Development and Standardization of a Test for Pragmatic Language Skills in Egyptian Arabic: The Egyptian Arabic Pragmatic Language Test (EAPLT).

PubMed

Khodeir, Mona S; Hegazi, Mona A; Saleh, Marwa M

2018-03-19

The aim of this study was to standardize an Egyptian Arabic Pragmatic Language Test (EAPLT) using linguistically and socially suitable questions and pictures in order to be able to address specific deficits in this language domain. Questions and pictures were designed for the EAPLT to assess 3 pragmatic language subsets: pragmatic skills, functions, and factors. Ten expert phoniatricians were asked to review the EAPLT and complete a questionnaire to assess the validity of the test items. The EAPLT was applied in 120 typically developing Arabic-speaking Egyptian children (64 females and 56 males) randomly selected by inclusion and exclusion criteria in the age range between 2 years, 1 month, 1 day and 9 years, 12 months, 31 days. Children's scores were used to calculate the means and standard deviations and the 5th and 95th percentiles to determine the age of the pragmatic skills acquisition. All experts have mostly agreed that the EAPLT gives a general idea about children's pragmatic language development. Test-retest reliability analysis proved the high reliability and internal consistency of the EAPLT subsets. A statistically significant correlation was found between the test subsets and age. The EAPLT is a valid and reliable Egyptian Arabic test that can be applied in order to detect a pragmatic language delay. © 2018 S. Karger AG, Basel.

Frontiers in Applied and Computational Mathematics 05’

DTIC Science & Technology

2005-03-01

dynamics, forcing subsets to have the same oscillation numbers and interleaving spiking times . Our analysis follows the theory of coupled systems of...continuum is described by a continuous- time stochastic process, as are their internal dynamics. Soluble factors, such as cytokines, are represent- ed...scale of a partide pas- sage time through the reaction zone. Both are realistic for many systems of physical interest. A higher order theory includes

Task Decomposition in Human Reliability Analysis

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

Boring, Ronald Laurids; Joe, Jeffrey Clark

2014-06-01

In the probabilistic safety assessments (PSAs) used in the nuclear industry, human failure events (HFEs) are determined as a subset of hardware failures, namely those hardware failures that could be triggered by human action or inaction. This approach is top-down, starting with hardware faults and deducing human contributions to those faults. Elsewhere, more traditionally human factors driven approaches would tend to look at opportunities for human errors first in a task analysis and then identify which of those errors is risk significant. The intersection of top-down and bottom-up approaches to defining HFEs has not been carefully studied. Ideally, both approachesmore » should arrive at the same set of HFEs. This question remains central as human reliability analysis (HRA) methods are generalized to new domains like oil and gas. The HFEs used in nuclear PSAs tend to be top-down— defined as a subset of the PSA—whereas the HFEs used in petroleum quantitative risk assessments (QRAs) are more likely to be bottom-up—derived from a task analysis conducted by human factors experts. The marriage of these approaches is necessary in order to ensure that HRA methods developed for top-down HFEs are also sufficient for bottom-up applications.« less

Performance bounds for modal analysis using sparse linear arrays

NASA Astrophysics Data System (ADS)

Li, Yuanxin; Pezeshki, Ali; Scharf, Louis L.; Chi, Yuejie

2017-05-01

We study the performance of modal analysis using sparse linear arrays (SLAs) such as nested and co-prime arrays, in both first-order and second-order measurement models. We treat SLAs as constructed from a subset of sensors in a dense uniform linear array (ULA), and characterize the performance loss of SLAs with respect to the ULA due to using much fewer sensors. In particular, we claim that, provided the same aperture, in order to achieve comparable performance in terms of Cramér-Rao bound (CRB) for modal analysis, SLAs require more snapshots, of which the number is about the number of snapshots used by ULA times the compression ratio in the number of sensors. This is shown analytically for the case with one undamped mode, as well as empirically via extensive numerical experiments for more complex scenarios. Moreover, the misspecified CRB proposed by Richmond and Horowitz is also studied, where SLAs suffer more performance loss than their ULA counterpart.

Accelerated time-of-flight (TOF) PET image reconstruction using TOF bin subsetization and TOF weighting matrix pre-computation.

PubMed

Mehranian, Abolfazl; Kotasidis, Fotis; Zaidi, Habib

2016-02-07

Time-of-flight (TOF) positron emission tomography (PET) technology has recently regained popularity in clinical PET studies for improving image quality and lesion detectability. Using TOF information, the spatial location of annihilation events is confined to a number of image voxels along each line of response, thereby the cross-dependencies of image voxels are reduced, which in turns results in improved signal-to-noise ratio and convergence rate. In this work, we propose a novel approach to further improve the convergence of the expectation maximization (EM)-based TOF PET image reconstruction algorithm through subsetization of emission data over TOF bins as well as azimuthal bins. Given the prevalence of TOF PET, we elaborated the practical and efficient implementation of TOF PET image reconstruction through the pre-computation of TOF weighting coefficients while exploiting the same in-plane and axial symmetries used in pre-computation of geometric system matrix. In the proposed subsetization approach, TOF PET data were partitioned into a number of interleaved TOF subsets, with the aim of reducing the spatial coupling of TOF bins and therefore to improve the convergence of the standard maximum likelihood expectation maximization (MLEM) and ordered subsets EM (OSEM) algorithms. The comparison of on-the-fly and pre-computed TOF projections showed that the pre-computation of the TOF weighting coefficients can considerably reduce the computation time of TOF PET image reconstruction. The convergence rate and bias-variance performance of the proposed TOF subsetization scheme were evaluated using simulated, experimental phantom and clinical studies. Simulations demonstrated that as the number of TOF subsets is increased, the convergence rate of MLEM and OSEM algorithms is improved. It was also found that for the same computation time, the proposed subsetization gives rise to further convergence. The bias-variance analysis of the experimental NEMA phantom and a clinical FDG-PET study also revealed that for the same noise level, a higher contrast recovery can be obtained by increasing the number of TOF subsets. It can be concluded that the proposed TOF weighting matrix pre-computation and subsetization approaches enable to further accelerate and improve the convergence properties of OSEM and MLEM algorithms, thus opening new avenues for accelerated TOF PET image reconstruction.

Accelerated time-of-flight (TOF) PET image reconstruction using TOF bin subsetization and TOF weighting matrix pre-computation

NASA Astrophysics Data System (ADS)

Mehranian, Abolfazl; Kotasidis, Fotis; Zaidi, Habib

2016-02-01

Time-of-flight (TOF) positron emission tomography (PET) technology has recently regained popularity in clinical PET studies for improving image quality and lesion detectability. Using TOF information, the spatial location of annihilation events is confined to a number of image voxels along each line of response, thereby the cross-dependencies of image voxels are reduced, which in turns results in improved signal-to-noise ratio and convergence rate. In this work, we propose a novel approach to further improve the convergence of the expectation maximization (EM)-based TOF PET image reconstruction algorithm through subsetization of emission data over TOF bins as well as azimuthal bins. Given the prevalence of TOF PET, we elaborated the practical and efficient implementation of TOF PET image reconstruction through the pre-computation of TOF weighting coefficients while exploiting the same in-plane and axial symmetries used in pre-computation of geometric system matrix. In the proposed subsetization approach, TOF PET data were partitioned into a number of interleaved TOF subsets, with the aim of reducing the spatial coupling of TOF bins and therefore to improve the convergence of the standard maximum likelihood expectation maximization (MLEM) and ordered subsets EM (OSEM) algorithms. The comparison of on-the-fly and pre-computed TOF projections showed that the pre-computation of the TOF weighting coefficients can considerably reduce the computation time of TOF PET image reconstruction. The convergence rate and bias-variance performance of the proposed TOF subsetization scheme were evaluated using simulated, experimental phantom and clinical studies. Simulations demonstrated that as the number of TOF subsets is increased, the convergence rate of MLEM and OSEM algorithms is improved. It was also found that for the same computation time, the proposed subsetization gives rise to further convergence. The bias-variance analysis of the experimental NEMA phantom and a clinical FDG-PET study also revealed that for the same noise level, a higher contrast recovery can be obtained by increasing the number of TOF subsets. It can be concluded that the proposed TOF weighting matrix pre-computation and subsetization approaches enable to further accelerate and improve the convergence properties of OSEM and MLEM algorithms, thus opening new avenues for accelerated TOF PET image reconstruction.

Feature relevance assessment for the semantic interpretation of 3D point cloud data

NASA Astrophysics Data System (ADS)

Weinmann, M.; Jutzi, B.; Mallet, C.

2013-10-01

The automatic analysis of large 3D point clouds represents a crucial task in photogrammetry, remote sensing and computer vision. In this paper, we propose a new methodology for the semantic interpretation of such point clouds which involves feature relevance assessment in order to reduce both processing time and memory consumption. Given a standard benchmark dataset with 1.3 million 3D points, we first extract a set of 21 geometric 3D and 2D features. Subsequently, we apply a classifier-independent ranking procedure which involves a general relevance metric in order to derive compact and robust subsets of versatile features which are generally applicable for a large variety of subsequent tasks. This metric is based on 7 different feature selection strategies and thus addresses different intrinsic properties of the given data. For the example of semantically interpreting 3D point cloud data, we demonstrate the great potential of smaller subsets consisting of only the most relevant features with 4 different state-of-the-art classifiers. The results reveal that, instead of including as many features as possible in order to compensate for lack of knowledge, a crucial task such as scene interpretation can be carried out with only few versatile features and even improved accuracy.

Variable Neighborhood Search Heuristics for Selecting a Subset of Variables in Principal Component Analysis

ERIC Educational Resources Information Center

Brusco, Michael J.; Singh, Renu; Steinley, Douglas

2009-01-01

The selection of a subset of variables from a pool of candidates is an important problem in several areas of multivariate statistics. Within the context of principal component analysis (PCA), a number of authors have argued that subset selection is crucial for identifying those variables that are required for correct interpretation of the…

Ordering Elements and Subsets: Examples for Student Understanding

ERIC Educational Resources Information Center

Mellinger, Keith E.

2004-01-01

Teaching the art of counting can be quite difficult. Many undergraduate students have difficulty separating the ideas of permutation, combination, repetition, etc. This article develops some examples to help explain some of the underlying theory while looking carefully at the selection of various subsets of objects from a larger collection. The…

Barrett's Oesophagus in an Achalasia Patient: Immunological Analysis and Comparison with a Group of Achalasia Patients

PubMed Central

Torres-Landa, Samuel; Coss-Adame, Enrique; Valdovinos, Miguel A.; Alejandro-Medrano, Edgar; Ramos-Ávalos, Bárbara; Martínez-Benítez, Braulio

2016-01-01

The aim of the study was to characterize the presence of diverse CD4 and CD8 T cell subsets and regulatory cells in peripheral blood and lower oesophageal sphincter (LES) from a young patient with BE/achalasia without treatment versus achalasia group. In order to characterize the circulating cells in this patient, a cytometric analysis was performed. LES tissue was evaluated by double-immunostaining procedure. Five healthy blood donors, 5 type achalasia patients, and 5 oesophagus tissue samples (gastrooesophageal junction) from transplant donors were included as control groups. A conspicuous systemic inflammation was determined in BE/achalasia patient and achalasia versus healthy volunteer group. Nonetheless, a predominance of Th22, Th2, IFN-α-producing T cells, Tregs, Bregs, and pDCregs was observed in BE/achalasia patient versus achalasia group. A low percentage of Th1 subset in BE/achalasia versus achalasia group was determined. A noticeable increase in tissue of Th22, Th17, Th2, Tregs, Bregs, and pDCregs was observed in BE/achalasia versus achalasia group. Th1 subset was lower in the BE/achalasia patient versus achalasia group. This study suggests that inflammation is a possible factor in the pathogenesis of BE/achalasia. Further research needs to be performed to understand the specific cause of the correlation between BE and achalasia. PMID:27752370

Analysis of EPA's endocrine screening battery and recommendations for further review.

PubMed

Schapaugh, Adam W; McFadden, Lisa G; Zorrilla, Leah M; Geter, David R; Stuchal, Leah D; Sunger, Neha; Borgert, Christopher J

2015-08-01

EPA's Endocrine Disruptor Screening Program Tier 1 battery consists of eleven assays intended to identify the potential of a chemical to interact with the estrogen, androgen, thyroid, or steroidogenesis systems. We have collected control data from a subset of test order recipients from the first round of screening. The analysis undertaken herein demonstrates that the EPA should review all testing methods prior to issuing further test orders. Given the frequency with which certain performance criteria were violated, a primary focus of that review should consider adjustments to these standards to better reflect biological variability. A second focus should be to provide detailed, assay-specific direction on when results should be discarded; no clear guidance exists on the degree to which assays need to be re-run for failing to meet performance criteria. A third focus should be to identify permissible differences in study design and execution that have a large influence on endpoint variance. Experimental guidelines could then be re-defined such that endpoint variances are reduced and performance criteria are violated less frequently. It must be emphasized that because we were restricted to a subset (approximately half) of the control data, our analyses serve only as examples to underscore the importance of a detailed, rigorous, and comprehensive evaluation of the performance of the battery. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Query-Driven Visualization and Analysis

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

Ruebel, Oliver; Bethel, E. Wes; Prabhat, Mr.

2012-11-01

This report focuses on an approach to high performance visualization and analysis, termed query-driven visualization and analysis (QDV). QDV aims to reduce the amount of data that needs to be processed by the visualization, analysis, and rendering pipelines. The goal of the data reduction process is to separate out data that is "scientifically interesting'' and to focus visualization, analysis, and rendering on that interesting subset. The premise is that for any given visualization or analysis task, the data subset of interest is much smaller than the larger, complete data set. This strategy---extracting smaller data subsets of interest and focusing ofmore » the visualization processing on these subsets---is complementary to the approach of increasing the capacity of the visualization, analysis, and rendering pipelines through parallelism. This report discusses the fundamental concepts in QDV, their relationship to different stages in the visualization and analysis pipelines, and presents QDV's application to problems in diverse areas, ranging from forensic cybersecurity to high energy physics.« less

Computer access security code system

NASA Technical Reports Server (NTRS)

Collins, Earl R., Jr. (Inventor)

1990-01-01

A security code system for controlling access to computer and computer-controlled entry situations comprises a plurality of subsets of alpha-numeric characters disposed in random order in matrices of at least two dimensions forming theoretical rectangles, cubes, etc., such that when access is desired, at least one pair of previously unused character subsets not found in the same row or column of the matrix is chosen at random and transmitted by the computer. The proper response to gain access is transmittal of subsets which complete the rectangle, and/or a parallelepiped whose opposite corners were defined by first groups of code. Once used, subsets are not used again to absolutely defeat unauthorized access by eavesdropping, and the like.

Comparative Expression Profiling of Distinct T Cell Subsets Undergoing Oxidative Stress

PubMed Central

Lichtenfels, Rudolf; Mougiakakos, Dimitrios; Johansson, C. Christian; Dressler, Sven P.; Recktenwald, Christian V.; Kiessling, Rolf; Seliger, Barbara

2012-01-01

The clinical outcome of adoptive T cell transfer-based immunotherapies is often limited due to different escape mechanisms established by tumors in order to evade the hosts' immune system. The establishment of an immunosuppressive micromilieu by tumor cells along with distinct subsets of tumor-infiltrating lymphocytes is often associated with oxidative stress that can affect antigen-specific memory/effector cytotoxic T cells thereby substantially reducing their frequency and functional activation. Therefore, protection of tumor-reactive cytotoxic T lymphocytes from oxidative stress may enhance the anti-tumor-directed immune response. In order to better define the key pathways/proteins involved in the response to oxidative stress a comparative 2-DE-based proteome analysis of naïve CD45RA+ and their memory/effector CD45RO+ T cell counterparts in the presence and absence of low dose hydrogen peroxide (H2O2) was performed in this pilot study. Based on the profiling data of these T cell subpopulations under the various conditions, a series of differentially expressed spots were defined, members thereof identified by mass spectrometry and subsequently classified according to their cellular function and localization. Representative targets responding to oxidative stress including proteins involved in signaling pathways, in regulating the cellular redox status as well as in shaping/maintaining the structural cell integrity were independently verified at the transcript and protein level under the same conditions in both T cell subsets. In conclusion the resulting profiling data describe complex, oxidative stress-induced, but not strictly concordant changes within the respective expression profiles of CD45RA+ and CD45RO+ T cells. Some of the differentially expressed genes/proteins might be further exploited as potential targets toward modulating the redox capacity of the distinct lymphocyte subsets thereby providing the basis for further studies aiming at rendering them more resistant to tumor micromilieu-induced oxidative stress. PMID:22911781

Isolation and Flow Cytometry Analysis of Innate Lymphoid Cells from the Intestinal Lamina Propria.

PubMed

Gronke, Konrad; Kofoed-Nielsen, Michael; Diefenbach, Andreas

2017-01-01

The intestinal mucosa constitutes the biggest surface area of the body. It is constantly challenged by bacteria, commensal and pathogenic, protozoa, and food-derived irritants. In order to maintain homeostasis, a complex network of signaling circuits has evolved that includes contributions of immune cells. In recent years a subset of lymphocytes, which belong to the innate immune system, has caught particular attention. These so-called innate lymphoid cells (ILC) reside within the lamina propria of the small and large intestines and rapidly respond to environmental challenges. They provide immunity to various types of infections but may also contribute to organ homeostasis as they produce factors acting on epithelial cells thereby enhancing barrier integrity. Here, we describe how these cells can be isolated from their environment and provide an in-depth protocol how to visualize the various ILC subsets by flow cytometry.

Top-down and bottom-up definitions of human failure events in human reliability analysis

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

Boring, Ronald Laurids

2014-10-01

In the probabilistic risk assessments (PRAs) used in the nuclear industry, human failure events (HFEs) are determined as a subset of hardware failures, namely those hardware failures that could be triggered by human action or inaction. This approach is top-down, starting with hardware faults and deducing human contributions to those faults. Elsewhere, more traditionally human factors driven approaches would tend to look at opportunities for human errors first in a task analysis and then identify which of those errors is risk significant. The intersection of top-down and bottom-up approaches to defining HFEs has not been carefully studied. Ideally, both approachesmore » should arrive at the same set of HFEs. This question is crucial, however, as human reliability analysis (HRA) methods are generalized to new domains like oil and gas. The HFEs used in nuclear PRAs tend to be top-down—defined as a subset of the PRA—whereas the HFEs used in petroleum quantitative risk assessments (QRAs) often tend to be bottom-up—derived from a task analysis conducted by human factors experts. The marriage of these approaches is necessary in order to ensure that HRA methods developed for top-down HFEs are also sufficient for bottom-up applications.« less

Forecasting Advancement Rates to Petty Officer Third Class for U.S. Navy Hospital Corpsmen

DTIC Science & Technology

2014-06-01

variable. c. Designation of Data Subsets for Cross-Validation In order to maintain the integrity of the analysis and test the fitted models’ predictive...two models, an H-L goodness-of-fit test is conducted on the 1,524 individual Sailors within the designated test data set; the results of which are...the total number of sea months, the proportion of vacancies to test takers, Armed Forces Qualification Test score, and performance mark average

Clustering, Seriation, and Subset Extraction of Confusion Data

ERIC Educational Resources Information Center

Brusco, Michael J.; Steinley, Douglas

2006-01-01

The study of confusion data is a well established practice in psychology. Although many types of analytical approaches for confusion data are available, among the most common methods are the extraction of 1 or more subsets of stimuli, the partitioning of the complete stimulus set into distinct groups, and the ordering of the stimulus set. Although…

Heterogeneity in Neutrophil Microparticles Reveals Distinct Proteome and Functional Properties*

PubMed Central

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

2013-01-01

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

Comparative analysis of QSAR models for predicting pK(a) of organic oxygen acids and nitrogen bases from molecular structure.

PubMed

Yu, Haiying; Kühne, Ralph; Ebert, Ralf-Uwe; Schüürmann, Gerrit

2010-11-22

For 1143 organic compounds comprising 580 oxygen acids and 563 nitrogen bases that cover more than 17 orders of experimental pK(a) (from -5.00 to 12.23), the pK(a) prediction performances of ACD, SPARC, and two calibrations of a semiempirical quantum chemical (QC) AM1 approach have been analyzed. The overall root-mean-square errors (rms) for the acids are 0.41, 0.58 (0.42 without ortho-substituted phenols with intramolecular H-bonding), and 0.55 and for the bases are 0.65, 0.70, 1.17, and 1.27 for ACD, SPARC, and both QC methods, respectively. Method-specific performances are discussed in detail for six acid subsets (phenols and aromatic and aliphatic carboxylic acids with different substitution patterns) and nine base subsets (anilines, primary, secondary and tertiary amines, meta/para-substituted and ortho-substituted pyridines, pyrimidines, imidazoles, and quinolines). The results demonstrate an overall better performance for acids than for bases but also a substantial variation across subsets. For the overall best-performing ACD, rms ranges from 0.12 to 1.11 and 0.40 to 1.21 pK(a) units for the acid and base subsets, respectively. With regard to the squared correlation coefficient r², the results are 0.86 to 0.96 (acids) and 0.79 to 0.95 (bases) for ACD, 0.77 to 0.95 (acids) and 0.85 to 0.97 (bases) for SPARC, and 0.64 to 0.87 (acids) and 0.43 to 0.83 (bases) for the QC methods, respectively. Attention is paid to structural and method-specific causes for observed pitfalls. The significant subset dependence of the prediction performances suggests a consensus modeling approach.

Structure, organization, and sequence of alpha satellite DNA from human chromosome 17: evidence for evolution by unequal crossing-over and an ancestral pentamer repeat shared with the human X chromosome.

PubMed

Waye, J S; Willard, H F

1986-09-01

The centromeric regions of all human chromosomes are characterized by distinct subsets of a diverse tandemly repeated DNA family, alpha satellite. On human chromosome 17, the predominant form of alpha satellite is a 2.7-kilobase-pair higher-order repeat unit consisting of 16 alphoid monomers. We present the complete nucleotide sequence of the 16-monomer repeat, which is present in 500 to 1,000 copies per chromosome 17, as well as that of a less abundant 15-monomer repeat, also from chromosome 17. These repeat units were approximately 98% identical in sequence, differing by the exclusion of precisely 1 monomer from the 15-monomer repeat. Homologous unequal crossing-over is suggested as a probable mechanism by which the different repeat lengths on chromosome 17 were generated, and the putative site of such a recombination event is identified. The monomer organization of the chromosome 17 higher-order repeat unit is based, in part, on tandemly repeated pentamers. A similar pentameric suborganization has been previously demonstrated for alpha satellite of the human X chromosome. Despite the organizational similarities, substantial sequence divergence distinguishes these subsets. Hybridization experiments indicate that the chromosome 17 and X subsets are more similar to each other than to the subsets found on several other human chromosomes. We suggest that the chromosome 17 and X alpha satellite subsets may be related components of a larger alphoid subfamily which have evolved from a common ancestral repeat into the contemporary chromosome-specific subsets.

Technical Proceedings fo the Symposium on Military Information Systems Engineering (Panel 11 on Information Processing Technology, Defence Research Group).

DTIC Science & Technology

1991-12-27

session. The following gives the flavour of the comments made. 17. Prototyping captures requirements. The prototype exercises requirements and allows the...can modify the data in a given sub-set. These sub-sets can be used as granules of database distribu- tion in order to simplify access control. (3

OPTIMAL NETWORK TOPOLOGY DESIGN

NASA Technical Reports Server (NTRS)

Yuen, J. H.

1994-01-01

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

Decision Variants for the Automatic Determination of Optimal Feature Subset in RF-RFE.

PubMed

Chen, Qi; Meng, Zhaopeng; Liu, Xinyi; Jin, Qianguo; Su, Ran

2018-06-15

Feature selection, which identifies a set of most informative features from the original feature space, has been widely used to simplify the predictor. Recursive feature elimination (RFE), as one of the most popular feature selection approaches, is effective in data dimension reduction and efficiency increase. A ranking of features, as well as candidate subsets with the corresponding accuracy, is produced through RFE. The subset with highest accuracy (HA) or a preset number of features (PreNum) are often used as the final subset. However, this may lead to a large number of features being selected, or if there is no prior knowledge about this preset number, it is often ambiguous and subjective regarding final subset selection. A proper decision variant is in high demand to automatically determine the optimal subset. In this study, we conduct pioneering work to explore the decision variant after obtaining a list of candidate subsets from RFE. We provide a detailed analysis and comparison of several decision variants to automatically select the optimal feature subset. Random forest (RF)-recursive feature elimination (RF-RFE) algorithm and a voting strategy are introduced. We validated the variants on two totally different molecular biology datasets, one for a toxicogenomic study and the other one for protein sequence analysis. The study provides an automated way to determine the optimal feature subset when using RF-RFE.

Topology design and performance analysis of an integrated communication network

NASA Technical Reports Server (NTRS)

Li, V. O. K.; Lam, Y. F.; Hou, T. C.; Yuen, J. H.

1985-01-01

A research study on the topology design and performance analysis for the Space Station Information System (SSIS) network is conducted. It is begun with a survey of existing research efforts in network topology design. Then a new approach for topology design is presented. It uses an efficient algorithm to generate candidate network designs (consisting of subsets of the set of all network components) in increasing order of their total costs, and checks each design to see if it forms an acceptable network. This technique gives the true cost-optimal network, and is particularly useful when the network has many constraints and not too many components. The algorithm for generating subsets is described in detail, and various aspects of the overall design procedure are discussed. Two more efficient versions of this algorithm (applicable in specific situations) are also given. Next, two important aspects of network performance analysis: network reliability and message delays are discussed. A new model is introduced to study the reliability of a network with dependent failures. For message delays, a collection of formulas from existing research results is given to compute or estimate the delays of messages in a communication network without making the independence assumption. The design algorithm coded in PASCAL is included as an appendix.

Performance Analysis of Relay Subset Selection for Amplify-and-Forward Cognitive Relay Networks

PubMed Central

Qureshi, Ijaz Mansoor; Malik, Aqdas Naveed; Zubair, Muhammad

2014-01-01

Cooperative communication is regarded as a key technology in wireless networks, including cognitive radio networks (CRNs), which increases the diversity order of the signal to combat the unfavorable effects of the fading channels, by allowing distributed terminals to collaborate through sophisticated signal processing. Underlay CRNs have strict interference constraints towards the secondary users (SUs) active in the frequency band of the primary users (PUs), which limits their transmit power and their coverage area. Relay selection offers a potential solution to the challenges faced by underlay networks, by selecting either single best relay or a subset of potential relay set under different design requirements and assumptions. The best relay selection schemes proposed in the literature for amplify-and-forward (AF) based underlay cognitive relay networks have been very well studied in terms of outage probability (OP) and bit error rate (BER), which is deficient in multiple relay selection schemes. The novelty of this work is to study the outage behavior of multiple relay selection in the underlay CRN and derive the closed-form expressions for the OP and BER through cumulative distribution function (CDF) of the SNR received at the destination. The effectiveness of relay subset selection is shown through simulation results. PMID:24737980

Algorithm For Solution Of Subset-Regression Problems

NASA Technical Reports Server (NTRS)

Verhaegen, Michel

1991-01-01

Reliable and flexible algorithm for solution of subset-regression problem performs QR decomposition with new column-pivoting strategy, enables selection of subset directly from originally defined regression parameters. This feature, in combination with number of extensions, makes algorithm very flexible for use in analysis of subset-regression problems in which parameters have physical meanings. Also extended to enable joint processing of columns contaminated by noise with those free of noise, without using scaling techniques.

Morphological and physiological analysis of type-5 and other bipolar cells in the Mouse Retina.

PubMed

Hellmer, C B; Zhou, Y; Fyk-Kolodziej, B; Hu, Z; Ichinose, T

2016-02-19

Retinal bipolar cells are second-order neurons in the visual system, which initiate multiple image feature-based neural streams. Among more than ten types of bipolar cells, type-5 cells are thought to play a role in motion detection pathways. Multiple subsets of type-5 cells have been reported; however, detailed characteristics of each subset have not yet been elucidated. Here, we found that they exhibit distinct morphological features as well as unique voltage-gated channel expression. We have conducted electrophysiological and immunohistochemical analysis of retinal bipolar cells. We defined type-5 cells by their axon terminal ramification in the inner plexiform layer between the border of ON/OFF sublaminae and the ON choline acetyltransferase (ChAT) band. We found three subsets of type-5 cells: XBCs had the widest axon terminals that stratified at a close approximation of the ON ChAT band as well as exhibiting large voltage-gated Na(+) channel activity, type-5-1 cells had compact terminals and no Na(+) channel activity, and type-5-2 cells contained umbrella-shaped terminals as well as large voltage-gated Na(+) channel activity. Hyperpolarization-activated cyclic nucleotide-gated (HCN) currents were also evoked in all type-5 bipolar cells. We found that XBCs and type-5-2 cells exhibited larger HCN currents than type-5-1 cells. Furthermore, the former two types showed stronger HCN1 expression than the latter. Our previous observations (Ichinose et al., 2014) match the current study: low temporal tuning cells that we named 5S corresponded to 5-1 in this study, while high temporal tuning 5f cells from the previous study corresponded to 5-2 cells. Taken together, we found three subsets of type-5 bipolar cells based on their morphologies and physiological features. Copyright © 2015 IBRO. Published by Elsevier Ltd. All rights reserved.

Localization of spontaneous magnetoencephalographic activity of neonates and fetuses using independent component and Hilbert phase analysis.

PubMed

Vairavan, Srinivasan; Eswaran, Hari; Preissl, Hubert; Wilson, James D; Haddad, Naim; Lowery, Curtis L; Govindan, Rathinaswamy B

2010-01-01

The fetal magnetoencephalogram (fMEG) is measured in the presence of large interference from maternal and fetal magnetocardiograms (mMCG and fMCG). These cardiac interferences can be attenuated by orthogonal projection (OP) technique of the corresponding spatial vectors. However, the OP technique redistributes the fMEG signal among the channels and also leaves some cardiac residuals (partially attenuated mMCG and fMCG) due to loss of stationarity in the signal. In this paper, we propose a novel way to extract and localize the neonatal and fetal spontaneous brain activity by using independent component analysis (ICA) technique. In this approach, we perform ICA on a small subset of sensors for 1-min duration. The independent components obtained are further investigated for the presence of discontinuous patterns as identified by the Hilbert phase analysis and are used as decision criteria for localizing the spontaneous brain activity. In order to locate the region of highest spontaneous brain activity content, this analysis is performed on the sensor subsets, which are traversed across the entire sensor space. The region of the spontaneous brain activity as identified by the proposed approach correlated well with the neonatal and fetal head location. In addition, the burst duration and the inter-burst interval computed for the identified discontinuous brain patterns are in agreement with the reported values.

Research on the application of a decoupling algorithm for structure analysis

NASA Technical Reports Server (NTRS)

Denman, E. D.

1980-01-01

The mathematical theory for decoupling mth-order matrix differential equations is presented. It is shown that the decoupling precedure can be developed from the algebraic theory of matrix polynomials. The role of eigenprojectors and latent projectors in the decoupling process is discussed and the mathematical relationships between eigenvalues, eigenvectors, latent roots, and latent vectors are developed. It is shown that the eigenvectors of the companion form of a matrix contains the latent vectors as a subset. The spectral decomposition of a matrix and the application to differential equations is given.

A method for simplifying the analysis of traffic accidents injury severity on two-lane highways using Bayesian networks.

PubMed

Mujalli, Randa Oqab; de Oña, Juan

2011-10-01

This study describes a method for reducing the number of variables frequently considered in modeling the severity of traffic accidents. The method's efficiency is assessed by constructing Bayesian networks (BN). It is based on a two stage selection process. Several variable selection algorithms, commonly used in data mining, are applied in order to select subsets of variables. BNs are built using the selected subsets and their performance is compared with the original BN (with all the variables) using five indicators. The BNs that improve the indicators' values are further analyzed for identifying the most significant variables (accident type, age, atmospheric factors, gender, lighting, number of injured, and occupant involved). A new BN is built using these variables, where the results of the indicators indicate, in most of the cases, a statistically significant improvement with respect to the original BN. It is possible to reduce the number of variables used to model traffic accidents injury severity through BNs without reducing the performance of the model. The study provides the safety analysts a methodology that could be used to minimize the number of variables used in order to determine efficiently the injury severity of traffic accidents without reducing the performance of the model. Copyright © 2011 Elsevier Ltd. All rights reserved.

Texture analysis of tissues in Gleason grading of prostate cancer

NASA Astrophysics Data System (ADS)

Alexandratou, Eleni; Yova, Dido; Gorpas, Dimitris; Maragos, Petros; Agrogiannis, George; Kavantzas, Nikolaos

2008-02-01

Prostate cancer is a common malignancy among maturing men and the second leading cause of cancer death in USA. Histopathological grading of prostate cancer is based on tissue structural abnormalities. Gleason grading system is the gold standard and is based on the organization features of prostatic glands. Although Gleason score has contributed on cancer prognosis and on treatment planning, its accuracy is about 58%, with this percentage to be lower in GG2, GG3 and GG5 grading. On the other hand it is strongly affected by "inter- and intra observer variations", making the whole process very subjective. Therefore, there is need for the development of grading tools based on imaging and computer vision techniques for a more accurate prostate cancer prognosis. The aim of this paper is the development of a novel method for objective grading of biopsy specimen in order to support histopathological prognosis of the tumor. This new method is based on texture analysis techniques, and particularly on Gray Level Co-occurrence Matrix (GLCM) that estimates image properties related to second order statistics. Histopathological images of prostate cancer, from Gleason grade2 to Gleason grade 5, were acquired and subjected to image texture analysis. Thirteen texture characteristics were calculated from this matrix as they were proposed by Haralick. Using stepwise variable selection, a subset of four characteristics were selected and used for the description and classification of each image field. The selected characteristics profile was used for grading the specimen with the multiparameter statistical method of multiple logistic discrimination analysis. The subset of these characteristics provided 87% correct grading of the specimens. The addition of any of the remaining characteristics did not improve significantly the diagnostic ability of the method. This study demonstrated that texture analysis techniques could provide valuable grading decision support to the pathologists, concerning prostate cancer prognosis.

Analysis of Information Content in High-Spectral Resolution Sounders using Subset Selection Analysis

NASA Technical Reports Server (NTRS)

Velez-Reyes, Miguel; Joiner, Joanna

1998-01-01

In this paper, we summarize the results of the sensitivity analysis and data reduction carried out to determine the information content of AIRS and IASI channels. The analysis and data reduction was based on the use of subset selection techniques developed in the linear algebra and statistical community to study linear dependencies in high dimensional data sets. We applied the subset selection method to study dependency among channels by studying the dependency among their weighting functions. Also, we applied the technique to study the information provided by the different levels in which the atmosphere is discretized for retrievals and analysis. Results from the method correlate well with intuition in many respects and point out to possible modifications for band selection in sensor design and number and location of levels in the analysis process.

An overview of the NASA Langley Atmospheric Data Center: Online tools to effectively disseminate Earth science data products

NASA Astrophysics Data System (ADS)

Parker, L.; Dye, R. A.; Perez, J.; Rinsland, P.

2012-12-01

Over the past decade the Atmospheric Science Data Center (ASDC) at NASA Langley Research Center has archived and distributed a variety of satellite mission and aircraft campaign data sets. These datasets posed unique challenges to the user community at large due to the sheer volume and variety of the data and the lack of intuitive features in the order tools available to the investigator. Some of these data sets also lack sufficient metadata to provide rudimentary data discovery. To meet the needs of emerging users, the ASDC addressed issues in data discovery and delivery through the use of standards in data and access methods, and distribution through appropriate portals. The ASDC is currently undergoing a refresh of its webpages and Ordering Tools that will leverage updated collection level metadata in an effort to enhance the user experience. The ASDC is now providing search and subset capability to key mission satellite data sets. The ASDC has collaborated with Science Teams to accommodate prospective science users in the climate and modeling communities. The ASDC is using a common framework that enables more rapid development and deployment of search and subset tools that provide enhanced access features for the user community. Features of the Search and Subset web application enables a more sophisticated approach to selecting and ordering data subsets by parameter, date, time, and geographic area. The ASDC has also applied key practices from satellite missions to the multi-campaign aircraft missions executed for Earth Venture-1 and MEaSUReS

How do I order MISR data?

Atmospheric Science Data Center

2017-10-12

... and archived at the NASA Langley Research Center Atmospheric Science Data Center (ASDC). A MISR Order and Customization Tool is ... Pool (an on-line, short-term data cache that provides a Web interface and FTP access). Specially subsetted and/or reformatted MISR data ...

Reverse Engineering a Signaling Network Using Alternative Inputs

PubMed Central

Tanaka, Hiromasa; Yi, Tau-Mu

2009-01-01

One of the goals of systems biology is to reverse engineer in a comprehensive fashion the arrow diagrams of signal transduction systems. An important tool for ordering pathway components is genetic epistasis analysis, and here we present a strategy termed Alternative Inputs (AIs) to perform systematic epistasis analysis. An alternative input is defined as any genetic manipulation that can activate the signaling pathway instead of the natural input. We introduced the concept of an “AIs-Deletions matrix” that summarizes the outputs of all combinations of alternative inputs and deletions. We developed the theory and algorithms to construct a pairwise relationship graph from the AIs-Deletions matrix capturing both functional ordering (upstream, downstream) and logical relationships (AND, OR), and then interpreting these relationships into a standard arrow diagram. As a proof-of-principle, we applied this methodology to a subset of genes involved in yeast mating signaling. This experimental pilot study highlights the robustness of the approach and important technical challenges. In summary, this research formalizes and extends classical epistasis analysis from linear pathways to more complex networks, facilitating computational analysis and reconstruction of signaling arrow diagrams. PMID:19898612

Artificial nose, NIR and UV-visible spectroscopy for the characterisation of the PDO Chianti Classico olive oil.

PubMed

Forina, M; Oliveri, P; Bagnasco, L; Simonetti, R; Casolino, M C; Nizzi Grifi, F; Casale, M

2015-11-01

An authentication study of the Italian PDO (Protected Designation of Origin) olive oil Chianti Classico, based on artificial nose, near-infrared and UV-visible spectroscopy, with a set of samples representative of the whole Chianti Classico production area and a considerable number of samples from other Italian PDO regions was performed. The signals provided by the three analytical techniques were used both individually and jointly, after fusion of the respective variables, in order to build a model for the Chianti Classico PDO olive oil. Different signal pre-treatments were performed in order to investigate their importance and their effects in enhancing and extracting information from experimental data, correcting backgrounds or removing baseline variations. Stepwise-Linear Discriminant Analysis (STEP-LDA) was used as a feature selection technique and, afterward, Linear Discriminant Analysis (LDA) and the class-modelling technique Quadratic Discriminant Analysis-UNEQual dispersed classes (QDA-UNEQ) were applied to sub-sets of selected variables, in order to obtain efficient models capable of characterising the extra virgin olive oils produced in the Chianti Classico PDO area. Copyright © 2015 Elsevier B.V. All rights reserved.

Sparse principal component analysis in medical shape modeling

NASA Astrophysics Data System (ADS)

Sjöstrand, Karl; Stegmann, Mikkel B.; Larsen, Rasmus

2006-03-01

Principal component analysis (PCA) is a widely used tool in medical image analysis for data reduction, model building, and data understanding and exploration. While PCA is a holistic approach where each new variable is a linear combination of all original variables, sparse PCA (SPCA) aims at producing easily interpreted models through sparse loadings, i.e. each new variable is a linear combination of a subset of the original variables. One of the aims of using SPCA is the possible separation of the results into isolated and easily identifiable effects. This article introduces SPCA for shape analysis in medicine. Results for three different data sets are given in relation to standard PCA and sparse PCA by simple thresholding of small loadings. Focus is on a recent algorithm for computing sparse principal components, but a review of other approaches is supplied as well. The SPCA algorithm has been implemented using Matlab and is available for download. The general behavior of the algorithm is investigated, and strengths and weaknesses are discussed. The original report on the SPCA algorithm argues that the ordering of modes is not an issue. We disagree on this point and propose several approaches to establish sensible orderings. A method that orders modes by decreasing variance and maximizes the sum of variances for all modes is presented and investigated in detail.

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

PubMed

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

2006-07-01

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

';Best' Practices for Aggregating Subset Results from Archived Datasets

NASA Astrophysics Data System (ADS)

Baskin, W. E.; Perez, J.

2013-12-01

In response to the exponential growth in science data analysis and visualization capabilities Data Centers have been developing new delivery mechanisms to package and deliver large volumes of aggregated subsets of archived data. New standards are evolving to help data providers and application programmers deal with growing needs of the science community. These standards evolve from the best practices gleaned from new products and capabilities. The NASA Atmospheric Sciences Data Center (ASDC) has developed and deployed production provider-specific search and subset web applications for the CALIPSO, CERES, TES, and MOPITT missions. This presentation explores several use cases that leverage aggregated subset results and examines the standards and formats ASDC developers applied to the delivered files as well as the implementation strategies for subsetting and processing the aggregated products. The following topics will be addressed: - Applications of NetCDF CF conventions to aggregated level 2 satellite subsets - Data-Provider-Specific format requirements vs. generalized standards - Organization of the file structure of aggregated NetCDF subset output - Global Attributes of individual subsetted files vs. aggregated results - Specific applications and framework used for subsetting and delivering derivative data files

Spontaneous and natural cytotoxicity receptor-mediated cytotoxicity are effector functions of distinct natural killer subsets in hepatitis C virus-infected chimpanzees.

PubMed

Verstrepen, B E; Nieuwenhuis, I G; Mooij, P; Bogers, W M; Boonstra, A; Koopman, G

2016-07-01

In humans, CD16 and CD56 are used to identify functionally distinct natural killer (NK) subsets. Due to ubiquitous CD56 expression, this marker cannot be used to distinguish between NK cell subsets in chimpanzees. Therefore, functional analysis of distinct NK subsets during hepatitis C virus (HCV) infection has never been performed in these animals. In the present study an alternative strategy was used to identify four distinct NK subsets on the basis of the expression of CD16 and CD94. The expression of activating and inhibiting surface receptors showed that these subsets resemble human NK subsets. CD107 expression was used to determine degranulation of the different subsets in naive and HCV-infected chimpanzees. In HCV-infected chimpanzees increased spontaneous cytotoxicity was observed in CD94(high/dim) CD16(pos) and CD94(low) CD16(pos) subsets. By contrast, increased natural cytotoxicity receptor (NCR)- mediated degranulation after NKp30 and NKp44 triggering was demonstrated in the CD94(dim) CD16(neg) subset. Our findings suggest that spontaneous and NCR-mediated cytotoxicity are effector functions of distinct NK subsets in HCV-infected chimpanzees. © 2016 British Society for Immunology.

Tumor and liver determinants of prognosis in unresectable hepatocellular carcinoma: a case cohort study.

PubMed

Carr, Brian I; Buch, Shama C; Kondragunta, Venkateswarlu; Pancoska, Petr; Branch, Robert A

2008-08-01

A total of 967 patients with unresectable and untransplantable, biopsy-proven hepatocellular carcinoma (HCC) were prospectively evaluated at baseline and followed up till death. Survival was the end-point for all analyses. We found in our overall analysis, that male gender, ascites, cirrhosis, portal vein thrombosis (PVT), elevated alpha-fetoprotein (AFP) or bilirubin or alkaline phosphatases were each statistically significant adverse prognostic factors. Patients with normal AFP survived longer than those with elevated AFP, in the presence of PVT, large or bilobar tumors or cirrhosis. We used a bivariate analysis to separate patient subgroups based on poor liver function and aggressive tumor characteristics. In subgroup analysis based on these subsets, there was clear discrimination in survival between subsets; in addition both cirrhosis and presence of PVT were significant, independent but modest risk factors. The results of this large dataset show that amongst nonsurgical HCC patients, there are clear subsets with longer survival than other subsets. This data also supports the concept of heterogeneity of HCC.

Development of a Support Vector Machine - Based Image Analysis System for Focal Liver Lesions Classification in Magnetic Resonance Images

NASA Astrophysics Data System (ADS)

Gatos, I.; Tsantis, S.; Karamesini, M.; Skouroliakou, A.; Kagadis, G.

2015-09-01

Purpose: The design and implementation of a computer-based image analysis system employing the support vector machine (SVM) classifier system for the classification of Focal Liver Lesions (FLLs) on routine non-enhanced, T2-weighted Magnetic Resonance (MR) images. Materials and Methods: The study comprised 92 patients; each one of them has undergone MRI performed on a Magnetom Concerto (Siemens). Typical signs on dynamic contrast-enhanced MRI and biopsies were employed towards a three class categorization of the 92 cases: 40-benign FLLs, 25-Hepatocellular Carcinomas (HCC) within Cirrhotic liver parenchyma and 27-liver metastases from Non-Cirrhotic liver. Prior to FLLs classification an automated lesion segmentation algorithm based on Marcov Random Fields was employed in order to acquire each FLL Region of Interest. 42 texture features derived from the gray-level histogram, co-occurrence and run-length matrices and 12 morphological features were obtained from each lesion. Stepwise multi-linear regression analysis was utilized to avoid feature redundancy leading to a feature subset that fed the multiclass SVM classifier designed for lesion classification. SVM System evaluation was performed by means of leave-one-out method and ROC analysis. Results: Maximum accuracy for all three classes (90.0%) was obtained by means of the Radial Basis Kernel Function and three textural features (Inverse- Different-Moment, Sum-Variance and Long-Run-Emphasis) that describe lesion's contrast, variability and shape complexity. Sensitivity values for the three classes were 92.5%, 81.5% and 96.2% respectively, whereas specificity values were 94.2%, 95.3% and 95.5%. The AUC value achieved for the selected subset was 0.89 with 0.81 - 0.94 confidence interval. Conclusion: The proposed SVM system exhibit promising results that could be utilized as a second opinion tool to the radiologist in order to decrease the time/cost of diagnosis and the need for patients to undergo invasive examination.

RNA-seq Analysis Reveals Unique Transcriptome Signatures in Systemic Lupus Erythematosus Patients with Distinct Autoantibody Specificities

PubMed Central

Rai, Richa; Chauhan, Sudhir Kumar; Singh, Vikas Vikram; Rai, Madhukar; Rai, Geeta

2016-01-01

Systemic lupus erythematosus (SLE) patients exhibit immense heterogeneity which is challenging from the diagnostic perspective. Emerging high throughput sequencing technologies have been proved to be a useful platform to understand the complex and dynamic disease processes. SLE patients categorised based on autoantibody specificities are reported to have differential immuno-regulatory mechanisms. Therefore, we performed RNA-seq analysis to identify transcriptomics of SLE patients with distinguished autoantibody specificities. The SLE patients were segregated into three subsets based on the type of autoantibodies present in their sera (anti-dsDNA+ group with anti-dsDNA autoantibody alone; anti-ENA+ group having autoantibodies against extractable nuclear antigens (ENA) only, and anti-dsDNA+ENA+ group having autoantibodies to both dsDNA and ENA). Global transcriptome profiling for each SLE patients subsets was performed using Illumina® Hiseq-2000 platform. The biological relevance of dysregulated transcripts in each SLE subsets was assessed by ingenuity pathway analysis (IPA) software. We observed that dysregulation in the transcriptome expression pattern was clearly distinct in each SLE patients subsets. IPA analysis of transcripts uniquely expressed in different SLE groups revealed specific biological pathways to be affected in each SLE subsets. Multiple cytokine signaling pathways were specifically dysregulated in anti-dsDNA+ patients whereas Interferon signaling was predominantly dysregulated in anti-ENA+ patients. In anti-dsDNA+ENA+ patients regulation of actin based motility by Rho pathway was significantly affected. The granulocyte gene signature was a common feature to all SLE subsets; however, anti-dsDNA+ group showed relatively predominant expression of these genes. Dysregulation of Plasma cell related transcripts were higher in anti-dsDNA+ and anti-ENA+ patients as compared to anti-dsDNA+ ENA+. Association of specific canonical pathways with the uniquely expressed transcripts in each SLE subgroup indicates that specific immunological disease mechanisms are operative in distinct SLE patients’ subsets. This ‘sub-grouping’ approach could further be useful for clinical evaluation of SLE patients and devising targeted therapeutics. PMID:27835693

Whole grain intake, determined by dietary records and plasma alkylresorcinol concentrations, is low among pregnant women in Singapore.

PubMed

Ross, Alastair B; Colega, Marjorelee T; Lim, Ai Lin; Silva-Zolezzi, Irma; Macé, Katherine; Saw, Seang Mei; Kwek, Kenneth; Gluckman, Peter; Godfrey, Keith M; Chong, Yap-Seng; Chong, Mary F F

2015-01-01

To quantify whole grain intake in pregnant women in Singapore in order to provide the first detailed analysis of whole grain intake in an Asian country and in pregnant women. Analysis of 24-h diet recalls in a cross-sectional cohort study and analysis of a biomarker of whole grain intake (plasma alkylresorcinols) in a subset of subjects. The Growing Up in Singapore Towards healthy Outcomes-mother offspring cohort study based in Singapore. 998 pregnant mothers with complete 24-h recalls taken during their 26-28th week of gestation. Plasma samples from a randomly select subset of 100 subjects were analysed for plasma alkylresorcinols. Median (IQR) whole grain intake for the cohort and the 30% who reported eating whole grains were 0 (IQR 0, 9) and 23.6 (IQR 14.6, 44.2) g/day respectively. Plasma alkylresorcinol concentrations were very low [median (IQR)=9 (3, 15) nmol/L], suggesting low intake of whole grain wheat in this population. Plasma alkylresorcinols were correlated with whole grain wheat intake (Spearman's r=0.35; p<0.01). Whole grain intake among pregnant mothers in Singapore was well below the 2-3 (60-95 g) servings of whole grains per day recommended by the Singapore Health Promotion Board. Efforts to increase whole grain intake should be supported to encourage people to choose whole grains over refined grains in their diet.

Systems Level Analysis of Systemic Sclerosis Shows a Network of Immune and Profibrotic Pathways Connected with Genetic Polymorphisms

PubMed Central

Mahoney, J. Matthew; Taroni, Jaclyn; Martyanov, Viktor; Wood, Tammara A.; Greene, Casey S.; Pioli, Patricia A.; Hinchcliff, Monique E.; Whitfield, Michael L.

2015-01-01

Systemic sclerosis (SSc) is a rare systemic autoimmune disease characterized by skin and organ fibrosis. The pathogenesis of SSc and its progression are poorly understood. The SSc intrinsic gene expression subsets (inflammatory, fibroproliferative, normal-like, and limited) are observed in multiple clinical cohorts of patients with SSc. Analysis of longitudinal skin biopsies suggests that a patient's subset assignment is stable over 6–12 months. Genetically, SSc is multi-factorial with many genetic risk loci for SSc generally and for specific clinical manifestations. Here we identify the genes consistently associated with the intrinsic subsets across three independent cohorts, show the relationship between these genes using a gene-gene interaction network, and place the genetic risk loci in the context of the intrinsic subsets. To identify gene expression modules common to three independent datasets from three different clinical centers, we developed a consensus clustering procedure based on mutual information of partitions, an information theory concept, and performed a meta-analysis of these genome-wide gene expression datasets. We created a gene-gene interaction network of the conserved molecular features across the intrinsic subsets and analyzed their connections with SSc-associated genetic polymorphisms. The network is composed of distinct, but interconnected, components related to interferon activation, M2 macrophages, adaptive immunity, extracellular matrix remodeling, and cell proliferation. The network shows extensive connections between the inflammatory- and fibroproliferative-specific genes. The network also shows connections between these subset-specific genes and 30 SSc-associated polymorphic genes including STAT4, BLK, IRF7, NOTCH4, PLAUR, CSK, IRAK1, and several human leukocyte antigen (HLA) genes. Our analyses suggest that the gene expression changes underlying the SSc subsets may be long-lived, but mechanistically interconnected and related to a patients underlying genetic risk. PMID:25569146

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

NASA Technical Reports Server (NTRS)

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

2000-01-01

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

Stable phenotype of B-cell subsets following cryopreservation and thawing of normal human lymphocytes stored in a tissue biobank.

PubMed

Rasmussen, Simon Mylius; Bilgrau, Anders Ellern; Schmitz, Alexander; Falgreen, Steffen; Bergkvist, Kim Steve; Tramm, Anette Mai; Baech, John; Jacobsen, Chris Ladefoged; Gaihede, Michael; Kjeldsen, Malene Krag; Bødker, Julie Støve; Dybkaer, Karen; Bøgsted, Martin; Johnsen, Hans Erik

2015-01-01

Cryopreservation is an acknowledged procedure to store vital cells for future biomarker analyses. Few studies, however, have analyzed the impact of the cryopreservation on phenotyping. We have performed a controlled comparison of cryopreserved and fresh cellular aliquots prepared from individual healthy donors. We studied circulating B-cell subset membrane markers and global gene expression, respectively by multiparametric flow cytometry and microarray data. Extensive statistical analysis of the generated data tested the concept that "overall, there are no phenotypic differences between cryopreserved and fresh B-cell subsets." Subsequently, we performed an uncontrolled comparison of tonsil tissue samples. By multiparametric flow analysis, we documented no significant changes following cryopreservation of subset frequencies or membrane intensity for the differentiation markers CD19, CD20, CD22, CD27, CD38, CD45, and CD200. By gene expression profiling following cryopreservation, across all samples, only 16 out of 18708 genes were significantly up or down regulated, including FOSB, KLF4, RBP7, ANXA1 or CLC, DEFA3, respectively. Implementation of cryopreserved tissue in our research program allowed us to present a performance analysis, by comparing cryopreserved and fresh tonsil tissue. As expected, phenotypic differences were identified, but to an extent that did not affect the performance of the cryopreserved tissue to generate specific B-cell subset associated gene signatures and assign subset phenotypes to independent tissue samples. We have confirmed our working concept and illustrated the usefulness of vital cryopreserved cell suspensions for phenotypic studies of the normal B-cell hierarchy; however, storage procedures need to be delineated by tissue-specific comparative analysis. © 2014 Clinical Cytometry Society.

Stable Phenotype Of B-Cell Subsets Following Cryopreservation and Thawing of Normal Human Lymphocytes Stored in a Tissue Biobank.

PubMed

Rasmussen, Simon Mylius; Bilgrau, Anders Ellern; Schmitz, Alexander; Falgreen, Steffen; Bergkvist, Kim Steve; Tramm, Anette Mai; Baech, John; Jacobsen, Chris Ladefoged; Gaihede, Michael; Kjeldsen, Malene Krag; Bødker, Julie Støve; Dybkaer, Karen; Bøgsted, Martin; Johnsen, Hans Erik

2014-09-20

Background Cryopreservation is an acknowledged procedure to store vital cells for future biomarker analyses. Few studies, however, have analyzed the impact of the cryopreservation on phenotyping. Methods We have performed a controlled comparison of cryopreserved and fresh cellular aliquots prepared from individual healthy donors. We studied circulating B-cell subset membrane markers and global gene expression, respectively by multiparametric flow cytometry and microarray data. Extensive statistical analysis of the generated data tested the concept that "overall, there are phenotypic differences between cryopreserved and fresh B-cell subsets". Subsequently, we performed a consecutive uncontrolled comparison of tonsil tissue samples. Results By multiparametric flow analysis, we documented no significant changes following cryopreservation of subset frequencies or membrane intensity for the differentiation markers CD19, CD20, CD22, CD27, CD38, CD45, and CD200. By gene expression profiling following cryopreservation, across all samples, only 16 out of 18708 genes were significantly up or down regulated, including FOSB, KLF4, RBP7, ANXA1 or CLC, DEFA3, respectively. Implementation of cryopreserved tissue in our research program allowed us to present a performance analysis, by comparing cryopreserved and fresh tonsil tissue. As expected, phenotypic differences were identified, but to an extent that did not affect the performance of the cryopreserved tissue to generate specific B-cell subset associated gene signatures and assign subset phenotypes to independent tissue samples. Conclusions We have confirmed our working concept and illustrated the usefulness of vital cryopreserved cell suspensions for phenotypic studies of the normal B-cell hierarchy; however, storage procedures need to be delineated by tissue specific comparative analysis. © 2014 Clinical Cytometry Society. Copyright © 2014 Clinical Cytometry Society.

Significance of settling model structures and parameter subsets in modelling WWTPs under wet-weather flow and filamentous bulking conditions.

PubMed

Ramin, Elham; Sin, Gürkan; Mikkelsen, Peter Steen; Plósz, Benedek Gy

2014-10-15

Current research focuses on predicting and mitigating the impacts of high hydraulic loadings on centralized wastewater treatment plants (WWTPs) under wet-weather conditions. The maximum permissible inflow to WWTPs depends not only on the settleability of activated sludge in secondary settling tanks (SSTs) but also on the hydraulic behaviour of SSTs. The present study investigates the impacts of ideal and non-ideal flow (dry and wet weather) and settling (good settling and bulking) boundary conditions on the sensitivity of WWTP model outputs to uncertainties intrinsic to the one-dimensional (1-D) SST model structures and parameters. We identify the critical sources of uncertainty in WWTP models through global sensitivity analysis (GSA) using the Benchmark simulation model No. 1 in combination with first- and second-order 1-D SST models. The results obtained illustrate that the contribution of settling parameters to the total variance of the key WWTP process outputs significantly depends on the influent flow and settling conditions. The magnitude of the impact is found to vary, depending on which type of 1-D SST model is used. Therefore, we identify and recommend potential parameter subsets for WWTP model calibration, and propose optimal choice of 1-D SST models under different flow and settling boundary conditions. Additionally, the hydraulic parameters in the second-order SST model are found significant under dynamic wet-weather flow conditions. These results highlight the importance of developing a more mechanistic based flow-dependent hydraulic sub-model in second-order 1-D SST models in the future. Copyright © 2014 Elsevier Ltd. All rights reserved.

77 FR 43879 - Self-Regulatory Organizations; NYSE Arca, Inc.; Notice of Designation of a Longer Period for...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-26

... Proposed Rule Change Amending NYSE Arca Equities Rule 7.31(h) To Add a PL Select Order Type July 20, 2012...(h) to add a PL Select Order type. The proposed rule change was published for comment in the Federal... security at a specified, undisplayed price. The PL Select Order would be a subset of the PL Order that...

Dynamic equilibrium of heterogeneous and interconvertible multipotent hematopoietic cell subsets

PubMed Central

Weston, Wendy; Zayas, Jennifer; Perez, Ruben; George, John; Jurecic, Roland

2014-01-01

Populations of hematopoietic stem cells and progenitors are quite heterogeneous and consist of multiple cell subsets with distinct phenotypic and functional characteristics. Some of these subsets also appear to be interconvertible and oscillate between functionally distinct states. The multipotent hematopoietic cell line EML has emerged as a unique model to study the heterogeneity and interconvertibility of multipotent hematopoietic cells. Here we describe extensive phenotypic and functional heterogeneity of EML cells which stems from the coexistence of multiple cell subsets. Each of these subsets is phenotypically and functionally heterogeneous, and displays distinct multilineage differentiation potential, cell cycle profile, proliferation kinetics, and expression pattern of HSC markers and some of the key lineage-associated transcription factors. Analysis of their maintenance revealed that on a population level all EML cell subsets exhibit cell-autonomous interconvertible properties, with the capacity to generate all other subsets and re-establish complete parental EML cell population. Moreover, all EML cell subsets generated during multiple cell generations maintain their distinct phenotypic and functional signatures and interconvertible properties. The model of EML cell line suggests that interconvertible multipotent hematopoietic cell subsets coexist in a homeostatically maintained dynamic equilibrium which is regulated by currently unknown cell-intrinsic mechanisms. PMID:24903657

Dynamic equilibrium of heterogeneous and interconvertible multipotent hematopoietic cell subsets.

PubMed

Weston, Wendy; Zayas, Jennifer; Perez, Ruben; George, John; Jurecic, Roland

2014-06-06

Populations of hematopoietic stem cells and progenitors are quite heterogeneous and consist of multiple cell subsets with distinct phenotypic and functional characteristics. Some of these subsets also appear to be interconvertible and oscillate between functionally distinct states. The multipotent hematopoietic cell line EML has emerged as a unique model to study the heterogeneity and interconvertibility of multipotent hematopoietic cells. Here we describe extensive phenotypic and functional heterogeneity of EML cells which stems from the coexistence of multiple cell subsets. Each of these subsets is phenotypically and functionally heterogeneous, and displays distinct multilineage differentiation potential, cell cycle profile, proliferation kinetics, and expression pattern of HSC markers and some of the key lineage-associated transcription factors. Analysis of their maintenance revealed that on a population level all EML cell subsets exhibit cell-autonomous interconvertible properties, with the capacity to generate all other subsets and re-establish complete parental EML cell population. Moreover, all EML cell subsets generated during multiple cell generations maintain their distinct phenotypic and functional signatures and interconvertible properties. The model of EML cell line suggests that interconvertible multipotent hematopoietic cell subsets coexist in a homeostatically maintained dynamic equilibrium which is regulated by currently unknown cell-intrinsic mechanisms.

WE-DE-201-04: Cross Validation of Knowledge-Based Treatment Planning for Prostate LDR Brachytherapy Using Principle Component Analysis

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

Roper, J; Ghavidel, B; Godette, K

Purpose: To validate a knowledge-based algorithm for prostate LDR brachytherapy treatment planning. Methods: A dataset of 100 cases was compiled from an active prostate seed implant service. Cases were randomized into 10 subsets. For each subset, the 90 remaining library cases were registered to a common reference frame and then characterized on a point by point basis using principle component analysis (PCA). Each test case was converted to PCA vectors using the same process and compared with each library case using a Mahalanobis distance to evaluate similarity. Rank order PCA scores were used to select the best-matched library case. Themore » seed arrangement was extracted from the best-matched case and used as a starting point for planning the test case. Any subsequent modifications were recorded that required input from a treatment planner to achieve V100>95%, V150<60%, V200<20%. To simulate operating-room planning constraints, seed activity was held constant, and the seed count could not increase. Results: The computational time required to register test-case contours and evaluate PCA similarity across the library was 10s. Preliminary analysis of 2 subsets shows that 9 of 20 test cases did not require any seed modifications to obtain an acceptable plan. Five test cases required fewer than 10 seed modifications or a grid shift. Another 5 test cases required approximately 20 seed modifications. An acceptable plan was not achieved for 1 outlier, which was substantially larger than its best match. Modifications took between 5s and 6min. Conclusion: A knowledge-based treatment planning algorithm for prostate LDR brachytherapy is being cross validated using 100 prior cases. Preliminary results suggest that for this size library, acceptable plans can be achieved without planner input in about half of the cases while varying amounts of planner input are needed in remaining cases. Computational time and planning time are compatible with clinical practice.« less

Development of a psychological test to measure ability-based emotional intelligence in the Indonesian workplace using an item response theory.

PubMed

Fajrianthi; Zein, Rizqy Amelia

2017-01-01

This study aimed to develop an emotional intelligence (EI) test that is suitable to the Indonesian workplace context. Airlangga Emotional Intelligence Test (Tes Kecerdasan Emosi Airlangga [TKEA]) was designed to measure three EI domains: 1) emotional appraisal, 2) emotional recognition, and 3) emotional regulation. TKEA consisted of 120 items with 40 items for each subset. TKEA was developed based on the Situational Judgment Test (SJT) approach. To ensure its psychometric qualities, categorical confirmatory factor analysis (CCFA) and item response theory (IRT) were applied to test its validity and reliability. The study was conducted on 752 participants, and the results showed that test information function (TIF) was 3.414 (ability level = 0) for subset 1, 12.183 for subset 2 (ability level = -2), and 2.398 for subset 3 (level of ability = -2). It is concluded that TKEA performs very well to measure individuals with a low level of EI ability. It is worth to note that TKEA is currently at the development stage; therefore, in this study, we investigated TKEA's item analysis and dimensionality test of each TKEA subset.

Nonuniform update for sparse target recovery in fluorescence molecular tomography accelerated by ordered subsets.

PubMed

Zhu, Dianwen; Li, Changqing

2014-12-01

Fluorescence molecular tomography (FMT) is a promising imaging modality and has been actively studied in the past two decades since it can locate the specific tumor position three-dimensionally in small animals. However, it remains a challenging task to obtain fast, robust and accurate reconstruction of fluorescent probe distribution in small animals due to the large computational burden, the noisy measurement and the ill-posed nature of the inverse problem. In this paper we propose a nonuniform preconditioning method in combination with L (1) regularization and ordered subsets technique (NUMOS) to take care of the different updating needs at different pixels, to enhance sparsity and suppress noise, and to further boost convergence of approximate solutions for fluorescence molecular tomography. Using both simulated data and phantom experiment, we found that the proposed nonuniform updating method outperforms its popular uniform counterpart by obtaining a more localized, less noisy, more accurate image. The computational cost was greatly reduced as well. The ordered subset (OS) technique provided additional 5 times and 3 times speed enhancements for simulation and phantom experiments, respectively, without degrading image qualities. When compared with the popular L (1) algorithms such as iterative soft-thresholding algorithm (ISTA) and Fast iterative soft-thresholding algorithm (FISTA) algorithms, NUMOS also outperforms them by obtaining a better image in much shorter period of time.

Variation in geographic access to specialist inpatient hospices in England and Wales.

PubMed

Gatrell, Anthony C; Wood, D Justin

2012-07-01

We seek to map and describe variation in geographic access to the set of 189 specialist adult inpatient hospices in England and Wales. Using almost 35,000 small Census areas (Local Super Output Areas: LSOAs) as our units of analysis, the locations of hospices, and estimated drive times from LSOAs to hospices we construct an accessibility 'score' for each LSOA, for England and Wales as a whole. Data on cancer mortality are used as a proxy for the 'demand' for hospice care and we then identify that subset of small areas in which accessibility (service supply) is relatively poor yet the potential 'demand' for hospice services is above average. That subset is then filtered according to the deprivation score for each LSOA, in order to identify those LSOAs which are also above average in terms of deprivation. While urban areas are relatively well served, large parts of England and Wales have poor access to hospices, and there is a risk that the needs of those living in relatively deprived areas may be unmet. Copyright © 2012 Elsevier Ltd. All rights reserved.

Bootstrapping under constraint for the assessment of group behavior in human contact networks

NASA Astrophysics Data System (ADS)

Tremblay, Nicolas; Barrat, Alain; Forest, Cary; Nornberg, Mark; Pinton, Jean-François; Borgnat, Pierre

2013-11-01

The increasing availability of time- and space-resolved data describing human activities and interactions gives insights into both static and dynamic properties of human behavior. In practice, nevertheless, real-world data sets can often be considered as only one realization of a particular event. This highlights a key issue in social network analysis: the statistical significance of estimated properties. In this context, we focus here on the assessment of quantitative features of specific subset of nodes in empirical networks. We present a method of statistical resampling based on bootstrapping groups of nodes under constraints within the empirical network. The method enables us to define acceptance intervals for various null hypotheses concerning relevant properties of the subset of nodes under consideration in order to characterize by a statistical test its behavior as “normal” or not. We apply this method to a high-resolution data set describing the face-to-face proximity of individuals during two colocated scientific conferences. As a case study, we show how to probe whether colocating the two conferences succeeded in bringing together the two corresponding groups of scientists.

Modulation Depth Estimation and Variable Selection in State-Space Models for Neural Interfaces

PubMed Central

Hochberg, Leigh R.; Donoghue, John P.; Brown, Emery N.

2015-01-01

Rapid developments in neural interface technology are making it possible to record increasingly large signal sets of neural activity. Various factors such as asymmetrical information distribution and across-channel redundancy may, however, limit the benefit of high-dimensional signal sets, and the increased computational complexity may not yield corresponding improvement in system performance. High-dimensional system models may also lead to overfitting and lack of generalizability. To address these issues, we present a generalized modulation depth measure using the state-space framework that quantifies the tuning of a neural signal channel to relevant behavioral covariates. For a dynamical system, we develop computationally efficient procedures for estimating modulation depth from multivariate data. We show that this measure can be used to rank neural signals and select an optimal channel subset for inclusion in the neural decoding algorithm. We present a scheme for choosing the optimal subset based on model order selection criteria. We apply this method to neuronal ensemble spike-rate decoding in neural interfaces, using our framework to relate motor cortical activity with intended movement kinematics. With offline analysis of intracortical motor imagery data obtained from individuals with tetraplegia using the BrainGate neural interface, we demonstrate that our variable selection scheme is useful for identifying and ranking the most information-rich neural signals. We demonstrate that our approach offers several orders of magnitude lower complexity but virtually identical decoding performance compared to greedy search and other selection schemes. Our statistical analysis shows that the modulation depth of human motor cortical single-unit signals is well characterized by the generalized Pareto distribution. Our variable selection scheme has wide applicability in problems involving multisensor signal modeling and estimation in biomedical engineering systems. PMID:25265627

Altered dynamics of Candida albicans phagocytosis by macrophages and PMNs when both phagocyte subsets are present.

PubMed

Rudkin, Fiona M; Bain, Judith M; Walls, Catriona; Lewis, Leanne E; Gow, Neil A R; Erwig, Lars P

2013-10-29

An important first line of defense against Candida albicans infections is the killing of fungal cells by professional phagocytes of the innate immune system, such as polymorphonuclear cells (PMNs) and macrophages. In this study, we employed live-cell video microscopy coupled with dynamic image analysis tools to provide insights into the complexity of C. albicans phagocytosis when macrophages and PMNs were incubated with C. albicans alone and when both phagocyte subsets were present. When C. albicans cells were incubated with only one phagocyte subtype, PMNs had a lower overall phagocytic capacity than macrophages, despite engulfing fungal cells at a higher rate once fungal cells were bound to the phagocyte surface. PMNs were more susceptible to C. albicans-mediated killing than macrophages, irrespective of the number of C. albicans cells ingested. In contrast, when both phagocyte subsets were studied in coculture, the two cell types phagocytosed and cleared C. albicans at equal rates and were equally susceptible to killing by the fungus. The increase in macrophage susceptibility to C. albicans-mediated killing was a consequence of macrophages taking up a higher proportion of hyphal cells under these conditions. In the presence of both PMNs and macrophages, C. albicans yeast cells were predominantly cleared by PMNs, which migrated at a greater speed toward fungal cells and engulfed bound cells more rapidly. These observations demonstrate that the phagocytosis of fungal pathogens depends on, and is modified by, the specific phagocyte subsets present at the site of infection. Extensive work investigating fungal cell phagocytosis by macrophages and PMNs of the innate immune system has been carried out. These studies have been informative but have examined this phenomenon only when one phagocyte subset is present. The current study employed live-cell video microscopy to break down C. albicans phagocytosis into its component parts and examine the effect of a single phagocyte subset, versus a mixed phagocyte population, on these individual stages. Through this approach, we identified that the rate of fungal cell engulfment and rate of phagocyte killing altered significantly when both macrophages and PMNs were incubated in coculture with C. albicans compared to the rate of either phagocyte subset incubated alone with the fungus. This research highlights the significance of studying pathogen-host cell interactions with a combination of phagocytes in order to gain a greater understanding of the interactions that occur between cells of the host immune system in response to fungal invasion.

Random or predictable?: Adoption patterns of chronic care management practices in physician organizations.

PubMed

Miake-Lye, Isomi M; Chuang, Emmeline; Rodriguez, Hector P; Kominski, Gerald F; Yano, Elizabeth M; Shortell, Stephen M

2017-08-24

Theories, models, and frameworks used by implementation science, including Diffusion of Innovations, tend to focus on the adoption of one innovation, when often organizations may be facing multiple simultaneous adoption decisions. For instance, despite evidence that care management practices (CMPs) are helpful in managing chronic illness, there is still uneven adoption by physician organizations. This exploratory paper leverages this natural variation in uptake to describe inter-organizational patterns in adoption of CMPs and to better understand how adoption choices may be related to one another. We assessed a cross section of national survey data from physician organizations reporting on the use of 20 CMPs (5 each for asthma, congestive heart failure, depression, and diabetes). Item response theory was used to explore patterns in adoption, first considering all 20 CMPs together and then by subsets according to disease focus or CMP type (e.g., registries, patient reminders). Mokken scale analysis explored whether adoption choices were linked by disease focus or CMP type and whether a consistent ordering of adoption choices was present. The Mokken scale for all 20 CMPs demonstrated medium scalability (H = 0.43), but no consistent ordering. Scales for subsets of CMPs sharing a disease focus had medium scalability (0.4 < H < 0.5), while subsets sharing a CMP type had strong scalability (H > 0.5). Scales for CMP type consistently ranked diabetes CMPs as most adoptable and depression CMPs as least adoptable. Within disease focus scales, patient reminders were ranked as the most adoptable CMP, while clinician feedback and patient education were ranked the least adoptable. Patterns of adoption indicate that innovation characteristics may influence adoption. CMP dissemination efforts may be strengthened by encouraging traditionally non-adopting organizations to focus on more adoptable practices first and then describing a pathway for the adoption of subsequent CMPs. Clarifying why certain CMPs are "less adoptable" may also provide insights into how to overcome CMP adoption constraints.

Calibration and Data Analysis of the MC-130 Air Balance

NASA Technical Reports Server (NTRS)

Booth, Dennis; Ulbrich, N.

2012-01-01

Design, calibration, calibration analysis, and intended use of the MC-130 air balance are discussed. The MC-130 balance is an 8.0 inch diameter force balance that has two separate internal air flow systems and one external bellows system. The manual calibration of the balance consisted of a total of 1854 data points with both unpressurized and pressurized air flowing through the balance. A subset of 1160 data points was chosen for the calibration data analysis. The regression analysis of the subset was performed using two fundamentally different analysis approaches. First, the data analysis was performed using a recently developed extension of the Iterative Method. This approach fits gage outputs as a function of both applied balance loads and bellows pressures while still allowing the application of the iteration scheme that is used with the Iterative Method. Then, for comparison, the axial force was also analyzed using the Non-Iterative Method. This alternate approach directly fits loads as a function of measured gage outputs and bellows pressures and does not require a load iteration. The regression models used by both the extended Iterative and Non-Iterative Method were constructed such that they met a set of widely accepted statistical quality requirements. These requirements lead to reliable regression models and prevent overfitting of data because they ensure that no hidden near-linear dependencies between regression model terms exist and that only statistically significant terms are included. Finally, a comparison of the axial force residuals was performed. Overall, axial force estimates obtained from both methods show excellent agreement as the differences of the standard deviation of the axial force residuals are on the order of 0.001 % of the axial force capacity.

Effects of Number of Animals Monitored on Representations of Cattle Group Movement Characteristics and Spatial Occupancy

PubMed Central

Liu, Tong; Green, Angela R.; Rodríguez, Luis F.; Ramirez, Brett C.; Shike, Daniel W.

2015-01-01

The number of animals required to represent the collective characteristics of a group remains a concern in animal movement monitoring with GPS. Monitoring a subset of animals from a group instead of all animals can reduce costs and labor; however, incomplete data may cause information losses and inaccuracy in subsequent data analyses. In cattle studies, little work has been conducted to determine the number of cattle within a group needed to be instrumented considering subsequent analyses. Two different groups of cattle (a mixed group of 24 beef cows and heifers, and another group of 8 beef cows) were monitored with GPS collars at 4 min intervals on intensively managed pastures and corn residue fields in 2011. The effects of subset group size on cattle movement characterization and spatial occupancy analysis were evaluated by comparing the results between subset groups and the entire group for a variety of summarization parameters. As expected, more animals yield better results for all parameters. Results show the average group travel speed and daily travel distances are overestimated as subset group size decreases, while the average group radius is underestimated. Accuracy of group centroid locations and group radii are improved linearly as subset group size increases. A kernel density estimation was performed to quantify the spatial occupancy by cattle via GPS location data. Results show animals among the group had high similarity of spatial occupancy. Decisions regarding choosing an appropriate subset group size for monitoring depend on the specific use of data for subsequent analysis: a small subset group may be adequate for identifying areas visited by cattle; larger subset group size (e.g. subset group containing more than 75% of animals) is recommended to achieve better accuracy of group movement characteristics and spatial occupancy for the use of correlating cattle locations with other environmental factors. PMID:25647571

[Varicocele and coincidental abacterial prostato-vesiculitis: negative role about the sperm output].

PubMed

Vicari, Enzo; La Vignera, Sandro; Tracia, Angelo; Cardì, Francesco; Donati, Angelo

2003-03-01

To evaluate the frequency and the role of a coincidentally expressed abacterial prostato-vesiculitis (PV) on sperm output in patients with left varicocele (Vr). We evaluated 143 selected infertile patients (mean age 27 years, range 21-43), with oligo- and/or astheno- and/or teratozoospermia (OAT) subdivided in two groups. Group A included 76 patients with previous varicocelectomy and persistent OAT. Group B included 67 infertile patients (mean age 26 years, range 21-37) with OAT and not varicocelectomized. Patients with Vr and coincidental didymo-epididymal ultrasound (US) abnormalities were excluded from the study. Following rectal prostato-vesicular ultrasonography, each group was subdivided in two subsets on the basis of the absence (group A: subset Vr-/PV-; and group B: subset Vr+/PV-) or the presence of an abacterial PV (group A: subset Vr-/PV+; group B: subset Vr+/PV+). Particularly, PV was present in 47.4% and 41.8% patients of groups A and B, respectively. This coincidental pathology was ipsilateral with Vr in the 61% of the cases. Semen analysis was performed in all patients. Patients of group A showed a total sperm number significantly higher than those found in group B. In presence of PV, sperm parameters were not significantly different between matched--subsets (Vr-/PV+ vs. Vr+/PV+). In absence of PV, the sperm density, the total sperm number and the percentage of forward motility from subset with previous varicocelectomy (Vr-/PV) exhibited values significantly higher than those found in the matched--subset (Vr+/PV-). Sperm analysis alone performed in patients with left Vr is not a useful prognostic post-varicocelectomy marker. Since following varicocelectomy a lack of sperm response could mask another coincidental pathology, the identification through US scans of a possible PV may be mandatory. On the other hand, an integrated uro-andrological approach, including US scans, allows to enucleate subsets of patients with Vr alone, who will have an expected better sperm response following Vr repair.

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

PubMed

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

2018-08-01

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

ESMPy and OpenClimateGIS: Python Interfaces for High Performance Grid Remapping and Geospatial Dataset Manipulation

NASA Astrophysics Data System (ADS)

O'Kuinghttons, Ryan; Koziol, Benjamin; Oehmke, Robert; DeLuca, Cecelia; Theurich, Gerhard; Li, Peggy; Jacob, Joseph

2016-04-01

The Earth System Modeling Framework (ESMF) Python interface (ESMPy) supports analysis and visualization in Earth system modeling codes by providing access to a variety of tools for data manipulation. ESMPy started as a Python interface to the ESMF grid remapping package, which provides mature and robust high-performance and scalable grid remapping between 2D and 3D logically rectangular and unstructured grids and sets of unconnected data. ESMPy now also interfaces with OpenClimateGIS (OCGIS), a package that performs subsetting, reformatting, and computational operations on climate datasets. ESMPy exposes a subset of ESMF grid remapping utilities. This includes bilinear, finite element patch recovery, first-order conservative, and nearest neighbor grid remapping methods. There are also options to ignore unmapped destination points, mask points on source and destination grids, and provide grid structure in the polar regions. Grid remapping on the sphere takes place in 3D Cartesian space, so the pole problem is not an issue as it can be with other grid remapping software. Remapping can be done between any combination of 2D and 3D logically rectangular and unstructured grids with overlapping domains. Grid pairs where one side of the regridding is represented by an appropriate set of unconnected data points, as is commonly found with observational data streams, is also supported. There is a developing interoperability layer between ESMPy and OpenClimateGIS (OCGIS). OCGIS is a pure Python, open source package designed for geospatial manipulation, subsetting, and computation on climate datasets stored in local NetCDF files or accessible remotely via the OPeNDAP protocol. Interfacing with OCGIS has brought GIS-like functionality to ESMPy (i.e. subsetting, coordinate transformations) as well as additional file output formats (i.e. CSV, ESRI Shapefile). ESMPy is distinguished by its strong emphasis on open source, community governance, and distributed development. The user base has grown quickly, and the package is integrating with several other software tools and frameworks. These include the Ultrascale Visualization Climate Data Analysis Tools (UV-CDAT), Iris, PyFerret, cfpython, and the Community Surface Dynamics Modeling System (CSDMS). ESMPy minimum requirements include Python 2.6, Numpy 1.6.1 and an ESMF installation. Optional dependencies include NetCDF and OCGIS-related dependencies: GDAL, Shapely, and Fiona. ESMPy is regression tested nightly, and supported on Darwin, Linux and Cray systems with the GNU compiler suite and MPI communications. OCGIS is supported on Linux, and also undergoes nightly regression testing. Both packages are installable from Anaconda channels. Upcoming development plans for ESMPy involve development of a higher order conservative grid remapping method. Future OCGIS development will focus on mesh and location stream interoperability and streamlined access to ESMPy's MPI implementation.

Domino: Extracting, Comparing, and Manipulating Subsets across Multiple Tabular Datasets

PubMed Central

Gratzl, Samuel; Gehlenborg, Nils; Lex, Alexander; Pfister, Hanspeter; Streit, Marc

2016-01-01

Answering questions about complex issues often requires analysts to take into account information contained in multiple interconnected datasets. A common strategy in analyzing and visualizing large and heterogeneous data is dividing it into meaningful subsets. Interesting subsets can then be selected and the associated data and the relationships between the subsets visualized. However, neither the extraction and manipulation nor the comparison of subsets is well supported by state-of-the-art techniques. In this paper we present Domino, a novel multiform visualization technique for effectively representing subsets and the relationships between them. By providing comprehensive tools to arrange, combine, and extract subsets, Domino allows users to create both common visualization techniques and advanced visualizations tailored to specific use cases. In addition to the novel technique, we present an implementation that enables analysts to manage the wide range of options that our approach offers. Innovative interactive features such as placeholders and live previews support rapid creation of complex analysis setups. We introduce the technique and the implementation using a simple example and demonstrate scalability and effectiveness in a use case from the field of cancer genomics. PMID:26356916

Development of a psychological test to measure ability-based emotional intelligence in the Indonesian workplace using an item response theory

PubMed Central

Fajrianthi; Zein, Rizqy Amelia

2017-01-01

This study aimed to develop an emotional intelligence (EI) test that is suitable to the Indonesian workplace context. Airlangga Emotional Intelligence Test (Tes Kecerdasan Emosi Airlangga [TKEA]) was designed to measure three EI domains: 1) emotional appraisal, 2) emotional recognition, and 3) emotional regulation. TKEA consisted of 120 items with 40 items for each subset. TKEA was developed based on the Situational Judgment Test (SJT) approach. To ensure its psychometric qualities, categorical confirmatory factor analysis (CCFA) and item response theory (IRT) were applied to test its validity and reliability. The study was conducted on 752 participants, and the results showed that test information function (TIF) was 3.414 (ability level = 0) for subset 1, 12.183 for subset 2 (ability level = −2), and 2.398 for subset 3 (level of ability = −2). It is concluded that TKEA performs very well to measure individuals with a low level of EI ability. It is worth to note that TKEA is currently at the development stage; therefore, in this study, we investigated TKEA’s item analysis and dimensionality test of each TKEA subset. PMID:29238234

Maximizing and minimizing investment concentration with constraints of budget and investment risk

NASA Astrophysics Data System (ADS)

Shinzato, Takashi

2018-01-01

In this paper, as a first step in examining the properties of a feasible portfolio subset that is characterized by budget and risk constraints, we assess the maximum and minimum of the investment concentration using replica analysis. To do this, we apply an analytical approach of statistical mechanics. We note that the optimization problem considered in this paper is the dual problem of the portfolio optimization problem discussed in the literature, and we verify that these optimal solutions are also dual. We also present numerical experiments, in which we use the method of steepest descent that is based on Lagrange's method of undetermined multipliers, and we compare the numerical results to those obtained by replica analysis in order to assess the effectiveness of our proposed approach.

Systemic sclerosis: a world wide global analysis.

PubMed

Coral-Alvarado, Paola; Pardo, Aryce L; Castaño-Rodriguez, Natalia; Rojas-Villarraga, Adriana; Anaya, Juan-Manuel

2009-07-01

The objective of this study was to analyze epidemiological tendencies of systemic sclerosis (SSc) around the world in order to identify possible local variations in the presentation and occurrence of the disease. A systematic review of the literature was performed through electronic databases using the keywords "Systemic Sclerosis" and "Clinical Characteristics." Out of a total of 167 articles, 41 were included in the analysis. Significant differences in the mean age at the time of diagnosis, subsets of SSc, clinical characteristics, and presence of antibodies were found between different regions of the word. Because variations in both additive and nonadditive genetic factors and the environmental variance are specific to the investigated population, ethnicity and geography are important characteristics to be considered in the study of SSc and other autoimmune diseases.

Integration by parts and Pohozaev identities for space-dependent fractional-order operators

NASA Astrophysics Data System (ADS)

Grubb, Gerd

2016-08-01

Consider a classical elliptic pseudodifferential operator P on Rn of order 2a (0 < a < 1) with even symbol. For example, P = A(x , D) a where A (x , D) is a second-order strongly elliptic differential operator; the fractional Laplacian (- Δ) a is a particular case. For solutions u of the Dirichlet problem on a bounded smooth subset Ω ⊂Rn, we show an integration-by-parts formula with a boundary integral involving (d-a u)|∂Ω, where d (x) = dist (x , ∂ Ω). This extends recent results of Ros-Oton, Serra and Valdinoci, to operators that are x-dependent, nonsymmetric, and have lower-order parts. We also generalize their formula of Pohozaev-type, that can be used to prove unique continuation properties, and nonexistence of nontrivial solutions of semilinear problems. An illustration is given with P =(- Δ +m2) a. The basic step in our analysis is a factorization of P, P ∼P-P+, where we set up a calculus for the generalized pseudodifferential operators P± that come out of the construction.

Higher-order Fourier analysis over finite fields and applications

NASA Astrophysics Data System (ADS)

Hatami, Pooya

Higher-order Fourier analysis is a powerful tool in the study of problems in additive and extremal combinatorics, for instance the study of arithmetic progressions in primes, where the traditional Fourier analysis comes short. In recent years, higher-order Fourier analysis has found multiple applications in computer science in fields such as property testing and coding theory. In this thesis, we develop new tools within this theory with several new applications such as a characterization theorem in algebraic property testing. One of our main contributions is a strong near-equidistribution result for regular collections of polynomials. The densities of small linear structures in subsets of Abelian groups can be expressed as certain analytic averages involving linear forms. Higher-order Fourier analysis examines such averages by approximating the indicator function of a subset by a function of bounded number of polynomials. Then, to approximate the average, it suffices to know the joint distribution of the polynomials applied to the linear forms. We prove a near-equidistribution theorem that describes these distributions for the group F(n/p) when p is a fixed prime. This fundamental fact was previously known only under various extra assumptions about the linear forms or the field size. We use this near-equidistribution theorem to settle a conjecture of Gowers and Wolf on the true complexity of systems of linear forms. Our next application is towards a characterization of testable algebraic properties. We prove that every locally characterized affine-invariant property of functions f : F(n/p) → R with n∈ N, is testable. In fact, we prove that any such property P is proximity-obliviously testable. More generally, we show that any affine-invariant property that is closed under subspace restrictions and has "bounded complexity" is testable. We also prove that any property that can be described as the property of decomposing into a known structure of low-degree polynomials is locally characterized and is, hence, testable. We discuss several notions of regularity which allow us to deduce algorithmic versions of various regularity lemmas for polynomials by Green and Tao and by Kaufman and Lovett. We show that our algorithmic regularity lemmas for polynomials imply algorithmic versions of several results relying on regularity, such as decoding Reed-Muller codes beyond the list decoding radius (for certain structured errors), and prescribed polynomial decompositions. Finally, motivated by the definition of Gowers norms, we investigate norms defined by different systems of linear forms. We give necessary conditions on the structure of systems of linear forms that define norms. We prove that such norms can be one of only two types, and assuming that |F p| is sufficiently large, they essentially are equivalent to either a Gowers norm or Lp norms.

Reference ranges of hematology and lymphocyte subsets in healthy Korean native cattle (Hanwoo) and Holstein dairy cattle.

PubMed

Kim, Yun-Mi; Lee, Jin-A; Jung, Bock-Gie; Kim, Tae-Hoon; Lee, Bong-Joo; Suh, Guk-Hyun

2016-06-01

There are no accurate reference ranges for hematology parameters and lymphocyte subsets in Korean native beef cattle (Hanwoo). This study was performed to establish reliable reference ranges of hematology and lymphocyte subsets using a large number of Hanwoo cattle (n = 350) and to compare differences between Hanwoo and Holstein dairy cattle (n = 334). Additionally, age-related changes in lymphocyte subsets were studied. Bovine leukocyte subpopulation analysis was performed using mono or dual color flow cytometry. The leukocyte subpopulations investigated in healthy cattle included: CD2(+) cells, sIgM(+) cells, MHC class II(+) cells, CD3(+) CD4(+) cells, CD3(+) CD8(+) cells, and WC1(+) cells. Although Hanwoo and Holstein cattle are the same species, results showed several differences in hematology and lymphocyte subsets between Hanwoo and Holstein cattle. This study is the first report to establish reference ranges of hematology and lymphocyte subsets in adult Hanwoo cattle. © 2015 Japanese Society of Animal Science.

MODIS Interactive Subsetting Tool (MIST)

NASA Astrophysics Data System (ADS)

McAllister, M.; Duerr, R.; Haran, T.; Khalsa, S. S.; Miller, D.

2008-12-01

In response to requests from the user community, NSIDC has teamed with the Oak Ridge National Laboratory Distributive Active Archive Center (ORNL DAAC) and the Moderate Resolution Data Center (MrDC) to provide time series subsets of satellite data covering stations in the Greenland Climate Network (GC-NET) and the International Arctic Systems for Observing the Atmosphere (IASOA) network. To serve these data NSIDC created the MODIS Interactive Subsetting Tool (MIST). MIST works with 7 km by 7 km subset time series of certain Version 5 (V005) MODIS products over GC-Net and IASOA stations. User- selected data are delivered in a text Comma Separated Value (CSV) file format. MIST also provides online analysis capabilities that include generating time series and scatter plots. Currently, MIST is a Beta prototype and NSIDC intends that user requests will drive future development of the tool. The intent of this poster is to introduce MIST to the MODIS data user audience and illustrate some of the online analysis capabilities.

On the Hardness of Subset Sum Problem from Different Intervals

NASA Astrophysics Data System (ADS)

Kogure, Jun; Kunihiro, Noboru; Yamamoto, Hirosuke

The subset sum problem, which is often called as the knapsack problem, is known as an NP-hard problem, and there are several cryptosystems based on the problem. Assuming an oracle for shortest vector problem of lattice, the low-density attack algorithm by Lagarias and Odlyzko and its variants solve the subset sum problem efficiently, when the “density” of the given problem is smaller than some threshold. When we define the density in the context of knapsack-type cryptosystems, weights are usually assumed to be chosen uniformly at random from the same interval. In this paper, we focus on general subset sum problems, where this assumption may not hold. We assume that weights are chosen from different intervals, and make analysis of the effect on the success probability of above algorithms both theoretically and experimentally. Possible application of our result in the context of knapsack cryptosystems is the security analysis when we reduce the data size of public keys.

Flow cytometric analysis of extracellular vesicle subsets in plasma: impact of swarm by particles of non-interest.

PubMed

Libregts, S F W M; Arkesteijn, G J A; Németh, A; Nolte-'t Hoen, E N M; Wauben, M H M

2018-05-20

Essentials Extracellular vesicles (EVs) in biological fluids are promising biomarkers for disease. Fluorescence-based flow cytometric analysis is suitable to detect low abundant EV subsets. Particles of non-interest can induce false-positive light scatter and fluorescent signals. Interference of particles of non-interest can be monitored by analyzing serial dilutions. Background Extracellular vesicles (EVs) in plasma are increasingly being recognized as potential biomarkers. EV analysis for diagnostic purposes should be robust and should allow analysis of EV subsets with a wide range of abundance and in a large number of patient samples. Flow cytometry offers possibilities to meet these criteria, as it allows multiparameter analysis of individual EVs. However, analysis of plasma EVs is challenging, because of their size and heterogeneity, and the presence of other submicrometer-sized particles in plasma that could interfere with EV analysis. Objectives To explore whether fluorescence-based flow cytometric analysis of EV subsets is suitable when the EVs of interest are present in low abundance in a background of non-labeled or differently labeled EVs and particles. Methods Fluorescently labeled EVs of interest were spiked at different ratios in full plasma, purified plasma components, or (non-)fluorescent polystyrene beads, and subsequently analyzed by flow cytometry with fluorescence threshold triggering. Results We found that light scatter detection of low-abundance or rare EV subsets during fluorescence threshold triggering was severely affected by particles of non-interest, owing to coincidence and swarming. Importantly, we show that interfering particles labeled with different fluorophores induced false-positive fluorescent signals on the particles of interest. These unwanted effects could only be discerned and controlled by performing serial dilutions and analyzing light scatter and fluorescence parameters. Conclusions We demonstrate how particles of non-interest in plasma can impact on the light scatter and fluorescence detection of low-abundance EVs of interest during fluorescence-based flow cytometric analysis, and provide a means to prevent erroneous data interpretation. © 2018 The Authors. Journal of Thrombosis and Haemostasis published by Wiley Periodicals, Inc. on behalf of International Society on Thrombosis and Haemostasis.

One Size Does Not Fit All: Human Failure Event Decomposition and Task Analysis

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

Ronald Laurids Boring, PhD

2014-09-01

In the probabilistic safety assessments (PSAs) used in the nuclear industry, human failure events (HFEs) are determined as a subset of hardware failures, namely those hardware failures that could be triggered or exacerbated by human action or inaction. This approach is top-down, starting with hardware faults and deducing human contributions to those faults. Elsewhere, more traditionally human factors driven approaches would tend to look at opportunities for human errors first in a task analysis and then identify which of those errors is risk significant. The intersection of top-down and bottom-up approaches to defining HFEs has not been carefully studied. Ideally,more » both approaches should arrive at the same set of HFEs. This question remains central as human reliability analysis (HRA) methods are generalized to new domains like oil and gas. The HFEs used in nuclear PSAs tend to be top-down—defined as a subset of the PSA—whereas the HFEs used in petroleum quantitative risk assessments (QRAs) are more likely to be bottom-up—derived from a task analysis conducted by human factors experts. The marriage of these approaches is necessary in order to ensure that HRA methods developed for top-down HFEs are also sufficient for bottom-up applications. In this paper, I first review top-down and bottom-up approaches for defining HFEs and then present a seven-step guideline to ensure a task analysis completed as part of human error identification decomposes to a level suitable for use as HFEs. This guideline illustrates an effective way to bridge the bottom-up approach with top-down requirements.« less

Memory and long-range correlations in chess games

NASA Astrophysics Data System (ADS)

Schaigorodsky, Ana L.; Perotti, Juan I.; Billoni, Orlando V.

2014-01-01

In this paper we report the existence of long-range memory in the opening moves of a chronologically ordered set of chess games using an extensive chess database. We used two mapping rules to build discrete time series and analyzed them using two methods for detecting long-range correlations; rescaled range analysis and detrended fluctuation analysis. We found that long-range memory is related to the level of the players. When the database is filtered according to player levels we found differences in the persistence of the different subsets. For high level players, correlations are stronger at long time scales; whereas in intermediate and low level players they reach the maximum value at shorter time scales. This can be interpreted as a signature of the different strategies used by players with different levels of expertise. These results are robust against the assignation rules and the method employed in the analysis of the time series.

Whole-rock analyses of core samples from the 1988 drilling of Kilauea Iki lava lake, Hawaii

USGS Publications Warehouse

Helz, Rosalind Tuthill; Taggart, Joseph E.

2010-01-01

This report presents and evaluates 64 major-element analyses of previously unanalyzed Kilauea Iki drill core, plus three samples from the 1959 and 1960 eruptions of Kilauea, obtained by X-ray fluorescence (XRF) analysis during the period 1992 to 1995. All earlier major-element analyses of Kilauea Iki core, obtained by classical (gravimetric) analysis, were reported and evaluated in Helz and others (1994). In order to assess how well the newer data compare with this earlier suite of analyses, a subset of 24 samples, which had been analyzed by classical analysis, was reanalyzed using the XRF technique; those results are presented and evaluated in this report also. The XRF analyses have not been published previously. This report also provides an overview of how the chemical variations observed in these new data fit in with the chemical zonation patterns and petrologic processes inferred in earlier studies of Kilauea Iki.

Archive Management of NASA Earth Observation Data to Support Cloud Analysis

NASA Technical Reports Server (NTRS)

Lynnes, Christopher; Baynes, Kathleen; McInerney, Mark A.

2017-01-01

NASA collects, processes and distributes petabytes of Earth Observation (EO) data from satellites, aircraft, in situ instruments and model output, with an order of magnitude increase expected by 2024. Cloud-based web object storage (WOS) of these data can simplify the execution of such an increase. More importantly, it can also facilitate user analysis of those volumes by making the data available to the massively parallel computing power in the cloud. However, storing EO data in cloud WOS has a ripple effect throughout the NASA archive system with unexpected challenges and opportunities. One challenge is modifying data servicing software (such as Web Coverage Service servers) to access and subset data that are no longer on a directly accessible file system, but rather in cloud WOS. Opportunities include refactoring of the archive software to a cloud-native architecture; virtualizing data products by computing on demand; and reorganizing data to be more analysis-friendly.

Statistical iterative reconstruction for streak artefact reduction when using multidetector CT to image the dento-alveolar structures.

PubMed

Dong, J; Hayakawa, Y; Kober, C

2014-01-01

When metallic prosthetic appliances and dental fillings exist in the oral cavity, the appearance of metal-induced streak artefacts is not avoidable in CT images. The aim of this study was to develop a method for artefact reduction using the statistical reconstruction on multidetector row CT images. Adjacent CT images often depict similar anatomical structures. Therefore, reconstructed images with weak artefacts were attempted using projection data of an artefact-free image in a neighbouring thin slice. Images with moderate and strong artefacts were continuously processed in sequence by successive iterative restoration where the projection data was generated from the adjacent reconstructed slice. First, the basic maximum likelihood-expectation maximization algorithm was applied. Next, the ordered subset-expectation maximization algorithm was examined. Alternatively, a small region of interest setting was designated. Finally, the general purpose graphic processing unit machine was applied in both situations. The algorithms reduced the metal-induced streak artefacts on multidetector row CT images when the sequential processing method was applied. The ordered subset-expectation maximization and small region of interest reduced the processing duration without apparent detriments. A general-purpose graphic processing unit realized the high performance. A statistical reconstruction method was applied for the streak artefact reduction. The alternative algorithms applied were effective. Both software and hardware tools, such as ordered subset-expectation maximization, small region of interest and general-purpose graphic processing unit achieved fast artefact correction.

Data Point Averaging for Computational Fluid Dynamics Data

NASA Technical Reports Server (NTRS)

Norman, Jr., David (Inventor)

2016-01-01

A system and method for generating fluid flow parameter data for use in aerodynamic heating analysis. Computational fluid dynamics data is generated for a number of points in an area on a surface to be analyzed. Sub-areas corresponding to areas of the surface for which an aerodynamic heating analysis is to be performed are identified. A computer system automatically determines a sub-set of the number of points corresponding to each of the number of sub-areas and determines a value for each of the number of sub-areas using the data for the sub-set of points corresponding to each of the number of sub-areas. The value is determined as an average of the data for the sub-set of points corresponding to each of the number of sub-areas. The resulting parameter values then may be used to perform an aerodynamic heating analysis.

Data Point Averaging for Computational Fluid Dynamics Data

NASA Technical Reports Server (NTRS)

Norman, David, Jr. (Inventor)

2014-01-01

A system and method for generating fluid flow parameter data for use in aerodynamic heating analysis. Computational fluid dynamics data is generated for a number of points in an area on a surface to be analyzed. Sub-areas corresponding to areas of the surface for which an aerodynamic heating analysis is to be performed are identified. A computer system automatically determines a sub-set of the number of points corresponding to each of the number of sub-areas and determines a value for each of the number of sub-areas using the data for the sub-set of points corresponding to each of the number of sub-areas. The value is determined as an average of the data for the sub-set of points corresponding to each of the number of sub-areas. The resulting parameter values then may be used to perform an aerodynamic heating analysis.

Analysis of Normal Human Mammary Epigenomes Reveals Cell-Specific Active Enhancer States and Associated Transcription Factor Networks.

PubMed

Pellacani, Davide; Bilenky, Misha; Kannan, Nagarajan; Heravi-Moussavi, Alireza; Knapp, David J H F; Gakkhar, Sitanshu; Moksa, Michelle; Carles, Annaick; Moore, Richard; Mungall, Andrew J; Marra, Marco A; Jones, Steven J M; Aparicio, Samuel; Hirst, Martin; Eaves, Connie J

2016-11-15

The normal adult human mammary gland is a continuous bilayered epithelial system. Bipotent and myoepithelial progenitors are prominent and unique components of the outer (basal) layer. The inner (luminal) layer includes both luminal-restricted progenitors and a phenotypically separable fraction that lacks progenitor activity. We now report an epigenomic comparison of these three subsets with one another, with their associated stromal cells, and with three immortalized, non-tumorigenic human mammary cell lines. Each genome-wide analysis contains profiles for six histone marks, methylated DNA, and RNA transcripts. Analysis of these datasets shows that each cell type has unique features, primarily within genomic regulatory regions, and that the cell lines group together. Analyses of the promoter and enhancer profiles place the luminal progenitors in between the basal cells and the non-progenitor luminal subset. Integrative analysis reveals networks of subset-specific transcription factors. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Automated sinkhole detection using a DEM subsetting technique and fill tools at Mammoth Cave National Park

NASA Astrophysics Data System (ADS)

Wall, J.; Bohnenstiehl, D. R.; Levine, N. S.

2013-12-01

An automated workflow for sinkhole detection is developed using Light Detection and Ranging (Lidar) data from Mammoth Cave National Park (MACA). While the park is known to sit within a karst formation, the generally dense canopy cover and the size of the park (~53,000 acres) creates issues for sinkhole inventorying. Lidar provides a useful remote sensing technology for peering beneath the canopy in hard to reach areas of the park. In order to detect sinkholes, a subsetting technique is used to interpolate a Digital Elevation Model (DEM) thereby reducing edge effects. For each subset, standard GIS fill tools are used to fill depressions within the DEM. The initial DEM is then subtracted from the filled DEM resulting in detected depressions or sinkholes. Resulting depressions are then described in terms of size and geospatial trend.

Day-Ahead PM2.5 Concentration Forecasting Using WT-VMD Based Decomposition Method and Back Propagation Neural Network Improved by Differential Evolution

PubMed Central

Wang, Deyun; Liu, Yanling; Luo, Hongyuan; Yue, Chenqiang; Cheng, Sheng

2017-01-01

Accurate PM2.5 concentration forecasting is crucial for protecting public health and atmospheric environment. However, the intermittent and unstable nature of PM2.5 concentration series makes its forecasting become a very difficult task. In order to improve the forecast accuracy of PM2.5 concentration, this paper proposes a hybrid model based on wavelet transform (WT), variational mode decomposition (VMD) and back propagation (BP) neural network optimized by differential evolution (DE) algorithm. Firstly, WT is employed to disassemble the PM2.5 concentration series into a number of subsets with different frequencies. Secondly, VMD is applied to decompose each subset into a set of variational modes (VMs). Thirdly, DE-BP model is utilized to forecast all the VMs. Fourthly, the forecast value of each subset is obtained through aggregating the forecast results of all the VMs obtained from VMD decomposition of this subset. Finally, the final forecast series of PM2.5 concentration is obtained by adding up the forecast values of all subsets. Two PM2.5 concentration series collected from Wuhan and Tianjin, respectively, located in China are used to test the effectiveness of the proposed model. The results demonstrate that the proposed model outperforms all the other considered models in this paper. PMID:28704955

Profiling dendritic cell subsets in head and neck squamous cell tonsillar cancer and benign tonsils.

PubMed

Abolhalaj, Milad; Askmyr, David; Sakellariou, Christina Alexandra; Lundberg, Kristina; Greiff, Lennart; Lindstedt, Malin

2018-05-23

Dendritic cells (DCs) have a key role in orchestrating immune responses and are considered important targets for immunotherapy against cancer. In order to develop effective cancer vaccines, detailed knowledge of the micromilieu in cancer lesions is warranted. In this study, flow cytometry and human transcriptome arrays were used to characterize subsets of DCs in head and neck squamous cell tonsillar cancer and compare them to their counterparts in benign tonsils to evaluate subset-selective biomarkers associated with tonsillar cancer. We describe, for the first time, four subsets of DCs in tonsillar cancer: CD123 + plasmacytoid DCs (pDC), CD1c + , CD141 + , and CD1c - CD141 - myeloid DCs (mDC). An increased frequency of DCs and an elevated mDC/pDC ratio were shown in malignant compared to benign tonsillar tissue. The microarray data demonstrates characteristics specific for tonsil cancer DC subsets, including expression of immunosuppressive molecules and lower expression levels of genes involved in development of effector immune responses in DCs in malignant tonsillar tissue, compared to their counterparts in benign tonsillar tissue. Finally, we present target candidates selectively expressed by different DC subsets in malignant tonsils and confirm expression of CD206/MRC1 and CD207/Langerin on CD1c + DCs at protein level. This study descibes DC characteristics in the context of head and neck cancer and add valuable steps towards future DC-based therapies against tonsillar cancer.

Natural Killer Cells Promote Fetal Development through the Secretion of Growth-Promoting Factors.

PubMed

Fu, Binqing; Zhou, Yonggang; Ni, Xiang; Tong, Xianhong; Xu, Xiuxiu; Dong, Zhongjun; Sun, Rui; Tian, Zhigang; Wei, Haiming

2017-12-19

Natural killer (NK) cells are present in large populations at the maternal-fetal interface during early pregnancy. However, the role of NK cells in fetal growth is unclear. Here, we have identified a CD49a + Eomes + subset of NK cells that secreted growth-promoting factors (GPFs), including pleiotrophin and osteoglycin, in both humans and mice. The crosstalk between HLA-G and ILT2 served as a stimulus for GPF-secreting function of this NK cell subset. Decreases in this GPF-secreting NK cell subset impaired fetal development, resulting in fetal growth restriction. The transcription factor Nfil3, but not T-bet, affected the function and the number of this decidual NK cell subset. Adoptive transfer of induced CD49a + Eomes + NK cells reversed impaired fetal growth and rebuilt an appropriate local microenvironment. These findings reveal properties of NK cells in promoting fetal growth. In addition, this research proposes approaches for therapeutic administration of NK cells in order to reverse restricted nourishments within the uterine microenvironment during early pregnancy. Copyright © 2017 Elsevier Inc. All rights reserved.

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

PubMed

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

2017-10-31

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

Automatic Nuclei Segmentation in H&E Stained Breast Cancer Histopathology Images

PubMed Central

Veta, Mitko; van Diest, Paul J.; Kornegoor, Robert; Huisman, André; Viergever, Max A.; Pluim, Josien P. W.

2013-01-01

The introduction of fast digital slide scanners that provide whole slide images has led to a revival of interest in image analysis applications in pathology. Segmentation of cells and nuclei is an important first step towards automatic analysis of digitized microscopy images. We therefore developed an automated nuclei segmentation method that works with hematoxylin and eosin (H&E) stained breast cancer histopathology images, which represent regions of whole digital slides. The procedure can be divided into four main steps: 1) pre-processing with color unmixing and morphological operators, 2) marker-controlled watershed segmentation at multiple scales and with different markers, 3) post-processing for rejection of false regions and 4) merging of the results from multiple scales. The procedure was developed on a set of 21 breast cancer cases (subset A) and tested on a separate validation set of 18 cases (subset B). The evaluation was done in terms of both detection accuracy (sensitivity and positive predictive value) and segmentation accuracy (Dice coefficient). The mean estimated sensitivity for subset A was 0.875 (±0.092) and for subset B 0.853 (±0.077). The mean estimated positive predictive value was 0.904 (±0.075) and 0.886 (±0.069) for subsets A and B, respectively. For both subsets, the distribution of the Dice coefficients had a high peak around 0.9, with the vast majority of segmentations having values larger than 0.8. PMID:23922958

Automatic nuclei segmentation in H&E stained breast cancer histopathology images.

PubMed

Veta, Mitko; van Diest, Paul J; Kornegoor, Robert; Huisman, André; Viergever, Max A; Pluim, Josien P W

2013-01-01

The introduction of fast digital slide scanners that provide whole slide images has led to a revival of interest in image analysis applications in pathology. Segmentation of cells and nuclei is an important first step towards automatic analysis of digitized microscopy images. We therefore developed an automated nuclei segmentation method that works with hematoxylin and eosin (H&E) stained breast cancer histopathology images, which represent regions of whole digital slides. The procedure can be divided into four main steps: 1) pre-processing with color unmixing and morphological operators, 2) marker-controlled watershed segmentation at multiple scales and with different markers, 3) post-processing for rejection of false regions and 4) merging of the results from multiple scales. The procedure was developed on a set of 21 breast cancer cases (subset A) and tested on a separate validation set of 18 cases (subset B). The evaluation was done in terms of both detection accuracy (sensitivity and positive predictive value) and segmentation accuracy (Dice coefficient). The mean estimated sensitivity for subset A was 0.875 (±0.092) and for subset B 0.853 (±0.077). The mean estimated positive predictive value was 0.904 (±0.075) and 0.886 (±0.069) for subsets A and B, respectively. For both subsets, the distribution of the Dice coefficients had a high peak around 0.9, with the vast majority of segmentations having values larger than 0.8.

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

PubMed Central

Danielle, Borra; Tibor, Verduna; Stefano, Massaglia

2017-01-01

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

ECS Maintenance Wed. 12/28

Atmospheric Science Data Center

2016-12-27

Date(s):  Wednesday, December 28, 2016 Time:  12 am - 12 pm EDT Event Impact:  The Data Pool, MISR order and browse tools, TAD, TES and MOPITT Search and Subset Applications, and Reverb will be unavailable...

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

PubMed

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

2003-07-01

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

South Australian Scleroderma Register: analysis of deceased patients.

PubMed

Bond, C; Pile, K D; McNeil, J D; Ahern, M J; Smith, M D; Cleland, L G; Roberts-Thomson, P J

1998-11-01

The demographic, clinical, pathological and serological features of 123 decreased patients with systemic sclerosis have been analysed. These patients consisted of all identified patients dying with this disease in South Australia between 1983 and 1996 inclusive. There were 85 females and 38 males, with the ratio of limited:diffuse:overlap disease subset being 9:5:1. Disease characteristics revealed that patients with the limited disease tended to be female with high frequencies of the centromere autoantibody, while patients with the diffuse disease had equal gender representation with the frequent presence of nucleolar, speckled or homogeneous antinuclear antibody. Mean duration of disease and mean age of death for the limited:diffuse:overlap subsets differed significantly between groups (p < 0.05) and were 16.5, 9.3 and 10.9 years and 71.9, 57.8 and 52.8 years respectively. Cumulative survival curves for the subsets differed highly significantly, with patients with the limited diseases dying more commonly from right heart failure (documented terminally in 25% of the centromere positive limited subset), cardiovascular disease or cancer, while patients with the diffuse subset died from respiratory failure, renal failure or cardiovascular disease. In conclusion, this retrospective analysis has revealed that scleroderma is a relatively common but clinically heterogeneous disorder. There are important clinical and prognostic implications in defining limited versus diffuse versus overlap disease.

On optimal fuzzy best proximity coincidence points of fuzzy order preserving proximal Ψ(σ, α)-lower-bounding asymptotically contractive mappings in non-Archimedean fuzzy metric spaces.

PubMed

De la Sen, Manuel; Abbas, Mujahid; Saleem, Naeem

2016-01-01

This paper discusses some convergence properties in fuzzy ordered proximal approaches defined by [Formula: see text]-sequences of pairs, where [Formula: see text] is a surjective self-mapping and [Formula: see text] where Aand Bare nonempty subsets of and abstract nonempty set X and [Formula: see text] is a partially ordered non-Archimedean fuzzy metric space which is endowed with a fuzzy metric M, a triangular norm * and an ordering [Formula: see text] The fuzzy set M takes values in a sequence or set [Formula: see text] where the elements of the so-called switching rule [Formula: see text] are defined from [Formula: see text] to a subset of [Formula: see text] Such a switching rule selects a particular realization of M at the nth iteration and it is parameterized by a growth evolution sequence [Formula: see text] and a sequence or set [Formula: see text] which belongs to the so-called [Formula: see text]-lower-bounding mappings which are defined from [0, 1] to [0, 1]. Some application examples concerning discrete systems under switching rules and best approximation solvability of algebraic equations are discussed.

Integrative genome-wide analysis of the determinants of RNA splicing in kidney renal clear cell carcinoma.

PubMed

Lehmann, Kjong-Van; Kahles, André; Kandoth, Cyriac; Lee, William; Schultz, Nikolaus; Stegle, Oliver; Rätsch, Gunnar

2015-01-01

We present a genome-wide analysis of splicing patterns of 282 kidney renal clear cell carcinoma patients in which we integrate data from whole-exome sequencing of tumor and normal samples, RNA-seq and copy number variation. We proposed a scoring mechanism to compare splicing patterns in tumor samples to normal samples in order to rank and detect tumor-specific isoforms that have a potential for new biomarkers. We identified a subset of genes that show introns only observable in tumor but not in normal samples, ENCODE and GEUVADIS samples. In order to improve our understanding of the underlying genetic mechanisms of splicing variation we performed a large-scale association analysis to find links between somatic or germline variants with alternative splicing events. We identified 915 cis- and trans-splicing quantitative trait loci (sQTL) associated with changes in splicing patterns. Some of these sQTL have previously been associated with being susceptibility loci for cancer and other diseases. Our analysis also allowed us to identify the function of several COSMIC variants showing significant association with changes in alternative splicing. This demonstrates the potential significance of variants affecting alternative splicing events and yields insights into the mechanisms related to an array of disease phenotypes.

The mass of Mars, Phobos, and Deimos, from the analysis of the Mariner 9 and Viking Orbiter tracking data

NASA Technical Reports Server (NTRS)

Smith, D. E.; Lemoine, F. G.; Fricke, S. K.

1994-01-01

We have estimated the mass of Phobos, Deimos, and Mars using the Viking Orbiter and Mariner 9 tracking data. We divided the data into 282 arcs and sorted the data by periapse height, by inclination, and by satellite. The data were processed with the GEODYN/SOLVE orbit determination programs, which have previously been used to analyze planetary tracking data. The a priori Mars gravity field applied in this study was the 50th degree and order GMM-1 (Goddard Mars Model-1) model. The subsets of data were carefully edited to remove any arcs with close encounters of less than 500 km with either Phobos or Deimos. Whereas previous investigators have used close flybys (less than 500 km) to estimate the satellite masses, we have attempted to estimate the masses of Phobos and Deimos from multiday arcs which only included more distant encounters. The subsets of data were further edited to eliminate spurious data near solar conjunction (Nov.-Dec. 1976 and January 1979). In addition, the Viking-1 data from Oct. through Dec. 1978 were also excluded because of the low periapse altitude (as low as 232 km) and thus high sensitivity to atmospheric drag.

Screening for depression in clinical practice: reliability and validity of a five-item subset of the CES-Depression.

PubMed

Bohannon, Richard W; Maljanian, Rose; Goethe, John

2003-12-01

Individuals with chronic disease are not screened routinely for depression. Availability of an abbreviated test with demonstrated reliability and validity might encourage screening so we explored the reliability and validity of a 5-item subset of the 20-item Center for Epidemiological Studies Depression Scale among inner-city outpatients with chronic asthma or diabetes. Most patients were female (73.1%) and Hispanic (61.8%). Acceptable reliability was shown by Cronbach alpha (.76) for the subset of 5 items. Validity was supported by the high correlation of .91 between patients' scores on the 5-item subset and the full 20 items. The 5 items reflected a single factor (eigenvalue = 2.66). Receiver operating characteristic curve analysis identified cut-points for the 5 items that were sensitive (> .84) and specific (> or = .80) in identifying patients classified as depressed by full 20 items. The reduced patient and clinician burden of the subset of 5 items, as well as its desirable psychometric properties, support broader application of this subset as a screening tool for depression.

Feature Selection for Speech Emotion Recognition in Spanish and Basque: On the Use of Machine Learning to Improve Human-Computer Interaction

PubMed Central

Arruti, Andoni; Cearreta, Idoia; Álvarez, Aitor; Lazkano, Elena; Sierra, Basilio

2014-01-01

Study of emotions in human–computer interaction is a growing research area. This paper shows an attempt to select the most significant features for emotion recognition in spoken Basque and Spanish Languages using different methods for feature selection. RekEmozio database was used as the experimental data set. Several Machine Learning paradigms were used for the emotion classification task. Experiments were executed in three phases, using different sets of features as classification variables in each phase. Moreover, feature subset selection was applied at each phase in order to seek for the most relevant feature subset. The three phases approach was selected to check the validity of the proposed approach. Achieved results show that an instance-based learning algorithm using feature subset selection techniques based on evolutionary algorithms is the best Machine Learning paradigm in automatic emotion recognition, with all different feature sets, obtaining a mean of 80,05% emotion recognition rate in Basque and a 74,82% in Spanish. In order to check the goodness of the proposed process, a greedy searching approach (FSS-Forward) has been applied and a comparison between them is provided. Based on achieved results, a set of most relevant non-speaker dependent features is proposed for both languages and new perspectives are suggested. PMID:25279686

On the use of higher order wave forms in the search for gravitational waves emitted by compact binary coalescences

NASA Astrophysics Data System (ADS)

McKechan, David J. A.

2010-11-01

This thesis concerns the use, in gravitational wave data analysis, of higher order wave form models of the gravitational radiation emitted by compact binary coalescences. We begin with an introductory chapter that includes an overview of the theory of general relativity, gravitational radiation and ground-based interferometric gravitational wave detectors. We then discuss, in Chapter 2, the gravitational waves emitted by compact binary coalescences, with an explanation of higher order waveforms and how they differ from leading order waveforms we also introduce the post-Newtonian formalism. In Chapter 3 the method and results of a gravitational wave search for low mass compact binary coalescences using a subset of LIGO's 5th science run data are presented and in the subsequent chapter we examine how one could use higher order waveforms in such analyses. We follow the development of a new search algorithm that incorporates higher order waveforms with promising results for detection efficiency and parameter estimation. In Chapter 5, a new method of windowing time-domain waveforms that offers benefit to gravitational wave searches is presented. The final chapter covers the development of a game designed as an outreach project to raise public awareness and understanding of the search for gravitational waves.

Iterative CT reconstruction using coordinate descent with ordered subsets of data

NASA Astrophysics Data System (ADS)

Noo, F.; Hahn, K.; Schöndube, H.; Stierstorfer, K.

2016-04-01

Image reconstruction based on iterative minimization of a penalized weighted least-square criteria has become an important topic of research in X-ray computed tomography. This topic is motivated by increasing evidence that such a formalism may enable a significant reduction in dose imparted to the patient while maintaining or improving image quality. One important issue associated with this iterative image reconstruction concept is slow convergence and the associated computational effort. For this reason, there is interest in finding methods that produce approximate versions of the targeted image with a small number of iterations and an acceptable level of discrepancy. We introduce here a novel method to produce such approximations: ordered subsets in combination with iterative coordinate descent. Preliminary results demonstrate that this method can produce, within 10 iterations and using only a constant image as initial condition, satisfactory reconstructions that retain the noise properties of the targeted image.

An intelligent data model for the storage of structured grids

NASA Astrophysics Data System (ADS)

Clyne, John; Norton, Alan

2013-04-01

With support from the U.S. National Science Foundation we have developed, and currently maintain, VAPOR: a geosciences-focused, open source visual data analysis package. VAPOR enables highly interactive exploration, as well as qualitative and quantitative analysis of high-resolution simulation outputs using only a commodity, desktop computer. The enabling technology behind VAPOR's ability to interact with a data set, whose size would overwhelm all but the largest analysis computing resources, is a progressive data access file format, called the VAPOR Data Collection (VDC). The VDC is based on the discrete wavelet transform and their information compaction properties. Prior to analysis, raw data undergo a wavelet transform, concentrating the information content into a fraction of the coefficients. The coefficients are then sorted by their information content (magnitude) into a small number of bins. Data are reconstructed by applying an inverse wavelet transform. If all of the coefficient bins are used during reconstruction the process is lossless (up to floating point round-off). If only a subset of the bins are used, an approximation of the original data is produced. A crucial point here is that the principal benefit to reconstruction from a subset of wavelet coefficients is a reduction in I/O. Further, if smaller coefficients are simply discarded, or perhaps stored on more capacious tertiary storage, secondary storage requirements (e.g. disk) can be reduced as well. In practice, these reductions in I/O or storage can be on the order of tens or even hundreds. This talk will briefly describe the VAPOR Data Collection, and will present real world success stories from the geosciences that illustrate how progressive data access enables highly interactive exploration of Big Data.

Identifying developmental toxicity pathways for a subset of ToxCast chemicals using human embryonic stem cells and metabolomics

EPA Science Inventory

Metabolomics analysis was performed on the supernatant of human embryonic stem (hES) cell cultures exposed to a blinded subset of 11 chemicals selected from the chemical library of EPA's ToxCast™ chemical screening and prioritization research project. Metabolites from hES cultur...

Transcriptional and functional profiling defines human small intestinal macrophage subsets.

PubMed

Bujko, Anna; Atlasy, Nader; Landsverk, Ole J B; Richter, Lisa; Yaqub, Sheraz; Horneland, Rune; Øyen, Ole; Aandahl, Einar Martin; Aabakken, Lars; Stunnenberg, Hendrik G; Bækkevold, Espen S; Jahnsen, Frode L

2018-02-05

Macrophages (Mfs) are instrumental in maintaining immune homeostasis in the intestine, yet studies on the origin and heterogeneity of human intestinal Mfs are scarce. Here, we identified four distinct Mf subpopulations in human small intestine (SI). Assessment of their turnover in duodenal transplants revealed that all Mf subsets were completely replaced over time; Mf1 and Mf2, phenotypically similar to peripheral blood monocytes (PBMos), were largely replaced within 3 wk, whereas two subsets with features of mature Mfs, Mf3 and Mf4, exhibited significantly slower replacement. Mf3 and Mf4 localized differently in SI; Mf3 formed a dense network in mucosal lamina propria, whereas Mf4 was enriched in submucosa. Transcriptional analysis showed that all Mf subsets were markedly distinct from PBMos and dendritic cells. Compared with PBMos, Mf subpopulations showed reduced responsiveness to proinflammatory stimuli but were proficient at endocytosis of particulate and soluble material. These data provide a comprehensive analysis of human SI Mf population and suggest a precursor-progeny relationship with PBMos. © 2018 Bujko et al.

Preliminary experimental results from a MARS Micro-CT system.

PubMed

He, Peng; Yu, Hengyong; Thayer, Patrick; Jin, Xin; Xu, Qiong; Bennett, James; Tappenden, Rachael; Wei, Biao; Goldstein, Aaron; Renaud, Peter; Butler, Anthony; Butler, Phillip; Wang, Ge

2012-01-01

The Medipix All Resolution System (MARS) system is a commercial spectral/multi-energy micro-CT scanner designed and assembled by the MARS Bioimaging, Ltd. in New Zealand. This system utilizes the state-of-the-art Medipix photon-counting, energy-discriminating detector technology developed by a collaboration at European Organization for Nuclear Research (CERN). In this paper, we report our preliminary experimental results using this system, including geometrical alignment, photon energy characterization, protocol optimization, and spectral image reconstruction. We produced our scan datasets with a multi-material phantom, and then applied ordered subset-simultaneous algebraic reconstruction technique (OS-SART) to reconstruct images in different energy ranges and principal component analysis (PCA) to evaluate spectral deviation among the energy ranges.

High-Throughput Characterization of Intrinsic Disorder in Proteins from the Protein Structure Initiative

PubMed Central

Johnson, Derrick E.; Xue, Bin; Sickmeier, Megan D.; Meng, Jingwei; Cortese, Marc S.; Oldfield, Christopher J.; Le Gall, Tanguy; Dunker, A. Keith; Uversky, Vladimir N.

2012-01-01

The identification of intrinsically disordered proteins (IDPs) among the targets that fail to form satisfactory crystal structures in the Protein Structure Initiative represent a key to reducing the costs and time for determining three-dimensional structures of proteins. To help in this endeavor, several Protein Structure Initiative Centers were asked to send samples of both crystallizable proteins and proteins that failed to crystallize. The abundance of intrinsic disorder in these proteins was evaluated via computational analysis using Predictors of Natural Disordered Regions (PONDR®) and the potential cleavage sites and corresponding fragments were determined. Then, the target proteins were analyzed for intrinsic disorder by their resistance to limited proteolysis. The rates of tryptic digestion of sample target proteins were compared to those of lysozyme/myoglobin, apo-myoglobin and α-casein as standards of ordered, partially disordered and completely disordered proteins, respectively. At the next stage, the protein samples were subjected to both far-UV and near-UV circular dichroism (CD) analysis. For most of the samples, a good agreement between CD data, predictions of disorder and the rates of limited tryptic digestion was established. Further experimentation is being performed on a smaller subset of these samples in order to obtain more detailed information on the ordered/disordered nature of the proteins. PMID:22651963

Investigation of production method, geographical origin and species authentication in commercially relevant shrimps using stable isotope ratio and/or multi-element analyses combined with chemometrics: an exploratory analysis.

PubMed

Ortea, Ignacio; Gallardo, José M

2015-03-01

Three factors defining the traceability of a food product are production method (wild or farmed), geographical origin and biological species, which have to be checked and guaranteed, not only in order to avoid mislabelling and commercial fraud, but also to address food safety issues and to comply with legal regulations. The aim of this study was to determine whether these three factors could be differentiated in shrimps using stable isotope ratio analysis of carbon and nitrogen and/or multi-element composition. Different multivariate statistics methods were applied to different data subsets in order to evaluate their performance in terms of classification or predictive ability. Although the success rates varied depending on the dataset used, the combination of both techniques allowed the correct classification of 100% of the samples according to their actual origin and method of production, and 93.5% according to biological species. Even though further studies including a larger number of samples in each group are needed in order to validate these findings, we can conclude that these methodologies should be considered for studies regarding seafood product authenticity. Copyright © 2014 Elsevier Ltd. All rights reserved.

Roughness in Lattice Ordered Effect Algebras

PubMed Central

Xin, Xiao Long; Hua, Xiu Juan; Zhu, Xi

2014-01-01

Many authors have studied roughness on various algebraic systems. In this paper, we consider a lattice ordered effect algebra and discuss its roughness in this context. Moreover, we introduce the notions of the interior and the closure of a subset and give some of their properties in effect algebras. Finally, we use a Riesz ideal induced congruence and define a function e(a, b) in a lattice ordered effect algebra E and build a relationship between it and congruence classes. Then we study some properties about approximation of lattice ordered effect algebras. PMID:25170523

Visual analytics in cheminformatics: user-supervised descriptor selection for QSAR methods.

PubMed

Martínez, María Jimena; Ponzoni, Ignacio; Díaz, Mónica F; Vazquez, Gustavo E; Soto, Axel J

2015-01-01

The design of QSAR/QSPR models is a challenging problem, where the selection of the most relevant descriptors constitutes a key step of the process. Several feature selection methods that address this step are concentrated on statistical associations among descriptors and target properties, whereas the chemical knowledge is left out of the analysis. For this reason, the interpretability and generality of the QSAR/QSPR models obtained by these feature selection methods are drastically affected. Therefore, an approach for integrating domain expert's knowledge in the selection process is needed for increase the confidence in the final set of descriptors. In this paper a software tool, which we named Visual and Interactive DEscriptor ANalysis (VIDEAN), that combines statistical methods with interactive visualizations for choosing a set of descriptors for predicting a target property is proposed. Domain expertise can be added to the feature selection process by means of an interactive visual exploration of data, and aided by statistical tools and metrics based on information theory. Coordinated visual representations are presented for capturing different relationships and interactions among descriptors, target properties and candidate subsets of descriptors. The competencies of the proposed software were assessed through different scenarios. These scenarios reveal how an expert can use this tool to choose one subset of descriptors from a group of candidate subsets or how to modify existing descriptor subsets and even incorporate new descriptors according to his or her own knowledge of the target property. The reported experiences showed the suitability of our software for selecting sets of descriptors with low cardinality, high interpretability, low redundancy and high statistical performance in a visual exploratory way. Therefore, it is possible to conclude that the resulting tool allows the integration of a chemist's expertise in the descriptor selection process with a low cognitive effort in contrast with the alternative of using an ad-hoc manual analysis of the selected descriptors. Graphical abstractVIDEAN allows the visual analysis of candidate subsets of descriptors for QSAR/QSPR. In the two panels on the top, users can interactively explore numerical correlations as well as co-occurrences in the candidate subsets through two interactive graphs.

Different responses to oxidized low-density lipoproteins in human polarized macrophages

PubMed Central

2011-01-01

Background Oxidized low-density lipoprotein (oxLDL) uptake by macrophages plays an important role in foam cell formation. It has been suggested the presence of heterogeneous subsets of macrophage, such as M1 and M2, in human atherosclerotic lesions. To evaluate which types of macrophages contribute to atherogenesis, we performed cDNA microarray analysis to determine oxLDL-induced transcriptional alterations of each subset of macrophages. Results Human monocyte-derived macrophages were polarized toward the M1 or M2 subset, followed by treatment with oxLDL. Then gene expression levels during oxLDL treatment in each subset of macrophages were evaluated by cDNA microarray analysis and quantitative real-time RT-PCR. In terms of high-ranking upregulated genes and functional ontologies, the alterations during oxLDL treatment in M2 macrophages were similar to those in nonpolarized macrophages (M0). Molecular network analysis showed that most of the molecules in the oxLDL-induced highest scoring molecular network of M1 macrophages were directly or indirectly related to transforming growth factor (TGF)-β1. Hierarchical cluster analysis revealed commonly upregulated genes in all subset of macrophages, some of which contained antioxidant response elements (ARE) in their promoter regions. A cluster of genes that were specifically upregulated in M1 macrophages included those encoding molecules related to nuclear factor of kappa light polypeptide gene enhancer in B-cells (NF-κB) signaling pathway. Quantitative real-time RT-PCR showed that the gene expression of interleukin (IL)-8 after oxLDL treatment in M2 macrophages was markedly lower than those in M0 and M1 cells. HMOX1 gene expression levels were almost the same in all 3 subsets of macrophages even after oxLDL treatment. Conclusions The present study demonstrated transcriptional alterations in polarized macrophages during oxLDL treatment. The data suggested that oxLDL uptake may affect TGF-β1- and NF-κB-mediated functions of M1 macrophages, but not those of M0 or M2 macrophages. It is likely that M1 macrophages characteristically respond to oxLDL. PMID:21199582

CT image reconstruction with half precision floating-point values.

PubMed

Maaß, Clemens; Baer, Matthias; Kachelrieß, Marc

2011-07-01

Analytic CT image reconstruction is a computationally demanding task. Currently, the even more demanding iterative reconstruction algorithms find their way into clinical routine because their image quality is superior to analytic image reconstruction. The authors thoroughly analyze a so far unconsidered but valuable tool of tomorrow's reconstruction hardware (CPU and GPU) that allows implementing the forward projection and backprojection steps, which are the computationally most demanding parts of any reconstruction algorithm, much more efficiently. Instead of the standard 32 bit floating-point values (float), a recently standardized floating-point value with 16 bit (half) is adopted for data representation in image domain and in rawdata domain. The reduction in the total data amount reduces the traffic on the memory bus, which is the bottleneck of today's high-performance algorithms, by 50%. In CT simulations and CT measurements, float reconstructions (gold standard) and half reconstructions are visually compared via difference images and by quantitative image quality evaluation. This is done for analytical reconstruction (filtered backprojection) and iterative reconstruction (ordered subset SART). The magnitude of quantization noise, which is caused by a reduction in the data precision of both rawdata and image data during image reconstruction, is negligible. This is clearly shown for filtered backprojection and iterative ordered subset SART reconstruction. In filtered backprojection, the implementation of the backprojection should be optimized for low data precision if the image data are represented in half format. In ordered subset SART image reconstruction, no adaptations are necessary and the convergence speed remains unchanged. Half precision floating-point values allow to speed up CT image reconstruction without compromising image quality.

Functional characterization of a regulatory human T-cell subpopulation increasing during autologous MLR.

PubMed Central

Cosulich, M E; Risso, A; Canonica, G W; Bargellesi, A

1986-01-01

The present study was undertaken to investigate the heterogeneity of helper T cells in humans using two different monoclonal antibodies: 5/9 and MLR4. The former identifies 15-20% of resting T lymphocytes from peripheral blood and corresponds to an anti-helper/inducer T cell. The second antibody, MLR4, recognizes 5% of total T lymphocytes and partially overlaps with the 5/9+ T cells. In order to investigate functional differences within the 5/9+ cells, we separated two different subsets (5/9+ MLR+ and 5/9+ MLR4-) by a rosetting technique. Although both subsets provide help for Ig synthesis in a PWM-stimulated culture, only the 5/9+ MLR4- fraction gave a proliferative response in both autologous and allogeneic MLR and to soluble protein antigens. The effect of radiation on the ability of the two subsets to provide help for Ig synthesis showed that the 5/9+ MLR4+ subset is highly radiation-sensitive, while 5/9+ MLR- is relatively radiation-resistant. In a further series of experiments, 5/9+ MLR4+ cells isolated after activation in an autologous MLR but not by Con A, were no longer able to induce T-cell differentiation but now showed a strong suppressor effect. The 5/9+ MLR4- subset separated from the same cultures did not display any suppressor function. These data demonstrate in fresh PBL the existence of a radiation-sensitive regulatory subset exerting a helper activity, and which acquires suppressor activity after activation in autologous MLR. PMID:2936679

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

PubMed Central

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

2017-01-01

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

A Preliminary Analysis of LANDSAT-4 Thematic Mapper Radiometric Performance

NASA Technical Reports Server (NTRS)

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

1984-01-01

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

AIRS Data Subsetting Service at the Goddard Earth Sciences (GES) DISC/DAAC

NASA Technical Reports Server (NTRS)

Vicente, Gilberto A.; Qin, Jianchun; Li, Jason; Gerasimov, Irina; Savtchenko, Andrey

2004-01-01

The AIRS mission, as a combination of the Atmospheric Infrared Sounder (AIRS), the Advanced Microwave Sounding Unit (AMSU) and the Humidity Sounder for Brazil (HSB), brings climate research and weather prediction into 21st century. From NASA' Aqua spacecraft, the AIRS/AMSU/HSB instruments measure humidity, temperature, cloud properties and the amounts of greenhouse gases. The AIRS also reveals land and sea- surface temperatures. Measurements from these three instruments are analyzed . jointly to filter out the effects of clouds from the IR data in order to derive clear-column air-temperature profiles and surface temperatures with high vertical resolution and accuracy. Together, they constitute an advanced operational sounding data system that have contributed to improve global modeling efforts and numerical weather prediction; enhance studies of the global energy and water cycles, the effects of greenhouse gases, and atmosphere-surface interactions; and facilitate monitoring of climate variations and trends. The high data volume generated by the AIRS/AMSU/HSB instruments and the complexity of its data format (Hierarchical Data Format, HDF) are barriers to AIRS data use. Although many researchers are interested in only a fraction of the data they receive or request, they are forced to run their algorithms on a much larger data set to extract the information of interest. In order to better server its users, the GES DISC/DAAC, provider of long-term archives and distribution services as well science support for the AIRS/AMSU/HSB data products, has developed various tools for performing channels, variables, parameter, spatial and derived products subsetting, resampling and reformatting operations. This presentation mainly describes the web-enabled subsetting services currently available at the GES DISC/DAAC that provide subsetting functions for all the Level 1B and Level 2 data products from the AIRS/AMSU/HSB instruments.

Comparison between flowcytometry and immunoperoxidase staining for the enumeration of lymphocyte subsets.

PubMed

Dhaliwal, J S; Malar, B; Quck, C K; Sukumaran, K D; Hassan, K

1991-06-01

Immunoperoxidase staining was compared with flowcytometry for the enumeration of lymphocyte subsets. The percentages obtained for peripheral blood lymphocytes using immunoperoxidase (CD3 = 76 CD4 = 27.9, B = 10.7 CD4/CD8 = 1.8) differed significantly from those obtained by flowcytometry (CD3 = 65.7 CD4 = 39.4, CD8 = 25.6, B = 16.7, HLA DR = 11.9 CD4/CD8 = 1.54) for certain subsets (CD3, CD4, B). There was no significant difference in lymphocyte subsets between children and adults using the same method. These differences are probably due to the different methods used to prepare lymphocytes for analysis. Other factors that should also be considered are the presence of CD4 antigen on monocytes and CD8 on natural killer cells.

Optimizing tertiary storage organization and access for spatio-temporal datasets

NASA Technical Reports Server (NTRS)

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

1994-01-01

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

On the relationship between NMR-derived amide order parameters and protein backbone entropy changes

PubMed Central

Sharp, Kim A.; O’Brien, Evan; Kasinath, Vignesh; Wand, A. Joshua

2015-01-01

Molecular dynamics simulations are used to analyze the relationship between NMR-derived squared generalized order parameters of amide NH groups and backbone entropy. Amide order parameters (O2NH) are largely determined by the secondary structure and average values appear unrelated to the overall flexibility of the protein. However, analysis of the more flexible subset (O2NH < 0.8) shows that these report both on the local flexibility of the protein and on a different component of the conformational entropy than that reported by the side chain methyl axis order parameters, O2axis. A calibration curve for backbone entropy vs. O2NH is developed which accounts for both correlations between amide group motions of different residues, and correlations between backbone and side chain motions. This calibration curve can be used with experimental values of O2NH changes obtained by NMR relaxation measurements to extract backbone entropy changes, e.g. upon ligand binding. In conjunction with our previous calibration for side chain entropy derived from measured O2axis values this provides a prescription for determination of the total protein conformational entropy changes from NMR relaxation measurements. PMID:25739366

On the relationship between NMR-derived amide order parameters and protein backbone entropy changes.

PubMed

Sharp, Kim A; O'Brien, Evan; Kasinath, Vignesh; Wand, A Joshua

2015-05-01

Molecular dynamics simulations are used to analyze the relationship between NMR-derived squared generalized order parameters of amide NH groups and backbone entropy. Amide order parameters (O(2) NH ) are largely determined by the secondary structure and average values appear unrelated to the overall flexibility of the protein. However, analysis of the more flexible subset (O(2) NH  < 0.8) shows that these report both on the local flexibility of the protein and on a different component of the conformational entropy than that reported by the side chain methyl axis order parameters, O(2) axis . A calibration curve for backbone entropy vs. O(2) NH is developed, which accounts for both correlations between amide group motions of different residues, and correlations between backbone and side chain motions. This calibration curve can be used with experimental values of O(2) NH changes obtained by NMR relaxation measurements to extract backbone entropy changes, for example, upon ligand binding. In conjunction with our previous calibration for side chain entropy derived from measured O(2) axis values this provides a prescription for determination of the total protein conformational entropy changes from NMR relaxation measurements. © 2015 Wiley Periodicals, Inc.

All-Possible-Subsets for MANOVA and Factorial MANOVAs: Less than a Weekend Project

ERIC Educational Resources Information Center

Nimon, Kim; Zientek, Linda Reichwein; Kraha, Amanda

2016-01-01

Multivariate techniques are increasingly popular as researchers attempt to accurately model a complex world. MANOVA is a multivariate technique used to investigate the dimensions along which groups differ, and how these dimensions may be used to predict group membership. A concern in a MANOVA analysis is to determine if a smaller subset of…

Optimized diffusion gradient orientation schemes for corrupted clinical DTI data sets.

PubMed

Dubois, J; Poupon, C; Lethimonnier, F; Le Bihan, D

2006-08-01

A method is proposed for generating schemes of diffusion gradient orientations which allow the diffusion tensor to be reconstructed from partial data sets in clinical DT-MRI, should the acquisition be corrupted or terminated before completion because of patient motion. A general energy-minimization electrostatic model was developed in which the interactions between orientations are weighted according to their temporal order during acquisition. In this report, two corruption scenarios were specifically considered for generating relatively uniform schemes of 18 and 60 orientations, with useful subsets of 6 and 15 orientations. The sets and subsets were compared to conventional sets through their energy, condition number and rotational invariance. Schemes of 18 orientations were tested on a volunteer. The optimized sets were similar to uniform sets in terms of energy, condition number and rotational invariance, whether the complete set or only a subset was considered. Diffusion maps obtained in vivo were close to those for uniform sets whatever the acquisition time was. This was not the case with conventional schemes, whose subset uniformity was insufficient. With the proposed approach, sets of orientations responding to several corruption scenarios can be generated, which is potentially useful for imaging uncooperative patients or infants.

Listeria arpJ gene modifies T helper type 2 subset differentiation.

PubMed

Kanoh, Makoto; Maruyama, Saho; Shen, Hua; Matsumoto, Akira; Shinomiya, Hiroto; Przybilla, Karin; Gouin, Edith; Cossart, Pascale; Goebel, Werner; Asano, Yoshihiro

2015-07-15

Although the T-cell subset differentiation pathway has been characterized extensively from the view of host gene regulation, the effects of genes of the pathogen on T-cell subset differentiation during infection have yet to be elucidated. Especially, the bacterial genes that are responsible for this shift have not yet been determined. Utilizing a single-gene-mutation Listeria panel, we investigated genes involved in the host-pathogen interaction that are required for the initiation of T-cell subset differentiation in the early phase of pathogen infection. We demonstrate that the induction of T helper types 1 and 2 (Th1 and Th2) subsets are separate phenomena and are mediated by distinct Listeria genes. We identified several candidate Listeria genes that appear to be involved in the host-Listeria interaction. Among them, arpJ is the strongest candidate gene for inhibiting Th2 subset induction. Furthermore, the analysis utilizing arpJ-deficient Listeria monocytogenes (Lm) revealed that the tumor necrosis factor (TNF) superfamily (Tnfsf) 9-TNF receptor superfamily (Tnfrsf) 9 interaction inhibits the Th2 response during Lm infection. arpJ is the candidate gene for inhibiting Th2 T-cell subset induction. The arpJ gene product influences the expression of Tnfsf/Tnfrsf on antigen-presenting cells and inhibits the Th2 T-cell subset differentiation during Listeria infection. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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

NASA Technical Reports Server (NTRS)

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

2001-01-01

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

Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph.

PubMed

Ma, Hong-Wu; Zhao, Xue-Ming; Yuan, Ying-Jin; Zeng, An-Ping

2004-08-12

Metabolic networks are organized in a modular, hierarchical manner. Methods for a rational decomposition of the metabolic network into relatively independent functional subsets are essential to better understand the modularity and organization principle of a large-scale, genome-wide network. Network decomposition is also necessary for functional analysis of metabolism by pathway analysis methods that are often hampered by the problem of combinatorial explosion due to the complexity of metabolic network. Decomposition methods proposed in literature are mainly based on the connection degree of metabolites. To obtain a more reasonable decomposition, the global connectivity structure of metabolic networks should be taken into account. In this work, we use a reaction graph representation of a metabolic network for the identification of its global connectivity structure and for decomposition. A bow-tie connectivity structure similar to that previously discovered for metabolite graph is found also to exist in the reaction graph. Based on this bow-tie structure, a new decomposition method is proposed, which uses a distance definition derived from the path length between two reactions. An hierarchical classification tree is first constructed from the distance matrix among the reactions in the giant strong component of the bow-tie structure. These reactions are then grouped into different subsets based on the hierarchical tree. Reactions in the IN and OUT subsets of the bow-tie structure are subsequently placed in the corresponding subsets according to a 'majority rule'. Compared with the decomposition methods proposed in literature, ours is based on combined properties of the global network structure and local reaction connectivity rather than, primarily, on the connection degree of metabolites. The method is applied to decompose the metabolic network of Escherichia coli. Eleven subsets are obtained. More detailed investigations of the subsets show that reactions in the same subset are really functionally related. The rational decomposition of metabolic networks, and subsequent studies of the subsets, make it more amenable to understand the inherent organization and functionality of metabolic networks at the modular level. http://genome.gbf.de/bioinformatics/

Efficiencies in freight & passenger routing & scheduling.

DOT National Transportation Integrated Search

2015-08-01

The problem we study concerns routing a fleet of capacitated vehicles in real time to collect : shipment orders placed by a known set of customers. On each day of operation, only a subset of : all customers request service. Some of these requests are...

Diagnosing Warm Frontal Cloud Formation in a GCM: A Novel Approach Using Conditional Subsetting

NASA Technical Reports Server (NTRS)

Booth, James F.; Naud, Catherine M.; DelGenio, Anthony D.

2013-01-01

This study analyzes characteristics of clouds and vertical motion across extratropical cyclone warm fronts in the NASA Goddard Institute for Space Studies general circulation model. The validity of the modeled clouds is assessed using a combination of satellite observations from CloudSat, Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observations (CALIPSO), Advanced Microwave Scanning Radiometer for Earth Observing System (AMSR-E), and the NASA Modern-Era Retrospective Analysis for Research and Applications (MERRA) reanalysis. The analysis focuses on developing cyclones, to test the model's ability to generate their initial structure. To begin, the extratropical cyclones and their warm fronts are objectively identified and cyclone-local fields are mapped into a vertical transect centered on the surface warm front. To further isolate specific physics, the cyclones are separated using conditional subsetting based on additional cyclone-local variables, and the differences between the subset means are analyzed. Conditional subsets are created based on 1) the transect clouds and 2) vertical motion; 3) the strength of the temperature gradient along the warm front, as well as the storm-local 4) wind speed and 5) precipitable water (PW). The analysis shows that the model does not generate enough frontal cloud, especially at low altitude. The subsetting results reveal that, compared to the observations, the model exhibits a decoupling between cloud formation at high and low altitudes across warm fronts and a weak sensitivity to moisture. These issues are caused in part by the parameterized convection and assumptions in the stratiform cloud scheme that are valid in the subtropics. On the other hand, the model generates proper covariability of low-altitude vertical motion and cloud at the warm front and a joint dependence of cloudiness on wind and PW.

VizieR Online Data Catalog: DIBs in APOGEE telluric standard star spectra (Elyajouri+, 2017)

NASA Astrophysics Data System (ADS)

Elyajouri, M.; Lallement, R.; Monreal-Ibero, A.; Capitanio, L.; Cox, N. L. J.

2017-04-01

A subset of ~60 target stars from the APOGEE TSS list described in Sect. 3 has been observed in the visible with NARVAL, the spectropolarimeter of the Bernard Lyot telescope (2m) at Pic du Midi observatory, used in high-resolution spectroscopic mode (R~=80000). For all data the signal-to-noise ratio (S/N) is between 50 and 100. Two targets were observed twice in order check the estimated uncertainties. An additional subset of five targets was observed with the SOPHIE spectrograph at the 1.93m telescope of the Haute-Provence Observatory at a resolving power R~=39000. (1 data file).

Stem and Progenitor Cell Subsets Are Affected by JAK2 Signaling and Can Be Monitored by Flow Cytometry

PubMed Central

Iida, Ryuji; Welner, Robert S.; Zhao, Wanke; Alberola-lla, José; Medina, Kay L.; Zhao, Zhizhuang Joe; Kincade, Paul W.

2014-01-01

Although extremely rare, hematopoietic stem cells (HSCs) are divisible into subsets that differ with respect to differentiation potential and cell surface marker expression. For example, we recently found that CD86− CD150+ CD48− HSCs have limited potential for lymphocyte production. This could be an important new tool for studying hematological abnormalities. Here, we analyzed HSC subsets with a series of stem cell markers in JAK2V617F transgenic (Tg) mice, where the mutation is sufficient to cause myeloproliferative neoplasia with lymphocyte deficiency. Total numbers of HSC were elevated 3 to 20 fold in bone marrow of JAK2V617F mice. Careful analysis suggested the accumulation involved multiple HSC subsets, but particularly those characterized as CD150HI CD86− CD18L°CD41+ and excluding Hoechst dye. Real-Time PCR analysis of their HSC revealed that the erythropoiesis associated gene transcripts Gata1, Klf1 and Epor were particularly high. Flow cytometry analyses based on two differentiation schemes for multipotent progenitors (MPP) also suggested alteration by JAK2 signals. The low CD86 on HSC and multipotent progenitors paralleled the large reductions we found in lymphoid progenitors, but the few that were produced functioned normally when sorted and placed in culture. Either of two HSC subsets conferred disease when transplanted. Thus, flow cytometry can be used to observe the influence of abnormal JAK2 signaling on stem and progenitor subsets. Markers that similarly distinguish categories of human HSCs might be very valuable for monitoring such conditions. They could also serve as indicators of HSC fitness and suitability for transplantation. PMID:24699465

An exploration of the properties of the CORE problem list subset and how it facilitates the implementation of SNOMED CT

PubMed Central

Xu, Julia

2015-01-01

Objective Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT) is the emergent international health terminology standard for encoding clinical information in electronic health records. The CORE Problem List Subset was created to facilitate the terminology’s implementation. This study evaluates the CORE Subset’s coverage and examines its growth pattern as source datasets are being incorporated. Methods Coverage of frequently used terms and the corresponding usage of the covered terms were assessed by “leave-one-out” analysis of the eight datasets constituting the current CORE Subset. The growth pattern was studied using a retrospective experiment, growing the Subset one dataset at a time and examining the relationship between the size of the starting subset and the coverage of frequently used terms in the incoming dataset. Linear regression was used to model that relationship. Results On average, the CORE Subset covered 80.3% of the frequently used terms of the left-out dataset, and the covered terms accounted for 83.7% of term usage. There was a significant positive correlation between the CORE Subset’s size and the coverage of the frequently used terms in an incoming dataset. This implies that the CORE Subset will grow at a progressively slower pace as it gets bigger. Conclusion The CORE Problem List Subset is a useful resource for the implementation of Systematized Nomenclature of Medicine Clinical Terms in electronic health records. It offers good coverage of frequently used terms, which account for a high proportion of term usage. If future datasets are incorporated into the CORE Subset, it is likely that its size will remain small and manageable. PMID:25725003

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

NASA Astrophysics Data System (ADS)

Ayoobi, Iman; Tangestani, Majid H.

2017-10-01

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

Potential linkage for schizophrenia on chromosome 22q12-q13: A replication study

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

Schwab, S.G.; Bondy, B.; Wildenauer, D.B.

1995-10-09

In an attempt to replicate a potential linkage on chromosome 22q12-q13.1 reported by Pulver et al., we have analyzed 4 microsatellite markers which span this chromosomal region, including the IL2RB locus, for linkage with schizophrenia in 30 families from Israel and Germany. Linkage analysis by pairwise lod score analysis as well as by multipoint analysis did not provide evidence for a single major gene locus. However, a lod score of Z{sub max} = 0.612 was obtained for a dominant model of inheritance with the marker D22S304 at recombination fraction 0.2 by pairwise analysis. In addition, using a nonparametric method, sibmore » pair analysis, a P value of 0.068 corresponding to a lod score of 0.48 was obtained for this marker. This finding, together with those of Pulver et al., is suggestive of a genetic factor in this region, predisposing for schizophrenia in a subset of families. Further studies using nonparametric methods should be conducted in order to clarify this point. 32 refs., 1 fig., 4 tabs.« less

Using NASA's Giovanni Web Portal to Access and Visualize Satellite-based Earth Science Data in the Classroom

NASA Technical Reports Server (NTRS)

Lloyd, Steven; Acker, James G.; Prados, Ana I.; Leptoukh, Gregory G.

2008-01-01

One of the biggest obstacles for the average Earth science student today is locating and obtaining satellite-based remote sensing data sets in a format that is accessible and optimal for their data analysis needs. At the Goddard Earth Sciences Data and Information Services Center (GES-DISC) alone, on the order of hundreds of Terabytes of data are available for distribution to scientists, students and the general public. The single biggest and time-consuming hurdle for most students when they begin their study of the various datasets is how to slog through this mountain of data to arrive at a properly sub-setted and manageable data set to answer their science question(s). The GES DISC provides a number of tools for data access and visualization, including the Google-like Mirador search engine and the powerful GES-DISC Interactive Online Visualization ANd aNalysis Infrastructure (Giovanni) web interface.

Stable Scalp EEG Spatiospectral Patterns Across Paradigms Estimated by Group ICA.

PubMed

Labounek, René; Bridwell, David A; Mareček, Radek; Lamoš, Martin; Mikl, Michal; Slavíček, Tomáš; Bednařík, Petr; Baštinec, Jaromír; Hluštík, Petr; Brázdil, Milan; Jan, Jiří

2018-01-01

Electroencephalography (EEG) oscillations reflect the superposition of different cortical sources with potentially different frequencies. Various blind source separation (BSS) approaches have been developed and implemented in order to decompose these oscillations, and a subset of approaches have been developed for decomposition of multi-subject data. Group independent component analysis (Group ICA) is one such approach, revealing spatiospectral maps at the group level with distinct frequency and spatial characteristics. The reproducibility of these distinct maps across subjects and paradigms is relatively unexplored domain, and the topic of the present study. To address this, we conducted separate group ICA decompositions of EEG spatiospectral patterns on data collected during three different paradigms or tasks (resting-state, semantic decision task and visual oddball task). K-means clustering analysis of back-reconstructed individual subject maps demonstrates that fourteen different independent spatiospectral maps are present across the different paradigms/tasks, i.e. they are generally stable.

Energy-Discriminative Performance of a Spectral Micro-CT System

PubMed Central

He, Peng; Yu, Hengyong; Bennett, James; Ronaldson, Paul; Zainon, Rafidah; Butler, Anthony; Butler, Phil; Wei, Biao; Wang, Ge

2013-01-01

Experiments were performed to evaluate the energy-discriminative performance of a spectral (multi-energy) micro-CT system. The system, designed by MARS (Medipix All Resolution System) Bio-Imaging Ltd. (Christchurch, New Zealand), employs a photon-counting energy-discriminative detector technology developed by CERN (European Organization for Nuclear Research). We used the K-edge attenuation characteristic of some known materials to calibrate the detector’s photon energy discrimination. For tomographic analysis, we used the compressed sensing (CS) based ordered-subset simultaneous algebraic reconstruction techniques (OS-SART) to reconstruct sample images, which is effective to reduce noise and suppress artifacts. Unlike conventional CT, the principal component analysis (PCA) method can be applied to extract and quantify additional attenuation information from a spectral CT dataset. Our results show that the spectral CT has a good energy-discriminative performance and provides more attenuation information than the conventional CT. PMID:24004864

Uncertainty Analysis via Failure Domain Characterization: Polynomial Requirement Functions

NASA Technical Reports Server (NTRS)

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

2011-01-01

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

Association analysis using USDA diverse rice (Oryza sativa L.) germplasm collections to identify loci influencing grain quality traits

USDA-ARS?s Scientific Manuscript database

he USDA rice (Oryza sativa L.) core subset (RCS) was assembled to represent the genetic diversity of the entire USDA-ARS National Small Grains Collection and consists of 1,794 accessions from 114 countries. The USDA rice mini-core (MC) is a subset of 217 accessions from the RCS and was selected to ...

Flight Regime Recognition Analysis for the Army UH-60A IMDS Usage

DTIC Science & Technology

2006-12-01

61 Figure 34. The Behavior of The Parameter Weight.On.Wheels........................... 65 Figure 35. The ... Behavior of a Take-off Regime in Subsetting Process ................ 68 xi Figure 36. Subsetting the Big Data into Smaller Sets (WOW, Flags...of components can be extended to their true lifetime (Bechhoefer, n.d.) This is directly related to the accurate representation of regime

Antigen presenting capacity of murine splenic myeloid cells.

PubMed

Hey, Ying-Ying; Quah, Benjamin; O'Neill, Helen C

2017-01-11

The spleen is an important site for hematopoiesis. It supports development of myeloid cells from bone marrow-derived precursors entering from blood. Myeloid subsets in spleen are not well characterised although dendritic cell (DC) subsets are clearly defined in terms of phenotype, development and functional role. Recently a novel dendritic-like cell type in spleen named 'L-DC' was distinguished from other known dendritic and myeloid cells by its distinct phenotype and developmental origin. That study also redefined splenic eosinophils as well as resident and inflammatory monocytes in spleen. L-DC are shown to be distinct from known splenic macrophages and monocyte subsets. Using a new flow cytometric procedure, it has been possible to identify and isolate L-DC in order to assess their functional competence and ability to activate T cells both in vivo and in vitro. L-DC are readily accessible to antigen given intravenously through receptor-mediated endocytosis. They are also capable of CD8 + T cell activation through antigen cross presentation, with subsequent induction of cytotoxic effector T cells. L-DC are MHCII - cells and unable to activate CD4 + T cells, a property which clearly distinguishes them from conventional DC. The myeloid subsets of resident monocytes, inflammatory monocytes, neutrophils and eosinophils, were found to have varying capacities to take up antigen, but were uniformly unable to activate either CD4 + T cells or CD8 + T cells. The results presented here demonstrate that L-DC in spleen are distinct from other myeloid cells in that they can process antigen for CD8 + T cell activation and induction of cytotoxic effector function, while both L-DC and myeloid subsets remain unable to activate CD4 + T cells. The L-DC subset in spleen is therefore distinct as an antigen presenting cell.

Archive Management of NASA Earth Observation Data to Support Cloud Analysis

NASA Technical Reports Server (NTRS)

Lynnes, Christopher; Baynes, Kathleen; McInerney, Mark

2017-01-01

NASA collects, processes and distributes petabytes of Earth Observation (EO) data from satellites, aircraft, in situ instruments and model output, with an order of magnitude increase expected by 2024. Cloud-based web object storage (WOS) of these data can simplify the execution of such an increase. More importantly, it can also facilitate user analysis of those volumes by making the data available to the massively parallel computing power in the cloud. However, storing EO data in cloud WOS has a ripple effect throughout the NASA archive system with unexpected challenges and opportunities. One challenge is modifying data servicing software (such as Web Coverage Service servers) to access and subset data that are no longer on a directly accessible file system, but rather in cloud WOS. Opportunities include refactoring of the archive software to a cloud-native architecture; virtualizing data products by computing on demand; and reorganizing data to be more analysis-friendly. Reviewed by Mark McInerney ESDIS Deputy Project Manager.

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

PubMed

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

1997-02-01

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

Postinjection single photon transmission tomography with ordered-subset algorithms for whole-body PET imaging

NASA Astrophysics Data System (ADS)

Bai, Chuanyong; Kinahan, P. E.; Brasse, D.; Comtat, C.; Townsend, D. W.

2002-02-01

We have evaluated the penalized ordered-subset transmission reconstruction (OSTR) algorithm for postinjection single photon transmission scanning. The OSTR algorithm of Erdogan and Fessler (1999) uses a more accurate model for transmission tomography than ordered-subsets expectation-maximization (OSEM) when OSEM is applied to the logarithm of the transmission data. The OSTR algorithm is directly applicable to postinjection transmission scanning with a single photon source, as emission contamination from the patient mimics the effect, in the original derivation of OSTR, of random coincidence contamination in a positron source transmission scan. Multiple noise realizations of simulated postinjection transmission data were reconstructed using OSTR, filtered backprojection (FBP), and OSEM algorithms. Due to the nonspecific task performance, or multiple uses, of the transmission image, multiple figures of merit were evaluated, including image noise, contrast, uniformity, and root mean square (rms) error. We show that: 1) the use of a three-dimensional (3-D) regularizing image roughness penalty with OSTR improves the tradeoffs in noise, contrast, and rms error relative to the use of a two-dimensional penalty; 2) OSTR with a 3-D penalty has improved tradeoffs in noise, contrast, and rms error relative to FBP or OSEM; and 3) the use of image standard deviation from a single realization to estimate the true noise can be misleading in the case of OSEM. We conclude that using OSTR with a 3-D penalty potentially allows for shorter postinjection transmission scans in single photon transmission tomography in positron emission tomography (PET) relative to FBP or OSEM reconstructed images with the same noise properties. This combination of singles+OSTR is particularly suitable for whole-body PET oncology imaging.

Unified User Interface to Support Effective and Intuitive Data Discovery, Dissemination, and Analysis at NASA GES DISC

NASA Technical Reports Server (NTRS)

Petrenko, M.; Hegde, M.; Bryant, K.; Johnson, J. E.; Ritrivi, A.; Shen, S.; Volmer, B.; Pham, L. B.

2015-01-01

Goddard Earth Sciences Data and Information Services Center (GES DISC) has been providing access to scientific data sets since 1990s. Beginning as one of the first Earth Observing System Data and Information System (EOSDIS) archive centers, GES DISC has evolved to offer a wide range of science-enabling services. With a growing understanding of needs and goals of its science users, GES DISC continues to improve and expand on its broad set of data discovery and access tools, sub-setting services, and visualization tools. Nonetheless, the multitude of the available tools, a partial overlap of functionality, and independent and uncoupled interfaces employed by these tools often leave the end users confused as of what tools or services are the most appropriate for a task at hand. As a result, some the services remain underutilized or largely unknown to the users, significantly reducing the availability of the data and leading to a great loss of scientific productivity. In order to improve the accessibility of GES DISC tools and services, we have designed and implemented UUI, the Unified User Interface. UUI seeks to provide a simple, unified, and intuitive one-stop shop experience for the key services available at GES DISC, including sub-setting (Simple Subset Wizard), granule file search (Mirador), plotting (Giovanni), and other services. In this poster, we will discuss the main lessons, obstacles, and insights encountered while designing the UUI experience. We will also present the architecture and technology behind UUI, including NodeJS, Angular, and Mongo DB, as well as speculate on the future of the tool at GES DISC as well as in a broader context of the Space Science Informatics.

Statistical Learning of Origin-Specific Statically Optimal Individualized Treatment Rules

PubMed Central

van der Laan, Mark J.; Petersen, Maya L.

2008-01-01

Consider a longitudinal observational or controlled study in which one collects chronological data over time on a random sample of subjects. The time-dependent process one observes on each subject contains time-dependent covariates, time-dependent treatment actions, and an outcome process or single final outcome of interest. A statically optimal individualized treatment rule (as introduced in van der Laan et. al. (2005), Petersen et. al. (2007)) is a treatment rule which at any point in time conditions on a user-supplied subset of the past, computes the future static treatment regimen that maximizes a (conditional) mean future outcome of interest, and applies the first treatment action of the latter regimen. In particular, Petersen et. al. (2007) clarified that, in order to be statically optimal, an individualized treatment rule should not depend on the observed treatment mechanism. Petersen et. al. (2007) further developed estimators of statically optimal individualized treatment rules based on a past capturing all confounding of past treatment history on outcome. In practice, however, one typically wishes to find individualized treatment rules responding to a user-supplied subset of the complete observed history, which may not be sufficient to capture all confounding. The current article provides an important advance on Petersen et. al. (2007) by developing locally efficient double robust estimators of statically optimal individualized treatment rules responding to such a user-supplied subset of the past. However, failure to capture all confounding comes at a price; the static optimality of the resulting rules becomes origin-specific. We explain origin-specific static optimality, and discuss the practical importance of the proposed methodology. We further present the results of a data analysis in which we estimate a statically optimal rule for switching antiretroviral therapy among patients infected with resistant HIV virus. PMID:19122792

Technical Analysis of SSP-21 Protocol

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

Bromberger, S.

As part of the California Energy Systems for the Twenty-First Century (CES-21) program, in December 2016 San Diego Gas and Electric (SDG&E) contracted with Lawrence Livermore National Laboratory (LLNL) to perform an independent verification and validation (IV&V) of a white paper describing their Secure SCADA Protocol for the Twenty-First Century (SSP-21) in order to analyze the effectiveness and propriety of cryptographic protocol use within the SSP-21 specification. SSP-21 is designed to use cryptographic protocols to provide (optional) encryption, authentication, and nonrepudiation, among other capabilities. The cryptographic protocols to be used reflect current industry standards; future versions of SSP-21 will usemore » other advanced technologies to provide a subset of security services.« less

Feature Selection in Classification of Eye Movements Using Electrooculography for Activity Recognition

PubMed Central

Mala, S.; Latha, K.

2014-01-01

Activity recognition is needed in different requisition, for example, reconnaissance system, patient monitoring, and human-computer interfaces. Feature selection plays an important role in activity recognition, data mining, and machine learning. In selecting subset of features, an efficient evolutionary algorithm Differential Evolution (DE), a very efficient optimizer, is used for finding informative features from eye movements using electrooculography (EOG). Many researchers use EOG signals in human-computer interactions with various computational intelligence methods to analyze eye movements. The proposed system involves analysis of EOG signals using clearness based features, minimum redundancy maximum relevance features, and Differential Evolution based features. This work concentrates more on the feature selection algorithm based on DE in order to improve the classification for faultless activity recognition. PMID:25574185

Feature selection in classification of eye movements using electrooculography for activity recognition.

PubMed

Mala, S; Latha, K

2014-01-01

Activity recognition is needed in different requisition, for example, reconnaissance system, patient monitoring, and human-computer interfaces. Feature selection plays an important role in activity recognition, data mining, and machine learning. In selecting subset of features, an efficient evolutionary algorithm Differential Evolution (DE), a very efficient optimizer, is used for finding informative features from eye movements using electrooculography (EOG). Many researchers use EOG signals in human-computer interactions with various computational intelligence methods to analyze eye movements. The proposed system involves analysis of EOG signals using clearness based features, minimum redundancy maximum relevance features, and Differential Evolution based features. This work concentrates more on the feature selection algorithm based on DE in order to improve the classification for faultless activity recognition.

Evolutionary Approach for Relative Gene Expression Algorithms

PubMed Central

Czajkowski, Marcin

2014-01-01

A Relative Expression Analysis (RXA) uses ordering relationships in a small collection of genes and is successfully applied to classiffication using microarray data. As checking all possible subsets of genes is computationally infeasible, the RXA algorithms require feature selection and multiple restrictive assumptions. Our main contribution is a specialized evolutionary algorithm (EA) for top-scoring pairs called EvoTSP which allows finding more advanced gene relations. We managed to unify the major variants of relative expression algorithms through EA and introduce weights to the top-scoring pairs. Experimental validation of EvoTSP on public available microarray datasets showed that the proposed solution significantly outperforms in terms of accuracy other relative expression algorithms and allows exploring much larger solution space. PMID:24790574

Logic analysis of complex systems by characterizing failure phenomena to achieve diagnosis and fault-isolation

NASA Technical Reports Server (NTRS)

Wong, J. T.; Andre, W. L.

1981-01-01

A recent result shows that, for a certain class of systems, the interdependency among the elements of such a system together with the elements constitutes a mathematical structure a partially ordered set. It is called a loop free logic model of the system. On the basis of an intrinsic property of the mathematical structure, a characterization of system component failure in terms of maximal subsets of bad test signals of the system was obtained. Also, as a consequence, information concerning the total number of failure components in the system was deduced. Detailed examples are given to show how to restructure real systems containing loops into loop free models for which the result is applicable.

Elucidation of Seventeen Human Peripheral Blood B cell Subsets and Quantification of the Tetanus Response Using a Density-Based Method for the Automated Identification of Cell Populations in Multidimensional Flow Cytometry Data

PubMed Central

Qian, Yu; Wei, Chungwen; Lee, F. Eun-Hyung; Campbell, John; Halliley, Jessica; Lee, Jamie A.; Cai, Jennifer; Kong, Megan; Sadat, Eva; Thomson, Elizabeth; Dunn, Patrick; Seegmiller, Adam C.; Karandikar, Nitin J.; Tipton, Chris; Mosmann, Tim; Sanz, Iñaki; Scheuermann, Richard H.

2011-01-01

Background Advances in multi-parameter flow cytometry (FCM) now allow for the independent detection of larger numbers of fluorochromes on individual cells, generating data with increasingly higher dimensionality. The increased complexity of these data has made it difficult to identify cell populations from high-dimensional FCM data using traditional manual gating strategies based on single-color or two-color displays. Methods To address this challenge, we developed a novel program, FLOCK (FLOw Clustering without K), that uses a density-based clustering approach to algorithmically identify biologically relevant cell populations from multiple samples in an unbiased fashion, thereby eliminating operator-dependent variability. Results FLOCK was used to objectively identify seventeen distinct B cell subsets in a human peripheral blood sample and to identify and quantify novel plasmablast subsets responding transiently to tetanus and other vaccinations in peripheral blood. FLOCK has been implemented in the publically available Immunology Database and Analysis Portal – ImmPort (http://www.immport.org) for open use by the immunology research community. Conclusions FLOCK is able to identify cell subsets in experiments that use multi-parameter flow cytometry through an objective, automated computational approach. The use of algorithms like FLOCK for FCM data analysis obviates the need for subjective and labor intensive manual gating to identify and quantify cell subsets. Novel populations identified by these computational approaches can serve as hypotheses for further experimental study. PMID:20839340

SVP-like MADS-box protein from Carya cathayensis forms higher-order complexes.

PubMed

Wang, Jingjing; Hou, Chuanming; Huang, Jianqin; Wang, Zhengjia; Xu, Yingwu

2015-03-01

To properly regulate plant flowering time and construct floral pattern, MADS-domain containing transcription factors must form multimers including homo- and hetero-dimers. They are also active in forming hetero-higher-order complexes with three to five different molecules. However, it is not well known if a MADS-box protein can also form homo-higher-order complex. In this study a biochemical approach is utilized to provide insight into the complex formation for an SVP-like MADS-box protein cloned from hickory. The results indicated that the protein is a heterogeneous higher-order complex with the peak population containing over 20 monomers. Y2H verified the protein to form homo-complex in yeast cells. Western blot of the hickory floral bud sample revealed that the protein exists in higher-order polymers in native. Deletion assays indicated that the flexible C-terminal residues are mainly responsible for the higher-order polymer formation and the heterogeneity. Current results provide direct biochemical evidences for an active MADS-box protein to be a high order complex, much higher than a quartermeric polymer. Analysis suggests that a MADS-box subset may be able to self-assemble into large complexes, and thereby differentiate one subfamily from the other in a higher-order structural manner. Present result is a valuable supplement to the action of mechanism for MADS-box proteins in plant development. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Feature selection with harmony search.

PubMed

Diao, Ren; Shen, Qiang

2012-12-01

Many search strategies have been exploited for the task of feature selection (FS), in an effort to identify more compact and better quality subsets. Such work typically involves the use of greedy hill climbing (HC), or nature-inspired heuristics, in order to discover the optimal solution without going through exhaustive search. In this paper, a novel FS approach based on harmony search (HS) is presented. It is a general approach that can be used in conjunction with many subset evaluation techniques. The simplicity of HS is exploited to reduce the overall complexity of the search process. The proposed approach is able to escape from local solutions and identify multiple solutions owing to the stochastic nature of HS. Additional parameter control schemes are introduced to reduce the effort and impact of parameter configuration. These can be further combined with the iterative refinement strategy, tailored to enforce the discovery of quality subsets. The resulting approach is compared with those that rely on HC, genetic algorithms, and particle swarm optimization, accompanied by in-depth studies of the suggested improvements.

Random-subset fitting of digital holograms for fast three-dimensional particle tracking [invited].

PubMed

Dimiduk, Thomas G; Perry, Rebecca W; Fung, Jerome; Manoharan, Vinothan N

2014-09-20

Fitting scattering solutions to time series of digital holograms is a precise way to measure three-dimensional dynamics of microscale objects such as colloidal particles. However, this inverse-problem approach is computationally expensive. We show that the computational time can be reduced by an order of magnitude or more by fitting to a random subset of the pixels in a hologram. We demonstrate our algorithm on experimentally measured holograms of micrometer-scale colloidal particles, and we show that 20-fold increases in speed, relative to fitting full frames, can be attained while introducing errors in the particle positions of 10 nm or less. The method is straightforward to implement and works for any scattering model. It also enables a parallelization strategy wherein random-subset fitting is used to quickly determine initial guesses that are subsequently used to fit full frames in parallel. This approach may prove particularly useful for studying rare events, such as nucleation, that can only be captured with high frame rates over long times.

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

PubMed

Sun, Yingqiang; Lu, Chengbo; Li, Xiaobo

2018-05-17

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

The brief family relationship scale: a brief measure of the relationship dimension in family functioning.

PubMed

Fok, Carlotta Ching Ting; Allen, James; Henry, David

2014-02-01

The Relationship dimension of the Family Environment Scale, which consists of the Cohesion, Expressiveness, and Conflict subscales, measures a person's perception of the quality of his or her family relationship functioning. This study investigates an adaptation of the Relationship dimension of the Family Environment Scale for Alaska Native youth. The authors tested the adapted measure, the Brief Family Relationship Scale, for psychometric properties and internal structure with 284 12- to 18-year-old predominately Yup'ik Eskimo Alaska Native adolescents from rural, remote communities. This non-Western cultural group is hypothesized to display higher levels of collectivism traditionally organized around an extended kinship family structure. Results demonstrate a subset of the adapted items function satisfactorily, a three-response alternative format provided meaningful information, and the subscale's underlying structure is best described through three distinct first-order factors, organized under one higher order factor. Convergent and discriminant validity of the Brief Family Relationship Scale was assessed through correlational analysis.

On the visible size and geometry of aggressively expanding civilizations at cosmological distances

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

Olson, S. Jay, E-mail: stephanolson@boisestate.edu

2016-04-01

If a subset of advanced civilizations in the universe choose to rapidly expand into unoccupied space, these civilizations would have the opportunity to grow to a cosmological scale over the course of billions of years. If such life also makes observable changes to the galaxies they inhabit, then it is possible that vast domains of life-saturated galaxies could be visible from the Earth. Here, we describe the shape and angular size of these domains as viewed from the Earth, and calculate median visible sizes for a variety of scenarios. We also calculate the total fraction of the sky that shouldmore » be covered by at least one domain. In each of the 27 scenarios we examine, the median angular size of the nearest domain is within an order of magnitude of a percent of the whole celestial sphere. Observing such a domain would likely require an analysis of galaxies on the order of a Gly from the Earth.« less

Accelerating an Ordered-Subset Low-Dose X-Ray Cone Beam Computed Tomography Image Reconstruction with a Power Factor and Total Variation Minimization.

PubMed

Huang, Hsuan-Ming; Hsiao, Ing-Tsung

2016-01-01

In recent years, there has been increased interest in low-dose X-ray cone beam computed tomography (CBCT) in many fields, including dentistry, guided radiotherapy and small animal imaging. Despite reducing the radiation dose, low-dose CBCT has not gained widespread acceptance in routine clinical practice. In addition to performing more evaluation studies, developing a fast and high-quality reconstruction algorithm is required. In this work, we propose an iterative reconstruction method that accelerates ordered-subsets (OS) reconstruction using a power factor. Furthermore, we combine it with the total-variation (TV) minimization method. Both simulation and phantom studies were conducted to evaluate the performance of the proposed method. Results show that the proposed method can accelerate conventional OS methods, greatly increase the convergence speed in early iterations. Moreover, applying the TV minimization to the power acceleration scheme can further improve the image quality while preserving the fast convergence rate.

Plate-based diversity subset screening: an efficient paradigm for high throughput screening of a large screening file.

PubMed

Bell, Andrew S; Bradley, Joseph; Everett, Jeremy R; Knight, Michelle; Loesel, Jens; Mathias, John; McLoughlin, David; Mills, James; Sharp, Robert E; Williams, Christine; Wood, Terence P

2013-05-01

The screening files of many large companies, including Pfizer, have grown considerably due to internal chemistry efforts, company mergers and acquisitions, external contracted synthesis, or compound purchase schemes. In order to screen the targets of interest in a cost-effective fashion, we devised an easy-to-assemble, plate-based diversity subset (PBDS) that represents almost the entire computed chemical space of the screening file whilst comprising only a fraction of the plates in the collection. In order to create this file, we developed new design principles for the quality assessment of screening plates: the Rule of 40 (Ro40) and a plate selection process that insured excellent coverage of both library chemistry and legacy chemistry space. This paper describes the rationale, design, construction, and performance of the PBDS, that has evolved into the standard paradigm for singleton (one compound per well) high-throughput screening in Pfizer since its introduction in 2006.

Accelerating an Ordered-Subset Low-Dose X-Ray Cone Beam Computed Tomography Image Reconstruction with a Power Factor and Total Variation Minimization

PubMed Central

Huang, Hsuan-Ming; Hsiao, Ing-Tsung

2016-01-01

In recent years, there has been increased interest in low-dose X-ray cone beam computed tomography (CBCT) in many fields, including dentistry, guided radiotherapy and small animal imaging. Despite reducing the radiation dose, low-dose CBCT has not gained widespread acceptance in routine clinical practice. In addition to performing more evaluation studies, developing a fast and high-quality reconstruction algorithm is required. In this work, we propose an iterative reconstruction method that accelerates ordered-subsets (OS) reconstruction using a power factor. Furthermore, we combine it with the total-variation (TV) minimization method. Both simulation and phantom studies were conducted to evaluate the performance of the proposed method. Results show that the proposed method can accelerate conventional OS methods, greatly increase the convergence speed in early iterations. Moreover, applying the TV minimization to the power acceleration scheme can further improve the image quality while preserving the fast convergence rate. PMID:27073853

Detection of Nitrogen Content in Rubber Leaves Using Near-Infrared (NIR) Spectroscopy with Correlation-Based Successive Projections Algorithm (SPA).

PubMed

Tang, Rongnian; Chen, Xupeng; Li, Chuang

2018-05-01

Near-infrared spectroscopy is an efficient, low-cost technology that has potential as an accurate method in detecting the nitrogen content of natural rubber leaves. Successive projections algorithm (SPA) is a widely used variable selection method for multivariate calibration, which uses projection operations to select a variable subset with minimum multi-collinearity. However, due to the fluctuation of correlation between variables, high collinearity may still exist in non-adjacent variables of subset obtained by basic SPA. Based on analysis to the correlation matrix of the spectra data, this paper proposed a correlation-based SPA (CB-SPA) to apply the successive projections algorithm in regions with consistent correlation. The result shows that CB-SPA can select variable subsets with more valuable variables and less multi-collinearity. Meanwhile, models established by the CB-SPA subset outperform basic SPA subsets in predicting nitrogen content in terms of both cross-validation and external prediction. Moreover, CB-SPA is assured to be more efficient, for the time cost in its selection procedure is one-twelfth that of the basic SPA.

VARIABLE SELECTION FOR QUALITATIVE INTERACTIONS IN PERSONALIZED MEDICINE WHILE CONTROLLING THE FAMILY-WISE ERROR RATE

PubMed Central

Gunter, Lacey; Zhu, Ji; Murphy, Susan

2012-01-01

For many years, subset analysis has been a popular topic for the biostatistics and clinical trials literature. In more recent years, the discussion has focused on finding subsets of genomes which play a role in the effect of treatment, often referred to as stratified or personalized medicine. Though highly sought after, methods for detecting subsets with altering treatment effects are limited and lacking in power. In this article we discuss variable selection for qualitative interactions with the aim to discover these critical patient subsets. We propose a new technique designed specifically to find these interaction variables among a large set of variables while still controlling for the number of false discoveries. We compare this new method against standard qualitative interaction tests using simulations and give an example of its use on data from a randomized controlled trial for the treatment of depression. PMID:22023676

Molecular Signatures in Skin Associated with Clinical Improvement During Mycophenolate Treatment in Systemic Sclerosis

PubMed Central

Hinchcliff, Monique; Huang, Chiang-Ching; Wood, Tammara A.; Mahoney, J. Matthew; Martyanov, Viktor; Bhattacharyya, Swati; Tamaki, Zenshiro; Lee, Jungwha; Carns, Mary; Podlusky, Sofia; Sirajuddin, Arlene; Shah, Sanjiv J; Chang, Rowland W.; Lafyatis, Robert; Varga, John; Whitfield, Michael L.

2013-01-01

Heterogeneity in systemic sclerosis/SSc confounds clinical trials. We previously identified ‘intrinsic’ gene expression subsets by analysis of SSc skin. Here we test the hypotheses that skin gene expression signatures including intrinsic subset are associated with skin score/MRSS improvement during mycophenolate mofetil (MMF) treatment. Gene expression and intrinsic subset assignment were measured in 12 SSc patients’ biopsies and ten controls at baseline, and from serial biopsies of one cyclophosphamide-treated patient, and nine MMF-treated patients. Gene expression changes during treatment were determined using paired t-tests corrected for multiple hypothesis testing. MRSS improved in four of seven MMF-treated patients classified as the inflammatory intrinsic subset. Three patients without MRSS improvement were classified as normal-like or fibroproliferative intrinsic subsets. 321 genes (FDR <5%) were differentially expressed at baseline between patients with and without MRSS improvement during treatment. Expression of 571 genes (FDR <10%) changed between pre- and post-MMF treatment biopsies for patients demonstrating MRSS improvement. Gene expression changes in skin are only seen in patients with MRSS improvement. Baseline gene expression in skin, including intrinsic subset assignment, may identify SSc patients whose MRSS will improve during MMF treatment, suggesting that gene expression in skin may allow targeted treatment in SSc. PMID:23677167

Mixed input to olfactory glomeruli from two subsets of ciliated sensory neurons does not impede relay neuron specificity in the crucian carp.

PubMed

Hansson, Kenth-Arne; Døving, Kjell B; Skjeldal, Frode M

2015-10-01

The consensus view of olfactory processing is that the axons of receptor-specific primary olfactory sensory neurons (OSNs) converge to a small subset of glomeruli, thus preserving the odour identity before the olfactory information is processed in higher brain centres. In the present study, we show that two different subsets of ciliated OSNs with different odorant specificities converge to the same glomeruli. In order to stain different ciliated OSNs in the crucian carp Carassius carassius we used two different chemical odorants, a bile salt and a purported alarm substance, together with fluorescent dextrans. The dye is transported within the axons and stains glomeruli in the olfactory bulb. Interestingly, the axons from the ciliated OSNs co-converge to the same glomeruli. Despite intermingled innervation of glomeruli, axons and terminal fields from the two different subsets of ciliated OSNs remained mono-coloured. By 4-6 days after staining, the dye was transported trans-synaptically to separately stained axons of relay neurons. These findings demonstrate that specificity of the primary neurons is retained in the olfactory pathways despite mixed innervation of the olfactory glomeruli. The results are discussed in relation to the emerging concepts about non-mammalian glomeruli. © 2015. Published by The Company of Biologists Ltd.

Changes in hematological indices and lymphocyte subsets in response to whole blood donation in healthy male donors.

PubMed

Borai, Anwar; Livingstone, Callum; Alsobhi, Enaam; Al Sofyani, Abeer; Balgoon, Dalal; Farzal, Anwar; Almohammadi, Mohammed; Al-Amri, Abdulafattah; Bahijri, Suhad; Alrowaili, Daad; Bassiuni, Wafaa; Saleh, Ayman; Alrowaili, Norah; Abdelaal, Mohamed

2017-04-01

Whole blood donation has immunomodulatory effects, and most of these have been observed at short intervals following blood donation. This study aimed to investigate the impact of whole blood donation on lymphocyte subsets over a typical inter-donation interval. Healthy male subjects were recruited to study changes in complete blood count (CBC) (n = 42) and lymphocyte subsets (n = 16) before and at four intervals up to 106 days following blood donation. Repeated measures ANOVA were used to compare quantitative variables between different visits. Following blood donation, changes in CBC and erythropoietin were as expected. The neutrophil count increased by 11.3% at 8 days (p < .001). Novel changes were observed in lymphocyte subsets as the CD4/CD8 ratio increased by 9.2% (p < .05) at 8 days and 13.7% (p < .05) at 22 days. CD16-56 cells decreased by 16.2% (p < .05) at 8 days. All the subsets had returned to baseline by 106 days. Regression analysis showed that the changes in CD16-56 cells and CD4/CD8 ratio were not significant (Wilk's lambda = 0.15 and 0.94, respectively) when adjusted for BMI. In conclusion, following whole blood donation, there are transient changes in lymphocyte subsets. The effect of BMI on lymphocyte subsets and the effect of this immunomodulation on the immune response merit further investigation.

VisFlow - Web-based Visualization Framework for Tabular Data with a Subset Flow Model.

PubMed

Yu, Bowen; Silva, Claudio T

2017-01-01

Data flow systems allow the user to design a flow diagram that specifies the relations between system components which process, filter or visually present the data. Visualization systems may benefit from user-defined data flows as an analysis typically consists of rendering multiple plots on demand and performing different types of interactive queries across coordinated views. In this paper, we propose VisFlow, a web-based visualization framework for tabular data that employs a specific type of data flow model called the subset flow model. VisFlow focuses on interactive queries within the data flow, overcoming the limitation of interactivity from past computational data flow systems. In particular, VisFlow applies embedded visualizations and supports interactive selections, brushing and linking within a visualization-oriented data flow. The model requires all data transmitted by the flow to be a data item subset (i.e. groups of table rows) of some original input table, so that rendering properties can be assigned to the subset unambiguously for tracking and comparison. VisFlow features the analysis flexibility of a flow diagram, and at the same time reduces the diagram complexity and improves usability. We demonstrate the capability of VisFlow on two case studies with domain experts on real-world datasets showing that VisFlow is capable of accomplishing a considerable set of visualization and analysis tasks. The VisFlow system is available as open source on GitHub.

Towards semi-automatic rock mass discontinuity orientation and set analysis from 3D point clouds

NASA Astrophysics Data System (ADS)

Guo, Jiateng; Liu, Shanjun; Zhang, Peina; Wu, Lixin; Zhou, Wenhui; Yu, Yinan

2017-06-01

Obtaining accurate information on rock mass discontinuities for deformation analysis and the evaluation of rock mass stability is important. Obtaining measurements for high and steep zones with the traditional compass method is difficult. Photogrammetry, three-dimensional (3D) laser scanning and other remote sensing methods have gradually become mainstream methods. In this study, a method that is based on a 3D point cloud is proposed to semi-automatically extract rock mass structural plane information. The original data are pre-treated prior to segmentation by removing outlier points. The next step is to segment the point cloud into different point subsets. Various parameters, such as the normal, dip/direction and dip, can be calculated for each point subset after obtaining the equation of the best fit plane for the relevant point subset. A cluster analysis (a point subset that satisfies some conditions and thus forms a cluster) is performed based on the normal vectors by introducing the firefly algorithm (FA) and the fuzzy c-means (FCM) algorithm. Finally, clusters that belong to the same discontinuity sets are merged and coloured for visualization purposes. A prototype system is developed based on this method to extract the points of the rock discontinuity from a 3D point cloud. A comparison with existing software shows that this method is feasible. This method can provide a reference for rock mechanics, 3D geological modelling and other related fields.

A Negative Partition Relation

PubMed Central

Hajnal, A.

1971-01-01

If the continuum hypothesis is assumed, there is a graph G whose vertices form an ordered set of type ω12; G does not contain triangles or complete even graphs of form [[unk]0,[unk]0], and there is no independent subset of vertices of type ω12. PMID:16591893

Spatial and temporal study of nitrate concentration in groundwater by means of coregionalization

USGS Publications Warehouse

D'Agostino, V.; Greene, E.A.; Passarella, G.; Vurro, M.

1998-01-01

Spatial and temporal behavior of hydrochemical parameters in groundwater can be studied using tools provided by geostatistics. The cross-variogram can be used to measure the spatial increments between observations at two given times as a function of distance (spatial structure). Taking into account the existence of such a spatial structure, two different data sets (sampled at two different times), representing concentrations of the same hydrochemical parameter, can be analyzed by cokriging in order to reduce the uncertainty of the estimation. In particular, if one of the two data sets is a subset of the other (that is, an undersampled set), cokriging allows us to study the spatial distribution of the hydrochemical parameter at that time, while also considering the statistical characteristics of the full data set established at a different time. This paper presents an application of cokriging by using temporal subsets to study the spatial distribution of nitrate concentration in the aquifer of the Lucca Plain, central Italy. Three data sets of nitrate concentration in groundwater were collected during three different periods in 1991. The first set was from 47 wells, but the second and the third are undersampled and represent 28 and 27 wells, respectively. Comparing the result of cokriging with ordinary kriging showed an improvement of the uncertainty in terms of reducing the estimation variance. The application of cokriging to the undersampled data sets reduced the uncertainty in estimating nitrate concentration and at the same time decreased the cost of the field sampling and laboratory analysis.Spatial and temporal behavior of hydrochemical parameters in groundwater can be studied using tools provided by geostatistics. The cross-variogram can be used to measure the spatial increments between observations at two given times as a function of distance (spatial structure). Taking into account the existence of such a spatial structure, two different data sets (sampled at two different times), representing concentrations of the same hydrochemical parameter, can be analyzed by cokriging in order to reduce the uncertainty of the estimation. In particular, if one of the two data sets is a subset of the other (that is, an undersampled set), cokriging allows us to study the spatial distribution of the hydrochemical parameter at that time, while also considering the statistical characteristics of the full data set established at a different time. This paper presents an application of cokriging by using temporal subsets to study the spatial distribution of nitrate concentration in the aquifer of the Lucca Plain, central Italy. Three data sets of nitrate concentration in groundwater were collected during three different periods in 1991. The first set was from 47 wells, but the second and the third are undersampled and represent 28 and 27 wells, respectively. Comparing the result of cokriging with ordinary kriging showed an improvement of the uncertainty in terms of reducing the estimation variance. The application of cokriging to the undersampled data sets reduced the uncertainty in estimating nitrate concentration and at the same time decreased the cost of the field sampling and laboratory analysis.

Column Subset Selection, Matrix Factorization, and Eigenvalue Optimization

DTIC Science & Technology

2008-07-01

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

Influence of Cognitive Functioning on Age-Related Performance Declines in Visuospatial Sequence Learning.

PubMed

Krüger, Melanie; Hinder, Mark R; Puri, Rohan; Summers, Jeffery J

2017-01-01

Objectives: The aim of this study was to investigate how age-related performance differences in a visuospatial sequence learning task relate to age-related declines in cognitive functioning. Method: Cognitive functioning of 18 younger and 18 older participants was assessed using a standardized test battery. Participants then undertook a perceptual visuospatial sequence learning task. Various relationships between sequence learning and participants' cognitive functioning were examined through correlation and factor analysis. Results: Older participants exhibited significantly lower performance than their younger counterparts in the sequence learning task as well as in multiple cognitive functions. Factor analysis revealed two independent subsets of cognitive functions associated with performance in the sequence learning task, related to either the processing and storage of sequence information (first subset) or problem solving (second subset). Age-related declines were only found for the first subset of cognitive functions, which also explained a significant degree of the performance differences in the sequence learning task between age-groups. Discussion: The results suggest that age-related performance differences in perceptual visuospatial sequence learning can be explained by declines in the ability to process and store sequence information in older adults, while a set of cognitive functions related to problem solving mediates performance differences independent of age.

Designs and adaptive analysis plans for pivotal clinical trials of therapeutics and companion diagnostics.

PubMed

Simon, Richard

2008-06-01

Developments in genomics and biotechnology provide unprecedented opportunities for the development of effective therapeutics and companion diagnostics for matching the right drug to the right patient. Effective co-development involves many new challenges with increased opportunity for success as well as delay and failure. Clinical trial designs and adaptive analysis plans for the prospective design of pivotal trials of new therapeutics and companion diagnostics are reviewed. Effective co-development requires careful prospective planning of the design and analysis strategy for pivotal clinical trials. Randomized clinical trials continue to be important for evaluating the effectiveness of new treatments, but the target populations for analysis should be prospectively specified based on the companion diagnostic. Post hoc analyses of traditionally designed randomized clinical trials are often deeply problematic. Clear separation is generally required of the data used for developing the diagnostic test, including their threshold of positivity, from the data used for evaluating treatment effectiveness in subsets determined by the test. Adaptive analysis can be used to provide flexibility to the analysis but the use of such methods requires careful planning and prospective definition in order to assure that the pivotal trial adequately limits the chance of erroneous conclusions.

B-cell subset alterations and correlated factors in HIV-1 infection.

PubMed

Pensieroso, Simone; Galli, Laura; Nozza, Silvia; Ruffin, Nicolas; Castagna, Antonella; Tambussi, Giuseppe; Hejdeman, Bo; Misciagna, Donatella; Riva, Agostino; Malnati, Mauro; Chiodi, Francesca; Scarlatti, Gabriella

2013-05-15

During HIV-1 infection, the development, phenotype, and functionality of B cells are impaired. Transitional B cells and aberrant B-cell populations arise in blood, whereas a declined percentage of resting memory B cells is detected. Our study aimed at pinpointing the demographic, immunological, and viral factors driving these pathological findings, and the role of antiretroviral therapy in reverting these alterations. B-cell phenotype and correlating factors were evaluated. Variations in B-cell subsets were evaluated by flow cytometry in HIV-1-infected individuals naive to therapy, elite controllers, and patients treated with antiretroviral drugs (virological control or failure). Multivariable analysis was performed to identify variables independently associated with the B-cell alterations. Significant differences were observed among patients' groups in relation to all B-cell subsets. Resting memory B cells were preserved in patients naive to therapy and elite controllers, but reduced in treated patients. Individuals naive to therapy and experiencing multidrug failure, as well as elite controllers, had significantly higher levels of activated memory B cells compared to healthy controls. In the multivariate analysis, plasma viral load and nadir CD4 T cells independently correlated with major B-cell alterations. Coinfection with hepatitis C but not hepatitis B virus also showed an impact on specific B-cell subsets. Successful protracted antiretroviral treatment led to normalization of all B-cell subsets with exception of resting memory B cells. Our results indicate that viremia and nadir CD4 T cells are important prognostic markers of B-cell perturbations and provide evidence that resting memory B-cell depletion during chronic infection is not reverted upon successful antiretroviral therapy.

In Situ Microscopy Analysis Reveals Local Innate Immune Response Developed around Brucella Infected Cells in Resistant and Susceptible Mice

PubMed Central

Copin, Richard; Vitry, Marie-Alice; Hanot Mambres, Delphine; Machelart, Arnaud; De Trez, Carl; Vanderwinden, Jean-Marie; Magez, Stefan; Akira, Shizuo; Ryffel, Bernhard; Carlier, Yves; Letesson, Jean-Jacques; Muraille, Eric

2012-01-01

Brucella are facultative intracellular bacteria that chronically infect humans and animals causing brucellosis. Brucella are able to invade and replicate in a broad range of cell lines in vitro, however the cells supporting bacterial growth in vivo are largely unknown. In order to identify these, we used a Brucella melitensis strain stably expressing mCherry fluorescent protein to determine the phenotype of infected cells in spleen and liver, two major sites of B. melitensis growth in mice. In both tissues, the majority of primary infected cells expressed the F4/80 myeloid marker. The peak of infection correlated with granuloma development. These structures were mainly composed of CD11b+ F4/80+ MHC-II+ cells expressing iNOS/NOS2 enzyme. A fraction of these cells also expressed CD11c marker and appeared similar to inflammatory dendritic cells (DCs). Analysis of genetically deficient mice revealed that differentiation of iNOS+ inflammatory DC, granuloma formation and control of bacterial growth were deeply affected by the absence of MyD88, IL-12p35 and IFN-γ molecules. During chronic phase of infection in susceptible mice, we identified a particular subset of DC expressing both CD11c and CD205, serving as a reservoir for the bacteria. Taken together, our results describe the cellular nature of immune effectors involved during Brucella infection and reveal a previously unappreciated role for DC subsets, both as effectors and reservoir cells, in the pathogenesis of brucellosis. PMID:22479178

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

PubMed Central

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

2016-01-01

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

Evaluation of reconstruction techniques in regional cerebral blood flow SPECT using trade-off plots: a Monte Carlo study.

PubMed

Olsson, Anna; Arlig, Asa; Carlsson, Gudrun Alm; Gustafsson, Agnetha

2007-09-01

The image quality of single photon emission computed tomography (SPECT) depends on the reconstruction algorithm used. The purpose of the present study was to evaluate parameters in ordered subset expectation maximization (OSEM) and to compare systematically with filtered back-projection (FBP) for reconstruction of regional cerebral blood flow (rCBF) SPECT, incorporating attenuation and scatter correction. The evaluation was based on the trade-off between contrast recovery and statistical noise using different sizes of subsets, number of iterations and filter parameters. Monte Carlo simulated SPECT studies of a digital human brain phantom were used. The contrast recovery was calculated as measured contrast divided by true contrast. Statistical noise in the reconstructed images was calculated as the coefficient of variation in pixel values. A constant contrast level was reached above 195 equivalent maximum likelihood expectation maximization iterations. The choice of subset size was not crucial as long as there were > or = 2 projections per subset. The OSEM reconstruction was found to give 5-14% higher contrast recovery than FBP for all clinically relevant noise levels in rCBF SPECT. The Butterworth filter, power 6, achieved the highest stable contrast recovery level at all clinically relevant noise levels. The cut-off frequency should be chosen according to the noise level accepted in the image. Trade-off plots are shown to be a practical way of deciding the number of iterations and subset size for the OSEM reconstruction and can be used for other examination types in nuclear medicine.

Immune reconstitution after allogeneic hematopoietic stem cell transplantation in children: a single institution study of 59 patients.

PubMed

Kim, Hyun O; Oh, Hyun Jin; Lee, Jae Wook; Jang, Pil-Sang; Chung, Nack-Gyun; Cho, Bin; Kim, Hack-Ki

2013-01-01

Lymphocyte subset recovery is an important factor that determines the success of hematopoietic stem cell transplantation (HSCT). Temporal differences in the recovery of lymphocyte subsets and the factors influencing this recovery are important variables that affect a patient's post-transplant immune reconstitution, and therefore require investigation. The time taken to achieve lymphocyte subset recovery and the factors influencing this recovery were investigated in 59 children who had undergone HSCT at the Department of Pediatrics, The Catholic University of Korea Seoul St. Mary's Hospital, and who had an uneventful follow-up period of at least 1 year. Analyses were carried out at 3 and 12 months post-transplant. An additional study was performed 1 month post-transplant to evaluate natural killer (NK) cell recovery. The impact of pre- and post-transplant variables, including diagnosis of Epstein-Barr virus (EBV) DNAemia posttransplant, on lymphocyte recovery was evaluated. THE LYMPHOCYTE SUBSETS RECOVERED IN THE FOLLOWING ORDER: NK cells, cytotoxic T cells, B cells, and helper T cells. At 1 month post-transplant, acute graft-versus-host disease was found to contribute significantly to the delay of CD16(+)/56(+) cell recovery. Younger patients showed delayed recovery of both CD3(+)/CD8(+) and CD19(+) cells. EBV DNAemia had a deleterious impact on the recovery of both CD3(+) and CD3(+)/CD4(+) lymphocytes at 1 year post-transplant. In our pediatric allogeneic HSCT cohort, helper T cells were the last subset to recover. Younger age and EBV DNAemia had a negative impact on the post-transplant recovery of T cells and B cells.

Characterization of Conserved and Nonconserved Imprinted Genes in Swine

USDA-ARS?s Scientific Manuscript database

Genomic imprinting results in the silencing of a subset of mammalian alleles due to parent-of-origin inheritance. Due to the nature of their expression patterns they play a critical role in placental and early embryonic development. In order to increase our understanding of imprinted genes specifi...

Let's Do It: Paper Dot Plates Give Numbers Meaning.

ERIC Educational Resources Information Center

Thompson, Charles S.; Van de Walle, John

1980-01-01

Described are activities using paper plates with dots drawn on them which place a heavy emphasis on matching and ordering sets, on developing mental images of sets, and on perceiving sets of a certain size as composed of smaller subsets. Also suggested are activities involving numerals. (Author/TG)

76 FR 24363 - Adjudication and Enforcement

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-02

... proceedings under section 337 of the Tariff Act of 1930. The Supplement to the Strategic Human Capital Plan... in another subset of cases. In order to better allocate its resources, OUII may have to assign... in the Federal Register. The new rule will have no substantive effect on Commission practice in...

Clusters of Colleges and Universities: An Empirically Determined System.

ERIC Educational Resources Information Center

Korb, Roslyn

A technique for classifying higher education institutions was developed in order to identify homogenous subsets of institutions and to compare an institution with its empirically determined peers. The majority of the data were obtained from a 4-year longitudinal file that merged the finance, faculty, enrollment, and institutional characteristics…

Long High Redshift GRB and Xrt/swift Lightcurves

NASA Astrophysics Data System (ADS)

Arkhangelskaja, Irene

At February of 2010 the volume of Swift GRB subset with known redshift consisted of more than 150 bursts. Long GRB redshift distribution analysis has shown that confidence level of single peak approximation of this distribution is only ˜60%. Moreover, more than 40% of GRB are in very heavy tails outside 3σ level for this fit. More detailed analysis of long GRB redshift distribution reveals that at 97% confidence level at least two subgroups could be separated with following parameters: = 0.9 ± 0.1 and = 2.7 ± 0.2. It allows to make conclusion that Swift long GRB sources subset is not uniform. In the presented article attention is paid on the measure of discrepancy of long GRB with z>3 and subset of other long GRB with known redshifts. XRT/Swift lightcurves for these groups of GRB were considered and it have shown that at least 90% XRT/Swift lightcurves for GRB with z>3 are more complicated and have got a number of maxima.

Identification of petroleum hydrocarbons using a reduced number of PAHs selected by Procrustes rotation.

PubMed

Fernández-Varela, R; Andrade, J M; Muniategui, S; Prada, D; Ramírez-Villalobos, F

2010-04-01

Identifying petroleum-related products released into the environment is a complex and difficult task. To achieve this, polycyclic aromatic hydrocarbons (PAHs) are of outstanding importance nowadays. Despite traditional quantitative fingerprinting uses straightforward univariate statistical analyses to differentiate among oils and to assess their sources, a multivariate strategy based on Procrustes rotation (PR) was applied in this paper. The aim of PR is to select a reduced subset of PAHs still capable of performing a satisfactory identification of petroleum-related hydrocarbons. PR selected two subsets of three (C(2)-naphthalene, C(2)-dibenzothiophene and C(2)-phenanthrene) and five (C(1)-decahidronaphthalene, naphthalene, C(2)-phenanthrene, C(3)-phenanthrene and C(2)-fluoranthene) PAHs for each of the two datasets studied here. The classification abilities of each subset of PAHs were tested using principal components analysis, hierarchical cluster analysis and Kohonen neural networks and it was demonstrated that they unraveled the same patterns as the overall set of PAHs. (c) 2009 Elsevier Ltd. All rights reserved.

A novel iris transillumination grading scale allowing flexible assessment with quantitative image analysis and visual matching.

PubMed

Wang, Chen; Brancusi, Flavia; Valivullah, Zaheer M; Anderson, Michael G; Cunningham, Denise; Hedberg-Buenz, Adam; Power, Bradley; Simeonov, Dimitre; Gahl, William A; Zein, Wadih M; Adams, David R; Brooks, Brian

2018-01-01

To develop a sensitive scale of iris transillumination suitable for clinical and research use, with the capability of either quantitative analysis or visual matching of images. Iris transillumination photographic images were used from 70 study subjects with ocular or oculocutaneous albinism. Subjects represented a broad range of ocular pigmentation. A subset of images was subjected to image analysis and ranking by both expert and nonexpert reviewers. Quantitative ordering of images was compared with ordering by visual inspection. Images were binned to establish an 8-point scale. Ranking consistency was evaluated using the Kendall rank correlation coefficient (Kendall's tau). Visual ranking results were assessed using Kendall's coefficient of concordance (Kendall's W) analysis. There was a high degree of correlation among the image analysis, expert-based and non-expert-based image rankings. Pairwise comparisons of the quantitative ranking with each reviewer generated an average Kendall's tau of 0.83 ± 0.04 (SD). Inter-rater correlation was also high with Kendall's W of 0.96, 0.95, and 0.95 for nonexpert, expert, and all reviewers, respectively. The current standard for assessing iris transillumination is expert assessment of clinical exam findings. We adapted an image-analysis technique to generate quantitative transillumination values. Quantitative ranking was shown to be highly similar to a ranking produced by both expert and nonexpert reviewers. This finding suggests that the image characteristics used to quantify iris transillumination do not require expert interpretation. Inter-rater rankings were also highly similar, suggesting that varied methods of transillumination ranking are robust in terms of producing reproducible results.

CXCR3 expression defines a novel subset of innate CD8+ T cells that enhance immunity against bacterial infection and cancer upon stimulation with IL-15

PubMed Central

Oghumu, Steve; Terrazas, Cesar A.; Varikuti, Sanjay; Kimble, Jennifer; Vadia, Stephen; Yu, Lianbo; Seveau, Stephanie; Satoskar, Abhay R.

2015-01-01

Innate CD8+ T cells are a heterogeneous population with developmental pathways distinct from conventional CD8+ T cells. However, their biology, classification, and functions remain incompletely understood. We recently demonstrated the existence of a novel population of chemokine (C-X-C motif) receptor 3 (CXCR3)-positive innate CD8+ T cells. Here, we investigated the functional properties of this subset and identified effector molecules and pathways which mediate their function. Adoptive transfer of IL-15 activated CXCR3+ innate CD8+ T cells conferred increased protection against Listeria monocytogenes infection in susceptible IFN-γ−/− mice compared with similarly activated CXCR3− subset. This was associated with enhanced proliferation and IFN-γ production in CXCR3+ cells. Further, CXCR3+ innate cells showed enhanced cytotoxicity against a tumor cell line in vitro. In depth analysis of the CXCR3+ subset showed increased gene expression of Ccl5, Klrc1, CtsW, GP49a, IL-2Rβ, Atp5e, and Ly6c but reduced IFN-γR2 and Art2b. Ingenuity pathway analysis revealed an up-regulation of genes associated with T-cell activation, proliferation, cytotoxicity, and translational initiation in CXCR3+ populations. Our results demonstrate that CXCR3 expression in innate CD8+ T cells defines a subset with enhanced cytotoxic potential and protective antibacterial immune functions. Immunotherapeutic approaches against infectious disease and cancer could utilize CXCR3+ innate CD8+ T-cell populations as novel clinical intervention strategies.—Oghumu, S., Terrazas, C. A., Varikuti, S., Kimble, J., Vadia, S., Yu, L., Seveau, S., Satoskar, A. R. CXCR3 expression defines a novel subset of innate CD8+ T cells that enhance immunity against bacterial infection and cancer upon stimulation with IL-15. PMID:25466888

Systematic wavelength selection for improved multivariate spectral analysis

DOEpatents

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

1995-01-01

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

Position Affects Performance in Multiple-Object Tracking in Rugby Union Players

PubMed Central

Martín, Andrés; Sfer, Ana M.; D'Urso Villar, Marcela A.; Barraza, José F.

2017-01-01

We report an experiment that examines the performance of rugby union players and a control group composed of graduate student with no sport experience, in a multiple-object tracking task. It compares the ability of 86 high level rugby union players grouped as Backs and Forwards and the control group, to track a subset of randomly moving targets amongst the same number of distractors. Several difficulties were included in the experimental design in order to evaluate possible interactions between the relevant variables. Results show that the performance of the Backs is better than that of the other groups, but the occurrence of interactions precludes an isolated groups analysis. We interpret the results within the framework of visual attention and discuss both, the implications of our results and the practical consequences. PMID:28951725

Frustration in protein elastic network models

NASA Astrophysics Data System (ADS)

Lezon, Timothy; Bahar, Ivet

2010-03-01

Elastic network models (ENMs) are widely used for studying the equilibrium dynamics of proteins. The most common approach in ENM analysis is to adopt a uniform force constant or a non-specific distance dependent function to represent the force constant strength. Here we discuss the influence of sequence and structure in determining the effective force constants between residues in ENMs. Using a novel method based on entropy maximization, we optimize the force constants such that they exactly reporduce a subset of experimentally determined pair covariances for a set of proteins. We analyze the optimized force constants in terms of amino acid types, distances, contact order and secondary structure, and we demonstrate that including frustrated interactions in the ENM is essential for accurately reproducing the global modes in the middle of the frequency spectrum.

Skin lesion computational diagnosis of dermoscopic images: Ensemble models based on input feature manipulation.

PubMed

Oliveira, Roberta B; Pereira, Aledir S; Tavares, João Manuel R S

2017-10-01

The number of deaths worldwide due to melanoma has risen in recent times, in part because melanoma is the most aggressive type of skin cancer. Computational systems have been developed to assist dermatologists in early diagnosis of skin cancer, or even to monitor skin lesions. However, there still remains a challenge to improve classifiers for the diagnosis of such skin lesions. The main objective of this article is to evaluate different ensemble classification models based on input feature manipulation to diagnose skin lesions. Input feature manipulation processes are based on feature subset selections from shape properties, colour variation and texture analysis to generate diversity for the ensemble models. Three subset selection models are presented here: (1) a subset selection model based on specific feature groups, (2) a correlation-based subset selection model, and (3) a subset selection model based on feature selection algorithms. Each ensemble classification model is generated using an optimum-path forest classifier and integrated with a majority voting strategy. The proposed models were applied on a set of 1104 dermoscopic images using a cross-validation procedure. The best results were obtained by the first ensemble classification model that generates a feature subset ensemble based on specific feature groups. The skin lesion diagnosis computational system achieved 94.3% accuracy, 91.8% sensitivity and 96.7% specificity. The input feature manipulation process based on specific feature subsets generated the greatest diversity for the ensemble classification model with very promising results. Copyright © 2017 Elsevier B.V. All rights reserved.

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

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

Findlay, Rick; Kautsky, Mark

2015-12-01

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

Ecomorphological analysis of bovid mandibles from Laetoli Tanzania using 3D geometric morphometrics: Implications for hominin paleoenvironmental reconstruction.

PubMed

Forrest, Frances L; Plummer, Thomas W; Raaum, Ryan L

2018-01-01

The current study describes a new method of mandibular ecological morphology (ecomorphology). Three-dimensional geometric morphometrics (3D GM) was used to quantify mandibular shape variation between extant bovids with different feeding preferences. Landmark data were subjected to generalized Procrustes analysis (GPA), principal components analysis (PCA), and discriminant function analysis (DFA). The PCA resulted in a continuum from grazers to browsers along PC1 and DFA classified 88% or more of the modern specimens to the correct feeding category. The protocol was reduced to a subset of landmarks on the mandibular corpus in order to make it applicable to incomplete fossils. The reduced landmark set resulted in greater overlap between feeding categories but maintained the same continuum as the complete landmark model. The DFA resubstitution and jackknife analyses resulted in classification success rates of 85% and 80%, respectively. The reduced landmark model was applied to fossil mandibles from the Upper Laetolil Beds (∼4.3-3.5 Ma) and Upper Ndolanya Beds (∼2.7-2.6 Ma) at Laetoli, Tanzania in order to assess antelope diet, and indirectly evaluate paleo-vegetation structure. The majority of the fossils were classified by the DFA as browsers or mixed feeders preferring browse. Our results indicate a continuous presence of wooded habitats and are congruent with recent environmental studies at Laetoli indicating a mosaic woodland-bushland-grassland savanna ecosystem. Copyright © 2017 Elsevier Ltd. All rights reserved.

DistributedFBA.jl: High-level, high-performance flux balance analysis in Julia

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

Heirendt, Laurent; Thiele, Ines; Fleming, Ronan M. T.

Flux balance analysis and its variants are widely used methods for predicting steady-state reaction rates in biochemical reaction networks. The exploration of high dimensional networks with such methods is currently hampered by software performance limitations. DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia. It is tailored to solve multiple flux balance analyses on a subset or all the reactions of large and huge-scale networks, on any number of threads or nodes. DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia. It is tailored to solve multiple flux balance analyses on amore » subset or all the reactions of large and huge-scale networks, on any number of threads or nodes.« less

DistributedFBA.jl: High-level, high-performance flux balance analysis in Julia

DOE PAGES

Heirendt, Laurent; Thiele, Ines; Fleming, Ronan M. T.

2017-01-16

Flux balance analysis and its variants are widely used methods for predicting steady-state reaction rates in biochemical reaction networks. The exploration of high dimensional networks with such methods is currently hampered by software performance limitations. DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia. It is tailored to solve multiple flux balance analyses on a subset or all the reactions of large and huge-scale networks, on any number of threads or nodes. DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia. It is tailored to solve multiple flux balance analyses on amore » subset or all the reactions of large and huge-scale networks, on any number of threads or nodes.« less

Extended B cell phenotype in patients with myalgic encephalomyelitis/chronic fatigue syndrome: a cross‐sectional study

PubMed Central

Mensah, F.; Bansal, A.; Berkovitz, S.; Sharma, A.; Reddy, V.; Leandro, M. J.

2016-01-01

Summary Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a heterogeneous condition of unknown aetiology characterized by multiple symptoms including fatigue, post‐exertional malaise and cognitive impairment, lasting for at least 6 months. Recently, two clinical trials of B cell depletion therapy with rituximab (anti‐CD20) reported convincing improvement in symptoms. A possible but undefined role for B cells has therefore been proposed. Studies of the relative percentages of B cell subsets in patients with ME/CFS have not revealed any reproducible differences from healthy controls (HC). In order to explore whether more subtle alterations in B cell subsets related to B cell differentiation exist in ME/CFS patients we used flow cytometry to immunophenotype CD19+ B cells. The panel utilized immunoglobulin (Ig)D, CD27 and CD38 (classical B cell subsets) together with additional markers. A total of 38 patients fulfilling Canadian, Centre for Disease Control and Fukuda ME/CFS criteria and 32 age‐ and sex‐matched HC were included. We found no difference in percentages of classical subsets between ME/CFS patients and HC. However, we observed an increase in frequency (P < 0·01) and expression (MFI; P = 0·03) of CD24 on total B cells, confined to IgD+ subsets. Within memory subsets, a higher frequency of CD21+CD38– B cells (>20%) was associated with the presence of ME/CFS [odds ratio: 3·47 (1·15–10·46); P = 0·03] compared with HC, and there was a negative correlation with disease duration. In conclusion, we identified possible changes in B cell phenotype in patients with ME/CFS. These may reflect altered B cell function and, if confirmed in other patient cohorts, could provide a platform for studies based on clinical course or responsiveness to rituximab therapy. PMID:26646713

On the reduced dynamics of a subset of interacting bosonic particles

NASA Astrophysics Data System (ADS)

Gessner, Manuel; Buchleitner, Andreas

2018-03-01

The quantum dynamics of a subset of interacting bosons in a subspace of fixed particle number is described in terms of symmetrized many-particle states. A suitable partial trace operation over the von Neumann equation of an N-particle system produces a hierarchical expansion for the subdynamics of M ≤ N particles. Truncating this hierarchy with a pure product state ansatz yields the general, nonlinear coherent mean-field equation of motion. In the special case of a contact interaction potential, this reproduces the Gross-Pitaevskii equation. To account for incoherent effects on top of the mean-field evolution, we discuss possible extensions towards a second-order perturbation theory that accounts for interaction-induced decoherence in form of a nonlinear Lindblad-type master equation.

Flexible ordering of antibody class switch and V(D)J joining during B-cell ontogeny

PubMed Central

Kumar, Satyendra; Wuerffel, Robert; Achour, Ikbel; Lajoie, Bryan; Sen, Ranjan; Dekker, Job; Feeney, Ann J.; Kenter, Amy L.

2013-01-01

V(D)J joining is mediated by RAG recombinase during early B-lymphocyte development in the bone marrow (BM). Activation-induced deaminase initiates isotype switching in mature B cells of secondary lymphoid structures. Previous studies questioned the strict ontological partitioning of these processes. We show that pro-B cells undergo robust switching to a subset of immunoglobulin H (IgH) isotypes. Chromatin studies reveal that in pro-B cells, the spatial organization of the Igh locus may restrict switching to this subset of isotypes. We demonstrate that in the BM, V(D)J joining and switching are interchangeably inducible, providing an explanation for the hyper-IgE phenotype of Omenn syndrome. PMID:24240234

Replica amplification of nucleic acid arrays

DOEpatents

Church, George M.

2002-01-01

A method of producing a plurality of a nucleic acid array, comprising, in order, the steps of amplifying in situ nucleic acid molecules of a first randomly-patterned, immobilized nucleic acid array comprising a heterogeneous pool of nucleic acid molecules affixed to a support, transferring at least a subset of the nucleic acid molecules produced by such amplifying to a second support, and affixing the subset so transferred to the second support to form a second randomly-patterned, immobilized nucleic acid array, wherein the nucleic acid molecules of the second array occupy positions that correspond to those of the nucleic acid molecules from which they were amplified on the first array, so that the first array serves as a template to produce a plurality, is disclosed.

A protective role of murine langerin+ cells in immune responses to cutaneous vaccination with microneedle patches

PubMed Central

Pulit-Penaloza, Joanna A.; Esser, E. Stein; Vassilieva, Elena V.; Lee, Jeong Woo; Taherbhai, Misha T.; Pollack, Brian P.; Prausnitz, Mark R.; Compans, Richard W.; Skountzou, Ioanna

2014-01-01

Cutaneous vaccination with microneedle patches offers several advantages over more frequently used approaches for vaccine delivery, including improved protective immunity. However, the involvement of specific APC subsets and their contribution to the induction of immunity following cutaneous vaccine delivery is not well understood. A better understanding of the functions of individual APC subsets in the skin will allow us to target specific skin cell populations in order to further enhance vaccine efficacy. Here we use a Langerin-EGFP-DTR knock-in mouse model to determine the contribution of langerin+ subsets of skin APCs in the induction of adaptive immune responses following cutaneous microneedle delivery of influenza vaccine. Depletion of langerin+ cells prior to vaccination resulted in substantial impairment of both Th1 and Th2 responses, and decreased post-challenge survival rates, in mice vaccinated cutaneously but not in those vaccinated via the intramuscular route or in non-depleted control mice. Our results indicate that langerin+ cells contribute significantly to the induction of protective immune responses following cutaneous vaccination with a subunit influenza vaccine. PMID:25130187

Research on allocation efficiency of the daisy chain allocation algorithm

NASA Astrophysics Data System (ADS)

Shi, Jingping; Zhang, Weiguo

2013-03-01

With the improvement of the aircraft performance in reliability, maneuverability and survivability, the number of the control effectors increases a lot. How to distribute the three-axis moments into the control surfaces reasonably becomes an important problem. Daisy chain method is simple and easy to be carried out in the design of the allocation system. But it can not solve the allocation problem for entire attainable moment subset. For the lateral-directional allocation problem, the allocation efficiency of the daisy chain can be directly measured by the area of its subset of attainable moments. Because of the non-linear allocation characteristic, the subset of attainable moments of daisy-chain method is a complex non-convex polygon, and it is difficult to solve directly. By analyzing the two-dimensional allocation problems with a "micro-element" idea, a numerical calculation algorithm is proposed to compute the area of the non-convex polygon. In order to improve the allocation efficiency of the algorithm, a genetic algorithm with the allocation efficiency chosen as the fitness function is proposed to find the best pseudo-inverse matrix.

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

NASA Technical Reports Server (NTRS)

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

1999-01-01

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

A Mathematical Modelling Approach to One-Day Cricket Batting Orders

PubMed Central

Bukiet, Bruce; Ovens, Matthews

2006-01-01

While scoring strategies and player performance in cricket have been studied, there has been little published work about the influence of batting order with respect to One-Day cricket. We apply a mathematical modelling approach to compute efficiently the expected performance (runs distribution) of a cricket batting order in an innings. Among other applications, our method enables one to solve for the probability of one team beating another or to find the optimal batting order for a set of 11 players. The influence of defence and bowling ability can be taken into account in a straightforward manner. In this presentation, we outline how we develop our Markov Chain approach to studying the progress of runs for a batting order of non- identical players along the lines of work in baseball modelling by Bukiet et al., 1997. We describe the issues that arise in applying such methods to cricket, discuss ideas for addressing these difficulties and note limitations on modelling batting order for One-Day cricket. By performing our analysis on a selected subset of the possible batting orders, we apply the model to quantify the influence of batting order in a game of One Day cricket using available real-world data for current players. Key Points Batting order does effect the expected runs distribution in one-day cricket. One-day cricket has fewer data points than baseball, thus extreme values have greater effect on estimated probabilities. Dismissals rare and probabilities very small by comparison to baseball. Probability distribution for lower order batsmen is potentially skewed due to increased risk taking. Full enumeration of all possible line-ups is impractical using a single average computer. PMID:24357943

A mathematical modelling approach to one-day cricket batting orders.

PubMed

Bukiet, Bruce; Ovens, Matthews

2006-01-01

While scoring strategies and player performance in cricket have been studied, there has been little published work about the influence of batting order with respect to One-Day cricket. We apply a mathematical modelling approach to compute efficiently the expected performance (runs distribution) of a cricket batting order in an innings. Among other applications, our method enables one to solve for the probability of one team beating another or to find the optimal batting order for a set of 11 players. The influence of defence and bowling ability can be taken into account in a straightforward manner. In this presentation, we outline how we develop our Markov Chain approach to studying the progress of runs for a batting order of non- identical players along the lines of work in baseball modelling by Bukiet et al., 1997. We describe the issues that arise in applying such methods to cricket, discuss ideas for addressing these difficulties and note limitations on modelling batting order for One-Day cricket. By performing our analysis on a selected subset of the possible batting orders, we apply the model to quantify the influence of batting order in a game of One Day cricket using available real-world data for current players. Key PointsBatting order does effect the expected runs distribution in one-day cricket.One-day cricket has fewer data points than baseball, thus extreme values have greater effect on estimated probabilities.Dismissals rare and probabilities very small by comparison to baseball.Probability distribution for lower order batsmen is potentially skewed due to increased risk taking.Full enumeration of all possible line-ups is impractical using a single average computer.

Unidimensional factor models imply weaker partial correlations than zero-order correlations.

PubMed

van Bork, Riet; Grasman, Raoul P P P; Waldorp, Lourens J

2018-06-01

In this paper we present a new implication of the unidimensional factor model. We prove that the partial correlation between two observed variables that load on one factor given any subset of other observed variables that load on this factor lies between zero and the zero-order correlation between these two observed variables. We implement this result in an empirical bootstrap test that rejects the unidimensional factor model when partial correlations are identified that are either stronger than the zero-order correlation or have a different sign than the zero-order correlation. We demonstrate the use of the test in an empirical data example with data consisting of fourteen items that measure extraversion.

Voxels in the Brain: Neuroscience, Informatics and Changing Notions of Objectivity.

ERIC Educational Resources Information Center

Beaulieu, Anne

2001-01-01

Examines a subset of tools (atlases of the brain) developed in the Human Brain Project (HBP) in order to understand how the use of these tools changes the practice of science. Discusses the redefinition of what constitutes 'objective' neuroscientific knowledge according to both technological possibilities built into these tools and the constraints…

A Multi-Institutional Investigation of Students' Preinstructional Ideas about Cosmology

ERIC Educational Resources Information Center

Bailey, Janelle M.; Sanchez, Roxanne; Coble, Kim; Larrieu, Donna; Cochran, Geraldine; Cominsky, Lynn R.

2012-01-01

In order to improve instruction in introductory astronomy, we are investigating students' preinstructional ideas about a number of cosmology topics. This article describes one aspect of this large research study in which 1270 students responded to a subset of three questions each from a larger set of questions about the following areas: definition…

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

PubMed

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

2008-09-05

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

Longitudinal Analysis of Whole Blood Transcriptomes to Explore Molecular Signatures Associated With Acute Renal Allograft Rejection

PubMed Central

Shin, Heesun; Günther, Oliver; Hollander, Zsuzsanna; Wilson-McManus, Janet E.; Ng, Raymond T.; Balshaw, Robert; Keown, Paul A.; McMaster, Robert; McManus, Bruce M.; Isbel, Nicole M.; Knoll, Greg; Tebbutt, Scott J.

2014-01-01

In this study, we explored a time course of peripheral whole blood transcriptomes from kidney transplantation patients who either experienced an acute rejection episode or did not in order to better delineate the immunological and biological processes measureable in blood leukocytes that are associated with acute renal allograft rejection. Using microarrays, we generated gene expression data from 24 acute rejectors and 24 nonrejectors. We filtered the data to obtain the most unambiguous and robustly expressing probe sets and selected a subset of patients with the clearest phenotype. We then performed a data-driven exploratory analysis using data reduction and differential gene expression analysis tools in order to reveal gene expression signatures associated with acute allograft rejection. Using a template-matching algorithm, we then expanded our analysis to include time course data, identifying genes whose expression is modulated leading up to acute rejection. We have identified molecular phenotypes associated with acute renal allograft rejection, including a significantly upregulated signature of neutrophil activation and accumulation following transplant surgery that is common to both acute rejectors and nonrejectors. Our analysis shows that this expression signature appears to stabilize over time in nonrejectors but persists in patients who go on to reject the transplanted organ. In addition, we describe an expression signature characteristic of lymphocyte activity and proliferation. This lymphocyte signature is significantly downregulated in both acute rejectors and nonrejectors following surgery; however, patients who go on to reject the organ show a persistent downregulation of this signature relative to the neutrophil signature. PMID:24526836

Gendered uncertainty and variation in physicians' decisions for coronary heart disease: the double-edged sword of "atypical symptoms".

PubMed

Welch, Lisa C; Lutfey, Karen E; Gerstenberger, Eric; Grace, Matthew

2012-09-01

Nonmedical factors and diagnostic certainty contribute to variation in clinical decision making, but the process by which this occurs remains unclear. We examine how physicians' interpretations of patient sex-gender affect diagnostic certainty and, in turn, decision making for coronary heart disease. Data are from a factorial experiment of 256 physicians who viewed 1 of 16 video vignettes with different patient-actors presenting the same symptoms of coronary heart disease. Physician participants completed a structured interview and provided a narrative about their decision-making processes. Quantitative analysis showed that diagnostic uncertainty reduces the likelihood that physicians will order tests and medications appropriate for an urgent cardiac condition in particular. Qualitative analysis revealed that a subset of physicians applied knowledge that women have "atypical symptoms" as a generalization, which engendered uncertainty for some. Findings are discussed in relation to social-psychological processes that underlie clinical decision making and the social framing of medical knowledge.

On the Temporal Variability of Low-Mode Internal Tides in the Deep Ocean

NASA Technical Reports Server (NTRS)

Ray, Richard D.; Zaron, E. D.

2010-01-01

In situ measurements of internal tides are typically characterized by high temporal variability, with strong dependence on stratification, mesoscale eddies, and background currents commonly observed. Thus, it is surprising to find phase-locked internal tides detectable by satellite altimetry. An important question is how much tidal variability is missed by altimetry. We address this question in several ways. We subset the altimetry by season and find only very small changes -- an important exception being internal tides in the South China Sea where we observe strong seasonal dependence. A wavenumber-domain analysis confirms that throughout most of the global ocean there is little temporal variability in altimetric internal-tide signals, at least in the first baroclinic mode, which is the mode that dominates surface elevation. The analysis shows higher order modes to be significantly more variable. The results of this study have important practical implications for the anticipated SWOT wide-swath altimeter mission, for which removal of internal tide signals is critical for observing non-tidal submesoscale phenomena.

Gendered Uncertainty and Variation in Physicians’ Decisions for Coronary Heart Disease: The Double-Edged Sword of “Atypical Symptoms”*

PubMed Central

Welch, Lisa C.; Lutfey, Karen E.; Gerstenberger, Eric; Grace, Matthew

2013-01-01

Nonmedical factors and diagnostic certainty contribute to variation in clinical decision making, but the process by which this occurs remains unclear. We examine how physicians’ interpretations of patient sex/gender affect diagnostic certainty and, in turn, decision making for coronary heart disease (CHD). Data are from a factorial experiment of 256 physicians who viewed one of 16 video vignettes with different patient-actors presenting the same CHD symptoms. Physician participants completed a structured interview and provided a narrative about their decision-making processes. Quantitative analysis showed that diagnostic uncertainty reduces the likelihood that physicians will order tests and medications appropriate for an urgent cardiac condition in particular. Qualitative analysis revealed that a subset of physicians applied knowledge that women have “atypical symptoms” as a generalization, which engendered uncertainty for some. Findings are discussed in relation to social-psychological processes that underlie clinical decision making and the social framing of medical knowledge. PMID:22933590

3D visualization software to analyze topological outcomes of topoisomerase reactions

PubMed Central

Darcy, I. K.; Scharein, R. G.; Stasiak, A.

2008-01-01

The action of various DNA topoisomerases frequently results in characteristic changes in DNA topology. Important information for understanding mechanistic details of action of these topoisomerases can be provided by investigating the knot types resulting from topoisomerase action on circular DNA forming a particular knot type. Depending on the topological bias of a given topoisomerase reaction, one observes different subsets of knotted products. To establish the character of topological bias, one needs to be aware of all possible topological outcomes of intersegmental passages occurring within a given knot type. However, it is not trivial to systematically enumerate topological outcomes of strand passage from a given knot type. We present here a 3D visualization software (TopoICE-X in KnotPlot) that incorporates topological analysis methods in order to visualize, for example, knots that can be obtained from a given knot by one intersegmental passage. The software has several other options for the topological analysis of mechanisms of action of various topoisomerases. PMID:18440983

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

PubMed

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

1991-01-01

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

Association of the proprotein convertase subtilisin/kexin-type 2 (PCSK2) gene with type 2 diabetes in an African American population

PubMed Central

Leak, Tennille S.; Keene, Keith L.; Langefeld, Carl D.; Gallagher, Carla J.; Mychaleckyj, Josyf C.; Freedman, Barry I.; Bowden, Donald W.; Rich, Stephen S.; Sale, Michèle M.

2009-01-01

In a genome-wide scan for type 2 diabetes (T2DM) in African American (AA) families, ordered subsets analysis (OSA) provided evidence for linkage to chromosome 20p in a subset with later age at diagnosis (max. LOD 2.57, P = 0.008). The proprotein convertase subtilisin/kexin-type 2 (PCSK2) gene is within the LOD-1 interval of this linkage peak. Twenty-nine single nucleotide polymorphisms (SNPs) were genotyped across this gene in 380 unrelated AA individuals with T2DM and end-stage renal disease (T2DM-ESRD), 278 AA controls, 96 European Americans (EA) and 120 Yoruba Nigerian (YRI) controls. In addition, 22 ancestry-informative markers (AIMs) were genotyped in all AA subjects, 120 YRI, and 96 EA controls. ADMIXMAP was used to model the distributions of admixture and generate score tests of allelic and haplotypic association. Association with T2DM was observed among 4 SNPs: rs2021785 (admixture-adjusted Pa = 0.00014), rs1609659 (Pa = 0.028), rs4814597 (Pa = 0.039) and rs2269023 (Pa = 0.043). None of the PCSK2 SNPs were associated with age at T2DM diagnosis. A variant in the PCKS2 gene, rs2021785, appears to play a role in susceptibility to T2DM in this AA population. PMID:17618154

Space Suit Joint Torque Measurement Method Validation

NASA Technical Reports Server (NTRS)

Valish, Dana; Eversley, Karina

2012-01-01

In 2009 and early 2010, a test method was developed and performed to quantify the torque required to manipulate joints in several existing operational and prototype space suits. This was done in an effort to develop joint torque requirements appropriate for a new Constellation Program space suit system. The same test method was levied on the Constellation space suit contractors to verify that their suit design met the requirements. However, because the original test was set up and conducted by a single test operator there was some question as to whether this method was repeatable enough to be considered a standard verification method for Constellation or other future development programs. In order to validate the method itself, a representative subset of the previous test was repeated, using the same information that would be available to space suit contractors, but set up and conducted by someone not familiar with the previous test. The resultant data was compared using graphical and statistical analysis; the results indicated a significant variance in values reported for a subset of the re-tested joints. Potential variables that could have affected the data were identified and a third round of testing was conducted in an attempt to eliminate and/or quantify the effects of these variables. The results of the third test effort will be used to determine whether or not the proposed joint torque methodology can be applied to future space suit development contracts.

An Extension of Dominance Analysis to Canonical Correlation Analysis

ERIC Educational Resources Information Center

Huo, Yan; Budescu, David V.

2009-01-01

Dominance analysis (Budescu, 1993) offers a general framework for determination of relative importance of predictors in univariate and multivariate multiple regression models. This approach relies on pairwise comparisons of the contribution of predictors in all relevant subset models. In this article we extend dominance analysis to canonical…

Lupus erythematosus tumidus: a series of 26 cases.

PubMed

Vieira, Vanessa; Del Pozo, Jesús; Yebra-Pimentel, Maria Teresa; Martínez, Walter; Fonseca, Eduardo

2006-05-01

To study 26 cases of lupus erythematosus tumidus (LET), a subset of chronic cutaneous lupus erythematosus (CCLE), referred to in the literature as a rare entity. A retrospective study was conducted of 26 patients diagnosed with LET between 1996 and 2002. The clinical characteristics, histopathologic and laboratory findings, response to treatment, association with other subsets of lupus, course, and diagnostic criteria were analyzed. The incidence by sex was similar. The mean age of presentation was 49.19 years. The clinical presentation usually involved erythematous, edematous plaques located on the face, chest, back, or extremities, related to sun exposure. A dermal lymphocytic infiltrate with a perivascular disposition and differing degrees of mucin deposition was observed in all cases. Minimal epidermal changes were present in 18 cases, and 11 of these also showed minimal dermal-epidermal changes. Only one case showed dermal-epidermal changes without any epidermal alteration. Direct immunofluorescence test was performed in 15 patients, and 11 were negative. All cases showed a benign course without systemic manifestations. The response to topical steroids or antimalarial treatment was excellent, but a seasonal recurrence was usually observed. Discussion No defined criteria for LET are universally accepted. The main controversies are the acceptance of LET as a separate subset of CCLE, and the histopathologic diagnostic features, mainly the presence or absence of epidermal and dermal-epidermal changes in these lesions. No inflexible histologic criteria should be employed for the diagnosis of LET. This subset of lupus erythematosus is characterized by intense photosensitivity, definite clinical lesions, a benign course, the absence of systemic disease, good response to antimalarial treatment, and a tendency to recur. More studies should be performed in order to establish the true incidence of LET because this subset of CCLE is probably underestimated.

Attenuation correction strategies for multi-energy photon emitters using SPECT

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

Pretorius, P.H.; King, M.A.; Pan, T.S.

1996-12-31

The aim of this study was to investigate whether the photopeak window projections from different energy photons can be combined into a single window for reconstruction or if it is better to not combine the projections due to differences in the attenuation maps required for each photon energy. The mathematical cardiac torso (MCAT) phantom was modified to simulate the uptake of Ga-67 in the human body. Four spherical hot tumors were placed in locations which challenged attenuation correction. An analytical 3D projector with attenuation and detector response included was used to generate projection sets. Data were reconstructed using filtered backprojectionmore » (FBP) reconstruction with Butterworth filtering in conjunction with one iteration of Chang attenuation correction, and with 5 and 10 iterations of ordered-subset maximum-likelihood expectation-maximization reconstruction. To serve as a standard for comparison, the projection sets obtained from the two energies were first reconstructed separately using their own attenuation maps. The emission data obtained from both energies were added and reconstructed using the following attenuation strategies: (1) the 93 keV attenuation map for attenuation correction, (2) the 185 keV attenuation map for attenuation correction, (3) using a weighted mean obtained from combining the 93 keV and 185 keV maps, and (4) an ordered subset approach which combines both energies. The central count ratio (CCR) and total count ratio (TCR) were used to compare the performance of the different strategies. Compared to the standard method, results indicate an over-estimation with strategy 1, an under-estimation with strategy 2 and comparable results with strategies 3 and 4. In all strategies, the CCR`s of sphere 4 were under-estimated, although TCR`s were comparable to that of the other locations. The weighted mean and ordered subset strategies for attenuation correction were of comparable accuracy to reconstruction of the windows separately.« less

Mayo Registry for Telemetry Efficacy in Arrest (MR TEA) study: An analysis of code status change following cardiopulmonary arrest.

PubMed

Snipelisky, David; Ray, Jordan; Matcha, Gautam; Roy, Archana; Chirila, Razvan; Maniaci, Michael; Bosworth, Veronica; Whitman, Anastasia; Lewis, Patricia; Vadeboncoeur, Tyler; Kusumoto, Fred; Burton, M Caroline

2015-07-01

Code status discussions are important during a hospitalization, yet variation in its practice exists. No data have assessed the likelihood of patients to change code status following a cardiopulmonary arrest. A retrospective review of all patients that experienced a cardiopulmonary arrest between May 1, 2008 and June 30, 2014 at an academic medical center was performed. The proportion of code status modifications to do not resuscitate (DNR) from full code was assessed. Baseline clinical characteristics, resuscitation factors, and 24-h post-resuscitation, hospital, and overall survival rates were compared between the two subsets. A total of 157 patients survived the index event and were included. One hundred and fifteen (73.2%) patients did not have a change in code status following the index event, while 42 (26.8%) changed code status to DNR. Clinical characteristics were similar between subsets, although patients in the change to DNR subset were older (average age 67.7 years) compared to the full code subset (average age 59.2 years; p = 0.005). Patients in the DNR subset had longer overall resuscitation efforts with less attempts at defibrillation. Compared to the DNR subset, patients that remained full code demonstrated higher 24-h post-resuscitation (n = 108, 93.9% versus n = 32, 76.2%; p = 0.001) and hospital (n = 50, 43.5% versus n = 6, 14.3%; p = 0.001) survival rates. Patients in the DNR subset were more likely to have neurologic deficits on discharge and shorter overall survival. Patient code status wishes do tend to change during critical periods within a hospitalization, adding emphasis for continued code status evaluation. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Label-free haemogram using wavelength modulated Raman spectroscopy for identifying immune-cell subset

NASA Astrophysics Data System (ADS)

Ashok, Praveen C.; Praveen, Bavishna B.; Campbell, Elaine C.; Dholakia, Kishan; Powis, Simon J.

2014-03-01

Leucocytes in the blood of mammals form a powerful protective system against a wide range of dangerous pathogens. There are several types of immune cells that has specific role in the whole immune system. The number and type of immune cells alter in the disease state and identifying the type of immune cell provides information about a person's state of health. There are several immune cell subsets that are essentially morphologically identical and require external labeling to enable discrimination. Here we demonstrate the feasibility of using Wavelength Modulated Raman Spectroscopy (WMRS) with suitable machine learning algorithms as a label-free method to distinguish between different closely lying immune cell subset. Principal Component Analysis (PCA) was performed on WMRS data from single cells, obtained using confocal Raman microscopy for feature reduction, followed by Support Vector Machine (SVM) for binary discrimination of various cell subset, which yielded an accuracy >85%. The method was successful in discriminating between untouched and unfixed purified populations of CD4+CD3+ and CD8+CD3+ T lymphocyte subsets, and CD56+CD3- natural killer cells with a high degree of specificity. It was also proved sensitive enough to identify unique Raman signatures that allow clear discrimination between dendritic cell subsets, comprising CD303+CD45+ plasmacytoid and CD1c+CD141+ myeloid dendritic cells. The results of this study clearly show that WMRS is highly sensitive and can distinguish between cell types that are morphologically identical.

Feature Selection and Pedestrian Detection Based on Sparse Representation.

PubMed

Yao, Shihong; Wang, Tao; Shen, Weiming; Pan, Shaoming; Chong, Yanwen; Ding, Fei

2015-01-01

Pedestrian detection have been currently devoted to the extraction of effective pedestrian features, which has become one of the obstacles in pedestrian detection application according to the variety of pedestrian features and their large dimension. Based on the theoretical analysis of six frequently-used features, SIFT, SURF, Haar, HOG, LBP and LSS, and their comparison with experimental results, this paper screens out the sparse feature subsets via sparse representation to investigate whether the sparse subsets have the same description abilities and the most stable features. When any two of the six features are fused, the fusion feature is sparsely represented to obtain its important components. Sparse subsets of the fusion features can be rapidly generated by avoiding calculation of the corresponding index of dimension numbers of these feature descriptors; thus, the calculation speed of the feature dimension reduction is improved and the pedestrian detection time is reduced. Experimental results show that sparse feature subsets are capable of keeping the important components of these six feature descriptors. The sparse features of HOG and LSS possess the same description ability and consume less time compared with their full features. The ratios of the sparse feature subsets of HOG and LSS to their full sets are the highest among the six, and thus these two features can be used to best describe the characteristics of the pedestrian and the sparse feature subsets of the combination of HOG-LSS show better distinguishing ability and parsimony.

Defining an essence of structure determining residue contacts in proteins.

PubMed

Sathyapriya, R; Duarte, Jose M; Stehr, Henning; Filippis, Ioannis; Lappe, Michael

2009-12-01

The network of native non-covalent residue contacts determines the three-dimensional structure of a protein. However, not all contacts are of equal structural significance, and little knowledge exists about a minimal, yet sufficient, subset required to define the global features of a protein. Characterisation of this "structural essence" has remained elusive so far: no algorithmic strategy has been devised to-date that could outperform a random selection in terms of 3D reconstruction accuracy (measured as the Ca RMSD). It is not only of theoretical interest (i.e., for design of advanced statistical potentials) to identify the number and nature of essential native contacts-such a subset of spatial constraints is very useful in a number of novel experimental methods (like EPR) which rely heavily on constraint-based protein modelling. To derive accurate three-dimensional models from distance constraints, we implemented a reconstruction pipeline using distance geometry. We selected a test-set of 12 protein structures from the four major SCOP fold classes and performed our reconstruction analysis. As a reference set, series of random subsets (ranging from 10% to 90% of native contacts) are generated for each protein, and the reconstruction accuracy is computed for each subset. We have developed a rational strategy, termed "cone-peeling" that combines sequence features and network descriptors to select minimal subsets that outperform the reference sets. We present, for the first time, a rational strategy to derive a structural essence of residue contacts and provide an estimate of the size of this minimal subset. Our algorithm computes sparse subsets capable of determining the tertiary structure at approximately 4.8 A Ca RMSD with as little as 8% of the native contacts (Ca-Ca and Cb-Cb). At the same time, a randomly chosen subset of native contacts needs about twice as many contacts to reach the same level of accuracy. This "structural essence" opens new avenues in the fields of structure prediction, empirical potentials and docking.

Defining an Essence of Structure Determining Residue Contacts in Proteins

PubMed Central

Sathyapriya, R.; Duarte, Jose M.; Stehr, Henning; Filippis, Ioannis; Lappe, Michael

2009-01-01

The network of native non-covalent residue contacts determines the three-dimensional structure of a protein. However, not all contacts are of equal structural significance, and little knowledge exists about a minimal, yet sufficient, subset required to define the global features of a protein. Characterisation of this “structural essence” has remained elusive so far: no algorithmic strategy has been devised to-date that could outperform a random selection in terms of 3D reconstruction accuracy (measured as the Ca RMSD). It is not only of theoretical interest (i.e., for design of advanced statistical potentials) to identify the number and nature of essential native contacts—such a subset of spatial constraints is very useful in a number of novel experimental methods (like EPR) which rely heavily on constraint-based protein modelling. To derive accurate three-dimensional models from distance constraints, we implemented a reconstruction pipeline using distance geometry. We selected a test-set of 12 protein structures from the four major SCOP fold classes and performed our reconstruction analysis. As a reference set, series of random subsets (ranging from 10% to 90% of native contacts) are generated for each protein, and the reconstruction accuracy is computed for each subset. We have developed a rational strategy, termed “cone-peeling” that combines sequence features and network descriptors to select minimal subsets that outperform the reference sets. We present, for the first time, a rational strategy to derive a structural essence of residue contacts and provide an estimate of the size of this minimal subset. Our algorithm computes sparse subsets capable of determining the tertiary structure at approximately 4.8 Å Ca RMSD with as little as 8% of the native contacts (Ca-Ca and Cb-Cb). At the same time, a randomly chosen subset of native contacts needs about twice as many contacts to reach the same level of accuracy. This “structural essence” opens new avenues in the fields of structure prediction, empirical potentials and docking. PMID:19997489

Identity and Diversity of Human Peripheral Th and T Regulatory Cells Defined by Single-Cell Mass Cytometry.

PubMed

Kunicki, Matthew A; Amaya Hernandez, Laura C; Davis, Kara L; Bacchetta, Rosa; Roncarolo, Maria-Grazia

2018-01-01

Human CD3 + CD4 + Th cells, FOXP3 + T regulatory (Treg) cells, and T regulatory type 1 (Tr1) cells are essential for ensuring peripheral immune response and tolerance, but the diversity of Th, Treg, and Tr1 cell subsets has not been fully characterized. Independent functional characterization of human Th1, Th2, Th17, T follicular helper (Tfh), Treg, and Tr1 cells has helped to define unique surface molecules, transcription factors, and signaling profiles for each subset. However, the adequacy of these markers to recapitulate the whole CD3 + CD4 + T cell compartment remains questionable. In this study, we examined CD3 + CD4 + T cell populations by single-cell mass cytometry. We characterize the CD3 + CD4 + Th, Treg, and Tr1 cell populations simultaneously across 23 memory T cell-associated surface and intracellular molecules. High-dimensional analysis identified several new subsets, in addition to the already defined CD3 + CD4 + Th, Treg, and Tr1 cell populations, for a total of 11 Th cell, 4 Treg, and 1 Tr1 cell subsets. Some of these subsets share markers previously thought to be selective for Treg, Th1, Th2, Th17, and Tfh cells, including CD194 (CCR4) + FOXP3 + Treg and CD183 (CXCR3) + T-bet + Th17 cell subsets. Unsupervised clustering displayed a phenotypic organization of CD3 + CD4 + T cells that confirmed their diversity but showed interrelation between the different subsets, including similarity between Th1-Th2-Tfh cell populations and Th17 cells, as well as similarity of Th2 cells with Treg cells. In conclusion, the use of single-cell mass cytometry provides a systems-level characterization of CD3 + CD4 + T cells in healthy human blood, which represents an important baseline reference to investigate abnormalities of different subsets in immune-mediated pathologies. Copyright © 2017 by The American Association of Immunologists, Inc.

Linkage analysis of autopsy-confirmed familial Alzheimer disease supports an Alzheimer disease locus in 8q24.

PubMed

Sillén, Anna; Brohede, Jesper; Forsell, Charlotte; Lilius, Lena; Andrade, Jorge; Odeberg, Jacob; Kimura, Toru; Winblad, Bengt; Graff, Caroline

2011-01-01

We have previously reported the results of an extended genome-wide scan of Swedish Alzheimer disease (AD)-affected families; in this paper, we analyzed a subset of these families with autopsy-confirmed AD. We report the fine-mapping, using both microsatellite markers and single-nucleotide polymorphisms (SNPs), in the observed maximum logarithm of the odds (LOD)-2 unit (LOD(max)-2) region under the identified linkage peak, linkage analysis of the fine-mapping data with additionally analyzed pedigrees, and association analysis of SNPs selected from candidate genes in the linked interval. The subset was made on the criterion of at least one autopsy-confirmed AD case per family, resulting in 24 families. Linkage analysis of a family subset having at least one autopsy-confirmed AD case showed a significant nonparametric single-point LOD score of 4.4 in 8q24. Fine-mapping under the linkage peak with 10 microsatellite markers yielded an increase in the multipoint (mpt) LOD score from 2.1 to 3.0. SNP genotyping was performed on 21 selected candidate transcripts of the LOD(max)-2 region. Both family-based association and linkage analysis were performed on extended material from 30 families, resulting in a suggestive linkage at peak marker rs6577853 (mpt LOD score = 2.4). The 8q24 region has been implicated to be involved in AD etiology. Copyright © 2011 S. Karger AG, Basel.

Analysis of facial motion patterns during speech using a matrix factorization algorithm

PubMed Central

Lucero, Jorge C.; Munhall, Kevin G.

2008-01-01

This paper presents an analysis of facial motion during speech to identify linearly independent kinematic regions. The data consists of three-dimensional displacement records of a set of markers located on a subject’s face while producing speech. A QR factorization with column pivoting algorithm selects a subset of markers with independent motion patterns. The subset is used as a basis to fit the motion of the other facial markers, which determines facial regions of influence of each of the linearly independent markers. Those regions constitute kinematic “eigenregions” whose combined motion produces the total motion of the face. Facial animations may be generated by driving the independent markers with collected displacement records. PMID:19062866

Chronic Low-Grade Inflammation in Childhood Obesity Is Associated with Decreased IL-10 Expression by Monocyte Subsets.

PubMed

Mattos, Rafael T; Medeiros, Nayara I; Menezes, Carlos A; Fares, Rafaelle C G; Franco, Eliza P; Dutra, Walderez O; Rios-Santos, Fabrício; Correa-Oliveira, Rodrigo; Gomes, Juliana A S

2016-01-01

Chronic low-grade inflammation is related to the development of comorbidities and poor prognosis in obesity. Monocytes are main sources of cytokines and play a pivotal role in inflammation. We evaluated monocyte frequency, phenotype and cytokine profile of monocyte subsets, to determine their association with the pathogenesis of childhood obesity. Children with obesity were evaluated for biochemical and anthropometric parameters. Monocyte subsets were characterized by flow cytometry, considering cytokine production and activation/recognition molecules. Correlation analysis between clinical parameters and immunological data delineated the monocytes contribution for low-grade inflammation. We observed a higher frequency of non-classical monocytes in the childhood obesity group (CO) than normal-weight group (NW). All subsets displayed higher TLR4 expression in CO, but their recognition and antigen presentation functions seem to be diminished due to lower expression of CD40, CD80/86 and HLA-DR. All subsets showed a lower expression of IL-10 in CO and correlation analyses showed changes in IL-10 expression profile. The lower expression of IL-10 may be decisive for the maintenance of the low-grade inflammation status in CO, especially for alterations in non-classical monocytes profile. These cells may contribute to supporting inflammation and loss of regulation in the immune response of children with obesity.

Chronic Low-Grade Inflammation in Childhood Obesity Is Associated with Decreased IL-10 Expression by Monocyte Subsets

PubMed Central

Mattos, Rafael T.; Medeiros, Nayara I.; Menezes, Carlos A.; Fares, Rafaelle C. G.; Franco, Eliza P.; Dutra, Walderez O.; Rios-Santos, Fabrício; Correa-Oliveira, Rodrigo; Gomes, Juliana A. S.

2016-01-01

Chronic low-grade inflammation is related to the development of comorbidities and poor prognosis in obesity. Monocytes are main sources of cytokines and play a pivotal role in inflammation. We evaluated monocyte frequency, phenotype and cytokine profile of monocyte subsets, to determine their association with the pathogenesis of childhood obesity. Children with obesity were evaluated for biochemical and anthropometric parameters. Monocyte subsets were characterized by flow cytometry, considering cytokine production and activation/recognition molecules. Correlation analysis between clinical parameters and immunological data delineated the monocytes contribution for low-grade inflammation. We observed a higher frequency of non-classical monocytes in the childhood obesity group (CO) than normal-weight group (NW). All subsets displayed higher TLR4 expression in CO, but their recognition and antigen presentation functions seem to be diminished due to lower expression of CD40, CD80/86 and HLA-DR. All subsets showed a lower expression of IL-10 in CO and correlation analyses showed changes in IL-10 expression profile. The lower expression of IL-10 may be decisive for the maintenance of the low-grade inflammation status in CO, especially for alterations in non-classical monocytes profile. These cells may contribute to supporting inflammation and loss of regulation in the immune response of children with obesity. PMID:27977792

A Single HIV-1 Cluster and a Skewed Immune Homeostasis Drive the Early Spread of HIV among Resting CD4+ Cell Subsets within One Month Post-Infection

PubMed Central

Avettand-Fenoël, Véronique; Nembot, Georges; Mélard, Adeline; Blanc, Catherine; Lascoux-Combe, Caroline; Slama, Laurence; Allegre, Thierry; Allavena, Clotilde; Yazdanpanah, Yazdan; Duvivier, Claudine; Katlama, Christine; Goujard, Cécile; Seksik, Bao Chau Phung; Leplatois, Anne; Molina, Jean-Michel; Meyer, Laurence; Autran, Brigitte; Rouzioux, Christine

2013-01-01

Optimizing therapeutic strategies for an HIV cure requires better understanding the characteristics of early HIV-1 spread among resting CD4+ cells within the first month of primary HIV-1 infection (PHI). We studied the immune distribution, diversity, and inducibility of total HIV-DNA among the following cell subsets: monocytes, peripheral blood activated and resting CD4 T cells, long-lived (naive [TN] and central-memory [TCM]) and short-lived (transitional-memory [TTM] and effector-memory cells [TEM]) resting CD4+T cells from 12 acutely-infected individuals recruited at a median 36 days from infection. Cells were sorted for total HIV-DNA quantification, phylogenetic analysis and inducibility, all studied in relation to activation status and cell signaling. One month post-infection, a single CCR5-restricted viral cluster was massively distributed in all resting CD4+ subsets from 88% subjects, while one subject showed a slight diversity. High levels of total HIV-DNA were measured among TN (median 3.4 log copies/million cells), although 10-fold less (p = 0.0005) than in equally infected TCM (4.5), TTM (4.7) and TEM (4.6) cells. CD3−CD4+ monocytes harbored a low viral burden (median 2.3 log copies/million cells), unlike equally infected resting and activated CD4+ T cells (4.5 log copies/million cells). The skewed repartition of resting CD4 subsets influenced their contribution to the pool of resting infected CD4+T cells, two thirds of which consisted of short-lived TTM and TEM subsets, whereas long-lived TN and TCM subsets contributed the balance. Each resting CD4 subset produced HIV in vitro after stimulation with anti-CD3/anti-CD28+IL-2 with kinetics and magnitude varying according to subset differentiation, while IL-7 preferentially induced virus production from long-lived resting TN cells. In conclusion, within a month of infection, a clonal HIV-1 cluster is massively distributed among resting CD4 T-cell subsets with a flexible inducibility, suggesting that subset activation and skewed immune homeostasis determine the conditions of viral dissemination and early establishment of the HIV reservoir. PMID:23691172

Optimized hyperspectral band selection using hybrid genetic algorithm and gravitational search algorithm

NASA Astrophysics Data System (ADS)

Zhang, Aizhu; Sun, Genyun; Wang, Zhenjie

2015-12-01

The serious information redundancy in hyperspectral images (HIs) cannot contribute to the data analysis accuracy, instead it require expensive computational resources. Consequently, to identify the most useful and valuable information from the HIs, thereby improve the accuracy of data analysis, this paper proposed a novel hyperspectral band selection method using the hybrid genetic algorithm and gravitational search algorithm (GA-GSA). In the proposed method, the GA-GSA is mapped to the binary space at first. Then, the accuracy of the support vector machine (SVM) classifier and the number of selected spectral bands are utilized to measure the discriminative capability of the band subset. Finally, the band subset with the smallest number of spectral bands as well as covers the most useful and valuable information is obtained. To verify the effectiveness of the proposed method, studies conducted on an AVIRIS image against two recently proposed state-of-the-art GSA variants are presented. The experimental results revealed the superiority of the proposed method and indicated that the method can indeed considerably reduce data storage costs and efficiently identify the band subset with stable and high classification precision.

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

PubMed Central

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

2014-01-01

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

Phenotypic and functional characterization of earthworm coelomocyte subsets: Linking light scatter-based cell typing and imaging of the sorted populations.

PubMed

Engelmann, Péter; Hayashi, Yuya; Bodó, Kornélia; Ernszt, Dávid; Somogyi, Ildikó; Steib, Anita; Orbán, József; Pollák, Edit; Nyitrai, Miklós; Németh, Péter; Molnár, László

2016-12-01

Flow cytometry is a common approach to study invertebrate immune cells including earthworm coelomocytes. However, the link between light-scatter- and microscopy-based phenotyping remains obscured. Here we show, by means of light scatter-based cell sorting, both subpopulations (amoebocytes and eleocytes) can be physically isolated with good sort efficiency and purity confirmed by downstream morphological and cytochemical applications. Immunocytochemical analysis using anti-EFCC monoclonal antibodies combined with phalloidin staining has revealed antigenically distinct, sorted subsets. Screening of lectin binding capacity indicated wheat germ agglutinin (WGA) as the strongest reactor to amoebocytes. This is further evidenced by WGA inhibition assays that suggest high abundance of N-acetyl-d-glucosamine in amoebocytes. Post-sort phagocytosis assays confirmed the functional differences between amoebocytes and eleocytes, with the former being in favor of bacterial engulfment. This study has proved successful in linking flow cytometry and microscopy analysis and provides further experimental evidence of phenotypic and functional heterogeneity in earthworm coelomocyte subsets. Copyright © 2016 Elsevier Ltd. All rights reserved.

On Proportionate and Truthful International Alliance Contributions: An Analysis of IncentiveCompatible Cost Sharing Mechanisms to Burden Sharing

DTIC Science & Technology

2017-03-23

Therefore, the mecha- nism induces a stable cost sharing scheme wherein a subset of colluding players will not all benefit . In a subset of colluding...goods are not divisible and are not excludable. Cost sharing mechanisms specific to public goods have been researched extensively in the literature...Jackson & Moulin [1992] consider the sharing of cost for an indivisible public project among many players, and their work was extended by Bag [1997] to

Hypervelocity Impact Test Fragment Modeling: Modifications to the Fragment Rotation Analysis and Lightcurve Code

NASA Technical Reports Server (NTRS)

Gouge, Michael F.

2011-01-01

Hypervelocity impact tests on test satellites are performed by members of the orbital debris scientific community in order to understand and typify the on-orbit collision breakup process. By analysis of these test satellite fragments, the fragment size and mass distributions are derived and incorporated into various orbital debris models. These same fragments are currently being put to new use using emerging technologies. Digital models of these fragments are created using a laser scanner. A group of computer programs referred to as the Fragment Rotation Analysis and Lightcurve code uses these digital representations in a multitude of ways that describe, measure, and model on-orbit fragments and fragment behavior. The Dynamic Rotation subroutine generates all of the possible reflected intensities from a scanned fragment as if it were observed to rotate dynamically while in orbit about the Earth. This calls an additional subroutine that graphically displays the intensities and the resulting frequency of those intensities as a range of solar phase angles in a Probability Density Function plot. This document reports the additions and modifications to the subset of the Fragment Rotation Analysis and Lightcurve concerned with the Dynamic Rotation and Probability Density Function plotting subroutines.

Highly Efficient Design-of-Experiments Methods for Combining CFD Analysis and Experimental Data

NASA Technical Reports Server (NTRS)

Anderson, Bernhard H.; Haller, Harold S.

2009-01-01

It is the purpose of this study to examine the impact of "highly efficient" Design-of-Experiments (DOE) methods for combining sets of CFD generated analysis data with smaller sets of Experimental test data in order to accurately predict performance results where experimental test data were not obtained. The study examines the impact of micro-ramp flow control on the shock wave boundary layer (SWBL) interaction where a complete paired set of data exist from both CFD analysis and Experimental measurements By combining the complete set of CFD analysis data composed of fifteen (15) cases with a smaller subset of experimental test data containing four/five (4/5) cases, compound data sets (CFD/EXP) were generated which allows the prediction of the complete set of Experimental results No statistical difference were found to exist between the combined (CFD/EXP) generated data sets and the complete Experimental data set composed of fifteen (15) cases. The same optimal micro-ramp configuration was obtained using the (CFD/EXP) generated data as obtained with the complete set of Experimental data, and the DOE response surfaces generated by the two data sets were also not statistically different.

Genome investigation suggests MdSHN3, an APETALA2-domain transcription factor gene, to be a positive regulator of apple fruit cuticle formation and an inhibitor of russet development

PubMed Central

Lashbrooke, Justin; Aharoni, Asaph; Costa, Fabrizio

2015-01-01

The outer epidermal layer of apple fruit is covered by a protective cuticle. Composed of a polymerized cutin matrix embedded with waxes, the cuticle is a natural waterproof barrier and protects against several abiotic and biotic stresses. In terms of apple production, the cuticle is essential to maintain long post-harvest storage, while severe failure of the cuticle can result in the formation of a disorder known as russet. Apple russet results from micro-cracking of the cuticle and the formation of a corky suberized layer. This is typically an undesirable consumer trait, and negatively impacts the post-harvest storage of apples. In order to identify genetic factors controlling cuticle biosynthesis (and thus preventing russet) in apple, a quantitative trait locus (QTL) mapping survey was performed on a full-sib population. Two genomic regions located on chromosomes 2 and 15 that could be associated with russeting were identified. Apples with compromised cuticles were identified through a novel and high-throughput tensile analysis of the skin, while histological analysis confirmed cuticle failure in a subset of the progeny. Additional genomic investigation of the determined QTL regions identified a set of underlying genes involved in cuticle biosynthesis. Candidate gene expression profiling by quantitative real-time PCR on a subset of the progeny highlighted the specific expression pattern of a SHN1/WIN1 transcription factor gene (termed MdSHN3) on chromosome 15. Orthologues of SHN1/WIN1 have been previously shown to regulate cuticle formation in Arabidopsis, tomato, and barley. The MdSHN3 transcription factor gene displayed extremely low expression in lines with improper cuticle formation, suggesting it to be a fundamental regulator of cuticle biosynthesis in apple fruit. PMID:26220084

Position of Social Determinants of Health in Urban Man-Made Lakes

PubMed Central

Shojaei, Parisa; Karimlou, Masoud; Mohammadi, Farahnaz; Afzali, Hosein Malek; Forouzan, Ameneh Setareh

2013-01-01

Background and Objective: A social determinants approach proposes that enhancing living conditions in areas such as income, housing, transportation, employment, education, social support, and health services is central to improving the health of urban populations. Urban development projects can be costly but have health impacts. The benefit derived from the creation of man-made lakes in developing countries is usually associated with great risks; however, the evidence for physical and non-physical health benefits of urban man-made lake is unclear. The aim of this paper is to formulate a conceptual framework of associations between urban man-made lakes and social determinants of health. Method: This study was a qualitative study carried out using one focus group discussion and 16 individual interviews. Data were analyzed based on deductive-inductive content analysis approach. Results: Participants’ points of view were analyzed within 261 codes. Data analysis matrix was the conceptual framework of social determinants of health commission and its sub-groups, thus, two structural and mediating determinants categories as well as their sub-sets were created accordingly. In addition, some extra sub-sets including environment, air quality, weather changes, noise pollution, pathogenesis, quality of life, shortage of available resources, region popularity, ethnicity, tourism, social and physical development of children, unintentional injuries, aesthetic, and spirituality were extracted beyond the matrix factors, which were placed in each of above categories based on their thematic content. Conclusion: This paper has illustrated that the quality and type of man-made lake provided within communities can have a significant and sustained impact on community’s health and wellbeing. Therefore, in order to strengthen positive effects and reduce negative effects of any developmental projects within community, their impacts on public health should be taken into consideration. PMID:24171878

Characterization with microturbulence simulations of the zero particle flux condition in case of a TCV discharge showing toroidal rotation reversal

NASA Astrophysics Data System (ADS)

Mariani, A.; Merlo, G.; Brunner, S.; Merle, A.; Sauter, O.; Görler, T.; Jenko, F.; Told, D.

2016-11-01

In view of the stabilization effect of sheared plasma rotation on microturbulence, it is important to study the intrinsic rotation that develops in tokamaks that present negligible external toroidal torque, like ITER. Remarkable observations have been made on TCV, analysing discharges without NBI injection, as reported in [A. Bortolon et al. 2006 Phys. Rev. Lett. 97] and exhibiting a rotation inversion occurring in conjunction with a relatively small change in the plasma density. We focus in particular on a limited L-mode TCV shot published in [B. P. Duval et al. 2008 Phys. Plasmas 15], that shows a rotation reversal during a density ramp up. In view of performing a momentum transport analysis on this TCV shot, some constraints have to be considered to reduce the uncertainty on the experimental parameters. One useful constraint is the zero particle flux condition, resulting from the absence of direct particle fuelling to the plasma core. In this work, a preliminary study of the reconstruction of the zero particle flux hyper-surface in the physical parameters space is presented, taking into account the effect of the main impurity (carbon) and beginning to explore the effect of collisions, in order to find a subset of this hyper-surface within the experimental error bars. The analysis is done performing gyrokinetic simulations with the local (flux-tube) version of the Eulerian code GENE [Jenko et al 2000 Phys. Plasmas 7 1904], computing the fluxes with a Quasi-Linear model, according to [E. Fable et al. 2010 PPCF 52], and validating the QL results with Non-Linear simulations in a subset of cases.

Position of social determinants of health in urban man-made lakes plans.

PubMed

Shojaei, Parisa; Karimloo, Masoud; Mohammadi, Farahnaz; Malek Afzali, Hossein; Forouzan, Ameneh Setareh

2013-09-04

A social determinants approach proposes that enhancing living conditions in areas such as income, housing, transportation, employment, education, social support, and health services is central to improving the health of urban populations. Urban development projects can be costly but have health impacts. The benefit derived from the creation of man-made lakes in developing countries is usually associated with great risks; however, the evidence for physical and non-physical health benefits of urban man-made lake is unclear. The aim of this paper is to formulate a conceptual framework of associations between urban man-made lakes and social determinants of health. This study was a qualitative study carried out using one focus group discussion and 16 individual interviews. Data were analyzed based on deductive-inductive content analysis approach. Participants' points of view were analyzed within 261 codes. Data analysis matrix was the conceptual framework of social determinants of health commission and its sub-groups, thus, two structural and mediating determinants categories as well as their sub-sets were created accordingly. In addition, some extra sub-sets including environment, air quality, weather changes, noise pollution, pathogenesis, quality of life, shortage of available resources, region popularity, ethnicity, tourism, social and physical development of children, unintentional injuries, aesthetic, and spirituality were extracted beyond the matrix factors, which were placed in each of above categories based on their thematic content. This paper has illustrated that the quality and type of man-made lake provided within communities can have a significant and sustained impact on community's health and wellbeing. Therefore, in order to strengthen positive effects and reduce negative effects of any developmental projects within community, their impacts on public health should be taken into consideration.

A general procedure to generate models for urban environmental-noise pollution using feature selection and machine learning methods.

PubMed

Torija, Antonio J; Ruiz, Diego P

2015-02-01

The prediction of environmental noise in urban environments requires the solution of a complex and non-linear problem, since there are complex relationships among the multitude of variables involved in the characterization and modelling of environmental noise and environmental-noise magnitudes. Moreover, the inclusion of the great spatial heterogeneity characteristic of urban environments seems to be essential in order to achieve an accurate environmental-noise prediction in cities. This problem is addressed in this paper, where a procedure based on feature-selection techniques and machine-learning regression methods is proposed and applied to this environmental problem. Three machine-learning regression methods, which are considered very robust in solving non-linear problems, are used to estimate the energy-equivalent sound-pressure level descriptor (LAeq). These three methods are: (i) multilayer perceptron (MLP), (ii) sequential minimal optimisation (SMO), and (iii) Gaussian processes for regression (GPR). In addition, because of the high number of input variables involved in environmental-noise modelling and estimation in urban environments, which make LAeq prediction models quite complex and costly in terms of time and resources for application to real situations, three different techniques are used to approach feature selection or data reduction. The feature-selection techniques used are: (i) correlation-based feature-subset selection (CFS), (ii) wrapper for feature-subset selection (WFS), and the data reduction technique is principal-component analysis (PCA). The subsequent analysis leads to a proposal of different schemes, depending on the needs regarding data collection and accuracy. The use of WFS as the feature-selection technique with the implementation of SMO or GPR as regression algorithm provides the best LAeq estimation (R(2)=0.94 and mean absolute error (MAE)=1.14-1.16 dB(A)). Copyright © 2014 Elsevier B.V. All rights reserved.

Data approximation using a blending type spline construction

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

Dalmo, Rune; Bratlie, Jostein

2014-11-18

Generalized expo-rational B-splines (GERBS) is a blending type spline construction where local functions at each knot are blended together by C{sup k}-smooth basis functions. One way of approximating discrete regular data using GERBS is by partitioning the data set into subsets and fit a local function to each subset. Partitioning and fitting strategies can be devised such that important or interesting data points are interpolated in order to preserve certain features. We present a method for fitting discrete data using a tensor product GERBS construction. The method is based on detection of feature points using differential geometry. Derivatives, which aremore » necessary for feature point detection and used to construct local surface patches, are approximated from the discrete data using finite differences.« less

'A giant mess'--making sense of complexity in the accounts of people with fibromyalgia.

PubMed

Dennis, Nicola L; Larkin, Michael; Derbyshire, Stuart W G

2013-11-01

The diagnosis of fibromyalgia is based on self-report and indirect measures and thus is unavoidably influenced by patients' own understanding of their symptoms. In order to provide appropriate support for people with fibromyalgia, it is important to understand variation in patients' interpretations of their own symptoms. Twenty people with fibromyalgia participated in email interviews exploring their experiences, history and diagnosis. Respondents answered a series of questions in their own time. Rich accounts were elicited. A hermeneutic phenomenological approach linked two stages of analysis. In the first instance, an in-depth, inductive analysis was developed around a subset of eight transcripts, using interpretative phenomenological analysis. The outcomes of this work were then used to inform a template analysis, which was applied to the remaining 12 transcripts, in order to extend and check the credibility of the in-depth analysis. Participants described enduring the course of a 'giant mess' of unpleasant symptoms, some of which were understood to be symptoms of fibromyalgia and some the interactive or parallel effects of comorbid illness. The respondents also demonstrated their considerable efforts at imposing order and sense on complexity and multiplicity, in terms of the instability of their symptoms. They expressed ambivalence towards diagnosis, doctors and medication, and we noted that each of the above areas appeared to come together to create a context of relational uncertainty, which undermined the security of connections to family, friends, colleagues and the workplace. Three key issues were discussed. First, there was not one overall symptom (e.g., pain) driving the unpleasantness of fibromyalgia; second, participants spent excessive time and energy trying to manage forces outside their control; third, because there is no definitive 'fibromyalgia experience', each diagnosis is unique, and our participants often appeared to be struggling to understand the course of their illness. Issues of stigma and legitimacy need to be considered carefully by health professionals in the context of the complex and uncertain experience of patients. © 2013 The British Psychological Society.

Psychometric properties of the college survey for students with brain injury: individuals with and without traumatic brain injury.

PubMed

Kennedy, Mary R T; Krause, Miriam O; O'Brien, Katy H

2014-01-01

The psychometric properties of the college challenges sub-set from The College Survey for Students with Brain Injury (CSS-BI) were investigated with adults with and without traumatic brain injury (TBI). Adults with and without TBI completed the CSS-BI. A sub-set of participants with TBI were interviewed, intentional and convergent validity were investigated, and the internal structure of the college challenges was analysed with exploratory factor analysis/principle component analysis. Respondents with TBI understood the items describing college challenges with evidence of intentional validity. More individuals with TBI than controls endorsed eight of the 13 college challenges. Those who reported more health issues endorsed more college challenges, demonstrating preliminary convergent validity. Cronbach's alphas of >0.85 demonstrated acceptable internal reliability. Factor analysis revealed a four-factor model for those with TBI: studying and learning (Factor 1), time management and organization (Factor 2), social (Factor 3) and nervousness/anxiety (Factor 4). This model explained 72% and 69% of the variance for those with and without TBI, respectively. The college challenges sub-set from the CSS-BI identifies challenges that individuals with TBI face when going to college. Some challenges were related to two factors in the model, demonstrating the inter-connections of these experiences.

Infliximab for chronic cutaneous sarcoidosis: a subset analysis from a double-blind randomized clinical trial.

PubMed

Baughman, Robert P; Judson, Marc A; Lower, Elyse E; Drent, Marjolein; Costabel, Ulrich; Flavin, Susan; Lo, Kim Hung; Barnathan, Elliot S

2016-01-15

Limited evidence exists demonstrating an effective treatment for chronic cutaneous sarcoidosis. To determine infliximab's effectiveness in sarcoidosis. We conducted a subset analysis from a randomized, double-blind, placebo-controlled trial for chronic pulmonary sarcoidosis to determine infliximab's effectiveness. Patients with chronic cutaneous sarcoidosis received infliximab (3 or 5 mg/kg) or placebo over 24 weeks. Of 138 patients, the subset analysis evaluated 17 patients with chronic facial and another 9 patients with nonfacial skin involvement. The SASI evaluated lesions for degree of erythema, desquamation, induration, and percentage of area involved. Facial and nonfacial lesions were scored in a blinded manner. Among 5 placebo-treated and 12 infliximab-treated patients, an improvement was observed with infliximab versus placebo in change from baseline to weeks 12 and 24 in desquamation (P<0.005) and induration (P<0.01) at week 24. Erythema, percentage of area involved and the evaluation of paired photographs did not reveal significant differences. Sample size; more extensive disease in placebo patients; chronic therapy upon enrollment; lung as primary organ of sarcoidosis involvement; limited investigator experience with SASI. Infliximab appears to be a beneficial treatment for chronic cutaneous sarcoidosis. The SASI scoring system demonstrated significant improvement versus placebo in lesion desquamation and induration.

An Atlas of Computed Equivalent Widths of Quasar Broad Emission Lines

NASA Astrophysics Data System (ADS)

Korista, Kirk; Baldwin, Jack; Ferland, Gary; Verner, Dima

We present graphically the results of several thousand photoionization calculations of broad emission-line clouds in quasars, spanning 7 orders of magnitude in hydrogen ionizing flux and particle density. The equivalent widths of 42 quasar emission lines are presented as contours in the particle density-ionizing flux plane for a typical incident continuum shape, solar chemical abundances, and cloud column density of N(H) = 1023 cm-2. Results are similarly given for a small subset of emission lines for two other column densities (1022 and 1024 cm-2), five other incident continuum shapes, and a gas metallicity of 5 Z⊙. These graphs should prove useful in the analysis of quasar emission-line data and in the detailed modeling of quasar broad emission-line regions. The digital results of these emission-line grids and many more are available over the Internet.

Assessment of awareness of connectedness as a culturally-based protective factor for Alaska native youth.

PubMed

Mohatt, Nathaniel V; Fok, Carlotta Ching Ting; Burket, Rebekah; Henry, David; Allen, James

2011-10-01

Research with Native Americans has identified connectedness as a culturally based protective factor against substance abuse and suicide. Connectedness refers to the interrelated welfare of the individual, one's family, one's community, and the natural environment. We developed an 18-item quantitative assessment of awareness of connectedness and tested it with 284 Alaska Native youth. Evaluation with confirmatory factor analysis and item response theory identified a 12-item subset that functions satisfactorily in a second-order four-factor model. The proposed Awareness of Connectedness Scale (ACS) displays good convergent and discriminant validity, and correlates positively with hypothesized protective factors such as reasons for living and communal mastery. The measure has utility in the study of culture-specific protective factors and as an outcomes measure for behavioral health programs with Native American youth.

Assessment of Awareness of Connectedness as a Culturally-based Protective Factor for Alaska Native Youth

PubMed Central

Mohatt, Nathaniel V.; Fok, Carlotta Ching Ting; Burket, Rebekah; Henry, David; Allen, James

2011-01-01

Research with Native Americans has identified connectedness as a culturally-based protective factor against substance abuse and suicide. Connectedness refers to the interrelated welfare of the individual, one’s family, one’s community, and the natural environment. We developed an 18-item quantitative assessment of awareness of connectedness and tested it with 284 Alaska Native youth. Evaluation with confirmatory factor analysis and item response theory identified a 12-item subset that functions satisfactorily in a second-order, four-factor model. The proposed Awareness of Connectedness Scale displays good convergent and discriminant validity and correlates positively with hypothesized protective factors such as reasons for living and communal mastery. The measure has utility in the study of culture-specific protective factors and as an outcomes measure for behavioral health programs with Native American youth. PMID:21988583

Complexity and dynamics of topological and community structure in complex networks

NASA Astrophysics Data System (ADS)

Berec, Vesna

2017-07-01

Complexity is highly susceptible to variations in the network dynamics, reflected on its underlying architecture where topological organization of cohesive subsets into clusters, system's modular structure and resulting hierarchical patterns, are cross-linked with functional dynamics of the system. Here we study connection between hierarchical topological scales of the simplicial complexes and the organization of functional clusters - communities in complex networks. The analysis reveals the full dynamics of different combinatorial structures of q-th-dimensional simplicial complexes and their Laplacian spectra, presenting spectral properties of resulting symmetric and positive semidefinite matrices. The emergence of system's collective behavior from inhomogeneous statistical distribution is induced by hierarchically ordered topological structure, which is mapped to simplicial complex where local interactions between the nodes clustered into subcomplexes generate flow of information that characterizes complexity and dynamics of the full system.

Leaving Librarianship: A Study of the Determinants and Consequences of Occupational Turnover

ERIC Educational Resources Information Center

Rathbun-Grubb, Susan R.

2009-01-01

The purpose of this study was to better understand occupational turnover among librarians and archivists by examining the careers of individuals who have left or intend to leave the profession, in order to identify the factors associated with turnover, and to discover the career outcomes of those who leave. The dissertation analyzes a subset of…

Comparison of the Incremental Validity of the Old and New MCAT.

ERIC Educational Resources Information Center

Wolf, Fredric M.; And Others

The predictive and incremental validity of both the Old and New Medical College Admission Test (MCAT) was examined and compared with a sample of over 300 medical students. Results of zero order and incremental validity coefficients, as well as prediction models resulting from all possible subsets regression analyses using Mallow's Cp criterion,…

"My Future Doesn't Know ME": Time and Subjectivity in Poetry by Young People

ERIC Educational Resources Information Center

Conrad, Rachel

2012-01-01

This article explores children's imaginative representations of time in relation to self-experience. Poems published in a young poets' anthology edited by Naomi Shihab Nye are analyzed in order to discern models of temporality and subjectivity imagined by young writers. A "dynamic temporality" is seen in a subset of poems which manipulate time…

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

ERIC Educational Resources Information Center

Fink, Richard T.

1972-01-01

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

Call Me "Madame": Re-Presenting Culture in the French Language Classroom

ERIC Educational Resources Information Center

Siskin, H. Jay

2007-01-01

This study examines autobiographies of American teachers of French in order to make explicit their beliefs regarding French language and culture. The themes of class and power are prominent in these teachers' belief systems, as is the desire for self-transformation through mastery of French and miming a subset of French behaviors. These notions…

Improved dynamic analysis method using load-dependent Ritz vectors

NASA Technical Reports Server (NTRS)

Escobedo-Torres, J.; Ricles, J. M.

1993-01-01

The dynamic analysis of large space structures is important in order to predict their behavior under operating conditions. Computer models of large space structures are characterized by having a large number of degrees of freedom, and the computational effort required to carry out the analysis is very large. Conventional methods of solution utilize a subset of the eigenvectors of the system, but for systems with many degrees of freedom, the solution of the eigenproblem is in many cases the most costly phase of the analysis. For this reason, alternate solution methods need to be considered. It is important that the method chosen for the analysis be efficient and that accurate results be obtainable. It is important that the method chosen for the analysis be efficient and that accurate results be obtainable. The load dependent Ritz vector method is presented as an alternative to the classical normal mode methods for obtaining dynamic responses of large space structures. A simplified model of a space station is used to compare results. Results show that the load dependent Ritz vector method predicts the dynamic response better than the classical normal mode method. Even though this alternate method is very promising, further studies are necessary to fully understand its attributes and limitations.

mESAdb: microRNA Expression and Sequence Analysis Database

PubMed Central

Kaya, Koray D.; Karakülah, Gökhan; Yakıcıer, Cengiz M.; Acar, Aybar C.; Konu, Özlen

2011-01-01

microRNA expression and sequence analysis database (http://konulab.fen.bilkent.edu.tr/mirna/) (mESAdb) is a regularly updated database for the multivariate analysis of sequences and expression of microRNAs from multiple taxa. mESAdb is modular and has a user interface implemented in PHP and JavaScript and coupled with statistical analysis and visualization packages written for the R language. The database primarily comprises mature microRNA sequences and their target data, along with selected human, mouse and zebrafish expression data sets. mESAdb analysis modules allow (i) mining of microRNA expression data sets for subsets of microRNAs selected manually or by motif; (ii) pair-wise multivariate analysis of expression data sets within and between taxa; and (iii) association of microRNA subsets with annotation databases, HUGE Navigator, KEGG and GO. The use of existing and customized R packages facilitates future addition of data sets and analysis tools. Furthermore, the ability to upload and analyze user-specified data sets makes mESAdb an interactive and expandable analysis tool for microRNA sequence and expression data. PMID:21177657

mESAdb: microRNA expression and sequence analysis database.

PubMed

Kaya, Koray D; Karakülah, Gökhan; Yakicier, Cengiz M; Acar, Aybar C; Konu, Ozlen

2011-01-01

microRNA expression and sequence analysis database (http://konulab.fen.bilkent.edu.tr/mirna/) (mESAdb) is a regularly updated database for the multivariate analysis of sequences and expression of microRNAs from multiple taxa. mESAdb is modular and has a user interface implemented in PHP and JavaScript and coupled with statistical analysis and visualization packages written for the R language. The database primarily comprises mature microRNA sequences and their target data, along with selected human, mouse and zebrafish expression data sets. mESAdb analysis modules allow (i) mining of microRNA expression data sets for subsets of microRNAs selected manually or by motif; (ii) pair-wise multivariate analysis of expression data sets within and between taxa; and (iii) association of microRNA subsets with annotation databases, HUGE Navigator, KEGG and GO. The use of existing and customized R packages facilitates future addition of data sets and analysis tools. Furthermore, the ability to upload and analyze user-specified data sets makes mESAdb an interactive and expandable analysis tool for microRNA sequence and expression data.

Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33

PubMed Central

Wang, Zhaoming; Zhu, Bin; Zhang, Mingfeng; Parikh, Hemang; Jia, Jinping; Chung, Charles C.; Sampson, Joshua N.; Hoskins, Jason W.; Hutchinson, Amy; Burdette, Laurie; Ibrahim, Abdisamad; Hautman, Christopher; Raj, Preethi S.; Abnet, Christian C.; Adjei, Andrew A.; Ahlbom, Anders; Albanes, Demetrius; Allen, Naomi E.; Ambrosone, Christine B.; Aldrich, Melinda; Amiano, Pilar; Amos, Christopher; Andersson, Ulrika; Andriole, Gerald; Andrulis, Irene L.; Arici, Cecilia; Arslan, Alan A.; Austin, Melissa A.; Baris, Dalsu; Barkauskas, Donald A.; Bassig, Bryan A.; Beane Freeman, Laura E.; Berg, Christine D.; Berndt, Sonja I.; Bertazzi, Pier Alberto; Biritwum, Richard B.; Black, Amanda; Blot, William; Boeing, Heiner; Boffetta, Paolo; Bolton, Kelly; Boutron-Ruault, Marie-Christine; Bracci, Paige M.; Brennan, Paul; Brinton, Louise A.; Brotzman, Michelle; Bueno-de-Mesquita, H. Bas; Buring, Julie E.; Butler, Mary Ann; Cai, Qiuyin; Cancel-Tassin, Geraldine; Canzian, Federico; Cao, Guangwen; Caporaso, Neil E.; Carrato, Alfredo; Carreon, Tania; Carta, Angela; Chang, Gee-Chen; Chang, I-Shou; Chang-Claude, Jenny; Che, Xu; Chen, Chien-Jen; Chen, Chih-Yi; Chen, Chung-Hsing; Chen, Constance; Chen, Kuan-Yu; Chen, Yuh-Min; Chokkalingam, Anand P.; Chu, Lisa W.; Clavel-Chapelon, Francoise; Colditz, Graham A.; Colt, Joanne S.; Conti, David; Cook, Michael B.; Cortessis, Victoria K.; Crawford, E. David; Cussenot, Olivier; Davis, Faith G.; De Vivo, Immaculata; Deng, Xiang; Ding, Ti; Dinney, Colin P.; Di Stefano, Anna Luisa; Diver, W. Ryan; Duell, Eric J.; Elena, Joanne W.; Fan, Jin-Hu; Feigelson, Heather Spencer; Feychting, Maria; Figueroa, Jonine D.; Flanagan, Adrienne M.; Fraumeni, Joseph F.; Freedman, Neal D.; Fridley, Brooke L.; Fuchs, Charles S.; Gago-Dominguez, Manuela; Gallinger, Steven; Gao, Yu-Tang; Gapstur, Susan M.; Garcia-Closas, Montserrat; Garcia-Closas, Reina; Gastier-Foster, Julie M.; Gaziano, J. Michael; Gerhard, Daniela S.; Giffen, Carol A.; Giles, Graham G.; Gillanders, Elizabeth M.; Giovannucci, Edward L.; Goggins, Michael; Gokgoz, Nalan; Goldstein, Alisa M.; Gonzalez, Carlos; Gorlick, Richard; Greene, Mark H.; Gross, Myron; Grossman, H. Barton; Grubb, Robert; Gu, Jian; Guan, Peng; Haiman, Christopher A.; Hallmans, Goran; Hankinson, Susan E.; Harris, Curtis C.; Hartge, Patricia; Hattinger, Claudia; Hayes, Richard B.; He, Qincheng; Helman, Lee; Henderson, Brian E.; Henriksson, Roger; Hoffman-Bolton, Judith; Hohensee, Chancellor; Holly, Elizabeth A.; Hong, Yun-Chul; Hoover, Robert N.; Hosgood, H. Dean; Hsiao, Chin-Fu; Hsing, Ann W.; Hsiung, Chao Agnes; Hu, Nan; Hu, Wei; Hu, Zhibin; Huang, Ming-Shyan; Hunter, David J.; Inskip, Peter D.; Ito, Hidemi; Jacobs, Eric J.; Jacobs, Kevin B.; Jenab, Mazda; Ji, Bu-Tian; Johansen, Christoffer; Johansson, Mattias; Johnson, Alison; Kaaks, Rudolf; Kamat, Ashish M.; Kamineni, Aruna; Karagas, Margaret; Khanna, Chand; Khaw, Kay-Tee; Kim, Christopher; Kim, In-Sam; Kim, Jin Hee; Kim, Yeul Hong; Kim, Young-Chul; Kim, Young Tae; Kang, Chang Hyun; Jung, Yoo Jin; Kitahara, Cari M.; Klein, Alison P.; Klein, Robert; Kogevinas, Manolis; Koh, Woon-Puay; Kohno, Takashi; Kolonel, Laurence N.; Kooperberg, Charles; Kratz, Christian P.; Krogh, Vittorio; Kunitoh, Hideo; Kurtz, Robert C.; Kurucu, Nilgun; Lan, Qing; Lathrop, Mark; Lau, Ching C.; Lecanda, Fernando; Lee, Kyoung-Mu; Lee, Maxwell P.; Le Marchand, Loic; Lerner, Seth P.; Li, Donghui; Liao, Linda M.; Lim, Wei-Yen; Lin, Dongxin; Lin, Jie; Lindstrom, Sara; Linet, Martha S.; Lissowska, Jolanta; Liu, Jianjun; Ljungberg, Börje; Lloreta, Josep; Lu, Daru; Ma, Jing; Malats, Nuria; Mannisto, Satu; Marina, Neyssa; Mastrangelo, Giuseppe; Matsuo, Keitaro; McGlynn, Katherine A.; McKean-Cowdin, Roberta; McNeill, Lorna H.; McWilliams, Robert R.; Melin, Beatrice S.; Meltzer, Paul S.; Mensah, James E.; Miao, Xiaoping; Michaud, Dominique S.; Mondul, Alison M.; Moore, Lee E.; Muir, Kenneth; Niwa, Shelley; Olson, Sara H.; Orr, Nick; Panico, Salvatore; Park, Jae Yong; Patel, Alpa V.; Patino-Garcia, Ana; Pavanello, Sofia; Peeters, Petra H. M.; Peplonska, Beata; Peters, Ulrike; Petersen, Gloria M.; Picci, Piero; Pike, Malcolm C.; Porru, Stefano; Prescott, Jennifer; Pu, Xia; Purdue, Mark P.; Qiao, You-Lin; Rajaraman, Preetha; Riboli, Elio; Risch, Harvey A.; Rodabough, Rebecca J.; Rothman, Nathaniel; Ruder, Avima M.; Ryu, Jeong-Seon; Sanson, Marc; Schned, Alan; Schumacher, Fredrick R.; Schwartz, Ann G.; Schwartz, Kendra L.; Schwenn, Molly; Scotlandi, Katia; Seow, Adeline; Serra, Consol; Serra, Massimo; Sesso, Howard D.; Severi, Gianluca; Shen, Hongbing; Shen, Min; Shete, Sanjay; Shiraishi, Kouya; Shu, Xiao-Ou; Siddiq, Afshan; Sierrasesumaga, Luis; Sierri, Sabina; Loon Sihoe, Alan Dart; Silverman, Debra T.; Simon, Matthias; Southey, Melissa C.; Spector, Logan; Spitz, Margaret; Stampfer, Meir; Stattin, Par; Stern, Mariana C.; Stevens, Victoria L.; Stolzenberg-Solomon, Rachael Z.; Stram, Daniel O.; Strom, Sara S.; Su, Wu-Chou; Sund, Malin; Sung, Sook Whan; Swerdlow, Anthony; Tan, Wen; Tanaka, Hideo; Tang, Wei; Tang, Ze-Zhang; Tardon, Adonina; Tay, Evelyn; Taylor, Philip R.; Tettey, Yao; Thomas, David M.; Tirabosco, Roberto; Tjonneland, Anne; Tobias, Geoffrey S.; Toro, Jorge R.; Travis, Ruth C.; Trichopoulos, Dimitrios; Troisi, Rebecca; Truelove, Ann; Tsai, Ying-Huang; Tucker, Margaret A.; Tumino, Rosario; Van Den Berg, David; Van Den Eeden, Stephen K.; Vermeulen, Roel; Vineis, Paolo; Visvanathan, Kala; Vogel, Ulla; Wang, Chaoyu; Wang, Chengfeng; Wang, Junwen; Wang, Sophia S.; Weiderpass, Elisabete; Weinstein, Stephanie J.; Wentzensen, Nicolas; Wheeler, William; White, Emily; Wiencke, John K.; Wolk, Alicja; Wolpin, Brian M.; Wong, Maria Pik; Wrensch, Margaret; Wu, Chen; Wu, Tangchun; Wu, Xifeng; Wu, Yi-Long; Wunder, Jay S.; Xiang, Yong-Bing; Xu, Jun; Yang, Hannah P.; Yang, Pan-Chyr; Yatabe, Yasushi; Ye, Yuanqing; Yeboah, Edward D.; Yin, Zhihua; Ying, Chen; Yu, Chong-Jen; Yu, Kai; Yuan, Jian-Min; Zanetti, Krista A.; Zeleniuch-Jacquotte, Anne; Zheng, Wei; Zhou, Baosen; Mirabello, Lisa; Savage, Sharon A.; Kraft, Peter; Chanock, Stephen J.; Yeager, Meredith; Landi, Maria Terese; Shi, Jianxin; Chatterjee, Nilanjan; Amundadottir, Laufey T.

2014-01-01

Genome-wide association studies (GWAS) have mapped risk alleles for at least 10 distinct cancers to a small region of 63 000 bp on chromosome 5p15.33. This region harbors the TERT and CLPTM1L genes; the former encodes the catalytic subunit of telomerase reverse transcriptase and the latter may play a role in apoptosis. To investigate further the genetic architecture of common susceptibility alleles in this region, we conducted an agnostic subset-based meta-analysis (association analysis based on subsets) across six distinct cancers in 34 248 cases and 45 036 controls. Based on sequential conditional analysis, we identified as many as six independent risk loci marked by common single-nucleotide polymorphisms: five in the TERT gene (Region 1: rs7726159, P = 2.10 × 10−39; Region 3: rs2853677, P = 3.30 × 10−36 and PConditional = 2.36 × 10−8; Region 4: rs2736098, P = 3.87 × 10−12 and PConditional = 5.19 × 10−6, Region 5: rs13172201, P = 0.041 and PConditional = 2.04 × 10−6; and Region 6: rs10069690, P = 7.49 × 10−15 and PConditional = 5.35 × 10−7) and one in the neighboring CLPTM1L gene (Region 2: rs451360; P = 1.90 × 10−18 and PConditional = 7.06 × 10−16). Between three and five cancers mapped to each independent locus with both risk-enhancing and protective effects. Allele-specific effects on DNA methylation were seen for a subset of risk loci, indicating that methylation and subsequent effects on gene expression may contribute to the biology of risk variants on 5p15.33. Our results provide strong support for extensive pleiotropy across this region of 5p15.33, to an extent not previously observed in other cancer susceptibility loci. PMID:25027329

Efficacy and safety of flavocoxid compared with naproxen in subjects with osteoarthritis of the knee- a subset analysis.

PubMed

Levy, Robert; Khokhlov, Alexander; Kopenkin, Sergey; Bart, Boris; Ermolova, Tatiana; Kantemirova, Raiasa; Mazurov, Vadim; Bell, Marjorie; Caldron, Paul; Pillai, Lakshmi; Burnett, Bruce

2010-12-01

twice-daily flavocoxid, a cyclooxygenase and 5-lipoxygenase inhibitor with potent antioxidant activity of botanical origin, was evaluated for 12 weeks in a randomized, double-blind, active-comparator study against naproxen in 220 subjects with moderate-severe osteoarthritis (OA) of the knee. As previously reported, both groups noted a significant reduction in the signs and symptoms of OA with no detectable differences in efficacy between the groups when the entire intent-to-treat population was considered. This post-hoc analysis compares the efficacy of flavocoxid to naproxen in different subsets of patients, specifically those related to age, gender, and disease severity as reported at baseline for individual response parameters. in the original randomized, double-blind study, 220 subjects were assigned to receive either flavocoxid (500 mg twice daily) or naproxen (500 mg twice daily) for 12 weeks. In this subgroup analysis, primary outcome measures including the Western Ontario and McMaster Universities OA index and subscales, timed walk, and secondary efficacy variables, including investigator global assessment for disease and global response to treatment, subject visual analog scale for discomfort, overall disease activity, global response to treatment, index joint tenderness and mobility, were evaluated for differing trends between the study groups. subset analyses revealed some statistically significant differences and some notable trends in favor of the flavocoxid group. These trends became stronger the longer the subjects continued on therapy. These observations were specifically noted in older subjects (>60 years), males and in subjects with milder disease, particularly those with lower subject global assessment of disease activity and investigator global assessment for disease and faster walking times at baseline. initial analysis of the entire intent-to-treat population revealed that flavocoxid was as effective as naproxen in managing the signs and symptoms of OA of the knee. Detailed analyses of subject subsets demonstrated distinct trends in favor of flavocoxid for specific groups of subjects.

Lie group classification of first-order delay ordinary differential equations

NASA Astrophysics Data System (ADS)

Dorodnitsyn, Vladimir A.; Kozlov, Roman; Meleshko, Sergey V.; Winternitz, Pavel

2018-05-01

A group classification of first-order delay ordinary differential equations (DODEs) accompanied by an equation for the delay parameter (delay relation) is presented. A subset of such systems (delay ordinary differential systems or DODSs), which consists of linear DODEs and solution-independent delay relations, have infinite-dimensional symmetry algebras—as do nonlinear ones that are linearizable by an invertible transformation of variables. Genuinely nonlinear DODSs have symmetry algebras of dimension n, . It is shown how exact analytical solutions of invariant DODSs can be obtained using symmetry reduction.

Predictive equations for the estimation of body size in seals and sea lions (Carnivora: Pinnipedia)

PubMed Central

Churchill, Morgan; Clementz, Mark T; Kohno, Naoki

2014-01-01

Body size plays an important role in pinniped ecology and life history. However, body size data is often absent for historical, archaeological, and fossil specimens. To estimate the body size of pinnipeds (seals, sea lions, and walruses) for today and the past, we used 14 commonly preserved cranial measurements to develop sets of single variable and multivariate predictive equations for pinniped body mass and total length. Principal components analysis (PCA) was used to test whether separate family specific regressions were more appropriate than single predictive equations for Pinnipedia. The influence of phylogeny was tested with phylogenetic independent contrasts (PIC). The accuracy of these regressions was then assessed using a combination of coefficient of determination, percent prediction error, and standard error of estimation. Three different methods of multivariate analysis were examined: bidirectional stepwise model selection using Akaike information criteria; all-subsets model selection using Bayesian information criteria (BIC); and partial least squares regression. The PCA showed clear discrimination between Otariidae (fur seals and sea lions) and Phocidae (earless seals) for the 14 measurements, indicating the need for family-specific regression equations. The PIC analysis found that phylogeny had a minor influence on relationship between morphological variables and body size. The regressions for total length were more accurate than those for body mass, and equations specific to Otariidae were more accurate than those for Phocidae. Of the three multivariate methods, the all-subsets approach required the fewest number of variables to estimate body size accurately. We then used the single variable predictive equations and the all-subsets approach to estimate the body size of two recently extinct pinniped taxa, the Caribbean monk seal (Monachus tropicalis) and the Japanese sea lion (Zalophus japonicus). Body size estimates using single variable regressions generally under or over-estimated body size; however, the all-subset regression produced body size estimates that were close to historically recorded body length for these two species. This indicates that the all-subset regression equations developed in this study can estimate body size accurately. PMID:24916814

UNCLES: method for the identification of genes differentially consistently co-expressed in a specific subset of datasets.

PubMed

Abu-Jamous, Basel; Fa, Rui; Roberts, David J; Nandi, Asoke K

2015-06-04

Collective analysis of the increasingly emerging gene expression datasets are required. The recently proposed binarisation of consensus partition matrices (Bi-CoPaM) method can combine clustering results from multiple datasets to identify the subsets of genes which are consistently co-expressed in all of the provided datasets in a tuneable manner. However, results validation and parameter setting are issues that complicate the design of such methods. Moreover, although it is a common practice to test methods by application to synthetic datasets, the mathematical models used to synthesise such datasets are usually based on approximations which may not always be sufficiently representative of real datasets. Here, we propose an unsupervised method for the unification of clustering results from multiple datasets using external specifications (UNCLES). This method has the ability to identify the subsets of genes consistently co-expressed in a subset of datasets while being poorly co-expressed in another subset of datasets, and to identify the subsets of genes consistently co-expressed in all given datasets. We also propose the M-N scatter plots validation technique and adopt it to set the parameters of UNCLES, such as the number of clusters, automatically. Additionally, we propose an approach for the synthesis of gene expression datasets using real data profiles in a way which combines the ground-truth-knowledge of synthetic data and the realistic expression values of real data, and therefore overcomes the problem of faithfulness of synthetic expression data modelling. By application to those datasets, we validate UNCLES while comparing it with other conventional clustering methods, and of particular relevance, biclustering methods. We further validate UNCLES by application to a set of 14 real genome-wide yeast datasets as it produces focused clusters that conform well to known biological facts. Furthermore, in-silico-based hypotheses regarding the function of a few previously unknown genes in those focused clusters are drawn. The UNCLES method, the M-N scatter plots technique, and the expression data synthesis approach will have wide application for the comprehensive analysis of genomic and other sources of multiple complex biological datasets. Moreover, the derived in-silico-based biological hypotheses represent subjects for future functional studies.

Circulating B cells in type 1 diabetics exhibit fewer maturation-associated phenotypes.

PubMed

Hanley, Patrick; Sutter, Jennifer A; Goodman, Noah G; Du, Yangzhu; Sekiguchi, Debora R; Meng, Wenzhao; Rickels, Michael R; Naji, Ali; Luning Prak, Eline T

2017-10-01

Although autoantibodies have been used for decades as diagnostic and prognostic markers in type 1 diabetes (T1D), further analysis of developmental abnormalities in B cells could reveal tolerance checkpoint defects that could improve individualized therapy. To evaluate B cell developmental progression in T1D, immunophenotyping was used to classify circulating B cells into transitional, mature naïve, mature activated, and resting memory subsets. Then each subset was analyzed for the expression of additional maturation-associated markers. While the frequencies of B cell subsets did not differ significantly between patients and controls, some T1D subjects exhibited reduced proportions of B cells that expressed transmembrane activator and CAML interactor (TACI) and Fas receptor (FasR). Furthermore, some T1D subjects had B cell subsets with lower frequencies of class switching. These results suggest circulating B cells exhibit variable maturation phenotypes in T1D. These phenotypic variations may correlate with differences in B cell selection in individual T1D patients. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Simian immunodeficiency virus infection induces severe loss of intestinal central memory T cells which impairs CD4+ T-cell restoration during antiretroviral therapy.

PubMed

Verhoeven, D; Sankaran, S; Dandekar, S

2007-08-01

Simian immunodeficiency virus (SIV) infection leads to severe loss of intestinal CD4(+) T cells and, as compared to peripheral blood, restoration of these cells is slow during antiretroviral therapy (ART). Mechanisms for this delay have not been examined in context of which specific CD4(+) memory subsets or lost and fail to regenerate during ART. Fifteen rhesus macaques were infected with SIV, five of which received ART (FTC/PMPA) for 30 weeks. Viral loads were measured by real-time PCR. Flow cytometric analysis determined changes in T-cell subsets and their proliferative state. Changes in proliferative CD4(+) memory subsets during infection accelerated their depletion. This reduced the central memory CD4(+) T-cell pool and contributed to slow CD4(+) T-cell restoration during ART. There was a lack of restoration of the CD4(+) central memory and effector memory T-cell subsets in gut-associated lymphoid tissue during ART, which may contribute to the altered intestinal T-cell homeostasis in SIV infection.

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

PubMed

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

1986-01-01

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

Geospatial Analysis of Food Environment Demonstrates Associations with Gestational Diabetes

PubMed Central

KAHR, Maike K.; SUTER, Melissa A.; BALLAS, Jerasimos; RAMIN, Susan M.; MONGA, Manju; LEE, Wesley; HU, Min; SHOPE, Cindy D.; CHESNOKOVA, Arina; KRANNICH, Laura; GRIFFIN, Emily N.; MASTROBATTISTA, Joan; DILDY, Gary A.; STREHLOW, Stacy L.; RAMPHUL, Ryan; HAMILTON, Winifred J; AAGAARD, Kjersti M.

2015-01-01

Background Gestational diabetes mellitus (GDM) is one of most common complications of pregnancy, with incidence rates varying by maternal age, race/ethnicity, obesity, parity, and family history. Given its increasing prevalence in recent decades, co-variant environmental and sociodemographic factors may be additional determinants of GDM occurrence. Objectives We hypothesized that environmental risk factors, in particular measures of the food environment, may be a diabetes contributor. We employed geospatial modeling in a populous U.S. county to characterize the association of the relative availability of fast food restaurants and supermarkets to GDM. Study Design Utilizing a perinatal database with over 4900 encoded antenatal and outcome variables inclusive of zip code data, 8912 consecutive pregnancies were analyzed for correlations between GDM and food environment based on county-wide food permit registration data. Linkage between pregnancies and food environment was achieved on the basis of validated 5 digit zip code data. The prevalence of supermarkets and fast food restaurants per 100,000 inhabitants for each zip code were gathered from publicly available food permit sources. In order to independently authenticate our findings with objective data, we measured hemoglobin A1c (HbA1c) levels as a function of geospatial distribution of food environment in a matched subset (n=80). Results Residence in neighborhoods with a high prevalence of fast food restaurants (fourth quartile) was significantly associated with an increased risk of developing GDM (relative to first quartile, aOR: 1.63 [95% CI 1.21–2.19]). In multivariate analysis, this association held true after controlling for potential confounders (p=0.002). Measurement of HbA1c levels in a matched subset were significantly increased in association with residence in a zip code with a higher fast food/supermarket ratio (n=80, r=0.251 p<0.05). Conclusions As demonstrated by geospatial analysis, a relationship of food environment and risk for gestational diabetes was identified. PMID:26319053

Genome-wide SNP discovery and population structure analysis in pepper (Capsicum annuum) using genotyping by sequencing.

PubMed

Taranto, F; D'Agostino, N; Greco, B; Cardi, T; Tripodi, P

2016-11-21

Knowledge on population structure and genetic diversity in vegetable crops is essential for association mapping studies and genomic selection. Genotyping by sequencing (GBS) represents an innovative method for large scale SNP detection and genotyping of genetic resources. Herein we used the GBS approach for the genome-wide identification of SNPs in a collection of Capsicum spp. accessions and for the assessment of the level of genetic diversity in a subset of 222 cultivated pepper (Capsicum annum) genotypes. GBS analysis generated a total of 7,568,894 master tags, of which 43.4% uniquely aligned to the reference genome CM334. A total of 108,591 SNP markers were identified, of which 105,184 were in C. annuum accessions. In order to explore the genetic diversity of C. annuum and to select a minimal core set representing most of the total genetic variation with minimum redundancy, a subset of 222 C. annuum accessions were analysed using 32,950 high quality SNPs. Based on Bayesian and Hierarchical clustering it was possible to divide the collection into three clusters. Cluster I had the majority of varieties and landraces mainly from Southern and Northern Italy, and from Eastern Europe, whereas clusters II and III comprised accessions of different geographical origins. Considering the genome-wide genetic variation among the accessions included in cluster I, a second round of Bayesian (K = 3) and Hierarchical (K = 2) clustering was performed. These analysis showed that genotypes were grouped not only based on geographical origin, but also on fruit-related features. GBS data has proven useful to assess the genetic diversity in a collection of C. annuum accessions. The high number of SNP markers, uniformly distributed on the 12 chromosomes, allowed the accessions to be distinguished according to geographical origin and fruit-related features. SNP markers and information on population structure developed in this study will undoubtedly support genome-wide association mapping studies and marker-assisted selection programs.

[Changes of monocyte and monocyte-platelet aggregates in different subgroups of thrombotic events in patients with acute myocardial infarction during PCI].

PubMed

Wang, Sheng; Sun, Cuifang; Liao, Wang; Wu, Zhongwei; Wang, Yudai; Huang, Xiuxian; Lu, Sijia; Dong, Xiaoli; Shuai, Fujie; Li, Bin

2017-07-01

Objective To investigate the impact of thrombotic events on the alterations of monocyte and monocyte-platelet aggregates (MPAs) in patients with acute myocardial infarction (AMI) during percutaneous coronary intervention (PCI). Methods Blood was collected before PCI for flow cytometry. Monocyte subsets and MPAs were detected by four-color platform (CDl4-APC, CDl6-PE-Cy7, CD86-PE and CD41-Alexa Fluor R 488). According to the expression of the platelet surface marker CD41, the number of monocyte subsets and MPAs was analyzed using the fluorescent microspheres of absolute counting tube. The Wilcoxon rank sum test and receiver operating characteristic (ROC) curve analysis were performed. Results CD14 + CD16 ++ monocytes in intraprocedural thrombotic events (IPTE) group were significantly fewer than those in non-IPTE group, and the percentage in total mononuclear cells decreased. Compared with non-IPTE group, MPA binding ratio and monocyte subset MPA binding ratio were significantly higher in IPTE group. ROC analysis showed that MPA binding ratio and subgroup MPA binding ratio had a better predictive value for IPTE in patients with AMI. Conclusion The CD14 + CD16 ++ monocytes in IPTE group were significantly fewer than those in the non-IPTE group. MPA binding ratio and MPA binding ratio of monocyte subsets were significantly higher in the IPTE group than in the non-IPTE group, so they have a good predictive value for IPTE in patients with AMI.

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

PubMed Central

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

2008-01-01

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

Creating a non-linear total sediment load formula using polynomial best subset regression model

NASA Astrophysics Data System (ADS)

Okcu, Davut; Pektas, Ali Osman; Uyumaz, Ali

2016-08-01

The aim of this study is to derive a new total sediment load formula which is more accurate and which has less application constraints than the well-known formulae of the literature. 5 most known stream power concept sediment formulae which are approved by ASCE are used for benchmarking on a wide range of datasets that includes both field and flume (lab) observations. The dimensionless parameters of these widely used formulae are used as inputs in a new regression approach. The new approach is called Polynomial Best subset regression (PBSR) analysis. The aim of the PBRS analysis is fitting and testing all possible combinations of the input variables and selecting the best subset. Whole the input variables with their second and third powers are included in the regression to test the possible relation between the explanatory variables and the dependent variable. While selecting the best subset a multistep approach is used that depends on significance values and also the multicollinearity degrees of inputs. The new formula is compared to others in a holdout dataset and detailed performance investigations are conducted for field and lab datasets within this holdout data. Different goodness of fit statistics are used as they represent different perspectives of the model accuracy. After the detailed comparisons are carried out we figured out the most accurate equation that is also applicable on both flume and river data. Especially, on field dataset the prediction performance of the proposed formula outperformed the benchmark formulations.

Finding high-order analytic post-Newtonian parameters from a high-precision numerical self-force calculation

NASA Astrophysics Data System (ADS)

Shah, Abhay G.; Friedman, John L.; Whiting, Bernard F.

2014-03-01

We present a novel analytic extraction of high-order post-Newtonian (pN) parameters that govern quasicircular binary systems. Coefficients in the pN expansion of the energy of a binary system can be found from corresponding coefficients in an extreme-mass-ratio inspiral computation of the change ΔU in the redshift factor of a circular orbit at fixed angular velocity. Remarkably, by computing this essentially gauge-invariant quantity to accuracy greater than one part in 10225, and by assuming that a subset of pN coefficients are rational numbers or products of π and a rational, we obtain the exact analytic coefficients. We find the previously unexpected result that the post-Newtonian expansion of ΔU (and of the change ΔΩ in the angular velocity at fixed redshift factor) have conservative terms at half-integral pN order beginning with a 5.5 pN term. This implies the existence of a corresponding 5.5 pN term in the expansion of the energy of a binary system. Coefficients in the pN series that do not belong to the subset just described are obtained to accuracy better than 1 part in 10265-23n at nth pN order. We work in a radiation gauge, finding the radiative part of the metric perturbation from the gauge-invariant Weyl scalar ψ0 via a Hertz potential. We use mode-sum renormalization, and find high-order renormalization coefficients by matching a series in L=ℓ+1/2 to the large-L behavior of the expression for ΔU. The nonradiative parts of the perturbed metric associated with changes in mass and angular momentum are calculated in the Schwarzschild gauge.

Mediating Effects of Patients' Stigma and Self-Efficacy on Relationships Between Doctors' Empathy Abilities and Patients' Cellular Immunity in Male Breast Cancer Patients.

PubMed

Yang, Ningxi; Cao, Yingnan; Li, Xiaoyan; Li, Shiyue; Yan, Hong; Geng, Qingshan

2018-06-12

BACKGROUND Doctors' empathy is closely related to patients' health. This study aimed to examine whether patients' stigma and self-efficacy play a mediating role in the relationship between doctors' empathy abilities and patients' cellular immunity in male patients with breast cancer. MATERIAL AND METHODS Doctors' empathy scores and patients' demographic data, disease condition, stigma, and self-efficacy were measured. Patient T cell subset was tested at admission and 3 months after the operation and was compared by paired t test. The multivariate linear regression model was applied to analyze the factors influencing the immune index. Pearson correlation analysis and structural equation modeling were applied to explore the relationships among patients' stigma, self-efficacy, and cellular immunity and doctors' empathy abilities. RESULTS At the 2 time points, only the change in NK subset was statistically significant, while the changes in percentage of CD3+, CD4+, CD8+, and B cells were not statistically significant. The doctors' empathy abilities were negatively correlated with patients' stigma and were positively related to patients' self-efficacy. Patients' stigma was negatively related to NK subset, while self-efficacy was positively associated with NK subset. Patients' stigma and self-efficacy played a mediating role in the relationship between doctors' empathy abilities and patients' NK subset, and stigma had a stronger effect than self-efficacy. CONCLUSIONS Doctors' empathy abilities affected breast cancer patients' NK subset through their stigma and self-efficacy. The mental health of male breast cancer patients need more attention and empathy education needs to be improved.

Support for the existence of invertible maps between electronic densities and non-analytic 1-body external potentials in non-relativistic time-dependent quantum mechanics

NASA Astrophysics Data System (ADS)

Mosquera, Martín A.

2017-10-01

Provided the initial state, the Runge-Gross theorem establishes that the time-dependent (TD) external potential of a system of non-relativistic electrons determines uniquely their TD electronic density, and vice versa (up to a constant in the potential). This theorem requires the TD external potential and density to be Taylor-expandable around the initial time of the propagation. This paper presents an extension without this restriction. Given the initial state of the system and evolution of the density due to some TD scalar potential, we show that a perturbative (not necessarily weak) TD potential that induces a non-zero divergence of the external force-density, inside a small spatial subset and immediately after the initial propagation time, will cause a change in the density within that subset, implying that the TD potential uniquely determines the TD density. In this proof, we assume unitary evolution of wavefunctions and first-order differentiability (which does not imply analyticity) in time of the internal and external force-densities, electronic density, current density, and their spatial derivatives over the small spatial subset and short time interval.

A Parameter Subset Selection Algorithm for Mixed-Effects Models

DOE PAGES

Schmidt, Kathleen L.; Smith, Ralph C.

2016-01-01

Mixed-effects models are commonly used to statistically model phenomena that include attributes associated with a population or general underlying mechanism as well as effects specific to individuals or components of the general mechanism. This can include individual effects associated with data from multiple experiments. However, the parameterizations used to incorporate the population and individual effects are often unidentifiable in the sense that parameters are not uniquely specified by the data. As a result, the current literature focuses on model selection, by which insensitive parameters are fixed or removed from the model. Model selection methods that employ information criteria are applicablemore » to both linear and nonlinear mixed-effects models, but such techniques are limited in that they are computationally prohibitive for large problems due to the number of possible models that must be tested. To limit the scope of possible models for model selection via information criteria, we introduce a parameter subset selection (PSS) algorithm for mixed-effects models, which orders the parameters by their significance. In conclusion, we provide examples to verify the effectiveness of the PSS algorithm and to test the performance of mixed-effects model selection that makes use of parameter subset selection.« less

Multivariate Cluster Analysis.

ERIC Educational Resources Information Center

McRae, Douglas J.

Procedures for grouping students into homogeneous subsets have long interested educational researchers. The research reported in this paper is an investigation of a set of objective grouping procedures based on multivariate analysis considerations. Four multivariate functions that might serve as criteria for adequate grouping are given and…

Automation and Preclinical Evaluation of a Dedicated Emission Mammotomography System for Fully 3-D Molecular Breast Imaging

DTIC Science & Technology

2008-10-01

concentrated aqueous 99m Tc and taped to the exterior surface of the breast phantom to act as fiducial markers for registration purposes. Two...34 Physica Medica, vol. 21, pp. 48-55, 2006. [16] H. Erdogan and J. A. Fessler, "Ordered subsets algorithms for transmission tomography," Phys Med Biol

Keeping the Teacher at Arm's Length: Student Resistance in Writing Conferences in Two High School Classrooms

ERIC Educational Resources Information Center

Consalvo, Annamary; Maloch, Beth

2015-01-01

The purpose of this paper is to explore a subset of findings taken from yearlong qualitative study of writing conferences in two diversely populated, urban high school classrooms. Drawing on multiple data sources, we used case study and discourse analytic methods to follow two focal students across the year in order to examine instructional and…

Concentration of the L{sub 1}-norm of trigonometric polynomials and entire functions

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

Malykhin, Yu V; Ryutin, K S

2014-11-30

For any sufficiently large n, the minimal measure of a subset of [−π,π] on which some nonzero trigonometric polynomial of order ≤n gains half of the L{sub 1}-norm is shown to be π/(n+1). A similar result for entire functions of exponential type is established. Bibliography: 13 titles.

Inside the Black Box of School Reform: Explaining the How and Why of Change at "Getting Results" Schools

ERIC Educational Resources Information Center

McDougall, Dennis; Saunders, William M.; Goldenberg, Claude

2007-01-01

This article reports key findings from a process-focused external evaluation that compared a subset of "Getting Results" project schools and comparison schools in order to understand the dynamics of school-wide reform efforts at these primary schools. Findings shed light on the "black box" of school reform and illuminate the…

Prioritizing molecular markers to test for in the initial workup of advanced non-small cell lung cancer: wants versus needs.

PubMed

West, Howard

2017-09-01

The current standard of care for molecular marker testing in patients with advanced non-small cell lung cancer (NSCLC) has been evolving over several years and is a product of the quality of the evidence supporting a targeted therapy for a specific molecular marker, the pre-test probability of that marker in the population, and the magnitude of benefit seen with that treatment. Among the markers that have one or more matched targeted therapies, only a few are in the subset for which they should be considered as most clearly worthy of prioritizing to detect in the first line setting in order to have them supplant other first line alternatives, and in only a subset of patients, as defined currently by NSCLC histology. Specifically, this currently includes testing for an activating epidermal growth factor receptor ( EGFR ) mutation or an anaplastic lymphoma kinase ( ALK ) or ROS1 rearrangement. This article reviews the history and data supporting the prioritization of these markers in patients with non-squamous NSCLC, a histologically selected population in whom the probability of these markers combined with the anticipated efficacy of targeted therapies against them is high enough to favor these treatments in the first line setting. In reviewing the evidence supporting this very limited core subset of most valuable molecular markers to detect in the initial workup of such patients, we can also see the criteria by which other actionable markers need to reach in order to be widely recognized as reliably valuable enough to warrant prioritization to detect in the initial workup of advanced NSCLC as well.

Microcomputer package for statistical analysis of microbial populations.

PubMed

Lacroix, J M; Lavoie, M C

1987-11-01

We have developed a Pascal system to compare microbial populations from different ecological sites using microcomputers. The values calculated are: the coverage value and its standard error, the minimum similarity and the geometric similarity between two biological samples, and the Lambda test consisting of calculating the ratio of the mean similarity between two subsets by the mean similarity within subsets. This system is written for Apple II, IBM or compatible computers, but it can work for any computer which can use CP/M, if the programs are recompiled for such a system.

Theoretical analysis on the measurement errors of local 2D DIC: Part I temporal and spatial uncertainty quantification of displacement measurements

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

Wang, Yueqi; Lava, Pascal; Reu, Phillip

This study presents a theoretical uncertainty quantification of displacement measurements by subset-based 2D-digital image correlation. A generalized solution to estimate the random error of displacement measurement is presented. The obtained solution suggests that the random error of displacement measurements is determined by the image noise, the summation of the intensity gradient in a subset, the subpixel part of displacement, and the interpolation scheme. The proposed method is validated with virtual digital image correlation tests.

Theoretical analysis on the measurement errors of local 2D DIC: Part I temporal and spatial uncertainty quantification of displacement measurements

DOE PAGES

Wang, Yueqi; Lava, Pascal; Reu, Phillip; ...

2015-12-23

This study presents a theoretical uncertainty quantification of displacement measurements by subset-based 2D-digital image correlation. A generalized solution to estimate the random error of displacement measurement is presented. The obtained solution suggests that the random error of displacement measurements is determined by the image noise, the summation of the intensity gradient in a subset, the subpixel part of displacement, and the interpolation scheme. The proposed method is validated with virtual digital image correlation tests.

Clinical effect of stereotyped B-cell receptor immunoglobulins in chronic lymphocytic leukaemia: a retrospective multicentre study.

PubMed

Baliakas, Panagiotis; Hadzidimitriou, Anastasia; Sutton, Lesley-Ann; Minga, Eva; Agathangelidis, Andreas; Nichelatti, Michele; Tsanousa, Athina; Scarfò, Lydia; Davis, Zadie; Yan, Xiao-Jie; Shanafelt, Tait; Plevova, Karla; Sandberg, Yorick; Vojdeman, Fie Juhl; Boudjogra, Myriam; Tzenou, Tatiana; Chatzouli, Maria; Chu, Charles C; Veronese, Silvio; Gardiner, Anne; Mansouri, Larry; Smedby, Karin E; Pedersen, Lone Bredo; van Lom, Kirsten; Giudicelli, Véronique; Francova, Hana Skuhrova; Nguyen-Khac, Florence; Panagiotidis, Panagiotis; Juliusson, Gunnar; Angelis, Lefteris; Anagnostopoulos, Achilles; Lefranc, Marie-Paule; Facco, Monica; Trentin, Livio; Catherwood, Mark; Montillo, Marco; Geisler, Christian H; Langerak, Anton W; Pospisilova, Sarka; Chiorazzi, Nicholas; Oscier, David; Jelinek, Diane F; Darzentas, Nikos; Belessi, Chrysoula; Davi, Frederic; Rosenquist, Richard; Ghia, Paolo; Stamatopoulos, Kostas

2014-11-01

About 30% of cases of chronic lymphocytic leukaemia (CLL) carry quasi-identical B-cell receptor immunoglobulins and can be assigned to distinct stereotyped subsets. Although preliminary evidence suggests that B-cell receptor immunoglobulin stereotypy is relevant from a clinical viewpoint, this aspect has never been explored in a systematic manner or in a cohort of adequate size that would enable clinical conclusions to be drawn. For this retrospective, multicentre study, we analysed 8593 patients with CLL for whom immunogenetic data were available. These patients were followed up in 15 academic institutions throughout Europe (in Czech Republic, Denmark, France, Greece, Italy, Netherlands, Sweden, and the UK) and the USA, and data were collected between June 1, 2012, and June 7, 2013. We retrospectively assessed the clinical implications of CLL B-cell receptor immunoglobulin stereotypy, with a particular focus on 14 major stereotyped subsets comprising cases expressing unmutated (U-CLL) or mutated (M-CLL) immunoglobulin heavy chain variable genes. The primary outcome of our analysis was time to first treatment, defined as the time between diagnosis and date of first treatment. 2878 patients were assigned to a stereotyped subset, of which 1122 patients belonged to one of 14 major subsets. Stereotyped subsets showed significant differences in terms of age, sex, disease burden at diagnosis, CD38 expression, and cytogenetic aberrations of prognostic significance. Patients within a specific subset generally followed the same clinical course, whereas patients in different stereotyped subsets-despite having the same immunoglobulin heavy variable gene and displaying similar immunoglobulin mutational status-showed substantially different times to first treatment. By integrating B-cell receptor immunoglobulin stereotypy (for subsets 1, 2, and 4) into the well established Döhner cytogenetic prognostic model, we showed these, which collectively account for around 7% of all cases of CLL and represent both U-CLL and M-CLL, constituted separate clinical entities, ranging from very indolent (subset 4) to aggressive disease (subsets 1 and 2). The molecular classification of chronic lymphocytic leukaemia based on B-cell receptor immunoglobulin stereotypy improves the Döhner hierarchical model and refines prognostication beyond immunoglobulin mutational status, with potential implications for clinical decision making, especially within prospective clinical trials. European Union; General Secretariat for Research and Technology of Greece; AIRC; Italian Ministry of Health; AIRC Regional Project with Fondazione CARIPARO and CARIVERONA; Regione Veneto on Chronic Lymphocytic Leukemia; Nordic Cancer Union; Swedish Cancer Society; Swedish Research Council; and National Cancer Institute (NIH). Copyright © 2014 Elsevier Ltd. All rights reserved.

Dynamic graphs, community detection, and Riemannian geometry

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

Bakker, Craig; Halappanavar, Mahantesh; Visweswara Sathanur, Arun

A community is a subset of a wider network where the members of that subset are more strongly connected to each other than they are to the rest of the network. In this paper, we consider the problem of identifying and tracking communities in graphs that change over time {dynamic community detection} and present a framework based on Riemannian geometry to aid in this task. Our framework currently supports several important operations such as interpolating between and averaging over graph snapshots. We compare these Riemannian methods with entry-wise linear interpolation and that the Riemannian methods are generally better suited tomore » dynamic community detection. Next steps with the Riemannian framework include developing higher-order interpolation methods (e.g. the analogues of polynomial and spline interpolation) and a Riemannian least-squares regression method for working with noisy data.« less

Global uniqueness in an inverse problem for time fractional diffusion equations

NASA Astrophysics Data System (ADS)

Kian, Y.; Oksanen, L.; Soccorsi, E.; Yamamoto, M.

2018-01-01

Given (M , g), a compact connected Riemannian manifold of dimension d ⩾ 2, with boundary ∂M, we consider an initial boundary value problem for a fractional diffusion equation on (0 , T) × M, T > 0, with time-fractional Caputo derivative of order α ∈ (0 , 1) ∪ (1 , 2). We prove uniqueness in the inverse problem of determining the smooth manifold (M , g) (up to an isometry), and various time-independent smooth coefficients appearing in this equation, from measurements of the solutions on a subset of ∂M at fixed time. In the "flat" case where M is a compact subset of Rd, two out the three coefficients ρ (density), a (conductivity) and q (potential) appearing in the equation ρ ∂tα u - div (a∇u) + qu = 0 on (0 , T) × M are recovered simultaneously.

Upper bounds on sequential decoding performance parameters

NASA Technical Reports Server (NTRS)

Jelinek, F.

1974-01-01

This paper presents the best obtainable random coding and expurgated upper bounds on the probabilities of undetectable error, of t-order failure (advance to depth t into an incorrect subset), and of likelihood rise in the incorrect subset, applicable to sequential decoding when the metric bias G is arbitrary. Upper bounds on the Pareto exponent are also presented. The G-values optimizing each of the parameters of interest are determined, and are shown to lie in intervals that in general have nonzero widths. The G-optimal expurgated bound on undetectable error is shown to agree with that for maximum likelihood decoding of convolutional codes, and that on failure agrees with the block code expurgated bound. Included are curves evaluating the bounds for interesting choices of G and SNR for a binary-input quantized-output Gaussian additive noise channel.

Evaluation of a Post-Processing Approach for Multiscale Analysis of Biphasic Mechanics of Chondrocytes

PubMed Central

Sibole, Scott C.; Maas, Steve; Halloran, Jason P.; Weiss, Jeffrey A.; Erdemir, Ahmet

2014-01-01

Understanding the mechanical behavior of chondrocytes as a result of cartilage tissue mechanics has significant implications for both evaluation of mechanobiological function and to elaborate on damage mechanisms. A common procedure for prediction of chondrocyte mechanics (and of cell mechanics in general) relies on a computational post-processing approach where tissue level deformations drive cell level models. Potential loss of information in this numerical coupling approach may cause erroneous cellular scale results, particularly during multiphysics analysis of cartilage. The goal of this study was to evaluate the capacity of 1st and 2nd order data passing to predict chondrocyte mechanics by analyzing cartilage deformations obtained for varying complexity of loading scenarios. A tissue scale model with a sub-region incorporating representation of chondron size and distribution served as control. The postprocessing approach first required solution of a homogeneous tissue level model, results of which were used to drive a separate cell level model (same characteristics as the subregion of control model). The 1st data passing appeared to be adequate for simplified loading of the cartilage and for a subset of cell deformation metrics, e.g., change in aspect ratio. The 2nd order data passing scheme was more accurate, particularly when asymmetric permeability of the tissue boundaries were considered. Yet, the method exhibited limitations for predictions of instantaneous metrics related to the fluid phase, e.g., mass exchange rate. Nonetheless, employing higher-order data exchange schemes may be necessary to understand the biphasic mechanics of cells under lifelike tissue loading states for the whole time history of the simulation. PMID:23809004

Isolation of mouse pancreatic alpha, beta, duct and acinar populations with cell surface markers.

PubMed

Dorrell, Craig; Grompe, Maria T; Pan, Fong Cheng; Zhong, Yongping; Canaday, Pamela S; Shultz, Leonard D; Greiner, Dale L; Wright, Chris V; Streeter, Philip R; Grompe, Markus

2011-06-06

Tools permitting the isolation of live pancreatic cell subsets for culture and/or molecular analysis are limited. To address this, we developed a collection of monoclonal antibodies with selective surface labeling of endocrine and exocrine pancreatic cell types. Cell type labeling specificity and cell surface reactivity were validated on mouse pancreatic sections and by gene expression analysis of cells isolated using FACS. Five antibodies which marked populations of particular interest were used to isolate and study viable populations of purified pancreatic ducts, acinar cells, and subsets of acinar cells from whole pancreatic tissue or of alpha or beta cells from isolated mouse islets. Gene expression analysis showed the presence of known endocrine markers in alpha and beta cell populations and revealed that TTR and DPPIV are primarily expressed in alpha cells whereas DGKB and GPM6A have a beta cell specific expression profile. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Correlation of solar wind parameters with Pc5 activity at all local times.

NASA Astrophysics Data System (ADS)

Baker, G. J.; Donovan, E. F.; Jackel, B. J.

2001-12-01

Using ten years of data from the CANOPUS Churchill line of magnetometers, we investigate the statistical properties of Pc5 pulsations, and the band-limited spectral power in the Pc5 frequency range (ie., 1.7-6.7 mHz). In order to determine the band-limited Pc5 power, we apodize with a 45 minute Hanning window, and detrend the data with the best-fit second order polynomial. For each station, we slide the window along in one minute increments, producing time series of absolute power measurements at one minute intervals. In addition, Pc5 pulsations were identified by eye for six of the seven Churchill line stations. Our criterion for classifying a magnetic perturbation as a Pc5 pulsation was that it was nearly monochromatic, and its amplitude did not decrease over at least four periods. Applying this criterion guarantees that the relative power in the Pc5 band is high. We then have a complete data set of Pc5 powers, and a subset corresponding to times when there were Pc5 pulsations present according to our classification. Initial results show the well known correlation between solar wind speed (IMP 8 one hour averages obtained via OMNIWEB) and Pc5 power. For example, for magnetic local times between 0600 and 1000, we obtain correlation coefficients between the logarithm of the band-limited power and the solar wind speed of 0.72 and 0.77, for the case of the entire data set, and the subset, respectively. In this paper, we present results of multivariate analysis of the Pc5 data base and solar wind data, designed to elucidate correlations at all local times. We discuss our results within the context of earlier studies by Engerbretson et al. [JGR, volume 103, 26721-26283, 1998] and Vennerstrom [JGR, volume 104, 10145-10157, 1999].

Molecular Analysis of Non-Small Cell Lung Cancer (NSCLC) Identifies Subsets with Different Sensitivity to Insulin like Growth Factor I Receptor (IGF-IR) Inhibition

PubMed Central

Gualberto, Antonio; Dolled-Filhart, Marisa; Gustavson, Mark; Christiansen, Jason; Wang, Yu-Fen; Hixon, Mary L.; Reynolds, Jennifer; McDonald, Sandra; Ang, Agnes; Rimm, David L.; Langer, Corey J.; Blakely, Johnetta; Garland, Linda; Paz-Ares, Luis G.; Karp, Daniel D.; Lee, Adrian V.

2010-01-01

Purpose Identify molecular determinants of sensitivity of NSCLC to anti-insulin like growth factor receptor (IGF-IR) therapy. Experimental Design 216 tumor samples were investigated. 165 consisted of retrospective analyses of banked tissue and an additional 51 were from patients enrolled in a phase 2 study of figitumumab (F), a monoclonal antibody against the IGF-IR, in stage IIIb/IV NSCLC. Biomarkers assessed included IGF-IR, EGFR, IGF-2, IGF-2R, IRS-1, IRS-2, vimentin and E-cadherin. Sub-cellular localization of IRS-1 and phosphorylation levels of MAPK and Akt1 were also analyzed. Results IGF-IR was differentially expressed across histological subtypes (P=0.04), with highest levels observed in squamous cell tumors. Elevated IGF-IR expression was also observed in a small number of squamous cell tumors responding to chemotherapy combined with F (p=0.008). Since no other biomarker/response interaction was observed using classical histological sub-typing, a molecular approach was undertaken to segment NSCLC into mechanism-based subpopulations. Principal component analysis and unsupervised Bayesian clustering identified 3 NSCLC subsets that resembled the steps of the epithelial-to-mesenchymal transition: E-cadherin high/IRS-1 low (Epithelial-like), E-cadherin intermediate/IRS-1 high (Transitional) and E-cadherin low/IRS-1 low (Mesenchymal-like). Several markers of the IGF-IR pathway were over-expressed in the Transitional subset. Furthermore, a higher response rate to the combination of chemotherapy and F was observed in Transitional tumors (71%) compared to those in the Mesenchymal-like subset (32%, p=0.03). Only one Epithelial-like tumor was identified in the phase 2 study, suggesting that advanced NSCLC has undergone significant de-differentiation at diagnosis. Conclusion NSCLC comprises molecular subsets with differential sensitivity to IGF-IR inhibition. PMID:20670944

Orthotopic AY-27 rat bladder urothelial cell carcinoma model presented an elevated methemoglobin proportion in the increased total hemoglobin content when evaluated in vivo by single-fiber reflectance spectroscopy

NASA Astrophysics Data System (ADS)

Sun, Tengfei; Davis, Carole A.; Hurst, Robert E.; Slaton, Joel W.; Piao, Daqing

2017-02-01

In vivo single-fiber reflectance spectroscopy (SfRS) was performed on an orthotopic AY-27 rat bladder urothelial cell carcinoma model to explore potential spectroscopic features revealing neoplastic changes. AY-27 bladder tumor cells were intravesically instilled in four rats and allowed to implant and grow for one week, with two additional rats as the control. A total of 107 SfRS measurements were taken from 27 sites on two control bladders and 80 from four AY-27 treated bladders. The spectral profiles obtained from AY-27 treated bladders revealed various levels of a methemoglobin (MetHb) characteristic spectral feature around 635nm. A multisegment spectral analysis method estimated concentrations of five chromophore compositions including oxyhemoglobin, deoxyhemoglobin, MetHb, lipid and water. The total hemoglobin concentration ([HbT]), the MetHb proportion in the total hemoglobin and the lipid volume content showed possible correlations. The 80 measurements from the AY-27 treated bladders could separate to three sub-sets according to the MetHb proportion. Specifically, 72 were in subset 1 with low proportion (5.3%<[MetHb]<7%), 6 in subset 2 with moderate proportion (7%<[MetHb]<30%), and 2 in subset 3 with significant proportion (>30%). When grouped according to [MetHB], the [HbT] increased from 368 μM of subset 1 to 488 μM of subset 2 to 541 μM of subset 3, in comparison to the 285 μM of the control. The increased total hemoglobin and the elevation of MetHb proportion may signify angiogenesis and degradation in hemoglobin oxygen-transport. Additionally, the lipid volume content decreased from 2.58% in the control to <0.2% in the tumor groups, indicating disruption of subepithelium tissue architecture.

Discovering biclusters in gene expression data based on high-dimensional linear geometries

PubMed Central

Gan, Xiangchao; Liew, Alan Wee-Chung; Yan, Hong

2008-01-01

Background In DNA microarray experiments, discovering groups of genes that share similar transcriptional characteristics is instrumental in functional annotation, tissue classification and motif identification. However, in many situations a subset of genes only exhibits consistent pattern over a subset of conditions. Conventional clustering algorithms that deal with the entire row or column in an expression matrix would therefore fail to detect these useful patterns in the data. Recently, biclustering has been proposed to detect a subset of genes exhibiting consistent pattern over a subset of conditions. However, most existing biclustering algorithms are based on searching for sub-matrices within a data matrix by optimizing certain heuristically defined merit functions. Moreover, most of these algorithms can only detect a restricted set of bicluster patterns. Results In this paper, we present a novel geometric perspective for the biclustering problem. The biclustering process is interpreted as the detection of linear geometries in a high dimensional data space. Such a new perspective views biclusters with different patterns as hyperplanes in a high dimensional space, and allows us to handle different types of linear patterns simultaneously by matching a specific set of linear geometries. This geometric viewpoint also inspires us to propose a generic bicluster pattern, i.e. the linear coherent model that unifies the seemingly incompatible additive and multiplicative bicluster models. As a particular realization of our framework, we have implemented a Hough transform-based hyperplane detection algorithm. The experimental results on human lymphoma gene expression dataset show that our algorithm can find biologically significant subsets of genes. Conclusion We have proposed a novel geometric interpretation of the biclustering problem. We have shown that many common types of bicluster are just different spatial arrangements of hyperplanes in a high dimensional data space. An implementation of the geometric framework using the Fast Hough transform for hyperplane detection can be used to discover biologically significant subsets of genes under subsets of conditions for microarray data analysis. PMID:18433477

Characterization of human invariant natural killer T subsets in health and disease using a novel invariant natural killer T cell-clonotypic monoclonal antibody, 6B11.

PubMed

Montoya, Carlos J; Pollard, David; Martinson, Jeffrey; Kumari, Kumud; Wasserfall, Clive; Mulder, Candice B; Rugeles, Maria T; Atkinson, Mark A; Landay, Alan L; Wilson, S Brian

2007-09-01

Identification of human CD1d-restricted T-cell receptor (TCR)-invariant natural killer T (iNKT) cells has been dependent on utilizing combinations of monoclonal antibodies or CD1d tetramers, which do not allow for the most specific analysis of this T-cell subpopulation. A novel monoclonal antibody (clone 6B11), specific for the invariant CDR3 loop of human canonical Valpha24Jalpha18 TCR alpha chain, was developed and used to specifically characterize iNKT cells. In healthy individuals studied for up to 1 year, a wide but stable frequency of circulating iNKT cells (range: 0.01-0.92%) was observed, with no differences in frequency by gender. Four stable iNKT cell subsets were characterized in peripheral blood based on the expression of CD4 and CD8, with CD8(+) iNKT cells being a phenotypic and functionally different subset from CD4(+) and double negative iNKT cells; in particular, LAG-3 was preferentially expressed on CD8(+) iNKT cells. In addition, a strong negative linear correlation between the frequency of total iNKT cells and percentage of the CD4(+) subset was observed. In terms of their potential association with disease, patients at risk for type 1 diabetes had significantly expanded frequencies of double negative iNKT cells when compared to matched controls and first-degree relatives. Moreover, peripheral blood CD4(+) iNKT cells were the highest producers of interleukin-4, while the production of interferon-gamma and tumour necrosis factor-alpha was similar amongst all iNKT cell subsets. These differences in iNKT cell subsets suggest that in humans the relative ratio of iNKT cell subsets may influence susceptibility vs. resistance to immune-mediated diseases.

Characterization of human invariant natural killer T subsets in health and disease using a novel invariant natural killer T cell-clonotypic monoclonal antibody, 6B11

PubMed Central

Montoya, Carlos J; Pollard, David; Martinson, Jeffrey; Kumari, Kumud; Wasserfall, Clive; Mulder, Candice B; Rugeles, Maria T; Atkinson, Mark A; Landay, Alan L; Wilson, S Brian

2007-01-01

Identification of human CD1d-restricted T-cell receptor (TCR)-invariant natural killer T (iNKT) cells has been dependent on utilizing combinations of monoclonal antibodies or CD1d tetramers, which do not allow for the most specific analysis of this T-cell subpopulation. A novel monoclonal antibody (clone 6B11), specific for the invariant CDR3 loop of human canonical Vα24Jα18 TCR α chain, was developed and used to specifically characterize iNKT cells. In healthy individuals studied for up to 1 year, a wide but stable frequency of circulating iNKT cells (range: 0·01–0·92%) was observed, with no differences in frequency by gender. Four stable iNKT cell subsets were characterized in peripheral blood based on the expression of CD4 and CD8, with CD8+ iNKT cells being a phenotypic and functionally different subset from CD4+ and double negative iNKT cells; in particular, LAG-3 was preferentially expressed on CD8+ iNKT cells. In addition, a strong negative linear correlation between the frequency of total iNKT cells and percentage of the CD4+ subset was observed. In terms of their potential association with disease, patients at risk for type 1 diabetes had significantly expanded frequencies of double negative iNKT cells when compared to matched controls and first-degree relatives. Moreover, peripheral blood CD4+ iNKT cells were the highest producers of interleukin-4, while the production of interferon-γ and tumour necrosis factor-α was similar amongst all iNKT cell subsets. These differences in iNKT cell subsets suggest that in humans the relative ratio of iNKT cell subsets may influence susceptibility vs. resistance to immune-mediated diseases. PMID:17662044

Vineland-II adaptive behavior profile of children with attention-deficit/hyperactivity disorder or specific learning disorders.

PubMed

Balboni, Giulia; Incognito, Oriana; Belacchi, Carmen; Bonichini, Sabrina; Cubelli, Roberto

2017-02-01

The evaluation of adaptive behavior is informative in children with attention-deficit/hyperactivity disorder (ADHD) or specific learning disorders (SLD). However, the few investigations available have focused only on the gross level of domains of adaptive behavior. To investigate which item subsets of the Vineland-II can discriminate children with ADHD or SLD from peers with typical development. Student's t-tests, ROC analysis, logistic regression, and linear discriminant function analysis were used to compare 24 children with ADHD, 61 elementary students with SLD, and controls matched on age, sex, school level attended, and both parents' education level. Several item subsets that address not only ADHD core symptoms, but also understanding in social context and development of interpersonal relationships, allowed discrimination of children with ADHD from controls. The combination of four item subsets (Listening and attending, Expressing complex ideas, Social communication, and Following instructions) classified children with ADHD with both sensitivity and specificity of 87.5%. Only Reading skills, Writing skills, and Time and dates discriminated children with SLD from controls. Evaluation of Vineland-II scores at the level of item content categories is a useful procedure for an efficient clinical description. Copyright © 2016 Elsevier Ltd. All rights reserved.

Classification Preictal and Interictal Stages via Integrating Interchannel and Time-Domain Analysis of EEG Features.

PubMed

Lin, Lung-Chang; Chen, Sharon Chia-Ju; Chiang, Ching-Tai; Wu, Hui-Chuan; Yang, Rei-Cheng; Ouyang, Chen-Sen

2017-03-01

The life quality of patients with refractory epilepsy is extremely affected by abrupt and unpredictable seizures. A reliable method for predicting seizures is important in the management of refractory epilepsy. A critical factor in seizure prediction involves the classification of the preictal and interictal stages. This study aimed to develop an efficient, automatic, quantitative, and individualized approach for preictal/interictal stage identification. Five epileptic children, who had experienced at least 2 episodes of seizures during a 24-hour video EEG recording, were included. Artifact-free preictal and interictal EEG epochs were acquired, respectively, and characterized with 216 global feature descriptors. The best subset of 5 discriminative descriptors was identified. The best subsets showed differences among the patients. Statistical analysis revealed most of the 5 descriptors in each subset were significantly different between the preictal and interictal stages for each patient. The proposed approach yielded weighted averages of 97.50% correctness, 96.92% sensitivity, 97.78% specificity, and 95.45% precision on classifying test epochs. Although the case number was limited, this study successfully integrated a new EEG analytical method to classify preictal and interictal EEG segments and might be used further in predicting the occurrence of seizures.

Annotating spatio-temporal datasets for meaningful analysis in the Web

NASA Astrophysics Data System (ADS)

Stasch, Christoph; Pebesma, Edzer; Scheider, Simon

2014-05-01

More and more environmental datasets that vary in space and time are available in the Web. This comes along with an advantage of using the data for other purposes than originally foreseen, but also with the danger that users may apply inappropriate analysis procedures due to lack of important assumptions made during the data collection process. In order to guide towards a meaningful (statistical) analysis of spatio-temporal datasets available in the Web, we have developed a Higher-Order-Logic formalism that captures some relevant assumptions in our previous work [1]. It allows to proof on meaningful spatial prediction and aggregation in a semi-automated fashion. In this poster presentation, we will present a concept for annotating spatio-temporal datasets available in the Web with concepts defined in our formalism. Therefore, we have defined a subset of the formalism as a Web Ontology Language (OWL) pattern. It allows capturing the distinction between the different spatio-temporal variable types, i.e. point patterns, fields, lattices and trajectories, that in turn determine whether a particular dataset can be interpolated or aggregated in a meaningful way using a certain procedure. The actual annotations that link spatio-temporal datasets with the concepts in the ontology pattern are provided as Linked Data. In order to allow data producers to add the annotations to their datasets, we have implemented a Web portal that uses a triple store at the backend to store the annotations and to make them available in the Linked Data cloud. Furthermore, we have implemented functions in the statistical environment R to retrieve the RDF annotations and, based on these annotations, to support a stronger typing of spatio-temporal datatypes guiding towards a meaningful analysis in R. [1] Stasch, C., Scheider, S., Pebesma, E., Kuhn, W. (2014): "Meaningful spatial prediction and aggregation", Environmental Modelling & Software, 51, 149-165.

Proteome Characterization Centers - TCGA

Cancer.gov

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

Analysis of the access patterns at GSFC distributed active archive center

NASA Technical Reports Server (NTRS)

Johnson, Theodore; Bedet, Jean-Jacques

1996-01-01

The Goddard Space Flight Center (GSFC) Distributed Active Archive Center (DAAC) has been operational for more than two years. Its mission is to support existing and pre Earth Observing System (EOS) Earth science datasets, facilitate the scientific research, and test Earth Observing System Data and Information System (EOSDIS) concepts. Over 550,000 files and documents have been archived, and more than six Terabytes have been distributed to the scientific community. Information about user request and file access patterns, and their impact on system loading, is needed to optimize current operations and to plan for future archives. To facilitate the management of daily activities, the GSFC DAAC has developed a data base system to track correspondence, requests, ingestion and distribution. In addition, several log files which record transactions on Unitree are maintained and periodically examined. This study identifies some of the users' requests and file access patterns at the GSFC DAAC during 1995. The analysis is limited to the subset of orders for which the data files are under the control of the Hierarchical Storage Management (HSM) Unitree. The results show that most of the data volume ordered was for two data products. The volume was also mostly made up of level 3 and 4 data and most of the volume was distributed on 8 mm and 4 mm tapes. In addition, most of the volume ordered was for deliveries in North America although there was a significant world-wide use. There was a wide range of request sizes in terms of volume and number of files ordered. On an average 78.6 files were ordered per request. Using the data managed by Unitree, several caching algorithms have been evaluated for both hit rate and the overhead ('cost') associated with the movement of data from near-line devices to disks. The algorithm called LRU/2 bin was found to be the best for this workload, but the STbin algorithm also worked well.

Space debris characterization in support of a satellite breakup model

NASA Technical Reports Server (NTRS)

Fortson, Bryan H.; Winter, James E.; Allahdadi, Firooz A.

1992-01-01

The Space Kinetic Impact and Debris Branch began an ambitious program to construct a fully analytical model of the breakup of a satellite under hypervelocity impact. In order to provide empirical data with which to substantiate the model, debris from hypervelocity experiments conducted in a controlled laboratory environment were characterized to provide information of its mass, velocity, and ballistic coefficient distributions. Data on the debris were collected in one master data file, and a simple FORTRAN program allows users to describe the debris from any subset of these experiments that may be of interest to them. A statistical analysis was performed, allowing users to determine the precision of the velocity measurements for the data. Attempts are being made to include and correlate other laboratory data, as well as those data obtained from the explosion or collision of spacecraft in low earth orbit.

NanoSIMS Determination of Carbon and Oxygen Isotopic Compositions of Presolar Graphites from the Murchison Meteorite

NASA Technical Reports Server (NTRS)

Stadermann, F. J.; Croat, T. K.; Bernatowicz, T.

2004-01-01

Graphite from the Murchison density separate KFC1 (2.15 - 2.20 g/cu cm) has previously been studied by combined SEM/EDX and ion microprobe analysis. These studies found several distinct morphological types of graphites and C isotopic compositions that vary over more than 3 orders of magnitude, clearly establishing their presolar origin. Subsequent TEM measurements of a subset of these particles found abundant embedded crystals of metal (Zr, Mo, Ti, Ru) carbides which were incorporated during the growth of the graphites. A new TEM study of a large set of KFC1 graphites led to the discovery of another type of presolar material, Ru-Fe metal. Here we report results of the C and O isotopic measurements in the same graphite sections, which makes it possible for the first time to directly correlate isotopic and TEM data of KFC1 grains.

Quantum Mechanical Metric for Internal Cohesion in Cement Crystals

PubMed Central

Dharmawardhana, C. C.; Misra, A.; Ching, Wai-Yim

2014-01-01

Calcium silicate hydrate (CSH) is the main binding phase of Portland cement, the single most important structural material in use worldwide. Due to the complex structure and chemistry of CSH at various length scales, the focus has progressively turned towards its atomic level comprehension. We study electronic structure and bonding of a large subset of the known CSH minerals. Our results reveal a wide range of contributions from each type of bonding, especially hydrogen bonding, which should enable critical analysis of spectroscopic measurements and construction of realistic C-S-H models. We find the total bond order density (TBOD) as the ideal overall metric for assessing crystal cohesion of these complex materials and should replace conventional measures such as Ca:Si ratio. A rarely known orthorhombic phase Suolunite is found to have higher cohesion (TBOD) in comparison to Jennite and Tobermorite, which are considered the backbone of hydrated Portland cement. PMID:25476741

Diverging biological roles among human monocyte subsets in the context of tuberculosis infection.

PubMed

Balboa, Luciana; Barrios-Payan, Jorge; González-Domínguez, Erika; Lastrucci, Claire; Lugo-Villarino, Geanncarlo; Mata-Espinoza, Dulce; Schierloh, Pablo; Kviatcovsky, Denise; Neyrolles, Olivier; Maridonneau-Parini, Isabelle; Sánchez-Torres, Carmen; Sasiain, María del Carmen; Hernández-Pando, Rogelio

2015-08-01

Circulating monocytes (Mo) play an essential role in the host immune response to chronic infections. We previously demonstrated that CD16(pos) Mo were expanded in TB (tuberculosis) patients, correlated with disease severity and were refractory to dendritic cell differentiation. In the present study, we investigated whether human Mo subsets (CD16(neg) and CD16(pos)) differed in their ability to influence the early inflammatory response against Mycobacterium tuberculosis. We first evaluated the capacity of the Mo subsets to migrate and engage a microbicidal response in vitro. Accordingly, CD16(neg) Mo were more prone to migrate in response to different mycobacteria-derived gradients, were more resistant to M. tuberculosis intracellular growth and produced higher reactive oxygen species than their CD16(pos) counterpart. To assess further the functional dichotomy among the human Mo subsets, we carried out an in vivo analysis by adapting a hybrid mouse model (SCID/Beige, where SCID is severe combined immunodeficient) to transfer each Mo subset, track their migratory fate during M. tuberculosis infection, and determine their impact on the host immune response. In M. tuberculosis-infected mice, the adoptively transferred CD16(neg) Mo displayed a higher lung migration index, induced a stronger pulmonary infiltration of murine leucocytes expressing pro- and anti-inflammatory cytokines, and significantly decreased the bacterial burden, in comparison with CD16(pos) Mo. Collectively, our results indicate that human Mo subsets display divergent biological roles in the context of M. tuberculosis infection, a scenario in which CD16(neg) Mo may contribute to the anti-mycobacterial immune response, whereas CD16(pos) Mo might promote microbial resilience, shedding light on a key aspect of the physiopathology of TB disease.

B cell subset distribution is altered in patients with severe periodontitis.

PubMed

Demoersman, Julien; Pochard, Pierre; Framery, Camille; Simon, Quentin; Boisramé, Sylvie; Soueidan, Assem; Pers, Jacques-Olivier

2018-01-01

Several studies have recently highlighted the implication of B cells in physiopathogenesis of periodontal disease by showing that a B cell deficiency leads to improved periodontal parameters. However, the detailed profiles of circulating B cell subsets have not yet been investigated in patients with severe periodontitis (SP). We hypothesised that an abnormal distribution of B cell subsets could be detected in the blood of patients with severe periodontal lesions, as already reported for patients with chronic inflammatory diseases as systemic autoimmune diseases. Fifteen subjects with SP and 13 subjects without periodontitis, according to the definition proposed by the CDC periodontal disease surveillance work group, were enrolled in this pilot observational study. Two flow cytometry panels were designed to analyse the circulating B and B1 cell subset distribution in association with the RANKL expression. A significantly higher percentage of CD27+ memory B cells was observed in patients with SP. Among these CD27+ B cells, the proportion of the switched memory subset was significantly higher. At the same time, human B1 cells, which were previously associated with a regulatory function (CD20+CD69-CD43+CD27+CD11b+), decreased in SP patients. The RANKL expression increased in every B cell subset from the SP patients and was significantly greater in activated B cells than in the subjects without periodontitis. These preliminary results demonstrate the altered distribution of B cells in the context of severe periodontitis. Further investigations with a larger cohort of patients can elucidate if the analysis of the B cell compartment distribution can reflect the periodontal disease activity and be a reliable marker for its prognosis (clinical trial registration number: NCT02833285, B cell functions in periodontitis).

Distinct Roles for CXCR6(+) and CXCR6(-) CD4(+) T Cells in the Pathogenesis of Chronic Colitis.

PubMed

Mandai, Yasushi; Takahashi, Daisuke; Hase, Koji; Obata, Yuuki; Furusawa, Yukihiro; Ebisawa, Masashi; Nakagawa, Tomoo; Sato, Toru; Katsuno, Tatsuro; Saito, Yasushi; Shimaoka, Takeshi; Yokosuka, Osamu; Yokote, Kotaro; Ohno, Hiroshi

2013-01-01

CD4(+) T cells play a central role in the development of inflammatory bowel disease (IBD) via high-level production of effector cytokines such as IFN-γ and TNF-α. To better characterize the colitogenic CD4(+) T cells, we examined their expression of CXCR6, a chemokine receptor that is expressed by T cells upon activation and is upregulated in several inflammatory diseases. We found that 80% of colonic lamina propria CD4(+) T cells expressed CXCR6 in the CD45RB(high) T cell-transferred colitis model. CXCR6 expression was similarly upregulated in inflamed mucosa of patients with Crohn's disease. Although surface marker analysis demonstrated that both CXCR6(+) and CXCR6(-) CD4(+) T-cell subsets consist of the cells with effector and effector-memory cells, the more cells in the CXCR6(+) subset produced IFN-γ and TNF-α compared to CXCR6(-) subset, and only the CXCR6(+) subset produced IL-17A. Nevertheless, adoptive retransfer of lamina propria CXCR6(+) T cells into Rag1 (-/-) recipients failed to induce the disease due to limited expansion of the transferred cells. By contrast, retransfer of CXCR6(-) cells evoked colitis similar to that observed in CD4(+)CD45RB(high) T cell-transferred mice, and resulted in their conversion into CXCR6(+) cells. Collectively, these observations suggest that the CXCR6(+)CD4(+) T-cell subset consists of terminally differentiated effector cells that serve as the major source of effector cytokines in the inflamed tissue, whereas CXCR6(-)CD4(+) T-cell subset serves as a colitogenic memory compartment that retains the ability to proliferate and differentiate into CXCR6(+)CD4(+) T cells.

Distinct Roles for CXCR6+ and CXCR6− CD4+ T Cells in the Pathogenesis of Chronic Colitis

PubMed Central

Hase, Koji; Obata, Yuuki; Furusawa, Yukihiro; Ebisawa, Masashi; Nakagawa, Tomoo; Sato, Toru; Katsuno, Tatsuro; Saito, Yasushi; Shimaoka, Takeshi; Yokosuka, Osamu; Yokote, Kotaro; Ohno, Hiroshi

2013-01-01

CD4+ T cells play a central role in the development of inflammatory bowel disease (IBD) via high-level production of effector cytokines such as IFN-γ and TNF-α. To better characterize the colitogenic CD4+ T cells, we examined their expression of CXCR6, a chemokine receptor that is expressed by T cells upon activation and is upregulated in several inflammatory diseases. We found that 80% of colonic lamina propria CD4+ T cells expressed CXCR6 in the CD45RBhigh T cell-transferred colitis model. CXCR6 expression was similarly upregulated in inflamed mucosa of patients with Crohn’s disease. Although surface marker analysis demonstrated that both CXCR6+ and CXCR6− CD4+ T-cell subsets consist of the cells with effector and effector-memory cells, the more cells in the CXCR6+ subset produced IFN-γ and TNF-α compared to CXCR6− subset, and only the CXCR6+ subset produced IL-17A. Nevertheless, adoptive retransfer of lamina propria CXCR6+ T cells into Rag1 −/− recipients failed to induce the disease due to limited expansion of the transferred cells. By contrast, retransfer of CXCR6− cells evoked colitis similar to that observed in CD4+CD45RBhigh T cell-transferred mice, and resulted in their conversion into CXCR6+ cells. Collectively, these observations suggest that the CXCR6+CD4+ T-cell subset consists of terminally differentiated effector cells that serve as the major source of effector cytokines in the inflamed tissue, whereas CXCR6−CD4+ T-cell subset serves as a colitogenic memory compartment that retains the ability to proliferate and differentiate into CXCR6+CD4+ T cells. PMID:23840334

B cell subset distribution is altered in patients with severe periodontitis

PubMed Central

Demoersman, Julien; Pochard, Pierre; Framery, Camille; Simon, Quentin; Boisramé, Sylvie; Soueidan, Assem

2018-01-01

Several studies have recently highlighted the implication of B cells in physiopathogenesis of periodontal disease by showing that a B cell deficiency leads to improved periodontal parameters. However, the detailed profiles of circulating B cell subsets have not yet been investigated in patients with severe periodontitis (SP). We hypothesised that an abnormal distribution of B cell subsets could be detected in the blood of patients with severe periodontal lesions, as already reported for patients with chronic inflammatory diseases as systemic autoimmune diseases. Fifteen subjects with SP and 13 subjects without periodontitis, according to the definition proposed by the CDC periodontal disease surveillance work group, were enrolled in this pilot observational study. Two flow cytometry panels were designed to analyse the circulating B and B1 cell subset distribution in association with the RANKL expression. A significantly higher percentage of CD27+ memory B cells was observed in patients with SP. Among these CD27+ B cells, the proportion of the switched memory subset was significantly higher. At the same time, human B1 cells, which were previously associated with a regulatory function (CD20+CD69-CD43+CD27+CD11b+), decreased in SP patients. The RANKL expression increased in every B cell subset from the SP patients and was significantly greater in activated B cells than in the subjects without periodontitis. These preliminary results demonstrate the altered distribution of B cells in the context of severe periodontitis. Further investigations with a larger cohort of patients can elucidate if the analysis of the B cell compartment distribution can reflect the periodontal disease activity and be a reliable marker for its prognosis (clinical trial registration number: NCT02833285, B cell functions in periodontitis). PMID:29447240

Genome Comparison of Human and Non-Human Malaria Parasites Reveals Species Subset-Specific Genes Potentially Linked to Human Disease

PubMed Central

Frech, Christian; Chen, Nansheng

2011-01-01

Genes underlying important phenotypic differences between Plasmodium species, the causative agents of malaria, are frequently found in only a subset of species and cluster at dynamically evolving subtelomeric regions of chromosomes. We hypothesized that chromosome-internal regions of Plasmodium genomes harbour additional species subset-specific genes that underlie differences in human pathogenicity, human-to-human transmissibility, and human virulence. We combined sequence similarity searches with synteny block analyses to identify species subset-specific genes in chromosome-internal regions of six published Plasmodium genomes, including Plasmodium falciparum, Plasmodium vivax, Plasmodium knowlesi, Plasmodium yoelii, Plasmodium berghei, and Plasmodium chabaudi. To improve comparative analysis, we first revised incorrectly annotated gene models using homology-based gene finders and examined putative subset-specific genes within syntenic contexts. Confirmed subset-specific genes were then analyzed for their role in biological pathways and examined for molecular functions using publicly available databases. We identified 16 genes that are well conserved in the three primate parasites but not found in rodent parasites, including three key enzymes of the thiamine (vitamin B1) biosynthesis pathway. Thirteen genes were found to be present in both human parasites but absent in the monkey parasite P. knowlesi, including genes specifically upregulated in sporozoites or gametocytes that could be linked to parasite transmission success between humans. Furthermore, we propose 15 chromosome-internal P. falciparum-specific genes as new candidate genes underlying increased human virulence and detected a currently uncharacterized cluster of P. vivax-specific genes on chromosome 6 likely involved in erythrocyte invasion. In conclusion, Plasmodium species harbour many chromosome-internal differences in the form of protein-coding genes, some of which are potentially linked to human disease and thus promising leads for future laboratory research. PMID:22215999

The involvement of plasmacytoid cells in HIV infection and pathogenesis.

PubMed

Aiello, Alessandra; Giannessi, Flavia; Percario, Zulema A; Affabris, Elisabetta

2018-04-01

Plasmacytoid dendritic cells (pDCs) are a unique dendritic cell subset that are specialized in type I interferon (IFN) production. pDCs are key players in the antiviral immune response and serve as bridge between innate and adaptive immunity. Although pDCs do not represent the main reservoir of the Human Immunodeficiency Virus (HIV), they are a crucial subset in HIV infection as they influence viral transmission, target cell infection and antigen presentation. pDCs act as inflammatory and immunosuppressive cells, thus contributing to HIV disease progression. This review provides a state of art analysis of the interactions between HIV and pDCs and their potential roles in HIV transmission, chronic immune activation and immunosuppression. A thorough understanding of the roles of pDCs in HIV infection will help to improve therapeutic strategies to fight HIV infection, and will further increase our knowledge on this important immune cell subset. Copyright © 2018 Elsevier Ltd. All rights reserved.

Optimization of oncological {sup 18}F-FDG PET/CT imaging based on a multiparameter analysis

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

Menezes, Vinicius O., E-mail: vinicius@radtec.com.br; Machado, Marcos A. D.; Queiroz, Cleiton C.

2016-02-15

Purpose: This paper describes a method to achieve consistent clinical image quality in {sup 18}F-FDG scans accounting for patient habitus, dose regimen, image acquisition, and processing techniques. Methods: Oncological PET/CT scan data for 58 subjects were evaluated retrospectively to derive analytical curves that predict image quality. Patient noise equivalent count rate and coefficient of variation (CV) were used as metrics in their analysis. Optimized acquisition protocols were identified and prospectively applied to 179 subjects. Results: The adoption of different schemes for three body mass ranges (<60 kg, 60–90 kg, >90 kg) allows improved image quality with both point spread functionmore » and ordered-subsets expectation maximization-3D reconstruction methods. The application of this methodology showed that CV improved significantly (p < 0.0001) in clinical practice. Conclusions: Consistent oncological PET/CT image quality on a high-performance scanner was achieved from an analysis of the relations existing between dose regimen, patient habitus, acquisition, and processing techniques. The proposed methodology may be used by PET/CT centers to develop protocols to standardize PET/CT imaging procedures and achieve better patient management and cost-effective operations.« less

Nonsynchronous updating in the multiverse of cellular automata

NASA Astrophysics Data System (ADS)

Reia, Sandro M.; Kinouchi, Osame

2015-04-01

In this paper we study updating effects on cellular automata rule space. We consider a subset of 6144 order-3 automata from the space of 262144 bidimensional outer-totalistic rules. We compare synchronous to asynchronous and sequential updatings. Focusing on two automata, we discuss how update changes destroy typical structures of these rules. Besides, we show that the first-order phase transition in the multiverse of synchronous cellular automata, revealed with the use of a recently introduced control parameter, seems to be robust not only to changes in update schema but also to different initial densities.

The Use of Software Agents for Autonomous Control of a DC Space Power System

NASA Technical Reports Server (NTRS)

May, Ryan D.; Loparo, Kenneth A.

2014-01-01

In order to enable manned deep-space missions, the spacecraft must be controlled autonomously using on-board algorithms. A control architecture is proposed to enable this autonomous operation for an spacecraft electric power system and then implemented using a highly distributed network of software agents. These agents collaborate and compete with each other in order to implement each of the control functions. A subset of this control architecture is tested against a steadystate power system simulation and found to be able to solve a constrained optimization problem with competing objectives using only local information.

Nonsynchronous updating in the multiverse of cellular automata.

PubMed

Reia, Sandro M; Kinouchi, Osame

2015-04-01

In this paper we study updating effects on cellular automata rule space. We consider a subset of 6144 order-3 automata from the space of 262144 bidimensional outer-totalistic rules. We compare synchronous to asynchronous and sequential updatings. Focusing on two automata, we discuss how update changes destroy typical structures of these rules. Besides, we show that the first-order phase transition in the multiverse of synchronous cellular automata, revealed with the use of a recently introduced control parameter, seems to be robust not only to changes in update schema but also to different initial densities.

Recent Developments in the Treatment of Spinal Epidural Abscesses

PubMed Central

Eltorai, Adam E.M.; Naqvi, Syed S.; Seetharam, Ashok; Brea, Bielinsky A.; Simon, Chad

2017-01-01

Spinal epidural abscess (SEA) is a serious condition that can be challenging to diagnose due to nonspecific symptomology and delayed presentation. Despite this, it requires prompt recognition and management in order to prevent permanent neurologic sequelae. Several recent studies have improved our understanding of SEA. Herein, we summarize the recent literature from the past 10 years relevant to SEA diagnosis, management and outcome. While surgical care remains the mainstay of treatment, a select subset of SEA patients may be managed without operative intervention. Multidisciplinary management involves internal medicine, infectious disease, critical care, and spine surgeons in order to optimize care. PMID:28713526

Equilibrium relations and bipolar cognitive mapping for online analytical processing with applications in international relations and strategic decision support.

PubMed

Zhang, Wen-Ran

2003-01-01

Bipolar logic, bipolar sets, and equilibrium relations are proposed for bipolar cognitive mapping and visualization in online analytical processing (OLAP) and online analytical mining (OLAM). As cognitive models, cognitive maps (CMs) hold great potential for clustering and visualization. Due to the lack of a formal mathematical basis, however, CM-based OLAP and OLAM have not gained popularity. Compared with existing approaches, bipolar cognitive mapping has a number of advantages. First, bipolar CMs are formal logical models as well as cognitive models. Second, equilibrium relations (with polarized reflexivity, symmetry, and transitivity), as bipolar generalizations and fusions of equivalence relations, provide a theoretical basis for bipolar visualization and coordination. Third, an equilibrium relation or CM induces bipolar partitions that distinguish disjoint coalition subsets not involved in any conflict, disjoint coalition subsets involved in a conflict, disjoint conflict subsets, and disjoint harmony subsets. Finally, equilibrium energy analysis leads to harmony and stability measures for strategic decision and multiagent coordination. Thus, this work bridges a gap for CM-based clustering and visualization in OLAP and OLAM. Basic ideas are illustrated with example CMs in international relations.

A non-linear data mining parameter selection algorithm for continuous variables

PubMed Central

Razavi, Marianne; Brady, Sean

2017-01-01

In this article, we propose a new data mining algorithm, by which one can both capture the non-linearity in data and also find the best subset model. To produce an enhanced subset of the original variables, a preferred selection method should have the potential of adding a supplementary level of regression analysis that would capture complex relationships in the data via mathematical transformation of the predictors and exploration of synergistic effects of combined variables. The method that we present here has the potential to produce an optimal subset of variables, rendering the overall process of model selection more efficient. This algorithm introduces interpretable parameters by transforming the original inputs and also a faithful fit to the data. The core objective of this paper is to introduce a new estimation technique for the classical least square regression framework. This new automatic variable transformation and model selection method could offer an optimal and stable model that minimizes the mean square error and variability, while combining all possible subset selection methodology with the inclusion variable transformations and interactions. Moreover, this method controls multicollinearity, leading to an optimal set of explanatory variables. PMID:29131829

Comparative phenotypic and functional analysis of migratory dendritic cell subsets from human oral mucosa and skin

PubMed Central

van de Ven, Rieneke; Thon, Maria; Gibbs, Susan; de Gruijl, Tanja D.

2017-01-01

Antigen exposure to oral mucosa is generally thought to lead to immune tolerance induction. However, very little is known about the subset composition and function of dendritic cells (DC) migrating from human oral mucosa. Here we show that migratory DC from healthy human gingival explants consist of the same phenotypic subsets in the same frequency distribution as DC migrating from human skin. The gingival CD1a+ Langerhans cell and interstitial DC subsets lacked CXCR4 expression in contrast to their cutaneous counterparts, pointing to different migration mechanisms, consistent with previous observations in constructed skin and gingival equivalents. Remarkably, without any exogenous conditioning, gingival explants released higher levels of inflammatory cytokines than human skin explants, resulting in higher DC migration rates and a superior ability of migrated DC to prime allogeneic T cells and to induce type-1 effector T cell differentiation. From these observations we conclude that rather than an intrinsic ability to induce T cell tolerance, DC migrating from oral mucosa may have a propensity to induce effector T cell immunity and maintain a high state of alert against possible pathogenic intruders in the steady state. These findings may have implications for oral immunization strategies. PMID:28704477

Defining Mononuclear Phagocyte Subset Homology Across Several Distant Warm-Blooded Vertebrates Through Comparative Transcriptomics

PubMed Central

Vu Manh, Thien-Phong; Elhmouzi-Younes, Jamila; Urien, Céline; Ruscanu, Suzana; Jouneau, Luc; Bourge, Mickaël; Moroldo, Marco; Foucras, Gilles; Salmon, Henri; Marty, Hélène; Quéré, Pascale; Bertho, Nicolas; Boudinot, Pierre; Dalod, Marc; Schwartz-Cornil, Isabelle

2015-01-01

Mononuclear phagocytes are organized in a complex system of ontogenetically and functionally distinct subsets, that has been best described in mouse and to some extent in human. Identification of homologous mononuclear phagocyte subsets in other vertebrate species of biomedical, economic, and environmental interest is needed to improve our knowledge in physiologic and physio-pathologic processes, and to design intervention strategies against a variety of diseases, including zoonotic infections. We developed a streamlined approach combining refined cell sorting and integrated comparative transcriptomics analyses which revealed conservation of the mononuclear phagocyte organization across human, mouse, sheep, pigs and, in some respect, chicken. This strategy should help democratizing the use of omics analyses for the identification and study of cell types across tissues and species. Moreover, we identified conserved gene signatures that enable robust identification and universal definition of these cell types. We identified new evolutionarily conserved gene candidates and gene interaction networks for the molecular regulation of the development or functions of these cell types, as well as conserved surface candidates for refined subset phenotyping throughout species. A phylogenetic analysis revealed that orthologous genes of the conserved signatures exist in teleost fishes and apparently not in Lamprey. PMID:26150816

The depth estimation of 3D face from single 2D picture based on manifold learning constraints

NASA Astrophysics Data System (ADS)

Li, Xia; Yang, Yang; Xiong, Hailiang; Liu, Yunxia

2018-04-01

The estimation of depth is virtual important in 3D face reconstruction. In this paper, we propose a t-SNE based on manifold learning constraints and introduce K-means method to divide the original database into several subset, and the selected optimal subset to reconstruct the 3D face depth information can greatly reduce the computational complexity. Firstly, we carry out the t-SNE operation to reduce the key feature points in each 3D face model from 1×249 to 1×2. Secondly, the K-means method is applied to divide the training 3D database into several subset. Thirdly, the Euclidean distance between the 83 feature points of the image to be estimated and the feature point information before the dimension reduction of each cluster center is calculated. The category of the image to be estimated is judged according to the minimum Euclidean distance. Finally, the method Kong D will be applied only in the optimal subset to estimate the depth value information of 83 feature points of 2D face images. Achieving the final depth estimation results, thus the computational complexity is greatly reduced. Compared with the traditional traversal search estimation method, although the proposed method error rate is reduced by 0.49, the number of searches decreases with the change of the category. In order to validate our approach, we use a public database to mimic the task of estimating the depth of face images from 2D images. The average number of searches decreased by 83.19%.

Evaluation of subset matching methods and forms of covariate balance.

PubMed

de Los Angeles Resa, María; Zubizarreta, José R

2016-11-30

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

Feature selection for the classification of traced neurons.

PubMed

López-Cabrera, José D; Lorenzo-Ginori, Juan V

2018-06-01

The great availability of computational tools to calculate the properties of traced neurons leads to the existence of many descriptors which allow the automated classification of neurons from these reconstructions. This situation determines the necessity to eliminate irrelevant features as well as making a selection of the most appropriate among them, in order to improve the quality of the classification obtained. The dataset used contains a total of 318 traced neurons, classified by human experts in 192 GABAergic interneurons and 126 pyramidal cells. The features were extracted by means of the L-measure software, which is one of the most used computational tools in neuroinformatics to quantify traced neurons. We review some current feature selection techniques as filter, wrapper, embedded and ensemble methods. The stability of the feature selection methods was measured. For the ensemble methods, several aggregation methods based on different metrics were applied to combine the subsets obtained during the feature selection process. The subsets obtained applying feature selection methods were evaluated using supervised classifiers, among which Random Forest, C4.5, SVM, Naïve Bayes, Knn, Decision Table and the Logistic classifier were used as classification algorithms. Feature selection methods of types filter, embedded, wrappers and ensembles were compared and the subsets returned were tested in classification tasks for different classification algorithms. L-measure features EucDistanceSD, PathDistanceSD, Branch_pathlengthAve, Branch_pathlengthSD and EucDistanceAve were present in more than 60% of the selected subsets which provides evidence about their importance in the classification of this neurons. Copyright © 2018 Elsevier B.V. All rights reserved.

23 CFR 973.210 - Indian lands bridge management system (BMS).

Code of Federal Regulations, 2013 CFR

2013-04-01

... analysis (as appropriate, considering size of structure, traffic volume, and structural condition). The investment analysis may include the ability to: (1) Identify alternative strategies to improve bridge... analyzing data for all bridges in the inventory or any subset. The minimum analyses shall include: (i) A...

Feature extraction across individual time series observations with spikes using wavelet principal component analysis.

PubMed

Røislien, Jo; Winje, Brita

2013-09-20

Clinical studies frequently include repeated measurements of individuals, often for long periods. We present a methodology for extracting common temporal features across a set of individual time series observations. In particular, the methodology explores extreme observations within the time series, such as spikes, as a possible common temporal phenomenon. Wavelet basis functions are attractive in this sense, as they are localized in both time and frequency domains simultaneously, allowing for localized feature extraction from a time-varying signal. We apply wavelet basis function decomposition of individual time series, with corresponding wavelet shrinkage to remove noise. We then extract common temporal features using linear principal component analysis on the wavelet coefficients, before inverse transformation back to the time domain for clinical interpretation. We demonstrate the methodology on a subset of a large fetal activity study aiming to identify temporal patterns in fetal movement (FM) count data in order to explore formal FM counting as a screening tool for identifying fetal compromise and thus preventing adverse birth outcomes. Copyright © 2013 John Wiley & Sons, Ltd.

Fleet analysis of headway distance for autonomous driving.

PubMed

Ivanco, Andrej

2017-12-01

Modern automobiles are going through a paradigm shift, where the driver may no longer be needed to drive the vehicle. As the self-driving vehicles are making their way to public roads the automakers have to ensure the naturalistic driving feel to gain drivers' confidence and accelerate adoption rates. This paper filters and analyzes a subset of radar data collected from SHRP2 with focus on characterizing the naturalistic headway distance with respect to the vehicle speed. The paper identifies naturalistic headway distance and compares it with the previous findings from the literature. A clear relation between time headway and speed was confirmed and quantified. A significant difference exists among individual drivers which supports a need to further refine the analysis. By understanding the relationship between human driving and their surroundings, the naturalistic driving behavior can be quantified and used to increase the adoption rates of autonomous driving. Dangerous and safety-compromising driving can be identified as well in order to avoid its replication in the control algorithms. Copyright © 2017 National Safety Council and Elsevier Ltd. All rights reserved.

All Roads Lead to Rome: Exploring Human Migration to the Eternal City through Biochemistry of Skeletons from Two Imperial-Era Cemeteries (1st-3rd c AD)

PubMed Central

Killgrove, Kristina; Montgomery, Janet

2016-01-01

Migration within the Roman Empire occurred at multiple scales and was engaged in both voluntarily and involuntarily. Because of the lengthy tradition of classical studies, bioarchaeological analyses must be fully contextualized within the bounds of history, material culture, and epigraphy. In order to assess migration to Rome within an updated contextual framework, strontium isotope analysis was performed on 105 individuals from two cemeteries associated with Imperial Rome—Casal Bertone and Castellaccio Europarco—and oxygen and carbon isotope analyses were performed on a subset of 55 individuals. Statistical analysis and comparisons with expected local ranges found several outliers who likely immigrated to Rome from elsewhere. Demographics of the immigrants show men and children migrated, and a comparison of carbon isotopes from teeth and bone samples suggests the immigrants may have significantly changed their diet. These data represent the first physical evidence of individual migrants to Imperial Rome. This case study demonstrates the importance of employing bioarchaeology to generate a deeper understanding of a complex ancient urban center. PMID:26863610

All Roads Lead to Rome: Exploring Human Migration to the Eternal City through Biochemistry of Skeletons from Two Imperial-Era Cemeteries (1st-3rd c AD).

PubMed

Killgrove, Kristina; Montgomery, Janet

2016-01-01

Migration within the Roman Empire occurred at multiple scales and was engaged in both voluntarily and involuntarily. Because of the lengthy tradition of classical studies, bioarchaeological analyses must be fully contextualized within the bounds of history, material culture, and epigraphy. In order to assess migration to Rome within an updated contextual framework, strontium isotope analysis was performed on 105 individuals from two cemeteries associated with Imperial Rome-Casal Bertone and Castellaccio Europarco-and oxygen and carbon isotope analyses were performed on a subset of 55 individuals. Statistical analysis and comparisons with expected local ranges found several outliers who likely immigrated to Rome from elsewhere. Demographics of the immigrants show men and children migrated, and a comparison of carbon isotopes from teeth and bone samples suggests the immigrants may have significantly changed their diet. These data represent the first physical evidence of individual migrants to Imperial Rome. This case study demonstrates the importance of employing bioarchaeology to generate a deeper understanding of a complex ancient urban center.

Atomistic modeling of the low-frequency mechanical modes and Raman spectra of icosahedral virus capsids

NASA Astrophysics Data System (ADS)

Dykeman, Eric C.; Sankey, Otto F.

2010-02-01

We describe a technique for calculating the low-frequency mechanical modes and frequencies of a large symmetric biological molecule where the eigenvectors of the Hessian matrix are determined with full atomic detail. The method, which follows order N methods used in electronic structure theory, determines the subset of lowest-frequency modes while using group theory to reduce the complexity of the problem. We apply the method to three icosahedral viruses of various T numbers and sizes; the human viruses polio and hepatitis B, and the cowpea chlorotic mottle virus, a plant virus. From the normal-mode eigenvectors, we use a bond polarizability model to predict a low-frequency Raman scattering profile for the viruses. The full atomic detail in the displacement patterns combined with an empirical potential-energy model allows a comparison of the fully atomic normal modes with elastic network models and normal-mode analysis with only dihedral degrees of freedom. We find that coarse-graining normal-mode analysis (particularly the elastic network model) can predict the displacement patterns for the first few (˜10) low-frequency modes that are global and cooperative.

Determination of total polyphenol index in wines employing a voltammetric electronic tongue.

PubMed

Cetó, Xavier; Gutiérrez, Juan Manuel; Gutiérrez, Manuel; Céspedes, Francisco; Capdevila, Josefina; Mínguez, Santiago; Jiménez-Jorquera, Cecilia; del Valle, Manel

2012-06-30

This work reports the application of a voltammetric electronic tongue system (ET) made from an array of modified graphite-epoxy composites plus a gold microelectrode in the qualitative and quantitative analysis of polyphenols found in wine. Wine samples were analyzed using cyclic voltammetry without any sample pretreatment. The obtained responses were preprocessed employing discrete wavelet transform (DWT) in order to compress and extract significant features from the voltammetric signals, and the obtained approximation coefficients fed a multivariate calibration method (artificial neural network-ANN-or partial least squares-PLS-) which accomplished the quantification of total polyphenol content. External test subset samples results were compared with the ones obtained with the Folin-Ciocalteu (FC) method and UV absorbance polyphenol index (I(280)) as reference values, with highly significant correlation coefficients of 0.979 and 0.963 in the range from 50 to 2400 mg L(-1) gallic acid equivalents, respectively. In a separate experiment, qualitative discrimination of different polyphenols found in wine was also assessed by principal component analysis (PCA). Copyright © 2012 Elsevier B.V. All rights reserved.

Analyzing Process Data from Game/Scenario-Based Tasks: An Edit Distance Approach

ERIC Educational Resources Information Center

Hao, Jiangang; Shu, Zhan; von Davier, Alina

2015-01-01

Students' activities in game/scenario-based tasks (G/SBTs) can be characterized by a sequence of time-stamped actions of different types with different attributes. For a subset of G/SBTs in which only the order of the actions is of great interest, the process data can be well characterized as a string of characters (i.e., action string) if we…

Factor Analysis Methods and Validity Evidence: A Systematic Review of Instrument Development across the Continuum of Medical Education

ERIC Educational Resources Information Center

Wetzel, Angela Payne

2011-01-01

Previous systematic reviews indicate a lack of reporting of reliability and validity evidence in subsets of the medical education literature. Psychology and general education reviews of factor analysis also indicate gaps between current and best practices; yet, a comprehensive review of exploratory factor analysis in instrument development across…

Attenuation correction strategies for multi-energy photon emitters using SPECT

NASA Astrophysics Data System (ADS)

Pretorius, P. H.; King, M. A.; Pan, T.-S.; Hutton, B. F.

1997-06-01

The aim of this study was to investigate whether the photopeak window projections from different energy photons can be combined into a single window for reconstruction or if it is better to not combine the projections due to differences in the attenuation maps required for each photon energy. The mathematical cardiac torso (MCAT) phantom was modified to simulate the uptake of Ga-67 in the human body. Four spherical hot tumors were placed in locations which challenged attenuation correction. An analytical 3D projector with attenuation and detector response included was used to generate projection sets. Data were reconstructed using filtered backprojection (FBP) reconstruction with Butterworth filtering in conjunction with one iteration of Chang attenuation correction, and with 5 and 10 iterations of ordered-subset maximum-likelihood expectation maximization (ML-OS) reconstruction. To serve as a standard for comparison, the projection sets obtained from the two energies were first reconstructed separately using their own attenuation maps. The emission data obtained from both energies were added and reconstructed using the following attenuation strategies: 1) the 93 keV attenuation map for attenuation correction, 2) the 185 keV attenuation map for attenuation correction, 3) using a weighted mean obtained from combining the 93 keV and 185 keV maps, and 4) an ordered subset approach which combines both energies. The central count ratio (CCR) and total count ratio (TCR) were used to compare the performance of the different strategies. Compared to the standard method, results indicate an over-estimation with strategy 1, an under-estimation with strategy 2 and comparable results with strategies 3 and 4. In all strategies, the CCRs of sphere 4 (in proximity to the liver, spleen and backbone) were under-estimated, although TCRs were comparable to that of the other locations. The weighted mean and ordered subset strategies for attenuation correction were of comparable accuracy to reconstruction of the windows separately. They are recommended for multi-energy photon SPECT imaging quantitation when there is a need to combine the acquisitions of multiple windows.

Decision Support System Requirements Definition for Human Extravehicular Activity Based on Cognitive Work Analysis

PubMed Central

Miller, Matthew James; McGuire, Kerry M.; Feigh, Karen M.

2016-01-01

The design and adoption of decision support systems within complex work domains is a challenge for cognitive systems engineering (CSE) practitioners, particularly at the onset of project development. This article presents an example of applying CSE techniques to derive design requirements compatible with traditional systems engineering to guide decision support system development. Specifically, it demonstrates the requirements derivation process based on cognitive work analysis for a subset of human spaceflight operations known as extravehicular activity. The results are presented in two phases. First, a work domain analysis revealed a comprehensive set of work functions and constraints that exist in the extravehicular activity work domain. Second, a control task analysis was performed on a subset of the work functions identified by the work domain analysis to articulate the translation of subject matter states of knowledge to high-level decision support system requirements. This work emphasizes an incremental requirements specification process as a critical component of CSE analyses to better situate CSE perspectives within the early phases of traditional systems engineering design. PMID:28491008

Decision Support System Requirements Definition for Human Extravehicular Activity Based on Cognitive Work Analysis.

PubMed

Miller, Matthew James; McGuire, Kerry M; Feigh, Karen M

2017-06-01

The design and adoption of decision support systems within complex work domains is a challenge for cognitive systems engineering (CSE) practitioners, particularly at the onset of project development. This article presents an example of applying CSE techniques to derive design requirements compatible with traditional systems engineering to guide decision support system development. Specifically, it demonstrates the requirements derivation process based on cognitive work analysis for a subset of human spaceflight operations known as extravehicular activity . The results are presented in two phases. First, a work domain analysis revealed a comprehensive set of work functions and constraints that exist in the extravehicular activity work domain. Second, a control task analysis was performed on a subset of the work functions identified by the work domain analysis to articulate the translation of subject matter states of knowledge to high-level decision support system requirements. This work emphasizes an incremental requirements specification process as a critical component of CSE analyses to better situate CSE perspectives within the early phases of traditional systems engineering design.

Specifications of a continual reassessment method design for phase I trials of combined drugs†

PubMed Central

Wages, Nolan A.; Conaway, Mark R.

2013-01-01

In studies of combinations of agents in phase I oncology trials, the dose–toxicity relationship may not be monotone for all combinations, in which case the toxicity probabilities follow a partial order. The continual reassessment method for partial orders (PO-CRM) is a design for phase I trials of combinations that leans upon identifying possible complete orders associated with the partial order. This article addresses some practical design considerations not previously undertaken when describing the PO-CRM. We describe an approach in choosing a proper subset of possible orderings, formulated according to the known toxicity relationships within a matrix of combination therapies. Other design issues, such as working model selection and stopping rules, are also discussed. We demonstrate the practical ability of PO-CRM as a phase I design for combinations through its use in a recent trial designed at the University of Virginia Cancer Center. PMID:23729323

The Long Noncoding RNA Landscape of the Mouse Eye.

PubMed

Chen, Weiwei; Yang, Shuai; Zhou, Zhonglou; Zhao, Xiaoting; Zhong, Jiayun; Reinach, Peter S; Yan, Dongsheng

2017-12-01

Long noncoding RNAs (lncRNAs) are important regulators of diverse biological functions. However, an extensive in-depth analysis of their expression profile and function in mammalian eyes is still lacking. Here we describe comprehensive landscapes of stage-dependent and tissue-specific lncRNA expression in the mouse eye. Affymetrix transcriptome array profiled lncRNA signatures from six different ocular tissue subsets (i.e., cornea, lens, retina, RPE, choroid, and sclera) in newborn and 8-week-old mice. Quantitative RT-PCR analysis validated array findings. Cis analyses and Gene Ontology (GO) annotation of protein-coding genes adjacent to signature lncRNA loci clarified potential lncRNA roles in maintaining tissue identity and regulating eye maturation during the aforementioned phase. In newborn and 8-week-old mice, we identified 47,332 protein-coding and noncoding gene transcripts. LncRNAs comprise 19,313 of these transcripts annotated in public data banks. During this maturation phase of these six different tissue subsets, more than 1000 lncRNAs expression levels underwent ≥2-fold changes. qRT-PCR analysis confirmed part of the gene microarray analysis results. K-means clustering identified 910 lncRNAs in the P0 groups and 686 lncRNAs in the postnatal 8-week-old groups, suggesting distinct tissue-specific lncRNA clusters. GO analysis of protein-coding genes proximal to lncRNA signatures resolved close correlations with their tissue-specific functional maturation between P0 and 8 weeks of age in the 6 tissue subsets. Characterizating maturational changes in lncRNA expression patterns as well as tissue-specific lncRNA signatures in six ocular tissues suggest important contributions made by lncRNA to the control of developmental processes in the mouse eye.

Systematics of the cusp anomalous dimension

NASA Astrophysics Data System (ADS)

Henn, Johannes M.; Huber, Tobias

2012-11-01

We study the velocity-dependent cusp anomalous dimension in supersymmetric Yang-Mills theory. In a paper by Correa, Maldacena, Sever, and one of the present authors, a scaling limit was identified in which the ladder diagrams are dominant and are mapped onto a Schrödinger problem. We show how to solve the latter in perturbation theory and provide an algorithm to compute the solution at any loop order. The answer is written in terms of harmonic polylogarithms. Moreover, we give evidence for two curious properties of the result. Firstly, we observe that the result can be written using a subset of harmonic polylogarithms only, at least up to six loops. Secondly, we show that in a light-like limit, only single zeta values appear in the asymptotic expansion, again up to six loops. We then extend the analysis of the scaling limit to systematically include subleading terms. This leads to a Schrödinger-type equation, but with an inhomogeneous term. We show how its solution can be computed in perturbation theory, in a way similar to the leading order case. Finally, we analyze the strong coupling limit of these subleading contributions and compare them to the string theory answer. We find agreement between the two calculations.

Meta-analysis of cancer gene expression signatures reveals new cancer genes, SAGE tags and tumor associated regions of co-regulation

PubMed Central

Kavak, Erşen; Ünlü, Mustafa; Nistér, Monica; Koman, Ahmet

2010-01-01

Cancer is among the major causes of human death and its mechanism(s) are not fully understood. We applied a novel meta-analysis approach to multiple sets of merged serial analysis of gene expression and microarray cancer data in order to analyze transcriptome alterations in human cancer. Our methodology, which we denote ‘COgnate Gene Expression patterNing in tumours’ (COGENT), unmasked numerous genes that were differentially expressed in multiple cancers. COGENT detected well-known tumor-associated (TA) genes such as TP53, EGFR and VEGF, as well as many multi-cancer, but not-yet-tumor-associated genes. In addition, we identified 81 co-regulated regions on the human genome (RIDGEs) by using expression data from all cancers. Some RIDGEs (28%) consist of paralog genes while another subset (30%) are specifically dysregulated in tumors but not in normal tissues. Furthermore, a significant number of RIDGEs are associated with GC-rich regions on the genome. All assembled data is freely available online (www.oncoreveal.org) as a tool implementing COGENT analysis of multi-cancer genes and RIDGEs. These findings engender a deeper understanding of cancer biology by demonstrating the existence of a pool of under-studied multi-cancer genes and by highlighting the cancer-specificity of some TA-RIDGEs. PMID:20621981

Is adaptation or transformation needed? Active nanomaterials and risk analysis

NASA Astrophysics Data System (ADS)

Kuzma, Jennifer; Roberts, John Patrick

2016-07-01

Nanotechnology has been a key area of funding and policy for the United States and globally for the past two decades. Since nanotechnology research and development became a focus and nanoproducts began to permeate the market, scholars and scientists have been concerned about how to assess the risks that they may pose to human health and the environment. The newest generation of nanomaterials includes biomolecules that can respond to and influence their environments, and there is a need to explore whether and how existing risk-analysis frameworks are challenged by such novelty. To fill this niche, we used a modified approach of upstream oversight assessment (UOA), a subset of anticipatory governance. We first selected case studies of "active nanomaterials," that are early in research and development and designed for use in multiple sectors, and then considered them under several, key risk-analysis frameworks. We found two ways in which the cases challenge the frameworks. The first category relates to how to assess risk under a narrow framing of the term (direct health and environmental harm), and the second involves the definition of what constitutes a "risk" worthy of assessment and consideration in decision making. In light of these challenges, we propose some changes for risk analysis in the face of active nanostructures in order to improve risk governance.

The tempo and mode of New World monkey evolution and biogeography in the context of phylogenomic analysis.

PubMed

Jameson Kiesling, Natalie M; Yi, Soojin V; Xu, Ke; Gianluca Sperone, F; Wildman, Derek E

2015-01-01

The development and evolution of organisms is heavily influenced by their environment. Thus, understanding the historical biogeography of taxa can provide insights into their evolutionary history, adaptations and trade-offs realized throughout time. In the present study we have taken a phylogenomic approach to infer New World monkey phylogeny, upon which we have reconstructed the biogeographic history of extant platyrrhines. In order to generate sufficient phylogenetic signal within the New World monkey clade, we carried out a large-scale phylogenetic analysis of approximately 40 kb of non-genic genomic DNA sequence in a 36 species subset of extant New World monkeys. Maximum parsimony, maximum likelihood and Bayesian inference analysis all converged on a single optimal tree topology. Divergence dating and biogeographic analysis reconstruct the timing and geographic location of divergence events. The ancestral area reconstruction describes the geographic locations of the last common ancestor of extant platyrrhines and provides insight into key biogeographic events occurring during platyrrhine diversification. Through these analyses we conclude that the diversification of the platyrrhines took place concurrently with the establishment and diversification of the Amazon rainforest. This suggests that an expanding rainforest environment rather than geographic isolation drove platyrrhine diversification. Copyright © 2014 Elsevier Inc. All rights reserved.

Offsite radiological consequence analysis for the bounding flammable gas accident

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

CARRO, C.A.

2003-03-19

The purpose of this analysis is to calculate the offsite radiological consequence of the bounding flammable gas accident. DOE-STD-3009-94, ''Preparation Guide for U.S. Department of Energy Nonreactor Nuclear Facility Documented Safety Analyses'', requires the formal quantification of a limited subset of accidents representing a complete set of bounding conditions. The results of these analyses are then evaluated to determine if they challenge the DOE-STD-3009-94, Appendix A, ''Evaluation Guideline,'' of 25 rem total effective dose equivalent in order to identify and evaluate safety class structures, systems, and components. The bounding flammable gas accident is a detonation in a single-shell tank (SST).more » A detonation versus a deflagration was selected for analysis because the faster flame speed of a detonation can potentially result in a larger release of respirable material. As will be shown, the consequences of a detonation in either an SST or a double-shell tank (DST) are approximately equal. A detonation in an SST was selected as the bounding condition because the estimated respirable release masses are the same and because the doses per unit quantity of waste inhaled are generally greater for SSTs than for DSTs. Appendix A contains a DST analysis for comparison purposes.« less

On sample size and different interpretations of snow stability datasets

NASA Astrophysics Data System (ADS)

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

2009-04-01

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

Use of supplemental long-chain omega-3 fatty acids and risk for cardiac death: An updated meta-analysis and review of research gaps.

PubMed

Maki, Kevin C; Palacios, Orsolya M; Bell, Marjorie; Toth, Peter P

Randomized controlled trials (RCTs) assessing use of long-chain omega-3 polyunsaturated fatty acids (LC-OM3), primarily eicosapentaenoic acid, and/or docosahexaenoic acid have shown mixed results. The objectives of the study were to update and further explore the available RCT data regarding LC-OM3 supplementation and risk for cardiac death and to propose testable hypotheses for the mixed results obtained in RCTs regarding supplemental LC-OM3 use and cardiac risk. A literature search was conducted using PubMed and Ovid/MEDLINE for RCTs assessing LC-OM3 supplements or pharmaceuticals with intervention periods of at least 6 months and reporting on the outcome of cardiac death. Meta-analysis was used to compare cumulative frequencies of cardiac death events between the LC-OM3 and control groups, including sensitivity and subset analyses. Fourteen RCTs were identified for the primary analysis (71,899 subjects). In the LC-OM3 arms, 1613 cardiac deaths were recorded (4.48% of subjects), compared with 1746 cardiac deaths in the control groups (4.87% of subjects). The pooled relative risk estimate showed an 8.0% (95% confidence interval 1.6%, 13.9%, P = .015) lower risk in the LC-OM3 arms vs controls. Subset analyses showed numerically larger effects (12.9%-29.1% lower risks, all P < .05) in subsets of RCTs with eicosapentaenoic acid + docosahexaenoic acid dosages >1 g/d and higher risk samples (secondary prevention, baseline mean or median triglycerides ≥150 mg/dL, low-density lipoprotein cholesterol ≥130 mg/dL, statin use <40% of subjects). Heterogeneity was low (I 2  ≤ 15.5%, P > .05) for the primary and subset analyses. LC-OM3 supplementation is associated with a modest reduction in cardiac death. Copyright © 2017 National Lipid Association. Published by Elsevier Inc. All rights reserved.

Single-cell analysis of lymphokine imbalance in asymptomatic HIV-1 infection: evidence for a major alteration within the CD8+ T cell subset

PubMed Central

Sousa, A E; Victorino, R M M

1998-01-01

In this study we investigated at single-cell level by flow cytometry the potential of T cell cytokine production in asymptomatic HIV-1-infected subjects with > 200 CD4 counts and possible correlation with T helper cell depletion and viral load. Mitogen-stimulated peripheral blood mononuclear cells from 32 HIV-1+ patients and 16 healthy subjects were intracytoplasmically stained for IL-2, interferon-gamma (IFN-γ), IL-4 or IL-10, and the frequency of cytokine-producing cells was assessed in total T cells, CD4, CD8 and CD45RO subsets as well as in CD69+CD3+ gated lymphocytes. HIV-1+ patients, irrespective of their degree of CD4 depletion, exhibited a major increase in IFN-γ+ CD8 T cells, largely due to CD28− cells, as well as a decrease in the capacity of CD8 T cells to produce IL-2. Patients with > 500 CD4 counts showed a diminished frequency of IL-4 expression in CD4 T cells and a negative correlation was found between this parameter and the ex vivo CD4 counts in the 32 patients. Analysis of patients stratified according to viral load revealed a significantly higher proportion of IL-2-producing CD4 cells in the group with < 5000 RNA copies/ml. In short, using single-cell analysis and an antigen-presenting cell-independent stimulus, we have not been able to find any significant cytokine imbalances in the CD4 subset, suggesting that the well described T helper defects are not due to intrinsic alterations in the potential of CD4 T cells to produce cytokines. On the other hand, the major disturbances in the CD8 T lymphocytes agree with the marked activation and possible replicative senescence of CD8 T cells and emphasize the role of this subset in HIV immunopathogenesis. PMID:9649194

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Selective principal component regression analysis of fluorescence hyperspectral image to assess aflatoxin contamination in corn

USDA-ARS?s Scientific Manuscript database

Selective principal component regression analysis (SPCR) uses a subset of the original image bands for principal component transformation and regression. For optimal band selection before the transformation, this paper used genetic algorithms (GA). In this case, the GA process used the regression co...

Analysis of variograms with various sample sizes from a multispectral image

USDA-ARS?s Scientific Manuscript database

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

Analysis of variograms with various sample sizes from a multispectral image

USDA-ARS?s Scientific Manuscript database

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

Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33.

PubMed

Wang, Zhaoming; Zhu, Bin; Zhang, Mingfeng; Parikh, Hemang; Jia, Jinping; Chung, Charles C; Sampson, Joshua N; Hoskins, Jason W; Hutchinson, Amy; Burdette, Laurie; Ibrahim, Abdisamad; Hautman, Christopher; Raj, Preethi S; Abnet, Christian C; Adjei, Andrew A; Ahlbom, Anders; Albanes, Demetrius; Allen, Naomi E; Ambrosone, Christine B; Aldrich, Melinda; Amiano, Pilar; Amos, Christopher; Andersson, Ulrika; Andriole, Gerald; Andrulis, Irene L; Arici, Cecilia; Arslan, Alan A; Austin, Melissa A; Baris, Dalsu; Barkauskas, Donald A; Bassig, Bryan A; Beane Freeman, Laura E; Berg, Christine D; Berndt, Sonja I; Bertazzi, Pier Alberto; Biritwum, Richard B; Black, Amanda; Blot, William; Boeing, Heiner; Boffetta, Paolo; Bolton, Kelly; Boutron-Ruault, Marie-Christine; Bracci, Paige M; Brennan, Paul; Brinton, Louise A; Brotzman, Michelle; Bueno-de-Mesquita, H Bas; Buring, Julie E; Butler, Mary Ann; Cai, Qiuyin; Cancel-Tassin, Geraldine; Canzian, Federico; Cao, Guangwen; Caporaso, Neil E; Carrato, Alfredo; Carreon, Tania; Carta, Angela; Chang, Gee-Chen; Chang, I-Shou; Chang-Claude, Jenny; Che, Xu; Chen, Chien-Jen; Chen, Chih-Yi; Chen, Chung-Hsing; Chen, Constance; Chen, Kuan-Yu; Chen, Yuh-Min; Chokkalingam, Anand P; Chu, Lisa W; Clavel-Chapelon, Francoise; Colditz, Graham A; Colt, Joanne S; Conti, David; Cook, Michael B; Cortessis, Victoria K; Crawford, E David; Cussenot, Olivier; Davis, Faith G; De Vivo, Immaculata; Deng, Xiang; Ding, Ti; Dinney, Colin P; Di Stefano, Anna Luisa; Diver, W Ryan; Duell, Eric J; Elena, Joanne W; Fan, Jin-Hu; Feigelson, Heather Spencer; Feychting, Maria; Figueroa, Jonine D; Flanagan, Adrienne M; Fraumeni, Joseph F; Freedman, Neal D; Fridley, Brooke L; Fuchs, Charles S; Gago-Dominguez, Manuela; Gallinger, Steven; Gao, Yu-Tang; Gapstur, Susan M; Garcia-Closas, Montserrat; Garcia-Closas, Reina; Gastier-Foster, Julie M; Gaziano, J Michael; Gerhard, Daniela S; Giffen, Carol A; Giles, Graham G; Gillanders, Elizabeth M; Giovannucci, Edward L; Goggins, Michael; Gokgoz, Nalan; Goldstein, Alisa M; Gonzalez, Carlos; Gorlick, Richard; Greene, Mark H; Gross, Myron; Grossman, H Barton; Grubb, Robert; Gu, Jian; Guan, Peng; Haiman, Christopher A; Hallmans, Goran; Hankinson, Susan E; Harris, Curtis C; Hartge, Patricia; Hattinger, Claudia; Hayes, Richard B; He, Qincheng; Helman, Lee; Henderson, Brian E; Henriksson, Roger; Hoffman-Bolton, Judith; Hohensee, Chancellor; Holly, Elizabeth A; Hong, Yun-Chul; Hoover, Robert N; Hosgood, H Dean; Hsiao, Chin-Fu; Hsing, Ann W; Hsiung, Chao Agnes; Hu, Nan; Hu, Wei; Hu, Zhibin; Huang, Ming-Shyan; Hunter, David J; Inskip, Peter D; Ito, Hidemi; Jacobs, Eric J; Jacobs, Kevin B; Jenab, Mazda; Ji, Bu-Tian; Johansen, Christoffer; Johansson, Mattias; Johnson, Alison; Kaaks, Rudolf; Kamat, Ashish M; Kamineni, Aruna; Karagas, Margaret; Khanna, Chand; Khaw, Kay-Tee; Kim, Christopher; Kim, In-Sam; Kim, Jin Hee; Kim, Yeul Hong; Kim, Young-Chul; Kim, Young Tae; Kang, Chang Hyun; Jung, Yoo Jin; Kitahara, Cari M; Klein, Alison P; Klein, Robert; Kogevinas, Manolis; Koh, Woon-Puay; Kohno, Takashi; Kolonel, Laurence N; Kooperberg, Charles; Kratz, Christian P; Krogh, Vittorio; Kunitoh, Hideo; Kurtz, Robert C; Kurucu, Nilgun; Lan, Qing; Lathrop, Mark; Lau, Ching C; Lecanda, Fernando; Lee, Kyoung-Mu; Lee, Maxwell P; Le Marchand, Loic; Lerner, Seth P; Li, Donghui; Liao, Linda M; Lim, Wei-Yen; Lin, Dongxin; Lin, Jie; Lindstrom, Sara; Linet, Martha S; Lissowska, Jolanta; Liu, Jianjun; Ljungberg, Börje; Lloreta, Josep; Lu, Daru; Ma, Jing; Malats, Nuria; Mannisto, Satu; Marina, Neyssa; Mastrangelo, Giuseppe; Matsuo, Keitaro; McGlynn, Katherine A; McKean-Cowdin, Roberta; McNeill, Lorna H; McWilliams, Robert R; Melin, Beatrice S; Meltzer, Paul S; Mensah, James E; Miao, Xiaoping; Michaud, Dominique S; Mondul, Alison M; Moore, Lee E; Muir, Kenneth; Niwa, Shelley; Olson, Sara H; Orr, Nick; Panico, Salvatore; Park, Jae Yong; Patel, Alpa V; Patino-Garcia, Ana; Pavanello, Sofia; Peeters, Petra H M; Peplonska, Beata; Peters, Ulrike; Petersen, Gloria M; Picci, Piero; Pike, Malcolm C; Porru, Stefano; Prescott, Jennifer; Pu, Xia; Purdue, Mark P; Qiao, You-Lin; Rajaraman, Preetha; Riboli, Elio; Risch, Harvey A; Rodabough, Rebecca J; Rothman, Nathaniel; Ruder, Avima M; Ryu, Jeong-Seon; Sanson, Marc; Schned, Alan; Schumacher, Fredrick R; Schwartz, Ann G; Schwartz, Kendra L; Schwenn, Molly; Scotlandi, Katia; Seow, Adeline; Serra, Consol; Serra, Massimo; Sesso, Howard D; Severi, Gianluca; Shen, Hongbing; Shen, Min; Shete, Sanjay; Shiraishi, Kouya; Shu, Xiao-Ou; Siddiq, Afshan; Sierrasesumaga, Luis; Sierri, Sabina; Loon Sihoe, Alan Dart; Silverman, Debra T; Simon, Matthias; Southey, Melissa C; Spector, Logan; Spitz, Margaret; Stampfer, Meir; Stattin, Par; Stern, Mariana C; Stevens, Victoria L; Stolzenberg-Solomon, Rachael Z; Stram, Daniel O; Strom, Sara S; Su, Wu-Chou; Sund, Malin; Sung, Sook Whan; Swerdlow, Anthony; Tan, Wen; Tanaka, Hideo; Tang, Wei; Tang, Ze-Zhang; Tardon, Adonina; Tay, Evelyn; Taylor, Philip R; Tettey, Yao; Thomas, David M; Tirabosco, Roberto; Tjonneland, Anne; Tobias, Geoffrey S; Toro, Jorge R; Travis, Ruth C; Trichopoulos, Dimitrios; Troisi, Rebecca; Truelove, Ann; Tsai, Ying-Huang; Tucker, Margaret A; Tumino, Rosario; Van Den Berg, David; Van Den Eeden, Stephen K; Vermeulen, Roel; Vineis, Paolo; Visvanathan, Kala; Vogel, Ulla; Wang, Chaoyu; Wang, Chengfeng; Wang, Junwen; Wang, Sophia S; Weiderpass, Elisabete; Weinstein, Stephanie J; Wentzensen, Nicolas; Wheeler, William; White, Emily; Wiencke, John K; Wolk, Alicja; Wolpin, Brian M; Wong, Maria Pik; Wrensch, Margaret; Wu, Chen; Wu, Tangchun; Wu, Xifeng; Wu, Yi-Long; Wunder, Jay S; Xiang, Yong-Bing; Xu, Jun; Yang, Hannah P; Yang, Pan-Chyr; Yatabe, Yasushi; Ye, Yuanqing; Yeboah, Edward D; Yin, Zhihua; Ying, Chen; Yu, Chong-Jen; Yu, Kai; Yuan, Jian-Min; Zanetti, Krista A; Zeleniuch-Jacquotte, Anne; Zheng, Wei; Zhou, Baosen; Mirabello, Lisa; Savage, Sharon A; Kraft, Peter; Chanock, Stephen J; Yeager, Meredith; Landi, Maria Terese; Shi, Jianxin; Chatterjee, Nilanjan; Amundadottir, Laufey T

2014-12-15

Genome-wide association studies (GWAS) have mapped risk alleles for at least 10 distinct cancers to a small region of 63 000 bp on chromosome 5p15.33. This region harbors the TERT and CLPTM1L genes; the former encodes the catalytic subunit of telomerase reverse transcriptase and the latter may play a role in apoptosis. To investigate further the genetic architecture of common susceptibility alleles in this region, we conducted an agnostic subset-based meta-analysis (association analysis based on subsets) across six distinct cancers in 34 248 cases and 45 036 controls. Based on sequential conditional analysis, we identified as many as six independent risk loci marked by common single-nucleotide polymorphisms: five in the TERT gene (Region 1: rs7726159, P = 2.10 × 10(-39); Region 3: rs2853677, P = 3.30 × 10(-36) and PConditional = 2.36 × 10(-8); Region 4: rs2736098, P = 3.87 × 10(-12) and PConditional = 5.19 × 10(-6), Region 5: rs13172201, P = 0.041 and PConditional = 2.04 × 10(-6); and Region 6: rs10069690, P = 7.49 × 10(-15) and PConditional = 5.35 × 10(-7)) and one in the neighboring CLPTM1L gene (Region 2: rs451360; P = 1.90 × 10(-18) and PConditional = 7.06 × 10(-16)). Between three and five cancers mapped to each independent locus with both risk-enhancing and protective effects. Allele-specific effects on DNA methylation were seen for a subset of risk loci, indicating that methylation and subsequent effects on gene expression may contribute to the biology of risk variants on 5p15.33. Our results provide strong support for extensive pleiotropy across this region of 5p15.33, to an extent not previously observed in other cancer susceptibility loci. Published by Oxford University Press 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Stem-like plasticity and heterogeneity of circulating tumor cells: current status and prospect challenges in liver cancer

PubMed Central

Correnti, Margherita; Raggi, Chiara

2017-01-01

Poor prognosis and high recurrence remain leading causes of primary liver cancerassociated mortality. The spread of circulating tumor cells (CTCs) in the blood plays a major role in the initiation of metastasis and tumor recurrence after surgery. Nevertheless, only a subset of CTCs can survive, migrate to distant sites and establish secondary tumors. Consistent with cancer stem cell (CSC) hypothesis, stem-like CTCs might represent a potential source for cancer relapse and distant metastasis. Thus, identification of stem-like metastasis-initiating CTC-subset may provide useful clinically prognostic information. This review will emphasize the most relevant findings of CTCs in the context of stem-like biology associated to liver carcinogenesis. In this view, the emerging field of stem-like CTCs may deliver substantial contribution in liver cancer field in order to move to personalized approaches for diagnosis, prognosis and therapy. PMID:27738343

A web-based platform for virtual screening.

PubMed

Watson, Paul; Verdonk, Marcel; Hartshorn, Michael J

2003-09-01

A fully integrated, web-based, virtual screening platform has been developed to allow rapid virtual screening of large numbers of compounds. ORACLE is used to store information at all stages of the process. The system includes a large database of historical compounds from high throughput screenings (HTS) chemical suppliers, ATLAS, containing over 3.1 million unique compounds with their associated physiochemical properties (ClogP, MW, etc.). The database can be screened using a web-based interface to produce compound subsets for virtual screening or virtual library (VL) enumeration. In order to carry out the latter task within ORACLE a reaction data cartridge has been developed. Virtual libraries can be enumerated rapidly using the web-based interface to the cartridge. The compound subsets can be seamlessly submitted for virtual screening experiments, and the results can be viewed via another web-based interface allowing ad hoc querying of the virtual screening data stored in ORACLE.

Superiorization with level control

NASA Astrophysics Data System (ADS)

Cegielski, Andrzej; Al-Musallam, Fadhel

2017-04-01

The convex feasibility problem is to find a common point of a finite family of closed convex subsets. In many applications one requires something more, namely finding a common point of closed convex subsets which minimizes a continuous convex function. The latter requirement leads to an application of the superiorization methodology which is actually settled between methods for convex feasibility problem and the convex constrained minimization. Inspired by the superiorization idea we introduce a method which sequentially applies a long-step algorithm for a sequence of convex feasibility problems; the method employs quasi-nonexpansive operators as well as subgradient projections with level control and does not require evaluation of the metric projection. We replace a perturbation of the iterations (applied in the superiorization methodology) by a perturbation of the current level in minimizing the objective function. We consider the method in the Euclidean space in order to guarantee the strong convergence, although the method is well defined in a Hilbert space.

Estimation of the lower and upper bounds on the probability of failure using subset simulation and random set theory

NASA Astrophysics Data System (ADS)

Alvarez, Diego A.; Uribe, Felipe; Hurtado, Jorge E.

2018-02-01

Random set theory is a general framework which comprises uncertainty in the form of probability boxes, possibility distributions, cumulative distribution functions, Dempster-Shafer structures or intervals; in addition, the dependence between the input variables can be expressed using copulas. In this paper, the lower and upper bounds on the probability of failure are calculated by means of random set theory. In order to accelerate the calculation, a well-known and efficient probability-based reliability method known as subset simulation is employed. This method is especially useful for finding small failure probabilities in both low- and high-dimensional spaces, disjoint failure domains and nonlinear limit state functions. The proposed methodology represents a drastic reduction of the computational labor implied by plain Monte Carlo simulation for problems defined with a mixture of representations for the input variables, while delivering similar results. Numerical examples illustrate the efficiency of the proposed approach.

Comparison of Different EHG Feature Selection Methods for the Detection of Preterm Labor

PubMed Central

Alamedine, D.; Khalil, M.; Marque, C.

2013-01-01

Numerous types of linear and nonlinear features have been extracted from the electrohysterogram (EHG) in order to classify labor and pregnancy contractions. As a result, the number of available features is now very large. The goal of this study is to reduce the number of features by selecting only the relevant ones which are useful for solving the classification problem. This paper presents three methods for feature subset selection that can be applied to choose the best subsets for classifying labor and pregnancy contractions: an algorithm using the Jeffrey divergence (JD) distance, a sequential forward selection (SFS) algorithm, and a binary particle swarm optimization (BPSO) algorithm. The two last methods are based on a classifier and were tested with three types of classifiers. These methods have allowed us to identify common features which are relevant for contraction classification. PMID:24454536

Beyond NK cells: the expanding universe of innate lymphoid cells.

PubMed

Cella, Marina; Miller, Hannah; Song, Christina

2014-01-01

For a long time, natural killer (NK) cells were thought to be the only innate immune lymphoid population capable of responding to invading pathogens under the influence of changing environmental cues. In the last few years, an increasing amount of evidence has shown that a number of different innate lymphoid cell (ILC) populations found at mucosal sites rapidly respond to locally produced cytokines in order to establish or maintain homeostasis. These ILC populations closely mirror the phenotype of adaptive T helper subsets in their repertoire of secreted soluble factors. Early in the immune response, ILCs are responsible for setting the stage to mount an adaptive T cell response that is appropriate for the incoming insult. Here, we review the diversity of ILC subsets and discuss similarities and differences between ILCs and NK cells in function and key transcriptional factors required for their development.

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.

Enhancing the Discrimination Ability of a Gas Sensor Array Based on a Novel Feature Selection and Fusion Framework.

PubMed

Deng, Changjian; Lv, Kun; Shi, Debo; Yang, Bo; Yu, Song; He, Zhiyi; Yan, Jia

2018-06-12

In this paper, a novel feature selection and fusion framework is proposed to enhance the discrimination ability of gas sensor arrays for odor identification. Firstly, we put forward an efficient feature selection method based on the separability and the dissimilarity to determine the feature selection order for each type of feature when increasing the dimension of selected feature subsets. Secondly, the K-nearest neighbor (KNN) classifier is applied to determine the dimensions of the optimal feature subsets for different types of features. Finally, in the process of establishing features fusion, we come up with a classification dominance feature fusion strategy which conducts an effective basic feature. Experimental results on two datasets show that the recognition rates of Database I and Database II achieve 97.5% and 80.11%, respectively, when k = 1 for KNN classifier and the distance metric is correlation distance (COR), which demonstrates the superiority of the proposed feature selection and fusion framework in representing signal features. The novel feature selection method proposed in this paper can effectively select feature subsets that are conducive to the classification, while the feature fusion framework can fuse various features which describe the different characteristics of sensor signals, for enhancing the discrimination ability of gas sensors and, to a certain extent, suppressing drift effect.

Unique capabilities of AC frequency scanning and its implementation on a Mars Organic Molecule Analyzer linear ion trap.

PubMed

Snyder, Dalton T; Kaplan, Desmond A; Danell, Ryan M; van Amerom, Friso H W; Pinnick, Veronica T; Brinckerhoff, William B; Mahaffy, Paul R; Cooks, R Graham

2017-06-21

A limitation of conventional quadrupole ion trap scan modes which use rf amplitude control for mass scanning is that, in order to detect a subset of an ion population, the rest of the ion population must also be interrogated. That is, ions cannot be detected out of order; they must be detected in order of either increasing or decreasing mass-to-charge (m/z). However, an ion trap operated in the ac frequency scan mode, where the rf amplitude is kept constant and instead the ac frequency is used for mass-selective operations, has no such limitation because any variation in the ac frequency affects only the subset of ions whose secular frequencies match the perturbation frequency. Hence, an ion trap operated in the ac frequency scan mode can perform any arbitrary mass scan, as well as a sequence of scans, using a single ion injection; we demonstrate both capabilities here. Combining these two capabilities, we demonstrate the acquisition of a full mass spectrum, a product ion spectrum, and a second generation product ion spectrum using a single ion injection event. We further demonstrate a "segmented scan" in which different mass ranges are interrogated at different rf amplitudes in order to improve resolution over a portion of the mass range, and a "periodic scan" in which ions are continuously introduced into the ion trap to achieve a nearly 100% duty cycle. These unique scan modes, along with other characteristics of ac frequency scanning, are particularly appropriate for miniature ion trap mass spectrometers. Hence, implementation of ac frequency scanning on a prototype of the Mars Organic Molecule Analyzer mass spectrometer is also described.

Analyzing lichen indicator data in the Forest Inventory and Analysis Program

Treesearch

Susan Will-Wolf

2010-01-01

Lichens are one of several forest health indicators sampled every year for a subset of plots on the permanent grid established by the Forest Inventory and Analysis (FIA) Program of the U.S. Department of Agriculture Forest Service. This report reviews analysis procedures for standard FIA lichen indicator data. Analyses of lichen data contribute to state, regional, and...

The Analysis of Dimensionality Reduction Techniques in Cryptographic Object Code Classification

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

Jason L. Wright; Milos Manic

2010-05-01

This paper compares the application of three different dimension reduction techniques to the problem of locating cryptography in compiled object code. A simple classi?er is used to compare dimension reduction via sorted covariance, principal component analysis, and correlation-based feature subset selection. The analysis concentrates on the classi?cation accuracy as the number of dimensions is increased.

Association of bladder sensation measures and bladder diary in patients with urinary incontinence.

PubMed

King, Ashley B; Wolters, Jeff P; Klausner, Adam P; Rapp, David E

2012-04-01

Investigation suggests the involvement of afferent actions in the pathophysiology of urinary incontinence. Current diagnostic modalities do not allow for the accurate identification of sensory dysfunction. We previously reported urodynamic derivatives that may be useful in assessing bladder sensation. We sought to further investigate these derivatives by assessing for a relationship with 3-day bladder diary. Subset analysis was performed in patients without stress urinary incontinence (SUI) attempting to isolate patients with urgency symptoms. No association was demonstrated between bladder diary parameters and urodynamic derivatives (r coefficient range (-0.06 to 0.08)(p > 0.05)). However, subset analysis demonstrated an association between detrusor overactivity (DO) and bladder urgency velocity (BUV), with a lower BUV identified in patients without DO. Subset analysis of patients with isolated urgency/urge incontinence identified weak associations between voiding frequency and FSR (r = 0.39) and between daily incontinence episodes and BUV (r = 0.35). However, these associations failed to demonstrate statistical significance. No statistical association was seen between bladder diary and urodynamic derivatives. This is not unexpected, given that bladder diary parameters may reflect numerous pathologies including not only sensory dysfunction but also SUI and DO. However, weak associations were identified in patients without SUI and, further, a statistical relationship between DO and BUV was seen. Additional research is needed to assess the utility of FSR/BUV in characterizing sensory dysfunction, especially in patients without concurrent pathology (e.g. SUI, DO).

3D tomographic imaging with the γ-eye planar scintigraphic gamma camera

NASA Astrophysics Data System (ADS)

Tunnicliffe, H.; Georgiou, M.; Loudos, G. K.; Simcox, A.; Tsoumpas, C.

2017-11-01

γ-eye is a desktop planar scintigraphic gamma camera (100 mm × 50 mm field of view) designed by BET Solutions as an affordable tool for dynamic, whole body, small-animal imaging. This investigation tests the viability of using γ-eye for the collection of tomographic data for 3D SPECT reconstruction. Two software packages, QSPECT and STIR (software for tomographic image reconstruction), have been compared. Reconstructions have been performed using QSPECT’s implementation of the OSEM algorithm and STIR’s OSMAPOSL (Ordered Subset Maximum A Posteriori One Step Late) and OSSPS (Ordered Subsets Separable Paraboloidal Surrogate) algorithms. Reconstructed images of phantom and mouse data have been assessed in terms of spatial resolution, sensitivity to varying activity levels and uniformity. The effect of varying the number of iterations, the voxel size (1.25 mm default voxel size reduced to 0.625 mm and 0.3125 mm), the point spread function correction and the weight of prior terms were explored. While QSPECT demonstrated faster reconstructions, STIR outperformed it in terms of resolution (as low as 1 mm versus 3 mm), particularly when smaller voxel sizes were used, and in terms of uniformity, particularly when prior terms were used. Little difference in terms of sensitivity was seen throughout.

Uses of NHANES biomarker data for chemical risk ...

EPA Pesticide Factsheets

Background. Each year, the US NHANES measures hundreds of chemical biomarkers in samples from thousands of study participants. These biomarker measurements are meant to track trends and identify subsets of the US population with elevated exposures. There is now interest in further utilizing the NHANES data to inform chemical risk assessments. Objectives. This article highlights: 1) the extent to which NHANES chemical biomarker data have been evaluated, 2) groups of chemicals that have been studied, 3) data analysis approaches, and 4) opportunities for using these data to inform chemical risk assessments.Methods. A literature search (1999-2013) was performed to identify publications in which NHANES data were reported. Manual curation identified only the subset of publications that clearly utilized chemical biomarker data. This subset was evaluated for chemical groupings, data analysis approaches, and overall trends.Results. A small percentage of yearly NHANES-related publications reported on chemical biomarkers (8% yearly average). Of eleven chemical groups, metals/metalloids were most frequently evaluated (49%), followed by pesticides (9%) and environmental phenols (7%). Studies of multiple chemical groups were also common (8%). Publications linking chemical biomarkers to health metrics have increased dramatically in recent years. New studies are addressing challenges related to NHANES data interpretation in health risk contexts.Conclusions. This articl

Rapid activation of spleen dendritic cell subsets following lymphocytic choriomeningitis virus infection of mice: analysis of the involvement of type 1 IFN.

PubMed

Montoya, Maria; Edwards, Matthew J; Reid, Delyth M; Borrow, Persephone

2005-02-15

In this study, we report the dynamic changes in activation and functions that occur in spleen dendritic cell (sDC) subsets following infection of mice with a natural murine pathogen, lymphocytic choriomeningitis virus (LCMV). Within 24 h postinfection (pi), sDCs acquired the ability to stimulate naive LCMV-specific CD8+ T cells ex vivo. Conventional (CD11chigh CD8+ and CD4+) sDC subsets rapidly up-regulated expression of costimulatory molecules and began to produce proinflammatory cytokines. Their tendency to undergo apoptosis ex vivo simultaneously increased, and in vivo the number of conventional DCs in the spleen decreased markedly, dropping approximately 2-fold by day 3 pi. Conversely, the number of plasmacytoid (CD11clowB220+) DCs in the spleen increased, so that they constituted almost 40% of sDCs by day 3 pi. Type 1 IFN production was up-regulated in plasmacytoid DCs by 24 h pi. Analysis of DC activation and maturation in mice unable to respond to type 1 IFNs implicated these cytokines in driving infection-associated phenotypic activation of conventional DCs and their enhanced tendency to undergo apoptosis, but also indicated the existence of type 1 IFN-independent pathways for the functional maturation of DCs during LCMV infection.

Long noncoding RNAs (lncRNAs) dynamics evidence immunomodulation during ISAV-Infected Atlantic salmon (Salmo salar).

PubMed

Boltaña, Sebastian; Valenzuela-Miranda, Diego; Aguilar, Andrea; Mackenzie, Simon; Gallardo-Escárate, Cristian

2016-03-04

Despite evidence for participation in the host response to infection, the roles of many long non-coding RNAs (lncRNAs) remain unknown. Therefore, the aims of this study were to identify lncRNAs in Atlantic salmon (Salmo salar) and evaluate their transcriptomic regulation during ISA virus (ISAV) infection, an Orthomyxoviridae virus associated with high mortalities in salmonid aquaculture. Using next-generation sequencing, whole-transcriptome analysis of the Salmo salar response to ISAV infection was performed, identifying 5,636 putative lncRNAs with a mean length of 695 base pairs. The transcriptional modulation evidenced a similar number of differentially expressed lncRNAs in the gills (3,294), head-kidney (3,275), and liver (3,325) over the course of the infection. Moreover, analysis of a subset of these lncRNAs showed the following: (i) Most were similarly regulated in response to ISA virus infection; (ii) The transcript subsets were uniquely modulated in each tissue (gills, liver, and head-kidney); and (iii) A subset of lncRNAs were upregulated for each tissue and time analysed, indicating potential markers for ISAV infection. These findings represent the first discovery of widespread differential expression of lncRNAs in response to virus infection in non-model species, suggesting that lncRNAs could be involved in regulating the host response during ISAV infection.

Radiographic estimation in seropositive and seronegative rheumatoid arthritis

PubMed Central

Sahatçiu-Meka, Vjollca; Rexhepi, Sylejman; Manxhuka-Kërliu, Suzana; Rexhepi, Mjellma

2011-01-01

Long since it have been suggested that a subpopulation of patients with rheumatoid arthritis, diagnosed with negative rheumatoid factor tests, represents a clinical entity quite distinct from that of seropositive rheumatoid arthritis (RA). Our aim was to establish a scientific comparative analysis between seronegative and seropositive rheumatoid arthritis, regarding some radiological and clinical parameters, applied for the first time on patients from Kosovo. Two hundred fifty patients with rheumatoid arthritis according to the American College of Rheumatology criteria were retrospectively studied by analysis the radiographic damage and clinical parameters of the disease, using a data base. All examinees were between 25-60 years of age (Xb=49.96, SD=10.37) with disease duration between 1-27 years (Xb = 6.41, SD=6.47). All patients underwent a standardised evaluation radiographs. Baseline standardised poster anterior radiographs of hands and feet and radiographs of other joints, depending on indications, were assessed. Erythrocyte sedimentation rate values correlated with the radiological damages and statistical difference was found for seronegative subset (r=0.24, p<0.01). Longer duration of the disease resulted in the increase of radiological changes in both subsets (r=0.66, p<0.01) seronegative, (r=0.49, p<0.01) seropositive. Anatomic changes of IInd and IIIrd level were nearly equally distributed in both subsets, 76 (60.8%) seronegative, 75 (60%) seropositive. Radiological damages are nearly equal in both subsets, elevate in relation to the duration of the disease and correlate with ESR values. Regarding the sero-status, differences within sex, with some exceptions, are not relevant. Although there are some definite quantitative and qualitative differences regarding sero-status, obviously there is a great deal of overlap between the two groups. PMID:21875421

Radiographic estimation in seropositive and seronegative rheumatoid arthritis.

PubMed

Sahatçiu-Meka, Vjollca; Rexhepi, Sylejman; Manxhuka-Kërliu, Suzana; Rexhepi, Mjellma

2011-08-01

Long since it have been suggested that a subpopulation of patients with rheumatoid arthritis, diagnosed with negative rheumatoid factor tests, represents a clinical entity quite distinct from that of seropositive rheumatoid arthritis (RA). Our aim was to establish a scientific comparative analysis between seronegative and seropositive rheumatoid arthritis, regarding some radiological and clinical parameters, applied for the first time on patients from Kosovo. Two hundred fifty patients with rheumatoid arthritis according to the American College of Rheumatology criteria were retrospectively studied by analysis the radiographic damage and clinical parameters of the disease, using a data base. All examinees were between 25-60 years of age (Xb=49.96, SD=10.37) with disease duration between 1-27 years (Xb = 6.41, SD=6.47). All patients underwent a standardised evaluation radiographs. Baseline standardised poster anterior radiographs of hands and feet and radiographs of other joints, depending on indications, were assessed. Erythrocyte sedimentation rate values correlated with the radiological damages and statistical difference was found for seronegative subset (r=0.24, p<0.01). Longer duration of the disease resulted in the increase of radiological changes in both subsets (r=0.66, p<0.01) seronegative, (r=0.49, p<0.01) seropositive. Anatomic changes of IInd and IIIrd level were nearly equally distributed in both subsets, 76 (60.8%) seronegative, 75 (60%) seropositive. Radiological damages are nearly equal in both subsets, elevate in relation to the duration of the disease and correlate with ESR values. Regarding the sero-status, differences within sex, with some exceptions, are not relevant. Although there are some definite quantitative and qualitative differences regarding sero-status, obviously there is a great deal of overlap between the two groups.

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

PubMed

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

2013-11-01

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

A Concise and Practical Framework for the Development and Usability Evaluation of Patient Information Websites.

PubMed

Peute, L W; Knijnenburg, S L; Kremer, L C; Jaspers, M W M

2015-01-01

The Website Developmental Model for the Healthcare Consumer (WDMHC) is an extensive and successfully evaluated framework that incorporates user-centered design principles. However, due to its extensiveness its application is limited. In the current study we apply a subset of the WDMHC framework in a case study concerning the development and evaluation of a website aimed at childhood cancer survivors (CCS). To assess whether the implementation of a limited subset of the WDMHC-framework is sufficient to deliver a high-quality website with few usability problems, aimed at a specific patient population. The website was developed using a six-step approach divided into three phases derived from the WDMHC: 1) information needs analysis, mock-up creation and focus group discussion; 2) website prototype development; and 3) heuristic evaluation (HE) and think aloud analysis (TA). The HE was performed by three double experts (knowledgeable both in usability engineering and childhood cancer survivorship), who assessed the site using the Nielsen heuristics. Eight end-users were invited to complete three scenarios covering all functionality of the website by TA. The HE and TA were performed concurrently on the website prototype. The HE resulted in 29 unique usability issues; the end-users performing the TA encountered eleven unique problems. Four issues specifically revealed by HE concerned cosmetic design flaws, whereas two problems revealed by TA were related to website content. Based on the subset of the WDMHC framework we were able to deliver a website that closely matched the expectancy of the end-users and resulted in relatively few usability problems during end-user testing. With the successful application of this subset of the WDMHC, we provide developers with a clear and easily applicable framework for the development of healthcare websites with high usability aimed at specific medical populations.

Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium

PubMed Central

Finak, Greg; Langweiler, Marc; Jaimes, Maria; Malek, Mehrnoush; Taghiyar, Jafar; Korin, Yael; Raddassi, Khadir; Devine, Lesley; Obermoser, Gerlinde; Pekalski, Marcin L.; Pontikos, Nikolas; Diaz, Alain; Heck, Susanne; Villanova, Federica; Terrazzini, Nadia; Kern, Florian; Qian, Yu; Stanton, Rick; Wang, Kui; Brandes, Aaron; Ramey, John; Aghaeepour, Nima; Mosmann, Tim; Scheuermann, Richard H.; Reed, Elaine; Palucka, Karolina; Pascual, Virginia; Blomberg, Bonnie B.; Nestle, Frank; Nussenblatt, Robert B.; Brinkman, Ryan Remy; Gottardo, Raphael; Maecker, Holden; McCoy, J Philip

2016-01-01

Standardization of immunophenotyping requires careful attention to reagents, sample handling, instrument setup, and data analysis, and is essential for successful cross-study and cross-center comparison of data. Experts developed five standardized, eight-color panels for identification of major immune cell subsets in peripheral blood. These were produced as pre-configured, lyophilized, reagents in 96-well plates. We present the results of a coordinated analysis of samples across nine laboratories using these panels with standardized operating procedures (SOPs). Manual gating was performed by each site and by a central site. Automated gating algorithms were developed and tested by the FlowCAP consortium. Centralized manual gating can reduce cross-center variability, and we sought to determine whether automated methods could streamline and standardize the analysis. Within-site variability was low in all experiments, but cross-site variability was lower when central analysis was performed in comparison with site-specific analysis. It was also lower for clearly defined cell subsets than those based on dim markers and for rare populations. Automated gating was able to match the performance of central manual analysis for all tested panels, exhibiting little to no bias and comparable variability. Standardized staining, data collection, and automated gating can increase power, reduce variability, and streamline analysis for immunophenotyping. PMID:26861911

Update on laser vision correction using wavefront analysis with the CustomCornea system and LADARVision 193-nm excimer laser

NASA Astrophysics Data System (ADS)

Maguen, Ezra I.; Salz, James J.; McDonald, Marguerite B.; Pettit, George H.; Papaioannou, Thanassis; Grundfest, Warren S.

2002-06-01

A study was undertaken to assess whether results of laser vision correction with the LADARVISION 193-nm excimer laser (Alcon-Autonomous technologies) can be improved with the use of wavefront analysis generated by a proprietary system including a Hartman-Schack sensor and expressed using Zernicke polynomials. A total of 82 eyes underwent LASIK in several centers with an improved algorithm, using the CustomCornea system. A subgroup of 48 eyes of 24 patients was randomized so that one eye undergoes conventional treatment and one eye undergoes treatment based on wavefront analysis. Treatment parameters were equal for each type of refractive error. 83% of all eyes had uncorrected vision of 20/20 or better and 95% were 20/25 or better. In all groups, uncorrected visual acuities did not improve significantly in eyes treated with wavefront analysis compared to conventional treatments. Higher order aberrations were consistently better corrected in eyes undergoing treatment based on wavefront analysis for LASIK at 6 months postop. In addition, the number of eyes with reduced RMS was significantly higher in the subset of eyes treated with a wavefront algorithm (38% vs. 5%). Wavefront technology may improve the outcomes of laser vision correction with the LADARVISION excimer laser. Further refinements of the technology and clinical trials will contribute to this goal.

The Use of Cluster Analysis in Typological Research on Community College Students

ERIC Educational Resources Information Center

Bahr, Peter Riley; Bielby, Rob; House, Emily

2011-01-01

One useful and increasingly popular method of classifying students is known commonly as cluster analysis. The variety of techniques that comprise the cluster analytic family are intended to sort observations (for example, students) within a data set into subsets (clusters) that share similar characteristics and differ in meaningful ways from other…

Estimating Uncertainty in N2O Emissions from US Cropland Soils

USDA-ARS?s Scientific Manuscript database

A Monte Carlo analysis was combined with an empirically-based approach to quantify uncertainties in soil N2O emissions from US croplands estimated with the DAYCENT simulation model. Only a subset of croplands was simulated in the Monte Carlo analysis which was used to infer uncertainties across the ...

14 CFR Appendix M to Part 25 - Fuel Tank System Flammability Reduction Means

Code of Federal Regulations, 2013 CFR

2013-01-01

..., ground testing, and flight testing, or any combination of these, that: (1) Validate the parameters used... either ground or takeoff/climb phases of flight during warm days. The analysis must consider the following conditions. (1) The analysis must use the subset of those flights that begin with a sea level...

14 CFR Appendix M to Part 25 - Fuel Tank System Flammability Reduction Means

Code of Federal Regulations, 2014 CFR

2014-01-01

..., ground testing, and flight testing, or any combination of these, that: (1) Validate the parameters used... either ground or takeoff/climb phases of flight during warm days. The analysis must consider the following conditions. (1) The analysis must use the subset of those flights that begin with a sea level...

14 CFR Appendix M to Part 25 - Fuel Tank System Flammability Reduction Means

Code of Federal Regulations, 2012 CFR

2012-01-01

..., ground testing, and flight testing, or any combination of these, that: (1) Validate the parameters used... either ground or takeoff/climb phases of flight during warm days. The analysis must consider the following conditions. (1) The analysis must use the subset of those flights that begin with a sea level...

Practitioner Representations of Environmental Uncertainty: An Application of Discriminant Analysis.

ERIC Educational Resources Information Center

Acharya, Lalit

Multiple discriminant analysis was used to analyze the structure of a perceived environmental uncertainty variable employed previously in research on public relations roles. Data came from a subset (N=229) of a national sample of public relations practitioners belonging to the Public Relations Society of America, who completed a set of scaled…

Toolsets for Airborne Data (TAD): Enhanced Airborne Data Merging Functionality through Spatial and Temporal Subsetting

NASA Astrophysics Data System (ADS)

Early, A. B.; Chen, G.; Beach, A. L., III; Northup, E. A.

2016-12-01

NASA has conducted airborne tropospheric chemistry studies for over three decades. These field campaigns have generated a great wealth of observations, including a wide range of the trace gases and aerosol properties. The Atmospheric Science Data Center (ASDC) at NASA Langley Research Center in Hampton Virginia originally developed the Toolsets for Airborne Data (TAD) web application in September 2013 to meet the user community needs for manipulating aircraft data for scientific research on climate change and air quality relevant issues. The analysis of airborne data typically requires data subsetting, which can be challenging and resource intensive for end users. In an effort to streamline this process, the TAD toolset enhancements will include new data subsetting features and updates to the current database model. These will include two subsetters: temporal and spatial, and vertical profile. The temporal and spatial subsetter will allow users to both focus on data from a specific location and/or time period. The vertical profile subsetter will retrieve data collected during an individual aircraft ascent or descent spiral. This effort will allow for the automation of the typically labor-intensive manual data subsetting process, which will provide users with data tailored to their specific research interests. The development of these enhancements will be discussed in this presentation.

CD4+VEGFR1(HIGH) T cell as a novel Treg subset regulates inflammatory bowel disease in lymphopenic mice.

PubMed

Shin, Jin-Young; Yoon, Il-Hee; Lim, Jong-Hyung; Shin, Jun-Seop; Nam, Hye-Young; Kim, Yong-Hee; Cho, Hyoung-Soo; Hong, So-Hee; Kim, Jung-Sik; Lee, Won-Woo; Park, Chung-Gyu

2015-09-01

Regulatory T cells (Tregs) are a specialized subpopulation of T cells that control the immune response and thereby maintain immune system homeostasis and tolerance to self-antigens. Many subsets of CD4(+) Tregs have been identified, including Foxp3(+), Tr1, Th3, and Foxp3neg iT(R)35 cells. In this study, we identified a new subset of CD4(+)VEGFR1(high) Tregs that have immunosuppressive capacity. CD4(+)VEGFR1high T cells, which constitute approximately 1.0% of CD4(+) T cells, are hyporesponsive to T-cell antigen receptor stimulation. Surface marker and FoxP3 expression analysis revealed that CD4(+)VEGFR1(high) T cells are distinct from known Tregs. CD4(+)VEGFR1(high) T cells suppressed the proliferation of CD4(+)CD25(-) T cell as efficiently as CD4(+)CD25(high) natural Tregs in a contact-independent manner. Furthermore, adoptive transfer of CD4(+)VEGFR1(+) T cells from wild type to RAG-2-deficient C57BL/6 mice inhibited effector T-cell-mediated inflammatory bowel disease. Thus, we report CD4(+) VEGFR1(high) T cells as a novel subset of Tregs that regulate the inflammatory response in the intestinal tract.

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

PubMed Central

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

2016-01-01

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

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

PubMed

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

2016-01-01

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

Residual settlements detection of ocean reclaimed lands with multi-platform SAR time series and SBAS technique: a case study of Shanghai Pudong International Airport

NASA Astrophysics Data System (ADS)

Yu, Lei; Yang, Tianliang; Zhao, Qing; Pepe, Antonio; Dong, Hongbin; Sun, Zhibin

2017-09-01

Shanghai Pudong International airport is one of the three major international airports in China. The airport is located at the Yangtze estuary which is a sensitive belt of sea and land interaction region. The majority of the buildings and facilities in the airport are built on ocean-reclaimed lands and silt tidal flat. Residual ground settlement could probably occur after the completion of the airport construction. The current status of the ground settlement of the airport and whether it is within a safe range are necessary to be investigated. In order to continuously monitor the ground settlement of the airport, two Synthetic Aperture Radar (SAR) time series, acquired by X-band TerraSAR-X (TSX) and TanDEM-X (TDX) sensors from December 2009 to December 2010 and from April 2013 to July 2015, were used for analyzing with SBAS technique. We firstly obtained ground deformation measurement of each SAR subset. Both of the measurements show that obvious ground subsidence phenomenon occurred at the airport, especially in the second runway, the second terminal, the sixth cargo plane and the eighth apron. The maximum vertical ground deformation rates of both SAR subset measurements were greater than -30 mm/year, while the cumulative ground deformations reached up to -30 mm and -35 mm respectively. After generation of SBAS-retrieved ground deformation for each SAR subset, we performed a joint analysis to combine time series of each common coherent point by applying a geotechnical model. The results show that three centralized areas of ground deformation existed in the airport, mainly distributed in the sixth cargo plane, the fifth apron and the fourth apron, The maximum vertical cumulative ground subsidence was more than -70 mm. In addition, by analyzing the combined time series of four selected points, we found that the ground deformation rates of the points located at the second runway, the third runway, and the second terminal, were progressively smaller as time goes by. It indicates that the stabilities of the foundation around these points were gradually enhanced.

Behçet's: A Disease or a Syndrome? Answer from an Expression Profiling Study.

PubMed

Oğuz, Ali Kemal; Yılmaz, Seda Taşır; Oygür, Çağdaş Şahap; Çandar, Tuba; Sayın, Irmak; Kılıçoğlu, Sibel Serin; Ergün, İhsan; Ateş, Aşkın; Özdağ, Hilal; Akar, Nejat

2016-01-01

Behçet's disease (BD) is a chronic, relapsing, multisystemic inflammatory disorder with unanswered questions regarding its etiology/pathogenesis and classification. Distinct manifestation based subsets, pronounced geographical variations in expression, and discrepant immunological abnormalities raised the question whether Behçet's is "a disease or a syndrome". To answer the preceding question we aimed to display and compare the molecular mechanisms underlying distinct subsets of BD. For this purpose, the expression data of the gene expression profiling and association study on BD by Xavier et al (2013) was retrieved from GEO database and reanalysed by gene expression data analysis/visualization and bioinformatics enrichment tools. There were 15 BD patients (B) and 14 controls (C). Three subsets of BD patients were generated: MB (isolated mucocutaneous manifestations, n = 7), OB (ocular involvement, n = 4), and VB (large vein thrombosis, n = 4). Class comparison analyses yielded the following numbers of differentially expressed genes (DEGs); B vs C: 4, MB vs C: 5, OB vs C: 151, VB vs C: 274, MB vs OB: 215, MB vs VB: 760, OB vs VB: 984. Venn diagram analysis showed that there were no common DEGs in the intersection "MB vs C" ∩ "OB vs C" ∩ "VB vs C". Cluster analyses successfully clustered distinct expressions of BD. During gene ontology term enrichment analyses, categories with relevance to IL-8 production (MB vs C) and immune response to microorganisms (OB vs C) were differentially enriched. Distinct subsets of BD display distinct expression profiles and different disease associated pathways. Based on these clear discrepancies, the designation as "Behçet's syndrome" (BS) should be encouraged and future research should take into consideration the immunogenetic heterogeneity of BS subsets. Four gene groups, namely, negative regulators of inflammation (CD69, CLEC12A, CLEC12B, TNFAIP3), neutrophil granule proteins (LTF, OLFM4, AZU1, MMP8, DEFA4, CAMP), antigen processing and presentation proteins (CTSS, ERAP1), and regulators of immune response (LGALS2, BCL10, ITCH, CEACAM8, CD36, IL8, CCL4, EREG, NFKBIZ, CCR2, CD180, KLRC4, NFAT5) appear to be instrumental in BS immunopathogenesis.

Thermodynamics of gravitational clustering phenomena: N-body self-gravitating gas on the sphere {{{S}}^{3}}\\subset {{{R}}^{4}}

NASA Astrophysics Data System (ADS)

Tello-Ortiz, F.; Velazquez, L.

2016-10-01

This work is devoted to the thermodynamics of gravitational clustering, a collective phenomenon with a great relevance in the N-body cosmological problem. We study a classical self-gravitating gas of identical non-relativistic particles defined on the sphere {{{S}}3}\\subset {{{R}}4} by considering gravitational interaction that corresponds to this geometric space. The analysis is performed within microcanonical description of an isolated Hamiltonian system by combining continuum approximation and the steepest descend method. According to numerical solution of resulting equations, the gravitational clustering can be associated with two microcanonical phase transitions. A first phase transition with a continuous character is associated with breakdown of SO(4) symmetry of this model. The second one is the gravitational collapse, whose continuous or discontinuous character crucially depends on the regularization of short-range divergence of gravitation potential. We also derive the thermodynamic limit of this model system, the astrophysical counterpart of the Gibbs-Duhem relation, the order parameters that characterize its phase transitions and the equation of state. Other interesting behavior is the existence of states with negative heat capacities, which appear when the effects of gravitation turn dominant for energies sufficiently low. Finally, we comment on the relevance of some of these results in the study of astrophysical and cosmological situations. Special interest deserves the gravitational modification of the equation of state due to the local inhomogeneities of matter distribution. Although this feature is systematically neglected in studies about universe expansion, the same one is able to mimic an effect that is attributed to the dark energy: a negative pressure.

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

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

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

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

A Framework for Propagation of Uncertainties in the Kepler Data Analysis Pipeline

NASA Technical Reports Server (NTRS)

Clarke, Bruce D.; Allen, Christopher; Bryson, Stephen T.; Caldwell, Douglas A.; Chandrasekaran, Hema; Cote, Miles T.; Girouard, Forrest; Jenkins, Jon M.; Klaus, Todd C.; Li, Jie;

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

PubMed

Roberts, Lynne D; Povee, Kate

2014-01-01

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

CD27 natural killer cell subsets play different roles during the pre-onset stage of experimental autoimmune encephalomyelitis.

PubMed

Gao, Ming; Yang, Yan; Li, Daling; Ming, Bingxia; Chen, Huoying; Sun, Yan; Xiao, Yifan; Lai, Lin; Zou, Huijuan; Xu, Yong; Xiong, Ping; Tan, Zheng; Gong, Feili; Zheng, Fang

2016-08-01

NK cells participate in the development of human multiple sclerosis (MS) and mouse experimental autoimmune encephalomyelitis (EAE), but the roles of different NK cell subsets in disease onset remain poorly understood. In this study, murine NK cells were divided into CD27(high) and CD27(low/-) subsets. The CD27(high) subset was decreased and the CD27(low/-) subset was increased in lymphoid organs during the pre-onset stage of EAE. Compared with the counterpart in naïve mice, the CD27(high) subset showed lower expression of Ly49D, Ly49H and NKG2D, and less production of IFN-γ, whereas the CD27(low/-) subset showed similar expression of the above mentioned surface receptors but higher cytotoxic activity in EAE mice. Compared with the CD27(high) subset, the CD27(low/-) subset exhibited increased promotion of DC maturation and no significant inhibition of T cells proliferation and Th17 cells differentiation in vitro Additionally, adoptive transfer of the CD27(low/-) subset, but not the CD27(high) subset, exacerbated the severity of EAE. Collectively, our data suggest the CD27 NK cell subsets play different roles in controlling EAE onset, which provide a new understanding for the regulation of NK cell subsets in early autoimmune disease. © The Author(s) 2016.

Earth Mover's Distance (EMD): A True Metric for Comparing Biomarker Expression Levels in Cell Populations.

PubMed

Orlova, Darya Y; Zimmerman, Noah; Meehan, Stephen; Meehan, Connor; Waters, Jeffrey; Ghosn, Eliver E B; Filatenkov, Alexander; Kolyagin, Gleb A; Gernez, Yael; Tsuda, Shanel; Moore, Wayne; Moss, Richard B; Herzenberg, Leonore A; Walther, Guenther

2016-01-01

Changes in the frequencies of cell subsets that (co)express characteristic biomarkers, or levels of the biomarkers on the subsets, are widely used as indices of drug response, disease prognosis, stem cell reconstitution, etc. However, although the currently available computational "gating" tools accurately reveal subset frequencies and marker expression levels, they fail to enable statistically reliable judgements as to whether these frequencies and expression levels differ significantly between/among subject groups. Here we introduce flow cytometry data analysis pipeline which includes the Earth Mover's Distance (EMD) metric as solution to this problem. Well known as an informative quantitative measure of differences between distributions, we present three exemplary studies showing that EMD 1) reveals clinically-relevant shifts in two markers on blood basophils responding to an offending allergen; 2) shows that ablative tumor radiation induces significant changes in the murine colon cancer tumor microenvironment; and, 3) ranks immunological differences in mouse peritoneal cavity cells harvested from three genetically distinct mouse strains.

Classification of Medical Datasets Using SVMs with Hybrid Evolutionary Algorithms Based on Endocrine-Based Particle Swarm Optimization and Artificial Bee Colony Algorithms.

PubMed

Lin, Kuan-Cheng; Hsieh, Yi-Hsiu

2015-10-01

The classification and analysis of data is an important issue in today's research. Selecting a suitable set of features makes it possible to classify an enormous quantity of data quickly and efficiently. Feature selection is generally viewed as a problem of feature subset selection, such as combination optimization problems. Evolutionary algorithms using random search methods have proven highly effective in obtaining solutions to problems of optimization in a diversity of applications. In this study, we developed a hybrid evolutionary algorithm based on endocrine-based particle swarm optimization (EPSO) and artificial bee colony (ABC) algorithms in conjunction with a support vector machine (SVM) for the selection of optimal feature subsets for the classification of datasets. The results of experiments using specific UCI medical datasets demonstrate that the accuracy of the proposed hybrid evolutionary algorithm is superior to that of basic PSO, EPSO and ABC algorithms, with regard to classification accuracy using subsets with a reduced number of features.

Effect of Occupant and Impact Factors on Forces within Neck: II. Analysis of Specific Subsets

NASA Astrophysics Data System (ADS)

Shaibani, Saami J.

2000-03-01

The forces generated in the cervical spine were evaluated for a substantial number of motor-vehicle occupants in an associated study.[1] Correlation between these forces and various occupant- and impact-related parameters was generally not high for the broad groupings of the population considered at that time. In this research, smaller subsets with more elements in common were extracted from the data to try to detect any underlying relationships that might exist for the neck force. Although correlation coefficients for these subsets were higher than those for the previous groupings in more than three-quarters of the matches undertaken, the values still did not indicate consistently good fits. This suggests that there is no simple relationship for the force within the cervical spine and this, in turn, means that the potential for neck injury has to be evaluated on a case-by-case basis. 1. Effect of Occupant and Impact Factors on Forces within Neck: I. Overview of Large Population, Bull. Am. Phys. Soc. in press (2000).

A Fixed Point Theorem in Weak Topology for Successively Recurrent System of Set-Valued Mapping Equations and Its Applications

NASA Astrophysics Data System (ADS)

Horiuchi, Kazuo

Let us introduce n (≥ 2) mappings fi(i = 1, …, n ≡ 0) defined on reflexive real Banach spaces Xi-1 and let fi : Xi-1 → Yi be completely continuous on bounded convex closed subsets X_{i-1}^{(0)} \\\\subset X_{i-1}. Moreover, let us introduce n set-valued mappings F_i : X_{i-1} \\\\times Y_i \\\\to {\\\\cal F}_c(X_i) (the family of all non-empty compact subsets of Xi), (i=1, …, n ≡ 0). Here, we have a fixed point theorem in weak topology on the successively recurrent system of set-valued mapping equations: xi ∈ Fi(xi-1, fi(xi-1)), (i=1, …, n ≡ 0). This theorem can be applied immediately to analysis of the availability of system of circular networks of channels undergone by uncertain fluctuations and to evaluation of the tolerability of behaviors of those systems.

Phylogenetic relationships in Epidendroideae (Orchidaceae), one of the great flowering plant radiations: progressive specialization and diversification.

PubMed

Freudenstein, John V; Chase, Mark W

2015-03-01

The largest subfamily of orchids, Epidendroideae, represents one of the most significant diversifications among flowering plants in terms of pollination strategy, vegetative adaptation and number of species. Although many groups in the subfamily have been resolved, significant relationships in the tree remain unclear, limiting conclusions about diversification and creating uncertainty in the classification. This study brings together DNA sequences from nuclear, plastid and mitochrondrial genomes in order to clarify relationships, to test associations of key characters with diversification and to improve the classification. Sequences from seven loci were concatenated in a supermatrix analysis for 312 genera representing most of epidendroid diversity. Maximum-likelihood and parsimony analyses were performed on this matrix and on subsets of the data to generate trees and to investigate the effect of missing values. Statistical character-associated diversification analyses were performed. Likelihood and parsimony analyses yielded highly resolved trees that are in strong agreement and show significant support for many key clades. Many previously proposed relationships among tribes and subtribes are supported, and some new relationships are revealed. Analyses of subsets of the data suggest that the relatively high number of missing data for the full analysis is not problematic. Diversification analyses show that epiphytism is most strongly associated with diversification among epidendroids, followed by expansion into the New World and anther characters that are involved with pollinator specificity, namely early anther inflexion, cellular pollinium stalks and the superposed pollinium arrangement. All tested characters show significant association with speciation in Epidendroideae, suggesting that no single character accounts for the success of this group. Rather, it appears that a succession of key features appeared that have contributed to diversification, sometimes in parallel. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Genome investigation suggests MdSHN3, an APETALA2-domain transcription factor gene, to be a positive regulator of apple fruit cuticle formation and an inhibitor of russet development.

PubMed

Lashbrooke, Justin; Aharoni, Asaph; Costa, Fabrizio

2015-11-01

The outer epidermal layer of apple fruit is covered by a protective cuticle. Composed of a polymerized cutin matrix embedded with waxes, the cuticle is a natural waterproof barrier and protects against several abiotic and biotic stresses. In terms of apple production, the cuticle is essential to maintain long post-harvest storage, while severe failure of the cuticle can result in the formation of a disorder known as russet. Apple russet results from micro-cracking of the cuticle and the formation of a corky suberized layer. This is typically an undesirable consumer trait, and negatively impacts the post-harvest storage of apples. In order to identify genetic factors controlling cuticle biosynthesis (and thus preventing russet) in apple, a quantitative trait locus (QTL) mapping survey was performed on a full-sib population. Two genomic regions located on chromosomes 2 and 15 that could be associated with russeting were identified. Apples with compromised cuticles were identified through a novel and high-throughput tensile analysis of the skin, while histological analysis confirmed cuticle failure in a subset of the progeny. Additional genomic investigation of the determined QTL regions identified a set of underlying genes involved in cuticle biosynthesis. Candidate gene expression profiling by quantitative real-time PCR on a subset of the progeny highlighted the specific expression pattern of a SHN1/WIN1 transcription factor gene (termed MdSHN3) on chromosome 15. Orthologues of SHN1/WIN1 have been previously shown to regulate cuticle formation in Arabidopsis, tomato, and barley. The MdSHN3 transcription factor gene displayed extremely low expression in lines with improper cuticle formation, suggesting it to be a fundamental regulator of cuticle biosynthesis in apple fruit. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation.

PubMed

Dueck, Hannah; Khaladkar, Mugdha; Kim, Tae Kyung; Spaethling, Jennifer M; Francis, Chantal; Suresh, Sangita; Fisher, Stephen A; Seale, Patrick; Beck, Sheryl G; Bartfai, Tamas; Kuhn, Bernhard; Eberwine, James; Kim, Junhyong

2015-06-09

Differentiation of metazoan cells requires execution of different gene expression programs but recent single-cell transcriptome profiling has revealed considerable variation within cells of seeming identical phenotype. This brings into question the relationship between transcriptome states and cell phenotypes. Additionally, single-cell transcriptomics presents unique analysis challenges that need to be addressed to answer this question. We present high quality deep read-depth single-cell RNA sequencing for 91 cells from five mouse tissues and 18 cells from two rat tissues, along with 30 control samples of bulk RNA diluted to single-cell levels. We find that transcriptomes differ globally across tissues with regard to the number of genes expressed, the average expression patterns, and within-cell-type variation patterns. We develop methods to filter genes for reliable quantification and to calibrate biological variation. All cell types include genes with high variability in expression, in a tissue-specific manner. We also find evidence that single-cell variability of neuronal genes in mice is correlated with that in rats consistent with the hypothesis that levels of variation may be conserved. Single-cell RNA-sequencing data provide a unique view of transcriptome function; however, careful analysis is required in order to use single-cell RNA-sequencing measurements for this purpose. Technical variation must be considered in single-cell RNA-sequencing studies of expression variation. For a subset of genes, biological variability within each cell type appears to be regulated in order to perform dynamic functions, rather than solely molecular noise.

Linear retrieval and global measurements of wind speed from the Seasat SMMR

NASA Technical Reports Server (NTRS)

Pandey, P. C.

1983-01-01

Retrievals of wind speed (WS) from Seasat Scanning Multichannel Microwave Radiometer (SMMR) were performed using a two-step statistical technique. Nine subsets of two to five SMMR channels were examined for wind speed retrieval. These subsets were derived by using a leaps and bound procedure based on the coefficient of determination selection criteria to a statistical data base of brightness temperatures and geophysical parameters. Analysis of Monsoon Experiment and ocean station PAPA data showed a strong correlation between sea surface temperature and water vapor. This relation was used in generating the statistical data base. Global maps of WS were produced for one and three month periods.

Children's Social Desirability and Dietary Reports.

PubMed

Baxter, Suzanne Domel; Smith, Albert F; Litaker, Mark S; Baglio, Michelle L; Guinn, Caroline H; Shaffer, Nicole M

2004-01-01

We investigated telephone administration of the Children's Social Desirability (CSD) scale and our adaptation for children of the Social Desirability for Food scale (C-SDF). Each of 100 4th-graders completed 2 telephone interviews 28 days apart. CSD scores had adequate internal consistency and test-retest reliability, and a 14-item subset was identified that sufficiently measures the same construct. Our C-SDF scale performed less well in terms of internal consistency and test-retest reliability; factor analysis revealed 2 factors, 1 of which was moderately related to the CSD. The 14-item subset of the CSD scale may help researchers understand error in children's dietary reports.

Children's Social Desirability and Dietary Reports

PubMed Central

Baxter, Suzanne Domel; Smith, Albert F.; Litaker, Mark S.; Baglio, Michelle L.; Guinn, Caroline H.; Shaffer, Nicole M.

2005-01-01

We investigated telephone administration of the Children's Social Desirability (CSD) scale and our adaptation for children of the Social Desirability for Food scale (C-SDF). Each of 100 4th-graders completed 2 telephone interviews 28 days apart. CSD scores had adequate internal consistency and test—retest reliability, and a 14-item subset was identified that sufficiently measures the same construct. Our C-SDF scale performed less well in terms of internal consistency and test—retest reliability; factor analysis revealed 2 factors, 1 of which was moderately related to the CSD. The 14-item subset of the CSD scale may help researchers understand error in children's dietary reports. PMID:15068757

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

PubMed

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

2016-09-01

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

Meta-analysis of the effect of pregrazing pasture mass on pasture intake, milk production, and grazing behavior of dairy cows strip-grazing temperate grasslands.

PubMed

Pérez-Prieto, L A; Delagarde, R

2012-09-01

Grazing management is a key factor in pasture-based dairy systems, which can be improved given advanced knowledge of the effects of pregrazing pasture mass (PM) on the performance of dairy cows. The aim of this study was to quantify the effects of PM on the pasture intake, milk production, milk composition, and grazing behavior of strip- or rotational-grazing dairy cows, based on a meta-analysis of published research papers. A database was created that included experiments in which the effects of PM on pasture intake and milk production of dairy cows were studied. Papers were selected only if at least 2 PM were compared under similar experimental conditions, particularly the same pasture allowance (SPA). The final database included 15 papers with 27 PM comparisons. For analytical purposes, the database was subdivided into 3 subsets that varied according to the estimation height at which pasture allowance was determined; that is, where PM were compared at the SPA above ground level (SPA(0) subset), above 2 to 3 cm (SPA(3) subset), and above 4 to 5 cm (SPA(5) subset). Statistical analyses were conducted on the entire database (global analysis) and within each subset using linear model procedures. An interaction between PM and estimation height was found for pasture intake and milk production in the global analysis. On the basis of the predictive equations, pasture intake increased by 1.58 kg of dry matter/d per tonne increase in PM when PM were compared at SPA(0), was not affected by PM when PM were compared at SPA(3), and decreased by 0.65 kg of dry matter/d per tonne increase in PM when PM were compared at SPA(5). This is consistent with the effect of PM on milk production, which was positive and negative (1.04 and -0.79 kg/t of PM, respectively) when PM were compared at SPA(0) and SPA(5), respectively. Grazing time was only slightly affected by PM, irrespective of estimation height, because the effect of PM on pasture intake was mainly dependent on the variation in pasture intake rate. Pasture intake rate increased with increasing PM at SPA(0) but decreased with increasing PM at SPA(5). This meta-analysis clearly demonstrates that the effects of PM on pasture intake, milk production, and behavior of strip-grazing dairy cows depend largely on the height at which the PM and pasture allowance are measured. These results have methodological implications for future grazing research because it can be recommended that PM be compared at similar levels of pasture availability (i.e., at the same pasture allowance above 2 to 3 cm) to avoid possible misinterpretations of results. They also reveal the benefits of improving grazing management and intake prediction through modeling in pasture-based dairy systems. Copyright © 2012 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Decisions with Uncertain Consequences—A Total Ordering on Loss-Distributions

PubMed Central

König, Sandra; Schauer, Stefan

2016-01-01

Decisions are often based on imprecise, uncertain or vague information. Likewise, the consequences of an action are often equally unpredictable, thus putting the decision maker into a twofold jeopardy. Assuming that the effects of an action can be modeled by a random variable, then the decision problem boils down to comparing different effects (random variables) by comparing their distribution functions. Although the full space of probability distributions cannot be ordered, a properly restricted subset of distributions can be totally ordered in a practically meaningful way. We call these loss-distributions, since they provide a substitute for the concept of loss-functions in decision theory. This article introduces the theory behind the necessary restrictions and the hereby constructible total ordering on random loss variables, which enables decisions under uncertainty of consequences. Using data obtained from simulations, we demonstrate the practical applicability of our approach. PMID:28030572

Molecular Biology and Prevention of Endometrial Cancer. Addendum

DTIC Science & Technology

2008-07-01

2) A subset of adenocarcinoma cases from the International DES Registry (IDESR) was analyzed for MSI 3) A case-control study of the CASH database... DES in- utero , for methylation and mutation of PTEN and MLH1 in order to determine if estrogen induces genetic alterations in these tumors...current trial within the “Gynecologic Disease Program”. Aim 2: To analyze vaginal and cervical adenocarcinomas , that have arisen in women exposed to

Reconfiguration Schemes for Fault-Tolerant Processor Arrays

DTIC Science & Technology

1992-10-15

partially notion of linear schedule are easily related to similar ordered subset of a multidimensional integer lattice models and concepts used in [11-[131...and several other (called indec set). The points of this lattice correspond works. to (i.e.. are the indices of) computations, and the partial There are...These data dependencies are represented as vectors that of all computations of the algorithm is to be minimized. connect points of the lattice . If a

Functional heterogeneity of human effector CD8+ T cells.

PubMed

Takata, Hiroshi; Naruto, Takuya; Takiguchi, Masafumi

2012-02-09

Effector CD8(+) T cells are believed to be terminally differentiated cells having cytotoxic activity and the ability to produce effector cytokines such as INF-γ and TNF-α. We investigated the difference between CXCR1(+) and CXCR1(-) subsets of human effector CD27(-)CD28(-)CD8(+) T cells. The subsets expressed cytolytic molecules similarly and exerted substantial cytolytic activity, whereas only the CXCR1(-) subset had IL-2 productivity and self-proliferative activity and was more resistant to cell death than the CXCR1(+) subset. These differences were explained by the specific up-regulation of CAMK4, SPRY2, and IL-7R in the CXCR1(-) subset and that of pro-apoptotic death-associated protein kinase 1 (DAPK1) in the CXCR1(+) subset. The IL-2 producers were more frequently found in the IL-7R(+) subset of the CXCR1(-) effector CD8(+) T cells than in the IL-7R(-) subset. IL-7/IL-7R signaling promoted cell survival only in the CXCR1(-) subset. The present study has highlighted a novel subset of effector CD8(+) T cells producing IL-2 and suggests the importance of this subset in the homeostasis of effector CD8(+) T cells.

Simultaneous modelling of multi-purpose/multi-stop activity patterns and quantities consumed

NASA Astrophysics Data System (ADS)

Roy, John R.; Smith, Nariida C.; Xu, Blake

Whereas for commuting travel there is a one-to-one correspondence between commuters and jobs, and for commodity flows a one-to-one correspondence between the size of orders and the shipping cost of the commodities, the situation is much more complex for retail/service travel. A typical shopper may make a single trip or multi-stop tour to buy/consume a quite diverse set of commodities/services at different locations in quite variable quantities. At the same time, the general pattern of the tour is clearly dependent on the activities and goods available at potential stops. These interdependencies have been alluded to in the literature, especially by spatial economists. However, until some preliminary work by the first author, there has been no attempt to formally include these interdependencies in a general model. This paper presents a framework for achieving this goal by developing an evolutionary set of models starting from the simplest forms available. From the above, it is clear that such interdependency models will inevitably have high dimensionality and combinatorial complexity. This rules out a simultaneous treatment of all the events using an individual choice approach. If an individual choice approach is to be applied in a tractable manner, the set of interdependent events needs to be segmented into several subsets, with simultaneity recognised within each subset, but a mere sequential progression occurring between subsets. In this paper, full event interdependencies are retained at the expense of modelling market segments of consumers rather than a sample of representative individuals. We couple the travel and consumption events in the only feasible way, by modelling the tours as discrete entities, in conjunction with the amount of each commodity consumed per stop on each such tour in terms of the continuous quantities of microeconomics. This is performed both under a budget/income constraint from microeconomics and a time budget constraint from time geography. The model considers both physical trips and tele-orders.

Simulating the Performance of Ground-Based Optical Asteroid Surveys

NASA Astrophysics Data System (ADS)

Christensen, Eric J.; Shelly, Frank C.; Gibbs, Alex R.; Grauer, Albert D.; Hill, Richard E.; Johnson, Jess A.; Kowalski, Richard A.; Larson, Stephen M.

2014-11-01

We are developing a set of asteroid survey simulation tools in order to estimate the capability of existing and planned ground-based optical surveys, and to test a variety of possible survey cadences and strategies. The survey simulator is composed of several layers, including a model population of solar system objects and an orbital integrator, a site-specific atmospheric model (including inputs for seeing, haze and seasonal cloud cover), a model telescope (with a complete optical path to estimate throughput), a model camera (including FOV, pixel scale, and focal plane fill factor) and model source extraction and moving object detection layers with tunable detection requirements. We have also developed a flexible survey cadence planning tool to automatically generate nightly survey plans. Inputs to the cadence planner include camera properties (FOV, readout time), telescope limits (horizon, declination, hour angle, lunar and zenithal avoidance), preferred and restricted survey regions in RA/Dec, ecliptic, and Galactic coordinate systems, and recent coverage by other asteroid surveys. Simulated surveys are created for a subset of current and previous NEO surveys (LINEAR, Pan-STARRS and the three Catalina Sky Survey telescopes), and compared against the actual performance of these surveys in order to validate the model’s performance. The simulator tracks objects within the FOV of any pointing that were not discovered (e.g. too few observations, too trailed, focal plane array gaps, too fast or slow), thus dividing the population into “discoverable” and “discovered” subsets, to inform possible survey design changes. Ongoing and future work includes generating a realistic “known” subset of the model NEO population, running multiple independent simulated surveys in coordinated and uncoordinated modes, and testing various cadences to find optimal strategies for detecting NEO sub-populations. These tools can also assist in quantifying the efficiency of novel yet unverified survey cadences (e.g. the baseline LSST cadence) that sparsely spread the observations required for detection over several days or weeks.

Iterative Stable Alignment and Clustering of 2D Transmission Electron Microscope Images

PubMed Central

Yang, Zhengfan; Fang, Jia; Chittuluru, Johnathan; Asturias, Francisco J.; Penczek, Pawel A.

2012-01-01

SUMMARY Identification of homogeneous subsets of images in a macromolecular electron microscopy (EM) image data set is a critical step in single-particle analysis. The task is handled by iterative algorithms, whose performance is compromised by the compounded limitations of image alignment and K-means clustering. Here we describe an approach, iterative stable alignment and clustering (ISAC) that, relying on a new clustering method and on the concepts of stability and reproducibility, can extract validated, homogeneous subsets of images. ISAC requires only a small number of simple parameters and, with minimal human intervention, can eliminate bias from two-dimensional image clustering and maximize the quality of group averages that can be used for ab initio three-dimensional structural determination and analysis of macromolecular conformational variability. Repeated testing of the stability and reproducibility of a solution within ISAC eliminates heterogeneous or incorrect classes and introduces critical validation to the process of EM image clustering. PMID:22325773

A Novel Collection of snRNA-Like Promoters with Tissue-Specific Transcription Properties

PubMed Central

Garritano, Sonia; Gigoni, Arianna; Costa, Delfina; Malatesta, Paolo; Florio, Tullio; Cancedda, Ranieri; Pagano, Aldo

2012-01-01

We recently identified a novel dataset of snRNA-like trascriptional units in the human genome. The investigation of a subset of these elements showed that they play relevant roles in physiology and/or pathology. In this work we expand our collection of small RNAs taking advantage of a newly developed algorithm able to identify genome sequence stretches with RNA polymerase (pol) III type 3 promoter features thus constituting putative pol III binding sites. The bioinformatic analysis of a subset of these elements that map in introns of protein-coding genes in antisense configuration suggest their association with alternative splicing, similarly to other recently characterized small RNAs. Interestingly, the analysis of the transcriptional activity of these novel promoters shows that they are active in a cell-type specific manner, in accordance with the emerging body of evidence of a tissue/cell-specific activity of pol III. PMID:23109855

A novel collection of snRNA-like promoters with tissue-specific transcription properties.

PubMed

Garritano, Sonia; Gigoni, Arianna; Costa, Delfina; Malatesta, Paolo; Florio, Tullio; Cancedda, Ranieri; Pagano, Aldo

2012-01-01

We recently identified a novel dataset of snRNA-like trascriptional units in the human genome. The investigation of a subset of these elements showed that they play relevant roles in physiology and/or pathology. In this work we expand our collection of small RNAs taking advantage of a newly developed algorithm able to identify genome sequence stretches with RNA polymerase (pol) III type 3 promoter features thus constituting putative pol III binding sites. The bioinformatic analysis of a subset of these elements that map in introns of protein-coding genes in antisense configuration suggest their association with alternative splicing, similarly to other recently characterized small RNAs. Interestingly, the analysis of the transcriptional activity of these novel promoters shows that they are active in a cell-type specific manner, in accordance with the emerging body of evidence of a tissue/cell-specific activity of pol III.

Diagnostic support for glaucoma using retinal images: a hybrid image analysis and data mining approach.

PubMed

Yu, Jin; Abidi, Syed Sibte Raza; Artes, Paul; McIntyre, Andy; Heywood, Malcolm

2005-01-01

The availability of modern imaging techniques such as Confocal Scanning Laser Tomography (CSLT) for capturing high-quality optic nerve images offer the potential for developing automatic and objective methods for diagnosing glaucoma. We present a hybrid approach that features the analysis of CSLT images using moment methods to derive abstract image defining features. The features are then used to train classifers for automatically distinguishing CSLT images of normal and glaucoma patient. As a first, in this paper, we present investigations in feature subset selction methods for reducing the relatively large input space produced by the moment methods. We use neural networks and support vector machines to determine a sub-set of moments that offer high classification accuracy. We demonstratee the efficacy of our methods to discriminate between healthy and glaucomatous optic disks based on shape information automatically derived from optic disk topography and reflectance images.

High-dimensional cluster analysis with the Masked EM Algorithm

PubMed Central

Kadir, Shabnam N.; Goodman, Dan F. M.; Harris, Kenneth D.

2014-01-01

Cluster analysis faces two problems in high dimensions: first, the “curse of dimensionality” that can lead to overfitting and poor generalization performance; and second, the sheer time taken for conventional algorithms to process large amounts of high-dimensional data. We describe a solution to these problems, designed for the application of “spike sorting” for next-generation high channel-count neural probes. In this problem, only a small subset of features provide information about the cluster member-ship of any one data vector, but this informative feature subset is not the same for all data points, rendering classical feature selection ineffective. We introduce a “Masked EM” algorithm that allows accurate and time-efficient clustering of up to millions of points in thousands of dimensions. We demonstrate its applicability to synthetic data, and to real-world high-channel-count spike sorting data. PMID:25149694

MSL: A Measure to Evaluate Three-dimensional Patterns in Gene Expression Data

PubMed Central

Gutiérrez-Avilés, David; Rubio-Escudero, Cristina

2015-01-01

Microarray technology is highly used in biological research environments due to its ability to monitor the RNA concentration levels. The analysis of the data generated represents a computational challenge due to the characteristics of these data. Clustering techniques are widely applied to create groups of genes that exhibit a similar behavior. Biclustering relaxes the constraints for grouping, allowing genes to be evaluated only under a subset of the conditions. Triclustering appears for the analysis of longitudinal experiments in which the genes are evaluated under certain conditions at several time points. These triclusters provide hidden information in the form of behavior patterns from temporal experiments with microarrays relating subsets of genes, experimental conditions, and time points. We present an evaluation measure for triclusters called Multi Slope Measure, based on the similarity among the angles of the slopes formed by each profile formed by the genes, conditions, and times of the tricluster. PMID:26124630

Global meta-analysis reveals low consistency of biodiversity congruence relationships.

PubMed

Westgate, Martin J; Barton, Philip S; Lane, Peter W; Lindenmayer, David B

2014-05-21

Knowledge of the number and distribution of species is fundamental to biodiversity conservation efforts, but this information is lacking for the majority of species on earth. Consequently, subsets of taxa are often used as proxies for biodiversity; but this assumes that different taxa display congruent distribution patterns. Here we use a global meta-analysis to show that studies of cross-taxon congruence rarely give consistent results. Instead, species richness congruence is highest at extreme spatial scales and close to the equator, while congruence in species composition is highest at large extents and grain sizes. Studies display highest variance in cross-taxon congruence when conducted in areas with dissimilar areal extents (for species richness) or latitudes (for species composition). These results undermine the assumption that a subset of taxa can be representative of biodiversity. Therefore, researchers whose goal is to prioritize locations or actions for conservation should use data from a range of taxa.

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

Treesearch

Joseph M. McCollum; Jamie K. Cochran

2005-01-01

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

The Vineland-II in Preschool Children with Autism Spectrum Disorders: An Item Content Category Analysis

ERIC Educational Resources Information Center

Balboni, Giulia; Tasso, Alessandra; Muratori, Filippo; Cubelli, Roberto

2016-01-01

We investigated which item subsets of the Vineland-II can discriminate low-functioning preschoolers with ASD from matched peers with other neurodevelopmental disorders, using a regression analysis derived from a normative sample to account for cognitive and linguistic competencies. At variance with the typical profile, a pattern with Communication…

Crown-condition classification: a guide to data collection and analysis

Treesearch

Michael E. Schomaker; Stanley J. Zarnoch; William A. Bechtold; David J. Latelle; William G. Burkman; Susan M. Cox

2007-01-01

The Forest Inventory and Analysis (FIA) Program of the Forest Service, U.S. Department of Agriculture, conducts a national inventory of forests across the United States. A systematic subset of permanent inventory plots in 38 States is currently sampled every year for numerous forest health indicators. One of these indicators, crown-condition classification, is designed...

Water quality parameter measurement using spectral signatures

NASA Technical Reports Server (NTRS)

White, P. E.

1973-01-01

Regression analysis is applied to the problem of measuring water quality parameters from remote sensing spectral signature data. The equations necessary to perform regression analysis are presented and methods of testing the strength and reliability of a regression are described. An efficient algorithm for selecting an optimal subset of the independent variables available for a regression is also presented.

Understanding deformation mechanisms during powder compaction using principal component analysis of compression data.

PubMed

Roopwani, Rahul; Buckner, Ira S

2011-10-14

Principal component analysis (PCA) was applied to pharmaceutical powder compaction. A solid fraction parameter (SF(c/d)) and a mechanical work parameter (W(c/d)) representing irreversible compression behavior were determined as functions of applied load. Multivariate analysis of the compression data was carried out using PCA. The first principal component (PC1) showed loadings for the solid fraction and work values that agreed with changes in the relative significance of plastic deformation to consolidation at different pressures. The PC1 scores showed the same rank order as the relative plasticity ranking derived from the literature for common pharmaceutical materials. The utility of PC1 in understanding deformation was extended to binary mixtures using a subset of the original materials. Combinations of brittle and plastic materials were characterized using the PCA method. The relationships between PC1 scores and the weight fractions of the mixtures were typically linear showing ideal mixing in their deformation behaviors. The mixture consisting of two plastic materials was the only combination to show a consistent positive deviation from ideality. The application of PCA to solid fraction and mechanical work data appears to be an effective means of predicting deformation behavior during compaction of simple powder mixtures. Copyright © 2011 Elsevier B.V. All rights reserved.

Detection of semi-volatile organic compounds in permeable ...

EPA Pesticide Factsheets

Abstract The Edison Environmental Center (EEC) has a research and demonstration permeable parking lot comprised of three different permeable systems: permeable asphalt, porous concrete and interlocking concrete permeable pavers. Water quality and quantity analysis has been ongoing since January, 2010. This paper describes a subset of the water quality analysis, analysis of semivolatile organic compounds (SVOCs) to determine if hydrocarbons were in water infiltrated through the permeable surfaces. SVOCs were analyzed in samples collected from 11 dates over a 3 year period, from 2/8/2010 to 4/1/2013.Results are broadly divided into three categories: 42 chemicals were never detected; 12 chemicals (11 chemical test) were detected at a rate of less than 10% or less; and 22 chemicals were detected at a frequency of 10% or greater (ranging from 10% to 66.5% detections). Fundamental and exploratory statistical analyses were performed on these latter analyses results by grouping results by surface type. The statistical analyses were limited due to low frequency of detections and dilutions of samples which impacted detection limits. The infiltrate data through three permeable surfaces were analyzed as non-parametric data by the Kaplan-Meier estimation method for fundamental statistics; there were some statistically observable difference in concentration between pavement types when using Tarone-Ware Comparison Hypothesis Test. Additionally Spearman Rank order non-parame

Target Detection Routine (TADER). User’s Guide.

DTIC Science & Technology

1987-09-01

o System range capability subset (one record - omitted for standoff SLAR and penetrating system) o System inherent detection probability subset ( IELT ...records, i.e., one per element type) * System capability modifier subset/A=1, E=1 ( IELT records) o System capability modifier subset/A=1, E=2 ( IELT ...records) s System capability modifier subset/A=2, E=1 ( IELT records) o System capability modifier subset/A=2, E=2 ( IELT records) Unit Data Set (one set

Cellular sources and targets of IFN-gamma-mediated protection against viral demyelination and neurological deficits.

PubMed

Murray, Paul D; McGavern, Dorian B; Pease, Larry R; Rodriguez, Moses

2002-03-01

IFN-gamma is an anti-viral and immunomodulatory cytokine critical for resistance to multiple pathogens. Using mice with targeted disruption of the gene for IFN-gamma, we previously demonstrated that this cytokine is critical for resistance to viral persistence and demyelination in the Theiler's virus model of multiple sclerosis. During viral infections, IFN-gamma is produced by natural killer (NK) cells, CD4(+) and CD8(+) T cells; however, the proportions of lymphocyte subsets responding to virus infection influences the contributions to IFN-gamma-mediated protection. To determine the lymphocyte subsets that produce IFN-gamma to maintain resistance, we used adoptive transfer strategies to generate mice with lymphocyte-specific deficiencies in IFN-gamma-production. We demonstrate that IFN-gamma production by both CD4(+) and CD8(+) T cell subsets is critical for resistance to Theiler's murine encephalomyelitis virus (TMEV)-induced demyelination and neurological disease, and that CD4(+) T cells make a greater contribution to IFN-gamma-mediated protection. To determine the cellular targets of IFN-gamma-mediated responses, we used adoptive transfer studies and bone marrow chimerism to generate mice in which either hematopoietic or somatic cells lacked the ability to express IFN-gamma receptor. We demonstrate that IFN-gamma receptor must be present on central nervous system glia, but not bone marrow-derived lymphocytes, in order to maintain resistance to TMEV-induced demyelination.

Cellular sources and targets of IFN-γ-mediated protection against viral demyelination and neurological deficits

PubMed Central

Murray, Paul D.; McGavern, Dorian B.; Pease, Larry R.; Rodriguez, Moses

2017-01-01

IFN-γ is an anti-viral and immunomodulatory cytokine critical for resistance to multiple pathogens. Using mice with targeted disruption of the gene for IFN-γ, we previously demonstrated that this cytokine is critical for resistance to viral persistence and demyelination in the Theiler’s virus model of multiple sclerosis. During viral infections, IFN-γ is produced by natural killer (NK) cells, CD4+ and CD8+ T cells; however, the proportions of lymphocyte subsets responding to virus infection influences the contributions to IFN-γ-mediated protection. To determine the lymphocyte subsets that produce IFN-γ to maintain resistance, we used adoptive transfer strategies to generate mice with lymphocyte-specific deficiencies in IFN-γ-production. We demonstrate that IFN-γ production by both CD4+ and CD8+ T cell subsets is critical for resistance to Theiler’s murine encephalomyelitis virus (TMEV)-induced demyelination and neurological disease, and that CD4+ T cells make a greater contribution to IFN-γ-mediated protection. To determine the cellular targets of IFN-γ-mediated responses, we used adoptive transfer studies and bone marrow chimerism to generate mice in which either hematopoietic or somatic cells lacked the ability to express IFN-γ receptor. We demonstrate that IFN-γ receptor must be present on central nervous system glia, but not bone marrow-derived lymphocytes, in order to maintain resistance to TMEV-induced demyelination. PMID:11857334

Psychosocial factors of caregiver burden in child caregivers: results from the new national study of caregiving.

PubMed

Cohen, Steven A; Cook, Sarah; Kelley, Lauren; Sando, Trisha; Bell, Allison E

2015-08-07

Over 50 million informal caregivers in the United States provide care to an aging adult, saving the economy hundreds of billions of dollars annually from costly hospitalization or institutionalization. Despite the benefits associated with caregiving, caregiver stress can lead to negative physical and mental health consequences, or "caregiver burden". Given these potential negative consequences of caregiver burden, it is important not only to understand the multidimensional components of burden but to also understand the experience from the perspective of the caregiver themselves. Therefore, the objectives of our study are to use exploratory factor analysis to obtain a set of latent factors among a subset of caregiver burden questions identified in previous studies and assess their reliability. All data was obtained from the 2011 National Study of Caregiving (NSOC). Exploratory factor analysis (EFA) was performed to identify a set of latent factors assessing four domains of caregiver burden in "child caregivers": those informal caregivers who provide care to a parent or stepparent. Sensitivity analysis was also conducted by repeating the EFA on demographic subsets of caregivers. After multiple factor analyses, four consistent caregiver burden factors emerged from the 23 questions analyzed: Negative emotional, positive emotional, social, and financial. Reliability of each factor varied, and was strongest for the positive emotional domain for caregiver burden. These domains were generally consistent across demographic subsets of informal caregivers. These results provide researchers a more comprehensive understanding of caregiver burden to target interventions to protect caregiver health and maintain this vital component of the US health care system.

Efficacy measures associated to a plantar pressure based classification system in diabetic foot medicine.

PubMed

Deschamps, Kevin; Matricali, Giovanni Arnoldo; Desmet, Dirk; Roosen, Philip; Keijsers, Noel; Nobels, Frank; Bruyninckx, Herman; Staes, Filip

2016-09-01

The concept of 'classification' has, similar to many other diseases, been found to be fundamental in the field of diabetic medicine. In the current study, we aimed at determining efficacy measures of a recently published plantar pressure based classification system. Technical efficacy of the classification system was investigated by applying a high resolution, pixel-level analysis on the normalized plantar pressure pedobarographic fields of the original experimental dataset consisting of 97 patients with diabetes and 33 persons without diabetes. Clinical efficacy was assessed by considering the occurence of foot ulcers at the plantar aspect of the forefoot in this dataset. Classification efficacy was assessed by determining the classification recognition rate as well as its sensitivity and specificity using cross-validation subsets of the experimental dataset together with a novel cohort of 12 patients with diabetes. Pixel-level comparison of the four groups associated to the classification system highlighted distinct regional differences. Retrospective analysis showed the occurence of eleven foot ulcers in the experimental dataset since their gait analysis. Eight out of the eleven ulcers developed in a region of the foot which had the highest forces. Overall classification recognition rate exceeded 90% for all cross-validation subsets. Sensitivity and specificity of the four groups associated to the classification system exceeded respectively the 0.7 and 0.8 level in all cross-validation subsets. The results of the current study support the use of the novel plantar pressure based classification system in diabetic foot medicine. It may particularly serve in communication, diagnosis and clinical decision making. Copyright © 2016 Elsevier B.V. All rights reserved.

Colon cancer: it's CIN or CIMP.

PubMed

Issa, Jean-Pierre

2008-10-01

Combined genetic and epigenetic analysis of sporadic colon cancer suggest that it can no longer be viewed as a single disease. There are at least three different subsets with distinct clinico-pathologic features, with important implications for preventions, screening, and therapy.

Effect of Long-Term Hormonal Therapy (vs Short-Term Hormonal Therapy): A Secondary Analysis of Intermediate-Risk Prostate Cancer Patients Treated on NRG Oncology RTOG 9202

PubMed Central

Mirhadi, Amin J.; Zhang, Qiang; Hanks, Gerald E.; Lepor, Herbert; Grignon, David J.; Peters, Christopher A.; Rosenthal, Seth A.; Zeitzer, Kenneth; Radwan, John S.; Lawton, Colleen; Parliament, Matthew B.; Reznik, Robert S.; Sandler, Howard M.

2017-01-01

Purpose NRG Oncology RTOG 9202 was a randomized trial testing long-term adjuvant androgen deprivation (LTAD) versus initial androgen deprivation only (STAD) with external beam radiation therapy (RT) in mostly high-risk and some intermediate-risk prostate cancer patients. RTOG 9408 found an overall survival (OS) advantage in patients with cT1b-T2b disease and prostate-specific antigen (PSA) <20 ng/mL, with benefit observed mostly among intermediate-risk patients. It was still unknown whether intermediate-risk patients would experience an additional survival benefit with LTAD; thus, we performed a secondary analysis to explore whether LTAD had any incremental benefit beyond STAD among the intermediate-risk subset of RTOG 9202. The study endpoints were OS, disease-specific survival (DSS), and PSA failure (PSAF). Methods and Materials An analysis was performed for all patients enrolled in RTOG 9202 defined as intermediate-risk (cT2 disease, PSA<10 ng/mL, and Gleason score = 7 or cT2 disease, PSA 10-20 ng/mL, and Gleason score <7). This review yielded 133 patients: 74 (STAD) and 59 (LTAD). The Kaplan-Meier method was used to estimate OS; the cumulative incidence approach was used to estimate DSS and PSAF. A 2-sided test was used, with significance level defined to be .05. Results With over 11 years of median follow-up, 39 STAD patients were alive and 33 LTAD patients were alive. There was no difference in OS (10-year estimates, 61% STAD vs 65% LTAD; P=.53), DSS (10-year DSS, 96% vs 97%; P=.72), or PSAF (10-year PSAF, 53% vs 55%; P=.99) between groups. Conclusion LTAD did not confer a benefit in terms of OS, DSS, or PSAF rates in the intermediate-risk subset in this study. Whereas the subset was relatively small, treatment assignment was randomly applied, and a trend in favor of LTAD would have been of interest. Given the small number of disease-specific deaths observed and lack of benefit with respect to our endpoints, this secondary analysis does not suggest that exploration of longer hormonal therapy is worth testing in the intermediate-risk prostate cancer subset. PMID:28126300

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

NASA Astrophysics Data System (ADS)

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

2004-12-01

This is the first of a series of papers on the theme of automated pollen analysis. The automation of pollen analysis could result in numerous advantages for the reconstruction of past environments, with larger data sets made practical, objectivity and fine resolution sampling. There are also applications in apiculture and medicine. Previous work on the classification of pollen using texture measures has been successful with small numbers of pollen taxa. However, as the number of pollen taxa to be identified increases, more features may be required to achieve a successful classification. This paper describes the use of simple geometric measures to augment the texture measures. The feasibility of this new approach is tested using scanning electron microscope (SEM) images of 12 taxa of fresh pollen taken from reference material collected on Henderson Island, Polynesia. Pollen images were captured directly from a SEM connected to a PC. A threshold grey-level was set and binary images were then generated. Pollen edges were then located and the boundaries were traced using a chain coding system. A number of simple geometric variables were calculated directly from the chain code of the pollen and a variable selection procedure was used to choose the optimal subset to be used for classification. The efficiency of these variables was tested using a leave-one-out classification procedure. The system successfully split the original 12 taxa sample into five sub-samples containing no more than six pollen taxa each. The further subdivision of echinate pollen types was then attempted with a subset of four pollen taxa. A set of difference codes was constructed for a range of displacements along the chain code. From these difference codes probability variables were calculated. A variable selection procedure was again used to choose the optimal subset of probabilities that may be used for classification. The efficiency of these variables was again tested using a leave-one-out classification procedure. The proportion of correctly classified pollen ranged from 81% to 100% depending on the subset of variables used. The best set of variables had an overall classification rate averaging at about 95%. This is comparable with the classification rates from the earlier texture analysis work for other types of pollen. Copyright

Statistical analysis and ANN modeling for predicting hydrological extremes under climate change scenarios: the example of a small Mediterranean agro-watershed.

PubMed

Kourgialas, Nektarios N; Dokou, Zoi; Karatzas, George P

2015-05-01

The purpose of this study was to create a modeling management tool for the simulation of extreme flow events under current and future climatic conditions. This tool is a combination of different components and can be applied in complex hydrogeological river basins, where frequent flood and drought phenomena occur. The first component is the statistical analysis of the available hydro-meteorological data. Specifically, principal components analysis was performed in order to quantify the importance of the hydro-meteorological parameters that affect the generation of extreme events. The second component is a prediction-forecasting artificial neural network (ANN) model that simulates, accurately and efficiently, river flow on an hourly basis. This model is based on a methodology that attempts to resolve a very difficult problem related to the accurate estimation of extreme flows. For this purpose, the available measurements (5 years of hourly data) were divided in two subsets: one for the dry and one for the wet periods of the hydrological year. This way, two ANNs were created, trained, tested and validated for a complex Mediterranean river basin in Crete, Greece. As part of the second management component a statistical downscaling tool was used for the creation of meteorological data according to the higher and lower emission climate change scenarios A2 and B1. These data are used as input in the ANN for the forecasting of river flow for the next two decades. The final component is the application of a meteorological index on the measured and forecasted precipitation and flow data, in order to assess the severity and duration of extreme events. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

A New Reliability Analysis Model of the Chegongzhuang Heat-Supplying Tunnel Structure Considering the Coupling of Pipeline Thrust and Thermal Effect

PubMed Central

Zhang, Jiawen; He, Shaohui; Wang, Dahai; Liu, Yangpeng; Yao, Wenbo; Liu, Xiabing

2018-01-01

Based on the operating Chegongzhuang heat-supplying tunnel in Beijing, the reliability of its lining structure under the action of large thrust and thermal effect is studied. According to the characteristics of a heat-supplying tunnel service, a three-dimensional numerical analysis model was established based on the mechanical tests on the in-situ specimens. The stress and strain of the tunnel structure were obtained before and after the operation. Compared with the field monitoring data, the rationality of the model was verified. After extracting the internal force of the lining structure, the improved method of subset simulation was proposed as the performance function to calculate the reliability of the main control section of the tunnel. In contrast to the traditional calculation method, the analytic relationship between the sample numbers in the subset simulation method and Monte Carlo method was given. The results indicate that the lining structure is greatly influenced by coupling in the range of six meters from the fixed brackets, especially the tunnel floor. The improved subset simulation method can greatly save computation time and improve computational efficiency under the premise of ensuring the accuracy of calculation. It is suitable for the reliability calculation of tunnel engineering, because “the lower the probability, the more efficient the calculation.” PMID:29401691

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

PubMed

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

2004-08-01

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

Bevacizumab in Treatment of High-Risk Ovarian Cancer—A Cost-Effectiveness Analysis

PubMed Central

Herzog, Thomas J.; Hu, Lilian; Monk, Bradley J.; Kiet, Tuyen; Blansit, Kevin; Kapp, Daniel S.; Yu, Xinhua

2014-01-01

Objective. The objective of this study was to evaluate a cost-effectiveness strategy of bevacizumab in a subset of high-risk advanced ovarian cancer patients with survival benefit. Methods. A subset analysis of the International Collaboration on Ovarian Neoplasms 7 trial showed that additions of bevacizumab (B) and maintenance bevacizumab (mB) to paclitaxel (P) and carboplatin (C) improved the overall survival (OS) of high-risk advanced cancer patients. Actual and estimated costs of treatment were determined from Medicare payment. Incremental cost-effectiveness ratio per life-year saved was established. Results. The estimated cost of PC is $535 per cycle; PCB + mB (7.5 mg/kg) is $3,760 per cycle for the first 6 cycles and then $3,225 per cycle for 12 mB cycles. Of 465 high-risk stage IIIC (>1 cm residual) or stage IV patients, the previously reported OS after PC was 28.8 months versus 36.6 months in those who underwent PCB + mB. With an estimated 8-month improvement in OS, the incremental cost-effectiveness ratio of B was $167,771 per life-year saved. Conclusion. In this clinically relevant subset of women with high-risk advanced ovarian cancer with overall survival benefit after bevacizumab, our economic model suggests that the incremental cost of bevacizumab was approximately $170,000. PMID:24721817

Long noncoding RNAs (lncRNAs) dynamics evidence immunomodulation during ISAV-Infected Atlantic salmon (Salmo salar)

PubMed Central

Boltaña, Sebastian; Valenzuela-Miranda, Diego; Aguilar, Andrea; Mackenzie, Simon; Gallardo-Escárate, Cristian

2016-01-01

Despite evidence for participation in the host response to infection, the roles of many long non-coding RNAs (lncRNAs) remain unknown. Therefore, the aims of this study were to identify lncRNAs in Atlantic salmon (Salmo salar) and evaluate their transcriptomic regulation during ISA virus (ISAV) infection, an Orthomyxoviridae virus associated with high mortalities in salmonid aquaculture. Using next-generation sequencing, whole-transcriptome analysis of the Salmo salar response to ISAV infection was performed, identifying 5,636 putative lncRNAs with a mean length of 695 base pairs. The transcriptional modulation evidenced a similar number of differentially expressed lncRNAs in the gills (3,294), head-kidney (3,275), and liver (3,325) over the course of the infection. Moreover, analysis of a subset of these lncRNAs showed the following: (i) Most were similarly regulated in response to ISA virus infection; (ii) The transcript subsets were uniquely modulated in each tissue (gills, liver, and head-kidney); and (iii) A subset of lncRNAs were upregulated for each tissue and time analysed, indicating potential markers for ISAV infection. These findings represent the first discovery of widespread differential expression of lncRNAs in response to virus infection in non-model species, suggesting that lncRNAs could be involved in regulating the host response during ISAV infection. PMID:26939752

Subsetting Tools for Enabling Easy Access to International Airborne Chemistry Data

NASA Astrophysics Data System (ADS)

Northup, E. A.; Chen, G.; Quam, B. M.; Beach, A. L., III; Silverman, M. L.; Early, A. B.

2017-12-01

In response to the Research Opportunities in Earth and Space Science (ROSES) 2015 release announcement for Advancing Collaborative Connections for Earth System Science (ACCESS), researchers at NASA Langley Research Center (LaRC) proposed to extend the capabilities of the existing Toolsets for Airborne Data (TAD) to include subsetting functionality to allow for easier access to international airborne field campaign data. Airborne field studies are commonly used to gain a detailed understanding of atmospheric processes for scientific research on international climate change and air quality issues. To accommodate the rigorous process for manipulating airborne field study chemistry data, and to lessen barriers for researchers, TAD was created with the ability to geolocate data from various sources measured on different time scales from a single flight. The analysis of airborne chemistry data typically requires data subsetting, which can be challenging and resource-intensive for end users. In an effort to streamline this process, new data subsetting features and updates to the current database model will be added to the TAD toolset. These will include two subsetters: temporal and spatial, and vertical profile. The temporal and spatial subsetter will allow users to both focus on data from a specific location and/or time period. The vertical profile subsetter will retrieve data collected during an individual aircraft ascent or descent spiral. These new web-based tools will allow for automation of the typically labor-intensive manual data subsetting process, which will provide users with data tailored to their specific research interests. The system has been designed to allow for new in-situ airborne missions to be added as they become available, with only minor pre-processing required. The development of these enhancements will be discussed in this presentation.

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

PubMed Central

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

2010-01-01

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

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

PubMed

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

2010-10-14

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

CCR6+ Th cell distribution differentiates systemic lupus erythematosus patients based on anti-dsDNA antibody status.

PubMed

Zhong, Wei; Jiang, Zhenyu; Wu, Jiang; Jiang, Yanfang; Zhao, Ling

2018-01-01

Systemic lupus erythematosus (SLE) disease has been shown to be associated with the generation of multiple auto-antibodies. Among these, anti-dsDNA antibodies (anti-DNAs) are specific and play a pathogenic role in SLE. Indeed, anti-DNA + SLE patients display a worse disease course. The generation of these pathogenic anti-DNAs has been attributed to the interaction between aberrant T helper (Th) cells and autoimmune B cells. Thus, in this study we have investigated whether CCR6 + Th cells have the ability to differentiate SLE patients based on anti-DNA status, and if their distribution has any correlation with disease activity. We recruited 25 anti-DNA + and 25 anti-DNA - treatment-naive onset SLE patients, matched for various clinical characteristics in our nested matched case-control study. CCR6 + Th cells and their additional subsets were analyzed in each patient by flow cytometry. Anti-DNA + SLE patients specifically had a higher percentage of Th cells expressing CCR6 and CXCR3. Further analysis of CCR6 + Th cell subsets showed that anti-DNA + SLE patients had elevated proportions of Th9, Th17, Th17.1 and CCR4/CXCR3 double-negative (DN) cells. However, the proportions of CCR6 - Th subsets, including Th1 and Th2 cells, did not show any association with anti-DNA status. Finally, we identified a correlation between CCR6 + Th subsets and clinical indicators, specifically in anti-DNA + SLE patients. Our data indicated that CCR6 + Th cells and their subsets were elevated and correlated with disease activity in anti-DNA + SLE patients. We speculated that CCR6 + Th cells may contribute to distinct disease severity in anti-DNA + SLE patients.

Metabolic Profile as a Potential Modifier of Long-Term Radiation Effects on Peripheral Lymphocyte Subsets in Atomic Bomb Survivors.

PubMed

Yoshida, Kengo; Nakashima, Eiji; Kyoizumi, Seishi; Hakoda, Masayuki; Hayashi, Tomonori; Hida, Ayumi; Ohishi, Waka; Kusunoki, Yoichiro

2016-09-01

Immune system impairments reflected by the composition and function of circulating lymphocytes are still observed in atomic bomb survivors, and metabolic abnormalities including altered blood triglyceride and cholesterol levels have also been detected in such survivors. Based on closely related features of immune and metabolic profiles of individuals, we investigated the hypothesis that long-term effects of radiation exposure on lymphocyte subsets might be modified by metabolic profiles in 3,113 atomic bomb survivors who participated in health examinations at the Radiation Effect Research Foundation, Hiroshima and Nagasaki, in 2000-2002. The lymphocyte subsets analyzed involved T-, B- and NK-cell subsets, and their percentages in the lymphocyte fraction were assessed using flow cytometry. Health examinations included metabolic indicators, body mass index, serum levels of total cholesterol, high-density lipoprotein cholesterol, C-reactive protein and hemoglobin A1c, as well as diabetes and fatty liver diagnoses. Standard regression analyses indicated that several metabolic indicators of obesity/related disease, particularly high-density lipoprotein cholesterol levels, were positively associated with type-1 helper T- and B-cell percentages but were inversely associated with naïve CD4 T and NK cells. A regression analysis adjusted for high-density lipoprotein cholesterol revealed a radiation dose relationship with increasing NK-cell percentage. Additionally, an interaction effect was suggested between radiation dose and C-reactive protein on B-cell percentage with a negative coefficient of the interaction term. Collectively, these findings suggest that radiation exposure and subsequent metabolic profile changes, potentially in relationship to obesity-related inflammation, lead to such long-term alterations in lymphocyte subset composition. Because this study is based on cross-sectional and exploratory analyses, the implications regarding radiation exposure, metabolic profiles and circulating lymphocytes warrant future longitudinal and molecular mechanistic studies.

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

PubMed Central

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

2017-01-01

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

Evaluation of diagnostic tools that tertiary teachers can apply to profile their students' conceptions

NASA Astrophysics Data System (ADS)

Schultz, Madeleine; Lawrie, Gwendolyn A.; Bailey, Chantal H.; Bedford, Simon B.; Dargaville, Tim R.; O'Brien, Glennys; Tasker, Roy; Thompson, Christopher D.; Williams, Mark; Wright, Anthony H.

2017-03-01

A multi-institution collaborative team of Australian chemistry education researchers, teaching a total of over 3000 first year chemistry students annually, has explored a tool for diagnosing students' prior conceptions as they enter tertiary chemistry courses. Five core topics were selected and clusters of diagnostic items were assembled linking related concepts in each topic together. An ordered multiple choice assessment strategy was adopted to enable provision of formative feedback to students through combination of the specific distractors that they chose. Concept items were either sourced from existing research instruments or developed by the project team. The outcome is a diagnostic tool consisting of five topic clusters of five concept items that has been delivered in large introductory chemistry classes at five Australian institutions. Statistical analysis of data has enabled exploration of the composition and validity of the instrument including a comparison between delivery of the complete 25 item instrument with subsets of five items, clustered by topic. This analysis revealed that most items retained their validity when delivered in small clusters. Tensions between the assembly, validation and delivery of diagnostic instruments for the purposes of acquiring robust psychometric research data versus their pragmatic use are considered in this study.

Population and allelic variation of A-to-I RNA editing in human transcriptomes.

PubMed

Park, Eddie; Guo, Jiguang; Shen, Shihao; Demirdjian, Levon; Wu, Ying Nian; Lin, Lan; Xing, Yi

2017-07-28

A-to-I RNA editing is an important step in RNA processing in which specific adenosines in some RNA molecules are post-transcriptionally modified to inosines. RNA editing has emerged as a widespread mechanism for generating transcriptome diversity. However, there remain significant knowledge gaps about the variation and function of RNA editing. In order to determine the influence of genetic variation on A-to-I RNA editing, we integrate genomic and transcriptomic data from 445 human lymphoblastoid cell lines by combining an RNA editing QTL (edQTL) analysis with an allele-specific RNA editing (ASED) analysis. We identify 1054 RNA editing events associated with cis genetic polymorphisms. Additionally, we find that a subset of these polymorphisms is linked to genome-wide association study signals of complex traits or diseases. Finally, compared to random cis polymorphisms, polymorphisms associated with RNA editing variation are located closer spatially to their respective editing sites and have a more pronounced impact on RNA secondary structure. Our study reveals widespread cis variation in RNA editing among genetically distinct individuals and sheds light on possible phenotypic consequences of such variation on complex traits and diseases.

Feature Selection Using Information Gain for Improved Structural-Based Alert Correlation

PubMed Central

Siraj, Maheyzah Md; Zainal, Anazida; Elshoush, Huwaida Tagelsir; Elhaj, Fatin

2016-01-01

Grouping and clustering alerts for intrusion detection based on the similarity of features is referred to as structurally base alert correlation and can discover a list of attack steps. Previous researchers selected different features and data sources manually based on their knowledge and experience, which lead to the less accurate identification of attack steps and inconsistent performance of clustering accuracy. Furthermore, the existing alert correlation systems deal with a huge amount of data that contains null values, incomplete information, and irrelevant features causing the analysis of the alerts to be tedious, time-consuming and error-prone. Therefore, this paper focuses on selecting accurate and significant features of alerts that are appropriate to represent the attack steps, thus, enhancing the structural-based alert correlation model. A two-tier feature selection method is proposed to obtain the significant features. The first tier aims at ranking the subset of features based on high information gain entropy in decreasing order. The‏ second tier extends additional features with a better discriminative ability than the initially ranked features. Performance analysis results show the significance of the selected features in terms of the clustering accuracy using 2000 DARPA intrusion detection scenario-specific dataset. PMID:27893821

Noise models for low counting rate coherent diffraction imaging.

PubMed

Godard, Pierre; Allain, Marc; Chamard, Virginie; Rodenburg, John

2012-11-05

Coherent diffraction imaging (CDI) is a lens-less microscopy method that extracts the complex-valued exit field from intensity measurements alone. It is of particular importance for microscopy imaging with diffraction set-ups where high quality lenses are not available. The inversion scheme allowing the phase retrieval is based on the use of an iterative algorithm. In this work, we address the question of the choice of the iterative process in the case of data corrupted by photon or electron shot noise. Several noise models are presented and further used within two inversion strategies, the ordered subset and the scaled gradient. Based on analytical and numerical analysis together with Monte-Carlo studies, we show that any physical interpretations drawn from a CDI iterative technique require a detailed understanding of the relationship between the noise model and the used inversion method. We observe that iterative algorithms often assume implicitly a noise model. For low counting rates, each noise model behaves differently. Moreover, the used optimization strategy introduces its own artefacts. Based on this analysis, we develop a hybrid strategy which works efficiently in the absence of an informed initial guess. Our work emphasises issues which should be considered carefully when inverting experimental data.

Biodiversity of genes encoding anti-microbial traits within plant associated microbes

PubMed Central

Mousa, Walaa K.; Raizada, Manish N.

2015-01-01

The plant is an attractive versatile home for diverse associated microbes. A subset of these microbes produces a diversity of anti-microbial natural products including polyketides, non-ribosomal peptides, terpenoids, heterocylic nitrogenous compounds, volatile compounds, bacteriocins, and lytic enzymes. In recent years, detailed molecular analysis has led to a better understanding of the underlying genetic mechanisms. New genomic and bioinformatic tools have permitted comparisons of orthologous genes between species, leading to predictions of the associated evolutionary mechanisms responsible for diversification at the genetic and corresponding biochemical levels. The purpose of this review is to describe the biodiversity of biosynthetic genes of plant-associated bacteria and fungi that encode selected examples of antimicrobial natural products. For each compound, the target pathogen and biochemical mode of action are described, in order to draw attention to the complexity of these phenomena. We review recent information of the underlying molecular diversity and draw lessons through comparative genomic analysis of the orthologous coding sequences (CDS). We conclude by discussing emerging themes and gaps, discuss the metabolic pathways in the context of the phylogeny and ecology of their microbial hosts, and discuss potential evolutionary mechanisms that led to the diversification of biosynthetic gene clusters. PMID:25914708

Analysis of metabolic syndrome components in >15 000 african americans identifies pleiotropic variants: results from the population architecture using genomics and epidemiology study.

PubMed

Carty, Cara L; Bhattacharjee, Samsiddhi; Haessler, Jeff; Cheng, Iona; Hindorff, Lucia A; Aroda, Vanita; Carlson, Christopher S; Hsu, Chun-Nan; Wilkens, Lynne; Liu, Simin; Selvin, Elizabeth; Jackson, Rebecca; North, Kari E; Peters, Ulrike; Pankow, James S; Chatterjee, Nilanjan; Kooperberg, Charles

2014-08-01

Metabolic syndrome (MetS) refers to the clustering of cardiometabolic risk factors, including dyslipidemia, central adiposity, hypertension, and hyperglycemia, in individuals. Identification of pleiotropic genetic factors associated with MetS traits may shed light on key pathways or mediators underlying MetS. Using the Metabochip array in 15 148 African Americans from the Population Architecture using Genomics and Epidemiology (PAGE) study, we identify susceptibility loci and investigate pleiotropy among genetic variants using a subset-based meta-analysis method, ASsociation-analysis-based-on-subSETs (ASSET). Unlike conventional models that lack power when associations for MetS components are null or have opposite effects, Association-analysis-based-on-subsets uses 1-sided tests to detect positive and negative associations for components separately and combines tests accounting for correlations among components. With Association-analysis-based-on-subsets, we identify 27 single nucleotide polymorphisms in 1 glucose and 4 lipids loci (TCF7L2, LPL, APOA5, CETP, and APOC1/APOE/TOMM40) significantly associated with MetS components overall, all P<2.5e-7, the Bonferroni adjusted P value. Three loci replicate in a Hispanic population, n=5172. A novel African American-specific variant, rs12721054/APOC1, and rs10096633/LPL are associated with ≥3 MetS components. We find additional evidence of pleiotropy for APOE, TOMM40, TCF7L2, and CETP variants, many with opposing effects (eg, the same rs7901695/TCF7L2 allele is associated with increased odds of high glucose and decreased odds of central adiposity). We highlight a method to increase power in large-scale genomic association analyses and report a novel variant associated with all MetS components in African Americans. We also identify pleiotropic associations that may be clinically useful in patient risk profiling and for informing translational research of potential gene targets and medications. © 2014 American Heart Association, Inc.

Ecological impacts of tropical forest fragmentation: how consistent are patterns in species richness and nestedness?

PubMed

Hill, Jane K; Gray, Michael A; Khen, Chey Vun; Benedick, Suzan; Tawatao, Noel; Hamer, Keith C

2011-11-27

Large areas of tropical forest now exist as remnants scattered across agricultural landscapes, and so understanding the impacts of forest fragmentation is important for biodiversity conservation. We examined species richness and nestedness among tropical forest remnants in birds (meta-analysis of published studies) and insects (field data for fruit-feeding Lepidoptera (butterflies and moths) and ants). Species-area relationships were evident in all four taxa, and avian and insect assemblages in remnants typically were nested subsets of those in larger areas. Avian carnivores and nectarivores and predatory ants were more nested than other guilds, implying that the sequential loss of species was more predictable in these groups, and that fragmentation alters the trophic organization of communities. For butterflies, the ordering of fragments to achieve maximum nestedness was by fragment area, suggesting that differences among fragments were driven mainly by extinction. In contrast for moths, maximum nestedness was achieved by ordering species by wing length; species with longer wings (implying better dispersal) were more likely to occur at all sites, including low diversity sites, suggesting that differences among fragments were driven more strongly by colonization. Although all four taxa exhibited high levels of nestedness, patterns of species turnover were also idiosyncratic, and thus even species-poor sites contributed to landscape-scale biodiversity, particularly for insects.

National Hydrography Dataset Plus (NHDPlus)

EPA Pesticide Factsheets

The NHDPlus Version 1.0 is an integrated suite of application-ready geospatial data sets that incorporate many of the best features of the National Hydrography Dataset (NHD) and the National Elevation Dataset (NED). The NHDPlus includes a stream network (based on the 1:100,000-scale NHD), improved networking, naming, and value-added attributes (VAA's). NHDPlus also includes elevation-derived catchments (drainage areas) produced using a drainageenforcement technique first broadly applied in New England, and thus dubbed The New-England Method. This technique involves burning-in the 1:100,000-scale NHD and when available building walls using the national WatershedBoundary Dataset (WBD). The resulting modified digital elevation model(HydroDEM) is used to produce hydrologic derivatives that agree with the NHDand WBD. An interdisciplinary team from the U. S. Geological Survey (USGS), U.S. Environmental Protection Agency (USEPA), and contractors, over the lasttwo years has found this method to produce the best quality NHD catchments using an automated process.The VAAs include greatly enhanced capabilities for upstream and downstream navigation, analysis and modeling. Examples include: retrieve all flowlines (predominantly confluence-to-confluence stream segments) and catchments upstream of a given flowline using queries rather than by slower flowline-by flowline navigation; retrieve flowlines by stream order; subset a stream level path sorted in hydrologic order for st

GPU-based prompt gamma ray imaging from boron neutron capture therapy.

PubMed

Yoon, Do-Kun; Jung, Joo-Young; Jo Hong, Key; Sil Lee, Keum; Suk Suh, Tae

2015-01-01

The purpose of this research is to perform the fast reconstruction of a prompt gamma ray image using a graphics processing unit (GPU) computation from boron neutron capture therapy (BNCT) simulations. To evaluate the accuracy of the reconstructed image, a phantom including four boron uptake regions (BURs) was used in the simulation. After the Monte Carlo simulation of the BNCT, the modified ordered subset expectation maximization reconstruction algorithm using the GPU computation was used to reconstruct the images with fewer projections. The computation times for image reconstruction were compared between the GPU and the central processing unit (CPU). Also, the accuracy of the reconstructed image was evaluated by a receiver operating characteristic (ROC) curve analysis. The image reconstruction time using the GPU was 196 times faster than the conventional reconstruction time using the CPU. For the four BURs, the area under curve values from the ROC curve were 0.6726 (A-region), 0.6890 (B-region), 0.7384 (C-region), and 0.8009 (D-region). The tomographic image using the prompt gamma ray event from the BNCT simulation was acquired using the GPU computation in order to perform a fast reconstruction during treatment. The authors verified the feasibility of the prompt gamma ray image reconstruction using the GPU computation for BNCT simulations.

PET Image Reconstruction Incorporating 3D Mean-Median Sinogram Filtering

NASA Astrophysics Data System (ADS)

Mokri, S. S.; Saripan, M. I.; Rahni, A. A. Abd; Nordin, A. J.; Hashim, S.; Marhaban, M. H.

2016-02-01

Positron Emission Tomography (PET) projection data or sinogram contained poor statistics and randomness that produced noisy PET images. In order to improve the PET image, we proposed an implementation of pre-reconstruction sinogram filtering based on 3D mean-median filter. The proposed filter is designed based on three aims; to minimise angular blurring artifacts, to smooth flat region and to preserve the edges in the reconstructed PET image. The performance of the pre-reconstruction sinogram filter prior to three established reconstruction methods namely filtered-backprojection (FBP), Maximum likelihood expectation maximization-Ordered Subset (OSEM) and OSEM with median root prior (OSEM-MRP) is investigated using simulated NCAT phantom PET sinogram as generated by the PET Analytical Simulator (ASIM). The improvement on the quality of the reconstructed images with and without sinogram filtering is assessed according to visual as well as quantitative evaluation based on global signal to noise ratio (SNR), local SNR, contrast to noise ratio (CNR) and edge preservation capability. Further analysis on the achieved improvement is also carried out specific to iterative OSEM and OSEM-MRP reconstruction methods with and without pre-reconstruction filtering in terms of contrast recovery curve (CRC) versus noise trade off, normalised mean square error versus iteration, local CNR versus iteration and lesion detectability. Overall, satisfactory results are obtained from both visual and quantitative evaluations.

Ecological impacts of tropical forest fragmentation: how consistent are patterns in species richness and nestedness?

PubMed Central

Hill, Jane K.; Gray, Michael A.; Khen, Chey Vun; Benedick, Suzan; Tawatao, Noel; Hamer, Keith C.

2011-01-01

Large areas of tropical forest now exist as remnants scattered across agricultural landscapes, and so understanding the impacts of forest fragmentation is important for biodiversity conservation. We examined species richness and nestedness among tropical forest remnants in birds (meta-analysis of published studies) and insects (field data for fruit-feeding Lepidoptera (butterflies and moths) and ants). Species–area relationships were evident in all four taxa, and avian and insect assemblages in remnants typically were nested subsets of those in larger areas. Avian carnivores and nectarivores and predatory ants were more nested than other guilds, implying that the sequential loss of species was more predictable in these groups, and that fragmentation alters the trophic organization of communities. For butterflies, the ordering of fragments to achieve maximum nestedness was by fragment area, suggesting that differences among fragments were driven mainly by extinction. In contrast for moths, maximum nestedness was achieved by ordering species by wing length; species with longer wings (implying better dispersal) were more likely to occur at all sites, including low diversity sites, suggesting that differences among fragments were driven more strongly by colonization. Although all four taxa exhibited high levels of nestedness, patterns of species turnover were also idiosyncratic, and thus even species-poor sites contributed to landscape-scale biodiversity, particularly for insects. PMID:22006967

PANTHER. Trajectory Analysis

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

Rintoul, Mark Daniel; Wilson, Andrew T.; Valicka, Christopher G.

We want to organize a body of trajectories in order to identify, search for, classify and predict behavior among objects such as aircraft and ships. Existing compari- son functions such as the Fr'echet distance are computationally expensive and yield counterintuitive results in some cases. We propose an approach using feature vectors whose components represent succinctly the salient information in trajectories. These features incorporate basic information such as total distance traveled and distance be- tween start/stop points as well as geometric features related to the properties of the convex hull, trajectory curvature and general distance geometry. Additionally, these features can generallymore » be mapped easily to behaviors of interest to humans that are searching large databases. Most of these geometric features are invariant under rigid transformation. We demonstrate the use of different subsets of these features to iden- tify trajectories similar to an exemplar, cluster a database of several hundred thousand trajectories, predict destination and apply unsupervised machine learning algorithms.« less

Trajectory analysis via a geometric feature space approach

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

Rintoul, Mark D.; Wilson, Andrew T.

This study aimed to organize a body of trajectories in order to identify, search for and classify both common and uncommon behaviors among objects such as aircraft and ships. Existing comparison functions such as the Fréchet distance are computationally expensive and yield counterintuitive results in some cases. We propose an approach using feature vectors whose components represent succinctly the salient information in trajectories. These features incorporate basic information such as the total distance traveled and the distance between start/stop points as well as geometric features related to the properties of the convex hull, trajectory curvature and general distance geometry. Additionally,more » these features can generally be mapped easily to behaviors of interest to humans who are searching large databases. Most of these geometric features are invariant under rigid transformation. Furthermore, we demonstrate the use of different subsets of these features to identify trajectories similar to an exemplar, cluster a database of several hundred thousand trajectories and identify outliers.« less

Analysis of neonatal brain lacking ATRX or MeCP2 reveals changes in nucleosome density, CTCF binding and chromatin looping

PubMed Central

Kernohan, Kristin D.; Vernimmen, Douglas; Gloor, Gregory B.; Bérubé, Nathalie G.

2014-01-01

ATRX and MeCP2 belong to an expanding group of chromatin-associated proteins implicated in human neurodevelopmental disorders, although their gene-regulatory activities are not fully resolved. Loss of ATRX prevents full repression of an imprinted gene network in the postnatal brain and in this study we address the mechanistic aspects of this regulation. We show that ATRX binds many imprinted domains individually but that transient co-localization between imprinted domains in the nuclei of neurons does not require ATRX. We demonstrate that MeCP2 is required for ATRX recruitment and that deficiency of either ATRX or MeCP2 causes decreased frequency of long-range chromatin interactions associated with altered nucleosome density at CTCF-binding sites and reduced CTCF occupancy. These findings indicate that MeCP2 and ATRX regulate gene expression at a subset of imprinted domains by maintaining a nucleosome configuration conducive to CTCF binding and to the maintenance of higher order chromatin structure. PMID:24990380

QFD-ANP Approach for the Conceptual Design of Research Vessels: A Case Study

NASA Astrophysics Data System (ADS)

Venkata Subbaiah, Kambagowni; Yeshwanth Sai, Koneru; Suresh, Challa

2016-10-01

Conceptual design is a subset of concept art wherein a new idea of product is created instead of a visual representation which would directly be used in a final product. The purpose is to understand the needs of conceptual design which are being used in engineering designs and to clarify the current conceptual design practice. Quality function deployment (QFD) is a customer oriented design approach for developing new or improved products and services to enhance customer satisfaction. House of quality (HOQ) has been traditionally used as planning tool of QFD which translates customer requirements (CRs) into design requirements (DRs). Factor analysis is carried out in order to reduce the CR portions of HOQ. The analytical hierarchical process is employed to obtain the priority ratings of CR's which are used in constructing HOQ. This paper mainly discusses about the conceptual design of an oceanographic research vessel using analytical network process (ANP) technique. Finally the QFD-ANP integrated methodology helps to establish the importance ratings of DRs.

Field of smart structures as seen by those working in it: survey results

NASA Astrophysics Data System (ADS)

Spillman, William B., Jr.; Sirkis, James S.; Gardiner, Peter T.

1995-04-01

There has been considerable discussion in the technical community on a number of questions concerned with smart materials and structures, such as what they are, whether smart materials can be considered a subset of smart structures, whether a smart structure and an intelligent structure are the same thing, etc. This discussion is both fueled and confused by the technical community due to the truly multidisciplinary nature of this new field. Smart materials and structures research involves so many technically diverse fields that it is quite common for one field to completely misunderstand the terminology and state-of-the-art in other fields. In order to ascertain whether a consensus is emerging on a number of these questions, the technical community was surveyed in a number of ways including via the Internet and by direct contact. The purpose of this survey in the final analysis was to better define the smart materials and structures field, its current status and its potential benefits. Results of the survey are presented and discussed.

Trajectory analysis via a geometric feature space approach

DOE PAGES

Rintoul, Mark D.; Wilson, Andrew T.

2015-10-05

This study aimed to organize a body of trajectories in order to identify, search for and classify both common and uncommon behaviors among objects such as aircraft and ships. Existing comparison functions such as the Fréchet distance are computationally expensive and yield counterintuitive results in some cases. We propose an approach using feature vectors whose components represent succinctly the salient information in trajectories. These features incorporate basic information such as the total distance traveled and the distance between start/stop points as well as geometric features related to the properties of the convex hull, trajectory curvature and general distance geometry. Additionally,more » these features can generally be mapped easily to behaviors of interest to humans who are searching large databases. Most of these geometric features are invariant under rigid transformation. Furthermore, we demonstrate the use of different subsets of these features to identify trajectories similar to an exemplar, cluster a database of several hundred thousand trajectories and identify outliers.« less

Validation of use of subsets of teeth when applying the total mouth periodontal score (TMPS) system in dogs.

PubMed

Harvey, Colin E; Laster, Larry; Shofer, Frances S

2012-01-01

A total mouth periodontal score (TMPS) system in dogs has been described previously. Use of buccal and palatal/lingual surfaces of all teeth requires observation and recording of 120 gingivitis scores and 120 periodontitis scores. Although the result is a reliable, repeatable assessment of the extent of periodontal disease in the mouth, observing and recording 240 data points is time-consuming. Using data from a previously reported study of periodontal disease in dogs, correlation analysis was used to determine whether use of any of seven different subsets of teeth can generate TMPS subset gingivitis and periodontitis scores that are highly correlated with TMPS all-site, all-teeth scores. Overall, gingivitis scores were less highly correlated than periodontitis scores. The minimal tooth set with a significant intra-class correlation (> or = 0.9 of means of right and left sides) for both gingivitis scores and attachment loss measurements consisted of the buccal surface of the maxillary third incisor canine, third premolar fourth premolar; and first molar teeth; and, the mandibular canine, third premolar, fourth premolar and first molar teeth on one side (9 teeth, 15 root sites). Use of this subset of teeth, which reduces the number of data points per dog from 240 to 30 for gingivitis and periodontitis at each scoring episode, is recommended when calculating the gingivitis and periodontitis scores using the TMPS system.

Oligoclonal T cell expansions in patients with Behçet's disease

PubMed Central

DIRESKENELI, H; EKSIOGLU-DEMIRALP, E; KIBAROGLU, A; YAVUZ, S; ERGUN, T; AKOGLU, T

1999-01-01

Behçet's disease (BD) is a multisystem disorder with oral and genital ulcers, mucocutaneous, ocular, joint, vascular and central nervous system involvement. In this study, the peripheral T cell repertoire was analysed in patients with BD with MoAbs against T cell receptor (TCR) Vβ gene products in CD4+ and CD8+ T cell compartments, and these were compared with rheumatoid arthritis (RA) patients and healthy controls (HC). In the CD4+ T cell compartment, oligoclonal TCR Vβ expression was observed in 56% of BD (10/18), 71% of RA (5/7) patients and 21% (3/14) of HC. In the CD8+ T cell group 50% of BD (9/18), 57% of RA patients and 28% of HC (4/14) had an oligoclonal TCR repertoire. An increase of TCR Vβ5.1 subset was observed in five BD patients among CD8+ T cells. Other elevations of TCR Vβ subsets were heterogeneously distributed with one to three different Vβ subsets. Our results suggest an antigen-driven oligoclonal increase of T cells in BD. There was no overall increase in any Vβ group to suggest a superantigen effect. Analysis of the responsible antigens causing the increase in T cell subsets may give insights into the aetiopathogenesis of BD and immunomodulation of these T cells may lead to new treatments. PMID:10403931

Human dendritic cell subsets display distinct interactions with the pathogenic mould Aspergillus fumigatus.

PubMed

Lother, Jasmin; Breitschopf, Tanja; Krappmann, Sven; Morton, C Oliver; Bouzani, Maria; Kurzai, Oliver; Gunzer, Matthias; Hasenberg, Mike; Einsele, Hermann; Loeffler, Juergen

2014-11-01

The mould Aspergillus fumigatus is primarily an opportunistic pathogen of immunocompromised patients. Once fungal spores have been inhaled they encounter cells of the innate immune system, which include dendritic cells (DCs). DCs are the key antigen-presenting cells of the immune system and distinct subtypes, which differ in terms of origin, morphology and function. This study has systematically compared the interactions between A. fumigatus and myeloid DCs (mDCs), plasmacytoid DCs (pDCs) and monocyte-derived DCs (moDCs). Analyses were performed by time-lapse video microscopy, scanning electron microscopy, plating assays, flow cytometry, 25-plex ELISA and transwell assays. The three subsets of DCs displayed distinct responses to the fungus with mDCs and moDCs showing the greatest similarities. mDCs and moDCs both produced rough convolutions and occasionally phagocytic cups upon exposure to A. fumigatus whereas pDCs maintained a smooth appearance. Both mDCs and moDCs phagocytosed conidia and germ tubes, while pDCs did not phagocytose any fungi. Analysis of cytokine release and maturation markers revealed specific differences in pro- and anti-inflammatory patterns between the different DC subsets. These distinct characteristics between the DC subsets highlight their differences and suggest specific roles of moDCs, mDCs and pDCs during their interaction with A. fumigatus in vivo. Copyright © 2014 Elsevier GmbH. All rights reserved.

Application of artificial neural networks for conformity analysis of fuel performed with an optical fiber sensor

NASA Astrophysics Data System (ADS)

Possetti, Gustavo Rafael Collere; Coradin, Francelli Klemba; Côcco, Lílian Cristina; Yamamoto, Carlos Itsuo; de Arruda, Lucia Valéria Ramos; Falate, Rosane; Muller, Marcia; Fabris, José Luís

2008-04-01

The liquid fuel quality control is an important issue that brings benefits for the State, for the consumers and for the environment. The conformity analysis, in special for gasoline, demands a rigorous sampling technique among gas stations and other economic agencies, followed by a series of standard physicochemical tests. Such procedures are commonly expensive and time demanding and, moreover, a specialist is often required to carry out the tasks. Such drawbacks make the development of alternative analysis tools an important research field. The fuel refractive index is an additional parameter to help the fuel conformity analysis, besides the prospective optical fiber sensors, which operate like transducers with singular properties. When this parameter is correlated with the sample density, it becomes possible to determine conformity zones that cannot be analytically defined. This work presents an application of artificial neural networks based on Radial Basis Function to determine these zones. A set of 45 gasoline samples, collected in several gas stations and previously analyzed according to the rules of Agência Nacional do Petróleo, Gás Natural e Biocombustíveis, a Brazilian regulatory agency, constituted the database to build two neural networks. The input variables of first network are the samples refractive indices, measured with an Abbe refractometer, and the density of the samples measured with a digital densimeter. For the second network the input variables included, besides the samples densities, the wavelength response of a long-period grating to the samples refractive indices. The used grating was written in an optical fiber using the point-to-point technique by submitting the fiber to consecutive electrical arcs from a splice machine. The output variables of both Radial Basis Function Networks are represented by the conformity status of each sample, according to report of tests carried out following the American Society for Testing and Materials and/or Brazilian Association of Technical Rules standards. A subset of 35 samples, randomly chosen from the database, was used to design and calibrate (train) both networks. The two networks topologies (numbers of Radial Basis Function neurons of the hidden layer and function radius) were built in order to minimize the root mean square error. The subset composed by the other 10 samples was used to validate the final networks architectures. The obtained results have demonstrated that both networks reach a good predictive capability.

Logical analysis of diffuse large B-cell lymphomas.

PubMed

Alexe, G; Alexe, S; Axelrod, D E; Hammer, P L; Weissmann, D

2005-07-01

The goal of this study is to re-examine the oligonucleotide microarray dataset of Shipp et al., which contains the intensity levels of 6817 genes of 58 patients with diffuse large B-cell lymphoma (DLBCL) and 19 with follicular lymphoma (FL), by means of the combinatorics, optimisation, and logic-based methodology of logical analysis of data (LAD). The motivations for this new analysis included the previously demonstrated capabilities of LAD and its expected potential (1) to identify different informative genes than those discovered by conventional statistical methods, (2) to identify combinations of gene expression levels capable of characterizing different types of lymphoma, and (3) to assemble collections of such combinations that if considered jointly are capable of accurately distinguishing different types of lymphoma. The central concept of LAD is a pattern or combinatorial biomarker, a concept that resembles a rule as used in decision tree methods. LAD is able to exhaustively generate the collection of all those patterns which satisfy certain quality constraints, through a systematic combinatorial process guided by clear optimization criteria. Then, based on a set covering approach, LAD aggregates the collection of patterns into classification models. In addition, LAD is able to use the information provided by large collections of patterns in order to extract subsets of variables, which collectively are able to distinguish between different types of disease. For the differential diagnosis of DLBCL versus FL, a model based on eight significant genes is constructed and shown to have a sensitivity of 94.7% and a specificity of 100% on the test set. For the prognosis of good versus poor outcome among the DLBCL patients, a model is constructed on another set consisting also of eight significant genes, and shown to have a sensitivity of 87.5% and a specificity of 90% on the test set. The genes selected by LAD also work well as a basis for other kinds of statistical analysis, indicating their robustness. These two models exhibit accuracies that compare favorably to those in the original study. In addition, the current study also provides a ranking by importance of the genes in the selected significant subsets as well as a library of dozens of combinatorial biomarkers (i.e. pairs or triplets of genes) that can serve as a source of mathematically generated, statistically significant research hypotheses in need of biological explanation.

Self-Organization of Vocabularies under Different Interaction Orders.

PubMed

Vera, Javier

2017-01-01

Traditionally, the formation of vocabularies has been studied by agent-based models (primarily, the naming game) in which random pairs of agents negotiate word-meaning associations at each discrete time step. This article proposes a first approximation to a novel question: To what extent is the negotiation of word-meaning associations influenced by the order in which agents interact? Automata networks provide the adequate mathematical framework to explore this question. Computer simulations suggest that on two-dimensional lattices the typical features of the formation of word-meaning associations are recovered under random schemes that update small fractions of the population at the same time; by contrast, if larger subsets of the population are updated, a periodic behavior may appear.

Refined Weyl Law for Homogeneous Perturbations of the Harmonic Oscillator

NASA Astrophysics Data System (ADS)

Doll, Moritz; Gannot, Oran; Wunsch, Jared

2018-02-01

Let H denote the harmonic oscillator Hamiltonian on R}^d,} perturbed by an isotropic pseudodifferential operator of order 1. We consider the Schrödinger propagator {U(t)=e^{-itH},} and find that while sing-supp Tr U(t) \\subset 2 π Z as in the unperturbed case, there exists a large class of perturbations in dimensions {d ≥ 2 for which the singularities of {Tr U(t)} at nonzero multiples of {2 π} are weaker than the singularity at t = 0. The remainder term in the Weyl law is of order {o(λ^{d-1})} , improving in these cases the {o(λ^{d-1})} remainder previously established by Helffer-Robert.

Enhanced Product Generation at NASA Data Centers Through Grid Technology

NASA Technical Reports Server (NTRS)

Barkstrom, Bruce R.; Hinke, Thomas H.; Gavali, Shradha; Seufzer, William J.

2003-01-01

This paper describes how grid technology can support the ability of NASA data centers to provide customized data products. A combination of grid technology and commodity processors are proposed to provide the bandwidth necessary to perform customized processing of data, with customized data subsetting providing the initial example. This customized subsetting engine can be used to support a new type of subsetting, called phenomena-based subsetting, where data is subsetted based on its association with some phenomena, such as mesoscale convective systems or hurricanes. This concept is expanded to allow the phenomena to be detected in one type of data, with the subsetting requirements transmitted to the subsetting engine to subset a different type of data. The subsetting requirements are generated by a data mining system and transmitted to the subsetter in the form of an XML feature index that describes the spatial and temporal extent of the phenomena. For this work, a grid-based mining system called the Grid Miner is used to identify the phenomena and generate the feature index. This paper discusses the value of grid technology in facilitating the development of a high performance customized product processing and the coupling of a grid mining system to support phenomena-based subsetting.

HPV-Associated Head and Neck Cancer: Unique Features of Epidemiology and Clinical Management

PubMed Central

Maxwell, Jessica H.; Grandis, Jennifer R.; Ferris, Robert L.

2017-01-01

Human papillomavirus (HPV) is a recently identified causative agent for a subset of head and neck cancers, primarily in the oropharynx, and is largely responsible for the rising worldwide incidence of oropharyngeal cancer (OPC). Patients with HPV-positive OPC have distinct risk factor profiles and generally have a better prognosis than patients with traditional, HPV-negative, head and neck cancer. Concurrent chemotherapy and radiation is a widely accepted primary treatment modality for many patients with HPV-positive OPC. However, recent advances in surgical modalities, including transoral laser and robotic surgery, have led to the reemergence of primary surgical treatment for HPV-positive patients. Clinical trials are under way to determine optimal treatment strategies for the growing subset of patients with HPV-positive OPC. Similarly, identifying those patients with HPV-positive cancer who are at risk for recurrence and poor survival is critical in order to tailor individual treatment regimens and avoid potential undertreatment. PMID:26332002

On the properties of energy stable flux reconstruction schemes for implicit large eddy simulation

NASA Astrophysics Data System (ADS)

Vermeire, B. C.; Vincent, P. E.

2016-12-01

We begin by investigating the stability, order of accuracy, and dispersion and dissipation characteristics of the extended range of energy stable flux reconstruction (E-ESFR) schemes in the context of implicit large eddy simulation (ILES). We proceed to demonstrate that subsets of the E-ESFR schemes are more stable than collocation nodal discontinuous Galerkin methods recovered with the flux reconstruction approach (FRDG) for marginally-resolved ILES simulations of the Taylor-Green vortex. These schemes are shown to have reduced dissipation and dispersion errors relative to FRDG schemes of the same polynomial degree and, simultaneously, have increased Courant-Friedrichs-Lewy (CFL) limits. Finally, we simulate turbulent flow over an SD7003 aerofoil using two of the most stable E-ESFR schemes identified by the aforementioned Taylor-Green vortex experiments. Results demonstrate that subsets of E-ESFR schemes appear more stable than the commonly used FRDG method, have increased CFL limits, and are suitable for ILES of complex turbulent flows on unstructured grids.

Post-processing images from the WFIRST-AFTA coronagraph testbed

NASA Astrophysics Data System (ADS)

Zimmerman, Neil T.; Ygouf, Marie; Pueyo, Laurent; Soummer, Remi; Perrin, Marshall D.; Mennesson, Bertrand; Cady, Eric; Mejia Prada, Camilo

2016-01-01

The concept for the exoplanet imaging instrument on WFIRST-AFTA relies on the development of mission-specific data processing tools to reduce the speckle noise floor. No instruments have yet functioned on the sky in the planet-to-star contrast regime of the proposed coronagraph (1E-8). Therefore, starlight subtraction algorithms must be tested on a combination of simulated and laboratory data sets to give confidence that the scientific goals can be reached. The High Contrast Imaging Testbed (HCIT) at Jet Propulsion Lab has carried out several technology demonstrations for the instrument concept, demonstrating 1E-8 raw (absolute) contrast. Here, we have applied a mock reference differential imaging strategy to HCIT data sets, treating one subset of images as a reference star observation and another subset as a science target observation. We show that algorithms like KLIP (Karhunen-Loève Image Projection), by suppressing residual speckles, enable the recovery of exoplanet signals at contrast of order 2E-9.

Large scale affinity calculations of cyclodextrin host-guest complexes: Understanding the role of reorganization in the molecular recognition process

PubMed Central

Wickstrom, Lauren; He, Peng; Gallicchio, Emilio; Levy, Ronald M.

2013-01-01

Host-guest inclusion complexes are useful models for understanding the structural and energetic aspects of molecular recognition. Due to their small size relative to much larger protein-ligand complexes, converged results can be obtained rapidly for these systems thus offering the opportunity to more reliably study fundamental aspects of the thermodynamics of binding. In this work, we have performed a large scale binding affinity survey of 57 β-cyclodextrin (CD) host guest systems using the binding energy distribution analysis method (BEDAM) with implicit solvation (OPLS-AA/AGBNP2). Converged estimates of the standard binding free energies are obtained for these systems by employing techniques such as parallel Hamitionian replica exchange molecular dynamics, conformational reservoirs and multistate free energy estimators. Good agreement with experimental measurements is obtained in terms of both numerical accuracy and affinity rankings. Overall, average effective binding energies reproduce affinity rank ordering better than the calculated binding affinities, even though calculated binding free energies, which account for effects such as conformational strain and entropy loss upon binding, provide lower root mean square errors when compared to measurements. Interestingly, we find that binding free energies are superior rank order predictors for a large subset containing the most flexible guests. The results indicate that, while challenging, accurate modeling of reorganization effects can lead to ligand design models of superior predictive power for rank ordering relative to models based only on ligand-receptor interaction energies. PMID:25147485

Mitochondrial and nuclear genes suggest that stony corals are monophyletic but most families of stony corals are not (Order Scleractinia, Class Anthozoa, Phylum Cnidaria).

PubMed

Fukami, Hironobu; Chen, Chaolun Allen; Budd, Ann F; Collins, Allen; Wallace, Carden; Chuang, Yao-Yang; Chen, Chienhsun; Dai, Chang-Feng; Iwao, Kenji; Sheppard, Charles; Knowlton, Nancy

2008-09-16

Modern hard corals (Class Hexacorallia; Order Scleractinia) are widely studied because of their fundamental role in reef building and their superb fossil record extending back to the Triassic. Nevertheless, interpretations of their evolutionary relationships have been in flux for over a decade. Recent analyses undermine the legitimacy of traditional suborders, families and genera, and suggest that a non-skeletal sister clade (Order Corallimorpharia) might be imbedded within the stony corals. However, these studies either sampled a relatively limited array of taxa or assembled trees from heterogeneous data sets. Here we provide a more comprehensive analysis of Scleractinia (127 species, 75 genera, 17 families) and various outgroups, based on two mitochondrial genes (cytochrome oxidase I, cytochrome b), with analyses of nuclear genes (ss-tubulin, ribosomal DNA) of a subset of taxa to test unexpected relationships. Eleven of 16 families were found to be polyphyletic. Strikingly, over one third of all families as conventionally defined contain representatives from the highly divergent "robust" and "complex" clades. However, the recent suggestion that corallimorpharians are true corals that have lost their skeletons was not upheld. Relationships were supported not only by mitochondrial and nuclear genes, but also often by morphological characters which had been ignored or never noted previously. The concordance of molecular characters and more carefully examined morphological characters suggests a future of greater taxonomic stability, as well as the potential to trace the evolutionary history of this ecologically important group using fossils.

Efficient Orchestration of Data Centers Via Comprehensive and Application Aware Trade Off Exploration

DTIC Science & Technology

2016-12-01

proposes to save power by concentrating traffic over a small subset of links. data center architecture [12], as depicted in Figure 1.1. The fat-tree... architecture is a physical network topology commonly used in data networks representing a hier- archical multi-rooted tree consisting of four levels...milliseconds) is an order of magnitude faster than the GASO variants (tens of seconds). 3.4.3 LAW for Architectures of Different Dimensions In this section

Man-portable Vector Time Domain EMI Sensor and Discrimination Processing

DTIC Science & Technology

2012-04-16

points of each winding are coincident. Each receiver coil is wound helically on a set of 10 grooves etched on the surface of the cube; 36- gauge wire...subset of the data, and inject various levels of noise into the position of the MPV in order to gauge the robustness of the discrimination results...as possible. The quantity φ also provides a metric to gauge goodness of fit, being essentially an average percent error: Benjamin Barrowes, Kevin

Perturbative reduction of derivative order in EFT

NASA Astrophysics Data System (ADS)

Glavan, Dražen

2018-02-01

Higher derivative corrections are ubiquitous in effective field theories, which seemingly introduces new degrees of freedom at successive orders. This is actually an artefact of the implicit local derivative expansion defining effective field theories. We argue that higher derivative corrections that introduce additional degrees of freedom should be removed and their effects captured either by lower derivative corrections, or special combinations of higher derivative corrections not propagating extra degrees of freedom. Three methods adapted for this task are examined and field redefinitions are found to be most appropriate. First order higher derivative corrections in a scalar tensor theory are removed by field redefinition and it is found that their effects are captured by a subset of Horndeski theories. A case is made for restricting the effective field theory expansions in principle to only terms not introducing additional degrees of freedom.

Conformal field theory construction for non-Abelian hierarchy wave functions

NASA Astrophysics Data System (ADS)

Tournois, Yoran; Hermanns, Maria

2017-12-01

The fractional quantum Hall effect is the paradigmatic example of topologically ordered phases. One of its most fascinating aspects is the large variety of different topological orders that may be realized, in particular non-Abelian ones. Here we analyze a class of non-Abelian fractional quantum Hall model states which are generalizations of the Abelian Haldane-Halperin hierarchy. We derive their topological properties and show that the quasiparticles obey non-Abelian fusion rules of type su (q)k . For a subset of these states we are able to derive the conformal field theory description that makes the topological properties—in particular braiding—of the state manifest. The model states we study provide explicit wave functions for a large variety of interesting topological orders, which may be relevant for certain fractional quantum Hall states observed in the first excited Landau level.

The Comparative Effectiveness of Different Item Analysis Techniques in Increasing Change Score Reliability.

ERIC Educational Resources Information Center

Crocker, Linda M.; Mehrens, William A.

Four new methods of item analysis were used to select subsets of items which would yield measures of attitude change. The sample consisted of 263 students at Michigan State University who were tested on the Inventory of Beliefs as freshmen and retested on the same instrument as juniors. Item change scores and total change scores were computed for…

A first look at measurement error on FIA plots using blind plots in the Pacific Northwest

Treesearch

Susanna Melson; David Azuma; Jeremy S. Fried

2002-01-01

Measurement error in the Forest Inventory and Analysis work of the Pacific Northwest Station was estimated with a recently implemented blind plot measurement protocol. A small subset of plots was revisited by a crew having limited knowledge of the first crew's measurements. This preliminary analysis of the first 18 months' blind plot data indicates that...

Analysis of Xq27-28 linkage in the international consortium for prostate cancer genetics (ICPCG) families.

PubMed

Bailey-Wilson, Joan E; Childs, Erica J; Cropp, Cheryl D; Schaid, Daniel J; Xu, Jianfeng; Camp, Nicola J; Cannon-Albright, Lisa A; Farnham, James M; George, Asha; Powell, Isaac; Carpten, John D; Giles, Graham G; Hopper, John L; Severi, Gianluca; English, Dallas R; Foulkes, William D; Mæhle, Lovise; Møller, Pål; Eeles, Rosalind; Easton, Douglas; Guy, Michelle; Edwards, Steve; Badzioch, Michael D; Whittemore, Alice S; Oakley-Girvan, Ingrid; Hsieh, Chih-Lin; Dimitrov, Latchezar; Stanford, Janet L; Karyadi, Danielle M; Deutsch, Kerry; McIntosh, Laura; Ostrander, Elaine A; Wiley, Kathleen E; Isaacs, Sarah D; Walsh, Patrick C; Thibodeau, Stephen N; McDonnell, Shannon K; Hebbring, Scott; Lange, Ethan M; Cooney, Kathleen A; Tammela, Teuvo L J; Schleutker, Johanna; Maier, Christiane; Bochum, Sylvia; Hoegel, Josef; Grönberg, Henrik; Wiklund, Fredrik; Emanuelsson, Monica; Cancel-Tassin, Geraldine; Valeri, Antoine; Cussenot, Olivier; Isaacs, William B

2012-06-19

Genetic variants are likely to contribute to a portion of prostate cancer risk. Full elucidation of the genetic etiology of prostate cancer is difficult because of incomplete penetrance and genetic and phenotypic heterogeneity. Current evidence suggests that genetic linkage to prostate cancer has been found on several chromosomes including the X; however, identification of causative genes has been elusive. Parametric and non-parametric linkage analyses were performed using 26 microsatellite markers in each of 11 groups of multiple-case prostate cancer families from the International Consortium for Prostate Cancer Genetics (ICPCG). Meta-analyses of the resultant family-specific linkage statistics across the entire 1,323 families and in several predefined subsets were then performed. Meta-analyses of linkage statistics resulted in a maximum parametric heterogeneity lod score (HLOD) of 1.28, and an allele-sharing lod score (LOD) of 2.0 in favor of linkage to Xq27-q28 at 138 cM. In subset analyses, families with average age at onset less than 65 years exhibited a maximum HLOD of 1.8 (at 138 cM) versus a maximum regional HLOD of only 0.32 in families with average age at onset of 65 years or older. Surprisingly, the subset of families with only 2-3 affected men and some evidence of male-to-male transmission of prostate cancer gave the strongest evidence of linkage to the region (HLOD = 3.24, 134 cM). For this subset, the HLOD was slightly increased (HLOD = 3.47 at 134 cM) when families used in the original published report of linkage to Xq27-28 were excluded. Although there was not strong support for linkage to the Xq27-28 region in the complete set of families, the subset of families with earlier age at onset exhibited more evidence of linkage than families with later onset of disease. A subset of families with 2-3 affected individuals and with some evidence of male to male disease transmission showed stronger linkage signals. Our results suggest that the genetic basis for prostate cancer in our families is much more complex than a single susceptibility locus on the X chromosome, and that future explorations of the Xq27-28 region should focus on the subset of families identified here with the strongest evidence of linkage to this region.

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

USGS Publications Warehouse

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

1984-01-01

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

Java Source Code Analysis for API Migration to Embedded Systems

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

Winter, Victor; McCoy, James A.; Guerrero, Jonathan

Embedded systems form an integral part of our technological infrastructure and oftentimes play a complex and critical role within larger systems. From the perspective of reliability, security, and safety, strong arguments can be made favoring the use of Java over C in such systems. In part, this argument is based on the assumption that suitable subsets of Java’s APIs and extension libraries are available to embedded software developers. In practice, a number of Java-based embedded processors do not support the full features of the JVM. For such processors, source code migration is a mechanism by which key abstractions offered bymore » APIs and extension libraries can made available to embedded software developers. The analysis required for Java source code-level library migration is based on the ability to correctly resolve element references to their corresponding element declarations. A key challenge in this setting is how to perform analysis for incomplete source-code bases (e.g., subsets of libraries) from which types and packages have been omitted. This article formalizes an approach that can be used to extend code bases targeted for migration in such a manner that the threats associated the analysis of incomplete code bases are eliminated.« less

Elite and Status Attainment Models of Inequality of Opportunity

ERIC Educational Resources Information Center

Myles, John F.; Srensen, Aage B.

1975-01-01

With changes in method, analysis of the process of attainment of various occupations and sub-sets of occupations such as elites can bring about the desired comparability between elite and status attainment studies of equality of opportunity. (Author/AM)

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

PubMed

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

2013-03-22

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

Sensitivity of control-augmented structure obtained by a system decomposition method

NASA Technical Reports Server (NTRS)

Sobieszczanskisobieski, Jaroslaw; Bloebaum, Christina L.; Hajela, Prabhat

1988-01-01

The verification of a method for computing sensitivity derivatives of a coupled system is presented. The method deals with a system whose analysis can be partitioned into subsets that correspond to disciplines and/or physical subsystems that exchange input-output data with each other. The method uses the partial sensitivity derivatives of the output with respect to input obtained for each subset separately to assemble a set of linear, simultaneous, algebraic equations that are solved for the derivatives of the coupled system response. This sensitivity analysis is verified using an example of a cantilever beam augmented with an active control system to limit the beam's dynamic displacements under an excitation force. The verification shows good agreement of the method with reference data obtained by a finite difference technique involving entire system analysis. The usefulness of a system sensitivity method in optimization applications by employing a piecewise-linear approach to the same numerical example is demonstrated. The method's principal merits are its intrinsically superior accuracy in comparison with the finite difference technique, and its compatibility with the traditional division of work in complex engineering tasks among specialty groups.

Statistical analysis on experimental calibration data for flowmeters in pressure pipes

NASA Astrophysics Data System (ADS)

Lazzarin, Alessandro; Orsi, Enrico; Sanfilippo, Umberto

2017-08-01

This paper shows a statistical analysis on experimental calibration data for flowmeters (i.e.: electromagnetic, ultrasonic, turbine flowmeters) in pressure pipes. The experimental calibration data set consists of the whole archive of the calibration tests carried out on 246 flowmeters from January 2001 to October 2015 at Settore Portate of Laboratorio di Idraulica “G. Fantoli” of Politecnico di Milano, that is accredited as LAT 104 for a flow range between 3 l/s and 80 l/s, with a certified Calibration and Measurement Capability (CMC) - formerly known as Best Measurement Capability (BMC) - equal to 0.2%. The data set is split into three subsets, respectively consisting in: 94 electromagnetic, 83 ultrasonic and 69 turbine flowmeters; each subset is analysed separately from the others, but then a final comparison is carried out. In particular, the main focus of the statistical analysis is the correction C, that is the difference between the flow rate Q measured by the calibration facility (through the accredited procedures and the certified reference specimen) minus the flow rate QM contemporarily recorded by the flowmeter under calibration, expressed as a percentage of the same QM .

The success of assisted reproduction technologies in relation to composition of the total regulatory T cell (Treg) pool and different Treg subsets.

PubMed

Schlossberger, V; Schober, L; Rehnitz, J; Schaier, M; Zeier, M; Meuer, S; Schmitt, E; Toth, B; Strowitzki, T; Steinborn, A

2013-11-01

Are there differences in composition of the total regulatory T cell (Treg) pool and distinct Treg subsets (naïve CD45RA(+)-Tregs, HLA-DR(-)- and HLA-DR(+)-memory Tregs) between successfully and non-successfully IVF/ICSI-treated women? Non-successfully IVF/ICSI-treated women have a decreased percentage of naïve CD45RA(+)-Tregs and an increased percentage of HLA-DR(-)-memory Tregs within the total Treg pool. Immunosuppressive Tregs play a significant role in human reproduction and studies have shown that their number and function are reduced in reproductive failure and complications of pregnancy such as pre-eclampsia and preterm labor. However, no data exist concerning the importance of Tregs for a successful outcome following assisted reproduction technologies. Blood samples were obtained from 210 women undergoing IVF/ICSI treatment, where 14 patients were excluded due to biochemical pregnancy or missed abortion. Age control blood samples were collected from 20 neonates and 176 healthy female volunteers. The study was performed between October 2010 and March 2012. In this study, we determined prospectively the quantity and composition of the total CD4(+)CD127(low+/-)CD25(+)FoxP3(+)-Treg pool and three different Treg subsets (naïve CD45RA(+)-Tregs, HLA-DR(-)- and HLA-DR(+)-memory Tregs) in all women undergoing IVF/ICSI treatment. We examined whether there were differences between those who became pregnant (n = 36) and those who did not (n = 160). The blood samples were collected within 1 h before the embryo transfer and analyzed by six-color flow cytometry. In order to evaluate these results with regard to the normal age-related changes in composition of the total Treg pool, the same analysis was performed using samples of umbilical cord blood and from healthy female volunteers aged between 17 and 76 years. The composition of the total Treg pool was documented for successfully IVF/ICSI-treated women (n = 5) throughout their pregnancy and we assessed the suppressive activity of each Treg subset in pregnant (n = 10) compared with non-pregnant women (n = 10) using suppression assays. The percentage of CD4(+)CD127(low+/-)CD25(+)FoxP3(+)-Tregs within the total CD4(+)-T cell pool did not change with age and did not differ between IVF/ICSI-treated women who did or did not become pregnant. For the total Treg pool, the percentage of the naïve CD45RA(+)-Tregs decreased continuously, while the percentage of HLA-DR(-)- and HLA-DR(+)-memory Tregs increased with aging. From the age of about 40 years, the increase in HLA-DR(+)-memory Tregs in particular became less pronounced, indicating that conversion of naïve CD45RA(+)Tregs into HLA-DR(+)-memory Tregs decreases with age. Women who did not achieve a pregnancy with IVF/ICSI were older than those who did (P < 0.01). However, multiple logistic regression analysis revealed that irrespective of age, the percentage of naïve CD45RA(+)-Tregs within the total Treg pool was decreased (P < 0.05), while the percentage of HLA-DR(-)-memory Tregs was increased (P < 0.01) in women who did not become pregnant compared with those who did. At the beginning of pregnancy, naïve CD45RA(+)-Tregs showed a major decrease but increased again during pregnancy and these cells showed a higher suppressive activity (P < 0.0001) in pregnant compared with non-pregnant women. There was a large variation in the percentages of the Treg subsets within the total Treg pool between successfully and non-successfully IVF/ICSI-treated women. Therefore, their determination would not allow us to predict the IVF/ICSI outcome with sufficient specificity and sensitivity. We did not examine the antigen specificity of the Treg subsets and therefore could not discern whether the naïve CD45RA(+)-Tregs recognized maternal or paternal antigens. Our findings suggest that Tregs, especially the naïve CD45RA(+)-Treg subset, may play a role in determining the probability of both becoming pregnant and maintenance of the pregnancy. This work was supported by the German Research Council (DFG) grant STE 885/3-2 (to A.S.). All authors declare to have no conflict of interest.