and CD4 + CD25 + Tim3 + cells in PBMCs were significantly lower in the MS group than in the control group, whereas no significant differences were detected regarding the percentages of CD3 + Tim3 + in PBMCs and T cell subsets. The serum concentrations of galectin-9, IL-17, and IFN-γ all were increased in MS patients compared with healthy controls. Our results support that Tim3 and related cytokines may be involved in the onset of MS. Copyright © 2016 Elsevier Ltd. All rights reserved.

Design and methods of the Southeast Stream Quality Assessment (SESQA), 2014

USGS Publications Warehouse

Journey, Celeste A.; Van Metre, Peter C.; Bell, Amanda H.; Button, Daniel T.; Garrett, Jessica D.; Nakagaki, Naomi; Qi, Sharon L.; Bradley, Paul M.

2015-07-15

This report provides a detailed description of the SESQA study components, including surveys of ecological conditions, routine water sampling, deployment of passive polar organic compound integrative samplers for pesticides and contaminants of emerging concern, and synoptic sediment sampling and toxicity testing at all urban, confined animal feeding operation, and reference sites. Continuous water-quality monitoring and daily pesticide sampling efforts conducted at a subset of urban sites are also described.

Density-Dependent Quantized Least Squares Support Vector Machine for Large Data Sets.

PubMed

Nan, Shengyu; Sun, Lei; Chen, Badong; Lin, Zhiping; Toh, Kar-Ann

2017-01-01

Based on the knowledge that input data distribution is important for learning, a data density-dependent quantization scheme (DQS) is proposed for sparse input data representation. The usefulness of the representation scheme is demonstrated by using it as a data preprocessing unit attached to the well-known least squares support vector machine (LS-SVM) for application on big data sets. Essentially, the proposed DQS adopts a single shrinkage threshold to obtain a simple quantization scheme, which adapts its outputs to input data density. With this quantization scheme, a large data set is quantized to a small subset where considerable sample size reduction is generally obtained. In particular, the sample size reduction can save significant computational cost when using the quantized subset for feature approximation via the Nyström method. Based on the quantized subset, the approximated features are incorporated into LS-SVM to develop a data density-dependent quantized LS-SVM (DQLS-SVM), where an analytic solution is obtained in the primal solution space. The developed DQLS-SVM is evaluated on synthetic and benchmark data with particular emphasis on large data sets. Extensive experimental results show that the learning machine incorporating DQS attains not only high computational efficiency but also good generalization performance.

Methods of analysis by the U.S. Geological Survey National Water Quality Laboratory : evaluation of alkaline persulfate digestion as an alternative to Kjeldahl digestion for determination of total and dissolved nitrogen and phosphorus in water

USGS Publications Warehouse

Patton, Charles J.; Kryskalla, Jennifer R.

2003-01-01

Alkaline persulfate digestion was evaluated and validated as a more sensitive, accurate, and less toxic alternative to Kjeldahl digestion for routine determination of nitrogen and phosphorus in surface- and ground-water samples in a large-scale and geographically diverse study conducted by U.S. Geological Survey (USGS) between October 1, 2001, and September 30, 2002. Data for this study were obtained from about 2,100 surface- and ground-water samples that were analyzed for Kjeldahl nitrogen and Kjeldahl phosphorus in the course of routine operations at the USGS National Water Quality Laboratory (NWQL). These samples were analyzed independently for total nitrogen and total phosphorus using an alkaline persulfate digestion method developed by the NWQL Methods Research and Development Program. About half of these samples were collected during nominally high-flow (April-June) conditions and the other half were collected during nominally low-flow (August-September) conditions. The number of filtered and whole-water samples analyzed from each flow regime was about equal.By operational definition, Kjeldahl nitrogen (ammonium + organic nitrogen) and alkaline persulfate digestion total nitrogen (ammonium + nitrite + nitrate + organic nitrogen) are not equivalent. It was necessary, therefore, to reconcile this operational difference by subtracting nitrate + nitrite concentra-tions from alkaline persulfate dissolved and total nitrogen concentrations prior to graphical and statistical comparisons with dissolved and total Kjeldahl nitrogen concentrations. On the basis of two-population paired t-test statistics, the means of all nitrate-corrected alkaline persulfate nitrogen and Kjeldahl nitrogen concentrations (2,066 paired results) were significantly different from zero at the p = 0.05 level. Statistically, the means of Kjeldahl nitrogen concentrations were greater than those of nitrate-corrected alkaline persulfate nitrogen concentrations. Experimental evidence strongly suggests, however, that this apparent low bias resulted from nitrate interference in the Kjeldahl digestion method rather than low nitrogen recovery by the alkaline persulfate digestion method. Typically, differences between means of Kjeldahl nitrogen and nitrate-corrected alkaline persulfate nitrogen in low-nitrate concentration (< 0.1 milligram nitrate nitrogen per liter) subsets of filtered surface- and ground-water samples were statistically equivalent to zero at the p =level.Paired analytical results for dissolved and total phosphorus in Kjeldahl and alkaline persulfate digests were directly comparable because both digestion methods convert all forms of phosphorus in water samples to orthophosphate. On the basis of two-population paired t-test statistics, the means of all Kjeldahl phosphorus and alkaline persulfate phosphorus concentrations (2,093 paired results) were not significantly different from zero at the p = 0.05 level. For some subsets of these data, which were grouped according to water type and flow conditions at the time of sample collection, differences between means of Kjeldahl phosphorus and alkaline persulfate phosphorus concentrations were not equivalent to zero at the p = 0.05 level. Differences between means of these subsets, however, were less than the method detection limit for phosphorus (0.007 milligram phosphorus per liter) by the alkaline persulfate digestion method, and were therefore analytically insignificant.This report provides details of the alkaline persulfate digestion procedure, interference studies, recovery of various nitrogen- and phosphorus-containing compounds, and other analytical figures of merit. The automated air-segmented continuous flow methods developed to determine nitrate and orthophosphate in the alkaline persulfate digests also are described. About 125 microliters of digested sample are required to determine nitrogen and phosphorus in parallel at a rate of about 100 samples per hour with less than 1-percent sample in

Optimal Frequency-Domain System Realization with Weighting

NASA Technical Reports Server (NTRS)

Juang, Jer-Nan; Maghami, Peiman G.

1999-01-01

Several approaches are presented to identify an experimental system model directly from frequency response data. The formulation uses a matrix-fraction description as the model structure. Frequency weighting such as exponential weighting is introduced to solve a weighted least-squares problem to obtain the coefficient matrices for the matrix-fraction description. A multi-variable state-space model can then be formed using the coefficient matrices of the matrix-fraction description. Three different approaches are introduced to fine-tune the model using nonlinear programming methods to minimize the desired cost function. The first method uses an eigenvalue assignment technique to reassign a subset of system poles to improve the identified model. The second method deals with the model in the real Schur or modal form, reassigns a subset of system poles, and adjusts the columns (rows) of the input (output) influence matrix using a nonlinear optimizer. The third method also optimizes a subset of poles, but the input and output influence matrices are refined at every optimization step through least-squares procedures.

Antimicrobial Resistance of Campylobacter Isolates from Retail Meat in the United States between 2002 and 2007▿

PubMed Central

Zhao, S.; Young, S. R.; Tong, E.; Abbott, J. W.; Womack, N.; Friedman, S. L.; McDermott, P. F.

2010-01-01

The emergence of antimicrobial resistance in Campylobacter spp. has been a growing public health concern globally. The objectives of this study were to determine the prevalence, antimicrobial susceptibility, and genetic relatedness of Campylobacter spp. recovered by the National Antimicrobial Resistance Monitoring System (NARMS) retail meat program. Retail meat samples (n = 24,566) from 10 U.S. states collected between 2002 and 2007, consisting of 6,138 chicken breast, 6,109 ground turkey, 6,171 ground beef, and 6,148 pork chop samples, were analyzed. A total of 2,258 Campylobacter jejuni, 925 Campylobacter coli, and 7 Campylobacter lari isolates were identified. Chicken breast samples showed the highest contamination rate (49.9%), followed by ground turkey (1.6%), whereas both pork chops and ground beef had <0.5% contamination. The most common resistance was to doxycycline/tetracycline (46.6%), followed by nalidixic acid (18.5%), ciprofloxacin (17.4%), azithromycin and erythromycin (2.8%), telithromycin (2.4%), clindamycin (2.2%), and gentamicin (<0.1%). In a subset of isolates tested, no resistance to meropenem and florfenicol was seen. C. coli isolates showed higher resistance rates to antimicrobials, with the exception of doxycycline/tetracycline, than those seen for C. jejuni. Pulsed-field gel electrophoresis (PFGE) fingerprinting resulted in 1,226 PFGE profiles among the 2,318 isolates, with many clones being widely dispersed throughout the 6-year sampling period. PMID:20971875

Antimicrobial resistance of Campylobacter isolates from retail meat in the United States between 2002 and 2007.

PubMed

Zhao, S; Young, S R; Tong, E; Abbott, J W; Womack, N; Friedman, S L; McDermott, P F

2010-12-01

The emergence of antimicrobial resistance in Campylobacter spp. has been a growing public health concern globally. The objectives of this study were to determine the prevalence, antimicrobial susceptibility, and genetic relatedness of Campylobacter spp. recovered by the National Antimicrobial Resistance Monitoring System (NARMS) retail meat program. Retail meat samples (n = 24,566) from 10 U.S. states collected between 2002 and 2007, consisting of 6,138 chicken breast, 6,109 ground turkey, 6,171 ground beef, and 6,148 pork chop samples, were analyzed. A total of 2,258 Campylobacter jejuni, 925 Campylobacter coli, and 7 Campylobacter lari isolates were identified. Chicken breast samples showed the highest contamination rate (49.9%), followed by ground turkey (1.6%), whereas both pork chops and ground beef had <0.5% contamination. The most common resistance was to doxycycline/tetracycline (46.6%), followed by nalidixic acid (18.5%), ciprofloxacin (17.4%), azithromycin and erythromycin (2.8%), telithromycin (2.4%), clindamycin (2.2%), and gentamicin (<0.1%). In a subset of isolates tested, no resistance to meropenem and florfenicol was seen. C. coli isolates showed higher resistance rates to antimicrobials, with the exception of doxycycline/tetracycline, than those seen for C. jejuni. Pulsed-field gel electrophoresis (PFGE) fingerprinting resulted in 1,226 PFGE profiles among the 2,318 isolates, with many clones being widely dispersed throughout the 6-year sampling period.

Multiple contexts and adolescent body mass index: Schools, neighborhoods, and social networks.

PubMed

Evans, Clare R; Onnela, Jukka-Pekka; Williams, David R; Subramanian, S V

2016-08-01

Adolescent health and behaviors are influenced by multiple contexts, including schools, neighborhoods, and social networks, yet these contexts are rarely considered simultaneously. In this study we combine social network community detection analysis and cross-classified multilevel modeling in order to compare the contributions of each of these three contexts to the total variation in adolescent body mass index (BMI). Wave 1 of the National Longitudinal Study of Adolescent to Adult Health is used, and for robustness we conduct the analysis in both the core sample (122 schools; N = 14,144) and a sub-set of the sample (16 schools; N = 3335), known as the saturated sample due to its completeness of neighborhood data. After adjusting for relevant covariates, we find that the school-level and neighborhood-level contributions to the variance are modest compared with the network community-level (σ(2)school = 0.069, σ(2)neighborhood = 0.144, σ(2)network = 0.463). These results are robust to two alternative algorithms for specifying network communities, and to analysis in the saturated sample. While this study does not determine whether network effects are attributable to social influence or selection, it does highlight the salience of adolescent social networks and indicates that they may be a promising context to address in the design of health promotion programs. Copyright © 2016 Elsevier Ltd. All rights reserved.

VizieR Online Data Catalog: Lyα profile in 43 Green Pea galaxies (Yang+, 2017)

NASA Astrophysics Data System (ADS)

Yang, H.; Malhotra, S.; Gronke, M.; Rhoads, J. E.; Leitherer, C.; Wofford, A.; Jiang, T.; Dijkstra, M.; Tilvi, V.; Wang, J.

2018-03-01

In SDSS DR7, a sample of 251 Green Peas was observed as serendipitous spectroscopic targets (Cardamone+ 2009MNRAS.399.1191C). A subset of 66 Green Peas have sufficient signal-to-noise ratio (S/N) in both continuum and emission lines (Hα, Hβ, and [OIII]λ5007) to study galactic properties. In Paper I (Yang+ 2016ApJ...820..130Y), we matched these 66 Green Peas with the COS archive and studied Lyα escape in a sample of 12 Green Peas with COS UV spectra. To address the bias and expand the sample size, we took the Lyα spectra of 20 additional Green Peas (PI S. Malhotra, GO 14201). We also supplement this sample with 11 additional Green Peas from published literature. In total, we have 43 Green Peas from six HST programs -- 20 galaxies from GO 14201 (PI S. Malhotra), 9 galaxies from GO 12928 (PI A. Henry; Henry+ 2015ApJ...809...19H), 7 galaxies from GO 11727 and GO 13017 (PI T. Heckman; Heckman+ 2011ApJ...730....5H ; Alexandroff+ 2015ApJ...810..104A), 2 galaxies from GO 13293 (PI A. Jaskot; Jaskot & Oey 2014ApJ...791L..19J), and 5 galaxies from GO 13744 (PI T. Thuan; Izotov+ 2016MNRAS.461.3683I). (4 data files).

Application of Sequential Quadratic Programming to Minimize Smart Active Flap Rotor Hub Loads

NASA Technical Reports Server (NTRS)

Kottapalli, Sesi; Leyland, Jane

2014-01-01

In an analytical study, SMART active flap rotor hub loads have been minimized using nonlinear programming constrained optimization methodology. The recently developed NLPQLP system (Schittkowski, 2010) that employs Sequential Quadratic Programming (SQP) as its core algorithm was embedded into a driver code (NLP10x10) specifically designed to minimize active flap rotor hub loads (Leyland, 2014). Three types of practical constraints on the flap deflections have been considered. To validate the current application, two other optimization methods have been used: i) the standard, linear unconstrained method, and ii) the nonlinear Generalized Reduced Gradient (GRG) method with constraints. The new software code NLP10x10 has been systematically checked out. It has been verified that NLP10x10 is functioning as desired. The following are briefly covered in this paper: relevant optimization theory; implementation of the capability of minimizing a metric of all, or a subset, of the hub loads as well as the capability of using all, or a subset, of the flap harmonics; and finally, solutions for the SMART rotor. The eventual goal is to implement NLP10x10 in a real-time wind tunnel environment.

Transcriptional Mechanisms of Proneural Factors and REST in Regulating Neuronal Reprogramming of Astrocytes

PubMed Central

Masserdotti, Giacomo; Gillotin, Sébastien; Sutor, Bernd; Drechsel, Daniela; Irmler, Martin; Jørgensen, Helle F.; Sass, Steffen; Theis, Fabian J.; Beckers, Johannes; Berninger, Benedikt; Guillemot, François; Götz, Magdalena

2015-01-01

Summary Direct lineage reprogramming induces dramatic shifts in cellular identity, employing poorly understood mechanisms. Recently, we demonstrated that expression of Neurog2 or Ascl1 in postnatal mouse astrocytes generates glutamatergic or GABAergic neurons. Here, we take advantage of this model to study dynamics of neuronal cell fate acquisition at the transcriptional level. We found that Neurog2 and Ascl1 rapidly elicited distinct neurogenic programs with only a small subset of shared target genes. Within this subset, only NeuroD4 could by itself induce neuronal reprogramming in both mouse and human astrocytes, while co-expression with Insm1 was required for glutamatergic maturation. Cultured astrocytes gradually became refractory to reprogramming, in part by the repressor REST preventing Neurog2 from binding to the NeuroD4 promoter. Notably, in astrocytes refractory to Neurog2 activation, the underlying neurogenic program remained amenable to reprogramming by exogenous NeuroD4. Our findings support a model of temporal hierarchy for cell fate change during neuronal reprogramming. PMID:26119235

The Fortran-P Translator: Towards Automatic Translation of Fortran 77 Programs for Massively Parallel Processors

DOE PAGES

O'keefe, Matthew; Parr, Terence; Edgar, B. Kevin; ...

1995-01-01

Massively parallel processors (MPPs) hold the promise of extremely high performance that, if realized, could be used to study problems of unprecedented size and complexity. One of the primary stumbling blocks to this promise has been the lack of tools to translate application codes to MPP form. In this article we show how applications codes written in a subset of Fortran 77, called Fortran-P, can be translated to achieve good performance on several massively parallel machines. This subset can express codes that are self-similar, where the algorithm applied to the global data domain is also applied to each subdomain. Wemore » have found many codes that match the Fortran-P programming style and have converted them using our tools. We believe a self-similar coding style will accomplish what a vectorizable style has accomplished for vector machines by allowing the construction of robust, user-friendly, automatic translation systems that increase programmer productivity and generate fast, efficient code for MPPs.« less

The Circulatory System [and] Instructor's Guide: The Circulatory System. Health Occupations Education Module: Instructional Materials in Anatomy and Physiology for Pennsylvania Health Occupations Programs.

ERIC Educational Resources Information Center

National Evaluation Systems, Inc., Amherst, MA.

This module on the circulatory system is one of 17 modules designed for individualized instruction in health occupations education programs at both the secondary and postsecondary levels. It is part of an eight-unit subset on anatomy and physiology within the set of 17 modules. Following a preface which explains to the student how to use the…

Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM

PubMed Central

Gagnon, Jessica K.; Law, Sean M.; Brooks, Charles L.

2016-01-01

Protein-ligand docking is a commonly used method for lead identification and refinement. While traditional structure-based docking methods represent the receptor as a rigid body, recent developments have been moving toward the inclusion of protein flexibility. Proteins exist in an inter-converting ensemble of conformational states, but effectively and efficiently searching the conformational space available to both the receptor and ligand remains a well-appreciated computational challenge. To this end, we have developed the Flexible CDOCKER method as an extension of the family of complete docking solutions available within CHARMM. This method integrates atomically detailed side chain flexibility with grid-based docking methods, maintaining efficiency while allowing the protein and ligand configurations to explore their conformational space simultaneously. This is in contrast to existing approaches that use induced-fit like sampling, such as Glide or Autodock, where the protein or the ligand space is sampled independently in an iterative fashion. Presented here are developments to the CHARMM docking methodology to incorporate receptor flexibility and improvements to the sampling protocol as demonstrated with re-docking trials on a subset of the CCDC/Astex set. These developments within CDOCKER achieve docking accuracy competitive with or exceeding the performance of other widely utilized docking programs. PMID:26691274

Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM.

PubMed

Gagnon, Jessica K; Law, Sean M; Brooks, Charles L

2016-03-30

Protein-ligand docking is a commonly used method for lead identification and refinement. While traditional structure-based docking methods represent the receptor as a rigid body, recent developments have been moving toward the inclusion of protein flexibility. Proteins exist in an interconverting ensemble of conformational states, but effectively and efficiently searching the conformational space available to both the receptor and ligand remains a well-appreciated computational challenge. To this end, we have developed the Flexible CDOCKER method as an extension of the family of complete docking solutions available within CHARMM. This method integrates atomically detailed side chain flexibility with grid-based docking methods, maintaining efficiency while allowing the protein and ligand configurations to explore their conformational space simultaneously. This is in contrast to existing approaches that use induced-fit like sampling, such as Glide or Autodock, where the protein or the ligand space is sampled independently in an iterative fashion. Presented here are developments to the CHARMM docking methodology to incorporate receptor flexibility and improvements to the sampling protocol as demonstrated with re-docking trials on a subset of the CCDC/Astex set. These developments within CDOCKER achieve docking accuracy competitive with or exceeding the performance of other widely utilized docking programs. © 2015 Wiley Periodicals, Inc.

Serum proteomics reveals systemic dysregulation of innate immunity in type 1 diabetes

PubMed Central

Fillmore, Thomas L.; Schepmoes, Athena A.; Clauss, Therese R.W.; Gritsenko, Marina A.; Mueller, Patricia W.; Rewers, Marian; Atkinson, Mark A.; Smith, Richard D.

2013-01-01

Using global liquid chromatography-mass spectrometry (LC-MS)–based proteomics analyses, we identified 24 serum proteins that were significantly variant between those with type 1 diabetes (T1D) and healthy controls. Functionally, these proteins represent innate immune responses, the activation cascade of complement, inflammatory responses, and blood coagulation. Targeted verification analyses were performed on 52 surrogate peptides representing these proteins, with serum samples from an antibody standardization program cohort of 100 healthy control and 50 type 1 diabetic subjects. 16 peptides were verified as having very good discriminating power, with areas under the receiver operating characteristic curve ≥0.8. Further validation with blinded serum samples from an independent cohort (10 healthy control and 10 type 1 diabetics) demonstrated that peptides from platelet basic protein and C1 inhibitor achieved both 100% sensitivity and 100% specificity for classification of samples. The disease specificity of these proteins was assessed using sera from 50 age-matched type 2 diabetic individuals, and a subset of proteins, C1 inhibitor in particular, were exceptionally good discriminators between these two forms of diabetes. The panel of biomarkers distinguishing those with T1D from healthy controls and those with type 2 diabetes suggests that dysregulated innate immune responses may be associated with the development of this disorder. PMID:23277452

Serum proteomics reveals systemic dysregulation of innate immunity in type 1 diabetes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Qibin; Fillmore, Thomas L.; Schepmoes, Athena A.

Using global liquid chromatography-mass spectrometry (LC-MS)-based proteomics analyses, we identified 24 serum proteins significantly variant between those with type 1 diabetes and healthy controls. Functionally, these proteins represent innate immune responses, the activation cascade of complement, inflammatory responses and blood coagulation. Targeted verification analyses were performed on 52 surrogate peptides representing these proteins with serum samples from an antibody standardization program cohort of 100 healthy control and 50 type 1 diabetic subjects, and 16 peptides were verified having very good discriminating power, with areas under the receiver operator characteristic curve ≥ 0.8. Further validation with blinded serum samples from anmore » independent cohort (10 healthy control and 10 type 1 diabetic) demonstrated that peptides from platelet basic protein and C1 inhibitor achieved both 100% sensitivity and 100% specificity for classification of samples. The disease specificity of these proteins was assessed using serum from 50 age matched type 2 diabetic individuals, and a subset of proteins, particularly C1 inhibitor were exceptionally good discriminators between these two forms of diabetes. The panel of biomarkers distinguishing those with type 1 diabetes from healthy control and type 2 diabetes suggests dysregulated innate immune responses may be associated with the development of this disorder.« less

Limits of Generalizing in Education Research: Why Criteria for Research Generalization Should Include Population Heterogeneity and Uses of Knowledge Claims

ERIC Educational Resources Information Center

Ercikan, Kadriye; Roth, Wolff-Michael

2014-01-01

Context: Generalization is a critical concept in all research designed to generate knowledge that applies to all elements of a unit (population) while studying only a subset of these elements (sample). Commonly applied criteria for generalizing focus on experimental design or representativeness of samples of the population of units. The criteria…

Fashion, Paper Dolls and Multiplicatives

ERIC Educational Resources Information Center

Ura, Suzana Kaori; Stein-Barana, Alzira C. M.; Munhoz, Deisy P.

2011-01-01

The multiplicative principle is the tool allowing the counting of groups that can be described by a sequence of events. An event is a subset of sample space, i.e. a collection of possible outcomes, which may be equal to or smaller than the sample space as a whole. It is important that students understand this basic principle early on and know how…

Ground-based digital imagery for tree stem analysis

Treesearch

Neil Clark; Daniel L. Schmoldt; Randolph H. Wynne; Matthew F. Winn; Philip A. Araman

2000-01-01

In the USA, a subset of permanent forest sample plots within each geographic region are intensively measured to obtain estimates of tree volume and products. The detailed field measurements required for this type of sampling are both time consuming and error prone. We are attempting to reduce both of these factors with the aid of a commercially-available solid-state...

The Support Needs of Children with Intellectual Disability and Autism: Implications for Supports Planning and Subgroup Classification

ERIC Educational Resources Information Center

Shogren, Karrie A.; Shaw, Leslie A.; Wehmeyer, Michael L.; Thompson, James R.; Lang, Kyle M.; Tassé, Marc J.; Schalock, Robert L.

2017-01-01

The Supports Intensity Scale-Children's version (SIS-C) was developed to provide a standardized measure of support needs of children with intellectual disability. Over half of the norming sample had a secondary diagnosis of autism. Using this subset of the sample, we engaged in exploratory analysis to examine the degree to which latent clusters…

Oregon ground-water quality and its relation to hydrogeological factors; a statistical approach

USGS Publications Warehouse

Miller, T.L.; Gonthier, J.B.

1984-01-01

An appraisal of Oregon ground-water quality was made using existing data accessible through the U.S. Geological Survey computer system. The data available for about 1,000 sites were separated by aquifer units and hydrologic units. Selected statistical moments were described for 19 constituents including major ions. About 96 percent of all sites in the data base were sampled only once. The sample data were classified by aquifer unit and hydrologic unit and analysis of variance was run to determine if significant differences exist between the units within each of these two classifications for the same 19 constituents on which statistical moments were determined. Results of the analysis of variance indicated both classification variables performed about the same, but aquifer unit did provide more separation for some constituents. Samples from the Rogue River basin were classified by location within the flow system and type of flow system. The samples were then analyzed using analysis of variance on 14 constituents to determine if there were significant differences between subsets classified by flow path. Results of this analysis were not definitive, but classification as to the type of flow system did indicate potential for segregating water-quality data into distinct subsets. (USGS)

Querying Co-regulated Genes on Diverse Gene Expression Datasets Via Biclustering.

PubMed

Deveci, Mehmet; Küçüktunç, Onur; Eren, Kemal; Bozdağ, Doruk; Kaya, Kamer; Çatalyürek, Ümit V

2016-01-01

Rapid development and increasing popularity of gene expression microarrays have resulted in a number of studies on the discovery of co-regulated genes. One important way of discovering such co-regulations is the query-based search since gene co-expressions may indicate a shared role in a biological process. Although there exist promising query-driven search methods adapting clustering, they fail to capture many genes that function in the same biological pathway because microarray datasets are fraught with spurious samples or samples of diverse origin, or the pathways might be regulated under only a subset of samples. On the other hand, a class of clustering algorithms known as biclustering algorithms which simultaneously cluster both the items and their features are useful while analyzing gene expression data, or any data in which items are related in only a subset of their samples. This means that genes need not be related in all samples to be clustered together. Because many genes only interact under specific circumstances, biclustering may recover the relationships that traditional clustering algorithms can easily miss. In this chapter, we briefly summarize the literature using biclustering for querying co-regulated genes. Then we present a novel biclustering approach and evaluate its performance by a thorough experimental analysis.

Enhanced sensitivity to glucocorticoids in cytarabine-resistant AML.

PubMed

Malani, D; Murumägi, A; Yadav, B; Kontro, M; Eldfors, S; Kumar, A; Karjalainen, R; Majumder, M M; Ojamies, P; Pemovska, T; Wennerberg, K; Heckman, C; Porkka, K; Wolf, M; Aittokallio, T; Kallioniemi, O

2017-05-01

We sought to identify drugs that could counteract cytarabine resistance in acute myeloid leukemia (AML) by generating eight resistant variants from MOLM-13 and SHI-1 AML cell lines by long-term drug treatment. These cells were compared with 66 ex vivo chemorefractory samples from cytarabine-treated AML patients. The models and patient cells were subjected to genomic and transcriptomic profiling and high-throughput testing with 250 emerging and clinical oncology compounds. Genomic profiling uncovered deletion of the deoxycytidine kinase (DCK) gene in both MOLM-13- and SHI-1-derived cytarabine-resistant variants and in an AML patient sample. Cytarabine-resistant SHI-1 variants and a subset of chemorefractory AML patient samples showed increased sensitivity to glucocorticoids that are often used in treatment of lymphoid leukemia but not AML. Paired samples taken from AML patients before treatment and at relapse also showed acquisition of glucocorticoid sensitivity. Enhanced glucocorticoid sensitivity was only seen in AML patient samples that were negative for the FLT3 mutation (P=0.0006). Our study shows that development of cytarabine resistance is associated with increased sensitivity to glucocorticoids in a subset of AML, suggesting a new therapeutic strategy that should be explored in a clinical trial of chemorefractory AML patients carrying wild-type FLT3.

Enhanced sensitivity to glucocorticoids in cytarabine-resistant AML

PubMed Central

Malani, D; Murumägi, A; Yadav, B; Kontro, M; Eldfors, S; Kumar, A; Karjalainen, R; Majumder, M M; Ojamies, P; Pemovska, T; Wennerberg, K; Heckman, C; Porkka, K; Wolf, M; Aittokallio, T; Kallioniemi, O

2017-01-01

We sought to identify drugs that could counteract cytarabine resistance in acute myeloid leukemia (AML) by generating eight resistant variants from MOLM-13 and SHI-1 AML cell lines by long-term drug treatment. These cells were compared with 66 ex vivo chemorefractory samples from cytarabine-treated AML patients. The models and patient cells were subjected to genomic and transcriptomic profiling and high-throughput testing with 250 emerging and clinical oncology compounds. Genomic profiling uncovered deletion of the deoxycytidine kinase (DCK) gene in both MOLM-13- and SHI-1-derived cytarabine-resistant variants and in an AML patient sample. Cytarabine-resistant SHI-1 variants and a subset of chemorefractory AML patient samples showed increased sensitivity to glucocorticoids that are often used in treatment of lymphoid leukemia but not AML. Paired samples taken from AML patients before treatment and at relapse also showed acquisition of glucocorticoid sensitivity. Enhanced glucocorticoid sensitivity was only seen in AML patient samples that were negative for the FLT3 mutation (P=0.0006). Our study shows that development of cytarabine resistance is associated with increased sensitivity to glucocorticoids in a subset of AML, suggesting a new therapeutic strategy that should be explored in a clinical trial of chemorefractory AML patients carrying wild-type FLT3. PMID:27833094

A Large Ordinary Chondrite Shower in the Dominion Range

NASA Technical Reports Server (NTRS)

Satterwhite, C. E.; Righter, K.; Harrington, R.; McBride, K. M.; Funk, R.

2017-01-01

The US Antarctic Meteorite Program has visited the Dominion Range in the Transantarctic Mountains during several different seasons, including the 1985, 2003, 2008, 2010, and 2014 seasons. Total recovered meteorites from this region is over 2000. The 2008 and 2010 seasons have been fully classified and, respectively) revealing the presence of a large meteorite shower that comprises approximately 60% of all samples recovered in those two seasons. The oil immersion classification suggests that this shower is LL chondrite material, whereas published magnetic susceptibility (MS; log chi) measurements yield L chondrite values. However, usually random sampling of a large collection like this would uncover EOC material for which we have prepared thin sections. In this case, no LL chondrite materials have been found in thin section, suggesting that the shower might instead be an L chondrite. L and LL chondrites are notoriously difficult to distinguish using oil immersion techniques. To better characterize this large group of samples, we have decided to examine some of the large members of this group, using EMPA analysis of the olivines to verify the classifications. With a compositional link between this subset of samples, and the MS measurements, we can more confidently classify the samples making up this pairing group. Subsequently, more accurate and meaningful comparisons may be drawn between this pairing group and some other Antarctic pairing groups such as from the Queen Alexandra Range (QUE), and Lewis Cliffs Ice Tongue (LEW). electron microprobe analysis

Estuarine water quality in parks of the Northeast Coastal and Barrier Network: Development and early implementation of vital signs estuarine nutrient-enrichment monitoring, 2003-06

USGS Publications Warehouse

Kopp, Blaine S.; Nielsen, Martha; Glisic, Dejan; Neckles, Hilary A.

2009-01-01

This report documents results of pilot tests of a protocol for monitoring estuarine nutrient enrichment for the Vital Signs Monitoring Program of the National Park Service Northeast Coastal and Barrier Network. Data collected from four parks during protocol development in 2003-06 are presented: Gateway National Recreation Area, Colonial National Historic Park, Fire Island National Seashore, and Assateague Island National Seashore. The monitoring approach incorporates several spatial and temporal designs to address questions at a hierarchy of scales. Indicators of estuarine response to nutrient enrichment were sampled using a probability design within park estuaries during a late-summer index period. Monitoring variables consisted of dissolved-oxygen concentration, chlorophyll a concentration, water temperature, salinity, attenuation of downwelling photosynthetically available radiation (PAR), and turbidity. The statistical sampling design allowed the condition of unsampled locations to be inferred from the distribution of data from a set of randomly positioned "probability" stations. A subset of sampling stations was sampled repeatedly during the index period, and stations were not rerandomized in subsequent years. These "trend stations" allowed us to examine temporal variability within the index period, and to improve the sensitivity of the monitoring protocol to detecting change through time. Additionally, one index site in each park was equipped for continuous monitoring throughout the index period. Thus, the protocol includes elements of probabilistic and targeted spatial sampling, and the temporal intensity ranges from snapshot assessments to continuous monitoring.

The use of isotypic control antibodies in the analysis of CD3+ and CD3+, CD4+ lymphocyte subsets by flow cytometry. Are they really necessary?

PubMed

Sreenan, J J; Tbakhi, A; Edinger, M G; Tubbs, R R

1997-02-01

Isotypic control reagents are defined as irrelevant antibodies of the same immunoglobulin class as the relevant reagent antibody in a flow cytometry panel. The use of the isotypic control antibody has been advocated as a necessary quality control measure in analysis of flow cytometry. The purpose of this study was to determine the necessity of an isotypic control antibody in the analysis of CD3+ and CD3+, CD4+ lymphocyte subsets. We performed a prospective study of 46 consecutive patient samples received for lymphocyte subset analysis to determine the need for the isotypic control. For each sample, a sham buffer (autocontrol) and isotypic control reagent were stained for three-color immunofluorescence, processed, and identically analyzed with Attractors software. The Attractors software allowed independent, multiparametric, simultaneous gating; was able to identically and reproducibly process each list mode file; and yielded population data in spreadsheet form. Statistical analysis (Fisher's z test) revealed no difference between the CD3+ autocontrol and CD3+ isotypic control (correlation = 1, P < .0001) or between the CD3+, CD4+ autocontrol and the CD3+, CD4+ isotypic control (correlation = 1, P < .0001). The elimination of the isotypic control reagent resulted in a total cost savings of $3.36 per test. Additionally, the subtraction of isotypic background can artifactually depress population enumeration. The use of an isotypic control antibody is not necessary to analyze flow cytometric data that result in discrete cell populations, such as CD3+ and CD3+, CD4+ lymphocyte subsets. The elimination of this unnecessary quality control measure results in substantial cost savings.

Reproducibility, stability, and biological variability of thrombin generation using calibrated automated thrombography in healthy dogs.

PubMed

Cuq, Benoît; Blois, Shauna L; Wood, R Darren; Monteith, Gabrielle; Abrams-Ogg, Anthony C; Bédard, Christian; Wood, Geoffrey A

2018-06-01

Thrombin plays a central role in hemostasis and thrombosis. Calibrated automated thrombography (CAT), a thrombin generation assay, may be a useful test for hemostatic disorders in dogs. To describe CAT results in a group of healthy dogs, and assess preanalytical variables and biological variability. Forty healthy dogs were enrolled. Lag time (Lag), time to peak (ttpeak), peak thrombin generation (peak), and endogenous thrombin potential (ETP) were measured. Direct jugular venipuncture and winged-needle catheter-assisted saphenous venipuncture were used to collect samples from each dog, and results were compared between methods. Sample stability at -80°C was assessed over 12 months in a subset of samples. Biological variability of CAT was assessed via nested ANOVA using samples obtained weekly from a subset of 9 dogs for 4 consecutive weeks. Samples for CAT were stable at -80°C over 12 months of storage. Samples collected via winged-needle catheter venipuncture showed poor repeatability compared to direct venipuncture samples; there was also poor agreement between the 2 sampling methods. Intra-individual variability of CAT parameters was below 25%; inter-individual variability ranged from 36.9% to 78.5%. Measurement of thrombin generation using CAT appears to be repeatable in healthy dogs, and samples are stable for at least 12 months when stored at -80°C. Direct venipuncture sampling is recommended for CAT. Low indices of individuality suggest that subject-based reference intervals are more suitable when interpreting CAT results. © 2018 American Society for Veterinary Clinical Pathology.

Characterization of Machine Variability and Progressive Heat Treatment in Selective Laser Melting of Inconel 718

NASA Technical Reports Server (NTRS)

Prater, T.; Tilson, W.; Jones, Z.

2015-01-01

The absence of an economy of scale in spaceflight hardware makes additive manufacturing an immensely attractive option for propulsion components. As additive manufacturing techniques are increasingly adopted by government and industry to produce propulsion hardware in human-rated systems, significant development efforts are needed to establish these methods as reliable alternatives to conventional subtractive manufacturing. One of the critical challenges facing powder bed fusion techniques in this application is variability between machines used to perform builds. Even with implementation of robust process controls, it is possible for two machines operating at identical parameters with equivalent base materials to produce specimens with slightly different material properties. The machine variability study presented here evaluates 60 specimens of identical geometry built using the same parameters. 30 samples were produced on machine 1 (M1) and the other 30 samples were built on machine 2 (M2). Each of the 30-sample sets were further subdivided into three subsets (with 10 specimens in each subset) to assess the effect of progressive heat treatment on machine variability. The three categories for post-processing were: stress relief, stress relief followed by hot isostatic press (HIP), and stress relief followed by HIP followed by heat treatment per AMS 5664. Each specimen (a round, smooth tensile) was mechanically tested per ASTM E8. Two formal statistical techniques, hypothesis testing for equivalency of means and one-way analysis of variance (ANOVA), were applied to characterize the impact of machine variability and heat treatment on six material properties: tensile stress, yield stress, modulus of elasticity, fracture elongation, and reduction of area. This work represents the type of development effort that is critical as NASA, academia, and the industrial base work collaboratively to establish a path to certification for additively manufactured parts. For future flight programs, NASA and its commercial partners will procure parts from vendors who will use a diverse range of machines to produce parts and, as such, it is essential that the AM community develop a sound understanding of the degree to which machine variability impacts material properties.

Damage evolution analysis of coal samples under cyclic loading based on single-link cluster method

NASA Astrophysics Data System (ADS)

Zhang, Zhibo; Wang, Enyuan; Li, Nan; Li, Xuelong; Wang, Xiaoran; Li, Zhonghui

2018-05-01

In this paper, the acoustic emission (AE) response of coal samples under cyclic loading is measured. The results show that there is good positive relation between AE parameters and stress. The AE signal of coal samples under cyclic loading exhibits an obvious Kaiser Effect. The single-link cluster (SLC) method is applied to analyze the spatial evolution characteristics of AE events and the damage evolution process of coal samples. It is found that a subset scale of the SLC structure becomes smaller and smaller when the number of cyclic loading increases, and there is a negative linear relationship between the subset scale and the degree of damage. The spatial correlation length ξ of an SLC structure is calculated. The results show that ξ fluctuates around a certain value from the second cyclic loading process to the fifth cyclic loading process, but spatial correlation length ξ clearly increases in the sixth loading process. Based on the criterion of microcrack density, the coal sample failure process is the transformation from small-scale damage to large-scale damage, which is the reason for changes in the spatial correlation length. Through a systematic analysis, the SLC method is an effective method to research the damage evolution process of coal samples under cyclic loading, and will provide important reference values for studying coal bursts.

Robust best linear estimator for Cox regression with instrumental variables in whole cohort and surrogates with additive measurement error in calibration sample

PubMed Central

Wang, Ching-Yun; Song, Xiao

2017-01-01

SUMMARY Biomedical researchers are often interested in estimating the effect of an environmental exposure in relation to a chronic disease endpoint. However, the exposure variable of interest may be measured with errors. In a subset of the whole cohort, a surrogate variable is available for the true unobserved exposure variable. The surrogate variable satisfies an additive measurement error model, but it may not have repeated measurements. The subset in which the surrogate variables are available is called a calibration sample. In addition to the surrogate variables that are available among the subjects in the calibration sample, we consider the situation when there is an instrumental variable available for all study subjects. An instrumental variable is correlated with the unobserved true exposure variable, and hence can be useful in the estimation of the regression coefficients. In this paper, we propose a nonparametric method for Cox regression using the observed data from the whole cohort. The nonparametric estimator is the best linear combination of a nonparametric correction estimator from the calibration sample and the difference of the naive estimators from the calibration sample and the whole cohort. The asymptotic distribution is derived, and the finite sample performance of the proposed estimator is examined via intensive simulation studies. The methods are applied to the Nutritional Biomarkers Study of the Women’s Health Initiative. PMID:27546625

Size, time, and asynchrony matter: the species-area relationship for parasites of freshwater fishes.

PubMed

Zelmer, Derek A

2014-10-01

The tendency to attribute species-area relationships to "island biogeography" effectively bypasses the examination of specific mechanisms that act to structure parasite communities. Positive covariation between fish size and infrapopulation richness should not be examined within the typical extinction-based paradigm, but rather should be addressed from the standpoint of differences in colonization potential among individual hosts. Although most mechanisms producing the aforementioned pattern constitute some variation of passive sampling, the deterministic aspects of the accumulation of parasite individuals by fish hosts makes untenable the suggestion that infracommunities of freshwater fishes are stochastic assemblages. At the component community level, application of extinction-dependent mechanisms might be appropriate, given sufficient time for colonization, but these structuring forces likely act indirectly through their effects on the host community to increase the probability of parasite persistence. At all levels, the passive sampling hypothesis is a relevant null model. The tendency for mechanisms that produce species-area relationships to produce nested subset patterns means that for most systems, the passive sampling hypothesis can be addressed through the application of appropriate null models of nested subset structure.

A reassessment of IgM memory subsets in humans

PubMed Central

Bagnara, Davide; Squillario, Margherita; Kipling, David; Mora, Thierry; Walczak, Aleksandra M.; Da Silva, Lucie; Weller, Sandra; Dunn-Walters, Deborah K.; Weill, Jean-Claude; Reynaud, Claude-Agnès

2015-01-01

From paired blood and spleen samples from three adult donors we performed high-throughput V-h sequencing of human B-cell subsets defined by IgD and CD27 expression: IgD+CD27+ (“MZ”), IgD−CD27+(“memory”, including IgM (“IgM-only”), IgG and IgA) and IgD−CD27− cells (“double-negative”, including IgM, IgG and IgA). 91,294 unique sequences clustered in 42,670 clones, revealing major clonal expansions in each of these subsets. Among these clones, we further analyzed those shared sequences from different subsets or tissues for Vh-gene mutation, H-CDR3-length, and Vh/Jh usage, comparing these different characteristics with all sequences from their subset of origin, for which these parameters constitute a distinct signature. The IgM-only repertoire profile differed notably from that of MZ B cells by a higher mutation frequency, and lower Vh4 and higher Jh6 gene usage. Strikingly, IgM sequences from clones shared between the MZ and the memory IgG/IgA compartments showed a mutation and repertoire profile of IgM-only and not of MZ B cells. Similarly, all IgM clonal relationships (between MZ, IgM-only, and double-negative compartments) involved sequences with the characteristics of IgM-only B cells. Finally, clonal relationships between tissues suggested distinct recirculation characteristics between MZ and switched B cells. The “IgM-only” subset (including cells with its repertoire signature but higher IgD or lower CD27 expression levels) thus appear as the only subset showing precursor-product relationships with CD27+ switched memory B cells, indicating that they represent germinal center-derived IgM memory B cells, and that IgM memory and MZ B cells constitute two distinct entities. PMID:26355154

A Reassessment of IgM Memory Subsets in Humans.

PubMed

Bagnara, Davide; Squillario, Margherita; Kipling, David; Mora, Thierry; Walczak, Aleksandra M; Da Silva, Lucie; Weller, Sandra; Dunn-Walters, Deborah K; Weill, Jean-Claude; Reynaud, Claude-Agnès

2015-10-15

From paired blood and spleen samples from three adult donors, we performed high-throughput VH sequencing of human B cell subsets defined by IgD and CD27 expression: IgD(+)CD27(+) ("marginal zone [MZ]"), IgD(-)CD27(+) ("memory," including IgM ["IgM-only"], IgG and IgA) and IgD(-)CD27(-) cells ("double-negative," including IgM, IgG, and IgA). A total of 91,294 unique sequences clustered in 42,670 clones, revealing major clonal expansions in each of these subsets. Among these clones, we further analyzed those shared sequences from different subsets or tissues for VH gene mutation, H-CDR3-length, and VH/JH usage, comparing these different characteristics with all sequences from their subset of origin for which these parameters constitute a distinct signature. The IgM-only repertoire profile differed notably from that of MZ B cells by a higher mutation frequency and lower VH4 and higher JH6 gene usage. Strikingly, IgM sequences from clones shared between the MZ and the memory IgG/IgA compartments showed a mutation and repertoire profile of IgM-only and not of MZ B cells. Similarly, all IgM clonal relationships (among MZ, IgM-only, and double-negative compartments) involved sequences with the characteristics of IgM-only B cells. Finally, clonal relationships between tissues suggested distinct recirculation characteristics between MZ and switched B cells. The "IgM-only" subset (including cells with its repertoire signature but higher IgD or lower CD27 expression levels) thus appear as the only subset showing precursor-product relationships with CD27(+) switched memory B cells, indicating that they represent germinal center-derived IgM memory B cells and that IgM memory and MZ B cells constitute two distinct entities. Copyright © 2015 by The American Association of Immunologists, Inc.

Method for Statically Checking an Object-oriented Computer Program Module

NASA Technical Reports Server (NTRS)

Bierhoff, Kevin M. (Inventor); Aldrich, Jonathan (Inventor)

2012-01-01

A method for statically checking an object-oriented computer program module includes the step of identifying objects within a computer program module, at least one of the objects having a plurality of references thereto, possibly from multiple clients. A discipline of permissions is imposed on the objects identified within the computer program module. The permissions enable tracking, from among a discrete set of changeable states, a subset of states each object might be in. A determination is made regarding whether the imposed permissions are violated by a potential reference to any of the identified objects. The results of the determination are output to a user.

Family homework and school-based sex education: delaying early adolescents' sexual behavior.

PubMed

Grossman, Jennifer M; Frye, Alice; Charmaraman, Linda; Erkut, Sumru

2013-11-01

Early sexual activity can undermine adolescents' future school success and health outcomes. The purpose of this study was to assess the role of a family homework component of a comprehensive sex education intervention in delaying sexual initiation for early adolescents and to explore what social and contextual factors prevent adolescents from completing these family homework activities. This mixed methods study included 6th- and 7th-grade survey responses from 706 students at 11 middle school schools receiving a sex education intervention, as well as interviews from a subset of 33, 7th-grade students from the larger sample. Adolescents who completed more family homework assignments were less likely to have vaginal intercourse in 7th grade than those who completed fewer assignments, after controlling for self-reports of having had vaginal intercourse in 6th grade and demographic variables. Participants' explanations for not completing assignments included personal, curriculum, and family-based reasons. Family homework activities designed to increase family communication about sexual issues can delay sex among early adolescents and contribute to school-based sex education programs. Successful sex education programs must identify and address barriers to family homework completion. © 2013, American School Health Association.

Genetic diversity, kinship analysis, and broodstock management of captive Atlantic sturgeon for population restoration

USGS Publications Warehouse

Henderson, A.P.; Spidle, A.P.; King, T.L.

2005-01-01

Captive Atlantic sturgeon Acipenser oxyrinchus considered for use as broodstock in a restoration program were genotyped using nuclear DNA microsatellites and compared to wild collections from the Hudson River, New York (source of parents of the captive sturgeon) and from Albemarle Sound, North Carolina. Because the potential broodfish were the progeny of a small number of parents, maintaining genetic diversity and minimizing inbreeding is essential to a successful breeding and supplementation program. The microsatellite loci used in this analysis generated unique multilocus genotypes for each of 136 Atlantic sturgeon. Analyses indicated significant genetic separation between the New York and North Carolina collections and correctly identified the potential broodstock as a subset of the Hudson River population. Pairwise genetic distance (-In proportion of shared alleles) between half and full siblings in the potential broodfish was as great as 1.386, a value exceeded by only 36% of the sampled broodfish pairs available for mating. Because the current broodstock population does not seem to have deviated far from their ancestral population in the Hudson River, progeny from that broodstock, or the parents themselves, would seem to be genetically suitable for release back into the Hudson River.

Long-term environmental monitoring for assessment of change: measurement inconsistencies over time and potential solutions.

PubMed

Ellingsen, Kari E; Yoccoz, Nigel G; Tveraa, Torkild; Hewitt, Judi E; Thrush, Simon F

2017-10-30

The importance of long-term environmental monitoring and research for detecting and understanding changes in ecosystems and human impacts on natural systems is widely acknowledged. Over the last decades, a number of critical components for successful long-term monitoring have been identified. One basic component is quality assurance/quality control protocols to ensure consistency and comparability of data. In Norway, the authorities require environmental monitoring of the impacts of the offshore petroleum industry on the Norwegian continental shelf, and in 1996, a large-scale regional environmental monitoring program was established. As a case study, we used a sub-set of data from this monitoring to explore concepts regarding best practices for long-term environmental monitoring. Specifically, we examined data from physical and chemical sediment samples and benthic macroinvertebrate assemblages from 11 stations from six sampling occasions during the period 1996-2011. Despite the established quality assessment and quality control protocols for this monitoring program, we identified several data challenges, such as missing values and outliers, discrepancies in variable and station names, changes in procedures without calibration, and different taxonomic resolution. Furthermore, we show that the use of different laboratories over time makes it difficult to draw conclusions with regard to some of the observed changes. We offer recommendations to facilitate comparison of data over time. We also present a new procedure to handle different taxonomic resolution, so valuable historical data is not discarded. These topics have a broader relevance and application than for our case study.

Survival of porcine reproductive and respiratory syndrome virus in houseflies

PubMed Central

Otake, Satoshi; Dee, Scott A.; Moon, Roger D.; Rossow, Kurt D.; Trincado, Carlos; Farnham, MacDonald; Pijoan, Carlos

2003-01-01

The objectives of the study were to determine the duration of porcine reproductive and respiratory syndrome virus (PRRSV) survival in houseflies (Musca domestica Linnaeus) following feeding on an infected pig, and to determine whether the virus was present on the exterior surface or within the internal viscera of the fly. A total of 210 laboratory-colonized houseflies were allowed to feed to repletion on a pig, experimentally infected with PRRSV on day 7 postinoculation, and then maintained alive under laboratory conditions (27°C). Two subsets (A and B) of 30 flies were collected at each of the following sampling points; 0, 6, and 12 hours post feeding (pf). Subset A contained an extra group of 30 flies collected at 24 hours pf due to the availability of extra flies. Flies in subset A were processed as whole fly homogenates, while the exterior surface washes and digestive organs were collected from flies in subset B. Whole fly homogenates, collected at 0, 6, and 12 hours pf, were positive by both polymerase chain reaction (PCR) and swine bioassay. Digestive organs, collected at 0 and 12 hours pf, were positive by PCR and swine bioassay. The PRRSV RNA was detected by PCR from the exterior surface wash of subset B flies collected at 0, 6, and 12 hours pf; however, only the subset collected at 0 hour pf was swine bioassay-positive. This study indicates that infectious PRRSV can survive within the intestinal tract of houseflies for up to 12 hours following feeding on an infected pig, but only for a short period on the exterior surface of the flies. PMID:12889726

UPEML: a machine-portable CDC Update emulator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mehlhorn, T.A.; Young, M.F.

1984-12-01

UPEML is a machine-portable CDC Update emulation program. UPEML is written in ANSI standard Fortran-77 and is relatively simple and compact. It is capable of emulating a significant subset of the standard CDC Update functions including program library creation and subsequent modification. Machine-portability is an essential attribute of UPEML. It was written primarily to facilitate the use of CDC-based scientific packages on alternate computer systems such as the VAX 11/780 and the IBM 3081.

A Production-Quality Unix Very High Speed Integrated Circuit (VHSIC) Hardware Description Language (VHDL) Subset Analyzer.

DTIC Science & Technology

1987-12-01

1985:55; Nash, 1984:18). Because of this, the Department of Defense began a program , VHDL, to standardize a hardware description language for VHSIC... Deitel , 1984:507-508). This operating system (or environment) is in general use in the commercial world. Universities, given the responsibility to ...though not necessarily exhaustive) test suite designed to exercise each VHDL grammar rule and associated program modules as thor- oughly as possible. The

F-35 Joint Strike Fighter (JSF) Program

DTIC Science & Technology

2012-02-16

Operational Test and Evaluation ( IOT &E), a subset of SDD.61 The eight partner countries are expected to purchase hundreds of F-35s, with the United...Netherlands have agreed to participate in the IOT &E program. UK, the senior F-35 partner, will have the strongest participation in the IOT &E phase...testing. (Telephone conversation with OSD/AT&L, October 3, 2007.) Other partner nations are still weighing their option to participate in the IOT &E

Integration of T Cell Receptor, Notch and Cytokine Signals Programs in Mouse γδ T Cell Effector Differentiation.

PubMed

Zarin, Payam; In, Tracy S H; Chen, Edward L Y; Singh, Jastaranpreet; Wong, Gladys W; Mohtashami, Mahmood; Wiest, David L; Anderson, Michele K; Zúñiga-Pflücker, Juan Carlos

2018-05-13

γδ T-cells perform a wide range of tissue and disease specific functions that are dependent on the effector cytokines produced by these cells. However, the aggregate signals required for the development of interferon-γ (IFNγ) and interleukin-17 (IL-17) producing γδ T-cells remain unknown. Here, we define the cues involved in the functional programming of γδ T-cells, by examining the roles of T-cell receptor (TCR), Notch, and cytokine-receptor signaling. KN6 γδTCR-transduced Rag2 -/- T-cell progenitors were cultured on stromal cells variably expressing TCR and Notch ligands, supplemented with different cytokines. We found that distinct combinations of these signals are required to program IFNγ versus IL-17 producing γδ T cell subsets, with Notch and weak TCR ligands optimally enabling development of γδ17 cells in the presence of IL-1β, IL-21 and IL-23. Notably, these cytokines were also shown to be required for the intrathymic development of γδ17 cells. Together, this work provides a framework of how signals downstream of TCR, Notch and cytokine receptors integrate to program the effector function of IFNγ and IL-17 producing γδ T-cell subsets. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

TOWARD PRECISE AGES FOR SINGLE STARS IN THE FIELD. GYROCHRONOLOGY CONSTRAINTS AT SEVERAL Gyr USING WIDE BINARIES. I. AGES FOR INITIAL SAMPLE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chaname, Julio; Ramirez, Ivan

2012-02-10

We present a program designed to obtain age-rotation measurements of solar-type dwarfs to be used in the calibration of gyrochronology relations at ages of several Gyr. This is a region of parameter space crucial for the large-scale study of the Milky Way, and where the only constraint available today is that provided by the Sun. Our program takes advantage of a set of wide binaries selected so that one component is an evolved star and the other is a main-sequence star of FGK type. In this way, we obtain the age of the system from the evolved star, while themore » rotational properties of the main-sequence component provide the information relevant for gyrochronology regarding the spin-down of solar-type stars. By mining currently available catalogs of wide binaries, we assemble a sample of 37 pairs well positioned for our purposes: 19 with turnoff or subgiant primaries and 18 with white dwarf components. Using high-resolution optical spectroscopy, we measure precise stellar parameters for a subset of 15 of the pairs with turnoff/subgiant components and use these to derive isochronal ages for the corresponding systems. Ages for 16 of the 18 pairs with white dwarf components are taken from the literature. The ages of this initial sample of 31 wide binaries range from 1 to 9 Gyr, with precisions better than {approx}20% for almost half of these systems. When combined with measurements of the rotation period of their main-sequence components, these wide binary systems would potentially provide a similar number of points useful for the calibration of gyrochronology relations at very old ages.« less

The Effects of an Integrated Community Case Management Strategy on the Appropriate Treatment of Children and Child Mortality in Kono District, Sierra Leone: A Program Evaluation.

PubMed

Ratnayake, Ruwan; Ratto, Jeffrey; Hardy, Colleen; Blanton, Curtis; Miller, Laura; Choi, Mary; Kpaleyea, John; Momoh, Pheabean; Barbera, Yolanda

2017-09-01

Integrated community case management (iCCM) aims to reduce child mortality in areas with poor access to health care. iCCM was implemented in 2009 in Kono district, Sierra Leone, a postconflict area with high under-five mortality rates (U5MRs). We evaluated iCCM's impact and effects on child health using cluster surveys in 2010 (midterm) and 2013 (endline) to compare indicators on child mortality, coverage of appropriate treatment, timely access to care, quality of care, and recognition of community health workers (CHWs). The sample size was powered to detect a 28% decline in U5MR. Clusters were selected proportional to population size. All households were sampled to measure mortality and systematic random sampling was used to measure coverage in a subset of households. We used program data to evaluate utilization and access; 5,257 (2010) and 3,649 (2013) households were surveyed. U5MR did not change significantly (4.54 [95% confidence interval [CI]: 3.47-5.60] to 3.95 [95% CI: 3.06-4.83] deaths per 1,000 per month ( P = 0.4)) though a relative change smaller than 28% could not be detected. CHWs were the first source of care for 52% (2010) and 50.9% (2013) of children. Coverage of appropriate treatment of fever by CHWs or peripheral health units increased from 45.5% [95% CI: 39.2-52.0] to 58.2% [95% CI: 50.5-65.5] ( P = 0.01); changes for diarrhea and pneumonia were not significant. The continued reliance on the CHW as the first source of care and improved coverage for the appropriate treatment of fever support iCCM's role in Kono district.

An Assessment of the Dimensionality of SAT-Mathematical.

ERIC Educational Resources Information Center

Lawrence, Ida M.; Dorans, Neil J.

Six editions of Scholastic Aptitude Test-Mathematical (SAT-M) were factor analyzed using confirmatory and exploratory methods. Confirmatory factor analyses (using the LISREL VI program) were conducted on correlation matrices among item parcels--sums of scores on a small subset of items. Item parcels were constructed to yield correlation matrices…

Adjunct laboratory tests in support of US/German salt characterization program

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buchholz, Stuart A.

2014-07-01

In summary, the goal of this activity is to complete a subset of a test matrix on salt from the Waste Isolation Pilot Plant (WIPP) undertaken by German research groups. The work will be performed at RESPEC in Rapid City, South Dakota, and is divided into three tasks.

Elucidating tectonic events and processes from variably tectonized conglomerate clast detrital geochronology: examples from the Hongliuhe Formation in the southern Central Asian Orogenic Belt, NW China

NASA Astrophysics Data System (ADS)

Cleven, Nathan; Lin, Shoufa; Davis, Donald; Xiao, Wenjiao; Guilmette, Carl

2017-04-01

This work expands upon detrital zircon geochronology with a sampling and analysis strategy dating granitoid conglomerate clasts that exhibit differing degrees of internal ductile deformation. As deformation textures within clastic material reflect the variation and history of tectonization in the source region of a deposit, we outline a dating methodology that can provide details of the provenance's tectonomagmatic history from deformation-relative age distributions. The method involves bulk samples of solely granitoid clasts, as they are representative of the magmatic framework within the provenance. The clasts are classified and sorted into three subsets: undeformed, slightly deformed, and deformed. LA-ICPMS U-Pb geochronology is performed on zircon separates of each subset. Our case study, involving the Permian Hongliuhe Formation in the southern Central Asian Orogenic Belt, analyzes each of the three clast subsets, as well as sandstone detrital samples, at three stratigraphic levels to yield a profile of the unroofed provenance. The age spectra of the clast samples exhibit different, wider distributions than sandstone samples, considered an effect of proximity to the respective provenance. Comparisons of clast data to sandstone data, as well as comparisons between stratigraphic levels, yield indications of key tectonic processes, in addition to the typical characteristics provided by detrital geochronology. The clast data indicates a minimal lag time, implying rapid exhumation rates, whereas sandstone data alone would indicate a 90 m.y. lag time. Early Paleozoic arc building episodes appear as Ordovician peaks in sandstone data, and Silurian-Devonian peaks in clast data, indicating a younging of magmatism towards the proximal provenance. A magmatic hiatus starts in the Devonian, correlating with the latest age of deformed clasts, interpreted as timing of collisional tectonics. Provenance interpretation using the correlations seen between the clast and sandstone data proves to be more detailed and more robust than that determined from sandstone samples alone. The variably tectonized clast detrital geochronology method offers a regional reconnaissance tool that can address the practical limits of studying regional granitoid distributions.

Factors Affecting Detection of Hepatitis E Virus on Canadian Retail Pork Chops and Pork Livers Assayed Using Real-Time RT-PCR.

PubMed

Wilhelm, B J; Leblanc, D; Avery, B; Pearl, D L; Houde, A; Rajić, A; McEwen, S A

2016-03-01

We collected 599 Canadian retail pork chops and 283 pork livers routinely (usually weekly) from April 2011 to March 2012 using the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) retail sampling platform. Samples were assayed using validated real-time (q) reverse transcriptase polymerase chain reaction (RT-PCR) and nested classical RT-PCR for the detection of hepatitis E virus (HEV), porcine enteric calicivirus (PEC) and rotavirus (RV). The presence of Escherichia coli, Salmonella spp. and Campylobacter spp. was measured on a subset of our samples. Exact logistic regression models were fitted for predictors for HEV detection, for each assay. For both assays, sample type (pork chop versus liver) was a significant predictor for HEV RNA detection. For nested classical RT-PCR but not qRT-PCR, region of sample collection was a significant predictor (P = 0.008) of HEV detection. Odds of HEV detection were greatest in spring relative to other seasons. E. coli was a significant predictor for HEV RNA detection using the qRT-PCR (P = 0.03). Overall, the prevalence of E. coli, Salmonella spp. and Campylobacter spp. was significantly greater than HEV, PEC or RV on our retail pork samples. Our sparse data set for the detection of PEC and RV precluded modelling of risk factors for the detection of these viruses. © 2015 Zoonoses and Public Health © 2015 Her Majesty the Queen in Right of Canada Reproduced with the permission of the Minister of the Public Health Agency of Canada.

Engineering Design Handbook: Development Guide for Reliability. Part Three. Reliability Prediction

DTIC Science & Technology

1976-01-01

Populations 4-3 4-7 IFR and DFR Distributions 4-3 CHAPTER 5. SOME ADVANCED MATHEMATICAL TECHNIQUES 5-0 List of Symbols 5-1 5-1 Introduction...Aß,CJE= sets AFyAGSFJBc ~ events that units UA and -\\AAA E{] EB £H T $£ T UB are Failed or Good subsets "of A£,CJ),E s-expected value of...i.e., the sample space is all possible values that can arise. Each value is called a sample point. There are six sample points in the sample space

Exploring impacts of multi-year, community-based care programs for orphans and vulnerable children: a case study from Kenya.

PubMed

Larson, Bruce A; Wambua, Nancy; Masila, Juliana; Wangai, Susan; Rohr, Julia; Brooks, Mohamad; Bryant, Malcolm

2013-01-01

The Community-Based Care for Orphans and Vulnerable Children (CBCO) program operated in Kenya during 2006-2010. In Eastern Province, the program provided support to approximately 3000 orphans and vulnerable children (OVC) living in 1500 households. A primary focus of the program was to support savings and loan associations composed of OVC caregivers (typically elderly women) to improve household and OVC welfare. Cross-sectional data were collected in 2011 from 1500 randomly selected households from 3 populations: program participants (CBCO group, n=500), households in the same villages as program participants but not in the program (the local-community-group = Group L, n=300), and households living in nearby villages where the program did not operate (the adjacent-community-group, Group A, n=700). Primary welfare outcomes evaluated are household food security, as measured by the Household Food Insecurity Access instrument, and OVC educational attainment. We compared outcomes between the CBCO and the subset of Group L not meeting program eligibility criteria (L-N) to investigate disparities within local communities. We compared outcomes between the CBCO group and the subset of Group A meeting eligibility criteria (A-E) to consider program impact. We compared outcomes between households not eligible for the program in the local and adjacent community groups (L-N and A-N) to consider if the adjacent communities are similar to the local communities. In May-June 2011, at the end of the OVC program, the majority of CBCO households continued to be severely food insecure, with rates similar to other households living in nearby communities. Participation rates in primary school are high, reflecting free primary education. Among the 18-22 year olds who were "children" during the program years, relatively few children completed secondary school across all study groups. Although the CBCO program likely provided useful services and benefits to program participants, disparities continued to exist in food security and educational outcomes between program participants and their non-OVC peers in the local community. Outcomes for CBCO households were similar to those observed for OVC households in adjacent communities.

Exploring impacts of multi-year, community-based care programs for orphans and vulnerable children: A case study from Kenya

PubMed Central

Larson, Bruce A.; Wambua, Nancy; Masila, Juliana; Wangai, Susan; Rohr, Julia; Brooks, Mohamad; Bryant, Malcolm

2013-01-01

The Community-Based Care for Orphans and Vulnerable Children (CBCO) program operated in Kenya during 2006–2010. In Eastern Province, the program provided support to approximately 3000 orphans and vulnerable children (OVC) living in 1500 households. A primary focus of the program was to support savings and loan associations composed of OVC caregivers (typically elderly women) to improve household and OVC welfare. Cross-sectional data were collected in 2011 from 1500 randomly selected households from 3 populations: program participants (CBCO group, n = 500), households in the same villages as program participants but not in the program (the local-community-group = Group L, n = 300), and households living in nearby villages where the program did not operate (the adjacent-community-group, Group A, n = 700). Primary welfare outcomes evaluated are household food security, as measured by the Household Food Insecurity Access instrument, and OVC educational attainment. We compared outcomes between the CBCO and the subset of Group L not meeting program eligibility criteria (L-N) to investigate disparities within local communities. We compared outcomes between the CBCO group and the subset of Group A meeting eligibility criteria (A-E) to consider program impact. We compared outcomes between households not eligible for the program in the local and adjacent community groups (L-N and A-N) to consider if the adjacent communities are similar to the local communities. In May-June 2011, at the end of the OVC program, the majority of CBCO households continued to be severely food insecure, with rates similar to other households living in nearby communities. Participation rates in primary school are high, reflecting free primary education. Among the 18–22 year olds who were “children” during the program years, relatively few children completed secondary school across all study groups. Although the CBCO program likely provided useful services and benefits to program participants, disparities continued to exist in food security and educational outcomes between program participants and their non-OVC peers in the local community. Outcomes for CBCO households were similar to those observed for OVC households in adjacent communities. PMID:23745629

Do employee health management programs work?

PubMed

Serxner, Seth; Gold, Daniel; Meraz, Angela; Gray, Ann

2009-01-01

Current peer review literature clearly documents the economic return and Return-on-Investment (ROI) for employee health management (EHM) programs. These EHM programs are defined as: health promotion, self-care, disease management, and case management programs. The evaluation literature for the sub-set of health promotion and disease management programs is examined in this article for specific evidence of the level of economic return in medical benefit cost reduction or avoidance. The article identifies the methodological challenges associated with determination of economic return for EHM programs and summarizes the findings from 23 articles that included 120 peer review study results. The article identifies the average ROI and percent health plan cost impact to be expected for both types of EHM programs, the expected time period for its occurrence, and caveats related to its measurement.

Implementation and Outcomes of Forensic Housing First Programs.

PubMed

Kriegel, Liat S; Henwood, Benjamin F; Gilmer, Todd P

2016-01-01

This mixed-method study used administrative data from 68 supportive housing programs and evaluative and qualitative site visit data from a subset of four forensic programs to (a) compare fidelity to the Housing First model and residential client outcomes between forensic and nonforensic programs and (b) investigate whether and how providers working in forensic programs can navigate competing Housing First principles and criminal justice mandates. Quantitative findings suggested that forensic programs were less likely to follow a harm reduction approach to substance use and clients in those programs were more likely to live in congregate settings. Qualitative findings suggested that an interplay of court involvement, limited resources, and risk environments influenced staff decisions regarding housing and treatment. Existing mental health and criminal justice collaborations necessitate adaptation to the Housing First model to accommodate client needs.

EmpiriciSN: Re-sampling Observed Supernova/Host Galaxy Populations Using an XD Gaussian Mixture Model

NASA Astrophysics Data System (ADS)

Holoien, Thomas W.-S.; Marshall, Philip J.; Wechsler, Risa H.

2017-06-01

We describe two new open-source tools written in Python for performing extreme deconvolution Gaussian mixture modeling (XDGMM) and using a conditioned model to re-sample observed supernova and host galaxy populations. XDGMM is new program that uses Gaussian mixtures to perform density estimation of noisy data using extreme deconvolution (XD) algorithms. Additionally, it has functionality not available in other XD tools. It allows the user to select between the AstroML and Bovy et al. fitting methods and is compatible with scikit-learn machine learning algorithms. Most crucially, it allows the user to condition a model based on the known values of a subset of parameters. This gives the user the ability to produce a tool that can predict unknown parameters based on a model that is conditioned on known values of other parameters. EmpiriciSN is an exemplary application of this functionality, which can be used to fit an XDGMM model to observed supernova/host data sets and predict likely supernova parameters using a model conditioned on observed host properties. It is primarily intended to simulate realistic supernovae for LSST data simulations based on empirical galaxy properties.

EmpiriciSN: Re-sampling Observed Supernova/Host Galaxy Populations Using an XD Gaussian Mixture Model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Holoien, Thomas W. -S.; Marshall, Philip J.; Wechsler, Risa H.

We describe two new open-source tools written in Python for performing extreme deconvolution Gaussian mixture modeling (XDGMM) and using a conditioned model to re-sample observed supernova and host galaxy populations. XDGMM is new program that uses Gaussian mixtures to perform density estimation of noisy data using extreme deconvolution (XD) algorithms. Additionally, it has functionality not available in other XD tools. It allows the user to select between the AstroML and Bovy et al. fitting methods and is compatible with scikit-learn machine learning algorithms. Most crucially, it allows the user to condition a model based on the known values of amore » subset of parameters. This gives the user the ability to produce a tool that can predict unknown parameters based on a model that is conditioned on known values of other parameters. EmpiriciSN is an exemplary application of this functionality, which can be used to fit an XDGMM model to observed supernova/host data sets and predict likely supernova parameters using a model conditioned on observed host properties. It is primarily intended to simulate realistic supernovae for LSST data simulations based on empirical galaxy properties.« less

A review of Soviet plasma engine development

NASA Technical Reports Server (NTRS)

Barnett, John W.

1990-01-01

The Soviet Union has maintained a substantial and successful electric propulsion research and development effort since the 1950s; however, American researchers are generally unfamiliar with the Soviet accomplishments. Sources of information about Soviet electric propulsion research are noted. The development of plasma engines, a subset of the electric propulsion effort, is reviewed using numerous Soviet sources. The operational principles and status of several engines of the closed electron drift and high-current types are discussed. With recognition of the limited knowledge of the current Soviet program, the Soviet and American programs are compared, revealing some differences in program formulation and emphasis.

Residential Customer Enrollment in Time-based Rate and Enabling Technology Programs: Smart Grid Investment Grant Consumer Behavior Study Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Todd, Annika; Cappers, Peter; Goldman, Charles

2013-05-01

The U.S. Department of Energy’s (DOE’s) Smart Grid Investment Grant (SGIG) program is working with a subset of the 99 SGIG projects undertaking Consumer Behavior Studies (CBS), which examine the response of mass market consumers (i.e., residential and small commercial customers) to time-varying electricity prices (referred to herein as time-based rate programs) in conjunction with the deployment of advanced metering infrastructure (AMI) and associated technologies. The effort presents an opportunity to advance the electric industry’s understanding of consumer behavior.

Leveraging technology and staffing in developing a new liaison program.

PubMed

Williams, Jeff; McCrillis, Aileen; McGowan, Richard; Nicholson, Joey; Surkis, Alisa; Thompson, Holly; Vieira, Dorice

2014-01-01

With nearly all library resources and services delivered digitally, librarians working for the New York University Health Sciences Library struggled with maintaining awareness of changing user needs, understanding barriers faced in using library resources and services, and determining knowledge management challenges across the organization. A liaison program was created to provide opportunities for librarians to meaningfully engage with users. The program was directed toward a subset of high-priority user groups to provide focused engagement with these users. Responsibility for providing routine reference service was reduced for liaison librarians to provide maximum time to engage with their assigned user communities.

Immune cell subsets, cytokine and cortisol levels during the first week of life in neonates born to pre-eclamptic mothers.

PubMed

Sava, Florentina; Toldi, Gergely; Treszl, András; Hajdú, Júlia; Harmath, Ágnes; Rigó, János; Tulassay, Tivadar; Vásárhelyi, Barna

2017-06-01

To address the hypothesis that pre-eclampsia (PE) impacts the fetal immune system, we investigated the prevalence of distinct immune cell subsets along with plasma cortisol and cytokine levels in pre-term newborns of PE mothers. Cord blood and peripheral blood samples on the 1st, 3rd and 7th postnatal days of life were collected from 14 pre-term infants affected by PE and 14 non-PE pregnancies. We measured plasma cortisol and cytokine levels with immunoassays and assessed the prevalence of T, NK and DC subsets using flow cytometry. The prevalence of CD4+ cells was lower in PE infants, while that of memory T cells was higher. Myeloid DCs had a lower prevalence in PE neonates. Cytokine and cortisol levels were lower in PE neonates. Our observations show that PE pregnancies are associated with altered newborn immune status during the first week of life. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Association of plasma cell subsets in the bone marrow and free light chain concentrations in the serum of monoclonal gammopathy patients.

PubMed

Ayliffe, Michael John; Behrens, Judith; Stern, Simon; Sumar, Nazira

2012-08-01

This study investigated bone marrow plasma cell subsets and monoclonal free light chain concentrations in blood of monoclonal gammopathy patients. 54 bone marrow samples were stained by double immunofluorescence to enumerate cellular subsets making either intact monoclonal immunoglobulin or free light chains only. Blood taken at the same time was assayed for free light chains by an automated immunoassay. Patients were assigned to three cellular population categories: single intact monoclonal immunoglobulin (59%), dual monoclonal immunoglobulin and free light chain only (31%), or single free light chain only (9%). The median affected free light chain concentration of each group was 75 mg/l, 903 mg/l and 3320 mg/l, respectively, but with substantial overlap. In myeloma patients the difference in serum free light chain concentrations between patients with free light chain only marrow cells and those without was statistically significant. Serum free light chain levels >600 mg/l result mostly from marrow cells restricted to free light chain production.

An Improved Search Approach for Solving Non-Convex Mixed-Integer Non Linear Programming Problems

NASA Astrophysics Data System (ADS)

Sitopu, Joni Wilson; Mawengkang, Herman; Syafitri Lubis, Riri

2018-01-01

The nonlinear mathematical programming problem addressed in this paper has a structure characterized by a subset of variables restricted to assume discrete values, which are linear and separable from the continuous variables. The strategy of releasing nonbasic variables from their bounds, combined with the “active constraint” method, has been developed. This strategy is used to force the appropriate non-integer basic variables to move to their neighbourhood integer points. Successful implementation of these algorithms was achieved on various test problems.

A study of the temporal variability of atrazine in private well water. Part I: Study design, implementation, and database development

USGS Publications Warehouse

Lorber, M.; Johnson, Kevin; Kross, B.; Pinsky, P.; Burmeister, L.; Thurman, M.; Wilkins, A.; Hallberg, G.

1997-01-01

In 1988, the Iowa Department of Natural Resources, along with the University of Iowa conducted the Statewide Rural Well Water Survey, commonly known as SWRL. A total of 686 private rural drinking water wells was selected by use of a probability sample and tested for pesticides and nitrates. Sixty-eight of these wells, the '10% repeat' wells, were additionally sampled in October, 1990 and June, 1991. Starting in November, 1991, the University of Iowa, with sponsorship from the United States Environmental Protection Agency, revisited these wells to begin a study of the temporal variability of atrazine and nitrates in wells. Other wells, which had originally tested positive for atrazine in SWRL but were not in the 10% repeat population, were added to the study population. Temporal sampling for a year-long period began in February of 1992 and concluded in January of 1993. All wells were sampled monthly, one subset was sampled weekly, and a second subset was sampled for 14-day consecutive periods. Two unique aspects of this study were the use of an immunoassay technique to screen for triazines before gas chromatography/mass spectrometry (GC/MS) analysis and quantification of atrazine, and the use of well owners to sample the wells. A total of 1771 samples from 83 wells are in the final data base for this study. This paper reviews the study design, the analytical methodologies, and development of the data base. A companion paper discusses the analysis of the data from this survey.

AN ARCGIS TOOL FOR CREATING POPULATIONS OF WATERSHEDS

EPA Science Inventory

For the Landscape Investigations for Pesticides Study in the Midwest, the goal is to sample a representative subset of watersheds selected statistically from a target population of watersheds within the glaciated corn belt. This area stretches from Ohio to Iowa and includes parts...

A novel, privacy-preserving cryptographic approach for sharing sequencing data

PubMed Central

Cassa, Christopher A; Miller, Rachel A; Mandl, Kenneth D

2013-01-01

Objective DNA samples are often processed and sequenced in facilities external to the point of collection. These samples are routinely labeled with patient identifiers or pseudonyms, allowing for potential linkage to identity and private clinical information if intercepted during transmission. We present a cryptographic scheme to securely transmit externally generated sequence data which does not require any patient identifiers, public key infrastructure, or the transmission of passwords. Materials and methods This novel encryption scheme cryptographically protects participant sequence data using a shared secret key that is derived from a unique subset of an individual’s genetic sequence. This scheme requires access to a subset of an individual’s genetic sequence to acquire full access to the transmitted sequence data, which helps to prevent sample mismatch. Results We validate that the proposed encryption scheme is robust to sequencing errors, population uniqueness, and sibling disambiguation, and provides sufficient cryptographic key space. Discussion Access to a set of an individual’s genotypes and a mutually agreed cryptographic seed is needed to unlock the full sequence, which provides additional sample authentication and authorization security. We present modest fixed and marginal costs to implement this transmission architecture. Conclusions It is possible for genomics researchers who sequence participant samples externally to protect the transmission of sequence data using unique features of an individual’s genetic sequence. PMID:23125421

Java PathFinder User Guide

NASA Technical Reports Server (NTRS)

Havelund, Klaus

1999-01-01

The JAVA PATHFINDER, JPF, is a translator from a subset of JAVA 1.0 to PROMELA, the programming language of the SPIN model checker. The purpose of JPF is to establish a framework for verification and debugging of JAVA programming based on model checking. The main goal is to automate program verification such that a programmer can apply it in the daily work without the need for a specialist to manually reformulate a program into a different notation in order to analyze the program. The system is especially suited for analyzing multi-threaded JAVA applications, where normal testing usually falls short. The system can find deadlocks and violations of boolean assertions stated by the programmer in a special assertion language. This document explains how to Use JPF.

Quantization of high dimensional Gaussian vector using permutation modulation with application to information reconciliation in continuous variable QKD

NASA Astrophysics Data System (ADS)

Daneshgaran, Fred; Mondin, Marina; Olia, Khashayar

This paper is focused on the problem of Information Reconciliation (IR) for continuous variable Quantum Key Distribution (QKD). The main problem is quantization and assignment of labels to the samples of the Gaussian variables observed at Alice and Bob. Trouble is that most of the samples, assuming that the Gaussian variable is zero mean which is de-facto the case, tend to have small magnitudes and are easily disturbed by noise. Transmission over longer and longer distances increases the losses corresponding to a lower effective Signal-to-Noise Ratio (SNR) exasperating the problem. Quantization over higher dimensions is advantageous since it allows for fractional bit per sample accuracy which may be needed at very low SNR conditions whereby the achievable secret key rate is significantly less than one bit per sample. In this paper, we propose to use Permutation Modulation (PM) for quantization of Gaussian vectors potentially containing thousands of samples. PM is applied to the magnitudes of the Gaussian samples and we explore the dependence of the sign error probability on the magnitude of the samples. At very low SNR, we may transmit the entire label of the PM code from Bob to Alice in Reverse Reconciliation (RR) over public channel. The side information extracted from this label can then be used by Alice to characterize the sign error probability of her individual samples. Forward Error Correction (FEC) coding can be used by Bob on each subset of samples with similar sign error probability to aid Alice in error correction. This can be done for different subsets of samples with similar sign error probabilities leading to an Unequal Error Protection (UEP) coding paradigm.

A Letter on Ancaiani et al. "Evaluating Scientific Research in Italy: The 2004-10 Research Evaluation Exercise"

ERIC Educational Resources Information Center

Baccini, Alberto; De Nicolao, Giuseppe

2017-01-01

This letter documents some problems in Ancaiani et al. (2015). Namely the evaluation of concordance, based on Cohen's kappa, reported by Ancaiani et al. was not computed on the whole random sample of 9,199 articles, but on a subset of 7,597 articles. The kappas relative to the whole random sample were in the range 0.07-0.15, indicating an…

Microbiota of the Small Intestine Is Selectively Engulfed by Phagocytes of the Lamina Propria and Peyer’s Patches

PubMed Central

Morikawa, Masatoshi; Tsujibe, Satoshi; Kiyoshima-Shibata, Junko; Watanabe, Yohei; Kato-Nagaoka, Noriko; Shida, Kan; Matsumoto, Satoshi

2016-01-01

Phagocytes such as dendritic cells and macrophages, which are distributed in the small intestinal mucosa, play a crucial role in maintaining mucosal homeostasis by sampling the luminal gut microbiota. However, there is limited information regarding microbial uptake in a steady state. We investigated the composition of murine gut microbiota that is engulfed by phagocytes of specific subsets in the small intestinal lamina propria (SILP) and Peyer’s patches (PP). Analysis of bacterial 16S rRNA gene amplicon sequences revealed that: 1) all the phagocyte subsets in the SILP primarily engulfed Lactobacillus (the most abundant microbe in the small intestine), whereas CD11bhi and CD11bhiCD11chi cell subsets in PP mostly engulfed segmented filamentous bacteria (indigenous bacteria in rodents that are reported to adhere to intestinal epithelial cells); and 2) among the Lactobacillus species engulfed by the SILP cell subsets, L. murinus was engulfed more frequently than L. taiwanensis, although both these Lactobacillus species were abundant in the small intestine under physiological conditions. These results suggest that small intestinal microbiota is selectively engulfed by phagocytes that localize in the adjacent intestinal mucosa in a steady state. These observations may provide insight into the crucial role of phagocytes in immune surveillance of the small intestinal mucosa. PMID:27701454

Microbiota of the Small Intestine Is Selectively Engulfed by Phagocytes of the Lamina Propria and Peyer's Patches.

PubMed

Morikawa, Masatoshi; Tsujibe, Satoshi; Kiyoshima-Shibata, Junko; Watanabe, Yohei; Kato-Nagaoka, Noriko; Shida, Kan; Matsumoto, Satoshi

2016-01-01

Phagocytes such as dendritic cells and macrophages, which are distributed in the small intestinal mucosa, play a crucial role in maintaining mucosal homeostasis by sampling the luminal gut microbiota. However, there is limited information regarding microbial uptake in a steady state. We investigated the composition of murine gut microbiota that is engulfed by phagocytes of specific subsets in the small intestinal lamina propria (SILP) and Peyer's patches (PP). Analysis of bacterial 16S rRNA gene amplicon sequences revealed that: 1) all the phagocyte subsets in the SILP primarily engulfed Lactobacillus (the most abundant microbe in the small intestine), whereas CD11bhi and CD11bhiCD11chi cell subsets in PP mostly engulfed segmented filamentous bacteria (indigenous bacteria in rodents that are reported to adhere to intestinal epithelial cells); and 2) among the Lactobacillus species engulfed by the SILP cell subsets, L. murinus was engulfed more frequently than L. taiwanensis, although both these Lactobacillus species were abundant in the small intestine under physiological conditions. These results suggest that small intestinal microbiota is selectively engulfed by phagocytes that localize in the adjacent intestinal mucosa in a steady state. These observations may provide insight into the crucial role of phagocytes in immune surveillance of the small intestinal mucosa.

A prospective gating method to acquire a diverse set of free-breathing CT images for model-based 4DCT

NASA Astrophysics Data System (ADS)

O'Connell, D.; Ruan, D.; Thomas, D. H.; Dou, T. H.; Lewis, J. H.; Santhanam, A.; Lee, P.; Low, D. A.

2018-02-01

Breathing motion modeling requires observation of tissues at sufficiently distinct respiratory states for proper 4D characterization. This work proposes a method to improve sampling of the breathing cycle with limited imaging dose. We designed and tested a prospective free-breathing acquisition protocol with a simulation using datasets from five patients imaged with a model-based 4DCT technique. Each dataset contained 25 free-breathing fast helical CT scans with simultaneous breathing surrogate measurements. Tissue displacements were measured using deformable image registration. A correspondence model related tissue displacement to the surrogate. Model residual was computed by comparing predicted displacements to image registration results. To determine a stopping criteria for the prospective protocol, i.e. when the breathing cycle had been sufficiently sampled, subsets of N scans where 5  ⩽  N  ⩽  9 were used to fit reduced models for each patient. A previously published metric was employed to describe the phase coverage, or ‘spread’, of the respiratory trajectories of each subset. Minimum phase coverage necessary to achieve mean model residual within 0.5 mm of the full 25-scan model was determined and used as the stopping criteria. Using the patient breathing traces, a prospective acquisition protocol was simulated. In all patients, phase coverage greater than the threshold necessary for model accuracy within 0.5 mm of the 25 scan model was achieved in six or fewer scans. The prospectively selected respiratory trajectories ranked in the (97.5  ±  4.2)th percentile among subsets of the originally sampled scans on average. Simulation results suggest that the proposed prospective method provides an effective means to sample the breathing cycle with limited free-breathing scans. One application of the method is to reduce the imaging dose of a previously published model-based 4DCT protocol to 25% of its original value while achieving mean model residual within 0.5 mm.

Breast Cancer--Screening Behavior among Rural California American Indian Women

ERIC Educational Resources Information Center

Hodge, Felicia Schanche

2009-01-01

A community-based Wellness Circles Program was designed and implemented at 13 sites in California to evaluate a culturally appropriate community-based health care model for American Indian families. Data obtained from the Behavioral Risk Factor Surveillance System (BRFSS) that was administered to a subset of women demonstrate that American Indian…

Exploring the Relationship between Student Involvement in GEAR UP and Academic Achievement

ERIC Educational Resources Information Center

Kennedy, Renea F.

2016-01-01

The purpose of this study was to examine the relationship between GEAR UP academic support services and student achievement. GEAR UP is an evidence-based college readiness program. This study focused on a subset of academic support services designed to impact student achievement including: academic mentoring, math tutoring, English tutoring, study…

Minority Students and Faculty in Higher Music Education

ERIC Educational Resources Information Center

Clements, Allen

2009-01-01

This article offers a brief summary of the current minority situation in university and college music programs in the United States. Research in this area has concentrated to varying degrees on specific subsets of the minority population (e.g., African Americans, Hispanics, Native Americans, Asians) as well as on minorities in a more general…

Story Based Activities Enhance Literacy Skills in Preschool Children

ERIC Educational Resources Information Center

Yazici, Elçin; Bolay, Hayrunnisa

2017-01-01

We investigated the impact of story-based activities on literacy skills in pre-school children. The efficacy of story-based activities program were tested by literacy skills survey test. Results showed that, the scores of overall literacy skills and all subsets skills in the study group (n = 45) were statistically significantly higher than the…

Stabilizing Developmental Language Trajectories in Infants/Toddlers: A Preliminary Study

ERIC Educational Resources Information Center

Marvin, Christine; Kuhn, Miriam; Knoche, Lisa

2013-01-01

Parents' interactions with their children can have influential effects on children's language outcomes. Special supports may be needed however, when young children live in poverty and show developmental delays early in life. This study analyzed data for a subset of children enrolled in Early Head Start (EHS) programs and participating in a…

Politics and Paradox! The Case of an Urban Alternative

ERIC Educational Resources Information Center

Tallerico, Marilyn; Burstyn, Joan N.

2005-01-01

In recent decades, a number of factors have contributed to the growth of alternative educational programs in urban settings. Public perception of cities as dangerous places and national media attention to high profile incidents of school violence are two influences. Here, Tallerico and Burstyn center on a subset of in-depth interview data provided…

Using Brief Experimental Analysis to Intensify Tier 3 Reading Interventions

ERIC Educational Resources Information Center

Coolong-Chaffin, Melissa; Wagner, Dana

2015-01-01

As implementation of multi-tiered systems of support becomes common practice across the nation, practitioners continue to need strategies for intensifying interventions and supports for the subset of students who fail to make adequate progress despite strong programs at Tiers 1 and 2. Experts recommend making several changes to the structure and…

Sequential computation of elementary modes and minimal cut sets in genome-scale metabolic networks using alternate integer linear programming

DOE Office of Scientific and Technical Information (OSTI.GOV)

Song, Hyun-Seob; Goldberg, Noam; Mahajan, Ashutosh

Elementary (flux) modes (EMs) have served as a valuable tool for investigating structural and functional properties of metabolic networks. Identification of the full set of EMs in genome-scale networks remains challenging due to combinatorial explosion of EMs in complex networks. It is often, however, that only a small subset of relevant EMs needs to be known, for which optimization-based sequential computation is a useful alternative. Most of the currently available methods along this line are based on the iterative use of mixed integer linear programming (MILP), the effectiveness of which significantly deteriorates as the number of iterations builds up. Tomore » alleviate the computational burden associated with the MILP implementation, we here present a novel optimization algorithm termed alternate integer linear programming (AILP). Results: Our algorithm was designed to iteratively solve a pair of integer programming (IP) and linear programming (LP) to compute EMs in a sequential manner. In each step, the IP identifies a minimal subset of reactions, the deletion of which disables all previously identified EMs. Thus, a subsequent LP solution subject to this reaction deletion constraint becomes a distinct EM. In cases where no feasible LP solution is available, IP-derived reaction deletion sets represent minimal cut sets (MCSs). Despite the additional computation of MCSs, AILP achieved significant time reduction in computing EMs by orders of magnitude. The proposed AILP algorithm not only offers a computational advantage in the EM analysis of genome-scale networks, but also improves the understanding of the linkage between EMs and MCSs.« less

Robust best linear estimator for Cox regression with instrumental variables in whole cohort and surrogates with additive measurement error in calibration sample.

PubMed

Wang, Ching-Yun; Song, Xiao

2016-11-01

Biomedical researchers are often interested in estimating the effect of an environmental exposure in relation to a chronic disease endpoint. However, the exposure variable of interest may be measured with errors. In a subset of the whole cohort, a surrogate variable is available for the true unobserved exposure variable. The surrogate variable satisfies an additive measurement error model, but it may not have repeated measurements. The subset in which the surrogate variables are available is called a calibration sample. In addition to the surrogate variables that are available among the subjects in the calibration sample, we consider the situation when there is an instrumental variable available for all study subjects. An instrumental variable is correlated with the unobserved true exposure variable, and hence can be useful in the estimation of the regression coefficients. In this paper, we propose a nonparametric method for Cox regression using the observed data from the whole cohort. The nonparametric estimator is the best linear combination of a nonparametric correction estimator from the calibration sample and the difference of the naive estimators from the calibration sample and the whole cohort. The asymptotic distribution is derived, and the finite sample performance of the proposed estimator is examined via intensive simulation studies. The methods are applied to the Nutritional Biomarkers Study of the Women's Health Initiative. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Functional Impact of Alternative Splicing in Cancer.

PubMed

Climente-González, Héctor; Porta-Pardo, Eduard; Godzik, Adam; Eyras, Eduardo

2017-08-29

Alternative splicing changes are frequently observed in cancer and are starting to be recognized as important signatures for tumor progression and therapy. However, their functional impact and relevance to tumorigenesis remain mostly unknown. We carried out a systematic analysis to characterize the potential functional consequences of alternative splicing changes in thousands of tumor samples. This analysis revealed that a subset of alternative splicing changes affect protein domain families that are frequently mutated in tumors and potentially disrupt protein-protein interactions in cancer-related pathways. Moreover, there was a negative correlation between the number of these alternative splicing changes in a sample and the number of somatic mutations in drivers. We propose that a subset of the alternative splicing changes observed in tumors may represent independent oncogenic processes that could be relevant to explain the functional transformations in cancer, and some of them could potentially be considered alternative splicing drivers (AS drivers). Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Optimization of black-box models with uncertain climatic inputs—Application to sunflower ideotype design

PubMed Central

Picheny, Victor; Trépos, Ronan; Casadebaig, Pierre

2017-01-01

Accounting for the interannual climatic variations is a well-known issue for simulation-based studies of environmental systems. It often requires intensive sampling (e.g., averaging the simulation outputs over many climatic series), which hinders many sequential processes, in particular optimization algorithms. We propose here an approach based on a subset selection in a large basis of climatic series, using an ad-hoc similarity function and clustering. A non-parametric reconstruction technique is introduced to estimate accurately the distribution of the output of interest using only the subset sampling. The proposed strategy is non-intrusive and generic (i.e. transposable to most models with climatic data inputs), and can be combined to most “off-the-shelf” optimization solvers. We apply our approach to sunflower ideotype design using the crop model SUNFLO. The underlying optimization problem is formulated as a multi-objective one to account for risk-aversion. Our approach achieves good performances even for limited computational budgets, outperforming significantly standard strategies. PMID:28542198

Age of Local Galactic Disk from the Wdlf for Cpmbs

NASA Astrophysics Data System (ADS)

Smith, J. Allyn; Oswalt, Terry D.; Wood, Matt A.; Silvestri, Nicole M.

We present the white dwarf luminosity function (WDLF) for common proper motion systems. This WDLF was derived using the 1/Vmax method pioneered by Schmidt (1975) and detailed by Liebert Dahn and Monet (1988). New cooling models were used to determine the luminosities of the white dwarfs and the age of the local Galactic disk. Comparison to WDLFs developed using older colling models (Wood 1995) will be examined for changes in the derived disk age. Kinematic data is available for a subset of the WDs in the sample. Separate luminosity functions will be examined for each of the statistically significant subsets. JAS acknowledges support from NASA GSRP Fellowship NGT-51086.

The importance of quality control in validating concentrations of contaminants of emerging concern in source and treated drinking water samples.

PubMed

Batt, Angela L; Furlong, Edward T; Mash, Heath E; Glassmeyer, Susan T; Kolpin, Dana W

2017-02-01

A national-scale survey of 247 contaminants of emerging concern (CECs), including organic and inorganic chemical compounds, and microbial contaminants, was conducted in source and treated drinking water samples from 25 treatment plants across the United States. Multiple methods were used to determine these CECs, including six analytical methods to measure 174 pharmaceuticals, personal care products, and pesticides. A three-component quality assurance/quality control (QA/QC) program was designed for the subset of 174 CECs which allowed us to assess and compare performances of the methods used. The three components included: 1) a common field QA/QC protocol and sample design, 2) individual investigator-developed method-specific QA/QC protocols, and 3) a suite of 46 method comparison analytes that were determined in two or more analytical methods. Overall method performance for the 174 organic chemical CECs was assessed by comparing spiked recoveries in reagent, source, and treated water over a two-year period. In addition to the 247 CECs reported in the larger drinking water study, another 48 pharmaceutical compounds measured did not consistently meet predetermined quality standards. Methodologies that did not seem suitable for these analytes are overviewed. The need to exclude analytes based on method performance demonstrates the importance of additional QA/QC protocols. Published by Elsevier B.V.

Comparison of the Functional microRNA Expression in Immune Cell Subsets of Neonates and Adults

PubMed Central

Yu, Hong-Ren; Hsu, Te-Yao; Huang, Hsin-Chun; Kuo, Ho-Chang; Li, Sung-Chou; Yang, Kuender D.; Hsieh, Kai-Sheng

2016-01-01

Diversity of biological molecules in newborn and adult immune cells contributes to differences in cell function and atopic properties. Micro RNAs (miRNAs) are reported to involve in the regulation of immune system. Therefore, determining the miRNA expression profile of leukocyte subpopulations is important for understanding immune system regulation. In order to explore the unique miRNA profiling that contribute to altered immune in neonates, we comprehensively analyzed the functional miRNA signatures of eight leukocyte subsets (polymorphonuclear cells, monocytes, CD4+ T cells, CD8+ T cells, natural killer cells, B cells, plasmacytoid dendritic cells, and myeloid dendritic cells) from both neonatal and adult umbilical cord and peripheral blood samples, respectively. We observed distinct miRNA profiles between adult and neonatal blood leukocyte subsets, including unique miRNA signatures for each cell lineage. Leukocyte miRNA signatures were altered after stimulation. Adult peripheral leukocytes had higher let-7b-5p expression levels compared to neonatal cord leukocytes across multiple subsets, irrespective of stimulation. Transfecting neonatal monocytes with a let-7b-5p mimic resulted in a reduction of LPS-induced interleukin (IL)-6 and TNF-α production, while transfection of a let-7b-5p inhibitor into adult monocytes enhanced IL-6 and TNF-α production. With this functional approach, we provide intact differential miRNA expression profiling of specific immune cell subsets between neonates and adults. These studies serve as a basis to further understand the altered immune response observed in neonates and advance the development of therapeutic strategies. PMID:28066425

TCF4-Targeting miR-124 is Differentially Expressed amongst Dendritic Cell Subsets

PubMed Central

Han, Sun Murray; Na, Hye Young; Ham, Onju; Choi, Wanho; Sohn, Moah; Ryu, Seul Hye; In, Hyunju; Hwang, Ki-Chul

2016-01-01

Dendritic cells (DCs) are professional antigen-presenting cells that sample their environment and present antigens to naïve T lymphocytes for the subsequent antigen-specific immune responses. DCs exist in a range of distinct subpopulations including plasmacytoid DCs (pDCs) and classical DCs (cDCs), with the latter consisting of the cDC1 and cDC2 lineages. Although the roles of DC-specific transcription factors across the DC subsets have become understood, the posttranscriptional mechanisms that regulate DC development are yet to be elucidated. MicroRNAs (miRNAs) are pivotal posttranscriptional regulators of gene expression in a myriad of biological processes, but their contribution to the immune system is just beginning to surface. In this study, our in-house probe collection was screened to identify miRNAs possibly involved in DC development and function by targeting the transcripts of relevant mouse transcription factors. Examination of DC subsets from the culture of mouse bone marrow with Flt3 ligand identified high expression of miR-124 which was able to target the transcript of TCF4, a transcription factor critical for the development and homeostasis of pDCs. Further expression profiling of mouse DC subsets isolated from in vitro culture as well as via ex vivo purification demonstrated that miR-124 was outstandingly expressed in CD24+ cDC1 cells compared to in pDCs and CD172α+ cDC2 cells. These results imply that miR-124 is likely involved in the processes of DC subset development by posttranscriptional regulation of a transcription factor(s). PMID:26937233

Occupational exposure to formaldehyde and alterations in lymphocyte subsets

PubMed Central

Hosgood, H. Dean; Zhang, Luoping; Tang, Xiaojiang; Vermeulen, Roel; Hao, Zhenyue; Shen, Min; Qiu, Chuangyi; Ge, Yichen; Hua, Ming; Ji, Zhiying; Li, Senhua; Xiong, Jun; Reiss, Boris; Liu, Songwang; Xin, Kerry X.; Azuma, Mariko; Xie, Yuxuan; Freeman, Laura Beane; Ruan, Xiaolin; Guo, Weihong; Galvan, Noe; Blair, Aaron; Li, Laiyu; Huang, Hanlin; Smith, Martyn T.; Rothman, Nathaniel; Lan, Qing

2012-01-01

Background Formaldehyde is used in many occupational settings, most notably in manufacturing, health care, and embalming. Formaldehyde has been classified as a human carcinogen, but its mechanism of action remains uncertain. Methods We carried out a cross-sectional study of 43 formaldehyde exposed-workers and 51 unexposed age and sex-matched controls in Guangdong, China to study formaldehyde’s early biologic effects. To follow-up our previous report that the total lymphocyte count was decreased in formaldehyde-exposed workers compared to controls, we evaluated each major lymphocyte subset (i.e., CD4+ T cells, CD8+ T cells, natural killer (NK) cells, and B cells) and T cell lymphocyte subset (CD4+ naïve and memory T cells, CD8+ naïve and memory T cells, and regulatory T cells). Linear regression of each subset was used to test for differences between exposed workers and controls, adjusting for potential confounders. Results Total NK cell and T cell counts were about 24% (p=0.037) and 16% (p=0.0042) lower, respectively, among exposed workers. Among certain T cell subsets, decreased counts among exposed workers were observed for CD8+ T cells (p=0.026), CD8+ effector memory T cells (p=0.018), and regulatory T cells (CD4+FoxP3+: p=0.04; CD25+FoxP3+: p=0.008). Conclusions Formaldehyde exposed-workers experienced decreased counts of NK cells, regulatory T cells, and CD8+ effector memory T cells; however, due to the small sample size these findings need to be confirmed in larger studies. PMID:22767408

Characterization of Plasma Membrane Proteins from Ovarian Cancer Cells Using Mass Spectrometry

DOE PAGES

Springer, David L.; Auberry, Deanna L.; Ahram, Mamoun; ...

2004-01-01

To determine how the repertoire of plasma membrane proteins change with disease state, specifically related to cancer, several methods for preparation of plasma membrane proteins were evaluated. Cultured cells derived from stage IV ovarian tumors were grown to 90% confluence and harvested in buffer containing CHAPS detergent. This preparation was centrifuged at low speed to remove insoluble cellular debris resulting in a crude homogenate. Glycosylated proteins in the crude homogenate were selectively enriched using lectin affinity chromatography. The crude homogenate and the lectin purified sample were prepared for mass spectrometric evaluation. The general procedure for protein identification began with trypsinmore » digestion of protein fractions followed by separation by reversed phase liquid chromatography that was coupled directly to a conventional tandem mass spectrometer (i.e. LCQ ion trap). Mass and fragmentation data for the peptides were searched against a human proteome data base using the informatics program SEQUEST. Using this procedure 398 proteins were identified with high confidence, including receptors, membrane-associated ligands, proteases, phosphatases, as well as structural and adhesion proteins. Results indicate that lectin chromatography provides a select subset of proteins and that the number and quality of the identifications improve as does the confidence of the protein identifications for this subset. These results represent the first step in development of methods to separate and successfully identify plasma membrane proteins from advanced ovarian cancer cells. Further characterization of plasma membrane proteins will contribute to our understanding of the mechanisms underlying progression of this deadly disease and may lead to new targeted interventions as well as new biomarkers for diagnosis.« less

Sparse sampling and reconstruction for electron and scanning probe microscope imaging

DOEpatents

Anderson, Hyrum; Helms, Jovana; Wheeler, Jason W.; Larson, Kurt W.; Rohrer, Brandon R.

2015-07-28

Systems and methods for conducting electron or scanning probe microscopy are provided herein. In a general embodiment, the systems and methods for conducting electron or scanning probe microscopy with an undersampled data set include: driving an electron beam or probe to scan across a sample and visit a subset of pixel locations of the sample that are randomly or pseudo-randomly designated; determining actual pixel locations on the sample that are visited by the electron beam or probe; and processing data collected by detectors from the visits of the electron beam or probe at the actual pixel locations and recovering a reconstructed image of the sample.

The impact of the State Children's Health Insurance Program's unborn child ruling expansions on foreign-born Latina prenatal care and birth outcomes, 2000-2007.

PubMed

Drewry, Jonathan; Sen, Bisakha; Wingate, Martha; Bronstein, Janet; Foster, E Michael; Kotelchuck, Milton

2015-07-01

The 2002 "unborn child ruling" resulted in State Children's Health Insurance Program (SCHIP) expansion for states to cover prenatal care for low-income women without health insurance. Foreign-born Latinas who do not qualify for Medicaid coverage theoretically should have benefited most from the policy ruling given their documented low rates of prenatal care utilization. This study compares prenatal care utilization and subsequent birth outcomes among foreign-born Latinas in six states that used the unborn child ruling to expand coverage to those in ten states that did not implement the expansion. This policy analysis examines cross-sectional pooled US natality data from the pre-enactment years (2000-2003) versus post-enactment years (2004-2007) to estimate the effect of the UCR on prenatal care utilization and birth outcome measures for foreign-born Latinas. Then using a difference-in-difference estimator, we assessed these differences across time for states that did or did not enact the unborn child ruling. Analyses were then replicated on a high-risk subset of the population (single foreign-born Latinas with lower levels of education). The SCHIP unborn child ruling policy expansion increased PNCU over time in the six enacting states. Foreign-born Latinas in expansion enacting states experienced increases in prenatal care utilization though only the high-risk subset were statistically significant. Birth outcomes did not change. The SCHIP unborn child ruling policy was associated with enhanced PNC for a subset of high-risk foreign-born Latinas.

Partners for Kids Care Coordination: Lessons From the Field.

PubMed

Weier, Rory Cusack; Gardner, William; Conkol, Kimberly; Pajer, Kathleen; Kelleher, Kelly J

2017-05-01

The goal of this trial was to present a case study of care coordination for children and youth with special health care needs from an exclusively pediatric accountable care organization, and compare precare and postcare data on their use of inpatient and emergency department services. This pre-post comparison of the health care utilization included a subset of 733 children enrolled in Partners for Kids care coordination funded through a delegation arrangement with several Medicaid managed care plans. We compared inpatient admissions, hospital bed days, 30-day hospital readmissions, and emergency department visits during the 6 months before their enrollment in the coordination program versus the 6 months after enrollment. Approximately 16 000 referrals to the Partners for Kids care coordination program were made for an estimated 12 000 children. A total of 3072 unique individual children were enrolled; the most common condition classification was mental, behavioral, and neurodevelopmental disorders (25% of enrolled children). Due to rapid turnover/churn in Medicaid managed care eligibility, the subset of children with continuous enrollment was limited to 733 children. Among this subset, the counts of inpatient admissions, bed days, and 30-day readmissions between the pre-enrollment and post-enrollment period decreased ( P < .05). These results suggest that it is possible for an accountable care organization to reduce inpatient and emergency department utilization. Going forward, the most important tasks of the care coordination team are to overcome obstacles to referral and participation and to develop methods to achieve better measures of patient-reported outcomes. Copyright © 2017 by the American Academy of Pediatrics.

Global Characterization of Protein Altering Mutations in Prostate Cancer

DTIC Science & Technology

2011-08-01

integrative analyses of somatic mutation with gene expression and copy number change data collected on the same samples. To date, we have performed...implications for resistance to cancer therapeutics. We have also identified a subset of genes that appear to be recurrently mutated in our discovery set, and...integrative analyses of somatic mutation with gene expression and copy number change data collected on the same samples. Body This is a “synergy” project

Evaluation of verifiability in HAL/S. [programming language for aerospace computers

NASA Technical Reports Server (NTRS)

Young, W. D.; Tripathi, A. R.; Good, D. I.; Browne, J. C.

1979-01-01

The ability of HAL/S to write verifiable programs, a characteristic which is highly desirable in aerospace applications, is lacking since many of the features of HAL/S do not lend themselves to existing verification techniques. The methods of language evaluation are described along with the means in which language features are evaluated for verifiability. These methods are applied in this study to various features of HAL/S to identify specific areas in which the language fails with respect to verifiability. Some conclusions are drawn for the design of programming languages for aerospace applications and ongoing work to identify a verifiable subset of HAL/S is described.

Rotavirus surveillance in urban and rural areas of Niger, April 2010-March 2012.

PubMed

Page, Anne-Laure; Jusot, Viviane; Mamaty, Abdoul-Aziz; Adamou, Lagare; Kaplon, Jérôme; Pothier, Pierre; Djibo, Ali; Manzo, Mahamane L; Toure, Brahima; Langendorf, Céline; Collard, Jean-Marc; Grais, Rebecca F

2014-04-01

Knowledge of rotavirus epidemiology is necessary to make informed decisions about vaccine introduction and to evaluate vaccine impact. During April 2010-March 2012, rotavirus surveillance was conducted among 9,745 children <5 years of age in 14 hospitals/health centers in Niger, where rotavirus vaccine has not been introduced. Study participants had acute watery diarrhea and moderate to severe dehydration, and 20% of the children were enrolled in a nutrition program. Of the 9,745 children, 30.6% were rotavirus positive. Genotyping of a subset of positive samples showed a variety of genotypes during the first year, although G2P[4] predominated. G12 genotypes, including G12P[8], which has emerged as a predominant strain in western Africa, represented >80% of isolates during the second year. Hospitalization and death rates and severe dehydration among rotavirus case-patients did not differ during the 2 years. The emergence of G12P[8] warrants close attention to the characteristics of associated epidemics and possible prevention measures.

On the occurrence of false positives in tests of migration under an isolation with migration model

PubMed Central

Hey, Jody; Chung, Yujin; Sethuraman, Arun

2015-01-01

The population genetic study of divergence is often done using a Bayesian genealogy sampler, like those implemented in IMa2 and related programs, and these analyses frequently include a likelihood-ratio test of the null hypothesis of no migration between populations. Cruickshank and Hahn (2014, Molecular Ecology, 23, 3133–3157) recently reported a high rate of false positive test results with IMa2 for data simulated with small numbers of loci under models with no migration and recent splitting times. We confirm these findings and discover that they are caused by a failure of the assumptions underlying likelihood ratio tests that arises when using marginal likelihoods for a subset of model parameters. We also show that for small data sets, with little divergence between samples from two populations, an excellent fit can often be found by a model with a low migration rate and recent splitting time and a model with a high migration rate and a deep splitting time. PMID:26456794

Resources for comparing the speed and performance of medical autocoders.

PubMed

Berman, Jules J

2004-06-15

Concept indexing is a popular method for characterizing medical text, and is one of the most important early steps in many data mining efforts. Concept indexing differs from simple word or phrase indexing because concepts are typically represented by a nomenclature code that binds a medical concept to all equivalent representations. A concept search on the term renal cell carcinoma would be expected to find occurrences of hypernephroma, and renal carcinoma (concept equivalents). The purpose of this study is to provide freely available resources to compare speed and performance among different autocoders. These tools consist of: 1) a public domain autocoder written in Perl (a free and open source programming language that installs on any operating system); 2) a nomenclature database derived from the unencumbered subset of the publicly available Unified Medical Language System; 3) a large corpus of autocoded output derived from a publicly available medical text. A simple lexical autocoder was written that parses plain-text into a listing of all 1,2,3, and 4-word strings contained in text, assigning a nomenclature code for text strings that match terms in the nomenclature. The nomenclature used is the unencumbered subset of the 2003 Unified Medical Language System (UMLS). The unencumbered subset of UMLS was reduced to exclude homonymous one-word terms and proper names, resulting in a term/code data dictionary containing about a half million medical terms. The Online Mendelian Inheritance in Man (OMIM), a 92+ Megabyte publicly available medical opus, was used as sample medical text for the autocoder. The autocoding Perl script is remarkably short, consisting of just 38 command lines. The 92+ Megabyte OMIM file was completely autocoded in 869 seconds on a 2.4 GHz processor (less than 10 seconds per Megabyte of text). The autocoded output file (9,540,442 bytes) contains 367,963 coded terms from OMIM and is distributed with this manuscript. A public domain Perl script is provided that can parse through plain-text files of any length, matching concepts against an external nomenclature. The script and associated files can be used freely to compare the speed and performance of autocoding software.

Uses of NHANES biomarker data for chemical risk assessment: Trends, challenges and opportunities

EPA Science Inventory

Background. Each year, the US NHANES measures hundreds of chemical biomarkers in samples from thousands of study participants. These biomarker measurements are meant to track trends and identify subsets of the US population with elevated exposures. There is now interest in furth...

Developmental Trajectories of Early Communication Skills

ERIC Educational Resources Information Center

Maatta, Sira; Laakso, Marja-Leena; Tolvanen, Asko; Ahonen, Timo; Aro, Tuija

2012-01-01

Purpose: This study focused on developmental trajectories of prelinguistic communication skills and their connections to later parent-reported language difficulties. Method: The participants represent a subset of a community-based sample of 508 children. Data include parent reports of prelinguistic communication skills at 12, 15, 18, and 21 months…

Evaluation of a novel mentor program to improve surgical care for US hospitals.

PubMed

Berian, Julia R; Thomas, Juliana M; Minami, Christina A; Farrell, Paula R; O'Leary, Kevin J; Williams, Mark V; Prachand, Vivek N; Halverson, Amy L; Bilimoria, Karl Y; Johnson, Julie K

2017-04-01

To evaluate a novel mentor program for 27 US surgeons, charged with improving quality at their respective hospitals, having been paired 1:1 with 27 surgeon mentors through a state-wide quality improvement (QI) initiative. Mixed-methods utilizing quantitative surveys and in-depth semi-structured interviews. The Illinois Surgical Quality Improvement Collaborative (ISQIC) utilized a novel Mentor Program to guide surgeons new to QI. All mentor-mentee pairs received the survey (n = 27). Purposive sampling identified a subset of mentors (n = 8) and mentees (n = 4) for in-depth semi-structured interviews. Surgeons with expertise in QI mentored surgeons new to QI. (i) Quantitative: self-reported satisfaction with the mentor program; (ii) Qualitative: key themes suggesting actions and strategies to facilitate mentorship in QI. Mentees expressed satisfaction with the mentor program (n = 24, 88.9%) and agreed that mentorship is vital to ISQIC (n = 24, 88.9%). Analysis of interview data revealed four key themes: (i) nuances of data management, (ii) culture of quality and safety, (iii) mentor-mentee relationship and (iv) logistics. Strategies from these key themes include: utilize raw data for in-depth QI understanding, facilitate presentations to build QI support, identify opportunities for in-person meetings and establish scheduled conference calls. The mentor's role required sharing experiences and acting as a resource. The mentee's role required actively bringing questions and identifying barriers. Mentorship plays a vital role in advancing surgeon knowledge and engagement with QI in ISQIC. Key themes in mentorship reflect strategies to best facilitate mentorship, which may serve as a guide to other collaboratives. © The Author 2017. Published by Oxford University Press in association with the International Society for Quality in Health Care. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

A linear programming model for protein inference problem in shotgun proteomics.

PubMed

Huang, Ting; He, Zengyou

2012-11-15

Assembling peptides identified from tandem mass spectra into a list of proteins, referred to as protein inference, is an important issue in shotgun proteomics. The objective of protein inference is to find a subset of proteins that are truly present in the sample. Although many methods have been proposed for protein inference, several issues such as peptide degeneracy still remain unsolved. In this article, we present a linear programming model for protein inference. In this model, we use a transformation of the joint probability that each peptide/protein pair is present in the sample as the variable. Then, both the peptide probability and protein probability can be expressed as a formula in terms of the linear combination of these variables. Based on this simple fact, the protein inference problem is formulated as an optimization problem: minimize the number of proteins with non-zero probabilities under the constraint that the difference between the calculated peptide probability and the peptide probability generated from peptide identification algorithms should be less than some threshold. This model addresses the peptide degeneracy issue by forcing some joint probability variables involving degenerate peptides to be zero in a rigorous manner. The corresponding inference algorithm is named as ProteinLP. We test the performance of ProteinLP on six datasets. Experimental results show that our method is competitive with the state-of-the-art protein inference algorithms. The source code of our algorithm is available at: https://sourceforge.net/projects/prolp/. zyhe@dlut.edu.cn. Supplementary data are available at Bioinformatics Online.

AMMI adjustment for statistical analysis of an international wheat yield trial.

PubMed

Crossa, J; Fox, P N; Pfeiffer, W H; Rajaram, S; Gauch, H G

1991-01-01

Multilocation trials are important for the CIMMYT Bread Wheat Program in producing high-yielding, adapted lines for a wide range of environments. This study investigated procedures for improving predictive success of a yield trial, grouping environments and genotypes into homogeneous subsets, and determining the yield stability of 18 CIMMYT bread wheats evaluated at 25 locations. Additive Main effects and Multiplicative Interaction (AMMI) analysis gave more precise estimates of genotypic yields within locations than means across replicates. This precision facilitated formation by cluster analysis of more cohesive groups of genotypes and locations for biological interpretation of interactions than occurred with unadjusted means. Locations were clustered into two subsets for which genotypes with positive interactions manifested in high, stable yields were identified. The analyses highlighted superior selections with both broad and specific adaptation.

Can a Simple Dietary Index Derived from a Sub-Set of Questionnaire Items Assess Diet Quality in a Sample of Australian Adults?

PubMed Central

Trapp, Georgina S. A.; Knuiman, Matthew; Hooper, Paula; Ambrosini, Gina L.

2018-01-01

Large, longitudinal surveys often lack consistent dietary data, limiting the use of existing tools and methods that are available to measure diet quality. This study describes a method that was used to develop a simple index for ranking individuals according to their diet quality in a longitudinal study. The RESIDential Environments (RESIDE) project (2004–2011) collected dietary data in varying detail, across four time points. The most detailed dietary data were collected using a 24-item questionnaire at the final time point (n = 555; age ≥ 25 years). At preceding time points, sub-sets of the 24 items were collected. A RESIDE dietary guideline index (RDGI) that was based on the 24-items was developed to assess diet quality in relation to the Australian Dietary Guidelines. The RDGI scores were regressed on the longitudinal sub-sets of six and nine questionnaire items at T4, from which two simple index scores (S-RDGI1 and S-RDGI2) were predicted. The S-RDGI1 and S-RDGI2 showed reasonable agreement with the RDGI (Spearman’s rho = 0.78 and 0.84; gross misclassification = 1.8%; correct classification = 64.9% and 69.7%; and, Cohen’s weighted kappa = 0.58 and 0.64, respectively). For all of the indices, higher diet quality was associated with being female, undertaking moderate to high amounts of physical activity, not smoking, and self-reported health. The S-RDGI1 and S-RDGI2 explained 62% and 73% of the variation in RDGI scores, demonstrating that a large proportion of the variability in diet quality scores can be captured using a relatively small sub-set of questionnaire items. The methods described in this study can be applied elsewhere, in situations where limited dietary data are available, to generate a sample-specific score for ranking individuals according to diet quality. PMID:29652828

Can a Simple Dietary Index Derived from a Sub-Set of Questionnaire Items Assess Diet Quality in a Sample of Australian Adults?

PubMed

Bivoltsis, Alexia; Trapp, Georgina S A; Knuiman, Matthew; Hooper, Paula; Ambrosini, Gina L

2018-04-13

Large, longitudinal surveys often lack consistent dietary data, limiting the use of existing tools and methods that are available to measure diet quality. This study describes a method that was used to develop a simple index for ranking individuals according to their diet quality in a longitudinal study. The RESIDential Environments (RESIDE) project (2004-2011) collected dietary data in varying detail, across four time points. The most detailed dietary data were collected using a 24-item questionnaire at the final time point ( n = 555; age ≥ 25 years). At preceding time points, sub-sets of the 24 items were collected. A RESIDE dietary guideline index (RDGI) that was based on the 24-items was developed to assess diet quality in relation to the Australian Dietary Guidelines. The RDGI scores were regressed on the longitudinal sub-sets of six and nine questionnaire items at T4, from which two simple index scores (S-RDGI1 and S-RDGI2) were predicted. The S-RDGI1 and S-RDGI2 showed reasonable agreement with the RDGI (Spearman's rho = 0.78 and 0.84; gross misclassification = 1.8%; correct classification = 64.9% and 69.7%; and, Cohen's weighted kappa = 0.58 and 0.64, respectively). For all of the indices, higher diet quality was associated with being female, undertaking moderate to high amounts of physical activity, not smoking, and self-reported health. The S-RDGI1 and S-RDGI2 explained 62% and 73% of the variation in RDGI scores, demonstrating that a large proportion of the variability in diet quality scores can be captured using a relatively small sub-set of questionnaire items. The methods described in this study can be applied elsewhere, in situations where limited dietary data are available, to generate a sample-specific score for ranking individuals according to diet quality.

A statistical approach to selecting and confirming validation targets in -omics experiments

PubMed Central

2012-01-01

Background Genomic technologies are, by their very nature, designed for hypothesis generation. In some cases, the hypotheses that are generated require that genome scientists confirm findings about specific genes or proteins. But one major advantage of high-throughput technology is that global genetic, genomic, transcriptomic, and proteomic behaviors can be observed. Manual confirmation of every statistically significant genomic result is prohibitively expensive. This has led researchers in genomics to adopt the strategy of confirming only a handful of the most statistically significant results, a small subset chosen for biological interest, or a small random subset. But there is no standard approach for selecting and quantitatively evaluating validation targets. Results Here we present a new statistical method and approach for statistically validating lists of significant results based on confirming only a small random sample. We apply our statistical method to show that the usual practice of confirming only the most statistically significant results does not statistically validate result lists. We analyze an extensively validated RNA-sequencing experiment to show that confirming a random subset can statistically validate entire lists of significant results. Finally, we analyze multiple publicly available microarray experiments to show that statistically validating random samples can both (i) provide evidence to confirm long gene lists and (ii) save thousands of dollars and hundreds of hours of labor over manual validation of each significant result. Conclusions For high-throughput -omics studies, statistical validation is a cost-effective and statistically valid approach to confirming lists of significant results. PMID:22738145

An Educational Programming Framework for a Subset of Students with Diverse Learning Needs: Borderline Intellectual Functioning

ERIC Educational Resources Information Center

Shaw, Steven R.

2008-01-01

Students with intelligence test scores between 70 and 85 frequently fall into the gap between general and special education. Students with borderline intellectual functioning are a large population at-risk for school failure. Recent educational trends (e.g., the use of response to intervention models of special education eligibility,…

Quality Authorizing for Online and Blended-Learning Charter Schools. NACSA Monograph

ERIC Educational Resources Information Center

Watson, John; Rapp, Chris

2011-01-01

Online charter schools are one key subset of the K-12 online education landscape, which also includes state virtual schools, district-level online programs, private providers of both individual courses and entire schools, and others. As of late 2010, online and blended charter schools existed in more than 20 states, serving more than 100,000…

Characterization of alpha beta and gamma delta T cell subsets expressing IL-17A in ruminants and swine

USDA-ARS?s Scientific Manuscript database

As part of our ongoing program to expand reagents available for research in cattle, we developed a monoclonal antibody (mAb) to bovine IL-17A, a multifunctional cytokine centrally involved in regulating innate and adaptive immune responses. Initial comparative studies demonstrated the mAb recognizes...

Tree failures and accidents in recreation areas: a guide to data management for hazard control

Treesearch

Lee A. Paine; James W. Clarke

1978-01-01

A data management system has been developed for storage and retrieval of tree failure and hazard data, with provision for computer analyses and presentation of results in useful tables. This system emphasizes important relationships between tree characteristics, environmental factors, and the resulting hazard. The analysis programs permit easy selection of subsets of...

Forest Inventory and Analysis and Forest Health Monitoring: Piecing the Quilt

Treesearch

Joseph M. McCollum; Jamie K. Cochran

2005-01-01

Against the backdrop of a discussion about patchwork quilt assembly, the authors present background information on global grids. They show how to compose hexagons, an important task in systematically developing a subset of Forest Health Monitoring (FHM) Program plots from Forest Inventory and Analysis (FIA) plots. Finally, they outline the FHM and FIA grids, along with...

Custom Search Engines: Tools & Tips

ERIC Educational Resources Information Center

Notess, Greg R.

2008-01-01

Few have the resources to build a Google or Yahoo! from scratch. Yet anyone can build a search engine based on a subset of the large search engines' databases. Use Google Custom Search Engine or Yahoo! Search Builder or any of the other similar programs to create a vertical search engine targeting sites of interest to users. The basic steps to…

Working with Latino Families: Challenges Faced by Educators and Civic Leaders

ERIC Educational Resources Information Center

Lieshoff, Sylvia Cobos

2007-01-01

This article analyzes a subset of data gathered during a survey of 155 school systems and communities across the nation. The data were obtained from a capability survey as part of the application for a Toyota Family Literacy Program (TFLP) grant. Educators and civic leaders in 38 states responded to questions about their five greatest challenges…

FIADB vegetation diversity and structure indicator (VEG)

Treesearch

Bethany K. Schulz; Kevin Dobelbower

2012-01-01

The Vegetation Diversity and Structure (VEG) Indicator is a suite of measurements including an inventory of vascular plants on an extensive systematic network of forest plots across the United States. This network is a subset of the standard forest inventory plots established by the U.S. Forest Service Forest Inventory and Analysis program. The VEG indicator provides...

Concentration data for anthropogenic organic compounds in ground water, surface water, and finished water of selected community water systems in the United States, 2002-05

USGS Publications Warehouse

Carter, Janet M.; Delzer, Gregory C.; Kingsbury, James A.; Hopple, Jessica A.

2007-01-01

The National Water-Quality Assessment Program of the U.S. Geological Survey began implementing Source Water-Quality Assessments (SWQAs) in 2001 that focus on characterizing the quality of source water and finished water of aquifers and major rivers used by some of the larger community water systems (CWSs) in the United States. As used for SWQA studies, source water is the raw (ambient) water collected at the supply well prior to water treatment (for ground water) or the raw (ambient) water collected from the river near the intake (for surface water), and finished water is the water that is treated and ready to be delivered to consumers. Finished water is collected before entering the distribution system. SWQA studies are conducted in two phases, and the objectives of SWQA studies are twofold: (1) to determine the occurrence and, for rivers, seasonal changes in concentrations of a broad list of anthropogenic organic compounds (AOCs) in aquifers and rivers that have some of the largest withdrawals for drinking-water supply (phase 1), and (2) for those AOCs found to occur most frequently in source water, characterize the extent to which these compounds are present in finished water (phase 2). These objectives were met for SWQA studies by collecting ground-water and surface-water (source) samples and analyzing these samples for 258 AOCs during phase 1. Samples from a subset of wells and surface-water sites located in areas with substantial agricultural production in the watershed were analyzed for 19 additional AOCs, for a total of 277 compounds analyzed for SWQA studies. The 277 compounds were classified according to the following 13 primary use or source groups: (1) disinfection by-products; (2) fumigant-related compounds; (3) fungicides; (4) gasoline hydrocarbons, oxygenates, and oxygenate degradates; (5) herbicides and herbicide degradates; (6) insecticides and insecticide degradates; (7) manufacturing additives; (8) organic synthesis compounds; (9) pavement- and combustion-derived compounds; (10) personal care and domestic use products; (11) plant- or animal-derived biochemicals; (12) refrigerants and propellants; and (13) solvents. Source and finished water samples were collected during phase 2 and analyzed for constituents that were detected frequently during phase 1. This report presents concentration data for AOCs in ground water, surface water, and finished water of CWSs sampled for SWQA studies during 2002-05. Specifically, this report presents the analytical results of samples collected during phase 1 including (1) samples from 221 wells that were analyzed for 258 AOCs; (2) monthly samples from 9 surface-water sites that were analyzed for 258 AOCs during phase 1; and (3) samples from a subset of the wells and surface-water sites located in areas with substantial agricultural production that were analyzed for 3 additional pesticides and 16 pesticide degradates. Samples collected during phase 2 were analyzed for selected AOCs that were detected most frequently in source water during phase 1 sampling; analytical results for phase 2 are presented for (1) samples of source water and finished water from 94 wells; and (2) samples of source water and finished water samples that were collected monthly and during selected flow conditions at 8 surface-water sites. Results of quality-assurance/quality-control samples collected for SWQA studies during 2002-05 also are presented.

Central station applications planning activities and supporting studies. [application of photovoltaic technology to power generation plants

NASA Technical Reports Server (NTRS)

Leonard, S. L.; Siegel, B.

1980-01-01

The application of photovoltaic technology in central station (utility) power generation plants is considered. A program of data collection and analysis designed to provide additional information about the subset of the utility market that was identified as the initial target for photovoltaic penetration, the oil-dependent utilities (especially muncipals) of the U.S. Sunbelt, is described along with a series of interviews designed to ascertain utility industry opinions about the National Photovoltaic Program as it relates to central station applications.

Automated Verification of Design Patterns with LePUS3

NASA Technical Reports Server (NTRS)

Nicholson, Jonathan; Gasparis, Epameinondas; Eden, Ammon H.; Kazman, Rick

2009-01-01

Specification and [visual] modelling languages are expected to combine strong abstraction mechanisms with rigour, scalability, and parsimony. LePUS3 is a visual, object-oriented design description language axiomatized in a decidable subset of the first-order predicate logic. We demonstrate how LePUS3 is used to formally specify a structural design pattern and prove ( verify ) whether any JavaTM 1.4 program satisfies that specification. We also show how LePUS3 specifications (charts) are composed and how they are verified fully automatically in the Two-Tier Programming Toolkit.

NATIONAL-SCALE ASSESSMENT OF AIR TOXICS RISKS ...

EPA Pesticide Factsheets

The national-scale assessment of air toxics risks is a modeling assessment which combines emission inventory development, atmospheric fate and transport modeling, exposure modeling, and risk assessment to characterize the risk associated with inhaling air toxics from outdoor sources. This national-scale effort will be initiated for the base year 1996 and repeated every three years thereafter to track trends and inform program development. Provide broad-scale understanding of inhalation risks for a subset of atmospherically-emitted air toxics to inform further data-gathering efforts and priority-setting for the EPA's Air Toxics Programs.

Automating Veterans Administration libraries: II. Implementation at the Kansas City Medical Center Library.

PubMed

Smith, V K; Ting, S C

1987-04-01

In 1985, the Kansas City Veterans Administration Medical Center began implementation of the Decentralized Hospital Computer Program (DHCP). An integrated library system, a subset of that program, was started by the medical library for acquisitions and an outline catalog. To test the system, staff of the Neurology Service were trained to use the outline catalog and electronic mail to request interlibrary loans and literature searches. In implementing the project with the Neurology Service, the library is paving the way for many types of electronic access and interaction with the library.

The Bootstrap, the Jackknife, and the Randomization Test: A Sampling Taxonomy.

PubMed

Rodgers, J L

1999-10-01

A simple sampling taxonomy is defined that shows the differences between and relationships among the bootstrap, the jackknife, and the randomization test. Each method has as its goal the creation of an empirical sampling distribution that can be used to test statistical hypotheses, estimate standard errors, and/or create confidence intervals. Distinctions between the methods can be made based on the sampling approach (with replacement versus without replacement) and the sample size (replacing the whole original sample versus replacing a subset of the original sample). The taxonomy is useful for teaching the goals and purposes of resampling schemes. An extension of the taxonomy implies other possible resampling approaches that have not previously been considered. Univariate and multivariate examples are presented.

Extremely red objects in the fields of high redshift radio galaxies

NASA Technical Reports Server (NTRS)

Persson, S. E.; Mccarthy, P. J.; Dressler, Alan; Matthews, Keith

1993-01-01

We are engaged in a program of infrared imaging photometry of high redshift radio galaxies. The observations are being done using NICMOS2 and NICMOS3 arrays on the DuPont 100-inch telescope at Las Campanas Observatory. In addition, Persson and Matthews are measuring the spectral energy distributions of normal cluster galaxies in the redshift range 0 to 1. These measurements are being done with a 58 x 62 InSb array on the Palomar 5-m telescope. During the course of these observations we have imaged roughly 20 square arcminutes of sky to limiting magnitudes greater than 20 in the J, H, and K passbands (3 sigma in 3 square arcseconds). We have detected several relatively bright, extremely red, extended objects during the course of this work. Because the radio galaxy program requires Thuan-Gunn gri photometry, we are able to construct rough photometric energy distributions for many of the objects. A sample of the galaxy magnitudes within 4 arcseconds diameter is given. All the detections are real; either the objects show up at several wavelengths, or in subsets of the data. The reddest object in the table, 9ab'B' was found in a field of galaxies in a rich cluster at z = 0.4; 9ab'A' lies 8 arcseconds from it.

Characteristics and Clinical Practices of Rural Marriage and Family Therapists

ERIC Educational Resources Information Center

Morris, James

2007-01-01

This report presents a subset of data collected from the American Association for Marriage and Family Therapy (AAMFT) Practice Research Network project conducted in 2002. A sample of 47 clinical members of AAMFT who indicated they practiced in a rural community provided descriptive information on demographic characteristics, training, clinical…

Cultural Participation in the Philadelphia Area.

ERIC Educational Resources Information Center

Hanford, Terry; And Others

Described are the results of two separate surveys of cross-sections of the Philadelphia public concerning their cultural behavior, attitudes, and perceptions. The more recent survey was conducted in 1984 with a random telephone sample of 404 Philadelphia residents. The other survey consisted of a subset of approximately 400 Philadelphia area…

Lymphocyte Subsets and Interleukin-2 Receptors in Autistic Children.

ERIC Educational Resources Information Center

Denney, Douglas R.; And Others

1996-01-01

Blood samples were obtained from 10 male autistic children, ages 7-15 years, and 10 controls. The children with autism had a lower percentage of helper-inducer cells and a lower helper:suppressor ratio, with both measures inversely related to the severity of autistic symptoms. (Author/DB)

Benchmarking 2011: Trends in Education Philanthropy

ERIC Educational Resources Information Center

Grantmakers for Education, 2011

2011-01-01

The analysis in "Benchmarking 2011" is based on data from an unduplicated sample of 184 education grantmaking organizations--approximately two-thirds of Grantmakers for Education's (GFE's) network of grantmakers--who responded to an online survey consisting of fixed-choice and open-ended questions. Because a different subset of funders elects to…

Self-Concept and Social Interaction in a Deaf Population.

ERIC Educational Resources Information Center

Garrison, Wayne M; And Others

Investigated were self concept levels of 109 deaf college students, and examined were social interaction behaviors among a subset of 27 Ss from the study sample. Results of the Tennessee Self Concept Scale indicated a response pattern demonstrating psychological distress or maladjustment, but reliability and comprehension analysis suggested that a…

Variation in Cognitive Failures: An Individual Differences Investigation of Everyday Attention and Memory Failures

ERIC Educational Resources Information Center

Unsworth, Nash; Brewer, Gene A.; Spillers, Gregory J.

2012-01-01

The present study examined individual differences in everyday cognitive failures assessed by diaries. A large sample of participants completed various cognitive ability measures in the laboratory. Furthermore, a subset of these participants also recorded everyday cognitive failures (attention, retrospective memory, and prospective memory failures)…

A new mosaic method for three-dimensional surface

NASA Astrophysics Data System (ADS)

Yuan, Yun; Zhu, Zhaokun; Ding, Yongjun

2011-08-01

Three-dimensional (3-D) data mosaic is a indispensable link in surface measurement and digital terrain map generation. With respect to the mosaic problem of the local unorganized cloud points with rude registration and mass mismatched points, a new mosaic method for 3-D surface based on RANSAC is proposed. Every circular of this method is processed sequentially by random sample with additional shape constraint, data normalization of cloud points, absolute orientation, data denormalization of cloud points, inlier number statistic, etc. After N random sample trials the largest consensus set is selected, and at last the model is re-estimated using all the points in the selected subset. The minimal subset is composed of three non-colinear points which form a triangle. The shape of triangle is considered in random sample selection in order to make the sample selection reasonable. A new coordinate system transformation algorithm presented in this paper is used to avoid the singularity. The whole rotation transformation between the two coordinate systems can be solved by twice rotations expressed by Euler angle vector, each rotation has explicit physical means. Both simulation and real data are used to prove the correctness and validity of this mosaic method. This method has better noise immunity due to its robust estimation property, and has high accuracy as the shape constraint is added to random sample and the data normalization added to the absolute orientation. This method is applicable for high precision measurement of three-dimensional surface and also for the 3-D terrain mosaic.

Estimating rare events in biochemical systems using conditional sampling.

PubMed

Sundar, V S

2017-01-28

The paper focuses on development of variance reduction strategies to estimate rare events in biochemical systems. Obtaining this probability using brute force Monte Carlo simulations in conjunction with the stochastic simulation algorithm (Gillespie's method) is computationally prohibitive. To circumvent this, important sampling tools such as the weighted stochastic simulation algorithm and the doubly weighted stochastic simulation algorithm have been proposed. However, these strategies require an additional step of determining the important region to sample from, which is not straightforward for most of the problems. In this paper, we apply the subset simulation method, developed as a variance reduction tool in the context of structural engineering, to the problem of rare event estimation in biochemical systems. The main idea is that the rare event probability is expressed as a product of more frequent conditional probabilities. These conditional probabilities are estimated with high accuracy using Monte Carlo simulations, specifically the Markov chain Monte Carlo method with the modified Metropolis-Hastings algorithm. Generating sample realizations of the state vector using the stochastic simulation algorithm is viewed as mapping the discrete-state continuous-time random process to the standard normal random variable vector. This viewpoint opens up the possibility of applying more sophisticated and efficient sampling schemes developed elsewhere to problems in stochastic chemical kinetics. The results obtained using the subset simulation method are compared with existing variance reduction strategies for a few benchmark problems, and a satisfactory improvement in computational time is demonstrated.

Multiclass cancer classification using a feature subset-based ensemble from microRNA expression profiles.

PubMed

Piao, Yongjun; Piao, Minghao; Ryu, Keun Ho

2017-01-01

Cancer classification has been a crucial topic of research in cancer treatment. In the last decade, messenger RNA (mRNA) expression profiles have been widely used to classify different types of cancers. With the discovery of a new class of small non-coding RNAs; known as microRNAs (miRNAs), various studies have shown that the expression patterns of miRNA can also accurately classify human cancers. Therefore, there is a great demand for the development of machine learning approaches to accurately classify various types of cancers using miRNA expression data. In this article, we propose a feature subset-based ensemble method in which each model is learned from a different projection of the original feature space to classify multiple cancers. In our method, the feature relevance and redundancy are considered to generate multiple feature subsets, the base classifiers are learned from each independent miRNA subset, and the average posterior probability is used to combine the base classifiers. To test the performance of our method, we used bead-based and sequence-based miRNA expression datasets and conducted 10-fold and leave-one-out cross validations. The experimental results show that the proposed method yields good results and has higher prediction accuracy than popular ensemble methods. The Java program and source code of the proposed method and the datasets in the experiments are freely available at https://sourceforge.net/projects/mirna-ensemble/. Copyright © 2016 Elsevier Ltd. All rights reserved.

Functional Differences between Human NKp44(-) and NKp44(+) RORC(+) Innate Lymphoid Cells.

PubMed

Hoorweg, Kerim; Peters, Charlotte P; Cornelissen, Ferry; Aparicio-Domingo, Patricia; Papazian, Natalie; Kazemier, Geert; Mjösberg, Jenny M; Spits, Hergen; Cupedo, Tom

2012-01-01

Human RORC(+) lymphoid tissue inducer cells are part of a rapidly expanding family of innate lymphoid cells (ILC) that participate in innate and adaptive immune responses as well as in lymphoid tissue (re) modeling. The assessment of a potential role for innate lymphocyte-derived cytokines in human homeostasis and disease is hampered by a poor characterization of RORC(+) innate cell subsets and a lack of knowledge on the distribution of these cells in adults. Here we show that functionally distinct subsets of human RORC(+) innate lymphoid cells are enriched for secretion of IL-17a or IL-22. Both subsets have an activated phenotype and can be distinguished based on the presence or absence of the natural cytotoxicity receptor NKp44. NKp44(+) IL-22 producing cells are present in tonsils while NKp44(-) IL-17a producing cells are present in fetal developing lymph nodes. Development of human intestinal NKp44(+) ILC is a programmed event that is independent of bacterial colonization and these cells colonize the fetal intestine during the first trimester. In the adult intestine, NKp44(+) ILC are the main ILC subset producing IL-22. NKp44(-) ILC remain present throughout adulthood in peripheral non-inflamed lymph nodes as resting, non-cytokine producing cells. However, upon stimulation lymph node ILC can swiftly initiate cytokine transcription suggesting that secondary human lymphoid organs may function as a reservoir for innate lymphoid cells capable of participating in inflammatory responses.

Circulating CXCR5+CD4+ T Follicular-Like Helper Cell and Memory B Cell Responses to Human Papillomavirus Vaccines

PubMed Central

Matsui, Ken; Adelsberger, Joseph W.; Kemp, Troy J.; Baseler, Michael W.; Ledgerwood, Julie E.; Pinto, Ligia A.

2015-01-01

Through the interaction of T follicular helper (Tfh) cells and B cells, efficacious vaccines can generate high-affinity, pathogen-neutralizing antibodies, and memory B cells. Using CXCR5, CXCR3, CCR6, CCR7, PD1, and ICOS as markers, Tfh-like cells can be identified in the circulation and be classified into three functionally distinct subsets that are PD1+ICOS+, PD1+ ICOS-, or PD1-ICOS-. We used these markers to identify different subsets of CXCR5+CD4+ Tfh-like cells in response to highly immunogenic and efficacious vaccines for human papillomaviruses (HPV): Cervarix and Gardasil. In this small study, we used PBMC samples from 11 Gardasil recipients, and 8 Cervarix recipients from the Vaccine Research Center 902 Study to examine the induction of circulating Tfh-like cells and IgD-CD38HiCD27+ memory B cells by flow cytometry. PD1+ICOS+ CXCR3+CCR6-CXCR5+CD4+ (Tfh1-like) cells were induced and peaked on Day (D) 7 post-first vaccination, but not as much on D7 post-third vaccination. We also observed a trend toward increase in PD1+ICOS+ CXCR3-CCR6-CXCR5+CD4+ (Tfh2-like) cells for both vaccines, and PD1+ICOS+ CXCR3-CCR6+CXCR5+CD4+ (Tfh17-like) subset was induced by Cervarix post-first vaccination. There were also minimal changes in the other cellular subsets. In addition, Cervarix recipients had more memory B cells post-first vaccination than did Gardasil recipients at D14 and D30. We found frequencies of memory B cells at D30 correlated with anti-HPV16 and 18 antibody titers from D30, and the induction levels of memory B cells at D30 and PD1+ICOS+Tfh1-like cells at D7 post-first vaccination correlated for Cervarix. Our study showed that induction of circulating CXCR5+CD4+ Tfh-like subsets can be detected following immunization with HPV vaccines, and potentially be useful as a marker of immunogenicity of vaccines. However, further investigations should be extended to different cohorts with larger sample size to better understand the functions of these T cells, as well as their relationship with B cells and antibodies. PMID:26333070

Serum BAFF and APRIL Levels, T-Lymphocyte Subsets, and Immunoglobulins after B-Cell Depletion Using the Monoclonal Anti-CD20 Antibody Rituximab in Myalgic Encephalopathy/Chronic Fatigue Syndrome.

PubMed

Lunde, Sigrid; Kristoffersen, Einar K; Sapkota, Dipak; Risa, Kristin; Dahl, Olav; Bruland, Ove; Mella, Olav; Fluge, Øystein

2016-01-01

Myalgic Encephalopathy/Chronic Fatigue Syndrome (ME/CFS) is a disease of unknown etiology. We have previously suggested clinical benefit from B-cell depletion using the monoclonal anti-CD20 antibody rituximab in a randomized and placebo-controlled study. Prolonged responses were then demonstrated in an open-label phase-II study with maintenance rituximab treatment. Using blood samples from patients in the previous two clinical trials, we investigated quantitative changes in T-lymphocyte subsets, in immunoglobulins, and in serum levels of two B-cell regulating cytokines during follow-up. B-lymphocyte activating factor of the tumor necrosis family (BAFF) in baseline serum samples was elevated in 70 ME/CFS patients as compared to 56 healthy controls (p = 0.011). There were no significant differences in baseline serum BAFF levels between patients with mild, moderate, or severe ME/CFS, or between responders and non-responders to rituximab. A proliferation-inducing ligand (APRIL) serum levels were not significantly different in ME/CFS patients compared to healthy controls at baseline, and no changes in serum levels were seen during follow-up. Immunophenotyping of peripheral blood T-lymphocyte subsets and T-cell activation markers at multiple time points during follow-up showed no significant differences over time, between rituximab and placebo groups, or between responders and non-responders to rituximab. Baseline serum IgG levels were significantly lower in patients with subsequent response after rituximab therapy compared to non-responders (p = 0.03). In the maintenance study, slight but significant reductions in mean serum immunoglobulin levels were observed at 24 months compared to baseline; IgG 10.6-9.5 g/L, IgA 1.8-1.5 g/L, and IgM 0.97-0.70 g/L. Although no functional assays were performed, the lack of significant associations of T- and NK-cell subset numbers with B-cell depletion, as well as the lack of associations to clinical responses, suggest that B-cell regulatory effects on T-cell or NK-cell subsets are not the main mechanisms for the observed improvements in ME/CFS symptoms observed in the two previous trials. The modest increase in serum BAFF levels at baseline may indicate an activated B-lymphocyte system in a subgroup of ME/CFS patients.

Serum BAFF and APRIL Levels, T-Lymphocyte Subsets, and Immunoglobulins after B-Cell Depletion Using the Monoclonal Anti-CD20 Antibody Rituximab in Myalgic Encephalopathy/Chronic Fatigue Syndrome

PubMed Central

Lunde, Sigrid; Kristoffersen, Einar K.; Sapkota, Dipak; Risa, Kristin; Dahl, Olav; Bruland, Ove; Mella, Olav; Fluge, Øystein

2016-01-01

Myalgic Encephalopathy/Chronic Fatigue Syndrome (ME/CFS) is a disease of unknown etiology. We have previously suggested clinical benefit from B-cell depletion using the monoclonal anti-CD20 antibody rituximab in a randomized and placebo-controlled study. Prolonged responses were then demonstrated in an open-label phase-II study with maintenance rituximab treatment. Using blood samples from patients in the previous two clinical trials, we investigated quantitative changes in T-lymphocyte subsets, in immunoglobulins, and in serum levels of two B-cell regulating cytokines during follow-up. B-lymphocyte activating factor of the tumor necrosis family (BAFF) in baseline serum samples was elevated in 70 ME/CFS patients as compared to 56 healthy controls (p = 0.011). There were no significant differences in baseline serum BAFF levels between patients with mild, moderate, or severe ME/CFS, or between responders and non-responders to rituximab. A proliferation-inducing ligand (APRIL) serum levels were not significantly different in ME/CFS patients compared to healthy controls at baseline, and no changes in serum levels were seen during follow-up. Immunophenotyping of peripheral blood T-lymphocyte subsets and T-cell activation markers at multiple time points during follow-up showed no significant differences over time, between rituximab and placebo groups, or between responders and non-responders to rituximab. Baseline serum IgG levels were significantly lower in patients with subsequent response after rituximab therapy compared to non-responders (p = 0.03). In the maintenance study, slight but significant reductions in mean serum immunoglobulin levels were observed at 24 months compared to baseline; IgG 10.6–9.5 g/L, IgA 1.8–1.5 g/L, and IgM 0.97–0.70 g/L. Although no functional assays were performed, the lack of significant associations of T- and NK-cell subset numbers with B-cell depletion, as well as the lack of associations to clinical responses, suggest that B-cell regulatory effects on T-cell or NK-cell subsets are not the main mechanisms for the observed improvements in ME/CFS symptoms observed in the two previous trials. The modest increase in serum BAFF levels at baseline may indicate an activated B-lymphocyte system in a subgroup of ME/CFS patients. PMID:27536947

Wrappers for Performance Enhancement and Oblivious Decision Graphs

DTIC Science & Technology

1995-09-01

always select all relevant features. We test di erent search engines to search the space of feature subsets and introduce compound operators to speed...distinct instances from the original dataset appearing in the test set is thus 0:632m. The 0i accuracy estimate is derived by using bootstrap sample...i for training and the rest of the instances for testing . Given a number b, the number of bootstrap samples, let 0i be the accuracy estimate for

Artificial neural networks applied to quantitative elemental analysis of organic material using PIXE

NASA Astrophysics Data System (ADS)

Correa, R.; Chesta, M. A.; Morales, J. R.; Dinator, M. I.; Requena, I.; Vila, I.

2006-08-01

An artificial neural network (ANN) has been trained with real-sample PIXE (particle X-ray induced emission) spectra of organic substances. Following the training stage ANN was applied to a subset of similar samples thus obtaining the elemental concentrations in muscle, liver and gills of Cyprinus carpio. Concentrations obtained with the ANN method are in full agreement with results from one standard analytical procedure, showing the high potentiality of ANN in PIXE quantitative analyses.

Comparative study of feature selection with ensemble learning using SOM variants

NASA Astrophysics Data System (ADS)

Filali, Ameni; Jlassi, Chiraz; Arous, Najet

2017-03-01

Ensemble learning has succeeded in the growth of stability and clustering accuracy, but their runtime prohibits them from scaling up to real-world applications. This study deals the problem of selecting a subset of the most pertinent features for every cluster from a dataset. The proposed method is another extension of the Random Forests approach using self-organizing maps (SOM) variants to unlabeled data that estimates the out-of-bag feature importance from a set of partitions. Every partition is created using a various bootstrap sample and a random subset of the features. Then, we show that the process internal estimates are used to measure variable pertinence in Random Forests are also applicable to feature selection in unsupervised learning. This approach aims to the dimensionality reduction, visualization and cluster characterization at the same time. Hence, we provide empirical results on nineteen benchmark data sets indicating that RFS can lead to significant improvement in terms of clustering accuracy, over several state-of-the-art unsupervised methods, with a very limited subset of features. The approach proves promise to treat with very broad domains.

Validation of the Abdominal Pain Index Using a Revised Scoring Method

PubMed Central

Sherman, Amanda L.; Smith, Craig A.; Walker, Lynn S.

2015-01-01

Objective Evaluate the psychometric properties of child- and parent-report versions of the four-item Abdominal Pain Index (API) in children with functional abdominal pain (FAP) and healthy controls, using a revised scoring method that facilitates comparisons of scores across samples and time. Methods Pediatric patients aged 8–18 years with FAP and controls completed the API at baseline (N = 1,967); a subset of their parents (N = 290) completed the API regarding the child’s pain. Subsets of patients completed follow-up assessments at 2 weeks (N = 231), 3 months (N = 330), and 6 months (N = 107). Subsets of both patients (N = 389) and healthy controls (N = 172) completed a long-term follow-up assessment (mean age at follow-up = 20.21 years, SD = 3.75). Results The API demonstrated good concurrent, discriminant, and construct validity, as well as good internal consistency. Conclusion We conclude that the API, using the revised scoring method, is a useful, reliable, and valid measure of abdominal pain severity. PMID:25617048

Use of the SF-8 to assess health-related quality of life for a chronically ill, low-income population participating in the Central Louisiana Medication Access Program (CMAP).

PubMed

Lefante, John J; Harmon, Gary N; Ashby, Keith M; Barnard, David; Webber, Larry S

2005-04-01

The utility of the SF-8 for assessing health-related quality of life (HRQL) is demonstrated. Race and gender differences in physical component (PCS) and mental component (MCS) summary scores among participants in the CENLA Medication Access Program (CMAP), along with comparisons to the United States population are made. Age-adjusted multiple linear regression analyses were used to compare 1687 CMAP participants to the US population. Internal race and gender comparisons, adjusting for age and the number of self reported diagnoses, were also obtained. The paired t-test was used to assess 6-month change in PCS and MCS scores for a subset of 342 participants. CMAP participants have PCS and MCS scores that are significantly 10-12 points lower than the US population, indicating lower self-reported HRQL. Females have significantly higher PCS and significantly lower MCS than males. African-Americans have significantly higher MCS than Caucasians. Significant increases in both PCS and MCS were observed for the subset of participants after 6 months of intervention. The expected lower baseline PCS and MCS measures and the expected associations with age and number of diagnoses indicate that the SF-8 survey is an effective tool for measuring the HRQL of participants in this program. Preliminary results indicate significant increases in both PCS and MCS 6 months after intervention.

Selecting Feature Subsets Based on SVM-RFE and the Overlapping Ratio with Applications in Bioinformatics.

PubMed

Lin, Xiaohui; Li, Chao; Zhang, Yanhui; Su, Benzhe; Fan, Meng; Wei, Hai

2017-12-26

Feature selection is an important topic in bioinformatics. Defining informative features from complex high dimensional biological data is critical in disease study, drug development, etc. Support vector machine-recursive feature elimination (SVM-RFE) is an efficient feature selection technique that has shown its power in many applications. It ranks the features according to the recursive feature deletion sequence based on SVM. In this study, we propose a method, SVM-RFE-OA, which combines the classification accuracy rate and the average overlapping ratio of the samples to determine the number of features to be selected from the feature rank of SVM-RFE. Meanwhile, to measure the feature weights more accurately, we propose a modified SVM-RFE-OA (M-SVM-RFE-OA) algorithm that temporally screens out the samples lying in a heavy overlapping area in each iteration. The experiments on the eight public biological datasets show that the discriminative ability of the feature subset could be measured more accurately by combining the classification accuracy rate with the average overlapping degree of the samples compared with using the classification accuracy rate alone, and shielding the samples in the overlapping area made the calculation of the feature weights more stable and accurate. The methods proposed in this study can also be used with other RFE techniques to define potential biomarkers from big biological data.

Methods to increase reproducibility in differential gene expression via meta-analysis

PubMed Central

Sweeney, Timothy E.; Haynes, Winston A.; Vallania, Francesco; Ioannidis, John P.; Khatri, Purvesh

2017-01-01

Findings from clinical and biological studies are often not reproducible when tested in independent cohorts. Due to the testing of a large number of hypotheses and relatively small sample sizes, results from whole-genome expression studies in particular are often not reproducible. Compared to single-study analysis, gene expression meta-analysis can improve reproducibility by integrating data from multiple studies. However, there are multiple choices in designing and carrying out a meta-analysis. Yet, clear guidelines on best practices are scarce. Here, we hypothesized that studying subsets of very large meta-analyses would allow for systematic identification of best practices to improve reproducibility. We therefore constructed three very large gene expression meta-analyses from clinical samples, and then examined meta-analyses of subsets of the datasets (all combinations of datasets with up to N/2 samples and K/2 datasets) compared to a ‘silver standard’ of differentially expressed genes found in the entire cohort. We tested three random-effects meta-analysis models using this procedure. We showed relatively greater reproducibility with more-stringent effect size thresholds with relaxed significance thresholds; relatively lower reproducibility when imposing extraneous constraints on residual heterogeneity; and an underestimation of actual false positive rate by Benjamini–Hochberg correction. In addition, multivariate regression showed that the accuracy of a meta-analysis increased significantly with more included datasets even when controlling for sample size. PMID:27634930

Volume 19, Issue8 (December 2004)Articles in the Current Issue:Research ArticleTowards automation of palynology 1: analysis of pollen shape and ornamentation using simple geometric measures, derived from scanning electron microscope images

NASA Astrophysics Data System (ADS)

Treloar, W. J.; Taylor, G. E.; Flenley, J. R.

2004-12-01

This is the first of a series of papers on the theme of automated pollen analysis. The automation of pollen analysis could result in numerous advantages for the reconstruction of past environments, with larger data sets made practical, objectivity and fine resolution sampling. There are also applications in apiculture and medicine. Previous work on the classification of pollen using texture measures has been successful with small numbers of pollen taxa. However, as the number of pollen taxa to be identified increases, more features may be required to achieve a successful classification. This paper describes the use of simple geometric measures to augment the texture measures. The feasibility of this new approach is tested using scanning electron microscope (SEM) images of 12 taxa of fresh pollen taken from reference material collected on Henderson Island, Polynesia. Pollen images were captured directly from a SEM connected to a PC. A threshold grey-level was set and binary images were then generated. Pollen edges were then located and the boundaries were traced using a chain coding system. A number of simple geometric variables were calculated directly from the chain code of the pollen and a variable selection procedure was used to choose the optimal subset to be used for classification. The efficiency of these variables was tested using a leave-one-out classification procedure. The system successfully split the original 12 taxa sample into five sub-samples containing no more than six pollen taxa each. The further subdivision of echinate pollen types was then attempted with a subset of four pollen taxa. A set of difference codes was constructed for a range of displacements along the chain code. From these difference codes probability variables were calculated. A variable selection procedure was again used to choose the optimal subset of probabilities that may be used for classification. The efficiency of these variables was again tested using a leave-one-out classification procedure. The proportion of correctly classified pollen ranged from 81% to 100% depending on the subset of variables used. The best set of variables had an overall classification rate averaging at about 95%. This is comparable with the classification rates from the earlier texture analysis work for other types of pollen. Copyright

Periconceptional growth hormone treatment alters fetal growth and development in lambs.

PubMed

Koch, J M; Wilmoth, T A; Wilson, M E

2010-05-01

Research in the area of fetal programming has focused on intrauterine growth restriction. Few studies have attempted to examine programming mechanisms that ultimately lead to lambs with a greater potential for postnatal growth. We previously demonstrated that treatment of ewes with GH at the time of breeding led to an increase in birth weight. Therefore, the objective of this study was to determine the effects of a single injection of sustained-release GH given during the periconceptional period on fetal growth and development and to determine if the GH axis would be altered in these offspring. Estrus was synchronized using 2 injections of PGF(2alpha); at the time of the second injection, ewes assigned to treatment were also given an injection of sustained-release GH. A maternal jugular vein sample was taken weekly to analyze IGF-I as a proxy for GH to estimate the duration of the treatment effect. In ewes treated with GH, IGF-I increased (P < 0.05) by wk 1 and remained elevated until wk 4 postinjection. Lambs were weighed, crown-rump length and abdominal girth were determined, and a plasma sample was collected. In a subset of male lambs, liver, heart, and brain weights were obtained, as well as left and right ventricular wall thicknesses. On postnatal d 100, a subset of ewe lambs were weighed and challenged with an intravenous injection of GHRH. Lambs from treated ewes had increased (P < 0.05) birth weight and abdominal girth compared with control lambs; however, there was no difference in crown-rump length. Expression of GH receptor and IGF-I were increased (P < 0.05) in lambs gestated by GH-treated ewes compared with control ewes. The left ventricular wall was thinner (P < 0.05) from lambs in the GH-treated group compared with control lambs. On postnatal d 100, those ewe lambs born to ewes treated with GH continued to be heavier (P < 0.05) and had no IGF-I response to GHRH challenge. In conclusion, treating ewes with a single injection of GH appeared to alter fetal growth and development. Lambs born to ewes treated with GH were larger at birth and had altered organ development, which may indicate that early maternal GH treatment may lead to permanent changes in the developing fetus. The ewe lambs maintained their growth performance to at least 100 d of postnatal life and appeared to have an altered GH axis, as demonstrated by the altered response to GHRH.

Terahertz imaging with compressed sensing and phase retrieval.

PubMed

Chan, Wai Lam; Moravec, Matthew L; Baraniuk, Richard G; Mittleman, Daniel M

2008-05-01

We describe a novel, high-speed pulsed terahertz (THz) Fourier imaging system based on compressed sensing (CS), a new signal processing theory, which allows image reconstruction with fewer samples than traditionally required. Using CS, we successfully reconstruct a 64 x 64 image of an object with pixel size 1.4 mm using a randomly chosen subset of the 4096 pixels, which defines the image in the Fourier plane, and observe improved reconstruction quality when we apply phase correction. For our chosen image, only about 12% of the pixels are required for reassembling the image. In combination with phase retrieval, our system has the capability to reconstruct images with only a small subset of Fourier amplitude measurements and thus has potential application in THz imaging with cw sources.

Wind Information Uplink to Aircraft Performing Interval Management Operations

NASA Technical Reports Server (NTRS)

Ahmad, Nashat; Barmore, Bryan; Swieringa, Kurt

2015-01-01

The accuracy of the wind information used to generate trajectories for aircraft performing Interval Management (IM) operations is critical to the success of an IM operation. There are two main forms of uncertainty in the wind information used by the Flight Deck Interval Management (FIM) equipment. The first is the accuracy of the forecast modeling done by the weather provider. The second is that only a small subset of the forecast data can be uplinked to the aircraft for use by the FIM equipment, resulting in loss of additional information. This study focuses on what subset of forecast data, such as the number and location of the points where the wind is sampled should be made available to uplink to the aircraft.

Trauma Collaborative Care Intervention: Effect on Surgeon Confidence in Managing Psychosocial Complications After Orthopaedic Trauma.

PubMed

Wegener, Stephen T; Carroll, Eben A; Gary, Joshua L; McKinley, Todd O; OʼToole, Robert V; Sietsema, Debra L; Castillo, Renan C; Frey, Katherine P; Scharfstein, Daniel O; Huang, Yanjie; Collins, Susan C J; MacKenzie, Ellen J

2017-08-01

The impact of the Trauma Collaborative Care (TCC) program on surgeon confidence in managing the psychosocial sequelae of orthopaedic trauma was evaluated as part of a larger prospective, multisite, cluster clinical trial. We compared confidence and perceived resource availability among surgeons practicing in trauma centers that implemented the TCC program with orthopaedic trauma surgeons in similar trauma centers that did not implement the TCC. Prospective cohort design. Level-I trauma centers. Attending surgeons and fellows (N = 95 Pre and N = 82 Post). Self-report 10-item measure of surgeon confidence in managing psychosocial issues associated with trauma and perceived availability of support resources. Analyses, performed on the entire sample and repeated on the subset of 52 surgeons who responded to the survey at both times points, found surgeons at intervention sites experienced a significantly greater positive improvement (P < 0.05) in their (1) belief that they have strategies to help orthopaedic trauma patients change their psychosocial situation; (2) confidence in making appropriate referrals for orthopaedic trauma patients with psychosocial problems; and (3) belief that they have access to information to guide the management of psychosocial issues related to recovery. Initial data suggest that the establishment of the TCC program can improve surgeons' perceived availability of resources and their confidence in managing the psychosocial sequelae after injury. Further studies will be required to determine if this translates into beneficial patient effects. Therapeutic Level II. See Instructions for Authors for a complete description of levels of evidence.

Microscope use in clinical veterinary practice and potential implications for veterinary school curricula.

PubMed

Stewart, Sherry M; Dowers, Kristy L; Cerda, Jacey R; Schoenfeld-Tacher, Regina M; Kogan, Lori R

2014-01-01

Microscopy (skill of using a microscope) and the concepts of cytology (study of cells) and histology (study of tissues) are most often taught in professional veterinary medicine programs through the traditional method of glass slides and light microscopes. Several limiting factors in veterinary training programs are encouraging educators to explore innovative options for teaching microscopy skills and the concepts of cytology and histology. An anonymous online survey was administered through the Colorado Veterinary Medical Association to Colorado veterinarians working in private practice. It was designed to assess their current usage of microscopes for cytological and histological evaluation of specimens and their perceptions of microscope use in their veterinary education. The first part of the survey was answered by 183 veterinarians, with 104 indicating they had an onsite diagnostic lab. Analysis pertaining to the use of the microscope in practice and in veterinary programs was conducted on this subset. Most respondents felt the amount of time spent in the curriculum using a microscope was just right for basic microscope use and using the microscope for viewing and learning about normal and abnormal histological sections and clinical cytology. Participants felt more emphasis could be placed on clinical and diagnostic cytology. Study results suggest that practicing veterinarians frequently use microscopes for a wide variety of cytological diagnostics. However, only two respondents indicated they prepared samples for histological evaluation. Veterinary schools should consider these results against the backdrop of pressure to implement innovative teaching techniques to meet the changing needs of the profession.

Residential indoor PM2.5 in wood stove homes: follow-up of the Libby changeout program

PubMed Central

Noonan, Curtis W.; Navidi, William; Sheppard, Lianne; Palmer, Christopher P.; Bergauff, Megan; Hooper, Kathi; Ward, Tony J.

2012-01-01

In 2005 through 2008 a small rural mountain valley community engaged in a wood stove changeout program to address concerns of poor ambient air quality. During this program we assessed changes to indoor air quality before and after the introduction of a new, lower emission wood stove. We previously reported a greater than 70% reduction in indoor PM2.5 concentrations in homes following the installation of a new EPA-certified stove within the home. We report here on follow-up of the experiences in these and other homes over three winters of sample collection. In 21 homes, we compared pre-changeout PM2.5 concentrations (mean (sd) = 45.0 (33.0) μg/m3) to multiple post-changeout measures of PM2.5 concentrations using a DustTrak. The mean reduction (and 95% confidence interval) from pre-changeout to post-changeout was −18.5 μg/m3 (−31.9, −5.2), adjusting for ambient PM2.5, ambient temperature, and other factors. Findings across homes and across years were highly variable, and a subset of homes did not experience a reduction in PM2.5 following changeout. Reductions were also observed for organic carbon, elemental carbon, and levoglucosan, but increases were observed for dehydroabietic acid and abietic acid. Despite overall improvements in indoor air quality, the varied response across homes may be due to factors other than the introduction of a new wood stove. PMID:22607315

Genetic heterogeneity in Finnish hereditary prostate cancer using ordered subset analysis

PubMed Central

Simpson, Claire L; Cropp, Cheryl D; Wahlfors, Tiina; George, Asha; Jones, MaryPat S; Harper, Ursula; Ponciano-Jackson, Damaris; Tammela, Teuvo; Schleutker, Johanna; Bailey-Wilson, Joan E

2013-01-01

Prostate cancer (PrCa) is the most common male cancer in developed countries and the second most common cause of cancer death after lung cancer. We recently reported a genome-wide linkage scan in 69 Finnish hereditary PrCa (HPC) families, which replicated the HPC9 locus on 17q21-q22 and identified a locus on 2q37. The aim of this study was to identify and to detect other loci linked to HPC. Here we used ordered subset analysis (OSA), conditioned on nonparametric linkage to these loci to detect other loci linked to HPC in subsets of families, but not the overall sample. We analyzed the families based on their evidence for linkage to chromosome 2, chromosome 17 and a maximum score using the strongest evidence of linkage from either of the two loci. Significant linkage to a 5-cM linkage interval with a peak OSA nonparametric allele-sharing LOD score of 4.876 on Xq26.3-q27 (ΔLOD=3.193, empirical P=0.009) was observed in a subset of 41 families weakly linked to 2q37, overlapping the HPCX1 locus. Two peaks that were novel to the analysis combining linkage evidence from both primary loci were identified; 18q12.1-q12.2 (OSA LOD=2.541, ΔLOD=1.651, P=0.03) and 22q11.1-q11.21 (OSA LOD=2.395, ΔLOD=2.36, P=0.006), which is close to HPC6. Using OSA allows us to find additional loci linked to HPC in subsets of families, and underlines the complex genetic heterogeneity of HPC even in highly aggregated families. PMID:22948022

Barriers to care and service needs among chronically homeless persons in a housing first program.

PubMed

Parker, R David; Albrecht, Helmut A

2012-01-01

In 2010, more than 600,000 people in the United States experienced homelessness. Efficient and cost-effective housing methods that reduce homelessness need to be implemented. Housing Ready programs are the standard method that often has set requirements including earned income and sobriety, among others. These programs enable a subset of the homeless to become housed. However, chronically homeless persons, who use the most resources, are often not successful at enrollment or maintaining enrollment. Housing First (H1) is a method focusing on chronically homeless persons. Housing First places a client in housing and provides services after stabilization. This article assessed differences between chronically homeless persons in a H1 program and chronically homeless persons who are not in H1. A case-control study imbedded within a homeless service program collected sociodemographic and service variables, including access and barriers to care. Although the sample was 100% native English speaking, 22% of homeless persons reported that their providers do not speak their same language. All (100%) of participants had a disabling condition under HUD guidelines, but only 17.78% of homeless controls reported having a disabling condition. There were no differences on housing status based on income, gender, race, or age. The lack of differences between these groups indicates that a H1 program can be a clear derivation from the more common Housing Ready programs that have specific requirements for participation. Provider communication may negatively impact an individual's ability to transition from homelessness. Furthermore, chronically homeless persons not in intensive case management are less likely to understand the eligibility requirements for housing and, therefore, self-disqualify because of this lack of knowledge. Intentional communication and education for chronically homeless persons are 2 examples where case managers could improve the ability of the chronically homeless to obtain housing.

Distinct myeloid cell subsets promote meningeal remodeling and vascular repair after mild traumatic brain injury.

PubMed

Russo, Matthew V; Latour, Lawrence L; McGavern, Dorian B

2018-05-01

Mild traumatic brain injury (mTBI) can cause meningeal vascular injury and cell death that spreads into the brain parenchyma and triggers local inflammation and recruitment of peripheral immune cells. The factors that dictate meningeal recovery after mTBI are unknown at present. Here we demonstrated that most patients who had experienced mTBI resolved meningeal vascular damage within 2-3 weeks, although injury persisted for months in a subset of patients. To understand the recovery process, we studied a mouse model of mTBI and found extensive meningeal remodeling that was temporally reliant on infiltrating myeloid cells with divergent functions. Inflammatory myelomonocytic cells scavenged dead cells in the lesion core, whereas wound-healing macrophages proliferated along the lesion perimeter and promoted angiogenesis through the clearance of fibrin and production of the matrix metalloproteinase MMP-2. Notably, a secondary injury experienced during the acute inflammatory phase aborted this repair program and enhanced inflammation, but a secondary injury experienced during the wound-healing phase did not. Our findings demonstrate that meningeal vasculature can undergo regeneration after mTBI that is dependent on distinct myeloid cell subsets.

The SIMRAND methodology: Theory and application for the simulation of research and development projects

NASA Technical Reports Server (NTRS)

Miles, R. F., Jr.

1986-01-01

A research and development (R&D) project often involves a number of decisions that must be made concerning which subset of systems or tasks are to be undertaken to achieve the goal of the R&D project. To help in this decision making, SIMRAND (SIMulation of Research ANd Development Projects) is a methodology for the selection of the optimal subset of systems or tasks to be undertaken on an R&D project. Using alternative networks, the SIMRAND methodology models the alternative subsets of systems or tasks under consideration. Each path through an alternative network represents one way of satisfying the project goals. Equations are developed that relate the system or task variables to the measure of reference. Uncertainty is incorporated by treating the variables of the equations probabilistically as random variables, with cumulative distribution functions assessed by technical experts. Analytical techniques of probability theory are used to reduce the complexity of the alternative networks. Cardinal utility functions over the measure of preference are assessed for the decision makers. A run of the SIMRAND Computer I Program combines, in a Monte Carlo simulation model, the network structure, the equations, the cumulative distribution functions, and the utility functions.

Histone Deacetylases 5 and 9 Govern Responsiveness of the Heart to a Subset of Stress Signals and Play Redundant Roles in Heart Development

PubMed Central

Chang, Shurong; McKinsey, Timothy A.; Zhang, Chun Li; Richardson, James A.; Hill, Joseph A.; Olson, Eric N.

2004-01-01

The adult heart responds to stress signals by hypertrophic growth, which is often accompanied by activation of a fetal cardiac gene program and eventual cardiac demise. We showed previously that histone deacetylase 9 (HDAC9) acts as a suppressor of cardiac hypertrophy and that mice lacking HDAC9 are sensitized to cardiac stress signals. Here we report that mice lacking HDAC5 display a similar cardiac phenotype and develop profoundly enlarged hearts in response to pressure overload resulting from aortic constriction or constitutive cardiac activation of calcineurin, a transducer of cardiac stress signals. In contrast, mice lacking either HDAC5 or HDAC9 show a hypertrophic response to chronic β-adrenergic stimulation identical to that of wild-type littermates, suggesting that these HDACs modulate a specific subset of cardiac stress response pathways. We also show that compound mutant mice lacking both HDAC5 and HDAC9 show a propensity for lethal ventricular septal defects and thin-walled myocardium. These findings reveal central roles for HDACs 5 and 9 in the suppression of a subset of cardiac stress signals as well as redundant functions in the control of cardiac development. PMID:15367668

Histone deacetylases 5 and 9 govern responsiveness of the heart to a subset of stress signals and play redundant roles in heart development.

PubMed

Chang, Shurong; McKinsey, Timothy A; Zhang, Chun Li; Richardson, James A; Hill, Joseph A; Olson, Eric N

2004-10-01

The adult heart responds to stress signals by hypertrophic growth, which is often accompanied by activation of a fetal cardiac gene program and eventual cardiac demise. We showed previously that histone deacetylase 9 (HDAC9) acts as a suppressor of cardiac hypertrophy and that mice lacking HDAC9 are sensitized to cardiac stress signals. Here we report that mice lacking HDAC5 display a similar cardiac phenotype and develop profoundly enlarged hearts in response to pressure overload resulting from aortic constriction or constitutive cardiac activation of calcineurin, a transducer of cardiac stress signals. In contrast, mice lacking either HDAC5 or HDAC9 show a hypertrophic response to chronic beta-adrenergic stimulation identical to that of wild-type littermates, suggesting that these HDACs modulate a specific subset of cardiac stress response pathways. We also show that compound mutant mice lacking both HDAC5 and HDAC9 show a propensity for lethal ventricular septal defects and thin-walled myocardium. These findings reveal central roles for HDACs 5 and 9 in the suppression of a subset of cardiac stress signals as well as redundant functions in the control of cardiac development.

The optical and near-infrared colors of galaxies, 1: The photometric data

NASA Technical Reports Server (NTRS)

Bershady, Matthew A.; Hereld, Mark; Kron, Richard G.; Koo, David C.; Munn, Jeffrey A.; Majewski, Steven R.

1994-01-01

We present optical and near-infrared photometry and spectroscopic redshifts of a well defined sample of 171 field galaxies selected from three high galactic latitude fields. This data set forms the basis for subsequent studies to characterize the trends, dispersion, and evolution of rest-frame colors and image structure. A subset of 143 galaxies constitutes a magnitude-limited sample to B approx. 19.9-20.75 (depending on field), with a median redshift of 0.14, and a maximum redshift of 0.54. This subset is statistically representative in its sampling of the apparent color distribution of galaxies. Thirty six galaxies were selected to have the reddest red-optical colors in two redshift intervals between 0.2 less than z less than 0.3. Photometric passbands are similar to U, B, V, I, and K, and sample galaxy spectral energy distributions between 0.37 and 2.2 micrometers in the observed frame, or down to 0.26 micrometers in the rest frame for the most distant galaxies. B and K images of the entire sample are assembled to form the first optical and near-infrared atlas of a statistically-representative sample of field galaxies. We discuss techniques for faint field-galaxy photometry, including a working definition of a total magnitude, and a method for matching magnitudes in different passbands and different seeing conditions to ensure reliable, integrated colors. Photographic saturation, which substantially affects the brightest 12% of our sample in the optical bands, is corrected with a model employing measured plate-density distributions for each galaxy, calibrated via similar measurements for stars as a function of known saturation level. Both the relative and absolute calibration of our photometry are demonstrated.

The importance of quality control in validating concentrations ...

EPA Pesticide Factsheets

A national-scale survey of 247 contaminants of emerging concern (CECs), including organic and inorganic chemical compounds, and microbial contaminants, was conducted in source and treated drinking water samples from 25 treatment plants across the United States. Multiple methods were used to determine these CECs, including six analytical methods to measure 174 pharmaceuticals, personal care products, and pesticides. A three-component quality assurance/quality control (QA/QC) program was designed for the subset of 174 CECs which allowed us to assess and compare performances of the methods used. The three components included: 1) a common field QA/QC protocol and sample design, 2) individual investigator-developed method-specific QA/QC protocols, and 3) a suite of 46 method comparison analytes that were determined in two or more analytical methods. Overall method performance for the 174 organic chemical CECs was assessed by comparing spiked recoveries in reagent, source, and treated water over a two-year period. In addition to the 247 CECs reported in the larger drinking water study, another 48 pharmaceutical compounds measured did not consistently meet predetermined quality standards. Methodologies that did not seem suitable for these analytes are overviewed. The need to exclude analytes based on method performance demonstrates the importance of additional QA/QC protocols. This paper compares the method performance of six analytical methods used to measure 174 emer

Beyond Picture Naming: Norms and Patient Data for a Verb Generation Task**

PubMed Central

Kurland, Jacquie; Reber, Alisson; Stokes, Polly

2014-01-01

Purpose The current study aimed to: 1) acquire a set of verb generation to picture norms; and 2) probe its utility as an outcomes measure in aphasia treatment. Method Fifty healthy volunteers participated in Phase I, the verb generation normative sample. They generated verbs for 218 pictures of common objects (ISI=5s). In Phase II, four persons with aphasia (PWA) generated verbs for 60 objects (ISI=10s). Their stimuli consisted of objects which were: 1) recently trained (for object naming; n=20); 2) untrained (a control set; n=20); or 3) from a set of pictures named correctly at baseline (n=20). Verb generation was acquired twice: two months into, and following, a six-month home practice program. Results No objects elicited perfect verb agreement in the normed sample. Stimuli with the highest percent agreement were mostly artifacts and dominant verbs primary functional associates. Although not targeted in treatment or home practice, PWA mostly improved performance in verb generation post-practice. Conclusions A set of clinically and experimentally useful verb generation norms was acquired for a subset of the Snodgrass and Vanderwart (1980) picture set. More cognitively demanding than confrontation naming, this task may help to fill the sizeable gap between object picture naming and propositional speech. PMID:24686752

Oral dendritic cells mediate antigen-specific tolerance by stimulating TH1 and regulatory CD4+ T cells.

PubMed

Mascarell, Laurent; Lombardi, Vincent; Louise, Anne; Saint-Lu, Nathalie; Chabre, Henri; Moussu, Hélène; Betbeder, Didier; Balazuc, Anne-Marie; Van Overtvelt, Laurence; Moingeon, Philippe

2008-09-01

A detailed characterization of oral antigen-presenting cells is critical to improve second-generation sublingual allergy vaccines. To characterize oral dendritic cells (DCs) within lingual and buccal tissues from BALB/c mice with respect to their surface phenotype, distribution, and capacity to polarize CD4(+) T-cell responses. In situ analysis of oral DCs was performed by immunohistology. Purified DCs were tested in vitro for their capacity to capture, process, and present the ovalbumin antigen to naive CD4(+) T cells. In vivo priming of ovalbumin-specific T cells adoptively transferred to BALB/c mice was analyzed by cytofluorometry in cervical lymph nodes after sublingual administration of mucoadhesive ovalbumin. Three subsets of oral DCs with a distinct tissue distribution were identified: (1) a minor subset of CD207(+) Langerhans cells located in the mucosa itself, (2) a major subpopulation of CD11b(+)CD11c(-) and CD11b(+)CD11c(+) myeloid DCs at the mucosal/submucosal interface, and (3) B220(+)120G8(+) plasmacytoid DCs found in submucosal tissues. Purified myeloid and plasmacytoid oral DCs capture and process the antigen efficiently and are programmed to elicit IFN-gamma and/or IL-10 production together with a suppressive function in naive CD4(+) T cells. Targeting the ovalbumin antigen to oral DCs in vivo by using mucoadhesive particles establishes tolerance in the absence of cell depletion through the stimulation of IFN-gamma and IL-10-producing CD4(+) regulatory T cells in cervical lymph nodes. The oral immune system is composed of various subsets of tolerogenic DCs organized in a compartmentalized manner and programmed to induce T(H)1/regulatory T-cell responses.

Application of the biosafety RAM and eProtocol software programs to streamline institutional biosafety committee processes at the USDA-National Animal Disease Center

USDA-ARS?s Scientific Manuscript database

The National Animal Disease Center (NADC) conducts basic and applied research on endemic animal diseases of high priority that adversely affect U.S. livestock production or trade. Experiments conducted at this Center vary in range and scope, with a subset involving synthetic or recombinant nucleic a...

Strengthening Ties: The Case for Building a Social Policy Centered on Families

ERIC Educational Resources Information Center

Longman, Phillip; Mundy, Liza; Black, Rachel; Bornfreund, Laura; Byrum, Greta; Cramer, Reid; Gangadharan, Seeta Peña; Guernsey, Lisa; Lieberman, Abbie; Lynn, Barry; McCarthy, Mary Alice

2015-01-01

Most of the social and economic policies in the U.S. do not explicitly address or take into account the growing importance of families as sources of human capital and determinants of individual success. Even the small subsets of programs that we conventionally frame as part of "family policy" are often based on long-defunct assumptions…

A computer program for fast and easy typing of partial endoglucanase gene sequence into phylotypes and sequevars 1&2 (select agents) of Ralstonia solanacearum

USDA-ARS?s Scientific Manuscript database

The phytopathogen Ralstonia solanacearum is a species complex that contains a subset of strains that are quarantined or select agent pathogens. An unidentified R. solanacearum strain is considered a select agent in the US until proven otherwise, which can be done by phylogenetic analysis of a partia...

This Is My Story: Participatory Performance for HIV and AIDS Education at the University of Malawi

ERIC Educational Resources Information Center

Jaganath, D.; Mulenga, C.; Hoffman, R. M.; Hamilton, J.; Boneh, G.

2014-01-01

University students represent a subset of young men and women at risk for HIV in high prevalence settings. Innovative programs are needed to raise awareness on the unique issues around HIV and AIDS in the university campus, while training student leaders for peer-based education. The Process and Collaboration for Empowerment and Discussion (PACED)…

Exploring the Experiences of Lesbian, Gay, Bisexual, and Questioning Adolescents in Foster Care

ERIC Educational Resources Information Center

Gallegos, Anne; White, Catherine Roller; Ryan, Caitlin; O'Brien, Kirk; Pecora, Peter J.; Thomas, Preneka

2011-01-01

This article is based on the findings from a subset of gender identity and sexual orientation questions from The Casey Field Office Mental Health Study (CFOMH). It aims to contribute the experiences of youth in the care of Casey Family Programs to the increasing body of research on lesbian, gay, bisexual, transgender, or questioning (LGBTQ) youth…

EPA Facility Registry Service (FRS): ICIS

EPA Pesticide Factsheets

This web feature service contains location and facility identification information from EPA's Facility Registry Service (FRS) for the subset of facilities that link to the Integrated Compliance Information System (ICIS). When complete, ICIS will provide a database that will contain integrated enforcement and compliance information across most of EPA's programs. The vision for ICIS is to replace EPA's independent databases that contain enforcement data with a single repository for that information. Currently, ICIS contains all Federal Administrative and Judicial enforcement actions and a subset of the Permit Compliance System (PCS), which supports the National Pollutant Discharge Elimination System (NPDES). ICIS exchanges non-sensitive enforcement/compliance activities, non-sensitive formal enforcement actions and NPDES information with FRS. This web feature service contains the enforcement/compliance activities and formal enforcement action related facilities; the NPDES facilities are contained in the PCS_NPDES web feature service. FRS identifies and geospatially locates facilities, sites or places subject to environmental regulations or of environmental interest. Using vigorous verification and data management procedures, FRS integrates facility data from EPA's national program systems, other federal agencies, and State and tribal master facility records and provides EPA with a centrally managed, single source of comprehensive and authoritative information on f

Analysis of the single-vehicle cyclic inventory routing problem

NASA Astrophysics Data System (ADS)

Aghezzaf, El-Houssaine; Zhong, Yiqing; Raa, Birger; Mateo, Manel

2012-11-01

The single-vehicle cyclic inventory routing problem (SV-CIRP) consists of a repetitive distribution of a product from a single depot to a selected subset of customers. For each customer, selected for replenishments, the supplier collects a corresponding fixed reward. The objective is to determine the subset of customers to replenish, the quantity of the product to be delivered to each and to design the vehicle route so that the resulting profit (difference between the total reward and the total logistical cost) is maximised while preventing stockouts at each of the selected customers. This problem appears often as a sub-problem in many logistical problems. In this article, the SV-CIRP is formulated as a mixed-integer program with a nonlinear objective function. After a thorough analysis of the structure of the problem and its features, an exact algorithm for its solution is proposed. This exact algorithm requires only solutions of linear mixed-integer programs. Values of a savings-based heuristic for this problem are compared to the optimal values obtained for a set of some test problems. In general, the gap may get as large as 25%, which justifies the effort to continue exploring and developing exact and approximation algorithms for the SV-CIRP.

Hybrid 3-D rocket trajectory program. Part 1: Formulation and analysis. Part 2: Computer programming and user's instruction. [computerized simulation using three dimensional motion analysis

NASA Technical Reports Server (NTRS)

Huang, L. C. P.; Cook, R. A.

1973-01-01

Models utilizing various sub-sets of the six degrees of freedom are used in trajectory simulation. A 3-D model with only linear degrees of freedom is especially attractive, since the coefficients for the angular degrees of freedom are the most difficult to determine and the angular equations are the most time consuming for the computer to evaluate. A computer program is developed that uses three separate subsections to predict trajectories. A launch rail subsection is used until the rocket has left its launcher. The program then switches to a special 3-D section which computes motions in two linear and one angular degrees of freedom. When the rocket trims out, the program switches to the standard, three linear degrees of freedom model.

Wavelet-Smoothed Interpolation of Masked Scientific Data for JPEG 2000 Compression

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brislawn, Christopher M.

2012-08-13

How should we manage scientific data with 'holes'? Some applications, like JPEG 2000, expect logically rectangular data, but some sources, like the Parallel Ocean Program (POP), generate data that isn't defined on certain subsets. We refer to grid points that lack well-defined, scientifically meaningful sample values as 'masked' samples. Wavelet-smoothing is a highly scalable interpolation scheme for regions with complex boundaries on logically rectangular grids. Computation is based on forward/inverse discrete wavelet transforms, so runtime complexity and memory scale linearly with respect to sample count. Efficient state-of-the-art minimal realizations yield small constants (O(10)) for arithmetic complexity scaling, and in-situ implementationmore » techniques make optimal use of memory. Implementation in two dimensions using tensor product filter banks is straighsorward and should generalize routinely to higher dimensions. No hand-tuning required when the interpolation mask changes, making the method aeractive for problems with time-varying masks. Well-suited for interpolating undefined samples prior to JPEG 2000 encoding. The method outperforms global mean interpolation, as judged by both SNR rate-distortion performance and low-rate artifact mitigation, for data distributions whose histograms do not take the form of sharply peaked, symmetric, unimodal probability density functions. These performance advantages can hold even for data whose distribution differs only moderately from the peaked unimodal case, as demonstrated by POP salinity data. The interpolation method is very general and is not tied to any particular class of applications, could be used for more generic smooth interpolation.« less

AST: an automated sequence-sampling method for improving the taxonomic diversity of gene phylogenetic trees.

PubMed

Zhou, Chan; Mao, Fenglou; Yin, Yanbin; Huang, Jinling; Gogarten, Johann Peter; Xu, Ying

2014-01-01

A challenge in phylogenetic inference of gene trees is how to properly sample a large pool of homologous sequences to derive a good representative subset of sequences. Such a need arises in various applications, e.g. when (1) accuracy-oriented phylogenetic reconstruction methods may not be able to deal with a large pool of sequences due to their high demand in computing resources; (2) applications analyzing a collection of gene trees may prefer to use trees with fewer operational taxonomic units (OTUs), for instance for the detection of horizontal gene transfer events by identifying phylogenetic conflicts; and (3) the pool of available sequences is biased towards extensively studied species. In the past, the creation of subsamples often relied on manual selection. Here we present an Automated sequence-Sampling method for improving the Taxonomic diversity of gene phylogenetic trees, AST, to obtain representative sequences that maximize the taxonomic diversity of the sampled sequences. To demonstrate the effectiveness of AST, we have tested it to solve four problems, namely, inference of the evolutionary histories of the small ribosomal subunit protein S5 of E. coli, 16 S ribosomal RNAs and glycosyl-transferase gene family 8, and a study of ancient horizontal gene transfers from bacteria to plants. Our results show that the resolution of our computational results is almost as good as that of manual inference by domain experts, hence making the tool generally useful to phylogenetic studies by non-phylogeny specialists. The program is available at http://csbl.bmb.uga.edu/~zhouchan/AST.php.

AST: An Automated Sequence-Sampling Method for Improving the Taxonomic Diversity of Gene Phylogenetic Trees

PubMed Central

Zhou, Chan; Mao, Fenglou; Yin, Yanbin; Huang, Jinling; Gogarten, Johann Peter; Xu, Ying

2014-01-01

A challenge in phylogenetic inference of gene trees is how to properly sample a large pool of homologous sequences to derive a good representative subset of sequences. Such a need arises in various applications, e.g. when (1) accuracy-oriented phylogenetic reconstruction methods may not be able to deal with a large pool of sequences due to their high demand in computing resources; (2) applications analyzing a collection of gene trees may prefer to use trees with fewer operational taxonomic units (OTUs), for instance for the detection of horizontal gene transfer events by identifying phylogenetic conflicts; and (3) the pool of available sequences is biased towards extensively studied species. In the past, the creation of subsamples often relied on manual selection. Here we present an Automated sequence-Sampling method for improving the Taxonomic diversity of gene phylogenetic trees, AST, to obtain representative sequences that maximize the taxonomic diversity of the sampled sequences. To demonstrate the effectiveness of AST, we have tested it to solve four problems, namely, inference of the evolutionary histories of the small ribosomal subunit protein S5 of E. coli, 16 S ribosomal RNAs and glycosyl-transferase gene family 8, and a study of ancient horizontal gene transfers from bacteria to plants. Our results show that the resolution of our computational results is almost as good as that of manual inference by domain experts, hence making the tool generally useful to phylogenetic studies by non-phylogeny specialists. The program is available at http://csbl.bmb.uga.edu/~zhouchan/AST.php. PMID:24892935

Very early disengagement and subsequent re-engagement in primary care Office Based Opioid Treatment (OBOT) with buprenorphine.

PubMed

Hui, David; Weinstein, Zoe M; Cheng, Debbie M; Quinn, Emily; Kim, Hyunjoong; Labelle, Colleen; Samet, Jeffrey H

2017-08-01

Patients with opioid use disorder often require multiple treatment attempts before achieving stable recovery. Rates of disengagement from buprenorphine are highest in the first month of treatment and termination of buprenorphine therapy results in return to use rates as high as 90%. To better characterize these at-risk patients, this study aims to describe: 1) the frequency and characteristics of patients with very early disengagement (≤1month) from Office Based Opioid Treatment (OBOT) with buprenorphine and 2) the frequency and characteristics of patients who re-engage in care at this same OBOT clinic within 2years, among the subset of very early disengagers. This is a retrospective cohort study of adult patients enrolled in a large urban OBOT program. Descriptive statistics were used to characterize the sample and the proportion of patients with very early (≤1month) disengagement and their re-engagement. Multivariable logistic regression models were used to identify patient characteristics associated with the outcomes of very early disengagement and re-engagement. Potential predictors included: sex, age, race/ethnicity, education, employment, opioid use history, prior substance use treatments, urine drug testing, and psychiatric diagnoses. Overall, very early disengagement was unusual, with only 8.4% (104/1234) of patients disengaging within the first month. Among the subset of very early disengagers with 2years of follow-up, the proportion who re-engaged with this OBOT program in the subsequent 2years was 11.9% (10/84). Urine drug test positive for opiates within the first month (AOR: 2.01, 95% CI: 1.02-3.93) was associated with increased odds of very early disengagement. Transferring from another buprenorphine prescriber (AOR: 0.09, 95% CI: 0.01-0.70) was associated with decreased odds of very early disengagement. No characteristics were significantly associated with re-engagement. Early disengagement is uncommon; however, continued opioid use appeared to be associated with higher odds of treatment disengagement and these patients may warrant additional support. Re-engagement was uncommon, suggesting the need for a more formal explicit system to encourage and facilitate re-engagement among patients who disengage. Copyright © 2017 Elsevier Inc. All rights reserved.

AOIPS data base management systems support for GARP data sets

NASA Technical Reports Server (NTRS)

Gary, J. P.

1977-01-01

A data base management system is identified, developed to provide flexible access to data sets produced by GARP during its data systems tests. The content and coverage of the data base are defined and a computer-aided, interactive information storage and retrieval system, implemented to facilitate access to user specified data subsets, is described. The computer programs developed to provide the capability were implemented on the highly interactive, minicomputer-based AOIPS and are referred to as the data retrieval system (DRS). Implemented as a user interactive but menu guided system, the DRS permits users to inventory the data tape library and create duplicate or subset data sets based on a user selected window defined by time and latitude/longitude boundaries. The DRS permits users to select, display, or produce formatted hard copy of individual data items contained within the data records.

Estimated cost savings associated with the transfer of office-administered specialty pharmaceuticals to a specialty pharmacy provider in a Medical Injectable Drug program.

PubMed

Baldini, Christopher G; Culley, Eric J

2011-01-01

A large managed care organization (MCO) in western Pennsylvania initiated a Medical Injectable Drug (MID) program in 2002 that transferred a specific subset of specialty drugs from physician reimbursement under the traditional "buy-and-bill" model in the medical benefit to MCO purchase from a specialty pharmacy provider (SPP) that supplied physician offices with the MIDs. The MID program was initiated with 4 drugs in 2002 (palivizumab and 3 hyaluronate products/derivatives) growing to more than 50 drugs by 2007-2008. To (a) describe the MID program as a method to manage the cost and delivery of this subset of specialty drugs, and (b) estimate the MID program cost savings in 2007 and 2008 in an MCO with approximately 4.6 million members. Cost savings generated by the MID program were calculated by comparing the total actual expenditure (plan cost plus member cost) on medications included in the MID program for calendar years 2007 and 2008 with the total estimated expenditure that would have been paid to physicians during the same time period for the same medication if reimbursement had been made using HCPCS (J code) billing under the physician "buy-and-bill" reimbursement rates. For the approximately 50 drugs in the MID program in 2007 and 2008, the drug cost savings in 2007 were estimated to be $15.5 million (18.2%) or $290 per claim ($0.28 per member per month [PMPM]) and about $13 million (12.7%) or $201 per claim ($0.23 PMPM) in 2008. Although 28% of MID claims continued to be billed by physicians using J codes in 2007 and 22% in 2008, all claims for MIDs were limited to the SPP reimbursement rates. This MID program was associated with health plan cost savings of approximately $28.5 million over 2 years, achieved by the transfer of about 50 physician-administered injectable pharmaceuticals from reimbursement to physicians to reimbursement to a single SPP and payment of physician claims for MIDs at the SPP reimbursement rates.

Reproducibility of Respondent-Driven Sampling (RDS) in Repeat Surveys of Men Who have Sex with Men, Unguja, Zanzibar.

PubMed

Khatib, Ahmed; Haji, Shaaban; Khamis, Maryam; Said, Christen; Khalid, Farhat; Dahoma, Mohammed; Ali, Ameir; Othman, Asha; Welty, Susie; McFarland, Willi

2017-07-01

To assess the reproducibility of respondent-driven sampling (RDS) in obtaining comparable samples across two survey rounds, we conducted integrated bio-behavioral surveillance surveys (IBBSS) using RDS in 2007 and 2011 among men who have sex with men (MSM) on Unguja island in Zanzibar. Differences in the two rounds were assessed by comparing RDS-adjusted population estimates, stratified estimates, and bottleneck plots. Participants in the 2011 survey round were younger (31.4 vs. 9.9% under 19 years old, p < 0.001), more likely to have tested for HIV in the last year (53.7 vs. 10.6%, p < 0.001), and less likely to have injected drugs in the last 3 months (1.0 vs. 23.2%, p < 0.001) compared to participants in the 2007 round. HIV prevalence was 12.3% in 2007 compared to 2.6% in 2011 (p < 0.001). The difference in HIV prevalence persisted after stratifying and adjusting for known differences in the two surveys rounds. Bottleneck plots suggest that recruitment chains were "trapped" in the social networks of MSM who injected drugs to a greater extent in 2007 than in 2011. We conclude that the two rounds of RDS sampled different subsets of the MSM population on Unguja, particularly with respect to inclusion of MSM within the social networks of people who inject drugs. Findings underscore the need to evaluate the reproducibility of RDS in repeated rounds of IBBSS and to develop new sampling methods for key populations at high risk for HIV in order to track the epidemic, develop evidence-based prevention and care programs, and assess their impact.

A comparison of human papillomavirus testing of clinician-collected and self-collected samples during follow-up after screen-and-treat.

PubMed

Taylor, Sylvia; Wang, Chunhui; Wright, Thomas C; Denny, Lynette; Kuhn, Louise

2011-08-15

Screen-and-treat cervical cancer prevention programs based on high-risk human papillomavirus (HPV) testing and cryotherapy have been shown to be effective in resource-limited settings. However, because cryotherapy is not 100% effective, follow-up is needed after treatment to detect post-treatment failures. We compared the test performances of high-risk HPV testing (Hybrid Capture 2) using self-collected and clinician-collected samples as well as cervical cytology for identifying cervical intraepithelial neoplasia grades 2 or 3 or invasive cervical cancer (CIN2+) among women who did (n=812) and did not (n=1858) undergo cryotherapy in a South African screen-and-treat trial. At 6 months after enrolment (and after cryotherapy, if performed), women were tested using all three screening methods and then underwent colposcopy/biopsy. A predefined subset of women (n=1,455) had extended follow-up with colposcopy/biopsy at 12 months. A total of 33 and 91 cases of CIN2+ were detected among treated and untreated women, respectively. The sensitivity of HPV testing using clinician-collected samples and cervical cytology did not differ by treatment status. HPV testing of clinician-collected samples detected the most cases of CIN2+ among both treated (85%) and untreated (91%) women (p=0.31). Cytology (at a cutoff of atypical squamous cells of undetermined significance or greater) detected 76% of cases among both treated and untreated women. However, the sensitivity of HPV testing using self-collected samples was significantly lower among treated versus untreated women (55% vs. 78%, p=0.01). HPV testing using self-collected vaginal specimens may be useful in primary screening but performs poorly for detecting post-treatment failures. Copyright © 2010 UICC.

COMT val108/158 met genotype affects neural but not cognitive processing in healthy individuals.

PubMed

Dennis, Nancy A; Need, Anna C; LaBar, Kevin S; Waters-Metenier, Sheena; Cirulli, Elizabeth T; Kragel, James; Goldstein, David B; Cabeza, Roberto

2010-03-01

The relationship between cognition and a functional polymorphism in the catechol-O-methlytransferase (COMT) gene, val108/158met, is one of debate in the literature. Furthermore, based on the dopaminergic differences associated with the COMT val108/158met genotype, neural differences during cognition may be present, regardless of genotypic differences in cognitive performance. To investigate these issues the current study aimed to 1) examine the effects of COMT genotype using a large sample of healthy individuals (n = 496-1218) and multiple cognitive measures, and using a subset of the sample (n = 22), 2) examine whether COMT genotype effects medial temporal lobe (MTL) and frontal activity during successful relational memory processing, and 3) investigate group differences in functional connectivity associated with successful relational memory processing. Results revealed no significant group difference in cognitive performance between COMT genotypes in any of the 19 cognitive measures. However, in the subset sample, COMT val homozygotes exhibited significantly decreased MTL and increased prefrontal activity during both successful relational encoding and retrieval, and reduced connectivity between these regions compared with met homozygotes. Taken together, the results suggest that although the COMT val108/158met genotype has no effect on cognitive behavioral measures in healthy individuals, it is associated with differences in neural process underlying cognitive output.

Internet Pornography Use, Perceived Addiction, and Religious/Spiritual Struggles.

PubMed

Grubbs, Joshua B; Exline, Julie J; Pargament, Kenneth I; Volk, Fred; Lindberg, Matthew J

2017-08-01

Prior work has demonstrated that religious beliefs and moral attitudes are often related to sexual functioning. The present work sought to examine another possibility: Do sexual attitudes and behaviors have a relationship with religious and spiritual functioning? More specifically, do pornography use and perceived addiction to Internet pornography predict the experience of religious and spiritual struggle? It was expected that feelings of perceived addiction to Internet pornography would indeed predict such struggles, both cross-sectionally and over time, but that actual pornography use would not. To test these ideas, two studies were conducted using a sample of undergraduate students (N = 1519) and a sample of adult Internet users in the U.S. (N = 713). Cross-sectional analyses in both samples found that elements of perceived addiction were related to the experience of religious and spiritual struggle. Additionally, longitudinal analyses over a 1-year time span with a subset of undergraduates (N = 156) and a subset of adult web users (N = 366) revealed that perceived addiction to Internet pornography predicted unique variance in struggle over time, even when baseline levels of struggle and other related variables were held constant. Collectively, these findings identify perceived addiction to Internet pornography as a reliable predictor of religious and spiritual struggle.

Accuracy of CNV Detection from GWAS Data.

PubMed

Zhang, Dandan; Qian, Yudong; Akula, Nirmala; Alliey-Rodriguez, Ney; Tang, Jinsong; Gershon, Elliot S; Liu, Chunyu

2011-01-13

Several computer programs are available for detecting copy number variants (CNVs) using genome-wide SNP arrays. We evaluated the performance of four CNV detection software suites--Birdsuite, Partek, HelixTree, and PennCNV-Affy--in the identification of both rare and common CNVs. Each program's performance was assessed in two ways. The first was its recovery rate, i.e., its ability to call 893 CNVs previously identified in eight HapMap samples by paired-end sequencing of whole-genome fosmid clones, and 51,440 CNVs identified by array Comparative Genome Hybridization (aCGH) followed by validation procedures, in 90 HapMap CEU samples. The second evaluation was program performance calling rare and common CNVs in the Bipolar Genome Study (BiGS) data set (1001 bipolar cases and 1033 controls, all of European ancestry) as measured by the Affymetrix SNP 6.0 array. Accuracy in calling rare CNVs was assessed by positive predictive value, based on the proportion of rare CNVs validated by quantitative real-time PCR (qPCR), while accuracy in calling common CNVs was assessed by false positive/false negative rates based on qPCR validation results from a subset of common CNVs. Birdsuite recovered the highest percentages of known HapMap CNVs containing >20 markers in two reference CNV datasets. The recovery rate increased with decreased CNV frequency. In the tested rare CNV data, Birdsuite and Partek had higher positive predictive values than the other software suites. In a test of three common CNVs in the BiGS dataset, Birdsuite's call was 98.8% consistent with qPCR quantification in one CNV region, but the other two regions showed an unacceptable degree of accuracy. We found relatively poor consistency between the two "gold standards," the sequence data of Kidd et al., and aCGH data of Conrad et al. Algorithms for calling CNVs especially common ones need substantial improvement, and a "gold standard" for detection of CNVs remains to be established.

Newcastle disease B1 vaccine strain in wild rock pigeons in Atlanta, Georgia

USDA-ARS?s Scientific Manuscript database

From June to October of 2012, samples were collected from wild Rock Pigeons (Columba livia) in urban neighborhoods of Atlanta, Georgia to ascertain the prevalence of pigeon paramyxovirus serotype-1 (PPMV-1). PPMV-1 strains are a subset of avian paramyxovirus serotype-1 (APMV-1) commonly isolated fro...

A Method for Establishing a Depreciated Monetary Value for Print Collections.

ERIC Educational Resources Information Center

Marman, Edward

1995-01-01

Outlines a method for establishing a depreciated value of a library collection and includes an example of applying the formula for calculating depreciation. The method is based on the useful life of books, other print, and audio visual materials; their original cost; and on sampling subsets or sections of the collection. (JKP)

Variations in Latino Parenting Practices and Their Effects on Child Cognitive Developmental Outcomes

ERIC Educational Resources Information Center

De Von Figueroa-Moseley, Colmar; Ramey, Craig T.; Keltner, Bette; Lanzi, Robin G.

2006-01-01

This research examines variations in parenting and its effects on child cognitive outcomes across Latino subgroups from a national sampling that utilized a subset of 995 former Head Start Latino parents and children. Comparisons of the Parenting Dimension Inventory scaled scores revealed Latino subgroup differences on nurturance and consistency.…

Psychometric Properties of the Alabama Parenting Questionnaire-Preschool Revision

ERIC Educational Resources Information Center

Clerkin, Suzanne M.; Marks, David J.; Policaro, Katia L.; Halperin, Jeffrey M.

2007-01-01

The psychometric properties of the Alabama Parenting Questionnaire-Preschool Revision (APQ-PR) were explored in a sample of hyperactive-inattentive preschool children (N = 47) and nonimpaired controls (N = 113). A subset of parents completed the questionnaire on 2 occasions, approximately 1 year apart. Factor analysis revealed a 3-factor solution,…

Effect of School Policy on Tobacco Use by School Personnel in Bihar, India.

ERIC Educational Resources Information Center

Sinha, Dhirendra N.; Gupta, Prakash C.; Warren, Charles W.; Asma, Samira

2004-01-01

This study examined the relationship between school tobacco policies and tobacco use prevalence among school personnel. Two subsets of schools were identified in Bihar, India: Federal schools (with a tobacco policy), and State schools (without a tobacco policy). Stratified probability samples of 50 schools each were selected. The survey was…

Who Stays? Who Leaves? An Examination of Sex Differences in Staying and Leaving.

ERIC Educational Resources Information Center

Poole, Millicent E.; Low, B. C.

The purpose of this study was to examine the major determinants of the "staying" and "leaving" process for samples of Melbourne (Australia) male and female adolescents. Sixty attitudinal statements were obtained from 796 adolescents and factor analysed. The subset of independent variables, together with a set of personality and…

The Acoustic Correlates of Perceived Masculinity, Perceived Femininity, and Perceived Sexual Orientation

ERIC Educational Resources Information Center

Munson, Benjamin

2007-01-01

Previous studies have shown that a subset of gay, lesbian, and bisexual (GLB) and heterosexual adults produce distinctive patterns of phonetic variation that allow listeners to detect their sexual orientation from audio-only samples of read speech. The current investigation examined the extent to which judgments of sexual orientation from speech…

Predictors of Daily Blood Glucose Monitoring in Appalachian Ohio

ERIC Educational Resources Information Center

Raffle, Holly; Ware, Lezlee J.; Ruhil, Anirudh V. S.; Hamel-Lambert, Jane; Denham, Sharon A.

2012-01-01

Objective: To determine factors contributing to successful diabetes self-management in Appalachia, as evidenced by daily blood glucose monitoring. Methods: A telephone survey (N = 3841) was conducted to assess health status and health care access. The current investigation is limited to the subset of this sample who report having diabetes (N =…

Participant-Based Monitoring of Indoor and Outdoor Nitrogen Dioxide, Volatile Organic Compounds, and Polycyclic Aromatic Hydrocarbons among MICA-Air Households

EPA Science Inventory

The Mechanistic Indicators of Childhood Asthma (MICA) study in Detroit, Michigan introduced a participant-based approach to reduce the resource burden associated with collection of indoor and outdoor residential air sampling data. A subset of participants designated as MICA-Air c...

77 FR 76043 - Agency Information Collection Activities: Proposed Collection; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-26

... a pretest of these questions on a sampled set of 2012 MEPS-IC survey respondents. A telephone pretest was conducted in the spring and summer of 2012. The results of this pretest, conducted under the Census Bureau's generic pretest clearance process, led to AHRQ recommending that a subset of the tested...

Family Influences on Adolescents’ Birth Control and Condom Use, Likelihood of Sexually Transmitted Infections

ERIC Educational Resources Information Center

Kao, Tsui-Sui Annie; Manczak, Melissa

2013-01-01

This study explored the relationships among personal factors, family structure and family function, adolescents’ self-efficacy for safe sex, and sexual behaviors among sexually active adolescents. A subset sample from the first three waves of the National Longitudinal Study of Adolescent Health (Add Health) was selected for this exploratory…

Time-dependent Reliability of Dynamic Systems using Subset Simulation with Splitting over a Series of Correlated Time Intervals

DTIC Science & Technology

2013-08-01

cost due to potential warranty costs, repairs and loss of market share. Reliability is the probability that the system will perform its intended...MCMC and splitting sampling schemes. Our proposed SS/ STP method is presented in Section 4, including accuracy bounds and computational effort

Practitioner Representations of Environmental Uncertainty: An Application of Discriminant Analysis.

ERIC Educational Resources Information Center

Acharya, Lalit

Multiple discriminant analysis was used to analyze the structure of a perceived environmental uncertainty variable employed previously in research on public relations roles. Data came from a subset (N=229) of a national sample of public relations practitioners belonging to the Public Relations Society of America, who completed a set of scaled…

ORGANIC CHARACTERIZATION OF AIRBORNE PARTICLES: INTERLABORATORY COMPARISON STUDIES AND THE DEVELOPMENT OF STANDARDS AND REFERENCE MATERIALS

EPA Science Inventory

Investigators characterizing and quantifying the organic compounds in particulate matter (PM) have completed the second interlaboratory comparison study. The first study used a subset of SRM1649a sieved to <63um(API) as an unknown sample, an extract of API, and SRM1649a for u...

Comparative analysis of monocytic and granulocytic myeloid-derived suppressor cell subsets in patients with gastrointestinal malignancies.

PubMed

Duffy, Austin; Zhao, Fei; Haile, Lydia; Gamrekelashvili, Jaba; Fioravanti, Suzanne; Ma, Chi; Kapanadze, Tamar; Compton, Kathryn; Figg, William D; Greten, Tim F

2013-02-01

Myeloid-derived suppressor cells (MDSC) are a heterogenous population of cells comprising myeloid progenitor cells and immature myeloid cells, which have the ability to suppress the effector immune response. In humans, MDSC have not been well characterized owing to the lack of specific markers, although it is possible to broadly classify the MDSC phenotypes described in the literature as being predominantly granulocytic (expressing markers such as CD15, CD66, CD33) or monocytic (expressing CD14). In this study, we set out to perform a direct comparative analysis across both granulocytic and monocytic MDSC subsets in terms of their frequency, absolute number, and function in the peripheral blood of patients with advanced GI cancer. We also set out to determine the optimal method of sample processing given that this is an additional source of heterogeneity. Our findings demonstrate consistent changes across sample processing methods for monocytic MDSC, suggesting that reliance upon cryopreserved PBMC is acceptable. Although we did not see an increase in the population of granulocytic MDSC, these cells were found to be more suppressive than their monocytic counterparts.

Food safety and inspection service regulatory testing program for Escherichia coli O157:H7 in raw ground beef.

PubMed

Naugle, Alecia Larew; Holt, Kristin G; Levine, Priscilla; Eckel, Ron

2005-03-01

We analyzed raw ground beef testing data to determine whether a decrease in the rate of Escherichia coli O157:H7-positive raw ground beef samples has occurred since the inception of Food Safety and Inspection Service (U.S. Department of Agriculture) regulatory actions and microbiological testing concerning this commodity and pathogen. A main effects log-linear Poisson regression model was constructed to evaluate the association between fiscal year and the rate of E. coli O157:H7-positive raw ground beef samples while controlling for the effect of season for the subset of test results obtained from fiscal year (FY)2000 through FY2003. Rate ratios were used to compare the rate of E. coli O157:H7-positive raw ground beef samples between sequential years to identify year-to-year differences. Of the 26,521 raw ground beef samples tested from FY2000 through FY2003, 189 (0.71%) tested positive for E. coli O157:H7. Year-to-year comparisons identified a 50% reduction in the rate of positive ground beef samples from FY2002 to FY2003 when controlling for season (95% CI, 10 to 72% decrease; P = 0.02). This decrease was the only significant year-to-year change in the rate of E. coli O157:H7-positive raw ground beef samples but was consistent in samples obtained from both federally inspected establishments and retail outlets. We believe this decrease is attributed to specific regulatory actions by Food Safety and Inspection Service and subsequent actions implemented by the industry, with the goal of reducing E. coli O157:H7 adulteration of raw ground beef. Continued monitoring is necessary to confirm that the decrease in the rate of E. coli O157:H7 in raw ground beef samples we observed here represents the beginning of a sustained trend.

Perspex machine: V. Compilation of C programs

NASA Astrophysics Data System (ADS)

Spanner, Matthew P.; Anderson, James A. D. W.

2006-01-01

The perspex machine arose from the unification of the Turing machine with projective geometry. The original, constructive proof used four special, perspective transformations to implement the Turing machine in projective geometry. These four transformations are now generalised and applied in a compiler, implemented in Pop11, that converts a subset of the C programming language into perspexes. This is interesting both from a geometrical and a computational point of view. Geometrically, it is interesting that program source can be converted automatically to a sequence of perspective transformations and conditional jumps, though we find that the product of homogeneous transformations with normalisation can be non-associative. Computationally, it is interesting that program source can be compiled for a Reduced Instruction Set Computer (RISC), the perspex machine, that is a Single Instruction, Zero Exception (SIZE) computer.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alam, Ujjaini; Lasue, Jeremie, E-mail: ujjaini.alam@gmail.com, E-mail: jeremie.lasue@irap.omp.eu

We examine three SNe Type Ia datasets: Union2.1, JLA and Panstarrs to check their consistency using cosmology blind statistical analyses as well as cosmological parameter fitting. We find that the Panstarrs dataset is the most stable of the three to changes in the data, although it does not, at the moment, go to high enough redshifts to tightly constrain the equation of state of dark energy, w . The Union2.1, drawn from several different sources, appears to be somewhat susceptible to changes within the dataset. The JLA reconstructs well for a smaller number of cosmological parameters. At higher degrees ofmore » freedom, the dependence of its errors on redshift can lead to varying results between subsets. Panstarrs is inconsistent with the other two datasets at about 2σ confidence level, and JLA and Union2.1 are about 1σ away from each other. For the Ω{sub 0} {sub m} − w cosmological reconstruction, with no additional data, the 1σ range of values in w for selected subsets of each dataset is two times larger for JLA and Union2.1 as compared to Panstarrs. The range in Ω{sub 0} {sub m} for the same subsets remains approximately similar for all three datasets. We find that although there are differences in the fitting and correction techniques used in the different samples, the most important criterion is the selection of the SNe, a slightly different SNe selection can lead to noticeably different results both in the purely statistical analysis and in cosmological reconstruction. We note that a single, high quality low redshift sample could help decrease the uncertainties in the result. We also note that lack of homogeneity in the magnitude errors may bias the results and should either be modeled, or its effect neutralized by using other, complementary datasets. A supernova sample with high quality data at both high and low redshifts, constructed from a few surveys to avoid heterogeneity in the sample, and with homogeneous errors, would result in a more robust cosmological reconstruction.« less

Minimal Residual Disease Assessment and Risk-based Therapy in Acute Lymphoblastic Leukemia.

PubMed

Bassan, Renato; Intermesoli, Tamara; Scattolin, Annamaria; Viero, Piera; Maino, Elena; Sancetta, Rosaria; Carobolante, Francesca; Gianni, Francesca; Stefanoni, Paola; Tosi, Manuela; Spinelli, Orietta; Rambaldi, Alessandro

2017-07-01

The study of minimal residual disease (MRD) in adult patients with acute lymphoblastic leukemia (ALL) allows a greater refinement of the individual risk classification and is the best support for risk-specific therapy with or without allogeneic hematopoietic cell transplantation (HCT). Using case-specific sensitive molecular probes or multiparametric flow cytometry on marrow samples obtained from the end of induction until midconsolidation, MRD assays can detect up to 1 leukemic cell of 10,000 total mononuclear cells (sensitivity, 0.01%; ie, ≥10 4 ). This cutoff, presently bound to technical limitations and subject to improvement, reflects the individual chemosensitivity and is strongly correlated with treatment outcome. The chance for cure is approximately 70% in the MRD-negative subset but only 20% to 30% in MRD-positive patients, in any diagnostic and risk subset. As shown by prospective trials from Germany, Italy, Spain, and France-Switzerland-Belgium, approximately 50% to 70% of unselected adult patients with Philadelphia-negative ALL achieve and maintain an early MRD response, whereas the remainder do not, including a substantial proportion of clinically standard-risk patients, and require an HCT to avert at least partially the risk of relapse. Along with the diffusion of more effective "pediatric-inspired" chemotherapy programs, the MRD analysis is an integral part of a modern management strategy, guiding the decision process to transplant or not, in which case nonrelapse mortality using HCT in first remission-still 10% to 20%-is totally abolished. The use of new agents such as monoclonal antibodies, small inhibitors, and chimeric antigen receptor T cells is opening a new era of MRD-directed therapies, that will further increase survival rates. Copyright © 2017 Elsevier Inc. All rights reserved.

Insights into soil carbon dynamics across climatic and geologic gradients from time-series and fraction-specific radiocarbon analysis

NASA Astrophysics Data System (ADS)

van der Voort, Tessa Sophia; Hagedorn, Frank; Zell, Claudia; McIntyre, Cameron; Eglinton, Tim

2016-04-01

Understanding the interaction between soil organic matter (SOM) and climatic, geologic and ecological factors is essential for the understanding of potential susceptibility and vulnerability to climate and land use change. Radiocarbon constitutes a powerful tool for unraveling SOM dynamics and is increasingly used in studies of carbon turnover. The complex and inherently heterogeneous nature of SOM renders it challenging to assess the processes that govern SOM stability by solely looking at the bulk signature on a plot-scale level. This project combines bulk radiocarbon measurements on a regional-scale spanning wide climatic and geologic gradients with a more in-depth approach for a subset of locations. For this subset, time-series and carbon pool-specific radiocarbon data has been acquired for both topsoil and deeper soils. These well-studied sites are part of the Long-Term Forest Ecosystem Research (LWF) program of the Swiss Federal Institute for Forest, Snow and Landscape research (WSL). Statistical analysis was performed to examine relationships of radiocarbon signatures with variables such as temperature, precipitation and elevation. Bomb-curve modeling was applied determine carbon turnover using time-series data. Results indicate that (1) there is no significant correlation between Δ14C signature and environmental conditions except a weak positive correlation with mean annual temperature, (2) vertical gradients in Δ14C signatures in surface and deeper soils are highly similar despite covering disparate soil-types and climatic systems, and (3) radiocarbon signatures vary significantly between time-series samples and carbon pools. Overall, this study provides a uniquely comprehensive dataset that allows for a better understanding of links between carbon dynamics and environmental settings, as well as for pool-specific and long-term trends in carbon (de)stabilization.

dbVOR: a database system for importing pedigree, phenotype and genotype data and exporting selected subsets.

PubMed

Baron, Robert V; Conley, Yvette P; Gorin, Michael B; Weeks, Daniel E

2015-03-18

When studying the genetics of a human trait, we typically have to manage both genome-wide and targeted genotype data. There can be overlap of both people and markers from different genotyping experiments; the overlap can introduce several kinds of problems. Most times the overlapping genotypes are the same, but sometimes they are different. Occasionally, the lab will return genotypes using a different allele labeling scheme (for example 1/2 vs A/C). Sometimes, the genotype for a person/marker index is unreliable or missing. Further, over time some markers are merged and bad samples are re-run under a different sample name. We need a consistent picture of the subset of data we have chosen to work with even though there might possibly be conflicting measurements from multiple data sources. We have developed the dbVOR database, which is designed to hold data efficiently for both genome-wide and targeted experiments. The data are indexed for fast retrieval by person and marker. In addition, we store pedigree and phenotype data for our subjects. The dbVOR database allows us to select subsets of the data by several different criteria and to merge their results into a coherent and consistent whole. Data may be filtered by: family, person, trait value, markers, chromosomes, and chromosome ranges. The results can be presented in columnar, Mega2, or PLINK format. dbVOR serves our needs well. It is freely available from https://watson.hgen.pitt.edu/register . Documentation for dbVOR can be found at https://watson.hgen.pitt.edu/register/docs/dbvor.html .

Nestedness in assemblages of helminth parasites of bats: a function of geography, environment, or host nestedness?

PubMed

Warburton, Elizabeth M; Van Der Mescht, Luther; Khokhlova, Irina S; Krasnov, Boris R; Vonhof, Maarten J

2018-05-01

Nested subsets occur in ecological communities when species-poor communities are subsets of larger, species-rich communities. Understanding this pattern can help elucidate species colonization abilities, extinction risks, and general structuring of biological communities. Here, we evaluate nestedness in a poorly studied host-parasite system, bats and their helminths, across the Japanese archipelago and within its different bioclimatic regions. We hypothesized that (1) if helminth communities are nested across geographic sites at the level of the archipelago, then broad-scale processes, like colonization-extinction dynamics, mainly structure parasite assemblages; (2) if helminth communities are nested across geographic sites at the level of the bioclimatic region, then fine-scale environmental variation plays a significant role in species nestedness; (3) if helminth community nestedness mirrors host species nestedness, then communities are nested because the habitats they occupy are nested; and (4) if nestedness does not occur or if it is not correlated with any geographical or host data, then passive sampling could be responsible for the patterns of parasite assemblage in our sample. We found that helminth communities were nested across host species throughout the archipelago but, when considering each bioclimatic region, helminths in only one region were significantly more nested than the null model. Helminth communities were also nested across sites within all four bioclimatic regions. These results suggest that helminths form nested subsets across the archipelago due to broad-scale processes that reflect the overall lineages of their mammalian hosts; however, at the regional scale, environmental processes related to nestedness of their habitats drive parasite community nestedness.

Persistent Super-Utilization of Acute Care Services Among Subgroups of Veterans Experiencing Homelessness.

PubMed

Szymkowiak, Dorota; Montgomery, Ann Elizabeth; Johnson, Erin E; Manning, Todd; O'Toole, Thomas P

2017-10-01

Acute health care utilization often occurs among persons experiencing homelessness. However, knowing which individuals will be persistent super-utilizers of acute care is less well understood. The objective of the study was to identify those more likely to be persistent super-utilizers of acute care services. We conducted a latent class analysis of secondary data from the Veterans Health Administration Corporate Data Warehouse, and Homeless Operations Management and Evaluation System. The study sample included 16,912 veterans who experienced homelessness and met super-utilizer criteria in any quarter between July 1, 2014 and December 31, 2015. The latent class analysis included veterans' diagnoses and acute care utilization. Medical, mental health, and substance use morbidity rates were high. More than half of the sample utilized Veterans Health Administration Homeless Programs concurrently with their super-utilization of acute care. There were 7 subgroups of super-utilizers, which varied considerably on the degree to which their super-utilization persisted over time. Approximately a third of the sample met super-utilizer criteria for ≥3 quarters; this group was older and disproportionately male, non-Hispanic white, and unmarried, with lower rates of post-9/11 service and higher rates of rural residence and service-connected disability. They were much more likely to be currently homeless with more medical, mental health, and substance use morbidity. Only a subset of homeless veterans were persistent super-utilizers, suggesting the need for more targeted interventions.

Construction of Core Collections Suitable for Association Mapping to Optimize Use of Mediterranean Olive (Olea europaea L.) Genetic Resources

PubMed Central

El Bakkali, Ahmed; Haouane, Hicham; Moukhli, Abdelmajid; Costes, Evelyne; Van Damme, Patrick; Khadari, Bouchaib

2013-01-01

Phenotypic characterisation of germplasm collections is a decisive step towards association mapping analyses, but it is particularly expensive and tedious for woody perennial plant species. Characterisation could be more efficient if focused on a reasonably sized subset of accessions, or so-called core collection (CC), reflecting the geographic origin and variability of the germplasm. The questions that arise concern the sample size to use and genetic parameters that should be optimized in a core collection to make it suitable for association mapping. Here we investigated these questions in olive (Olea europaea L.), a perennial fruit species. By testing different sampling methods and sizes in a worldwide olive germplasm bank (OWGB Marrakech, Morocco) containing 502 unique genotypes characterized by nuclear and plastid loci, a two-step sampling method was proposed. The Shannon-Weaver diversity index was found to be the best criterion to be maximized in the first step using the Core Hunter program. A primary core collection of 50 entries (CC50) was defined that captured more than 80% of the diversity. This latter was subsequently used as a kernel with the Mstrat program to capture the remaining diversity. 200 core collections of 94 entries (CC94) were thus built for flexibility in the choice of varieties to be studied. Most entries of both core collections (CC50 and CC94) were revealed to be unrelated due to the low kinship coefficient, whereas a genetic structure spanning the eastern and western/central Mediterranean regions was noted. Linkage disequilibrium was observed in CC94 which was mainly explained by a genetic structure effect as noted for OWGB Marrakech. Since they reflect the geographic origin and diversity of olive germplasm and are of reasonable size, both core collections will be of major interest to develop long-term association studies and thus enhance genomic selection in olive species. PMID:23667437

Chronic Binge Alcohol Administration Increases Intestinal T-Cell Proliferation and Turnover in Rhesus Macaques.

PubMed

Veazey, Ronald S; Amedee, Angela; Wang, Xiaolei; Bernice Kaack, M; Porretta, Constance; Dufour, Jason; Welsh, David; Happel, Kyle; Pahar, Bapi; Molina, Patricia E; Nelson, Steve; Bagby, Gregory J

2015-08-01

Alcohol use results in changes in intestinal epithelial cell turnover and microbial translocation, yet less is known about the consequences on intestinal lymphocytes in the gut. Here, we compared T-cell subsets in the intestine of macaques before and after 3 months of chronic alcohol administration to examine the effects of alcohol on intestinal T-cell subsets. Rhesus macaques received either alcohol or isocaloric sucrose as a control treatment daily over a 3-month period via indwelling gastric catheters. Intestinal lymphocyte subsets were identified in biopsy samples by flow cytometry. Twenty-four hours prior to sampling, animals were inoculated with bromo-deoxyuridine (BrdU) to assess lymphocyte proliferation. Immunohistochemistry was performed on tissue samples to quantitate CD3+ cells. Animals receiving alcohol had increased rates of intestinal T-cell turnover of both CD4+ and CD8+ T cells as reflected by increased BrdU incorporation. However, absolute numbers of T cells were decreased in intestinal tissues as evidenced by immunohistochemistry for total CD3 expression per mm(2) intestinal lamina propria in tissue sections. Combining immunohistochemistry and flow cytometry data showed that the absolute numbers of CD8+ T cells were significantly decreased, whereas absolute numbers of total CD4+ T cells were minimally decreased. Collectively, these data indicate that alcohol exposure to the small intestine results in marked loss of CD3+ T cells, accompanied by marked increases in CD4+ and CD8+ T-cell proliferation and turnover, which we speculate is an attempt to maintain stable numbers of T cells in tissues. This suggests that alcohol results in accelerated T-cell turnover in the gut, which may contribute to premature T-cell senescence. Further, these data indicate that chronic alcohol administration results in increased levels of HIV target cells (proliferating CD4+ T cells) that may support higher levels of HIV replication in intestinal tissues. Copyright © 2015 by the Research Society on Alcoholism.

Chronic binge alcohol administration increases intestinal T cell proliferation and turnover in rhesus macaques

PubMed Central

Veazey, Ronald S.; Amedee, Angela; Wang, Xiaolei; Kaack, M. Bernice; Porretta, Constance; Dufour, Jason; Welsh, David; Happel, Kyle; Pahar, Bapi; Molina, Patricia E.; Nelson, Steve; Bagby, Gregory J.

2015-01-01

Background Alcohol use results in changes in intestinal epithelial cell turnover and microbial translocation, yet less in known about the consequences on intestinal lymphocytes in the gut. Here we compared T cell subsets in the intestine of macaques before and after 3 months of chronic alcohol administration to examine the effects of alcohol on intestinal T cell subsets. Methods Rhesus macaques received either alcohol or isocaloric sucrose as a control treatment daily over a 3 month period via indwelling gastric catheters. Intestinal lymphocytes subsets were identified in biopsy samples by flow cytometry. Twenty-four hours prior to sampling, animals were inoculated with BrdU to assess lymphocyte proliferation. Immunohistochemistry was performed on tissue samples to quantitate CD3+ cells. Results Animals receiving alcohol had increased rates of intestinal T cell turnover of both CD4+ and CD8+ T cells as reflected by increased BrdU incorporation. However, absolute numbers of T cells were decreased in intestinal tissues as evidenced by immunohistochemistry for total CD3 expression per mm2 intestinal lamina propria in tissue sections. Combining immunohistochemistry and flow cytometry data showed that the absolute numbers of CD8+ T cells were significantly decreased, whereas total of CD4+ T cells were minimally decreased. Conclusions Collectively, these data indicate alcohol exposure to the small intestine results in marked loss of CD3+ T cells, accompanied by marked increases in CD4+ and CD8+ T cell proliferation and turnover, which we speculate is an attempt to maintain stable numbers of T cells in tissues. This suggests alcohol results in accelerated T cell turnover in the gut, which may contribute to premature T cell senescence. Further these data indicate that chronic alcohol administration results in increased levels of HIV target cells (proliferating CD4+ T cells) that may support higher levels of HIV replication in intestinal tissues. PMID:26146859

Development and Validation of a Predictive Model to Identify Individuals Likely to Have Undiagnosed Chronic Obstructive Pulmonary Disease Using an Administrative Claims Database.

PubMed

Moretz, Chad; Zhou, Yunping; Dhamane, Amol D; Burslem, Kate; Saverno, Kim; Jain, Gagan; Devercelli, Giovanna; Kaila, Shuchita; Ellis, Jeffrey J; Hernandez, Gemzel; Renda, Andrew

2015-12-01

Despite the importance of early detection, delayed diagnosis of chronic obstructive pulmonary disease (COPD) is relatively common. Approximately 12 million people in the United States have undiagnosed COPD. Diagnosis of COPD is essential for the timely implementation of interventions, such as smoking cessation programs, drug therapies, and pulmonary rehabilitation, which are aimed at improving outcomes and slowing disease progression. To develop and validate a predictive model to identify patients likely to have undiagnosed COPD using administrative claims data. A predictive model was developed and validated utilizing a retro-spective cohort of patients with and without a COPD diagnosis (cases and controls), aged 40-89, with a minimum of 24 months of continuous health plan enrollment (Medicare Advantage Prescription Drug [MAPD] and commercial plans), and identified between January 1, 2009, and December 31, 2012, using Humana's claims database. Stratified random sampling based on plan type (commercial or MAPD) and index year was performed to ensure that cases and controls had a similar distribution of these variables. Cases and controls were compared to identify demographic, clinical, and health care resource utilization (HCRU) characteristics associated with a COPD diagnosis. Stepwise logistic regression (SLR), neural networking, and decision trees were used to develop a series of models. The models were trained, validated, and tested on randomly partitioned subsets of the sample (Training, Validation, and Test data subsets). Measures used to evaluate and compare the models included area under the curve (AUC); index of the receiver operating characteristics (ROC) curve; sensitivity, specificity, positive predictive value (PPV); and negative predictive value (NPV). The optimal model was selected based on AUC index on the Test data subset. A total of 50,880 cases and 50,880 controls were included, with MAPD patients comprising 92% of the study population. Compared with controls, cases had a statistically significantly higher comorbidity burden and HCRU (including hospitalizations, emergency room visits, and medical procedures). The optimal predictive model was generated using SLR, which included 34 variables that were statistically significantly associated with a COPD diagnosis. After adjusting for covariates, anticholinergic bronchodilators (OR = 3.336) and tobacco cessation counseling (OR = 2.871) were found to have a large influence on the model. The final predictive model had an AUC of 0.754, sensitivity of 60%, specificity of 78%, PPV of 73%, and an NPV of 66%. This claims-based predictive model provides an acceptable level of accuracy in identifying patients likely to have undiagnosed COPD in a large national health plan. Identification of patients with undiagnosed COPD may enable timely management and lead to improved health outcomes and reduced COPD-related health care expenditures.

Analysis of the νb{6} Asymmetric no Stretch Band of Nitromethane

NASA Astrophysics Data System (ADS)

Dawadi, Mahesh B.; Degliumberto, Lou; Perry, David S.; Mettee, Howard; Sams, Robert L.

2017-06-01

The b-type band near 1583 \\wn has been assigned for m ≤ 3, K''_{a} ≤ 10, J'' ≤ 20. The ground state combination differences derived from these assigned levels were fit with the RAM36 program with an RMS deviation of 0.0006 \\wn. The upper state levels are split into multiplets by perturbations. A subset of the available upper state combination differences for m = 0, K'_{a} ≤ 7, J' ≤ 10 were fit with the same program, but with rather poorer precision (0.01 \\wn) than for the ground state.

Integration Testing of Space Flight Systems

NASA Technical Reports Server (NTRS)

Honeycutt, Timothy; Sowards, Stephanie

2008-01-01

Based on the previous success' of Multi-Element Integration Testing (MEITs) for the International Space Station Program, these type of integrated tests have also been planned for the Constellation Program: MEIT (1) CEV to ISS (emulated) (2) CEV to Lunar Lander/EDS (emulated) (3) Future: Lunar Surface Systems and Mars Missions Finite Element Integration Test (FEIT) (1) CEV/CLV (2) Lunar Lander/EDS/CaL V Integrated Verification Tests (IVT) (1) Performed as a subset of the FEITs during the flight tests and then performed for every flight after Full Operational Capability (FOC) has been obtained with the flight and ground Systems.

Automating Veterans Administration libraries: II. Implementation at the Kansas City Medical Center Library.

PubMed Central

Smith, V K; Ting, S C

1987-01-01

In 1985, the Kansas City Veterans Administration Medical Center began implementation of the Decentralized Hospital Computer Program (DHCP). An integrated library system, a subset of that program, was started by the medical library for acquisitions and an outline catalog. To test the system, staff of the Neurology Service were trained to use the outline catalog and electronic mail to request interlibrary loans and literature searches. In implementing the project with the Neurology Service, the library is paving the way for many types of electronic access and interaction with the library. PMID:3594023

Dissolved metals and associated constituents in abandoned coal-mine discharges, Pennsylvania, USA. Part 1: Constituent quantities and correlations

USGS Publications Warehouse

Cravotta, C.A.

2008-01-01

Complete hydrochemical data are rarely reported for coal-mine discharges (CMD). This report summarizes major and trace-element concentrations and loadings for CMD at 140 abandoned mines in the Anthracite and Bituminous Coalfields of Pennsylvania. Clean-sampling and low-level analytical methods were used in 1999 to collect data that could be useful to determine potential environmental effects, remediation strategies, and quantities of valuable constituents. A subset of 10 sites was resampled in 2003 to analyze both the CMD and associated ochreous precipitates; the hydrochemical data were similar in 2003 and 1999. In 1999, the flow at the 140 CMD sites ranged from 0.028 to 2210 L s-1, with a median of 18.4 L s-1. The pH ranged from 2.7 to 7.3; concentrations (range in mg/L) of dissolved (0.45-??m pore-size filter) SO4 (34-2000), Fe (0.046-512), Mn (0.019-74), and Al (0.007-108) varied widely. Predominant metalloid elements were Si (2.7-31.3 mg L-1), B ( C > P = N = Se) were not elevated in the CMD samples compared to average river water or seawater. Compared to seawater, the CMD samples also were poor in halogens (Cl > Br > I > F), alkalies (Na > K > Li > Rb > Cs), most alkaline earths (Ca > Mg > Sr), and most metalloids but were enriched by two to four orders of magnitude with Fe, Al, Mn, Co, Be, Sc, Y and the lanthanide rare-earth elements, and one order of magnitude with Ni and Zn. The ochre samples collected at a subset of 10 sites in 2003 were dominantly goethite with minor ferrihydrite or lepidocrocite. None of the samples for this subset contained schwertmannite or was Al rich, but most contained minor aluminosilicate detritus. Compared to concentrations in global average shale, the ochres were rich in Fe, Ag, As and Au, but were poor in most other metals and rare earths. The ochres were not enriched compared to commercial ore deposits mined for Au or other valuable metals. Although similar to commercial Fe ores in composition, the ochres are dispersed and present in relatively small quantities at most sites. Nevertheless, the ochres could be valuable for use as pigment.

Impaired Subset Progression and Polyfunctionality of T Cells in Mice Exposed to Methamphetamine during Chronic LCMV Infection

PubMed Central

Sriram, Uma; Hill, Beth L.; Cenna, Jonathan M.; Gofman, Larisa; Fernandes, Nicole C.; Haldar, Bijayesh; Potula, Raghava

2016-01-01

Methamphetamine (METH) is a widely used psychostimulant that severely impacts the host’s innate and adaptive immune systems and has profound immunological implications. T cells play a critical role in orchestrating immune responses. We have shown recently how chronic exposure to METH affects T cell activation using a murine model of lymphocytic choriomeningitis virus (LCMV) infection. Using the TriCOM (trinary state combinations) feature of GemStone™ to study the polyfunctionality of T cells, we have analyzed how METH affected the cytokine production pattern over the course of chronic LCMV infection. Furthermore, we have studied in detail the effects of METH on splenic T cell functions, such as cytokine production and degranulation, and how they regulate each other. We used the Probability State Modeling (PSM) program to visualize the differentiation of effector/memory T cell subsets during LCMV infection and analyze the effects of METH on T cell subset progression. We recently demonstrated that METH increased PD-1 expression on T cells during viral infection. In this study, we further analyzed the impact of PD-1 expression on T cell functional markers as well as its expression in the effector/memory subsets. Overall, our study indicates that analyzing polyfunctionality of T cells can provide additional insight into T cell effector functions. Analysis of T cell heterogeneity is important to highlight changes in the evolution of memory/effector functions during chronic viral infections. Our study also highlights the impact of METH on PD-1 expression and its consequences on T cell responses. PMID:27760221

Impaired Subset Progression and Polyfunctionality of T Cells in Mice Exposed to Methamphetamine during Chronic LCMV Infection.

PubMed

Sriram, Uma; Hill, Beth L; Cenna, Jonathan M; Gofman, Larisa; Fernandes, Nicole C; Haldar, Bijayesh; Potula, Raghava

2016-01-01

Methamphetamine (METH) is a widely used psychostimulant that severely impacts the host's innate and adaptive immune systems and has profound immunological implications. T cells play a critical role in orchestrating immune responses. We have shown recently how chronic exposure to METH affects T cell activation using a murine model of lymphocytic choriomeningitis virus (LCMV) infection. Using the TriCOM (trinary state combinations) feature of GemStone™ to study the polyfunctionality of T cells, we have analyzed how METH affected the cytokine production pattern over the course of chronic LCMV infection. Furthermore, we have studied in detail the effects of METH on splenic T cell functions, such as cytokine production and degranulation, and how they regulate each other. We used the Probability State Modeling (PSM) program to visualize the differentiation of effector/memory T cell subsets during LCMV infection and analyze the effects of METH on T cell subset progression. We recently demonstrated that METH increased PD-1 expression on T cells during viral infection. In this study, we further analyzed the impact of PD-1 expression on T cell functional markers as well as its expression in the effector/memory subsets. Overall, our study indicates that analyzing polyfunctionality of T cells can provide additional insight into T cell effector functions. Analysis of T cell heterogeneity is important to highlight changes in the evolution of memory/effector functions during chronic viral infections. Our study also highlights the impact of METH on PD-1 expression and its consequences on T cell responses.

Peripheral Blood Lymphocyte Subset Counts in Pre-menopausal Women with Iron-Deficiency Anaemia

PubMed Central

Reza Keramati, Mohammad; Sadeghian, Mohammad Hadi; Ayatollahi, Hossein; Mahmoudi, Mahmoud; Khajedaluea, Mohammad; Tavasolian, Houman; Borzouei, Anahita

2011-01-01

Background: Iron-deficiency anaemia (IDA) is a major worldwide public health problem. Children and women of reproductive age are especially vulnerable to IDA, and it has been reported that these patients are more prone to infection. This study was done to evaluate alteration of lymphocyte subgroups in IDA. Methods: In this prospective study, we investigated lymphocyte subsets in pre-menopausal women with iron-deficiency anaemia; 50 normal subjects and 50 IDA (hypochromic microcytic) cases were enrolled. Experimental and control anticoagulated blood samples were evaluated using flow cytometry to determine the absolute and relative numbers of various lymphocyte subgroups. Finally, the results of the patient and control groups were compared. Results: Mean (SD) absolute counts of lymphocytes, CD3+ cells, CD3+/CD4+ subsets (T helper) and CD3+/CD8+ subsets (T cytotoxic) in the patient group were 2.08 (0.65) x 109/L, 1.53 (0.53) x 109/L, 0.87 (0.28) x 109/L, and 0.51 (0.24) x 109/L, respectively. The results showed significant differences between case and control groups in mean absolute counts of lymphocytes (P = 0.014), T lymphocytes (P = 0.009), helper T cells (P = 0.004), and cytotoxic T cells (P = 0.043). Conclusion: This study showed that absolute counts of peripheral blood T lymphocytes as a marker of cell-mediated immunity may be decreased in pre-menopausal women with iron-deficiency anaemia, and that these patients may be more prone to infection. PMID:22135572

An assessment of LANDSAT data acquisition history on identification and area estimation of corn and soybeans. [U.S. Corn Belti Indiana and Iowa

NASA Technical Reports Server (NTRS)

Hixson, M. M.; Bauer, M. E.; Scholz, D. K. (Principal Investigator)

1980-01-01

Multitemporally registered LANDSAT MSS data from four acquisitions during the 1978 growing season were used in classification of eight sample segments in Iowa and Indiana. The results illustrate that use of LANDSAT acquisition when corn has tasseled is critical, as this is the optimum time for separation of corn and soybeans. An early season acquisition when the summer crops appear as bare soil can be beneficial in reducing the confusion between these two crops and other cover types. A subset of one visible and one infrared band from each date was found to produce results not significantly different from the use of all bands. Selection of a subset of these bands may also be feasible for multitemporal analysis.

Optimal number of features as a function of sample size for various classification rules.

PubMed

Hua, Jianping; Xiong, Zixiang; Lowey, James; Suh, Edward; Dougherty, Edward R

2005-04-15

Given the joint feature-label distribution, increasing the number of features always results in decreased classification error; however, this is not the case when a classifier is designed via a classification rule from sample data. Typically (but not always), for fixed sample size, the error of a designed classifier decreases and then increases as the number of features grows. The potential downside of using too many features is most critical for small samples, which are commonplace for gene-expression-based classifiers for phenotype discrimination. For fixed sample size and feature-label distribution, the issue is to find an optimal number of features. Since only in rare cases is there a known distribution of the error as a function of the number of features and sample size, this study employs simulation for various feature-label distributions and classification rules, and across a wide range of sample and feature-set sizes. To achieve the desired end, finding the optimal number of features as a function of sample size, it employs massively parallel computation. Seven classifiers are treated: 3-nearest-neighbor, Gaussian kernel, linear support vector machine, polynomial support vector machine, perceptron, regular histogram and linear discriminant analysis. Three Gaussian-based models are considered: linear, nonlinear and bimodal. In addition, real patient data from a large breast-cancer study is considered. To mitigate the combinatorial search for finding optimal feature sets, and to model the situation in which subsets of genes are co-regulated and correlation is internal to these subsets, we assume that the covariance matrix of the features is blocked, with each block corresponding to a group of correlated features. Altogether there are a large number of error surfaces for the many cases. These are provided in full on a companion website, which is meant to serve as resource for those working with small-sample classification. For the companion website, please visit http://public.tgen.org/tamu/ofs/ e-dougherty@ee.tamu.edu.

Use Of The Operational Air Quality Monitor (AQM) For In-Flight Water Testing Project

NASA Technical Reports Server (NTRS)

Macatangay, Ariel

2014-01-01

A primary requirement for manned spaceflight is Environmental Health which ensures air and water contaminants, acoustic profiles, microbial flora, and radiation exposures within the cabin are maintained to levels needed for crew health and for vehicle system functionality. The reliance on ground analyses of returned samples is a limitation in the current environmental monitoring strategy that will prevent future Exploration missions beyond low-Earth orbit. This proposal attempts to address this shortcoming by advancing in-flight analyses of water and air. Ground analysis of in-flight, air and water samples typically employ vapor-phase analysis by gas chromatography-mass spectrometry (GC-MS) to identify and quantify organic compounds present in the samples. We envision the use of newly-developed direct ionization approaches as the most viable avenue leading towards an integrated analytical platform for the monitoring of water, air, and, potentially bio-samples in the cabin environment. Development of an in-flight instrument capable of analyzing air and water samples would be the logical next step to meeting the environmental monitoring needs of Exploration missions. Currently, the Air Quality Monitor (AQM) on-board ISS provides this specific information for a number of target compounds in the air. However, there is a significant subset of common target compounds between air and water. Naturally, the following question arises, "Can the AQM be used for both air and water quality monitoring?" Previous directorate-level IR&D funding led to the development of a water sample introduction method for mass spectrometry using electrothermal vaporization (ETV). This project will focus on the integration of the ETV with a ground-based AQM. The capabilities of this integrated platform will be evaluated using a subset of toxicologically important compounds.

Iodine in food- and dietary supplement–composition databases123

PubMed Central

Pehrsson, Pamela R; Patterson, Kristine Y; Spungen, Judith H; Wirtz, Mark S; Andrews, Karen W; Dwyer, Johanna T; Swanson, Christine A

2016-01-01

The US Food and Drug Administration (FDA) and the Nutrient Data Laboratory (NDL) of the USDA Agricultural Research Service have worked independently on determining the iodine content of foods and dietary supplements and are now harmonizing their efforts. The objective of the current article is to describe the harmonization plan and the results of initial iodine analyses accomplished under that plan. For many years, the FDA’s Total Diet Study (TDS) has measured iodine concentrations in selected foods collected in 4 regions of the country each year. For more than a decade, the NDL has collected and analyzed foods as part of the National Food and Nutrient Analysis Program; iodine analysis is now being added to the program. The NDL recently qualified a commercial laboratory to conduct iodine analysis of foods by an inductively coupled plasma mass spectrometry (ICP-MS) method. Co-analysis of a set of samples by the commercial laboratory using the ICP-MS method and by the FDA laboratory using its standard colorimetric method yielded comparable results. The FDA recently reviewed historical TDS data for trends in the iodine content of selected foods, and the NDL analyzed samples of a limited subset of those foods for iodine. The FDA and the NDL are working to combine their data on iodine in foods and to produce an online database that can be used for estimating iodine intake from foods in the US population. In addition, the NDL continues to analyze dietary supplements for iodine and, in collaboration with the NIH Office of Dietary Supplements, to publish the data online in the Dietary Supplement Ingredient Database. The goal is to provide, through these 2 harmonized databases and the continuing TDS focus on iodine, improved tools for estimating iodine intake in population studies. PMID:27534627

Egg-laying sequence influences egg mercury concentrations and egg size in three bird species: Implications for contaminant monitoring programs.

PubMed

Ackerman, Joshua T; Eagles-Smith, Collin A; Herzog, Mark P; Yee, Julie L; Hartman, C Alex

2016-06-01

Bird eggs are commonly used in contaminant monitoring programs and toxicological risk assessments, but intraclutch variation and sampling methodology could influence interpretability. The authors examined the influence of egg-laying sequence on egg mercury concentrations and burdens in American avocets, black-necked stilts, and Forster's terns. The average decline in mercury concentrations between the first and last eggs laid was 33% for stilts, 22% for terns, and 11% for avocets, and most of this decline occurred between the first and second eggs laid (24% for stilts, 18% for terns, and 9% for avocets). Trends in egg size with egg-laying order were inconsistent among species, and overall differences in egg volume, mass, length, and width were <3%. The authors summarized the literature, and among 17 species studied, mercury concentrations generally declined by 16% between the first and second eggs laid. Despite the strong effect of egg-laying sequence, most of the variance in egg mercury concentrations still occurred among clutches (75-91%) rather than within clutches (9%-25%). Using simulations, the authors determined that accurate estimation of a population's mean egg mercury concentration using only a single random egg from a subset of nests would require sampling >60 nests to represent a large population (10% accuracy) or ≥14 nests to represent a small colony that contained <100 nests (20% accuracy). Environ Toxicol Chem 2016;35:1458-1469. Published 2015 Wiley Periodicals Inc. on behalf of SETAC. This article is a US Government work and, as such, is in the public domain in the United States of America. Published 2015 Wiley Periodicals Inc. on behalf of SETAC. This article is a US Government work and, as such, is in the public domain in the United States of America.

Countrywide Reassessment of Schistosoma mansoni Infection in Burundi Using a Urine-Circulating Cathodic Antigen Rapid Test: Informing the National Control Program

PubMed Central

Ortu, Giuseppina; Ndayishimiye, Onésime; Clements, Michelle; Kayugi, Donatien; Campbell, Carl H.; Lamine, Mariama Sani; Zivieri, Antonio; Magalhaes, Ricardo Soares; Binder, Sue; King, Charles H.; Fenwick, Alan; Colley, Daniel G.; Jourdan, Peter Mark

2017-01-01

Following implementation of the national control program, a reassessment of Schistosoma mansoni prevalence was conducted in Burundi to determine the feasibility of moving toward elimination. A countrywide cluster-randomized cross-sectional study was performed in May 2014. At least 25 schools were sampled from each of five eco-epidemiological risk zones for schistosomiasis. Fifty randomly selected children 13–14 years of age per school were included for a single urine-circulating cathodic antigen (CCA) rapid test and, in a subset of schools, for duplicate Kato-Katz slide preparation from a single stool sample. A total of 17,331 children from 347 schools were tested using CCA. The overall prevalence of S. mansoni infection, when CCA trace results were considered negative, was 13.5% (zone range [zr] = 4.6–17.8%), and when CCA trace results were considered positive, it was 42.8% (zr = 34.3–49.9%). In 170 schools, prevalence of this infection determined using Kato-Katz method was 1.5% (zr ==0–2.7%). The overall mean intensity of S. mansoni infection determined using Kato-Katz was 0.85 eggs per gram (standard deviation = 10.86). A majority of schools (84%) were classified as non-endemic (prevalence = 0) using Kato-Katz; however, a similar proportion of schools were classified as endemic when CCA trace results were considered negative (85%) and nearly all (98%) were endemic when CCA trace results were considered positive. The findings of this nationwide reassessment using a CCA rapid test indicate that Schistosoma infection is still widespread in Burundi, although its average intensity is probably low. Further evidence is now needed to determine the association between CCA rapid test positivity and low-intensity disease transmission. PMID:28115675

Program for Research on Dietary Supplements in Military Operations and Healthcare Metabolically Optimized Brain - JWF

DTIC Science & Technology

2014-05-01

Alcohol; Vitamins / Minerals / Antioxidants / Dietary supplements (not specified); Herbal Medicine (Subsets: Ginseng and Gingko Biloba); Diet...looking specifically at the role of glucose (Hoyland 2008). c. Other Intervention Groupings considered: i. Herbal Medicine : 58 abstracts identified...involved herbal medicine (excluding gingko biloba and ginseng) as an intervention on the healthy adult population. 31 separate herb or herbal

Efficient Transmission of DoD PKI Certificates in Tactical Networks

DTIC Science & Technology

2010-01-01

011 the COlll- mand line. To extract individual fields from cert ifica tes, we used the X.509 subset of the C API included with OpenSSL (vl.O.0-bcta2...www.disa.mil/nces. [17J NSA Suite Il Cryptogt"aphy. http://vvv . nsa.gov/ial programs/suiteb_cryptography/index.shtml. [18J OpenSSL : The Open Source toolk

Optimal Subset Selection of Time-Series MODIS Images and Sample Data Transfer with Random Forests for Supervised Classification Modelling

PubMed Central

Zhou, Fuqun; Zhang, Aining

2016-01-01

Nowadays, various time-series Earth Observation data with multiple bands are freely available, such as Moderate Resolution Imaging Spectroradiometer (MODIS) datasets including 8-day composites from NASA, and 10-day composites from the Canada Centre for Remote Sensing (CCRS). It is challenging to efficiently use these time-series MODIS datasets for long-term environmental monitoring due to their vast volume and information redundancy. This challenge will be greater when Sentinel 2–3 data become available. Another challenge that researchers face is the lack of in-situ data for supervised modelling, especially for time-series data analysis. In this study, we attempt to tackle the two important issues with a case study of land cover mapping using CCRS 10-day MODIS composites with the help of Random Forests’ features: variable importance, outlier identification. The variable importance feature is used to analyze and select optimal subsets of time-series MODIS imagery for efficient land cover mapping, and the outlier identification feature is utilized for transferring sample data available from one year to an adjacent year for supervised classification modelling. The results of the case study of agricultural land cover classification at a regional scale show that using only about a half of the variables we can achieve land cover classification accuracy close to that generated using the full dataset. The proposed simple but effective solution of sample transferring could make supervised modelling possible for applications lacking sample data. PMID:27792152

Estrogen and androgen receptor activities of hydraulic fracturing chemicals and surface and ground water in a drilling-dense region

USGS Publications Warehouse

Kassotis, Christopher D.; Tillitt, Donald E.; Davis, J. Wade; Hormann, Anette M.; Nagel, Susan C.

2014-01-01

The rapid rise in natural gas extraction using hydraulic fracturing increases the potential for contamination of surface and ground water from chemicals used throughout the process. Hundreds of products containing more than 750 chemicals and components are potentially used throughout the extraction process, including more than 100 known or suspected endocrine-disrupting chemicals. We hypothesized thataselected subset of chemicalsusedin natural gas drilling operationsandalso surface and ground water samples collected in a drilling-dense region of Garfield County, Colorado, would exhibit estrogen and androgen receptor activities. Water samples were collected, solid-phase extracted, and measured for estrogen and androgen receptor activities using reporter gene assays in human cell lines. Of the 39 unique water samples, 89%, 41%, 12%, and 46% exhibited estrogenic, antiestrogenic, androgenic, and antiandrogenic activities, respectively. Testing of a subset of natural gas drilling chemicals revealed novel antiestrogenic, novel antiandrogenic, and limited estrogenic activities. The Colorado River, the drainage basin for this region, exhibited moderate levels of estrogenic, antiestrogenic, and antiandrogenic activities, suggesting that higher localized activity at sites with known natural gas–related spills surrounding the river might be contributing to the multiple receptor activities observed in this water source. The majority of water samples collected from sites in a drilling-dense region of Colorado exhibited more estrogenic, antiestrogenic, or antiandrogenic activities than reference sites with limited nearby drilling operations. Our data suggest that natural gas drilling operationsmayresult in elevated endocrine-disrupting chemical activity in surface and ground water.

Optimal Subset Selection of Time-Series MODIS Images and Sample Data Transfer with Random Forests for Supervised Classification Modelling.

PubMed

Zhou, Fuqun; Zhang, Aining

2016-10-25

Nowadays, various time-series Earth Observation data with multiple bands are freely available, such as Moderate Resolution Imaging Spectroradiometer (MODIS) datasets including 8-day composites from NASA, and 10-day composites from the Canada Centre for Remote Sensing (CCRS). It is challenging to efficiently use these time-series MODIS datasets for long-term environmental monitoring due to their vast volume and information redundancy. This challenge will be greater when Sentinel 2-3 data become available. Another challenge that researchers face is the lack of in-situ data for supervised modelling, especially for time-series data analysis. In this study, we attempt to tackle the two important issues with a case study of land cover mapping using CCRS 10-day MODIS composites with the help of Random Forests' features: variable importance, outlier identification. The variable importance feature is used to analyze and select optimal subsets of time-series MODIS imagery for efficient land cover mapping, and the outlier identification feature is utilized for transferring sample data available from one year to an adjacent year for supervised classification modelling. The results of the case study of agricultural land cover classification at a regional scale show that using only about a half of the variables we can achieve land cover classification accuracy close to that generated using the full dataset. The proposed simple but effective solution of sample transferring could make supervised modelling possible for applications lacking sample data.

CD4 T cell subsets in the Mucosa are CD28+Ki-67−HLA-DR−CD69+ but show differential infection based on α4β7 receptor expression during acute SIV infection

PubMed Central

Kader, Muhamuda; Bixler, Sandra; Roederer, Mario; Veazey, Ronald; Mattapallil, Joseph J.

2009-01-01

Background CD4 T cell depletion in the mucosa has been well documented during acute HIV and SIV infections. The demonstration the HIV/SIV can use the α4β7 receptor for viral entry suggests that these viruses selectively target CD4 T cells in the mucosa that express high levels of α4β7 receptor. Methods Mucosal samples obtained from SIV infected rhesus macaques during the early phase of infection were used for immunophenotypic analysis. CD4 T cell subsets were sorted based on the expression of β7 and CD95 to quantify the level of SIV infection in different subsets of CD4 T cells. Changes in IL-17, IL-21, IL-23 and TGFβ mRNA expression was determined using Taqman PCR. Results CD4 T cells in the mucosa were found to harbor two major population of cells; ~25% of CD4 T cells expressed the α4+β7hi phenotype, whereas the rest of the 75% expressed an α4+β7int phenotype. Both the subsets were predominantly CD28+Ki-67− HLA-DR− but CD69+, and expressed detectable levels of CCR5 on their surface. Interestingly, however, α4+β7hiCD4 T cells were found to harbor more SIV than the α4+β7int subsets at day 10 pi. Early infection was associated with a dramatic increase in the expression of IL-17, and IL-17 promoting cytokines IL-21, IL-23, and TGFβ that stayed high even after the loss of mucosal CD4 T cells. Conclusions Our results suggest that the differential expression of the α4β7 receptor contributes to the differences in the extent of infection in CD4 T cell subsets in the mucosa. Early infection associated dysregulation of the IL-17 network in mucosal tissues involves other non-Th-17 cells that likely contributes to the pro-inflammatory environment in the mucosa during acute stages of SIV infection. PMID:19863675

MSC products for the simulation of tire behavior

NASA Technical Reports Server (NTRS)

Muskivitch, John C.

1995-01-01

The modeling of tires and the simulation of tire behavior are complex problems. The MacNeal-Schwendler Corporation (MSC) has a number of finite element analysis products that can be used to address the complexities of tire modeling and simulation. While there are many similarities between the products, each product has a number of capabilities that uniquely enable it to be used for a specific aspect of tire behavior. This paper discusses the following programs: (1) MSC/NASTRAN - general purpose finite element program for linear and nonlinear static and dynamic analysis; (2) MSC/ADAQUS - nonlinear statics and dynamics finite element program; (3) MSC/PATRAN AFEA (Advanced Finite Element Analysis) - general purpose finite element program with a subset of linear and nonlinear static and dynamic analysis capabilities with an integrated version of MSC/PATRAN for pre- and post-processing; and (4) MSC/DYTRAN - nonlinear explicit transient dynamics finite element program.

Using Data to Effectively Manage a National Screening Program

PubMed Central

Yancy, Brandie; Royalty, Janet E.; Marroulis, Steve; Mattingly, Cindy; Benard, Vicki B.; DeGroff, Amy

2015-01-01

The National Breast and Cervical Cancer Early Detection Program (NBCCEDP) of the Centers for Disease Control and Prevention (CDC) is implemented through cooperative agreements with state health departments, US territories, and tribal health organizations (grantees). Grantees typically contract with clinicians and other providers to deliver breast and cervical cancer screening and diagnostic services. As required by the CDC, grantees report biannually a subset of patient and clinical level program data known as the Minimum Data Elements. Rigorous processes are in place to ensure the completeness and quality of program data collection. In this article, the authors describe the NBCCEDP data-collection processes and data management system and discusses how data are used for 1) program monitoring and improvement, 2) evaluation and research, and 3) policy development and analysis. They also provide 2 examples of how grantees use data to improve their performance. PMID:25099900

Assessment of Automated Analyses of Cell Migration on Flat and Nanostructured Surfaces

PubMed Central

Grădinaru, Cristian; Łopacińska, Joanna M.; Huth, Johannes; Kestler, Hans A.; Flyvbjerg, Henrik; Mølhave, Kristian

2012-01-01

Motility studies of cells often rely on computer software that analyzes time-lapse recorded movies and establishes cell trajectories fully automatically. This raises the question of reproducibility of results, since different programs could yield significantly different results of such automated analysis. The fact that the segmentation routines of such programs are often challenged by nanostructured surfaces makes the question more pertinent. Here we illustrate how it is possible to track cells on bright field microscopy images with image analysis routines implemented in an open-source cell tracking program, PACT (Program for Automated Cell Tracking). We compare the automated motility analysis of three cell tracking programs, PACT, Autozell, and TLA, using the same movies as input for all three programs. We find that different programs track overlapping, but different subsets of cells due to different segmentation methods. Unfortunately, population averages based on such different cell populations, differ significantly in some cases. Thus, results obtained with one software package are not necessarily reproducible by other software. PMID:24688640

Multiple Choice Knapsack Problem: example of planning choice in transportation.

PubMed

Zhong, Tao; Young, Rhonda

2010-05-01

Transportation programming, a process of selecting projects for funding given budget and other constraints, is becoming more complex as a result of new federal laws, local planning regulations, and increased public involvement. This article describes the use of an integer programming tool, Multiple Choice Knapsack Problem (MCKP), to provide optimal solutions to transportation programming problems in cases where alternative versions of projects are under consideration. In this paper, optimization methods for use in the transportation programming process are compared and then the process of building and solving the optimization problems is discussed. The concepts about the use of MCKP are presented and a real-world transportation programming example at various budget levels is provided. This article illustrates how the use of MCKP addresses the modern complexities and provides timely solutions in transportation programming practice. While the article uses transportation programming as a case study, MCKP can be useful in other fields where a similar decision among a subset of the alternatives is required. Copyright 2009 Elsevier Ltd. All rights reserved.

Inference methods for spatial variation in species richness and community composition when not all species are detected

USGS Publications Warehouse

Nichols, J.D.; Boulinier, T.; Hines, J.E.; Pollock, K.H.; Sauer, J.R.

1998-01-01

Inferences about spatial variation in species richness and community composition are important both to ecological hypotheses about the structure and function of communities and to community-level conservation and management. Few sampling programs for animal communities provide censuses, and usually some species present. We present estimators useful for drawing inferences about comparative species richness and composition between different sampling locations when not all species are detected in sampling efforts. Based on capture-recapture models using the robust design, our methods estimate relative species richness, proportion of species in one location that are also found in another, and number of species found in one location but not in another. The methods use data on the presence or absence of each species at different sampling occasions (or locations) to estimate the number of species not detected at any occasions (or locations). This approach permits estimation of the number of species in the sampled community and in subsets of the community useful for estimating the fraction of species shared by two communities. We provide an illustration of our estimation methods by comparing bird species richness and composition in two locations sampled by routes of the North American Breeding Bird Survey. In this example analysis, the two locations (an associated bird communities) represented different levels of urbanization. Estimates of relative richness, proportion of shared species, and number of species present on one route but not the other indicated that the route with the smaller fraction of urban area had greater richness and a larer number of species that were not found on the more urban route than vice versa. We developed a software package, COMDYN, for computing estimates based on the methods. Because these estimation methods explicitly deal with sampling in which not all species are detected, we recommend their use for addressing questions about species richness and community composition.

Achievement, Assessment, and Learning: A Study of Emergent Bilingual Students in Mainstream Content Classrooms

ERIC Educational Resources Information Center

Logan-Terry, Aubrey Elizabeth

2012-01-01

This dissertation investigates and problematizes emergent bilingual students' achievement gaps in an existing corpus of middle-school science assessment data. I first characterize achievement gaps across national data, state data, and the corpus of approximately 27,000 students as an analytic backdrop. I then sample a subset of the 6th grade…

Word Decoding Development in Incremental Phonics Instruction in a Transparent Orthography

ERIC Educational Resources Information Center

Schaars, Moniek M.; Segers, Eliane; Verhoeven, Ludo

2017-01-01

The present longitudinal study aimed to investigate the development of word decoding skills during incremental phonics instruction in Dutch as a transparent orthography. A representative sample of 973 Dutch children in the first grade (M[subscript age] = 6;1, SD = 0;5) was exposed to incremental subsets of Dutch grapheme-phoneme correspondences…

Comparison of the Incremental Validity of the Old and New MCAT.

ERIC Educational Resources Information Center

Wolf, Fredric M.; And Others

The predictive and incremental validity of both the Old and New Medical College Admission Test (MCAT) was examined and compared with a sample of over 300 medical students. Results of zero order and incremental validity coefficients, as well as prediction models resulting from all possible subsets regression analyses using Mallow's Cp criterion,…

Emergence of Autism Spectrum Disorder in Children from Simplex Families: Relations to Parental Perceptions of Etiology

ERIC Educational Resources Information Center

Goin-Kochel, Robin P.; Mire, Sarah S.; Dempsey, Allison G.

2015-01-01

Current research describes a four-category scheme of Autism Spectrum Disorder (ASD) onset: early, regressive, plateau, delay + regression. To replicate prevalence of different onset types, ASD onset (per the "Autism Diagnostic Interview-Revised") was examined in a large North American sample; for a subset, parents' causal beliefs were…

The Vineland-II in Preschool Children with Autism Spectrum Disorders: An Item Content Category Analysis

ERIC Educational Resources Information Center

Balboni, Giulia; Tasso, Alessandra; Muratori, Filippo; Cubelli, Roberto

2016-01-01

We investigated which item subsets of the Vineland-II can discriminate low-functioning preschoolers with ASD from matched peers with other neurodevelopmental disorders, using a regression analysis derived from a normative sample to account for cognitive and linguistic competencies. At variance with the typical profile, a pattern with Communication…

Serologic survey for viral and bacterial infections in western populations of Canada Lynx (Lynx canadensis)

Treesearch

Roman Biek; Randall L. Zarnke; Colin Gillin; Margaret Wild; John R. Squires; Mary Poss

2002-01-01

A serologic survey for exposure to pathogens in Canada lynx (Lynx canadensis) in western North America was conducted. Samples from 215 lynx from six study areas were tested for antibodies to feline parvovirus (FPV), feline coronavirus, canine distemper virus, feline calicivirus, feline herpesvirus, Yersinia pestis, and Francisella tularensis. A subset of...

Investigating Optimal Learning Moments in U.S. and Finnish Science Classes

ERIC Educational Resources Information Center

Schneider, Barbara; Krajcik, Joseph; Lavonen, Jari; Salmela-Aro, Katariina; Broda, Michael; Spicer, Justina; Bruner, Justin; Moeller, Julia; Linnansaari, Janna; Juuti, Kalle; Viljaranta, Jaana

2016-01-01

This study explores how often students are engaged in their science classes and their affective states during these times, using an innovative methodology that records these experiences "in situ". Sampling a subset of high schools in the U.S. and Finland, we collected over 7,000 momentary responses from 344 students over the course of a…

School Violence: Associations with Control, Security/Enforcement, Educational/Therapeutic Approaches, and Demographic Factors

ERIC Educational Resources Information Center

Nickerson, Amanda B.; Martens, Matthew P.

2008-01-01

This study examined the extent to which three approaches to violence prevention and response were associated with the incidence of school crime and disruption after accounting for the influence of demographic variables. Secondary data analyses were conducted with four subsets of the sample of principals who completed the National Center for…

Regulatory CD4 T cells inhibit HIV-1 expression of other CD4 T cell subsets via interactions with cell surface regulatory proteins.

PubMed

Zhang, Mingce; Robinson, Tanya O; Duverger, Alexandra; Kutsch, Olaf; Heath, Sonya L; Cron, Randy Q

2018-03-01

During chronic HIV-1 infection, regulatory CD4 T cells (Tregs) frequently represent the largest subpopulation of CD4 T cell subsets, implying relative resistant to HIV-1. When HIV-1 infection of CD4 T cells was explored in vitro and ex vivo from patient samples, Tregs possessed lower levels of HIV-1 DNA and RNA in comparison with conventional effector and memory CD4 T cells. Moreover, Tregs suppressed HIV-1 expression in other CD4 T cells in an in vitro co-culture system. This suppression was mediated in part via multiple inhibitory surface proteins expressed on Tregs. Antibody blockade of CTLA-4, PD-1, and GARP on Tregs resulted in increased HIV-1 DNA integration and mRNA expression in neighboring CD4 T cells. Moreover, antibody blockade of Tregs inhibitory proteins resulted in increased HIV-1 LTR transcription in co-cultured CD4 T cells. Thus, Tregs inhibit HIV-1 infection of other CD4 T cell subsets via interactions with inhibitory cell surface proteins. Copyright © 2018 Elsevier Inc. All rights reserved.

Predicting ovarian malignancy: application of artificial neural networks to transvaginal and color Doppler flow US.

PubMed

Biagiotti, R; Desii, C; Vanzi, E; Gacci, G

1999-02-01

To compare the performance of artificial neural networks (ANNs) with that of multiple logistic regression (MLR) models for predicting ovarian malignancy in patients with adnexal masses by using transvaginal B-mode and color Doppler flow ultrasonography (US). A total of 226 adnexal masses were examined before surgery: Fifty-one were malignant and 175 were benign. The data were divided into training and testing subsets by using a "leave n out method." The training subsets were used to compute the optimum MLR equations and to train the ANNs. The cross-validation subsets were used to estimate the performance of each of the two models in predicting ovarian malignancy. At testing, three-layer back-propagation networks, based on the same input variables selected by using MLR (i.e., women's ages, papillary projections, random echogenicity, peak systolic velocity, and resistance index), had a significantly higher sensitivity than did MLR (96% vs 84%; McNemar test, p = .04). The Brier scores for ANNs were significantly lower than those calculated for MLR (Student t test for paired samples, P = .004). ANNs might have potential for categorizing adnexal masses as either malignant or benign on the basis of multiple variables related to demographic and US features.

Automated large-scale file preparation, docking, and scoring: evaluation of ITScore and STScore using the 2012 Community Structure-Activity Resource benchmark.

PubMed

Grinter, Sam Z; Yan, Chengfei; Huang, Sheng-You; Jiang, Lin; Zou, Xiaoqin

2013-08-26

In this study, we use the recently released 2012 Community Structure-Activity Resource (CSAR) data set to evaluate two knowledge-based scoring functions, ITScore and STScore, and a simple force-field-based potential (VDWScore). The CSAR data set contains 757 compounds, most with known affinities, and 57 crystal structures. With the help of the script files for docking preparation, we use the full CSAR data set to evaluate the performances of the scoring functions on binding affinity prediction and active/inactive compound discrimination. The CSAR subset that includes crystal structures is used as well, to evaluate the performances of the scoring functions on binding mode and affinity predictions. Within this structure subset, we investigate the importance of accurate ligand and protein conformational sampling and find that the binding affinity predictions are less sensitive to non-native ligand and protein conformations than the binding mode predictions. We also find the full CSAR data set to be more challenging in making binding mode predictions than the subset with structures. The script files used for preparing the CSAR data set for docking, including scripts for canonicalization of the ligand atoms, are offered freely to the academic community.

An enhancement of binary particle swarm optimization for gene selection in classifying cancer classes

PubMed Central

2013-01-01

Background Gene expression data could likely be a momentous help in the progress of proficient cancer diagnoses and classification platforms. Lately, many researchers analyze gene expression data using diverse computational intelligence methods, for selecting a small subset of informative genes from the data for cancer classification. Many computational methods face difficulties in selecting small subsets due to the small number of samples compared to the huge number of genes (high-dimension), irrelevant genes, and noisy genes. Methods We propose an enhanced binary particle swarm optimization to perform the selection of small subsets of informative genes which is significant for cancer classification. Particle speed, rule, and modified sigmoid function are introduced in this proposed method to increase the probability of the bits in a particle’s position to be zero. The method was empirically applied to a suite of ten well-known benchmark gene expression data sets. Results The performance of the proposed method proved to be superior to other previous related works, including the conventional version of binary particle swarm optimization (BPSO) in terms of classification accuracy and the number of selected genes. The proposed method also requires lower computational time compared to BPSO. PMID:23617960

Validation of the Abdominal Pain Index using a revised scoring method.

PubMed

Laird, Kelsey T; Sherman, Amanda L; Smith, Craig A; Walker, Lynn S

2015-06-01

Evaluate the psychometric properties of child- and parent-report versions of the four-item Abdominal Pain Index (API) in children with functional abdominal pain (FAP) and healthy controls, using a revised scoring method that facilitates comparisons of scores across samples and time. Pediatric patients aged 8-18 years with FAP and controls completed the API at baseline (N = 1,967); a subset of their parents (N = 290) completed the API regarding the child's pain. Subsets of patients completed follow-up assessments at 2 weeks (N = 231), 3 months (N = 330), and 6 months (N = 107). Subsets of both patients (N = 389) and healthy controls (N = 172) completed a long-term follow-up assessment (mean age at follow-up = 20.21 years, SD = 3.75). The API demonstrated good concurrent, discriminant, and construct validity, as well as good internal consistency. We conclude that the API, using the revised scoring method, is a useful, reliable, and valid measure of abdominal pain severity. © The Author 2015. Published by Oxford University Press on behalf of the Society of Pediatric Psychology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Theory and models for planning and evaluating institutional influenza prevention and control programs.

PubMed

Russell, Margaret L; Thurston, Wilfreda E; Henderson, Elizabeth A

2003-10-01

Low rates of staff influenza vaccine coverage occur in many health care facilities. Many programs do not offer vaccination to physicians or to volunteers, and some programs do not measure coverage or do so only for a subset of staff. The use of theory in planning and evaluation may prevent these problems and lead to more effective programs. We discuss the use of theory in the planning and evaluation of health programs and demonstrate how it can be used for the evaluation and planning of a hospital or nursing home influenza control program. The application of theory required explicit statement of the goals of the program and examination of the assumptions underlying potential program activities. This indicated that staff should probably be considered as employees, volunteers, physicians, and contractors of the facility. It also directed attention to evidence-based strategies for increasing vaccination rates. The application of a program planning model to a problem of institutional influenza prevention may prevent planners from excluding important target populations and failing to monitor the important indicators of program success.

Self-efficacy in weight management.

PubMed

Clark, M M; Abrams, D B; Niaura, R S; Eaton, C A; Rossi, J S

1991-10-01

Self-efficacy is an important mediating mechanism in advancing understanding of the treatment of obesity. This study developed and validated the Weight Efficacy Life-Style Questionnaire (WEL), improving on previous studies by the use of clinical populations, cross-validation of the initial factor analysis, exploration of the best fitting theoretical model of self-efficacy, and examination of change in treatment. The resulting 20-item WEL consists of five situational factors: Negative Emotions, Availability, Social Pressure, Physical Discomfort, and Positive Activities. A hierarchical model was found to provide the best fit to the data. Results from two separate clinical treatment studies (total N = 382) show that the WEL is sensitive to changes in global scores as well as to a subset of the five situational factor scores. Treatment programs may be incomplete if they change only a subset of the situational dimensions of self-efficacy. Theoretical and clinical implications are discussed.

Reliability-based design optimization using a generalized subset simulation method and posterior approximation

NASA Astrophysics Data System (ADS)

Ma, Yuan-Zhuo; Li, Hong-Shuang; Yao, Wei-Xing

2018-05-01

The evaluation of the probabilistic constraints in reliability-based design optimization (RBDO) problems has always been significant and challenging work, which strongly affects the performance of RBDO methods. This article deals with RBDO problems using a recently developed generalized subset simulation (GSS) method and a posterior approximation approach. The posterior approximation approach is used to transform all the probabilistic constraints into ordinary constraints as in deterministic optimization. The assessment of multiple failure probabilities required by the posterior approximation approach is achieved by GSS in a single run at all supporting points, which are selected by a proper experimental design scheme combining Sobol' sequences and Bucher's design. Sequentially, the transformed deterministic design optimization problem can be solved by optimization algorithms, for example, the sequential quadratic programming method. Three optimization problems are used to demonstrate the efficiency and accuracy of the proposed method.

Core Hunter 3: flexible core subset selection.

PubMed

De Beukelaer, Herman; Davenport, Guy F; Fack, Veerle

2018-05-31

Core collections provide genebank curators and plant breeders a way to reduce size of their collections and populations, while minimizing impact on genetic diversity and allele frequency. Many methods have been proposed to generate core collections, often using distance metrics to quantify the similarity of two accessions, based on genetic marker data or phenotypic traits. Core Hunter is a multi-purpose core subset selection tool that uses local search algorithms to generate subsets relying on one or more metrics, including several distance metrics and allelic richness. In version 3 of Core Hunter (CH3) we have incorporated two new, improved methods for summarizing distances to quantify diversity or representativeness of the core collection. A comparison of CH3 and Core Hunter 2 (CH2) showed that these new metrics can be effectively optimized with less complex algorithms, as compared to those used in CH2. CH3 is more effective at maximizing the improved diversity metric than CH2, still ensures a high average and minimum distance, and is faster for large datasets. Using CH3, a simple stochastic hill-climber is able to find highly diverse core collections, and the more advanced parallel tempering algorithm further increases the quality of the core and further reduces variability across independent samples. We also evaluate the ability of CH3 to simultaneously maximize diversity, and either representativeness or allelic richness, and compare the results with those of the GDOpt and SimEli methods. CH3 can sample equally representative cores as GDOpt, which was specifically designed for this purpose, and is able to construct cores that are simultaneously more diverse, and either are more representative or have higher allelic richness, than those obtained by SimEli. In version 3, Core Hunter has been updated to include two new core subset selection metrics that construct cores for representativeness or diversity, with improved performance. It combines and outperforms the strengths of other methods, as it (simultaneously) optimizes a variety of metrics. In addition, CH3 is an improvement over CH2, with the option to use genetic marker data or phenotypic traits, or both, and improved speed. Core Hunter 3 is freely available on http://www.corehunter.org .

Is it time for a new classification of mast cells? What do we know about mast cell heterogeneity?

PubMed

Frossi, Barbara; Mion, Francesca; Sibilano, Riccardo; Danelli, Luca; Pucillo, Carlo E M

2018-03-01

Mast cells (MCs) are derived from committed precursors that leave the hematopoietic tissue, migrate in the blood, and colonize peripheral tissues where they terminally differentiate under microenvironment stimuli. They are distributed in almost all vascularized tissues where they act both as immune effectors and housekeeping cells, contributing to tissue homeostasis. Historically, MCs were classified into 2 subtypes, according to tryptic enzymes expression. However, MCs display a striking heterogeneity that reflects a complex interplay between different microenvironmental signals delivered by various tissues, and a differentiation program that decides their identity. Moreover, tissue-specific MCs show a trained memory, which contributes to shape their function in a specific microenvironment. In this review, we summarize the current state of our understanding of MC heterogeneity that reflects their different tissue experiences. We describe the discovery of unique cell molecules that can be used to distinguish specific MC subsets in vivo, and discuss how the improved ability to recognize these subsets provided new insights into the biology of MCs. These recent advances will be helpful for the understanding of the specific role of individual MC subsets in the control of tissue homeostasis, and in the regulation of pathological conditions such as infection, autoimmunity, and cancer. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Effect of strength training on orthostatic hypotension in older adults.

PubMed

Brilla, L R; Stephens, A B; Knutzen, K M; Caine, D

1998-01-01

This preliminary study attempted to identify the frequency of orthostatic hypotension (OH) in community dwelling older adults who volunteered to participate in an 8-week, heavy-resistance, strength-training program. It also assessed the effect of the strength-training program on OH. From a larger study (n = 53) on high-resistance strength training in older adults (mean age 71.4 +/- 6.6 years), a subset of subjects (n = 24), mean age 71.0 +/- 5.8 years, was evaluated who met at least one criterion for OH. All subjects were tested for resting blood pressures (BP) and heart rates (HR) in the supine, sitting, and standing positions. Also noted was their response to orthostatism in rising from a cot after 10 minutes and rising from a chair after 5 minutes. The subset was not different from the overall group in gender ratio, age, or effect of medication on BP. The treatment was an 8-week strength-training program at 80% of their one repetition maximum. Significant changes (P < 0.05) were shown in supine diastolic BP (+3.2 mm Hg), sitting systolic BP (-3.9), and standing HR (+4.9 beats per minute). In response to the orthostatic challenge, significant (P < 0.05) improvements were shown in systolic BP (+9.7 mm Hg), diastolic BP (+4.7), and HR (+3.2 beats per minute) for the rise from chair, and in diastolic BP (+6.7 mm Hg) rise from the cot. These data show that OH is not uncommon (45%) in community dwelling older adults. A strength training program in older adults has little effect on resting BP, but elicits a positive adaptation to an orthostatic challenge.

Identifying marker genes in transcription profiling data using a mixture of feature relevance experts.

PubMed

Chow, M L; Moler, E J; Mian, I S

2001-03-08

Transcription profiling experiments permit the expression levels of many genes to be measured simultaneously. Given profiling data from two types of samples, genes that most distinguish the samples (marker genes) are good candidates for subsequent in-depth experimental studies and developing decision support systems for diagnosis, prognosis, and monitoring. This work proposes a mixture of feature relevance experts as a method for identifying marker genes and illustrates the idea using published data from samples labeled as acute lymphoblastic and myeloid leukemia (ALL, AML). A feature relevance expert implements an algorithm that calculates how well a gene distinguishes samples, reorders genes according to this relevance measure, and uses a supervised learning method [here, support vector machines (SVMs)] to determine the generalization performances of different nested gene subsets. The mixture of three feature relevance experts examined implement two existing and one novel feature relevance measures. For each expert, a gene subset consisting of the top 50 genes distinguished ALL from AML samples as completely as all 7,070 genes. The 125 genes at the union of the top 50s are plausible markers for a prototype decision support system. Chromosomal aberration and other data support the prediction that the three genes at the intersection of the top 50s, cystatin C, azurocidin, and adipsin, are good targets for investigating the basic biology of ALL/AML. The same data were employed to identify markers that distinguish samples based on their labels of T cell/B cell, peripheral blood/bone marrow, and male/female. Selenoprotein W may discriminate T cells from B cells. Results from analysis of transcription profiling data from tumor/nontumor colon adenocarcinoma samples support the general utility of the aforementioned approach. Theoretical issues such as choosing SVM kernels and their parameters, training and evaluating feature relevance experts, and the impact of potentially mislabeled samples on marker identification (feature selection) are discussed.

An Investigation of Unified Memory Access Performance in CUDA

PubMed Central

Landaverde, Raphael; Zhang, Tiansheng; Coskun, Ayse K.; Herbordt, Martin

2015-01-01

Managing memory between the CPU and GPU is a major challenge in GPU computing. A programming model, Unified Memory Access (UMA), has been recently introduced by Nvidia to simplify the complexities of memory management while claiming good overall performance. In this paper, we investigate this programming model and evaluate its performance and programming model simplifications based on our experimental results. We find that beyond on-demand data transfers to the CPU, the GPU is also able to request subsets of data it requires on demand. This feature allows UMA to outperform full data transfer methods for certain parallel applications and small data sizes. We also find, however, that for the majority of applications and memory access patterns, the performance overheads associated with UMA are significant, while the simplifications to the programming model restrict flexibility for adding future optimizations. PMID:26594668

Robust model selection and the statistical classification of languages

NASA Astrophysics Data System (ADS)

García, J. E.; González-López, V. A.; Viola, M. L. L.

2012-10-01

In this paper we address the problem of model selection for the set of finite memory stochastic processes with finite alphabet, when the data is contaminated. We consider m independent samples, with more than half of them being realizations of the same stochastic process with law Q, which is the one we want to retrieve. We devise a model selection procedure such that for a sample size large enough, the selected process is the one with law Q. Our model selection strategy is based on estimating relative entropies to select a subset of samples that are realizations of the same law. Although the procedure is valid for any family of finite order Markov models, we will focus on the family of variable length Markov chain models, which include the fixed order Markov chain model family. We define the asymptotic breakdown point (ABDP) for a model selection procedure, and we show the ABDP for our procedure. This means that if the proportion of contaminated samples is smaller than the ABDP, then, as the sample size grows our procedure selects a model for the process with law Q. We also use our procedure in a setting where we have one sample conformed by the concatenation of sub-samples of two or more stochastic processes, with most of the subsamples having law Q. We conducted a simulation study. In the application section we address the question of the statistical classification of languages according to their rhythmic features using speech samples. This is an important open problem in phonology. A persistent difficulty on this problem is that the speech samples correspond to several sentences produced by diverse speakers, corresponding to a mixture of distributions. The usual procedure to deal with this problem has been to choose a subset of the original sample which seems to best represent each language. The selection is made by listening to the samples. In our application we use the full dataset without any preselection of samples. We apply our robust methodology estimating a model which represent the main law for each language. Our findings agree with the linguistic conjecture, related to the rhythm of the languages included on our dataset.

Computer-assisted semen analysis and its utility for profiling boar semen samples.

PubMed

Didion, B A

2008-11-01

Achieving and maintaining a successful swine AI program depends on a number of factors, including accurate semen evaluation, typically sperm motility, morphology and concentration. Computer-Assisted Semen Analysis or CASA (i.e., image analysis with a phase-contrast microscope and computer measurements of motion parameters) objectively evaluates sperm motion characteristics, morphology and concentration. A total of 3077 semen collections were evaluated with CASA (on the day of collection), and a semen dose subset was used for single-sire AI of 6266 females over 6 months. Fertility data from these inseminations were fitted with models including farm/stud, line, boar, parity, mating week, semen age at mating and boar age at mating. The residuals from these models showed no correlation for any CASA semen unique motion parameter, which could be due to the level of sperm concentration, the number of inseminations per estrus, and the low number of females mated per boar. Future studies to expand CASA/fertility analysis need to address these constraints and may include analysis of extended boar semen after storage for 1 week.

A Mixed-Method Study on Correlates of HIV-Related Stigma Among Gay and Bisexual Men in the Southern United States.

PubMed

Berg, Rigmor C; Carter, Dakota; Ross, Michael W

Societal prejudice against people living with HIV infection is a formidable public health challenge that can negatively impact health and well-being. We recruited a multiethnic sample of 129 gay and bisexual men living with HIV who completed a brief survey; a subset of participants completed semi-structured qualitative interviews to contextualize the data. In bivariate analyses, stigma was positively and significantly correlated with depression (r = .402, p < .001) and negatively correlated with social support (r = -.482, p < .001). Qualitative interview results captured the mental suffering caused by stigma and coping strategies the men had developed. Although some of the coping strategies reduced the likelihood of experiencing acts of stigmatization, they also exacerbated the psychological stress of living with a stigmatized disease and limited the potential for social support. Our results highlight the need to scale up stigma-reduction programs, particularly those that can bolster social support networks. Copyright © 2017 Association of Nurses in AIDS Care. Published by Elsevier Inc. All rights reserved.

Risk assessment of nonylphenol and its ethoxylates in U.S. river water and sediment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weeks, J.A.; Adams, W.J.; Guiney, P.D.

1994-12-31

A comprehensive program addressing the risks of nonylphenol (NP) and its ethoxylates (NPE) in aquatic environments of the United States has been undertaken by the Alkyl Phenol Ethoxylates Panel of the Chemical Manufacturers Association cooperating with EPA. Several hundred million pounds of NPE surfactants are used in the US each year. Nonylphenol can be an intermediate product of degradation of nonylphenol ethoxylates. A survey of those river reaches most likely to contain NPE and NP residues was conducted based on a random sample of a subset of the EPA River Reach File defined by certain selection criteria. Applying enhanced analyticalmore » techniques, little or no NP and NPE were found in river water at most locations, while low levels were usually detected in sediment. Acute and chronic toxicity tests using a variety of organisms have also been completed. New results are presented for shrimp, fish, tadpoles, midges, and algae. The risk of NP to the aquatic environment is examined by comparison of observed levels with toxicity benchmarks, and by application of equilibrium partitioning theory to calculate sediment interstitial chemical concentrations.« less

Novel Non-Intrusive Trans-Dermal Remote Wireless Micro-Fluidic Monitoring System Applied to Continuous Glucose and Lactate Assays for Casualty Care and Combat Readiness Assessment

DTIC Science & Technology

2004-09-01

identification of the lettered features. 2.2 BFIT Sampling Chip The BFIT sampling chip is a flexible patch-like chip with a multilayer polymeric metal...PPy) and glucose oxidase (GOD). The BFIT fabrication process uses SU8 as a principal structural material consisting of five steps (Figure 2). This...process is a subset of an earlier technology developed for the polymer material PDMS.11,12,13,14,15 The first step was the deposition of a Teflon

Evaluation of the Military Functional Assessment Program: Inter rater Reliability of Task Scores

DTIC Science & Technology

2017-09-19

return-to-duty. Performance on the tasks is rated by a non-commissioned officer (NCO), occupational therapist, physical therapist, and mental health ...and additional ratings are provided on a subset of the tasks by an occupational therapist (OT), physical therapist (PT), and mental health (MH...3National Intrepid Center of Excellence United States Army Aeromedical Research Laboratory Aircrew Health and Performance Division September 2017

Core Competencies for 4-H Volunteer Leaders Differentiated by Occupation, Level of Education, and College Major: Implications for Leadership Education

ERIC Educational Resources Information Center

Nestor, Patrick; McKee, Renee K.; Culp, Ken, III

2006-01-01

The purpose of this study was to demographically describe 4-H volunteer leaders' competencies for effective delivery of 4-H youth development programs. As a subset of the data, occupation, level of education, college major of the volunteer leaders, staff and faculty were gathered as the primary focus of the article. The study was descriptive and…

A Framework for Empirical Discovery.

DTIC Science & Technology

1986-09-24

history of science reveal distinct classes of defined terms. Some systems have focused on one subset of these classes, while other programs have...the operators in detail, presenting examples of each from the history of science . 2.1 Defining Numeric Terms The most obvious operator for defining...laws; they can also simplify the process of discovering such laws. Let us consider some examples from the history of science in which the definition of

A global look into human T cell subsets before and after cryopreservation using multiparametric flow cytometry and two-dimensional visualization analysis.

PubMed

Lemieux, Jennifer; Jobin, Christine; Simard, Carl; Néron, Sonia

2016-07-01

The cryopreservation of human lymphocytes is an essential step for the achievement of several cellular therapies. Besides, T cells are considered as promising actors in cancer therapy for their cytotoxic and regulatory properties. Consequently, the development of tools to monitor the impact of freezing and thawing processes on their fine distribution may be an asset to achieve quality control in cellular therapy. In this study, the phenotypes of freshly isolated human mononuclear cells were compared to those observed following one cycle of cryopreservation and rest periods 0h, 1h and 24h after thawing but before staining. T cells were scrutinized for their distribution according to naive, memory effector, regulatory and helper subsets. Flow cytometry analyses were done using eight-color antibody panels as proposed by the Human Immunophenotyping Consortium. Data were further analyzed by using conventional directed gating and clustering software, namely SPADE and viSNE. Overall, SPADE and viSNE tools were very efficient to monitor the outcome of PBMC populations and T cell subsets. T cells were more sensitive to cryopreservation than other cells. Our results indicated that submitting the thawed cells to a 1h rest period improved the detection of some cell markers when compared to fresh samples. In contrast, cells submitted to a 24h rest period, or to none, were less representative of fresh sample distribution. The heterogeneity of PBMC, as well as the effects of freeze-thaw cycle on their distribution, can be easily monitored by using SPADE and viSNE. Copyright © 2016 Elsevier B.V. All rights reserved.

HIF-2α mediates a marked increase in migration and stemness characteristics in a subset of glioma cells under hypoxia by activating an Oct-4/Sox-2-Mena (INV) axis.

PubMed

Bhagat, Mohita; Palanichamy, Jayanth Kumar; Ramalingam, Pradeep; Mudassir, Madeeha; Irshad, Khushboo; Chosdol, Kunzang; Sarkar, Chitra; Seth, Pankaj; Goswami, Sumanta; Sinha, Subrata; Chattopadhyay, Parthaprasad

2016-05-01

Hypoxia is a salient feature of most solid tumors and plays a central role in tumor progression owing to its multiple contributions to therapeutic resistance, metastasis, angiogenesis and stemness properties. Reports exist in literature about hypoxia increasing stemness characteristics and invasiveness potential of malignant cells. In order to delineate molecular crosstalk among factors driving glioma progression, we used knockdown and overexpression strategies. We have demonstrated that U87MG and A172 glioma cells inherently have a subset of cells with high migratory potential due to migration-inducing Mena transcripts. These cells also have elevated stemness markers (Sox-2 and Oct-4). There was a significant increase of number in this subset of migratory cells on exposure to hypoxia with corresponding elevation (over 1000 fold) in migration-inducing Mena transcripts. We were able to demonstrate that a HIF-2α-Sox-2/Oct-4-Mena (INV) axis that is strongly activated in hypoxia and markedly increases the migratory potential of the cells. Such cells also formed tumor spheres with greater efficiency. We have correlated our in-vitro results with human glioblastoma samples and found that hypoxia, invasiveness and stemness markers correlated well in native tumor samples. This study identifies a novel signaling mechanism mediated by HIF-2α in regulating invasiveness and stemness characteristics, suggesting that under hypoxic conditions, some tumor cells acquire more migratory potential by increased Pan Mena and Mena INV expression as a consequence of this HIF-2α mediated increase in Oct-4 and Sox-2. These properties would help the cells to form a new nidus after local invasion or metastasis. Copyright © 2016 Elsevier Ltd. All rights reserved.

Oral Health and Blood Pressure: The IPC Cohort.

PubMed

Darnaud, Christelle; Thomas, Frédérique; Pannier, Bruno; Danchin, Nicolas; Bouchard, Philippe

2015-10-01

Chronic periodontal diseases involve bacteria-induced inflammation of the tissues supporting the teeth. An inflammatory origin for hypertension has been proposed, and periodontal diseases are associated with an increased risk of vascular disease. The present study was performed to assess whether oral health conditions were associated with the risk of hypertension in adult population. The sample comprised 102,330 subjects, who underwent medical and oral examinations between 2002 and 2011. A full-mouth clinical examination was performed using simplified plaque index, calculus index, and simplified modified gingival index to assess dental plaque, dental calculus and gingival inflammation. The number of teeth was recorded. Biological parameters, including blood pressure were assessed. A subset analysis according to age (<65 or ≥65 years) was conducted. The association between blood pressure and oral conditions was explored using a logistic regression approach. In the sample of subject ≥65 years, no significant association was found between oral variables and the risk of hypertension. In subset <65 years, oral variables and risk of hypertension were associated. Insufficient masticatory function and missing teeth (>10) showed odds ratio (OR) = 1.20 [95% CI = 1.08-1.32] and OR = 1.17 [95% CI = 1.04-1.31], respectively. Hypertension was also associated with high level of dental plaque [OR = 1.90, 95% CI = 1.55-2.33], dental calculus [OR = 1.18, 95% CI = 1.07-1.29] and gingival inflammation [OR = 1.56, 95% CI = 1.35-1.80] Moreover, in this subset <65 years, the risk of hypertension increases with the number of dental exposure. The present study indicates that insufficient masticatory function, poor oral hygiene, and oral inflammation are associated with hypertension in subject <65. © American Journal of Hypertension, Ltd 2015. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Flow cytometry analysis of T-cell subsets in cerebrospinal fluid of narcolepsy type 1 patients with long-lasting disease.

PubMed

Moresco, Monica; Lecciso, Mariangela; Ocadlikova, Darina; Filardi, Marco; Melzi, Silvia; Kornum, Birgitte Rahbek; Antelmi, Elena; Pizza, Fabio; Mignot, Emmanuel; Curti, Antonio; Plazzi, Giuseppe

2018-04-01

Type 1 narcolepsy (NT1) is a central hypersomnia linked to the destruction of hypocretin-producing neurons. A great body of genetic and epidemiological data points to likely autoimmune disease aetiology. Recent reports have characterized peripheral blood T-cell subsets in NT1, whereas data regarding the cerebrospinal fluid (CSF) immune cell composition are lacking. The current study aimed to characterize the T-cell and natural killer (NK) cell subsets in NT1 patients with long disease course. Immune cell subsets from CSF and peripheral blood mononuclear cell (PBMC) samples were analysed by flow cytometry in two age-balanced and sex-balanced groups of 14 NT1 patients versus 14 healthy controls. The frequency of CSF cell groups was compared with PBMCs. Non-parametric tests were used for statistical analyses. The NT1 patients did not show significant differences of CSF immune cell subsets compared to controls, despite a trend towards higher CD4 + terminally differentiated effector memory T cells. T cells preferentially displayed a memory phenotype in the CSF compared to PBMCs. Furthermore, a reduced frequency of CD4 + terminally differentiated effector memory T cells and an increased frequency of NK CD56 bright cells was observed in PBMCs from patients compared to controls. Finally, the ratio between CSF and peripheral CD4 + terminally differentiated effector memory T cells was two-fold increased in NT1 patients versus controls. Significant differences in PBMCs and in CSF/PBMC ratios of immune cell profile were found in NT1 patients compared to healthy controls. These differences might have arisen from the different HLA status, or be primary or secondary to hypocretin deficiency. Further functional studies in patients close to disease onset are required to understand NT1 pathophysiology. Copyright © 2017 Elsevier B.V. All rights reserved.

Molecular Analysis of Non-Small Cell Lung Cancer (NSCLC) Identifies Subsets with Different Sensitivity to Insulin like Growth Factor I Receptor (IGF-IR) Inhibition

PubMed Central

Gualberto, Antonio; Dolled-Filhart, Marisa; Gustavson, Mark; Christiansen, Jason; Wang, Yu-Fen; Hixon, Mary L.; Reynolds, Jennifer; McDonald, Sandra; Ang, Agnes; Rimm, David L.; Langer, Corey J.; Blakely, Johnetta; Garland, Linda; Paz-Ares, Luis G.; Karp, Daniel D.; Lee, Adrian V.

2010-01-01

Purpose Identify molecular determinants of sensitivity of NSCLC to anti-insulin like growth factor receptor (IGF-IR) therapy. Experimental Design 216 tumor samples were investigated. 165 consisted of retrospective analyses of banked tissue and an additional 51 were from patients enrolled in a phase 2 study of figitumumab (F), a monoclonal antibody against the IGF-IR, in stage IIIb/IV NSCLC. Biomarkers assessed included IGF-IR, EGFR, IGF-2, IGF-2R, IRS-1, IRS-2, vimentin and E-cadherin. Sub-cellular localization of IRS-1 and phosphorylation levels of MAPK and Akt1 were also analyzed. Results IGF-IR was differentially expressed across histological subtypes (P=0.04), with highest levels observed in squamous cell tumors. Elevated IGF-IR expression was also observed in a small number of squamous cell tumors responding to chemotherapy combined with F (p=0.008). Since no other biomarker/response interaction was observed using classical histological sub-typing, a molecular approach was undertaken to segment NSCLC into mechanism-based subpopulations. Principal component analysis and unsupervised Bayesian clustering identified 3 NSCLC subsets that resembled the steps of the epithelial-to-mesenchymal transition: E-cadherin high/IRS-1 low (Epithelial-like), E-cadherin intermediate/IRS-1 high (Transitional) and E-cadherin low/IRS-1 low (Mesenchymal-like). Several markers of the IGF-IR pathway were over-expressed in the Transitional subset. Furthermore, a higher response rate to the combination of chemotherapy and F was observed in Transitional tumors (71%) compared to those in the Mesenchymal-like subset (32%, p=0.03). Only one Epithelial-like tumor was identified in the phase 2 study, suggesting that advanced NSCLC has undergone significant de-differentiation at diagnosis. Conclusion NSCLC comprises molecular subsets with differential sensitivity to IGF-IR inhibition. PMID:20670944

Wavenumber selection method to determine the concentration of cocaine and adulterants in cocaine samples.

PubMed

Kahmann, A; Anzanello, M J; Fogliatto, F S; Marcelo, M C A; Ferrão, M F; Ortiz, R S; Mariotti, K C

2018-04-15

Street cocaine is typically altered with several compounds that increase its harmful health-related side effects, most notably depression, convulsions, and severe damages to the cardiovascular system, lungs, and brain. Thus, determining the concentration of cocaine and adulterants in seized drug samples is important from both health and forensic perspectives. Although FTIR has been widely used to identify the fingerprint and concentration of chemical compounds, spectroscopy datasets are usually comprised of thousands of highly correlated wavenumbers which, when used as predictors in regression models, tend to undermine the predictive performance of multivariate techniques. In this paper, we propose an FTIR wavenumber selection method aimed at identifying FTIR spectra intervals that best predict the concentration of cocaine and adulterants (e.g. caffeine, phenacetin, levamisole, and lidocaine) in cocaine samples. For that matter, the Mutual Information measure is integrated into a Quadratic Programming problem with the objective of minimizing the probability of retaining redundant wavenumbers, while maximizing the relationship between retained wavenumbers and compounds' concentrations. Optimization outputs guide the order of inclusion of wavenumbers in a predictive model, using a forward-based wavenumber selection method. After the inclusion of each wavenumber, parameters of three alternative regression models are estimated, and each model's prediction error is assessed through the Mean Average Error (MAE) measure; the recommended subset of retained wavenumbers is the one that minimizes the prediction error with maximum parsimony. Using our propositions in a dataset of 115 cocaine samples we obtained a best prediction model with average MAE of 0.0502 while retaining only 2.29% of the original wavenumbers, increasing the predictive precision by 0.0359 when compared to a model using the complete set of wavenumbers as predictors. Copyright © 2018 Elsevier B.V. All rights reserved.

Decomposition of complex microbial behaviors into resource-based stress responses

PubMed Central

Carlson, Ross P.

2009-01-01

Motivation: Highly redundant metabolic networks and experimental data from cultures likely adapting simultaneously to multiple stresses can complicate the analysis of cellular behaviors. It is proposed that the explicit consideration of these factors is critical to understanding the competitive basis of microbial strategies. Results: Wide ranging, seemingly unrelated Escherichia coli physiological fluxes can be simply and accurately described as linear combinations of a few ecologically relevant stress adaptations. These strategies were identified by decomposing the central metabolism of E.coli into elementary modes (mathematically defined biochemical pathways) and assessing the resource investment cost–benefit properties for each pathway. The approach capitalizes on the inherent tradeoffs related to investing finite resources like nitrogen into different pathway enzymes when the pathways have varying metabolic efficiencies. The subset of ecologically competitive pathways represented 0.02% of the total permissible pathways. The biological relevance of the assembled strategies was tested against 10 000 randomly constructed pathway subsets. None of the randomly assembled collections were able to describe all of the considered experimental data as accurately as the cost-based subset. The results suggest these metabolic strategies are biologically significant. The current descriptions were compared with linear programming (LP)-based flux descriptions using the Euclidean distance metric. The current study's pathway subset described the experimental fluxes with better accuracy than the LP results without having to test multiple objective functions or constraints and while providing additional ecological insight into microbial behavior. The assembled pathways seem to represent a generalized set of strategies that can describe a wide range of microbial responses and hint at evolutionary processes where a handful of successful metabolic strategies are utilized simultaneously in different combinations to adapt to diverse conditions. Contact: rossc@biofilms.montana.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19008248

Burden of orofacial pain in a socially deprived and culturally diverse area of the United Kingdom.

PubMed

Joury, Easter; Bernabe, Eduardo; Gallagher, Jennifer E; Marcenes, Wagner

2018-07-01

Little is known about the burden and impact of orofacial pain in deprived areas, and whether it mediates the relationship between socioeconomic position and impacts on daily life. We analysed data from a representative sample of 2168 adults, aged 16 to 65 years, from the East London Oral Health Inequality study. Participants completed a validated questionnaire on demographics, socioeconomic position (area deprivation), orofacial pain (by anatomical site) in the past month, and impacts related to oral conditions on daily life. Negative binomial regression models with robust variance estimator were fitted. The prevalence of orofacial pain was high (30.2%). The most common subset of orofacial pain was intraoral pain (27.5%). The prevalence of pain related to temporomandibular disorders was 6.8%. The most common subsets of intraoral pain were tooth (20.4%) and gingival (11.4%) pain. Orofacial pain, its subsets (intraoral and temporomandibular disorder-related pain), and intraoral pain subsets (tooth and gingival pain) consistently showed associations with all dimensions of impacts on daily life that were highly statistically significant: functional limitation, psychological discomfort, disabilities, and handicap. Socioeconomic inequalities were present in orofacial pain and some dimensions of impacts on daily life. Orofacial pain did not mediate the relationship between area deprivation and impacts on daily life. Our study demonstrated a substantial burden and impact of orofacial pain in a socially deprived and culturally diverse area of the United Kingdom. To address this burden, interventions that lie within the remit of health services are needed to improve access to dental care for adults with orofacial pain.

Selecting a climate model subset to optimise key ensemble properties

NASA Astrophysics Data System (ADS)

Herger, Nadja; Abramowitz, Gab; Knutti, Reto; Angélil, Oliver; Lehmann, Karsten; Sanderson, Benjamin M.

2018-02-01

End users studying impacts and risks caused by human-induced climate change are often presented with large multi-model ensembles of climate projections whose composition and size are arbitrarily determined. An efficient and versatile method that finds a subset which maintains certain key properties from the full ensemble is needed, but very little work has been done in this area. Therefore, users typically make their own somewhat subjective subset choices and commonly use the equally weighted model mean as a best estimate. However, different climate model simulations cannot necessarily be regarded as independent estimates due to the presence of duplicated code and shared development history. Here, we present an efficient and flexible tool that makes better use of the ensemble as a whole by finding a subset with improved mean performance compared to the multi-model mean while at the same time maintaining the spread and addressing the problem of model interdependence. Out-of-sample skill and reliability are demonstrated using model-as-truth experiments. This approach is illustrated with one set of optimisation criteria but we also highlight the flexibility of cost functions, depending on the focus of different users. The technique is useful for a range of applications that, for example, minimise present-day bias to obtain an accurate ensemble mean, reduce dependence in ensemble spread, maximise future spread, ensure good performance of individual models in an ensemble, reduce the ensemble size while maintaining important ensemble characteristics, or optimise several of these at the same time. As in any calibration exercise, the final ensemble is sensitive to the metric, observational product, and pre-processing steps used.

GEOTHERM user guide

USGS Publications Warehouse

Swanson, James R.

1977-01-01

GEOTHERM is a computerized geothermal resources file developed by the U.S. Geological Survey. The file contains data on geothermal fields, wells, and chemical analyses from the United states and international sources. The General Information Processing System (GIPSY) in the IBM 370/155 computer is used to store and retrieve data. The GIPSY retrieval program contains simple commands which can be used to search the file, select a narrowly defined subset, sort the records, and output the data in a variety of forms. Eight commands are listed and explained so that the GEOTHERM file can be accessed directly by geologists. No programming experience is necessary to retrieve data from the file.

An Analysis of Methodologies and Best Practices for Rapidly Acquiring Technologies to Meet Urgent Warfighter Needs

DTIC Science & Technology

2008-03-01

projects are a very small and unique subset of the typical acquisition and S& T programs and require a unique culture, operating environment, and...ll f th th t I’ l l 3 i t b t th ’ d b d I d ’ t k if it’ b h t i t ti l d b f l h t i i o em a ve seen are eve n program managemen , u ere s...Abstract The rapidly changing global security environment that today’s military operates within requires an ever increasing ability to quickly

Maternal Separations During the Reentry Years for 100 Infants Raised in a Prison Nursery

PubMed Central

Byrne, Mary W.; Goshin, Lorie; Blanchard-Lewis, Barbara

2011-01-01

Prison nurseries prevent maternal separations related to incarceration for the small subset of children whose pregnant mothers are incarcerated in states with such programs. For a cohort of 100 children accepted by corrections into one prison nursery, subsequent separation patterns are analyzed. The largest numbers are caused by corrections’ removal of infants from the nursery and infants reaching a one-year age limit. Criminal recidivism and substance abuse relapse threaten continued mothering during reentry. Focused and coordinated services are needed during prison stay and reentry years to sustain mothering for women and children accepted into prison nursery programs. PMID:22328865

EPA Facility Registry System (FRS): NEPT

EPA Pesticide Factsheets

This web feature service contains location and facility identification information from EPA's Facility Registry System (FRS) for the subset of facilities that link to the National Environmental Performance Track (NEPT) Program dataset. FRS identifies and geospatially locates facilities, sites or places subject to environmental regulations or of environmental interest. Using vigorous verification and data management procedures, FRS integrates facility data from EPA's national program systems, other federal agencies, and State and tribal master facility records and provides EPA with a centrally managed, single source of comprehensive and authoritative information on facilities. Additional information on FRS is available at the EPA website https://www.epa.gov/enviro/facility-registry-service-frs

EPA Facility Registry Service (FRS): NEI

EPA Pesticide Factsheets

This web feature service contains location and facility identification information from EPA's Facility Registry Service (FRS) for the subset of facilities that link to the National Emissions Inventory (NEI) Program dataset. FRS identifies and geospatially locates facilities, sites or places subject to environmental regulations or of environmental interest. Using vigorous verification and data management procedures, FRS integrates facility data from EPA's national program systems, other federal agencies, and State and tribal master facility records and provides EPA with a centrally managed, single source of comprehensive and authoritative information on facilities. Additional information on FRS is available at the EPA website https://www.epa.gov/enviro/facility-registry-service-frs

A genetic algorithm-based framework for wavelength selection on sample categorization.

PubMed

Anzanello, Michel J; Yamashita, Gabrielli; Marcelo, Marcelo; Fogliatto, Flávio S; Ortiz, Rafael S; Mariotti, Kristiane; Ferrão, Marco F

2017-08-01

In forensic and pharmaceutical scenarios, the application of chemometrics and optimization techniques has unveiled common and peculiar features of seized medicine and drug samples, helping investigative forces to track illegal operations. This paper proposes a novel framework aimed at identifying relevant subsets of attenuated total reflectance Fourier transform infrared (ATR-FTIR) wavelengths for classifying samples into two classes, for example authentic or forged categories in case of medicines, or salt or base form in cocaine analysis. In the first step of the framework, the ATR-FTIR spectra were partitioned into equidistant intervals and the k-nearest neighbour (KNN) classification technique was applied to each interval to insert samples into proper classes. In the next step, selected intervals were refined through the genetic algorithm (GA) by identifying a limited number of wavelengths from the intervals previously selected aimed at maximizing classification accuracy. When applied to Cialis®, Viagra®, and cocaine ATR-FTIR datasets, the proposed method substantially decreased the number of wavelengths needed to categorize, and increased the classification accuracy. From a practical perspective, the proposed method provides investigative forces with valuable information towards monitoring illegal production of drugs and medicines. In addition, focusing on a reduced subset of wavelengths allows the development of portable devices capable of testing the authenticity of samples during police checking events, avoiding the need for later laboratorial analyses and reducing equipment expenses. Theoretically, the proposed GA-based approach yields more refined solutions than the current methods relying on interval approaches, which tend to insert irrelevant wavelengths in the retained intervals. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

High-resolution microbiome profiling uncovers Fusobacterium nucleatum, Lactobacillus gasseri/johnsonii, and Lactobacillus vaginalis associated to oral and oropharyngeal cancer in saliva from HPV positive and HPV negative patients treated with surgery and chemo-radiation

PubMed Central

Guerrero-Preston, Rafael; White, James Robert; Godoy-Vitorino, Filipa; Rodríguez-Hilario, Arnold; Navarro, Kelvin; González, Herminio; Michailidi, Christina; Jedlicka, Anne; Canapp, Sierra; Bondy, Jessica; Dziedzic, Amanda; Mora-Lagos, Barbara; Rivera-Alvarez, Gustavo; Ili-Gangas, Carmen; Brebi-Mieville, Priscilla; Westra, William; Koch, Wayne; Kang, Hyunseok; Marchionni, Luigi; Kim, Young; Sidransky, David

2017-01-01

Microbiome studies show altered microbiota in head and neck squamous cell carcinoma (HNSCC), both in terms of taxonomic composition and metabolic capacity. These studies utilized a traditional bioinformatics methodology, which allows for accurate taxonomic assignment down to the genus level, but cannot accurately resolve species level membership. We applied Resphera Insight, a high-resolution methodology for 16S rRNA taxonomic assignment that is able to provide species-level context in its assignments of 16S rRNA next generation sequencing (NGS) data. Resphera Insight applied to saliva samples from HNSCC patients and healthy controls led to the discovery that a subset of HNSCC saliva samples is significantly enriched with commensal species from the vaginal flora, including Lactobacillus gasseri/johnsonii (710x higher in saliva) and Lactobacillus vaginalis (52x higher in saliva). These species were not observed in normal saliva from Johns Hopkins patients, nor in 16S rRNA NGS saliva samples from the Human Microbiome Project (HMP). Interestingly, both species were only observed in saliva from Human Papilloma Virus (HPV) positive and HPV negative oropharyngeal cancer patients. We confirmed the representation of both species in HMP data obtained from mid-vagina (n=128) and vaginal introitus (n=121) samples. Resphera Insight also led to the discovery that Fusobacterium nucleatum, an oral cavity flora commensal bacterium linked to colon cancer, is enriched (600x higher) in saliva from a subset of HNSCC patients with advanced tumors stages. Together, these high-resolution analyses on 583 samples suggest a possible role for bacterial species in the therapeutic outcome of HPV positive and HPV negative HNSCC patients. PMID:29340028

Random sample consensus combined with partial least squares regression (RANSAC-PLS) for microbial metabolomics data mining and phenotype improvement.

PubMed

Teoh, Shao Thing; Kitamura, Miki; Nakayama, Yasumune; Putri, Sastia; Mukai, Yukio; Fukusaki, Eiichiro

2016-08-01

In recent years, the advent of high-throughput omics technology has made possible a new class of strain engineering approaches, based on identification of possible gene targets for phenotype improvement from omic-level comparison of different strains or growth conditions. Metabolomics, with its focus on the omic level closest to the phenotype, lends itself naturally to this semi-rational methodology. When a quantitative phenotype such as growth rate under stress is considered, regression modeling using multivariate techniques such as partial least squares (PLS) is often used to identify metabolites correlated with the target phenotype. However, linear modeling techniques such as PLS require a consistent metabolite-phenotype trend across the samples, which may not be the case when outliers or multiple conflicting trends are present in the data. To address this, we proposed a data-mining strategy that utilizes random sample consensus (RANSAC) to select subsets of samples with consistent trends for construction of better regression models. By applying a combination of RANSAC and PLS (RANSAC-PLS) to a dataset from a previous study (gas chromatography/mass spectrometry metabolomics data and 1-butanol tolerance of 19 yeast mutant strains), new metabolites were indicated to be correlated with tolerance within certain subsets of the samples. The relevance of these metabolites to 1-butanol tolerance were then validated from single-deletion strains of corresponding metabolic genes. The results showed that RANSAC-PLS is a promising strategy to identify unique metabolites that provide additional hints for phenotype improvement, which could not be detected by traditional PLS modeling using the entire dataset. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Fiber-Content Measurement of Wool-Cashmere Blends Using Near-Infrared Spectroscopy.

PubMed

Zhou, Jinfeng; Wang, Rongwu; Wu, Xiongying; Xu, Bugao

2017-10-01

Cashmere and wool are two protein fibers with analogous geometrical attributes, but distinct physical properties. Due to its scarcity and unique features, cashmere is a much more expensive fiber than wool. In the textile production, cashmere is often intentionally blended with fine wool in order to reduce the material cost. To identify the fiber contents of a wool-cashmere blend is important to quality control and product classification. The goal of this study is to develop a reliable method for estimating fiber contents in wool-cashmere blends based on near-infrared (NIR) spectroscopy. In this study, we prepared two sets of cashmere-wool blends by using either whole fibers or fiber snippets in 11 different blend ratios of the two fibers and collected the NIR spectra of all the 22 samples. Of the 11 samples in each set, six were used as a subset for calibration and five as a subset for validation. By referencing the NIR band assignment to chemical bonds in protein, we identified six characteristic wavelength bands where the NIR absorbance powers of the two fibers were significantly different. We then performed the chemometric analysis with two multilinear regression (MLR) equations to predict the cashmere content (CC) in a blended sample. The experiment with these samples demonstrated that the predicted CCs from the MLR models were consistent with the CCs given in the preparations of the two sample sets (whole fiber or snippet), and the errors of the predicted CCs could be limited to 0.5% if the testing was performed over at least 25 locations. The MLR models seem to be reliable and accurate enough for estimating the cashmere content in a wool-cashmere blend and have potential to be used for tackling the cashmere adulteration problem.