Leaf habit does not determine the investment in both physical and chemical defences and pair-wise correlations between these defensive traits.

PubMed

Moreira, X; Pearse, I S

2017-05-01

Plant life-history strategies associated with resource acquisition and economics (e.g. leaf habit) are thought to be fundamental determinants of the traits and mechanisms that drive herbivore pressure, resource allocation to plant defensive traits, and the simultaneous expression (positive correlations) or trade-offs (negative correlations) between these defensive traits. In particular, it is expected that evergreen species - which usually grow slower and support constant herbivore pressure in comparison with deciduous species - will exhibit higher levels of both physical and chemical defences and a higher predisposition to the simultaneous expression of physical and chemical defensive traits. Here, by using a dataset which included 56 oak species (Quercus genus), we investigated whether leaf habit of plant species governs the investment in both physical and chemical defences and pair-wise correlations between these defensive traits. Our results showed that leaf habit does not determine the production of most leaf physical and chemical defences. Although evergreen oak species had higher levels of leaf toughness and specific leaf mass (physical defences) than deciduous oak species, both traits are essentially prerequisites for evergreenness. Similarly, our results also showed that leaf habit does not determine pair-wise correlations between defensive traits because most physical and chemical defensive traits were simultaneously expressed in both evergreen and deciduous oak species. Our findings indicate that leaf habit does not substantially contribute to oak species differences in plant defence investment. © 2017 German Botanical Society and The Royal Botanical Society of the Netherlands.

DincRNA: a comprehensive web-based bioinformatics toolkit for exploring disease associations and ncRNA function.

PubMed

Cheng, Liang; Hu, Yang; Sun, Jie; Zhou, Meng; Jiang, Qinghua

2018-06-01

DincRNA aims to provide a comprehensive web-based bioinformatics toolkit to elucidate the entangled relationships among diseases and non-coding RNAs (ncRNAs) from the perspective of disease similarity. The quantitative way to illustrate relationships of pair-wise diseases always depends on their molecular mechanisms, and structures of the directed acyclic graph of Disease Ontology (DO). Corresponding methods for calculating similarity of pair-wise diseases involve Resnik's, Lin's, Wang's, PSB and SemFunSim methods. Recently, disease similarity was validated suitable for calculating functional similarities of ncRNAs and prioritizing ncRNA-disease pairs, and it has been widely applied for predicting the ncRNA function due to the limited biological knowledge from wet lab experiments of these RNAs. For this purpose, a large number of algorithms and priori knowledge need to be integrated. e.g. 'pair-wise best, pairs-average' (PBPA) and 'pair-wise all, pairs-maximum' (PAPM) methods for calculating functional similarities of ncRNAs, and random walk with restart (RWR) method for prioritizing ncRNA-disease pairs. To facilitate the exploration of disease associations and ncRNA function, DincRNA implemented all of the above eight algorithms based on DO and disease-related genes. Currently, it provides the function to query disease similarity scores, miRNA and lncRNA functional similarity scores, and the prioritization scores of lncRNA-disease and miRNA-disease pairs. http://bio-annotation.cn:18080/DincRNAClient/. biofomeng@hotmail.com or qhjiang@hit.edu.cn. Supplementary data are available at Bioinformatics online.

NIST-NRC Comparison of Total Immersion Liquid-in-Glass Thermometers

NASA Astrophysics Data System (ADS)

Hill, K. D.; Gee, D. J.; Cross, C. D.; Strouse, G. F.

2009-02-01

The use of liquid-in-glass (LIG) thermometers is described in many documentary standards in the fields of environmental testing, material testing, and material transfer. Many national metrology institutes, including the National Institute of Standards and Technology (NIST) and the National Research Council of Canada (NRC), list calibration services for these thermometers among the Calibration Measurement Capabilities of Appendix C of the BIPM Key Comparison Database. NIST and NRC arranged a bilateral comparison of a set of total-immersion ASTM-type LIG thermometers to validate their uncertainty claims. Two each of ASTM thermometer types 62C through 69C were calibrated at NIST and at NRC at four temperatures distributed over the range appropriate to each thermometer, in addition to the ice point. Collectively, the thermometers span a temperature range of - 38 °C to 305 °C. In total, 160 measurements (80 pairs) comprise the comparison data set. Pair-wise differences ( T NIST- T NRC) were formed for each thermometer at each temperature. For 8 of the 80 pairs (10 %), the differences exceed the k = 2 combined uncertainties. These results support the claimed capabilities of NIST and NRC for the calibration of LIG thermometers.

A SAS(®) macro implementation of a multiple comparison post hoc test for a Kruskal-Wallis analysis.

PubMed

Elliott, Alan C; Hynan, Linda S

2011-04-01

The Kruskal-Wallis (KW) nonparametric analysis of variance is often used instead of a standard one-way ANOVA when data are from a suspected non-normal population. The KW omnibus procedure tests for some differences between groups, but provides no specific post hoc pair wise comparisons. This paper provides a SAS(®) macro implementation of a multiple comparison test based on significant Kruskal-Wallis results from the SAS NPAR1WAY procedure. The implementation is designed for up to 20 groups at a user-specified alpha significance level. A Monte-Carlo simulation compared this nonparametric procedure to commonly used parametric multiple comparison tests. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Evaluation of key driver categories influencing sustainable waste management development with the analytic hierarchy process (AHP): Serbia example.

PubMed

Tot, Bojana; Srđević, Bojan; Vujić, Bogdana; Russo, Mário Augusto Tavares; Vujić, Goran

2016-08-01

The problems of waste management have become increasingly complex in recent decades. The increasing amount of generated waste, adopted legislation in the field of waste management, administrative issues, economic impacts and social awareness are important drivers in achieving a sustainable waste management system. However, in practice, there are many other drivers that are often mutually in conflict. The purpose of this research is to define the precise driver and their corresponding sub-drivers, which are relevant for developing a waste management system and, on the basis of their importance, to determine which has the predominant influence on the slow development of a waste management system at the national and regional level, within the Republic of Serbia and similar countries of southeast Europe. This research presents two levels of decision making: the first is a pair-wise comparison of the drivers in relation to the goal and the second is a pair-wise comparison of the sub-drivers in relation to the driver and in relation to the goal. Results of performed analyses on the waste management drivers were integrated via the decision-making process supported by an analytic hierarchy process (AHP). The final results of this research shows that the Institutional-Administrative driver is the most important for developing a sustainable waste management system. © The Author(s) 2016.

Comparing methods for modelling spreading cell fronts.

PubMed

Markham, Deborah C; Simpson, Matthew J; Maini, Philip K; Gaffney, Eamonn A; Baker, Ruth E

2014-07-21

Spreading cell fronts play an essential role in many physiological processes. Classically, models of this process are based on the Fisher-Kolmogorov equation; however, such continuum representations are not always suitable as they do not explicitly represent behaviour at the level of individual cells. Additionally, many models examine only the large time asymptotic behaviour, where a travelling wave front with a constant speed has been established. Many experiments, such as a scratch assay, never display this asymptotic behaviour, and in these cases the transient behaviour must be taken into account. We examine the transient and the asymptotic behaviour of moving cell fronts using techniques that go beyond the continuum approximation via a volume-excluding birth-migration process on a regular one-dimensional lattice. We approximate the averaged discrete results using three methods: (i) mean-field, (ii) pair-wise, and (iii) one-hole approximations. We discuss the performance of these methods, in comparison to the averaged discrete results, for a range of parameter space, examining both the transient and asymptotic behaviours. The one-hole approximation, based on techniques from statistical physics, is not capable of predicting transient behaviour but provides excellent agreement with the asymptotic behaviour of the averaged discrete results, provided that cells are proliferating fast enough relative to their rate of migration. The mean-field and pair-wise approximations give indistinguishable asymptotic results, which agree with the averaged discrete results when cells are migrating much more rapidly than they are proliferating. The pair-wise approximation performs better in the transient region than does the mean-field, despite having the same asymptotic behaviour. Our results show that each approximation only works in specific situations, thus we must be careful to use a suitable approximation for a given system, otherwise inaccurate predictions could be made. Copyright © 2014 Elsevier Ltd. All rights reserved.

Development and evaluation of learning module on clinical decision-making in Prosthodontics.

PubMed

Deshpande, Saee; Lambade, Dipti; Chahande, Jayashree

2015-01-01

Best practice strategies for helping students learn the reasoning skills of problem solving and critical thinking (CT) remain a source of conjecture, particularly with regard to CT. The dental education literature is fundamentally devoid of research on the cognitive components of clinical decision-making. This study was aimed to develop and evaluate the impact of blended learning module on clinical decision-making skills of dental graduates for planning prosthodontics rehabilitation. An interactive teaching module consisting of didactic lectures on clinical decision-making and a computer-assisted case-based treatment planning software was developed Its impact on cognitive knowledge gain in clinical decision-making was evaluated using an assessment involving problem-based multiple choice questions and paper-based case scenarios. Mean test scores were: Pretest (17 ± 1), posttest 1 (21 ± 2) and posttest 2 (43 ± 3). Comparison of mean scores was done with one-way ANOVA test. There was overall significant difference in between mean scores at all the three points (P < 0.001). A pair-wise comparison of mean scores was done with Bonferroni test. The mean difference is significant at the 0.05 level. The pair-wise comparison shows that posttest 2 score is significantly higher than posttest 1 and posttest 1 is significantly higher than pretest that is, pretest 2 > posttest 1 > pretest. Blended teaching methods employing didactic lectures on the clinical decision-making as well as computer assisted case-based learning can be used to improve quality of clinical decision-making in prosthodontic rehabilitation for dental graduates.

Comparison of the social contact patterns among school-age children in specific seasons, locations, and times.

PubMed

Luh, Dih-Ling; You, Zhi-Shin; Chen, Szu-Chieh

2016-03-01

Social contact patterns among school-age children play an important role in the epidemiology of infectious disease. This study explored how people interact in specific seasons (flu season and non-flu season), environmental settings (city and county), and times (weekend and weekday). We conducted a survey of junior high school students (grades 7-8) using an established questionnaire during May-June 2013 and December 2013. The sample size with pair-wise comparisons for the times (weekday/weekend) and stratification by location and seasons were 75, 87, 105 and 106, respectively. The sample size with pair-wise comparisons for the seasons (flu/non-flu) and stratification by location were 54 and 83, respectively. Conversation and skin-to-skin contact behaviors were surveyed through diary-based questionnaires, of which 665 valid questionnaires were returned. There was no difference in the number of contacts during the flu and non-flu seasons, with averages of 16.3 (S.D.=12.9) and 14.6 (S.D.=9.5) people, respectively. However, statistical analysis showed that the average number of contacts in Taichung City and Yilan County were significantly different (p<0.001). Weekdays were associated with 23-28% more contacts than weekend days during both the non-flu and flu seasons (p<0.001) (Wilcoxon signed-rank test). Our work has important implications for the dynamic modeling of infectious diseases and performance analysis of human contact numbers and contact characteristics for schoolchildren in specific seasons, places, and times. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Pair-Wise and Many-Body Dispersive Interactions Coupled to an Optimally Tuned Range-Separated Hybrid Functional.

PubMed

Agrawal, Piyush; Tkatchenko, Alexandre; Kronik, Leeor

2013-08-13

We propose a nonempirical, pair-wise or many-body dispersion-corrected, optimally tuned range-separated hybrid functional. This functional retains the advantages of the optimal-tuning approach in the prediction of the electronic structure. At the same time, it gains accuracy in the prediction of binding energies for dispersively bound systems, as demonstrated on the S22 and S66 benchmark sets of weakly bound dimers.

Evaluation of users' satisfaction on pedestrian facilities using pair-wise comparison approach

NASA Astrophysics Data System (ADS)

Zainol, R.; Ahmad, F.; Nordin, N. A.; Aripin, A. W. M.

2014-02-01

Global climate change issues demand people of the world to change the way they live today. Thus, current cities need to be redeveloped towards less use of carbon in their day to day operations. Pedestrianized environment is one of the approaches used in reducing carbon foot print in cities. Heritage cities are the first to be looked into since they were built in the era in which motorized vehicles were minimal. Therefore, the research explores users' satisfaction on assessment of physical attributes of pedestrianization in Melaka Historical City, a UNESCO World Heritage Site. It aims to examine users' satisfaction on pedestrian facilities provided within the study area using pair wise questionnaire comparison approach. A survey of 200 respondents using random sampling was conducted in six different sites namely Jonker Street, Church Street, Kota Street, Goldsmith Street, Merdeka Street to Taming Sari Tower and Merdeka Street to River Cruise terminal. The survey consists of an assessment tool based on a nine-point scale of users' satisfaction level of pathway properties, zebra pedestrian crossing, street furniture, personal safety, adjacent to traffic flow, aesthetic and amenities. Analytical hierarchical process (AHP) was used to avoid any biasness in analyzing the data collected. Findings show that Merdeka Street to Taming Sari Tower as the street that scores the highest satisfaction level that fulfils all the required needs of a pedestrianized environment. Similar assessment elements can be used to evaluate existing streets in other cities and these criteria should also be used in planning for future cities.

Systematic review with meta-analysis: comparative efficacy of immunosuppressants and biologics for reducing hospitalisation and surgery in Crohn's disease and ulcerative colitis.

PubMed

Mao, E J; Hazlewood, G S; Kaplan, G G; Peyrin-Biroulet, L; Ananthakrishnan, A N

2017-01-01

Crohn's disease (CD) and ulcerative colitis (UC) have a progressive course leading to hospitalisation and surgery. The ability of existing therapies to alter disease course is not clearly defined. To investigate the comparative efficacy of currently available inflammatory bowel disease (IBD) therapies to reduce hospitalisation and surgery. We conducted a systematic review in MEDLINE/PubMed for randomised controlled trials (RCT) published between January 1980 and May 2016 examining efficacy of biological or immunomodulator therapy in IBD. We performed direct comparisons of pooled proportions of hospitalisation and surgery. Pair-wise comparisons using a random-effects Bayesian network meta-analysis were performed to assess comparative efficacy of different treatments. We identified seven randomised controlled trials (5 CD; 2 UC) comparing three biologics and one immunomodulator with placebo. In CD, anti-TNF biologics significantly reduced hospitalisation [Odds ratio (OR) 0.46, 95% confidence interval (CI) 0.36-0.60] and surgery (OR 0.23, 95% CI 0.13-0.42) compared to placebo. No statistically significant reduction was noted with azathioprine or vedolizumab. Azathioprine was inferior to both infliximab and adalimumab in preventing CD-related hospitalisation (>97.5% probability). Anti-TNF biologics significantly reduced hospitalisation (OR 0.48, 95% CI 0.29-0.80) and surgery (OR 0.67, 95% CI 0.46-0.97) in UC. There were no statistically significant differences in the pair-wise comparisons between active treatments. In CD and UC, anti-TNF biologics are efficacious in reducing the odds of hospitalisation by half and surgery by 33-77%. Azathioprine and vedolizumab were not associated with a similar improvement, but robust conclusions may be limited due to paucity of RCTs. © 2016 John Wiley & Sons Ltd.

Application of the Refined Integral Method in the mathematical modeling of drug delivery from one-layer torus-shaped devices.

PubMed

Helbling, Ignacio M; Ibarra, Juan C D; Luna, Julio A

2012-02-28

A mathematical modeling of controlled release of drug from one-layer torus-shaped devices is presented. Analytical solutions based on Refined Integral Method (RIM) are derived. The validity and utility of the model are ascertained by comparison of the simulation results with matrix-type vaginal rings experimental release data reported in the literature. For the comparisons, the pair-wise procedure is used to measure quantitatively the fit of the theoretical predictions to the experimental data. A good agreement between the model prediction and the experimental data is observed. A comparison with a previously reported model is also presented. More accurate results are achieved for small A/C(s) ratios. Copyright © 2011 Elsevier B.V. All rights reserved.

Comparative Response of Platelet fV and Plasma fV to Activated Protein C and Relevance to a Model of Acute Traumatic Coagulopathy

DTIC Science & Technology

2014-06-12

inducing concen tration. To test this hypothesis, we investigated the concentration of aPC required to induce significant delays in clot time, decrease...instructions and mixed with 50 ml plasma ( pre incubated at 37 uC). The Mean Normal PT is listed as 13.5 s for this device, and INR is calculated by...and pair wise comparison Bonferroni posttests . Results Nanomolar aPC Is Required to Prolong PT/INR PT measurements in fVdp are delayed compared to

PTM Along Track Algorithm to Maintain Spacing During Same Direction Pair-Wise Trajectory Management Operations

NASA Technical Reports Server (NTRS)

Carreno, Victor A.

2015-01-01

Pair-wise Trajectory Management (PTM) is a cockpit based delegated responsibility separation standard. When an air traffic service provider gives a PTM clearance to an aircraft and the flight crew accepts the clearance, the flight crew will maintain spacing and separation from a designated aircraft. A PTM along track algorithm will receive state information from the designated aircraft and from the own ship to produce speed guidance for the flight crew to maintain spacing and separation

Matrix multiplication operations using pair-wise load and splat operations

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

Eichenberger, Alexandre E.; Gschwind, Michael K.; Gunnels, John A.

Mechanisms for performing a matrix multiplication operation are provided. A vector load operation is performed to load a first vector operand of the matrix multiplication operation to a first target vector register. A pair-wise load and splat operation is performed to load a pair of scalar values of a second vector operand and replicate the pair of scalar values within a second target vector register. An operation is performed on elements of the first target vector register and elements of the second target vector register to generate a partial product of the matrix multiplication operation. The partial product is accumulatedmore » with other partial products and a resulting accumulated partial product is stored. This operation may be repeated for a second pair of scalar values of the second vector operand.« less

In vitro assessment of competency for different lingual brackets in sliding mechanics.

PubMed

Lalithapriya, S; Kumaran, N Kurunji; Rajasigamani, K

2015-01-01

To determine the static frictional resistance of different lingual brackets at different second order angulations when coupled with stainless steel (SS) archwire in dry and wet conditions. Using a modified jig, frictional resistance was evaluated under different conditions for a total of 270 upper premolar lingual brackets (0.018″ × 0.025″ - conventional - 7(th) generation and STb, self-ligating - evolution) with no in-built tip or torque together with 0.016″ × 0.022″ straight length SS archwires. For conventional brackets, the archwire was secured with 0.008″ preformed SS short ligature ties. One way analysis of variance with Tukey HSD as post-hoc test was applied for degree wise and bracket wise comparison within dry condition and wet condition. For pair wise comparison Student's t-test was used. Under both conditions the static frictional resistance is significantly higher for self-ligating brackets at 0°, while at 5° and 10° it is higher for 7(th) generation brackets. Statistically, significant difference does not exist at 0° between conventional brackets and the same was found at 5° and 10° between STb and self-ligating brackets. With an increase in second order angulations, all the evaluated samples exhibited an increased frictional value. Wet condition samples obtained a higher value than their corresponding dry condition. The self-ligating bracket evaluated in this in vitro study is not beneficial in reducing friction during en-mass retraction due to its interactive clip type.

The optimal hormonal replacement modality selection for multiple organ procurement from brain-dead organ donors

PubMed Central

Mi, Zhibao; Novitzky, Dimitri; Collins, Joseph F; Cooper, David KC

2015-01-01

The management of brain-dead organ donors is complex. The use of inotropic agents and replacement of depleted hormones (hormonal replacement therapy) is crucial for successful multiple organ procurement, yet the optimal hormonal replacement has not been identified, and the statistical adjustment to determine the best selection is not trivial. Traditional pair-wise comparisons between every pair of treatments, and multiple comparisons to all (MCA), are statistically conservative. Hsu’s multiple comparisons with the best (MCB) – adapted from the Dunnett’s multiple comparisons with control (MCC) – has been used for selecting the best treatment based on continuous variables. We selected the best hormonal replacement modality for successful multiple organ procurement using a two-step approach. First, we estimated the predicted margins by constructing generalized linear models (GLM) or generalized linear mixed models (GLMM), and then we applied the multiple comparison methods to identify the best hormonal replacement modality given that the testing of hormonal replacement modalities is independent. Based on 10-year data from the United Network for Organ Sharing (UNOS), among 16 hormonal replacement modalities, and using the 95% simultaneous confidence intervals, we found that the combination of thyroid hormone, a corticosteroid, antidiuretic hormone, and insulin was the best modality for multiple organ procurement for transplantation. PMID:25565890

A Comparison of Online, Video Synchronous, and Traditional Learning Modes for an Introductory Undergraduate Physics Course

NASA Astrophysics Data System (ADS)

Faulconer, E. K.; Griffith, J.; Wood, B.; Acharyya, S.; Roberts, D.

2018-05-01

While the equivalence between online and traditional classrooms has been well-researched, very little of this includes college-level introductory Physics. Only one study explored Physics at the whole-class level rather than specific course components such as a single lab or a homework platform. In this work, we compared the failure rate, grade distribution, and withdrawal rates in an introductory undergraduate Physics course across several learning modes including traditional face-to-face instruction, synchronous video instruction, and online classes. Statistically significant differences were found for student failure rates, grade distribution, and withdrawal rates but yielded small effect sizes. Post-hoc pair-wise test was run to determine differences between learning modes. Online students had a significantly lower failure rate than students who took the class via synchronous video classroom. While statistically significant differences were found for grade distributions, the pair-wise comparison yielded no statistically significance differences between learning modes when using the more conservative Bonferroni correction in post-hoc testing. Finally, in this study, student withdrawal rates were lowest for students who took the class in person (in-person classroom and synchronous video classroom) than online. Students that persist in an online introductory Physics class are more likely to achieve an A than in other modes. However, the withdrawal rate is higher from online Physics courses. Further research is warranted to better understand the reasons for higher withdrawal rates in online courses. Finding the root cause to help eliminate differences in student performance across learning modes should remain a high priority for education researchers and the education community as a whole.

Selection of a suitable method for the preparation of polymeric nanoparticles: multi-criteria decision making approach.

PubMed

Krishnamoorthy, Kannan; Mahalingam, Manikandan

2015-03-01

The present study is aimed to select the suitable method for preparation of camptothecin loaded polymeric nanoparticles by utilizing the multi-criteria decision making method. Novel approaches of drug delivery by formulation using nanotechnology are revolutionizing the future of medicine. Recent years have witnessed unprecedented growth of research and application in the area of nanotechnology. Nanoparticles have become an important area of research in the field of drug delivery because they have the ability to deliver a wide range of drug to varying areas of body. Despite of extensive research and development, polymeric nanoparticles are frequently used to improve the therapeutic effect of drugs. A number of techniques are available for the preparation of polymeric nanoparticles. The Analytical Hierarchy Process (AHP) is a method for decision making, which are derived from individual judgements for qualitative factors, using the pair-wise comparison matrix. In AHP, a decision hierarchy is constructed with a goal, criteria and alternatives. The model uses three main criteria 1) Instrument, 2) Process and Output and 3) Cost. In addition, there are eight sub-criteria's as well as eight alternatives. Pair-wise comparison matrixes are used to obtain the overall priority weight and ranking for the selection of suitable method. Nanoprecipitation technique is the most suitable method for the preparation of camptothecin loaded polymeric nanoparticles with the highest overall priority weight of 0.297 CONCLUSION: In particular, the result indicates that the priority weights obtained from AHP could be defined as a multiple output for finding out the most suitable method for preparation of camptothecin loaded polymeric nanoparticles.

Evaluation of the 8th AJCC staging system for pathologically versus clinically staged pancreatic adenocarcinoma: A time to revisit a dogma?

PubMed

Abdel-Rahman, Omar

2018-02-01

The 8th edition of the American Joint Committee on Cancer (AJCC) staging system for pancreatic exocrine adenocarcinoma has been released. The current study seeks to assess the 7th and 8th editions among patients registered within the surveillance, epidemiology and end results (SEER) database. SEER database (2010-2013) has been accessed through SEER*Stat program and AJCC 8th edition stages were reconstructed utilizing the collaborative stage descriptions. Kaplan-Meier analysis of overall survival and pancreatic cancer-specific survival analyses (according to both 7th and 8th editions and according to whether pathological or clinical staging were conducted) has been performed. Multivariate analysis of factors affecting pancreatic cancer-specific survival was also conducted through a Cox proportional hazard model. A total of 18  948 patients with pancreatic adenocarcinoma were identified in the period from 2010-2013. Pancreatic cancer-specific survival among pathologically staged patients and according to the 8th edition showed significant differences for all pair wise comparisons among different stages (P < 0.0001) except for the comparison between stage IA and stage IB (P = 0.307) and the comparison between stage IB and stage IIA (P = 0.116). Moreover, P value for stage IA vs IIA was 0.014; while pancreatic cancer-specific survival according to the 7th edition among pathologically staged patients showed significant differences for all pair wise comparisons among different stages (P < 0.0001) except for the comparison between IA and IB (P = 0.072), the comparison between stage IIA and stage IIB (P = 0.065), the comparison between stage IIA and stage III (P = 0.059) and the comparison between IIB and III (P = 0.595). Among clinically staged patients (i.e. those who did not undergo initial radical surgery), the prognostic performance of both 7th and 8th stages for both overall survival and pancreatic cancer-specific survival was limited. There is clearly a need to have two staging systems for pancreatic adenocarcinoma: pathological and clinical staging systems. Copyright © 2018 First Affiliated Hospital, Zhejiang University School of Medicine in China. Published by Elsevier B.V. All rights reserved.

Integrated Mueller-matrix near-infrared imaging and point-wise spectroscopy improves colonic cancer detection

PubMed Central

Wang, Jianfeng; Zheng, Wei; Lin, Kan; Huang, Zhiwei

2016-01-01

We report the development and implementation of a unique integrated Mueller-matrix (MM) near-infrared (NIR) imaging and Mueller-matrix point-wise diffuse reflectance (DR) spectroscopy technique for improving colonic cancer detection and diagnosis. Point-wise MM DR spectra can be acquired from any suspicious tissue areas indicated by MM imaging. A total of 30 paired colonic tissue specimens (normal vs. cancer) were measured using the integrated MM imaging and point-wise MM DR spectroscopy system. Polar decomposition algorithms are employed on the acquired images and spectra to derive three polarization metrics including depolarization, diattentuation and retardance for colonic tissue characterization. The decomposition results show that tissue depolarization and retardance are significantly decreased (p<0.001, paired 2-sided Student’s t-test, n = 30); while the tissue diattentuation is significantly increased (p<0.001, paired 2-sided Student’s t-test, n = 30) associated with colonic cancer. Further partial least squares discriminant analysis (PLS-DA) and leave-one tissue site-out, cross validation (LOSCV) show that the combination of the three polarization metrics provide the best diagnostic accuracy of 95.0% (sensitivity: 93.3%, and specificity: 96.7%) compared to either of the three polarization metrics (sensitivities of 93.3%, 83.3%, and 80.0%; and specificities of 90.0%, 96.7%, and 80.0%, respectively, for the depolarization, diattentuation and retardance metrics) for colonic cancer detection. This work suggests that the integrated MM NIR imaging and point-wise MM NIR diffuse reflectance spectroscopy has the potential to improve the early detection and diagnosis of malignant lesions in the colon. PMID:27446640

Pharmacokinetic analysis and comparison of caffeine administered rapidly or slowly in coffee chilled or hot versus chilled energy drink in healthy young adults.

PubMed

White, John R; Padowski, Jeannie M; Zhong, Yili; Chen, Gang; Luo, Shaman; Lazarus, Philip; Layton, Matthew E; McPherson, Sterling

2016-01-01

There is a paucity of data describing the impact of type of beverage (coffee versus energy drink), different rates of consumption and different temperature of beverages on the pharmacokinetic disposition of caffeine. Additionally, there is concern that inordinately high levels of caffeine may result from the rapid consumption of cold energy drinks. The objective of this study was to compare the pharmacokinetics of caffeine under various drink temperature, rate of consumption and vehicle (coffee versus energy drink) conditions. Five caffeine (dose = 160 mg) conditions were evaluated in an open-label, group-randomized, crossover fashion. After the administration of each caffeine dose, 10 serial plasma samples were harvested. Caffeine concentration was measured via liquid chromatography-mass spectrometry (LC-MS), and those concentrations were assessed by non-compartmental pharmacokinetic analysis. The calculated mean pharmacokinetic parameters were analyzed statistically by one-way repeated measures analysis of variance (RM ANOVA). If differences were found, each group was compared to the other by all pair-wise multiple comparison. Twenty-four healthy subjects ranging in age from 18 to 30 completed the study. The mean caffeine concentration time profiles were similar with overlapping SDs at all measured time points. The ANOVA revealed significant differences in mean Cmax and Vd ss/F, but no pair-wise comparisons reached statistical significance. No other differences in pharmacokinetic parameters were found. The results of this study are consistent with previous caffeine pharmacokinetic studies and suggest that while rate of consumption, temperature of beverage and vehicle (coffee versus energy drink) may be associated with slightly different pharmacokinetic parameters, the overall impact of these variables is small. This study suggests that caffeine absorption and exposure from coffee and energy drink is similar irrespective of beverage temperature or rate of consumption.

Pharmacokinetic analysis and comparison of caffeine administered rapidly or slowly in coffee chilled or hot versus chilled energy drink in healthy young adults

PubMed Central

White, John R.; Padowski, Jeannie M.; Zhong, Yili; Chen, Gang; Luo, Shaman; Lazarus, Philip; Layton, Matthew E.; McPherson, Sterling

2016-01-01

Abstract Context: There is a paucity of data describing the impact of type of beverage (coffee versus energy drink), different rates of consumption and different temperature of beverages on the pharmacokinetic disposition of caffeine. Additionally, there is concern that inordinately high levels of caffeine may result from the rapid consumption of cold energy drinks. Objective: The objective of this study was to compare the pharmacokinetics of caffeine under various drink temperature, rate of consumption and vehicle (coffee versus energy drink) conditions. Materials: Five caffeine (dose = 160 mg) conditions were evaluated in an open-label, group-randomized, crossover fashion. After the administration of each caffeine dose, 10 serial plasma samples were harvested. Caffeine concentration was measured via liquid chromatography–mass spectrometry (LC–MS), and those concentrations were assessed by non-compartmental pharmacokinetic analysis. The calculated mean pharmacokinetic parameters were analyzed statistically by one-way repeated measures analysis of variance (RM ANOVA). If differences were found, each group was compared to the other by all pair-wise multiple comparison. Results: Twenty-four healthy subjects ranging in age from 18 to 30 completed the study. The mean caffeine concentration time profiles were similar with overlapping SDs at all measured time points. The ANOVA revealed significant differences in mean C max and V d ss/F, but no pair-wise comparisons reached statistical significance. No other differences in pharmacokinetic parameters were found. Discussion: The results of this study are consistent with previous caffeine pharmacokinetic studies and suggest that while rate of consumption, temperature of beverage and vehicle (coffee versus energy drink) may be associated with slightly different pharmacokinetic parameters, the overall impact of these variables is small. Conclusion: This study suggests that caffeine absorption and exposure from coffee and energy drink is similar irrespective of beverage temperature or rate of consumption. PMID:27100333

Selection of a Suitable Method for the Preparation of Polymeric Nanoparticles: Multi-Criteria Decision Making Approach

PubMed Central

Krishnamoorthy, Kannan; Mahalingam, Manikandan

2015-01-01

Purpose: The present study is aimed to select the suitable method for preparation of camptothecin loaded polymeric nanoparticles by utilizing the multi-criteria decision making method. Novel approaches of drug delivery by formulation using nanotechnology are revolutionizing the future of medicine. Recent years have witnessed unprecedented growth of research and application in the area of nanotechnology. Nanoparticles have become an important area of research in the field of drug delivery because they have the ability to deliver a wide range of drug to varying areas of body. Methods: Despite of extensive research and development, polymeric nanoparticles are frequently used to improve the therapeutic effect of drugs. A number of techniques are available for the preparation of polymeric nanoparticles. The Analytical Hierarchy Process (AHP) is a method for decision making, which are derived from individual judgements for qualitative factors, using the pair-wise comparison matrix. In AHP, a decision hierarchy is constructed with a goal, criteria and alternatives. Results: The model uses three main criteria 1) Instrument, 2) Process and Output and 3) Cost. In addition, there are eight sub-criteria’s as well as eight alternatives. Pair-wise comparison matrixes are used to obtain the overall priority weight and ranking for the selection of suitable method. Nanoprecipitation technique is the most suitable method for the preparation of camptothecin loaded polymeric nanoparticles with the highest overall priority weight of 0.297 Conclusion: In particular, the result indicates that the priority weights obtained from AHP could be defined as a multiple output for finding out the most suitable method for preparation of camptothecin loaded polymeric nanoparticles. PMID:25789220

Student goal orientation in learning inquiry skills with modifiable software advisors

NASA Astrophysics Data System (ADS)

Shimoda, Todd A.; White, Barbara Y.; Frederiksen, John R.

2002-03-01

A computer support environment (SCI-WISE) for learning and doing science inquiry projects was designed. SCI-WISE incorporates software advisors that give general advice about a skill such as hypothesizing. By giving general advice (rather than step-by-step procedures), the system is intended to help students conduct experiments that are more epistemologically authentic. Also, students using SCI-WISE can select the type of advice the advisors give and when they give advice, as well as modify the advisors' knowledge bases. The system is based partly on a theoretical framework of levels of agency and goal orientation. This framework assumes that giving students higher levels of agency facilitates higher-level goal orientations (such as mastery or knowledge building as opposed to task completion) that in turn produce higher levels of competence. A study of sixth grade science students was conducted. Students took a pretest questionnaire that measured their goal orientations for science projects and their inquiry skills. The students worked in pairs on an open-ended inquiry project that requires complex reasoning about human memory. The students used one of two versions of SCI-WISE - one that was modifiable and one that was not. After finishing the project, the students took a posttest questionnaire similar to the pretest, and evaluated the version of the system they used. The main results showed that (a) there was no correlation of goal orientation with grade point average, (b) knowledge-oriented students using the modifiable version tended to rate SCI-WISE more helpful than task-oriented students, and (c) knowledge-oriented pairs using the nonmodifiable version tended to have higher posttest inquiry skills scores than other pair types.

Cardiovascular risk with non-steroidal anti-inflammatory drugs: systematic review of population-based controlled observational studies.

PubMed

McGettigan, Patricia; Henry, David

2011-09-01

Randomised trials have highlighted the cardiovascular risks of non-steroidal anti-inflammatory drugs (NSAIDs) in high doses and sometimes atypical settings. Here, we provide estimates of the comparative risks with individual NSAIDs at typical doses in community settings. We performed a systematic review of community-based controlled observational studies. We conducted comprehensive literature searches, extracted adjusted relative risk (RR) estimates, and pooled the estimates for major cardiovascular events associated with use of individual NSAIDs, in different doses, and in populations with low and high background risks of cardiovascular events. We also compared individual drugs in pair-wise (within study) analyses, generating ratios of RRs (RRRs). Thirty case-control studies included 184,946 cardiovascular events, and 21 cohort studies described outcomes in >2.7 million exposed individuals. Of the extensively studied drugs (ten or more studies), the highest overall risks were seen with rofecoxib, 1.45 (95% CI 1.33, 1.59), and diclofenac, 1.40 (1.27, 1.55), and the lowest with ibuprofen, 1.18 (1.11, 1.25), and naproxen, 1.09 (1.02, 1.16). In a sub-set of studies, risk was elevated with low doses of rofecoxib, 1.37 (1.20, 1.57), celecoxib, 1.26 (1.09, 1.47), and diclofenac, 1.22 (1.12, 1.33), and rose in each case with higher doses. Ibuprofen risk was seen only with higher doses. Naproxen was risk-neutral at all doses. Of the less studied drugs etoricoxib, 2.05 (1.45, 2.88), etodolac, 1.55 (1.28, 1.87), and indomethacin, 1.30 (1.19, 1.41), had the highest risks. In pair-wise comparisons, etoricoxib had a higher RR than ibuprofen, RRR = 1.68 (99% CI 1.14, 2.49), and naproxen, RRR = 1.75 (1.16, 2.64); etodolac was not significantly different from naproxen and ibuprofen. Naproxen had a significantly lower risk than ibuprofen, RRR = 0.92 (0.87, 0.99). RR estimates were constant with different background risks for cardiovascular disease and rose early in the course of treatment. This review suggests that among widely used NSAIDs, naproxen and low-dose ibuprofen are least likely to increase cardiovascular risk. Diclofenac in doses available without prescription elevates risk. The data for etoricoxib were sparse, but in pair-wise comparisons this drug had a significantly higher RR than naproxen or ibuprofen. Indomethacin is an older, rather toxic drug, and the evidence on cardiovascular risk casts doubt on its continued clinical use. Please see later in the article for the Editors' Summary.

Building dynamic population graph for accurate correspondence detection.

PubMed

Du, Shaoyi; Guo, Yanrong; Sanroma, Gerard; Ni, Dong; Wu, Guorong; Shen, Dinggang

2015-12-01

In medical imaging studies, there is an increasing trend for discovering the intrinsic anatomical difference across individual subjects in a dataset, such as hand images for skeletal bone age estimation. Pair-wise matching is often used to detect correspondences between each individual subject and a pre-selected model image with manually-placed landmarks. However, the large anatomical variability across individual subjects can easily compromise such pair-wise matching step. In this paper, we present a new framework to simultaneously detect correspondences among a population of individual subjects, by propagating all manually-placed landmarks from a small set of model images through a dynamically constructed image graph. Specifically, we first establish graph links between models and individual subjects according to pair-wise shape similarity (called as forward step). Next, we detect correspondences for the individual subjects with direct links to any of model images, which is achieved by a new multi-model correspondence detection approach based on our recently-published sparse point matching method. To correct those inaccurate correspondences, we further apply an error detection mechanism to automatically detect wrong correspondences and then update the image graph accordingly (called as backward step). After that, all subject images with detected correspondences are included into the set of model images, and the above two steps of graph expansion and error correction are repeated until accurate correspondences for all subject images are established. Evaluations on real hand X-ray images demonstrate that our proposed method using a dynamic graph construction approach can achieve much higher accuracy and robustness, when compared with the state-of-the-art pair-wise correspondence detection methods as well as a similar method but using static population graph. Copyright © 2015 Elsevier B.V. All rights reserved.

DockTrina: docking triangular protein trimers.

PubMed

Popov, Petr; Ritchie, David W; Grudinin, Sergei

2014-01-01

In spite of the abundance of oligomeric proteins within a cell, the structural characterization of protein-protein interactions is still a challenging task. In particular, many of these interactions involve heteromeric complexes, which are relatively difficult to determine experimentally. Hence there is growing interest in using computational techniques to model such complexes. However, assembling large heteromeric complexes computationally is a highly combinatorial problem. Nonetheless the problem can be simplified greatly by considering interactions between protein trimers. After dimers and monomers, triangular trimers (i.e. trimers with pair-wise contacts between all three pairs of proteins) are the most frequently observed quaternary structural motifs according to the three-dimensional (3D) complex database. This article presents DockTrina, a novel protein docking method for modeling the 3D structures of nonsymmetrical triangular trimers. The method takes as input pair-wise contact predictions from a rigid body docking program. It then scans and scores all possible combinations of pairs of monomers using a very fast root mean square deviation test. Finally, it ranks the predictions using a scoring function which combines triples of pair-wise contact terms and a geometric clash penalty term. The overall approach takes less than 2 min per complex on a modern desktop computer. The method is tested and validated using a benchmark set of 220 bound and seven unbound protein trimer structures. DockTrina will be made available at http://nano-d.inrialpes.fr/software/docktrina. Copyright © 2013 Wiley Periodicals, Inc.

Measuring pair-wise molecular interactions in a complex mixture

NASA Astrophysics Data System (ADS)

Chakraborty, Krishnendu; Varma, Manoj M.; Venkatapathi, Murugesan

2016-03-01

Complex biological samples such as serum contain thousands of proteins and other molecules spanning up to 13 orders of magnitude in concentration. Present measurement techniques do not permit the analysis of all pair-wise interactions between the components of such a complex mixture to a given target molecule. In this work we explore the use of nanoparticle tags which encode the identity of the molecule to obtain the statistical distribution of pair-wise interactions using their Localized Surface Plasmon Resonance (LSPR) signals. The nanoparticle tags are chosen such that the binding between two molecules conjugated to the respective nanoparticle tags can be recognized by the coupling of their LSPR signals. This numerical simulation is done by DDA to investigate this approach using a reduced system consisting of three nanoparticles (a gold ellipsoid with aspect ratio 2.5 and short axis 16 nm, and two silver ellipsoids with aspect ratios 3 and 2 and short axes 8 nm and 10 nm respectively) and the set of all possible dimers formed between them. Incident light was circularly polarized and all possible particle and dimer orientations were considered. We observed that minimum peak separation between two spectra is 5 nm while maximum is 184nm.

Multi-criteria analysis of potential recovery facilities in a reverse supply chain

NASA Astrophysics Data System (ADS)

Nukala, Satish; Gupta, Surendra M.

2005-11-01

Analytic Hierarchy Process (AHP) has been employed by researchers for solving multi-criteria analysis problems. However, AHP is often criticized for its unbalanced scale of judgments and failure to precisely handle the inherent uncertainty and vagueness in carrying out the pair-wise comparisons. With an objective to address these drawbacks, in this paper, we employ a fuzzy approach in selecting potential recovery facilities in the strategic planning of a reverse supply chain network that addresses the decision maker's level of confidence in the fuzzy assessments and his/her attitude towards risk. A numerical example is considered to illustrate the methodology.

Is central dogma a global property of cellular information flow?

PubMed Central

Piras, Vincent; Tomita, Masaru; Selvarajoo, Kumar

2012-01-01

The central dogma of molecular biology has come under scrutiny in recent years. Here, we reviewed high-throughput mRNA and protein expression data of Escherichia coli, Saccharomyces cerevisiae, and several mammalian cells. At both single cell and population scales, the statistical comparisons between the entire transcriptomes and proteomes show clear correlation structures. In contrast, the pair-wise correlations of single transcripts to proteins show nullity. These data suggest that the organizing structure guiding cellular processes is observed at omics-wide scale, and not at single molecule level. The central dogma, thus, globally emerges as an average integrated flow of cellular information. PMID:23189060

Is central dogma a global property of cellular information flow?

PubMed

Piras, Vincent; Tomita, Masaru; Selvarajoo, Kumar

2012-01-01

The central dogma of molecular biology has come under scrutiny in recent years. Here, we reviewed high-throughput mRNA and protein expression data of Escherichia coli, Saccharomyces cerevisiae, and several mammalian cells. At both single cell and population scales, the statistical comparisons between the entire transcriptomes and proteomes show clear correlation structures. In contrast, the pair-wise correlations of single transcripts to proteins show nullity. These data suggest that the organizing structure guiding cellular processes is observed at omics-wide scale, and not at single molecule level. The central dogma, thus, globally emerges as an average integrated flow of cellular information.

The effect of design modifications to the typographical layout of the New York State elementary science learning standards on user preference and process time

NASA Astrophysics Data System (ADS)

Arnold, Jeffery E.

The purpose of this study was to determine the effect of four different design layouts of the New York State elementary science learning standards on user processing time and preference. Three newly developed layouts contained the same information as the standards core curriculum. In this study, the layout of the core guide is referred to as Book. The layouts of the new documents are referred to as Chart, Map, and Tabloid based on the format used to convey content hierarchy information. Most notably, all the new layouts feature larger page sizes, color, page tabs, and an icon based navigation system (IBNS). A convenience sample of 48 New York State educators representing three educator types (16 pre-service teachers, 16 in-service teachers, and 16 administrators) participated in the study. After completing timed tasks accurately, participants scored each layout based on preference. Educator type and layout were the independent variables, and process time and user preference were the dependent variables. A two-factor experimental design with Educator Type as the between variable and with repeated measures on Layout, the within variable, showed a significant difference in process time for Educator Type and Layout. The main effect for Educator Type (F(2, 45) = 8.03, p <.001) was significant with an observed power of .94, and an effect size of .26. The pair-wise comparisons for process time showed that pre-service teachers (p = .02) and administrators (p =.009) completed the assigned tasks more quickly when compared to in-service teachers. The main effect for Layout (F(3, 135) = 4.47, p =.01) was also significant with an observed power of .80, and an effect size of .09. Pair-wise comparisons showed that the newly developed Chart (p = .019) and Map (p = .032) layouts reduced overall process time when compared to the existing state learning standards (Book). The Layout X Educator type interaction was not significant. The same two-factor experimental design on preference, showed the main effect for Layout (F(3, 135) = 28.43, p =.001) was significant. The observed power was 1.0, with an effect size of .39. Pair-wise comparisons for preference scores showed that the Chart (p = .001), Map (p = .001), and Tabloid (p = .001) were preferred over the Book layout. The Layout Type X Educator Type interaction and the main effect for Educator Type were not significant. This study provides evidence that the newly developed design layouts improve usability (as measured by process time and preference scores) of the New York State elementary science learning standard documents. Features in the new layout design, such as the IBNS, may provide a foundation for a visual language and aid users in navigating standard documents across grade level and subject areas. Implications for the next generation of standard documents are presented.

Design and implementation of a hybrid MPI-CUDA model for the Smith-Waterman algorithm.

PubMed

Khaled, Heba; Faheem, Hossam El Deen Mostafa; El Gohary, Rania

2015-01-01

This paper provides a novel hybrid model for solving the multiple pair-wise sequence alignment problem combining message passing interface and CUDA, the parallel computing platform and programming model invented by NVIDIA. The proposed model targets homogeneous cluster nodes equipped with similar Graphical Processing Unit (GPU) cards. The model consists of the Master Node Dispatcher (MND) and the Worker GPU Nodes (WGN). The MND distributes the workload among the cluster working nodes and then aggregates the results. The WGN performs the multiple pair-wise sequence alignments using the Smith-Waterman algorithm. We also propose a modified implementation to the Smith-Waterman algorithm based on computing the alignment matrices row-wise. The experimental results demonstrate a considerable reduction in the running time by increasing the number of the working GPU nodes. The proposed model achieved a performance of about 12 Giga cell updates per second when we tested against the SWISS-PROT protein knowledge base running on four nodes.

C–IBI: Targeting cumulative coordination within an iterative protocol to derive coarse-grained models of (multi-component) complex fluids

DOE PAGES

de Oliveira, Tiago E.; Netz, Paulo A.; Kremer, Kurt; ...

2016-05-03

We present a coarse-graining strategy that we test for aqueous mixtures. The method uses pair-wise cumulative coordination as a target function within an iterative Boltzmann inversion (IBI) like protocol. We name this method coordination iterative Boltzmann inversion (C–IBI). While the underlying coarse-grained model is still structure based and, thus, preserves pair-wise solution structure, our method also reproduces solvation thermodynamics of binary and/or ternary mixtures. In addition, we observe much faster convergence within C–IBI compared to IBI. To validate the robustness, we apply C–IBI to study test cases of solvation thermodynamics of aqueous urea and a triglycine solvation in aqueous urea.

Broadband continuous wave source localization via pair-wise, cochleagram processing

NASA Astrophysics Data System (ADS)

Nosal, Eva-Marie; Frazer, L. Neil

2005-04-01

A pair-wise processor has been developed for the passive localization of broadband continuous-wave underwater sources. The algorithm uses sparse hydrophone arrays and does not require previous knowledge of the source signature. It is applicable in multiple source situations. A spectrogram/cochleagram version of the algorithm has been developed in order to utilize higher frequencies at longer ranges where signal incoherence, and limited computational resources, preclude the use of full waveforms. Simulations demonstrating the robustness of the algorithm with respect to noise and environmental mismatch will be presented, together with initial results from the analysis of humpback whale song recorded at the Pacific Missile Range Facility off Kauai. [Work supported by MHPCC and ONR.

Preliminary Assessment of Detection Efficiency for the Geostationary Lightning Mapper Using Intercomparisons with Ground-Based Systems

NASA Technical Reports Server (NTRS)

Bateman, Monte; Mach, Douglas; Blakeslee, Richard J.; Koshak, William

2018-01-01

As part of the calibration/validation (cal/val) effort for the Geostationary Lightning Mapper (GLM) on GOES-16, we need to assess instrument performance (detection efficiency and accuracy). One major effort is to calculate the detection efficiency of GLM by comparing to multiple ground-based systems. These comparisons will be done pair-wise between GLM and each other source. A complication in this process is that the ground-based systems sense different properties of the lightning signal than does GLM (e.g., RF vs. optical). Also, each system has a different time and space resolution and accuracy. Preliminary results indicate that GLM is performing at or above its specification.

Divergent ancestral lineages of newfound hantaviruses harbored by phylogenetically related crocidurine shrew species in Korea

PubMed Central

Arai, Satoru; Gu, Se Hun; Baek, Luck Ju; Tabara, Kenji; Bennett, Shannon; Oh, Hong-Shik; Takada, Nobuhiro; Kang, Hae Ji; Tanaka-Taya, Keiko; Morikawa, Shigeru; Okabe, Nobuhiko; Yanagihara, Richard; Song, Jin-Won

2012-01-01

Spurred by the recent isolation of a novel hantavirus, named Imjin virus (MJNV), from the Ussuri white-toothed shrew (Crocidura lasiura), targeted trapping was conducted for the phylogenetically related Asian lesser white-toothed shrew (Crocidura shantungensis). Pair-wise alignment and comparison of the S, M and L segments of a newfound hantavirus, designated Jeju virus (JJUV), indicated remarkably low nucleotide and amino acid sequence similarity with MJNV. Phylogenetic analyses, using maximum likelihood and Bayesian methods, showed divergent ancestral lineages for JJUV and MJNV, despite the close phylogenetic relationship of their reservoir soricid hosts. Also, no evidence of host switching was apparent in tanglegrams, generated by TreeMap 2.0β. PMID:22230701

Cardiovascular Risk with Non-Steroidal Anti-Inflammatory Drugs: Systematic Review of Population-Based Controlled Observational Studies

PubMed Central

McGettigan, Patricia; Henry, David

2011-01-01

Background Randomised trials have highlighted the cardiovascular risks of non-steroidal anti-inflammatory drugs (NSAIDs) in high doses and sometimes atypical settings. Here, we provide estimates of the comparative risks with individual NSAIDs at typical doses in community settings. Methods and Findings We performed a systematic review of community-based controlled observational studies. We conducted comprehensive literature searches, extracted adjusted relative risk (RR) estimates, and pooled the estimates for major cardiovascular events associated with use of individual NSAIDs, in different doses, and in populations with low and high background risks of cardiovascular events. We also compared individual drugs in pair-wise (within study) analyses, generating ratios of RRs (RRRs). Thirty case-control studies included 184,946 cardiovascular events, and 21 cohort studies described outcomes in >2.7 million exposed individuals. Of the extensively studied drugs (ten or more studies), the highest overall risks were seen with rofecoxib, 1.45 (95% CI 1.33, 1.59), and diclofenac, 1.40 (1.27, 1.55), and the lowest with ibuprofen, 1.18 (1.11, 1.25), and naproxen, 1.09 (1.02, 1.16). In a sub-set of studies, risk was elevated with low doses of rofecoxib, 1.37 (1.20, 1.57), celecoxib, 1.26 (1.09, 1.47), and diclofenac, 1.22 (1.12, 1.33), and rose in each case with higher doses. Ibuprofen risk was seen only with higher doses. Naproxen was risk-neutral at all doses. Of the less studied drugs etoricoxib, 2.05 (1.45, 2.88), etodolac, 1.55 (1.28, 1.87), and indomethacin, 1.30 (1.19, 1.41), had the highest risks. In pair-wise comparisons, etoricoxib had a higher RR than ibuprofen, RRR = 1.68 (99% CI 1.14, 2.49), and naproxen, RRR = 1.75 (1.16, 2.64); etodolac was not significantly different from naproxen and ibuprofen. Naproxen had a significantly lower risk than ibuprofen, RRR = 0.92 (0.87, 0.99). RR estimates were constant with different background risks for cardiovascular disease and rose early in the course of treatment. Conclusions This review suggests that among widely used NSAIDs, naproxen and low-dose ibuprofen are least likely to increase cardiovascular risk. Diclofenac in doses available without prescription elevates risk. The data for etoricoxib were sparse, but in pair-wise comparisons this drug had a significantly higher RR than naproxen or ibuprofen. Indomethacin is an older, rather toxic drug, and the evidence on cardiovascular risk casts doubt on its continued clinical use. Please see later in the article for the Editors' Summary PMID:21980265

Evaluation of the Wise Guys Male Responsibility Curriculum: Participant-Control Comparisons

ERIC Educational Resources Information Center

Gruchow, Harvey William; Brown, Roger K.

2011-01-01

Background: Although males are often the initiators of teen sexual activity, pregnancy prevention programs generally target females. To address this deficiency, the Wise Guys Male Responsibility Curriculum was developed to be delivered to adolescent males in weekly classroom sessions. Methods: Seventh grade participants (n = 124) in the Wise Guys…

Geographic Profiling to Assess the Risk of Rare Plant Poaching in Natural Areas

NASA Astrophysics Data System (ADS)

Young, John A.; van Manen, Frank T.; Thatcher, Cindy A.

2011-09-01

We demonstrate the use of an expert-assisted spatial model to examine geographic factors influencing the poaching risk of a rare plant (American ginseng, Panax quinquefolius L.) in Shenandoah National Park, Virginia, USA. Following principles of the analytic hierarchy process (AHP), we identified a hierarchy of 11 geographic factors deemed important to poaching risk and requested law enforcement personnel of the National Park Service to rank those factors in a series of pair-wise comparisons. We used those comparisons to determine statistical weightings of each factor and combined them into a spatial model predicting poaching risk. We tested the model using 69 locations of previous poaching incidents recorded by law enforcement personnel. These locations occurred more frequently in areas predicted by the model to have a higher risk of poaching than random locations. The results of our study can be used to evaluate resource protection strategies and to target law enforcement activities.

Mates but not sexes differ in migratory niche in a monogamous penguin species.

PubMed

Thiebot, Jean-Baptiste; Bost, Charles-André; Dehnhard, Nina; Demongin, Laurent; Eens, Marcel; Lepoint, Gilles; Cherel, Yves; Poisbleau, Maud

2015-09-01

Strong pair bonds generally increase fitness in monogamous organisms, but may also underlie the risk of hampering it when re-pairing fails after the winter season. We investigated whether partners would either maintain contact or offset this risk by exploiting sex-specific favourable niches during winter in a migratory monogamous seabird, the southern rockhopper penguin Eudyptes chrysocome. Using light-based geolocation, we show that although the spatial distribution of both sexes largely overlapped, pair-wise mates were located on average 595 ± 260 km (and up to 2500 km) apart during winter. Stable isotope data also indicated a marked overlap between sex-specific isotopic niches (δ¹³C and δ¹⁵N values) but a segregation of the feeding habitats (δ¹³C values) within pairs. Importantly, the tracked females remained longer (12 days) at sea than males, but all re-mated with their previous partners after winter. Our study provides multiple evidence that migratory species may well demonstrate pair-wise segregation even in the absence of sex-specific winter niches (spatial and isotopic). We suggest that dispersive migration patterns with sex-biased timings may be a sufficient proximal cause for generating such a situation in migratory animals.

Comparison of CPP-ACP, Tri-Calcium Phosphate and Hydroxyapatite on Remineralization of Artificial Caries Like Lesions on Primary Enamel -An in vitro Study.

PubMed

Bajaj, Meghna; Poornima, P; Praveen, S; Nagaveni, N B; Roopa, K B; Neena, I E; Bharath, K P

To compare CPP-ACP, Tri-calcium phosphate and Hydroxyapatite on remineralization of artificial caries like lesions on primary enamel. Ten extracted Primary molars coated with nail varnish, leaving a window of 2×4 mm on buccal and lingual surface were immersed in demineralizing solution for 96 hours and sectioned longitudinally to obtain 40 sections (4 sections per tooth) and were randomly divided into 4 groups (A to D) n=10; Group A: negative control, Group B: CPP-ACP, Group C: Tri-calcium phosphate, Group D: Hydroxyapatite. Sections were subjected to pH cycling for 10 days and were evaluated by polarized light microscope before and after treatment. Intra group comparison of demineralization and remineralization was done by paired t-test. One way ANOVA was used for multiple group comparisons followed by post HOC TUKEY'S Test for group wise comparisons. Remineralization was found more with Group D followed by Group B, C and A. Hydroxyapatite showed better remineralization when compared to CPP-ACP and Tri-calcium phosphate.

Adjustment for reporting bias in network meta-analysis of antidepressant trials

PubMed Central

2012-01-01

Background Network meta-analysis (NMA), a generalization of conventional MA, allows for assessing the relative effectiveness of multiple interventions. Reporting bias is a major threat to the validity of MA and NMA. Numerous methods are available to assess the robustness of MA results to reporting bias. We aimed to extend such methods to NMA. Methods We introduced 2 adjustment models for Bayesian NMA. First, we extended a meta-regression model that allows the effect size to depend on its standard error. Second, we used a selection model that estimates the propensity of trial results being published and in which trials with lower propensity are weighted up in the NMA model. Both models rely on the assumption that biases are exchangeable across the network. We applied the models to 2 networks of placebo-controlled trials of 12 antidepressants, with 74 trials in the US Food and Drug Administration (FDA) database but only 51 with published results. NMA and adjustment models were used to estimate the effects of the 12 drugs relative to placebo, the 66 effect sizes for all possible pair-wise comparisons between drugs, probabilities of being the best drug and ranking of drugs. We compared the results from the 2 adjustment models applied to published data and NMAs of published data and NMAs of FDA data, considered as representing the totality of the data. Results Both adjustment models showed reduced estimated effects for the 12 drugs relative to the placebo as compared with NMA of published data. Pair-wise effect sizes between drugs, probabilities of being the best drug and ranking of drugs were modified. Estimated drug effects relative to the placebo from both adjustment models were corrected (i.e., similar to those from NMA of FDA data) for some drugs but not others, which resulted in differences in pair-wise effect sizes between drugs and ranking. Conclusions In this case study, adjustment models showed that NMA of published data was not robust to reporting bias and provided estimates closer to that of NMA of FDA data, although not optimal. The validity of such methods depends on the number of trials in the network and the assumption that conventional MAs in the network share a common mean bias mechanism. PMID:23016799

Impact of HealthWise South Africa on polydrug use and high-risk sexual behavior.

PubMed

Tibbits, Melissa K; Smith, Edward A; Caldwell, Linda L; Flisher, Alan J

2011-08-01

This study was designed to evaluate the efficacy of the HealthWise South Africa HIV and substance abuse prevention program at impacting adolescents' polydrug use and sexual risk behaviors. HealthWise is a school-based intervention designed to promote social-emotional skills, increase knowledge and refusal skills relevant to substance use and sexual behaviors, and encourage healthy free time activities. Four intervention schools in one township near Cape Town, South Africa were matched to five comparison schools (N = 4040). The sample included equal numbers of male and female participants (Mean age = 14.0). Multiple regression was used to assess the impact of HealthWise on the outcomes of interest. Findings suggest that among virgins at baseline (beginning of eighth grade) who had sex by Wave 5 (beginning of 10th grade), HealthWise youth were less likely than comparison youth to engage in two or more risk behaviors at last sex. Additionally, HealthWise was effective at slowing the onset of frequent polydrug use among non-users at baseline and slowing the increase in this outcome among all participants. Program effects were not found for lifetime sexual activity, condomless sex refusal and past-month polydrug use. These findings suggest that HealthWise is a promising approach to HIV and substance abuse prevention.

A water market simulator considering pair-wise trades between agents

NASA Astrophysics Data System (ADS)

Huskova, I.; Erfani, T.; Harou, J. J.

2012-04-01

In many basins in England no further water abstraction licences are available. Trading water between water rights holders has been recognized as a potentially effective and economically efficient strategy to mitigate increasing scarcity. A screening tool that could assess the potential for trade through realistic simulation of individual water rights holders would help assess the solution's potential contribution to local water management. We propose an optimisation-driven water market simulator that predicts pair-wise trade in a catchment and represents its interaction with natural hydrology and engineered infrastructure. A model is used to emulate licence-holders' willingness to engage in short-term trade transactions. In their simplest form agents are represented using an economic benefit function. The working hypothesis is that trading behaviour can be partially predicted based on differences in marginal values of water over space and time and estimates of transaction costs on pair-wise trades. We discuss the further possibility of embedding rules, norms and preferences of the different water user sectors to more realistically represent the behaviours, motives and constraints of individual licence holders. The potential benefits and limitations of such a social simulation (agent-based) approach is contrasted with our simulator where agents are driven by economic optimization. A case study based on the Dove River Basin (UK) demonstrates model inputs and outputs. The ability of the model to suggest impacts of water rights policy reforms on trading is discussed.

Expression of Wise in chick embryos.

PubMed

Shigetani, Y; Itasaki, N

2007-08-01

We have performed in situ hybridization to study the expression of Wise in early chick embryos. Wise expression is first detectable in the ectoderm at posterior levels of late neurula. As development proceeds, Wise expression is seen in specific patterns in the ectoderm of the trunk region, pharyngeal arches, limb buds, and feather buds. In addition to these areas, particular cartilages such as the ones in the maxillary process and limbs start to express Wise at the late pharyngula stage, and the expression in these cartilages becomes stronger than that in epidermal components at later stages. Importantly, Wise is expressed in regions where other signaling molecules such as Wnt, Bmp, and Shh are known to function in morphogenesis and differentiation. Direct comparisons of the expression of Wise and these genes are also demonstrated. (c) 2007 Wiley-Liss, Inc.

Abnormal functional network connectivity among resting-state networks in children with frontal lobe epilepsy.

PubMed

Widjaja, E; Zamyadi, M; Raybaud, C; Snead, O C; Smith, M L

2013-12-01

Epilepsy is considered a disorder of neural networks. The aims of this study were to assess functional connectivity within resting-state networks and functional network connectivity across resting-state networks by use of resting-state fMRI in children with frontal lobe epilepsy and to relate changes in resting-state networks with neuropsychological function. Fifteen patients with frontal lobe epilepsy and normal MR imaging and 14 healthy control subjects were recruited. Spatial independent component analysis was used to identify the resting-state networks, including frontal, attention, default mode network, sensorimotor, visual, and auditory networks. The Z-maps of resting-state networks were compared between patients and control subjects. The relation between abnormal connectivity and neuropsychological function was assessed. Correlations from all pair-wise combinations of independent components were performed for each group and compared between groups. The frontal network was the only network that showed reduced connectivity in patients relative to control subjects. The remaining 5 networks demonstrated both reduced and increased functional connectivity within resting-state networks in patients. There was a weak association between connectivity in frontal network and executive function (P = .029) and a significant association between sensorimotor network and fine motor function (P = .004). Control subjects had 79 pair-wise independent components that showed significant temporal coherence across all resting-state networks except for default mode network-auditory network. Patients had 66 pairs of independent components that showed significant temporal coherence across all resting-state networks. Group comparison showed reduced functional network connectivity between default mode network-attention, frontal-sensorimotor, and frontal-visual networks and increased functional network connectivity between frontal-attention, default mode network-sensorimotor, and frontal-visual networks in patients relative to control subjects. We found abnormal functional connectivity within and across resting-state networks in children with frontal lobe epilepsy. Impairment in functional connectivity was associated with impaired neuropsychological function.

WISE Beholds a Pair of Dancing Galaxies

NASA Image and Video Library

2011-01-13

This image from NASA Wide-Field Infrared Explorer features two stunning galaxies engaged in an intergalactic dance. The galaxies, Messier 81 and Messier 82, swept by each other a few hundred million years ago.

Numerical approach for finite volume three-body interaction

NASA Astrophysics Data System (ADS)

Guo, Peng; Gasparian, Vladimir

2018-01-01

In the present work, we study a numerical approach to one dimensional finite volume three-body interaction, the method is demonstrated by considering a toy model of three spinless particles interacting with pair-wise δ -function potentials. The numerical results are compared with the exact solutions of three spinless bosons interaction when the strength of short-range interactions are set equal for all pairs.

First-principles anharmonic quantum calculations for peptide spectroscopy: VSCF calculations and comparison with experiments.

PubMed

Roy, Tapta Kanchan; Sharma, Rahul; Gerber, R Benny

2016-01-21

First-principles quantum calculations for anharmonic vibrational spectroscopy of three protected dipeptides are carried out and compared with experimental data. Using hybrid HF/MP2 potentials, the Vibrational Self-Consistent Field with Second-Order Perturbation Correction (VSCF-PT2) algorithm is used to compute the spectra without any ad hoc scaling or fitting. All of the vibrational modes (135 for the largest system) are treated quantum mechanically and anharmonically using full pair-wise coupling potentials to represent the interaction between different modes. In the hybrid potential scheme the MP2 method is used for the harmonic part of the potential and a modified HF method is used for the anharmonic part. The overall agreement between computed spectra and experiment is very good and reveals different signatures for different conformers. This study shows that first-principles spectroscopic calculations of good accuracy are possible for dipeptides hence it opens possibilities for determination of dipeptide conformer structures by comparison of spectroscopic calculations with experiment.

Geographic profiling to assess the risk of rare plant poaching in natural areas

USGS Publications Warehouse

Young, J.A.; Van Manen, F.T.; Thatcher, C.A.

2011-01-01

We demonstrate the use of an expert-assisted spatial model to examine geographic factors influencing the poaching risk of a rare plant (American ginseng, Panax quinquefolius L.) in Shenandoah National Park, Virginia, USA. Following principles of the analytic hierarchy process (AHP), we identified a hierarchy of 11 geographic factors deemed important to poaching risk and requested law enforcement personnel of the National Park Service to rank those factors in a series of pair-wise comparisons. We used those comparisons to determine statistical weightings of each factor and combined them into a spatial model predicting poaching risk. We tested the model using 69 locations of previous poaching incidents recorded by law enforcement personnel. These locations occurred more frequently in areas predicted by the model to have a higher risk of poaching than random locations. The results of our study can be used to evaluate resource protection strategies and to target law enforcement activities. ?? Springer Science+Business Media, LLC (outside the USA) 2011.

DIALIGN P: fast pair-wise and multiple sequence alignment using parallel processors.

PubMed

Schmollinger, Martin; Nieselt, Kay; Kaufmann, Michael; Morgenstern, Burkhard

2004-09-09

Parallel computing is frequently used to speed up computationally expensive tasks in Bioinformatics. Herein, a parallel version of the multi-alignment program DIALIGN is introduced. We propose two ways of dividing the program into independent sub-routines that can be run on different processors: (a) pair-wise sequence alignments that are used as a first step to multiple alignment account for most of the CPU time in DIALIGN. Since alignments of different sequence pairs are completely independent of each other, they can be distributed to multiple processors without any effect on the resulting output alignments. (b) For alignments of large genomic sequences, we use a heuristics by splitting up sequences into sub-sequences based on a previously introduced anchored alignment procedure. For our test sequences, this combined approach reduces the program running time of DIALIGN by up to 97%. By distributing sub-routines to multiple processors, the running time of DIALIGN can be crucially improved. With these improvements, it is possible to apply the program in large-scale genomics and proteomics projects that were previously beyond its scope.

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

Kreuzer, Helen W.; West, Jason B.; Ehleringer, James

Seeds of the castor plant Ricinus communis, also known as castor beans, are of forensic interest because they are the source of the poison ricin. We have tested whether stable isotope ratios of castor seeds and ricin prepared by various methods can be used as a forensic signature. We collected over 300 castor seed samples from locations around the world and measured the C, N, O, and H stable isotope ratios of the whole seeds, oil, and three types of ricin preparations. Our results demonstrate that N isotope ratios can be used to correlate ricin prepared by any of thesemore » methods to source seeds. Further, stable isotope ratios distinguished >99% of crude and purified ricin protein samples in pair-wise comparison tests. Stable isotope ratios therefore constitute a valuable forensic signature for ricin preparations.« less

Functional connectivity analysis in resting state fMRI with echo-state networks and non-metric clustering for network structure recovery

NASA Astrophysics Data System (ADS)

Wismüller, Axel; DSouza, Adora M.; Abidin, Anas Z.; Wang, Xixi; Hobbs, Susan K.; Nagarajan, Mahesh B.

2015-03-01

Echo state networks (ESN) are recurrent neural networks where the hidden layer is replaced with a fixed reservoir of neurons. Unlike feed-forward networks, neuron training in ESN is restricted to the output neurons alone thereby providing a computational advantage. We demonstrate the use of such ESNs in our mutual connectivity analysis (MCA) framework for recovering the primary motor cortex network associated with hand movement from resting state functional MRI (fMRI) data. Such a framework consists of two steps - (1) defining a pair-wise affinity matrix between different pixel time series within the brain to characterize network activity and (2) recovering network components from the affinity matrix with non-metric clustering. Here, ESNs are used to evaluate pair-wise cross-estimation performance between pixel time series to create the affinity matrix, which is subsequently subject to non-metric clustering with the Louvain method. For comparison, the ground truth of the motor cortex network structure is established with a task-based fMRI sequence. Overlap between the primary motor cortex network recovered with our model free MCA approach and the ground truth was measured with the Dice coefficient. Our results show that network recovery with our proposed MCA approach is in close agreement with the ground truth. Such network recovery is achieved without requiring low-pass filtering of the time series ensembles prior to analysis, an fMRI preprocessing step that has courted controversy in recent years. Thus, we conclude our MCA framework can allow recovery and visualization of the underlying functionally connected networks in the brain on resting state fMRI.

Blood-Based Gene Expression Profiles Models for Classification of Subsyndromal Symptomatic Depression and Major Depressive Disorder

PubMed Central

Yu, Shunying; Yuan, Chengmei; Hong, Wu; Wang, Zuowei; Cui, Jian; Shi, Tieliu; Fang, Yiru

2012-01-01

Subsyndromal symptomatic depression (SSD) is a subtype of subthreshold depressive and also lead to significant psychosocial functional impairment as same as major depressive disorder (MDD). Several studies have suggested that SSD is a transitory phenomena in the depression spectrum and is thus considered a subtype of depression. However, the pathophysioloy of depression remain largely obscure and studies on SSD are limited. The present study compared the expression profile and made the classification with the leukocytes by using whole-genome cRNA microarrays among drug-free first-episode subjects with SSD, MDD, and matched controls (8 subjects in each group). Support vector machines (SVMs) were utilized for training and testing on candidate signature expression profiles from signature selection step. Firstly, we identified 63 differentially expressed SSD signatures in contrast to control (P< = 5.0E-4) and 30 differentially expressed MDD signatures in contrast to control, respectively. Then, 123 gene signatures were identified with significantly differential expression level between SSD and MDD. Secondly, in order to conduct priority selection for biomarkers for SSD and MDD together, we selected top gene signatures from each group of pair-wise comparison results, and merged the signatures together to generate better profiles used for clearly classify SSD and MDD sets in the same time. In details, we tried different combination of signatures from the three pair-wise compartmental results and finally determined 48 gene expression signatures with 100% accuracy. Our finding suggested that SSD and MDD did not exhibit the same expressed genome signature with peripheral blood leukocyte, and blood cell–derived RNA of these 48 gene models may have significant value for performing diagnostic functions and classifying SSD, MDD, and healthy controls. PMID:22348066

InfAcrOnt: calculating cross-ontology term similarities using information flow by a random walk.

PubMed

Cheng, Liang; Jiang, Yue; Ju, Hong; Sun, Jie; Peng, Jiajie; Zhou, Meng; Hu, Yang

2018-01-19

Since the establishment of the first biomedical ontology Gene Ontology (GO), the number of biomedical ontology has increased dramatically. Nowadays over 300 ontologies have been built including extensively used Disease Ontology (DO) and Human Phenotype Ontology (HPO). Because of the advantage of identifying novel relationships between terms, calculating similarity between ontology terms is one of the major tasks in this research area. Though similarities between terms within each ontology have been studied with in silico methods, term similarities across different ontologies were not investigated as deeply. The latest method took advantage of gene functional interaction network (GFIN) to explore such inter-ontology similarities of terms. However, it only used gene interactions and failed to make full use of the connectivity among gene nodes of the network. In addition, all existent methods are particularly designed for GO and their performances on the extended ontology community remain unknown. We proposed a method InfAcrOnt to infer similarities between terms across ontologies utilizing the entire GFIN. InfAcrOnt builds a term-gene-gene network which comprised ontology annotations and GFIN, and acquires similarities between terms across ontologies through modeling the information flow within the network by random walk. In our benchmark experiments on sub-ontologies of GO, InfAcrOnt achieves a high average area under the receiver operating characteristic curve (AUC) (0.9322 and 0.9309) and low standard deviations (1.8746e-6 and 3.0977e-6) in both human and yeast benchmark datasets exhibiting superior performance. Meanwhile, comparisons of InfAcrOnt results and prior knowledge on pair-wise DO-HPO terms and pair-wise DO-GO terms show high correlations. The experiment results show that InfAcrOnt significantly improves the performance of inferring similarities between terms across ontologies in benchmark set.

Measurements and modeling of flow structure in the wake of a low profile wishbone vortex generator

NASA Technical Reports Server (NTRS)

Wendt, B. J.; Hingst, W. R.

1994-01-01

The results of an experimental examination of the vortex structures shed from a low profile 'wishbone' generator are presented. The vortex generator height relative to the turbulent boundary layer was varied by testing two differently sized models. Measurements of the mean three-dimensional velocity field were conducted in cross-stream planes downstream of the vortex generators. In all cases, a counter-rotating vortex pair was observed. Individual vortices were characterized by three descriptors derived from the velocity data; circulation, peak vorticity, and cross-stream location of peak vorticity. Measurements in the cross plane at two axial locations behind the smaller wishbone characterize the downstream development of the vortex pairs. A single region of stream wise velocity deficit is shared by both vortex cores. This is in contrast to conventional generators, where each core coincides with a region of velocity deficit. The measured cross-stream velocities for each case are compared to an Oseen model with matching descriptors. The best comparison occurs with the data from the larger wishbone.

From micro-correlations to macro-correlations

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

Eliazar, Iddo, E-mail: iddo.eliazar@intel.com

2016-11-15

Random vectors with a symmetric correlation structure share a common value of pair-wise correlation between their different components. The symmetric correlation structure appears in a multitude of settings, e.g. mixture models. In a mixture model the components of the random vector are drawn independently from a general probability distribution that is determined by an underlying parameter, and the parameter itself is randomized. In this paper we study the overall correlation of high-dimensional random vectors with a symmetric correlation structure. Considering such a random vector, and terming its pair-wise correlation “micro-correlation”, we use an asymptotic analysis to derive the random vector’smore » “macro-correlation” : a score that takes values in the unit interval, and that quantifies the random vector’s overall correlation. The method of obtaining macro-correlations from micro-correlations is then applied to a diverse collection of frameworks that demonstrate the method’s wide applicability.« less

Genetic diversity analysis of Varronia curassavica Jacq. accessions using ISSR markers.

PubMed

Brito, F A; Nizio, D A C; Silva, A V C; Diniz, L E C; Rabbani, A R C; Arrigoni-Blank, M F; Alvares-Carvalho, S V; Figueira, G M; Montanari Júnior, I; Blank, A F

2016-09-02

Varronia curassavica Jacq. is a medicinal and aromatic plant from Brazil with significant economic importance. Studies on genetic diversity in active germplasm banks (AGB) are essential for conservation and breeding programs. The aim of this study was to analyze the genetic diversity of V. curassavica accessions of the AGB of Medicinal and Aromatic Plants of the Federal University of Sergipe (UFS), using inter-simple sequence repeat molecular markers. Twenty-four primers were tested, and 14 were polymorphic and informative, resulting in 149 bands with 97.98% polymorphism. The UPGMA dendrogram divided the accessions into Clusters I and II. Jaccard similarity coefficients for pair-wise comparisons of accessions ranged between 0.24 and 0.78. The pairs of accessions VCUR-001/VCUR-503, VCUR-001/VCUR-504, and VCUR-104/VCUR-501 showed relatively low similarity (0.24), and the pair of accessions VCUR-402/VCUR- 403 showed medium similarity (0.78). Twenty-eight accessions were divided into three distinct clusters, according to the STRUCTURE analysis. The genetic diversity of V. curassavica in the AGB of UFS is low to medium, and it requires expansion. Accession VCUR-802 is the most suitable for selection in breeding program of this species, since it clearly represents all of the diversity present in the AGB.

Life history traits in selfing versus outcrossing annuals: exploring the 'time-limitation' hypothesis for the fitness benefit of self-pollination

PubMed Central

Snell, Rebecca; Aarssen, Lonnie W

2005-01-01

Background Most self-pollinating plants are annuals. According to the 'time-limitation' hypothesis, this association between selfing and the annual life cycle has evolved as a consequence of strong r-selection, involving severe time-limitation for completing the life cycle. Under this model, selection from frequent density-independent mortality in ephemeral habitats minimizes time to flower maturation, with selfing as a trade-off, and / or selection minimizes the time between flower maturation and ovule fertilization, in which case selfing has a direct fitness benefit. Predictions arising from this hypothesis were evaluated using phylogenetically-independent contrasts of several life history traits in predominantly selfing versus outcrossing annuals from a data base of 118 species distributed across 14 families. Data for life history traits specifically related to maturation and pollination times were obtained by monitoring the start and completion of different stages of reproductive development in a greenhouse study of selfing and outcrossing annuals from an unbiased sample of 25 species involving five pair-wise family comparisons and four pair-wise genus comparisons. Results Selfing annuals in general had significantly shorter plant heights, smaller flowers, shorter bud development times, shorter flower longevity and smaller seed sizes compared with their outcrossing annual relatives. Age at first flower did not differ significantly between selfing and outcrossing annuals. Conclusions This is the first multi-species study to report these general life-history differences between selfers and outcrossers among annuals exclusively. The results are all explained more parsimoniously by selection associated with time-limitation than by selection associated with pollinator/mate limitation. The shorter bud development time reported here for selfing annuals is predicted explicitly by the time-limitation hypothesis for the fitness benefit of selfing (and not by the alternative 'reproductive assurance' hypothesis associated with pollinator/mate limitation). Support for the time-limitation hypothesis is also evident from published surveys: whereas selfers and outcrossers are about equally represented among annual species as a whole, selfers occur in much higher frequencies among the annual species found in two of the most severely time-limited habitats where flowering plants grow – deserts and cultivated habitats. PMID:15707481

Three-dimensional validation of the impact of the quantity of teeth or tooth parts on the morphological difference between twin dentitions.

PubMed

Franco, A; Willems, G; Couto Souza, P H; Coucke, W; Thevissen, P

2016-07-01

The number of teeth involved in cases of bite-mark analysis is generally fewer in comparison to the number of teeth available for cases of dental identification. This decreases the amount of information available and can hamper the distinction between bite suspects. The opposite is true in cases of dental identification and the assumption is that more teeth contribute to a higher degree of specificity and the possibility of identification in these cases. Despite being broadly accepted in forensic dentistry, this hypothesis has never been scientifically tested. The present study aims to assess the impact of the quantity of teeth or tooth parts on morphological differences in twin dentitions. A sample of 344 dental casts collected from 86 pairs of twins was used. The dental casts were digitized using an automated motion device (XCAD 3D® (XCADCAM Technology®, São Paulo, SP, Brazil) and were imported as three-dimensional dental model images (3D-DMI) in Geomagic Studio® (3D Systems®, Rock Hill, SC, USA) software package. Sub samples were established based on the quantity of teeth and tooth parts studied. Pair wise morphological comparisons between the corresponding twin siblings were established and quantified. Increasing the quantity of teeth and tooth parts resulted in an increase of morphological difference between twin dentitions. More evident differences were observed comparing anterior vs. entire dentitions (p < 0.05) and complete vs. partial anterior dentitions (p < 0.05). Dental identifications and bite-mark analysis must include all the possibly related dental information to reach optimal comparison outcomes.

Evaluation of a proposed method for representing drug terminology.

PubMed Central

Cimino, J. J.; McNamara, T. J.; Meredith, T.; Broverman, C. A.; Eckert, K. C.; Moore, M.; Tyree, D. J.

1999-01-01

In the absence of a single, standard, multipurpose terminology for representing medications, the HL7 Vocabulary Technical Committee has sought to develop a model for such terms in a way that will provide a unified method for representing them and supporting interoperability among various terminology systems. We evaluated the preliminary model by obtaining terms, represented in our model, from three leading vendors of pharmacy system knowledge bases. A total of 2303 terms were obtained, and 3982 pair-wise comparisons were possible. We found that the components of the term descriptions matched 68-87% of the time and that the overall descriptions matched 53% of the time. The evaluation has identified a number of areas in the model where more rigorous definitions will be needed in order to improve the matching rate. This paper discusses the implications of these results. PMID:10566318

Improvements in approaches to forecasting and evaluation techniques

NASA Astrophysics Data System (ADS)

Weatherhead, Elizabeth

2014-05-01

The US is embarking on an experiment to make significant and sustained improvements in weather forecasting. The effort stems from a series of community conversations that recognized the rapid advancements in observations, modeling and computing techniques in the academic, governmental and private sectors. The new directions and initial efforts will be summarized, including information on possibilities for international collaboration. Most new projects are scheduled to start in the last half of 2014. Several advancements include ensemble forecasting with global models, and new sharing of computing resources. Newly developed techniques for evaluating weather forecast models will be presented in detail. The approaches use statistical techniques that incorporate pair-wise comparisons of forecasts with observations and account for daily auto-correlation to assess appropriate uncertainty in forecast changes. Some of the new projects allow for international collaboration, particularly on the research components of the projects.

Application of probabilistic fiber-tracking method of MR imaging to measure impact of cranial irradiation on structural brain connectivity in children treated for medulloblastoma

NASA Astrophysics Data System (ADS)

Duncan, Elizabeth C.; Reddick, Wilburn E.; Glass, John O.; Hyun, Jung Won; Ji, Qing; Li, Yimei; Gajjar, Amar

2016-03-01

We applied a modified probabilistic fiber-tracking method for the extraction of fiber pathways to quantify decreased white matter integrity as a surrogate of structural loss in connectivity due to cranial radiation therapy (CRT) as treatment for pediatric medulloblastoma. Thirty subjects were examined (n=8 average-risk, n=22 high-risk) and the groups did not differ significantly in age at examination. The pathway analysis created a structural connectome focused on sub-networks within the central executive network (CEN) for comparison between baseline and post-CRT scans and for comparison between standard and high dose CRT. A paired-wise comparison of the connectivity between baseline and post-CRT scans showed the irradiation did have a significant detrimental impact on white matter integrity (decreased fractional anisotropy (FA) and decreased axial diffusivity (AX)) in most of the CEN sub-networks. Group comparisons of the change in the connectivity revealed that patients receiving high dose CRT experienced significant AX decreases in all sub-networks while the patients receiving standard dose CRT had relatively stable AX measures across time. This study on pediatric patients with medulloblastoma demonstrated the utility of this method to identify specific sub-networks within the developing brain affected by CRT.

Phenotypic covariance at species’ borders

PubMed Central

2013-01-01

Background Understanding the evolution of species limits is important in ecology, evolution, and conservation biology. Despite its likely importance in the evolution of these limits, little is known about phenotypic covariance in geographically marginal populations, and the degree to which it constrains, or facilitates, responses to selection. We investigated phenotypic covariance in morphological traits at species’ borders by comparing phenotypic covariance matrices (P), including the degree of shared structure, the distribution of strengths of pair-wise correlations between traits, the degree of morphological integration of traits, and the ranks of matricies, between central and marginal populations of three species-pairs of coral reef fishes. Results Greater structural differences in P were observed between populations close to range margins and conspecific populations toward range centres, than between pairs of conspecific populations that were both more centrally located within their ranges. Approximately 80% of all pair-wise trait correlations within populations were greater in the north, but these differences were unrelated to the position of the sampled population with respect to the geographic range of the species. Conclusions Neither the degree of morphological integration, nor ranks of P, indicated greater evolutionary constraint at range edges. Characteristics of P observed here provide no support for constraint contributing to the formation of these species’ borders, but may instead reflect structural change in P caused by selection or drift, and their potential to evolve in the future. PMID:23714580

Phenotypic covariance at species' borders.

PubMed

Caley, M Julian; Cripps, Edward; Game, Edward T

2013-05-28

Understanding the evolution of species limits is important in ecology, evolution, and conservation biology. Despite its likely importance in the evolution of these limits, little is known about phenotypic covariance in geographically marginal populations, and the degree to which it constrains, or facilitates, responses to selection. We investigated phenotypic covariance in morphological traits at species' borders by comparing phenotypic covariance matrices (P), including the degree of shared structure, the distribution of strengths of pair-wise correlations between traits, the degree of morphological integration of traits, and the ranks of matricies, between central and marginal populations of three species-pairs of coral reef fishes. Greater structural differences in P were observed between populations close to range margins and conspecific populations toward range centres, than between pairs of conspecific populations that were both more centrally located within their ranges. Approximately 80% of all pair-wise trait correlations within populations were greater in the north, but these differences were unrelated to the position of the sampled population with respect to the geographic range of the species. Neither the degree of morphological integration, nor ranks of P, indicated greater evolutionary constraint at range edges. Characteristics of P observed here provide no support for constraint contributing to the formation of these species' borders, but may instead reflect structural change in P caused by selection or drift, and their potential to evolve in the future.

The Functional Architecture of Visual Object Recognition

DTIC Science & Technology

1991-07-01

different forms of agnosia can provide clues to the representations underlying normal object recognition (Farah, 1990). For example, the pair-wise...patterns of deficit and sparing occur. In a review of 99 published cases of agnosia , the observed patterns of co- occurrence implicated two underlying

Communicating with sentences: A multi-word naming game model

NASA Astrophysics Data System (ADS)

Lou, Yang; Chen, Guanrong; Hu, Jianwei

2018-01-01

Naming game simulates the process of naming an object by a single word, in which a population of communicating agents can reach global consensus asymptotically through iteratively pair-wise conversations. We propose an extension of the single-word model to a multi-word naming game (MWNG), simulating the case of describing a complex object by a sentence (multiple words). Words are defined in categories, and then organized as sentences by combining them from different categories. We refer to a formatted combination of several words as a pattern. In such an MWNG, through a pair-wise conversation, it requires the hearer to achieve consensus with the speaker with respect to both every single word in the sentence as well as the sentence pattern, so as to guarantee the correct meaning of the saying; otherwise, they fail reaching consensus in the interaction. We validate the model in three typical topologies as the underlying communication network, and employ both conventional and man-designed patterns in performing the MWNG.

Graph Curvature for Differentiating Cancer Networks

PubMed Central

Sandhu, Romeil; Georgiou, Tryphon; Reznik, Ed; Zhu, Liangjia; Kolesov, Ivan; Senbabaoglu, Yasin; Tannenbaum, Allen

2015-01-01

Cellular interactions can be modeled as complex dynamical systems represented by weighted graphs. The functionality of such networks, including measures of robustness, reliability, performance, and efficiency, are intrinsically tied to the topology and geometry of the underlying graph. Utilizing recently proposed geometric notions of curvature on weighted graphs, we investigate the features of gene co-expression networks derived from large-scale genomic studies of cancer. We find that the curvature of these networks reliably distinguishes between cancer and normal samples, with cancer networks exhibiting higher curvature than their normal counterparts. We establish a quantitative relationship between our findings and prior investigations of network entropy. Furthermore, we demonstrate how our approach yields additional, non-trivial pair-wise (i.e. gene-gene) interactions which may be disrupted in cancer samples. The mathematical formulation of our approach yields an exact solution to calculating pair-wise changes in curvature which was computationally infeasible using prior methods. As such, our findings lay the foundation for an analytical approach to studying complex biological networks. PMID:26169480

GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution

PubMed Central

Kinjo, Akira R.; Nakamura, Haruki

2012-01-01

Comparison and classification of protein structures are fundamental means to understand protein functions. Due to the computational difficulty and the ever-increasing amount of structural data, however, it is in general not feasible to perform exhaustive all-against-all structure comparisons necessary for comprehensive classifications. To efficiently handle such situations, we have previously proposed a method, now called GIRAF. We herein describe further improvements in the GIRAF protein structure search and alignment method. The GIRAF method achieves extremely efficient search of similar structures of ligand binding sites of proteins by exploiting database indexing of structural features of local coordinate frames. In addition, it produces refined atom-wise alignments by iterative applications of the Hungarian method to the bipartite graph defined for a pair of superimposed structures. By combining the refined alignments based on different local coordinate frames, it is made possible to align structures involving domain movements. We provide detailed accounts for the database design, the search and alignment algorithms as well as some benchmark results. PMID:27493524

Use of environmental tobacco smoke constituents as markers for exposure

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

LaKind, J.S.; Jenkins, R.A.; Naiman, D.Q.

1999-06-01

The 16-City Study analyzed for gas-phase environmental tobacco smoke (ETS) constituents (nicotine, 3-ethenyl pyridine [3-EP], and myosmine) and for particulate-phase constituents (respirable particulate matter [RSP], ultraviolet-absorbing particulate matter [UVPM], fluorescing particulate matter [FPM], scopoletin, and solanesol). In this second of three articles, the authors discuss the merits of each constituent as a marker for ETS and report pair-wise comparisons of the markers. Neither nicotine nor UVPM were good predictors for RSP. However, nicotine and UVPM were good qualitative predictors of each other. Nicotine was correlated with other gas-phase constituents. Comparisons between UVPM and other particulate-phase constituents were performed. Its relationmore » with FPM was excellent, with UVPM approximately 1 1/2 times FPM. The correlation between UVPM and solanesol was good, but the relationship between the two was not linear. The relation between UVPM and scopoletin was not good, largely because of noise in the scopoletin measures around its limit of detection. The authors considered the relation between nicotine and saliva cotinine, a metabolite of nicotine. The two were highly correlated on the group level.« less

Inter-comparison of multiple statistically downscaled climate datasets for the Pacific Northwest, USA

PubMed Central

Jiang, Yueyang; Kim, John B.; Still, Christopher J.; Kerns, Becky K.; Kline, Jeffrey D.; Cunningham, Patrick G.

2018-01-01

Statistically downscaled climate data have been widely used to explore possible impacts of climate change in various fields of study. Although many studies have focused on characterizing differences in the downscaling methods, few studies have evaluated actual downscaled datasets being distributed publicly. Spatially focusing on the Pacific Northwest, we compare five statistically downscaled climate datasets distributed publicly in the US: ClimateNA, NASA NEX-DCP30, MACAv2-METDATA, MACAv2-LIVNEH and WorldClim. We compare the downscaled projections of climate change, and the associated observational data used as training data for downscaling. We map and quantify the variability among the datasets and characterize the spatio-temporal patterns of agreement and disagreement among the datasets. Pair-wise comparisons of datasets identify the coast and high-elevation areas as areas of disagreement for temperature. For precipitation, high-elevation areas, rainshadows and the dry, eastern portion of the study area have high dissimilarity among the datasets. By spatially aggregating the variability measures into watersheds, we develop guidance for selecting datasets within the Pacific Northwest climate change impact studies. PMID:29461513

Inter-comparison of multiple statistically downscaled climate datasets for the Pacific Northwest, USA.

PubMed

Jiang, Yueyang; Kim, John B; Still, Christopher J; Kerns, Becky K; Kline, Jeffrey D; Cunningham, Patrick G

2018-02-20

Statistically downscaled climate data have been widely used to explore possible impacts of climate change in various fields of study. Although many studies have focused on characterizing differences in the downscaling methods, few studies have evaluated actual downscaled datasets being distributed publicly. Spatially focusing on the Pacific Northwest, we compare five statistically downscaled climate datasets distributed publicly in the US: ClimateNA, NASA NEX-DCP30, MACAv2-METDATA, MACAv2-LIVNEH and WorldClim. We compare the downscaled projections of climate change, and the associated observational data used as training data for downscaling. We map and quantify the variability among the datasets and characterize the spatio-temporal patterns of agreement and disagreement among the datasets. Pair-wise comparisons of datasets identify the coast and high-elevation areas as areas of disagreement for temperature. For precipitation, high-elevation areas, rainshadows and the dry, eastern portion of the study area have high dissimilarity among the datasets. By spatially aggregating the variability measures into watersheds, we develop guidance for selecting datasets within the Pacific Northwest climate change impact studies.

A spatial decision support system (SDSS) for sustainable tourism planning in Cameron Highlands, Malaysia

NASA Astrophysics Data System (ADS)

Aminu, M.; Matori, A. N.; Yusof, K. W.

2014-02-01

The study describes a methodological approach based on an integrated use of Geographic Information System (GIS) and Analytic Network Process (ANP) of Multi Criteria Evaluation (MCE) to determine nature conservation and tourism development priorities among the highland areas. A set of criteria and indicators were defined to evaluate the highlands biodiversity conservation and tourism development. Pair wise comparison technique was used in order to support solution of a decision problem by evaluating possible alternatives from different perspectives. After the weights have been derived from the pairwise comparison technique, the next step was to compute the unweighted supermatrix, weighted supermatrix and the limit matrix. The limit matrix was normalized to obtain the priorities and the results transferred into GIS environment. Elements evaluated and ranked were represented by criterion maps. Map layers reflecting the opinion of different experts involved were summed using the weighted overlay approach of GIS. Subsequently sustainable tourism development scenarios were generated. The generation of scenarios highlighted the critical issues of the decision problem because it allows one to gradually narrow down a problem.

The effect of fabric structure on the mechanical properties of warp knitted surgical mesh for hernia repair.

PubMed

Mirjavan, Mohammad; Asayesh, Azita; Asgharian Jeddi, Ali Asghar

2017-02-01

Surgical mesh is being used for healing hernia, pelvic organ prolapse, skull injuries and urinary incontinence. In this research the effect of fabric structure on the mechanical properties of warp knitted surgical meshes in comparison to abdominal fascia has been investigated. For this purpose, warp knitted surgical mesh with five different structures (Tricot, Pin-hole-net, quasi-Sandfly, Sandfly and quasi-Marquissite) were produced using polypropylene monofilament. Thereafter, their mechanical properties such as uniaxial tensile behavior in various directions (wale-wise (90°), course-wise (0°) and diagonal (45°)), bending resistance and crease recovery were analyzed. The meshes demonstrated different elastic modulus in various directions, which can be attributed to the pore shape (pore angle) and underlap angle in the structure of mesh. Except Pin-hole-net mesh, other produced meshes exhibited better level of orthotropy in comparison to abdominal fascia. The most flexible mesh in both wale-wise and course-wise directions was quasi-Sandfly and thereafter quasi-Marquissite. Tricot and Pin-hole-net manifested the highest crease recovery in wale-wise and coursewise directions respectively. The most desirable mesh in terms of porosity was quasi-Marquissite mesh. Overall, the quasi-Marquissite mesh was selected as the most suitable surgical mesh considering all advantages and disadvantages of each produced mesh in this study. Copyright © 2016 Elsevier Ltd. All rights reserved.

Robust group-wise rigid registration of point sets using t-mixture model

NASA Astrophysics Data System (ADS)

Ravikumar, Nishant; Gooya, Ali; Frangi, Alejandro F.; Taylor, Zeike A.

2016-03-01

A probabilistic framework for robust, group-wise rigid alignment of point-sets using a mixture of Students t-distribution especially when the point sets are of varying lengths, are corrupted by an unknown degree of outliers or in the presence of missing data. Medical images (in particular magnetic resonance (MR) images), their segmentations and consequently point-sets generated from these are highly susceptible to corruption by outliers. This poses a problem for robust correspondence estimation and accurate alignment of shapes, necessary for training statistical shape models (SSMs). To address these issues, this study proposes to use a t-mixture model (TMM), to approximate the underlying joint probability density of a group of similar shapes and align them to a common reference frame. The heavy-tailed nature of t-distributions provides a more robust registration framework in comparison to state of the art algorithms. Significant reduction in alignment errors is achieved in the presence of outliers, using the proposed TMM-based group-wise rigid registration method, in comparison to its Gaussian mixture model (GMM) counterparts. The proposed TMM-framework is compared with a group-wise variant of the well-known Coherent Point Drift (CPD) algorithm and two other group-wise methods using GMMs, using both synthetic and real data sets. Rigid alignment errors for groups of shapes are quantified using the Hausdorff distance (HD) and quadratic surface distance (QSD) metrics.

A Comparative Evaluation of the Linear Dimensional Accuracy of Four Impression Techniques using Polyether Impression Material.

PubMed

Manoj, Smita Sara; Cherian, K P; Chitre, Vidya; Aras, Meena

2013-12-01

There is much discussion in the dental literature regarding the superiority of one impression technique over the other using addition silicone impression material. However, there is inadequate information available on the accuracy of different impression techniques using polyether. The purpose of this study was to assess the linear dimensional accuracy of four impression techniques using polyether on a laboratory model that simulates clinical practice. The impression material used was Impregum Soft™, 3 M ESPE and the four impression techniques used were (1) Monophase impression technique using medium body impression material. (2) One step double mix impression technique using heavy body and light body impression materials simultaneously. (3) Two step double mix impression technique using a cellophane spacer (heavy body material used as a preliminary impression to create a wash space with a cellophane spacer, followed by the use of light body material). (4) Matrix impression using a matrix of polyether occlusal registration material. The matrix is loaded with heavy body material followed by a pick-up impression in medium body material. For each technique, thirty impressions were made of a stainless steel master model that contained three complete crown abutment preparations, which were used as the positive control. Accuracy was assessed by measuring eight dimensions (mesiodistal, faciolingual and inter-abutment) on stone dies poured from impressions of the master model. A two-tailed t test was carried out to test the significance in difference of the distances between the master model and the stone models. One way analysis of variance (ANOVA) was used for multiple group comparison followed by the Bonferroni's test for pair wise comparison. The accuracy was tested at α = 0.05. In general, polyether impression material produced stone dies that were smaller except for the dies produced from the one step double mix impression technique. The ANOVA revealed a highly significant difference for each dimension measured (except for the inter-abutment distance between the first and the second die) between any two groups of stone models obtained from the four impression techniques. Pair wise comparison for each measurement did not reveal any significant difference (except for the faciolingual distance of the third die) between the casts produced using the two step double mix impression technique and the matrix impression system. The two step double mix impression technique produced stone dies that showed the least dimensional variation. During fabrication of a cast restoration, laboratory procedures should not only compensate for the cement thickness, but also for the increase or decrease in die dimensions.

Optical coherence tomography-based decision making in exudative age-related macular degeneration: comparison of time- vs spectral-domain devices.

PubMed

Cukras, C; Wang, Y D; Meyerle, C B; Forooghian, F; Chew, E Y; Wong, W T

2010-05-01

To determine whether optical coherence tomography (OCT) device-type influences clinical grading of OCT imaging in the context of exudative age-related macular degeneration (AMD). Ninety-six paired OCT scans from 49 patients with active exudative AMD were obtained on both the time-domain Stratus OCT system and the spectral-domain Cirrus OCT system at the same visit. Three independent graders judged each scan for the presence of intraretinal fluid (IRF) or subretinal fluid (SRF). The degree of grader consensus was evaluated and the ability of the systems to detect the presence of disease activity was analysed. Cirrus OCT generated a higher degree of inter-grader consensus than Stratus OCT with higher intraclass correlation coefficients for all parameters analysed. A pair-wise comparison of Cirrus OCT with Stratus OCT systems revealed that Cirrus-based gradings more frequently reported the presence of SRF and IRF and detected overall neovascular activity at a higher rate (P<0.05) compared with Stratus-based gradings. The choice of time-domain (Stratus) vs spectra-domain (Cirrus) OCT systems has a measurable impact on clinical decision making in exudative AMD. Spectral-domain OCT systems may be able to generate more consensus in clinical interpretation and, in particular cases, detect disease activity not detected by time-domain systems. Clinical trials using OCT-based clinical evaluations of exudative AMD may need to account for these inter-system differences in planning and analysis.

Optical Coherence Tomography-Based Decision Making in Exudative Age-related Macular Degeneration: Comparison of Time- versus Spectral-Domain Devices

PubMed Central

Cukras, Catherine; Wang, Yunqing D.; Meyerle, Catherine B.; Forooghian, Farzin; Chew, Emily Y.; Wong, Wai T.

2010-01-01

Purpose To determine if optical coherence tomography (OCT) device-type influences clinical grading of OCT imaging in the context of exudative age-related macular degeneration (AMD). Methods Ninety-six paired OCT scans from 49 patients with active exudative AMD were obtained on both the time-domain Stratus™ OCT system and the spectral-domain Cirrus™ OCT system at the same visit. Three independent graders judged each scan for the presence of intraretinal fluid (IRF) or subretinal fluid (SRF). The degree of grader consensus was evaluated and the ability of the systems to detect the presence of disease activity was analyzed. Results Cirrus™ OCT generated a higher degree of inter-grader consensus than Stratus OCT with higher intraclass correlation coefficients (ICC) for all parameters analyzed. A pair-wise comparison of Cirrus™ OCT to Stratus™ OCT systems revealed that Cirrus™-based gradings more frequently reported the presence of SRF and IRF and detected overall neovascular activity at a higher rate (p<0.05) compared to Stratus™-based gradings Conclusions The choice of time-domain (Stratus™) versus spectra-domain (Cirrus™) OCT systems has a measurable impact on clinical decision making in exudative AMD. Spectral-domain OCT systems may be able to generate more consensus in clinical interpretation and, in particular cases, detect disease activity not detected by time-domain systems. Clinical trials employing OCT-based clinical evaluations of exudative AMD may need to account for these inter-system differences in planning and analysis. PMID:19696804

Comparison of predicted binders in Rhipicephalus (Boophilus) microplus intestine protein variants Bm86 Campo Grande strain, Bm86 and Bm95.

PubMed

Andreotti, Renato; Pedroso, Marisela S; Caetano, Alexandre R; Martins, Natália F

2008-01-01

This paper reports the sequence analysis of Bm86 Campo Grande strain comparing it with Bm86 and Bm95 antigens from the preparations TickGardPLUS and Gavac, respectively. The PCR product was cloned into pMOSBlue and sequenced. The secondary structure prediction tool PSIPRED was used to calculate alpha helices and beta strand contents of the predicted polypeptide. The hydrophobicity profile was calculated using the algorithms from the Hopp and Woods method, in addition to identification of potential MHC class-I binding regions in the antigens. Pair-wise alignment revealed that the similarity between Bm86 Campo Grande strain and Bm86 is 0.2% higher than that between Bm86 Campo Grande strain and Bm95 antigens. The identities were 96.5% and 96.3% respectively. Major suggestive differences in hydrophobicity were predicted among the sequences in two specific regions.

Surface Hold Advisor Using Critical Sections

NASA Technical Reports Server (NTRS)

Law, Caleb Hoi Kei (Inventor); Hsiao, Thomas Kun-Lung (Inventor); Mittler, Nathan C. (Inventor); Couluris, George J. (Inventor)

2013-01-01

The Surface Hold Advisor Using Critical Sections is a system and method for providing hold advisories to surface controllers to prevent gridlock and resolve crossing and merging conflicts among vehicles traversing a vertex-edge graph representing a surface traffic network on an airport surface. The Advisor performs pair-wise comparisons of current position and projected path of each vehicle with other surface vehicles to detect conflicts, determine critical sections, and provide hold advisories to traffic controllers recommending vehicles stop at entry points to protected zones around identified critical sections. A critical section defines a segment of the vertex-edge graph where vehicles are in crossing or merging or opposite direction gridlock contention. The Advisor detects critical sections without reference to scheduled, projected or required times along assigned vehicle paths, and generates hold advisories to prevent conflicts without requiring network path direction-of-movement rules and without requiring rerouting, rescheduling or other network optimization solutions.

Bayesian learning of visual chunks by human observers

PubMed Central

Orbán, Gergő; Fiser, József; Aslin, Richard N.; Lengyel, Máté

2008-01-01

Efficient and versatile processing of any hierarchically structured information requires a learning mechanism that combines lower-level features into higher-level chunks. We investigated this chunking mechanism in humans with a visual pattern-learning paradigm. We developed an ideal learner based on Bayesian model comparison that extracts and stores only those chunks of information that are minimally sufficient to encode a set of visual scenes. Our ideal Bayesian chunk learner not only reproduced the results of a large set of previous empirical findings in the domain of human pattern learning but also made a key prediction that we confirmed experimentally. In accordance with Bayesian learning but contrary to associative learning, human performance was well above chance when pair-wise statistics in the exemplars contained no relevant information. Thus, humans extract chunks from complex visual patterns by generating accurate yet economical representations and not by encoding the full correlational structure of the input. PMID:18268353

The Use of Weighted Graphs for Large-Scale Genome Analysis

PubMed Central

Zhou, Fang; Toivonen, Hannu; King, Ross D.

2014-01-01

There is an acute need for better tools to extract knowledge from the growing flood of sequence data. For example, thousands of complete genomes have been sequenced, and their metabolic networks inferred. Such data should enable a better understanding of evolution. However, most existing network analysis methods are based on pair-wise comparisons, and these do not scale to thousands of genomes. Here we propose the use of weighted graphs as a data structure to enable large-scale phylogenetic analysis of networks. We have developed three types of weighted graph for enzymes: taxonomic (these summarize phylogenetic importance), isoenzymatic (these summarize enzymatic variety/redundancy), and sequence-similarity (these summarize sequence conservation); and we applied these types of weighted graph to survey prokaryotic metabolism. To demonstrate the utility of this approach we have compared and contrasted the large-scale evolution of metabolism in Archaea and Eubacteria. Our results provide evidence for limits to the contingency of evolution. PMID:24619061

Insight On Colorectal Carcinoma Infiltration by Studying Perilesional Extracellular Matrix

PubMed Central

Nebuloni, Manuela; Albarello, Luca; Andolfo, Annapaola; Magagnotti, Cinzia; Genovese, Luca; Locatelli, Irene; Tonon, Giovanni; Longhi, Erika; Zerbi, Pietro; Allevi, Raffaele; Podestà, Alessandro; Puricelli, Luca; Milani, Paolo; Soldarini, Armando; Salonia, Andrea; Alfano, Massimo

2016-01-01

The extracellular matrix (ECM) from perilesional and colorectal carcinoma (CRC), but not healthy colon, sustains proliferation and invasion of tumor cells. We investigated the biochemical and physical diversity of ECM in pair-wised comparisons of healthy, perilesional and CRC specimens. Progressive linearization and degree of organization of fibrils was observed from healthy to perilesional and CRC ECM, and was associated with a steady increase of stiffness and collagen crosslinking. In the perilesional ECM these modifications coincided with increased vascularization, whereas in the neoplastic ECM they were associated with altered modulation of matrisome proteins, increased content of hydroxylated lysine and lysyl oxidase. This study identifies the increased stiffness and crosslinking of the perilesional ECM predisposing an environment suitable for CRC invasion as a phenomenon associated with vascularization. The increased stiffness of colon areas may represent a new predictive marker of desmoplastic region predisposing to invasion, thus offering new potential application for monitoring adenoma with invasive potential. PMID:26940881

Simplicity and Typical Rank Results for Three-Way Arrays

ERIC Educational Resources Information Center

ten Berge, Jos M. F.

2011-01-01

Matrices can be diagonalized by singular vectors or, when they are symmetric, by eigenvectors. Pairs of square matrices often admit simultaneous diagonalization, and always admit block wise simultaneous diagonalization. Generalizing these possibilities to more than two (non-square) matrices leads to methods of simplifying three-way arrays by…

A cross-sectional study of the temporal evolution of electricity consumption of six commercial buildings.

PubMed

Pickering, Ethan M; Hossain, Mohammad A; Mousseau, Jack P; Swanson, Rachel A; French, Roger H; Abramson, Alexis R

2017-01-01

Current approaches to building efficiency diagnoses include conventional energy audit techniques that can be expensive and time consuming. In contrast, virtual energy audits of readily available 15-minute-interval building electricity consumption are being explored to provide quick, inexpensive, and useful insights into building operation characteristics. A cross sectional analysis of six buildings in two different climate zones provides methods for data cleaning, population-based building comparisons, and relationships (correlations) of weather and electricity consumption. Data cleaning methods have been developed to categorize and appropriately filter or correct anomalous data including outliers, missing data, and erroneous values (resulting in < 0.5% anomalies). The utility of a cross-sectional analysis of a sample set of building's electricity consumption is found through comparisons of baseload, daily consumption variance, and energy use intensity. Correlations of weather and electricity consumption 15-minute interval datasets show important relationships for the heating and cooling seasons using computed correlations of a Time-Specific-Averaged-Ordered Variable (exterior temperature) and corresponding averaged variables (electricity consumption)(TSAOV method). The TSAOV method is unique as it introduces time of day as a third variable while also minimizing randomness in both correlated variables through averaging. This study found that many of the pair-wise linear correlation analyses lacked strong relationships, prompting the development of the new TSAOV method to uncover the causal relationship between electricity and weather. We conclude that a combination of varied HVAC system operations, building thermal mass, plug load use, and building set point temperatures are likely responsible for the poor correlations in the prior studies, while the correlation of time-specific-averaged-ordered temperature and corresponding averaged variables method developed herein adequately accounts for these issues and enables discovery of strong linear pair-wise correlation R values. TSAOV correlations lay the foundation for a new approach to building studies, that mitigates plug load interferences and identifies more accurate insights into weather-energy relationship for all building types. Over all six buildings analyzed the TSAOV method reported very significant average correlations per building of 0.94 to 0.82 in magnitude. Our rigorous statistics-based methods applied to 15-minute-interval electricity data further enables virtual energy audits of buildings to quickly and inexpensively inform energy savings measures.

A cross-sectional study of the temporal evolution of electricity consumption of six commercial buildings

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

Pickering, Ethan M.; Hossain, Mohammad A.; Mousseau, Jack P.

Current approaches to building efficiency diagnoses include conventional energy audit techniques that can be expensive and time consuming. In contrast, virtual energy audits of readily available 15-minute-interval building electricity consumption are being explored to provide quick, inexpensive, and useful insights into building operation characteristics. A cross sectional analysis of six buildings in two different climate zones provides methods for data cleaning, population-based building comparisons, and relationships (correlations) of weather and electricity consumption. Data cleaning methods have been developed to categorize and appropriately filter or correct anomalous data including outliers, missing data, and erroneous values (resulting in < 0.5% anomalies). Themore » utility of a cross-sectional analysis of a sample set of building's electricity consumption is found through comparisons of baseload, daily consumption variance, and energy use intensity. Correlations of weather and electricity consumption 15-minute interval datasets show important relationships for the heating and cooling seasons using computed correlations of a Time-Specific-Averaged- Ordered Variable (exterior temperature) and corresponding averaged variables (electricity consumption)(TSAOV method). The TSAOV method is unique as it introduces time of day as a third variable while also minimizing randomness in both correlated variables through averaging. This study found that many of the pair-wise linear correlation analyses lacked strong relationships, prompting the development of the new TSAOV method to uncover the causal relationship between electricity and weather. We conclude that a combination of varied HVAC system operations, building thermal mass, plug load use, and building set point temperatures are likely responsible for the poor correlations in the prior studies, while the correlation of time-specific-averaged-ordered temperature and corresponding averaged variables method developed herein adequately accounts for these issues and enables discovery of strong linear pair-wise correlation R values. TSAOV correlations lay the foundation for a new approach to building studies, that mitigates plug load interferences and identifies more accurate insights into weather-energy relationship for all building types. Over all six buildings analyzed the TSAOV method reported very significant average correlations per building of 0.94 to 0.82 in magnitude. Our rigorous statistics-based methods applied to 15- minute-interval electricity data further enables virtual energy audits of buildings to quickly and inexpensively inform energy savings measures.« less

A cross-sectional study of the temporal evolution of electricity consumption of six commercial buildings

DOE PAGES

Pickering, Ethan M.; Hossain, Mohammad A.; Mousseau, Jack P.; ...

2017-10-31

Current approaches to building efficiency diagnoses include conventional energy audit techniques that can be expensive and time consuming. In contrast, virtual energy audits of readily available 15-minute-interval building electricity consumption are being explored to provide quick, inexpensive, and useful insights into building operation characteristics. A cross sectional analysis of six buildings in two different climate zones provides methods for data cleaning, population-based building comparisons, and relationships (correlations) of weather and electricity consumption. Data cleaning methods have been developed to categorize and appropriately filter or correct anomalous data including outliers, missing data, and erroneous values (resulting in < 0.5% anomalies). Themore » utility of a cross-sectional analysis of a sample set of building's electricity consumption is found through comparisons of baseload, daily consumption variance, and energy use intensity. Correlations of weather and electricity consumption 15-minute interval datasets show important relationships for the heating and cooling seasons using computed correlations of a Time-Specific-Averaged- Ordered Variable (exterior temperature) and corresponding averaged variables (electricity consumption)(TSAOV method). The TSAOV method is unique as it introduces time of day as a third variable while also minimizing randomness in both correlated variables through averaging. This study found that many of the pair-wise linear correlation analyses lacked strong relationships, prompting the development of the new TSAOV method to uncover the causal relationship between electricity and weather. We conclude that a combination of varied HVAC system operations, building thermal mass, plug load use, and building set point temperatures are likely responsible for the poor correlations in the prior studies, while the correlation of time-specific-averaged-ordered temperature and corresponding averaged variables method developed herein adequately accounts for these issues and enables discovery of strong linear pair-wise correlation R values. TSAOV correlations lay the foundation for a new approach to building studies, that mitigates plug load interferences and identifies more accurate insights into weather-energy relationship for all building types. Over all six buildings analyzed the TSAOV method reported very significant average correlations per building of 0.94 to 0.82 in magnitude. Our rigorous statistics-based methods applied to 15- minute-interval electricity data further enables virtual energy audits of buildings to quickly and inexpensively inform energy savings measures.« less

A cross-sectional study of the temporal evolution of electricity consumption of six commercial buildings

PubMed Central

Hossain, Mohammad A.; Mousseau, Jack P.; Swanson, Rachel A.; French, Roger H.; Abramson, Alexis R.

2017-01-01

Current approaches to building efficiency diagnoses include conventional energy audit techniques that can be expensive and time consuming. In contrast, virtual energy audits of readily available 15-minute-interval building electricity consumption are being explored to provide quick, inexpensive, and useful insights into building operation characteristics. A cross sectional analysis of six buildings in two different climate zones provides methods for data cleaning, population-based building comparisons, and relationships (correlations) of weather and electricity consumption. Data cleaning methods have been developed to categorize and appropriately filter or correct anomalous data including outliers, missing data, and erroneous values (resulting in < 0.5% anomalies). The utility of a cross-sectional analysis of a sample set of building’s electricity consumption is found through comparisons of baseload, daily consumption variance, and energy use intensity. Correlations of weather and electricity consumption 15-minute interval datasets show important relationships for the heating and cooling seasons using computed correlations of a Time-Specific-Averaged-Ordered Variable (exterior temperature) and corresponding averaged variables (electricity consumption)(TSAOV method). The TSAOV method is unique as it introduces time of day as a third variable while also minimizing randomness in both correlated variables through averaging. This study found that many of the pair-wise linear correlation analyses lacked strong relationships, prompting the development of the new TSAOV method to uncover the causal relationship between electricity and weather. We conclude that a combination of varied HVAC system operations, building thermal mass, plug load use, and building set point temperatures are likely responsible for the poor correlations in the prior studies, while the correlation of time-specific-averaged-ordered temperature and corresponding averaged variables method developed herein adequately accounts for these issues and enables discovery of strong linear pair-wise correlation R values. TSAOV correlations lay the foundation for a new approach to building studies, that mitigates plug load interferences and identifies more accurate insights into weather-energy relationship for all building types. Over all six buildings analyzed the TSAOV method reported very significant average correlations per building of 0.94 to 0.82 in magnitude. Our rigorous statistics-based methods applied to 15-minute-interval electricity data further enables virtual energy audits of buildings to quickly and inexpensively inform energy savings measures. PMID:29088269

Social Experience Is Sufficient to Modulate Sleep Need of Drosophila without Increasing Wakefulness.

PubMed

Lone, Shahnaz Rahman; Potdar, Sheetal; Srivastava, Manishi; Sharma, Vijay Kumar

2016-01-01

Organisms quickly learn about their surroundings and display synaptic plasticity which is thought to be critical for their survival. For example, fruit flies Drosophila melanogaster exposed to highly enriched social environment are found to show increased synaptic connections and a corresponding increase in sleep. Here we asked if social environment comprising a pair of same-sex individuals could enhance sleep in the participating individuals. To study this, we maintained individuals of D. melanogaster in same-sex pairs for a period of 1 to 4 days, and after separation, monitored sleep of the previously socialized and solitary individuals under similar conditions. Males maintained in pairs for 3 or more days were found to sleep significantly more during daytime and showed a tendency to fall asleep sooner as compared to solitary controls (both measures together are henceforth referred to as "sleep-enhancement"). This sleep phenotype is not strain-specific as it is observed in males from three different "wild type" strains of D. melanogaster. Previous studies on social interaction mediated sleep-enhancement presumed 'waking experience' during the interaction to be the primary underlying cause; however, we found sleep-enhancement to occur without any significant increase in wakefulness. Furthermore, while sleep-enhancement due to group-wise social interaction requires Pigment Dispersing Factor (PDF) positive neurons; PDF positive and CRYPTOCHROME (CRY) positive circadian clock neurons and the core circadian clock genes are not required for sleep-enhancement to occur when males interact in pairs. Pair-wise social interaction mediated sleep-enhancement requires dopamine and olfactory signaling, while visual and gustatory signaling systems seem to be dispensable. These results suggest that socialization alone (without any change in wakefulness) is sufficient to cause sleep-enhancement in fruit fly D. melanogaster males, and that its neuronal control is context-specific.

Moment Preserving Adaptive Particle Weights using Octree Velocity Distributions for PIC Simulations

DTIC Science & Technology

2012-07-01

with prevention of runaway computational costs. The standard approach of merging of particles[1] using pair-wise coalescence (2:1 ratio), cannot...approximately 2:1. This is lower than 5.5:1 because, in each of the eight children cells, the number of particles ranges between 0- 11 rather than being

Effect of congenital blindness on the semantic representation of some everyday concepts.

PubMed

Connolly, Andrew C; Gleitman, Lila R; Thompson-Schill, Sharon L

2007-05-15

This study explores how the lack of first-hand experience with color, as a result of congenital blindness, affects implicit judgments about "higher-order" concepts, such as "fruits and vegetables" (FV), but not others, such as "household items" (HHI). We demonstrate how the differential diagnosticity of color across our test categories interacts with visual experience to produce, in effect, a category-specific difference in implicit similarity. Implicit pair-wise similarity judgments were collected by using an odd-man-out triad task. Pair-wise similarities for both FV and for HHI were derived from this task and were compared by using cluster analysis and regression analyses. Color was found to be a significant component in the structure of implicit similarity for FV for sighted participants but not for blind participants; and this pattern remained even when the analysis was restricted to blind participants who had good explicit color knowledge of the stimulus items. There was also no evidence that either subject group used color knowledge in making decisions about HHI, nor was there an indication of any qualitative differences between blind and sighted subjects' judgments on HHI.

Whole Protein Native Fitness Potentials

NASA Astrophysics Data System (ADS)

Faraggi, Eshel; Kloczkowski, Andrzej

2013-03-01

Protein structure prediction can be separated into two tasks: sample the configuration space of the protein chain, and assign a fitness between these hypothetical models and the native structure of the protein. One of the more promising developments in this area is that of knowledge based energy functions. However, standard approaches using pair-wise interactions have shown shortcomings demonstrated by the superiority of multi-body-potentials. These shortcomings are due to residue pair-wise interaction being dependent on other residues along the chain. We developed a method that uses whole protein information filtered through machine learners to score protein models based on their likeness to native structures. For all models we calculated parameters associated with the distance to the solvent and with distances between residues. These parameters, in addition to energy estimates obtained by using a four-body-potential, DFIRE, and RWPlus were used as training for machine learners to predict the fitness of the models. Testing on CASP 9 targets showed that our method is superior to DFIRE, RWPlus, and the four-body potential, which are considered standards in the field.

Development and preliminary psychometric properties of a well-being index for medical students.

PubMed

Dyrbye, Liselotte N; Szydlo, Daniel W; Downing, Steven M; Sloan, Jeff A; Shanafelt, Tait D

2010-01-27

Psychological distress is common among medical students but manifests in a variety of forms. Currently, no brief, practical tool exists to simultaneously evaluate these domains of distress among medical students. The authors describe the development of a subject-reported assessment (Medical Student Well-Being Index, MSWBI) intended to screen for medical student distress across a variety of domains and examine its preliminary psychometric properties. Relevant domains of distress were identified, items generated, and a screening instrument formed using a process of literature review, nominal group technique, input from deans and medical students, and correlation analysis from previously administered assessments. Eleven experts judged the clarity, relevance, and representativeness of the items. A Content Validity Index (CVI) was calculated. Interrater agreement was assessed using pair-wise percent agreement adjusted for chance agreement. Data from 2248 medical students who completed the MSWBI along with validated full-length instruments assessing domains of interest was used to calculate reliability and explore internal structure validity. Burnout (emotional exhaustion and depersonalization), depression, mental quality of life (QOL), physical QOL, stress, and fatigue were domains identified for inclusion in the MSWBI. Six of 7 items received item CVI-relevance and CVI-representativeness of >or=0.82. Overall scale CVI-relevance and CVI-representativeness was 0.94 and 0.91. Overall pair-wise percent agreement between raters was >or=85% for clarity, relevance, and representativeness. Cronbach's alpha was 0.68. Item by item percent pair-wise agreements and Phi were low, suggesting little overlap between items. The majority of MSWBI items had a >or=74% sensitivity and specificity for detecting distress within the intended domain. The results of this study provide evidence of reliability and content-related validity of the MSWBI. Further research is needed to assess remaining psychometric properties and establish scores for which intervention is warranted.

Development and preliminary psychometric properties of a well-being index for medical students

PubMed Central

2010-01-01

Background Psychological distress is common among medical students but manifests in a variety of forms. Currently, no brief, practical tool exists to simultaneously evaluate these domains of distress among medical students. The authors describe the development of a subject-reported assessment (Medical Student Well-Being Index, MSWBI) intended to screen for medical student distress across a variety of domains and examine its preliminary psychometric properties. Methods Relevant domains of distress were identified, items generated, and a screening instrument formed using a process of literature review, nominal group technique, input from deans and medical students, and correlation analysis from previously administered assessments. Eleven experts judged the clarity, relevance, and representativeness of the items. A Content Validity Index (CVI) was calculated. Interrater agreement was assessed using pair-wise percent agreement adjusted for chance agreement. Data from 2248 medical students who completed the MSWBI along with validated full-length instruments assessing domains of interest was used to calculate reliability and explore internal structure validity. Results Burnout (emotional exhaustion and depersonalization), depression, mental quality of life (QOL), physical QOL, stress, and fatigue were domains identified for inclusion in the MSWBI. Six of 7 items received item CVI-relevance and CVI-representativeness of ≥0.82. Overall scale CVI-relevance and CVI-representativeness was 0.94 and 0.91. Overall pair-wise percent agreement between raters was ≥85% for clarity, relevance, and representativeness. Cronbach's alpha was 0.68. Item by item percent pair-wise agreements and Phi were low, suggesting little overlap between items. The majority of MSWBI items had a ≥74% sensitivity and specificity for detecting distress within the intended domain. Conclusions The results of this study provide evidence of reliability and content-related validity of the MSWBI. Further research is needed to assess remaining psychometric properties and establish scores for which intervention is warranted. PMID:20105312

Lunatimonas lonarensis gen. nov., sp. nov., a haloalkaline bacterium of the family Cyclobacteriaceae with nitrate reducing activity.

PubMed

Srinivas, T N R; Aditya, S; Bhumika, V; Kumar, P Anil

2014-02-01

Novel pinkish-orange pigmented, Gram-negative staining, half-moon shaped, non-motile, strictly aerobic strains designated AK24(T) and AK26 were isolated from water and sediment samples of Lonar Lake, Buldhana district, Maharahstra, India. Both strains were positive for oxidase, catalase and β-galactosidase activities. The predominant fatty acids were iso-C15:0 (41.5%), anteiso-C15:0 (9.7%), iso-C17:0 3OH (9.6%), iso-C17:1 ω9c (10.2%) and C16:1 ω7c/C16:1 ω6c/iso-C15:0 2OH (summed feature 3) (14.4%). The strains contained MK-7 as the major respiratory quinone, and phosphatidylethanolamine and five unidentified lipids as the polar lipids. Blast analysis of the 16S rRNA gene sequence of strain AK24(T) showed that it was closely related to Aquiflexum balticum, with a pair-wise sequence similarity of 91.6%, as well as to Fontibacter ferrireducens, Belliella baltica and Indibacter alkaliphilus (91.3, 91.2 and 91.2% pair-wise sequence similarity, respectively), but it only had between 88.6 and 91.0% pair-wise sequence similarity to the rest of the family members. The MALDI-TOF assay reported no significant similarities for AK24(T) and AK26, since they potentially represented a new species. A MALDI MSP dendrogram showed close similarity between the two strains, but they maintained a distance from their phylogenetic neighbors. The genome of AK24(T) showed the presence of heavy metal tolerance genes, including the genes providing resistance to arsenic, cadmium, cobalt and zinc. A cluster of heat shock resistance genes was also found in the genome. Two lantibiotic producing genes, LanR and LasB, were also found in the genome of AK24(T). Strains AK24(T) and AK26 were very closely related to each other with 99.5% pair-wise sequence similarity. Phylogenetic analysis indicated that the strains were members of the family Cyclobacteriaceae and they clustered with the genus Mariniradius, as well as with the genera Aquiflexum, Cecembia, Fontibacter, Indibacter, and Shivajiella. DNA-DNA hybridization between strains AK24(T) and AK26 showed a relatedness of 82% and their rep-PCR banding patterns were very similar. Based on data from the current polyphasic study, it is proposed that the isolates be placed in a new genus and species with the name Lunatimonas lonarensis gen. nov., sp. nov. The type strain of Lunatimonas lonarensis is AK24(T) (=JCM 18822(T)=MTCC 11627(T)). Copyright © 2013 Elsevier GmbH. All rights reserved.

Epistasis between neurochemical gene polymorphisms and risk for ADHD

PubMed Central

Segurado, Ricardo; Bellgrove, Mark A; Manconi, Francesca; Gill, Michael; Hawi, Ziarah

2011-01-01

A number of genes with function related to synaptic neurochemistry have been genetically associated with attention deficit/hyperactivity disorder. However, susceptibility to the development of common psychiatric disorders by single variants acting alone, can so far only explain a small proportion of the heritability of the phenotype. It has been postulated that the unexplained ‘dark heritability' may at least in part be due to epistatic effects, which may account for the small observed marginal associations, and the difficulties with replication of positive findings. We undertook a comprehensive exploration of pair-wise interactions between genetic variants in 24 candidate genic regions involved in monoaminergic catabolism, anabolism, release, re-uptake and signal transmission in a sample of 177 parent-affected child trios using a case-only design and a case–pseudocontrol design using conditional logistic regression. Marker-pairs thresholded on interaction odds ratio (OR) and P-value are presented. We detected a number of interaction ORs >4.0, including an interesting correlation between markers in the ADRA1B and DBH genes in affected individuals, and several further interesting but smaller effects. These effects are no larger than you would expect by chance under the assumption of independence of all pair-wise relations; however, independence is unlikely. Furthermore, the size of these effects is of interest and attempts to replicate these results in other samples are anticipated. PMID:21368917

Progression in disability and regional grey matter atrophy in relapsing-remitting multiple sclerosis.

PubMed

Hofstetter, Louis; Naegelin, Yvonne; Filli, Lukas; Kuster, Pascal; Traud, Stefan; Smieskova, Renata; Mueller-Lenke, Nicole; Kappos, Ludwig; Gass, Achim; Sprenger, Till; Penner, Iris-Katharina; Nichols, Thomas E; Vrenken, Hugo; Barkhof, Frederik; Polman, Chris; Radue, Ernst-Wilhelm; Borgwardt, Stefan J; Bendfeldt, Kerstin

2014-02-01

In multiple sclerosis (MS) regional grey matter (GM) atrophy has been associated with disability progression. The aim of this study was to compare regional GM volume changes in relapsing-remitting MS (RRMS) patients with progressive and stable disability, using voxel-based morphometry (VBM). We acquired baseline and 1-year follow-up 3-dimensional (3D) T1-weighted magnetic resonance imaging (MRI) data of RRMS patients, using two 1.5-Tesla scanners. Patients were matched pair-wise with respect to age, gender, disease duration, medication, scanner and baseline Expanded Disability Status Scale (EDSS) into 13 pairs, with either progressive EDSS (≥ 1 point change y(-1)) or stable EDSS, as well as into 29 pairs with either progressive Multiple Sclerosis Functional Composite (MSFC) at ≥ 0.25% decrease in y(-1) in any component, or stable MSFC. We analysed longitudinal regional differences in GM volumes in the progressive and stable EDSS and MSFC groups, respectively, using VBM. Significant GM volume reductions occurred in the right precuneus, in the progressive EDSS group. Differential between-group effects occurred in the right precuneus and in the postcentral gyrus. Further longitudinal GM volume reductions occurred in the right orbicular gyrus, in the progressive MSFC group, but no between-group differences were observed (non-stationary cluster-wise inference, all P(corrected) < 0.05). These results suggested a direct association of disability progression and regional GM atrophy in RRMS.

Tomato Expression Database (TED): a suite of data presentation and analysis tools

PubMed Central

Fei, Zhangjun; Tang, Xuemei; Alba, Rob; Giovannoni, James

2006-01-01

The Tomato Expression Database (TED) includes three integrated components. The Tomato Microarray Data Warehouse serves as a central repository for raw gene expression data derived from the public tomato cDNA microarray. In addition to expression data, TED stores experimental design and array information in compliance with the MIAME guidelines and provides web interfaces for researchers to retrieve data for their own analysis and use. The Tomato Microarray Expression Database contains normalized and processed microarray data for ten time points with nine pair-wise comparisons during fruit development and ripening in a normal tomato variety and nearly isogenic single gene mutants impacting fruit development and ripening. Finally, the Tomato Digital Expression Database contains raw and normalized digital expression (EST abundance) data derived from analysis of the complete public tomato EST collection containing >150 000 ESTs derived from 27 different non-normalized EST libraries. This last component also includes tools for the comparison of tomato and Arabidopsis digital expression data. A set of query interfaces and analysis, and visualization tools have been developed and incorporated into TED, which aid users in identifying and deciphering biologically important information from our datasets. TED can be accessed at . PMID:16381976

Tomato Expression Database (TED): a suite of data presentation and analysis tools.

PubMed

Fei, Zhangjun; Tang, Xuemei; Alba, Rob; Giovannoni, James

2006-01-01

The Tomato Expression Database (TED) includes three integrated components. The Tomato Microarray Data Warehouse serves as a central repository for raw gene expression data derived from the public tomato cDNA microarray. In addition to expression data, TED stores experimental design and array information in compliance with the MIAME guidelines and provides web interfaces for researchers to retrieve data for their own analysis and use. The Tomato Microarray Expression Database contains normalized and processed microarray data for ten time points with nine pair-wise comparisons during fruit development and ripening in a normal tomato variety and nearly isogenic single gene mutants impacting fruit development and ripening. Finally, the Tomato Digital Expression Database contains raw and normalized digital expression (EST abundance) data derived from analysis of the complete public tomato EST collection containing >150,000 ESTs derived from 27 different non-normalized EST libraries. This last component also includes tools for the comparison of tomato and Arabidopsis digital expression data. A set of query interfaces and analysis, and visualization tools have been developed and incorporated into TED, which aid users in identifying and deciphering biologically important information from our datasets. TED can be accessed at http://ted.bti.cornell.edu.

Evidence for Divergent Evolution of Growth Temperature Preference in Sympatric Saccharomyces Species

PubMed Central

Gonçalves, Paula; Valério, Elisabete; Correia, Cláudia; de Almeida, João M. G. C. F.; Sampaio, José Paulo

2011-01-01

The genus Saccharomyces currently includes eight species in addition to the model yeast Saccharomyces cerevisiae, most of which can be consistently isolated from tree bark and soil. We recently found sympatric pairs of Saccharomyces species, composed of one cryotolerant and one thermotolerant species in oak bark samples of various geographic origins. In order to contribute to explain the occurrence in sympatry of Saccharomyces species, we screened Saccharomyces genomic data for protein divergence that might be correlated to distinct growth temperature preferences of the species, using the dN/dS ratio as a measure of protein evolution rates and pair-wise species comparisons. In addition to proteins previously implicated in growth at suboptimal temperatures, we found that glycolytic enzymes were among the proteins exhibiting higher than expected divergence when one cryotolerant and one thermotolerant species are compared. By measuring glycolytic fluxes and glycolytic enzymatic activities in different species and at different temperatures, we subsequently show that the unusual divergence of glycolytic genes may be related to divergent evolution of the glycolytic pathway aligning its performance to the growth temperature profiles of the different species. In general, our results support the view that growth temperature preference is a trait that may have undergone divergent selection in the course of ecological speciation in Saccharomyces. PMID:21674061

Parallel Evolution of Larval Feeding Behavior, Morphology, and Habitat in the Snail-Kiling fly Genus Tetanocera

NASA Astrophysics Data System (ADS)

Chapman, E. G.; Foote, B. A.; Malukiewicz, J.; Hoeh, W. R.

2005-05-01

Sciomyzid larvae (Diptera: Acalyptratae) display a wide range of feeding behaviors, typically preying on a wide variety of gastropods. The genus Tetanocera is particularly interesting because its species occupy five larval feeding groups with each species' larvae living in one of two habitat types (aquatic or terrestrial). We constructed a molecular phylogeny for Tetanocera, estimated evolutionary transitions in larval feeding behaviors and habitats that occurred during Tetanocera phylogenesis, and investigated potential correlations among larval habitat and morphological characteristics. Approximately 3800 base pairs (both mitochondrial and nuclear) of sequence data were used to build the phylogeny. Larval feeding groups and habitat type were mapped onto the phylogeny and pair-wise comparisons were used to evaluate potential associations between habitat and morphology. Feeding and habitat groups within Tetanocera were usually not monophyletic and it was estimated that Tetanocera lineages made at least three independent aquatic to terrestrial transitions. These parallel habitat shifts were typically accompanied by parallel character state changes in four morphological characteristics (larval color and three posterior spiracular disc characters). These larval habitat-morphology associations were statistically significant and consistent with the action of natural selection in facilitating the morphological changes that occurred during aquatic to terrestrial habitat transitions in Tetanocera.

Restructurable VLSI Program

DTIC Science & Technology

1981-03-31

logic testing element and a concomitant testability criterion ideally suited to dynamic circuit applications and appro- priate for automatic computer...making connections automatically . PF is an experimental feature which provides users with only four different chip sizes (full, half, quarter, and eighth...initial solution is found constructively which is improved by pair-wise swapping. Results show, however, that the constructive initial sorter , which

Quality Matters: Extension of Clusters of Residues with Good Hydrophobic Contacts Stabilize (Hyper)Thermophilic Proteins

PubMed Central

2015-01-01

Identifying determinant(s) of protein thermostability is key for rational and data-driven protein engineering. By analyzing more than 130 pairs of mesophilic/(hyper)thermophilic proteins, we identified the quality (residue-wise energy) of hydrophobic interactions as a key factor for protein thermostability. This distinguishes our study from previous ones that investigated predominantly structural determinants. Considering this key factor, we successfully discriminated between pairs of mesophilic/(hyper)thermophilic proteins (discrimination accuracy: ∼80%) and searched for structural weak spots in E. coli dihydrofolate reductase (classification accuracy: 70%). PMID:24437522

[Influence of autoclave sterilization on dimensional stability and detail reproduction of 5 additional silicone impression materials].

PubMed

Xu, Tong-kai; Sun, Zhi-hui; Jiang, Yong

2012-03-01

To evaluate the dimensional stability and detail reproduction of five additional silicone impression materials after autoclave sterilization. Impressions were made on the ISO 4823 standard mold containing several marking lines, in five kinds of additional silicone. All the impressions were sterilized by high temperature and pressure (135 °C, 212.8 kPa) for 25 min. Linear measurements of pre-sterilization and post-sterilization were made with a measuring microscope. Statistical analysis utilized single-factor analysis with pair-wise comparison of mean values when appropriate. Hypothesis testing was conducted at alpha = 0.05. No significant difference was found between the pre-sterilization and post-sterilization conditions for all locations, and all the absolute valuse of linear rate of change less than 8%. All the sterilization by the autoclave did not affect the surfuce detail reproduction of the 5 impression materials. The dimensional stability and detail reproduction of the five additional silicone impression materials in the study was unaffected by autoclave sterilization.

Novel tetra-nucleotide microsatellite DNA markers for assessing the evolutionary genetics and demographics of Northern Snakehead (Channa argus) invading North America

USGS Publications Warehouse

King, Timothy L.; Johnson, Robin L.

2011-01-01

We document the isolation and characterization of 19 tetra-nucleotide microsatellite DNA markers in northern snakehead (Channa argus) fish that recently colonized Meadow Lake, New York City, New York. These markers displayed moderate levels of allelic diversity (averaging 6.8 alleles/locus) and heterozygosity (averaging 74.2%). Demographic analyses suggested that the Meadow Lake collection has not achieved mutation-drift equilibrium. These results were consistent with instances of deviations from Hardy–Weinberg equilibrium and the presence of some linkage disequilibrium. A comparison of individual pair-wise distances suggested the presence of multiple differentiated groups of related individuals. Results of all analyses are consistent with a pattern of multiple, recent introductions. The microsatellite markers developed for C. argus yielded sufficient genetic diversity to potentially: (1) delineate kinship; (2) elucidate fine-scale population structure; (3) define management (eradication) units; (4) estimate dispersal rates; (5) estimate population sizes; and (6) provide unique demographic perspectives of control or eradication effectiveness.

Performance metrics for the assessment of satellite data products: an ocean color case study

PubMed Central

Seegers, Bridget N.; Stumpf, Richard P.; Schaeffer, Blake A.; Loftin, Keith A.; Werdell, P. Jeremy

2018-01-01

Performance assessment of ocean color satellite data has generally relied on statistical metrics chosen for their common usage and the rationale for selecting certain metrics is infrequently explained. Commonly reported statistics based on mean squared errors, such as the coefficient of determination (r2), root mean square error, and regression slopes, are most appropriate for Gaussian distributions without outliers and, therefore, are often not ideal for ocean color algorithm performance assessment, which is often limited by sample availability. In contrast, metrics based on simple deviations, such as bias and mean absolute error, as well as pair-wise comparisons, often provide more robust and straightforward quantities for evaluating ocean color algorithms with non-Gaussian distributions and outliers. This study uses a SeaWiFS chlorophyll-a validation data set to demonstrate a framework for satellite data product assessment and recommends a multi-metric and user-dependent approach that can be applied within science, modeling, and resource management communities. PMID:29609296

Electric Field Reconstruction in the Image Plane of a High-Contrast Coronagraph Using a Set of Pinholes around the Lyot Plane

NASA Technical Reports Server (NTRS)

Giveona, Amir; Shaklan, Stuart; Kern, Brian; Noecker, Charley; Kendrick, Steve; Wallace, Kent

2012-01-01

In a setup similar to the self coherent camera, we have added a set of pinholes in the diffraction ring of the Lyot plane in a high-contrast stellar Lyot coronagraph. We describe a novel complex electric field reconstruction from image plane intensity measurements consisting of light in the coronagraph's dark hole interfering with light from the pinholes. The image plane field is modified by letting light through one pinhole at a time. In addition to estimation of the field at the science camera, this method allows for self-calibration of the probes by letting light through the pinholes in various permutations while blocking the main Lyot opening. We present results of estimation and calibration from the High Contrast Imaging Testbed along with a comparison to the pair-wise deformable mirror diversity based estimation technique. Tests are carried out in narrow-band light and over a composite 10% bandpass.

Pythagorean fuzzy analytic hierarchy process to multi-criteria decision making

NASA Astrophysics Data System (ADS)

Mohd, Wan Rosanisah Wan; Abdullah, Lazim

2017-11-01

A numerous approaches have been proposed in the literature to determine the criteria of weight. The weight of criteria is very significant in the process of decision making. One of the outstanding approaches that used to determine weight of criteria is analytic hierarchy process (AHP). This method involves decision makers (DMs) to evaluate the decision to form the pair-wise comparison between criteria and alternatives. In classical AHP, the linguistic variable of pairwise comparison is presented in terms of crisp value. However, this method is not appropriate to present the real situation of the problems because it involved the uncertainty in linguistic judgment. For this reason, AHP has been extended by incorporating the Pythagorean fuzzy sets. In addition, no one has found in the literature proposed how to determine the weight of criteria using AHP under Pythagorean fuzzy sets. In order to solve the MCDM problem, the Pythagorean fuzzy analytic hierarchy process is proposed to determine the criteria weight of the evaluation criteria. Using the linguistic variables, pairwise comparison for evaluation criteria are made to the weights of criteria using Pythagorean fuzzy numbers (PFNs). The proposed method is implemented in the evaluation problem in order to demonstrate its applicability. This study shows that the proposed method provides us with a useful way and a new direction in solving MCDM problems with Pythagorean fuzzy context.

Assessing compositional variability through graphical analysis and Bayesian statistical approaches: case studies on transgenic crops.

PubMed

Harrigan, George G; Harrison, Jay M

2012-01-01

New transgenic (GM) crops are subjected to extensive safety assessments that include compositional comparisons with conventional counterparts as a cornerstone of the process. The influence of germplasm, location, environment, and agronomic treatments on compositional variability is, however, often obscured in these pair-wise comparisons. Furthermore, classical statistical significance testing can often provide an incomplete and over-simplified summary of highly responsive variables such as crop composition. In order to more clearly describe the influence of the numerous sources of compositional variation we present an introduction to two alternative but complementary approaches to data analysis and interpretation. These include i) exploratory data analysis (EDA) with its emphasis on visualization and graphics-based approaches and ii) Bayesian statistical methodology that provides easily interpretable and meaningful evaluations of data in terms of probability distributions. The EDA case-studies include analyses of herbicide-tolerant GM soybean and insect-protected GM maize and soybean. Bayesian approaches are presented in an analysis of herbicide-tolerant GM soybean. Advantages of these approaches over classical frequentist significance testing include the more direct interpretation of results in terms of probabilities pertaining to quantities of interest and no confusion over the application of corrections for multiple comparisons. It is concluded that a standardized framework for these methodologies could provide specific advantages through enhanced clarity of presentation and interpretation in comparative assessments of crop composition.

Effect of congenital blindness on the semantic representation of some everyday concepts

PubMed Central

Connolly, Andrew C.; Gleitman, Lila R.; Thompson-Schill, Sharon L.

2007-01-01

This study explores how the lack of first-hand experience with color, as a result of congenital blindness, affects implicit judgments about “higher-order” concepts, such as “fruits and vegetables” (FV), but not others, such as “household items” (HHI). We demonstrate how the differential diagnosticity of color across our test categories interacts with visual experience to produce, in effect, a category-specific difference in implicit similarity. Implicit pair-wise similarity judgments were collected by using an odd-man-out triad task. Pair-wise similarities for both FV and for HHI were derived from this task and were compared by using cluster analysis and regression analyses. Color was found to be a significant component in the structure of implicit similarity for FV for sighted participants but not for blind participants; and this pattern remained even when the analysis was restricted to blind participants who had good explicit color knowledge of the stimulus items. There was also no evidence that either subject group used color knowledge in making decisions about HHI, nor was there an indication of any qualitative differences between blind and sighted subjects' judgments on HHI. PMID:17483447

New hypothesis elucidates self-incompatibility in the olive tree regarding S-alleles dominance relationships as in the sporophytic model.

PubMed

Breton, Catherine M; Bervillé, André

2012-09-01

Most olive varieties are not strictly self-incompatible, nevertheless, they request foreign pollen to enhance fruit yield, and consequently orchards should contain pollinisers to ensure fruit set of the main variety. The best way to choose pollinisers is to experiment numerous crosses in a diallel design. Here, the genetic mode of inheritance of SI in the olive is deciphered and it does not correspond to the GSI type, but to the SSI type. It leaves S-allele dominance relationship expression in the male (pollen and pollen tube), but not in the female (stigma and style). Thus, a pair-wise combination of varieties may be inter-compatible in one direction (male to female, or female to male) and inter-incompatible in the other direction. Dominance relationships also explain different levels of self-pollination observed in varieties. Little efficient pollinisers were found and predicted in varieties; nevertheless, some new efficient pair-wise allele combinations are predicted and could be created. This model enables one to forecast compatibility without waiting for several years of yield records and to choose pollinisers in silico. Copyright © 2012 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.

Analysis of the “naming game” with learning errors in communications

NASA Astrophysics Data System (ADS)

Lou, Yang; Chen, Guanrong

2015-07-01

Naming game simulates the process of naming an objective by a population of agents organized in a certain communication network. By pair-wise iterative interactions, the population reaches consensus asymptotically. We study naming game with communication errors during pair-wise conversations, with error rates in a uniform probability distribution. First, a model of naming game with learning errors in communications (NGLE) is proposed. Then, a strategy for agents to prevent learning errors is suggested. To that end, three typical topologies of communication networks, namely random-graph, small-world and scale-free networks, are employed to investigate the effects of various learning errors. Simulation results on these models show that 1) learning errors slightly affect the convergence speed but distinctively increase the requirement for memory of each agent during lexicon propagation; 2) the maximum number of different words held by the population increases linearly as the error rate increases; 3) without applying any strategy to eliminate learning errors, there is a threshold of the learning errors which impairs the convergence. The new findings may help to better understand the role of learning errors in naming game as well as in human language development from a network science perspective.

Strategies for informed sample size reduction in adaptive controlled clinical trials

NASA Astrophysics Data System (ADS)

Arandjelović, Ognjen

2017-12-01

Clinical trial adaptation refers to any adjustment of the trial protocol after the onset of the trial. The main goal is to make the process of introducing new medical interventions to patients more efficient. The principal challenge, which is an outstanding research problem, is to be found in the question of how adaptation should be performed so as to minimize the chance of distorting the outcome of the trial. In this paper, we propose a novel method for achieving this. Unlike most of the previously published work, our approach focuses on trial adaptation by sample size adjustment, i.e. by reducing the number of trial participants in a statistically informed manner. Our key idea is to select the sample subset for removal in a manner which minimizes the associated loss of information. We formalize this notion and describe three algorithms which approach the problem in different ways, respectively, using (i) repeated random draws, (ii) a genetic algorithm, and (iii) what we term pair-wise sample compatibilities. Experiments on simulated data demonstrate the effectiveness of all three approaches, with a consistently superior performance exhibited by the pair-wise sample compatibilities-based method.

Analysis of the "naming game" with learning errors in communications.

PubMed

Lou, Yang; Chen, Guanrong

2015-07-16

Naming game simulates the process of naming an objective by a population of agents organized in a certain communication network. By pair-wise iterative interactions, the population reaches consensus asymptotically. We study naming game with communication errors during pair-wise conversations, with error rates in a uniform probability distribution. First, a model of naming game with learning errors in communications (NGLE) is proposed. Then, a strategy for agents to prevent learning errors is suggested. To that end, three typical topologies of communication networks, namely random-graph, small-world and scale-free networks, are employed to investigate the effects of various learning errors. Simulation results on these models show that 1) learning errors slightly affect the convergence speed but distinctively increase the requirement for memory of each agent during lexicon propagation; 2) the maximum number of different words held by the population increases linearly as the error rate increases; 3) without applying any strategy to eliminate learning errors, there is a threshold of the learning errors which impairs the convergence. The new findings may help to better understand the role of learning errors in naming game as well as in human language development from a network science perspective.

Evaluation of body-wise and organ-wise registrations for abdominal organs

NASA Astrophysics Data System (ADS)

Xu, Zhoubing; Panjwani, Sahil A.; Lee, Christopher P.; Burke, Ryan P.; Baucom, Rebeccah B.; Poulose, Benjamin K.; Abramson, Richard G.; Landman, Bennett A.

2016-03-01

Identifying cross-sectional and longitudinal correspondence in the abdomen on computed tomography (CT) scans is necessary for quantitatively tracking change and understanding population characteristics, yet abdominal image registration is a challenging problem. The key difficulty in solving this problem is huge variations in organ dimensions and shapes across subjects. The current standard registration method uses the global or body-wise registration technique, which is based on the global topology for alignment. This method (although producing decent results) has substantial influence of outliers, thus leaving room for significant improvement. Here, we study a new image registration approach using local (organ-wise registration) by first creating organ-specific bounding boxes and then using these regions of interest (ROIs) for aligning references to target. Based on Dice Similarity Coefficient (DSC), Mean Surface Distance (MSD) and Hausdorff Distance (HD), the organ-wise approach is demonstrated to have significantly better results by minimizing the distorting effects of organ variations. This paper compares exclusively the two registration methods by providing novel quantitative and qualitative comparison data and is a subset of the more comprehensive problem of improving the multi-atlas segmentation by using organ normalization.

Detection of longitudinal visual field progression in glaucoma using machine learning.

PubMed

Yousefi, Siamak; Kiwaki, Taichi; Zheng, Yuhui; Suigara, Hiroki; Asaoka, Ryo; Murata, Hiroshi; Lemij, Hans; Yamanishi, Kenji

2018-06-16

Global indices of standard automated perimerty are insensitive to localized losses, while point-wise indices are sensitive but highly variable. Region-wise indices sit in between. This study introduces a machine-learning-based index for glaucoma progression detection that outperforms global, region-wise, and point-wise indices. Development and comparison of a prognostic index. Visual fields from 2085 eyes of 1214 subjects were used to identify glaucoma progression patterns using machine learning. Visual fields from 133 eyes of 71 glaucoma patients were collected 10 times over 10 weeks to provide a no-change, test-retest dataset. The parameters of all methods were identified using visual field sequences in the test-retest dataset to meet fixed 95% specificity. An independent dataset of 270 eyes of 136 glaucoma patients and survival analysis were utilized to compare methods. The time to detect progression in 25% of the eyes in the longitudinal dataset using global mean deviation (MD) was 5.2 years (95% confidence interval, 4.1 - 6.5 years); 4.5 years (4.0 - 5.5) using region-wise, 3.9 years (3.5 - 4.6) using point-wise, and 3.5 years (3.1 - 4.0) using machine learning analysis. The time until 25% of eyes showed subsequently confirmed progression after two additional visits were included were 6.6 years (5.6 - 7.4 years), 5.7 years (4.8 - 6.7), 5.6 years (4.7 - 6.5), and 5.1 years (4.5 - 6.0) for global, region-wise, point-wise, and machine learning analyses, respectively. Machine learning analysis detects progressing eyes earlier than other methods consistently, with or without confirmation visits. In particular, machine learning detects more slowly progressing eyes than other methods. Copyright © 2018 Elsevier Inc. All rights reserved.

Evaluation of MERIS products from Baltic Sea coastal waters rich in CDOM

NASA Astrophysics Data System (ADS)

Beltrán-Abaunza, J. M.; Kratzer, S.; Brockmann, C.

2013-11-01

In this study, retrievals of the medium resolution imaging spectrometer (MERIS) reflectances and water quality products using 4 different coastal processing algorithms freely available are assessed by comparison against sea-truthing data. The study is based on a pair-wise comparison using processor-dependent quality flags for the retrieval of valid common macro-pixels. This assessment is required in order to ensure the reliability of monitoring systems based on MERIS data, such as the Swedish coastal and lake monitoring system (http.vattenkvalitet.se). The results show that the pre-processing with the Improved Contrast between Ocean and Land (ICOL) processor, correcting for adjacency effects, improve the retrieval of spectral reflectance for all processors, Therefore, it is recommended that the ICOL processor should be applied when Baltic coastal waters are investigated. Chlorophyll was retrieved best using the FUB (Free University of Berlin) processing algorithm, although overestimations in the range 18-26.5%, dependent on the compared pairs, were obtained. At low chlorophyll concentrations (< 2.5 mg m-3), random errors dominated in the retrievals with the MEGS (MERIS ground segment processor) processor. The lowest bias and random errors were obtained with MEGS for suspended particulate matter, for which overestimations in te range of 8-16% were found. Only the FUB retrieved CDOM (Coloured Dissolved Organic Matter) correlate with in situ values. However, a large systematic underestimation appears in the estimates that nevertheless may be corrected for by using a~local correction factor. The MEGS has the potential to be used as an operational processing algorithm for the Himmerfjärden bay and adjacent areas, but it requires further improvement of the atmospheric correction for the blue bands and better definition at relatively low chlorophyll concentrations in presence of high CDOM attenuation.

Exploring methodological frameworks for a mental task-based near-infrared spectroscopy brain-computer interface.

PubMed

Weyand, Sabine; Takehara-Nishiuchi, Kaori; Chau, Tom

2015-10-30

Near-infrared spectroscopy (NIRS) brain-computer interfaces (BCIs) enable users to interact with their environment using only cognitive activities. This paper presents the results of a comparison of four methodological frameworks used to select a pair of tasks to control a binary NIRS-BCI; specifically, three novel personalized task paradigms and the state-of-the-art prescribed task framework were explored. Three types of personalized task selection approaches were compared, including: user-selected mental tasks using weighted slope scores (WS-scores), user-selected mental tasks using pair-wise accuracy rankings (PWAR), and researcher-selected mental tasks using PWAR. These paradigms, along with the state-of-the-art prescribed mental task framework, where mental tasks are selected based on the most commonly used tasks in literature, were tested by ten able-bodied participants who took part in five NIRS-BCI sessions. The frameworks were compared in terms of their accuracy, perceived ease-of-use, computational time, user preference, and length of training. Most notably, researcher-selected personalized tasks resulted in significantly higher accuracies, while user-selected personalized tasks resulted in significantly higher perceived ease-of-use. It was also concluded that PWAR minimized the amount of data that needed to be collected; while, WS-scores maximized user satisfaction and minimized computational time. In comparison to the state-of-the-art prescribed mental tasks, our findings show that overall, personalized tasks appear to be superior to prescribed tasks with respect to accuracy and perceived ease-of-use. The deployment of personalized rather than prescribed mental tasks ought to be considered and further investigated in future NIRS-BCI studies. Copyright © 2015 Elsevier B.V. All rights reserved.

Evaluation of MERIS products from Baltic Sea coastal waters rich in CDOM

NASA Astrophysics Data System (ADS)

Beltrán-Abaunza, J. M.; Kratzer, S.; Brockmann, C.

2014-05-01

In this study, retrievals of the medium resolution imaging spectrometer (MERIS) reflectances and water quality products using four different coastal processing algorithms freely available are assessed by comparison against sea-truthing data. The study is based on a pair-wise comparison using processor-dependent quality flags for the retrieval of valid common macro-pixels. This assessment is required in order to ensure the reliability of monitoring systems based on MERIS data, such as the Swedish coastal and lake monitoring system (http://vattenkvalitet.se). The results show that the pre-processing with the Improved Contrast between Ocean and Land (ICOL) processor, correcting for adjacency effects, improves the retrieval of spectral reflectance for all processors. Therefore, it is recommended that the ICOL processor should be applied when Baltic coastal waters are investigated. Chlorophyll was retrieved best using the FUB (Free University of Berlin) processing algorithm, although overestimations in the range 18-26.5%, dependent on the compared pairs, were obtained. At low chlorophyll concentrations (< 2.5 mg m-3), data dispersion dominated in the retrievals with the MEGS (MERIS ground segment processor) processor. The lowest bias and data dispersion were obtained with MEGS for suspended particulate matter, for which overestimations in the range of 8-16% were found. Only the FUB retrieved CDOM (coloured dissolved organic matter) correlate with in situ values. However, a large systematic underestimation appears in the estimates that nevertheless may be corrected for by using a local correction factor. The MEGS has the potential to be used as an operational processing algorithm for the Himmerfjärden bay and adjacent areas, but it requires further improvement of the atmospheric correction for the blue bands and better definition at relatively low chlorophyll concentrations in the presence of high CDOM attenuation.

Partially restored resting-state functional connectivity in women recovered from anorexia nervosa.

PubMed

Boehm, Ilka; Geisler, Daniel; Tam, Friederike; King, Joseph A; Ritschel, Franziska; Seidel, Maria; Bernardoni, Fabio; Murr, Julia; Goschke, Thomas; Calhoun, Vince D; Roessner, Veit; Ehrlich, Stefan

2016-10-01

We have previously shown increased resting-state functional connectivity (rsFC) in the frontoparietal network (FPN) and the default mode network (DMN) in patients with acute anorexia nervosa. Based on these findings we investigated within-network rsFC in patients recovered from anorexia nervosa to examine whether these abnormalities are a state or trait marker of the disease. To extend the understanding of functional connectivity in patients with anorexia nervosa, we also estimated rsFC between large-scale networks. Girls and women recovered from anorexia nervosa and pair-wise, age- and sex-matched healthy controls underwent a resting-state fMRI scan. Using independent component analyses (ICA), we isolated the FPN, DMN and salience network. We used standard comparisons as well as a hypothesis-based approach to test the findings of our previous rsFC study in this recovered cohort. Temporal correlations between network time-course pairs were computed to investigate functional network connectivity (FNC). Thirty-one patients recovered from anorexia nervosa and 31 controls participated in our study. Standard group comparisons revealed reduced rsFC between the dorsolateral prefrontal cortex (dlPFC) and the FPN in the recovered group. Using a hypothesis-based approach we extended the previous finding of increased rsFC between the angular gyrus and the FPN in patients recovered from anorexia nervosa. No group differences in FNC were revealed. The study design did not allow us to conclude that the difference found in rsFC constitutes a scar effect of the disease. This study suggests that some abnormal rsFC patterns found in patients recovered from anorexia nervosa normalize after long-term weight restoration, while distorted rsFC in the FPN, a network that has been associated with cognitive control, may constitute a trait marker of the disorder.

Using Pair Wise Rankings in the Assessment of Adaptive Aiding

DTIC Science & Technology

2017-02-22

Aviation Psychology (ISAP) 9 – 11 May 2017 14. ABSTRACT In remotely piloted aircraft (RPA) operations, operator cognitive workload is an important concern...Force Research Laboratory Wright-Patterson AFB, Ohio In remotely piloted aircraft (RPA) operations, operator cognitive workload is an important...model in future research. Operator cognitive workload is an important concern in remotely piloted aircraft (RPA) operations. RPA use is

Blocking Strategies for Performing Entity Resolution in a Distributed Computing Environment

ERIC Educational Resources Information Center

Wang, Pei

2016-01-01

Entity resolution (ER) is an O(n[superscript 2]) problem where n is the number of records to be processed. The pair-wise nature of ER makes it impractical to perform on large datasets without the use of a technique called blocking. In blocking the records are separated into groups (called blocks) in such a way the records most likely to match are…

Electric Field Reconstruction in the Image Plane of a High-Contrast Coronagraph Using a Set of Pinholes Around the Lyot Plane

NASA Technical Reports Server (NTRS)

Giveon, Amir; Kern, Brian; Shaklan, Stuart; Wallace, Kent; Noecker, Charley

2012-01-01

The pair-wise estimation has been used now on various testbeds with different coronagraphs with the best contrast results to date. Pinholes estimate has been implemented and ready to be tested in closed loop correction. Pinholes estimate offers an independent method. We hope to improve the calibration process to gain better estimates.

ParallABEL: an R library for generalized parallelization of genome-wide association studies.

PubMed

Sangket, Unitsa; Mahasirimongkol, Surakameth; Chantratita, Wasun; Tandayya, Pichaya; Aulchenko, Yurii S

2010-04-29

Genome-Wide Association (GWA) analysis is a powerful method for identifying loci associated with complex traits and drug response. Parts of GWA analyses, especially those involving thousands of individuals and consuming hours to months, will benefit from parallel computation. It is arduous acquiring the necessary programming skills to correctly partition and distribute data, control and monitor tasks on clustered computers, and merge output files. Most components of GWA analysis can be divided into four groups based on the types of input data and statistical outputs. The first group contains statistics computed for a particular Single Nucleotide Polymorphism (SNP), or trait, such as SNP characterization statistics or association test statistics. The input data of this group includes the SNPs/traits. The second group concerns statistics characterizing an individual in a study, for example, the summary statistics of genotype quality for each sample. The input data of this group includes individuals. The third group consists of pair-wise statistics derived from analyses between each pair of individuals in the study, for example genome-wide identity-by-state or genomic kinship analyses. The input data of this group includes pairs of SNPs/traits. The final group concerns pair-wise statistics derived for pairs of SNPs, such as the linkage disequilibrium characterisation. The input data of this group includes pairs of individuals. We developed the ParallABEL library, which utilizes the Rmpi library, to parallelize these four types of computations. ParallABEL library is not only aimed at GenABEL, but may also be employed to parallelize various GWA packages in R. The data set from the North American Rheumatoid Arthritis Consortium (NARAC) includes 2,062 individuals with 545,080, SNPs' genotyping, was used to measure ParallABEL performance. Almost perfect speed-up was achieved for many types of analyses. For example, the computing time for the identity-by-state matrix was linearly reduced from approximately eight hours to one hour when ParallABEL employed eight processors. Executing genome-wide association analysis using the ParallABEL library on a computer cluster is an effective way to boost performance, and simplify the parallelization of GWA studies. ParallABEL is a user-friendly parallelization of GenABEL.

ProtPhylo: identification of protein-phenotype and protein-protein functional associations via phylogenetic profiling.

PubMed

Cheng, Yiming; Perocchi, Fabiana

2015-07-01

ProtPhylo is a web-based tool to identify proteins that are functionally linked to either a phenotype or a protein of interest based on co-evolution. ProtPhylo infers functional associations by comparing protein phylogenetic profiles (co-occurrence patterns of orthology relationships) for more than 9.7 million non-redundant protein sequences from all three domains of life. Users can query any of 2048 fully sequenced organisms, including 1678 bacteria, 255 eukaryotes and 115 archaea. In addition, they can tailor ProtPhylo to a particular kind of biological question by choosing among four main orthology inference methods based either on pair-wise sequence comparisons (One-way Best Hits and Best Reciprocal Hits) or clustering of orthologous proteins across multiple species (OrthoMCL and eggNOG). Next, ProtPhylo ranks phylogenetic neighbors of query proteins or phenotypic properties using the Hamming distance as a measure of similarity between pairs of phylogenetic profiles. Candidate hits can be easily and flexibly prioritized by complementary clues on subcellular localization, known protein-protein interactions, membrane spanning regions and protein domains. The resulting protein list can be quickly exported into a csv text file for further analyses. ProtPhylo is freely available at http://www.protphylo.org. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Hepatic Transcriptome Responses of Domesticated and Wild Turkey Embryos to Aflatoxin B₁.

PubMed

Monson, Melissa S; Cardona, Carol J; Coulombe, Roger A; Reed, Kent M

2016-01-06

The mycotoxin, aflatoxin B₁ (AFB₁) is a hepatotoxic, immunotoxic, and mutagenic contaminant of food and animal feeds. In poultry, AFB₁ can be maternally transferred to embryonated eggs, affecting development, viability and performance after hatch. Domesticated turkeys (Meleagris gallopavo) are especially sensitive to aflatoxicosis, while Eastern wild turkeys (M. g. silvestris) are likely more resistant. In ovo exposure provided a controlled AFB₁ challenge and comparison of domesticated and wild turkeys. Gene expression responses to AFB₁ in the embryonic hepatic transcriptome were examined using RNA-sequencing (RNA-seq). Eggs were injected with AFB₁ (1 μg) or sham control and dissected for liver tissue after 1 day or 5 days of exposure. Libraries from domesticated turkey (n = 24) and wild turkey (n = 15) produced 89.2 Gb of sequence. Approximately 670 M reads were mapped to a turkey gene set. Differential expression analysis identified 1535 significant genes with |log₂ fold change| ≥ 1.0 in at least one pair-wise comparison. AFB₁ effects were dependent on exposure time and turkey type, occurred more rapidly in domesticated turkeys, and led to notable up-regulation in cell cycle regulators, NRF2-mediated response genes and coagulation factors. Further investigation of NRF2-response genes may identify targets to improve poultry resistance.

On the role of tip curvature on flapping plates.

PubMed

Martin, Nathan; Gharib, Morteza

2018-01-09

During the flapping motion of a fish's tail, the caudal fin exhibits antero-posterior bending and dorso-ventral bending, the latter of which is referred to as chord-wise bending herein. The impact of chord-wise tip curvature on the hydrodynamic forces for flapping plates is investigated to explore potential mechanisms to improve the maneuverability or the performance of autonomous underwater vehicles. First, actuated chord-wise tip curvature is explored. Comparison of rigid curved geometries to a rigid flat plate as a baseline suggests that an increased curvature decreases the generated forces. An actuated plate with a dynamic tip curvature is created to illustrate a modulation of this decrease in forces. Second, the impact of curvature is isolated using curved plates with an identical planform area. Comparison of rigid curved geometries as a baseline corroborates the result that an increased curvature decreases the generated forces, with the exception that presenting a concave geometry into the flow increases the thrust and the efficiency. A passively-actuated plate is designed to capitalize on this effect by presenting a concave geometry into the flow throughout the cycle. The dynamically and passively actuated plates show potential to improve the maneuverability and the efficiency of autonomous underwater vehicles, respectively.

Statistical testing and power analysis for brain-wide association study.

PubMed

Gong, Weikang; Wan, Lin; Lu, Wenlian; Ma, Liang; Cheng, Fan; Cheng, Wei; Grünewald, Stefan; Feng, Jianfeng

2018-04-05

The identification of connexel-wise associations, which involves examining functional connectivities between pairwise voxels across the whole brain, is both statistically and computationally challenging. Although such a connexel-wise methodology has recently been adopted by brain-wide association studies (BWAS) to identify connectivity changes in several mental disorders, such as schizophrenia, autism and depression, the multiple correction and power analysis methods designed specifically for connexel-wise analysis are still lacking. Therefore, we herein report the development of a rigorous statistical framework for connexel-wise significance testing based on the Gaussian random field theory. It includes controlling the family-wise error rate (FWER) of multiple hypothesis testings using topological inference methods, and calculating power and sample size for a connexel-wise study. Our theoretical framework can control the false-positive rate accurately, as validated empirically using two resting-state fMRI datasets. Compared with Bonferroni correction and false discovery rate (FDR), it can reduce false-positive rate and increase statistical power by appropriately utilizing the spatial information of fMRI data. Importantly, our method bypasses the need of non-parametric permutation to correct for multiple comparison, thus, it can efficiently tackle large datasets with high resolution fMRI images. The utility of our method is shown in a case-control study. Our approach can identify altered functional connectivities in a major depression disorder dataset, whereas existing methods fail. A software package is available at https://github.com/weikanggong/BWAS. Copyright © 2018 Elsevier B.V. All rights reserved.

Assessing the effects of cocaine dependence and pathological gambling using group-wise sparse representation of natural stimulus FMRI data.

PubMed

Ren, Yudan; Fang, Jun; Lv, Jinglei; Hu, Xintao; Guo, Cong Christine; Guo, Lei; Xu, Jiansong; Potenza, Marc N; Liu, Tianming

2017-08-01

Assessing functional brain activation patterns in neuropsychiatric disorders such as cocaine dependence (CD) or pathological gambling (PG) under naturalistic stimuli has received rising interest in recent years. In this paper, we propose and apply a novel group-wise sparse representation framework to assess differences in neural responses to naturalistic stimuli across multiple groups of participants (healthy control, cocaine dependence, pathological gambling). Specifically, natural stimulus fMRI (N-fMRI) signals from all three groups of subjects are aggregated into a big data matrix, which is then decomposed into a common signal basis dictionary and associated weight coefficient matrices via an effective online dictionary learning and sparse coding method. The coefficient matrices associated with each common dictionary atom are statistically assessed for each group separately. With the inter-group comparisons based on the group-wise correspondence established by the common dictionary, our experimental results demonstrated that the group-wise sparse coding and representation strategy can effectively and specifically detect brain networks/regions affected by different pathological conditions of the brain under naturalistic stimuli.

Experimental congruence of interval scale production from paired comparisons and ranking for image evaluation

NASA Astrophysics Data System (ADS)

Handley, John C.; Babcock, Jason S.; Pelz, Jeff B.

2003-12-01

Image evaluation tasks are often conducted using paired comparisons or ranking. To elicit interval scales, both methods rely on Thurstone's Law of Comparative Judgment in which objects closer in psychological space are more often confused in preference comparisons by a putative discriminal random process. It is often debated whether paired comparisons and ranking yield the same interval scales. An experiment was conducted to assess scale production using paired comparisons and ranking. For this experiment a Pioneer Plasma Display and Apple Cinema Display were used for stimulus presentation. Observers performed rank order and paired comparisons tasks on both displays. For each of five scenes, six images were created by manipulating attributes such as lightness, chroma, and hue using six different settings. The intention was to simulate the variability from a set of digital cameras or scanners. Nineteen subjects, (5 females, 14 males) ranging from 19-51 years of age participated in this experiment. Using a paired comparison model and a ranking model, scales were estimated for each display and image combination yielding ten scale pairs, ostensibly measuring the same psychological scale. The Bradley-Terry model was used for the paired comparisons data and the Bradley-Terry-Mallows model was used for the ranking data. Each model was fit using maximum likelihood estimation and assessed using likelihood ratio tests. Approximate 95% confidence intervals were also constructed using likelihood ratios. Model fits for paired comparisons were satisfactory for all scales except those from two image/display pairs; the ranking model fit uniformly well on all data sets. Arguing from overlapping confidence intervals, we conclude that paired comparisons and ranking produce no conflicting decisions regarding ultimate ordering of treatment preferences, but paired comparisons yield greater precision at the expense of lack-of-fit.

Potential Drug-Drug Interactions among Patients prescriptions collected from Medicine Out-patient Setting.

PubMed

Farooqui, Riffat; Hoor, Talea; Karim, Nasim; Muneer, Mehtab

2018-01-01

To identify and evaluate the frequency, severity, mechanism and common pairs of drug-drug interactions (DDIs) in prescriptions by consultants in medicine outpatient department. This cross sectional descriptive study was done by Pharmacology department of Bahria University Medical & Dental College (BUMDC) in medicine outpatient department (OPD) of a private hospital in Karachi from December 2015 to January 2016. A total of 220 prescriptions written by consultants were collected. Medications given with patient's diagnosis were recorded. Drugs were analyzed for interactions by utilizing Medscape drug interaction checker, drugs.com checker and stockley`s drug interactions index. Two hundred eleven prescriptions were selected while remaining were excluded from the study because of unavailability of the prescribed drugs in the drug interaction checkers. In 211 prescriptions, two common diagnoses were diabetes mellitus (28.43%) and hypertension (27.96%). A total of 978 medications were given. Mean number of medications per prescription was 4.6. A total of 369 drug-drug interactions were identified in 211 prescriptions (175%). They were serious 4.33%, significant 66.12% and minor 29.53%. Pharmacokinetic and pharmacodynamic interactions were 37.94% and 51.21% respectively while 10.84% had unknown mechanism. Number wise common pairs of DDIs were Omeprazole-Losartan (S), Gabapentine- Acetaminophen (M), Losartan-Diclofenac (S). The frequency of DDIs is found to be too high in prescriptions of consultants from medicine OPD of a private hospital in Karachi. Significant drug-drug interactions were more and mostly caused by Pharmacodynamic mechanism. Number wise evaluation showed three common pairs of drugs involved in interactions.

Potential Drug-Drug Interactions among Patients prescriptions collected from Medicine Out-patient Setting

PubMed Central

Farooqui, Riffat; Hoor, Talea; Karim, Nasim; Muneer, Mehtab

2018-01-01

Objective: To identify and evaluate the frequency, severity, mechanism and common pairs of drug-drug interactions (DDIs) in prescriptions by consultants in medicine outpatient department. Methods: This cross sectional descriptive study was done by Pharmacology department of Bahria University Medical & Dental College (BUMDC) in medicine outpatient department (OPD) of a private hospital in Karachi from December 2015 to January 2016. A total of 220 prescriptions written by consultants were collected. Medications given with patient's diagnosis were recorded. Drugs were analyzed for interactions by utilizing Medscape drug interaction checker, drugs.com checker and stockley`s drug interactions index. Two hundred eleven prescriptions were selected while remaining were excluded from the study because of unavailability of the prescribed drugs in the drug interaction checkers. Results: In 211 prescriptions, two common diagnoses were diabetes mellitus (28.43%) and hypertension (27.96%). A total of 978 medications were given. Mean number of medications per prescription was 4.6. A total of 369 drug-drug interactions were identified in 211 prescriptions (175%). They were serious 4.33%, significant 66.12% and minor 29.53%. Pharmacokinetic and pharmacodynamic interactions were 37.94% and 51.21% respectively while 10.84% had unknown mechanism. Number wise common pairs of DDIs were Omeprazole-Losartan (S), Gabapentine- Acetaminophen (M), Losartan-Diclofenac (S). Conclusion: The frequency of DDIs is found to be too high in prescriptions of consultants from medicine OPD of a private hospital in Karachi. Significant drug-drug interactions were more and mostly caused by Pharmacodynamic mechanism. Number wise evaluation showed three common pairs of drugs involved in interactions. PMID:29643896

40 CFR 258.53 - Ground-water sampling and analysis requirements.

Code of Federal Regulations, 2011 CFR

2011-07-01

... include consistent sampling and analysis procedures that are designed to ensure monitoring results that... testing period. If a multiple comparisons procedure is used, the Type I experiment wise error rate for...

Genetic diversity and species diversity of stream fishes covary across a land-use gradient.

PubMed

Blum, Michael J; Bagley, Mark J; Walters, David M; Jackson, Suzanne A; Daniel, F Bernard; Chaloud, Deborah J; Cade, Brian S

2012-01-01

Genetic diversity and species diversity are expected to covary according to area and isolation, but may not always covary with environmental heterogeneity. In this study, we examined how patterns of genetic and species diversity in stream fishes correspond to local and regional environmental conditions. To do so, we compared population size, genetic diversity and divergence in central stonerollers (Campostoma anomalum) to measures of species diversity and turnover in stream fish assemblages among similarly sized watersheds across an agriculture-forest land-use gradient in the Little Miami River basin (Ohio, USA). Significant correlations were found in many, but not all, pair-wise comparisons. Allelic richness and species richness were strongly correlated, for example, but diversity measures based on allele frequencies and assemblage structure were not. In-stream conditions related to agricultural land use were identified as significant predictors of genetic diversity and species diversity. Comparisons to population size indicate, however, that genetic diversity and species diversity are not necessarily independent and that variation also corresponds to watershed location and glaciation history in the drainage basin. Our findings demonstrate that genetic diversity and species diversity can covary in stream fish assemblages, and illustrate the potential importance of scaling observations to capture responses to hierarchical environmental variation. More comparisons according to life history variation could further improve understanding of conditions that give rise to parallel variation in genetic diversity and species diversity, which in turn could improve diagnosis of anthropogenic influences on aquatic ecosystems.

Comparison between available serologic tests for detecting antibodies against Anaplasma phagocytophilum and Borrelia burgdorferi in horses in Canada.

PubMed

Schvartz, Gili; Epp, Tasha; Burgess, Hilary J; Chilton, Neil B; Lohmann, Katharina L

2015-07-01

To investigate the agreement between available serologic tests for the detection of antibodies against Anaplasma phagocytophilum and Borrelia burgdorferi, 50 serum samples from horses of unknown clinical status and at low risk for infection were tested. In addition to a point-of-care enzyme-linked immunosorbent assay (pocELISA), the evaluated tests included 2 indirect fluorescent antibody tests (IFATs) for antibodies against A. phagocytophilum and an IFAT, an ELISA confirmed with Western blot, and the Lyme multiplex assay for antibodies against B. burgdorferi. For each pair-wise comparison between serologic tests, the difference in the proportion of seropositive results as well as kappa and the prevalence-adjusted, bias-adjusted kappa were calculated. The proportion of seropositive results differed significantly in each pairwise comparison of tests for detection of antibodies against A. phagocytophilum, and between the pocELISA and IFAT as well as between the pocELISA and Lyme multiplex assay for detection of antibodies against B. burgdorferi. Agreement based on kappa varied from poor to fair while agreement was improved when evaluating prevalence-adjusted, bias-adjusted kappa. Lack of agreement may be explained by differences in methodology between the evaluated tests, cross-reactivity or false-positive and false-negative tests. In addition to the limitations of serologic test interpretation in the absence of clinical disease, this data suggest that screening of horses for exposure to tick-borne diseases in nonendemic areas may not be warranted. © 2015 The Author(s).

Genetic diversity and species diversity of stream fishes covary across a land-use gradient

USGS Publications Warehouse

Blum, M.J.; Bagley, M.J.; Walters, D.M.; Jackson, S.A.; Daniel, F.B.; Chaloud, D.J.; Cade, B.S.

2012-01-01

Genetic diversity and species diversity are expected to covary according to area and isolation, but may not always covary with environmental heterogeneity. In this study, we examined how patterns of genetic and species diversity in stream fishes correspond to local and regional environmental conditions. To do so, we compared population size, genetic diversity and divergence in central stonerollers (Campostoma anomalum) to measures of species diversity and turnover in stream fish assemblages among similarly sized watersheds across an agriculture-forest land-use gradient in the Little Miami River basin (Ohio, USA). Significant correlations were found in many, but not all, pair-wise comparisons. Allelic richness and species richness were strongly correlated, for example, but diversity measures based on allele frequencies and assemblage structure were not. In-stream conditions related to agricultural land use were identified as significant predictors of genetic diversity and species diversity. Comparisons to population size indicate, however, that genetic diversity and species diversity are not necessarily independent and that variation also corresponds to watershed location and glaciation history in the drainage basin. Our findings demonstrate that genetic diversity and species diversity can covary in stream fish assemblages, and illustrate the potential importance of scaling observations to capture responses to hierarchical environmental variation. More comparisons according to life history variation could further improve understanding of conditions that give rise to parallel variation in genetic diversity and species diversity, which in turn could improve diagnosis of anthropogenic influences on aquatic ecosystems. ?? 2011 Springer-Verlag.

The interactive evolution of human communication systems.

PubMed

Fay, Nicolas; Garrod, Simon; Roberts, Leo; Swoboda, Nik

2010-04-01

This paper compares two explanations of the process by which human communication systems evolve: iterated learning and social collaboration. It then reports an experiment testing the social collaboration account. Participants engaged in a graphical communication task either as a member of a community, where they interacted with seven different partners drawn from the same pool, or as a member of an isolated pair, where they interacted with the same partner across the same number of games. Participants' horizontal, pair-wise interactions led "bottom up" to the creation of an effective and efficient shared sign system in the community condition. Furthermore, the community-evolved sign systems were as effective and efficient as the local sign systems developed by isolated pairs. Finally, and as predicted by a social collaboration account, and not by an iterated learning account, interaction was critical to the creation of shared sign systems, with different isolated pairs establishing different local sign systems and different communities establishing different global sign systems. Copyright © 2010 Cognitive Science Society, Inc.

Ultrasound analysis of the vertebral artery during non-thrust cervical translatoric spinal manipulation.

PubMed

Creighton, Doug; Kondratek, Melodie; Krauss, John; Huijbregts, Peter; Qu, Harvey

2011-05-01

Cervical translatoric spinal manipulation (TSM) techniques have been suggested as a safer alternative to cervical thrust rotatory techniques. The objective of this study was to determine the effect of three C5-C6 non-thrust TSM techniques on vertebral artery (VA) lumen diameter (LD) and two blood flow velocity parameters. The two-tailed research hypothesis was that the TSM techniques would result in a significant change (increase or decrease) in blood flow velocity and arterial LD at the C5-C6 intertransverse portion of the VA. In a sample of 30 subjects representative of a clinical population, color-coded duplex Doppler diagnostic ultrasound imaging was used to collect data on LD, peak systolic velocity (PSV), and end diastolic velocity with the cervical spine positioned in neutral and in three different manipulation positions. Pair-wise mean differences between measurements at baseline (neutral position) and in all three manipulation positions were analyzed using two-tailed paired t-tests with alpha set at 0·05. Of the 18 paired comparisons, there were four statistically significant differences between measurements in the neutral position and a manipulation position, three concerning LD and one PSV. The three significant differences in LD ranged from 4·6 to 3·2% and were not associated with changes in blood flow velocity. The one significant change in PSV was only 6·6 cm/s. A value that still greatly exceeded the end diastolic velocity. No subject experienced symptoms associated with VA compromise. This study has provided evidence for the safety of the three lower cervical non-thrust TSM techniques on the current population studied. Further study is required on thrust versus non-thrust TSM techniques and on levels other than C5-C6.

Increasing the structural coverage of tuberculosis drug targets.

PubMed

Baugh, Loren; Phan, Isabelle; Begley, Darren W; Clifton, Matthew C; Armour, Brianna; Dranow, David M; Taylor, Brandy M; Muruthi, Marvin M; Abendroth, Jan; Fairman, James W; Fox, David; Dieterich, Shellie H; Staker, Bart L; Gardberg, Anna S; Choi, Ryan; Hewitt, Stephen N; Napuli, Alberto J; Myers, Janette; Barrett, Lynn K; Zhang, Yang; Ferrell, Micah; Mundt, Elizabeth; Thompkins, Katie; Tran, Ngoc; Lyons-Abbott, Sally; Abramov, Ariel; Sekar, Aarthi; Serbzhinskiy, Dmitri; Lorimer, Don; Buchko, Garry W; Stacy, Robin; Stewart, Lance J; Edwards, Thomas E; Van Voorhis, Wesley C; Myler, Peter J

2015-03-01

High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus "homolog-rescue" strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. Of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structures would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1 Å, >85% side chain identity, and ≥80% PSAPF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases. Copyright © 2014 Elsevier Ltd. All rights reserved.

Increasing the structural coverage of tuberculosis drug targets

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

Baugh, Loren; Phan, Isabelle; Begley, Darren W.

High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus “homolog-rescue” strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. We found that of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structuresmore » would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1 Å, >85% side chain identity, and ≥80% PS APF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases.« less

GenoMycDB: a database for comparative analysis of mycobacterial genes and genomes.

PubMed

Catanho, Marcos; Mascarenhas, Daniel; Degrave, Wim; Miranda, Antonio Basílio de

2006-03-31

Several databases and computational tools have been created with the aim of organizing, integrating and analyzing the wealth of information generated by large-scale sequencing projects of mycobacterial genomes and those of other organisms. However, with very few exceptions, these databases and tools do not allow for massive and/or dynamic comparison of these data. GenoMycDB (http://www.dbbm.fiocruz.br/GenoMycDB) is a relational database built for large-scale comparative analyses of completely sequenced mycobacterial genomes, based on their predicted protein content. Its central structure is composed of the results obtained after pair-wise sequence alignments among all the predicted proteins coded by the genomes of six mycobacteria: Mycobacterium tuberculosis (strains H37Rv and CDC1551), M. bovis AF2122/97, M. avium subsp. paratuberculosis K10, M. leprae TN, and M. smegmatis MC2 155. The database stores the computed similarity parameters of every aligned pair, providing for each protein sequence the predicted subcellular localization, the assigned cluster of orthologous groups, the features of the corresponding gene, and links to several important databases. Tables containing pairs or groups of potential homologs between selected species/strains can be produced dynamically by user-defined criteria, based on one or multiple sequence similarity parameters. In addition, searches can be restricted according to the predicted subcellular localization of the protein, the DNA strand of the corresponding gene and/or the description of the protein. Massive data search and/or retrieval are available, and different ways of exporting the result are offered. GenoMycDB provides an on-line resource for the functional classification of mycobacterial proteins as well as for the analysis of genome structure, organization, and evolution.

Increasing the structural coverage of tuberculosis drug targets

DOE PAGES

Baugh, Loren; Phan, Isabelle; Begley, Darren W.; ...

2014-12-19

High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus “homolog-rescue” strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. We found that of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structuresmore » would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1 Å, >85% side chain identity, and ≥80% PS APF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases.« less

Analysis of 12 X-STR loci in the population of south Croatia.

PubMed

Mršić, Gordan; Ozretić, Petar; Crnjac, Josip; Merkaš, Siniša; Račić, Ivana; Rožić, Sara; Sukser, Viktorija; Popović, Maja; Korolija, Marina

2017-02-01

The aim of the study was to assess forensic pertinence of 12 short tandem repeats (STRs) on X-chromosome in south Croatia population. Investigator ® Argus X-12 kit was used to co-amplify 12 STR loci belonging to four linkage groups (LGs) on X-chromosome in 99 male and 98 female DNA samples of unrelated donors. PCR products were analyzed by capillary electrophoresis. Population genetic and forensic parameters were calculated by the Arlequin and POPTREE2 software, and an on-line tool available at ChrX-STR.org. Hardy-Weinberg equilibrium was confirmed for all X-STR markers in female samples. Biallelic patterns at DXS10079 locus were detected in four male samples. Polymorphism information content for the most (DXS10135) and the least (DXS8378) informative markers was 0.9212 and 0.6347, respectively. In both male and female samples, combined power of discrimination exceeded 0.999999999. As confirmed by linkage disequilibrium test, significant association of marker pair DXS10074-DXS10079 (P = 0.0004) within LG2 and marker pair DXS10101-DXS10103 (P = 0.0003) within LG3 was found only in male samples. Number of observed haplotypes in our sample pool amounted 3.01, 7.53, 5 and 3.25% of the number of possible haplotypes for LG1, LG2, LG3 and LG4, respectively. According to haplotype diversity value of 0.9981, LG1 was the most informative. In comparison of south Croatia with 26 world populations, pair-wise [Formula: see text] values increase in parallel with geographical distance. Overall statistical assessment confirmed suitability of Investigator ® Argus X-12 kit for forensic casework in both identification and familial testing in the population of south Croatia.

Increasing the Structural Coverage of Tuberculosis Drug Targets

PubMed Central

Baugh, Loren; Phan, Isabelle; Begley, Darren W.; Clifton, Matthew C.; Armour, Brianna; Dranow, David M.; Taylor, Brandy M.; Muruthi, Marvin M.; Abendroth, Jan; Fairman, James W.; Fox, David; Dieterich, Shellie H.; Staker, Bart L.; Gardberg, Anna S.; Choi, Ryan; Hewitt, Stephen N.; Napuli, Alberto J.; Myers, Janette; Barrett, Lynn K.; Zhang, Yang; Ferrell, Micah; Mundt, Elizabeth; Thompkins, Katie; Tran, Ngoc; Lyons-Abbott, Sally; Abramov, Ariel; Sekar, Aarthi; Serbzhinskiy, Dmitri; Lorimer, Don; Buchko, Garry W.; Stacy, Robin; Stewart, Lance J.; Edwards, Thomas E.; Van Voorhis, Wesley C.; Myler, Peter J.

2015-01-01

High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus “homolog-rescue” strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. Of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structures would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1Å, >85% side chain identity, and ≥80% PSAPF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases. PMID:25613812

Pair-wise comparison analysis of differential expression of mRNAs in early and advanced stage primary colorectal adenocarcinomas

PubMed Central

Lau, Tze Pheng; Roslani, April Camilla; Lian, Lay Hoong; Chai, Hwa Chia; Lee, Ping Chin; Hilmi, Ida; Goh, Khean Lee; Chua, Kek Heng

2014-01-01

Objectives To characterise the mRNA expression patterns of early and advanced stage colorectal adenocarcinomas of Malaysian patients. Design Comparative expression analysis. Setting and participants We performed a combination of annealing control primer (ACP)-based PCR and reverse transcription-quantitative real-time PCR for the identification of differentially expressed genes (DEGs) associated with early and advanced stage primary colorectal tumours. We recruited four paired samples from patients with colorectal cancer (CRC) of Dukes’ A and B for the preliminary differential expression study, and a total of 27 paired samples, ranging from CRC stages I to IV, for subsequent confirmatory test. The tumouric samples were obtained from the patients with CRC undergoing curative surgical resection without preoperative chemoradiotherapy. The recruited patients with CRC were newly diagnosed with CRC, and were not associated with any hereditary syndromes, previously diagnosed cancer or positive family history of CRC. The paired non-cancerous tissue specimens were excised from macroscopically normal colonic mucosa distally located from the colorectal tumours. Primary and secondary outcome measures The differential mRNA expression patterns of early and advanced stage colorectal adenocarcinomas compared with macroscopically normal colonic mucosa were characterised by ACP-based PCR and reverse transcription-quantitative real-time PCR. Results The RPL35, RPS23 and TIMP1 genes were found to be overexpressed in both early and advanced stage colorectal adenocarcinomas (p<0.05). However, the ARPC2 gene was significantly underexpressed in early colorectal adenocarcinomas, while the advanced stage primary colorectal tumours exhibited an additional overexpression of the C6orf173 gene (p<0.05). Conclusions We characterised two distinctive gene expression patterns to aid in the stratification of primary colorectal neoplasms among Malaysian patients with CRC. Further work can be done to assess and compare the mRNA expression levels of these identified DEGs between each CRC stage group, stages I–IV. PMID:25107436

Assessment of data processing to improve reliability of microarray experiments using genomic DNA reference.

PubMed

Yang, Yunfeng; Zhu, Mengxia; Wu, Liyou; Zhou, Jizhong

2008-09-16

Using genomic DNA as common reference in microarray experiments has recently been tested by different laboratories. Conflicting results have been reported with regard to the reliability of microarray results using this method. To explain it, we hypothesize that data processing is a critical element that impacts the data quality. Microarray experiments were performed in a gamma-proteobacterium Shewanella oneidensis. Pair-wise comparison of three experimental conditions was obtained either with two labeled cDNA samples co-hybridized to the same array, or by employing Shewanella genomic DNA as a standard reference. Various data processing techniques were exploited to reduce the amount of inconsistency between both methods and the results were assessed. We discovered that data quality was significantly improved by imposing the constraint of minimal number of replicates, logarithmic transformation and random error analyses. These findings demonstrate that data processing significantly influences data quality, which provides an explanation for the conflicting evaluation in the literature. This work could serve as a guideline for microarray data analysis using genomic DNA as a standard reference.

Analytic hierarchy process helps select site for limestone quarry expansion in Barbados.

PubMed

Dey, Prasanta Kumar; Ramcharan, Eugene K

2008-09-01

Site selection is a key activity for quarry expansion to support cement production, and is governed by factors such as resource availability, logistics, costs, and socio-economic-environmental factors. Adequate consideration of all the factors facilitates both industrial productivity and sustainable economic growth. This study illustrates the site selection process that was undertaken for the expansion of limestone quarry operations to support cement production in Barbados. First, alternate sites with adequate resources to support a 25-year development horizon were identified. Second, technical and socio-economic-environmental factors were then identified. Third, a database was developed for each site with respect to each factor. Fourth, a hierarchical model in analytic hierarchy process (AHP) framework was then developed. Fifth, the relative ranking of the alternate sites was then derived through pair wise comparison in all the levels and through subsequent synthesizing of the results across the hierarchy through computer software (Expert Choice). The study reveals that an integrated framework using the AHP can help select a site for the quarry expansion project in Barbados.

Environmental management framework for wind farm siting: methodology and case study.

PubMed

Tegou, Leda-Ioanna; Polatidis, Heracles; Haralambopoulos, Dias A

2010-11-01

This paper develops an integrated framework to evaluate land suitability for wind farm siting that combines multi-criteria analysis (MCA) with geographical information systems (GIS); an application of the proposed framework for the island of Lesvos, Greece, is further illustrated. A set of environmental, economic, social, and technical constraints, based on recent Greek legislation, identifies the potential sites for wind power installation. Furthermore, the area under consideration is evaluated by a variety of criteria, such as wind power potential, land cover type, electricity demand, visual impact, land value, and distance from the electricity grid. The pair-wise comparison method in the context of the analytic hierarchy process (AHP) is applied to estimate the criteria weights in order to establish their relative importance in site evaluation. The overall suitability of the study region for wind farm siting is appraised through the weighted summation rule. Results showed that only a very small percentage of the total area of Lesvos could be suitable for wind farm installation, although favourable wind potential exists in many more areas of the island. Copyright 2010 Elsevier Ltd. All rights reserved.

Spatially resolved bimodal spectroscopy for classification/evaluation of mouse skin inflammatory and pre-cancerous stages

NASA Astrophysics Data System (ADS)

Díaz-Ayil, Gilberto; Amouroux, Marine; Clanché, Fabien; Granjon, Yves; Blondel, Walter C. P. M.

2009-07-01

Spatially-resolved bimodal spectroscopy (multiple AutoFluorescence AF excitation and Diffuse Reflectance DR), was used in vivo to discriminate various healthy and precancerous skin stages in a pre-clinical model (UV-irradiated mouse): Compensatory Hyperplasia CH, Atypical Hyperplasia AH and Dysplasia D. A specific data preprocessing scheme was applied to intensity spectra (filtering, spectral correction and intensity normalization), and several sets of spectral characteristics were automatically extracted and selected based on their discrimination power, statistically tested for every pair-wise comparison of histological classes. Data reduction with Principal Components Analysis (PCA) was performed and 3 classification methods were implemented (k-NN, LDA and SVM), in order to compare diagnostic performance of each method. Diagnostic performance was studied and assessed in terms of Sensibility (Se) and Specificity (Sp) as a function of the selected features, of the combinations of 3 different inter-fibres distances and of the numbers of principal components, such that: Se and Sp ~ 100% when discriminating CH vs. others; Sp ~ 100% and Se > 95% when discriminating Healthy vs. AH or D; Sp ~ 74% and Se ~ 63% for AH vs. D.

Manganese chloride tetrahydrate (CMC-001) enhanced liver MRI: evaluation of efficacy and safety in healthy volunteers.

PubMed

Albiin, Nils; Kartalis, Nikolaos; Bergquist, Annika; Sadigh, Bita; Brismar, Torkel B

2012-10-01

To evaluate the efficacy of three dose levels of the oral hepatobiliary manganese-based magnetic resonance imaging (MRI) contrast agent CMC-001, and assess its safety profile and patient acceptability. After ethics committee approval, 32 healthy volunteers (males/females: 18/14) were included. Liver MRI was performed before and 3 h after ingestion of 0.8, 0.4, and 0.2 g of CMC-001 on separate occasions. Liver-to-muscle signal intensity (SI) ratio from baseline to post-contrast and image quality was assessed. Adverse drug reactions/adverse events (ADRs/AEs) and clinico-laboratory tests were monitored. The increase in liver-to-muscle SI ratio was significantly higher after 0.8 g (0.696) compared to 0.4 g (0.458) and 0.2 g (0.223) (in all pair-wise comparisons, P < 0.0001). The overall image quality was superior after 0.8 g. ADRs/AEs were dose-related and predominantly of mild intensity. Liver MRI using 0.8 g CMC-001 has the highest efficacy and still acceptable ADRs and should therefore be preferred.

A multiple criteria analysis for household solid waste management in the urban community of Dakar.

PubMed

Kapepula, Ka-Mbayu; Colson, Gerard; Sabri, Karim; Thonart, Philippe

2007-01-01

Household solid waste management is a severe problem in big cities of developing countries. Mismanaged solid waste dumpsites produce bad sanitary, ecological and economic consequences for the whole population, especially for the poorest urban inhabitants. Dealing with this problem, this paper utilizes field data collected in the urban community of Dakar, in view of ranking nine areas of the city with respect to multiple criteria of nuisance. Nine criteria are built and organized in three families that represent three classical viewpoints: the production of wastes, their collection and their treatment. Thanks to the method PROMETHEE and the software ARGOS, we do a pair-wise comparison of the nine areas, which allows their multiple criteria rankings according to each viewpoint and then globally. Finding the worst and best areas in terms of nuisance for a better waste management in the city is our final purpose, fitting as well as possible the needs of the urban community. Based on field knowledge and on the literature, we suggest applying general and area-specific remedies to the household solid waste problems.

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

Szoka de Valladares, M.R.; Mack, S.

The DOE Hydrogen Program needs to develop criteria as part of a systematic evaluation process for proposal identification, evaluation and selection. The H Scan component of this process provides a framework in which a project proposer can fully describe their candidate technology system and its components. The H Scan complements traditional methods of capturing cost and technical information. It consists of a special set of survey forms designed to elicit information so expert reviewers can assess the proposal relative to DOE specified selection criteria. The Analytic Hierarchy Process (AHP) component of the decision process assembles the management defined evaluation andmore » selection criteria into a coherent multi-level decision construct by which projects can be evaluated in pair-wise comparisons. The AHP model will reflect management`s objectives and it will assist in the ranking of individual projects based on the extent to which each contributes to management`s objectives. This paper contains a detailed description of the products and activities associated with the planning and evaluation process: The objectives or criteria; the H Scan; and The Analytic Hierarchy Process (AHP).« less

Substance abuse intervention for health care workers: a preliminary report.

PubMed

Lapham, S C; Chang, I; Gregory, C

2000-05-01

The Workplace Managed Care Cooperative Agreement project targets 3,300 health care professionals in hospital, specialty clinic, and primary care settings located in metropolitan New Mexico communities. This project will evaluate whether enhancements to existing substance abuse prevention/early intervention programs can prevent the onset of risky drinking, reduce prevalence of risky drinking, better identify employees who abuse alcohol and drugs, and improve employee wellness. This article describes one such enhancement (Project WISE [Workplace Initiative in Substance Education]), implemented at Lovelace Health Systems. Project WISE includes relatively low-cost elements such as substance abuse awareness training, information on how to reduce drinking, and brief motivational counseling. Evaluation will consist of baseline comparisons of the intervention and comparison sites, a process evaluation, a qualitative analysis using focus groups, and an outcome evaluation using health and work records. Methodological challenges, solutions, and implications for researchers undertaking similar projects are presented.

The Ĝ Infrared Search for Extraterrestrial Civilizations with Large Energy Supplies. III. The Reddest Extended Sources in WISE

NASA Astrophysics Data System (ADS)

Griffith, Roger L.; Wright, Jason T.; Maldonado, Jessica; Povich, Matthew S.; Sigurđsson, Steinn; Mullan, Brendan

2015-04-01

Nearby Type iii (galaxy-spanning) Kardashev supercivilizations would have high mid-infrared (MIR) luminosities. We have used the Wide-field Infrared Survey Explorer (WISE) to survey ∼ 1× {{10}5} galaxies for extreme MIR emission, 1 × 103 times more galaxies than the only previous such search. We have calibrated the WISE All-sky Catalog pipeline products to improve their photometry for extended sources. We present 563 extended sources with |b|≥slant 10 and red MIR colors, having visually vetted them to remove artifacts. No galaxies in our sample host an alien civilization reprocessing more than 85% of its starlight into the MIR, and only 50 galaxies, including Arp 220, have MIR luminosities consistent with \\gt 50% reprocessing. Ninety of these (likely) extragalactic sources have little literature presence; in most cases, they are likely barely resolved galaxies or pairs of galaxies undergoing large amounts of star formation. Five are new to science and deserve further study. The Be star 48 Librae sits within a MIR nebula, and we suggest that it may be creating dust. WISE, 2MASS, and Spitzer imagery shows that IRAS 04287+6444 is consistent with a previously unnoticed, heavily extinguished cluster of young stellar objects. We identify five “passive” (i.e., red) spiral galaxies with unusually high MIR and low NUV luminosity. We search a set of H i dark galaxies for MIR emission and find none. These 90 poorly understood sources and 5 anomalous passive spirals deserve follow-up via both SETI and conventional astrophysics.

Testing of the ABBN-RF multigroup data library in photon transport calculations

NASA Astrophysics Data System (ADS)

Koscheev, Vladimir; Lomakov, Gleb; Manturov, Gennady; Tsiboulia, Anatoly

2017-09-01

Gamma radiation is produced via both of nuclear fuel and shield materials. Photon interaction is known with appropriate accuracy, but secondary gamma ray production known much less. The purpose of this work is studying secondary gamma ray production data from neutron induced reactions in iron and lead by using MCNP code and modern nuclear data as ROSFOND, ENDF/B-7.1, JEFF-3.2 and JENDL-4.0. Results of calculations show that all of these nuclear data have different photon production data from neutron induced reactions and have poor agreement with evaluated benchmark experiment. The ABBN-RF multigroup cross-section library is based on the ROSFOND data. It presented in two forms of micro cross sections: ABBN and MATXS formats. Comparison of group-wise calculations using both ABBN and MATXS data to point-wise calculations with the ROSFOND library shows a good agreement. The discrepancies between calculation and experimental C/E results in neutron spectra are in the limit of experimental errors. For the photon spectrum they are out of experimental errors. Results of calculations using group-wise and point-wise representation of cross sections show a good agreement both for photon and neutron spectra.

Numerical and experimental investigation of enhancement of heat transfer in dimpled rib heat exchanger tube

NASA Astrophysics Data System (ADS)

Kumar, Anil; Maithani, Rajesh; Suri, Amar Raj Singh

2017-12-01

In this study, numerical and experimental investigation has been carried out for a range of system and operating parameters in order to analyse the effect of dimpled rib on heat and fluid flow behaviours in heat exchanger tube. Tube has, stream wise spacing ( x/ d d ) range of 15-35, span wise spacing ( y/ d d ) range of 15-35, ratio of dimpled depth to print diameter ( e/ d d ) of 1.0 and Reynolds number ( Re n ) ranges from 4000 to 28,000. Simulations were carried out to obtain heat and fluid flow behaviour of smooth and rough tube, using commercial CFD software, ANSYS 16.0 (Fluent). Renormalization k - ɛ model was employed to assess the influence of dimpled on turbulent flow and velocity field. Simulation results show that, the enhancement of 3.18 times in heat transfer and 2.87 times enhancement in thermal hydraulic performance as a function of stream wise direction ( x/ d d ) of 15 and span wise direction ( y/ d d ) of 15 respectively. Comparison between numerical and experimental simulation results showed that good agreement as the data fell within ±10% error band.

Potential use of random amplified polymorphic DNA (RAPD) technique to study the genetic diversity in Indian mustard (Brassica juncea) and its relationship to heterosis.

PubMed

Jain, A; Bhatia, S; Banga, S S; Prakash, S; Lakshmikumaran, M

1994-04-01

RAPD assays were performed, using 34 arbitrary decamer oligonucleotide primers and six combinations of two primers, to detect inherent variations and genetic relationships among 12 Indian and 11 exotic B. juncea genotypes. Of 595 amplification products identified, 500 of them were polymorphic across all genotypes. A low level of genetic variability was detected among the Indian genotypes, while considerable polymorphism was present among the exotic ones. Based on the pair-wise comparisons of amplification products the genetic similarity was calculated using Jaccard's similarity coefficients and a dendrogram was constructed using an unweighted pair group method was arithmetical averages (UPGMA). On the basis of this analysis the genotypes were clustered into two groups, A and B. Group A comprised only exotic genotypes, whereas all the Indian genotypes and four of the exotic genotypes were clustered in group B. Almost similar genotypic rankings could also be established by computing as few as 200 amplification products. In general, a high per cent of heterosis was recorded in crosses involving Indian x exotic genotypes. On the other hand, when crosses were made amongst Indian or exotic genotypes, about 80% of them exhibited negative heterosis. Results from this study indicate that, despite the lack of direct correlation between the genetic distance and the degree of heterosis, genetic diversity forms a very useful guide not only for investigating the relationships among Brassica genotypes but also in the selection of parents for heterotic hybrid combinations.

Transcriptome instability as a molecular pan-cancer characteristic of carcinomas.

PubMed

Sveen, Anita; Johannessen, Bjarne; Teixeira, Manuel R; Lothe, Ragnhild A; Skotheim, Rolf I

2014-08-10

We have previously proposed transcriptome instability as a genome-wide, pre-mRNA splicing-related characteristic of colorectal cancer. Here, we explore the hypothesis of transcriptome instability being a general characteristic of cancer. Exon-level microarray expression data from ten cancer datasets were analyzed, including breast cancer, cervical cancer, colorectal cancer, gastric cancer, lung cancer, neuroblastoma, and prostate cancer (555 samples), as well as paired normal tissue samples from the colon, lung, prostate, and stomach (93 samples). Based on alternative splicing scores across the genomes, we calculated sample-wise relative amounts of aberrant exon skipping and inclusion. Strong and non-random (P < 0.001) correlations between these estimates and the expression levels of splicing factor genes (n = 280) were found in most cancer types analyzed (breast-, cervical-, colorectal-, lung- and prostate cancer). This suggests a biological explanation for the splicing variation. Surprisingly, these associations prevailed in pan-cancer analyses. This is in contrast to the tissue and cancer specific patterns observed in comparisons across healthy tissue samples from the colon, lung, prostate, and stomach, and between paired cancer-normal samples from the same four tissue types. Based on exon-level expression profiling and computational analyses of alternative splicing, we propose transcriptome instability as a molecular pan-cancer characteristic. The affected cancers show strong and non-random associations between low expression levels of splicing factor genes, and high amounts of aberrant exon skipping and inclusion, and vice versa, on a genome-wide scale.

Improving Arterial Spin Labeling by Using Deep Learning.

PubMed

Kim, Ki Hwan; Choi, Seung Hong; Park, Sung-Hong

2018-05-01

Purpose To develop a deep learning algorithm that generates arterial spin labeling (ASL) perfusion images with higher accuracy and robustness by using a smaller number of subtraction images. Materials and Methods For ASL image generation from pair-wise subtraction, we used a convolutional neural network (CNN) as a deep learning algorithm. The ground truth perfusion images were generated by averaging six or seven pairwise subtraction images acquired with (a) conventional pseudocontinuous arterial spin labeling from seven healthy subjects or (b) Hadamard-encoded pseudocontinuous ASL from 114 patients with various diseases. CNNs were trained to generate perfusion images from a smaller number (two or three) of subtraction images and evaluated by means of cross-validation. CNNs from the patient data sets were also tested on 26 separate stroke data sets. CNNs were compared with the conventional averaging method in terms of mean square error and radiologic score by using a paired t test and/or Wilcoxon signed-rank test. Results Mean square errors were approximately 40% lower than those of the conventional averaging method for the cross-validation with the healthy subjects and patients and the separate test with the patients who had experienced a stroke (P < .001). Region-of-interest analysis in stroke regions showed that cerebral blood flow maps from CNN (mean ± standard deviation, 19.7 mL per 100 g/min ± 9.7) had smaller mean square errors than those determined with the conventional averaging method (43.2 ± 29.8) (P < .001). Radiologic scoring demonstrated that CNNs suppressed noise and motion and/or segmentation artifacts better than the conventional averaging method did (P < .001). Conclusion CNNs provided superior perfusion image quality and more accurate perfusion measurement compared with those of the conventional averaging method for generation of ASL images from pair-wise subtraction images. © RSNA, 2017.

ParallABEL: an R library for generalized parallelization of genome-wide association studies

PubMed Central

2010-01-01

Background Genome-Wide Association (GWA) analysis is a powerful method for identifying loci associated with complex traits and drug response. Parts of GWA analyses, especially those involving thousands of individuals and consuming hours to months, will benefit from parallel computation. It is arduous acquiring the necessary programming skills to correctly partition and distribute data, control and monitor tasks on clustered computers, and merge output files. Results Most components of GWA analysis can be divided into four groups based on the types of input data and statistical outputs. The first group contains statistics computed for a particular Single Nucleotide Polymorphism (SNP), or trait, such as SNP characterization statistics or association test statistics. The input data of this group includes the SNPs/traits. The second group concerns statistics characterizing an individual in a study, for example, the summary statistics of genotype quality for each sample. The input data of this group includes individuals. The third group consists of pair-wise statistics derived from analyses between each pair of individuals in the study, for example genome-wide identity-by-state or genomic kinship analyses. The input data of this group includes pairs of SNPs/traits. The final group concerns pair-wise statistics derived for pairs of SNPs, such as the linkage disequilibrium characterisation. The input data of this group includes pairs of individuals. We developed the ParallABEL library, which utilizes the Rmpi library, to parallelize these four types of computations. ParallABEL library is not only aimed at GenABEL, but may also be employed to parallelize various GWA packages in R. The data set from the North American Rheumatoid Arthritis Consortium (NARAC) includes 2,062 individuals with 545,080, SNPs' genotyping, was used to measure ParallABEL performance. Almost perfect speed-up was achieved for many types of analyses. For example, the computing time for the identity-by-state matrix was linearly reduced from approximately eight hours to one hour when ParallABEL employed eight processors. Conclusions Executing genome-wide association analysis using the ParallABEL library on a computer cluster is an effective way to boost performance, and simplify the parallelization of GWA studies. ParallABEL is a user-friendly parallelization of GenABEL. PMID:20429914

Depression and disability: comparisons with common physical conditions in the Ibadan study of aging.

PubMed

Gureje, Oye; Ademola, Adedotun; Olley, Benjamin O

2008-11-01

To compare the effects of depression and chronic physical conditions on disability in elderly persons. Yoruba-speaking areas of Nigeria. Interviews. PATICIPANTS: Community-dwelling persons aged 65 and older. Face-to-face interviews were conducted with a representative sample of community-dwelling persons aged 65 and older (N=2,152) in the Yoruba-speaking areas of Nigeria (representing approximately 22% of the national population). Major depressive disorder (MDD) was assessed using the World Health Organization Composite International Diagnostic Interview. Chronic pain and medical disorders were assessed using self-report. Disorder-specific disability was evaluated using the Sheehan Disability Scale (SDS). MDD was highly comorbid with each of the medical conditions (odds ratio range 1.3-2.0). A higher proportion of persons with MDD (47.2%) were rated severely disabled globally than those with arthritis (20.6%), chronic spinal pain (24.2%), or high blood pressure (25.0%). Subjects with MDD were also more likely to be severely disabled in three of the four domains of the SDS. In pair-wise comparisons, persons with MDD had significantly higher levels of disability than those with any of the disorders, with differences in mean scores ranging between -3.74 and -27.50. To reduce the public health burden of depression, its prevention and treatment require more clinical and research attention than currently given by developing countries.

Analysis of Interferometric Synthetic Aperture Radar Phase Data at Brady Hot Springs, Nevada, USA Using Prior Information

NASA Astrophysics Data System (ADS)

Reinisch, E. C.; Ali, S. T.; Cardiff, M. A.; Morency, C.; Kreemer, C.; Feigl, K. L.; Team, P.

2016-12-01

Time-dependent deformation has been observed at Brady Hot Springs using interferometric synthetic aperture radar (InSAR) [Ali et al. 2016, http://dx.doi.org/10.1016/j.geothermics.2016.01.008]. Our goal is to evaluate multiple competing hypotheses to explain the observed deformation at Brady. To do so requires statistical tests that account for uncertainty. Graph theory is useful for such an analysis of InSAR data [Reinisch, et al. 2016, http://dx.doi.org/10.1007/s00190-016-0934-5]. In particular, the normalized edge Laplacian matrix calculated from the edge-vertex incidence matrix of the graph of the pair-wise data set represents its correlation and leads to a full data covariance matrix in the weighted least squares problem. This formulation also leads to the covariance matrix of the epoch-wise measurements, representing their relative uncertainties. While the formulation in terms of incidence graphs applies to any quantity derived from pair-wise differences, the modulo-2π ambiguity of wrapped phase renders the problem non-linear. The conventional practice is to unwrap InSAR phase before modeling, which can introduce mistakes without increasing the corresponding measurement uncertainty. To address this issue, we are applying Bayesian inference. To build the likelihood, we use three different observables: (a) wrapped phase [e.g., Feigl and Thurber 2009, http://dx.doi.org/10.1111/j.1365-246X.2008.03881.x]; (b) range gradients, as defined by Ali and Feigl [2012, http://dx.doi.org/10.1029/2012GC004112]; and (c) unwrapped phase, i.e. range change in mm, which we validate using GPS data. We apply our method to InSAR data taken over Brady Hot Springs geothermal field in Nevada as part of a project entitled "Poroelastic Tomography by Adjoint Inverse Modeling of Data from Seismology, Geodesy, and Hydrology" (PoroTomo) [ http://geoscience.wisc.edu/feigl/porotomo].

LHC constraints on color octet scalars

NASA Astrophysics Data System (ADS)

Hayreter, Alper; Valencia, German

2017-08-01

We extract constraints on the parameter space of the Manohar and Wise model by comparing the cross sections for dijet, top-pair, dijet-pair, t t ¯t t ¯ and b b ¯b b ¯ productions at the LHC with the strongest available experimental limits from ATLAS or CMS at 8 or 13 TeV. Overall we find mass limits around 1 TeV in the most sensitive regions of parameter space, and lower elsewhere. This is at odds with generic limits for color octet scalars often quoted in the literature where much larger production cross sections are assumed. The constraints that can be placed on coupling constants are typically weaker than those from existing theoretical considerations, with the exception of the parameter ηD.

The influence of presentation format on the "bigger is better" (BIB) effect.

PubMed

Bromgard, Gregg D; Trafimow, David; Silvera, David H

2013-04-01

Two experiments tested the "bigger is better" (BIB) effect, whereby bigger objects are perceived more favorably than smaller ones. In Experiment 1, participants directly compared pairs of objects and a strong BIB effect was obtained for both positively and negatively valenced stimuli. In Experiment 2, comparative and absolute evaluations were combined in a single experiment and the BIB effect was mediated for positively and negatively valenced stimuli. Taken in combination, the data support a complex hypothesis that pair-wise presentations induce a comparative process that causes a BIB effect. But when objects are evaluated separately, size and valence interact such that increased size evokes more positive ratings of positive objects and more negative ratings for negative objects.

Pair-Wise, Deformable Mirror, Image Plane-Based Diversity Electric Field Estimation for High Contrast Coronagraphy

NASA Technical Reports Server (NTRS)

Give'on, Amir; Kern, Brian D.; Shaklan, Stuart

2011-01-01

In this paper we describe the complex electric field reconstruction from image plane intensity measurements for high contrast coronagraphic imaging. A deformable mirror (DM) surface is modied with pairs of complementary shapes to create diversity in the image plane of the science camera where the intensity of the light is measured. Along with the Electric Field Conjugation correction algorithm, this estimation method has been used in various high contrast imaging testbeds to achieve the best contrasts to date both in narrow and in broad band light. We present the basic methodology of estimation in easy to follow list of steps, present results from HCIT and raise several open quations we are confronted with using this method.

Detecting phase separation of freeze-dried binary amorphous systems using pair-wise distribution function and multivariate data analysis.

PubMed

Chieng, Norman; Trnka, Hjalte; Boetker, Johan; Pikal, Michael; Rantanen, Jukka; Grohganz, Holger

2013-09-15

The purpose of this study is to investigate the use of multivariate data analysis for powder X-ray diffraction-pair-wise distribution function (PXRD-PDF) data to detect phase separation in freeze-dried binary amorphous systems. Polymer-polymer and polymer-sugar binary systems at various ratios were freeze-dried. All samples were analyzed by PXRD, transformed to PDF and analyzed by principal component analysis (PCA). These results were validated by differential scanning calorimetry (DSC) through characterization of glass transition of the maximally freeze-concentrate solute (Tg'). Analysis of PXRD-PDF data using PCA provides a more clear 'miscible' or 'phase separated' interpretation through the distribution pattern of samples on a score plot presentation compared to residual plot method. In a phase separated system, samples were found to be evenly distributed around the theoretical PDF profile. For systems that were miscible, a clear deviation of samples away from the theoretical PDF profile was observed. Moreover, PCA analysis allows simultaneous analysis of replicate samples. Comparatively, the phase behavior analysis from PXRD-PDF-PCA method was in agreement with the DSC results. Overall, the combined PXRD-PDF-PCA approach improves the clarity of the PXRD-PDF results and can be used as an alternative explorative data analytical tool in detecting phase separation in freeze-dried binary amorphous systems. Copyright © 2013 Elsevier B.V. All rights reserved.

Glutathione S-transferase Pi expression predicts response to adjuvant chemotherapy for stage C colon cancer: a matched historical control study

PubMed Central

2012-01-01

Background This study examined the association between overall survival and Glutathione S-transferase Pi (GST Pi) expression and genetic polymorphism in stage C colon cancer patients after resection alone versus resection plus 5-fluourouracil-based adjuvant chemotherapy. Methods Patients were drawn from a hospital registry of colorectal cancer resections. Those receiving chemotherapy after it was introduced in 1992 were compared with an age and sex matched control group from the preceding period. GST Pi expression was assessed by immunohistochemistry. Overall survival was analysed by the Kaplan-Meier method and Cox regression. Results From an initial 104 patients treated with chemotherapy and 104 matched controls, 26 were excluded because of non-informative immunohistochemistry, leaving 95 in the treated group and 87 controls. Survival did not differ significantly among patients with low GST Pi who did or did not receive chemotherapy and those with high GST Pi who received chemotherapy (lowest pair-wise p = 0.11) whereas patients with high GST Pi who did not receive chemotherapy experienced markedly poorer survival than any of the other three groups (all pair-wise p <0.01). This result was unaffected by GST Pi genotype. Conclusion Stage C colon cancer patients with low GST Pi did not benefit from 5-fluourouracil-based adjuvant chemotherapy whereas those with high GST Pi did. PMID:22639861

Glutathione S-transferase Pi expression predicts response to adjuvant chemotherapy for stage C colon cancer: a matched historical control study.

PubMed

Jankova, Lucy; Robertson, Graham; Chan, Charles; Tan, King L; Kohonen-Corish, Maija; Fung, Caroline L-S; Clarke, Candice; Lin, Betty P C; Molloy, Mark; Chapuis, Pierre H; Bokey, Les; Dent, Owen F; Clarke, Stephen J

2012-05-28

This study examined the association between overall survival and Glutathione S-transferase Pi (GST Pi) expression and genetic polymorphism in stage C colon cancer patients after resection alone versus resection plus 5-fluourouracil-based adjuvant chemotherapy. Patients were drawn from a hospital registry of colorectal cancer resections. Those receiving chemotherapy after it was introduced in 1992 were compared with an age and sex matched control group from the preceding period. GST Pi expression was assessed by immunohistochemistry. Overall survival was analysed by the Kaplan-Meier method and Cox regression. From an initial 104 patients treated with chemotherapy and 104 matched controls, 26 were excluded because of non-informative immunohistochemistry, leaving 95 in the treated group and 87 controls. Survival did not differ significantly among patients with low GST Pi who did or did not receive chemotherapy and those with high GST Pi who received chemotherapy (lowest pair-wise p = 0.11) whereas patients with high GST Pi who did not receive chemotherapy experienced markedly poorer survival than any of the other three groups (all pair-wise p <0.01). This result was unaffected by GST Pi genotype. Stage C colon cancer patients with low GST Pi did not benefit from 5-fluourouracil-based adjuvant chemotherapy whereas those with high GST Pi did.

Untargeted analysis of chromatographic data for green and fermented rooibos: Problem with size effect removal.

PubMed

Tobin, Jade; Walach, Jan; de Beer, Dalene; Williams, Paul J; Filzmoser, Peter; Walczak, Beata

2017-11-24

While analyzing chromatographic data, it is necessary to preprocess it properly before exploration and/or supervised modeling. To make chromatographic signals comparable, it is crucial to remove the scaling effect, caused by differences in overall sample concentrations. One of the efficient methods of signal scaling is Probabilistic Quotient Normalization (PQN) [1]. However, it can be applied only to data for which the majority of features do not vary systematically among the studied classes of signals. When studying the influence of the traditional "fermentation" (oxidation) process on the concentration of 56 individual peaks detected in rooibos plant material, this assumption is not fulfilled. In this case, the only possible solution is the analysis of pairwise log-ratios, which are not influenced by the scaling constant. To estimate significant features, i.e., peaks differentiating the studied classes of samples (green and fermented rooibos plant material), we propose the application of rPLR (robust pair-wise log-ratios) as proposed by Walach et al. [2]. It allows for fast computation and identification of the significant features in terms of original variables (peaks) which is problematic, while working with the unfolded pair-wise log ratios. As demonstrated, it can be applied to designed data sets and in the case of contaminated data, it allows proper conclusions. Copyright © 2017 Elsevier B.V. All rights reserved.

More powerful haplotype sharing by accounting for the mode of inheritance.

PubMed

Ziegler, Andreas; Ewhida, Adel; Brendel, Michael; Kleensang, André

2009-04-01

The concept of haplotype sharing (HS) has received considerable attention recently, and several haplotype association methods have been proposed. Here, we extend the work of Beckmann and colleagues [2005 Hum. Hered. 59:67-78] who derived an HS statistic (BHS) as special case of Mantel's space-time clustering approach. The Mantel-type HS statistic correlates genetic similarity with phenotypic similarity across pairs of individuals. While phenotypic similarity is measured as the mean-corrected cross product of phenotypes, we propose to incorporate information of the underlying genetic model in the measurement of the genetic similarity. Specifically, for the recessive and dominant modes of inheritance we suggest the use of the minimum and maximum of shared length of haplotypes around a marker locus for pairs of individuals. If the underlying genetic model is unknown, we propose a model-free HS Mantel statistic using the max-test approach. We compare our novel HS statistics to BHS using simulated case-control data and illustrate its use by re-analyzing data from a candidate region of chromosome 18q from the Rheumatoid Arthritis (RA) Consortium. We demonstrate that our approach is point-wise valid and superior to BHS. In the re-analysis of the RA data, we identified three regions with point-wise P-values<0.005 containing six known genes (PMIP1, MC4R, PIGN, KIAA1468, TNFRSF11A and ZCCHC2) which might be worth follow-up.

A comparison of somatic mutational spectra in healthy study populations from Russia, Sweden and USA

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

Noori, P; Hou, S; Jones, I M

Comparison of mutation spectra at the hypoxanthine-phosphoribosyl transferase (HPRT) gene of peripheral blood T lymphocytes may provide insight into the aetiology of somatic mutation contributing to carcinogenesis and other diseases. To increase knowledge of mutation spectra in healthy people, we have analyzed HPRT mutant T-cells of 50 healthy Russians originally recruited as controls for a study of Chernobyl clean-up workers (Jones et al. Radiation Res. 158, 2002, 424). Reverse transcriptase polymerase chain reactions and DNA sequencing identified 161 independent mutations among 176 thioguanine resistant mutants. Forty (40) mutations affected splicing mechanisms and 27 deletions or insertions of 1 to 60more » nucleotides were identified. Ninety four (94) single base substitutions were identified, including 62 different mutations at 55 different nucleotide positions, of which 19 had not previously been reported in human T-cells. Comparison of this base substitution spectrum with mutation spectra in a USA (Burkhart-Schultz et al. Carcinogenesis 17, 1996, 1871) and two Swedish populations (Podlutsky et al, Carcinogenesis 19, 1998, 557, Podlutsky et al. Mutation Res. 431, 1999, 325) revealed similarity in the type, frequency and distribution of mutations in the four spectra, consistent with aetiologies inherent in human metabolism. There were 15-19 identical mutations in the three pair-wise comparisons of Russian with USA and Swedish spectra. Intriguingly, there were 21 mutations unique to the Russian spectrum, and comparison by the Monte Carlo method of Adams and Skopek (J. Mol. Biol. 194, 1987, 391) indicated that the Russian spectrum was different from both Swedish spectra (P=0.007, 0.002) but not different from the USA spectrum (P=0.07), when Bonferroni correction for multiple comparisons was made (p < 0.008 required for significance). Age and smoking did not account for these differences. Other factors causing mutational differences need to be explored.« less

Intersatellite Calibration of Microwave Radiometers for GPM

NASA Astrophysics Data System (ADS)

Wilheit, T. T.

2010-12-01

The aim of the GPM mission is to measure precipitation globally with high temporal resolution by using a constellation of satellites logically united by the GPM Core Satellite which will be in a non-sunsynchronous, medium inclination orbit. The usefulness of the combined product depends on the consistency of precipitation retrievals from the various microwave radiometers. The calibration requirements for this consistency are quite daunting requiring a multi-layered approach. The radiometers can vary considerably in their frequencies, view angles, polarizations and spatial resolutions depending on their primary application and other constraints. The planned parametric algorithms will correct for the varying viewing parameters, but they are still vulnerable to calibration errors, both relative and absolute. The GPM Intersatellite Calibration Working Group (aka X-CAL) will adjust the calibration of all the radiometers to a common consensus standard for the GPM Level 1C product to be used in precipitation retrievals. Finally, each Precipitation Algorithm Working Group must have its own strategy for removing the residual errors. If the final adjustments are small, the credibility of the precipitation retrievals will be enhanced. Before intercomparing, the radiometers must be self consistent on a scan-wise and orbit-wise basis. Pre-screening for this consistency constitutes the first step in the intercomparison. The radiometers are then compared pair-wise with the microwave radiometer (GMI) on the GPM Core Satellite. Two distinct approaches are used for sake of cross-checking the results. On the one hand, nearly simultaneous observations are collected at the cross-over points of the orbits and the observations of one are converted to virtual observations of the other using a radiative transfer model to permit comparisons. The complementary approach collects histograms of brightness temperature from each instrument. In each case a model is needed to translate the observations from one set of viewing parameters to those of the GMI. For the conically scanning window channel radiometers, the models are reasonably complete. Currently we have compared TMI with Windsat and arrived at a preliminary consensus calibration based on the pair. This consensus calibration standard has been applied to TMI and is currently being compared with AMSR-E on the Aqua satellite. In this way we are implementing a rolling wave spin-up of X-CAL. In this sense, the launch of GPM core will simply provide one more radiometer to the constellation; one hopes it will be the best calibrated. Water vapor and temperature sounders will use a different scenario. Some of the precipitation retrieval algorithms will use sounding channels. The GMI will include typical water vapor sounding channels. The radiances are ingested directly via 3DVAR and 4DVAR techniques into forecast models by many operational weather forecast agencies. The residuals and calibration adjustments of this process will provide a measure of the relative calibration errors throughout the constellation. The use of the ARM Southern Great Plains site as a benchmark for calibrating the more opaque channels is also being investigated.

Type-II generalized family-wise error rate formulas with application to sample size determination.

PubMed

Delorme, Phillipe; de Micheaux, Pierre Lafaye; Liquet, Benoit; Riou, Jérémie

2016-07-20

Multiple endpoints are increasingly used in clinical trials. The significance of some of these clinical trials is established if at least r null hypotheses are rejected among m that are simultaneously tested. The usual approach in multiple hypothesis testing is to control the family-wise error rate, which is defined as the probability that at least one type-I error is made. More recently, the q-generalized family-wise error rate has been introduced to control the probability of making at least q false rejections. For procedures controlling this global type-I error rate, we define a type-II r-generalized family-wise error rate, which is directly related to the r-power defined as the probability of rejecting at least r false null hypotheses. We obtain very general power formulas that can be used to compute the sample size for single-step and step-wise procedures. These are implemented in our R package rPowerSampleSize available on the CRAN, making them directly available to end users. Complexities of the formulas are presented to gain insight into computation time issues. Comparison with Monte Carlo strategy is also presented. We compute sample sizes for two clinical trials involving multiple endpoints: one designed to investigate the effectiveness of a drug against acute heart failure and the other for the immunogenicity of a vaccine strategy against pneumococcus. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

An enquiry into the method of paired comparison: reliability, scaling, and Thurstone's Law of Comparative Judgment

Treesearch

Thomas C. Brown; George L. Peterson

2009-01-01

The method of paired comparisons is used to measure individuals' preference orderings of items presented to them as discrete binary choices. This paper reviews the theory and application of the paired comparison method, describes a new computer program available for eliciting the choices, and presents an analysis of methods for scaling paired choice data to...

Partially restored resting-state functional connectivity in women recovered from anorexia nervosa

PubMed Central

Boehm, Ilka; Geisler, Daniel; Tam, Friederike; King, Joseph A.; Ritschel, Franziska; Seidel, Maria; Bernardoni, Fabio; Murr, Julia; Goschke, Thomas; Calhoun, Vince D.; Roessner, Veit; Ehrlich, Stefan

2016-01-01

Background We have previously shown increased resting-state functional connectivity (rsFC) in the frontoparietal network (FPN) and the default mode network (DMN) in patients with acute anorexia nervosa. Based on these findings we investigated within-network rsFC in patients recovered from anorexia nervosa to examine whether these abnormalities are a state or trait marker of the disease. To extend the understanding of functional connectivity in patients with anorexia nervosa, we also estimated rsFC between large-scale networks. Methods Girls and women recovered from anorexia nervosa and pair-wise, age- and sex-matched healthy controls underwent a resting-state fMRI scan. Using independent component analyses (ICA), we isolated the FPN, DMN and salience network. We used standard comparisons as well as a hypothesis-based approach to test the findings of our previous rsFC study in this recovered cohort. Temporal correlations between network time-course pairs were computed to investigate functional network connectivity (FNC). Results Thirty-one patients recovered from anorexia nervosa and 31 controls participated in our study. Standard group comparisons revealed reduced rsFC between the dorsolateral prefrontal cortex (dlPFC) and the FPN in the recovered group. Using a hypothesis-based approach we extended the previous finding of increased rsFC between the angular gyrus and the FPN in patients recovered from anorexia nervosa. No group differences in FNC were revealed. Limitations The study design did not allow us to conclude that the difference found in rsFC constitutes a scar effect of the disease. Conclusion This study suggests that some abnormal rsFC patterns found in patients recovered from anorexia nervosa normalize after long-term weight restoration, while distorted rsFC in the FPN, a network that has been associated with cognitive control, may constitute a trait marker of the disorder. PMID:27045551

VizieR Online Data Catalog: Taurus ultra-wide pairs (Joncour+, 2017)

NASA Astrophysics Data System (ADS)

Joncour, I.; Duchene, G.; Moraux, E.

2017-05-01

Although a recent catalog of Taurus members has been released including newly detected mid-infrared Wide-field Infrared Survey Explorer (WISE) sources (Esplin et al., 2014, Cat. J/ApJ/784/126), we adopted the catalog containing 352 Taurus members that offers a full census of members down to 0.02 Mȯ(Luhman et al., 2010, Cat. J/ApJS/186/111; Rebull et al., 2010, Cat. J/ApJS/186/259), which we supplemented with stellar multiplicity data. (3 data files).

An Extremely Red and Two Other Nearby L Dwarf Candidates Previously Overlooked in 2MASS, WISE, and Other Surveys

NASA Astrophysics Data System (ADS)

Scholz, Ralf-Dieter; Bell, Cameron P. M.

2018-02-01

We present three new nearby L dwarf candidates, found in a continued combined color/proper motion search using WISE, 2MASS, and other survey data, where we included extended WISE sources and looked closer to the Galactic plane region. Their spectral types and distances were estimated from photometric comparisons to well-known L dwarfs with trigonometric parallaxes. The first object, 2MASS J07555430-3259589, is an extremely red L7.5p dwarf candidate at a photometric distance of about 16 pc. Its position, proper motion and distance are consistent with membership in the Carina-Near young moving group. The second one, 2MASS J07414279-0506464, is resolved in Gaia DR1 as a close binary (separation 0.3 arcsec), and we classify it as a equal-mass binary candidate consisting of two L5 dwarfs at 19 pc. Our nearest new neighbor, 2MASS J19251275+0700362, is an L7 dwarf candidate at 10 pc.

VoxelStats: A MATLAB Package for Multi-Modal Voxel-Wise Brain Image Analysis.

PubMed

Mathotaarachchi, Sulantha; Wang, Seqian; Shin, Monica; Pascoal, Tharick A; Benedet, Andrea L; Kang, Min Su; Beaudry, Thomas; Fonov, Vladimir S; Gauthier, Serge; Labbe, Aurélie; Rosa-Neto, Pedro

2016-01-01

In healthy individuals, behavioral outcomes are highly associated with the variability on brain regional structure or neurochemical phenotypes. Similarly, in the context of neurodegenerative conditions, neuroimaging reveals that cognitive decline is linked to the magnitude of atrophy, neurochemical declines, or concentrations of abnormal protein aggregates across brain regions. However, modeling the effects of multiple regional abnormalities as determinants of cognitive decline at the voxel level remains largely unexplored by multimodal imaging research, given the high computational cost of estimating regression models for every single voxel from various imaging modalities. VoxelStats is a voxel-wise computational framework to overcome these computational limitations and to perform statistical operations on multiple scalar variables and imaging modalities at the voxel level. VoxelStats package has been developed in Matlab(®) and supports imaging formats such as Nifti-1, ANALYZE, and MINC v2. Prebuilt functions in VoxelStats enable the user to perform voxel-wise general and generalized linear models and mixed effect models with multiple volumetric covariates. Importantly, VoxelStats can recognize scalar values or image volumes as response variables and can accommodate volumetric statistical covariates as well as their interaction effects with other variables. Furthermore, this package includes built-in functionality to perform voxel-wise receiver operating characteristic analysis and paired and unpaired group contrast analysis. Validation of VoxelStats was conducted by comparing the linear regression functionality with existing toolboxes such as glim_image and RMINC. The validation results were identical to existing methods and the additional functionality was demonstrated by generating feature case assessments (t-statistics, odds ratio, and true positive rate maps). In summary, VoxelStats expands the current methods for multimodal imaging analysis by allowing the estimation of advanced regional association metrics at the voxel level.

An analysis of relational complexity in an air traffic control conflict detection task.

PubMed

Boag, Christine; Neal, Andrew; Loft, Shayne; Halford, Graeme S

2006-11-15

Theoretical analyses of air traffic complexity were carried out using the Method for the Analysis of Relational Complexity. Twenty-two air traffic controllers examined static air traffic displays and were required to detect and resolve conflicts. Objective measures of performance included conflict detection time and accuracy. Subjective perceptions of mental workload were assessed by a complexity-sorting task and subjective ratings of the difficulty of different aspects of the task. A metric quantifying the complexity of pair-wise relations among aircraft was able to account for a substantial portion of the variance in the perceived complexity and difficulty of conflict detection problems, as well as reaction time. Other variables that influenced performance included the mean minimum separation between aircraft pairs and the amount of time that aircraft spent in conflict.

A Coulomb collision algorithm for weighted particle simulations

NASA Technical Reports Server (NTRS)

Miller, Ronald H.; Combi, Michael R.

1994-01-01

A binary Coulomb collision algorithm is developed for weighted particle simulations employing Monte Carlo techniques. Charged particles within a given spatial grid cell are pair-wise scattered, explicitly conserving momentum and implicitly conserving energy. A similar algorithm developed by Takizuka and Abe (1977) conserves momentum and energy provided the particles are unweighted (each particle representing equal fractions of the total particle density). If applied as is to simulations incorporating weighted particles, the plasma temperatures equilibrate to an incorrect temperature, as compared to theory. Using the appropriate pairing statistics, a Coulomb collision algorithm is developed for weighted particles. The algorithm conserves energy and momentum and produces the appropriate relaxation time scales as compared to theoretical predictions. Such an algorithm is necessary for future work studying self-consistent multi-species kinetic transport.

Item Response Modeling of Paired Comparison and Ranking Data

ERIC Educational Resources Information Center

Maydeu-Olivares, Alberto; Brown, Anna

2010-01-01

The comparative format used in ranking and paired comparisons tasks can significantly reduce the impact of uniform response biases typically associated with rating scales. Thurstone's (1927, 1931) model provides a powerful framework for modeling comparative data such as paired comparisons and rankings. Although Thurstonian models are generally…

ChIP-PIT: Enhancing the Analysis of ChIP-Seq Data Using Convex-Relaxed Pair-Wise Interaction Tensor Decomposition.

PubMed

Zhu, Lin; Guo, Wei-Li; Deng, Su-Ping; Huang, De-Shuang

2016-01-01

In recent years, thanks to the efforts of individual scientists and research consortiums, a huge amount of chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) experimental data have been accumulated. Instead of investigating them independently, several recent studies have convincingly demonstrated that a wealth of scientific insights can be gained by integrative analysis of these ChIP-seq data. However, when used for the purpose of integrative analysis, a serious drawback of current ChIP-seq technique is that it is still expensive and time-consuming to generate ChIP-seq datasets of high standard. Most researchers are therefore unable to obtain complete ChIP-seq data for several TFs in a wide variety of cell lines, which considerably limits the understanding of transcriptional regulation pattern. In this paper, we propose a novel method called ChIP-PIT to overcome the aforementioned limitation. In ChIP-PIT, ChIP-seq data corresponding to a diverse collection of cell types, TFs and genes are fused together using the three-mode pair-wise interaction tensor (PIT) model, and the prediction of unperformed ChIP-seq experimental results is formulated as a tensor completion problem. Computationally, we propose efficient first-order method based on extensions of coordinate descent method to learn the optimal solution of ChIP-PIT, which makes it particularly suitable for the analysis of massive scale ChIP-seq data. Experimental evaluation the ENCODE data illustrate the usefulness of the proposed model.

Inferring Weighted Directed Association Network from Multivariate Time Series with a Synthetic Method of Partial Symbolic Transfer Entropy Spectrum and Granger Causality

PubMed Central

Hu, Yanzhu; Ai, Xinbo

2016-01-01

Complex network methodology is very useful for complex system explorer. However, the relationships among variables in complex system are usually not clear. Therefore, inferring association networks among variables from their observed data has been a popular research topic. We propose a synthetic method, named small-shuffle partial symbolic transfer entropy spectrum (SSPSTES), for inferring association network from multivariate time series. The method synthesizes surrogate data, partial symbolic transfer entropy (PSTE) and Granger causality. A proper threshold selection is crucial for common correlation identification methods and it is not easy for users. The proposed method can not only identify the strong correlation without selecting a threshold but also has the ability of correlation quantification, direction identification and temporal relation identification. The method can be divided into three layers, i.e. data layer, model layer and network layer. In the model layer, the method identifies all the possible pair-wise correlation. In the network layer, we introduce a filter algorithm to remove the indirect weak correlation and retain strong correlation. Finally, we build a weighted adjacency matrix, the value of each entry representing the correlation level between pair-wise variables, and then get the weighted directed association network. Two numerical simulated data from linear system and nonlinear system are illustrated to show the steps and performance of the proposed approach. The ability of the proposed method is approved by an application finally. PMID:27832153

Non-random assembly of bacterioplankton communities in the subtropical north pacific ocean.

PubMed

Eiler, Alexander; Hayakawa, Darin H; Rappé, Michael S

2011-01-01

The exploration of bacterial diversity in the global ocean has revealed new taxa and previously unrecognized metabolic potential; however, our understanding of what regulates this diversity is limited. Using terminal restriction fragment length polymorphism (T-RFLP) data from bacterial small-subunit ribosomal RNA genes we show that, independent of depth and time, a large fraction of bacterioplankton co-occurrence patterns are non-random in the oligotrophic North Pacific subtropical gyre (NPSG). Pair-wise correlations of all identified operational taxonomic units (OTUs) revealed a high degree of significance, with 6.6% of the pair-wise co-occurrences being negatively correlated and 20.7% of them being positive. The most abundant OTUs, putatively identified as Prochlorococcus, SAR11, and SAR116 bacteria, were among the most correlated OTUs. As expected, bacterial community composition lacked statistically significant patterns of seasonality in the mostly stratified water column except in a few depth horizons of the sunlit surface waters, with higher frequency variations in community structure apparently related to populations associated with the deep chlorophyll maximum. Communities were structured vertically into epipelagic, mesopelagic, and bathypelagic populations. Permutation-based statistical analyses of T-RFLP data and their corresponding metadata revealed a broad range of putative environmental drivers controlling bacterioplankton community composition in the NPSG, including concentrations of inorganic nutrients and phytoplankton pigments. Together, our results suggest that deterministic forces such as environmental filtering and interactions among taxa determine bacterioplankton community patterns, and consequently affect ecosystem functions in the NPSG.

Image and the University.

ERIC Educational Resources Information Center

Hayes, Thomas J.

1993-01-01

It is argued that colleges tend to have a high opinion of themselves and would be wise to learn how their various publics (community, business community, guidance counselors, college-bound students, parents, current students, alumni, staff) perceive them. Comparison with competitors and monitoring of change over time is also recommended. (MSE)

Diffusion and imaging properties of three new lipophilic tracers, NeuroVue ™ Maroon, NeuroVue ™ Red and NeuroVue ™ Green and their use for double and triple labeling of neuronal profile.

PubMed Central

Fritzsch, B.; Muirhead, K.A.; Feng, Feng; D.Gray, B.; Ohlsson-Wilhelm, B. M.

2006-01-01

We describe here diffusion and imaging properties of three new lipophilic tracers, NeuroVue ™ Maroon (near infrared), NeuroVue ™ Red and NeuroVue ™ Green. Using pair wise comparisons between the new dyes and existing dyes (DiI, DiA, DiD, DiO, PKH2, PKH26) applied to the left and the right side of fixed spinal cord preparations, we show that NeuroVue Maroon (excitation max 647 nm) surpasses all other dyes in this study in signal to noise ratio. We also present data showing the utility of these new dyes for both double labeling and triple labeling in combination with each other or existing lipophilic tracers. Using mice bearing the PLP-eGFP transgene, we demonstrate that either NeuroVue Maroon or NeuroVue Red can readily be combined with eGFP labeling. Double labeling experiments using NeuroVue Red and eGFP allowed us to demonstrate that every fiber in the neonatal ear is surrounded by developing Schwann cells. PMID:16023922

Multiphase flows of N immiscible incompressible fluids: A reduction-consistent and thermodynamically-consistent formulation and associated algorithm

NASA Astrophysics Data System (ADS)

Dong, S.

2018-05-01

We present a reduction-consistent and thermodynamically consistent formulation and an associated numerical algorithm for simulating the dynamics of an isothermal mixture consisting of N (N ⩾ 2) immiscible incompressible fluids with different physical properties (densities, viscosities, and pair-wise surface tensions). By reduction consistency we refer to the property that if only a set of M (1 ⩽ M ⩽ N - 1) fluids are present in the system then the N-phase governing equations and boundary conditions will exactly reduce to those for the corresponding M-phase system. By thermodynamic consistency we refer to the property that the formulation honors the thermodynamic principles. Our N-phase formulation is developed based on a more general method that allows for the systematic construction of reduction-consistent formulations, and the method suggests the existence of many possible forms of reduction-consistent and thermodynamically consistent N-phase formulations. Extensive numerical experiments have been presented for flow problems involving multiple fluid components and large density ratios and large viscosity ratios, and the simulation results are compared with the physical theories or the available physical solutions. The comparisons demonstrate that our method produces physically accurate results for this class of problems.

Testing the myth: tolerant dogs and aggressive wolves.

PubMed

Range, Friederike; Ritter, Caroline; Virányi, Zsófia

2015-05-22

Cooperation is thought to be highly dependent on tolerance. For example, it has been suggested that dog-human cooperation has been enabled by selecting dogs for increased tolerance and reduced aggression during the course of domestication ('emotional reactivity hypothesis'). However, based on observations of social interactions among members of captive packs, a few dog-wolf comparisons found contradictory results. In this study, we compared intraspecies aggression and tolerance of dogs and wolves raised and kept under identical conditions by investigating their agonistic behaviours and cofeeding during pair-wise food competition tests, a situation that has been directly linked to cooperation. We found that in wolves, dominant and subordinate members of the dyads monopolized the food and showed agonistic behaviours to a similar extent, whereas in dogs these behaviours were privileges of the high-ranking individuals. The fact that subordinate dogs rarely challenged their higher-ranking partners suggests a steeper dominance hierarchy in dogs than in wolves. Finally, wolves as well as dogs showed only rare and weak aggression towards each other. Therefore, we suggest that wolves are sufficiently tolerant to enable wolf-wolf cooperation, which in turn might have been the basis for the evolution of dog-human cooperation (canine cooperation hypothesis).

Testing the myth: tolerant dogs and aggressive wolves

PubMed Central

Range, Friederike; Ritter, Caroline; Virányi, Zsófia

2015-01-01

Cooperation is thought to be highly dependent on tolerance. For example, it has been suggested that dog–human cooperation has been enabled by selecting dogs for increased tolerance and reduced aggression during the course of domestication (‘emotional reactivity hypothesis’). However, based on observations of social interactions among members of captive packs, a few dog–wolf comparisons found contradictory results. In this study, we compared intraspecies aggression and tolerance of dogs and wolves raised and kept under identical conditions by investigating their agonistic behaviours and cofeeding during pair-wise food competition tests, a situation that has been directly linked to cooperation. We found that in wolves, dominant and subordinate members of the dyads monopolized the food and showed agonistic behaviours to a similar extent, whereas in dogs these behaviours were privileges of the high-ranking individuals. The fact that subordinate dogs rarely challenged their higher-ranking partners suggests a steeper dominance hierarchy in dogs than in wolves. Finally, wolves as well as dogs showed only rare and weak aggression towards each other. Therefore, we suggest that wolves are sufficiently tolerant to enable wolf–wolf cooperation, which in turn might have been the basis for the evolution of dog–human cooperation (canine cooperation hypothesis). PMID:25904666

Sustainable Urban Forestry Potential Based Quantitative And Qualitative Measurement Using Geospatial Technique

NASA Astrophysics Data System (ADS)

Rosli, A. Z.; Reba, M. N. M.; Roslan, N.; Room, M. H. M.

2014-02-01

In order to maintain the stability of natural ecosystems around urban areas, urban forestry will be the best initiative to maintain and control green space in our country. Integration between remote sensing (RS) and geospatial information system (GIS) serves as an effective tool for monitoring environmental changes and planning, managing and developing a sustainable urbanization. This paper aims to assess capability of the integration of RS and GIS to provide information for urban forest potential sites based on qualitative and quantitative by using priority parameter ranking in the new township of Nusajaya. SPOT image was used to provide high spatial accuracy while map of topography, landuse, soils group, hydrology, Digital Elevation Model (DEM) and soil series data were applied to enhance the satellite image in detecting and locating present attributes and features on the ground. Multi-Criteria Decision Making (MCDM) technique provides structural and pair wise quantification and comparison elements and criteria for priority ranking for urban forestry purpose. Slope, soil texture, drainage, spatial area, availability of natural resource, and vicinity of urban area are criteria considered in this study. This study highlighted the priority ranking MCDM is cost effective tool for decision-making in urban forestry planning and landscaping.

Patch forest: a hybrid framework of random forest and patch-based segmentation

NASA Astrophysics Data System (ADS)

Xie, Zhongliu; Gillies, Duncan

2016-03-01

The development of an accurate, robust and fast segmentation algorithm has long been a research focus in medical computer vision. State-of-the-art practices often involve non-rigidly registering a target image with a set of training atlases for label propagation over the target space to perform segmentation, a.k.a. multi-atlas label propagation (MALP). In recent years, the patch-based segmentation (PBS) framework has gained wide attention due to its advantage of relaxing the strict voxel-to-voxel correspondence to a series of pair-wise patch comparisons for contextual pattern matching. Despite a high accuracy reported in many scenarios, computational efficiency has consistently been a major obstacle for both approaches. Inspired by recent work on random forest, in this paper we propose a patch forest approach, which by equipping the conventional PBS with a fast patch search engine, is able to boost segmentation speed significantly while retaining an equal level of accuracy. In addition, a fast forest training mechanism is also proposed, with the use of a dynamic grid framework to efficiently approximate data compactness computation and a 3D integral image technique for fast box feature retrieval.

Sockeye: A 3D Environment for Comparative Genomics

PubMed Central

Montgomery, Stephen B.; Astakhova, Tamara; Bilenky, Mikhail; Birney, Ewan; Fu, Tony; Hassel, Maik; Melsopp, Craig; Rak, Marcin; Robertson, A. Gordon; Sleumer, Monica; Siddiqui, Asim S.; Jones, Steven J.M.

2004-01-01

Comparative genomics techniques are used in bioinformatics analyses to identify the structural and functional properties of DNA sequences. As the amount of available sequence data steadily increases, the ability to perform large-scale comparative analyses has become increasingly relevant. In addition, the growing complexity of genomic feature annotation means that new approaches to genomic visualization need to be explored. We have developed a Java-based application called Sockeye that uses three-dimensional (3D) graphics technology to facilitate the visualization of annotation and conservation across multiple sequences. This software uses the Ensembl database project to import sequence and annotation information from several eukaryotic species. A user can additionally import their own custom sequence and annotation data. Individual annotation objects are displayed in Sockeye by using custom 3D models. Ensembl-derived and imported sequences can be analyzed by using a suite of multiple and pair-wise alignment algorithms. The results of these comparative analyses are also displayed in the 3D environment of Sockeye. By using the Java3D API to visualize genomic data in a 3D environment, we are able to compactly display cross-sequence comparisons. This provides the user with a novel platform for visualizing and comparing genomic feature organization. PMID:15123592

GPU-Meta-Storms: computing the structure similarities among massive amount of microbial community samples using GPU.

PubMed

Su, Xiaoquan; Wang, Xuetao; Jing, Gongchao; Ning, Kang

2014-04-01

The number of microbial community samples is increasing with exponential speed. Data-mining among microbial community samples could facilitate the discovery of valuable biological information that is still hidden in the massive data. However, current methods for the comparison among microbial communities are limited by their ability to process large amount of samples each with complex community structure. We have developed an optimized GPU-based software, GPU-Meta-Storms, to efficiently measure the quantitative phylogenetic similarity among massive amount of microbial community samples. Our results have shown that GPU-Meta-Storms would be able to compute the pair-wise similarity scores for 10 240 samples within 20 min, which gained a speed-up of >17 000 times compared with single-core CPU, and >2600 times compared with 16-core CPU. Therefore, the high-performance of GPU-Meta-Storms could facilitate in-depth data mining among massive microbial community samples, and make the real-time analysis and monitoring of temporal or conditional changes for microbial communities possible. GPU-Meta-Storms is implemented by CUDA (Compute Unified Device Architecture) and C++. Source code is available at http://www.computationalbioenergy.org/meta-storms.html.

Comparing masked target transform volume (MTTV) clutter metric to human observer evaluation of visual clutter

NASA Astrophysics Data System (ADS)

Camp, H. A.; Moyer, Steven; Moore, Richard K.

2010-04-01

The Night Vision and Electronic Sensors Directorate's current time-limited search (TLS) model, which makes use of the targeting task performance (TTP) metric to describe image quality, does not explicitly account for the effects of visual clutter on observer performance. The TLS model is currently based on empirical fits to describe human performance for a time of day, spectrum and environment. Incorporating a clutter metric into the TLS model may reduce the number of these empirical fits needed. The masked target transform volume (MTTV) clutter metric has been previously presented and compared to other clutter metrics. Using real infrared imagery of rural images with varying levels of clutter, NVESD is currently evaluating the appropriateness of the MTTV metric. NVESD had twenty subject matter experts (SME) rank the amount of clutter in each scene in a series of pair-wise comparisons. MTTV metric values were calculated and then compared to the SME observers rankings. The MTTV metric ranked the clutter in a similar manner to the SME evaluation, suggesting that the MTTV metric may emulate SME response. This paper is a first step in quantifying clutter and measuring the agreement to subjective human evaluation.

Integrating sensory evaluation in adaptive conjoint analysis to elaborate the conflicting influence of intrinsic and extrinsic attributes on food choice.

PubMed

Hoppert, Karin; Mai, Robert; Zahn, Susann; Hoffmann, Stefan; Rohm, Harald

2012-12-01

Sensory properties and packaging information are factors which considerably contribute to food choice. We present a new methodology in which sensory preference testing was integrated in adaptive conjoint analysis. By simultaneous variation of intrinsic and extrinsic attributes on identical levels, this procedure allows assessing the importance of attribute/level combinations on product selection. In a set-up with nine pair-wise comparisons and four subsequent calibration assessments, 101 young consumers evaluated vanilla yoghurt which was varied in fat content (four levels), sugar content (two levels) and flavour intensity (two levels); the same attribute/level combinations were also presented as extrinsic information. The results indicate that the evaluation of a particular attribute may largely diverge in intrinsic and in extrinsic processing. We noticed from our utility values that, for example, the acceptance of yoghurt increases with an increasing level of the actual fat content, whereas acceptance diminishes when a high fat content is labelled on the product. This article further implicates that neglecting these diverging relationships may lead to an over- or underestimation of the importance of an attribute for food choice. Copyright © 2012 Elsevier Ltd. All rights reserved.

Paired Comparisons.

DTIC Science & Technology

1982-05-01

including multidimensional scaling. Applications have arisen in many areas, but most notably in food technolog, marketing research, and sports ... competition .- An extensive bibliography on paired comparisons by Davidson and Farquhar (1976) contains some 400 references. - Paired comparisons have been...consideration of chess competition . Ford (1957) pro- posed the model independently. Both Zermelo and Ford concentrated on solution of normal equations for

68Ga-HBED-CC-PSMA PET/CT Versus Histopathology in Primary Localized Prostate Cancer: A Voxel-Wise Comparison

PubMed Central

Zamboglou, Constantinos; Schiller, Florian; Fechter, Tobias; Wieser, Gesche; Jilg, Cordula Annette; Chirindel, Alin; Salman, Nasr; Drendel, Vanessa; Werner, Martin; Mix, Michael; Meyer, Philipp Tobias; Grosu, Anca Ligia

2016-01-01

Purpose: We performed a voxel-wise comparison of 68Ga-HBED-CC-PSMA PET/CT with prostate histopathology to evaluate the performance of 68Ga-HBED-CC-PSMA for the detection and delineation of primary prostate cancer (PCa). Methodology: Nine patients with histopathological proven primary PCa underwent 68Ga-HBED-CC-PSMA PET/CT followed by radical prostatectomy. Resected prostates were scanned by ex-vivo CT in a special localizer and histopathologically prepared. Histopathological information was matched to ex-vivo CT. PCa volume (PCa-histo) and non-PCa tissue in the prostate (NPCa-histo) were processed to obtain a PCa-model, which was adjusted to PET-resolution (histo-PET). Each histo-PET was coregistered to in-vivo PSMA-PET/CT data. Results: Analysis of spatial overlap between histo-PET and PSMA PET revealed highly significant correlations (p < 10-5) in nine patients and moderate to high coefficients of determination (R²) from 42 to 82 % with an average of 60 ± 14 % in eight patients (in one patient R2 = 7 %). Mean SUVmean in PCa-histo and NPCa-histo was 5.6 ± 6.1 and 3.3 ± 2.5 (p = 0.012). Voxel-wise receiver-operating characteristic (ROC) analyses comparing the prediction by PSMA-PET with the non-smoothed tumor distribution from histopathology yielded an average area under the curve of 0.83 ± 0.12. Absolute and relative SUV (normalized to SUVmax) thresholds for achieving at least 90 % sensitivity were 3.19 ± 3.35 and 0.28 ± 0.09, respectively. Conclusions: Voxel-wise analyses revealed good correlations of 68Ga-HBED-CC-PSMA PET/CT and histopathology in eight out of nine patients. Thus, PSMA-PET allows a reliable detection and delineation of PCa as basis for PET-guided focal therapies. PMID:27446496

Gender differences in the effects of childhood adversity on alcohol, drug, and polysubstance-related disorders.

PubMed

Evans, Elizabeth A; Grella, Christine E; Upchurch, Dawn M

2017-07-01

To examine gender differences in the associations between childhood adversity and different types of substance use disorders and whether gender moderates these relationships. We analyzed data from 19,209 women and 13,898 men as provided by Wave 2 (2004-2005) of the National Epidemiologic Survey on Alcohol and Related Conditions (NESARC) to examine whether gender moderates the associations between childhood adversity and DSM-IV defined lifetime occurrence of alcohol, drug, and polysubstance-related disorders. We used multinomial logistic regression, weighted to be representative of the US adult civilian, noninstitutionalized population, and we calculated predicted probabilities by gender, controlling for covariates. To test which specific moderation contrasts were statistically significant, we conducted pair-wise comparisons corrected for multiple comparisons using Bonferroni's method. For each type of substance use disorder, risk was increased by more exposure to childhood adversity, and women had a lower risk than men. However, moderation effects revealed that with more experiences of childhood adversity, the gender gap in predicted probability for a disorder narrowed in relation to alcohol, it converged in relation to drugs such that risk among women surpassed that among men, and it widened in relation to polysubstances. Knowledge regarding substance-specific gender differences associated with childhood adversity exposure can inform evidence-based treatments. It may also be useful for shaping other types of gender-sensitive public health initiatives to ameliorate or prevent different types of substance use disorders.

Laparoscopic-guided abdominal wall nerve blocks in the pediatric population: a novel technique with comparison to ultrasound-guided blocks and local wound infiltration alone.

PubMed

Landmann, Alessandra; Visoiu, Mihaela; Malek, Marcus M

2018-03-01

Abdominal wall nerve blocks have been gaining popularity for the treatment of perioperative pain in children. Our aim was to compare a technique of surgeon-performed, laparoscopic abdominal wall nerve blocks to anesthesia-placed, ultrasound-guided abdominal wall nerve blocks and the current standard of local wound infiltration. After institutional review board approval was obtained, a retrospective chart review was performed of pediatric patients treated at a single institution during a 2-year period. Statistics were calculated using analysis of variance with post-hoc Bonferonni t tests for pair-wise comparisons. Included in this study were 380 patients who received ultrasound-guided abdominal wall nerve blocks (n = 125), laparoscopic-guided abdominal wall nerve blocks (n = 88), and local wound infiltration (n = 117). Groups were well matched for age, sex, and weight. There was no significant difference in pain scores within the first 8 hours or narcotic usage between groups. Local wound infiltration demonstrated the shortest overall time required to perform (P < .0001). Patients who received a surgeon-performed abdominal wall nerve block demonstrated a shorter duration of hospital stay when compared to the other groups (P = .02). Our study has demonstrated that laparoscopic-guided abdominal wall nerve blocks show similar efficacy to ultrasound-guided nerve blocks performed by pain management physicians without increasing time in the operating room. Copyright © 2017 Elsevier Inc. All rights reserved.

Brain Plasticity in Speech Training in Native English Speakers Learning Mandarin Tones

NASA Astrophysics Data System (ADS)

Heinzen, Christina Carolyn

The current study employed behavioral and event-related potential (ERP) measures to investigate brain plasticity associated with second-language (L2) phonetic learning based on an adaptive computer training program. The program utilized the acoustic characteristics of Infant-Directed Speech (IDS) to train monolingual American English-speaking listeners to perceive Mandarin lexical tones. Behavioral identification and discrimination tasks were conducted using naturally recorded speech, carefully controlled synthetic speech, and non-speech control stimuli. The ERP experiments were conducted with selected synthetic speech stimuli in a passive listening oddball paradigm. Identical pre- and post- tests were administered on nine adult listeners, who completed two-to-three hours of perceptual training. The perceptual training sessions used pair-wise lexical tone identification, and progressed through seven levels of difficulty for each tone pair. The levels of difficulty included progression in speaker variability from one to four speakers and progression through four levels of acoustic exaggeration of duration, pitch range, and pitch contour. Behavioral results for the natural speech stimuli revealed significant training-induced improvement in identification of Tones 1, 3, and 4. Improvements in identification of Tone 4 generalized to novel stimuli as well. Additionally, comparison between discrimination of across-category and within-category stimulus pairs taken from a synthetic continuum revealed a training-induced shift toward more native-like categorical perception of the Mandarin lexical tones. Analysis of the Mismatch Negativity (MMN) responses in the ERP data revealed increased amplitude and decreased latency for pre-attentive processing of across-category discrimination as a result of training. There were also laterality changes in the MMN responses to the non-speech control stimuli, which could reflect reallocation of brain resources in processing pitch patterns for the across-category lexical tone contrast. Overall, the results support the use of IDS characteristics in training non-native speech contrasts and provide impetus for further research.

Strengthening the Connection Between Space and Society: A Comparative Analysis of Supernovae Distribution in the Andromeda Galaxy for Secondary School Students

NASA Astrophysics Data System (ADS)

Borders, Kareen; Mendez, B.; Borders, K.; Thaller, M.; Plecki, M.; Usuda, K.

2011-05-01

In order to prepare students in grades 4-12 for a global workforce, NASA supports science, technology, engineering, and math (STEM) immersion education for secondary students. Secondary schools, through the NASA Explorer School program, the Spitzer Space Telescope, the National Optical Astronomy Observatory, and the WISE (Wide Field Infrared Survey Explorer) Telescope Teacher Ambassador program, offer authentic research opportunities for students. Spitzer and WISE studied the sky in infrared light. Among the objects WISE studied are asteroids, the coolest and dimmest stars, and the most luminous galaxies. The lessons learned from the NASA Explorer School program and Spitzer and WISE teacher and student programs can be applied to other programs, engaging students in authentic research experiences by using data from space-borne and earth-based observatories such Kitt Peak Observatory. Several ground based telescopes at Kitt Peak Observatory study visible light from objects such as supernovae. Utilizing a student research immersion philosophy along with data analysis skills learned from the Spitzer and WISE student research programs, an analysis of supernovae distribution with respect to location in the Andromeda galaxy was conducted using images of the Andromeda galaxy taken from the WIYN 0.9 meter telescope on Kitt Peak. A comparison was made between the 12 outer fields (spiral arms) and the 4 inner fields (central bulge). Novae were found by "blinking” images of each field throughout 100 epochs of data. Blinking is a technique used to compare images of fields and noting brightness (via x,y coordinates) in one field that is not visible in the same field during a different epoch. Although the central bulge was expected to contain more supernovae due to stellar density and proximity of stars to each other, analysis of data indicates that the there is also a concentration of supernovae that appeared in outer regions. WISE Telescope funding is gratefully acknowledged.

The cardioprotection granted by metoprolol is restricted to its administration prior to coronary reperfusion

PubMed Central

Ibanez, Borja; Cimmino, Giovanni; Prat-González, Susanna; Vilahur, Gemma; Hutter, Randolph; García, Mario J.; Fuster, Valentin; Sanz, Javier; Badimon, Lina; Badimon, Juan J.

2013-01-01

Background Myocardial infarct size is a strong predictor of cardiovascular events. Intravenous metoprolol before coronary reperfusion has been shown to reduce infarct size; however, it is unknown whether oral metoprolol initiated early after reperfusion, as clinical guidelines recommend, is similarly cardioprotective. We compared the extent of myocardial salvage associated with intravenous pre-reperfusion-metoprolol administration in comparison with oral post-reperfusion-metoprolol or placebo. We also studied the effect on suspected markers of reperfusion injury. Methods Thirty Yorkshire-pigs underwent a reperfused myocardial infarction, being randomized to pre-reperfusion-metoprolol, post-reperfusion-metoprolol or placebo. Cardiac magnetic resonance imaging was performed in eighteen pigs at day 3 for the quantification of salvaged myocardium. The amounts of at-risk and infarcted myocardium were quantified using T2-weighted and post-contrast delayed enhancement imaging, respectively. Twelve animals were sacrificed after 24 h for reperfusion injury analysis. Results The pre-reperfusion-metoprolol group had significantly larger salvaged myocardium than the post-reperfusion-metoprolol or the placebo groups (31±4%, 13±6%, and 7±3% of myocardium at-risk respectively). Post-mortem analyses suggest lesser myocardial reperfusion injury in the pre-reperfusion-metoprolol in comparison with the other 2 groups (lower neutrophil infiltration, decreased myocardial apoptosis, and higher activation of the salvage-kinase phospho-Akt). Salvaged myocardium and reperfusion injury pair wise comparisons proved there were significant differences between the pre-reperfusion-metoprolol and the other 2 groups, but not among the latter two. Conclusions The intravenous administration of metoprolol before coronary reperfusion results in larger myocardial salvage than its oral administration initiated early after reperfusion. If confirmed in the clinical setting, the timing and route of β-blocker initiation could be revisited. PMID:19913314

hSAGEing: an improved SAGE-based software for identification of human tissue-specific or common tumor markers and suppressors.

PubMed

Yang, Cheng-Hong; Chuang, Li-Yeh; Shih, Tsung-Mu; Chang, Hsueh-Wei

2010-12-17

SAGE (serial analysis of gene expression) is a powerful method of analyzing gene expression for the entire transcriptome. There are currently many well-developed SAGE tools. However, the cross-comparison of different tissues is seldom addressed, thus limiting the identification of common- and tissue-specific tumor markers. To improve the SAGE mining methods, we propose a novel function for cross-tissue comparison of SAGE data by combining the mathematical set theory and logic with a unique "multi-pool method" that analyzes multiple pools of pair-wise case controls individually. When all the settings are in "inclusion", the common SAGE tag sequences are mined. When one tissue type is in "inclusion" and the other types of tissues are not in "inclusion", the selected tissue-specific SAGE tag sequences are generated. They are displayed in tags-per-million (TPM) and fold values, as well as visually displayed in four kinds of scales in a color gradient pattern. In the fold visualization display, the top scores of the SAGE tag sequences are provided, along with cluster plots. A user-defined matrix file is designed for cross-tissue comparison by selecting libraries from publically available databases or user-defined libraries. The hSAGEing tool provides a combination of friendly cross-tissue analysis and an interface for comparing SAGE libraries for the first time. Some up- or down-regulated genes with tissue-specific or common tumor markers and suppressors are identified computationally. The tool is useful and convenient for in silico cancer transcriptomic studies and is freely available at http://bio.kuas.edu.tw/hSAGEing.

A Comparison of Apical Bacterial Extrusion in Manual, ProTaper Rotary, and One Shape Rotary Instrumentation Techniques.

PubMed

Mittal, Rakesh; Singla, Meenu G; Garg, Ashima; Dhawan, Anu

2015-12-01

Apical extrusion of irrigants and debris is an inherent limitation associated with cleaning and shaping of root canals and has been studied extensively because of its clinical relevance as a cause of flare-ups. Many factors affect the amount of extruded intracanal materials. The purpose of this study was to assess the bacterial extrusion by using manual, multiple-file continuous rotary system (ProTaper) and single-file continuous rotary system (One Shape). Forty-two human mandibular premolars were inoculated with Enterococcus faecalis by using a bacterial extrusion model. The teeth were divided into 3 experimental groups (n = 12) and 1 control group (n = 6). The root canals of experimental groups were instrumented according to the manufacturers' instructions by using manual technique, ProTaper rotary system, or One Shape rotary system. Sterilized saline was used as an irrigant, and bacterial extrusion was quantified as colony-forming units/milliliter. The results obtained were statistically analyzed by using one-way analysis of variance for intergroup comparison and post hoc Tukey test for pair-wise comparison. The level for accepting statistical significance was set at P < .05. All the instrumentation techniques resulted in bacterial extrusion, with manual step-back technique exhibiting significantly more bacterial extrusion than the engine-driven systems. Of the 2 engine-driven systems, ProTaper rotary extruded significantly more bacteria than One Shape rotary system (P < .05). The engine-driven nickel-titanium systems were associated with less apical extrusion. The instrument design may play a role in amount of extrusion. Copyright © 2015 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Analysis of functional redundancies within the Arabidopsis TCP transcription factor family.

PubMed

Danisman, Selahattin; van Dijk, Aalt D J; Bimbo, Andrea; van der Wal, Froukje; Hennig, Lars; de Folter, Stefan; Angenent, Gerco C; Immink, Richard G H

2013-12-01

Analyses of the functions of TEOSINTE-LIKE1, CYCLOIDEA, and PROLIFERATING CELL FACTOR1 (TCP) transcription factors have been hampered by functional redundancy between its individual members. In general, putative functionally redundant genes are predicted based on sequence similarity and confirmed by genetic analysis. In the TCP family, however, identification is impeded by relatively low overall sequence similarity. In a search for functionally redundant TCP pairs that control Arabidopsis leaf development, this work performed an integrative bioinformatics analysis, combining protein sequence similarities, gene expression data, and results of pair-wise protein-protein interaction studies for the 24 members of the Arabidopsis TCP transcription factor family. For this, the work completed any lacking gene expression and protein-protein interaction data experimentally and then performed a comprehensive prediction of potential functional redundant TCP pairs. Subsequently, redundant functions could be confirmed for selected predicted TCP pairs by genetic and molecular analyses. It is demonstrated that the previously uncharacterized class I TCP19 gene plays a role in the control of leaf senescence in a redundant fashion with TCP20. Altogether, this work shows the power of combining classical genetic and molecular approaches with bioinformatics predictions to unravel functional redundancies in the TCP transcription factor family.

Analysis of functional redundancies within the Arabidopsis TCP transcription factor family

PubMed Central

Danisman, Selahattin; de Folter, Stefan; Immink, Richard G. H.

2013-01-01

Analyses of the functions of TEOSINTE-LIKE1, CYCLOIDEA, and PROLIFERATING CELL FACTOR1 (TCP) transcription factors have been hampered by functional redundancy between its individual members. In general, putative functionally redundant genes are predicted based on sequence similarity and confirmed by genetic analysis. In the TCP family, however, identification is impeded by relatively low overall sequence similarity. In a search for functionally redundant TCP pairs that control Arabidopsis leaf development, this work performed an integrative bioinformatics analysis, combining protein sequence similarities, gene expression data, and results of pair-wise protein–protein interaction studies for the 24 members of the Arabidopsis TCP transcription factor family. For this, the work completed any lacking gene expression and protein–protein interaction data experimentally and then performed a comprehensive prediction of potential functional redundant TCP pairs. Subsequently, redundant functions could be confirmed for selected predicted TCP pairs by genetic and molecular analyses. It is demonstrated that the previously uncharacterized class I TCP19 gene plays a role in the control of leaf senescence in a redundant fashion with TCP20. Altogether, this work shows the power of combining classical genetic and molecular approaches with bioinformatics predictions to unravel functional redundancies in the TCP transcription factor family. PMID:24129704

Assessing Effects of Prenatal Alcohol Exposure Using Group-wise Sparse Representation of FMRI Data

PubMed Central

Lv, Jinglei; Jiang, Xi; Li, Xiang; Zhu, Dajiang; Zhao, Shijie; Zhang, Tuo; Hu, Xintao; Han, Junwei; Guo, Lei; Li, Zhihao; Coles, Claire; Hu, Xiaoping; Liu, Tianming

2015-01-01

Task-based fMRI activation mapping has been widely used in clinical neuroscience in order to assess different functional activity patterns in conditions such as prenatal alcohol exposure (PAE) affected brains and healthy controls. In this paper, we propose a novel, alternative approach of group-wise sparse representation of the fMRI data of multiple groups of subjects (healthy control, exposed non-dysmorphic PAE and exposed dysmorphic PAE) and assess the systematic functional activity differences among these three populations. Specifically, a common time series signal dictionary is learned from the aggregated fMRI signals of all three groups of subjects, and then the weight coefficient matrices (named statistical coefficient map (SCM)) associated with each common dictionary were statistically assessed for each group separately. Through inter-group comparisons based on the correspondence established by the common dictionary, our experimental results have demonstrated that the group-wise sparse coding strategy and the SCM can effectively reveal a collection of brain networks/regions that were affected by different levels of severity of PAE. PMID:26195294

THE EXEMPLAR T8 SUBDWARF COMPANION OF WOLF 1130

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

Mace, Gregory N.; McLean, Ian S.; Logsdon, Sarah E.

We have discovered a wide separation (188.''5) T8 subdwarf companion to the sdM1.5+WD binary Wolf 1130. Companionship of WISE J200520.38+542433.9 is verified through common proper motion over a ∼3 yr baseline. Wolf 1130 is located 15.83 ± 0.96 pc from the Sun, placing the brown dwarf at a projected separation of ∼3000 AU. Near-infrared colors and medium resolution (R ≈ 2000-4000) spectroscopy establish the uniqueness of this system as a high-gravity, low-metallicity benchmark. Although there are a number of low-metallicity T dwarfs in the literature, WISE J200520.38+542433.9 has the most extreme inferred metallicity to date with [Fe/H] = –0.64 ±more » 0.17 based on Wolf 1130. Model comparisons to this exemplar late-type subdwarf support it having an old age, a low metallicity, and a small radius. However, the spectroscopic peculiarities of WISE J200520.38+542433.9 underscore the importance of developing the low-metallicity parameter space of the most current atmospheric models.« less

On the accuracy and reproducibility of a novel probabilistic atlas-based generation for calculation of head attenuation maps on integrated PET/MR scanners.

PubMed

Chen, Kevin T; Izquierdo-Garcia, David; Poynton, Clare B; Chonde, Daniel B; Catana, Ciprian

2017-03-01

To propose an MR-based method for generating continuous-valued head attenuation maps and to assess its accuracy and reproducibility. Demonstrating that novel MR-based photon attenuation correction methods are both accurate and reproducible is essential prior to using them routinely in research and clinical studies on integrated PET/MR scanners. Continuous-valued linear attenuation coefficient maps ("μ-maps") were generated by combining atlases that provided the prior probability of voxel positions belonging to a certain tissue class (air, soft tissue, or bone) and an MR intensity-based likelihood classifier to produce posterior probability maps of tissue classes. These probabilities were used as weights to generate the μ-maps. The accuracy of this probabilistic atlas-based continuous-valued μ-map ("PAC-map") generation method was assessed by calculating the voxel-wise absolute relative change (RC) between the MR-based and scaled CT-based attenuation-corrected PET images. To assess reproducibility, we performed pair-wise comparisons of the RC values obtained from the PET images reconstructed using the μ-maps generated from the data acquired at three time points. The proposed method produced continuous-valued μ-maps that qualitatively reflected the variable anatomy in patients with brain tumor and agreed well with the scaled CT-based μ-maps. The absolute RC comparing the resulting PET volumes was 1.76 ± 2.33 %, quantitatively demonstrating that the method is accurate. Additionally, we also showed that the method is highly reproducible, the mean RC value for the PET images reconstructed using the μ-maps obtained at the three visits being 0.65 ± 0.95 %. Accurate and highly reproducible continuous-valued head μ-maps can be generated from MR data using a probabilistic atlas-based approach.

Selecting predictors for discriminant analysis of species performance: an example from an amphibious softwater plant.

PubMed

Vanderhaeghe, F; Smolders, A J P; Roelofs, J G M; Hoffmann, M

2012-03-01

Selecting an appropriate variable subset in linear multivariate methods is an important methodological issue for ecologists. Interest often exists in obtaining general predictive capacity or in finding causal inferences from predictor variables. Because of a lack of solid knowledge on a studied phenomenon, scientists explore predictor variables in order to find the most meaningful (i.e. discriminating) ones. As an example, we modelled the response of the amphibious softwater plant Eleocharis multicaulis using canonical discriminant function analysis. We asked how variables can be selected through comparison of several methods: univariate Pearson chi-square screening, principal components analysis (PCA) and step-wise analysis, as well as combinations of some methods. We expected PCA to perform best. The selected methods were evaluated through fit and stability of the resulting discriminant functions and through correlations between these functions and the predictor variables. The chi-square subset, at P < 0.05, followed by a step-wise sub-selection, gave the best results. In contrast to expectations, PCA performed poorly, as so did step-wise analysis. The different chi-square subset methods all yielded ecologically meaningful variables, while probable noise variables were also selected by PCA and step-wise analysis. We advise against the simple use of PCA or step-wise discriminant analysis to obtain an ecologically meaningful variable subset; the former because it does not take into account the response variable, the latter because noise variables are likely to be selected. We suggest that univariate screening techniques are a worthwhile alternative for variable selection in ecology. © 2011 German Botanical Society and The Royal Botanical Society of the Netherlands.

The Energy-Wise Homebuyer: A Guide to Selecting an Energy-Efficient Home.

ERIC Educational Resources Information Center

Hogarth, Peter T.; And Others

Presented is a guide for purchasers of new or used homes who wish to make informed comparisons of energy costs. Included are 12 energy features to look for, detailed energy checklists, and charts for calculating energy expenses. Among the considerations discussed are heating systems, insulation, thermostats, caulking and weatherstripping, and…

Comparison of Wood Composite Properties Using Cantilever-Beam Bending

Treesearch

Houjiang Zhang; John F. Hunt; Lujing Zhou

2015-01-01

Wood-based composite panels generally are first tested out-of-plane in the primarypanel directionfollowed by the cross panel direction, but rarely edgewise. While most applications use wood-based composites in the flat-wise orientation and only need the out-of-plane properties, there are construction configurations where edgewise properties are needed for improved...

WTA estimates using the method of paired comparison: tests of robustness

Treesearch

Patricia A. Champ; John B. Loomis

1998-01-01

The method of paired comparison is modified to allow choices between two alternative gains so as to estimate willingness to accept (WTA) without loss aversion. The robustness of WTA values for two public goods is tested with respect to sensitivity of theWTA measure to the context of the bundle of goods used in the paired comparison exercise and to the scope (scale) of...

Risk and the evolution of human exchange.

PubMed

Kaplan, Hillard S; Schniter, Eric; Smith, Vernon L; Wilson, Bart J

2012-08-07

Compared with other species, exchange among non-kin is a hallmark of human sociality in both the breadth of individuals and total resources involved. One hypothesis is that extensive exchange evolved to buffer the risks associated with hominid dietary specialization on calorie dense, large packages, especially from hunting. 'Lucky' individuals share food with 'unlucky' individuals with the expectation of reciprocity when roles are reversed. Cross-cultural data provide prima facie evidence of pair-wise reciprocity and an almost universal association of high-variance (HV) resources with greater exchange. However, such evidence is not definitive; an alternative hypothesis is that food sharing is really 'tolerated theft', in which individuals possessing more food allow others to steal from them, owing to the threat of violence from hungry individuals. Pair-wise correlations may reflect proximity providing greater opportunities for mutual theft of food. We report a laboratory experiment of foraging and food consumption in a virtual world, designed to test the risk-reduction hypothesis by determining whether people form reciprocal relationships in response to variance of resource acquisition, even when there is no external enforcement of any transfer agreements that might emerge. Individuals can forage in a high-mean, HV patch or a low-mean, low-variance (LV) patch. The key feature of the experimental design is that individuals can transfer resources to others. We find that sharing hardly occurs after LV foraging, but among HV foragers sharing increases dramatically over time. The results provide strong support for the hypothesis that people are pre-disposed to evaluate gains from exchange and respond to unsynchronized variance in resource availability through endogenous reciprocal trading relationships.

Twisted ribbon structure of paired helical filaments revealed by atomic force microscopy.

PubMed Central

Pollanen, M. S.; Markiewicz, P.; Bergeron, C.; Goh, M. C.

1994-01-01

Progressive deposition of phosphorylated tau into the paired helical filaments (PHF) that compose neurofibrillary tangles, dystrophic neurites, and neuropil threads is an obligate feature of Alzheimer's disease. The standard model of PHF structure, derived from electron microscopic studies, suggests that two 8- to 10-nm filaments each composed of three to four protofilaments are wound into a helix with a maximal diameter of -20 nm and a half period of 65 to 80 nm. However, recent vertical platinum-carbon replicas of PHF more closely resemble a thin helical ribbon without constitutive protofilaments. Here we report that native PHF imaged with an atomic force microscope appear as twisted ribbons rather than the generally accepted structure derived from electron microscopic studies. These data imply that the assembly of PHF is not due to the twisting of pair-wise filaments but rather the helical winding of self-associated tau molecules arranged into a flattened structure. Future structural models of PHF should be based on quantitative data obtained from imaging techniques, such as scanning probe microscopy, which do not require harsh specimen preparation procedures. Images Figure 1 PMID:8178938

Twisted ribbon structure of paired helical filaments revealed by atomic force microscopy.

PubMed

Pollanen, M S; Markiewicz, P; Bergeron, C; Goh, M C

1994-05-01

Progressive deposition of phosphorylated tau into the paired helical filaments (PHF) that compose neurofibrillary tangles, dystrophic neurites, and neuropil threads is an obligate feature of Alzheimer's disease. The standard model of PHF structure, derived from electron microscopic studies, suggests that two 8- to 10-nm filaments each composed of three to four protofilaments are wound into a helix with a maximal diameter of -20 nm and a half period of 65 to 80 nm. However, recent vertical platinum-carbon replicas of PHF more closely resemble a thin helical ribbon without constitutive protofilaments. Here we report that native PHF imaged with an atomic force microscope appear as twisted ribbons rather than the generally accepted structure derived from electron microscopic studies. These data imply that the assembly of PHF is not due to the twisting of pair-wise filaments but rather the helical winding of self-associated tau molecules arranged into a flattened structure. Future structural models of PHF should be based on quantitative data obtained from imaging techniques, such as scanning probe microscopy, which do not require harsh specimen preparation procedures.

Estimation of Disability Weights in the General Population of South Korea Using a Paired Comparison

PubMed Central

Ock, Minsu; Ahn, Jeonghoon; Yoon, Seok-Jun; Jo, Min-Woo

2016-01-01

We estimated the disability weights in the South Korean population by using a paired comparison-only model wherein ‘full health’ and ‘being dead’ were included as anchor points, without resorting to a cardinal method, such as person trade-off. The study was conducted via 2 types of survey: a household survey involving computer-assisted face-to-face interviews and a web-based survey (similar to that of the GBD 2010 disability weight study). With regard to the valuation methods, paired comparison, visual analogue scale (VAS), and standard gamble (SG) were used in the household survey, whereas paired comparison and population health equivalence (PHE) were used in the web-based survey. Accordingly, we described a total of 258 health states, with ‘full health’ and ‘being dead’ designated as anchor points. In the analysis, 4 models were considered: a paired comparison-only model; hybrid model between paired comparison and PHE; VAS model; and SG model. A total of 2,728 and 3,188 individuals participated in the household and web-based survey, respectively. The Pearson correlation coefficients of the disability weights of health states between the GBD 2010 study and the current models were 0.802 for Model 2, 0.796 for Model 1, 0.681 for Model 3, and 0.574 for Model 4 (all P-values<0.001). The discrimination of values according to health state severity was most suitable in Model 1. Based on these results, the paired comparison-only model was selected as the best model for estimating disability weights in South Korea, and for maintaining simplicity in the analysis. Thus, disability weights can be more easily estimated by using paired comparison alone, with ‘full health’ and ‘being dead’ as one of the health states. As noted in our study, we believe that additional evidence regarding the universality of disability weight can be observed by using a simplified methodology of estimating disability weights. PMID:27606626

Simultaneous Control of Error Rates in fMRI Data Analysis

PubMed Central

Kang, Hakmook; Blume, Jeffrey; Ombao, Hernando; Badre, David

2015-01-01

The key idea of statistical hypothesis testing is to fix, and thereby control, the Type I error (false positive) rate across samples of any size. Multiple comparisons inflate the global (family-wise) Type I error rate and the traditional solution to maintaining control of the error rate is to increase the local (comparison-wise) Type II error (false negative) rates. However, in the analysis of human brain imaging data, the number of comparisons is so large that this solution breaks down: the local Type II error rate ends up being so large that scientifically meaningful analysis is precluded. Here we propose a novel solution to this problem: allow the Type I error rate to converge to zero along with the Type II error rate. It works because when the Type I error rate per comparison is very small, the accumulation (or global) Type I error rate is also small. This solution is achieved by employing the Likelihood paradigm, which uses likelihood ratios to measure the strength of evidence on a voxel-by-voxel basis. In this paper, we provide theoretical and empirical justification for a likelihood approach to the analysis of human brain imaging data. In addition, we present extensive simulations that show the likelihood approach is viable, leading to ‘cleaner’ looking brain maps and operationally superiority (lower average error rate). Finally, we include a case study on cognitive control related activation in the prefrontal cortex of the human brain. PMID:26272730

Cytochrome b sequences in black-crowned night-herons (Nycticorax nycticorax) from heronries exposed to genotoxic contaminants

USGS Publications Warehouse

Dahl, Christopher R.; Bickham, John W.; Wickliffe, Jeffery K.; Custer, Thomas W.

2001-01-01

DNA sequence analysis of a 215 base-pair region of the mitochondrial cytochrome b gene was used to examine genetic variation and search for evidence of an increased mutation rate in black-crowned night-herons. We examined five populations exposed to environmental contamination (primarily PAHs and PCBs) and one reference population from the eastern U.S. There was no evidence of a high mutation rate even within populations previously shown to exhibit increased variation in DNA content among somatic cells as a result of petroleum exposure. Three haplotypes were observed among 99 individuals. The low level of variability could be evidence for a genetic bottleneck, or that cytochrome b is too conservative for use in population genetic studies of this species. With the exception of one population from Louisiana, pair-wise Phist estimates were very low, indicative of little population structure and potentially high rates of effective migration among populations.

Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation.

PubMed

Belaghzal, Houda; Dekker, Job; Gibcus, Johan H

2017-07-01

Chromosome conformation capture-based methods such as Hi-C have become mainstream techniques for the study of the 3D organization of genomes. These methods convert chromatin interactions reflecting topological chromatin structures into digital information (counts of pair-wise interactions). Here, we describe an updated protocol for Hi-C (Hi-C 2.0) that integrates recent improvements into a single protocol for efficient and high-resolution capture of chromatin interactions. This protocol combines chromatin digestion and frequently cutting enzymes to obtain kilobase (kb) resolution. It also includes steps to reduce random ligation and the generation of uninformative molecules, such as unligated ends, to improve the amount of valid intra-chromosomal read pairs. This protocol allows for obtaining information on conformational structures such as compartment and topologically associating domains, as well as high-resolution conformational features such as DNA loops. Copyright © 2017 Elsevier Inc. All rights reserved.

Iterative non-sequential protein structural alignment.

PubMed

Salem, Saeed; Zaki, Mohammed J; Bystroff, Christopher

2009-06-01

Structural similarity between proteins gives us insights into their evolutionary relationships when there is low sequence similarity. In this paper, we present a novel approach called SNAP for non-sequential pair-wise structural alignment. Starting from an initial alignment, our approach iterates over a two-step process consisting of a superposition step and an alignment step, until convergence. We propose a novel greedy algorithm to construct both sequential and non-sequential alignments. The quality of SNAP alignments were assessed by comparing against the manually curated reference alignments in the challenging SISY and RIPC datasets. Moreover, when applied to a dataset of 4410 protein pairs selected from the CATH database, SNAP produced longer alignments with lower rmsd than several state-of-the-art alignment methods. Classification of folds using SNAP alignments was both highly sensitive and highly selective. The SNAP software along with the datasets are available online at http://www.cs.rpi.edu/~zaki/software/SNAP.

Monitoring of human brain functions in risk decision-making task by diffuse optical tomography using voxel-wise general linear model

NASA Astrophysics Data System (ADS)

Lin, Zi-Jing; Li, Lin; Cazzell, Marry; Liu, Hanli

2013-03-01

Functional near-infrared spectroscopy (fNIRS) is a non-invasive imaging technique which measures the hemodynamic changes that reflect the brain activity. Diffuse optical tomography (DOT), a variant of fNIRS with multi-channel NIRS measurements, has demonstrated capability of three dimensional (3D) reconstructions of hemodynamic changes due to the brain activity. Conventional method of DOT image analysis to define the brain activation is based upon the paired t-test between two different states, such as resting-state versus task-state. However, it has limitation because the selection of activation and post-activation period is relatively subjective. General linear model (GLM) based analysis can overcome this limitation. In this study, we combine the 3D DOT image reconstruction with GLM-based analysis (i.e., voxel-wise GLM analysis) to investigate the brain activity that is associated with the risk-decision making process. Risk decision-making is an important cognitive process and thus is an essential topic in the field of neuroscience. The balloon analogue risk task (BART) is a valid experimental model and has been commonly used in behavioral measures to assess human risk taking action and tendency while facing risks. We have utilized the BART paradigm with a blocked design to investigate brain activations in the prefrontal and frontal cortical areas during decision-making. Voxel-wise GLM analysis was performed on 18human participants (10 males and 8females).In this work, we wish to demonstrate the feasibility of using voxel-wise GLM analysis to image and study cognitive functions in response to risk decision making by DOT. Results have shown significant changes in the dorsal lateral prefrontal cortex (DLPFC) during the active choice mode and a different hemodynamic pattern between genders, which are in good agreements with published literatures in functional magnetic resonance imaging (fMRI) and fNIRS studies.

Amino acid pair- and triplet-wise groupings in the interior of α-helical segments in proteins.

PubMed

de Sousa, Miguel M; Munteanu, Cristian R; Pazos, Alejandro; Fonseca, Nuno A; Camacho, Rui; Magalhães, A L

2011-02-21

A statistical approach has been applied to analyse primary structure patterns at inner positions of α-helices in proteins. A systematic survey was carried out in a recent sample of non-redundant proteins selected from the Protein Data Bank, which were used to analyse α-helix structures for amino acid pairing patterns. Only residues more than three positions apart from both termini of the α-helix were considered as inner. Amino acid pairings i, i+k (k=1, 2, 3, 4, 5), were analysed and the corresponding 20×20 matrices of relative global propensities were constructed. An analysis of (i, i+4, i+8) and (i, i+3, i+4) triplet patterns was also performed. These analysis yielded information on a series of amino acid patterns (pairings and triplets) showing either high or low preference for α-helical motifs and suggested a novel approach to protein alphabet reduction. In addition, it has been shown that the individual amino acid propensities are not enough to define the statistical distribution of these patterns. Global pair propensities also depend on the type of pattern, its composition and orientation in the protein sequence. The data presented should prove useful to obtain and refine useful predictive rules which can further the development and fine-tuning of protein structure prediction algorithms and tools. Copyright © 2010 Elsevier Ltd. All rights reserved.

Fired Cartridge Case Identification Using Optical Images and the Congruent Matching Cells (CMC) Method

PubMed Central

Tong, Mingsi; Song, John; Chu, Wei; Thompson, Robert M

2014-01-01

The Congruent Matching Cells (CMC) method for ballistics identification was invented at the National Institute of Standards and Technology (NIST). The CMC method is based on the correlation of pairs of small correlation cells instead of the correlation of entire images. Four identification parameters – TCCF, Tθ, Tx and Ty are proposed for identifying correlated cell pairs originating from the same firearm. The correlation conclusion (matching or non-matching) is determined by whether the number of CMC is ≥ 6. This method has been previously validated using a set of 780 pair-wise 3D topography images. However, most ballistic images stored in current local and national databases are in an optical intensity (grayscale) format. As a result, the reliability of applying the CMC method on optical intensity images is an important issue. In this paper, optical intensity images of breech face impressions captured on the same set of 40 cartridge cases are correlated and analyzed for the validation test of CMC method using optical images. This includes correlations of 63 pairs of matching images and 717 pairs of non-matching images under top ring lighting. Tests of the method do not produce any false identification (false positive) or false exclusion (false negative) results, which support the CMC method and the proposed identification criterion, C = 6, for firearm breech face identifications using optical intensity images. PMID:26601045

Male factor infertility: a twin study.

PubMed

Cloonan, Yona K; Holt, Victoria L; Goldberg, Jack

2007-05-01

There is a considerable body of literature on the causes of female infertility, but far less is known about male factor infertility. We conducted a classical twin study to estimate the genetic influence on 12-month male factor infertility. The study used the Vietnam Era Twin (VET) Registry, which includes male twin pairs born between 1939 and 1957, and who served in the US military between 1965 and 1975. In 1987, a health survey was mailed to all twins and obtained a 74% response rate. The current analyses comprised 1795 complete pairs in which both twins were married only once. Proband-wise concordance rates, tetrachoric correlations, and a bivariate probit model were used to calculate estimates of familial clustering and heritability for male factor infertility. The proband concordance rate for male factor infertility was 38% [95% CI 32.8, 42.4] in monozygotic (MZ) pairs and 33% [95% CI 28.0, 38.6] in dizygotic (DZ) pairs. The tetrachoric correlations for male infertility were 0.15 in MZ and 0.04 in DZ pairs. This pattern provides evidence of familial clustering, although genetic influence was not evident (P = 0.21). The current study identified that 12-month male factor infertility clustered within families. However, results suggest that factors unique to individual twins may play a more prominent role in male infertility than additive genetic effects or the common environment.

Fired Cartridge Case Identification Using Optical Images and the Congruent Matching Cells (CMC) Method.

PubMed

Tong, Mingsi; Song, John; Chu, Wei; Thompson, Robert M

2014-01-01

The Congruent Matching Cells (CMC) method for ballistics identification was invented at the National Institute of Standards and Technology (NIST). The CMC method is based on the correlation of pairs of small correlation cells instead of the correlation of entire images. Four identification parameters - T CCF, T θ, T x and T y are proposed for identifying correlated cell pairs originating from the same firearm. The correlation conclusion (matching or non-matching) is determined by whether the number of CMC is ≥ 6. This method has been previously validated using a set of 780 pair-wise 3D topography images. However, most ballistic images stored in current local and national databases are in an optical intensity (grayscale) format. As a result, the reliability of applying the CMC method on optical intensity images is an important issue. In this paper, optical intensity images of breech face impressions captured on the same set of 40 cartridge cases are correlated and analyzed for the validation test of CMC method using optical images. This includes correlations of 63 pairs of matching images and 717 pairs of non-matching images under top ring lighting. Tests of the method do not produce any false identification (false positive) or false exclusion (false negative) results, which support the CMC method and the proposed identification criterion, C = 6, for firearm breech face identifications using optical intensity images.

Transcriptional homeostasis of a mangrove species, Ceriops tagal, in saline environments, as revealed by microarray analysis.

PubMed

Liang, Shan; Fang, Lu; Zhou, Renchao; Tang, Tian; Deng, Shulin; Dong, Suisui; Huang, Yelin; Zhong, Cairong; Shi, Suhua

2012-01-01

Differential responses to the environmental stresses at the level of transcription play a critical role in adaptation. Mangrove species compose a dominant community in intertidal zones and form dense forests at the sea-land interface, and although the anatomical and physiological features associated with their salt-tolerant lifestyles have been well characterized, little is known about the impact of transcriptional phenotypes on their adaptation to these saline environments. We report the time-course transcript profiles in the roots of a true mangrove species, Ceriops tagal, as revealed by a series of microarray experiments. The expression of a total of 432 transcripts changed significantly in the roots of C. tagal under salt shock, of which 83 had a more than 2-fold change and were further assembled into 59 unigenes. Global transcription was stable at the early stage of salt stress and then was gradually dysregulated with the increased duration of the stress. Importantly, a pair-wise comparison of predicted homologous gene pairs revealed that the transcriptional regulations of most of the differentially expressed genes were highly divergent in C. tagal from that in salt-sensitive species, Arabidopsis thaliana. This work suggests that transcriptional homeostasis and specific transcriptional regulation are major events in the roots of C. tagal when subjected to salt shock, which could contribute to the establishment of adaptation to saline environments and, thus, facilitate the salt-tolerant lifestyle of this mangrove species. Furthermore, the candidate genes underlying the adaptation were identified through comparative analyses. This study provides a foundation for dissecting the genetic basis of the adaptation of mangroves to intertidal environments.

Transcriptomic Analysis Reveals Differential Gene Expressions for Cell Growth and Functional Secondary Metabolites in Induced Autotetraploid of Chinese Woad (Isatis indigotica Fort.)

PubMed Central

Zhou, Yingying; Kang, Lei; Liao, Shiying; Pan, Qi; Ge, Xianhong; Li, Zaiyun

2015-01-01

The giant organs and enhanced concentrations of secondary metabolites realized by autopolyploidy are attractive for breeding the respective medicinal and agricultural plants and studying the genetic mechanisms. The traditional medicinal plant Chinese woad (Isatis indigotica Fort., 2n = 2x = 14) is now still largely used for the diseases caused by bacteria and viruses in China. In this study, its autopolyploids (3x, 4x) were produced and characterized together with the 2x donor for their phenotype and transcriptomic alterations by using high-throughput RNA sequencing. With the increase of genome dosage, the giantism in cells and organs was obvious and the photosynthetic rate was higher. The 4x plants showed predominantly the normal meiotic chromosome pairing (bivalents and quadrivalents) and equal segregation and then produced the majority of 4x progeny. The total 70136 All-unigenes were de novo assembled, and 56,482 (80.53%) unigenes were annotated based on BLASTx searches of the public databases. From pair-wise comparisons between transcriptomic data of 2x, 3x, 4x plants, 1856 (2.65%)(2x vs 4x), 693(0.98%)(2x vs 3x), 1045(1.48%)(3x vs 4x) unigenes were detected to differentially expressed genes (DEGs), including both up- and down-regulated ones. These DEGs were mainly involved in cell growth (synthesis of expansin and pectin), cell wall organization, secondary metabolite biosynthesis, response to stress and photosynthetic pathways. The up-regulation of some DEGs for metabolic pathways of functional compounds in the induced autotetraploids substantiates the promising new type of this medicinal plant with the increased biomass and targeted metabolites. PMID:25739089

QueTAL: a suite of tools to classify and compare TAL effectors functionally and phylogenetically

PubMed Central

Pérez-Quintero, Alvaro L.; Lamy, Léo; Gordon, Jonathan L.; Escalon, Aline; Cunnac, Sébastien; Szurek, Boris; Gagnevin, Lionel

2015-01-01

Transcription Activator-Like (TAL) effectors from Xanthomonas plant pathogenic bacteria can bind to the promoter region of plant genes and induce their expression. DNA-binding specificity is governed by a central domain made of nearly identical repeats, each determining the recognition of one base pair via two amino acid residues (a.k.a. Repeat Variable Di-residue, or RVD). Knowing how TAL effectors differ from each other within and between strains would be useful to infer functional and evolutionary relationships, but their repetitive nature precludes reliable use of traditional alignment methods. The suite QueTAL was therefore developed to offer tailored tools for comparison of TAL effector genes. The program DisTAL considers each repeat as a unit, transforms a TAL effector sequence into a sequence of coded repeats and makes pair-wise alignments between these coded sequences to construct trees. The program FuncTAL is aimed at finding TAL effectors with similar DNA-binding capabilities. It calculates correlations between position weight matrices of potential target DNA sequence predicted from the RVD sequence, and builds trees based on these correlations. The programs accurately represented phylogenetic and functional relationships between TAL effectors using either simulated or literature-curated data. When using the programs on a large set of TAL effector sequences, the DisTAL tree largely reflected the expected species phylogeny. In contrast, FuncTAL showed that TAL effectors with similar binding capabilities can be found between phylogenetically distant taxa. This suite will help users to rapidly analyse any TAL effector genes of interest and compare them to other available TAL genes and should improve our understanding of TAL effectors evolution. It is available at http://bioinfo-web.mpl.ird.fr/cgi-bin2/quetal/quetal.cgi. PMID:26284082

Tool use without a tool: kinematic characteristics of pantomiming as compared to actual use and the effect of brain damage.

PubMed

Hermsdörfer, Joachim; Li, Yong; Randerath, Jennifer; Goldenberg, Georg; Johannsen, Leif

2012-04-01

Movement goals and task mechanics differ substantially between actual tool use and corresponding pantomimes. In addition, apraxia seems to be more severe during pantomime than during actual tool use. Comparisons of these two modes of action execution using quantitative methods of movement analyses are rare. In the present study, repetitive scooping movements with a ladle from a bowl into a plate were recorded and movement kinematics was analyzed. Brain-damaged patients using their ipsilesional hand and healthy control subjects were tested in three conditions: pantomime, demonstration with the tool only, and actual use in the normal context. Analysis of the hand trajectories during the transport component revealed clear differences between the tasks, such as slower actual use and moderate deficits in patients with left brain damage (LBD). LBD patients were particularly impaired in the scooping component: LBD patients with apraxia exhibited reduced hand rotation at the bowl and the plate. The deficit was most obvious during pantomime but actual use was also affected, and reduced hand rotation was consistent across conditions as indicated by strong pair-wise correlations between task conditions. In healthy control subjects, correlations between movement parameters were most evident between the pantomime and demonstration conditions but weak in correlation pairs involving actual use. From these findings and published neuroimaging evidence, we conclude that for a specific tool-use action, common motor schemas are activated but are adjusted and modified according to the actual task constraints and demands. An apraxic LBD individual can show a deficit across all three action conditions, but the severity can differ substantially between conditions.

A Probabilistic, Dynamic, and Attribute-wise Model of Intertemporal Choice

PubMed Central

Dai, Junyi; Busemeyer, Jerome R.

2014-01-01

Most theoretical and empirical research on intertemporal choice assumes a deterministic and static perspective, leading to the widely adopted delay discounting models. As a form of preferential choice, however, intertemporal choice may be generated by a stochastic process that requires some deliberation time to reach a decision. We conducted three experiments to investigate how choice and decision time varied as a function of manipulations designed to examine the delay duration effect, the common difference effect, and the magnitude effect in intertemporal choice. The results, especially those associated with the delay duration effect, challenged the traditional deterministic and static view and called for alternative approaches. Consequently, various static or dynamic stochastic choice models were explored and fit to the choice data, including alternative-wise models derived from the traditional exponential or hyperbolic discount function and attribute-wise models built upon comparisons of direct or relative differences in money and delay. Furthermore, for the first time, dynamic diffusion models, such as those based on decision field theory, were also fit to the choice and response time data simultaneously. The results revealed that the attribute-wise diffusion model with direct differences, power transformations of objective value and time, and varied diffusion parameter performed the best and could account for all three intertemporal effects. In addition, the empirical relationship between choice proportions and response times was consistent with the prediction of diffusion models and thus favored a stochastic choice process for intertemporal choice that requires some deliberation time to make a decision. PMID:24635188

Altered voxel-wise gray matter structural brain networks in schizophrenia: Association with brain genetic expression pattern.

PubMed

Liu, Feng; Tian, Hongjun; Li, Jie; Li, Shen; Zhuo, Chuanjun

2018-05-04

Previous seed- and atlas-based structural covariance/connectivity analyses have demonstrated that patients with schizophrenia is accompanied by aberrant structural connection and abnormal topological organization. However, it remains unclear whether this disruption is present in unbiased whole-brain voxel-wise structural covariance networks (SCNs) and whether brain genetic expression variations are linked with network alterations. In this study, ninety-five patients with schizophrenia and 95 matched healthy controls were recruited and gray matter volumes were extracted from high-resolution structural magnetic resonance imaging scans. Whole-brain voxel-wise gray matter SCNs were constructed at the group level and were further analyzed by using graph theory method. Nonparametric permutation tests were employed for group comparisons. In addition, regression modes along with random effect analysis were utilized to explore the associations between structural network changes and gene expression from the Allen Human Brain Atlas. Compared with healthy controls, the patients with schizophrenia showed significantly increased structural covariance strength (SCS) in the right orbital part of superior frontal gyrus and bilateral middle frontal gyrus, while decreased SCS in the bilateral superior temporal gyrus and precuneus. The altered SCS showed reproducible correlations with the expression profiles of the gene classes involved in therapeutic targets and neurodevelopment. Overall, our findings not only demonstrate that the topological architecture of whole-brain voxel-wise SCNs is impaired in schizophrenia, but also provide evidence for the possible role of therapeutic targets and neurodevelopment-related genes in gray matter structural brain networks in schizophrenia.

Streamline Basal Application of Herbicide for Small-Stem Hardwood Control

Treesearch

James H. Miller

1990-01-01

Abstract. The effectiveness of low-volume b a s a lapplication of herbicide - "streamline" application - was evaluated on 25 hardwood species and loblolly pine. Test mixtures were step-wise rates of Garlon 4 mixed in diesel fuel with a penatrant added. Most comparisons tested 1O%, 20%, and 30% mixtures of Garlon 4, while tests with...

On the mechanism of energy transduction in myosin subfragment 1.

PubMed Central

Botts, J; Takashi, R; Torgerson, P; Hozumi, T; Muhlrad, A; Mornet, D; Morales, M F

1984-01-01

It is proposed that the myosin subfragment 1 moiety of the muscle contractile apparatus is a self-contained "engine" whose operational plan is based on the interactive nature of ATP (or degradation intermediate) binding and actin binding, made possible by an intersite communication system. It is suggested that the spatial information required for examining this engine can, at least provisionally, be derived from fluorescence resonance energy transfer measurements interpreted by the Förster equation and that the existence of an intersite communication system can be deduced from piece-wise detection of interacting pairs of points. PMID:6585786

Extent of linkage disequilibrium, consistency of gametic phase, and imputation accuracy within and across Canadian dairy breeds.

PubMed

Larmer, S G; Sargolzaei, M; Schenkel, F S

2014-05-01

Genomic selection requires a large reference population to accurately estimate single nucleotide polymorphism (SNP) effects. In some Canadian dairy breeds, the available reference populations are not large enough for accurate estimation of SNP effects for traits of interest. If marker phase is highly consistent across multiple breeds, it is theoretically possible to increase the accuracy of genomic prediction for one or all breeds by pooling several breeds into a common reference population. This study investigated the extent of linkage disequilibrium (LD) in 5 major dairy breeds using a 50,000 (50K) SNP panel and 3 of the same breeds using the 777,000 (777K) SNP panel. Correlation of pair-wise SNP phase was also investigated on both panels. The level of LD was measured using the squared correlation of alleles at 2 loci (r(2)), and the consistency of SNP gametic phases was correlated using the signed square root of these values. Because of the high cost of the 777K panel, the accuracy of imputation from lower density marker panels [6,000 (6K) or 50K] was examined both within breed and using a multi-breed reference population in Holstein, Ayrshire, and Guernsey. Imputation was carried out using FImpute V2.2 and Beagle 3.3.2 software. Imputation accuracies were then calculated as both the proportion of correct SNP filled in (concordance rate) and allelic R(2). Computation time was also explored to determine the efficiency of the different algorithms for imputation. Analysis showed that LD values >0.2 were found in all breeds at distances at or shorter than the average adjacent pair-wise distance between SNP on the 50K panel. Correlations of r-values, however, did not reach high levels (<0.9) at these distances. High correlation values of SNP phase between breeds were observed (>0.94) when the average pair-wise distances using the 777K SNP panel were examined. High concordance rate (0.968-0.995) and allelic R(2) (0.946-0.991) were found for all breeds when imputation was carried out with FImpute from 50K to 777K. Imputation accuracy for Guernsey and Ayrshire was slightly lower when using the imputation method in Beagle. Computing time was significantly greater when using Beagle software, with all comparable procedures being 9 to 13 times less efficient, in terms of time, compared with FImpute. These findings suggest that use of a multi-breed reference population might increase prediction accuracy using the 777K SNP panel and that 777K genotypes can be efficiently and effectively imputed using the lower density 50K SNP panel. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Examining the efficiency and interdependence of US credit and stock markets through MF-DFA and MF-DXA approaches

NASA Astrophysics Data System (ADS)

Shahzad, Syed Jawad Hussain; Nor, Safwan Mohd; Mensi, Walid; Kumar, Ronald Ravinesh

2017-04-01

This study examines the power law properties of 11 US credit and stock markets at the industry level. We use multifractal detrended fluctuation analysis (MF-DFA) and multifractal detrended cross-correlation analysis (MF-DXA) to first investigate the relative efficiency of credit and stock markets and then evaluate the mutual interdependence between CDS-equity market pairs. The scaling exponents of the MF-DFA approach suggest that CDS markets are relatively more inefficient than their equity counterparts. However, Banks and Financial credit markets are relatively more efficient. Basic Materials (both CDS and equity indices) is the most inefficient sector of the US economy. The cross-correlation exponents obtained through MF-DXA also suggest that the relationship of the CDS and equity sectors within and across markets is multifractal for all pairs. Within the CDS market, Basic Materials is the most dependent sector, whereas equity market sectors can be divided into two distinct groups based on interdependence. The pair-wise dependence between Basic Materials sector CDSs and the equity index is also the highest. The degree of cross-correlation shows that the sectoral pairs of CDS and equity markets belong to a persistent cross-correlated series within selected time intervals.

Using expert opinion to prioritize impacts of climate change on sea turtles' nesting grounds.

PubMed

Fuentes, M M P B; Cinner, J E

2010-12-01

Managers and conservationists often need to prioritize which impacts from climate change to deal with from a long list of threats. However, data which allows comparison of the relative impact from climatic threats for decision-making is often unavailable. This is the case for the management of sea turtles in the face of climate change. The terrestrial life stages of sea turtles can be negatively impacted by various climatic processes, such as sea level rise, altered cyclonic activity, and increased sand temperatures. However, no study has systematically investigated the relative impact of each of these climatic processes, making it challenging for managers to prioritize their decisions and resources. To address this we offer a systematic method for eliciting expert knowledge to estimate the relative impact of climatic processes on sea turtles' terrestrial reproductive phase. For this we used as an example the world's largest population of green sea turtles and asked 22 scientists and managers to answer a paper based survey with a series of pair-wise comparison matrices that compared the anticipated impacts from each climatic process. Both scientists and managers agreed that increased sand temperature will likely cause the most threat to the reproductive output of the nGBR green turtle population followed by sea level rise, then altered cyclonic activity. The methodology used proved useful to determine the relative impact of the selected climatic processes on sea turtles' reproductive output and provided valuable information for decision-making. Thus, the methodological approach can potentially be applied to other species and ecosystems of management concern. Copyright © 2009 Elsevier Ltd. All rights reserved.

Comparison of cigarette smoking knowledge, attitudes, and practices among staff in perinatal and other substance abuse treatment settings.

PubMed

Miller-Thomas, Tonya; Leoutsakos, Jeannie-Marie S; Terplan, Mishka; Brigham, Emily P; Chisolm, Margaret S

2014-01-01

Despite the high prevalence and known morbidity and mortality caused by cigarette smoking, 60% to 70% of substance abuse treatment programs lack smoking cessation counseling or fail to offer pharmacotherapy for smoking cessation, including those programs designed to meet the needs of drug-dependent pregnant patients. Previous studies of staff knowledge, attitudes, and practices (S-KAP) at general substance abuse/HIV treatment programs have suggested that staff may contribute to the deficiency in smoking cessation treatment in these settings. It is not known whether similar deficiencies exist at perinatal substance abuse treatment programs. This study compared cigarette S-KAP in perinatal substance abuse (n = 41) and general substance abuse/HIV treatment (Veterans Affairs [VA] medical center, hospital-, and community-based) workforce samples (n = 335). Significant differences were seen between the 2 groups on all measures, but perinatal staff compared favorably to general staff only on measures of barriers to smoking cessation services. Perinatal staff compared unfavorably on all other measures: knowledge, beliefs/attitudes, self-efficacy, and smoking cessation practices. Pair-wise comparisons of knowledge and beliefs/attitudes revealed a significant difference between perinatal and VA staff; of self-efficacy, between perinatal and staff at all other settings; and of smoking cessation practices, between perinatal and VA and community-based staff. These results-showing deficiencies of perinatal staff on most S-KAP measures-are concerning and suggest that identifying gaps in and improving S-KAP in perinatal substance abuse programs is urgently needed, for which the VA may provide an efficacious model.

Labial soft tissue volume evaluation of different techniques for ridge preservation after tooth extraction: a randomized controlled clinical trial.

PubMed

Schneider, David; Schmidlin, Patrick R; Philipp, Alexander; Annen, Beat M; Ronay, Valerie; Hämmerle, Christoph H F; Attin, Thomas; Jung, Ronald E

2014-06-01

To volumetrically evaluate soft tissue changes of different ridge preservation techniques compared to spontaneous healing 6 months after tooth extraction. In each of 40 patients, one single-rooted tooth was extracted and four treatment modalities were randomly assigned to the following groups (n = 10 each): A) ß-tricalcium-phosphate-particles with a polylactid coating (ß-TCP), B) demineralized bovine bone mineral with 10% collagen covered with a collagen matrix (DBBM-C/CM), C) DBBM with 10% collagen covered with an autogenous soft tissue punch graft (DBBM-C/PG), D) spontaneous healing (control). Impressions were obtained before extraction and 6 months later, casts were digitized and volumetric changes at the buccal soft tissues were determined. One-way anova was performed and pair-wise Wilcoxon rank sum test with Bonferroni-Holm method was applied for comparison of differences between two groups. After 6 months, horizontal contour changes accounted for -1.7 ± 0.7 mm (A), -1.2 ± 0.5 mm (B), -1.2 ± 0.7 mm (C) and -1.8 ± 0.8 mm (D). None of the group comparisons reached statistical significance. Six months after tooth extraction all groups revealed a horizontal volume change in the buccal soft tissue contour. Application of DBBM-C/CM or DBBM-C/PG reduced the amount of volume resorption compared to ß-TCP or spontaneous healing without reaching statistically significant difference. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Evolutionary growth process of highly conserved sequences in vertebrate genomes.

PubMed

Ishibashi, Minaka; Noda, Akiko Ogura; Sakate, Ryuichi; Imanishi, Tadashi

2012-08-01

Genome sequence comparison between evolutionarily distant species revealed ultraconserved elements (UCEs) among mammals under strong purifying selection. Most of them were also conserved among vertebrates. Because they tend to be located in the flanking regions of developmental genes, they would have fundamental roles in creating vertebrate body plans. However, the evolutionary origin and selection mechanism of these UCEs remain unclear. Here we report that UCEs arose in primitive vertebrates, and gradually grew in vertebrate evolution. We searched for UCEs in two teleost fishes, Tetraodon nigroviridis and Oryzias latipes, and found 554 UCEs with 100% identity over 100 bps. Comparison of teleost and mammalian UCEs revealed 43 pairs of common, jawed-vertebrate UCEs (jUCE) with high sequence identities, ranging from 83.1% to 99.2%. Ten of them retain lower similarities to the Petromyzon marinus genome, and the substitution rates of four non-exonic jUCEs were reduced after the teleost-mammal divergence, suggesting that robust conservation had been acquired in the jawed vertebrate lineage. Our results indicate that prototypical UCEs originated before the divergence of jawed and jawless vertebrates and have been frozen as perfect conserved sequences in the jawed vertebrate lineage. In addition, our comparative sequence analyses of UCEs and neighboring regions resulted in a discovery of lineage-specific conserved sequences. They were added progressively to prototypical UCEs, suggesting step-wise acquisition of novel regulatory roles. Our results indicate that conserved non-coding elements (CNEs) consist of blocks with distinct evolutionary history, each having been frozen since different evolutionary era along the vertebrate lineage. Copyright © 2012 Elsevier B.V. All rights reserved.

Is there more valuable information in PWI datasets for a voxel-wise acute ischemic stroke tissue outcome prediction than what is represented by typical perfusion maps?

NASA Astrophysics Data System (ADS)

Forkert, Nils Daniel; Siemonsen, Susanne; Dalski, Michael; Verleger, Tobias; Kemmling, Andre; Fiehler, Jens

2014-03-01

The acute ischemic stroke is a leading cause for death and disability in the industry nations. In case of a present acute ischemic stroke, the prediction of the future tissue outcome is of high interest for the clinicians as it can be used to support therapy decision making. Within this context, it has already been shown that the voxel-wise multi-parametric tissue outcome prediction leads to more promising results compared to single channel perfusion map thresholding. Most previously published multi-parametric predictions employ information from perfusion maps derived from perfusion-weighted MRI together with other image sequences such as diffusion-weighted MRI. However, it remains unclear if the typically calculated perfusion maps used for this purpose really include all valuable information from the PWI dataset for an optimal tissue outcome prediction. To investigate this problem in more detail, two different methods to predict tissue outcome using a k-nearest-neighbor approach were developed in this work and evaluated based on 18 datasets of acute stroke patients with known tissue outcome. The first method integrates apparent diffusion coefficient and perfusion parameter (Tmax, MTT, CBV, CBF) information for the voxel-wise prediction, while the second method employs also apparent diffusion coefficient information but the complete perfusion information in terms of the voxel-wise residue functions instead of the perfusion parameter maps for the voxel-wise prediction. Overall, the comparison of the results of the two prediction methods for the 18 patients using a leave-one-out cross validation revealed no considerable differences. Quantitatively, the parameter-based prediction of tissue outcome led to a mean Dice coefficient of 0.474, while the prediction using the residue functions led to a mean Dice coefficient of 0.461. Thus, it may be concluded from the results of this study that the perfusion parameter maps typically derived from PWI datasets include all valuable perfusion information required for a voxel-based tissue outcome prediction, while the complete analysis of the residue functions does not add further benefits for the voxel-wise tissue outcome prediction and is also computationally more expensive.

Ethnic differences in lens parameters measured by ocular biometry in a cataract surgery population.

PubMed

Wang, Dajiang; Amoozgar, Behzad; Porco, Travis; Wang, Zhen; Lin, Shan C

2017-01-01

To investigate whether differences exist in lens position and other lens parameters among major ethnic groups with cataractous eyes, which may help explain racial differences in angle closure risk. This retrospective, cross-sectional study included 807 adult patients who had cataract surgery between years 2014 and 2016 at the University of California, San Francisco (UCSF). Adult patients of white, Asian, Hispanic and African-American ethnicity were included. Lens position (LP), defined as anterior chamber depth (ACD) + 1/2 lens thickness (LT), was assessed using measurements from optical biometry. Other assessed biometric parameters included axial length (AL), relative lens position (RLP) (defined as LP/AL), and anterior chamber depth (ACD). A total of 807 patients and 1361 eyes were included in this study from a database of patients having cataract surgery. Mean age was 69.2 years (age range from 18 to 101 years old), and 60.3% of patients were women. The mean LP measurements were 5.54±0.32 mm for white, 5.38±0.32 mm for Asian, 5.32±0.30 mm for Hispanic, and 5.40±0.28 mm for African-American participants. After adjusting for age, sex, and AL, significant differences were found when comparing LP in paired comparisons among White cohort with Asians (P<0.001), Hispanics (P<0.001) and African-Americans (P = 0.003). Additionally, when comparing RLP, similar significant results were found when comparing Whites with Asians (P<0.001), Hispanics (P<0.001) and African-Americans (P = 0.002). Lastly, pair-wise comparison of LT between ethnic groups showed significant differences while comparing Asians with Whites (P = 0.001) and Asians with African-Americans (P<0.001). The results of this study suggest that the LP of Hispanic, Asian, and African-American patients are significantly smaller than that of White patients, and among all ethnic groups, Hispanics and after Asians have the smallest LP (P<0.001) and RLP (P<0.001). These findings may have implications for the relative risk of angle closure and the potential IOP response after cataract surgery among different ethnic groups.

Biological Parametric Mapping: A Statistical Toolbox for Multi-Modality Brain Image Analysis

PubMed Central

Casanova, Ramon; Ryali, Srikanth; Baer, Aaron; Laurienti, Paul J.; Burdette, Jonathan H.; Hayasaka, Satoru; Flowers, Lynn; Wood, Frank; Maldjian, Joseph A.

2006-01-01

In recent years multiple brain MR imaging modalities have emerged; however, analysis methodologies have mainly remained modality specific. In addition, when comparing across imaging modalities, most researchers have been forced to rely on simple region-of-interest type analyses, which do not allow the voxel-by-voxel comparisons necessary to answer more sophisticated neuroscience questions. To overcome these limitations, we developed a toolbox for multimodal image analysis called biological parametric mapping (BPM), based on a voxel-wise use of the general linear model. The BPM toolbox incorporates information obtained from other modalities as regressors in a voxel-wise analysis, thereby permitting investigation of more sophisticated hypotheses. The BPM toolbox has been developed in MATLAB with a user friendly interface for performing analyses, including voxel-wise multimodal correlation, ANCOVA, and multiple regression. It has a high degree of integration with the SPM (statistical parametric mapping) software relying on it for visualization and statistical inference. Furthermore, statistical inference for a correlation field, rather than a widely-used T-field, has been implemented in the correlation analysis for more accurate results. An example with in-vivo data is presented demonstrating the potential of the BPM methodology as a tool for multimodal image analysis. PMID:17070709

A superpixel-based framework for automatic tumor segmentation on breast DCE-MRI

NASA Astrophysics Data System (ADS)

Yu, Ning; Wu, Jia; Weinstein, Susan P.; Gaonkar, Bilwaj; Keller, Brad M.; Ashraf, Ahmed B.; Jiang, YunQing; Davatzikos, Christos; Conant, Emily F.; Kontos, Despina

2015-03-01

Accurate and efficient automated tumor segmentation in breast dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is highly desirable for computer-aided tumor diagnosis. We propose a novel automatic segmentation framework which incorporates mean-shift smoothing, superpixel-wise classification, pixel-wise graph-cuts partitioning, and morphological refinement. A set of 15 breast DCE-MR images, obtained from the American College of Radiology Imaging Network (ACRIN) 6657 I-SPY trial, were manually segmented to generate tumor masks (as ground truth) and breast masks (as regions of interest). Four state-of-the-art segmentation approaches based on diverse models were also utilized for comparison. Based on five standard evaluation metrics for segmentation, the proposed framework consistently outperformed all other approaches. The performance of the proposed framework was: 1) 0.83 for Dice similarity coefficient, 2) 0.96 for pixel-wise accuracy, 3) 0.72 for VOC score, 4) 0.79 mm for mean absolute difference, and 5) 11.71 mm for maximum Hausdorff distance, which surpassed the second best method (i.e., adaptive geodesic transformation), a semi-automatic algorithm depending on precise initialization. Our results suggest promising potential applications of our segmentation framework in assisting analysis of breast carcinomas.

A new compound arithmetic crossover-based genetic algorithm for constrained optimisation in enterprise systems

NASA Astrophysics Data System (ADS)

Jin, Chenxia; Li, Fachao; Tsang, Eric C. C.; Bulysheva, Larissa; Kataev, Mikhail Yu

2017-01-01

In many real industrial applications, the integration of raw data with a methodology can support economically sound decision-making. Furthermore, most of these tasks involve complex optimisation problems. Seeking better solutions is critical. As an intelligent search optimisation algorithm, genetic algorithm (GA) is an important technique for complex system optimisation, but it has internal drawbacks such as low computation efficiency and prematurity. Improving the performance of GA is a vital topic in academic and applications research. In this paper, a new real-coded crossover operator, called compound arithmetic crossover operator (CAC), is proposed. CAC is used in conjunction with a uniform mutation operator to define a new genetic algorithm CAC10-GA. This GA is compared with an existing genetic algorithm (AC10-GA) that comprises an arithmetic crossover operator and a uniform mutation operator. To judge the performance of CAC10-GA, two kinds of analysis are performed. First the analysis of the convergence of CAC10-GA is performed by the Markov chain theory; second, a pair-wise comparison is carried out between CAC10-GA and AC10-GA through two test problems available in the global optimisation literature. The overall comparative study shows that the CAC performs quite well and the CAC10-GA defined outperforms the AC10-GA.

Integrating knowledge-based multi-criteria evaluation techniques with GIS for landfill site selection: A case study using AHP

NASA Astrophysics Data System (ADS)

Fagbohun, B. J.; Aladejana, O. O.

2016-09-01

A major challenge in most growing urban areas of developing countries, without a pre-existing land use plan is the sustainable and efficient management of solid wastes. Siting a landfill is a complicated task because of several environmental regulations. This challenge gives birth to the need to develop efficient strategies for the selection of proper waste disposal sites in accordance with all existing environmental regulations. This paper presents a knowledge-based multi-criteria decision analysis using GIS for the selection of suitable landfill site in Ado-Ekiti, Nigeria. In order to identify suitable sites for landfill, seven factors - land use/cover, geology, river, soil, slope, lineament and roads - were taken into consideration. Each factor was classified and ranked based on prior knowledge about the area and existing guidelines. Weights for each factor were determined through pair-wise comparison using Saaty's 9 point scale and AHP. The integration of factors according to their weights using weighted index overlay analysis revealed that 39.23 km2 within the area was suitable to site a landfill. The resulting suitable area was classified as high suitability covering 6.47 km2 (16.49%), moderate suitability 25.48 km2 (64.95%) and low suitability 7.28 km2 (18.56%) based on their overall weights.

Evaluation and application of multiple scoring functions for a virtual screening experiment

NASA Astrophysics Data System (ADS)

Xing, Li; Hodgkin, Edward; Liu, Qian; Sedlock, David

2004-05-01

In order to identify novel chemical classes of factor Xa inhibitors, five scoring functions (FlexX, DOCK, GOLD, ChemScore and PMF) were engaged to evaluate the multiple docking poses generated by FlexX. The compound collection was composed of confirmed potent factor Xa inhibitors and a subset of the LeadQuest® screening compound library. Except for PMF the other four scoring functions succeeded in reproducing the crystal complex (PDB code: 1FAX). During virtual screening the highest hit rate (80%) was demonstrated by FlexX at an energy cutoff of -40 kJ/mol, which is about 40-fold over random screening (2.06%). Limited results suggest that presenting more poses of a single molecule to the scoring functions could deteriorate their enrichment factors. A series of promising scaffolds with favorable binding scores was retrieved from LeadQuest. Consensus scoring by pair-wise intersection failed to enrich the hit rate yielded by single scorings (i.e. FlexX). We note that reported successes of consensus scoring in hit rate enrichment could be artificial because their comparisons were based on a selected subset of single scoring and a markedly reduced subset of double or triple scoring. The findings presented in this report are based upon a single biological system and support further studies.

Expression of myogenes in longissimus dorsi muscle during prenatal development in commercial and local Piau pigs.

PubMed

Reis, Evelyze Pinheiro Dos; Paixão, Débora Martins; Brustolini, Otávio José Bernardes; Silva, Fabyano Fonseca E; Silva, Walmir; Araújo, Flávio Marcos Gomes de; Salim, Anna Christina de Matos; Oliveira, Guilherme; Guimarães, Simone Eliza Facioni

2016-01-01

This study used qRT-PCR to examine variation in the expression of 13 myogenes during muscle development in four prenatal periods (21, 40, 70 and 90 days post-insemination) in commercial (the three-way Duroc, Landrace and Large-White cross) and local Piau pig breeds that differ in muscle mass. There was no variation in the expression of the CHD8, EID2B, HIF1AN, IKBKB, RSPO3, SOX7 and SUFU genes at the various prenatal ages or between breeds. The MAP2K1 and RBM24 genes showed similar expression between commercial and Piau pigs but greater expression (p < 0.05) in at least one prenatal period. Pair-wise comparisons of prenatal periods in each breed showed that only the CSRP3, LEF1, MRAS and MYOG genes had higher expression (p < 0.05) in at least one prenatal period in commercial and Piau pigs. Overall, these results identified the LEF1 gene as a primary candidate to account for differences in muscle mass between the pig breeds since activation of this gene may lead to greater myoblast fusion in the commercial breed compared to Piau pigs. Such fusion could explain the different muscularity between breeds in the postnatal periods.

Impact of cryopreservation on tetramer, cytokine flow cytometry, and ELISPOT

PubMed Central

Maecker, Holden T; Moon, James; Bhatia, Sonny; Ghanekar, Smita A; Maino, Vernon C; Payne, Janice K; Kuus-Reichel, Kristine; Chang, Jennie C; Summers, Amanda; Clay, Timothy M; Morse, Michael A; Lyerly, H Kim; DeLaRosa, Corazon; Ankerst, Donna P; Disis, Mary L

2005-01-01

Background Cryopreservation of PBMC and/or overnight shipping of samples are required for many clinical trials, despite their potentially adverse effects upon immune monitoring assays such as MHC-peptide tetramer staining, cytokine flow cytometry (CFC), and ELISPOT. In this study, we compared the performance of these assays on leukapheresed PBMC shipped overnight in medium versus cryopreserved PBMC from matched donors. Results Using CMV pp65 peptide pool stimulation or pp65 HLA-A2 tetramer staining, there was significant correlation between shipped and cryopreserved samples for each assay (p ≤ 0.001). The differences in response magnitude between cryopreserved and shipped PBMC specimens were not significant for most antigens and assays. There was significant correlation between CFC and ELISPOT assay using pp65 peptide pool stimulation, in both shipped and cryopreserved samples (p ≤ 0.001). Strong correlation was observed between CFC (using HLA-A2-restricted pp65 peptide stimulation) and tetramer staining (p < 0.001). Roughly similar sensitivity and specificity were observed between the three assays and between shipped and cryopreserved samples for each assay. Conclusion We conclude that all three assays show concordant results on shipped versus cryopreserved specimens, when using a peptide-based readout. The assays are also concordant with each other in pair wise comparisons using equivalent antigen systems. PMID:16026627

Examining Difference in Immigration Stress, Acculturation Stress and Mental Health Outcomes in Six Hispanic/Latino Nativity and Regional Groups.

PubMed

Cervantes, Richard C; Gattamorta, Karina A; Berger-Cardoso, Jodi

2018-02-27

Little is known about the specific behavioral health impact of acculturation stressors that affect Hispanic/Latino immigrant sub-groups. These immigration-related stressors and traumatic events may have differential impact on depression depending on country/region of origin. Using a measure of immigration and acculturation stress, the current study sought to determine differences in the impact of stress on six sub-groups of Hispanic immigrants. Data on stress and depression were examined using a large, representative adult immigrant sample (N = 641). Controlling for age, gender and years in the US, factorial analysis of covariance revealed significant differences on total Hispanic Stress Inventory 2 (HSI2) stress appraisal scores based on country/region of origin. Pair wise comparisons between country/region of origin groups revealed that Mexicans had higher levels of stress compared to Cuban or Dominican immigrants. Several patterns of differential stress were also found within sub-domains of the HSI2. Using regression models, HSI2 stress appraisals and their interaction with country of origin proved to not be significant predictors of depression (PHQ9), while gender and age were significant. Differences in HSI2 stress that are based on nativity may be moderated by cultural resilience that ultimately serves a protective role to prevent the onset of depression.

An Integrated Approach of Fuzzy Linguistic Preference Based AHP and Fuzzy COPRAS for Machine Tool Evaluation.

PubMed

Nguyen, Huu-Tho; Md Dawal, Siti Zawiah; Nukman, Yusoff; Aoyama, Hideki; Case, Keith

2015-01-01

Globalization of business and competitiveness in manufacturing has forced companies to improve their manufacturing facilities to respond to market requirements. Machine tool evaluation involves an essential decision using imprecise and vague information, and plays a major role to improve the productivity and flexibility in manufacturing. The aim of this study is to present an integrated approach for decision-making in machine tool selection. This paper is focused on the integration of a consistent fuzzy AHP (Analytic Hierarchy Process) and a fuzzy COmplex PRoportional ASsessment (COPRAS) for multi-attribute decision-making in selecting the most suitable machine tool. In this method, the fuzzy linguistic reference relation is integrated into AHP to handle the imprecise and vague information, and to simplify the data collection for the pair-wise comparison matrix of the AHP which determines the weights of attributes. The output of the fuzzy AHP is imported into the fuzzy COPRAS method for ranking alternatives through the closeness coefficient. Presentation of the proposed model application is provided by a numerical example based on the collection of data by questionnaire and from the literature. The results highlight the integration of the improved fuzzy AHP and the fuzzy COPRAS as a precise tool and provide effective multi-attribute decision-making for evaluating the machine tool in the uncertain environment.

Effect of Charged-Magnetic Grains in Protoplanetary Disks

NASA Astrophysics Data System (ADS)

Perry, Jonathan; Matthews, Lorin; Hyde, Truell

Effects of Charged-Magnetic Grains in Protoplanetary Disks Jonathan, Perry, Lorin Swint Matthews, and Truell W. Hyde Center for Astrophysics, Space Physics, and Engi-neering Research, addressPlaceNamePlaceNameplaceBaylor StreetPlaceTypeUniversity, Stree-taddressOne Bear Place 97316 Waco, TX 76798 USA The interaction and growth of dust grains is an important process in early planetesimal formation. The structure of aggregates formed from dust depend largely on the initial properties within the dust population, whether the grains are charged or uncharged, magnetic or non-magnetic. Theoretical simulations exam-ining pair-wise interactions between aggregates indicate that charged magnetic grains exhibit different growth behavior than populations consisting of exclusively charged or exclusively mag-netic grains. This study extends that work to predict how charged-magnetic grains influence grain growth within a protoplanetary disk. An N-body simulation containing various mixtures of dust materials is used to examine the differences in dust coagulation in the presence of charged magnetic aggregates. The growth of the dust aggregates is analyzed to determine the effects that charged magnetic grains contribute to the evolution of the dust cloud. Comparison of the rate of aggregation as well as the dynamic exponent relating mass of a cluster to the elapsed time will both be discussed.

Comparative Analysis of Households Solid Waste Management in Rural and Urban Ghana

PubMed Central

Appiah, Divine Odame; Poku, Adjoa Afriyie; Garsonu, Emmanuel Kofi

2016-01-01

The comparative analysis of solid waste management between rural and urban Ghana is largely lacking. This study investigated the solid waste situation and the organisation of solid waste management in both urban and rural settings from the perspective of households. The study employed cross-sectional survey covering both rural and urban districts in the Ashanti and Greater Accra Regions of Ghana. The study systematically sampled houses from which 400 households and respondents were randomly selected. Pearson's Chi square test was used to compare demographic and socioeconomic variables in rural and urban areas. Multivariate Test, Tests of Between-Subjects Effects, and Pair-Wise Comparisons were performed through one-way MANOVA to determine whether or not solid waste situations in rural and urban areas are significantly different. The results revealed that location significantly affects solid waste management in Ghana. Urban communities had lower mean scores than rural communities for poor solid waste situation in homes. However, urban communities had higher mean scores than rural communities for poor solid waste situation in principal streets and dumping sites. The study recommends that the local government authorities implement very comprehensive policies (sanitary inspection, infrastructure development, and community participation) that will take into consideration the specific solid waste management needs of both urban and rural areas. PMID:27807453

Expression of myogenes in longissimus dorsi muscle during prenatal development in commercial and local Piau pigs

PubMed Central

dos Reis, Evelyze Pinheiro; Paixão, Débora Martins; Brustolini, Otávio José Bernardes; Silva, Fabyano Fonseca e; Silva, Walmir; de Araújo, Flávio Marcos Gomes; Salim, Anna Christina de Matos; Oliveira, Guilherme; Guimarães, Simone Eliza Facioni

2016-01-01

Abstract This study used qRT-PCR to examine variation in the expression of 13 myogenes during muscle development in four prenatal periods (21, 40, 70 and 90 days post-insemination) in commercial (the three-way Duroc, Landrace and Large-White cross) and local Piau pig breeds that differ in muscle mass. There was no variation in the expression of the CHD8, EID2B, HIF1AN, IKBKB, RSPO3, SOX7 and SUFU genes at the various prenatal ages or between breeds. The MAP2K1 and RBM24 genes showed similar expression between commercial and Piau pigs but greater expression (p < 0.05) in at least one prenatal period. Pair-wise comparisons of prenatal periods in each breed showed that only the CSRP3, LEF1, MRAS and MYOG genes had higher expression (p < 0.05) in at least one prenatal period in commercial and Piau pigs. Overall, these results identified the LEF1 gene as a primary candidate to account for differences in muscle mass between the pig breeds since activation of this gene may lead to greater myoblast fusion in the commercial breed compared to Piau pigs. Such fusion could explain the different muscularity between breeds in the postnatal periods. PMID:27801482

Value for money - recasting the problem in terms of dynamic access prioritisation.

PubMed

Taylor, William J; Laking, George

2010-01-01

To develop an approach for achieving value for money in rehabilitation based on dynamic prioritisation of access to services according to individual capacity to benefit. A critical review of economic evaluation and adaptation of a prioritisation method used in determining access to elective surgical services in New Zealand to a rehabilitation context. The cost-effectiveness frontier is not straight but curved, suggesting that some people benefit more from a given intervention than others. An approach that identifies those most likely to benefit from inpatient rehabilitation following stroke (as an example) and enables access in order of capacity to benefit is presented in the context of a quality improvement programme. The approach is operationalised as a prioritisation tool that is dynamic in the sense that is can be reapplied subject to changes in the patient's clinical status. The steps proposed to develop such a tool include qualitative research with expert clinicians, pair-wise comparison of alternative scenarios (1000Minds survey), construction of an economic model of the tool's operation and an observational cohort study to help populate the model and calibrate the tool. A dynamic prioritisation approach to guide access to scarce health-care resources (such as inpatient rehabilitation following stroke) offers a transparent and equitable way of achieving value for money in the delivery of rehabilitation services.

Longitudinal study of a cooperation-driven, socio-scientific issue intervention on promoting students' critical thinking and self-regulation in learning science

NASA Astrophysics Data System (ADS)

Wang, Hsin-Hui; Chen, Hsiang-Ting; Lin, Huann-shyang; Huang, Yu-Ning; Hong, Zuway-R.

2017-10-01

This longitudinal study explored the effects of a Cooperation-driven Socioscientific Issue (CDSSI) intervention on junior high school students' perceptions of critical thinking (CT) and self-regulation (SR) in Taiwan. Forty-nine grade 7 students were randomly selected as an experimental group (EG) to attend a 3-semester 72-hour intervention; while another 49 grade 7 students from the same school were randomly selected as the comparison group (CG). All participants completed a 4-wave student questionnaire to assess their perceptions of CT and SR. In addition, 8 target students from the EG with the lowest scores on either CT or SR were purposefully recruited for weekly observation. These target students and their teachers were interviewed one month after the intervention in each semester. Analyses of covariance and paired-wise t-tests revealed that the EG students' perceptions of CT and SR in learning science were improved during the study and were significantly better than their counterparts' at the end of the study. Systematic interview and classroom observation results were consistent with the quantitative findings. This study adds empirical evidence and provides insights into how CDSSI can be integrated into planning and implementing effective pedagogical strategies aimed at increasing students' perceptions of CT and SR in learning science.

Ethnic variation of selected dental traits in Coorg

PubMed Central

Uthaman, Chancy; Sequeira, Peter Simon; Jain, Jithesh

2015-01-01

Purpose: In a country like India, in addition to the great innate diversity, there are distinct migrant populations with unique dental traits. Aim: To assess the distribution and degree of expression of cusp of Carabelli of maxillary first permanent molars and shoveling trait of maxillary central incisors, between three ethnic groups of Coorg, namely Kodavas, Tibetans, and Malayalees. Materials and Methods: A cross-sectional, indirect, anthropometric, study was carried out among 15- to 30-year-old subjects belonging to three different ethnic origins. A random sample consisting of 91 subjects were recruited for the study. The shovel trait of incisors and the Carabelli trait of molars were recorded according to the classification given by Hrdliƈka and Sousa et al., respectively. Statistical Analysis: The Kruskal-Wallis test was employed to determine the difference in three populations for shoveling and Carabelli traits. Mann-Whitney Test was used for pair-wise comparisons of three populations. Result: Of the total 91 subjects, 31 were Kodavas, 30 Malayalees and 30 Tibetans. There was a statistically significant difference in shoveling trait among the three ethnic groups. For Carabelli traits, there was no statistically significant difference among three ethnic groups. Conclusion: The present study findings showed that Tibetans have a higher degree of shoveling trait than the selected South Indian ethnic groups. PMID:26816457

Validation of the β-amy1 transcription profiling assay and selection of reference genes suited for a RT-qPCR assay in developing barley caryopsis.

PubMed

Ovesná, Jaroslava; Kučera, Ladislav; Vaculová, Kateřina; Štrymplová, Kamila; Svobodová, Ilona; Milella, Luigi

2012-01-01

Reverse transcription coupled with real-time quantitative PCR (RT-qPCR) is a frequently used method for gene expression profiling. Reference genes (RGs) are commonly employed to normalize gene expression data. A limited information exist on the gene expression and profiling in developing barley caryopsis. Expression stability was assessed by measuring the cycle threshold (Ct) range and applying both the GeNorm (pair-wise comparison of geometric means) and Normfinder (model-based approach) principles for the calculation. Here, we have identified a set of four RGs suitable for studying gene expression in the developing barley caryopsis. These encode the proteins GAPDH, HSP90, HSP70 and ubiquitin. We found a correlation between the frequency of occurrence of a transcript in silico and its suitability as an RG. This set of RGs was tested by comparing the normalized level of β-amylase (β-amy1) transcript with directly measured quantities of the BMY1 gene product in the developing barley caryopsis. This panel of genes could be used for other gene expression studies, as well as to optimize β-amy1 analysis for study of the impact of β-amy1 expression upon barley end-use quality.

Evaluating Dynamic Bivariate Correlations in Resting-state fMRI: A comparison study and a new approach

PubMed Central

Lindquist, Martin A.; Xu, Yuting; Nebel, Mary Beth; Caffo, Brain S.

2014-01-01

To date, most functional Magnetic Resonance Imaging (fMRI) studies have assumed that the functional connectivity (FC) between time series from distinct brain regions is constant across time. However, recently, there has been increased interest in quantifying possible dynamic changes in FC during fMRI experiments, as it is thought this may provide insight into the fundamental workings of brain networks. In this work we focus on the specific problem of estimating the dynamic behavior of pair-wise correlations between time courses extracted from two different regions of the brain. We critique the commonly used sliding-windows technique, and discuss some alternative methods used to model volatility in the finance literature that could also prove useful in the neuroimaging setting. In particular, we focus on the Dynamic Conditional Correlation (DCC) model, which provides a model-based approach towards estimating dynamic correlations. We investigate the properties of several techniques in a series of simulation studies and find that DCC achieves the best overall balance between sensitivity and specificity in detecting dynamic changes in correlations. We also investigate its scalability beyond the bivariate case to demonstrate its utility for studying dynamic correlations between more than two brain regions. Finally, we illustrate its performance in an application to test-retest resting state fMRI data. PMID:24993894

Comparative Analysis of Households Solid Waste Management in Rural and Urban Ghana.

PubMed

Boateng, Simon; Amoako, Prince; Appiah, Divine Odame; Poku, Adjoa Afriyie; Garsonu, Emmanuel Kofi

2016-01-01

The comparative analysis of solid waste management between rural and urban Ghana is largely lacking. This study investigated the solid waste situation and the organisation of solid waste management in both urban and rural settings from the perspective of households. The study employed cross-sectional survey covering both rural and urban districts in the Ashanti and Greater Accra Regions of Ghana. The study systematically sampled houses from which 400 households and respondents were randomly selected. Pearson's Chi square test was used to compare demographic and socioeconomic variables in rural and urban areas. Multivariate Test, Tests of Between-Subjects Effects, and Pair-Wise Comparisons were performed through one-way MANOVA to determine whether or not solid waste situations in rural and urban areas are significantly different. The results revealed that location significantly affects solid waste management in Ghana. Urban communities had lower mean scores than rural communities for poor solid waste situation in homes. However, urban communities had higher mean scores than rural communities for poor solid waste situation in principal streets and dumping sites. The study recommends that the local government authorities implement very comprehensive policies (sanitary inspection, infrastructure development, and community participation) that will take into consideration the specific solid waste management needs of both urban and rural areas.

Deciphering life history transcriptomes in different environments

PubMed Central

Etges, William J.; Trotter, Meredith V.; de Oliveira, Cássia C.; Rajpurohit, Subhash; Gibbs, Allen G.; Tuljapurkar, Shripad

2014-01-01

We compared whole transcriptome variation in six preadult stages and seven adult female ages in two populations of cactophilic Drosophila mojavensis reared on two host plants in order to understand how differences in gene expression influence standing life history variation. We used Singular Value Decomposition (SVD) to identify dominant trajectories of life cycle gene expression variation, performed pair-wise comparisons of stage and age differences in gene expression across the life cycle, identified when genes exhibited maximum levels of life cycle gene expression, and assessed population and host cactus effects on gene expression. Life cycle SVD analysis returned four significant components of transcriptional variation, revealing functional enrichment of genes responsible for growth, metabolic function, sensory perception, neural function, translation and aging. Host cactus effects on female gene expression revealed population and stage specific differences, including significant host plant effects on larval metabolism and development, as well as adult neurotransmitter binding and courtship behavior gene expression levels. In 3 - 6 day old virgin females, significant up-regulation of genes associated with meiosis and oogenesis was accompanied by down-regulation of genes associated with somatic maintenance, evidence for a life history tradeoff. The transcriptome of D. mojavensis reared in natural environments throughout its life cycle revealed core developmental transitions and genome wide influences on life history variation in natural populations. PMID:25442828

Development of Genetic Markers in Eucalyptus Species by Target Enrichment and Exome Sequencing

PubMed Central

Dasgupta, Modhumita Ghosh; Dharanishanthi, Veeramuthu; Agarwal, Ishangi; Krutovsky, Konstantin V.

2015-01-01

The advent of next-generation sequencing has facilitated large-scale discovery, validation and assessment of genetic markers for high density genotyping. The present study was undertaken to identify markers in genes supposedly related to wood property traits in three Eucalyptus species. Ninety four genes involved in xylogenesis were selected for hybridization probe based nuclear genomic DNA target enrichment and exome sequencing. Genomic DNA was isolated from the leaf tissues and used for on-array probe hybridization followed by Illumina sequencing. The raw sequence reads were trimmed and high-quality reads were mapped to the E. grandis reference sequence and the presence of single nucleotide variants (SNVs) and insertions/ deletions (InDels) were identified across the three species. The average read coverage was 216X and a total of 2294 SNVs and 479 InDels were discovered in E. camaldulensis, 2383 SNVs and 518 InDels in E. tereticornis, and 1228 SNVs and 409 InDels in E. grandis. Additionally, SNV calling and InDel detection were conducted in pair-wise comparisons of E. tereticornis vs. E. grandis, E. camaldulensis vs. E. tereticornis and E. camaldulensis vs. E. grandis. This study presents an efficient and high throughput method on development of genetic markers for family– based QTL and association analysis in Eucalyptus. PMID:25602379

Methane mitigation timelines to inform energy technology evaluation

NASA Astrophysics Data System (ADS)

Roy, Mandira; Edwards, Morgan R.; Trancik, Jessika E.

2015-11-01

Energy technologies emitting differing proportions of methane (CH4) and carbon dioxide (CO2) vary significantly in their relative climate impacts over time, due to the distinct atmospheric lifetimes and radiative efficiencies of the two gases. Standard technology comparisons using the global warming potential (GWP) with a fixed time horizon do not account for the timing of emissions in relation to climate policy goals. Here we develop a portfolio optimization model that incorporates changes in technology impacts based on the temporal proximity of emissions to a radiative forcing (RF) stabilization target. An optimal portfolio, maximizing allowed energy consumption while meeting the RF target, is obtained by year-wise minimization of the marginal RF impact in an intended stabilization year. The optimal portfolio calls for using certain higher-CH4-emitting technologies prior to an optimal switching year, followed by CH4-light technologies as the stabilization year approaches. We apply the model to evaluate transportation technology pairs and find that accounting for dynamic emissions impacts, in place of using the static GWP, can result in CH4 mitigation timelines and technology transitions that allow for significantly greater energy consumption while meeting a climate policy target. The results can inform the forward-looking evaluation of energy technologies by engineers, private investors, and policy makers.

Testing process predictions of models of risky choice: a quantitative model comparison approach

PubMed Central

Pachur, Thorsten; Hertwig, Ralph; Gigerenzer, Gerd; Brandstätter, Eduard

2013-01-01

This article presents a quantitative model comparison contrasting the process predictions of two prominent views on risky choice. One view assumes a trade-off between probabilities and outcomes (or non-linear functions thereof) and the separate evaluation of risky options (expectation models). Another view assumes that risky choice is based on comparative evaluation, limited search, aspiration levels, and the forgoing of trade-offs (heuristic models). We derived quantitative process predictions for a generic expectation model and for a specific heuristic model, namely the priority heuristic (Brandstätter et al., 2006), and tested them in two experiments. The focus was on two key features of the cognitive process: acquisition frequencies (i.e., how frequently individual reasons are looked up) and direction of search (i.e., gamble-wise vs. reason-wise). In Experiment 1, the priority heuristic predicted direction of search better than the expectation model (although neither model predicted the acquisition process perfectly); acquisition frequencies, however, were inconsistent with both models. Additional analyses revealed that these frequencies were primarily a function of what Rubinstein (1988) called “similarity.” In Experiment 2, the quantitative model comparison approach showed that people seemed to rely more on the priority heuristic in difficult problems, but to make more trade-offs in easy problems. This finding suggests that risky choice may be based on a mental toolbox of strategies. PMID:24151472

Longitudinally Jointed Edge-Wise Compression HoneyComb Composite Sandwich Coupon Testing And Fe Analysis: Three Methods of Strain Measurement, And Comparison

NASA Technical Reports Server (NTRS)

Farrokh, Babak; Rahim, Nur Aida Abul; Segal, Ken; Fan, Terry; Jones, Justin; Hodges, Ken; Mashni, Noah; Garg, Naman; Sang, Alex

2013-01-01

Three distinct strain measurement methods (i.e., foil resistance strain gages, fiber optic strain sensors, and a three-dimensional digital image photogrammetry that gives full field strain and displacement measurements) were implemented to measure strains on the back and front surfaces of a longitudinally jointed curved test article subjected to edge-wise compression testing, at NASA Goddard Space Flight Center, according to ASTM C364. The pre-test finite element analysis (FEA) was conducted to assess ultimate failure load and predict strain distribution pattern throughout the test coupon. The predicted strain pattern contours were then utilized as guidelines for installing the strain measurement instrumentations. The foil resistance strain gages and fiber optic strain sensors were bonded on the specimen at locations with nearly the same analytically predicted strain values, and as close as possible to each other, so that, comparisons between the measured strains by strain gages and fiber optic sensors, as well as the three-dimensional digital image photogrammetric system are relevant. The test article was loaded to failure (at 167 kN), at the compressive strain value of 10,000 micro epsilon. As a part of this study, the validity of the measured strains by fiber optic sensors is examined against the foil resistance strain gages and the three-dimensional digital image photogrammetric data, and comprehensive comparisons are made with FEA predictions.

Primary Care Clinicians' Perspectives on Reducing Low-Value Care in an Integrated Delivery System.

PubMed

Buist, Diana S M; Chang, Eva; Handley, Matt; Pardee, Roy; Gundersen, Gabrielle; Cheadle, Allen; Reid, Robert J

2016-01-01

Perceptions about low-value care (eg, medical tests and procedures that may be unnecessary and/or harmful) among clinicians with capitated salaries are unknown. Explore clinicians' perceived use of and responsibility for reducing low-value care by focusing on barriers to use, awareness of the Choosing Wisely campaign, and response to reports of peer-comparison resource use and practice patterns. Electronic, cross-sectional survey, distributed in 2013, to 304 salaried primary care physicians and physician assistants at Group Health Cooperative. Attitudes, awareness, and barriers of low-value care strategies and initiatives. A total of 189 clinicians responded (62% response rate). More than 90% believe cost is important to various stakeholders and believe it is fair to ask clinicians to be cost-conscious. Most found peer-comparison resource-use reports useful for understanding practice patterns and prompting peer discussions. Two-thirds of clinicians were aware of the Choosing Wisely campaign; among them, 97% considered it a legitimate information source. Although 88% reported being comfortable discussing low-value care with patients, 80% reported they would order tests or procedures when a patient insisted. As key barriers in reducing low-value care, clinicians identified time constraints (45%), overcoming patient preferences/values (44%), community standards (43%), fear of patients' dissatisfaction (41%), patients' knowledge about the harms of low-value care (38%), and availability of tools to support shared decision making (37%). Salaried clinicians are aware of rising health care costs and want to be stewards of limited health care resources. Evidence-based initiatives such as the Choosing Wisely campaign may help motivate clinicians to be conscientious stewards of limited health care resources.

Modelling heterogeneity variances in multiple treatment comparison meta-analysis--are informative priors the better solution?

PubMed

Thorlund, Kristian; Thabane, Lehana; Mills, Edward J

2013-01-11

Multiple treatment comparison (MTC) meta-analyses are commonly modeled in a Bayesian framework, and weakly informative priors are typically preferred to mirror familiar data driven frequentist approaches. Random-effects MTCs have commonly modeled heterogeneity under the assumption that the between-trial variance for all involved treatment comparisons are equal (i.e., the 'common variance' assumption). This approach 'borrows strength' for heterogeneity estimation across treatment comparisons, and thus, ads valuable precision when data is sparse. The homogeneous variance assumption, however, is unrealistic and can severely bias variance estimates. Consequently 95% credible intervals may not retain nominal coverage, and treatment rank probabilities may become distorted. Relaxing the homogeneous variance assumption may be equally problematic due to reduced precision. To regain good precision, moderately informative variance priors or additional mathematical assumptions may be necessary. In this paper we describe four novel approaches to modeling heterogeneity variance - two novel model structures, and two approaches for use of moderately informative variance priors. We examine the relative performance of all approaches in two illustrative MTC data sets. We particularly compare between-study heterogeneity estimates and model fits, treatment effect estimates and 95% credible intervals, and treatment rank probabilities. In both data sets, use of moderately informative variance priors constructed from the pair wise meta-analysis data yielded the best model fit and narrower credible intervals. Imposing consistency equations on variance estimates, assuming variances to be exchangeable, or using empirically informed variance priors also yielded good model fits and narrow credible intervals. The homogeneous variance model yielded high precision at all times, but overall inadequate estimates of between-trial variances. Lastly, treatment rankings were similar among the novel approaches, but considerably different when compared with the homogenous variance approach. MTC models using a homogenous variance structure appear to perform sub-optimally when between-trial variances vary between comparisons. Using informative variance priors, assuming exchangeability or imposing consistency between heterogeneity variances can all ensure sufficiently reliable and realistic heterogeneity estimation, and thus more reliable MTC inferences. All four approaches should be viable candidates for replacing or supplementing the conventional homogeneous variance MTC model, which is currently the most widely used in practice.

Rank-Order and Paired Comparisons as the Basis for Measurement.

ERIC Educational Resources Information Center

Linacre, John M.

Three case studies are presented demonstrating the application of straight-forward Rasch techniques to rank order data. Paired comparisons are the simplest form of rank ordering. A consumer preference test with 56 pairs of cups of coffee tasted by each of 26 consumers illustrates analysis of these rankings. When subjects are allowed the option of…

Elaboration on the Culturally Informed Iranian Hierarchical Wisdom Model: Comparison with Sternberg's ACCEL Model

ERIC Educational Resources Information Center

Karami, Sareh; Ghahremani, Mehdi

2017-01-01

Using a grounded theory approach to the study of historical texts and an expert interview, we developed the Iranian hierarchical wisdom model (IHWM; Karami & Ghahremani, 2016). According to IHWM, there are three levels to wisdom: practical intelligence, wise, and sage. In this article, we discuss the model and elaborate on it. Next, we examine…

Comparison between various patch wise strategies for reconstruction of ultra-spectral cubes captured with a compressive sensing system

NASA Astrophysics Data System (ADS)

Oiknine, Yaniv; August, Isaac Y.; Revah, Liat; Stern, Adrian

2016-05-01

Recently we introduced a Compressive Sensing Miniature Ultra-Spectral Imaging (CS-MUSI) system. The system is based on a single Liquid Crystal (LC) cell and a parallel sensor array where the liquid crystal cell performs spectral encoding. Within the framework of compressive sensing, the CS-MUSI system is able to reconstruct ultra-spectral cubes captured with only an amount of ~10% samples compared to a conventional system. Despite the compression, the technique is extremely complex computationally, because reconstruction of ultra-spectral images requires processing huge data cubes of Gigavoxel size. Fortunately, the computational effort can be alleviated by using separable operation. An additional way to reduce the reconstruction effort is to perform the reconstructions on patches. In this work, we consider processing on various patch shapes. We present an experimental comparison between various patch shapes chosen to process the ultra-spectral data captured with CS-MUSI system. The patches may be one dimensional (1D) for which the reconstruction is carried out spatially pixel-wise, or two dimensional (2D) - working on spatial rows/columns of the ultra-spectral cube, as well as three dimensional (3D).

Longitudinally Jointed Edge-wise Compression Honeycomb Composite Sandwich Coupon Testing and FE Analysis: Three Methods of Strain Measurement, and Comparison

NASA Technical Reports Server (NTRS)

Farrokh, Babak; AbdulRahim, Nur Aida; Segal, Ken; Fan, Terry; Jones, Justin; Hodges, Ken; Mashni, Noah; Garg, Naman; Sang, Alex; Gifford, Dawn;

RECOVIR Software for Identifying Viruses

NASA Technical Reports Server (NTRS)

Chakravarty, Sugoto; Fox, George E.; Zhu, Dianhui

2013-01-01

Most single-stranded RNA (ssRNA) viruses mutate rapidly to generate a large number of strains with highly divergent capsid sequences. Determining the capsid residues or nucleotides that uniquely characterize these strains is critical in understanding the strain diversity of these viruses. RECOVIR (an acronym for "recognize viruses") software predicts the strains of some ssRNA viruses from their limited sequence data. Novel phylogenetic-tree-based databases of protein or nucleic acid residues that uniquely characterize these virus strains are created. Strains of input virus sequences (partial or complete) are predicted through residue-wise comparisons with the databases. RECOVIR uses unique characterizing residues to identify automatically strains of partial or complete capsid sequences of picorna and caliciviruses, two of the most highly diverse ssRNA virus families. Partition-wise comparisons of the database residues with the corresponding residues of more than 300 complete and partial sequences of these viruses resulted in correct strain identification for all of these sequences. This study shows the feasibility of creating databases of hitherto unknown residues uniquely characterizing the capsid sequences of two of the most highly divergent ssRNA virus families. These databases enable automated strain identification from partial or complete capsid sequences of these human and animal pathogens.

Limited Agreement of Independent RNAi Screens for Virus-Required Host Genes Owes More to False-Negative than False-Positive Factors

PubMed Central

Wang, Zhishi; Craven, Mark; Newton, Michael A.; Ahlquist, Paul

2013-01-01

Systematic, genome-wide RNA interference (RNAi) analysis is a powerful approach to identify gene functions that support or modulate selected biological processes. An emerging challenge shared with some other genome-wide approaches is that independent RNAi studies often show limited agreement in their lists of implicated genes. To better understand this, we analyzed four genome-wide RNAi studies that identified host genes involved in influenza virus replication. These studies collectively identified and validated the roles of 614 cell genes, but pair-wise overlap among the four gene lists was only 3% to 15% (average 6.7%). However, a number of functional categories were overrepresented in multiple studies. The pair-wise overlap of these enriched-category lists was high, ∼19%, implying more agreement among studies than apparent at the gene level. Probing this further, we found that the gene lists implicated by independent studies were highly connected in interacting networks by independent functional measures such as protein-protein interactions, at rates significantly higher than predicted by chance. We also developed a general, model-based approach to gauge the effects of false-positive and false-negative factors and to estimate, from a limited number of studies, the total number of genes involved in a process. For influenza virus replication, this novel statistical approach estimates the total number of cell genes involved to be ∼2,800. This and multiple other aspects of our experimental and computational results imply that, when following good quality control practices, the low overlap between studies is primarily due to false negatives rather than false-positive gene identifications. These results and methods have implications for and applications to multiple forms of genome-wide analysis. PMID:24068911

Sythesis of MCMC and Belief Propagation

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

Ahn, Sungsoo; Chertkov, Michael; Shin, Jinwoo

Markov Chain Monte Carlo (MCMC) and Belief Propagation (BP) are the most popular algorithms for computational inference in Graphical Models (GM). In principle, MCMC is an exact probabilistic method which, however, often suffers from exponentially slow mixing. In contrast, BP is a deterministic method, which is typically fast, empirically very successful, however in general lacking control of accuracy over loopy graphs. In this paper, we introduce MCMC algorithms correcting the approximation error of BP, i.e., we provide a way to compensate for BP errors via a consecutive BP-aware MCMC. Our framework is based on the Loop Calculus (LC) approach whichmore » allows to express the BP error as a sum of weighted generalized loops. Although the full series is computationally intractable, it is known that a truncated series, summing up all 2-regular loops, is computable in polynomial-time for planar pair-wise binary GMs and it also provides a highly accurate approximation empirically. Motivated by this, we first propose a polynomial-time approximation MCMC scheme for the truncated series of general (non-planar) pair-wise binary models. Our main idea here is to use the Worm algorithm, known to provide fast mixing in other (related) problems, and then design an appropriate rejection scheme to sample 2-regular loops. Furthermore, we also design an efficient rejection-free MCMC scheme for approximating the full series. The main novelty underlying our design is in utilizing the concept of cycle basis, which provides an efficient decomposition of the generalized loops. In essence, the proposed MCMC schemes run on transformed GM built upon the non-trivial BP solution, and our experiments show that this synthesis of BP and MCMC outperforms both direct MCMC and bare BP schemes.« less

Genetic relatedness and disrupted social structure in a poached population of African elephants.

PubMed

Gobush, Kathleen; Kerr, Ben; Wasser, Samuel

2009-02-01

We use genetic measures of relatedness and observations of female bonding to examine the demographic signature of historically heavy poaching of a population of free-ranging African elephants. We collected dung samples to obtain DNA and observed behaviour from 102 elephant families over a 25-month period in 2003-2005 in Mikumi National Park, Tanzania. Poaching reduced the population by 75% in the decade prior to the 1989 ivory trade ban; park records indicate that poaching dropped significantly in Mikumi following the ban. Using 10 microsatellite loci, DNA was genotyped in 203 elephants and pair-wise relatedness was calculated among adult females within and between groups. The Mikumi population is characterized by small group size, considerable variation in group relatedness, females with no first-order adult relatives and females that form only weak social bonds. We used gene-drop analysis and a model of a genetically intact pedigree to compare our observed Mikumi group relatedness to a simulated genetically intact unpoached expectation. The majority of groups in Mikumi contain 2 to 3 adults; of these, 45% were classified as genetically disrupted. Bonding, quantified with a pair-wise association index, was significantly correlated with relatedness; however only half of the females formed strong bonds with other females, and relatedness was substantially lower for a given bond strength as compared to an unpoached population. Female African elephants without kin demonstrated considerable behavioural plasticity in this disturbed environment, grouping with other females lacking kin, with established groups, or remaining alone, unable to form any stable adult female-bonds. We interpret these findings as the remaining effect of poaching disturbance in Mikumi, despite a drop in the level of poaching since the commercial trade in ivory was banned 15 years ago.

76 T dwarfs from the UKIDSS LAS: benchmarks, kinematics and an updated space density

NASA Astrophysics Data System (ADS)

Burningham, Ben; Cardoso, C. V.; Smith, L.; Leggett, S. K.; Smart, R. L.; Mann, A. W.; Dhital, S.; Lucas, P. W.; Tinney, C. G.; Pinfield, D. J.; Zhang, Z.; Morley, C.; Saumon, D.; Aller, K.; Littlefair, S. P.; Homeier, D.; Lodieu, N.; Deacon, N.; Marley, M. S.; van Spaandonk, L.; Baker, D.; Allard, F.; Andrei, A. H.; Canty, J.; Clarke, J.; Day-Jones, A. C.; Dupuy, T.; Fortney, J. J.; Gomes, J.; Ishii, M.; Jones, H. R. A.; Liu, M.; Magazzú, A.; Marocco, F.; Murray, D. N.; Rojas-Ayala, B.; Tamura, M.

2013-07-01

We report the discovery of 76 new T dwarfs from the UKIRT Infrared Deep Sky Survey (UKIDSS) Large Area Survey (LAS). Near-infrared broad- and narrow-band photometry and spectroscopy are presented for the new objects, along with Wide-field Infrared Survey Explorer (WISE) and warm-Spitzer photometry. Proper motions for 128 UKIDSS T dwarfs are presented from a new two epoch LAS proper motion catalogue. We use these motions to identify two new benchmark systems: LHS 6176AB, a T8p+M4 pair and HD 118865AB, a T5.5+F8 pair. Using age constraints from the primaries and evolutionary models to constrain the radii, we have estimated their physical properties from their bolometric luminosity. We compare the colours and properties of known benchmark T dwarfs to the latest model atmospheres and draw two principal conclusions. First, it appears that the H - [4.5] and J - W2 colours are more sensitive to metallicity than has previously been recognized, such that differences in metallicity may dominate over differences in Teff when considering relative properties of cool objects using these colours. Secondly, the previously noted apparent dominance of young objects in the late-T dwarf sample is no longer apparent when using the new model grids and the expanded sample of late-T dwarfs and benchmarks. This is supported by the apparently similar distribution of late-T dwarfs and earlier type T dwarfs on reduced proper motion diagrams that we present. Finally, we present updated space densities for the late-T dwarfs, and compare our values to simulation predictions and those from WISE.

Dynamics of social behaviour at parturition in a gregarious ungulate.

PubMed

Pérez-Barbería, F J; Walker, D M

2018-05-01

Group living is the behavioural response that results when individuals assess the costs vs benefits of sociality, and these trade-offs vary across an animal's life. Here we quantitatively assess how periparturient condition (mother/non-mother) and births affect the dynamics of social interactions of a gregarious ungulate, and how such can help to explain evolutionary hypotheses of the mother-offspring bond. To achieve this we used data of the individual movement of a group of Scottish blackface sheep (Ovis aries) marked with GPS collars and properties of mathematical graphs (networks). Euclidean pair-wise distance between sheep were threshold at different percentiles to determine network links, and these thresholds have a profound effect on the connectivity of the resulting network. Births increased the average pair-wise distance between mothers, and between mothers and non-mothers, with less effect on the distance between non-mothers. Mothers occupied peripheral positions within the flock, more evident following births. Associations between individuals (i.e. network community change) were highly dynamic, though mothers were less likely to change community than non-mothers, especially after births. Births hampered individual communication within the flock (assessed via network closeness centrality), especially in mothers. Overall leadership (lead positioning relative to flock movement) was not associated to reproductive condition, and individual leadership rank was not affected by births. A ten minute GPS acquisition time was adequate to capture complex social dynamics in sheep movement. The results on mother's isolation behaviour support the hypotheses of selection for maternal imprint facilitation, reducing risks to nursing alien offspring, and group/multilevel selection on group formation. Copyright © 2018 Elsevier B.V. All rights reserved.

Risk and the evolution of human exchange

PubMed Central

Kaplan, Hillard S.; Schniter, Eric; Smith, Vernon L.; Wilson, Bart J.

2012-01-01

Compared with other species, exchange among non-kin is a hallmark of human sociality in both the breadth of individuals and total resources involved. One hypothesis is that extensive exchange evolved to buffer the risks associated with hominid dietary specialization on calorie dense, large packages, especially from hunting. ‘Lucky’ individuals share food with ‘unlucky’ individuals with the expectation of reciprocity when roles are reversed. Cross-cultural data provide prima facie evidence of pair-wise reciprocity and an almost universal association of high-variance (HV) resources with greater exchange. However, such evidence is not definitive; an alternative hypothesis is that food sharing is really ‘tolerated theft’, in which individuals possessing more food allow others to steal from them, owing to the threat of violence from hungry individuals. Pair-wise correlations may reflect proximity providing greater opportunities for mutual theft of food. We report a laboratory experiment of foraging and food consumption in a virtual world, designed to test the risk-reduction hypothesis by determining whether people form reciprocal relationships in response to variance of resource acquisition, even when there is no external enforcement of any transfer agreements that might emerge. Individuals can forage in a high-mean, HV patch or a low-mean, low-variance (LV) patch. The key feature of the experimental design is that individuals can transfer resources to others. We find that sharing hardly occurs after LV foraging, but among HV foragers sharing increases dramatically over time. The results provide strong support for the hypothesis that people are pre-disposed to evaluate gains from exchange and respond to unsynchronized variance in resource availability through endogenous reciprocal trading relationships. PMID:22513855

Using Paired Comparisons to Assess Maslow's Hierarchy of Needs.

ERIC Educational Resources Information Center

Strong, Lisa L.; Fiebert, Martin S.

Past studies which have examined need levels have identified individuals as functioning at specific need levels without an adequate assessment of the intensity of each need or a clear comparison with other need levels. To address these issues, a self-report inventory using a modified paired comparison format was developed to assess need potencies…

[Flicker comparison of optic disc photographs: sensitivity and specificity].

PubMed

Funk, Jens; Lagrèze, Wolf; Zeyen, Thierry

2002-12-01

Examination and documentation of the optic nerve head are essential in monitoring glaucoma patients. Even minor changes in optic nerve head morphology can be visualised using the so-called flicker test: Two optic nerve head photographs, taken at consecutive examinations, are superimposed by projection. When occluding the pictures in a rapid alternating fashion, changes in optic nerve head morphology appear as motion. In this study, we evaluated sensitivity and specificity of the flicker test. A set of 33 pairs of serial optic disc slides was used as gold standard. These 33 pairs had been classified earlier by 3 independent groups of experts. 23 had been classified as "no change over time", 10 had been classified as "change". All 33 pairs were now evaluated by flicker comparison in a masked fashion. Flicker comparison usually took 1 minute per pair of slides. Sensitivity was 90 %, specificity was 65 %. The sensitivity was reasonably high. The moderate specificity was due to some cases showing "change" with the flicker comparison which might have been overlooked by the expert groups. Flicker comparison is an easy, fast and reliable technique to evaluate pairs of consecutive optic disc photographs.

Multipole Algorithms for Molecular Dynamics Simulation on High Performance Computers.

NASA Astrophysics Data System (ADS)

Elliott, William Dewey

1995-01-01

A fundamental problem in modeling large molecular systems with molecular dynamics (MD) simulations is the underlying N-body problem of computing the interactions between all pairs of N atoms. The simplest algorithm to compute pair-wise atomic interactions scales in runtime {cal O}(N^2), making it impractical for interesting biomolecular systems, which can contain millions of atoms. Recently, several algorithms have become available that solve the N-body problem by computing the effects of all pair-wise interactions while scaling in runtime less than {cal O}(N^2). One algorithm, which scales {cal O}(N) for a uniform distribution of particles, is called the Greengard-Rokhlin Fast Multipole Algorithm (FMA). This work describes an FMA-like algorithm called the Molecular Dynamics Multipole Algorithm (MDMA). The algorithm contains several features that are new to N-body algorithms. MDMA uses new, efficient series expansion equations to compute general 1/r^{n } potentials to arbitrary accuracy. In particular, the 1/r Coulomb potential and the 1/r^6 portion of the Lennard-Jones potential are implemented. The new equations are based on multivariate Taylor series expansions. In addition, MDMA uses a cell-to-cell interaction region of cells that is closely tied to worst case error bounds. The worst case error bounds for MDMA are derived in this work also. These bounds apply to other multipole algorithms as well. Several implementation enhancements are described which apply to MDMA as well as other N-body algorithms such as FMA and tree codes. The mathematics of the cell -to-cell interactions are converted to the Fourier domain for reduced operation count and faster computation. A relative indexing scheme was devised to locate cells in the interaction region which allows efficient pre-computation of redundant information and prestorage of much of the cell-to-cell interaction. Also, MDMA was integrated into the MD program SIgMA to demonstrate the performance of the program over several simulation timesteps. One MD application described here highlights the utility of including long range contributions to Lennard-Jones potential in constant pressure simulations. Another application shows the time dependence of long range forces in a multiple time step MD simulation.

Connectopic mapping with resting-state fMRI.

PubMed

Haak, Koen V; Marquand, Andre F; Beckmann, Christian F

2018-04-15

Brain regions are often topographically connected: nearby locations within one brain area connect with nearby locations in another area. Mapping these connection topographies, or 'connectopies' in short, is crucial for understanding how information is processed in the brain. Here, we propose principled, fully data-driven methods for mapping connectopies using functional magnetic resonance imaging (fMRI) data acquired at rest by combining spectral embedding of voxel-wise connectivity 'fingerprints' with a novel approach to spatial statistical inference. We apply the approach in human primary motor and visual cortex, and show that it can trace biologically plausible, overlapping connectopies in individual subjects that follow these regions' somatotopic and retinotopic maps. As a generic mechanism to perform inference over connectopies, the new spatial statistics approach enables rigorous statistical testing of hypotheses regarding the fine-grained spatial profile of functional connectivity and whether that profile is different between subjects or between experimental conditions. The combined framework offers a fundamental alternative to existing approaches to investigating functional connectivity in the brain, from voxel- or seed-pair wise characterizations of functional association, towards a full, multivariate characterization of spatial topography. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

AllWISE counterparts to ROSAT and XMMSlew surveys done using NWAY (An accurate algorithm to pair sources simultaneously between N catalogs)

NASA Astrophysics Data System (ADS)

Salvato, M.; Buchner, j.; Budavari, T.; Dwelly, T.; Merloni, A.; Brusa, M.; Rau, A.; Fotopoulou, S.; Nandra, K.

2017-10-01

At the end of the mission, the eROSITA All-sky X-ray survey will provide the community with about 4 million of point-like sources, down to a limit of 10^{-14} erg/cm^2/s in the soft band and 2x10^{-13} erg/cm^2/s in the hard band. The brightest sources however have been already observed by ROSAT, but have been rarely used due to the large uncertainties in their positions, thus making the identification of their right multi-wavelength counterparts a demanding task with uncertain results. New all-sky Optical and IR surveys like GAIA and WISE allow us, for the first time, to provide reliable counterparts to all ROSAT sources, thanks also to the development of a new algorithm, NWAY, based on Bayesian statistic and adoption of color-magnitude priors. This paves the way to new programs of complete characterization of the bright X-ray sky, such as the SDSS-IV/SPIDERS survey started in 2014. In this talk I will briefly present the code and the multiwavelength properties of ROSAT and XMMSLEW counterparts.

Protein contact prediction using patterns of correlation.

PubMed

Hamilton, Nicholas; Burrage, Kevin; Ragan, Mark A; Huber, Thomas

2004-09-01

We describe a new method for using neural networks to predict residue contact pairs in a protein. The main inputs to the neural network are a set of 25 measures of correlated mutation between all pairs of residues in two "windows" of size 5 centered on the residues of interest. While the individual pair-wise correlations are a relatively weak predictor of contact, by training the network on windows of correlation the accuracy of prediction is significantly improved. The neural network is trained on a set of 100 proteins and then tested on a disjoint set of 1033 proteins of known structure. An average predictive accuracy of 21.7% is obtained taking the best L/2 predictions for each protein, where L is the sequence length. Taking the best L/10 predictions gives an average accuracy of 30.7%. The predictor is also tested on a set of 59 proteins from the CASP5 experiment. The accuracy is found to be relatively consistent across different sequence lengths, but to vary widely according to the secondary structure. Predictive accuracy is also found to improve by using multiple sequence alignments containing many sequences to calculate the correlations. Copyright 2004 Wiley-Liss, Inc.

Capturing pair-wise epistatic effects associated with three agronomic traits in barley.

PubMed

Xu, Yi; Wu, Yajun; Wu, Jixiang

2018-04-01

Genetic association mapping has been widely applied to determine genetic markers favorably associated with a trait of interest and provide information for marker-assisted selection. Many association mapping studies commonly focus on main effects due to intolerable computing intensity. This study aims to select several sets of DNA markers with potential epistasis to maximize genetic variations of some key agronomic traits in barley. By doing so, we integrated a MDR (multifactor dimensionality reduction) method with a forward variable selection approach. This integrated approach was used to determine single nucleotide polymorphism pairs with epistasis effects associated with three agronomic traits: heading date, plant height, and grain yield in barley from the barley Coordinated Agricultural Project. Our results showed that four, seven, and five SNP pairs accounted for 51.06, 45.66 and 40.42% for heading date, plant height, and grain yield, respectively with epistasis being considered, while corresponding contributions to these three traits were 45.32, 31.39, 31.31%, respectively without epistasis being included. The results suggested that epistasis model was more effective than non-epistasis model in this study and can be more preferred for other applications.

Data Wise in Action: Stories of Schools Using Data to Improve Teaching and Learning

ERIC Educational Resources Information Center

Boudett, Kathryn Parker, Ed.; Steele, Jennifer L., Ed.

2007-01-01

What does it look like when a school uses data wisely? "Data Wise in Action", a new companion and sequel to the bestselling "Data Wise", tells the stories of eight very different schools following the Data Wise process of using assessment results to improve teaching and learning. "Data Wise in Action" highlights the…

WISE Design for Knowledge Integration.

ERIC Educational Resources Information Center

Linn, Marcia C.; Clark, Douglas; Slotta, James D.

2003-01-01

Examines the implementation of Web-based Inquiry Science Environment (WISE), which can incorporate modeling tools and hand-held devices. Describes WISE design team practices, features of the WISE learning environment, and patterns of feature use in WISE library projects. (SOE)

Students' Perspective (Age Wise, Gender Wise and Year Wise) of Parameters Affecting the Undergraduate Engineering Education

ERIC Educational Resources Information Center

Kumari, Neeraj

2014-01-01

The objective of the study is to examine the students' perspective (age wise, gender wise and year wise) of parameters affecting the undergraduate engineering education system present in a private technical institution in NCR [National Capital Region], Haryana. It is a descriptive type of research in nature. The data has been collected with the…

Design and Analyses of High Aspect Ratio Nozzles for Distributed Propulsion Acoustic Measurements

NASA Technical Reports Server (NTRS)

Dippold, Vance F., III

2016-01-01

A series of three convergent round-to-rectangular high-aspect ratio nozzles were designed for acoustics measurements. The nozzles have exit area aspect ratios of 8:1, 12:1, and 16:1. With septa inserts, these nozzles will mimic an array of distributed propulsion system nozzles, as found on hybrid wing-body aircraft concepts. Analyses were performed for the three nozzle designs and showed that the flow through the nozzles was free of separated flow and shocks. The exit flow was mostly uniform with the exception of a pair of vortices at each span-wise end of the nozzle.

A modified GFP facilitates counting membrane protein subunits by step-wise photobleaching in Arabidopsis.

PubMed

Song, Kai; Xue, Yiqun; Wang, Xiaohua; Wan, Yinglang; Deng, Xin; Lin, Jinxing

2017-06-01

Membrane proteins exert functions by forming oligomers or molecular complexes. Currently, step-wise photobleaching has been applied to count the fluorescently labelled subunits in plant cells, for which an accurate and reliable control is required to distinguish individual subunits and define the basal fluorescence. However, the common procedure using immobilized GFP molecules is obviously not applicable for analysis in living plant cells. Using the spatial intensity distribution analysis (SpIDA), we found that the A206K mutation reduced the dimerization of GFP molecules. Further ectopic expression of Myristoyl-GFP A206K driven by the endogenous AtCLC2 promoter allowed imaging of individual molecules at a low expression level. As a result, the percentage of dimers in the transgenic pCLC2::Myristoyl-mGFP A206K line was significantly reduced in comparison to that of the pCLC2::Myristoyl-GFP line, confirming its application in defining the basal fluorescence intensity of GFP. Taken together, our results demonstrated that pCLC2::Myristoyl-mGFP A206K can be used as a standard control for monomer GFP, facilitating the analysis of the step-wise photobleaching of membrane proteins in Arabidopsis thaliana. Copyright © 2017 Elsevier GmbH. All rights reserved.

An evaluation of the genetic-matched pair study design using genome-wide SNP data from the European population.

PubMed

Lu, Timothy Tehua; Lao, Oscar; Nothnagel, Michael; Junge, Olaf; Freitag-Wolf, Sandra; Caliebe, Amke; Balascakova, Miroslava; Bertranpetit, Jaume; Bindoff, Laurence Albert; Comas, David; Holmlund, Gunilla; Kouvatsi, Anastasia; Macek, Milan; Mollet, Isabelle; Nielsen, Finn; Parson, Walther; Palo, Jukka; Ploski, Rafal; Sajantila, Antti; Tagliabracci, Adriano; Gether, Ulrik; Werge, Thomas; Rivadeneira, Fernando; Hofman, Albert; Uitterlinden, André Gerardus; Gieger, Christian; Wichmann, Heinz-Erich; Ruether, Andreas; Schreiber, Stefan; Becker, Christian; Nürnberg, Peter; Nelson, Matthew Roberts; Kayser, Manfred; Krawczak, Michael

2009-07-01

Genetic matching potentially provides a means to alleviate the effects of incomplete Mendelian randomization in population-based gene-disease association studies. We therefore evaluated the genetic-matched pair study design on the basis of genome-wide SNP data (309,790 markers; Affymetrix GeneChip Human Mapping 500K Array) from 2457 individuals, sampled at 23 different recruitment sites across Europe. Using pair-wise identity-by-state (IBS) as a matching criterion, we tried to derive a subset of markers that would allow identification of the best overall matching (BOM) partner for a given individual, based on the IBS status for the subset alone. However, our results suggest that, by following this approach, the prediction accuracy is only notably improved by the first 20 markers selected, and increases proportionally to the marker number thereafter. Furthermore, in a considerable proportion of cases (76.0%), the BOM of a given individual, based on the complete marker set, came from a different recruitment site than the individual itself. A second marker set, specifically selected for ancestry sensitivity using singular value decomposition, performed even more poorly and was no more capable of predicting the BOM than randomly chosen subsets. This leads us to conclude that, at least in Europe, the utility of the genetic-matched pair study design depends critically on the availability of comprehensive genotype information for both cases and controls.

A comparison of cylindrical and row trenched cooling holes with alignment angle of 0 degree near the combustor endwall

NASA Astrophysics Data System (ADS)

Kianpour, E.; Nor Azwadi, C. S.; Golshokouh, I.

2013-12-01

We studied the effects of cylindrical and row trenched cooling holes with alignment angle of 0° at BR=3.18 on the film cooling performance near the endwall surface of a combustor simulator. In this research, a three-dimensional presentation of gas turbine engine was simulated and analyzed with a commercial finite volume package FLUENT 6.2.26 to gain fundamental data. The current study has been performed with Reynolds-averaged Navier-Stokes turbulence model (RANS) on internal cooling passages. This combustor simulator combined the interaction of two rows of dilution jets, which were staggered in the stream wise direction and aligned in the span wise direction. The entire findings of the study declared that with using the row trenched holes near the enwall surface; film cooling effectiveness is doubled compared to the cooling performance of baseline case.

Optimal lay-up design of variable stiffness laminated composite plates by a layer-wise optimization technique

NASA Astrophysics Data System (ADS)

Houmat, A.

2018-02-01

The optimal lay-up design for the maximum fundamental frequency of variable stiffness laminated composite plates is investigated using a layer-wise optimization technique. The design variables are two fibre orientation angles per ply. Thin plate theory is used in conjunction with a p-element to calculate the fundamental frequencies of symmetrically and antisymmetrically laminated composite plates. Comparisons with existing optimal solutions for constant stiffness symmetrically laminated composite plates show excellent agreement. It is observed that the maximum fundamental frequency can be increased considerably using variable stiffness design as compared to constant stiffness design. In addition, optimal lay-ups for the maximum fundamental frequency of variable stiffness symmetrically and antisymmetrically laminated composite plates with different aspect ratios and various combinations of free, simply supported and clamped edge conditions are presented. These should prove a useful benchmark for optimal lay-ups of variable stiffness laminated composite plates.

GWFASTA: server for FASTA search in eukaryotic and microbial genomes.

PubMed

Issac, Biju; Raghava, G P S

2002-09-01

Similarity searches are a powerful method for solving important biological problems such as database scanning, evolutionary studies, gene prediction, and protein structure prediction. FASTA is a widely used sequence comparison tool for rapid database scanning. Here we describe the GWFASTA server that was developed to assist the FASTA user in similarity searches against partially and/or completely sequenced genomes. GWFASTA consists of more than 60 microbial genomes, eight eukaryote genomes, and proteomes of annotatedgenomes. Infact, it provides the maximum number of databases for similarity searching from a single platform. GWFASTA allows the submission of more than one sequence as a single query for a FASTA search. It also provides integrated post-processing of FASTA output, including compositional analysis of proteins, multiple sequences alignment, and phylogenetic analysis. Furthermore, it summarizes the search results organism-wise for prokaryotes and chromosome-wise for eukaryotes. Thus, the integration of different tools for sequence analyses makes GWFASTA a powerful toolfor biologists.

Does technique matter; a pilot study exploring weighting techniques for a multi-criteria decision support framework.

PubMed

van Til, Janine; Groothuis-Oudshoorn, Catharina; Lieferink, Marijke; Dolan, James; Goetghebeur, Mireille

2014-01-01

There is an increased interest in the use of multi-criteria decision analysis (MCDA) to support regulatory and reimbursement decision making. The EVIDEM framework was developed to provide pragmatic multi-criteria decision support in health care, to estimate the value of healthcare interventions, and to aid in priority-setting. The objectives of this study were to test 1) the influence of different weighting techniques on the overall outcome of an MCDA exercise, 2) the discriminative power in weighting different criteria of such techniques, and 3) whether different techniques result in similar weights in weighting the criteria set proposed by the EVIDEM framework. A sample of 60 Dutch and Canadian students participated in the study. Each student used an online survey to provide weights for 14 criteria with two different techniques: a five-point rating scale and one of the following techniques selected randomly: ranking, point allocation, pairwise comparison and best worst scaling. The results of this study indicate that there is no effect of differences in weights on value estimates at the group level. On an individual level, considerable differences in criteria weights and rank order occur as a result of the weight elicitation method used, and the ability of different techniques to discriminate in criteria importance. Of the five techniques tested, the pair-wise comparison of criteria has the highest ability to discriminate in weights when fourteen criteria are compared. When weights are intended to support group decisions, the choice of elicitation technique has negligible impact on criteria weights and the overall value of an innovation. However, when weights are used to support individual decisions, the choice of elicitation technique influences outcome and studies that use dissimilar techniques cannot be easily compared. Weight elicitation through pairwise comparison of criteria is preferred when taking into account its superior ability to discriminate between criteria and respondents' preferences.

Effect of five commercial mouth rinses on the microhardness of a nanofilled resin composite restorative material: An in vitro study

PubMed Central

Jyothi, KN; Crasta, Shanol; Venugopal, P

2012-01-01

Aim and Objectives: This in vitro study was designed to comparatively evaluate the effect of five commercial mouth rinses on the micro hardness of a nanofilled resin based restorative material. Materials and Methods: Fifty specimens of resin composite material (Filtek Z350XT, 3M ESPE, St.Paul, MN USA) were prepared and immersed in artificial saliva for 24 h. The base line micro hardness of specimens was recorded using Vicker's micro hardness tester (MMT – X7 Matsuzawa, Japan). The specimens were randomly distributed into five groups, each containing 10 specimens (n=10) as follows – Group I Listerine (alcohol based), Group II Periogard (alcohol based), Group III Colgate plax (alcohol based), Group IV C- prev (alcohol free), Group V Hiora(alcohol free). The specimens were immersed in 20 ml of mouth rinses and incubated for 24 h at 37°C. The post immersion micro hardness values of the specimens were recorded and the data was tabulated for statistical analysis. Kruskal–Wallis test was used for inter group comparison followed by pair wise comparison of groups using Mann–Whitney U test. The level of significance was set at P=0.05. Results: Significant reduction in the mean VHN (Vicker's micro hardness number) was observed in all the groups after exposure to the tested mouth rinses (P<0.01) and the reduction in mean VHN values were as follows: Group I 12.09, Group II 3.42, Group II 1.51, Group IV 1.03, Group V 0.57. Inter group comparison showed statistically significant reduction in micro hardness in Groups I and II compared to all other groups with P<0.001. There was no significant difference between Groups III, IV and V. Conclusion: All the mouth rinses showed a reduction in the microhardness of nanofilled resin composite material with listerine (Group I) containing maximum amount of alcohol, showing highest reduction in micro hardness value. PMID:22876004

Using structural equation modeling for network meta-analysis.

PubMed

Tu, Yu-Kang; Wu, Yun-Chun

2017-07-14

Network meta-analysis overcomes the limitations of traditional pair-wise meta-analysis by incorporating all available evidence into a general statistical framework for simultaneous comparisons of several treatments. Currently, network meta-analyses are undertaken either within the Bayesian hierarchical linear models or frequentist generalized linear mixed models. Structural equation modeling (SEM) is a statistical method originally developed for modeling causal relations among observed and latent variables. As random effect is explicitly modeled as a latent variable in SEM, it is very flexible for analysts to specify complex random effect structure and to make linear and nonlinear constraints on parameters. The aim of this article is to show how to undertake a network meta-analysis within the statistical framework of SEM. We used an example dataset to demonstrate the standard fixed and random effect network meta-analysis models can be easily implemented in SEM. It contains results of 26 studies that directly compared three treatment groups A, B and C for prevention of first bleeding in patients with liver cirrhosis. We also showed that a new approach to network meta-analysis based on the technique of unrestricted weighted least squares (UWLS) method can also be undertaken using SEM. For both the fixed and random effect network meta-analysis, SEM yielded similar coefficients and confidence intervals to those reported in the previous literature. The point estimates of two UWLS models were identical to those in the fixed effect model but the confidence intervals were greater. This is consistent with results from the traditional pairwise meta-analyses. Comparing to UWLS model with common variance adjusted factor, UWLS model with unique variance adjusted factor has greater confidence intervals when the heterogeneity was larger in the pairwise comparison. The UWLS model with unique variance adjusted factor reflects the difference in heterogeneity within each comparison. SEM provides a very flexible framework for univariate and multivariate meta-analysis, and its potential as a powerful tool for advanced meta-analysis is still to be explored.

The AGN activity in a sample of IR Luminous Major Mergers

NASA Astrophysics Data System (ADS)

Loiseau, N.; de Rosa, A.; Bianchi, S.; Bogdanovich, T.

2017-10-01

As part of our study of the nuclear activity in a sample of 70 IR luminous major mergers we obtained XMM-Newton data of 4 more pairs of these galaxies. This is part of our multiwavelength study of the nuclear activity in mergers and groups of galaxies (MAGNA collaboration). Our purpose is to understand in which cases one or both of the galaxies of the major merger would have a massive black hole, and if the interaction stage, or the mass/type of the galaxies have role in the enhanced AGN and/or Starburst activity. X-rays can be the best tool to detect hidden AGN. At present very few mergers of AGN simultaneously active have been detected, most of them serendipitously. We present here the X-ray data of these 4 pairs, which have been selected using their WISE colors as a diagnostic tool. We compare the results for these 8 galaxies with the data of the 33 merging galaxies of this sample previously detected with XMM-Newton or Chandra.

PLASS: Protein-ligand affinity statistical score a knowledge-based force-field model of interaction derived from the PDB

NASA Astrophysics Data System (ADS)

Ozrin, V. D.; Subbotin, M. V.; Nikitin, S. M.

2004-04-01

We have developed PLASS (Protein-Ligand Affinity Statistical Score), a pair-wise potential of mean-force for rapid estimation of the binding affinity of a ligand molecule to a protein active site. This scoring function is derived from the frequency of occurrence of atom-type pairs in crystallographic complexes taken from the Protein Data Bank (PDB). Statistical distributions are converted into distance-dependent contributions to the Gibbs free interaction energy for 10 atomic types using the Boltzmann hypothesis, with only one adjustable parameter. For a representative set of 72 protein-ligand structures, PLASS scores correlate well with the experimentally measured dissociation constants: a correlation coefficient R of 0.82 and RMS error of 2.0 kcal/mol. Such high accuracy results from our novel treatment of the volume correction term, which takes into account the inhomogeneous properties of the protein-ligand complexes. PLASS is able to rank reliably the affinity of complexes which have as much diversity as in the PDB.

Extrastriatal dopamine D2-receptor availability in social anxiety disorder.

PubMed

Plavén-Sigray, Pontus; Hedman, Erik; Victorsson, Pauliina; Matheson, Granville J; Forsberg, Anton; Djurfeldt, Diana R; Rück, Christian; Halldin, Christer; Lindefors, Nils; Cervenka, Simon

2017-05-01

Alterations in the dopamine system are hypothesized to influence the expression of social anxiety disorder (SAD) symptoms. However, molecular imaging studies comparing dopamine function between patients and control subjects have yielded conflicting results. Importantly, while all previous investigations focused on the striatum, findings from activation and blood flow studies indicate that prefrontal and limbic brain regions have a central role in the pathophysiology. The objective of this study was to investigate extrastriatal dopamine D2-receptor (D2-R) availability in SAD. We examined 12 SAD patients and 16 healthy controls using positron emission tomography and the high-affinity D2-R radioligand [ 11 C]FLB457. Parametric images of D2-R binding potential were derived using the Logan graphical method with cerebellum as reference region. Two-tailed one-way independent ANCOVAs, with age as covariate, were used to examine differences in D2-R availability between groups using both region-based and voxel-wise analyses. The region-based analysis showed a medium effect size of higher D2-R levels in the orbitofrontal cortex (OFC) in patients, although this result did not remain significant after correction for multiple comparisons. The voxel-wise comparison revealed elevated D2-R availability in patients within OFC and right dorsolateral prefrontal cortex after correction for multiple comparisons. These preliminary results suggest that an aberrant extrastriatal dopamine system may be part of the disease mechanism in SAD. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Evaluation of a computerized cognitive behavioural therapy programme, MindWise (2.0), for adults with mild-to-moderate depression and anxiety.

PubMed

Collins, Sarah; Byrne, Michael; Hawe, James; O'Reilly, Gary

2018-06-01

To investigate the acceptability and utility of a newly developed computerized cognitive behavioural therapy (cCBT) programme, MindWise (2.0), for adults attending Irish primary care psychology services. Adult primary care psychology service users across four rural locations in Ireland were invited to participate in this study. A total of 60 service users participated in the MindWise (2.0) treatment group and compared to 22 people in a comparison waiting list control group. Participants completed pre- and post-intervention outcome measures of anxiety, depression, and work/social functioning. At post-intervention, 25 of 60 people in the MindWise (2.0) condition had fully completed the programme and 19 of 22 people in the waiting list condition provided time 2 data. Relative to those in the control group, the MindWise (2.0) participants reported significantly reduced symptoms of anxiety and no change in depression or work/social functioning. The newly developed cCBT programme, MindWise (2.0), resulted in significant improvements on a measure of anxiety and may address some barriers to accessing more traditional face-to-face mental health services for adults in a primary care setting. Further programme development and related research appears both warranted and needed to lower programme drop-out, establish if gains in anxiety management are maintained over time, and support people in a primary care context with depression. There is a growing evidence base that computerized self-help programmes can assist in a stepped-care approach to adult mental health service provision. These programmes require further development to address issues such as high dropout, the development of equally effective transdiagnostic content, and greater effectiveness in the country of origin. This study evaluated the acceptability and utility of a brief online CBT programme for adults referred due to anxiety or low mood to primary care psychology services in the national health service in Ireland. Results indicate that 42% of people completed the programme and experienced a significant reduction in anxiety but not depression and no improvement in work or social adjustment compared to similar adults on a waiting list for services. This study suggests the programme warrants further development and research and may in time become a useful and suitable intervention within the national health service in Ireland. © 2017 The British Psychological Society.

Characterization of wise protein and its molecular mechanism to interact with both Wnt and BMP signals.

PubMed

Lintern, Katherine B; Guidato, Sonia; Rowe, Alison; Saldanha, José W; Itasaki, Nobue

2009-08-21

Cross-talk of BMP and Wnt signaling pathways has been implicated in many aspects of biological events during embryogenesis and in adulthood. A secreted protein Wise and its orthologs (Sostdc1, USAG-1, and Ectodin) have been shown to modulate Wnt signaling and also inhibit BMP signals. Modulation of Wnt signaling activity by Wise is brought about by an interaction with the Wnt co-receptor LRP6, whereas BMP inhibition is by binding to BMP ligands. Here we have investigated the mode of action of Wise on Wnt and BMP signals. It was found that Wise binds LRP6 through one of three loops formed by the cystine knot. The Wise deletion construct lacking the LRP6-interacting loop domain nevertheless binds BMP4 and inhibits BMP signals. Moreover, BMP4 does not interfere with Wise-LRP6 binding, suggesting separate domains for the physical interaction. Functional assays also show that the ability of Wise to block Wnt1 activity through LRP6 is not impeded by BMP4. In contrast, the ability of Wise to inhibit BMP4 is prevented by additional LRP6, implying a preference of Wise in binding LRP6 over BMP4. In addition to the interaction of Wise with BMP4 and LRP6, the molecular characteristics of Wise, such as glycosylation and association with heparan sulfate proteoglycans on the cell surface, are suggested. This study helps to understand the multiple functions of Wise at the molecular level and suggests a possible role for Wise in balancing Wnt and BMP signals.

Heat-Related Mortality in India: Excess All-Cause Mortality Associated with the 2010 Ahmedabad Heat Wave

PubMed Central

Azhar, Gulrez Shah; Mavalankar, Dileep; Nori-Sarma, Amruta; Rajiva, Ajit; Dutta, Priya; Jaiswal, Anjali; Sheffield, Perry; Knowlton, Kim; Hess, Jeremy J.; Azhar, Gulrez Shah; Deol, Bhaskar; Bhaskar, Priya Shekhar; Hess, Jeremy; Jaiswal, Anjali; Khosla, Radhika; Knowlton, Kim; Mavalankar, Mavalankar; Rajiva, Ajit; Sarma, Amruta; Sheffield, Perry

2014-01-01

Introduction In the recent past, spells of extreme heat associated with appreciable mortality have been documented in developed countries, including North America and Europe. However, far fewer research reports are available from developing countries or specific cities in South Asia. In May 2010, Ahmedabad, India, faced a heat wave where the temperatures reached a high of 46.8°C with an apparent increase in mortality. The purpose of this study is to characterize the heat wave impact and assess the associated excess mortality. Methods We conducted an analysis of all-cause mortality associated with a May 2010 heat wave in Ahmedabad, Gujarat, India, to determine whether extreme heat leads to excess mortality. Counts of all-cause deaths from May 1–31, 2010 were compared with the mean of counts from temporally matched periods in May 2009 and 2011 to calculate excess mortality. Other analyses included a 7-day moving average, mortality rate ratio analysis, and relationship between daily maximum temperature and daily all-cause death counts over the entire year of 2010, using month-wise correlations. Results The May 2010 heat wave was associated with significant excess all-cause mortality. 4,462 all-cause deaths occurred, comprising an excess of 1,344 all-cause deaths, an estimated 43.1% increase when compared to the reference period (3,118 deaths). In monthly pair-wise comparisons for 2010, we found high correlations between mortality and daily maximum temperature during the locally hottest “summer” months of April (r = 0.69, p<0.001), May (r = 0.77, p<0.001), and June (r = 0.39, p<0.05). During a period of more intense heat (May 19–25, 2010), mortality rate ratios were 1.76 [95% CI 1.67–1.83, p<0.001] and 2.12 [95% CI 2.03–2.21] applying reference periods (May 12–18, 2010) from various years. Conclusion The May 2010 heat wave in Ahmedabad, Gujarat, India had a substantial effect on all-cause excess mortality, even in this city where hot temperatures prevail through much of April-June. PMID:24633076

[Has the pregnancy outcome of women with pregestational diabetes mellitus improved in ten years?].

PubMed

Čechurová, Daniela; Krčma, Michal; Jankovec, Zdeněk; Dort, Jiří; Turek, Jan; Lacigová, Silvie; Rušavý, Zdeněk

2015-02-01

In spite of progress in medicine, studies from a number of countries indicate steadily increased risk of perinatal morbidity and mortality in the offspring of diabetic mothers. No data regarding the pregnancy outcome in women with diabetes mellitus type 1 and 2 (pregestational DM) have been published in the Czech Republic. The aim of the study was to evaluate the pregnancy course of women with pregestational DM and outcome of their offspring and to assess whether it has improved in ten years. A retrospective evaluation of pregnancy outcome of pregestational DM women followed up in the University Hospital Pilsen in years 2000-2009 (Group A, n = 107) and comparison with the period 1990-1997 (Group B, n = 39) were performed. Wilcoxon non-paired test, contingency tables, step-wise logistic regression and step-wise linear multiple regression methods were used for statistical analyses. Data is presented as median (interquartile range). Women from the Group A were older 28 (25, 31) vs 25 (22, 27) years, p = 0.01. Otherwise, the groups did not statistically significantly differ in diabetes duration, BMI, and representation of women with type 2 diabetes. A better glycemic control (HbA1c, mmol/mol) was achieved in the Group A in all trimesters - 1st trimester: 59 (47, 67) vs 66 (56, 76), 2nd trimester: 46 (40, 52) vs 54 (48, 59) and 3rd trimester: 46 (40, 51) vs 53 (47, 60), p = 0.01. The caesarean section rate decreased (65.2 % vs 87.5 %, p < 0.05). The incidence of the respiratory distress syndrome after adjustment for age and diabetes duration also decreased (8.9 % vs 18.2 %, p < 0.05). A decreasing trend in the rate of premature delivery before 34th week of gestation (1.1 % vs 6.3 %) and neonatal mortality (1.1 % vs 2.9 %) was observed, however, the differences were not statistically significant. The achieved improved glycemic control led to only a partial improvement in the course of pregnancy and outcome of the offspring of diabetic mothers.

Using WISE to Find Obscured AGN Activity in SDSS Mergers and Interactions

NASA Astrophysics Data System (ADS)

Weston, Madalyn; McIntosh, Daniel H.; Her, Xiachang; Rigby, Jane R.

2015-01-01

In simulations, major encounters between gas-rich galaxies are predicted to drive gas to the centers of interacting and merging systems triggering new star formation (SF) and fueling an active galactic nucleus (AGN). Depending on the rate of SF, large amounts of obscuring dust can make detection of merger-induced activity difficult and may be at the heart of the ongoing merger-AGN connection debate. To provide better constraints on the importance of obscured AGNs, we use data from the Wide-field Infrared Survey Explorer (WISE) for a comprehensive sample of over 1000 major galaxy interactions and ongoing mergers visually selected from the SDSS with Mstar>1e10 Msun and 0.01 < z < 0.08. We examine the [3.4]-[4.6] versus [4.6]-[12] micron color-color plane and find that most interactions and mergers have the same colors as normal (non-interacting and non-merging) galaxies, which define a narrow [3.4]-[4.6] micron locus and span a wide range in [4.6]-[12] micron colors from spectroscopically quiescent (blue, no dust) to galaxies with SF emission (dust-reddened). We find that 2-6% of mergers (and 2-3% of interactions) have unusually red [3.4]-[4.6] micron colors, which are associated with dust-obscured (Type-2) AGNs. We note that mergers (interactions) are 4-15 (3-8) times more likely to host a buried AGN than normal galaxies. We also find that optical emission-line AGNs (Seyferts) identified as mergers are 3-7 times more likely to be obscured than non-merging Seyferts. We investigate whether the obscured AGN subset of our sample have unique properties and find that their stellar masses, mass ratios, pair separations, and environments are not statistically different from those of the bulk of mergers and interactions with normal WISE colors. We note that among mergers and interactions with an AGN, the WISE-selected AGN favor higher [OIII] luminosities associated with higher AGN power than their unobscured counterparts. Our findings support an AGN-merger connection.

Mapping the neuropsychological profile of temporal lobe epilepsy using cognitive network topology and graph theory.

PubMed

Kellermann, Tanja S; Bonilha, Leonardo; Eskandari, Ramin; Garcia-Ramos, Camille; Lin, Jack J; Hermann, Bruce P

2016-10-01

Normal cognitive function is defined by harmonious interaction among multiple neuropsychological domains. Epilepsy has a disruptive effect on cognition, but how diverse cognitive abilities differentially interact with one another compared with healthy controls (HC) is unclear. This study used graph theory to analyze the community structure of cognitive networks in adults with temporal lobe epilepsy (TLE) compared with that in HC. Neuropsychological assessment was performed in 100 patients with TLE and 82 HC. For each group, an adjacency matrix was constructed representing pair-wise correlation coefficients between raw scores obtained in each possible test combination. For each cognitive network, each node corresponded to a cognitive test; each link corresponded to the correlation coefficient between tests. Global network structure, community structure, and node-wise graph theory properties were qualitatively assessed. The community structure in patients with TLE was composed of fewer, larger, more mixed modules, characterizing three main modules representing close relationships between the following: 1) aspects of executive function (EF), verbal and visual memory, 2) speed and fluency, and 3) speed, EF, perception, language, intelligence, and nonverbal memory. Conversely, controls exhibited a relative division between cognitive functions, segregating into more numerous, smaller modules consisting of the following: 1) verbal memory, 2) language, perception, and intelligence, 3) speed and fluency, and 4) visual memory and EF. Overall node-wise clustering coefficient and efficiency were increased in TLE. Adults with TLE demonstrate a less clear and poorly structured segregation between multiple cognitive domains. This panorama suggests a higher degree of interdependency across multiple cognitive domains in TLE, possibly indicating compensatory mechanisms to overcome functional impairments. Copyright © 2016 Elsevier Inc. All rights reserved.

Comparison of radio-telemetric home range analysis and acoustic detection for Little Brown Bat habitat evaluation

USGS Publications Warehouse

Coleman, Laci S.; Ford, W. Mark; Dobony, Christopher A.; Britzke, Eric R.

2014-01-01

With dramatic declines of bat populations due to mortality caused by Pseudogymnoascus destructans (White-nose Syndrome), assessing habitat preferences of bats in the northeastern US is now critical to guide the development of regional conservation efforts. In the summer of 2012, we conducted fixed-station simultaneous telemetry to determine nocturnal spatial use and fixed-kernel home-range estimates of available habitat of a Myotis lucifugus (Le Conte) (Little Brown Bat) maternity colony in an artificial bat house. In summers of 2011 and 2012, we also deployed a 52-ha grid of 4 × 4 Anabat acoustic detectors over five 6–8-day sampling periods in various riparian and non-riparian environments in close proximity to the same bat house. The mean telemetry home range of 143 ha for bats (n = 7) completely overlapped the acoustic grid. Rankings of habitats from telemetry data for these 7 bats and 5 additional bats not included in home-range calculations but added for habitat-use measures (n = 13) revealed a higher proportional use of forested riparian habitats than other types at the landscape scale. Pair-wise comparisons of habitats indicated that bats were found significantly closer to forested riparian habitats and forests than to open water, developed areas, fields, shrublands, or wetland habitats at the landscape scale. Acoustic sampling showed that naïve occupancy was 0.8 and 0.6 and mean nightly detection probabilities were 0.23 and 0.08 at riparian and non-riparian sites, respectively. Our findings suggest that Little Brown Bats select forested riparian and forested habitats for foraging at the landscape scale but may be most easily detected acoustically at riparian sites when a simple occupancy determination for an area is required.

Comparison of the recovery of Mycobacterium bovis isolates using the BACTEC MGIT 960 system, BACTEC 460 system, and Middlebrook 7H10 and 7H11 solid media.

PubMed

Hines, Nichole; Payeur, Janet B; Hoffman, Lorraine J

2006-05-01

The BACTEC Microbacteria Growth Indicator Tube (MGIT) 960 system was evaluated to determine how it compares with the BACTEC 460 radiometric system and solid media for recovery of Mycobacterium bovis from tissue samples. A total of 506 bovine lymph node samples were collected from abattoirs in the United States and Mexico between November 2003 and September 2004. Processed samples were inoculated into an MGIT 960 tube, BACTEC 460 vial, and Middlebrook 7H10 and Middlebrook 7H11 solid media. Ziehl-Neelsen slides were prepared to check for contaminants and confirm the presence of acid-fast positive bacilli. Samples containing acid-fast bacilli were confirmed as members of the Mycobacterium tuberculosis complex by a nucleic acid assay. Niacin and nitrate biochemical tests were used to distinguish M. bovis from M. tuberculosis isolates. Statistical analyses were performed to compare recovery rate, mean time to detection, contamination rates, as well as pair-wise comparisons in each category. The results showed that the MGIT 960 system had a higher recovery rate of M. bovis (122/129) than did the BACTEC 460 (102/129) and solid media system (96/129). The average time to detection was 15.8 days for the MGIT 960 system, 28.2 days for the BACTEC 460 system, and 43.4 days for solid media. Contamination rates were 6.9% for the MGIT 960 system, 3.4% for the BACTEC 460 system, and 21.7% for solid media. These results indicate the MGIT 960 system can be used as an alternative to the BACTEC 460 system for recovering M. bovis from tissue samples.

Feasibility, Acceptability and Findings from a Pilot Randomized Controlled Intervention Study on the Impact of a Book Designed to Inform Patients about Cancer Clinical Trials

PubMed Central

Carney, Patricia A.; Tucker, Erin K.; Newby, Timothy A.; Beer, Tomasz M.

2014-01-01

Objective To assess the feasibility, acceptability and changes in knowledge among cancer patients assigned to receive a 160 page book on experimental cancer therapies and clinical trials. Methods We enrolled 20 patients with cancer who had never participated in a clinical trial, and randomly assigned them to receive the book either during Week 1or Week 4 of the study. We collected baseline patient demographic and cancer related information as well as knowledge about cancer clinical trials at Week 0. Follow-up surveys were administered at Weeks 3 and 6 for both study groups. Comparisons were made within and between groups randomized to receive the book Early (at Week 1) to those who received it Later (at Week 4). Results One hundred percent of data were captured in both groups at baseline, which decreased to 77.8% by Week 6. The vast majority of participants found the book moderately or very useful (89% in the Early Group at Week 3 and 95.5% in the Late Group at Week 6). Within group pair-wise comparisons found significant difference between baseline and Week 6 in content-specific knowledge scores among participants in the Late Group (79% vs. 92.1%, p=0.01). Global knowledge scores increased significantly for variables reflecting knowledge that promotes decisions to participate in clinical trials. Conclusions Providing published reading material to patients with cancer is both feasible and acceptable. Offering information to patients about cancer clinical trials, using a book designed for patients with cancer may influence knowledge related to decision to participate in clinical trials. PMID:24127249

Nurses' and midwives' clinical leadership development needs: a mixed methods study.

PubMed

Casey, Mary; McNamara, Martin; Fealy, Gerard; Geraghty, Ruth

2011-07-01

This paper is a report of a descriptive study of nurses' and midwives' clinical leadership development needs. Nurses and midwives are expected to fulfil a leadership role at all levels, yet efforts to strategically support them are often unfocused. An analysis of clinical leadership development needs can provide the foundation for leadership initiatives to support staff. A mixed methods design was used. A questionnaire was sent to 911 nurses and midwives and 22 focus groups comprising 184 participants were conducted. Data were collected between March and June 2009 across all promotional grades of nurses and midwives in Ireland. Repeated measures anova with Greenhouse-Geisser adjustment was used for post hoc pair wise comparisons of the subscale dimensions of clinical leadership. anova with Tukey's post hoc method was used for comparison between grades on each individual subscale. Thematic analysis was undertaken on the focus group data. Results reveal that needs related to development of the profession were the highest for all grades. The staff grade expressed a higher need in relation to 'managing clinical area', 'managing the patient care' and 'skills for clinical leadership' than managers. Qualitative analysis yielded five themes; (1) clinical leadership and leaders from a nursing and midwifery perspective; (2) quality service from a nursing and midwifery perspective; (3) clinical leaders' roles and functions; (4) capital and (5) competences for clinical leaders and leadership and the context of clinical leadership. Clinical leadership concerns quality, safety and effectiveness. Nurses and midwives are ideally placed to offer the clinical leadership that is required to ensure these patient care outcomes. Development initiatives must address the leader and leadership competencies to support staff. © 2011 Blackwell Publishing Ltd.

Steroid hormone levels associated with passive and active smoking

PubMed Central

Soldin, Offie P.; Makambi, Kepher H.; Soldin, Steven J.; O’Mara, Daniel M.

2013-01-01

Context Cigarette tobacco smoke is a potent environmental contaminant known to adversely affect health including fertility and pregnancy. Objective To examine the associations between second-hand cigarette tobacco-smoke exposure, or active smoking and serum concentrations of steroid hormones using tandem mass spectrometry. Design Healthy women (18–45 y) from the general community in the Metropolitan Washington, DC were recruited at the follicular stage of their menstrual cycle. Participants were assigned to one of three study groups: active smokers (N= 107), passive smokers (N= 86), or non-smokers (N= 100). Classifications were based on a combination of self-reporting and serum cotinine concentrations. Methods Serum androgens, estrogens, progestins, androstenedione, aldosterone, cortisol, corticosterone, dehydroepiandrosterone (DHEA), dehydroepiandrosterone sulfate (DHEAS), 11-deoxycortisol and 25-hydroxy-vitamin D3 (25-OHVitD3) and cotinine were measured by isotope dilution tandem mass spectrometry (LC/MS/MS) (API-5000). Kruskal–Wallis tests were used to assess median differences among the three groups, with Dunn’s multiple comparison test for post hoc analysis. Results Serum estrone, estradiol, and estriol concentrations were lower in active and passive smokers than in non-smokers. The three study groups differed significantly in serum concentrations of 16-OHE1, aldosterone and 25-OHVitD3, as well as in the ratios of many of the steroids. Pair-wise comparison of the groups demonstrated significant differences in hormone concentrations between (i) smokers and nonsmokers for aldosterone: (ii) passive smokers and non-smokers for aldosterone, progesterone and estriol. Moreover, for smokers and passive smokers, there were no significant differences in these hormone concentrations. Conclusions Smoke exposure was associated with lower than normal median steroid hormone concentrations. These processes may be instrumental in explaining some adverse effects of tobacco smoke on female health and fertility. PMID:21396948

Methods for network meta-analysis of continuous outcomes using individual patient data: a case study in acupuncture for chronic pain.

PubMed

Saramago, Pedro; Woods, Beth; Weatherly, Helen; Manca, Andrea; Sculpher, Mark; Khan, Kamran; Vickers, Andrew J; MacPherson, Hugh

2016-10-06

Network meta-analysis methods, which are an extension of the standard pair-wise synthesis framework, allow for the simultaneous comparison of multiple interventions and consideration of the entire body of evidence in a single statistical model. There are well-established advantages to using individual patient data to perform network meta-analysis and methods for network meta-analysis of individual patient data have already been developed for dichotomous and time-to-event data. This paper describes appropriate methods for the network meta-analysis of individual patient data on continuous outcomes. This paper introduces and describes network meta-analysis of individual patient data models for continuous outcomes using the analysis of covariance framework. Comparisons are made between this approach and change score and final score only approaches, which are frequently used and have been proposed in the methodological literature. A motivating example on the effectiveness of acupuncture for chronic pain is used to demonstrate the methods. Individual patient data on 28 randomised controlled trials were synthesised. Consistency of endpoints across the evidence base was obtained through standardisation and mapping exercises. Individual patient data availability avoided the use of non-baseline-adjusted models, allowing instead for analysis of covariance models to be applied and thus improving the precision of treatment effect estimates while adjusting for baseline imbalance. The network meta-analysis of individual patient data using the analysis of covariance approach is advocated to be the most appropriate modelling approach for network meta-analysis of continuous outcomes, particularly in the presence of baseline imbalance. Further methods developments are required to address the challenge of analysing aggregate level data in the presence of baseline imbalance.

A comparison of low-carbohydrate vs. high-carbohydrate diets: energy restriction, nutrient quality and correlation to body mass index.

PubMed

Bowman, Shanthy A; Spence, Joseph T

2002-06-01

To evaluate free-living adults' diets that ranged from very low to high amounts of carbohydrate for their energy content, nutritional quality and correlation to Body Mass Index. Adults ages 19 years and older, who had complete dietary intake data on day-1 of the USDA's 1994 to 1996 Continuing Survey of Food Intakes by Individuals (CSFII 1994-1996), were divided into four groups--very low, low, moderate and high carbohydrate--based on the percent total energy from carbohydrate. Mean energy, nutrient, food intakes and Body Mass Index values were compared among the groups. SUDAAN software package was used for the data analysis and pair-wise mean comparisons (p < 0.05). The high-carbohydrate diet was lower in energy and energy density (number of kilocalories per gram of total amount of food consumed) than the other three diets. Macronutrient composition varied significantly among all the four groups. Nutrient density (amount of nutrient per 1,000 kilocalories of energy consumed) of vitamin A, carotene, vitamin C, folate, calcium, magnesium and iron increased and that of vitamin B12 and zinc decreased with an increase in the percent total energy from carbohydrate. The high-carbohydrate group ate more of low-fat foods, grain products and fruits. This group also had the lowest sodium intake. Adults eating a high-carbohydrate diet are more likely to have Body Mass Index values below 25. A study of diets of free-living adults in the U.S. showed that diets high in carbohydrate were both energy restrictive and nutritious and may be adopted for successful weight management.

Expert Elicitations of 2100 Emission of CO2

NASA Astrophysics Data System (ADS)

Ho, Emily; Bosetti, Valentina; Budescu, David; Keller, Klaus; van Vuuren, Detlef

2017-04-01

Emission scenarios such as Shared Socioeconomic Pathways (SSPs) and Representative Concentration Pathways (RCPs) are used intensively for climate research (e.g. climate change projections) and policy analysis. While the range of these scenarios provides an indication of uncertainty, these scenarios are typically not associated with probability values. Some studies (e.g. Vuuren et al, 2007; Gillingham et al., 2015) took a different approach associating baseline emission pathways (conditionally) with probability distributions. This paper summarizes three studies where climate change experts were asked to conduct pair-wise comparisons of possible ranges of 2100 greenhouse gas emissions and rate the relative likelihood of the ranges. The elicitation was performed under two sets of assumptions: 1) a situation where no climate policies are introduced beyond the ones already in place (baseline scenario), and 2) a situation in which countries have ratified the voluntary policies in line with the long term target embedded in the 2015 Paris Agreement. These indirect relative judgments were used to construct subjective cumulative distribution functions. We show that by using a ratio scaling method that invokes relative likelihoods of scenarios, a subjective probability distribution can be derived for each expert that expresses their beliefs in the projected greenhouse gas emissions range in 2100. This method is shown to elicit stable estimates that require minimal adjustment and is relatively invariant to the partition of the domain of interest. Experts also rated the method as being easy and intuitive to use. We also report results of a study that allowed participants to choose their own ranges of greenhouse gas emissions to remove potential anchoring bias. We discuss the implications of the use of this method for facilitating comparison and communication of beliefs among diverse users of climate science research.

DNA Barcodes of Asian Houbara Bustard (Chlamydotis undulata macqueenii)

PubMed Central

Arif, Ibrahim A.; Khan, Haseeb A.; Williams, Joseph B.; Shobrak, Mohammad; Arif, Waad I.

2012-01-01

Populations of Houbara Bustards have dramatically declined in recent years. Captive breeding and reintroduction programs have had limited success in reviving population numbers and thus new technological solutions involving molecular methods are essential for the long term survival of this species. In this study, we sequenced the 694 bp segment of COI gene of the four specimens of Asian Houbara Bustard (Chlamydotis undulata macqueenii). We also compared these sequences with earlier published barcodes of 11 individuals comprising different families of the orders Gruiformes, Ciconiiformes, Podicipediformes and Crocodylia (out group). The pair-wise sequence comparison showed a total of 254 variable sites across all the 15 sequences from different taxa. Three of the four specimens of Houbara Bustard had an identical sequence of COI gene and one individual showed a single nucleotide difference (G > A transition at position 83). Within the bustard family (Otididae), comparison among the three species (Asian Houbara Bustard, Great Bustard (Otis tarda) and the Little Bustard (Tetrax tetrax)), representing three different genera, showed 116 variable sites. For another family (Rallidae), the intra-family variable sites among the individuals of four different genera were found to be 146. The COI genetic distances among the 15 individuals varied from 0.000 to 0.431. Phylogenetic analysis using 619 bp nucleotide segment of COI clearly discriminated all the species representing different genera, families and orders. All the four specimens of Houbara Bustard formed a single clade and are clearly separated from other two individuals of the same family (Otis tarda and Tetrax tetrax). The nucleotide sequence of partial segment of COI gene effectively discriminated the closely related species. This is the first study reporting the barcodes of Houbara Bustard and would be helpful in future molecular studies, particularly for the conservation of this threatened bird in Saudi Arabia. PMID:22408462

The influence of cranio-cervical posture on maximal mouth opening and pressure pain threshold in patients with myofascial temporomandibular pain disorders.

PubMed

La Touche, Roy; París-Alemany, Alba; von Piekartz, Harry; Mannheimer, Jeffrey S; Fernández-Carnero, Josue; Rocabado, Mariano

2011-01-01

The aim of this study was to assess the influence of cranio-cervical posture on the maximal mouth opening (MMO) and pressure pain threshold (PPT) in patients with myofascial temporomandibular pain disorders. A total of 29 patients (19 females and 10 males) with myofascial temporomandibular pain disorders, aged 19 to 59 years participated in the study (mean years±SD; 34.69±10.83 y). MMO and the PPT (on the right side) of patients in neutral, retracted, and forward head postures were measured. A 1-way repeated measures analysis of variance followed by 3 pair-wise comparisons were used to determine differences. Comparisons indicated significant differences in PPT at 3 points within the trigeminal innervated musculature [masseter (M1 and M2) and anterior temporalis (T1)] among the 3 head postures [M1 (F=117.78; P<0.001), M2 (F=129.04; P<0.001), and T1 (F=195.44; P<0.001)]. There were also significant differences in MMO among the 3 head postures (F=208.06; P<0.001). The intrarater reliability on a given day-to-day basis was good with the interclass correlation coefficient ranging from 0.89 to 0.94 and 0.92 to 0.94 for PPT and MMO, respectively, among the different head postures. The results of this study shows that the experimental induction of different cranio-cervical postures influences the MMO and PPT values of the temporomandibular joint and muscles of mastication that receive motor and sensory innervation by the trigeminal nerve. Our results provide data that supports the biomechanical relationship between the cranio-cervical region and the dynamics of the temporomandibular joint, as well as trigeminal nociceptive processing in different cranio-cervical postures.

Efficacy of platelet rich fibrin in the treatment of human intrabony defects with or without bone graft: A randomized controlled trial

PubMed Central

Chandradas, Nikhil D.; Ravindra, Shivamurthy; Rangaraju, Vivekananda M.; Jain, Sheetal; Dasappa, Shivaprasad

2016-01-01

Aim: To evaluate the efficacy of platelet rich fibrin (PRF) with or without bone graft [demineralized bone matrix (DBM) graft] in the treatment of intrabony defects based on clinical and radiographic parameters. Materials and Methods: Thirty six intrabony defects in 36 patients were randomly divided into three different groups and were treated with group A (PRF with DBM) or group B (PRF alone) or group C [open flap debridement (OFD)]. Clinical parameters such as plaque index (PI), gingival index (GI), probing depth (PD), relative attachment level (RAL), and gingival recession (GR) were assessed at baseline and 9 months postoperatively; radiographic parameters such as linear bone growth (LBG) and percentage in bone fill (%BF) were calculated by using the image analysis software. Comparisons of groups were analyzed using Kruskal–Wallis analysis of variance test. Pair-wise comparison of groups was done by Mann-Whitney U test. Results: Mean PD reduction and RAL gain were greater in group A (4.25 ± 1.48, 3.92 ± 0.90) and group B (3.82 ± 0.75, 3.27 ± 0.65) than control (3.00 ± 1.21, 2.25 ± 0.62). Furthermore, statistically significant improvement in LBG and %BF was found in group A (3.47 ± 0.53, 61.53 ± 4.54) compared to group B (2.55 ± 0.61, 49.60 ± 14.08) and group C (1.21 ± 0.80, 24.69 ± 15.59). Conclusions: The study demonstrated that PRF improves clinical and radiological parameters compared to OFD alone in intrabony defects. Addition of DBM enhances the effects of PRF in RAL gain and radiographic defect fill. PMID:27652249

Wise, a context-dependent activator and inhibitor of Wnt signalling.

PubMed

Itasaki, Nobue; Jones, C Michael; Mercurio, Sara; Rowe, Alison; Domingos, Pedro M; Smith, James C; Krumlauf, Robb

2003-09-01

We have isolated a novel secreted molecule, Wise, by a functional screen for activities that alter the anteroposterior character of neuralised Xenopus animal caps. Wise encodes a secreted protein capable of inducing posterior neural markers at a distance. Phenotypes arising from ectopic expression or depletion of Wise resemble those obtained when Wnt signalling is altered. In animal cap assays, posterior neural markers can be induced by Wnt family members, and induction of these markers by Wise requires components of the canonical Wnt pathway. This indicates that in this context Wise activates the Wnt signalling cascade by mimicking some of the effects of Wnt ligands. Activation of the pathway was further confirmed by nuclear accumulation of beta-catenin driven by Wise. By contrast, in an assay for secondary axis induction, extracellularly Wise antagonises the axis-inducing ability of Wnt8. Thus, Wise can activate or inhibit Wnt signalling in a context-dependent manner. The Wise protein physically interacts with the Wnt co-receptor, lipoprotein receptor-related protein 6 (LRP6), and is able to compete with Wnt8 for binding to LRP6. These activities of Wise provide a new mechanism for integrating inputs through the Wnt coreceptor complex to modulate the balance of Wnt signalling.

Explanatory Supplement to the AllWISE Data Release Products

NASA Astrophysics Data System (ADS)

Cutri, R. M.; Wright, E. L.; Conrow, T.; Fowler, J. W.; Eisenhardt, P. R. M.; Grillmair, C.; Kirkpatrick, J. D.; Masci, F.; McCallon, H. L.; Wheelock, S. L.; Fajardo-Acosta, S.; Yan, L.; Benford, D.; Harbut, M.; Jarrett, T.; Lake, S.; Leisawitz, D.; Ressler, M. E.; Stanford, S. A.; Tsai, C. W.; Liu, F.; Helou, G.; Mainzer, A.; Gettings, D.; Gonzalez, A.; Hoffman, D.; Marsh, K. A.; Padgett, D.; Skrutskie, M. F.; Beck, R. P.; Papin, M.; Wittman, M.

2013-11-01

The AllWISE program builds upon the successful Wide-field Infrared Survey Explorer (WISE; Wright et al. 2010) mission by combining data from all WISE and NEOWISE (Mainzer et al. 2011) survey phases to form the most comprehensive view of the mid-infrared sky currently available. By combining the data from two complete sky coverage epochs in an advanced data processing system, AllWISE has generated new products that have enhanced photometric sensitivity and accuracy, and improved astrometric precision compared with the earlier WISE All-Sky Data Release. Exploiting the 6 month baseline between the WISE sky coverage epochs enables AllWISE to measure source motions for the first time, and to compute improved flux variability statistics. AllWISE data release products include: a Source Catalog that contains 4-band fluxes, positions, apparent motion measurements, and flux variability statistics for over 747 million objects detected at SNR>5 in the combined exposures; a Multiepoch Photometry Database containing over 42 billion time-tagged, single-exposure fluxes for each object detected on the combined exposures; and an Image Atlas of 18,240 4-band calibrated FITS images, depth-of-coverage and noise maps that cover the sky produced by coadding nearly 7.9 million single-exposure images from the cryogenic and post-cryogenic survey phases. The Explanatory Supplement to the AllWISE Data Release Products is a general guide for users of the AllWISE data. The Supplement contains detailed descriptions of the format and characteristics of the AllWISE data products, as well as a summary of cautionary notes that describe known limitations. The Supplement is an on-line document that is updated frequently to provide the most current information for users of the AllWISE data products. The Explanatory Supplement is maintained at: http://wise2.ipac.caltech.edu/docs/release/allwise/expsup/index.html AllWISE makes use of data from WISE, which is a joint project of the University of California, Los Angeles, and the Jet Propulsion Laboratory/California Institute of Technology, and NEOWISE, which is a project of the Jet Propulsion Laboratory/California Institute of Technology. WISE and NEOWISE are funded by the National Aeronautics and Space Administration.

A novel method for pair-matching using three-dimensional digital models of bone: mesh-to-mesh value comparison.

PubMed

Karell, Mara A; Langstaff, Helen K; Halazonetis, Demetrios J; Minghetti, Caterina; Frelat, Mélanie; Kranioti, Elena F

2016-09-01

The commingling of human remains often hinders forensic/physical anthropologists during the identification process, as there are limited methods to accurately sort these remains. This study investigates a new method for pair-matching, a common individualization technique, which uses digital three-dimensional models of bone: mesh-to-mesh value comparison (MVC). The MVC method digitally compares the entire three-dimensional geometry of two bones at once to produce a single value to indicate their similarity. Two different versions of this method, one manual and the other automated, were created and then tested for how well they accurately pair-matched humeri. Each version was assessed using sensitivity and specificity. The manual mesh-to-mesh value comparison method was 100 % sensitive and 100 % specific. The automated mesh-to-mesh value comparison method was 95 % sensitive and 60 % specific. Our results indicate that the mesh-to-mesh value comparison method overall is a powerful new tool for accurately pair-matching commingled skeletal elements, although the automated version still needs improvement.

Relationship of mode of conception and sex concordance with mortality/morbidity in preterm twins.

PubMed

Mirea, Lucia; Yang, Junmin; Paterson, Andrew D; Shah, Vibhuti; Bassil, Kate L; Lee, Shoo K; Shah, Prakesh S

2013-10-01

To assess the association of mode of conception and sex concordance with neonatal outcomes in very preterm twins. Twin pairs born at gestational age ≤ 32 weeks and admitted to a Level 3 neonatal intensive care unit (NICU) in 2010-2011 were retrospectively identified from the Canadian Neonatal Network™ database. A composite outcome representing neonatal mortality or any severe morbidity (intraventricular hemorrhage grades ≥ 3 or periventricular leukomalacia, retinopathy of prematurity stages ≥ 3, bronchopulmonary dysplasia, or necrotizing enterocolitis stages ≥ 2) was compared between twins conceived using assisted reproduction technologies (ARTs) or spontaneously (SP), and tested for association with sex concordance in individual-level and pair-wise multivariable logistic regression analyses. Study subjects included 1,508 twins from 216 ART (53 [25%] male-male, 104 [48%] male-female, and 59 [27%] female-female) and 538 SP (192 [36%] male-male, 123 [23%] male-female, and 223 [41%] female-female) pairs. No statistically significant association was detected between mode of conception and the composite outcome of mortality/morbidities. The composite outcome was significantly higher in same-sex than in opposite-sex twins (OR = 1.68; 95% CI = [1.09, 2.59]). This relationship was most pronounced in ART pairs (OR = 2.25; 95% CI = [1.02, 4.98]), with increased rates in one or both twins from male-male versus opposite-sex ART pairs (OR = 3.0; 95% CI = [1.07, 8.36]). Same-sex pairing was associated with higher mortality/morbidities in very preterm twins admitted to the NICU, and can be used in clinical practice to identify twins at higher risk of adverse neonatal outcomes.

The importance of group-wise registration in tract based spatial statistics study of neurodegeneration: a simulation study in Alzheimer's disease.

PubMed

Keihaninejad, Shiva; Ryan, Natalie S; Malone, Ian B; Modat, Marc; Cash, David; Ridgway, Gerard R; Zhang, Hui; Fox, Nick C; Ourselin, Sebastien

2012-01-01

Tract-based spatial statistics (TBSS) is a popular method for the analysis of diffusion tensor imaging data. TBSS focuses on differences in white matter voxels with high fractional anisotropy (FA), representing the major fibre tracts, through registering all subjects to a common reference and the creation of a FA skeleton. This work considers the effect of choice of reference in the TBSS pipeline, which can be a standard template, an individual subject from the study, a study-specific template or a group-wise average. While TBSS attempts to overcome registration error by searching the neighbourhood perpendicular to the FA skeleton for the voxel with maximum FA, this projection step may not compensate for large registration errors that might occur in the presence of pathology such as atrophy in neurodegenerative diseases. This makes registration performance and choice of reference an important issue. Substantial work in the field of computational anatomy has shown the use of group-wise averages to reduce biases while avoiding the arbitrary selection of a single individual. Here, we demonstrate the impact of the choice of reference on: (a) specificity (b) sensitivity in a simulation study and (c) a real-world comparison of Alzheimer's disease patients to controls. In (a) and (b), simulated deformations and decreases in FA were applied to control subjects to simulate changes of shape and WM integrity similar to what would be seen in AD patients, in order to provide a "ground truth" for evaluating the various methods of TBSS reference. Using a group-wise average atlas as the reference outperformed other references in the TBSS pipeline in all evaluations.

Voxel-wise grey matter asymmetry analysis in left- and right-handers.

PubMed

Ocklenburg, Sebastian; Friedrich, Patrick; Güntürkün, Onur; Genç, Erhan

2016-10-28

Handedness is thought to originate in the brain, but identifying its structural correlates in the cortex has yielded surprisingly incoherent results. One idea proclaimed by several authors is that structural grey matter asymmetries might underlie handedness. While some authors have found significant associations with handedness in different brain areas (e.g. in the central sulcus and precentral sulcus), others have failed to identify such associations. One method used by many researchers to determine structural grey matter asymmetries is voxel based morphometry (VBM). However, it has recently been suggested that the standard VBM protocol might not be ideal to assess structural grey matter asymmetries, as it establishes accurate voxel-wise correspondence across individuals but not across both hemispheres. This could potentially lead to biased and incoherent results. Recently, a new toolbox specifically geared at assessing structural asymmetries and involving accurate voxel-wise correspondence across hemispheres has been published [F. Kurth, C. Gaser, E. Luders. A 12-step user guide for analyzing voxel-wise gray matter asymmetries in statistical parametric mapping (SPM), Nat Protoc 10 (2015), 293-304]. Here, we used this new toolbox to re-assess grey matter asymmetry differences in left- vs. right-handers and linked them to quantitative measures of hand preference and hand skill. While we identified several significant left-right asymmetries in the overall sample, no difference between left- and right-handers reached significance after correction for multiple comparisons. These findings indicate that the structural brain correlates of handedness are unlikely to be rooted in macroscopic grey matter area differences that can be assessed with VBM. Future studies should focus on other potential structural correlates of handedness, e.g. structural white matter asymmetries. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

The Importance of Group-Wise Registration in Tract Based Spatial Statistics Study of Neurodegeneration: A Simulation Study in Alzheimer's Disease

PubMed Central

Keihaninejad, Shiva; Ryan, Natalie S.; Malone, Ian B.; Modat, Marc; Cash, David; Ridgway, Gerard R.; Zhang, Hui; Fox, Nick C.; Ourselin, Sebastien

2012-01-01

Tract-based spatial statistics (TBSS) is a popular method for the analysis of diffusion tensor imaging data. TBSS focuses on differences in white matter voxels with high fractional anisotropy (FA), representing the major fibre tracts, through registering all subjects to a common reference and the creation of a FA skeleton. This work considers the effect of choice of reference in the TBSS pipeline, which can be a standard template, an individual subject from the study, a study-specific template or a group-wise average. While TBSS attempts to overcome registration error by searching the neighbourhood perpendicular to the FA skeleton for the voxel with maximum FA, this projection step may not compensate for large registration errors that might occur in the presence of pathology such as atrophy in neurodegenerative diseases. This makes registration performance and choice of reference an important issue. Substantial work in the field of computational anatomy has shown the use of group-wise averages to reduce biases while avoiding the arbitrary selection of a single individual. Here, we demonstrate the impact of the choice of reference on: (a) specificity (b) sensitivity in a simulation study and (c) a real-world comparison of Alzheimer's disease patients to controls. In (a) and (b), simulated deformations and decreases in FA were applied to control subjects to simulate changes of shape and WM integrity similar to what would be seen in AD patients, in order to provide a “ground truth” for evaluating the various methods of TBSS reference. Using a group-wise average atlas as the reference outperformed other references in the TBSS pipeline in all evaluations. PMID:23139736

Dismounted Warrior Network Experiments

DTIC Science & Technology

2000-11-01

Foxtrot Locomotion Human Joystick ODT Joystick Foot Pedal + Head Orientation Visual Display Wireless HMD 4 Projection Desktop Single Screens (WISE... Biomechanics DI-Guy JackML DI-Guy Table 1. VICs Comparison Matrix VIC Alpha is the Dismounted Soldier Simulation (DSS) system developed by Veda, Inc. under a...using a pressure sensitive foot pedal . The user’s head is tracked with a magnetic sensor and is used to control steering through the environment. A

Comparisons of GLM and LMA Observations

NASA Astrophysics Data System (ADS)

Thomas, R. J.; Krehbiel, P. R.; Rison, W.; Stanley, M. A.; Attanasio, A.

2017-12-01

Observations from 3-dimensional VHF lightning mapping arrays (LMAs) provide a valuable basis for evaluating the spatial accuracy and detection efficiencies of observations from the recently launched, optical-based Geosynchronous Lightning Mapper (GLM). In this presentation, we describe results of comparing the LMA and GLM observations. First, the observations are compared spatially and temporally at the individual event (pixel) level for sets of individual discharges. For LMA networks in Florida, Colorado, and Oklahoma, the GLM observations are well correlated time-wise with LMA observations but are systematically offset by one- to two pixels ( 10 to 15 or 20 km) in a southwesterly direction from the actual lightning activity. The graphical comparisons show a similar location uncertainty depending on the altitude at which the scattered light is emitted from the parent cloud, due to being observed at slant ranges. Detection efficiencies (DEs) can be accurately determined graphically for intervals where individual flashes in a storm are resolved time-wise, and DEs and false alarm rates can be automated using flash sorting algorithms for overall and/or larger storms. This can be done as a function of flash size and duration, and generally shows high detection rates for larger flashes. Preliminary results during the May 1 2017 ER-2 overflight of Colorado storms indicate decreased detection efficiency if the storm is obscured by an overlying cloud layer.

Seeking Optimal Region-Of-Interest (ROI) Single-Value Summary Measures for fMRI Studies in Imaging Genetics

PubMed Central

Tong, Yunxia; Chen, Qiang; Nichols, Thomas E.; Rasetti, Roberta; Callicott, Joseph H.; Berman, Karen F.; Weinberger, Daniel R.; Mattay, Venkata S.

2016-01-01

A data-driven hypothesis-free genome-wide association (GWA) approach in imaging genetics studies allows screening the entire genome to discover novel genes that modulate brain structure, chemistry, and function. However, a whole brain voxel-wise analysis approach in such genome-wide based imaging genetic studies can be computationally intense and also likely has low statistical power since a stringent multiple comparisons correction is needed for searching over the entire genome and brain. In imaging genetics with functional magnetic resonance imaging (fMRI) phenotypes, since many experimental paradigms activate focal regions that can be pre-specified based on a priori knowledge, reducing the voxel-wise search to single-value summary measures within a priori ROIs could prove efficient and promising. The goal of this investigation is to evaluate the sensitivity and reliability of different single-value ROI summary measures and provide guidance in future work. Four different fMRI databases were tested and comparisons across different groups (patients with schizophrenia, their siblings, vs. normal control subjects; across genotype groups) were conducted. Our results show that four of these measures, particularly those that represent values from the top most-activated voxels within an ROI are more powerful at reliably detecting group differences and generating greater effect sizes than the others. PMID:26974435

Evaluation of the Fake Resistance of a Forced-choice Paired-comparison Computer Adaptive Personality Measure

DTIC Science & Technology

2008-08-01

version of NCAPS, participants higher in cognitive ability and reading ability were able to produce higher fakability scores. Higher intelligence ... intelligence and reading ability. Therefore, the adaptive paired- comparison NCAPS is very likely to provide scores close to the true trait scores for...regardless of the intelligence or reading levels associated with those taking the adaptive NCAPS; it will be difficult to fake the adaptive paired

Prevention and rehabilitation in Swedish public sector workplaces: Effects on co-workers' and leaders' health and psychosocial working conditions.

PubMed

Vinberg, Stig; Romild, Ulla; Landstad, Bodil J

2015-01-01

Leaders and co-workers in Swedish public sector organizations are exposed to demanding psychosocial working conditions; more knowledge about workplace-based interventions in this sector of working life is needed. To compare co-workers' and leaders' self-ratings of health and psychosocial working conditions, and investigate how prevention and rehabilitation in Swedish public sector workplaces affects these ratings. The longitudinal panel data consisted of 311 individuals (20 leaders, 291 co-workers) at 19 workplaces. Based on questionnaire data, statistical analyses were performed using Mann-Whitney U-Test, pair-wise Spearman correlations, a mixed between-within subjects ANOVA and Friedman's test. Results indicate differences in how the leaders and the co-workers judge their health and psychosocial working conditions. Leaders report work content that is more varied and interesting as well as more possibilities for personal development through work, yet they also report more tiredness, concern over managing their work situation and time pressure at work. Comparisons of mean values for used indicators show some improvements after one year, but also several non-significant or negative time trends two years after the interventions were initiated. The study provides some support for experienced differences between co-workers' and leaders' health and psychosocial working conditions in public sector workplaces, indicating the importance of different workplace-oriented prevention and rehabilitation interventions for these two categories of employees.

Epidemiology Characteristics, Methodological Assessment and Reporting of Statistical Analysis of Network Meta-Analyses in the Field of Cancer

PubMed Central

Ge, Long; Tian, Jin-hui; Li, Xiu-xia; Song, Fujian; Li, Lun; Zhang, Jun; Li, Ge; Pei, Gai-qin; Qiu, Xia; Yang, Ke-hu

2016-01-01

Because of the methodological complexity of network meta-analyses (NMAs), NMAs may be more vulnerable to methodological risks than conventional pair-wise meta-analysis. Our study aims to investigate epidemiology characteristics, conduction of literature search, methodological quality and reporting of statistical analysis process in the field of cancer based on PRISMA extension statement and modified AMSTAR checklist. We identified and included 102 NMAs in the field of cancer. 61 NMAs were conducted using a Bayesian framework. Of them, more than half of NMAs did not report assessment of convergence (60.66%). Inconsistency was assessed in 27.87% of NMAs. Assessment of heterogeneity in traditional meta-analyses was more common (42.62%) than in NMAs (6.56%). Most of NMAs did not report assessment of similarity (86.89%) and did not used GRADE tool to assess quality of evidence (95.08%). 43 NMAs were adjusted indirect comparisons, the methods used were described in 53.49% NMAs. Only 4.65% NMAs described the details of handling of multi group trials and 6.98% described the methods of similarity assessment. The median total AMSTAR-score was 8.00 (IQR: 6.00–8.25). Methodological quality and reporting of statistical analysis did not substantially differ by selected general characteristics. Overall, the quality of NMAs in the field of cancer was generally acceptable. PMID:27848997

An Integrated Approach of Fuzzy Linguistic Preference Based AHP and Fuzzy COPRAS for Machine Tool Evaluation

PubMed Central

Nguyen, Huu-Tho; Md Dawal, Siti Zawiah; Nukman, Yusoff; Aoyama, Hideki; Case, Keith

2015-01-01

Globalization of business and competitiveness in manufacturing has forced companies to improve their manufacturing facilities to respond to market requirements. Machine tool evaluation involves an essential decision using imprecise and vague information, and plays a major role to improve the productivity and flexibility in manufacturing. The aim of this study is to present an integrated approach for decision-making in machine tool selection. This paper is focused on the integration of a consistent fuzzy AHP (Analytic Hierarchy Process) and a fuzzy COmplex PRoportional ASsessment (COPRAS) for multi-attribute decision-making in selecting the most suitable machine tool. In this method, the fuzzy linguistic reference relation is integrated into AHP to handle the imprecise and vague information, and to simplify the data collection for the pair-wise comparison matrix of the AHP which determines the weights of attributes. The output of the fuzzy AHP is imported into the fuzzy COPRAS method for ranking alternatives through the closeness coefficient. Presentation of the proposed model application is provided by a numerical example based on the collection of data by questionnaire and from the literature. The results highlight the integration of the improved fuzzy AHP and the fuzzy COPRAS as a precise tool and provide effective multi-attribute decision-making for evaluating the machine tool in the uncertain environment. PMID:26368541

Bimodal spectroscopic evaluation of ultra violet-irradiated mouse skin inflammatory and precancerous stages: instrumentation, spectral feature extraction/selection and classification (k-NN, LDA and SVM)

NASA Astrophysics Data System (ADS)

Díaz-Ayil, G.; Amouroux, M.; Blondel, W. C. P. M.; Bourg-Heckly, G.; Leroux, A.; Guillemin, F.; Granjon, Y.

2009-07-01

This paper deals with the development and application of in vivo spatially-resolved bimodal spectroscopy (AutoFluorescence AF and Diffuse Reflectance DR), to discriminate various stages of skin precancer in a preclinical model (UV-irradiated mouse): Compensatory Hyperplasia CH, Atypical Hyperplasia AH and Dysplasia D. A programmable instrumentation was developed for acquiring AF emission spectra using 7 excitation wavelengths: 360, 368, 390, 400, 410, 420 and 430 nm, and DR spectra in the 390-720 nm wavelength range. After various steps of intensity spectra preprocessing (filtering, spectral correction and intensity normalization), several sets of spectral characteristics were extracted and selected based on their discrimination power statistically tested for every pair-wise comparison of histological classes. Data reduction with Principal Components Analysis (PCA) was performed and 3 classification methods were implemented (k-NN, LDA and SVM), in order to compare diagnostic performance of each method. Diagnostic performance was studied and assessed in terms of sensitivity (Se) and specificity (Sp) as a function of the selected features, of the combinations of 3 different inter-fibers distances and of the numbers of principal components, such that: Se and Sp ≈ 100% when discriminating CH vs. others; Sp ≈ 100% and Se > 95% when discriminating Healthy vs. AH or D; Sp ≈ 74% and Se ≈ 63%for AH vs. D.

Effect of Different Tube Potential Settings on Caries Detection using PSP Plate and Conventional Film.

PubMed

De Melo, Daniela Pita; Cruz, Adriana Dibo; Melo, Saulo Leonardo Sousa; De Farias, Julyanna Filgueiras GonçAlves; Haiter-Neto, Francisco; De Almeida, Solange Maria

2015-04-01

To compare intraoral Phosphor Stimulable Plate digital system and intraoral film using different tube settings on incipient proximal caries detection. Five blocks, with five teeth each, were radiographically examined using phosphor plates and F-speed films. The images were acquired in 07 different tube potentials from 50-80 kV. The films were digitized. Three oral radiologists scored the images for the presence of caries using a 5-point rating scale. The areas under ROC curve were calculated. The influence of tube kilovoltage was verified by ANOVA and pair wise comparisons performed using Tukey test. Mean ROC curve areas varied from 0.446-0.628 for digital images and 0.494-0.559 for conventional images. The tube setting of 70 kV presented the best result both for digital and conventional images. Considering the image type separately, 70 kV scored highest followed by 75 and 65 kV for digital images (p=0.084). For conventional image modality, even though 70 kV presented the best result, it did not differ significantly from 80 kV, not differing from 60 and 55 kV, which did not differ from 75, 65 and 50 kV (p=0.53). Phosphor plate digital images seem to be more susceptible to tube setting potential variations then digitized film images.

Sonomyographic responses during voluntary isometric ramp contraction of the human rectus femoris muscle.

PubMed

Chen, Xin; Zheng, Yong-Ping; Guo, Jing-Yi; Zhu, Zhenyu; Chan, Shing-Chow; Zhang, Zhiguo

2012-07-01

This paper aims to investigate the relationship between torque and muscle morphological change, which is derived from ultrasound image sequence and termed as sonomyography (SMG), during isometric ramp contraction of the rectus femoris (RF) muscle, and to further compare SMG with the electromyography (EMG) and mechanomyography (MMG), which represent the electrical and mechanical activities of the muscle. Nine subjects performed isometric ramp contraction of knee up to 90% of the maximal voluntary contraction (MVC) at speeds of 45, 22.5 and 15% MVC/s, and EMG, MMG and ultrasonography were simultaneously recorded from the RF muscle. Cross-sectional area, which was referred to as SMG, was automatically extracted from continuously captured ultrasound images using a newly developed image tracking algorithm. Polynomial regression analyses were applied to fit the EMG/MMG/SMG-to-torque relationships, and the regression coefficients of EMG, MMG, and SMG were compared. Moreover, the effect of contraction speed on SMG/EMG/MMG-to-torque relationships was tested by pair-wise comparisons of the mean relationship curves at different speeds for EMG, MMG and SMG. The results show that continuous SMG could provide important morphological parameters of continuous muscle contraction. Compared with EMG and MMG, SMG exhibits different changing patterns with the increase of torque during voluntary isometric ramp contraction, and it is less influenced by the contraction speed.

Response of the hepatic transcriptome to aflatoxin B1 in domestic turkey (Meleagris gallopavo).

PubMed

Monson, Melissa S; Settlage, Robert E; McMahon, Kevin W; Mendoza, Kristelle M; Rawal, Sumit; El-Nezami, Hani S; Coulombe, Roger A; Reed, Kent M

2014-01-01

Dietary exposure to aflatoxin B1 (AFB1) is detrimental to avian health and leads to major economic losses for the poultry industry. AFB1 is especially hepatotoxic in domestic turkeys (Meleagris gallopavo), since these birds are unable to detoxify AFB1 by glutathione-conjugation. The impacts of AFB1 on the turkey hepatic transcriptome and the potential protection from pretreatment with a Lactobacillus-based probiotic mixture were investigated through RNA-sequencing. Animals were divided into four treatment groups and RNA was subsequently recovered from liver samples. Four pooled RNA-seq libraries were sequenced to produce over 322 M reads totaling 13.8 Gb of sequence. Approximately 170,000 predicted transcripts were de novo assembled, of which 803 had significant differential expression in at least one pair-wise comparison between treatment groups. Functional analysis linked many of the transcripts significantly affected by AFB1 exposure to cancer, apoptosis, the cell cycle or lipid regulation. Most notable were transcripts from the genes encoding E3 ubiquitin-protein ligase Mdm2, osteopontin, S-adenosylmethionine synthase isoform type-2, and lipoprotein lipase. Expression was modulated by the probiotics, but treatment did not completely mitigate the effects of AFB1. Genes identified through transcriptome analysis provide candidates for further study of AFB1 toxicity and targets for efforts to improve the health of domestic turkeys exposed to AFB1.

Anti-smoking legislation and its effects on urinary cotinine and cadmium levels

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

Sánchez-Rodríguez, Jinny E., E-mail: jinnysanchez@isciii.es; Bartolomé, Mónica, E-mail: mbj@isciii.es; Cañas, Ana I, E-mail: acanas@isciii.es

Anti-smoking legislation has been associated with an improvement in health indicators. Since the cadmium (Cd) body burden in the general population is markedly increased by smoke exposure, we analyzed the impact of the more restrictive legislation that came into force in Spain in 2011 by measuring Cd and cotinine in first morning urine samples from 83 adults in Madrid (Spain) before (2010) and after (2011) introduction of this law. Individual pair-wise comparisons showed a reduction of creatinine corrected Cotinine and Cd levels for non-active smokers, i. e. those which urinary cotinine levels are below 50 μg/L. After the application ofmore » the stricter law, cotinine levels in urine only decreased in non-active smokers who self-reported not to be exposed to second-hand smoke. The reduction in second hand smoke exposure was significantly higher in weekends (Friday to Sunday) than in working days (Monday to Thursday). The decrease in U-Cd was highly significant in non-active smokers and, in general, correlated with lower creatinine excretion. Therefore correction by creatinine could bias urinary Cd results, at least for cotinine levels higher than 500 μg/L. The biochemical/toxicological benefits detected herein support the stricter application of anti-smoking legislation and emphasize the need to raise the awareness of the population as regards exposure at home.« less

Macroinvertebrate Responses to Constructed Riffles in the Cache River, Illinois, USA

NASA Astrophysics Data System (ADS)

Walther, Denise A.; Whiles, Matt R.

2008-04-01

Stream restoration practices are becoming increasingly common, but biological assessments of these improvements are still limited. Rock weirs, a type of constructed riffle, were implemented in the upper Cache River in southern Illinois, USA, in 2001 and 2003-2004 to control channel incision and protect high quality riparian wetlands as part of an extensive watershed-level restoration. Construction of the rock weirs provided an opportunity to examine biological responses to a common in-stream restoration technique. We compared macroinvertebrate assemblages on previously constructed rock weirs and newly constructed weirs to those on snags and scoured clay streambed, the two dominant substrates in the unrestored reaches of the river. We quantitatively sampled macroinvertebrates on these substrates on seven occasions during 2003 and 2004. Ephemeroptera, Plecoptera, and Trichoptera (EPT) biomass and aquatic insect biomass were significantly higher on rock weirs than the streambed for most sample periods. Snags supported intermediate EPT and aquatic insect biomass compared to rock weirs and the streambed. Nonmetric multidimensional scaling (NMDS) ordinations for 2003 and 2004 revealed distinct assemblage groups for rock weirs, snags, and the streambed. Analysis of similarity supported visual interpretation of NMDS plots. All pair-wise substrate comparisons differed significantly, except recently constructed weirs versus older weirs. Results indicate positive responses by macroinvertebrate assemblages to in-stream restoration in the Cache River. Moreover, these responses were not evident with more common measures of total density, biomass, and diversity.

Population structure of the banana weevil, an introduced pest in the Canary Islands, studied by RAPD analysis.

PubMed

Magaña, C; Beroiz, B; Hernández-Crespo, P; Montes de Oca, M; Carnero, A; Ortego, F; Castañera, P

2007-12-01

The banana weevil (BW), Cosmopolites sordidus (Coleoptera: Curculionidae), is one of the most important insect pests of bananas and plantains. The mobility and the origin of BW infestations at the Canary Islands (Tenerife, La Gomera and La Palma) have been analysed using Random Amplified Polymorphic DNA (RAPD) as molecular markers. Populations from Costa Rica, Colombia, Uganda and Madeira were also included for comparison. One hundred and fifteen reproducible bands from eight primers were obtained. The level of polymorphism in the populations from the Canary Islands (40-62%) was in the range of those found in other populations. Nei's genetic distances, pair-wise fixation index (FST) values indicate that the closest populations are Tenerife populations among themselves (Nei's genetic distance=0.054-0.100; FST=0.091-0.157) and Costa Rica and Colombia populations (Nei's genetic distance=0.049; FST=0.113). Our results indicate the existence of BW local biotypes with limited gene flow and affected by genetic drift. These results are compatible with a unique event of colonization at Tenerife; whereas, the outbreaks in La Gomera and La Palma may come from independent introductions. The Madeira population is phylogenetically and geographically closer to the Canary Islands populations, suggesting that it is the most likely source of the insects introduced in the Canary Islands.

Modularization and epistatic hierarchy determine homeostatic actions of multiple blood pressure quantitative trait loci.

PubMed

Chauvet, Cristina; Crespo, Kimberley; Ménard, Annie; Roy, Julie; Deng, Alan Y

2013-11-15

Hypertension, the most frequently diagnosed clinical condition world-wide, predisposes individuals to morbidity and mortality, yet its underlying pathological etiologies are poorly understood. So far, a large number of quantitative trait loci (QTLs) have been identified in both humans and animal models, but how they function together in determining overall blood pressure (BP) in physiological settings is unknown. Here, we systematically and comprehensively performed pair-wise comparisons of individual QTLs to create a global picture of their functionality in an inbred rat model. Rather than each of numerous QTLs contributing to infinitesimal BP increments, a modularized pattern arises: two epistatic 'blocks' constitute basic functional 'units' for nearly all QTLs, designated as epistatic module 1 (EM1) and EM2. This modularization dictates the magnitude and scope of BP effects. Any EM1 member can contribute to BP additively to that of EM2, but not to those of the same module. Members of each EM display epistatic hierarchy, which seems to reflect a related functional pathway. Rat homologues of 11 human BP QTLs belong to either EM1 or EM2. Unique insights emerge into the novel genetic mechanism and hierarchy determining BP in the Dahl salt-sensitive SS/Jr (DSS) rat model that implicate a portion of human QTLs. Elucidating the pathways underlying EM1 and EM2 may reveal the genetic regulation of BP.

First report of field evolved resistance to agrochemicals in dengue mosquito, Aedes albopictus (Diptera: Culicidae), from Pakistan.

PubMed

Khan, Hafiz Azhar Ali; Akram, Waseem; Shehzad, Khurram; Shaalan, Essam A

2011-07-22

Agrochemicals have been widely used in Pakistan for several years. This exposes mosquito populations, particularly those present around agricultural settings, to an intense selection pressure for insecticide resistance. The aim of the present study was to investigate the toxicity of representative agrochemicals against various populations of Aedes albopictus (Skuse) collected from three different regions from 2008-2010. For organophosphates and pyrethroids, the resistance ratios compared with susceptible Lab-PK were in the range of 157-266 fold for chlorpyrifos, 24-52 fold for profenofos, 41-71 fold for triazofos, and 15-26 fold for cypermethrin, 15-53 fold for deltamethrin and 21-58 fold for lambdacyhalothrin. The resistance ratios for carbamates and new insecticides were in the range of 13-22 fold for methomyl, 24-30 fold for thiodicarb, and 41-101 fold for indoxacarb, 14-27 fold for emamectin benzoate and 23-50 fold for spinosad. Pair wise comparisons of the log LC50s of insecticides revealed correlation among several insecticides, suggesting a possible cross resistance mechanism. Moreover, resistance remained stable across 3 years, suggesting field selection for general fitness had also taken place for various populations of Ae. albopictus. Moderate to high level of resistance to agrochemicals in Pakistani field populations of Ae. albopictus is reported here first time. The geographic extent of resistance is unknown but, if widespread, may lead to problems in future vector control.

A Computational Framework for Quantitative Evaluation of Movement during Rehabilitation

NASA Astrophysics Data System (ADS)

Chen, Yinpeng; Duff, Margaret; Lehrer, Nicole; Sundaram, Hari; He, Jiping; Wolf, Steven L.; Rikakis, Thanassis

2011-06-01

This paper presents a novel generalized computational framework for quantitative kinematic evaluation of movement in a rehabilitation clinic setting. The framework integrates clinical knowledge and computational data-driven analysis together in a systematic manner. The framework provides three key benefits to rehabilitation: (a) the resulting continuous normalized measure allows the clinician to monitor movement quality on a fine scale and easily compare impairments across participants, (b) the framework reveals the effect of individual movement components on the composite movement performance helping the clinician decide the training foci, and (c) the evaluation runs in real-time, which allows the clinician to constantly track a patient's progress and make appropriate adaptations to the therapy protocol. The creation of such an evaluation is difficult because of the sparse amount of recorded clinical observations, the high dimensionality of movement and high variations in subject's performance. We address these issues by modeling the evaluation function as linear combination of multiple normalized kinematic attributes y = Σwiφi(xi) and estimating the attribute normalization function φi(ṡ) by integrating distributions of idealized movement and deviated movement. The weights wi are derived from a therapist's pair-wise comparison using a modified RankSVM algorithm. We have applied this framework to evaluate upper limb movement for stroke survivors with excellent results—the evaluation results are highly correlated to the therapist's observations.

Error simulation of paired-comparison-based scaling methods

NASA Astrophysics Data System (ADS)

Cui, Chengwu

2000-12-01

Subjective image quality measurement usually resorts to psycho physical scaling. However, it is difficult to evaluate the inherent precision of these scaling methods. Without knowing the potential errors of the measurement, subsequent use of the data can be misleading. In this paper, the errors on scaled values derived form paired comparison based scaling methods are simulated with randomly introduced proportion of choice errors that follow the binomial distribution. Simulation results are given for various combinations of the number of stimuli and the sampling size. The errors are presented in the form of average standard deviation of the scaled values and can be fitted reasonably well with an empirical equation that can be sued for scaling error estimation and measurement design. The simulation proves paired comparison based scaling methods can have large errors on the derived scaled values when the sampling size and the number of stimuli are small. Examples are also given to show the potential errors on actually scaled values of color image prints as measured by the method of paired comparison.

PCTFPeval: a web tool for benchmarking newly developed algorithms for predicting cooperative transcription factor pairs in yeast.

PubMed

Lai, Fu-Jou; Chang, Hong-Tsun; Wu, Wei-Sheng

2015-01-01

Computational identification of cooperative transcription factor (TF) pairs helps understand the combinatorial regulation of gene expression in eukaryotic cells. Many advanced algorithms have been proposed to predict cooperative TF pairs in yeast. However, it is still difficult to conduct a comprehensive and objective performance comparison of different algorithms because of lacking sufficient performance indices and adequate overall performance scores. To solve this problem, in our previous study (published in BMC Systems Biology 2014), we adopted/proposed eight performance indices and designed two overall performance scores to compare the performance of 14 existing algorithms for predicting cooperative TF pairs in yeast. Most importantly, our performance comparison framework can be applied to comprehensively and objectively evaluate the performance of a newly developed algorithm. However, to use our framework, researchers have to put a lot of effort to construct it first. To save researchers time and effort, here we develop a web tool to implement our performance comparison framework, featuring fast data processing, a comprehensive performance comparison and an easy-to-use web interface. The developed tool is called PCTFPeval (Predicted Cooperative TF Pair evaluator), written in PHP and Python programming languages. The friendly web interface allows users to input a list of predicted cooperative TF pairs from their algorithm and select (i) the compared algorithms among the 15 existing algorithms, (ii) the performance indices among the eight existing indices, and (iii) the overall performance scores from two possible choices. The comprehensive performance comparison results are then generated in tens of seconds and shown as both bar charts and tables. The original comparison results of each compared algorithm and each selected performance index can be downloaded as text files for further analyses. Allowing users to select eight existing performance indices and 15 existing algorithms for comparison, our web tool benefits researchers who are eager to comprehensively and objectively evaluate the performance of their newly developed algorithm. Thus, our tool greatly expedites the progress in the research of computational identification of cooperative TF pairs.

PCTFPeval: a web tool for benchmarking newly developed algorithms for predicting cooperative transcription factor pairs in yeast

PubMed Central

2015-01-01

Background Computational identification of cooperative transcription factor (TF) pairs helps understand the combinatorial regulation of gene expression in eukaryotic cells. Many advanced algorithms have been proposed to predict cooperative TF pairs in yeast. However, it is still difficult to conduct a comprehensive and objective performance comparison of different algorithms because of lacking sufficient performance indices and adequate overall performance scores. To solve this problem, in our previous study (published in BMC Systems Biology 2014), we adopted/proposed eight performance indices and designed two overall performance scores to compare the performance of 14 existing algorithms for predicting cooperative TF pairs in yeast. Most importantly, our performance comparison framework can be applied to comprehensively and objectively evaluate the performance of a newly developed algorithm. However, to use our framework, researchers have to put a lot of effort to construct it first. To save researchers time and effort, here we develop a web tool to implement our performance comparison framework, featuring fast data processing, a comprehensive performance comparison and an easy-to-use web interface. Results The developed tool is called PCTFPeval (Predicted Cooperative TF Pair evaluator), written in PHP and Python programming languages. The friendly web interface allows users to input a list of predicted cooperative TF pairs from their algorithm and select (i) the compared algorithms among the 15 existing algorithms, (ii) the performance indices among the eight existing indices, and (iii) the overall performance scores from two possible choices. The comprehensive performance comparison results are then generated in tens of seconds and shown as both bar charts and tables. The original comparison results of each compared algorithm and each selected performance index can be downloaded as text files for further analyses. Conclusions Allowing users to select eight existing performance indices and 15 existing algorithms for comparison, our web tool benefits researchers who are eager to comprehensively and objectively evaluate the performance of their newly developed algorithm. Thus, our tool greatly expedites the progress in the research of computational identification of cooperative TF pairs. PMID:26677932

IRAC Photometry of the Coldest CatWISE-selected Brown Dwarfs

NASA Astrophysics Data System (ADS)

Meisner, Aaron; Kirkpatrick, J. Davy; Kirkpatrick, J. Davy; Eisenhardt, Peter; Marocco, Federico; Faherty, Jacqueline; Cushing, Michael; Wright, Edward

2018-05-01

We will obtain IRAC [3.6] and [4.5] photometry of 250 extremely cool brown dwarfs newly revealed by the powerful combination of WISE and NEOWISE imaging at 4.6 microns. Our CatWISE effort, which is an archival data analysis program using WISE and NEOWISE data, will improve upon the motion selection of AllWISE by enabling a >10x time baseline enhancement, from 0.5 years (AllWISE) to 6.5 years (CatWISE). As a result, CatWISE motion selection is expected to yield a dramatic 8-fold increase in the sample of known brown dwarfs at spectral types T5 and later (T < 1,200 K). Many of the coolest such CatWISE discoveries will be detected exclusively in the WISE 4.6 micron (W2) channel. WISE W1 (3.4 micron) nondetections, which we expect for the majority of our most interesting sources, will provide only limits on mid-infrared color. Spitzer can supply this critical datum by measuring accurate [3.6]-[4.5] colors of our discoveries. These Spitzer color measurements will permit photometric spectral type estimates, which in turn yield estimates for critical parameters including luminosity, distance, and near-infrared flux. Using large [3.6]-[4.5] color to pinpoint the coldest late T and Y dwarfs among our CatWISE sample will enable us to prioritize these objects for spectroscopic follow-up, better understand the bottom of the substellar mass function, and identify nearby giant planet analogs suitable for future atmospheric studies with JWST.

WISE Photometry for 400 million SDSS sources

DOE PAGES

Lang, Dustin; Hogg, David W.; Schlegel, David J.

2016-01-28

Here, we present photometry of images from the Wide-Field Infrared Survey Explorer (WISE) of over 400 million sources detected by the Sloan Digital Sky Survey (SDSS). We also use a "forced photometry" technique, using measured SDSS source positions, star-galaxy classification, and galaxy profiles to define the sources whose fluxes are to be measured in the WISE images. We perform photometry with The Tractor image modeling code, working on our "unWISE" coaddds and taking account of the WISE point-spread function and a noise model. The result is a measurement of the flux of each SDSS source in each WISE band. Manymore » sources have little flux in the WISE bands, so often the measurements we report are consistent with zero given our uncertainties. But, for many sources we get 3σ or 4σ measurements; these sources would not be reported by the "official" WISE pipeline and will not appear in the WISE catalog, yet they can be highly informative for some scientific questions. In addition, these small-signal measurements can be used in stacking analyses at the catalog level. The forced photometry approach has the advantage that we measure a consistent set of sources between SDSS and WISE, taking advantage of the resolution and depth of the SDSS images to interpret the WISE images; objects that are resolved in SDSS but blended together in WISE still have accurate measurements in our photometry. Our results, and the code used to produce them, are publicly available at http://unwise.me.« less

Wise Detections of Known QSOS at Redshifts Greater Than Six

NASA Technical Reports Server (NTRS)

Blain, Andrew W.; Assef, Roberto; Stern, Daniel; Tsai, Chao-Wei; Eisenhardt, Peter; Bridge, Carrie; Benford, Dominic; Jarrett, Tom; Cutri, Roc; Petty, Sara;

Wise retained in the endoplasmic reticulum inhibits Wnt signaling by reducing cell surface LRP6.

PubMed

Guidato, Sonia; Itasaki, Nobue

2007-10-15

The Wnt signaling pathway is tightly regulated by extracellular and intracellular modulators. Wise was isolated as a secreted protein capable of interacting with the Wnt co-receptor LRP6. Studies in Xenopus embryos revealed that Wise either enhances or inhibits the Wnt pathway depending on the cellular context. Here we show that the cellular localization of Wise has distinct effects on the Wnt pathway readout. While secreted Wise either synergizes or inhibits the Wnt signals depending on the partner ligand, ER-retained Wise consistently blocks the Wnt pathway. ER-retained Wise reduces LRP6 on the cell surface, making cells less susceptible to the Wnt signal. This study provides a cellular mechanism for the action of Wise and introduces the modulation of cellular susceptibility to Wnt signals as a novel mechanism of the regulation of the Wnt pathway.

Scalable load balancing for massively parallel distributed Monte Carlo particle transport

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

O'Brien, M. J.; Brantley, P. S.; Joy, K. I.

2013-07-01

In order to run computer simulations efficiently on massively parallel computers with hundreds of thousands or millions of processors, care must be taken that the calculation is load balanced across the processors. Examining the workload of every processor leads to an unscalable algorithm, with run time at least as large as O(N), where N is the number of processors. We present a scalable load balancing algorithm, with run time 0(log(N)), that involves iterated processor-pair-wise balancing steps, ultimately leading to a globally balanced workload. We demonstrate scalability of the algorithm up to 2 million processors on the Sequoia supercomputer at Lawrencemore » Livermore National Laboratory. (authors)« less

Solvent Effects on Protein Folding/Unfolding

NASA Astrophysics Data System (ADS)

García, A. E.; Hillson, N.; Onuchic, J. N.

Pressure effects on the hydrophobic potential of mean force led Hummer et al. to postulate a model for pressure denaturation of proteins in which denaturation occurs by means of water penetration into the protein interior, rather than by exposing the protein hydrophobic core to the solvent --- commonly used to describe temperature denaturation. We study the effects of pressure in protein folding/unfolding kinetics in an off-lattice minimalist model of a protein in which pressure effects have been incorporated by means of the pair-wise potential of mean force of hydrophobic groups in water. We show that pressure slows down the kinetics of folding by decreasing the reconfigurational diffusion coefficient and moves the location of the folding transition state.

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

Schmidt, T.; Imhof, A.; Ingold, G.

To vary the polarization vector of an APPLE II undulator continuously from 0 - 180 deg., all four magnet arrays need to be movable. Following the adjustable-phase undulator approach by R. Carr, a 3.4 m long fixed gap undulator for SLS with a gap of 11.6 mm has been constructed. It will be installed in fall 2006. The gap drive is replaced by a pair-wise shift of the magnet arrays to change the energy, while the polarization is changed by shifts of diagonal arrays. The high injection efficiency and standard operation top-up mode at the SLS allows this simplified undulatormore » design. The design as well as the operational aspects will be discussed.« less

Rotation invariant deep binary hashing for fast image retrieval

NASA Astrophysics Data System (ADS)

Dai, Lai; Liu, Jianming; Jiang, Aiwen

2017-07-01

In this paper, we study how to compactly represent image's characteristics for fast image retrieval. We propose supervised rotation invariant compact discriminative binary descriptors through combining convolutional neural network with hashing. In the proposed network, binary codes are learned by employing a hidden layer for representing latent concepts that dominate on class labels. A loss function is proposed to minimize the difference between binary descriptors that describe reference image and the rotated one. Compared with some other supervised methods, the proposed network doesn't have to require pair-wised inputs for binary code learning. Experimental results show that our method is effective and achieves state-of-the-art results on the CIFAR-10 and MNIST datasets.

Hierarchical structure of biological systems

PubMed Central

Alcocer-Cuarón, Carlos; Rivera, Ana L; Castaño, Victor M

2014-01-01

A general theory of biological systems, based on few fundamental propositions, allows a generalization of both Wierner and Berthalanffy approaches to theoretical biology. Here, a biological system is defined as a set of self-organized, differentiated elements that interact pair-wise through various networks and media, isolated from other sets by boundaries. Their relation to other systems can be described as a closed loop in a steady-state, which leads to a hierarchical structure and functioning of the biological system. Our thermodynamical approach of hierarchical character can be applied to biological systems of varying sizes through some general principles, based on the exchange of energy information and/or mass from and within the systems. PMID:24145961

Hierarchical structure of biological systems: a bioengineering approach.

PubMed

Alcocer-Cuarón, Carlos; Rivera, Ana L; Castaño, Victor M

2014-01-01

A general theory of biological systems, based on few fundamental propositions, allows a generalization of both Wierner and Berthalanffy approaches to theoretical biology. Here, a biological system is defined as a set of self-organized, differentiated elements that interact pair-wise through various networks and media, isolated from other sets by boundaries. Their relation to other systems can be described as a closed loop in a steady-state, which leads to a hierarchical structure and functioning of the biological system. Our thermodynamical approach of hierarchical character can be applied to biological systems of varying sizes through some general principles, based on the exchange of energy information and/or mass from and within the systems.

[Correlation between gaseous exchange rate, body temperature, and mitochondrial protein content in the liver of mice].

PubMed

Muradian, Kh K; Utko, N O; Mozzhukhina, T H; Pishel', I M; Litoshenko, O Ia; Bezrukov, V V; Fraĭfel'd, V E

2002-01-01

Correlative and regressive relations between the gaseous exchange, thermoregulation and mitochondrial protein content were analyzed by two- and three-dimensional statistics in mice. It has been shown that the pair wise linear methods of analysis did not reveal any significant correlation between the parameters under exploration. However, it became evident at three-dimensional and non-linear plotting for which the coefficients of multivariable correlation reached and even exceeded 0.7-0.8. The calculations based on partial differentiation of the multivariable regression equations allow to conclude that at certain values of VO2, VCO2 and body temperature negative relations between the systems of gaseous exchange and thermoregulation become dominating.

Assessing Vocational Interests in the Basque Country Using Paired Comparison Design

ERIC Educational Resources Information Center

Elosua, Paula

2007-01-01

This article proposes the Thurstonian paired comparison model to assess vocational preferences and uses this approach to evaluate the Realistic, Investigative, Artistic, Social, Enterprise, and Conventional (RIASEC) model in the Basque Country (Spain). First, one unrestricted model is estimated in the Structural Equation Modelling framework using…

Paired Comparison Evaluations of Managerial Effectiveness by Peers and Supervisors.

ERIC Educational Resources Information Center

Siegel, Laurence

1982-01-01

Solicited paired comparison evaluations for a group of savings and loan association branch managers. Peer evaluations were obtained from 16 of these managers; supervisory evaluations were obtained from four officers. Interjudge agreement (both within and between groups) was high. Peer-generated evaluations assisted officers in making acceptable…

Eye movements reflect and shape strategies in fraction comparison.

PubMed

Ischebeck, Anja; Weilharter, Marina; Körner, Christof

2016-01-01

The comparison of fractions is a difficult task that can often be facilitated by separately comparing components (numerators and denominators) of the fractions--that is, by applying so-called component-based strategies. The usefulness of such strategies depends on the type of fraction pair to be compared. We investigated the temporal organization and the flexibility of strategy deployment in fraction comparison by evaluating sequences of eye movements in 20 young adults. We found that component-based strategies could account for the response times and the overall number of fixations observed for the different fraction pairs. The analysis of eye movement sequences showed that the initial eye movements in a trial were characterized by stereotypical scanning patterns indicative of an exploratory phase that served to establish the kind of fraction pair presented. Eye movements that followed this phase adapted to the particular type of fraction pair and indicated the deployment of specific comparison strategies. These results demonstrate that participants employ eye movements systematically to support strategy use in fraction comparison. Participants showed a remarkable flexibility to adapt to the most efficient strategy on a trial-by-trial basis. Our results confirm the value of eye movement measurements in the exploration of strategic adaptation in complex tasks.

Evaluation of a metal artifact reduction algorithm applied to post-interventional flat detector CT in comparison to pre-treatment CT in patients with acute subarachnoid haemorrhage.

PubMed

Mennecke, Angelika; Svergun, Stanislav; Scholz, Bernhard; Royalty, Kevin; Dörfler, Arnd; Struffert, Tobias

2017-01-01

Metal artefacts can impair accurate diagnosis of haemorrhage using flat detector CT (FD-CT), especially after aneurysm coiling. Within this work we evaluate a prototype metal artefact reduction algorithm by comparison of the artefact-reduced and the non-artefact-reduced FD-CT images to pre-treatment FD-CT and multi-slice CT images. Twenty-five patients with acute aneurysmal subarachnoid haemorrhage (SAH) were selected retrospectively. FD-CT and multi-slice CT before endovascular treatment as well as FD-CT data sets after treatment were available for all patients. The algorithm was applied to post-treatment FD-CT. The effect of the algorithm was evaluated utilizing the pre-post concordance of a modified Fisher score, a subjective image quality assessment, the range of the Hounsfield units within three ROIs, and the pre-post slice-wise Pearson correlation. The pre-post concordance of the modified Fisher score, the subjective image quality, and the pre-post correlation of the ranges of the Hounsfield units were significantly higher for artefact-reduced than for non-artefact-reduced images. Within the metal-affected slices, the pre-post slice-wise Pearson correlation coefficient was higher for artefact-reduced than for non-artefact-reduced images. The overall diagnostic quality of the artefact-reduced images was improved and reached the level of the pre-interventional FD-CT images. The metal-unaffected parts of the image were not modified. • After coiling subarachnoid haemorrhage, metal artefacts seriously reduce FD-CT image quality. • This new metal artefact reduction algorithm is feasible for flat-detector CT. • After coiling, MAR is necessary for diagnostic quality of affected slices. • Slice-wise Pearson correlation is introduced to evaluate improvement of MAR in future studies. • Metal-unaffected parts of image are not modified by this MAR algorithm.

WiseView: Visualizing motion and variability of faint WISE sources

NASA Astrophysics Data System (ADS)

Caselden, Dan; Westin, Paul, III; Meisner, Aaron; Kuchner, Marc; Colin, Guillaume

2018-06-01

WiseView renders image blinks of Wide-field Infrared Survey Explorer (WISE) coadds spanning a multi-year time baseline in a browser. The software allows for easy visual identification of motion and variability for sources far beyond the single-frame detection limit, a key threshold not surmounted by many studies. WiseView transparently gathers small image cutouts drawn from many terabytes of unWISE coadds, facilitating access to this large and unique dataset. Users need only input the coordinates of interest and can interactively tune parameters including the image stretch, colormap and blink rate. WiseView was developed in the context of the Backyard Worlds: Planet 9 citizen science project, and has enabled hundreds of brown dwarf candidate discoveries by citizen scientists and professional astronomers.

Quicksilver: Fast predictive image registration - A deep learning approach.

PubMed

Yang, Xiao; Kwitt, Roland; Styner, Martin; Niethammer, Marc

2017-09-01

This paper introduces Quicksilver, a fast deformable image registration method. Quicksilver registration for image-pairs works by patch-wise prediction of a deformation model based directly on image appearance. A deep encoder-decoder network is used as the prediction model. While the prediction strategy is general, we focus on predictions for the Large Deformation Diffeomorphic Metric Mapping (LDDMM) model. Specifically, we predict the momentum-parameterization of LDDMM, which facilitates a patch-wise prediction strategy while maintaining the theoretical properties of LDDMM, such as guaranteed diffeomorphic mappings for sufficiently strong regularization. We also provide a probabilistic version of our prediction network which can be sampled during the testing time to calculate uncertainties in the predicted deformations. Finally, we introduce a new correction network which greatly increases the prediction accuracy of an already existing prediction network. We show experimental results for uni-modal atlas-to-image as well as uni-/multi-modal image-to-image registrations. These experiments demonstrate that our method accurately predicts registrations obtained by numerical optimization, is very fast, achieves state-of-the-art registration results on four standard validation datasets, and can jointly learn an image similarity measure. Quicksilver is freely available as an open-source software. Copyright © 2017 Elsevier Inc. All rights reserved.

Decomposition of P(CH 3) 3 on Ru(0001): comparison with PH 3 and PCl 3

NASA Astrophysics Data System (ADS)

Tao, H.-S.; Diebold, U.; Shinn, N. D.; Madey, T. E.

1997-04-01

The decomposition of P(CH 3) 3 adsorbed on Ru(0001) at 80 K is studied by soft X-ray photoelectron spectroscopy using synchrotron radiation. Using the chemical shifts in the P 2p core levels, we are able to identify various phosphorus-containing surface reaction products and follow their reactions on Ru(0001). It is found that P(CH 3) 3 undergoes a step-wise demethylation on Ru(0001), P(CH 3) 3 → P(CH 3) 2 → P(CH 3) → P, which is complete around ˜450 K. These results are compared with the decomposition of isostructural PH 3 and PCl 3 on Ru(0001). The decomposition of PH 3 involves a stable intermediate, labeled as PH x, and follows a reaction of: PH 3 → PH x → P, which is complete around ˜190 K. The conversion of chemisorbed phosphorus to ruthenium phosphide is observed and is complete around ˜700 K on Ru(0001). PCl 3 also follows a step-wise decomposition reaction, PCl 3 → PCl 2 → PCl → P, which is complete around ˜300 K. The energetics of the adsorption and the step-wise decomposition reactions of PH 3, PCl 3 and P(CH 3) 3 are estimated using the bond order conservation Morse potential (BOCMP) method. The energetics calculated using the BOCMP method agree qualitatively with the experimental data.

A WISE Selection of MIR AGN in Different Environments

NASA Astrophysics Data System (ADS)

Cheeseboro, Belinda D.; Norman, Dara J.

2015-01-01

This study was undertaken to understand the role of large scale environment in the evolution of MIR-selected AGN. In this study we examine AGN candidates in two types of environments: 7 clusters and 6 blank fields. Two types of clusters were studied in this project: 3 virialized and 4 non-virialized. The redshift of the clusters ranged 0.22≤z≤0.28. We used the mid-infrared WISE All-Sky database to identify AGN, applying various methods to refine our AGN candidate selection. To ascertain if there is an excess or deficit of MIR AGN in galaxy clusters vs. blank fields, we compared the AGN candidate distributions in virialized vs. non-virialized clusters to the blank fields. After close examination and comparison of the results to X-ray selected AGN from the Gilmour et al. (2009) study, we concluded that we do not detect an excess or deficit of MIR AGN in our clusters whether the cluster was virialized or non-virialized. This contrasted the conclusion of the Gilmour et al. (2009) study where there was an excess of X-Ray selected AGN in clusters.We also note an interesting feature in our WISE color-color plots that might be used for further investigation.Cheeseboro was supported by the NOAO/KPNO ResearchExperiences for Undergraduates (REU) Program which is funded by theNational Science Foundation Research Experiences for UndergraduatesProgram (AST-1262829).

Genetic and Environmental Factors in Invasive Cervical Cancer: Design and Methods of a Classical Twin Study.

PubMed

Machalek, Dorothy A; Wark, John D; Tabrizi, Sepehr N; Hopper, John L; Bui, Minh; Dite, Gillian S; Cornall, Alyssa M; Pitts, Marian; Gertig, Dorota; Erbas, Bircan; Garland, Suzanne M

2017-02-01

Persistent high-risk human papillomavirus (HPV) infection is a necessary prerequisite for development of cervical cancer and its precursor lesion, high-grade squamous intraepithelial lesion (HSIL). However, HPV infection is not sufficient to drive this process, and genetic and environmental factors may also play a role. The Cervical Cancer, Genetics and Environment Twin Study was established to investigate the environmental and genetic influences on variation in susceptibility to cervical pre-cancer in 25- to 69-year-old monozygotic (MZ) and dizygotic (DZ) twins recruited through the Australian Twin Registry. Reviews of Papanicolaou (Pap) screening histories were undertaken to identify individual women with a history of an abnormal Pap test. This was followed by detection of HPV in archival Pap smears of selected twin pairs to determine HPV persistence. Selected twin pairs also completed a detailed questionnaire on socio-demographic characteristics, sexual behavior, and HPV knowledge. In future analyses, under the assumptions of the classical twin design, case-wise concordance for persistent HPV infection and HSIL will be calculated for MZ and DZ twin pairs, and twin pairs (both MZ and DZ) who are discordant for the above outcomes will be used to assess the contributions of measured environmental risk factors. The study examines factors related to HPV persistence and development of HSIL among female MZ and DZ twins. The results will contribute to our understanding of the natural history of cervical HPV infection and the relative contributions of genetic and environmental factors in disease progression.

Quasar lenses and pairs in the VST-ATLAS and Gaia

NASA Astrophysics Data System (ADS)

Agnello, A.; Schechter, P. L.; Morgan, N. D.; Treu, T.; Grillo, C.; Malesani, D.; Anguita, T.; Apostolovski, Y.; Rusu, C. E.; Motta, V.; Rojas, K.; Chehade, B.; Shanks, T.

2018-04-01

We report on discovery results from a quasar lens search in the ATLAS-DR3 public footprint. Spectroscopic follow-up campaigns, conducted at the 2.6 m Nordic Optical Telescope (La Palma) and 3.6 m New Technology Telescope (La Silla) in 2016, yielded seven pairs of quasars exhibiting the same lines at the same redshift and monotonic flux ratios with wavelength (hereafter NIQs, nearly identical quasar pairs). Magellan spectra of A0140-1152 (01h40m03{^s.}0-11d52m19{^s.}0, zs = 1.807) confirm it as a lens with deflector at zl = 0.277 and Einstein radius θE = (0.73 ± 0.02) arcsec. Follow-up imaging of the NIQ A2213-2652 (22h13m38{^s.}4-26d52m27{^s.}1) reveals the deflector galaxy and confirms it as a lens. We show the use of spatial resolution from the Gaia mission to select lenses and list additional systems from a WISE-Gaia-ATLAS search, yielding three additional lenses (02h35m27{^s.}4-24d33m13{^s.}2, 02h59m33s-23d38m01{^s.}8, 01h46m32{^s.}9-11d33m39{^s.}0). The overall sample consists of 11 lenses/NIQs, plus three lenses known before 2016, over the ATLAS-DR3 footprint (≈3500 deg2). Finally, we discuss future prospects for objective classification of pair/NIQ/contaminant spectra.

Repeatability and Reproducibility of Decisions by Latent Fingerprint Examiners

PubMed Central

Ulery, Bradford T.; Hicklin, R. Austin; Buscaglia, JoAnn; Roberts, Maria Antonia

2012-01-01

The interpretation of forensic fingerprint evidence relies on the expertise of latent print examiners. We tested latent print examiners on the extent to which they reached consistent decisions. This study assessed intra-examiner repeatability by retesting 72 examiners on comparisons of latent and exemplar fingerprints, after an interval of approximately seven months; each examiner was reassigned 25 image pairs for comparison, out of total pool of 744 image pairs. We compare these repeatability results with reproducibility (inter-examiner) results derived from our previous study. Examiners repeated 89.1% of their individualization decisions, and 90.1% of their exclusion decisions; most of the changed decisions resulted in inconclusive decisions. Repeatability of comparison decisions (individualization, exclusion, inconclusive) was 90.0% for mated pairs, and 85.9% for nonmated pairs. Repeatability and reproducibility were notably lower for comparisons assessed by the examiners as “difficult” than for “easy” or “moderate” comparisons, indicating that examiners' assessments of difficulty may be useful for quality assurance. No false positive errors were repeated (n = 4); 30% of false negative errors were repeated. One percent of latent value decisions were completely reversed (no value even for exclusion vs. of value for individualization). Most of the inter- and intra-examiner variability concerned whether the examiners considered the information available to be sufficient to reach a conclusion; this variability was concentrated on specific image pairs such that repeatability and reproducibility were very high on some comparisons and very low on others. Much of the variability appears to be due to making categorical decisions in borderline cases. PMID:22427888

Spacewatch Survey for Asteroids and Comets

DTIC Science & Technology

2005-11-01

radar images. Relationship of Spacewatch to the WISE spacecraft mission: E. L. Wright of the UCLA Astronomy Dept. is the PI of the Wide-field Infrared ...Survey Explorer (WISE) MIDEX spacecraft mission. WISE will map the whole sky at thermal infrared wavelengths with 500 times more sensitivity than the...elongations. WISE=s detections in the thermal infrared will also provide a size-limited sample of asteroids instead of the brightness-limited surveys

SU-E-J-86: Lobar Lung Function Quantification by PET Galligas and CT Ventilation Imaging in Lung Cancer Patients

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

Eslick, E; Kipritidis, J; Keall, P

2014-06-01

Purpose: The purpose of this study was to quantify the lobar lung function using the novel PET Galligas ([68Ga]-carbon nanoparticle) ventilation imaging and the investigational CT ventilation imaging in lung cancer patients pre-treatment. Methods: We present results on our first three lung cancer patients (2 male, mean age 78 years) as part of an ongoing ethics approved study. For each patient a PET Galligas ventilation (PET-V) image and a pair of breath hold CT images (end-exhale and end-inhale tidal volumes) were acquired using a Siemens Biograph PET CT. CT-ventilation (CT-V) images were created from the pair of CT images usingmore » deformable image registration (DIR) algorithms and the Hounsfield Unit (HU) ventilation metric. A comparison of ventilation quantification from each modality was done on the lobar level and the voxel level. A Bland-Altman plot was used to assess the difference in mean percentage contribution of each lobe to the total lung function between the two modalities. For each patient, a voxel-wise Spearmans correlation was calculated for the whole lungs between the two modalities. Results: The Bland-Altman plot demonstrated strong agreement between PET-V and CT-V for assessment of lobar function (r=0.99, p<0.001; range mean difference: −5.5 to 3.0). The correlation between PET-V and CT-V at the voxel level was moderate(r=0.60, p<0.001). Conclusion: This preliminary study on the three patients data sets demonstrated strong agreement between PET and CT ventilation imaging for the assessment of pre-treatment lung function at the lobar level. Agreement was only moderate at the level of voxel correlations. These results indicate that CT ventilation imaging has potential for assessing pre-treatment lobar lung function in lung cancer patients.« less

A comparative study of progressive wear of four dental monolithic, veneered glass-ceramics.

PubMed

Zhang, Zhenzhen; Yi, Yuanping; Wang, Xuesong; Guo, Jiawen; Li, Ding; He, Lin; Zhang, Shaofeng

2017-10-01

This study evaluated the wear performance and wear mechanisms of four dental glass-ceramics, based on the microstructure and mechanical properties in the progressive wear process. Bar (N = 40, n = 10) and disk (N = 32, n = 8) specimens were prepared from (A) lithium disilicate glass-ceramic (LD), (B) leucite reinforced glass-ceramic (LEU), (C) feldspathic glass-ceramic (FEL), and (D) fluorapatite glass-ceramic (FLU). The bar specimens were tested for three-point flexural strength, hardness, fracture toughness and elastic modulus. The disk specimens paired with steatite antagonists were tested in a pin-on-disk tribometer with 10N up to 1000,000 wear cycles. The wear analysis of glass-ceramics was performed using a 3D profilometer after every 200,000 wear cycles. Wear loss of steatite antagonists was calculated by measuring the weight and density using sensitive balance and Archimedes' method. Wear morphologies and microstructures were analyzed by scanning electron microscopy (SEM). The crystalline phase compositions were determined using X-ray diffraction (XRD). One-way analysis of variance (ANOVA) was used to analyze the data. Multiple pair-wise comparison of means was performed by Tukey's post-hoc test. LD showed the highest fracture toughness, flexural strength, elastic modulus and crystallinity, followed by LEU and FEL, and FLU showed the lowest. However, the hardness of LD was lower than all the other three types of ceramics. For steatite antagonists, LD produced the least wear loss of antagonist, followed by LEU and FEL, and FLU had the most wear loss. For glass-ceramic materials, LD exhibited similar wear loss as LEU, but more than FLU and FEL did. Moreover, fracture occurred on the wear surface of FLU. In the progressive wear process, veneering porcelains showed better wear resistance but fluorapatite veneering porcelains appeared fracture surface. Monolithic lithium disilicate glass-ceramics with higher mechanical properties showed more wear loss, however, they did not fracture and produced less wear loss of antagonists. Copyright © 2017 Elsevier Ltd. All rights reserved.

Automated quantification of pulmonary emphysema from computed tomography scans: comparison of variation and correlation of common measures in a large cohort

NASA Astrophysics Data System (ADS)

Keller, Brad M.; Reeves, Anthony P.; Yankelevitz, David F.; Henschke, Claudia I.

2010-03-01

The purpose of this work was to retrospectively investigate the variation of standard indices of pulmonary emphysema from helical computed tomographic (CT) scans as related to inspiration differences over a 1 year interval and determine the strength of the relationship between these measures in a large cohort. 626 patients that had 2 scans taken at an interval of 9 months to 15 months (μ: 381 days, σ: 31 days) were selected for this work. All scans were acquired at a 1.25mm slice thickness using a low dose protocol. For each scan, the emphysema index (EI), fractal dimension (FD), mean lung density (MLD), and 15th percentile of the histogram (HIST) were computed. The absolute and relative changes for each measure were computed and the empirical 95% confidence interval was reported both in non-normalized and normalized scales. Spearman correlation coefficients are computed between the relative change in each measure and relative change in inspiration between each scan-pair, as well as between each pair-wise combination of the four measures. EI varied on a range of -10.5 to 10.5 on a non-normalized scale and -15 to 15 on a normalized scale, with FD and MLD showing slightly larger but comparable spreads, and HIST having a much larger variation. MLD was found to show the strongest correlation to inspiration change (r=0.85, p<0.001), and EI, FD, and HIST to have moderately strong correlation (r = 0.61-0.74, p<0.001). Finally, HIST showed very strong correlation to EI (r = 0.92, p<0.001), while FD showed the least strong relationship to EI (r = 0.82, p<0.001). This work shows that emphysema index and fractal dimension have the least variability overall of the commonly used measures of emphysema and that they offer the most unique quantification of emphysema relative to each other.

A fuzzy stochastic framework for managing hydro-environmental and socio-economic interactions under uncertainty

NASA Astrophysics Data System (ADS)

Subagadis, Yohannes Hagos; Schütze, Niels; Grundmann, Jens

2014-05-01

An amplified interconnectedness between a hydro-environmental and socio-economic system brings about profound challenges of water management decision making. In this contribution, we present a fuzzy stochastic approach to solve a set of decision making problems, which involve hydrologically, environmentally, and socio-economically motivated criteria subjected to uncertainty and ambiguity. The proposed methodological framework combines objective and subjective criteria in a decision making procedure for obtaining an acceptable ranking in water resources management alternatives under different type of uncertainty (subjective/objective) and heterogeneous information (quantitative/qualitative) simultaneously. The first step of the proposed approach involves evaluating the performance of alternatives with respect to different types of criteria. The ratings of alternatives with respect to objective and subjective criteria are evaluated by simulation-based optimization and fuzzy linguistic quantifiers, respectively. Subjective and objective uncertainties related to the input information are handled through linking fuzziness and randomness together. Fuzzy decision making helps entail the linguistic uncertainty and a Monte Carlo simulation process is used to map stochastic uncertainty. With this framework, the overall performance of each alternative is calculated using an Order Weighted Averaging (OWA) aggregation operator accounting for decision makers' experience and opinions. Finally, ranking is achieved by conducting pair-wise comparison of management alternatives. This has been done on the basis of the risk defined by the probability of obtaining an acceptable ranking and mean difference in total performance for the pair of management alternatives. The proposed methodology is tested in a real-world hydrosystem, to find effective and robust intervention strategies for the management of a coastal aquifer system affected by saltwater intrusion due to excessive groundwater extraction for irrigated agriculture and municipal use. The results show that the approach gives useful support for robust decision-making and is sensitive to the decision makers' degree of optimism.

Modelling heterogeneity variances in multiple treatment comparison meta-analysis – Are informative priors the better solution?

PubMed Central

2013-01-01

Background Multiple treatment comparison (MTC) meta-analyses are commonly modeled in a Bayesian framework, and weakly informative priors are typically preferred to mirror familiar data driven frequentist approaches. Random-effects MTCs have commonly modeled heterogeneity under the assumption that the between-trial variance for all involved treatment comparisons are equal (i.e., the ‘common variance’ assumption). This approach ‘borrows strength’ for heterogeneity estimation across treatment comparisons, and thus, ads valuable precision when data is sparse. The homogeneous variance assumption, however, is unrealistic and can severely bias variance estimates. Consequently 95% credible intervals may not retain nominal coverage, and treatment rank probabilities may become distorted. Relaxing the homogeneous variance assumption may be equally problematic due to reduced precision. To regain good precision, moderately informative variance priors or additional mathematical assumptions may be necessary. Methods In this paper we describe four novel approaches to modeling heterogeneity variance - two novel model structures, and two approaches for use of moderately informative variance priors. We examine the relative performance of all approaches in two illustrative MTC data sets. We particularly compare between-study heterogeneity estimates and model fits, treatment effect estimates and 95% credible intervals, and treatment rank probabilities. Results In both data sets, use of moderately informative variance priors constructed from the pair wise meta-analysis data yielded the best model fit and narrower credible intervals. Imposing consistency equations on variance estimates, assuming variances to be exchangeable, or using empirically informed variance priors also yielded good model fits and narrow credible intervals. The homogeneous variance model yielded high precision at all times, but overall inadequate estimates of between-trial variances. Lastly, treatment rankings were similar among the novel approaches, but considerably different when compared with the homogenous variance approach. Conclusions MTC models using a homogenous variance structure appear to perform sub-optimally when between-trial variances vary between comparisons. Using informative variance priors, assuming exchangeability or imposing consistency between heterogeneity variances can all ensure sufficiently reliable and realistic heterogeneity estimation, and thus more reliable MTC inferences. All four approaches should be viable candidates for replacing or supplementing the conventional homogeneous variance MTC model, which is currently the most widely used in practice. PMID:23311298

Estimating willingness to accept using paired comparison choice experiments: tests of robustness

Treesearch

David C. Kingsley; Thomas C. Brown

2013-01-01

Paired comparison (PC) choice experiments offer researchers and policy-makers an alternative nonmarket valuation method particularly apt when a ranking of the public's priorities across policy alternatives is paramount. Similar to contingent valuation, PC choice experiments estimate the total value associated with a specific environmental good or service. Similar...

Estimation of Effect Size from a Series of Experiments Involving Paired Comparisons.

ERIC Educational Resources Information Center

Gibbons, Robert D.; And Others

1993-01-01

A distribution theory is derived for a G. V. Glass-type (1976) estimator of effect size from studies involving paired comparisons. The possibility of combining effect sizes from studies involving a mixture of related and unrelated samples is also explored. Resulting estimates are illustrated using data from previous psychiatric research. (SLD)

Preference uncertainty, preference learning, and paired comparison experiments

Treesearch

David C. Kingsley; Thomas C. Brown

2010-01-01

Results from paired comparison experiments suggest that as respondents progress through a sequence of binary choices they become more consistent, apparently fine-tuning their preferences. Consistency may be indicated by the variance of the estimated valuation distribution measured by the error term in the random utility model. A significant reduction in the variance is...

Impact of deep learning on the normalization of reconstruction kernel effects in imaging biomarker quantification: a pilot study in CT emphysema

NASA Astrophysics Data System (ADS)

Jin, Hyeongmin; Heo, Changyong; Kim, Jong Hyo

2018-02-01

Differing reconstruction kernels are known to strongly affect the variability of imaging biomarkers and thus remain as a barrier in translating the computer aided quantification techniques into clinical practice. This study presents a deep learning application to CT kernel conversion which converts a CT image of sharp kernel to that of standard kernel and evaluates its impact on variability reduction of a pulmonary imaging biomarker, the emphysema index (EI). Forty cases of low-dose chest CT exams obtained with 120kVp, 40mAs, 1mm thickness, of 2 reconstruction kernels (B30f, B50f) were selected from the low dose lung cancer screening database of our institution. A Fully convolutional network was implemented with Keras deep learning library. The model consisted of symmetric layers to capture the context and fine structure characteristics of CT images from the standard and sharp reconstruction kernels. Pairs of the full-resolution CT data set were fed to input and output nodes to train the convolutional network to learn the appropriate filter kernels for converting the CT images of sharp kernel to standard kernel with a criterion of measuring the mean squared error between the input and target images. EIs (RA950 and Perc15) were measured with a software package (ImagePrism Pulmo, Seoul, South Korea) and compared for the data sets of B50f, B30f, and the converted B50f. The effect of kernel conversion was evaluated with the mean and standard deviation of pair-wise differences in EI. The population mean of RA950 was 27.65 +/- 7.28% for B50f data set, 10.82 +/- 6.71% for the B30f data set, and 8.87 +/- 6.20% for the converted B50f data set. The mean of pair-wise absolute differences in RA950 between B30f and B50f is reduced from 16.83% to 1.95% using kernel conversion. Our study demonstrates the feasibility of applying the deep learning technique for CT kernel conversion and reducing the kernel-induced variability of EI quantification. The deep learning model has a potential to improve the reliability of imaging biomarker, especially in evaluating the longitudinal changes of EI even when the patient CT scans were performed with different kernels.

Cool Astronomy: Education and Public Outreach for the WISE mission

NASA Astrophysics Data System (ADS)

Mendez, Bryan J.

2011-01-01

The Education and Public Outreach (E/PO) program of the Wide-field Infrared Survey Explorer (WISE) aims to educate and engage students, teachers, and the general public in the endeavor of science. We bring a collection of accomplished professionals in formal and informal astronomy education from around the nation to create learning materials and experiences that appeal to broad audiences. Our E/PO program trains teachers in science, technology, engineering, and mathematics (STEM) topics related to WISE; creates standards-based classroom resources and lessons using WISE data and WISE-related STEM topics; develops interactive programming for museums and science centers; and inspires the public with WISE science and images.

Munc18-1-regulated stage-wise SNARE assembly underlying synaptic exocytosis.

PubMed

Ma, Lu; Rebane, Aleksander A; Yang, Guangcan; Xi, Zhiqun; Kang, Yuhao; Gao, Ying; Zhang, Yongli

2015-12-23

Synaptic-soluble N-ethylmaleimide-sensitive factor attachment receptor (SNARE) proteins couple their stage-wise folding/assembly to rapid exocytosis of neurotransmitters in a Munc18-1-dependent manner. The functions of the different assembly stages in exocytosis and the role of Munc18-1 in SNARE assembly are not well understood. Using optical tweezers, we observed four distinct stages of assembly in SNARE N-terminal, middle, C-terminal, and linker domains (or NTD, MD, CTD, and LD, respectively). We found that SNARE layer mutations differentially affect SNARE assembly. Comparison of their effects on SNARE assembly and on exocytosis reveals that NTD and CTD are responsible for vesicle docking and fusion, respectively, whereas MD regulates SNARE assembly and fusion. Munc18-1 initiates SNARE assembly and structures t-SNARE C-terminus independent of syntaxin N-terminal regulatory domain (NRD) and stabilizes the half-zippered SNARE complex dependent upon the NRD. Our observations demonstrate distinct functions of SNARE domains whose assembly is intimately chaperoned by Munc18-1.

Optimum stacking sequence design of laminated composite circular plates with curvilinear fibres by a layer-wise optimization method

NASA Astrophysics Data System (ADS)

Guenanou, A.; Houmat, A.

2018-05-01

The optimum stacking sequence design for the maximum fundamental frequency of symmetrically laminated composite circular plates with curvilinear fibres is investigated for the first time using a layer-wise optimization method. The design variables are two fibre orientation angles per layer. The fibre paths are constructed using the method of shifted paths. The first-order shear deformation plate theory and a curved square p-element are used to calculate the objective function. The blending function method is used to model accurately the geometry of the circular plate. The equations of motion are derived using Lagrange's method. The numerical results are validated by means of a convergence test and comparison with published values for symmetrically laminated composite circular plates with rectilinear fibres. The material parameters, boundary conditions, number of layers and thickness are shown to influence the optimum solutions to different extents. The results should serve as a benchmark for optimum stacking sequences of symmetrically laminated composite circular plates with curvilinear fibres.

Pharmacological treatments in asthma-affected horses: A pair-wise and network meta-analysis.

PubMed

Calzetta, L; Roncada, P; di Cave, D; Bonizzi, L; Urbani, A; Pistocchini, E; Rogliani, P; Matera, M G

2017-11-01

Equine asthma is a disease characterised by reversible airflow obstruction, bronchial hyper-responsiveness and airway inflammation following exposure of susceptible horses to specific airborne agents. Although clinical remission can be achieved in a low-airborne dust environment, repeated exacerbations may lead to irreversible airway remodelling. The available data on the pharmacotherapy of equine asthma result from several small studies, and no head-to-head clinical trials have been conducted among the available medications. To assess the impact of the pharmacological interventions in equine asthma and compare the effect of different classes of drugs on lung function. Pair-wise and network meta-analysis. Literature searches for clinical trials on the pharmacotherapy of equine asthma were performed. The risk of publication bias was assessed by funnel plots and Egger's test. Changes in maximum transpulmonary or pleural pressure, pulmonary resistance and dynamic lung compliance vs. control were analysed via random-effects models and Bayesian networks. The results obtained from 319 equine asthma-affected horses were extracted from 32 studies. Bronchodilators, corticosteroids and chromones improved maximum transpulmonary or pleural pressure (range: -8.0 to -21.4 cmH 2 O; P<0.001). Bronchodilators, corticosteroids and furosemide reduced pulmonary resistance (range: -1.2 to -1.9 cmH 2 O/L/s; P<0.001), and weakly increased dynamic lung compliance. Inhaled β 2 -adrenoreceptor (β 2 -AR) agonists and inhaled corticosteroids had the highest probability of being the best therapies. Long-term treatments were more effective than short-term treatments. Weak publication bias was detected. This study demonstrates that long-term treatments with inhaled corticosteroids and long-acting β 2 -AR agonists may represent the first choice for treating equine asthma. Further high quality clinical trials are needed to clarify whether inhaled bronchodilators should be preferred to inhaled corticosteroids or vice versa, and to investigate the potential superiority of combination therapy in equine asthma. © 2017 EVJ Ltd.

Simulating Water Markets to Help Design Water Rights Regimes

NASA Astrophysics Data System (ADS)

Harou, J. J.; Erfani, T.; Huskova, I.; Binions, O.

2012-12-01

In many catchments in England no further licenses are available from the Environmental regulator that provides them. The possibility of trading water between license holders has been recognized as a potentially effective and economically efficient strategy to mitigate increasing scarcity. Although trading licenses has been possible since several years, it very rarely happens (roughly 50 trades in 8 years). Several barriers to trade exist including lack of sufficient and prolonged scarcity, license-holder unwillingness to risk future renewal, likelihood license will be downgraded during a trade, duration of time required for approving a trade, etc. Regulators seek to make policy changes so that their inability to grant new licenses will not harm the local and national economy. What policy changes will most cost-effectively increase trading and allow it to effectively reduce the economic cost of scarcity events? A screening tool that could help evaluate problems and advantages of different regulatory solutions, and that could serve to test, assuming transaction costs can be quantified, their effect on trading under specific conditions would be useful. We propose such a water market simulator that predicts economically efficient pair-wise trade (between willing buyers and sellers) and represents the interaction of trades with natural hydrological flows, engineered infrastructure and a particular regulatory regime. The model emulates license-holders' willingness to engage in short-term trade transactions. In their initial form different 'agents' (license holders) are represented using an economic benefit function of water use which is supplemented by rules to represent behavioral or other characteristics of realistic system behavior. A case study based on the river Ouse basin (UK) is made to test the model. The model simulates the catchment weekly over several years considering reservoirs and pair-wise specific transaction costs. Several regulatory policies are tested by evaluating their possible impact on transaction costs and then verifying impact on the number and type of predicted transactions.

Extent of Linkage Disequilibrium in the Domestic Cat, Felis silvestris catus, and Its Breeds

PubMed Central

Alhaddad, Hasan; Khan, Razib; Grahn, Robert A.; Gandolfi, Barbara; Mullikin, James C.; Cole, Shelley A.; Gruffydd-Jones, Timothy J.; Häggström, Jens; Lohi, Hannes; Longeri, Maria; Lyons, Leslie A.

2013-01-01

Domestic cats have a unique breeding history and can be used as models for human hereditary and infectious diseases. In the current era of genome-wide association studies, insights regarding linkage disequilibrium (LD) are essential for efficient association studies. The objective of this study is to investigate the extent of LD in the domestic cat, Felis silvestris catus, particularly within its breeds. A custom illumina GoldenGate Assay consisting of 1536 single nucleotide polymorphisms (SNPs) equally divided over ten 1 Mb chromosomal regions was developed, and genotyped across 18 globally recognized cat breeds and two distinct random bred populations. The pair-wise LD descriptive measure (r 2) was calculated between the SNPs in each region and within each population independently. LD decay was estimated by determining the non-linear least-squares of all pair-wise estimates as a function of distance using established models. The point of 50% decay of r2 was used to compare the extent of LD between breeds. The longest extent of LD was observed in the Burmese breed, where the distance at which r2 ≈ 0.25 was ∼380 kb, comparable to several horse and dog breeds. The shortest extent of LD was found in the Siberian breed, with an r2 ≈ 0.25 at approximately 17 kb, comparable to random bred cats and human populations. A comprehensive haplotype analysis was also conducted. The haplotype structure of each region within each breed mirrored the LD estimates. The LD of cat breeds largely reflects the breeds’ population history and breeding strategies. Understanding LD in diverse populations will contribute to an efficient use of the newly developed SNP array for the cat in the design of genome-wide association studies, as well as to the interpretation of results for the fine mapping of disease and phenotypic traits. PMID:23308248

Polar Desolvation and Position 226 of Pancreatic and Neutrophil Elastases Are Crucial to their Affinity for the Kunitz-Type Inhibitors ShPI-1 and ShPI-1/K13L.

PubMed

Hernández González, Jorge Enrique; García-Fernández, Rossana; Valiente, Pedro Alberto

2015-01-01

The Kunitz-type protease inhibitor ShPI-1 inhibits human neutrophil elastase (HNE, Ki = 2.35·10-8 M) but does not interact with the porcine pancreatic elastase (PPE); whereas its P1 site variant, ShPI-1/K13L, inhibits both HNE and PPE (Ki = 1.3·10-9 M, and Ki = 1.2·10-8 M, respectively). By employing a combination of molecular modeling tools, e.g., structural alignment, molecular dynamics simulations and Molecular Mechanics Generalized-Born/Poisson-Boltzmann Surface Area free energy calculations, we showed that D226 of HNE plays a critical role in the interaction of this enzyme with ShPI-1 through the formation of a strong salt bridge and hydrogen bonds with K13 at the inhibitor's P1 site, which compensate the unfavorable polar-desolvation penalty of the latter residue. Conversely, T226 of PPE is unable to establish strong interactions with K13, thereby precluding the insertion of K13 side-chain into the S1 subsite of this enzyme. An alternative conformation of K13 site-chain placed at the entrance of the S1 subsite of PPE, similar to that observed in the crystal structure of ShPI-1 in complex with chymotrypsin (PDB: 3T62), is also unfavorable due to the lack of stabilizing pair-wise interactions. In addition, our results suggest that the higher affinity of ShPI-1/K13L for both elastases mainly arises from the lower polar-desolvation penalty of L13 compared to that of K13, and not from stronger pair-wise interactions of the former residue with those of each enzyme. These results provide insights into the PPE and HNE inhibition and may contribute to the design of more potent and/or specific inhibitors toward one of these proteases.

Extent of linkage disequilibrium in the domestic cat, Felis silvestris catus, and its breeds.

PubMed

Alhaddad, Hasan; Khan, Razib; Grahn, Robert A; Gandolfi, Barbara; Mullikin, James C; Cole, Shelley A; Gruffydd-Jones, Timothy J; Häggström, Jens; Lohi, Hannes; Longeri, Maria; Lyons, Leslie A

2013-01-01

Domestic cats have a unique breeding history and can be used as models for human hereditary and infectious diseases. In the current era of genome-wide association studies, insights regarding linkage disequilibrium (LD) are essential for efficient association studies. The objective of this study is to investigate the extent of LD in the domestic cat, Felis silvestris catus, particularly within its breeds. A custom illumina GoldenGate Assay consisting of 1536 single nucleotide polymorphisms (SNPs) equally divided over ten 1 Mb chromosomal regions was developed, and genotyped across 18 globally recognized cat breeds and two distinct random bred populations. The pair-wise LD descriptive measure (r(2)) was calculated between the SNPs in each region and within each population independently. LD decay was estimated by determining the non-linear least-squares of all pair-wise estimates as a function of distance using established models. The point of 50% decay of r(2) was used to compare the extent of LD between breeds. The longest extent of LD was observed in the Burmese breed, where the distance at which r(2) ≈ 0.25 was ∼380 kb, comparable to several horse and dog breeds. The shortest extent of LD was found in the Siberian breed, with an r(2) ≈ 0.25 at approximately 17 kb, comparable to random bred cats and human populations. A comprehensive haplotype analysis was also conducted. The haplotype structure of each region within each breed mirrored the LD estimates. The LD of cat breeds largely reflects the breeds' population history and breeding strategies. Understanding LD in diverse populations will contribute to an efficient use of the newly developed SNP array for the cat in the design of genome-wide association studies, as well as to the interpretation of results for the fine mapping of disease and phenotypic traits.

Evaluation of Automated and Semi-Automated Scoring of Polysomnographic Recordings from a Clinical Trial Using Zolpidem in the Treatment of Insomnia

PubMed Central

Svetnik, Vladimir; Ma, Junshui; Soper, Keith A.; Doran, Scott; Renger, John J.; Deacon, Steve; Koblan, Ken S.

2007-01-01

Objective: To evaluate the performance of 2 automated systems, Morpheus and Somnolyzer24X7, with various levels of human review/editing, in scoring polysomnographic (PSG) recordings from a clinical trial using zolpidem in a model of transient insomnia. Methods: 164 all-night PSG recordings from 82 subjects collected during 2 nights of sleep, one under placebo and one under zolpidem (10 mg) treatment were used. For each recording, 6 different methods were used to provide sleep stage scores based on Rechtschaffen & Kales criteria: 1) full manual scoring, 2) automated scoring by Morpheus 3) automated scoring by Somnolyzer24X7, 4) automated scoring by Morpheus with full manual review, 5) automated scoring by Morpheus with partial manual review, 6) automated scoring by Somnolyzer24X7 with partial manual review. Ten traditional clinical efficacy measures of sleep initiation, maintenance, and architecture were calculated. Results: Pair-wise epoch-by-epoch agreements between fully automated and manual scores were in the range of intersite manual scoring agreements reported in the literature (70%-72%). Pair-wise epoch-by-epoch agreements between automated scores manually reviewed were higher (73%-76%). The direction and statistical significance of treatment effect sizes using traditional efficacy endpoints were essentially the same whichever method was used. As the degree of manual review increased, the magnitude of the effect size approached those estimated with fully manual scoring. Conclusion: Automated or semi-automated sleep PSG scoring offers valuable alternatives to costly, time consuming, and intrasite and intersite variable manual scoring, especially in large multicenter clinical trials. Reduction in scoring variability may also reduce the sample size of a clinical trial. Citation: Svetnik V; Ma J; Soper KA; Doran S; Renger JJ; Deacon S; Koblan KS. Evaluation of automated and semi-automated scoring of polysomnographic recordings from a clinical trial using zolpidem in the treatment of insomnia. SLEEP 2007;30(11):1562-1574. PMID:18041489

Public awareness and misunderstanding about DrinkWise Australia: a cross-sectional survey of Australian adults.

PubMed

Brennan, Emily; Wakefield, Melanie A; Durkin, Sarah J; Jernigan, David H; Dixon, Helen G; Pettigrew, Simone

2017-08-01

DrinkWise Australia is an alcohol industry Social Aspects/Public Relations Organisation (SAPRO). We assessed the Australian public's awareness of DrinkWise, beliefs about its funding source, and associations between funding beliefs and perceptions of DrinkWise. A total of 467 adult weekly drinkers completed an online cross-sectional survey in February 2016. Half the sample had heard of DrinkWise (48.6%); of these, the proportion aware that DrinkWise is industry funded (37.0%) was much smaller than the proportion believing it receives government funding (84.1%). Respondents who incorrectly believed DrinkWise receives government funding were more likely to hold a favourable perception of the organisation's credibility, trustworthiness and respectability than those who did not believe it receives government funding (75.9% vs. 58.3%; p=0.032). The drinking population is vulnerable to believing that alcohol industry public relations organisations such as DrinkWise are government funded, which in turn is associated with more favourable perceptions of the organisation's credibility, trustworthiness, and respectability. Implications for public health: Favourable perceptions of DrinkWise may enhance the industry's ability to delay or dilute potentially effective alcohol control policies. Future research should investigate whether educating the public about DrinkWise's alcohol industry funding alters the public's perception of how credible, trustworthy and respectable the organisation is. © 2017 The Authors.

WISE PHOTOMETRY FOR 400 MILLION SDSS SOURCES

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

Lang, Dustin; Hogg, David W.; Schlegel, David J., E-mail: dstndstn@gmail.com

2016-02-15

We present photometry of images from the Wide-Field Infrared Survey Explorer (WISE) of over 400 million sources detected by the Sloan Digital Sky Survey (SDSS). We use a “forced photometry” technique, using measured SDSS source positions, star–galaxy classification, and galaxy profiles to define the sources whose fluxes are to be measured in the WISE images. We perform photometry with The Tractor image modeling code, working on our “unWISE” coaddds and taking account of the WISE point-spread function and a noise model. The result is a measurement of the flux of each SDSS source in each WISE band. Many sources havemore » little flux in the WISE bands, so often the measurements we report are consistent with zero given our uncertainties. However, for many sources we get 3σ or 4σ measurements; these sources would not be reported by the “official” WISE pipeline and will not appear in the WISE catalog, yet they can be highly informative for some scientific questions. In addition, these small-signal measurements can be used in stacking analyses at the catalog level. The forced photometry approach has the advantage that we measure a consistent set of sources between SDSS and WISE, taking advantage of the resolution and depth of the SDSS images to interpret the WISE images; objects that are resolved in SDSS but blended together in WISE still have accurate measurements in our photometry. Our results, and the code used to produce them, are publicly available at http://unwise.me.« less

Evaluation of a Pair-Wise Conflict Detection and Resolution Algorithm in a Multiple Aircraft Scenario

NASA Technical Reports Server (NTRS)

Carreno, Victor A.

2002-01-01

The KB3D algorithm is a pairwise conflict detection and resolution (CD&R) algorithm. It detects and generates trajectory vectoring for an aircraft which has been predicted to be in an airspace minima violation within a given look-ahead time. It has been proven, using mechanized theorem proving techniques, that for a pair of aircraft, KB3D produces at least one vectoring solution and that all solutions produced are correct. Although solutions produced by the algorithm are mathematically correct, they might not be physically executable by an aircraft or might not solve multiple aircraft conflicts. This paper describes a simple solution selection method which assesses all solutions generated by KB3D and determines the solution to be executed. The solution selection method and KB3D are evaluated using a simulation in which N aircraft fly in a free-flight environment and each aircraft in the simulation uses KB3D to maintain separation. Specifically, the solution selection method filters KB3D solutions which are procedurally undesirable or physically not executable and uses a predetermined criteria for selection.

Inductive Game Theory and the Dynamics of Animal Conflict

PubMed Central

DeDeo, Simon; Krakauer, David C.; Flack, Jessica C.

2010-01-01

Conflict destabilizes social interactions and impedes cooperation at multiple scales of biological organization. Of fundamental interest are the causes of turbulent periods of conflict. We analyze conflict dynamics in an monkey society model system. We develop a technique, Inductive Game Theory, to extract directly from time-series data the decision-making strategies used by individuals and groups. This technique uses Monte Carlo simulation to test alternative causal models of conflict dynamics. We find individuals base their decision to fight on memory of social factors, not on short timescale ecological resource competition. Furthermore, the social assessments on which these decisions are based are triadic (self in relation to another pair of individuals), not pairwise. We show that this triadic decision making causes long conflict cascades and that there is a high population cost of the large fights associated with these cascades. These results suggest that individual agency has been over-emphasized in the social evolution of complex aggregates, and that pair-wise formalisms are inadequate. An appreciation of the empirical foundations of the collective dynamics of conflict is a crucial step towards its effective management. PMID:20485557

Inductive game theory and the dynamics of animal conflict.

PubMed

DeDeo, Simon; Krakauer, David C; Flack, Jessica C

2010-05-13

Conflict destabilizes social interactions and impedes cooperation at multiple scales of biological organization. Of fundamental interest are the causes of turbulent periods of conflict. We analyze conflict dynamics in an monkey society model system. We develop a technique, Inductive Game Theory, to extract directly from time-series data the decision-making strategies used by individuals and groups. This technique uses Monte Carlo simulation to test alternative causal models of conflict dynamics. We find individuals base their decision to fight on memory of social factors, not on short timescale ecological resource competition. Furthermore, the social assessments on which these decisions are based are triadic (self in relation to another pair of individuals), not pairwise. We show that this triadic decision making causes long conflict cascades and that there is a high population cost of the large fights associated with these cascades. These results suggest that individual agency has been over-emphasized in the social evolution of complex aggregates, and that pair-wise formalisms are inadequate. An appreciation of the empirical foundations of the collective dynamics of conflict is a crucial step towards its effective management.

Eye movements reflect and shape strategies in fraction comparison

PubMed Central

Ischebeck, Anja; Weilharter, Marina; Körner, Christof

2016-01-01

The comparison of fractions is a difficult task that can often be facilitated by separately comparing components (numerators and denominators) of the fractions—that is, by applying so-called component-based strategies. The usefulness of such strategies depends on the type of fraction pair to be compared. We investigated the temporal organization and the flexibility of strategy deployment in fraction comparison by evaluating sequences of eye movements in 20 young adults. We found that component-based strategies could account for the response times and the overall number of fixations observed for the different fraction pairs. The analysis of eye movement sequences showed that the initial eye movements in a trial were characterized by stereotypical scanning patterns indicative of an exploratory phase that served to establish the kind of fraction pair presented. Eye movements that followed this phase adapted to the particular type of fraction pair and indicated the deployment of specific comparison strategies. These results demonstrate that participants employ eye movements systematically to support strategy use in fraction comparison. Participants showed a remarkable flexibility to adapt to the most efficient strategy on a trial-by-trial basis. Our results confirm the value of eye movement measurements in the exploration of strategic adaptation in complex tasks. PMID:26039819

Identification and Small Sample Estimation of Thurstone's Unrestricted Model for Paired Comparisons Data

ERIC Educational Resources Information Center

Maydeu-Olivares, Alberto; Hernandez, Adolfo

2007-01-01

The interpretation of a Thurstonian model for paired comparisons where the utilities' covariance matrix is unrestricted proved to be difficult due to the comparative nature of the data. We show that under a suitable constraint the utilities' correlation matrix can be estimated, yielding a readily interpretable solution. This set of identification…

Neural Correlates of Encoding Predict Infants' Memory in the Paired-Comparison Procedure

ERIC Educational Resources Information Center

Snyder, Kelly A.

2010-01-01

The present study used event-related potentials (ERPs) to monitor infant brain activity during the initial encoding of a previously novel visual stimulus, and examined whether ERP measures of encoding predicted infants' subsequent performance on a visual memory task (i.e., the paired-comparison task). A late slow wave component of the ERP measured…

Paired comparison estimates of willingness to accept versus contingent valuation estimates of willingness to pay

Treesearch

John B. Loomis; George Peterson; Patricia A. Champ; Thomas C. Brown; Beatrice Lucero

1998-01-01

Estimating empirical measures of an individual's willingness to accept that are consistent with conventional economic theory, has proven difficult. The method of paired comparison offers a promising approach to estimate willingness to accept. This method involves having individuals make binary choices between receiving a particular good or a sum of money....

Inhibition of WISE preserves renal allograft function.

PubMed

Qian, Xueming; Yuan, Xiaodong; Vonderfecht, Steven; Ge, Xupeng; Lee, Jae; Jurisch, Anke; Zhang, Li; You, Andrew; Fitzpatrick, Vincent D; Williams, Alexia; Valente, Eliane G; Pretorius, Jim; Stevens, Jennitte L; Tipton, Barbara; Winters, Aaron G; Graham, Kevin; Harriss, Lindsey; Baker, Daniel M; Damore, Michael; Salimi-Moosavi, Hossein; Gao, Yongming; Elkhal, Abdallah; Paszty, Chris; Simonet, W Scott; Richards, William G; Tullius, Stefan G

2013-01-01

Wnt-modulator in surface ectoderm (WISE) is a secreted modulator of Wnt signaling expressed in the adult kidney. Activation of Wnt signaling has been observed in renal transplants developing interstitial fibrosis and tubular atrophy; however, whether WISE contributes to chronic changes is not well understood. Here, we found moderate to high expression of WISE mRNA in a rat model of renal transplantation and in kidneys from normal rats. Treatment with a neutralizing antibody against WISE improved proteinuria and graft function, which correlated with higher levels of β-catenin protein in kidney allografts. In addition, treatment with the anti-WISE antibody reduced infiltration of CD68(+) macrophages and CD8(+) T cells, attenuated glomerular and interstitial injury, and decreased biomarkers of renal injury. This treatment reduced expression of genes involved in immune responses and in fibrogenic pathways. In summary, WISE contributes to renal dysfunction by promoting tubular atrophy and interstitial fibrosis.

DriveWise: an interdisciplinary hospital-based driving assessment program.

PubMed

O'Connor, Margaret G; Kapust, Lissa R; Hollis, Ann M

2008-01-01

Health care professionals working with the elderly have opportunities through research and clinical practice to shape public policy affecting the older driver. This article describes DriveWise, an interdisciplinary hospital-based driving assessment program developed in response to clinical concerns about the driving safety of individuals with medical conditions. DriveWise clinicians use evidence-based, functional assessments to determine driving competence. In addition, the program was designed to meet the emotional needs of individuals whose driving safety has been called into question. To date, approximately 380 participants have been assessed through DriveWise. The following report details the DriveWise mission, DriveWise team members, and road test results. We continue to refine the assessment process to promote safety and support the dignity and independence of all participants. The DriveWise interdisciplinary approach to practice is a concrete example of how gerontological education across professions can have direct benefits to the older adult.

Measuring the Test-Wiseness of Medical Students.

ERIC Educational Resources Information Center

Harvill, Leo M.

The objectives for this study were to: (1) develop a valid, reliable measure of test-wiseness with equivalent forms for use with students in the health sciences; and (2) determine the level of test-wiseness of entering medical students. The test-wiseness areas included in this study were: similar options, umbrella term, item give-away, convergence…

WE-H-207A-05: Spatial Co-Localization of F-18 NaF Vs. F-18 FDG Defined Disease Volumes

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

Ferjancic, P; Harmon, S; Jeraj, R

Purpose: Both [F-18]NaF and [F-18]FDG show promise for quantitative PET/CT assessment in metastatic prostate cancer to bone. Broad agreement between the tracers has been shown but voxel-wise correspondence has not been explored in depth. This study evaluates the spatial co-localization of [F-18]NaF PET and [F-18]FDG PET in bone lesions. Methods: Seventy-three lesion contours were identified in six patients receiving dynamic NaF PET/CT and FDG PET/CT scans two hours apart using identical fields-of-view. Tracer uptake (SUV) reflecting 60 minutes post-injection was modeled from kinetic parameters. Lesions were segmented by a physician separately on NaF PET and FDG PET. PET images weremore » rigidly aligned using skeletal references on CT images. Lesion size, degree of overlap, voxel-wise tracer uptake values (SUV), and CT density distributions were compared using Dice coefficient, Positive Predictive Value (PPV), and Spearman rank correlation tests. Results: Across all patients, 42 lesions were identified on NaF PET (median 1.4 cm{sup 3}, range <1–204 cm{sup 3}) compared to 31 using FDG PET (median 1.8 cm{sup 3}, range <1–244 cm{sup 3}). Spatial cooccurrence was found in 25 lesion pairs. Lesions on NaF PET had PPV of 0.91 and on FDG a PPV of 0.65. Overall, NaF-defined lesions were 47% (±24%) larger by volume with moderate overlap to FDG, resulting in mean Dice coefficient of 34% (±22%). In areas of overlap, voxel-wise correlation of NaF and FDG SUV was moderate (ρ=0.56). Expanding to regions of non-spatial overlap, voxels contained in FDG-only contours were almost exclusively low HU (median 118), compared to dense regions of NaF-only voxels (median 250). In sclerotic sub-volumes (HU > 300) NaF-defined contours encompassed 83% of total FDG volume. Conclusion: Moderate voxel-wise correlation of FDG and NaF PET/CT uptake was observed. Spatial discrepancies in FDG and NaF PET/CT imaging of boney metastases could be influenced by poor sensitivity of FDG PET/CT in sclerotic regions. Funded by Prostate Cancer Foundation.« less

The Faintest WISE Debris Disks: Enhanced Methods for Detection and Verification

NASA Astrophysics Data System (ADS)

Patel, Rahul I.; Metchev, Stanimir A.; Heinze, Aren; Trollo, Joseph

2017-02-01

In an earlier study, we reported nearly 100 previously unknown dusty debris disks around Hipparcos main-sequence stars within 75 pc by selecting stars with excesses in individual WISE colors. Here, we further scrutinize the Hipparcos 75 pc sample to (1) gain sensitivity to previously undetected, fainter mid-IR excesses and (2) remove spurious excesses contaminated by previously unidentified blended sources. We improve on our previous method by adopting a more accurate measure of the confidence threshold for excess detection and by adding an optimally weighted color average that incorporates all shorter-wavelength WISE photometry, rather than using only individual WISE colors. The latter is equivalent to spectral energy distribution fitting, but only over WISE bandpasses. In addition, we leverage the higher-resolution WISE images available through the unWISE.me image service to identify contaminated WISE excesses based on photocenter offsets among the W3- and W4-band images. Altogether, we identify 19 previously unreported candidate debris disks. Combined with the results from our earlier study, we have found a total of 107 new debris disks around 75 pc Hipparcos main-sequence stars using precisely calibrated WISE photometry. This expands the 75 pc debris disk sample by 22% around Hipparcos main-sequence stars and by 20% overall (including non-main-sequence and non-Hipparcos stars).

Wise regulates bone deposition through genetic interactions with Lrp5.

PubMed

Ellies, Debra L; Economou, Androulla; Viviano, Beth; Rey, Jean-Philippe; Paine-Saunders, Stephenie; Krumlauf, Robb; Saunders, Scott

2014-01-01

In this study using genetic approaches in mouse we demonstrate that the secreted protein Wise plays essential roles in regulating early bone formation through its ability to modulate Wnt signaling via interactions with the Lrp5 co-receptor. In Wise-/- mutant mice we find an increase in the rate of osteoblast proliferation and a transient increase in bone mineral density. This change in proliferation is dependent upon Lrp5, as Wise;Lrp5 double mutants have normal bone mass. This suggests that Wise serves as a negative modulator of Wnt signaling in active osteoblasts. Wise and the closely related protein Sclerostin (Sost) are expressed in osteoblast cells during temporally distinct early and late phases in a manner consistent with the temporal onset of their respective increased bone density phenotypes. These data suggest that Wise and Sost may have common roles in regulating bone development through their ability to control the balance of Wnt signaling. We find that Wise is also required to potentiate proliferation in chondrocytes, serving as a potential positive modulator of Wnt activity. Our analyses demonstrate that Wise plays a key role in processes that control the number of osteoblasts and chondrocytes during bone homeostasis and provide important insight into mechanisms regulating the Wnt pathway during skeletal development.

Identification of coffee bean varieties using hyperspectral imaging: influence of preprocessing methods and pixel-wise spectra analysis.

PubMed

Zhang, Chu; Liu, Fei; He, Yong

2018-02-01

Hyperspectral imaging was used to identify and to visualize the coffee bean varieties. Spectral preprocessing of pixel-wise spectra was conducted by different methods, including moving average smoothing (MA), wavelet transform (WT) and empirical mode decomposition (EMD). Meanwhile, spatial preprocessing of the gray-scale image at each wavelength was conducted by median filter (MF). Support vector machine (SVM) models using full sample average spectra and pixel-wise spectra, and the selected optimal wavelengths by second derivative spectra all achieved classification accuracy over 80%. Primarily, the SVM models using pixel-wise spectra were used to predict the sample average spectra, and these models obtained over 80% of the classification accuracy. Secondly, the SVM models using sample average spectra were used to predict pixel-wise spectra, but achieved with lower than 50% of classification accuracy. The results indicated that WT and EMD were suitable for pixel-wise spectra preprocessing. The use of pixel-wise spectra could extend the calibration set, and resulted in the good prediction results for pixel-wise spectra and sample average spectra. The overall results indicated the effectiveness of using spectral preprocessing and the adoption of pixel-wise spectra. The results provided an alternative way of data processing for applications of hyperspectral imaging in food industry.

More Than a Pretty Picture: Making WISE Data Accessible to the Public

NASA Astrophysics Data System (ADS)

Ali, Nancy; Mendez, B.; Fricke, K.; Wright, E. L.; Eisenhardt, P. R.; Cutri, R. M.; Hurt, R.; WISE Team

2011-01-01

NASA's Wide-field Infrared Survey Explorer (WISE) has surveyed the sky in four bands of infrared light, creating a treasure trove of data. This data is of interest not only to the professional astronomical community, but also to educators, students and the general public. The Education and Public Outreach (E/PO) program for WISE is creating opportunities to make WISE data accessible to these audiences through the Internet as well as through teacher professional development programs. Shortly after WISE took its first light image in January 2010, images have been featured weekly on the WISE website. These images serve to engage the general public through "pretty pictures” that are accompanied by educational captions. Social media such as Facebook and Twitter are used to further engage the public with the images. For a more comprehensive view of WISE images, we are creating a guided tour of the infrared sky on the WorldWide Telescope. The public will be able to use the free WorldWide Telescope software to interact with WISE images and listen to narration that describes features of the Universe as seen in infrared light. We are also developing resources for teachers and students to access WISE data when in becomes public in 2011 to learn about astronomical imaging and to conduct authentic scientific investigations.

Three new cool brown dwarfs discovered with the wide-field infrared survey explorer (WISE) and an improved spectrum of the Y0 dwarf wise J041022.71+150248.4

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

Cushing, Michael C.; Kirkpatrick, J. Davy; Gelino, Christopher R.

2014-05-01

As part of a larger search of Wide-field Infrared Survey Explorer (WISE) data for cool brown dwarfs with effective temperatures less than 1000 K, we present the discovery of three new cool brown dwarfs with spectral types later than T7. Using low-resolution, near-infrared spectra obtained with the NASA Infrared Telescope Facility and the Hubble Space Telescope, we derive spectral types of T9.5 for WISE J094305.98+360723.5, T8 for WISE J200050.19+362950.1, and Y0: for WISE J220905.73+271143.9. The identification of WISE J220905.73+271143.9 as a Y dwarf brings the total number of spectroscopically confirmed Y dwarfs to 17. In addition, we present an improvedmore » spectrum (i.e., higher signal-to-noise ratio) of the Y0 dwarf WISE J041022.71+150248.4 that confirms the Cushing et al. classification of Y0. Spectrophotometric distance estimates place all three new brown dwarfs at distances less than 12 pc, with WISE J200050.19+362950.1 lying at a distance of only 3.9-8.0 pc. Finally, we note that brown dwarfs like WISE J200050.19+362950.1 that lie in or near the Galactic plane offer an exciting opportunity to directly measure the mass of a brown dwarf via astrometric microlensing.« less

Mutagenesis: Interactions with a parallel universe.

PubMed

Miller, Jeffrey H

Unexpected observations in mutagenesis research have led to a new perspective in this personal reflection based on years of studying mutagenesis. Many mutagens have been thought to operate via a single principal mechanism, with secondary effects usually resulting in only minor changes in the observed mutation frequencies and spectra. For example, we conceive of base analogs as resulting in direct mispairing as their main mechanism of mutagenesis. Recent studies now show that in fact even these simple mutagens can cause very large and unanticipated effects both in mutation frequencies and in the mutational spectra when used in certain pair-wise combinations. Here we characterize this leap in mutation frequencies as a transport to an alternate universe of mutagenesis. Copyright © 2018 Elsevier B.V. All rights reserved.

Shedding of dual structures in the wake of a surface-mounted low aspect ratio cone

NASA Astrophysics Data System (ADS)

Chen, Zixiang; Martinuzzi, Robert J.

2018-04-01

The periodic shedding of vortex pairs in the turbulent wake of a surface-mounted right cone of aspect ratio 0.867 protruding a thin turbulent boundary layer is investigated experimentally. A phase-averaged volumetric velocity field is reconstructed from planar stereoscopic particle image velocimetry. During a typical (phase-averaged) shedding cycle, counter-rotating base vortices alternately form. These are tilted and stretched to merge with stream-wise tip vortices. The merged structure sheds and is convected downstream. A synthesis of earlier observations suggests that a similar shedding process exists for other low aspect ratio tapered geometries and is more complex than the shedding patterns observed for cantilevered cylinders, despite similarities of the mean flow field structure.

Dynamics and mechanics of motor-filament systems

NASA Astrophysics Data System (ADS)

Kruse, K.; Jülicher, F.

2006-08-01

Motivated by the cytoskeleton of eukaryotic cells, we develop a general framework for describing the large-scale dynamics of an active filament network. In the cytoskeleton, active cross-links are formed by motor proteins that are able to induce relative motion between filaments. Starting from pair-wise interactions of filaments via such active processes, our framework is based on momentum conservation and an analysis of the momentum flux. This allows us to calculate the stresses in the filament network generated by the action of motor proteins. We derive effective theories for the filament dynamics which can be related to continuum theories of active polar gels. As an example, we discuss the stability of homogenous isotropic filament distributions in two spatial dimensions.

An Alternate Set of Basis Functions for the Electromagnetic Solution of Arbitrarily-Shaped, Three-Dimensional, Closed, Conducting Bodies Using Method of Moments

NASA Technical Reports Server (NTRS)

Mackenzie, Anne I.; Baginski, Michael E.; Rao, Sadasiva M.

2008-01-01

In this work, we present an alternate set of basis functions, each defined over a pair of planar triangular patches, for the method of moments solution of electromagnetic scattering and radiation problems associated with arbitrarily-shaped, closed, conducting surfaces. The present basis functions are point-wise orthogonal to the pulse basis functions previously defined. The prime motivation to develop the present set of basis functions is to utilize them for the electromagnetic solution of dielectric bodies using a surface integral equation formulation which involves both electric and magnetic cur- rents. However, in the present work, only the conducting body solution is presented and compared with other data.

DLGP: A database for lineage-conserved and lineage-specific gene pairs in animal and plant genomes.

PubMed

Wang, Dapeng

2016-01-15

The conservation of gene organization in the genome with lineage-specificity is an invaluable resource to decipher their potential functionality with diverse selective constraints, especially in higher animals and plants. Gene pairs appear to be the minimal structure for such kind of gene clusters that tend to reside in their preferred locations, representing the distinctive genomic characteristics in single species or a given lineage. Despite gene families having been investigated in a widespread manner, the definition of gene pair families in various taxa still lacks adequate attention. To address this issue, we report DLGP (http://lcgbase.big.ac.cn/DLGP/) that stores the pre-calculated lineage-based gene pairs in currently available 134 animal and plant genomes and inspect them under the same analytical framework, bringing out a set of innovational features. First, the taxonomy or lineage has been classified into four levels such as Kingdom, Phylum, Class and Order. It adopts all-to-all comparison strategy to identify the possible conserved gene pairs in all species for each gene pair in certain species and reckon those that are conserved in over a significant proportion of species in a given lineage (e.g. Primates, Diptera or Poales) as the lineage-conserved gene pairs. Furthermore, it predicts the lineage-specific gene pairs by retaining the above-mentioned lineage-conserved gene pairs that are not conserved in any other lineages. Second, it carries out pairwise comparison for the gene pairs between two compared species and creates the table including all the conserved gene pairs and the image elucidating the conservation degree of gene pairs in chromosomal level. Third, it supplies gene order browser to extend gene pairs to gene clusters, allowing users to view the evolution dynamics in the gene context in an intuitive manner. This database will be able to facilitate the particular comparison between animals and plants, between vertebrates and arthropods, and between monocots and eudicots, accounting for the significant contribution of gene pairs to speciation and diversification in specific lineages. Copyright © 2015 Elsevier Inc. All rights reserved.

Drop-wise and film-wise water condensation processes occurring on metallic micro-scaled surfaces

NASA Astrophysics Data System (ADS)

Starostin, Anton; Valtsifer, Viktor; Barkay, Zahava; Legchenkova, Irina; Danchuk, Viktor; Bormashenko, Edward

2018-06-01

Water condensation was studied on silanized (superhydrophobic) and fluorinated (superoleophobic) micro-rough aluminum surfaces of the same topography. Condensation on superhydrophobic surfaces occurred via film-wise mechanism, whereas on superoleophobic surfaces it was drop-wise. The difference in the pathways of condensation was attributed to the various energy barriers separating the Cassie and Wenzel wetting states on the investigated surfaces. The higher barriers inherent for superoleophobic surfaces promoted the drop-wise condensation. Triple-stage kinetics of growth of droplets condensed on superoleophobic surfaces is reported and discussed.

Medial prefrontal aberrations in major depressive disorder revealed by cytoarchitectonically informed voxel-based morphometry

PubMed Central

Bludau, Sebastian; Bzdok, Danilo; Gruber, Oliver; Kohn, Nils; Riedl, Valentin; Sorg, Christian; Palomero-Gallagher, Nicola; Müller, Veronika I.; Hoffstaedter, Felix; Amunts, Katrin; Eickhoff, Simon B.

2017-01-01

Objective The heterogeneous human frontal pole has been identified as a node in the dysfunctional network of major depressive disorder. The contribution of the medial (socio-affective) versus lateral (cognitive) frontal pole to major depression pathogenesis is currently unclear. The present study performs morphometric comparison of the microstructurally informed subdivisions of human frontal pole between depressed patients and controls using both uni- and multivariate statistics. Methods Multi-site voxel- and region-based morphometric MRI analysis of 73 depressed patients and 73 matched controls without psychiatric history. Frontal pole volume was first compared between depressed patients and controls by subdivision-wise classical morphometric analysis. In a second approach, frontal pole volume was compared by subdivision-naive multivariate searchlight analysis based on support vector machines. Results Subdivision-wise morphometric analysis found a significantly smaller medial frontal pole in depressed patients with a negative correlation of disease severity and duration. Histologically uninformed multivariate voxel-wise statistics provided converging evidence for structural aberrations specific to the microstructurally defined medial area of the frontal pole in depressed patients. Conclusions Across disparate methods, we demonstrated subregion specificity in the left medial frontal pole volume in depressed patients. Indeed, the frontal pole was shown to structurally and functionally connect to other key regions in major depression pathology like the anterior cingulate cortex and the amygdala via the uncinate fasciculus. Present and previous findings consolidate the left medial portion of the frontal pole as particularly altered in major depression. PMID:26621569

Teaching practical wisdom in medicine through clinical judgement, goals of care, and ethical reasoning.

PubMed

Kaldjian, Lauris Christopher

2010-09-01

Clinical decision making is a challenging task that requires practical wisdom-the practised ability to help patients choose wisely among available diagnostic and treatment options. But practical wisdom is not a concept one typically hears mentioned in medical training and practice. Instead, emphasis is placed on clinical judgement. The author draws from Aristotle and Aquinas to describe the virtue of practical wisdom and compare it with clinical judgement. From this comparison, the author suggests that a more complete understanding of clinical judgement requires its explicit integration with goals of care and ethical values. Although clinicians may be justified in assuming that goals of care and ethical values are implicit in routine decision making, it remains important for training purposes to encourage habits of clinical judgement that are consciously goal-directed and ethically informed. By connecting clinical judgement to patients' goals and values, clinical decisions are more likely to stay focused on the particular interests of individual patients. To cultivate wise clinical judgement among trainees, educational efforts should aim at the integration of clinical judgement, communication with patients about goals of care, and ethical reasoning. But ultimately, training in wise clinical judgement will take years of practice in the company of experienced clinicians who are able to demonstrate practical wisdom by example. By helping trainees develop clinical judgement that incorporates patients' goals of care and ethical reasoning, we may help lessen the risk that 'clinical judgement' will merely express 'the clinician's judgement.'

Economic valuation by the method of paired comparison, with emphasis on evaluation of the transitivity axiom

Treesearch

George L. Peterson; Thomas C. Brown

1998-01-01

The paired comparison (PC) method is used to investigate reliability, transitivity, and decision time for binary choices among goods and sums of money. The PC method reveals inconsistent choices and yields individual preference order over the set of items being compared. The data reported support the transitivity assumption and demonstrate high reliability for...

A one-year neonatal mouse carcinogenesis study of quinacrine dihydrochloride.

PubMed

Cancel, Aida M; Smith, Thomas; Rehkemper, Ursula; Dillberger, John E; Sokal, David; McClain, R Michael

2006-01-01

Quinacrine is an acridine derivative under investigation for its use in nonsurgical female sterilization. Safety issues regarding the carcinogenic potential of quinacrine have been raised because it is mutagenic and clastogenic in vitro. The objective of the study was to evaluate the carcinogenic potential of quinacrine dihydrochloride (quinacrine) in neonatal mice treated with single intraperitoneal doses on postpartum days 8 and 15 and observed for 52 weeks. Neonatal Crl: CD-1 mice of each sex were randomly allocated into four treatment groups (0, 10, 50, and 150 mg/kg), dosed twice with quinacrine suspended in carboxymethylcellulose, observed for 52 weeks post dose, and then euthanized, necropsied, and subjected to a full histopathological examination. In male mice, tumor incidence was not significantly increased at any site at any dose level. In female mice, the incidence of benign uterine endometrial stromal polyps was slightly greater at the mid and high dose (> or = 50 mg/kg), as was the incidence of endometrial hyperplasia. The incidence of polyps in these groups was not significantly greater than in controls by pair-wise comparison but was significantly greater (p = .042) by the linear trend test. The authors conclude that quinacrine administered twice to neonatal mice may have enhanced or accelerated the development of endometrial hyperplasia and uterine stromal polyps at higher doses. Because uterine stromal polyps are a commonly observed benign tumor in older mice, the significance of this finding is unclear and will require a weight of evidence evaluation for a conclusion on the carcinogenic potential of quinacrine.

Regionalisation of Hydrological Indices to Assess Land-Use Change Impacts in the Tropical Andes

NASA Astrophysics Data System (ADS)

Buytaert, W.; Ochoa Tocachi, B. F.

2014-12-01

Andean ecosystems are major water sources for cities and communities located in the Tropical Andes; however, there is a considerable lack of knowledge about their hydrology. Two problems are especially important: (i) the lack of monitoring to assess the impacts of historical land-use and cover change and degradation (LUCCD) at catchment scale, and (ii) the high variability in climatic and hydrological conditions that complicate the evaluation of land management practices. This study analyses how a reliable LUCCD impacts assessment can be performed in an environment of high variability combined with data-scarcity and low-quality records. We use data from participatory hydrological monitoring activities in 20 catchments distributed along the tropical Andes. A set of 46 hydrological indices is calculated and regionalized by relating them to 42 physical catchment properties. Principal Component Analysis (PCA) is performed to maximise available data while minimising redundancy in the sets of variables. Hydrological model parameters are constrained by estimated indices, and different behavioural predictions are assembled to provide a generalised response on which we assess LUCCD impacts. Results from this methodology show that the attributed effects of LUCCD in pair-wise catchment comparisons may be overstated or hidden by different sources of uncertainty, including measurement inaccuracies and model structural errors. We propose extrapolation and evaluation in ungauged catchments as a way to regionalize LUCCD predictions and to provide statistically significant conclusions in the Andean region. These estimations may deliver reliable knowledge to evaluate the hydrological impact of different watershed management practices.

First report of field evolved resistance to agrochemicals in dengue mosquito, Aedes albopictus (Diptera: Culicidae), from Pakistan

PubMed Central

2011-01-01

Background Agrochemicals have been widely used in Pakistan for several years. This exposes mosquito populations, particularly those present around agricultural settings, to an intense selection pressure for insecticide resistance. The aim of the present study was to investigate the toxicity of representative agrochemicals against various populations of Aedes albopictus (Skuse) collected from three different regions from 2008-2010. Results For organophosphates and pyrethroids, the resistance ratios compared with susceptible Lab-PK were in the range of 157-266 fold for chlorpyrifos, 24-52 fold for profenofos, 41-71 fold for triazofos, and 15-26 fold for cypermethrin, 15-53 fold for deltamethrin and 21-58 fold for lambdacyhalothrin. The resistance ratios for carbamates and new insecticides were in the range of 13-22 fold for methomyl, 24-30 fold for thiodicarb, and 41-101 fold for indoxacarb, 14-27 fold for emamectin benzoate and 23-50 fold for spinosad. Pair wise comparisons of the log LC50s of insecticides revealed correlation among several insecticides, suggesting a possible cross resistance mechanism. Moreover, resistance remained stable across 3 years, suggesting field selection for general fitness had also taken place for various populations of Ae. albopictus. Conclusion Moderate to high level of resistance to agrochemicals in Pakistani field populations of Ae. albopictus is reported here first time. The geographic extent of resistance is unknown but, if widespread, may lead to problems in future vector control. PMID:21781290

Evaluating 3D bone tissue engineered constructs with different seeding densities using the alamarBlue assay and the effect on in vivo bone formation.

PubMed

Wilson, C E; Dhert, W J A; Van Blitterswijk, C A; Verbout, A J; De Bruijn, J D

2002-12-01

Bone tissue engineering using patient derived cells seeded onto porous scaffolds has gained much attention in recent years. Evaluating the viability of these 3D constructs is an essential step in optimizing the process. The alamarBlue (aB) assay was evaluated for its potential to follow in vitro cell proliferation on architecturally standardized hydroxyapatite scaffolds. The impact of the aB assayed and seeding density on subsequent in vivo bone formation was investigated. Twelve scaffolds were seeded with various densities from 250 to 2.5x10(6) cells/scaffold and assay by aB at 5 time points during the 7-day culture period. Twelve additional scaffolds were seeded with 2.5x10(5) cells/scaffold. Two control and 2 aB treated scaffolds were subcutaneously implanted into each of 6 nude mice for 6 weeks. Four observers ranked bone formation using a pair wise comparison of histological sections form each mouse. The aB assay successfully followed cell proliferation, however, the diffusion kinetics of the 3D constructs must be considered. The influence of in vitro aB treatment on subsequent in vivo bone formation cannot be ruled out but was not shown to be significant in the current study. The aB assay appears to be quite promising for evaluating a maximum or end-point viability of 3D tissue engineered constructs. Finally, higher seeding densities resulted in more observed bone formation.

Evolutionary Insights from a Genetically Divergent Hantavirus Harbored by the European Common Mole (Talpa europaea)

PubMed Central

Kang, Hae Ji; Bennett, Shannon N.; Sumibcay, Laarni; Arai, Satoru; Hope, Andrew G.; Mocz, Gabor; Song, Jin-Won; Cook, Joseph A.; Yanagihara, Richard

2009-01-01

Background The discovery of genetically distinct hantaviruses in shrews (Order Soricomorpha, Family Soricidae) from widely separated geographic regions challenges the hypothesis that rodents (Order Rodentia, Family Muridae and Cricetidae) are the primordial reservoir hosts of hantaviruses and also predicts that other soricomorphs harbor hantaviruses. Recently, novel hantavirus genomes have been detected in moles of the Family Talpidae, including the Japanese shrew mole (Urotrichus talpoides) and American shrew mole (Neurotrichus gibbsii). We present new insights into the evolutionary history of hantaviruses gained from a highly divergent hantavirus, designated Nova virus (NVAV), identified in the European common mole (Talpa europaea) captured in Hungary. Methodology/Principal Findings Pair-wise alignment and comparison of the full-length S- and L-genomic segments indicated moderately low sequence similarity of 54–65% and 46–63% at the nucleotide and amino acid levels, respectively, between NVAV and representative rodent- and soricid-borne hantaviruses. Despite the high degree of sequence divergence, the predicted secondary structure of the NVAV nucleocapsid protein exhibited the characteristic coiled-coil domains at the amino-terminal end, and the L-segment motifs, typically found in hantaviruses, were well conserved. Phylogenetic analyses, using maximum-likelihood and Bayesian methods, showed that NVAV formed a distinct clade that was evolutionarily distant from all other hantaviruses. Conclusions Newly identified hantaviruses harbored by shrews and moles support long-standing virus-host relationships and suggest that ancestral soricomorphs, rather than rodents, may have been the early or original mammalian hosts. PMID:19582155

Understanding consumer preferences in the context of managed competition: evidence from a choice experiment in Colombia.

PubMed

Trujillo, Antonio J; Ruiz, Fernando; Bridges, John F P; Amaya, Jeannette L; Buttorff, Christine; Quiroga, Angélica M

2012-03-01

In many countries, health insurance coverage is the primary way for individuals to access care. Governments can support access through social insurance programmes; however, after a certain period, governments struggle to achieve universal coverage. Evidence suggests that complex individual behaviour may play a role. Using a choice experiment, this research explored consumer preferences for health insurance in Colombia. We also evaluated whether preferences differed across consumers with differing demographic and health status factors. A household field experiment was conducted in Bogotá in 2010. The sample consisted of 109 uninsured and 133 low-income insured individuals. Each individual evaluated 12 pair-wise comparisons of hypothetical health plans. We focused on six characteristics of health insurance: premium, out-of-pocket expenditure, chronic condition coverage, quality of care, family coverage and sick leave. A main effects orthogonal design was used to derive the 72 scenarios used in the choice experiment. Parameters were estimated using conditional logit models. Since price data were included, we estimated respondents' willingness to pay for characteristics. Consumers valued health benefits and family coverage more than other attributes. Additionally, differences in preferences can be exploited to increase coverage. The willingness to pay for benefits may partially cover the average cost of providing them. Policy makers might be able to encourage those insured via the subsidized system to enrol in the next level of the social health insurance scheme through expanding benefits to family members and expanding the level of chronic condition coverage.

RNA-Seq identification of candidate defense genes targeted by endophytic Bacillus cereus-mediated induced systemic resistance against Meloidogyne incognita in tomato.

PubMed

Hu, Haijing; Wang, Cong; Li, Xia; Tang, Yunyun; Wang, Yufang; Chen, Shuanglin; Yan, Shuzhen

2018-05-08

The endophytic bacteria Bacillus cereus BCM2 has shown great potential as a defense against the parasitic nematode Meloidogyne incognita. Here, we studied the endophytic bacteria-mediated plant defense against M. incognita and searched for defense-related candidate genes using RNA-Seq. The induced systemic resistance of BCM2 against M. incognita was tested using the split-root method. Pre-inoculated BCM2 on the inducer side was associated with a dramatic reduction in galls and egg masses at the responder side, but inoculated BCM2 alone did not produce the same effect. In order to investigate which plant defense-related genes are specifically activated by BCM2, four RNA samples from tomato roots were sequenced, and four high quality total clean bases were obtained, ranging from 6.64 to 6.75 Gb, with an average of 21558 total genes. The 34 candidate defense-related genes were identified by pair-wise comparison among libraries, representing the targets for BCM2 priming resistance against M. incognita. Functional characterization revealed that the plant-pathogen interaction pathway (ID: ko04626) was significantly enriched for BCM2-mediated M. incognita resistance. This study demonstrates that B. cereus BCM2 maintains a harmonious host-microbe relationship with tomato, but appeared to prime the plant, resulting in more vigorous defense response toward the infection nematode. This article is protected by copyright. All rights reserved.

Self-supervised online metric learning with low rank constraint for scene categorization.

PubMed

Cong, Yang; Liu, Ji; Yuan, Junsong; Luo, Jiebo

2013-08-01

Conventional visual recognition systems usually train an image classifier in a bath mode with all training data provided in advance. However, in many practical applications, only a small amount of training samples are available in the beginning and many more would come sequentially during online recognition. Because the image data characteristics could change over time, it is important for the classifier to adapt to the new data incrementally. In this paper, we present an online metric learning method to address the online scene recognition problem via adaptive similarity measurement. Given a number of labeled data followed by a sequential input of unseen testing samples, the similarity metric is learned to maximize the margin of the distance among different classes of samples. By considering the low rank constraint, our online metric learning model not only can provide competitive performance compared with the state-of-the-art methods, but also guarantees convergence. A bi-linear graph is also defined to model the pair-wise similarity, and an unseen sample is labeled depending on the graph-based label propagation, while the model can also self-update using the more confident new samples. With the ability of online learning, our methodology can well handle the large-scale streaming video data with the ability of incremental self-updating. We evaluate our model to online scene categorization and experiments on various benchmark datasets and comparisons with state-of-the-art methods demonstrate the effectiveness and efficiency of our algorithm.

Factors associated with having a usual source of care in an ethnically diverse sample of Asian American adults.

PubMed

Chang, Eva; Chan, Kitty S; Han, Hae-Ra

2014-09-01

Despite significant population increases, how Asian Americans ethnic subgroups vary in having a usual source of care (USC) is poorly understood. To examine how having a USC varies among Asian American ethnic subgroups (Chinese, Filipinos, Japanese, Koreans, Vietnamese, and South Asians), and the potential factors influencing variation in having a USC. Data were from 2005 and 2009 California Health Interview Survey. Logistic regressions and pair-wise comparisons were used to compare odds of having a USC among Asian ethnic adults (18-64 y) and to examine ethnicity-specific associations with immigration-related factors (English proficiency, length of residence, and living in an ethnically concordant neighborhood) and key enabling (employment, income, insurance), predisposing (education), and need (health status) factors. Models also adjusted for other sociodemographic factors. Significant differences in the magnitude of the variation and factors influencing having a USC were found across Asian subgroups. Korean and Japanese adults had 52%-69% lower adjusted odds of having a USC compared with Chinese. Among all Asian subgroups, uninsured adults had 85%-94% lower adjusted odds of having a USC. Patterns of associations with USC and key factors varied by specific Asian subgroup. Patterns of associations for USC varied by Asian subgroup, although uninsurance persisted significantly across all subgroups. Persistent variation and heterogenous associations suggest that targeted, ethnicity-specific policies and outreach are needed to improve having a USC for Asian American ethnic adults.

Evaluation of endogenous control gene(s) for gene expression studies in human blood exposed to 60Co γ-rays ex vivo.

PubMed

Vaiphei, S Thangminlal; Keppen, Joshua; Nongrum, Saibadaiahun; Chaubey, R C; Kma, L; Sharan, R N

2015-01-01

In gene expression studies, it is critical to normalize data using a stably expressed endogenous control gene in order to obtain accurate and reliable results. However, we currently do not have a universally applied endogenous control gene for normalization of data for gene expression studies, particularly those involving (60)Co γ-ray-exposed human blood samples. In this study, a comparative assessment of the gene expression of six widely used housekeeping endogenous control genes, namely 18S, ACTB, B2M, GAPDH, MT-ATP6 and CDKN1A, was undertaken for a range of (60)Co γ-ray doses (0.5, 1.0, 2.0 and 4.0 Gy) at 8.4 Gy min(-1) at 0 and 24 h post-irradiation time intervals. Using the NormFinder algorithm, real-time PCR data obtained from six individuals (three males and three females) were analyzed with respect to the threshold cycle (Ct) value and abundance, ΔCt pair-wise comparison, intra- and inter-group variability assessments, etc. GAPDH, either alone or in combination with 18S, was found to be the most suitable endogenous control gene and should be used in gene expression studies, especially those involving qPCR of γ-ray-exposed human blood samples. © The Author 2014. Published by Oxford University Press on behalf of The Japan Radiation Research Society and Japanese Society for Radiation Oncology.

Wise promotes coalescence of cells of neural crest and placode origins in the trigeminal region during head development.

PubMed

Shigetani, Yasuyo; Howard, Sara; Guidato, Sonia; Furushima, Kenryo; Abe, Takaya; Itasaki, Nobue

2008-07-15

While most cranial ganglia contain neurons of either neural crest or placodal origin, neurons of the trigeminal ganglion derive from both populations. The Wnt signaling pathway is known to be required for the development of neural crest cells and for trigeminal ganglion formation, however, migrating neural crest cells do not express any known Wnt ligands. Here we demonstrate that Wise, a Wnt modulator expressed in the surface ectoderm overlying the trigeminal ganglion, play a role in promoting the assembly of placodal and neural crest cells. When overexpressed in chick, Wise causes delamination of ectodermal cells and attracts migrating neural crest cells. Overexpression of Wise is thus sufficient to ectopically induce ganglion-like structures consisting of both origins. The function of Wise is likely synergized with Wnt6, expressed in an overlapping manner with Wise in the surface ectoderm. Electroporation of morpholino antisense oligonucleotides against Wise and Wnt6 causes decrease in the contact of neural crest cells with the delaminated placode-derived cells. In addition, targeted deletion of Wise in mouse causes phenotypes that can be explained by a decrease in the contribution of neural crest cells to the ophthalmic lobe of the trigeminal ganglion. These data suggest that Wise is able to function cell non-autonomously on neural crest cells and promote trigeminal ganglion formation.

An empirical examination of WISE/NEOWISE asteroid analysis and results

NASA Astrophysics Data System (ADS)

Myhrvold, Nathan

2018-11-01

Asteroid observations by the WISE space telescope and the analysis of those observations by the NEOWISE project have provided more information about the diameter, albedo, and other properties of approximately 164,000 asteroids, more than all other sources combined. The raw data set from this mission will likely be the largest and most important such data on asteroids available for many years. To put this trove of data to productive use, we must understand its strengths and weaknesses, and we need clear and reproducible methods for analyzing the data set. This study critically examines the WISE observational data and the NEOWISE results published in both the original papers and the NASA Planetary Data System (PDS). There seem to be multiple areas where the analysis might benefit from improvement or independent verification. The NEOWISE results were obtained by the application of 10 different modeling methods, many of which are not adequately explained or even defined, to 12 different combinations of WISE band data. More than half of NEOWISE results are based on a single band of data. The majority of curve fits to the data in the NEOWISE results are of poor quality, frequently missing most or all of the data points on which they are based. Complete misses occur for about 30% of single-band results, and among the results derived from the most common multiple-band combinations, about 43% miss all data points in at least one band. The NEOWISE data analysis relies on assumptions that are in many cases inconsistent with each other. A substantial fraction of WISE data was systematically excluded from the NEOWISE analysis. Building on methods developed by Hanuš et al. (2015), I show that error estimates for the WISE observational data were not well characterized, and all observations have true uncertainty at least a factor of 1.3-2.5 times larger than previously described, depending on the band. I also show that the error distribution is not well fit by a normal distribution. These findings are important because the Monte Carlo error-analysis method used by the NEOWISE project depends on both the observational errors and the normal distribution. An empirical comparison of published NEOWISE diameters to those in the literature that were estimated by using radar, occultation, or spacecraft (ROS) measurements shows that, for 129 results involving 105 asteroids, the NEOWISE diameters presented in tables of thermal-modeling results exactly match prior ROS results from the literature. While these are only a tiny fraction (0.06%) of the asteroids analyzed, they are important because they represent the only independent check on NEOWISE diameter accuracy. After removing the exact matches and adding additional ROS results, I find that the accuracy of diameter estimates for NEOWISE results depends strongly on the choice of data bands and on which of the 10 models was used. I show that systematic errors in the diameter estimates are much larger than previously described and range from - 5% to + 23%. In addition, random errors range from - 15% to + 19% when all four WISE bands were used, and from - 39% to + 57% in cases employing only the W2 band. The empirical results presented here show that much work remains to be done in analyzing data from the WISE/NEOWISE mission and interpreting it for asteroid science.

A Genomewide Linkage Scan of Cocaine Dependence and Major Depressive Episode in Two Populations

PubMed Central

Yang, Bao-Zhu; Han, Shizhong; Kranzler, Henry R; Farrer, Lindsay A; Gelernter, Joel

2011-01-01

Cocaine dependence (CD) and major depressive episode (MDE) frequently co-occur with poorer treatment outcome and higher relapse risk. Shared genetic risk was affirmed; to date, there have been no reports of genomewide linkage scans (GWLSs) surveying the susceptibility regions for comorbid CD and MDE (CD–MDE). We aimed to identify chromosomal regions and candidate genes susceptible to CD, MDE, and CD–MDE in African Americans (AAs) and European Americans (EAs). A total of 1896 individuals were recruited from 384 AA and 355 EA families, each with at least a sibling-pair with CD and/or opioid dependence. Array-based genotyping of about 6000 single-nucleotide polymorphisms was completed for all individuals. Parametric and non-parametric genomewide linkage analyses were performed. We found a genomewide-significant linkage peak on chromosome 7 at 183.4 cM for non-parametric analysis of CD–MDE in AAs (lod=3.8, genomewide empirical p=0.016; point-wise p=0.00001). A nearly genomewide significant linkage was identified for CD–MDE in EAs on chromosome 5 at 14.3 cM (logarithm of odds (lod)=2.95, genomewide empirical p=0.055; point-wise p=0.00012). Parametric analysis corroborated the findings in these two regions and improved the support for the peak on chromosome 5 so that it reached genomewide significance (heterogeneity lod=3.28, genomewide empirical p=0.046; point-wise p=0.00053). This is the first GWLS for CD–MDE. The genomewide significant linkage regions on chromosomes 5 and 7 harbor four particularly promising candidate genes: SRD5A1, UBE3C, PTPRN2, and VIPR2. Replication of the linkage findings in other populations is warranted, as is a focused analysis of the genes located in the linkage regions implicated here. PMID:21849985

Subthalamus stimulation in Parkinson disease: Accounting for the bilaterality of contacts.

PubMed

Lemaire, Jean-Jacques; Pereira, Bruno; Derost, Philippe; Vassal, François; Ulla, Miguel; Morand, Dominique; Coll, Guillaume; Gabrillargues, Jean; Marques, Ana; Debilly, Bérangère; Coste, Jérôme; Durif, Franck

2016-01-01

Deep brain stimulation (DBS) in Parkinson's disease uses bi-hemispheric high-frequency stimulation within the subthalamus, however, the specific impacts of bilaterality of DBS are still not clear. Thus, we aimed to study the individual-level clinical impact of locations of right-left contact pair-up accounting for each subthalamic nucleus (STN) anatomy. Contact locations and effects at 1 year were studied retrospectively in an unselected series of 53 patients operated between 2004 and 2010. Location of contacts was defined relatively to the main axis of STN used to map longitudinal and transversal positions, and STN membership (out meaning out-of-STN). Contact pairings were described via three methods: (i) Unified contact location (UCL) collapsing DBS into an all-in-one contact; (ii) balance of contact pair-up (BCPU), defined as symmetric or asymmetric regardless of laterality; (iii) hemisphere-wise most frequent contact pair-up (MFCP) regardless of BCPU. Clinical data were: mean levodopa equivalent dose, Unified Parkinson's Disease Rating Scale (UPDRS) motor score III without medication, UPDRS II and III speech sub-scores, UPDRS II freezing sub-score, 1 year versus preoperative values, with and without levodopa. Ad-hoc two-sided tests were used for statistical analysis. Worsening speech, was more frequent for UCL_out patients and when the left MFCP contact was rear and/or superolateral, however, it less frequent for BCPU-asymmetric patients. Worsening freezing was more frequent when the right MFCP contact was rear and superolateral. These results point to strategies for minimizing dysarthria and freezing as adverse effects of DBS.

Subthalamus stimulation in Parkinson disease: Accounting for the bilaterality of contacts

PubMed Central

Lemaire, Jean-Jacques; Pereira, Bruno; Derost, Philippe; Vassal, François; Ulla, Miguel; Morand, Dominique; Coll, Guillaume; Gabrillargues, Jean; Marques, Ana; Debilly, Bérangère; Coste, Jérôme; Durif, Franck

2016-01-01

Background: Deep brain stimulation (DBS) in Parkinson's disease uses bi-hemispheric high-frequency stimulation within the subthalamus, however, the specific impacts of bilaterality of DBS are still not clear. Thus, we aimed to study the individual-level clinical impact of locations of right-left contact pair-up accounting for each subthalamic nucleus (STN) anatomy. Methods: Contact locations and effects at 1 year were studied retrospectively in an unselected series of 53 patients operated between 2004 and 2010. Location of contacts was defined relatively to the main axis of STN used to map longitudinal and transversal positions, and STN membership (out meaning out-of-STN). Contact pairings were described via three methods: (i) Unified contact location (UCL) collapsing DBS into an all-in-one contact; (ii) balance of contact pair-up (BCPU), defined as symmetric or asymmetric regardless of laterality; (iii) hemisphere-wise most frequent contact pair-up (MFCP) regardless of BCPU. Clinical data were: mean levodopa equivalent dose, Unified Parkinson's Disease Rating Scale (UPDRS) motor score III without medication, UPDRS II and III speech sub-scores, UPDRS II freezing sub-score, 1 year versus preoperative values, with and without levodopa. Ad-hoc two-sided tests were used for statistical analysis. Results: Worsening speech, was more frequent for UCL_out patients and when the left MFCP contact was rear and/or superolateral, however, it less frequent for BCPU-asymmetric patients. Worsening freezing was more frequent when the right MFCP contact was rear and superolateral. Conclusions: These results point to strategies for minimizing dysarthria and freezing as adverse effects of DBS. PMID:27990316

Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences

PubMed Central

2018-01-01

Prediction of taxonomy for marker gene sequences such as 16S ribosomal RNA (rRNA) is a fundamental task in microbiology. Most experimentally observed sequences are diverged from reference sequences of authoritatively named organisms, creating a challenge for prediction methods. I assessed the accuracy of several algorithms using cross-validation by identity, a new benchmark strategy which explicitly models the variation in distances between query sequences and the closest entry in a reference database. When the accuracy of genus predictions was averaged over a representative range of identities with the reference database (100%, 99%, 97%, 95% and 90%), all tested methods had ≤50% accuracy on the currently-popular V4 region of 16S rRNA. Accuracy was found to fall rapidly with identity; for example, better methods were found to have V4 genus prediction accuracy of ∼100% at 100% identity but ∼50% at 97% identity. The relationship between identity and taxonomy was quantified as the probability that a rank is the lowest shared by a pair of sequences with a given pair-wise identity. With the V4 region, 95% identity was found to be a twilight zone where taxonomy is highly ambiguous because the probabilities that the lowest shared rank between pairs of sequences is genus, family, order or class are approximately equal. PMID:29682424

Double-Difference Global Adjoint Tomography

NASA Astrophysics Data System (ADS)

Orsvuran, R.; Bozdag, E.; Lei, W.; Tromp, J.

2017-12-01

The adjoint method allows us to incorporate full waveform simulations in inverse problems. Misfit functions play an important role in extracting the relevant information from seismic waveforms. In this study, our goal is to apply the Double-Difference (DD) methodology proposed by Yuan et al. (2016) to global adjoint tomography. Dense seismic networks, such as USArray, lead to higher-resolution seismic images underneath continents. However, the imbalanced distribution of stations and sources poses challenges in global ray coverage. We adapt double-difference multitaper measurements to global adjoint tomography. We normalize each DD measurement by its number of pairs, and if a measurement has no pair, as may frequently happen for data recorded at oceanic stations, classical multitaper measurements are used. As a result, the differential measurements and pair-wise weighting strategy help balance uneven global kernel coverage. Our initial experiments with minor- and major-arc surface waves show promising results, revealing more pronounced structure near dense networks while reducing the prominence of paths towards cluster of stations. We have started using this new measurement in global adjoint inversions, addressing azimuthal anisotropy in upper mantle. Meanwhile, we are working on combining the double-difference approach with instantaneous phase measurements to emphasize contributions of scattered waves in global inversions and extending it to body waves. We will present our results and discuss challenges and future directions in the context of global tomographic inversions.

Towards a consistent approach of measuring and modelling CO2 exchange with manual chambers

NASA Astrophysics Data System (ADS)

Huth, Vytas; Vaidya, Shrijana; Hoffmann, Mathias; Jurisch, Nicole; Günther, Anke; Gundlach, Laura; Hagemann, Ulrike; Elsgaard, Lars; Augustin, Jürgen

2016-04-01

Determining ecosystem CO2 exchange with the manual closed chamber method has been applied in the past for e.g. plant, soil or treatment on a wide range of terrestrial ecosystems. Its major limitation is the discontinuous data acquisation challenging any gap-filling procedures. In addition, both data acquisition and gap-filling of closed chamber data have been carried out in different ways in the past. The reliability and comparability of the derived results from different closed chamber studies has therefore remained unclear. Hence, this study compares two different approaches of obtaining fluxes of gross primary production (GPP) either via sunrise to noon or via gradually-shaded mid-day measurements of transparent chamber fluxes (i.e. net ecosystem exchange, NEE) and opaque chamber fluxes (i.e., ecosystem respiration, RECO) on a field experiment plot in NE Germany cropped with a lucerne-clover-grass mix. Additionally, we compare three approaches of pooling RECO data for consecutive modelling of annual balances of NEE, i.e. campaign-wise (single measurement day RECO models), seasonal-wise (one RECO model for the entire study period), and cluster-wise (two RECO models representing low-/high-vegetation-stage data) modelling. The annual NEE balances of the sunrise to noon measurements are insensitive towards differing RECO modelling approaches (-101 to -131 g C m-2), whereas the choice of modelling annual NEE balances with the shaded mid-day measurements must be taken carefully (-200 to 425 g C m-2). In addition, the campaign-wise RECO modelling approach is very sensitive to daily data pooling (sunrise vs. mid-day) and only advisable when the diurnal variability of CO2 fluxes and environmental parameters (i.e. photosynthetically active radiation, temperature) is sufficiently covered. The seasonal- and cluster-wise approaches lead to robust NEE balances with only little variation in terms of daily data collection. We therefore recommend sunrise to noon measurements and data pooling from adjacent measurement campaigns as long as pooling over e.g. harvest events and significant changes in plant development can be omitted. If, e.g. for extensive treatment comparisons, the sunrise to noon measurements are not feasible due to their higher workload, data pooling accounting for plant development is necessary.

Cryptanalysis and Improvements for the Quantum Private Comparison Protocol Using EPR Pairs

NASA Astrophysics Data System (ADS)

Wang, Cong; Xu, Gang; Yang, Yi-Xian

2013-07-01

In this paper, we carry out an in-depth analysis of the quantum private comparison (QPC) protocol with the semi-honest third party (TP). The security of QPC protocol using the EPR pairs is re-examined. Unfortunately, we find that TP can use the fake EPR pairs to steal all the secret information. Furthermore, we give two simple and feasible solutions to improve the original QPC protocol. It is shown that the improved protocol is secure, which can resist various kinds of attacks from both the outside eavesdroppers and the inside participants, even the semi-honest TP.

Explanatory Supplement to the WISE All-Sky Release Products

NASA Technical Reports Server (NTRS)

2012-01-01

The Wide-field Infrared Survey Explorer (WISE; Wright et al. 2010) surveyed the entire sky at 3.4, 4.6, 12 and 22 microns in 2010, achieving 5-sigma point source sensitivities per band better than 0.08, 0.11, 1 and 6 mJy in unconfused regions on the ecliptic. The WISE All-Sky Data Release, conducted on March 14, 2012, incorporates all data taken during the full cryogenic mission phase, 7 January 2010 to 6 August 20l0,that were processed with improved calibrations and reduction algorithms. Release data products include: (1) an Atlas of 18,240 match-filtered, calibrated and coadded image sets; (2) a Source Catalog containing positions and four-band photometry for over 563 million objects, and (3) an Explanatory Supplement. Ancillary products include a Reject Table that contains 284 million detections that were not selected for the Source Catalog because they are low signal-to-noise ratio or spurious detections of image artifacts, an archive of over 1.5 million sets of calibrated WISE Single-exposure images, and a database of 9.4 billion source extractions from those single images, and moving object tracklets identified by the NEOWISE program (Mainzer et aI. 2011). The WISE All-Sky Data Release products supersede those from the WISE Preliminary Data Release (Cutri et al. 2011). The Explanatory Supplement to the WISE All-Sky Data Release Products is a general guide for users of the WISE data. The Supplement contains an overview of the WISE mission, facilities, and operations, a detailed description of WISE data processing algorithms, a guide to the content and formals of the image and tabular data products, and cautionary notes that describe known limitations of the All-Sky Release products. Instructions for accessing the WISE data products via the services of the NASA/IPAC Infrared Science Archive are provided. The Supplement also provides analyses of the achieved sky coverage, photometric and astrometric characteristics and completeness and reliability of the All-Sky Release data products. The WISE All-Sky Release Explanatory Supplement is an on-line document that is updated frequently to provide the most current information for users of the WISE data products. The Explanatory Supplement is maintained at: http://wise2.ipac.caltech.edu/docs/release/allsky/expsup/index.html WISE is a joint project of the University of California, Los Angeles and the Jet Propulsion Laboratory/California Institute of Technology, funded by the National Aeronautics and Space Administration. NEOWISE is a project of the Jet Propulsion Laboratory/California Institute of Technology, funded by the Planetary Science Division of the National Aeronautics and Space Administration.

Tympanic ear thermometer assessment of body temperature among patients with cognitive disturbances. An acceptable and ethically desirable alternative?

PubMed

Aadal, Lena; Fog, Lisbet; Pedersen, Asger Roer

2016-12-01

Investigation of a possible relation between body temperature measurements by the current generation of tympanic ear and rectal thermometers. In Denmark, a national guideline recommends the rectal measurement. Subsequently, the rectal thermometers and tympanic ear devices are the most frequently used and first choice in Danish hospital wards. Cognitive changes constitute challenges with cooperating in rectal temperature assessments. With regard to diagnosing, ethics, safety and the patients' dignity, the tympanic ear thermometer might comprise a desirable alternative to rectal noninvasive measurement of body temperature during in-hospital-based neurorehabilitation. A prospective, descriptive cohort study. Consecutive inclusion of 27 patients. Linear regression models were used to analyse 284 simultaneous temperature measurements. Ethical approval for this study was granted by the Danish Data Protection Agency, and the study was completed in accordance with the Helsinki Declaration 2008. About 284 simultaneous rectal and ear temperature measurements on 27 patients were analysed. The patient-wise variability of measured temperatures was significantly higher for the ear measurements. Patient-wise linear regressions for the 25 patients with at least three pairs of simultaneous ear and rectal temperature measurements showed large interpatient variability of the association. A linear relationship between the rectal body temperature assessment and the temperature assessment employing the tympanic thermometer is weak. Both measuring methods reflect variance in temperature, but ear measurements showed larger variation. © 2016 Nordic College of Caring Science.

Teachers and Technology Use in Secondary Science Classrooms: Investigating the Experiences of Middle School Science Teachers Implementing the Web-based Inquiry Science Environment (WISE)

NASA Astrophysics Data System (ADS)

Schulz, Rachel Corinne

This study investigated the intended teacher use of a technology-enhanced learning tool, Web-based Inquiry Science Environment (WISE), and the first experiences of teachers new to using it and untrained in its use. The purpose of the study was to learn more about the factors embedded into the design of the technology that enabled it or hindered it from being used as intended. The qualitative research design applied grounded theory methods. Using theoretical sampling and a constant comparative analysis, a document review of WISE website led to a model of intended teacher use. The experiences of four middle school science teachers as they enacted WISE for the first time were investigated through ethnographic field observations, surveys and interviews using thematic analysis to construct narratives of each teachers use. These narratives were compared to the model of intended teacher use of WISE. This study found two levels of intended teacher uses for WISE. A basic intended use involved having student running the project to completion while the teacher provides feedback and assesses student learning. A more optimal description of intended use involved the supplementing the core curriculum with WISE as well as enhancing the core scope and sequence of instruction and aligning assessment with the goals of instruction through WISE. Moreover, WISE projects were optimally intended to be facilitated through student-centered teaching practices and inquiry-based instruction in a collaborative learning environment. It is also optimally intended for these projects to be shared with other colleagues for feedback and iterative development towards improving the Knowledge Integration of students. Of the four teachers who participated in this study, only one demonstrated the use of WISE as intended in the most basic way. This teacher also demonstrated the use of WISE in a number of optimal ways. Teacher confusion with certain tools available within WISE suggests that there may be a way to develop the user experience through these touch points and help teachers learn how to use the technology as they are selecting and setting up a project run. Further research may study whether improving these touch points can improve the teachers' use of WISE as intended both basically and optimally. It may also study whether or not teacher in basic and optimal ways directly impact student learning results.

WISE Choices? Understanding Occupational Decision-Making in a Climate of Equal Opportunities for Women in Science and Technology.

ERIC Educational Resources Information Center

Henwood, Flis

1996-01-01

Examines Women into Science and Engineering (WISE) discourse and explains why WISE has had limited success. It argues the WISE discourse limits the space women have to speak of the conflicts and contradictions they experience, and suggests the need for a greater understanding of how subjective experiences of gender and sexuality impinge upon work…

The Windy Island Soliton Experiment (WISE): Shallow Water and Basin Experiment Configuration and Preliminary Observations

DTIC Science & Technology

2009-02-19

Virginia 22203-1995 The Windy Island Soliton Experiment (WISE): Shallow Water and Basin Experiment Configuration and Preliminary Observations...case letters) The Windy Island Soliton Experiment (WISE): Shallow water and Basin Experiment Configuration and Preliminary Observations 5. FUNDING...release; distribution is unlimited 12b. DISTRIBUTION CODE 13. ABSTRACT (maximum 200 words) The Windy Islands Soliton Experiment (WISE) was

Automatic Video Analysis for Obstructive Sleep Apnea Diagnosis.

PubMed

Abad, Jorge; Muñoz-Ferrer, Aida; Cervantes, Miguel Ángel; Esquinas, Cristina; Marin, Alicia; Martínez, Carlos; Morera, Josep; Ruiz, Juan

2016-08-01

We investigated the diagnostic accuracy for the identification of obstructive sleep apnea (OSA) and its severity of a noninvasive technology based on image processing (SleepWise). This is an observational, prospective study to evaluate the degree of agreement between polysomnography (PSG) and SleepWise. We recruited 56 consecutive subjects with suspected OSA who were referred as outpatients to the Sleep Unit of the Hospital Universitari Germans Trias i Pujol (HUGTiP) from January 2013 to January 2014. All patients underwent laboratory PSG and image processing with SleepWise simultaneously the same night. Both PSG and SleepWise analyses were carried independently and blindly. We analyzed 50 of the 56 patients recruited. OSA was diagnosed through PSG in a total of 44 patients (88%) with a median apnea-hypopnea index (AHI) of 25.35 (24.9). According to SleepWise, 45 patients (90%) met the criteria for a diagnosis of OSA, with a median AHI of 22.8 (22.03). An analysis of the ability of PSG and SleepWise to classify patients by severity on the basis of their AHI shows that the two diagnostic systems distribute the different groups similarly. According to PSG, 23 patients (46%) had a diagnosis of severe OSA, 11 patients (22%) moderate OSA, and 10 patients (20%) mild OSA. According to SleepWise, 20, 13, and 12 patients (40%, 26%, and 24%, respectively) had a diagnosis of severe, moderate, and mild OSA respectively. For OSA diagnosis, SleepWise was found to have sensitivity of 100% and specificity of 83% in relation to PSG. The positive predictive value was 97% and the negative predictive value was 100%. The Bland-Altman plot comparing the mean AHI values obtained through PSG and SleepWise shows very good agreement between the two diagnostic techniques, with a bias of -3.85, a standard error of 12.18, and a confidence interval of -0.39 to -7.31. SleepWise was reasonably accurate for noninvasive and automatic diagnosis of OSA in outpatients. SleepWise determined the severity of OSA with high reliability. The current study including simultaneous laboratory PSG and SleepWise processing image is proposed as a reasonable validation standard. © 2016 Associated Professional Sleep Societies, LLC.

PageMan: an interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments.

PubMed

Usadel, Björn; Nagel, Axel; Steinhauser, Dirk; Gibon, Yves; Bläsing, Oliver E; Redestig, Henning; Sreenivasulu, Nese; Krall, Leonard; Hannah, Matthew A; Poree, Fabien; Fernie, Alisdair R; Stitt, Mark

2006-12-18

Microarray technology has become a widely accepted and standardized tool in biology. The first microarray data analysis programs were developed to support pair-wise comparison. However, as microarray experiments have become more routine, large scale experiments have become more common, which investigate multiple time points or sets of mutants or transgenics. To extract biological information from such high-throughput expression data, it is necessary to develop efficient analytical platforms, which combine manually curated gene ontologies with efficient visualization and navigation tools. Currently, most tools focus on a few limited biological aspects, rather than offering a holistic, integrated analysis. Here we introduce PageMan, a multiplatform, user-friendly, and stand-alone software tool that annotates, investigates, and condenses high-throughput microarray data in the context of functional ontologies. It includes a GUI tool to transform different ontologies into a suitable format, enabling the user to compare and choose between different ontologies. It is equipped with several statistical modules for data analysis, including over-representation analysis and Wilcoxon statistical testing. Results are exported in a graphical format for direct use, or for further editing in graphics programs.PageMan provides a fast overview of single treatments, allows genome-level responses to be compared across several microarray experiments covering, for example, stress responses at multiple time points. This aids in searching for trait-specific changes in pathways using mutants or transgenics, analyzing development time-courses, and comparison between species. In a case study, we analyze the results of publicly available microarrays of multiple cold stress experiments using PageMan, and compare the results to a previously published meta-analysis.PageMan offers a complete user's guide, a web-based over-representation analysis as well as a tutorial, and is freely available at http://mapman.mpimp-golm.mpg.de/pageman/. PageMan allows multiple microarray experiments to be efficiently condensed into a single page graphical display. The flexible interface allows data to be quickly and easily visualized, facilitating comparisons within experiments and to published experiments, thus enabling researchers to gain a rapid overview of the biological responses in the experiments.

A comparison of two scales for assessing health professional students’ attitude toward interprofessional learning

PubMed Central

Lie, Désirée Annabel; Fung, Cha Chi; Trial, Janet; Lohenry, Kevin

2013-01-01

Rationale The validated 19-item Readiness for Interprofessional Learning Scale (RIPLS) is often used for assessing attitudes toward interprofessional education (IPE). The 12-item Interdisciplinary Education Perception Scale (IEPS), also used for this purpose, has not been validated among the professions of medicine, pharmacy, and physician assistants (PAs). The discriminatory ability of the two scales has not been directly compared. Comparison of the two will aid educators in selecting the optimal scale. Objective To compare psychometric properties of the RIPLS and IEPS and to examine the ability of each scale to discriminate mean scores among student subgroups (gender, profession, seniority, and prior IPE exposure). Method We conducted a cross-sectional (Qualtrics©) survey (RIPLS and IEPS) of junior and senior students in medicine (n=360), pharmacy (n=360), and the PA profession (n=106). Descriptive statistics were used to report aggregate mean scores of subgroups. The internal consistency of each scale was assessed using Cronbach's α. Concurrent validity was measured by Pearson's correlation coefficients. Independent-sample t-tests and analysis of variances (ANOVAs) were performed to assess the discriminatory ability of each scale. Cohen's d effect sizes were calculated for all significant pair-wise comparisons. Results Response rate was 82%. Cronbach's α was 0.85 (RIPLS) and 0.91 (IEPS). The RIPLS discriminated scores by gender among junior students only, and scores by IPE exposure among all students. The IEPS distinguished score differences for the three professions among junior students and by prior IPE exposure for all three professions. Neither scale detected differences in mean scores by profession among all students or by level of training among the three professions. Conclusions Neither the RIPLS nor the IEPS has greater discriminatory ability for detecting attitude differences among the student subgroups. Reason for differences may be explained by slightly different scale constructs. The RIPLS is designed to assess students’ own attitude toward interprofessional learning, while the IEPS discerns perceived attitudes about team collaboration for students’ own professions and may be more appropriate for more advanced students. PMID:24300749

COMPARISON OF LAPAROSCOPIC SKILLS PERFORMANCE USING SINGLE-SITE ACCESS (SSA) DEVICES VS. AN INDEPENDENT-PORT SSA APPROACH

PubMed Central

Schill, Matthew R.; Varela, J. Esteban; Frisella, Margaret M.; Brunt, L. Michael

2015-01-01

Background We compared performance of validated laparoscopic tasks on four commercially available single site access (SSA) access devices (AD) versus an independent port (IP) SSA set-up. Methods A prospective, randomized comparison of laparoscopic skills performance on four AD (GelPOINT™, SILS™ Port, SSL Access System™, TriPort™) and one IP SSA set-up was conducted. Eighteen medical students (2nd–4th year), four surgical residents, and five attending surgeons were trained to proficiency in multi-port laparoscopy using four laparoscopic drills (peg transfer, bean drop, pattern cutting, extracorporeal suturing) in a laparoscopic trainer box. Drills were then performed in random order on each IP-SSA and AD-SSA set-up using straight laparoscopic instruments. Repetitions were timed and errors recorded. Data are mean ± SD, and statistical analysis was by two-way ANOVA with Tukey HSD post-hoc tests. Results Attending surgeons had significantly faster total task times than residents or students (p< 0.001), but the difference between residents and students was NS. Pair-wise comparisons revealed significantly faster total task times for the IP-SSA set-up compared to all four AD-SSA’s within the student group only (p<0.05). Total task times for residents and attending surgeons showed a similar profile, but the differences were NS. When data for the three groups was combined, the total task time was less for the IP-SSA set-up than for each of the four AD-SSA set-ups (p < 0.001). Similarly,, the IP-SSA set-up was significantly faster than 3 of 4 AD-SSA set-ups for peg transfer, 3 of 4 for pattern cutting, and 2 of 4 for suturing. No significant differences in error rates between IP-SSA and AD-SSA set-ups were detected. Conclusions When compared to an IP-SSA laparoscopic set-up, single site access devices are associated with longer task performance times in a trainer box model, independent of level of training. Task performance was similar across different SSA devices. PMID:21993938

Comparison of Interaural Electrode Pairing Methods for Bilateral Cochlear Implants

PubMed Central

Dietz, Mathias

2015-01-01

In patients with bilateral cochlear implants (CIs), pairing matched interaural electrodes and stimulating them with the same frequency band is expected to facilitate binaural functions such as binaural fusion, localization, and spatial release from masking. Because clinical procedures typically do not include patient-specific interaural electrode pairing, it remains the case that each electrode is allocated to a generic frequency range, based simply on the electrode number. Two psychoacoustic techniques for determining interaurally paired electrodes have been demonstrated in several studies: interaural pitch comparison and interaural time difference (ITD) sensitivity. However, these two methods are rarely, if ever, compared directly. A third, more objective method is to assess the amplitude of the binaural interaction component (BIC) derived from electrically evoked auditory brainstem responses for different electrode pairings; a method has been demonstrated to be a potential candidate for bilateral CI users. Here, we tested all three measures in the same eight CI users. We found good correspondence between the electrode pair producing the largest BIC and the electrode pair producing the maximum ITD sensitivity. The correspondence between the pairs producing the largest BIC and the pitch-matched electrode pairs was considerably weaker, supporting the previously proposed hypothesis that whilst place pitch might adapt over time to accommodate mismatched inputs, sensitivity to ITDs does not adapt to the same degree. PMID:26631108

Update on the Wide-field Infrared Survey Explorer (WISE)

NASA Technical Reports Server (NTRS)

Mainzer, Amanda K.; Eisenhardt, Peter; Wright, Edward L.; Liu, Feng-Chuan; Irace, William; Heinrichsen, Ingolf; Cutri, Roc; Duval, Valerie

2006-01-01

The Wide-field Infrared Survey Explorer (WISE), a NASA MIDEX mission, will survey the entire sky in four bands from 3.3 to 23 microns with a sensitivity 1000 times greater than the IRAS survey. The WISE survey will extend the Two Micron All Sky Survey into the thermal infrared and will provide an important catalog for the James Webb Space Telescope. Using 1024(sup 2) HgCdTe and Si:As arrays at 3.3, 4.7, 12 and 23 microns, WISE will find the most luminous galaxies in the universe, the closest stars to the Sun, and it will detect most of the main belt asteroids larger than 3 km. The single WISE instrument consists of a 40 cm diamond-turned aluminum afocal telescope, a two-stage solid hydrogen cryostat, a scan mirror mechanism, and reimaging optics giving 5 resolution (full-width-half-maximum). The use of dichroics and beamsplitters allows four color images of a 47' x47' field of view to be taken every 8.8 seconds, synchronized with the orbital motion to provide total sky coverage with overlap between revolutions. WISE will be placed into a Sun-synchronous polar orbit on a Delta 7320-10 launch vehicle. The WISE survey approach is simple and efficient. The three-axis-stabilized spacecraft rotates at a constant rate while the scan mirror freezes the telescope line of sight during each exposure. WISE has completed its mission Preliminary Design Review and its NASA Confirmation Review, and the project is awaiting confirmation from NASA to proceed to the Critical Design phase. Much of the payload hardware is now complete, and assembly of the payload will occur over the next year. WISE is scheduled to launch in late 2009; the project web site can be found at www.wise.ssl.berkeley.edu.

The WISE Satellite Development: Managing the Risks and the Opportunities

NASA Technical Reports Server (NTRS)

Duval, Valerie G.; Elwell, John D.; Howard, Joan F.; Irace, William R.; Liu, Feng-Chuan

2010-01-01

NASA's Wide-field Infrared Survey Explorer (WISE) MIDEX mission is surveying the entire sky in four infrared bands from 3.4 to 22 micrometers. The WISE instrument consists of a 40 cm telescope, a solid hydrogen cryostat, a scan mirror mechanism, and four 1K x1K infrared detectors. The WISE spacecraft bus provides communication, data handling, and avionics including instrument pointing. A Delta 7920 successfully launched WISE into a Sun-synchronous polar orbit on December 14, 2009. WISE was competitively selected by NASA as a Medium cost Explorer mission (MIDEX) in 2002. MIDEX missions are led by the Principal Investigator who delegates day-to-day management to the Project Manager. Given the tight cost cap and relatively short development schedule, NASA chose to extend the development period one year with an option to cancel the mission if certain criteria were not met. To meet this and other challenges, the WISE management team had to learn to work seamlessly across institutional lines and to recognize risks and opportunities in order to develop the flight hardware within the project resources. In spite of significant technical issues, the WISE satellite was delivered on budget and on schedule. This paper describes our management approach and risk posture, technical issues, and critical decisions made.

Wise Regulates Bone Deposition through Genetic Interactions with Lrp5

PubMed Central

Ellies, Debra L.; Economou, Androulla; Viviano, Beth; Rey, Jean-Philippe; Paine-Saunders, Stephenie; Krumlauf, Robb; Saunders, Scott

2014-01-01

In this study using genetic approaches in mouse we demonstrate that the secreted protein Wise plays essential roles in regulating early bone formation through its ability to modulate Wnt signaling via interactions with the Lrp5 co-receptor. In Wise−/− mutant mice we find an increase in the rate of osteoblast proliferation and a transient increase in bone mineral density. This change in proliferation is dependent upon Lrp5, as Wise;Lrp5 double mutants have normal bone mass. This suggests that Wise serves as a negative modulator of Wnt signaling in active osteoblasts. Wise and the closely related protein Sclerostin (Sost) are expressed in osteoblast cells during temporally distinct early and late phases in a manner consistent with the temporal onset of their respective increased bone density phenotypes. These data suggest that Wise and Sost may have common roles in regulating bone development through their ability to control the balance of Wnt signaling. We find that Wise is also required to potentiate proliferation in chondrocytes, serving as a potential positive modulator of Wnt activity. Our analyses demonstrate that Wise plays a key role in processes that control the number of osteoblasts and chondrocytes during bone homeostasis and provide important insight into mechanisms regulating the Wnt pathway during skeletal development. PMID:24789067

Inhibition of Wnt signaling by Wise (Sostdc1) and negative feedback from Shh controls tooth number and patterning.

PubMed

Ahn, Youngwook; Sanderson, Brian W; Klein, Ophir D; Krumlauf, Robb

2010-10-01

Mice carrying mutations in Wise (Sostdc1) display defects in many aspects of tooth development, including tooth number, size and cusp pattern. To understand the basis of these defects, we have investigated the pathways modulated by Wise in tooth development. We present evidence that, in tooth development, Wise suppresses survival of the diastema or incisor vestigial buds by serving as an inhibitor of Lrp5- and Lrp6-dependent Wnt signaling. Reducing the dosage of the Wnt co-receptor genes Lrp5 and Lrp6 rescues the Wise-null tooth phenotypes. Inactivation of Wise leads to elevated Wnt signaling and, as a consequence, vestigial tooth buds in the normally toothless diastema region display increased proliferation and continuous development to form supernumerary teeth. Conversely, gain-of-function studies show that ectopic Wise reduces Wnt signaling and tooth number. Our analyses demonstrate that the Fgf and Shh pathways are major downstream targets of Wise-regulated Wnt signaling. Furthermore, our experiments revealed that Shh acts as a negative-feedback regulator of Wnt signaling and thus determines the fate of the vestigial buds and later tooth patterning. These data provide insight into the mechanisms that control Wnt signaling in tooth development and into how crosstalk among signaling pathways controls tooth number and morphogenesis.

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

Patel, Rahul I.; Metchev, Stanimir A.; Trollo, Joseph

In an earlier study, we reported nearly 100 previously unknown dusty debris disks around Hipparcos main-sequence stars within 75 pc by selecting stars with excesses in individual WISE colors. Here, we further scrutinize the Hipparcos  75 pc sample to (1) gain sensitivity to previously undetected, fainter mid-IR excesses and (2) remove spurious excesses contaminated by previously unidentified blended sources. We improve on our previous method by adopting a more accurate measure of the confidence threshold for excess detection and by adding an optimally weighted color average that incorporates all shorter-wavelength WISE photometry, rather than using only individual WISE colors. Themore » latter is equivalent to spectral energy distribution fitting, but only over WISE bandpasses. In addition, we leverage the higher-resolution WISE images available through the unWISE.me image service to identify contaminated WISE excesses based on photocenter offsets among the W 3- and W 4-band images. Altogether, we identify 19 previously unreported candidate debris disks. Combined with the results from our earlier study, we have found a total of 107 new debris disks around 75 pc Hipparcos main-sequence stars using precisely calibrated WISE photometry. This expands the 75 pc debris disk sample by 22% around Hipparcos main-sequence stars and by 20% overall (including non-main-sequence and non- Hipparcos stars).« less

WISE Observations of Comets, Centaurs, & Scattered Disk Objects

NASA Technical Reports Server (NTRS)

Bauer, J.; Walker, R.; Mainzer, A.; Masiero, J.; Grav, T.; Cutri, R.; Dailey, J.; McMillan, R.; Lisse, C. M.; Fernandez, Y. R.;

Educational Materials - Burn Wise

EPA Pesticide Factsheets

Burn Wise outreach material. Burn Wise is a partnership program of that emphasizes the importance of burning the right wood, the right way, in the right wood-burning appliance to protect your home, health, and the air we breathe.

An automated tool for cortical feature analysis: Application to differences on 7 Tesla T2* -weighted images between young and older healthy subjects.

PubMed

Doan, Nhat Trung; van Rooden, Sanneke; Versluis, Maarten J; Buijs, Mathijs; Webb, Andrew G; van der Grond, Jeroen; van Buchem, Mark A; Reiber, Johan H C; Milles, Julien

2015-07-01

High field T 2 * -weighted MR images of the cerebral cortex are increasingly used to study tissue susceptibility changes related to aging or pathologies. This paper presents a novel automated method for the computation of quantitative cortical measures and group-wise comparison using 7 Tesla T 2 * -weighted magnitude and phase images. The cerebral cortex was segmented using a combination of T 2 * -weighted magnitude and phase information and subsequently was parcellated based on an anatomical atlas. Local gray matter (GM)/white matter (WM) contrast and cortical profiles, which depict the magnitude or phase variation across the cortex, were computed from the magnitude and phase images in each parcellated region and further used for group-wise comparison. Differences in local GM/WM contrast were assessed using linear regression analysis. Regional cortical profiles were compared both globally and locally using permutation testing. The method was applied to compare a group of 10 young volunteers with a group of 15 older subjects. Using local GM/WM contrast, significant differences were revealed in at least 13 of 17 studied regions. Highly significant differences between cortical profiles were shown in all regions. The proposed method can be a useful tool for studying cortical changes in normal aging and potentially in neurodegenerative diseases. Magn Reson Med 74:240-248, 2015. © 2014 Wiley Periodicals, Inc. © 2014 Wiley Periodicals, Inc.

On the mid-infrared variability of candidate eruptive variables (exors): A comparison between Spitzer and WISE data

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

Antoniucci, S.; Giannini, T.; Li Causi, G.

2014-02-10

Aiming to statistically study the variability in the mid-IR of young stellar objects, we have compared the 3.6, 4.5, and 24 μm Spitzer fluxes of 1478 sources belonging to the C2D (Cores to Disks) legacy program with the WISE fluxes at 3.4, 4.6, and 22 μm. From this comparison, we have selected a robust sample of 34 variable sources. Their variations were classified per spectral Class (according to the widely accepted scheme of Class I/flat/II/III protostars), and per star forming region. On average, the number of variable sources decreases with increasing Class and is definitely higher in Perseus and Ophiuchusmore » than in Chamaeleon and Lupus. According to the paradigm Class ≡ Evolution, the photometric variability can be considered to be a feature more pronounced in less evolved protostars, and, as such, related to accretion processes. Moreover, our statistical findings agree with the current knowledge of star formation activity in different regions. The 34 selected variables were further investigated for similarities with known young eruptive variables, namely the EXors. In particular, we analyzed (1) the shape of the spectral energy distribution, (2) the IR excess over the stellar photosphere, (3) magnitude versus color variations, and (4) output parameters of model fitting. This first systematic search for EXors ends up with 11 bona fide candidates that can be considered as suitable targets for monitoring or future investigations.« less

Understanding Young Exoplanet Analogs with WISE

NASA Astrophysics Data System (ADS)

Rice, Emily

We propose to tackle outstanding questions about the fundamental properties of young brown dwarfs, which are atmospheric analogs to massive gas giant exoplanets, using public archive data from the Wide-field Infrared Survey Explorer (WISE) combined with our extensive dataset of optical and near-infrared observations, including spectra, proper motions, and parallaxes. Using WISE data we will construct color-color diagrams, color- magnitude diagrams, and spectral energy distributions for our sample of candidate young brown dwarfs. We will fully characterize the spectral properties of the candidates and evaluate their membership in nearby young moving groups in order to obtain independent age estimates. The practical outcomes of this project will allow the research community to use observed colors and spectra to reliably constrain the properties - including effective temperature, gravity, and dust/cloud properties - of both brown dwarfs and gas giant exoplanets. We will also search for new young brown dwarfs in the WISE archive using colors and proper motions. The expanded sample of young brown dwarfs will be used to create a self-contained feedback loop to identify and address the shortcomings of cool atmosphere models and low-mass evolutionary tracks, both of which are already being used to infer the properties of massive exoplanets. Disentangling the effects of physical parameters on the observed properties of young brown dwarfs is directly relevant to studies of exoplanets. Direct observations of exoplanets are currently very limited, and young brown dwarfs are the laboratories in which we can solve existing problems before the onslaught of new observations from instruments capable of directly imaging exoplanets, including the Gemini Planet Imager, Project 1640 at the Palomar Observatory, SPHERE on the VLT, and the James Webb Space Telescope. This project addresses the goal of the NASA Science Mission Directorate to discover how the universe works; in particular, the results of our work will improve our understanding of objects at the intersection of stars and planets and be directly applicable to understanding the atmospheres of directly-imaged exoplanets. The assembled investigators are the absolute best team to accomplish this work. They have extensive and diverse observational experience in astrometry, photometry, and spectroscopy from the optical through the mid-IR, spanning nearly the entire spectral energy distribution of young brown dwarfs and encompassing their most fundamental observational properties. They have considerable experience mining large photometric catalogs and identifying low-gravity very low mass objects. The team maintains collaborations with two groups actively modelling brown dwarf and exoplanet atmospheres and interior evolution. The proposed research organically combines several ongoing projects into a cohesive program that will efficiently incorporate WISE data to disentangle the ambiguous and interdependent physical properties of young brown dwarfs. As a result of the team's previous observational projects, we have assembled a dataset that positions us to best interpret WISE observations brown dwarfs and identify new young brown dwarfs in the WISE archive. A significant parallax program is ongoing, and all of the computing resources and many of the analysis tools are already in place, including several well-tested pipelines for data reduction and analysis and model comparisons. The team will incorporate undergraduate students in the project through an existing NSF-funded REU program.

An Empirical Bayes Approach to Item Banking. Project Psychometric Aspects of Item Banking No. 6. Research Report 86-6.

ERIC Educational Resources Information Center

van der Linden, Wim J.; Eggen, Theo J. H. M.

A procedure for the sequential optimization of the calibration of an item bank is given. The procedure is based on an empirical Bayes approach to a reformulation of the Rasch model as a model for paired comparisons between the difficulties of test items in which ties are allowed to occur. First, it is indicated how a paired-comparisons design…

Burn Wise Educational Materials for Businesses

EPA Pesticide Factsheets

Burn Wise outreach material. Burn Wise is a partnership program of that emphasizes the importance of burning the right wood, the right way, in the right wood-burning appliance to protect your home, health, and the air we breathe.

The Visual Analogue Scale for Rating, Ranking and Paired-Comparison (VAS-RRP): A new technique for psychological measurement.

PubMed

Sung, Yao-Ting; Wu, Jeng-Shin

2018-04-17

Traditionally, the visual analogue scale (VAS) has been proposed to overcome the limitations of ordinal measures from Likert-type scales. However, the function of VASs to overcome the limitations of response styles to Likert-type scales has not yet been addressed. Previous research using ranking and paired comparisons to compensate for the response styles of Likert-type scales has suffered from limitations, such as that the total score of ipsative measures is a constant that cannot be analyzed by means of many common statistical techniques. In this study we propose a new scale, called the Visual Analogue Scale for Rating, Ranking, and Paired-Comparison (VAS-RRP), which can be used to collect rating, ranking, and paired-comparison data simultaneously, while avoiding the limitations of each of these data collection methods. The characteristics, use, and analytic method of VAS-RRPs, as well as how they overcome the disadvantages of Likert-type scales, ranking, and VASs, are discussed. On the basis of analyses of simulated and empirical data, this study showed that VAS-RRPs improved reliability, response style bias, and parameter recovery. Finally, we have also designed a VAS-RRP Generator for researchers' construction and administration of their own VAS-RRPs.

Joint coverage probability in a simulation study on Continuous-Time Markov Chain parameter estimation.

PubMed

Benoit, Julia S; Chan, Wenyaw; Doody, Rachelle S

2015-01-01

Parameter dependency within data sets in simulation studies is common, especially in models such as Continuous-Time Markov Chains (CTMC). Additionally, the literature lacks a comprehensive examination of estimation performance for the likelihood-based general multi-state CTMC. Among studies attempting to assess the estimation, none have accounted for dependency among parameter estimates. The purpose of this research is twofold: 1) to develop a multivariate approach for assessing accuracy and precision for simulation studies 2) to add to the literature a comprehensive examination of the estimation of a general 3-state CTMC model. Simulation studies are conducted to analyze longitudinal data with a trinomial outcome using a CTMC with and without covariates. Measures of performance including bias, component-wise coverage probabilities, and joint coverage probabilities are calculated. An application is presented using Alzheimer's disease caregiver stress levels. Comparisons of joint and component-wise parameter estimates yield conflicting inferential results in simulations from models with and without covariates. In conclusion, caution should be taken when conducting simulation studies aiming to assess performance and choice of inference should properly reflect the purpose of the simulation.

Accounting for Non-Gaussian Sources of Spatial Correlation in Parametric Functional Magnetic Resonance Imaging Paradigms I: Revisiting Cluster-Based Inferences.

PubMed

Gopinath, Kaundinya; Krishnamurthy, Venkatagiri; Sathian, K

2018-02-01

In a recent study, Eklund et al. employed resting-state functional magnetic resonance imaging data as a surrogate for null functional magnetic resonance imaging (fMRI) datasets and posited that cluster-wise family-wise error (FWE) rate-corrected inferences made by using parametric statistical methods in fMRI studies over the past two decades may have been invalid, particularly for cluster defining thresholds less stringent than p < 0.001; this was principally because the spatial autocorrelation functions (sACF) of fMRI data had been modeled incorrectly to follow a Gaussian form, whereas empirical data suggested otherwise. Here, we show that accounting for non-Gaussian signal components such as those arising from resting-state neural activity as well as physiological responses and motion artifacts in the null fMRI datasets yields first- and second-level general linear model analysis residuals with nearly uniform and Gaussian sACF. Further comparison with nonparametric permutation tests indicates that cluster-based FWE corrected inferences made with Gaussian spatial noise approximations are valid.

Cerebral glucose metabolic prediction from amnestic mild cognitive impairment to Alzheimer's dementia: a meta-analysis.

PubMed

Ma, Hai Rong; Sheng, Li Qin; Pan, Ping Lei; Wang, Gen Di; Luo, Rong; Shi, Hai Cun; Dai, Zhen Yu; Zhong, Jian Guo

2018-01-01

Brain 18 F-fluorodeoxyglucose positron emission tomography (FDG-PET) has been utilized to monitor disease conversion from amnestic mild cognitive impairment (aMCI) to Alzheimer's dementia (AD). However, the conversion patterns of FDG-PET metabolism across studies are not conclusive. We conducted a voxel-wise meta-analysis using Seed-based d Mapping that included 10 baseline voxel-wise FDG-PET comparisons between 93 aMCI converters and 129 aMCI non-converters from nine longitudinal studies. The most robust and reliable metabolic alterations that predicted conversion from aMCI to AD were localized in the left posterior cingulate cortex (PCC)/precuneus. Furthermore, meta-regression analyses indicated that baseline mean age and severity of cognitive impairment, and follow-up duration were significant moderators for metabolic alterations in aMCI converters. Our study revealed hypometabolism in the left PCC/precuneus as an early feature in the development of AD. This finding has important implications in understanding the neural substrates for AD conversion and could serve as a potential imaging biomarker for early detection of AD as well as for tracking disease progression at the predementia stage.

Cleavage Entropy as Quantitative Measure of Protease Specificity

PubMed Central

Fuchs, Julian E.; von Grafenstein, Susanne; Huber, Roland G.; Margreiter, Michael A.; Spitzer, Gudrun M.; Wallnoefer, Hannes G.; Liedl, Klaus R.

2013-01-01

A purely information theory-guided approach to quantitatively characterize protease specificity is established. We calculate an entropy value for each protease subpocket based on sequences of cleaved substrates extracted from the MEROPS database. We compare our results with known subpocket specificity profiles for individual proteases and protease groups (e.g. serine proteases, metallo proteases) and reflect them quantitatively. Summation of subpocket-wise cleavage entropy contributions yields a measure for overall protease substrate specificity. This total cleavage entropy allows ranking of different proteases with respect to their specificity, separating unspecific digestive enzymes showing high total cleavage entropy from specific proteases involved in signaling cascades. The development of a quantitative cleavage entropy score allows an unbiased comparison of subpocket-wise and overall protease specificity. Thus, it enables assessment of relative importance of physicochemical and structural descriptors in protease recognition. We present an exemplary application of cleavage entropy in tracing substrate specificity in protease evolution. This highlights the wide range of substrate promiscuity within homologue proteases and hence the heavy impact of a limited number of mutations on individual substrate specificity. PMID:23637583

Finite element approximation of the radiative transport equation in a medium with piece-wise constant refractive index

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

Lehtikangas, O., E-mail: Ossi.Lehtikangas@uef.fi; Tarvainen, T.; Department of Computer Science, University College London, Gower Street, London WC1E 6BT

2015-02-01

The radiative transport equation can be used as a light transport model in a medium with scattering particles, such as biological tissues. In the radiative transport equation, the refractive index is assumed to be constant within the medium. However, in biomedical media, changes in the refractive index can occur between different tissue types. In this work, light propagation in a medium with piece-wise constant refractive index is considered. Light propagation in each sub-domain with a constant refractive index is modeled using the radiative transport equation and the equations are coupled using boundary conditions describing Fresnel reflection and refraction phenomena onmore » the interfaces between the sub-domains. The resulting coupled system of radiative transport equations is numerically solved using a finite element method. The approach is tested with simulations. The results show that this coupled system describes light propagation accurately through comparison with the Monte Carlo method. It is also shown that neglecting the internal changes of the refractive index can lead to erroneous boundary measurements of scattered light.« less

Effect of tooth brushing on gloss retention and surface roughness of five bulk-fill resin composites.

PubMed

O'Neill, Catherine; Kreplak, Laurent; Rueggeberg, Frederick A; Labrie, Daniel; Shimokawa, Carlos Alberto Kenji; Price, Richard Bengt

2018-01-01

To determine the effects of tooth brushing on five bulk-fill resin based composites (RBCs). Ten samples of Filtek Supreme Enamel (control), Filtek One Bulk Fill, Tetric EvoCeram Bulk Fill, SonicFill 2, SDR flow+, and Admira Fusion X-tra were light cured for 20 seconds using the Valo Grand curing light. After 24 hours storage in air at 37°C, specimens were brushed in a random order using Colgate OpticWhite dentifrice and a soft toothbrush. Surface gloss was measured prior to brushing, after 5,000, 10,000 and 15,000 back and forth brushing cycles. Surface roughness was measured after 15,000 brushing cycles using atomic force microscopy (AFM) and selected scanning electron microscope (SEM) images were taken. The data was examined using ANOVA and pair-wise comparisons using Scheffe's post-hoc multiple comparison tests (α = 0.05). Surface gloss decreased and the surface roughness increased after brushing. Two-way ANOVA showed that both the RBC and the number of brushing cycles had a significant negative effect on the gloss. One-way ANOVA showed that the RBC had a significant effect on the roughness after 15,000 brushing cycles. For both gloss and roughness, brushing had the least effect on the nano-filled control and nano-filled bulk-fill RBC, and the greatest negative effect on Admira Fusion X-tra. The SEM images provided visual agreement. There was an excellent linear correlation (R 2  = 0.98) between the logarithm of the gloss and roughness. After brushing, the bulk-fill RBCs were all rougher than the control nano-filled RBC. The nano-filled bulk-fill RBC was the least affected by brushing. Bulk-fill RBCs lose their gloss faster and become rougher than the nanofilled conventional RBC, Filtek Supreme Ultra. The nanofilled bulk-fill RBC was the least affected by tooth brushing. © 2017 Wiley Periodicals, Inc.

Comparison of macroinvertebrate community structure between two riffle-based sampling protocols in Wyoming, Colorado, and Montana, 2000-2001

USGS Publications Warehouse

Peterson, David A.; Zumberge, Jeremy R.

2006-01-01

Samples of benthic macroinvertebrates were collected side-by-side from riffles at 12 stream sites in Wyoming, Colorado, and Montana during 2000-2001, following protocols established by the U.S. Geological Survey National Water-Quality Assessment (NAWQA) Program and the U.S. Environmental Protection Agency Environmental Monitoring and Assessment Program (EMAP). Samples from riffles were collected following NAWQA protocols, using a sampler with 425-micron net mesh-opening size from a total area of 1.25 m2 per sample in multiple riffles. Samples also were collected following EMAP protocols, using a sampler with 500-micron net mesh-opening size from a total area of 0.72 m2 per sample in multiple riffles. The taxonomic identification and enumeration of the samples followed procedures established for each program. Benthic macroinvertebrate community structure was compared between the data sets using individual metrics, a multimetric index, and multivariate analysis. Comparisons between the macroinvertebrate community structures were made after sequentially adjusting both data sets for: (1) ambiguous taxa, (2) taxonomic inconsistencies, and (3) differences in laboratory subsampling. After removal of ambiguous taxa, pair-wise differences in total taxa richness and Ephemeroptera taxa richness were statistically significant (p < 0.05). Differences between the data sets generally were not significant for richness of other taxa, tolerant taxa, semi-voltine taxa, functional feeding groups, diversity, and dominance. Sample scores calculated using the Wyoming Stream Integrity Index were not significantly different between the two data sets. After reconciling both data sets for taxonomic inconsistencies, total taxa richness and Ephemeroptera taxa richness remained significantly different between the data sets. After adjusting the data for differences in laboratory subsampling, the differences in taxa richness were no longer significant. Bray-Curtis similarity coefficients and non-metric multi-dimensional scaling were used to examine macroinvertebrate community structure. Similarity in community structure between sites was affected to a greater extent by taxa reconciliation than by adjustment for subsampling.

Veillonella, Firmicutes: Microbes disguised as Gram negatives.

PubMed

Vesth, Tammi; Ozen, Aslı; Andersen, Sandra C; Kaas, Rolf Sommer; Lukjancenko, Oksana; Bohlin, Jon; Nookaew, Intawat; Wassenaar, Trudy M; Ussery, David W

2013-12-20

The Firmicutes represent a major component of the intestinal microflora. The intestinal Firmicutes are a large, diverse group of organisms, many of which are poorly characterized due to their anaerobic growth requirements. Although most Firmicutes are Gram positive, members of the class Negativicutes, including the genus Veillonella, stain Gram negative. Veillonella are among the most abundant organisms of the oral and intestinal microflora of animals and humans, in spite of being strict anaerobes. In this work, the genomes of 24 Negativicutes, including eight Veillonella spp., are compared to 20 other Firmicutes genomes; a further 101 prokaryotic genomes were included, covering 26 phyla. Thus a total of 145 prokaryotic genomes were analyzed by various methods to investigate the apparent conflict of the Veillonella Gram stain and their taxonomic position within the Firmicutes. Comparison of the genome sequences confirms that the Negativicutes are distantly related to Clostridium spp., based on 16S rRNA, complete genomic DNA sequences, and a consensus tree based on conserved proteins. The genus Veillonella is relatively homogeneous: inter-genus pair-wise comparison identifies at least 1,350 shared proteins, although less than half of these are found in any given Clostridium genome. Only 27 proteins are found conserved in all analyzed prokaryote genomes. Veillonella has distinct metabolic properties, and significant similarities to genomes of Proteobacteria are not detected, with the exception of a shared LPS biosynthesis pathway. The clade within the class Negativicutes to which the genus Veillonella belongs exhibits unique properties, most of which are in common with Gram-positives and some with Gram negatives. They are only distantly related to Clostridia, but are even less closely related to Gram-negative species. Though the Negativicutes stain Gram-negative and possess two membranes, the genome and proteome analysis presented here confirm their place within the (mainly) Gram positive phylum of the Firmicutes. Further studies are required to unveil the evolutionary history of the Veillonella and other Negativicutes.

Veillonella, Firmicutes: Microbes disguised as Gram negatives

PubMed Central

Vesth, Tammi; Ozen, Aslı; Andersen, Sandra C.; Kaas, Rolf Sommer; Lukjancenko, Oksana; Bohlin, Jon; Nookaew, Intawat; Wassenaar, Trudy M.; Ussery, David W.

2013-01-01

The Firmicutes represent a major component of the intestinal microflora. The intestinal Firmicutes are a large, diverse group of organisms, many of which are poorly characterized due to their anaerobic growth requirements. Although most Firmicutes are Gram positive, members of the class Negativicutes, including the genus Veillonella, stain Gram negative. Veillonella are among the most abundant organisms of the oral and intestinal microflora of animals and humans, in spite of being strict anaerobes. In this work, the genomes of 24 Negativicutes, including eight Veillonella spp., are compared to 20 other Firmicutes genomes; a further 101 prokaryotic genomes were included, covering 26 phyla. Thus a total of 145 prokaryotic genomes were analyzed by various methods to investigate the apparent conflict of the Veillonella Gram stain and their taxonomic position within the Firmicutes. Comparison of the genome sequences confirms that the Negativicutes are distantly related to Clostridium spp., based on 16S rRNA, complete genomic DNA sequences, and a consensus tree based on conserved proteins. The genus Veillonella is relatively homogeneous: inter-genus pair-wise comparison identifies at least 1,350 shared proteins, although less than half of these are found in any given Clostridium genome. Only 27 proteins are found conserved in all analyzed prokaryote genomes. Veillonella has distinct metabolic properties, and significant similarities to genomes of Proteobacteria are not detected, with the exception of a shared LPS biosynthesis pathway. The clade within the class Negativicutes to which the genus Veillonella belongs exhibits unique properties, most of which are in common with Gram-positives and some with Gram negatives. They are only distantly related to Clostridia, but are even less closely related to Gram-negative species. Though the Negativicutes stain Gram-negative and possess two membranes, the genome and proteome analysis presented here confirm their place within the (mainly) Gram positive phylum of the Firmicutes. Further studies are required to unveil the evolutionary history of the Veillonella and other Negativicutes. PMID:24976898

Adenosine A1 receptor antagonist, L-97-1, improves survival and protects the kidney in a rat model of cecal ligation and puncture induced sepsis☆

PubMed Central

Wilson, Constance N.; Vance, Constance O.; Lechner, Melissa G.; Matuschak, George M.; Lechner, Andrew J.

2014-01-01

Previously it was reported that combining antibiotics with L-97-1, an adenosine A1 receptor antagonist, significantly improves survival and blocks acute lung injury induced by Yersinia pestis CO 99 in a rat model of pneumonic plague. In the current studies using a conscious rat model of cecal ligation and puncture (CLP) sepsis, L-97-1 was administered in daily intravenous infusions in combination with antibiotics to simulate the use of L-97-1 as an anti-sepsis therapeutic in the clinical setting. In these studies, when administered at 12 hours (h) following CLP, in combination with broad spectrum antibiotics, ceftriaxone and clindamycin, L-97-1 improves 7 day (d) survival [25%, 35%, and 75%, respectively for L-97-1 (10 mg/kg/h, 12.5 mg/kg/h, and 15 mg/kg/h) versus (vs.) 25% for antibiotics alone] in a dose-dependent manner. The addition of L-97-1, 15 mg/kg/h to antibiotics significantly increased 7 d survival following CLP compared to therapy with either antibiotics alone (P = 0.002) or L-97-1 at 15 mg/kg/h alone (P < 0.001) and was not significantly different than survival in sham CLP animals (Log-rank (Mantel-Cox) test with Bonferroni’s correction for multiple comparisons). Moreover, in these studies, in combination with antibiotics L-97-1 dose-dependently protects the kidney, significantly improving renal function at 24 h post CLP at 10 mg/kg/h (P < 0.001), 12.5 mg/kg/h (P < 0.0001), and 15 mg/kg/h (P < 0.0001) vs. antibiotics alone (ANOVA followed by Tukey’s post-hoc test for pair-wise comparisons). The results of these studies support efficacy for L-97-1 as an anti-sepsis therapeutic. PMID:25041842

Ultrasound measurement of inferior vena cava diameters by emergency department nurses.

PubMed

De Lorenzo, Robert A; Holbrook-Emmons, Victoria L

2014-01-01

Sonographic measurement of the inferior vena cava (IVC) diameter is a potentially important noninvasive estimate of fluid status. We researched whether nurses without prior ultrasonography experience could accurately obtain vena cava diameter measurements on models and subjects in comparison with those obtained by an expert sonographer. The design was a prospective educational study using a pre- and posttest of knowledge and a comparison of imaging performance between a subject and an expert sonographer. The setting was an urban teaching medical center with emergency nurses and a convenience sample of volunteer patients selected from the emergency department (ED). Nurses completed a written survey and a pretest to document prior training and experience in ultrasonography and assess baseline knowledge. A structured training program (3.5 hr in length) was provided over three sessions. Training consisted of didactic presentations, practice on phantoms (manikin models designed to provide the sonographic image of the human body when scanned by a trainee) and classmates, and one volunteer patient in the ED. Each nurse then measured IVC diameters on three different volunteer patients in transverse and longitudinal orientations using frozen images. An expert sonographer, blinded to subject results, performed the same examination. Correlations were determined, and a posttraining written examination was completed and results compared with the pretest using a pair-wise t test. Fourteen nurses, with a mean of 8 years' nursing experience (range = 2-18 years), participated. Nurse-expert R value correlation for the longitudinal orientation was 0.68 (95% confidence interval [CI] [0.35, 0.76]) and 0.59 (95% CI [0.47, 0.81]) for the transverse orientation. Posttest scores improved 8.2 percentage points (95% CI [4.0, 12.4]) from 83.3% to 91.5%. Following a brief training course, nurses with no prior sonography experience show moderately good correlation measuring the IVC diameter as compared with expert measurements, with better performance demonstrated in the longitudinal orientation.

In vitro study comparing fracture strength recovery of teeth restored with three esthetic bonding materials using different techniques.

PubMed

Rajput, Akhil; Ataide, Ida; Lambor, Rajan; Monteiro, Jeanne; Tar, Malika; Wadhawan, Neeraj

2010-01-01

Reattachment of the fractured fragment of a traumatized tooth (whenever available and usable) has become the treatment of choice in cases of uncomplicated crown fractures. Despite the presence of various bonding materials and techniques, laboratory data evaluating the biomechanical aspects of such procedures is largely lacking in the literature. The objective of this in vitro study was to evaluate the fracture strength recovery of incisors, following fragment restoration with three different techniques. A total of 90 extracted human maxillary central incisors were subjected to crown fractured under standard conditions. This was carried out by applying a compressive force from the buccal aspect of the clinical crown using a universal strength testing machine. The fractured teeth were equality distributed in three groups, defined on the basis of the technique used for reattachment: i) overcontour, ii) internal dentinal groove and iii) direct buildup. Each group was further subdivided into three subgroups on the basis of the intermediate restorative material used for reattachment, namely: i) hybrid composite (Filtek Z100 Universal Restorative, ii) nanocomposite (Filtek Z350) and iii) Ormocer (Voco Admira). Following reattachment, the crowns were re-fractured under standard conditions. The force required for fracture was recorded and was expressed as a percentage of the fracture strength of the intact tooth. The data was expressed as a percentage of the fracture strength of the intact tooth. The data was analyzed using two-way ANOVA and Bonferroni tests for pair-wise comparison. The results showed no statistically significant differences in fractures strength between the three groups (P > 0.05). However, comparison of the subgroups revealed statistically significant higher strength recovery percentages for the hybrid and the nanocomposite compared with the Ormocer material (P < 0.05). It was concluded that material properties have a significant influence on the success of reattachment procedures.

Comparison of scoring systems and outcome of patients admitted to a liver intensive care unit of a tertiary referral centre with severe variceal bleeding.

PubMed

Al-Freah, M A B; Gera, A; Martini, S; McPhail, M J W; Devlin, J; Harrison, P M; Shawcross, D; Abeles, R D; Taylor, N J; Auzinger, G; Bernal, W; Heneghan, M A; Wendon, J A

2014-06-01

Acute variceal haemorrhage (AVH) is associated with significant mortality. To determine outcome and factors associated with hospital mortality (HM) in patients with AVH admitted to intensive care unit (ICU) and to compare outcomes of patients requiring transfer to a tertiary ICU (transfer group, TG) to a local in-patient group (LG). A retrospective study of all adult patients (N = 177) admitted to ICU with AVH from 2000-2008 was performed. Median age was 48 years (16-80). Male represented 58%. Median MELD score was 16 (6-39), SOFA score was 8 (6-11). HM was higher in patients who had severe liver disease or critical illness measured by MELD, SOFA, APACHE II scores and number of failed organs (NFO), P < 0.05. Patients with day-1 lactate ≥ 2 mmol/L had increased HM (P < 0.001). MELD score performed as well as APACHE II, SOFA and NFO (P < 0.001) in predicting HM (AUROC = 0.84, 0.81, 0.79 and 0.82, respectively P > 0.05 for pair wise comparisons). Re-bleeding was associated with increased HM (56.9% vs. 31.6%, P = 0.002). The TG (n = 124) had less severe liver disease and critical illness and consequently had lower HM than local patients (32% vs. 57%, P = 0.002). TG patients with ≥2 endoscopies prior to transfer had increased 6-week mortality (P = 0.03). Time from bleeding to transfer ≥3 days was associated with re-bleeding (OR = 2.290, P = 0.043). MELD score was comparable to ICU prognostic models in predicting mortality. Blood lactate was also predictive of hospital mortality. Delays in referrals and repeated endoscopy were associated with increased re-bleeding and mortality in this group. © 2014 John Wiley & Sons Ltd.

Combination of monthly gravity field solutions from different processing centers

NASA Astrophysics Data System (ADS)

Jean, Yoomin; Meyer, Ulrich; Jäggi, Adrian

2015-04-01

Currently, the official GRACE Science Data System (SDS) monthly gravity field solutions are generated independently by the Centre for Space Research (CSR) and the German Research Centre for Geosciences (GFZ). Additional GRACE SDS monthly fields are provided by the Jet Propulsion Laboratory (JPL) for validation and outside the SDS by a number of other institutions worldwide. Although the adopted background models and processing standards have been harmonized more and more by the various processing centers during the past years, notable differences still exist and the users are more or less left alone with a decision which model to choose for their individual applications. Combinations are well-established in the area of other space geodetic techniques, such as the Global Navigation Satellite Systems (GNSS), Satellite Laser Ranging (SLR), and Very Long Baseline Interferometry (VLBI), where regular comparisons and combinations of space-geodetic products have tremendously increased the usefulness of the products in a wide range of disciplines and scientific applications. In the frame of the recently started Horizon 2020 project European Gravity Service for Improved Emergency Management (EGSIEM), a scientific combination service shall therefore be established to deliver the best gravity products for applications in Earth and environmental science research based on the unified knowledge of the European GRACE community. In a first step the large variety of available monthly GRACE gravity field solutions shall be mutually compared spatially and spectrally. We assess the noise of the raw as well as filtered solutions and compare the secular and seasonal periodic variations fitted to the monthly solutions. In a second step we will explore ways to generate combined solutions, e.g., based on a weighted average of the individual solutions using empirical weights derived from pair-wise comparisons. We will also assess the quality of such a combined solution and discuss the potential benefits for the GRACE and GRACE-FO user community.

Conformations of dendrimers in dilute solution

NASA Astrophysics Data System (ADS)

Timoshenko, Edward G.; Kuznetsov, Yuri A.; Connolly, Ronan

2002-11-01

Conformations of isolated homo-dendrimers of G=1-7 generations with D=1-6 spacers have been studied in the good and poor solvents, as well as across the coil-to-globule transition, by means of a version of the Gaussian self-consistent method and Monte Carlo simulation in continuous space based on the same coarse-grained model. The latter includes harmonic springs between connected monomers and the pair-wise Lennard-Jones potential with a hard core repulsion. The scaling law for the dendrimer size, the degrees of bond stretching and steric congestion, as well as the radial density, static structure factor, and asphericity have been analyzed. It is also confirmed that while smaller dendrimers have a dense core, larger ones develop a hollow domain at some separation from the center.

Single-Trial Classification of Multi-User P300-Based Brain-Computer Interface Using Riemannian Geometry.

PubMed

Korczowski, L; Congedo, M; Jutten, C

2015-08-01

The classification of electroencephalographic (EEG) data recorded from multiple users simultaneously is an important challenge in the field of Brain-Computer Interface (BCI). In this paper we compare different approaches for classification of single-trials Event-Related Potential (ERP) on two subjects playing a collaborative BCI game. The minimum distance to mean (MDM) classifier in a Riemannian framework is extended to use the diversity of the inter-subjects spatio-temporal statistics (MDM-hyper) or to merge multiple classifiers (MDM-multi). We show that both these classifiers outperform significantly the mean performance of the two users and analogous classifiers based on the step-wise linear discriminant analysis. More importantly, the MDM-multi outperforms the performance of the best player within the pair.

A comparative study for chest radiograph image retrieval using binary texture and deep learning classification.

PubMed

Anavi, Yaron; Kogan, Ilya; Gelbart, Elad; Geva, Ofer; Greenspan, Hayit

2015-08-01

In this work various approaches are investigated for X-ray image retrieval and specifically chest pathology retrieval. Given a query image taken from a data set of 443 images, the objective is to rank images according to similarity. Different features, including binary features, texture features, and deep learning (CNN) features are examined. In addition, two approaches are investigated for the retrieval task. One approach is based on the distance of image descriptors using the above features (hereon termed the "descriptor"-based approach); the second approach ("classification"-based approach) is based on a probability descriptor, generated by a pair-wise classification of each two classes (pathologies) and their decision values using an SVM classifier. Best results are achieved using deep learning features in a classification scheme.

Eigenvalue-eigenvector decomposition (EED) analysis of dissimilarity and covariance matrix obtained from total synchronous fluorescence spectral (TSFS) data sets of herbal preparations: Optimizing the classification approach

NASA Astrophysics Data System (ADS)

Tarai, Madhumita; Kumar, Keshav; Divya, O.; Bairi, Partha; Mishra, Kishor Kumar; Mishra, Ashok Kumar

2017-09-01

The present work compares the dissimilarity and covariance based unsupervised chemometric classification approaches by taking the total synchronous fluorescence spectroscopy data sets acquired for the cumin and non-cumin based herbal preparations. The conventional decomposition method involves eigenvalue-eigenvector analysis of the covariance of the data set and finds the factors that can explain the overall major sources of variation present in the data set. The conventional approach does this irrespective of the fact that the samples belong to intrinsically different groups and hence leads to poor class separation. The present work shows that classification of such samples can be optimized by performing the eigenvalue-eigenvector decomposition on the pair-wise dissimilarity matrix.

New Basis Functions for the Electromagnetic Solution of Arbitrarily-shaped, Three Dimensional Conducting Bodies Using Method of Moments

NASA Technical Reports Server (NTRS)

Mackenzie, Anne I.; Baginski, Michael E.; Rao, Sadasiva M.

2007-01-01

In this work, we present a new set of basis functions, de ned over a pair of planar triangular patches, for the solution of electromagnetic scattering and radiation problems associated with arbitrarily-shaped surfaces using the method of moments solution procedure. The basis functions are constant over the function subdomain and resemble pulse functions for one and two dimensional problems. Further, another set of basis functions, point-wise orthogonal to the first set, is also de ned over the same function space. The primary objective of developing these basis functions is to utilize them for the electromagnetic solution involving conducting, dielectric, and composite bodies. However, in the present work, only the conducting body solution is presented and compared with other data.

New Basis Functions for the Electromagnetic Solution of Arbitrarily-shaped, Three Dimensional Conducting Bodies using Method of Moments

NASA Technical Reports Server (NTRS)

Mackenzie, Anne I.; Baginski, Michael E.; Rao, Sadasiva M.

2008-01-01

In this work, we present a new set of basis functions, defined over a pair of planar triangular patches, for the solution of electromagnetic scattering and radiation problems associated with arbitrarily-shaped surfaces using the method of moments solution procedure. The basis functions are constant over the function subdomain and resemble pulse functions for one and two dimensional problems. Further, another set of basis functions, point-wise orthogonal to the first set, is also defined over the same function space. The primary objective of developing these basis functions is to utilize them for the electromagnetic solution involving conducting, dielectric, and composite bodies. However, in the present work, only the conducting body solution is presented and compared with other data.

Molecular epidemiology of Plum pox virus in Japan.

PubMed

Maejima, Kensaku; Himeno, Misako; Komatsu, Ken; Takinami, Yusuke; Hashimoto, Masayoshi; Takahashi, Shuichiro; Yamaji, Yasuyuki; Oshima, Kenro; Namba, Shigetou

2011-05-01

For a molecular epidemiological study based on complete genome sequences, 37 Plum pox virus (PPV) isolates were collected from the Kanto region in Japan. Pair-wise analyses revealed that all 37 Japanese isolates belong to the PPV-D strain, with low genetic diversity (less than 0.8%). In phylogenetic analysis of the PPV-D strain based on complete nucleotide sequences, the relationships of the PPV-D strain were reconstructed with high resolution: at the global level, the American, Canadian, and Japanese isolates formed their own distinct monophyletic clusters, suggesting that the routes of viral entry into these countries were independent; at the local level, the actual transmission histories of PPV were precisely reconstructed with high bootstrap support. This is the first description of the molecular epidemiology of PPV based on complete genome sequences.

Immediate effects of form-class constraints on spoken word recognition

PubMed Central

Magnuson, James S.; Tanenhaus, Michael K.; Aslin, Richard N.

2008-01-01

In many domains of cognitive processing there is strong support for bottom-up priority and delayed top-down (contextual) integration. We ask whether this applies to supra-lexical context that could potentially constrain lexical access. Previous findings of early context integration in word recognition have typically used constraints that can be linked to pair-wise conceptual relations between words. Using an artificial lexicon, we found immediate integration of syntactic expectations based on pragmatic constraints linked to syntactic categories rather than words: phonologically similar “nouns” and “adjectives” did not compete when a combination of syntactic and visual information strongly predicted form class. These results suggest that predictive context is integrated continuously, and that previous findings supporting delayed context integration stem from weak contexts rather than delayed integration. PMID:18675408

Speech Discrimination in Preschool Children: A Comparison of Two Tasks.

ERIC Educational Resources Information Center

Menary, Susan; And Others

1982-01-01

Eleven four-year-old children were tested for discrimination of the following word pairs: rope/robe, seat/seed, pick/pig, ice/eyes, and mouse/mouth. All word pairs were found to be discriminable, but performance on seat/seed and mouse/mouth was inferior to that of the other word pairs. (Author)

Stimulus-related independent component and voxel-wise analysis of human brain activity during free viewing of a feature film.

PubMed

Lahnakoski, Juha M; Salmi, Juha; Jääskeläinen, Iiro P; Lampinen, Jouko; Glerean, Enrico; Tikka, Pia; Sams, Mikko

2012-01-01

Understanding how the brain processes stimuli in a rich natural environment is a fundamental goal of neuroscience. Here, we showed a feature film to 10 healthy volunteers during functional magnetic resonance imaging (fMRI) of hemodynamic brain activity. We then annotated auditory and visual features of the motion picture to inform analysis of the hemodynamic data. The annotations were fitted to both voxel-wise data and brain network time courses extracted by independent component analysis (ICA). Auditory annotations correlated with two independent components (IC) disclosing two functional networks, one responding to variety of auditory stimulation and another responding preferentially to speech but parts of the network also responding to non-verbal communication. Visual feature annotations correlated with four ICs delineating visual areas according to their sensitivity to different visual stimulus features. In comparison, a separate voxel-wise general linear model based analysis disclosed brain areas preferentially responding to sound energy, speech, music, visual contrast edges, body motion and hand motion which largely overlapped the results revealed by ICA. Differences between the results of IC- and voxel-based analyses demonstrate that thorough analysis of voxel time courses is important for understanding the activity of specific sub-areas of the functional networks, while ICA is a valuable tool for revealing novel information about functional connectivity which need not be explained by the predefined model. Our results encourage the use of naturalistic stimuli and tasks in cognitive neuroimaging to study how the brain processes stimuli in rich natural environments.