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Sample records for multidimensional phenotypic profiling

  1. Fitness of multidimensional phenotypes in dynamic adaptive landscapes.

    PubMed

    Laughlin, Daniel C; Messier, Julie

    2015-08-01

    Phenotypic traits influence species distributions, but ecology lacks established links between multidimensional phenotypes and fitness for predicting species responses to environmental change. The common focus on single traits rather than multiple trait combinations limits our understanding of their adaptive value, and intraspecific trait covariation has been neglected in ecology despite its importance in evolutionary theory and its likely impact on species distributions. Here, we extend the adaptive landscape framework to ecological sorting of multidimensional phenotypes across environments and discuss how two analytical approaches can be used to quantify fitness as a function of the interaction between the phenotype and the environment. We encourage ecologists to consider how phenotypic integration will constrain species responses to environmental change.

  2. Confirmatory Factor Analysis and Profile Analysis via Multidimensional Scaling

    ERIC Educational Resources Information Center

    Kim, Se-Kang; Davison, Mark L.; Frisby, Craig L.

    2007-01-01

    This paper describes the Confirmatory Factor Analysis (CFA) parameterization of the Profile Analysis via Multidimensional Scaling (PAMS) model to demonstrate validation of profile pattern hypotheses derived from multidimensional scaling (MDS). Profile Analysis via Multidimensional Scaling (PAMS) is an exploratory method for identifying major…

  3. Multidimensional Clinical Phenotyping of an Adult Cystic Fibrosis Patient Population

    PubMed Central

    Conrad, Douglas J.; Bailey, Barbara A.

    2015-01-01

    Background Cystic Fibrosis (CF) is a multi-systemic disease resulting from mutations in the Cystic Fibrosis Transmembrane Regulator (CFTR) gene and has major manifestations in the sino-pulmonary, and gastro-intestinal tracts. Clinical phenotypes were generated using 26 common clinical variables to generate classes that overlapped quantiles of lung function and were based on multiple aspects of CF systemic disease. Methods The variables included age, gender, CFTR mutations, FEV1% predicted, FVC% predicted, height, weight, Brasfield chest xray score, pancreatic sufficiency status and clinical microbiology results. Complete datasets were compiled on 211 subjects. Phenotypes were identified using a proximity matrix generated by the unsupervised Random Forests algorithm and subsequent clustering by the Partitioning around Medoids (PAM) algorithm. The final phenotypic classes were then characterized and compared to a similar dataset obtained three years earlier. Findings Clinical phenotypes were identified using a clustering strategy that generated four and five phenotypes. Each strategy identified 1) a low lung health scores phenotype, 2) a younger, well-nourished, male-dominated class, 3) various high lung health score phenotypes that varied in terms of age, gender and nutritional status. This multidimensional clinical phenotyping strategy identified classes with expected microbiology results and low risk clinical phenotypes with pancreatic sufficiency. Interpretation This study demonstrated regional adult CF clinical phenotypes using non-parametric, continuous, ordinal and categorical data with a minimal amount of subjective data to identify clinically relevant phenotypes. These studies identified the relative stability of the phenotypes, demonstrated specific phenotypes consistent with published findings and identified others needing further study. PMID:25822311

  4. The Role of CT Scanning in Multidimensional Phenotyping of COPD

    PubMed Central

    2011-01-01

    Background: COPD is a heterogeneous disease characterized by airflow obstruction and diagnosed by lung function. CT imaging is emerging as an important, noninvasive tool in phenotyping COPD. However, the use of CT imaging in defining the disease heterogeneity above lung function is not fully known. Methods: Seventy-five patients with COPD (58 men, 17 women) were studied with CT imaging and with measures of airway inflammation. Airway physiology and health status were also determined. Results: The presence of emphysema (EM), bronchiectasis (BE), and bronchial wall thickening (BWT) was found in 67%, 27%, and 27% of subjects, respectively. The presence of EM was associated with lower lung function (mean difference % FEV1, −20%; 95% CI, −28 to −11; P < .001). There was no difference in airway inflammation, exacerbation frequency, or bacterial load in patients with EM alone or with BE and/or BWT ± EM. The diffusing capacity of the lung for carbon monoxide/alveolar volume ratio was the most sensitive and specific parameter in identifying EM (area under the receiver operator characteristic curve, 0.87; 95% CI, 0.79-0.96). Physiologic cluster analysis identified three clusters, two of which were EM predominant and the third characterized by a heterogeneous combination of EM and BE. Conclusions: The application of CT imaging can be useful as a tool in the multidimensional approach to phenotyping patients with COPD. PMID:21454400

  5. Multidimensional profiles of health locus of control in Hispanic Americans.

    PubMed

    Champagne, Brian R; Fox, Rina S; Mills, Sarah D; Sadler, Georgia Robins; Malcarne, Vanessa L

    2016-10-01

    Latent profile analysis identified health locus of control profiles among 436 Hispanic Americans who completed the Multidimensional Health Locus of Control scales. Results revealed four profiles: Internally Oriented-Weak, -Moderate, -Strong, and Externally Oriented. The profile groups were compared on sociocultural and demographic characteristics, health beliefs and behaviors, and physical and mental health outcomes. The Internally Oriented-Strong group had less cancer fatalism, religiosity, and equity health attributions, and more alcohol consumption than the other three groups; the Externally Oriented group had stronger equity health attributions and less alcohol consumption. Deriving multidimensional health locus of control profiles through latent profile analysis allows examination of the relationships of health locus of control subtypes to health variables.

  6. Multidimensional profiling of cell surface proteins and nuclear markers

    SciTech Connect

    Han, Ju; Chang, Hang; Andarawewa, Kumari; Yaswen, Paul; Helen Barcellos-Hoff, Mary; Parvin, Bahram

    2009-01-30

    Cell membrane proteins play an important role in tissue architecture and cell-cell communication. We hypothesize that segmentation and multidimensional characterization of the distribution of cell membrane proteins, on a cell-by-cell basis, enable improved classification of treatment groups and identify important characteristics that can otherwise be hidden. We have developed a series of computational steps to (i) delineate cell membrane protein signals and associate them with a specific nucleus; (ii) compute a coupled representation of the multiplexed DNA content with membrane proteins; (iii) rank computed features associated with such a multidimensional representation; (iv) visualize selected features for comparative evaluation through heatmaps; and (v) discriminate between treatment groups in an optimal fashion. The novelty of our method is in the segmentation of the membrane signal and the multidimensional representation of phenotypic signature on a cell-by-cell basis. To test the utility of this method, the proposed computational steps were applied to images of cells that have been irradiated with different radiation qualities in the presence and absence of other small molecules. These samples are labeled for their DNA content and E-cadherin membrane proteins. We demonstrate that multidimensional representations of cell-by-cell phenotypes improve predictive and visualization capabilities among different treatment groups, and identify hidden variables.

  7. Evolution of cooperation in a multidimensional phenotype space.

    PubMed

    Kroumi, Dhaker; Lessard, Sabin

    2015-06-01

    The emergence of cooperation in populations of selfish individuals is a fascinating topic that has inspired much theoretical work. An important model to study cooperation is the phenotypic model, where individuals are characterized by phenotypic properties that are visible to others. The phenotype of an individual can be represented for instance by a vector x = (x1,…,xn), where x1,…,xn are integers. The population can be well mixed in the sense that everyone is equally likely to interact with everyone else, but the behavioral strategies of the individuals can depend on their distance in the phenotype space. A cooperator can choose to help other individuals exhibiting the same phenotype and defects otherwise. Cooperation is said to be favored by selection if it is more abundant than defection in the stationary state. This means that the average frequency of cooperators in the stationary state strictly exceeds 1/2. Antal et al. (2009c) found conditions that ensure that cooperation is more abundant than defection in a one-dimensional (i.e. n = 1) and an infinite-dimensional (i.e. n = ∞) phenotype space in the case of the Prisoner's Dilemma under weak selection. However, reality lies between these two limit cases. In this paper, we derive the corresponding condition in the case of a phenotype space of any finite dimension. This is done by applying a perturbation method to study a mutation-selection equilibrium under weak selection. This condition is obtained in the limit of a large population size by using the ancestral process. The best scenario for cooperation to be more likely to evolve is found to be a high population-scaled phenotype mutation rate, a low population-scaled strategy mutation rate and a high phenotype space dimension. The biological intuition is that a high population-scaled phenotype mutation rate reduces the quantity of interactions between cooperators and defectors, while a high population-scaled strategy mutation rate introduces newly

  8. Evaluating the Invariance of Cognitive Profile Patterns Derived from Profile Analysis via Multidimensional Scaling (PAMS): A Bootstrapping Approach

    ERIC Educational Resources Information Center

    Kim, Se-Kang

    2010-01-01

    The aim of the current study is to validate the invariance of major profile patterns derived from multidimensional scaling (MDS) by bootstrapping. Profile Analysis via Multidimensional Scaling (PAMS) was employed to obtain profiles and bootstrapping was used to construct the sampling distributions of the profile coordinates and the empirical…

  9. Target deconvolution techniques in modern phenotypic profiling

    PubMed Central

    Lee, Jiyoun; Bogyo, Matthew

    2013-01-01

    The past decade has seen rapid growth in the use of diverse compound libraries in classical phenotypic screens to identify modulators of a given process. The subsequent process of identifying the molecular targets of active hits, also called ‘target deconvolution’, is an essential step for understanding compound mechanism of action and for using the identified hits as tools for further dissection of a given biological process. Recent advances in ‘omics’ technologies, coupled with in silico approaches and the reduced cost of whole genome sequencing, have greatly improved the workflow of target deconvolution and have contributed to a renaissance of ‘modern’ phenotypic profiling. In this review, we will outline how both new and old techniques are being used in the difficult process of target identification and validation as well as discuss some of the ongoing challenges remaining for phenotypic screening. PMID:23337810

  10. Human tissue profiling with multidimensional protein identification technology.

    PubMed

    Cagney, Gerard; Park, Stephen; Chung, Clement; Tong, Bianca; O'Dushlaine, Colm; Shields, Denis C; Emili, Andrew

    2005-01-01

    Profiling of tissues and cell types through systematic characterization of expressed genes or proteins shows promise as a basic research tool, and has potential applications in disease diagnosis and classification. We used multidimensional protein identification protein identification technology (MudPIT) to analyze proteomes for enriched nuclear extracts of eight human tissues: brain, heart, liver, lung, muscle, pancreas, spleen, and testis. We show that the method is approximately 80% reproducible. We address issues of relative abundance, tissue-specificity, and selectivity, and the significance of proteins whose expression does not correlate with that of the corresponding mRNA. Surprisingly, most proteins are detected in a single tissue. These proteins tend to fulfill specialist (and potentially tissue-specific) functions compared to proteins expressed in two or more tissues.

  11. Using Profile Analysis via Multidimensional Scaling (PAMS) to identify core profiles from the WMS-III.

    PubMed

    Frisby, Craig L; Kim, Se-Kang

    2008-03-01

    Profile Analysis via Multidimensional Scaling (PAMS) is a procedure for extracting latent core profiles in a multitest data set. The PAMS procedure offers several advantages compared with other profile analysis procedures. Most notably, PAMS estimates individual profile weights that reflect the degree to which an individual's observed profile approximates the shape and scatter of latent core profiles. The PAMS procedure was applied to index scores of nonreplicated participants from the standardization sample (N = 1,033) for the Wechsler Memory Scale--Third Edition (D. Tulsky, J. Zhu, & M. F. Ledbetter, 2002). PAMS extracted discrepant visual memory and auditory memory versus working memory core profiles for the complete 16- to 89-year-old sample and discrepant working memory and auditory memory versus working memory core profiles for the 75- to 89-year-old cohort. Implications for use of PAMS in future research are discussed.

  12. Bifactor Approach to Modeling Multidimensionality of Physical Self-Perception Profile

    ERIC Educational Resources Information Center

    Chung, ChihMing; Liao, Xiaolan; Song, Hairong; Lee, Taehun

    2016-01-01

    The multi-dimensionality of Physical Self-Perception Profile (PSPP) has been acknowledged by the use of correlated-factor model and second-order model. In this study, the authors critically endorse the bifactor model, as a substitute to address the multi-dimensionality of PSPP. To cross-validate the models, analyses are conducted first in…

  13. Multidimensional Profiling Platforms Reveal Metabolic Dysregulation caused by Organophosphorus Pesticides

    PubMed Central

    Medina-Cleghorn, Daniel; Heslin, Ann; Morris, Patrick J.; Mulvihill, Melinda M.; Nomura, Daniel K.

    2014-01-01

    We are environmentally exposed to countless synthetic chemicals on a daily basis with an increasing number of these chemical exposures linked to adverse health effects. However, our understanding of the (patho)physiological effects of these chemicals remains poorly understood, due in-part to a general lack of effort to systematically and comprehensively identify the direct interactions of environmental chemicals with biological macromolecules in mammalian systems in vivo. Here, we have used functional chemoproteomic and metabolomic platforms to broadly identify direct enzyme targets that are inhibited by widely used organophosphorus (OP) pesticides in vivo in mice and to determine metabolic alterations that are caused by these chemicals. We find that these pesticides directly inhibit over 20 serine hydrolases in vivo leading to widespread disruptions in lipid metabolism. Through identifying direct biological targets of OP pesticides, we show heretofore unrecognized modes of toxicity that may be associated with these agents and underscore the utility of utilizing multidimensional profiling approaches to obtain a more complete understanding of toxicities associated with environmental chemicals. PMID:24205821

  14. Equivalence of kernel machine regression and kernel distance covariance for multidimensional phenotype association studies.

    PubMed

    Hua, Wen-Yu; Ghosh, Debashis

    2015-09-01

    Associating genetic markers with a multidimensional phenotype is an important yet challenging problem. In this work, we establish the equivalence between two popular methods: kernel-machine regression (KMR), and kernel distance covariance (KDC). KMR is a semiparametric regression framework that models covariate effects parametrically and genetic markers non-parametrically, while KDC represents a class of methods that include distance covariance (DC) and Hilbert-Schmidt independence criterion (HSIC), which are nonparametric tests of independence. We show that the equivalence between the score test of KMR and the KDC statistic under certain conditions can lead to a novel generalization of the KDC test that incorporates covariates. Our contributions are 3-fold: (1) establishing the equivalence between KMR and KDC; (2) showing that the principles of KMR can be applied to the interpretation of KDC; (3) the development of a broader class of KDC statistics, where the class members are statistics corresponding to different kernel combinations. Finally, we perform simulation studies and an analysis of real data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) study. The ADNI study suggest that SNPs of FLJ16124 exhibit pairwise interaction effects that are strongly correlated to the changes of brain region volumes. PMID:25939365

  15. Equivalence of kernel machine regression and kernel distance covariance for multidimensional phenotype association studies.

    PubMed

    Hua, Wen-Yu; Ghosh, Debashis

    2015-09-01

    Associating genetic markers with a multidimensional phenotype is an important yet challenging problem. In this work, we establish the equivalence between two popular methods: kernel-machine regression (KMR), and kernel distance covariance (KDC). KMR is a semiparametric regression framework that models covariate effects parametrically and genetic markers non-parametrically, while KDC represents a class of methods that include distance covariance (DC) and Hilbert-Schmidt independence criterion (HSIC), which are nonparametric tests of independence. We show that the equivalence between the score test of KMR and the KDC statistic under certain conditions can lead to a novel generalization of the KDC test that incorporates covariates. Our contributions are 3-fold: (1) establishing the equivalence between KMR and KDC; (2) showing that the principles of KMR can be applied to the interpretation of KDC; (3) the development of a broader class of KDC statistics, where the class members are statistics corresponding to different kernel combinations. Finally, we perform simulation studies and an analysis of real data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) study. The ADNI study suggest that SNPs of FLJ16124 exhibit pairwise interaction effects that are strongly correlated to the changes of brain region volumes.

  16. A Grand Challenge. 2. Phenotypic Profiling of a Natural Product Library on Parkinson's Patient-Derived Cells.

    PubMed

    Vial, Marie-Laure; Zencak, Dusan; Grkovic, Tanja; Gorse, Alain-Dominique; Mackay-Sim, Alan; Mellick, George D; Wood, Stephen A; Quinn, Ronald J

    2016-08-26

    Harnessing the inherent biological relevance of natural products requires a method for the recognition of biological effects that may subsequently lead to the discovery of particular targets. An unbiased multidimensional profiling method was used to examine the activities of natural products on primary cells derived from a Parkinson's disease patient. The biological signature of 482 natural products was examined using multiparametric analysis to investigate known cellular pathways and organelles implicated in Parkinson's disease such as mitochondria, lysosomes, endosomes, apoptosis, and autophagy. By targeting several cell components simultaneously the chance of finding a phenotype was increased. The phenotypes were then clustered using an uncentered correlation. The multidimensional phenotypic screening showed that all natural products, in our screening set, were biologically relevant compounds as determined by an observed phenotypic effect. Multidimensional phenotypic screening can predict the cellular function and subcellular site of activity of new compounds, while the cluster analysis provides correlation with compounds with known mechanisms of action. This study reinforces the value of natural products as biologically relevant compounds. PMID:27447544

  17. Connecting synthetic chemistry decisions to cell and genome biology using small-molecule phenotypic profiling

    PubMed Central

    Wagner, Bridget K.; Clemons, Paul A.

    2009-01-01

    Discovering small-molecule modulators for thousands of gene products requires multiple stages of biological testing, specificity evaluation, and chemical optimization. Many cellular profiling methods, including cellular sensitivity, gene-expression, and cellular imaging, have emerged as methods to assess the functional consequences of biological perturbations. Cellular profiling methods applied to small-molecule science provide opportunities to use complex phenotypic information to prioritize and optimize small-molecule structures simultaneously against multiple biological endpoints. As throughput increases and cost decreases for such technologies, we see an emerging paradigm of using more information earlier in probe- and drug-discovery efforts. Moreover, increasing access to public datasets makes possible the construction of “virtual” profiles of small-molecule performance, even when multiplexed measurements were not performed or when multidimensional profiling was not the original intent. We review some key conceptual advances in small-molecule phenotypic profiling, emphasizing connections to other information, such as protein-binding measurements, genetic perturbations, and cell states. We argue that to maximally leverage these measurements in probe and drug discovery requires a fundamental connection to synthetic chemistry, allowing the consequences of synthetic decisions to be described in terms of changes in small-molecule profiles. Mining such data in the context of chemical structure and synthesis strategies can inform decisions about chemistry procurement and library development, leading to optimal small-molecule screening collections. PMID:19825513

  18. Development and Validation of a Short Form for the Multidimensional Work Ethic Profile

    ERIC Educational Resources Information Center

    Meriac, John P.; Woehr, David J.; Gorman, C. Allen; Thomas, Amanda L. E.

    2013-01-01

    The multidimensional work ethic profile (MWEP) has become one of the most widely-used inventories for measuring the work ethic construct. However, its length has been a potential barrier to even more widespread use. We developed a short form of the MWEP, the MWEP-SF. A subset of items from the original measure was identified, using item response…

  19. Advances in Human B Cell Phenotypic Profiling

    PubMed Central

    Kaminski, Denise A.; Wei, Chungwen; Qian, Yu; Rosenberg, Alexander F.; Sanz, Ignacio

    2012-01-01

    To advance our understanding and treatment of disease, research immunologists have been called-upon to place more centralized emphasis on impactful human studies. Such endeavors will inevitably require large-scale study execution and data management regulation (“Big Biology”), necessitating standardized and reliable metrics of immune status and function. A well-known example setting this large-scale effort in-motion is identifying correlations between eventual disease outcome and T lymphocyte phenotype in large HIV-patient cohorts using multiparameter flow cytometry. However, infection, immunodeficiency, and autoimmunity are also characterized by correlative and functional contributions of B lymphocytes, which to-date have received much less attention in the human Big Biology enterprise. Here, we review progress in human B cell phenotyping, analysis, and bioinformatics tools that constitute valuable resources for the B cell research community to effectively join in this effort. PMID:23087687

  20. Determining the significance of scale values from multidimensional scaling profile analysis using a resampling method.

    PubMed

    Ding, Cody S

    2005-02-01

    Although multidimensional scaling (MDS) profile analysis is widely used to study individual differences, there is no objective way to evaluate the statistical significance of the estimated scale values. In the present study, a resampling technique (bootstrapping) was used to construct confidence limits for scale values estimated from MDS profile analysis. These bootstrap confidence limits were used, in turn, to evaluate the significance of marker variables of the profiles. The results from analyses of both simulation data and real data suggest that the bootstrap method may be valid and may be used to evaluate hypotheses about the statistical significance of marker variables of MDS profiles. PMID:16097342

  1. Ameloblastoma Phenotypes Reflected in Distinct Transcriptome Profiles.

    PubMed

    Hu, Shijia; Parker, Joel; Divaris, Kimon; Padilla, Ricardo; Murrah, Valerie; Wright, John Timothy

    2016-01-01

    Ameloblastoma is a locally invasive benign neoplasm derived from odontogenic epithelium and presents with diverse phenotypes yet to be characterized molecularly. High recurrence rates of 50-80% with conservative treatment in some sub-types warrants radical surgical resections resulting in high morbidity. The objective of the study was to characterize the transcriptome of ameloblastoma and identify relevant genes and molecular pathways using normal odontogenic tissue (human "dentome") for comparison. Laser capture microdissection was used to obtain neoplastic epithelial tissue from 17 tumors which were examined using the Agilent 44 k whole genome microarray. Ameloblastoma separated into 2 distinct molecular clusters that were associated with pre-secretory ameloblast and odontoblast. Within the pre-secretory cluster, 9/10 of samples were of the follicular type while 6/7 of the samples in the odontoblast cluster were of the plexiform type (p < 0.05). Common pathways altered in both clusters included cell-cycle regulation, inflammatory and MAPkinase pathways, specifically known cancer-driving genes such as TP53 and members of the MAPkinase pathways. The pre-secretory ameloblast cluster exhibited higher activation of inflammatory pathways while the odontoblast cluster showed greater disturbances in transcription regulators. Our results are suggestive of underlying inter-tumor molecular heterogeneity of ameloblastoma sub-types and have implications for the use of tailored treatment. PMID:27491308

  2. Ameloblastoma Phenotypes Reflected in Distinct Transcriptome Profiles

    PubMed Central

    Hu, Shijia; Parker, Joel; Divaris, Kimon; Padilla, Ricardo; Murrah, Valerie; Wright, John Timothy

    2016-01-01

    Ameloblastoma is a locally invasive benign neoplasm derived from odontogenic epithelium and presents with diverse phenotypes yet to be characterized molecularly. High recurrence rates of 50–80% with conservative treatment in some sub-types warrants radical surgical resections resulting in high morbidity. The objective of the study was to characterize the transcriptome of ameloblastoma and identify relevant genes and molecular pathways using normal odontogenic tissue (human “dentome”) for comparison. Laser capture microdissection was used to obtain neoplastic epithelial tissue from 17 tumors which were examined using the Agilent 44 k whole genome microarray. Ameloblastoma separated into 2 distinct molecular clusters that were associated with pre-secretory ameloblast and odontoblast. Within the pre-secretory cluster, 9/10 of samples were of the follicular type while 6/7 of the samples in the odontoblast cluster were of the plexiform type (p < 0.05). Common pathways altered in both clusters included cell-cycle regulation, inflammatory and MAPkinase pathways, specifically known cancer-driving genes such as TP53 and members of the MAPkinase pathways. The pre-secretory ameloblast cluster exhibited higher activation of inflammatory pathways while the odontoblast cluster showed greater disturbances in transcription regulators. Our results are suggestive of underlying inter-tumor molecular heterogeneity of ameloblastoma sub-types and have implications for the use of tailored treatment. PMID:27491308

  3. Multidimensional assessment of neuroendocrine and psychopathological profiles in maltreated youth.

    PubMed

    Puetz, Vanessa B; Zweerings, Jana; Dahmen, Brigitte; Ruf, Caroline; Scharke, Wolfgang; Herpertz-Dahlmann, Beate; Konrad, Kerstin

    2016-09-01

    It has been debated whether children who have experienced early life stress (ELS), such as early caregiver separation show elevated risk for stress-related psychiatric disorders and a multi-symptom psychopathological profile that is not fully reflected in categorical assessments. In this study, we investigated dimensional measures of stress-related psychopathology in children in permanent out-of-home care, taking into account potential neuroendocrine interactions. In the current study, 25 children who had been placed in permanent out-of-home care before age 3 (years) and 26 controls (aged 10.6 ± 1.75 years) were investigated with categorical (DSM-IV) and dimensional assessments (CBCL) of psychopathology and diurnal salivary cortisol levels were assessed. Semi-structured interviews (K-DIPS) revealed no significant group differences in full-scale psychiatric diagnoses, whereas dimensional assessment (CBCL) revealed significant group differences in externalizing and total problem behaviours within the clinical range for children with ELS. Only children with ELS showed a combined symptom profile of clinical-range internalizing and externalizing problems. Lower morning cortisol values and subsequent flatter decline was found in subjects with ELS children compared to controls, showing group differences in diurnal cortisol secretion. Lower morning cortisol values were associated with more problem behaviour in the ELS group. Results show that ELS children exhibited increased psychopathological symptom severity and complexity associated with lower morning cortisol levels, which was not fully reflected in categorical assessments. This highlights the importance of incorporating dimensional assessments and neurobiological factors into psychopathological evaluations of children in out-of-home care in order to facilitate early identification of children at high risk for stress-related disorders. PMID:26875183

  4. The Impact of Time Perspective Latent Profiles on College Drinking: A Multidimensional Approach

    PubMed Central

    Braitman, Abby L.; Henson, James M.

    2015-01-01

    Background Zimbardo and Boyd’s1 time perspective, or the temporal framework individuals use to process information, has been shown to predict health behaviors such as alcohol use. Previous studies supported the predictive validity of individual dimensions of time perspective, with some dimensions acting as protective factors and others as risk factors. However, some studies produced findings contrary to the general body of literature. In addition, time perspective is a multidimensional construct, and the combination of perspectives may be more predictive than individual dimensions in isolation; consequently, multidimensional profiles are a more accurate measure of individual differences and more appropriate for predicting health behaviors. Objectives The current study identified naturally occurring profiles of time perspective and examined their association with risky alcohol use. Methods Data were collected from a college student sample (n = 431, mean age = 20.41 years) using an online survey. Time perspective profiles were identified using latent profile analysis. Results Bootstrapped regression models identified a protective class that engaged in significantly less overall drinking (β = −0.254) as well as engaging in significantly less episodic high risk drinking (β = −0.274). There was also emerging evidence of a high risk time perspective profile that was linked to more overall drinking (β = 0.198) and engaging in more high risk drinking (β = 0.245), though these differences were not significant. Conclusions/Importance These findings support examining time perspective in a multidimensional framework rather than individual dimensions in isolation. Implications include identifying students most in need of interventions, and tailoring interventions to target temporal framing in decision-making. PMID:25607806

  5. Rapid electrochemical phenotypic profiling of antibiotic-resistant bacteria.

    PubMed

    Besant, Justin D; Sargent, Edward H; Kelley, Shana O

    2015-07-01

    Rapid phenotyping of bacteria to identify drug-resistant strains is an important capability for the treatment and management of infectious disease. At present, the rapid determination of antibiotic susceptibility is hindered by the requirement that, in existing devices, bacteria must be pre-cultured for 2-3 days to reach detectable levels. Here we report a novel electrochemical approach that achieves rapid readout of the antibiotic susceptibility profile of a bacterial infection within one hour. The electrochemical reduction of a redox-active molecule is monitored that reports on levels of metabolically-active bacteria. Bacteria are captured in miniaturized wells, incubated with antimicrobials and monitored for resistance. This electrochemical phenotyping approach is effective with clinically-relevant levels of bacteria, and provides results comparable to culture-based analysis. Results, however, are delivered on a much faster timescale, with resistance profiles available after a one hour incubation period.

  6. Phenotype Microarray Profiling of Zymomonas mobilis ZM4

    SciTech Connect

    Bochner, Barry; Gomez, Vanessa; Ziman, michael; Yang, Shihui; Brown, Steven D

    2009-01-01

    In this study, we developed a Phenotype MicroArray{trademark} (PM) protocol to profile cellular phenotypes in Zymomonas mobilis, which included a standard set of nearly 2,000 assays for carbon, nitrogen, phosphorus and sulfur source utilization, nutrient stimulation, pH and osmotic stresses, and chemical sensitivities with 240 inhibitory chemicals. We observed two positive assays for C-source utilization (fructose and glucose) using the PM screen, which uses redox chemistry and cell respiration as a universal reporter to profile growth phenotypes in a high-throughput 96-well plate-based format. For nitrogen metabolism, the bacterium showed a positive test results for ammonia, aspartate, asparagine, glutamate, glutamine, and peptides. Z. mobilis appeared to use a diverse array of P-sources with two exceptions being pyrophosphate and tripolyphosphate. The assays suggested that Z. mobilis uses both inorganic and organic compounds as S-sources. No stimulation by nutrients was detected; however, there was evidence of partial inhibition by purines and pyrimidines, NAD, and deferoxamine. Z. mobilis was relatively resistant to acid pH, tolerating a pH down to about 4.0. It also tolerated phosphate, sulfate, and nitrate, but was rather sensitive to chloride and nitrite. Z. mobilis showed resistance to a large number of diverse chemicals that inhibit most bacteria. The information from PM analysis provides an overview of Z. mobilis physiology and a foundation for future comparisons of other wild-type and mutant Z. mobilis strains.

  7. Automated Analysis and Classification of Histological Tissue Features by Multi-Dimensional Microscopic Molecular Profiling

    PubMed Central

    Riordan, Daniel P.; Varma, Sushama; West, Robert B.; Brown, Patrick O.

    2015-01-01

    Characterization of the molecular attributes and spatial arrangements of cells and features within complex human tissues provides a critical basis for understanding processes involved in development and disease. Moreover, the ability to automate steps in the analysis and interpretation of histological images that currently require manual inspection by pathologists could revolutionize medical diagnostics. Toward this end, we developed a new imaging approach called multidimensional microscopic molecular profiling (MMMP) that can measure several independent molecular properties in situ at subcellular resolution for the same tissue specimen. MMMP involves repeated cycles of antibody or histochemical staining, imaging, and signal removal, which ultimately can generate information analogous to a multidimensional flow cytometry analysis on intact tissue sections. We performed a MMMP analysis on a tissue microarray containing a diverse set of 102 human tissues using a panel of 15 informative antibody and 5 histochemical stains plus DAPI. Large-scale unsupervised analysis of MMMP data, and visualization of the resulting classifications, identified molecular profiles that were associated with functional tissue features. We then directly annotated H&E images from this MMMP series such that canonical histological features of interest (e.g. blood vessels, epithelium, red blood cells) were individually labeled. By integrating image annotation data, we identified molecular signatures that were associated with specific histological annotations and we developed statistical models for automatically classifying these features. The classification accuracy for automated histology labeling was objectively evaluated using a cross-validation strategy, and significant accuracy (with a median per-pixel rate of 77% per feature from 15 annotated samples) for de novo feature prediction was obtained. These results suggest that high-dimensional profiling may advance the development of computer

  8. Examining Work Ethic across Populations: A Comparison of the Multidimensional Work Ethic Profile across Three Diverse Cultures

    ERIC Educational Resources Information Center

    Woehr, David J.; Arciniega, Luis M.; Lim, Doo H.

    2007-01-01

    The authors examined the measurement equivalence of the Multidimensional Work Ethic Profile (MWEP) across the diverse cultures of Korea, Mexico, and the United States. Korean- and Spanish-language versions of the MWEP were developed and evaluated relative to the original English version of the measure. Confirmatory factor analytic results…

  9. Comparing Longitudinal Profile Patterns of Mathematics and Reading in Early Child Longitudinal Study, Kindergarten: The Profile Analysis via Multidimensional Scaling (PAMS) Approach

    ERIC Educational Resources Information Center

    Kim, Se-Kang

    2010-01-01

    The aim of the study is to compare longitudinal patterns from Mathematics and Reading data from the direct child assessment of Early Child Longitudinal Study, Kindergarten (ECLS-K, US Department of Education, National Center for Education Statistics 2006), utilizing Profile Analysis via Multidimensional Scaling (PAMS). PAMS has been used initially…

  10. Assessing sub-clinical psychosis phenotypes in the general population--a multidimensional approach.

    PubMed

    Rössler, Wulf; Ajdacic-Gross, Vladeta; Müller, Mario; Rodgers, Stephanie; Haker, Helene; Hengartner, Michael P

    2015-02-01

    Several studies have demonstrated that expression of a psychosis phenotype can be observed below the threshold of its clinical detection. To date, however, no conceptual certainty has been reported for the validity and reliability of sub-clinical psychosis. Our main objectives were to assess the prevalence rates and severity of various psychosis symptoms in a representative community sample. Furthermore, we wanted to analyze which latent factors are depicted by several currently used psychosis questionnaires. We also examined how those latent factors for sub-clinical psychosis are linked to psychosocial factors, normal personality traits, and coping abilities related to chronic stress. Most of the eight subscales from the Paranoia Checklist and the Structured Interview for Assessing Perceptual Anomalies had a very similar type of distribution, i.e., an inverse Gaussian (Wald) distribution. This supported the notion of a continuity of psychotic symptoms, which we would expect to find for continuously distributed symptoms within the general population. Sub-clinical psychosis can be reduced to two different factors - one representing odd beliefs about the world and odd behavior, and the other one representing anomalous perceptions (such as hallucinations). Persons with odd beliefs and behavior are under greater burden and more susceptible to psychosocial risks than are persons with anomalous perceptions. These sub-clinical psychosis syndromes are also related to stable personality traits. In conclusion, we obtained strong support for the notion that there is no natural cut-off separating psychotic illness from good health. Sub-clinical psychosis of any kind is not trivial because it is associated with various types of social disability. PMID:25523751

  11. Next-generation biobanking of metastases to enable multidimensional molecular profiling in personalized medicine.

    PubMed

    Diaz, Zuanel; Aguilar-Mahecha, Adriana; Paquet, Eric R; Basik, Mark; Orain, Michèle; Camlioglu, Errol; Constantin, André; Benlimame, Naciba; Bachvarov, Dimcho; Jannot, Guillaume; Simard, Martin J; Chabot, Benoit; Gologan, Adrian; Klinck, Roscoe; Gagnon-Kugler, Thérèse; Lespérance, Bernard; Samson, Benoit; Kavan, Petr; Alcindor, Thierry; Dalfen, Richard; Lan, Cathy; Chabot, Catherine; Buchanan, Marguerite; Przybytkowski, Ewa; Qureshi, Samia; Rousseau, Caroline; Spatz, Alan; Têtu, Bernard; Batist, Gerald

    2013-11-01

    Great advances in analytical technology coupled with accelerated new drug development and growing understanding of biological challenges, such as tumor heterogeneity, have required a change in the focus for biobanking. Most current banks contain samples of primary tumors, but linking molecular signatures to therapeutic questions requires serial biopsies in the setting of metastatic disease, next-generation of biobanking. Furthermore, an integration of multidimensional analysis of various molecular components, that is, RNA, DNA, methylome, microRNAome and post-translational modifications of the proteome, is necessary for a comprehensive view of a tumor's biology. While data using such biopsies are now regularly presented, the preanalytical variables in tissue procurement and processing in multicenter studies are seldom detailed and therefore are difficult to duplicate or standardize across sites and across studies. In the context of a biopsy-driven clinical trial, we generated a detailed protocol that includes morphological evaluation and isolation of high-quality nucleic acids from small needle core biopsies obtained from liver metastases. The protocol supports stable shipping of samples to a central laboratory, where biopsies are subsequently embedded in support media. Designated pathologists must evaluate all biopsies for tumor content and macrodissection can be performed if necessary to meet our criteria of >60% neoplastic cells and <20% necrosis for genomic isolation. We validated our protocol in 40 patients who participated in a biopsy-driven study of therapeutic resistance in metastatic colorectal cancer. To ensure that our protocol was compatible with multiplex discovery platforms and that no component of the processing interfered with downstream enzymatic reactions, we performed array comparative genomic hybridization, methylation profiling, microRNA profiling, splicing variant analysis and gene expression profiling using genomic material isolated from

  12. Plasma exosome profiles from dairy cows with divergent fertility phenotypes.

    PubMed

    Mitchell, M D; Scholz-Romero, K; Reed, S; Peiris, H N; Koh, Y Q; Meier, S; Walker, C G; Burke, C R; Roche, J R; Rice, G; Salomon, C

    2016-09-01

    Cell-to-cell communication in physiological and pathological conditions may be influenced by neighboring cells, distant tissues, or local environmental factors. Exosomes are specific subsets of extracellular vesicles that internalize and deliver their content to near and distant sites. Exosomes may play a role in the maternal-embryo crosstalk vital for the recognition and maintenance of a pregnancy; however, their role in dairy cow reproduction has not been established. This study aimed to characterize the exosome profile in the plasma of 2 strains of dairy cow with divergent fertility phenotypes. Plasma was obtained and characterized on the basis of genetic ancestry as fertile (FERT; <23% North American genetics, New Zealand Holstein-Friesian strain, n=8) or subfertile (SUBFERT; >92% North American genetics, North American Holstein-Friesian strain, n=8). Exosomes were isolated by differential and buoyant density centrifugation and characterized by size distribution (nanoparticle tracking analysis, NanoSight NS500, NanoSight Ltd., Amesbury, UK), the presence of CD63 (Western blot), and their morphology (electron microscopy). The total number of exosomes was determined by quantifying the immunoreactive CD63 (ExoELISA kit, System Biosciences), and the protein content established by mass spectrometry. Enriched exosome fractions were identified as cup-shape vesicles with diameters around 100 nm and positive for the CD63 marker. The concentration of exosomes was 50% greater in FERT cows. Mass spectrometry identified 104 and 117 proteins in FERT and SUBFERT cows, of which 23 and 36 were unique, respectively. Gene ontology analysis revealed enrichment for proteins involved in immunomodulatory processes and cell-to-cell communication. Although the role of exosomes in dairy cow reproduction remains to be elucidated, their quantification and content in models with divergent fertility phenotypes could provide novel information to support both physiological and genetic

  13. Transcriptional Profiling of Egg Allergy and Relationship to Disease Phenotype

    PubMed Central

    Kosoy, Roman; Agashe, Charuta; Grishin, Alexander; Leung, Donald Y.; Wood, Robert A.; Sicherer, Scott H.; Jones, Stacie M.; Burks, A. Wesley; Davidson, Wendy F.; Lindblad, Robert W.; Dawson, Peter; Merad, Miriam; Kidd, Brian A.; Dudley, Joel T.; Sampson, Hugh A.

    2016-01-01

    Background Egg allergy is one of the most common food allergies of childhood. There is a lack of information on the immunologic basis of egg allergy beyond the role of IgE. Objective To use transcriptional profiling as a novel approach to uncover immunologic processes associated with different phenotypes of egg allergy. Methods Peripheral blood mononuclear cells (PBMCs) were obtained from egg-allergic children who were defined as reactive (BER) or tolerant (BET) to baked egg, and from food allergic controls (AC) who were egg non-allergic. PBMCs were stimulated with egg white protein. Gene transcription was measured by microarray after 24 h, and cytokine secretion by multiplex assay after 5 days. Results The transcriptional response of PBMCs to egg protein differed between BER and BET versus AC subjects. Compared to the AC group, the BER group displayed increased expression of genes associated with allergic inflammation as well as corresponding increased secretion of IL-5, IL-9 and TNF-α. A similar pattern was observed for the BET group. Further similarities in gene expression patterns between BER and BET groups, as well as some important differences, were revealed using a novel Immune Annotation resource developed for this project. This approach identified several novel processes not previously associated with egg allergy, including positive associations with TLR4-stimulated myeloid cells and activated NK cells, and negative associations with an induced Treg signature. Further pathway analysis of differentially expressed genes comparing BER to BET subjects showed significant enrichment of IFN-α and IFN-γ response genes, as well as genes associated with virally-infected DCs. Conclusions Transcriptional profiling identified several novel pathways and processes that differed when comparing the response to egg allergen in BET, BER, and AC groups. We conclude that this approach is a useful hypothesis-generating mechanism to identify novel immune processes associated

  14. Unique DNA methylome profiles in CpG island methylator phenotype colon cancers.

    PubMed

    Xu, Yaomin; Hu, Bo; Choi, Ae-Jin; Gopalan, Banu; Lee, Byron H; Kalady, Matthew F; Church, James M; Ting, Angela H

    2012-02-01

    A subset of colorectal cancers was postulated to have the CpG island methylator phenotype (CIMP), a higher propensity for CpG island DNA methylation. The validity of CIMP, its molecular basis, and its prognostic value remain highly controversial. Using MBD-isolated genome sequencing, we mapped and compared genome-wide DNA methylation profiles of normal, non-CIMP, and CIMP colon specimens. Multidimensional scaling analysis revealed that each specimen could be clearly classified as normal, non-CIMP, and CIMP, thus signifying that these three groups have distinctly different global methylation patterns. We discovered 3780 sites in various genomic contexts that were hypermethylated in both non-CIMP and CIMP colon cancers when compared with normal colon. An additional 2026 sites were found to be hypermethylated in CIMP tumors only; and importantly, 80% of these sites were located in CpG islands. These data demonstrate on a genome-wide level that the additional hypermethylation seen in CIMP tumors occurs almost exclusively at CpG islands and support definitively that these tumors were appropriately named. When these sites were examined more closely, we found that 25% were adjacent to sites that were also hypermethylated in non-CIMP tumors. Thus, CIMP is also characterized by more extensive methylation of sites that are already prone to be hypermethylated in colon cancer. These observations indicate that CIMP tumors have specific defects in controlling both DNA methylation seeding and spreading and serve as an important first step in delineating molecular mechanisms that control these processes. PMID:21990380

  15. Large-scale Phenotypic Profiling of Gene Deletion Mutants in Candida glabrata

    PubMed Central

    Tscherner, Michael; Kuchler, Karl

    2016-01-01

    Here, we describe a method enabling the phenotypic profiling of genome-scale deletion collections of fungal mutants to detect phenotypes for various stress conditions. These stress conditions include among many others antifungal drug susceptibility, temperature-induced and osmotic as well as heavy metal or oxidative stress. The protocol was extensively used to phenotype a collection of gene deletion mutants in the human fungal pathogen Candida glabrata (C. glabrata) (Schwarzmüller et al., 2014). PMID:27774498

  16. Toward a multidimensional understanding of residential neighborhood: a latent profile analysis of Los Angeles neighborhoods and longitudinal adult excess weight

    PubMed Central

    Jones, Malia; Huh, Jimi

    2015-01-01

    People are embedded in a complex socio-spatial context that may affect their weight status through multiple mechanisms, including food & physical activity opportunities and chronic stress exposure. However, research to date has been unable to resolve what features of neighborhoods are causally related to weight status. We used latent profile analysis to identify three “types” of neighborhoods (based on five dimensions of neighborhood social status) in Los Angeles, CA. Our neighborhood types were both substantively interpretable and predictive of excess weight in both cross-sectional and longitudinal models. Our results are promising for a research community attempting to operationalize neighborhoods as multidimensional, complex systems. PMID:24607872

  17. Two physically and serologically distinct lipopolysaccharide profiles in strains of Bordetella pertussis and their phenotype variants.

    PubMed Central

    Peppler, M S

    1984-01-01

    The lipopolysaccharide (LPS) from nine strains representing 18 phenotype variants of Bordetella pertussis could be grouped into one of two distinct profiles by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and silver staining. One group, representing the wild-type LPS profile of B. pertussis, consisted of two silver-staining bands: a dominant brown-amber a band and a faster-migrating, minor, black-staining b band. The second group, representing a variant LPS profile, consisted of a single black-staining band of similar mobility to the b band in the wild-type profile. By electrophoretic transfer (Western) blot analysis, mouse antiserum raised against whole cells of Tohama I (prototype wild-type LPS strain) recognized only the a band from all strains/phenotypes possessing the wild-type LPS profile. In contrast, mouse antiserum raised against whole cells of 134 (prototype variant LPS strain) recognized all b bands, regardless of strain/phenotype, and could be shown to cross-react weakly with the a band from Tohama I. These results and results from cohemagglutination and immunodiffusion analyses support the classification of B. pertussis into one of two physiologically and serologically distinct LPS phenotypes: Lps AB for the wild-type profile and Lps B for the variant profile. The relationship of LPS type and phenotypic, or "phase," variation is discussed. Images PMID:6317567

  18. Multi-parameter phenotypic profiling: using cellular effects to characterize small-molecule compounds.

    PubMed

    Feng, Yan; Mitchison, Timothy J; Bender, Andreas; Young, Daniel W; Tallarico, John A

    2009-07-01

    Multi-parameter phenotypic profiling of small molecules provides important insights into their mechanisms of action, as well as a systems level understanding of biological pathways and their responses to small molecule treatments. It therefore deserves more attention at an early step in the drug discovery pipeline. Here, we summarize the technologies that are currently in use for phenotypic profiling--including mRNA-, protein- and imaging-based multi-parameter profiling--in the drug discovery context. We think that an earlier integration of phenotypic profiling technologies, combined with effective experimental and in silico target identification approaches, can improve success rates of lead selection and optimization in the drug discovery process.

  19. Multidimensional risk profiles on teen parenthood: evidence from Britain in the 1970s.

    PubMed

    Russell, S T

    1998-01-01

    Research on the antecedents of teen parenthood has most often focused upon the role of the family of origin in creating the contexts within which teen parenthood occurs. A smaller body of work, however, has investigated the multidimensional character of teenagers' lives which extends beyond the family. The results of such exploration can help to provide a more complete understanding of the complexity of teenagers' lives and the varied factors which place them at risk of becoming young parents. The multidimensional character of teenagers' lives is studied together with the risk of becoming a parent among British youths during the 1970s. Data from the National Child Development Study on a British cohort which grew up during the 1970s are examined to assess the degree to which family characteristics from the teenage years mediate and are mediated by physical development, psychosocial characteristics, academic performance and attitudes, and future plans. Study findings suggest the existence of reciprocal relationships between adolescents' families, schools, and peer networks. Multidimensional risk factors show little variation by gender, while risk factors differ according to the marital status of the teen when he or she became a parent. PMID:12322038

  20. The Neuropsychological Profile of Autism and The Broad Autism Phenotype

    PubMed Central

    Losh, Molly; Adolphs, Ralph; Poe, Michele D.; Couture, Shannon; Penn, David; Baranek, Grace T.; Piven, Joseph

    2009-01-01

    Context There now exist multiple reports of a constellation of language, personality, and social-behavioral features present among relatives that mirror the symptom domains of autism, but much milder in expression. Studies of this ‘broad autism phenotype’ (BAP) may provide a potentially important, complementary approach for detecting the genes causing autism and defining associated neural circuitry, by identifying more refined phenotypes which can be measured quantitatively in both affected and unaffected individuals, and which are tied to functioning in particular regions of the brain. Objective To gain insights into neuropsychological features that index genetic liability to autism. Design Case-control. Setting General community. Participants Thirty-eight high-functioning individuals with autism and parents of autistic individuals, both with and without the BAP (N=83), as well as control groups. Main Outcome Measures A comprehensive battery of neuropsychological tasks tapping social cognition, executive function, and global/local processing strategies (central coherence). Results Both individuals with autism and parents with the BAP differed from controls on measures of social cognition, with performance in the other two domains more similar to controls. Conclusions Data suggest that the social cognitive domain may be an important target for linking phenotype to cognitive process to brain structure in autism, and may ultimately provide insights into genes involved in autism. PMID:19414711

  1. Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes

    PubMed Central

    Chen, Rui; Mias, George I.; Li-Pook-Than, Jennifer; Jiang, Lihua; Lam, Hugo Y. K.; Chen, Rong; Miriami, Elana; Karczewski, Konrad J.; Hariharan, Manoj; Dewey, Frederick E.; Cheng, Yong; Clark, Michael J.; Im, Hogune; Habegger, Lukas; Balasubramanian, Suganthi; O'Huallachain, Maeve; Dudley, Joel T.; Hillenmeyer, Sara; Haraksingh, Rajini; Sharon, Donald; Euskirchen, Ghia; Lacroute, Phil; Bettinger, Keith; Boyle, Alan P.; Kasowski, Maya; Grubert, Fabian; Seki, Scott; Garcia, Marco; Whirl-Carrillo, Michelle; Gallardo, Mercedes; Blasco, Maria A.; Greenberg, Peter L.; Snyder, Phyllis; Klein, Teri E.; Altman, Russ B.; Butte, Atul; Ashley, Euan A.; Nadeau, Kari C.; Gerstein, Mark; Tang, Hua; Snyder, Michael

    2012-01-01

    SUMMARY Personalized medicine is expected to benefit from combining genomic information with regular monitoring of physiological states by multiple high-throughput methods. Here we present an integrative Personal Omics Profile (iPOP), an analysis that combines genomic, transcriptomic, proteomic, metabolomic, and autoantibody profiles from a single individual over a 14-month period. Our iPOP analysis revealed various medical risks, including Type II diabetes. It also uncovered extensive, dynamic changes in diverse molecular components and biological pathways across healthy and diseased conditions. Extremely high coverage genomic and transcriptomic data, which provide the basis of our iPOP, discovered extensive heteroallelic changes during healthy and diseased states and an unexpected RNA editing mechanism. This study demonstrates that longitudinal iPOP can be used to interpret healthy and disease states by connecting genomic information with additional dynamic omics activity. PMID:22424236

  2. Phenotypic Profiling of Antibiotic Response Signatures in Escherichia coli Using Raman Spectroscopy

    PubMed Central

    Athamneh, A. I. M.; Alajlouni, R. A.; Wallace, R. S.; Seleem, M. N.

    2014-01-01

    Identifying the mechanism of action of new potential antibiotics is a necessary but time-consuming and costly process. Phenotypic profiling has been utilized effectively to facilitate the discovery of the mechanism of action and molecular targets of uncharacterized drugs. In this research, Raman spectroscopy was used to profile the phenotypic response of Escherichia coli to applied antibiotics. The use of Raman spectroscopy is advantageous because it is noninvasive, label free, and prone to automation, and its results can be obtained in real time. In this research, E. coli cultures were subjected to three times the MICs of 15 different antibiotics (representing five functional antibiotic classes) with known mechanisms of action for 30 min before being analyzed by Raman spectroscopy (using a 532-nm excitation wavelength). The resulting Raman spectra contained sufficient biochemical information to distinguish between profiles induced by individual antibiotics belonging to the same class. The collected spectral data were used to build a discriminant analysis model that identified the effects of unknown antibiotic compounds on the phenotype of E. coli cultures. Chemometric analysis showed the ability of Raman spectroscopy to predict the functional class of an unknown antibiotic and to identify individual antibiotics that elicit similar phenotypic responses. Results of this research demonstrate the power of Raman spectroscopy as a cellular phenotypic profiling methodology and its potential impact on antibiotic drug development research. PMID:24295982

  3. Transcriptional profiling identifies the metabolic phenotype of gonococcal biofilms.

    PubMed

    Falsetta, Megan L; Bair, Thomas B; Ku, Shan Chi; Vanden Hoven, Rachel N; Steichen, Christopher T; McEwan, Alastair G; Jennings, Michael P; Apicella, Michael A

    2009-09-01

    Neisseria gonorrhoeae, the etiologic agent of gonorrhea, is frequently asymptomatic in women, often leading to chronic infections. One factor contributing to this may be biofilm formation. N. gonorrhoeae can form biofilms on glass and plastic surfaces. There is also evidence that biofilm formation may occur during natural cervical infection. To further study the mechanism of gonococcal biofilm formation, we compared transcriptional profiles of N. gonorrhoeae biofilms to planktonic profiles. Biofilm RNA was extracted from N. gonorrhoeae 1291 grown for 48 h in continuous-flow chambers over glass. Planktonic RNA was extracted from the biofilm runoff. In comparing biofilm with planktonic growth, 3.8% of the genome was differentially regulated. Genes that were highly upregulated in biofilms included aniA, norB, and ccp. These genes encode enzymes that are central to anaerobic respiratory metabolism and stress tolerance. Downregulated genes included members of the nuo gene cluster, which encodes the proton-translocating NADH dehydrogenase. Furthermore, it was observed that aniA, ccp, and norB insertional mutants were attenuated for biofilm formation on glass and transformed human cervical epithelial cells. These data suggest that biofilm formation by the gonococcus may represent a response that is linked to the control of nitric oxide steady-state levels during infection of cervical epithelial cells. PMID:19528210

  4. Phenotyping drug polypharmacology via eicosanoid profiling of blood[S

    PubMed Central

    Song, Jiao; Liu, Xuejun; Rao, Tadimeti S.; Chang, Leon; Meehan, Michael J.; Blevitt, Jonathan M.; Wu, Jiejun; Dorrestein, Pieter C.; Milla, Marcos E.

    2015-01-01

    It is widely accepted that small-molecule drugs, despite their selectivity at primary targets, exert pharmacological effects (and safety liabilities) through a multiplicity of pathways. As such, it has proved extremely difficult to experimentally assess polypharmacology in an agnostic fashion. Profiling of metabolites produced as part of physiological responses to pharmacological stimuli provides a unique opportunity to explore drug pharmacology. A total of 122 eicosanoid lipids in human whole blood were monitored from 10 different donors upon stimulation with several inducers of immunological responses and treatment with modulators of prostaglandin (PG) and leukotriene biosynthesis, including clinical and investigational molecules. Such analysis revealed differentiation between drugs nominally targeting different eicosanoid biosynthetic enzymes, or even those designed to target the same enzyme. Profiled agents, some of them marketed products, affect eicosanoid biosynthesis in ways that cannot be predicted from information on their intended targets. As an example, we used this platform to discriminate drugs based on their ability to silence PG biosynthesis in response to bacterial lipopolysaccharide, resulting in differential pharmacological activity in an in vivo model of endotoxemia. Some of the observed effects are subject to variability among individuals, indicating a potential application of this methodology to the patient stratification, based on their responses to benchmark drugs and experimental compounds read on the eicosanome via a simple blood test. PMID:26022804

  5. Bacterial profiling of soil using genus-specific markers and multidimensional scaling.

    PubMed

    Lenz, Erin J; Foran, David R

    2010-11-01

    Forensic identification of soil based on microbial DNA fingerprinting has met with mixed success, with research efforts rarely considering temporal variability or local heterogeneity in soil's microbial makeup. In the research presented, the nitrogen fixing bacteria rhizobia were specifically examined. Soils were collected monthly from five habitats for 1 year, and quarterly in each cardinal direction from the main collection site. When all habitats were compared simultaneously using Terminal Restriction Fragment Length Polymorphism analysis of the rhizobial recA gene and multidimensional scaling, only two were differentiated over a year's time, however pairwise comparisons allowed four of five soils to be effectively differentiated. Adding in 10-foot distant soils as "questioned" samples correctly grouped them in 40-70% of cases, depending on restriction enzyme used. The results indicate that the technique has potential for forensic soil identification, although extensive anthropogenic manipulation of a soil makes such identification much more tentative. PMID:20533986

  6. Computational Models for Prediction of Yeast Strain Potential for Winemaking from Phenotypic Profiles

    PubMed Central

    Umek, Lan; Fonseca, Elza; Drumonde-Neves, João; Dequin, Sylvie; Zupan, Blaz; Schuller, Dorit

    2013-01-01

    Saccharomyces cerevisiae strains from diverse natural habitats harbour a vast amount of phenotypic diversity, driven by interactions between yeast and the respective environment. In grape juice fermentations, strains are exposed to a wide array of biotic and abiotic stressors, which may lead to strain selection and generate naturally arising strain diversity. Certain phenotypes are of particular interest for the winemaking industry and could be identified by screening of large number of different strains. The objective of the present work was to use data mining approaches to identify those phenotypic tests that are most useful to predict a strain's potential for winemaking. We have constituted a S. cerevisiae collection comprising 172 strains of worldwide geographical origins or technological applications. Their phenotype was screened by considering 30 physiological traits that are important from an oenological point of view. Growth in the presence of potassium bisulphite, growth at 40°C, and resistance to ethanol were mostly contributing to strain variability, as shown by the principal component analysis. In the hierarchical clustering of phenotypic profiles the strains isolated from the same wines and vineyards were scattered throughout all clusters, whereas commercial winemaking strains tended to co-cluster. Mann-Whitney test revealed significant associations between phenotypic results and strain's technological application or origin. Naïve Bayesian classifier identified 3 of the 30 phenotypic tests of growth in iprodion (0.05 mg/mL), cycloheximide (0.1 µg/mL) and potassium bisulphite (150 mg/mL) that provided most information for the assignment of a strain to the group of commercial strains. The probability of a strain to be assigned to this group was 27% using the entire phenotypic profile and increased to 95%, when only results from the three tests were considered. Results show the usefulness of computational approaches to simplify strain selection

  7. Active Learning Strategies for Phenotypic Profiling of High-Content Screens.

    PubMed

    Smith, Kevin; Horvath, Peter

    2014-06-01

    High-content screening is a powerful method to discover new drugs and carry out basic biological research. Increasingly, high-content screens have come to rely on supervised machine learning (SML) to perform automatic phenotypic classification as an essential step of the analysis. However, this comes at a cost, namely, the labeled examples required to train the predictive model. Classification performance increases with the number of labeled examples, and because labeling examples demands time from an expert, the training process represents a significant time investment. Active learning strategies attempt to overcome this bottleneck by presenting the most relevant examples to the annotator, thereby achieving high accuracy while minimizing the cost of obtaining labeled data. In this article, we investigate the impact of active learning on single-cell-based phenotype recognition, using data from three large-scale RNA interference high-content screens representing diverse phenotypic profiling problems. We consider several combinations of active learning strategies and popular SML methods. Our results show that active learning significantly reduces the time cost and can be used to reveal the same phenotypic targets identified using SML. We also identify combinations of active learning strategies and SML methods which perform better than others on the phenotypic profiling problems we studied.

  8. Shade Avoidance Components and Pathways in Adult Plants Revealed by Phenotypic Profiling

    PubMed Central

    Nozue, Kazunari; Tat, An V.; Kumar Devisetty, Upendra; Robinson, Matthew; Mumbach, Maxwell R.; Ichihashi, Yasunori; Lekkala, Saradadevi; Maloof, Julin N.

    2015-01-01

    Shade from neighboring plants limits light for photosynthesis; as a consequence, plants have a variety of strategies to avoid canopy shade and compete with their neighbors for light. Collectively the response to foliar shade is called the shade avoidance syndrome (SAS). The SAS includes elongation of a variety of organs, acceleration of flowering time, and additional physiological responses, which are seen throughout the plant life cycle. However, current mechanistic knowledge is mainly limited to shade-induced elongation of seedlings. Here we use phenotypic profiling of seedling, leaf, and flowering time traits to untangle complex SAS networks. We used over-representation analysis (ORA) of shade-responsive genes, combined with previous annotation, to logically select 59 known and candidate novel mutants for phenotyping. Our analysis reveals shared and separate pathways for each shade avoidance response. In particular, auxin pathway components were required for shade avoidance responses in hypocotyl, petiole, and flowering time, whereas jasmonic acid pathway components were only required for petiole and flowering time responses. Our phenotypic profiling allowed discovery of seventeen novel shade avoidance mutants. Our results demonstrate that logical selection of mutants increased success of phenotypic profiling to dissect complex traits and discover novel components. PMID:25874869

  9. Adolescent Risk Behaviors: Studying Typical and Atypical Individuals via Multidimensional Scaling Profile Analysis

    ERIC Educational Resources Information Center

    Dong, Yang; Ding, Cody

    2012-01-01

    Within the framework of problem behavior theory, the purpose of this study was to examine risk behavior profiles of typical and atypical adolescents and the differential outcomes of well-beings for these individuals in the United States. Based on the data from the survey of Health Behavior of School-Aged Children by World Health Organization,…

  10. Multi-dimensional dopant profiling with atomic resolution by scanning tunneling microscopy

    NASA Astrophysics Data System (ADS)

    Liu, Lequn

    Due to the random nature of ion implantation, dopant diffusion, and other processes involved in the doping of silicon devices, the dopant density in shallow junctions and short channels is subject to stochastic variations, which translate directly into variations in device behavior. Dopant profilers with nanometer scale or even atomic scale resolution are needed to properly measure these dopant fluctuations. This thesis presents a new approach for two- and three-dimensional dopant profiling with atomic resolution on the Si(100) surface by scanning tunneling microscopy (STM). The lack of surface states within the band gap of the perfect Si(100)2x1:H surface opens the way to STM studies of dopant distributions in Si(100). STM topographic images, dI/dV images and current image tunneling spectroscopy (CITS) were acquired across the lateral PN junctions of Si devices. Two-dimensional dopant (carrier) profiles were extracted from CITS data with 5A resolution. Moreover, the N and P type dopant induced features were observed in filled state and empty state STM images. The donor (Arsenic) induced feature appears as a protrusion in both the filled and empty state images, while the acceptor (Boron) induced feature appears as a hillock in the filled state image and a depression in the empty state image. The bias dependence, depth dependence and dopant concentration dependence of the dopant induced features were investigated in detail. Based on scattering theory, the numerical calculation was performed to achieve a fundamental understanding of dopant induced features, and the calculation results were in qualitative agreement with the experimental observations. The potential application of this study for 3D dopant profiling with atomic resolution on both P and N type samples is discussed, and the optimal scanning conditions are also suggested. This work reveals the real physical picture of randomly distributed dopants and may be useful to verify and calibrate TCAD simulators.

  11. cellXpress: a fast and user-friendly software platform for profiling cellular phenotypes

    PubMed Central

    2013-01-01

    Background High-throughput, image-based screens of cellular responses to genetic or chemical perturbations generate huge numbers of cell images. Automated analysis is required to quantify and compare the effects of these perturbations. However, few of the current freely-available bioimage analysis software tools are optimized for efficient handling of these images. Even fewer of them are designed to transform the phenotypic features measured from these images into discriminative profiles that can reveal biologically meaningful associations among the tested perturbations. Results We present a fast and user-friendly software platform called "cellXpress" to segment cells, measure quantitative features of cellular phenotypes, construct discriminative profiles, and visualize the resulting cell masks and feature values. We have also developed a suite of library functions to load the extracted features for further customizable analysis and visualization under the R computing environment. We systematically compared the processing speed, cell segmentation accuracy, and phenotypic-profile clustering performance of cellXpress to other existing bioimage analysis software packages or algorithms. We found that cellXpress outperforms these existing tools on three different bioimage datasets. We estimate that cellXpress could finish processing a genome-wide gene knockdown image dataset in less than a day on a modern personal desktop computer. Conclusions The cellXpress platform is designed to make fast and efficient high-throughput phenotypic profiling more accessible to the wider biological research community. The cellXpress installation packages for 64-bit Windows and Linux, user manual, installation guide, and datasets used in this analysis can be downloaded freely from http://www.cellXpress.org. PMID:24564609

  12. Multidimensional profiles of welfare and work dynamics: development, validation, and associations with child cognitive and mental health outcomes.

    PubMed

    Yoshikawa, H; Seidman, E

    2001-12-01

    This prospective longitudinal study addresses the research gap in the literature regarding multidimensional variation in welfare use and employment patterns, and relationships of such variation with parent earnings and child development outcomes. This study also aims to address the limitations of welfare dynamics studies that do not examine how multiple dimensions of welfare receipt and employment co-occur Cluster analysis was utilized, using monthly welfare and employment data from the National Longitudinal Survey of Youth, to examine variation within the welfare population in their welfare and work patterns across the first 5 years of children's lives. Six cluster profiles of welfare and work dynamics were found: Short-Term, Short-Term Work Exit, Working Cyclers, Nonworking Cyclers, Cycle to Long-Term Exit, and Long-Term. The clusters were validated using mother's 6th-year earnings as the criterion. The clusters' associations with child development outcomes in the cognitive and mental health domains (at ages 6 and 7) were then explored. Work following short-term welfare use was associated with higher child reading scores than that following long-term use (a moderate-size effect). Cycling on and off welfare in the context of high levels of employment was associated with higher child internalizing symptoms than cycling accompanied by low levels of employment (a moderate-size effect). Implications for evaluation of TANF welfare-to-work policies are discussed.

  13. Immune Neuroendocrine Phenotypes in Coturnix coturnix: Do Avian Species Show LEWIS/FISCHER-Like Profiles?

    PubMed Central

    Nazar, F. Nicolas; Barrios, Bibiana E.; Kaiser, Pete; Marin, Raul H.; Correa, Silvia G.

    2015-01-01

    Immunoneuroendocrinology studies have identified conserved communicational paths in birds and mammals, e.g. the Hypothalamus-Pituitary-Adrenal axis with anti-inflammatory activity mediated by glucocorticoids. Immune neuroendocrine phenotypes (INPs) have been proposed for mammals implying the categorization of a population in subgroups underlying divergent immune-neuroendocrine interactions. These phenotypes were studied in the context of the LEWIS/FISCHER paradigm (rats expressing high or low pro-inflammatory profiles, respectively). Although avian species have some common immunological mechanisms with mammals, they have also evolved some distinct strategies and, until now, it has not been studied whether birds may also share with mammals similar INPs. Based on corticosterone levels we determined the existence of two divergent groups in Coturnix coturnix that also differed in other immune-neuroendocrine responses. Quail with lowest corticosterone showed higher lymphoproliferative and antibody responses, interferon-γ and interleukin-1β mRNA expression levels and lower frequencies of leukocyte subpopulations distribution and interleukin-13 levels, than their higher corticosterone counterparts. Results suggest the existence of INPs in birds, comparable to mammalian LEWIS/FISCHER profiles, where basal corticosterone also underlies responses of comparable variables associated to the phenotypes. Concluding, INP may not be a mammalian distinct feature, leading to discuss whether these profiles represent a parallel phenomenon evolved in birds and mammals, or a common feature inherited from a reptilian ancestor millions of years ago. PMID:25793369

  14. Tissue-Specific Profiling Reveals Transcriptome Alterations in Arabidopsis Mutants Lacking Morphological Phenotypes[C][W

    PubMed Central

    Simon, Marissa; Bruex, Angela; Kainkaryam, Raghunandan M.; Zheng, Xiaohua; Huang, Ling; Woolf, Peter J.; Schiefelbein, John

    2013-01-01

    Traditional genetic analysis relies on mutants with observable phenotypes. Mutants lacking visible abnormalities may nevertheless exhibit molecular differences useful for defining gene function. To examine this, we analyzed tissue-specific transcript profiles from Arabidopsis thaliana transcription factor gene mutants with known roles in root epidermis development, but lacking a single-gene mutant phenotype due to genetic redundancy. We discovered substantial transcriptional changes in each mutant, preferentially affecting root epidermal genes in a manner consistent with the known double mutant effects. Furthermore, comparing transcript profiles of single and double mutants, we observed remarkable variation in the sensitivity of target genes to the loss of one or both paralogous genes, including preferential effects on specific branches of the epidermal gene network, likely reflecting the pathways of paralog subfunctionalization during evolution. In addition, we analyzed the root epidermal transcriptome of the transparent testa glabra2 mutant to clarify its role in the network. These findings provide insight into the molecular basis of genetic redundancy and duplicate gene diversification at the level of a specific gene regulatory network, and they demonstrate the usefulness of tissue-specific transcript profiling to define gene function in mutants lacking informative visible changes in phenotype. PMID:24014549

  15. Phenotypic Characterization of Retinoic Acid Differentiated SH-SY5Y Cells by Transcriptional Profiling

    PubMed Central

    Korecka, Joanna A.; van Kesteren, Ronald E.; Blaas, Eva; Spitzer, Sonia O.; Kamstra, Jorke H.; Smit, August B.; Swaab, Dick F.; Verhaagen, Joost; Bossers, Koen

    2013-01-01

    Multiple genetic and environmental factors play a role in the development and progression of Parkinson’s disease (PD). The main neuropathological hallmark of PD is the degeneration of dopaminergic (DAergic) neurons in the substantia nigra pars compacta. To study genetic and molecular contributors to the disease process, there is a great need for readily accessible cells with prominent DAergic features that can be used for reproducible in vitro cellular screening. Here, we investigated the molecular phenotype of retinoic acid (RA) differentiated SH-SY5Y cells using genome wide transcriptional profiling combined with gene ontology, transcription factor and molecular pathway analysis. We demonstrated that RA induces a general neuronal differentiation program in SH-SY5Y cells and that these cells develop a predominantly mature DAergic-like neurotransmitter phenotype. This phenotype is characterized by increased dopamine levels together with a substantial suppression of other neurotransmitter phenotypes, such as those for noradrenaline, acetylcholine, glutamate, serotonin and histamine. In addition, we show that RA differentiated SH-SY5Y cells express the dopamine and noradrenalin neurotransmitter transporters that are responsible for uptake of MPP(+), a well known DAergic cell toxicant. MPP(+) treatment alters mitochondrial activity according to its proposed cytotoxic effect in DAergic neurons. Taken together, RA differentiated SH-SY5Y cells have a DAergic-like phenotype, and provide a good cellular screening tool to find novel genes or compounds that affect cytotoxic processes that are associated with PD. PMID:23724009

  16. A GIS-based Computational Tool for Multidimensional Flow Velocity by Acoustic Doppler Current Profilers

    NASA Astrophysics Data System (ADS)

    Kim, D.; Winkler, M.; Muste, M.

    2015-06-01

    Acoustic Doppler Current Profilers (ADCPs) provide efficient and reliable flow measurements compared to other tools for characteristics of the riverine environments. In addition to originally targeted discharge measurements, ADCPs are increasingly utilized to assess river flow characteristics. The newly developed VMS (Velocity Mapping Software) aims at providing an efficient process for quality assurance, mapping velocity vectors for visualization and facilitating comparison with physical and numerical model results. VMS was designed to provide efficient and smooth work flows for processing groups of transects. The software allows the user to select group of files and subsequently to conduct statistical and graphical quality assurance on the files as a group or individually as appropriate. VMS also enables spatial averaging in horizontal and vertical plane for ADCP data in a single or multiple transects over the same or consecutive cross sections. The analysis results are displayed in numerical and graphical formats.

  17. Metabolic Profiling and Phenotyping of Central Nervous System Diseases: Metabolites Bring Insights into Brain Dysfunctions.

    PubMed

    Dumas, Marc-Emmanuel; Davidovic, Laetitia

    2015-09-01

    Metabolic phenotyping corresponds to the large-scale quantitative and qualitative analysis of the metabolome i.e., the low-molecular weight <1 KDa fraction in biological samples, and provides a key opportunity to advance neurosciences. Proton nuclear magnetic resonance and mass spectrometry are the main analytical platforms used for metabolic profiling, enabling detection and quantitation of a wide range of compounds of particular neuro-pharmacological and physiological relevance, including neurotransmitters, secondary messengers, structural lipids, as well as their precursors, intermediates and degradation products. Metabolic profiling is therefore particularly indicated for the study of central nervous system by probing metabolic and neurochemical profiles of the healthy or diseased brain, in preclinical models or in human samples. In this review, we introduce the analytical and statistical requirements for metabolic profiling. Then, we focus on key studies in the field of metabolic profiling applied to the characterization of animal models and human samples of central nervous system disorders. We highlight the potential of metabolic profiling for pharmacological and physiological evaluation, diagnosis and drug therapy monitoring of patients affected by brain disorders. Finally, we discuss the current challenges in the field, including the development of systems biology and pharmacology strategies improving our understanding of metabolic signatures and mechanisms of central nervous system diseases. PMID:25616565

  18. Multidimensional spectrometer

    DOEpatents

    Zanni, Martin Thomas; Damrauer, Niels H.

    2010-07-20

    A multidimensional spectrometer for the infrared, visible, and ultraviolet regions of the electromagnetic spectrum, and a method for making multidimensional spectroscopic measurements in the infrared, visible, and ultraviolet regions of the electromagnetic spectrum. The multidimensional spectrometer facilitates measurements of inter- and intra-molecular interactions.

  19. Gravitaional/Mechanical Factors Affect Gene Expression Profile and Phenotypic Specification of Human Mesenchymal Stem Cells

    NASA Astrophysics Data System (ADS)

    Monici, Monica; Romano, Giovanni; Cialdai, Francesca; Fusi, Fanco; Marziliano, Nicola; Benvenuti, Susana; Cellai, Ilaria; Egli, Marcel; Cogoli, Augusto

    2008-06-01

    Stem cell implantation is a promising approach for tissue repair. Unfortunately this possibility is strictly limited because these cells early withdraw from the cell cycler and seem to form passive, rather than active grafts. Therefore, the development of strategies capable of increasing the yield of phenotypic specification would be a primary aim in biomedical research. It is known that both biochemical and physical factors are needed for tissue homeostasis and their combination in a dose- and time-dependent manner is probably the key to in vitro and in vivo tissue regeneration. In this study, the effects of gravitational factors on human mesenchymal stem cell differentiation were investigated and compared with the ones caused by mechanical stress. The results showed that gene expression profile and phenotypic specification change according with the gravitational/ mechanical stress to which the hMSCs were exposed. Loading by hyperfuge and photomechanical stress by pulsed Nd:YAG laser induced osteoblastogenesis and chondrogenesis while microgravity favoured adipogenesis.

  20. Myoepithelial mRNA expression profiling reveals a common tumor-suppressor phenotype.

    PubMed

    Barsky, Sanford H

    2003-04-01

    A series of myoepithelial cell lines and xenografts derived from benign human myoepithelial tumors of diverse sources (salivary gland, breast, and lung) exhibit common mRNA expression profiles indicative of a tumor-suppressor phenotype. Previously established myoepithelial cell lines and xenografts (HMS-#; HMS-#X) were compared to nonmyoepithelial breast carcinoma cells (MDA-MB-231 and MDA-MB-468, and inflammatory breast carcinoma samples, IBCr, and IBCw), a normal mammary epithelial cell line (HMEC) and individual cases of human breast cancer (zcBT#T), and matched normal human breast tissues (zcBT#N) (overall samples = 22). The global gene expression profile (22,000 genes) of these individual samples was examined using Affymetrix Microarray Gene Chips and subsequently analyzed with both Affymetrix and DChip algorithms. The myoepithelial cell lines/xenografts were distinct and very different from the nonmyoepithelial breast carcinoma cells and the normal breast and breast tumor biopsies. Two hundred and seven specifically selected genes represented a subset of genes that distinguished (P < 0.05) all the myoepithelial cell lines/xenografts from all the other samples and which themselves exhibited hierarchical clustering. Further analysis of these genes revealed increased expression in genes belonging to the classes of extracellular matrix proteins, angiogenic inhibitors, and proteinase inhibitors and decreased expression belonging to the classes of angiogenic factors and proteinases. Developmental genes were also differentially expressed (either over or underexpressed). These studies confirm our previous impression that human myoepithelial cells express a distinct tumor-suppressor phenotype.

  1. OCT4 Remodels the Phenotype and Promotes Angiogenesis of HUVECs by Changing the Gene Expression Profile

    PubMed Central

    Mou, Yan; Yue, Zhen; Wang, Xiaotong; Li, Wenxue; Zhang, Haiying; Wang, Yang; Li, Ronggui; Sun, Xin

    2016-01-01

    It has been shown that forced expression of four mouse stem cell factors (OCT4, Sox2, Klf4, and c-Myc) changed the phenotype of rat endothelial cells to vascular progenitor cells. The present study aimed to explore whether the expression of OCT4 alone might change the phenotype of human umbilical vein endothelial cells (HUVECs) to endothelial progenitor cells and, if so, to examine the possible mechanism involved. A Matrigel-based in vitro angiogenesis assay was used to evaluate the angiogenesis of the cells; the gene expression profile was analyzed by an oligonucleotide probe-based gene array chip and validated by RT-QPCR. The cellular functions of the mRNAs altered by OCT4 were analyzed with Gene Ontology. We found that induced ectopic expression of mouse OCT4 in HUVECs significantly enhanced angiogenesis of the cells, broadly changed the gene expression profile and particularly increased the expression of CD133, CD34, and VEGFR2 (KDR) which are characteristic marker molecules for endothelial progenitor cells (EPCs). Furthermore by analyzing the cellular functions that were targeted by the mRNAs altered by OCT4 we found that stem cell maintenance and cell differentiation were among the top functional response targeted by up-regulated and down-regulated mRNAs upon forced expression of OCT4. These results support the argument that OCT4 remodels the phenotype of HUVECs from endothelial cells to EPCs by up-regulating the genes responsible for stem cell maintenance and down-regulating the genes for cell differentiation. PMID:27226779

  2. Expanding the phenotypic profile of boys with 47, XXY: the impact of familial learning disabilities.

    PubMed

    Samango-Sprouse, Carole A; Stapleton, Emily J; Mitchell, Francie L; Sadeghin, Teresa; Donahue, Thomas P; Gropman, Andrea L

    2014-06-01

    The aim of the study was to examine the impact of familial learning disabilities (FLD) on the phenotypic profile of 47, XXY males and the possibility that 47, XXY males with more severe cognitive deficits may be partially a consequence of familial dyslexia/reading disorder. We wondered if FLD could pose an additional risk for complex neurodevelopmental differences in 47, XXY. The neurodevelopmental profile of males with 47, XXY has been characterized by developmental dyspraxia, language-based learning disorders, executive dysfunction, reading, and attentional deficits. One hundred eighteen boys with 47, XXY diagnosed prenatally who did not receive early hormonal treatment were divided into two groups based on positive histories of FLD and given comprehensive neurodevelopmental evaluations between 36 and 108 months. The assessments included intelligence (nonverbal and verbal), neuromotor (fine and gross), speech, and language. The group with FLD performed significantly lower in multiple neurodevelopmental domains of the Wechsler of VIQ P = 0.015, FSIQ P = 0.0005, the Brief IQ P = 0.0525 of the Leiter, in Auditory Comprehension P = 0.0505, Expressive Communication P = 0.0055, and neuromotor domains of Manual Coordination P = 0.0032, Fine Motor Control P = 0.0378, and Motor Coordination P = 0.008. Our study demonstrates the influence of FLD on neurodevelopment and expands the phenotypic profile of 47, XXY, suggesting some neurodevelopmental variability is attributable to other factors than the additional X. FLD may increase the vulnerability of the 47, XXY children and anticipatory guidance should be provided to families. PMID:24715716

  3. Coping as Part of Motivational Resilience in School: A Multidimensional Measure of Families, Allocations, and Profiles of Academic Coping

    ERIC Educational Resources Information Center

    Skinner, Ellen; Pitzer, Jennifer; Steele, Joel

    2013-01-01

    A study was designed to examine a multidimensional measure of children's coping in the academic domain as part of a larger model of motivational resilience. Using items tapping multiple ways of dealing with academic problems, including five adaptive ways (strategizing, help-seeking, comfort-seeking, self-encouragement, and commitment) and six…

  4. Muscle transcriptomic profiles in pigs with divergent phenotypes for fatness traits

    PubMed Central

    2010-01-01

    Background Selection for increasing intramuscular fat content would definitively improve the palatability and juiciness of pig meat as well as the sensorial and organoleptic properties of cured products. However, evidences obtained in human and model organisms suggest that high levels of intramuscular fat might alter muscle lipid and carbohydrate metabolism. We have analysed this issue by determining the transcriptomic profiles of Duroc pigs with divergent phenotypes for 13 fatness traits. The strong aptitude of Duroc pigs to have high levels of intramuscular fat makes them a valuable model to analyse the mechanisms that regulate muscle lipid metabolism, an issue with evident implications in the elucidation of the genetic basis of human metabolic diseases such as obesity and insulin resistance. Results Muscle gene expression profiles of 68 Duroc pigs belonging to two groups (HIGH and LOW) with extreme phenotypes for lipid deposition and composition traits have been analysed. Microarray and quantitative PCR analysis showed that genes related to fatty acid uptake, lipogenesis and triacylglycerol synthesis were upregulated in the muscle tissue of HIGH pigs, which are fatter and have higher amounts of intramuscular fat than their LOW counterparts. Paradoxically, lipolytic genes also showed increased mRNA levels in the HIGH group suggesting the existence of a cycle where triacylglycerols are continuously synthesized and degraded. Several genes related to the insulin-signalling pathway, that is usually impaired in obese humans, were also upregulated. Finally, genes related to antigen-processing and presentation were downregulated in the HIGH group. Conclusion Our data suggest that selection for increasing intramuscular fat content in pigs would lead to a shift but not a disruption of the metabolic homeostasis of muscle cells. Future studies on the post-translational changes affecting protein activity or expression as well as information about protein location within the

  5. Mitochondria Biogenesis and Bioenergetics Gene Profiles in Isogenic Prostate Cells with Different Malignant Phenotypes

    PubMed Central

    Burch, Tanya C.; Rhim, Johng S.

    2016-01-01

    Background. The most significant hallmarks of cancer are directly or indirectly linked to deregulated mitochondria. In this study, we sought to profile mitochondria associated genes in isogenic prostate cell lines with different tumorigenic phenotypes from the same patient. Results. Two isogenic human prostate cell lines RC77N/E (nonmalignant cells) and RC77T/E (malignant cells) were profiled for expression of mitochondrial biogenesis and energy metabolism genes by qRT-PCR using the Human Mitochondria and the Mitochondrial Energy Metabolism RT2 PCR arrays. Forty-seven genes were differentially regulated between the two cell lines. The interaction and regulatory networks of these genes were generated by Ingenuity Pathway Analysis. UCP2 was the most significantly upregulated gene in primary adenocarcinoma cells in the current study. The overexpression of UCP2 upon malignant transformation was further validated using human prostatectomy clinical specimens. Conclusions. This study demonstrates the overexpression of multiple genes that are involved in mitochondria biogenesis, bioenergetics, and modulation of apoptosis. These genes may play a role in malignant transformation and disease progression. The upregulation of some of these genes in clinical samples indicates that some of the differentially transcribed genes could be the potential targets for therapeutic interventions. PMID:27478826

  6. Mitochondria Biogenesis and Bioenergetics Gene Profiles in Isogenic Prostate Cells with Different Malignant Phenotypes.

    PubMed

    Burch, Tanya C; Rhim, Johng S; Nyalwidhe, Julius O

    2016-01-01

    Background. The most significant hallmarks of cancer are directly or indirectly linked to deregulated mitochondria. In this study, we sought to profile mitochondria associated genes in isogenic prostate cell lines with different tumorigenic phenotypes from the same patient. Results. Two isogenic human prostate cell lines RC77N/E (nonmalignant cells) and RC77T/E (malignant cells) were profiled for expression of mitochondrial biogenesis and energy metabolism genes by qRT-PCR using the Human Mitochondria and the Mitochondrial Energy Metabolism RT(2) PCR arrays. Forty-seven genes were differentially regulated between the two cell lines. The interaction and regulatory networks of these genes were generated by Ingenuity Pathway Analysis. UCP2 was the most significantly upregulated gene in primary adenocarcinoma cells in the current study. The overexpression of UCP2 upon malignant transformation was further validated using human prostatectomy clinical specimens. Conclusions. This study demonstrates the overexpression of multiple genes that are involved in mitochondria biogenesis, bioenergetics, and modulation of apoptosis. These genes may play a role in malignant transformation and disease progression. The upregulation of some of these genes in clinical samples indicates that some of the differentially transcribed genes could be the potential targets for therapeutic interventions. PMID:27478826

  7. Quantitative NMR metabolite profiling of methicillin-resistant and methicillin-susceptible Staphylococcus aureus discriminates between biofilm and planktonic phenotypes.

    PubMed

    Ammons, Mary Cloud B; Tripet, Brian P; Carlson, Ross P; Kirker, Kelly R; Gross, Michael A; Stanisich, Jessica J; Copié, Valérie

    2014-06-01

    Wound bioburden in the form of colonizing biofilms is a major contributor to nonhealing wounds. Staphylococcus aureus is a Gram-positive, facultative anaerobe commonly found in chronic wounds; however, much remains unknown about the basic physiology of this opportunistic pathogen, especially with regard to the biofilm phenotype. Transcriptomic and proteomic analysis of S. aureus biofilms have suggested that S. aureus biofilms exhibit an altered metabolic state relative to the planktonic phenotype. Herein, comparisons of extracellular and intracellular metabolite profiles detected by (1)H NMR were conducted for methicillin-resistant (MRSA) and methicillin-susceptible (MSSA) S. aureus strains grown as biofilm and planktonic cultures. Principal component analysis distinguished the biofilm phenotype from the planktonic phenotype, and factor loadings analysis identified metabolites that contributed to the statistical separation of the biofilm from the planktonic phenotype, suggesting that key features distinguishing biofilm from planktonic growth include selective amino acid uptake, lipid catabolism, butanediol fermentation, and a shift in metabolism from energy production to assembly of cell-wall components and matrix deposition. These metabolite profiles provide a basis for the development of metabolite biomarkers that distinguish between biofilm and planktonic phenotypes in S. aureus and have the potential for improved diagnostic and therapeutic use in chronic wounds.

  8. Metabolomics profiling in plasma samples from glioma patients correlates with tumor phenotypes

    PubMed Central

    Zhao, Hua; Heimberger, Amy B.; Lu, Zhimin; Wu, Xifeng; Hodges, Tiffany R.; Song, Renduo; Shen, Jie

    2016-01-01

    Background Tumor-based molecular biomarkers have redefined in the classification gliomas. However, the association of systemic metabolomics with glioma phenotype has not been explored yet. Methods In this study, we conducted two-step (discovery and validation) metabolomic profiling in plasma samples from 87 glioma patients. The metabolomics data were tested for correlation with glioma grade (high vs low), glioblastoma (GBM) versus malignant gliomas, and IDH mutation status. Results Five metabolites, namely uracil, arginine, lactate, cystamine, and ornithine, significantly differed between high- and low-grade glioma patients in both the discovery and validation cohorts. When the discovery and validation cohorts were combined, we identified 29 significant metabolites with 18 remaining significant after adjusting for multiple comparisons. Those 18 significant metabolites separated high- from low-grade glioma patients with 91.1% accuracy. In the pathway analysis, a total of 18 significantly metabolic pathways were identified. Similarly, we identified 2 and 6 metabolites that significantly differed between GBM and non-GBM, and IDH mutation positive and negative patients after multiple comparison adjusting. Those 6 significant metabolites separated IDH1 mutation positive from negative glioma patients with 94.4% accuracy. Three pathways were identified to be associated with IDH mutation status. Within arginine and proline metabolism, levels of intermediate metabolites in creatine pathway were all significantly lower in IDH mutation positive than in negative patients, suggesting an increased activity of creatine pathway in IDH mutation positive tumors. Conclusion Our findings identified metabolites and metabolic pathways that differentiated tumor phenotypes. These may be useful as host biomarker candidates to further help glioma molecular classification. PMID:26967252

  9. Correlation of Lactobacillus rhamnosus Genotypes and Carbohydrate Utilization Signatures Determined by Phenotype Profiling

    PubMed Central

    Lambert, Jolanda; van Limpt, Kees; Wels, Michiel; Smokvina, Tamara; Knol, Jan; Kleerebezem, Michiel

    2015-01-01

    Lactobacillus rhamnosus is a bacterial species commonly colonizing the gastrointestinal (GI) tract of humans and also frequently used in food products. While some strains have been studied extensively, physiological variability among isolates of the species found in healthy humans or their diet is largely unexplored. The aim of this study was to characterize the diversity of carbohydrate utilization capabilities of human isolates and food-derived strains of L. rhamnosus in relation to their niche of isolation and genotype. We investigated the genotypic and phenotypic diversity of 25 out of 65 L. rhamnosus strains from various niches, mainly human feces and fermented dairy products. Genetic fingerprinting of the strains by amplified fragment length polymorphism (AFLP) identified 11 distinct subgroups at 70% similarity and suggested niche enrichment within particular genetic clades. High-resolution carbohydrate utilization profiling (OmniLog) identified 14 carbon sources that could be used by all of the strains tested for growth, while the utilization of 58 carbon sources differed significantly between strains, enabling the stratification of L. rhamnosus strains into three metabolic clusters that partially correlate with the genotypic clades but appear uncorrelated with the strain's origin of isolation. Draft genome sequences of 8 strains were generated and employed in a gene-trait matching (GTM) analysis together with the publicly available genomes of L. rhamnosus GG (ATCC 53103) and HN001 for several carbohydrates that were distinct for the different metabolic clusters: l-rhamnose, cellobiose, l-sorbose, and α-methyl-d-glucoside. From the analysis, candidate genes were identified that correlate with l-sorbose and α-methyl-d-glucoside utilization, and the proposed function of these genes could be confirmed by heterologous expression in a strain lacking the genes. This study expands our insight into the phenotypic and genotypic diversity of the species L. rhamnosus

  10. Robust Classification of Small-Molecule Mechanism of Action Using a Minimalist High-Content Microscopy Screen and Multidimensional Phenotypic Trajectory Analysis.

    PubMed

    Twarog, Nathaniel R; Low, Jonathan A; Currier, Duane G; Miller, Greg; Chen, Taosheng; Shelat, Anang A

    2016-01-01

    Phenotypic screening through high-content automated microscopy is a powerful tool for evaluating the mechanism of action of candidate therapeutics. Despite more than a decade of development, however, high content assays have yielded mixed results, identifying robust phenotypes in only a small subset of compound classes. This has led to a combinatorial explosion of assay techniques, analyzing cellular phenotypes across dozens of assays with hundreds of measurements. Here, using a minimalist three-stain assay and only 23 basic cellular measurements, we developed an analytical approach that leverages informative dimensions extracted by linear discriminant analysis to evaluate similarity between the phenotypic trajectories of different compounds in response to a range of doses. This method enabled us to visualize biologically-interpretable phenotypic tracks populated by compounds of similar mechanism of action, cluster compounds according to phenotypic similarity, and classify novel compounds by comparing them to phenotypically active exemplars. Hierarchical clustering applied to 154 compounds from over a dozen different mechanistic classes demonstrated tight agreement with published compound mechanism classification. Using 11 phenotypically active mechanism classes, classification was performed on all 154 compounds: 78% were correctly identified as belonging to one of the 11 exemplar classes or to a different unspecified class, with accuracy increasing to 89% when less phenotypically active compounds were excluded. Importantly, several apparent clustering and classification failures, including rigosertib and 5-fluoro-2'-deoxycytidine, instead revealed more complex mechanisms or off-target effects verified by more recent publications. These results show that a simple, easily replicated, minimalist high-content assay can reveal subtle variations in the cellular phenotype induced by compounds and can correctly predict mechanism of action, as long as the appropriate

  11. Methotrexate modulates folate phenotype and inflammatory profile in EA.hy 926 cells

    PubMed Central

    Summers, Carolyn M.; Hammons, Andrea L.; Arora, Jasbir; Zhang, Suhong; Jochems, Jeanine; Blair, Ian A.; Whitehead, Alexander S.

    2014-01-01

    EA.hy 926 cells grown under low folate conditions adopt a “pro-atherosclerotic” morphology and biochemical phenotype. Pharmacologically relevant doses of the antifolate drug methotrexate (MTX) were applied to EA.hy 926 cells maintained in normal (Hi) and low (Lo) folate culture media. Under both folate conditions, MTX caused inhibition of cell proliferation without significantly compromising metabolic activity. MTX treated Hi cells were depleted of folate derivatives, which were present in altered proportions relative to untreated cells. Transcript profiling using microarrays indicated that MTX treatment modified the transciptome in similar ways for both Hi and Lo cells. Many inflammation-related genes, most prominently those encoding C3 and IL-8, were up-regulated, whereas many genes involved in cell division were down-regulated. The results for C3 and IL-8 were confirmed by quantitative RT-PCR and ELISA. MTX appears to modify the inflammatory potential of EA.hy 926 cells such that its therapeutic properties may, at least under some conditions, be accompanied by the induction of a subset of gene products that promote and/or maintain comorbid pathologies. PMID:24657277

  12. The hairless gene of the mouse: relationship of phenotypic effects with expression profile and genotype.

    PubMed

    Cachón-González, M B; San-José, I; Cano, A; Vega, J A; García, N; Freeman, T; Schimmang, T; Stoye, J P

    1999-10-01

    Various mutations of the hairless (hr) gene of mice result in hair loss and other integument defects. To examine the role of the hr gene in mouse development, the expression profile of hr has been determined by in situ hybridisation and correlated to the nature of genetic changes and morphological abnormalities in different mutant animals. Four variant alleles have been characterised at the molecular level. hr/hr mice produce reduced, but significant, levels of hr mRNA whereas other alleles contain mutations which would be expected to preclude the synthesis of functional product, demonstrating a correlation between allelic variation at the hr locus and phenotypic severity. hr expression was shown to be widespread and temporally regulated. It was identified in novel tissues such as cartilage, developing tooth, inner ear, retina, and colon as well as in skin and brain. Analysis of mice homozygous for the rhino allele of hairless revealed that, although no morphological defects were detectable in many tissues normally expressing hr, previously undescribed abnormalities were present in several tissues including inner ear, retina, and colon. These findings indicate that the hairless gene product plays a wider role in development than previously suspected. Dev Dyn 1999;216:113-126. PMID:10536052

  13. The Matchmaker Exchange API: automating patient matching through the exchange of structured phenotypic and genotypic profiles.

    PubMed

    Buske, Orion J; Schiettecatte, François; Hutton, Benjamin; Dumitriu, Sergiu; Misyura, Andriy; Huang, Lijia; Hartley, Taila; Girdea, Marta; Sobreira, Nara; Mungall, Chris; Brudno, Michael

    2015-10-01

    Despite the increasing prevalence of clinical sequencing, the difficulty of identifying additional affected families is a key obstacle to solving many rare diseases. There may only be a handful of similar patients worldwide, and their data may be stored in diverse clinical and research databases. Computational methods are necessary to enable finding similar patients across the growing number of patient repositories and registries. We present the Matchmaker Exchange Application Programming Interface (MME API), a protocol and data format for exchanging phenotype and genotype profiles to enable matchmaking among patient databases, facilitate the identification of additional cohorts, and increase the rate with which rare diseases can be researched and diagnosed. We designed the API to be straightforward and flexible in order to simplify its adoption on a large number of data types and workflows. We also provide a public test data set, curated from the literature, to facilitate implementation of the API and development of new matching algorithms. The initial version of the API has been successfully implemented by three members of the Matchmaker Exchange and was immediately able to reproduce previously identified matches and generate several new leads currently being validated. The API is available at https://github.com/ga4gh/mme-apis. PMID:26255989

  14. The Matchmaker Exchange API: automating patient matching through the exchange of structured phenotypic and genotypic profiles.

    PubMed

    Buske, Orion J; Schiettecatte, François; Hutton, Benjamin; Dumitriu, Sergiu; Misyura, Andriy; Huang, Lijia; Hartley, Taila; Girdea, Marta; Sobreira, Nara; Mungall, Chris; Brudno, Michael

    2015-10-01

    Despite the increasing prevalence of clinical sequencing, the difficulty of identifying additional affected families is a key obstacle to solving many rare diseases. There may only be a handful of similar patients worldwide, and their data may be stored in diverse clinical and research databases. Computational methods are necessary to enable finding similar patients across the growing number of patient repositories and registries. We present the Matchmaker Exchange Application Programming Interface (MME API), a protocol and data format for exchanging phenotype and genotype profiles to enable matchmaking among patient databases, facilitate the identification of additional cohorts, and increase the rate with which rare diseases can be researched and diagnosed. We designed the API to be straightforward and flexible in order to simplify its adoption on a large number of data types and workflows. We also provide a public test data set, curated from the literature, to facilitate implementation of the API and development of new matching algorithms. The initial version of the API has been successfully implemented by three members of the Matchmaker Exchange and was immediately able to reproduce previously identified matches and generate several new leads currently being validated. The API is available at https://github.com/ga4gh/mme-apis.

  15. Correlation of Phenotypic Profiles Using Targeted Proteomics Identifies Mycobacterial Esx-1 Substrates

    PubMed Central

    2015-01-01

    The Esx/WXG-100 (ESAT-6/Wss) exporters are multiprotein complexes that promote protein translocation across the cytoplasmic membrane in a diverse range of pathogenic and nonpathogenic bacterial species. The Esx-1 (ESAT-6 System-1) system mediates virulence factor translocation in mycobacterial pathogens, including the human pathogen Mycobacterium tuberculosis. Although several genes have been associated with Esx-1-mediated transport and virulence, the contribution of individual Esx-1 genes to export is largely undefined. A unique aspect of Esx-1 export is that several substrates require each other for export/stability. We exploited substrate “codependency” to identify Esx-1 substrates. We simultaneously quantified changes in the levels of 13 Esx-1 proteins from both secreted and cytosolic protein fractions generated from 16 Esx-1-deficient Mycobacterium marinum strains in a single experiment using MRM/SRM targeted mass spectrometry. This expansion of measurable Esx-1 proteins allowed us to define statistical rules for assigning novel substrates using phenotypic profiles of known Esx-1 substrates. Using this approach, we identified three additional Esx-1 substrates encoded by the esx-1 region. Our studies begin to address how disruption of specific genes affects several proteins in the Esx-1 complex. Overall, our findings illuminate relationships between Esx-1 proteins and create a framework for the identification of secreted substrates applicable to other protein exporters and pathways. PMID:25106450

  16. Toxin profile, antibiotic resistance, and phenotypic and molecular characterization of Bacillus cereus in Sunsik.

    PubMed

    Chon, Jung-Whan; Kim, Jong-Hyun; Lee, Sun-Jin; Hyeon, Ji-Yeon; Seo, Kun-Ho

    2012-10-01

    Sunsik, a ready-to-eat food in Korea, is comprised of various agricultural and marine products, and has been an important concern in Bacillus cereus food poisoning. The aim of this study was to investigate the toxin profiles, genotypic and phenotypic patterns as well as antibiotic resistance of B. cereus strains isolated from Sunsik. A subtyping method known as automated repetitive sequence-based PCR system (DiversiLab™) was used to assess the intraspecific biodiversity of these isolates. Thirty-five B. cereus strains were isolated from 100 commercial Sunsik samples, all of which harbored at least 1 enterotoxin gene. The detection rates of nheABC, hblCDA, cytK, and entFM enterotoxin gene among all isolates were 97%, 86%, 77%, and 100%, respectively. Most strains also produced corresponding enterotoxins such as HBL (83%) and NHE (94%). One strain (2.9%) carried the emetic toxin genes, including ces and EM1, and was positive for the HEp-2 cell emetic toxin assay. Most strains were positive for various biochemical tests such as salicin hydrolysis (86%), starch fermentation (89%), hemolysis (89%), motility test (100%) and lecithinase hydrolysis (89%). All isolates were susceptible to most antibiotics although they were highly resistant to β-lactam antibiotics. By using the automated rep-PCR system, all isolates were successfully differentiated, indicating the diversity of B. cereus strains present in Sunsik.

  17. Inherited erythromelalgia due to mutations in SCN9A: natural history, clinical phenotype and somatosensory profile.

    PubMed

    McDonnell, Aoibhinn; Schulman, Betsy; Ali, Zahid; Dib-Hajj, Sulayman D; Brock, Fiona; Cobain, Sonia; Mainka, Tina; Vollert, Jan; Tarabar, Sanela; Waxman, Stephen G

    2016-04-01

    Inherited erythromelalgia, the first human pain syndrome linked to voltage-gated sodium channels, is widely regarded as a genetic model of human pain. Because inherited erythromelalgia was linked to gain-of-function changes of sodium channel Na(v)1.7 only a decade ago, the literature has mainly consisted of reports of genetic and/or clinical characterization of individual patients. This paper describes the pattern of pain, natural history, somatosensory profile, psychosocial status and olfactory testing of 13 subjects with primary inherited erythromelalgia with mutations of SCN9A, the gene encoding Na(v)1.7. Subjects were clinically profiled using questionnaires, quantitative sensory testing and olfaction testing during the in-clinic phase of the study. In addition, a detailed pain phenotype for each subject was obtained over a 3-month period at home using diaries, enabling subjects to self-report pain attacks, potential triggers, duration and severity of pain. All subjects reported pain and heat in the extremities (usually feet and/or hands), with pain attacks triggered by heat or exercise and relieved mainly by non-pharmacological manoeuvres such as cooling. A large proportion of pain attacks (355/1099; 32%) did not involve a specific trigger. There was considerable variability in the number, duration and severity of pain attacks between subjects, even those carrying the same mutation within a family, and within individuals over the 12-13 week observation period. Most subjects (11/13) had pain between attacks. For these subjects, mean pain severity between pain attacks was usually lower than that during an attack. Olfaction testing using the Sniffin'T test did not demonstrate hyperosmia. One subject had evidence of orthostatic hypotension. Overall, there was a statistically significant correlation between total Hospital Anxiety and Depression Scale scores (P= 0.005) and pain between attacks and for Hospital Anxiety and Depression Scale Depression scores and pain

  18. A semi-parametric approach to estimate risk functions associated with multi-dimensional exposure profiles: application to smoking and lung cancer

    PubMed Central

    2013-01-01

    Background A common characteristic of environmental epidemiology is the multi-dimensional aspect of exposure patterns, frequently reduced to a cumulative exposure for simplicity of analysis. By adopting a flexible Bayesian clustering approach, we explore the risk function linking exposure history to disease. This approach is applied here to study the relationship between different smoking characteristics and lung cancer in the framework of a population based case control study. Methods Our study includes 4658 males (1995 cases, 2663 controls) with full smoking history (intensity, duration, time since cessation, pack-years) from the ICARE multi-centre study conducted from 2001-2007. We extend Bayesian clustering techniques to explore predictive risk surfaces for covariate profiles of interest. Results We were able to partition the population into 12 clusters with different smoking profiles and lung cancer risk. Our results confirm that when compared to intensity, duration is the predominant driver of risk. On the other hand, using pack-years of cigarette smoking as a single summary leads to a considerable loss of information. Conclusions Our method estimates a disease risk associated to a specific exposure profile by robustly accounting for the different dimensions of exposure and will be helpful in general to give further insight into the effect of exposures that are accumulated through different time patterns. PMID:24152389

  19. Haptoglobin phenotype prevalence and cytokine profiles during Plasmodium falciparum infection in Dogon and Fulani ethnic groups living in Mali

    PubMed Central

    2013-01-01

    Background The Fulani are known to have a lower parasitaemia and less clinical episodes of malaria as compared to the Dogon sympatric ethnic group, living in Mali. Higher circulating malaria-specific antibody titers and increased pro-inflammatory cytokine levels have been shown in Fulani individuals. Several studies have tried to link haptoglobin (Hp) phenotypes with susceptibility to malaria, but without consensus. This study investigated the role of Hp phenotypes and cytokine levels in Dogon and Fulani during asymptomatic Plasmodium falciparum infection. Methods Two different cohorts were combined in this study: a 2008 cohort with 77 children aged between two and ten years and a 2001 cohort, with 82 children and adults, aged between 11 and 68 years. Hp phenotypes in plasma were measured by Western Blot. Circulating levels of sCD163, IL-6, IL-10, IFN-γ and TNF were measured by ELISA. Multiple regression analysis was performed to associate Hp phenotypes with cytokine profiles. In addition, in vitro stimulation of peripheral blood mononuclear cells (PBMCs) with Hp:Hb complexes was performed and cytokine release in corresponding supernatants were measured using cytometric bead array. Results The results revealed a higher Hp2-2 phenotype prevalence in the Fulani. The Hp2-2 phenotype was associated with a higher susceptibility to P. falciparum infection in Dogon, but not in Fulani. In concordance with previous studies, Fulani showed increased inflammatory mediators (IL-6, IFN-γ) and additionally also increased sCD163 levels compared to Dogon, irrespective of infection. Furthermore, infected individuals showed elevated sCD163 levels compared to uninfected individuals, in both Fulani and Dogon. Multiple regression analysis revealed that the Hp1-1 phenotype was associated with higher levels of TNF and IFN-γ, as compared to the Hp2-2 phenotype. In vitro stimulation of PBMCs with Hb:Hp1-1 complexes resulted in a pro-inflammatory cytokine profile, whilst stimulation with

  20. Exploring the Lean Phenotype of Glutathione-Depleted Mice: Thiol, Amino Acid and Fatty Acid Profiles

    PubMed Central

    Elshorbagy, Amany K.; Jernerén, Fredrik; Scudamore, Cheryl L.; McMurray, Fiona; Cater, Heather; Hough, Tertius; Cox, Roger; Refsum, Helga

    2016-01-01

    Background Although reduced glutathione (rGSH) is decreased in obese mice and humans, block of GSH synthesis by buthionine sulfoximine (BSO) results in a lean, insulin-sensitive phenotype. Data is lacking about the effect of BSO on GSH precursors, cysteine and glutamate. Plasma total cysteine (tCys) is positively associated with stearoyl-coenzyme A desaturase (SCD) activity and adiposity in humans and animal models. Objective To explore the phenotype, amino acid and fatty acid profiles in BSO-treated mice. Design Male C3H/HeH mice aged 11 weeks were fed a high-fat diet with or without BSO in drinking water (30 mmol/L) for 8 weeks. Amino acid and fatty acid changes were assessed, as well as food consumption, energy expenditure, locomotor activity, body composition and liver vacuolation (steatosis). Results Despite higher food intake, BSO decreased particularly fat mass but also lean mass (both P<0.001), and prevented fatty liver vacuolation. Physical activity increased during the dark phase. BSO decreased plasma free fatty acids and enhanced insulin sensitivity. BSO did not alter liver rGSH, but decreased plasma total GSH (tGSH) and rGSH (by ~70%), and liver tGSH (by 82%). Glutamate accumulated in plasma and liver. Urine excretion of cysteine and its precursors was increased by BSO. tCys, rCys and cystine decreased in plasma (by 23–45%, P<0.001 for all), but were maintained in liver, at the expense of decreased taurine. Free and total plasma concentrations of the SCD products, oleic and palmitoleic acids were decreased (by 27–38%, P <0.001 for all). Conclusion Counterintuitively, block of GSH synthesis decreases circulating tCys, raising the question of whether the BSO-induced obesity-resistance is linked to cysteine depletion. Cysteine-supplementation of BSO-treated mice is warranted to dissect the effects of cysteine and GSH depletion on energy metabolism. PMID:27788147

  1. A Person-Centered Perspective on Multidimensional Perfectionism in Canadian and Chinese University Students: A Multigroup Latent Profile Analysis

    ERIC Educational Resources Information Center

    Smith, Martin M.; Saklofske, Donald H.; Yan, Gonggu; Sherry, Simon B.

    2016-01-01

    This study investigated the generalizability of the tripartite model of perfectionism across Canadian and Chinese university students. Using latent profile analysis and indicators of perfectionistic strivings, perfectionistic concerns, and neuroticism in both groups, the authors derived a 3-profile solution: adaptive perfectionists, maladaptive…

  2. Peruvian Maca (Lepidium peruvianum): (II) Phytochemical Profiles of Four Prime Maca Phenotypes Grown in Two Geographically-Distant Locations.

    PubMed

    O Meissner, Henry; Mscisz, Alina; Piatkowska, Ewa; Baraniak, Marek; Mielcarek, Sebastian; Kedzia, Bogdan; Holderna-Kedzia, Elzbieta; Pisulewski, Pawel

    2016-03-01

    Peruvian Maca crops (Lepidium peruvianum), grown in two geographically-distant cultivation sites located at similar altitudes in the highlands of the Peruvian Andes (Junin at 4,200 m a.s.l. and Ancash 4,150 m a.s.l.), were used in the study. Four prime Maca phenotypes, distinguished by hypocotyl colours labelled as "Yellow", "Purple", "Red" and "Black" were selected to determine distribution in levels and corresponding ratios between individual Glucosinolates (Glucotropaeolin and m-methylglucotropaeolin) in an attempt to identify four Peruvian Maca phenotypes from analyses of powdered hypocotyls. There were highly significant differences (P<0.01) in hypocotyl weight/size of four Maca phenotypes harvested in two locations. The Junin crop represented a mostly "large" class (13.3 g) with "small" size hypocotyls (7.2 g), while a "small" class was predominant in Ancash (3.5 g). Powdered Yellow Maca showed significantly higher (P<0.001) microbial contamination than the other three, with Black Maca being the least infected. Only minor, statistically-confirmed differences were detected in nutritive characteristics between the four Maca phenotypes grown in Junin, however highly significant differences (P<0.01) in Glucosinolates existed between the Red and Black Maca grown in Junin and Ancash. Irrespective of the cultivation location, Red phenotypes showed the highest content of Total Glucosinolates, followed by Black and Purple, with the Yellow phenotype showing consistently lower levels. Highly significant P<0.01) differences determined in ratios of individual Glucosinolates between four Maca phenotypes grown in two locations, confirms an earlier assumption that sums of individual Glucosinolates, their ratios and profiles, may be feasible to explore in analytically identifying individual Maca phenotypes in pulverised marketed Maca products. PMID:27127450

  3. Peruvian Maca (Lepidium peruvianum): (II) Phytochemical Profiles of Four Prime Maca Phenotypes Grown in Two Geographically-Distant Locations

    PubMed Central

    O. Meissner, Henry; Mscisz, Alina; Piatkowska, Ewa; Baraniak, Marek; Mielcarek, Sebastian; Kedzia, Bogdan; Holderna-Kedzia, Elzbieta; Pisulewski, Pawel

    2016-01-01

    Peruvian Maca crops (Lepidium peruvianum), grown in two geographically-distant cultivation sites located at similar altitudes in the highlands of the Peruvian Andes (Junin at 4,200 m a.s.l. and Ancash 4,150 m a.s.l.), were used in the study. Four prime Maca phenotypes, distinguished by hypocotyl colours labelled as “Yellow”, “Purple”, “Red” and “Black” were selected to determine distribution in levels and corresponding ratios between individual Glucosinolates (Glucotropaeolin and m-methylglucotropaeolin) in an attempt to identify four Peruvian Maca phenotypes from analyses of powdered hypocotyls. There were highly significant differences (P<0.01) in hypocotyl weight/size of four Maca phenotypes harvested in two locations. The Junin crop represented a mostly “large” class (13.3 g) with “small” size hypocotyls (7.2 g), while a “small” class was predominant in Ancash (3.5 g). Powdered Yellow Maca showed significantly higher (P<0.001) microbial contamination than the other three, with Black Maca being the least infected. Only minor, statistically-confirmed differences were detected in nutritive characteristics between the four Maca phenotypes grown in Junin, however highly significant differences (P<0.01) in Glucosinolates existed between the Red and Black Maca grown in Junin and Ancash. Irrespective of the cultivation location, Red phenotypes showed the highest content of Total Glucosinolates, followed by Black and Purple, with the Yellow phenotype showing consistently lower levels. Highly significant P<0.01) differences determined in ratios of individual Glucosinolates between four Maca phenotypes grown in two locations, confirms an earlier assumption that sums of individual Glucosinolates, their ratios and profiles, may be feasible to explore in analytically identifying individual Maca phenotypes in pulverised marketed Maca products. PMID:27127450

  4. Senescence associated secretory phenotype profile from primary lung mice fibroblasts depends on the senescence induction stimuli.

    PubMed

    Maciel-Barón, L A; Morales-Rosales, S L; Aquino-Cruz, A A; Triana-Martínez, F; Galván-Arzate, S; Luna-López, A; González-Puertos, V Y; López-Díazguerrero, N E; Torres, C; Königsberg, Mina

    2016-02-01

    Cellular senescence is a multifactorial phenomenon of growth arrest and distorted function, which has been recognized as an important feature during tumor suppression mechanisms and a contributor to aging. Senescent cells have an altered secretion pattern called Senescence-Associated Secretory Phenotype (SASP) that comprises a complex mix of factors including cytokines, growth factors, chemokines, and matrix metalloproteinases. SASP has been related with local inflammation that leads to cellular transformation and neurodegenerative diseases. Various pathways for senescence induction have been proposed; the most studied is replicative senescence due to telomere attrition called replicative senescence (RS). However, senescence can be prematurely achieved when cells are exposed to diverse stimuli such as oxidative stress (stress-induced premature senescence, SIPS) or proteasome inhibition (proteasome inhibition-induced premature senescence, PIIPS). SASP has been characterized in RS and SIPS but not in PIIPS. Hence, our aim was to determine SASP components in primary lung fibroblasts obtained from CD-1 mice induced to senescence by PIIPS and compare them to RS and SIPS. Our results showed important variations in the 62 cytokines analyzed, while SIPS and RS showed an increase in the secretion of most cytokines, and in PIIPS only 13 were incremented. Variations in glutathione-redox balance were also observed in SIPS and RS, and not in PIIPS. All senescence types SASP displayed a pro-inflammatory profile and increased proliferation in L929 mice fibroblasts exposed to SASP. However, the behavior observed was not exactly the same, suggesting that the senescence induction pathway might encompass dissimilar responses in adjacent cells and promote different outcomes.

  5. Metabolomic and Gene Expression Profiles Exhibit Modular Genetic and Dietary Structure Linking Metabolic Syndrome Phenotypes in Drosophila.

    PubMed

    Williams, Stephanie; Dew-Budd, Kelly; Davis, Kristen; Anderson, Julie; Bishop, Ruth; Freeman, Kenda; Davis, Dana; Bray, Katherine; Perkins, Lauren; Hubickey, Joana; Reed, Laura K

    2015-12-01

    Genetic and environmental factors influence complex disease in humans, such as metabolic syndrome, and Drosophila melanogaster serves as an excellent model in which to test these factors experimentally. Here we explore the modularity of endophenotypes with an in-depth reanalysis of a previous study by Reed et al. (2014), where we raised 20 wild-type genetic lines of Drosophila larvae on four diets and measured gross phenotypes of body weight, total sugar, and total triglycerides, as well as the endophenotypes of metabolomic and whole-genome expression profiles. We then perform new gene expression experiments to test for conservation of phenotype-expression correlations across different diets and populations. We find that transcript levels correlated with gross phenotypes were enriched for puparial adhesion, metamorphosis, and central energy metabolism functions. The specific metabolites L-DOPA and N-arachidonoyl dopamine make physiological links between the gross phenotypes across diets, whereas leucine and isoleucine thus exhibit genotype-by-diet interactions. Between diets, we find low conservation of the endophenotypes that correlate with the gross phenotypes. Through the follow-up expression study, we found that transcript-trait correlations are well conserved across populations raised on a familiar diet, but on a novel diet, the transcript-trait correlations are no longer conserved. Thus, physiological canalization of metabolic phenotypes breaks down in a novel environment exposing cryptic variation. We cannot predict the physiological basis of disease in a perturbing environment from profiles observed in the ancestral environment. This study demonstrates that variation for disease traits within a population is acquired through a multitude of physiological mechanisms, some of which transcend genetic and environmental influences, and others that are specific to an individual's genetic and environmental context.

  6. Metabolomic and Gene Expression Profiles Exhibit Modular Genetic and Dietary Structure Linking Metabolic Syndrome Phenotypes in Drosophila.

    PubMed

    Williams, Stephanie; Dew-Budd, Kelly; Davis, Kristen; Anderson, Julie; Bishop, Ruth; Freeman, Kenda; Davis, Dana; Bray, Katherine; Perkins, Lauren; Hubickey, Joana; Reed, Laura K

    2015-12-01

    Genetic and environmental factors influence complex disease in humans, such as metabolic syndrome, and Drosophila melanogaster serves as an excellent model in which to test these factors experimentally. Here we explore the modularity of endophenotypes with an in-depth reanalysis of a previous study by Reed et al. (2014), where we raised 20 wild-type genetic lines of Drosophila larvae on four diets and measured gross phenotypes of body weight, total sugar, and total triglycerides, as well as the endophenotypes of metabolomic and whole-genome expression profiles. We then perform new gene expression experiments to test for conservation of phenotype-expression correlations across different diets and populations. We find that transcript levels correlated with gross phenotypes were enriched for puparial adhesion, metamorphosis, and central energy metabolism functions. The specific metabolites L-DOPA and N-arachidonoyl dopamine make physiological links between the gross phenotypes across diets, whereas leucine and isoleucine thus exhibit genotype-by-diet interactions. Between diets, we find low conservation of the endophenotypes that correlate with the gross phenotypes. Through the follow-up expression study, we found that transcript-trait correlations are well conserved across populations raised on a familiar diet, but on a novel diet, the transcript-trait correlations are no longer conserved. Thus, physiological canalization of metabolic phenotypes breaks down in a novel environment exposing cryptic variation. We cannot predict the physiological basis of disease in a perturbing environment from profiles observed in the ancestral environment. This study demonstrates that variation for disease traits within a population is acquired through a multitude of physiological mechanisms, some of which transcend genetic and environmental influences, and others that are specific to an individual's genetic and environmental context. PMID:26530416

  7. Metabolomic and Gene Expression Profiles Exhibit Modular Genetic and Dietary Structure Linking Metabolic Syndrome Phenotypes in Drosophila

    PubMed Central

    Williams, Stephanie; Dew-Budd, Kelly; Davis, Kristen; Anderson, Julie; Bishop, Ruth; Freeman, Kenda; Davis, Dana; Bray, Katherine; Perkins, Lauren; Hubickey, Joana; Reed, Laura K.

    2015-01-01

    Genetic and environmental factors influence complex disease in humans, such as metabolic syndrome, and Drosophila melanogaster serves as an excellent model in which to test these factors experimentally. Here we explore the modularity of endophenotypes with an in-depth reanalysis of a previous study by Reed et al. (2014), where we raised 20 wild-type genetic lines of Drosophila larvae on four diets and measured gross phenotypes of body weight, total sugar, and total triglycerides, as well as the endophenotypes of metabolomic and whole-genome expression profiles. We then perform new gene expression experiments to test for conservation of phenotype-expression correlations across different diets and populations. We find that transcript levels correlated with gross phenotypes were enriched for puparial adhesion, metamorphosis, and central energy metabolism functions. The specific metabolites L-DOPA and N-arachidonoyl dopamine make physiological links between the gross phenotypes across diets, whereas leucine and isoleucine thus exhibit genotype-by-diet interactions. Between diets, we find low conservation of the endophenotypes that correlate with the gross phenotypes. Through the follow-up expression study, we found that transcript-trait correlations are well conserved across populations raised on a familiar diet, but on a novel diet, the transcript-trait correlations are no longer conserved. Thus, physiological canalization of metabolic phenotypes breaks down in a novel environment exposing cryptic variation. We cannot predict the physiological basis of disease in a perturbing environment from profiles observed in the ancestral environment. This study demonstrates that variation for disease traits within a population is acquired through a multitude of physiological mechanisms, some of which transcend genetic and environmental influences, and others that are specific to an individual’s genetic and environmental context. PMID:26530416

  8. Multi-dimensional TOF-SIMS analysis for effective profiling of disease-related ions from the tissue surface.

    PubMed

    Park, Ji-Won; Jeong, Hyobin; Kang, Byeongsoo; Kim, Su Jin; Park, Sang Yoon; Kang, Sokbom; Kim, Hark Kyun; Choi, Joon Sig; Hwang, Daehee; Lee, Tae Geol

    2015-06-05

    Time-of-flight secondary ion mass spectrometry (TOF-SIMS) emerges as a promising tool to identify the ions (small molecules) indicative of disease states from the surface of patient tissues. In TOF-SIMS analysis, an enhanced ionization of surface molecules is critical to increase the number of detected ions. Several methods have been developed to enhance ionization capability. However, how these methods improve identification of disease-related ions has not been systematically explored. Here, we present a multi-dimensional SIMS (MD-SIMS) that combines conventional TOF-SIMS and metal-assisted SIMS (MetA-SIMS). Using this approach, we analyzed cancer and adjacent normal tissues first by TOF-SIMS and subsequently by MetA-SIMS. In total, TOF- and MetA-SIMS detected 632 and 959 ions, respectively. Among them, 426 were commonly detected by both methods, while 206 and 533 were detected uniquely by TOF- and MetA-SIMS, respectively. Of the 426 commonly detected ions, 250 increased in their intensities by MetA-SIMS, whereas 176 decreased. The integrated analysis of the ions detected by the two methods resulted in an increased number of discriminatory ions leading to an enhanced separation between cancer and normal tissues. Therefore, the results show that MD-SIMS can be a useful approach to provide a comprehensive list of discriminatory ions indicative of disease states.

  9. Multidimensional Profiles of Health Status: An Application of the Grade of Membership Model to the World Health Survey

    PubMed Central

    Andreotti, Alessandra; Minicuci, Nadia; Kowal, Paul; Chatterji, Somnath

    2009-01-01

    Background The World Health Organization (WHO) conducted the World Health Survey (WHS) between 2002 and 2004 in 70 countries to provide cross-population comparable data on health, health-related outcomes and risk factors. The aim of this study was to apply Grade of Membership (GoM) modelling as a means to condense extensive health information from the WHS into a set of easily understandable health profiles and to assign the degree to which an individual belongs to each profile. Principal Findings This paper described the application of the GoM models to summarize population health status using World Health Survey data. Grade of Membership analysis is a flexible, non-parametric, multivariate method, used to calculate health profiles from WHS self-reported health state and health conditions. The WHS dataset was divided into four country economic categories based on the World Bank economic groupings (high, upper-middle, lower-middle and low income economies) for separate GoM analysis. Three main health profiles were produced for each of the four areas: I. Robust; II. Intermediate; III. Frail; moreover population health, wealth and inequalities are defined for countries in each economic area as a means to put the health results into perspective. Conclusions These analyses have provided a robust method to better understand health profiles and the components which can help to identify healthy and non-healthy individuals. The obtained profiles have described concrete levels of health and have clearly delineated characteristics of healthy and non-healthy respondents. The GoM results provided both a useable way of summarising complex individual health information and a selection of intermediate determinants which can be targeted for interventions to improve health. As populations' age, and with limited budgets for additional costs for health care and social services, applying the GoM methods may assist with identifying higher risk profiles for decision-making and resource

  10. Phenotypic profile of expanded NK cells in chronic lymphoproliferative disorders: a surrogate marker for NK-cell clonality.

    PubMed

    Bárcena, Paloma; Jara-Acevedo, María; Tabernero, María Dolores; López, Antonio; Sánchez, María Luz; García-Montero, Andrés C; Muñoz-García, Noemí; Vidriales, María Belén; Paiva, Artur; Lecrevisse, Quentin; Lima, Margarida; Langerak, Anton W; Böttcher, Sebastian; van Dongen, Jacques J M; Orfao, Alberto; Almeida, Julia

    2015-12-15

    Currently, the lack of a universal and specific marker of clonality hampers the diagnosis and classification of chronic expansions of natural killer (NK) cells. Here we investigated the utility of flow cytometric detection of aberrant/altered NK-cell phenotypes as a surrogate marker for clonality, in the diagnostic work-up of chronic lymphoproliferative disorders of NK cells (CLPD-NK). For this purpose, a large panel of markers was evaluated by multiparametric flow cytometry on peripheral blood (PB) CD56(low) NK cells from 60 patients, including 23 subjects with predefined clonal (n = 9) and polyclonal (n = 14) CD56(low) NK-cell expansions, and 37 with CLPD-NK of undetermined clonality; also, PB samples from 10 healthy adults were included. Clonality was established using the human androgen receptor (HUMARA) assay. Clonal NK cells were found to show decreased expression of CD7, CD11b and CD38, and higher CD2, CD94 and HLADR levels vs. normal NK cells, together with a restricted repertoire of expression of the CD158a, CD158b and CD161 killer-associated receptors. In turn, NK cells from both clonal and polyclonal CLPD-NK showed similar/overlapping phenotypic profiles, except for high and more homogeneous expression of CD94 and HLADR, which was restricted to clonal CLPD-NK. We conclude that the CD94(hi)/HLADR+ phenotypic profile proved to be a useful surrogate marker for NK-cell clonality.

  11. Phenotypic profile of expanded NK cells in chronic lymphoproliferative disorders: a surrogate marker for NK-cell clonality

    PubMed Central

    Bárcena, Paloma; Jara-Acevedo, María; Tabernero, María Dolores; López, Antonio; Sánchez, María Luz; García-Montero, Andrés C.; Muñoz-García, Noemí; Vidriales, María Belén; Paiva, Artur; Lecrevisse, Quentin; Lima, Margarida; Langerak, Anton W.; Böttcher, Sebastian; van Dongen, Jacques J.M.

    2015-01-01

    Currently, the lack of a universal and specific marker of clonality hampers the diagnosis and classification of chronic expansions of natural killer (NK) cells. Here we investigated the utility of flow cytometric detection of aberrant/altered NK-cell phenotypes as a surrogate marker for clonality, in the diagnostic work-up of chronic lymphoproliferative disorders of NK cells (CLPD-NK). For this purpose, a large panel of markers was evaluated by multiparametric flow cytometry on peripheral blood (PB) CD56low NK cells from 60 patients, including 23 subjects with predefined clonal (n = 9) and polyclonal (n = 14) CD56low NK-cell expansions, and 37 with CLPD-NK of undetermined clonality; also, PB samples from 10 healthy adults were included. Clonality was established using the human androgen receptor (HUMARA) assay. Clonal NK cells were found to show decreased expression of CD7, CD11b and CD38, and higher CD2, CD94 and HLADR levels vs. normal NK cells, together with a restricted repertoire of expression of the CD158a, CD158b and CD161 killer-associated receptors. In turn, NK cells from both clonal and polyclonal CLPD-NK showed similar/overlapping phenotypic profiles, except for high and more homogeneous expression of CD94 and HLADR, which was restricted to clonal CLPD-NK. We conclude that the CD94hi/HLADR+ phenotypic profile proved to be a useful surrogate marker for NK-cell clonality. PMID:26556869

  12. Multi-parametric profiling network based on gene expression and phenotype data: a novel approach to developmental neurotoxicity testing.

    PubMed

    Nagano, Reiko; Akanuma, Hiromi; Qin, Xian-Yang; Imanishi, Satoshi; Toyoshiba, Hiroyoshi; Yoshinaga, Jun; Ohsako, Seiichiroh; Sone, Hideko

    2012-01-01

    The establishment of more efficient approaches for developmental neurotoxicity testing (DNT) has been an emerging issue for children's environmental health. Here we describe a systematic approach for DNT using the neuronal differentiation of mouse embryonic stem cells (mESCs) as a model of fetal programming. During embryoid body (EB) formation, mESCs were exposed to 12 chemicals for 24 h and then global gene expression profiling was performed using whole genome microarray analysis. Gene expression signatures for seven kinds of gene sets related to neuronal development and neuronal diseases were selected for further analysis. At the later stages of neuronal cell differentiation from EBs, neuronal phenotypic parameters were determined using a high-content image analyzer. Bayesian network analysis was then performed based on global gene expression and neuronal phenotypic data to generate comprehensive networks with a linkage between early events and later effects. Furthermore, the probability distribution values for the strength of the linkage between parameters in each network was calculated and then used in principal component analysis. The characterization of chemicals according to their neurotoxic potential reveals that the multi-parametric analysis based on phenotype and gene expression profiling during neuronal differentiation of mESCs can provide a useful tool to monitor fetal programming and to predict developmentally neurotoxic compounds. PMID:22312247

  13. Phenotypic profile of early-onset familial Alzheimer's disease caused by presenilin-1 E280A mutation.

    PubMed

    Sepulveda-Falla, Diego; Glatzel, Markus; Lopera, Francisco

    2012-01-01

    Presenilin 1 (PS1) mutations are the most common cause of early-onset familial Alzheimer's disease (EOFAD). They show a common phenotypic profile characterized by early age of onset, severe dementia and distinct neurodegeneration. The largest population of EOFAD carries the E280A mutation in PS1 and resides in Antioquia, Colombia, currently comprising around 5,000 individuals. Carriers start showing memory impairment in the third decade of life, followed by progressive impairment of language and other cognitive processes. They reach mild cognitive impairment around 45 and dementia around 50 years of age. There is some phenotypic variability among the carriers of this single PS1 mutation. Some patients present with epilepsy, verbal impairment, and cerebellar ataxia. Neuropathologically, PS1 E280A cases show pronounced brain atrophy, severe amyloid-β pathology, distinct hyperphosphorylated tau-related pathology, and cerebellar damage. The earliest event identified by functional magnetic imaging resonance is hyperactivation within the right anterior hippocampus around 33 years of age. This well-studied population with a clear pre-clinical profile and wide phenotypic variability in age of onset and clinical presentation is ideally suited for clinical trials and to study molecular mechanisms of Alzheimer's disease. PMID:22766738

  14. Phenotypic profiling of Raf inhibitors and mitochondrial toxicity in 3D tissue using biodynamic imaging.

    PubMed

    An, Ran; Merrill, Dan; Avramova, Larisa; Sturgis, Jennifer; Tsiper, Maria; Robinson, J Paul; Turek, John; Nolte, David D

    2014-04-01

    The existence of phenotypic differences in the drug responses of 3D tissue relative to 2D cell culture is a concern in high-content drug screening. Biodynamic imaging is an emerging technology that probes 3D tissue using short-coherence dynamic light scattering to measure the intracellular motions inside tissues in their natural microenvironments. The information content of biodynamic imaging is displayed through tissue dynamics spectroscopy (TDS) but has not previously been correlated against morphological image analysis of 2D cell culture. In this article, a set of mitochondria-affecting compounds (FCCP, valinomycin, nicardipine, ionomycin) and Raf kinase inhibitors (PLX4032, PLX4720, GDC, and sorafenib) are applied to multicellular tumor spheroids from two colon adenocarcinoma cell lines (HT-29 and DLD-1). These were screened by TDS and then compared against conventional image-based high-content analysis (HCA). The responses to the Raf inhibitors PLX4032 and PLX4720 are grouped separately by cell line, reflecting the Braf/Kras difference in these cell lines. There is a correlation between TDS and HCA phenotypic clustering for most cases, which demonstrates the ability of dynamic measurements to capture phenotypic responses to drugs. However, there are significant 2D versus 3D phenotypic differences exhibited by several of the drugs/cell lines.

  15. Phenotypic Profiling of Raf Inhibitors and Mitochondrial Toxicity in 3D Tissue Using Biodynamic Imaging

    PubMed Central

    An, Ran; Merrill, Dan; Avramova, Larisa; Sturgis, Jennifer; Tsiper, Maria; Robinson, J. Paul; Turek, John; Nolte, David D.

    2014-01-01

    The existence of phenotypic differences in the drug responses of 3D tissue relative to 2D cell culture is a concern in high-content drug screening. Biodynamic imaging is an emerging technology that probes 3D tissue using short-coherence dynamic light scattering to measure the intracellular motions inside tissues in their natural microenvironments. The information content of biodynamic imaging is displayed through tissue dynamics spectroscopy (TDS) but has not previously been correlated against morphological image analysis of 2D cell culture. In this article, a set of mitochondria-affecting compounds (FCCP, valinomycin, nicardipine, ionomycin) and Raf kinase inhibitors (PLX4032, PLX4720, GDC, and sorafenib) are applied to multicellular tumor spheroids from two colon adenocarcinoma cell lines (HT-29 and DLD-1). These were screened by TDS and then compared against conventional image-based high-content analysis (HCA). The responses to the Raf inhibitors PLX4032 and PLX4720 are grouped separately by cell line, reflecting the Braf/Kras difference in these cell lines. There is a correlation between TDS and HCA phenotypic clustering for most cases, which demonstrates the ability of dynamic measurements to capture phenotypic responses to drugs. However, there are significant 2D versus 3D phenotypic differences exhibited by several of the drugs/cell lines. PMID:24361645

  16. Adaptation of the Biolog Phenotype MicroArrayTM Technology to Profile the Obligate Anaerobe Geobacter metallireducens

    SciTech Connect

    Joyner, Dominique; Fortney, Julian; Chakraborty, Romy; Hazen, Terry

    2010-05-17

    The Biolog OmniLog? Phenotype MicroArray (PM) plate technology was successfully adapted to generate a select phenotypic profile of the strict anaerobe Geobacter metallireducens (G.m.). The profile generated for G.m. provides insight into the chemical sensitivity of the organism as well as some of its metabolic capabilities when grown with a basal medium containing acetate and Fe(III). The PM technology was developed for aerobic organisms. The reduction of a tetrazolium dye by the test organism represents metabolic activity on the array which is detected and measured by the OmniLog(R) system. We have previously adapted the technology for the anaerobic sulfate reducing bacterium Desulfovibrio vulgaris. In this work, we have taken the technology a step further by adapting it for the iron reducing obligate anaerobe Geobacter metallireducens. In an osmotic stress microarray it was determined that the organism has higher sensitivity to impermeable solutes 3-6percent KCl and 2-5percent NaNO3 that result in osmotic stress by osmosis to the cell than to permeable non-ionic solutes represented by 5-20percent ethylene glycol and 2-3percent urea. The osmotic stress microarray also includes an array of osmoprotectants and precursor molecules that were screened to identify substrates that would provide osmotic protection to NaCl stress. None of the substrates tested conferred resistance to elevated concentrations of salt. Verification studies in which G.m. was grown in defined medium amended with 100mM NaCl (MIC) and the common osmoprotectants betaine, glycine and proline supported the PM findings. Further verification was done by analysis of transcriptomic profiles of G.m. grown under 100mM NaCl stress that revealed up-regulation of genes related to degradation rather than accumulation of the above-mentioned osmoprotectants. The phenotypic profile, supported by additional analysis indicates that the accumulation of these osmoprotectants as a response to salt stress does not

  17. Plasma cytokine profiles related to smoking-sensitivity and phenotypes of chronic obstructive pulmonary disease.

    PubMed

    Nakamura, Miho; Nakamura, Hidetoshi; Minematsu, Naoto; Chubachi, Shotaro; Miyazaki, Masaki; Yoshida, Shuichi; Tsuduki, Keishi; Shirahata, Toru; Mashimo, Shuko; Takahashi, Saeko; Nakajima, Takahiro; Tateno, Hiroki; Fujishima, Seitaro; Betsuyaku, Tomoko

    2014-08-01

    Chronic obstructive pulmonary disease (COPD) develops only in smoking-sensitive smokers and manifests heterogeneous phenotypes, including emphysema and non-emphysema types. We aimed to identify biomarkers related to the smoking-sensitivity and phenotypes of COPD. Among 240 smokers suggestive of COPD, we studied on four groups defined by % forced expiratory volume in one second (FEV1) and computed tomography-based pulmonary emphysema. Plasma concentrations of 33 inflammatory markers were measured in four groups as well as Non-smokers using multiplex protein arrays. IL-5, IL-7 and IL-13 were identified to be associated with smoking sensitivity and IL-6 and IL-10 were candidate biomarkers for airway-lesion dominant COPD.

  18. Profiling the repertoire of phenotypes influenced by environmental cues that occur during asexual reproduction

    PubMed Central

    Dombrovsky, Aviv; Arthaud, Laury; Ledger, Terence N.; Tares, Sophie; Robichon, Alain

    2009-01-01

    The aphid Acyrthosiphon pisum population is composed of different morphs, such as winged and wingless parthenogens, males, and sexual females. The combined effect of reduced photoperiodicity and cold in fall triggers the apparition of sexual morphs. In contrast they reproduce asexually in spring and summer. In our current study, we provide evidence that clonal individuals display phenotypic variability within asexual morph categories. We describe that clones sharing the same morphological features, which arose from the same founder mother, constitute a repertoire of variants with distinct behavioral and physiological traits. Our results suggest that the prevailing environmental conditions influence the recruitment of adaptive phenotypes from a cohort of clonal individuals exhibiting considerable molecular diversity. However, we observed that the variability might be reduced or enhanced by external factors, but is never abolished in accordance with a model of stochastically produced phenotypes. This overall mechanism allows the renewal of colonies from a few adapted individuals that survive drastic episodic changes in a fluctuating environment. PMID:19635846

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

    PubMed

    Cheng, Yiming; Perocchi, Fabiana

    2015-07-01

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

  20. Sensory Ciliogenesis in Caenorhabditis elegans: Assignment of IFT Components into Distinct Modules Based on Transport and Phenotypic Profiles

    PubMed Central

    Ou, Guangshuo; Koga, Makato; Blacque, Oliver E.; Murayama, Takashi; Ohshima, Yasumi; Schafer, Jenny C.; Li, Chunmei; Yoder, Bradley K.

    2007-01-01

    Sensory cilium biogenesis within Caenorhabditis elegans neurons depends on the kinesin-2–dependent intraflagellar transport (IFT) of ciliary precursors associated with IFT particles to the axoneme tip. Here we analyzed the molecular organization of the IFT machinery by comparing the in vivo transport and phenotypic profiles of multiple proteins involved in IFT and ciliogenesis. Based on their motility in wild-type and bbs (Bardet-Biedl syndrome) mutants, IFT proteins were classified into groups with similar transport profiles that we refer to as “modules.” We also analyzed the distribution and transport of fluorescent IFT particles in multiple known ciliary mutants and 49 new ciliary mutants. Most of the latter mutants were snip-SNP mapped and one, namely dyf-14(ks69), was cloned and found to encode a conserved protein essential for ciliogenesis. The products of these ciliogenesis genes could also be assigned to the aforementioned set of modules or to specific aspects of ciliogenesis, based on IFT particle dynamics and ciliary mutant phenotypes. Although binding assays would be required to confirm direct physical interactions, the results are consistent with the hypothesis that the C. elegans IFT machinery has a modular design, consisting of modules IFT-subcomplex A, IFT-subcomplex B, and a BBS protein complex, in addition to motor and cargo modules, with each module contributing to distinct functional aspects of IFT or ciliogenesis. PMID:17314406

  1. Comparison of Gene Expression and Genome-Wide DNA Methylation Profiling between Phenotypically Normal Cloned Pigs and Conventionally Bred Controls

    PubMed Central

    Li, Shengting; Li, Jian; Lin, Lin; Nielsen, Anders Lade; Sørensen, Charlotte Brandt; Vajta, Gábor; Wang, Jun; Zhang, Xiuqing; Du, Yutao; Yang, Huanming; Bolund, Lars

    2011-01-01

    Animal breeding via Somatic Cell Nuclear Transfer (SCNT) has enormous potential in agriculture and biomedicine. However, concerns about whether SCNT animals are as healthy or epigenetically normal as conventionally bred ones are raised as the efficiency of cloning by SCNT is much lower than natural breeding or In-vitro fertilization (IVF). Thus, we have conducted a genome-wide gene expression and DNA methylation profiling between phenotypically normal cloned pigs and control pigs in two tissues (muscle and liver), using Affymetrix Porcine expression array as well as modified methylation-specific digital karyotyping (MMSDK) and Solexa sequencing technology. Typical tissue-specific differences with respect to both gene expression and DNA methylation were observed in muscle and liver from cloned as well as control pigs. Gene expression profiles were highly similar between cloned pigs and controls, though a small set of genes showed altered expression. Cloned pigs presented a more different pattern of DNA methylation in unique sequences in both tissues. Especially a small set of genomic sites had different DNA methylation status with a trend towards slightly increased methylation levels in cloned pigs. Molecular network analysis of the genes that contained such differential methylation loci revealed a significant network related to tissue development. In conclusion, our study showed that phenotypically normal cloned pigs were highly similar with normal breeding pigs in their gene expression, but moderate alteration in DNA methylation aspects still exists, especially in certain unique genomic regions. PMID:22022462

  2. Recycling Behavior: A Multidimensional Approach

    ERIC Educational Resources Information Center

    Meneses, Gonzalo Diaz; Palacio, Asuncion Beerli

    2005-01-01

    This work centers on the study of consumer recycling roles to examine the sociodemographic and psychographic profile of the distribution of recycling tasks and roles within the household. With this aim in mind, an empirical work was carried out, the results of which suggest that recycling behavior is multidimensional and comprises the undertaking…

  3. Adverse Selection? A Multi-Dimensional Profile of People Dispensed Opioid Analgesics for Persistent Non-Cancer Pain

    PubMed Central

    Rogers, Kris D.; Kemp, Anna; McLachlan, Andrew J.; Blyth, Fiona

    2013-01-01

    Objectives This study investigates utilisation patterns for prescription opioid analgesics in the Australian community and how these are associated with a framework of individual-level factors related to healthcare use. Methods Self-reported demographic and health information from participants in the 45 and Up Study cohort were linked to pharmaceutical claims from 2006–2009. Participants comprised 19,816 people with ≥1 opioid analgesic dispensing in the 12-months after recruitment to the cohort and 79,882 people not dispensed opioid analgesics. All participants were aged ≥45 years, were social security pharmaceutical beneficiaries, with no history of cancer. People dispensed opioid analgesics were classified as having acute (dispensing period <90 days), episodic (≥90 days and <3 ‘authority’ prescriptions for increased quantity supply) or long-term treatment (≥90 days and ≥3 authority prescriptions). Results Of participants dispensed opioid analgesic 52% received acute treatment, 25% episodic treatment and 23% long-term treatment. People dispensed opioid analgesics long-term had an average of 14.9 opioid analgesic prescriptions/year from 2.0 doctors compared with 1.5 prescriptions from 1.1 doctors for people receiving acute treatment. People dispensed opioid analgesics reported more need-related factors such as poorer physical functioning and higher psychological distress. Long-term users were more likely to have access-related factors such as low-income and living outside major cities. After simultaneous adjustment, association with predisposing health factors and access diminished, but indicators of need such as osteoarthritis treatment, paracetamol use, and poor physical function were the strongest predictors for all opioid analgesic users. Conclusions People dispensed opioid analgesics were in poorer health, reported higher levels of distress and poorer functioning than people not receiving opioid analgesics. Varying dispensing profiles were

  4. Liver transcriptome profile in pigs with extreme phenotypes of intramuscular fatty acid composition

    PubMed Central

    2012-01-01

    Background New advances in high-throughput technologies have allowed for the massive analysis of genomic data, providing new opportunities for the characterization of the transcriptome architectures. Recent studies in pigs have employed RNA-Seq to explore the transcriptome of different tissues in a reduced number of animals. The main goal of this study was the identification of differentially-expressed genes in the liver of Iberian x Landrace crossbred pigs showing extreme phenotypes for intramuscular fatty acid composition using RNA-Seq. Results The liver transcriptomes of two female groups (H and L) with phenotypically extreme intramuscular fatty acid composition were sequenced using RNA-Seq. A total of 146 and 180 unannotated protein-coding genes were identified in intergenic regions for the L and H groups, respectively. In addition, a range of 5.8 to 7.3% of repetitive elements was found, with SINEs being the most abundant elements. The expression in liver of 186 (L) and 270 (H) lncRNAs was also detected. The higher reproducibility of the RNA-Seq data was validated by RT-qPCR and porcine expression microarrays, therefore showing a strong correlation between RT-qPCR and RNA-Seq data (ranking from 0.79 to 0.96), as well as between microarrays and RNA-Seq (r=0.72). A differential expression analysis between H and L animals identified 55 genes differentially-expressed between groups. Pathways analysis revealed that these genes belong to biological functions, canonical pathways and three gene networks related to lipid and fatty acid metabolism. In concordance with the phenotypic classification, the pathways analysis inferred that linolenic and arachidonic acids metabolism was altered between extreme individuals. In addition, a connection was observed among the top three networks, hence suggesting that these genes are interconnected and play an important role in lipid and fatty acid metabolism. Conclusions In the present study RNA-Seq was used as a tool to explore

  5. Development of a 3D Tissue Culture–Based High-Content Screening Platform That Uses Phenotypic Profiling to Discriminate Selective Inhibitors of Receptor Tyrosine Kinases

    PubMed Central

    Booij, Tijmen H.; Klop, Maarten J. D.; Yan, Kuan; Szántai-Kis, Csaba; Szokol, Balint; Orfi, Laszlo; van de Water, Bob; Keri, Gyorgy; Price, Leo S.

    2016-01-01

    3D tissue cultures provide a more physiologically relevant context for the screening of compounds, compared with 2D cell cultures. Cells cultured in 3D hydrogels also show complex phenotypes, increasing the scope for phenotypic profiling. Here we describe a high-content screening platform that uses invasive human prostate cancer cells cultured in 3D in standard 384-well assay plates to study the activity of potential therapeutic small molecules and antibody biologics. Image analysis tools were developed to process 3D image data to measure over 800 phenotypic parameters. Multiparametric analysis was used to evaluate the effect of compounds on tissue morphology. We applied this screening platform to measure the activity and selectivity of inhibitors of the c-Met and epidermal growth factor (EGF) receptor (EGFR) tyrosine kinases in 3D cultured prostate carcinoma cells. c-Met and EGFR activity was quantified based on the phenotypic profiles induced by their respective ligands, hepatocyte growth factor and EGF. The screening method was applied to a novel collection of 80 putative inhibitors of c-Met and EGFR. Compounds were identified that induced phenotypic profiles indicative of selective inhibition of c-Met, EGFR, or bispecific inhibition of both targets. In conclusion, we describe a fully scalable high-content screening platform that uses phenotypic profiling to discriminate selective and nonselective (off-target) inhibitors in a physiologically relevant 3D cell culture setting. PMID:27412535

  6. Development of a 3D Tissue Culture-Based High-Content Screening Platform That Uses Phenotypic Profiling to Discriminate Selective Inhibitors of Receptor Tyrosine Kinases.

    PubMed

    Booij, Tijmen H; Klop, Maarten J D; Yan, Kuan; Szántai-Kis, Csaba; Szokol, Balint; Orfi, Laszlo; van de Water, Bob; Keri, Gyorgy; Price, Leo S

    2016-10-01

    3D tissue cultures provide a more physiologically relevant context for the screening of compounds, compared with 2D cell cultures. Cells cultured in 3D hydrogels also show complex phenotypes, increasing the scope for phenotypic profiling. Here we describe a high-content screening platform that uses invasive human prostate cancer cells cultured in 3D in standard 384-well assay plates to study the activity of potential therapeutic small molecules and antibody biologics. Image analysis tools were developed to process 3D image data to measure over 800 phenotypic parameters. Multiparametric analysis was used to evaluate the effect of compounds on tissue morphology. We applied this screening platform to measure the activity and selectivity of inhibitors of the c-Met and epidermal growth factor (EGF) receptor (EGFR) tyrosine kinases in 3D cultured prostate carcinoma cells. c-Met and EGFR activity was quantified based on the phenotypic profiles induced by their respective ligands, hepatocyte growth factor and EGF. The screening method was applied to a novel collection of 80 putative inhibitors of c-Met and EGFR. Compounds were identified that induced phenotypic profiles indicative of selective inhibition of c-Met, EGFR, or bispecific inhibition of both targets. In conclusion, we describe a fully scalable high-content screening platform that uses phenotypic profiling to discriminate selective and nonselective (off-target) inhibitors in a physiologically relevant 3D cell culture setting.

  7. Prevalent phenotypic and genotypic profile of enterotoxigenic Escherichia coli among Iranian children.

    PubMed

    Nazarian, Shahram; Gargari, Seyed Latif Mousavi; Rasooli, Iraj; Alerasol, Masoome; Bagheri, Samane; Alipoor, Shakiba Darvish

    2014-01-01

    Enterotoxigenic Escherichia coli (ETEC) is the most common cause of diarrhea among children. ETEC strains express colonization factors (CFs), which mediate adherence to the small intestinal epithelium and produce entrotoxins that induce diarrhea. Here, we characterized the phenotypes and genotypes of ETEC strains from 261 diarrheal stool samples from Iranian children. The prevalence of ETEC was 8.04%. Most of the isolates were positive for heat-labile and heat-stable toxins. CFA/I, CS3, CS2, and CS5 were detected from some of the clinical isolates. 33.3% of the isolates did not express CFs. The majority of ETEC isolates were identified as O127 and O128 serotypes, and 57% of the strains were resistant to more than 1 antimicrobial agent. Heat-labile enterotoxin activity was confirmed using the Y1 adrenal cell assay, rabbit ileal loop and adenylate cyclase activation tests. Regional phenotypic and genotypic characterization could help to elucidate the ecology and pathogenicity of ETEC to efficiently reduce the burden of illness brought about by ETEC. This study may lead to development of effective prophylactic measures. PMID:24647248

  8. Comparative gene expression profiles for highly similar aggressive phenotypes in male and female cichlid fishes (Julidochromis)

    PubMed Central

    Schumer, Molly; Krishnakant, Kavita; Renn, Suzy C. P.

    2011-01-01

    SUMMARY Julidochromis marlieri and Julidochromis transcriptus are two closely related Tanganyikan cichlids that have evolved different behavior and mating strategies since they diverged from their common ancestor. While J. transcriptus follows the ancestral pattern of male dominance, male-biased sexual size dimorphism and territoriality, the pattern is reversed in J. marlieri. In J. marlieri, females show all of these behavioral and morphological characteristics. This raises the question of whether female J. marlieri achieve the dominant phenotype by expressing the same genes as J. transcriptus males or whether novel brain gene expression patterns have evolved to produce a similar behavioral phenotype in the females of J. marlieri. This study used cDNA microarrays to investigate whether female J. marlieri and male J. transcriptus show conserved or divergent patterns of brain gene expression. Analysis of microarray data in both species showed certain gene expression patterns associated with sex role independent of gonadal sex and, to a lesser extent, gene expression patterns associated with sex independent of sex role. In general, these data suggest that while there has been substantial divergence in gene expression patterns between J. transcriptus and J. marlieri, we can detect a highly significant overlap for a core set of genes related to aggression in both species. These results suggest that the proximate mechanisms regulating aggressive behavior in J. transcriptus and J. marlieri may be shared. PMID:21900474

  9. Phenotypic Profiling of Scedosporium aurantiacum, an Opportunistic Pathogen Colonizing Human Lungs

    PubMed Central

    Kaur, Jashanpreet; Duan, Shu Yao; Vaas, Lea A. I.; Penesyan, Anahit; Meyer, Wieland; Paulsen, Ian T.; Nevalainen, Helena

    2015-01-01

    Genotyping studies of Australian Scedosporium isolates have revealed the strong prevalence of a recently described species: Scedosporium aurantiacum. In addition to occurring in the environment, this fungus is also known to colonise the respiratory tracts of cystic fibrosis (CF) patients. A high throughput Phenotype Microarray (PM) analysis using 94 assorted substrates (sugars, amino acids, hexose-acids and carboxylic acids) was carried out for four isolates exhibiting different levels of virulence, determined using a Galleria mellonella infection model. A significant difference was observed in the substrate utilisation patterns of strains displaying differential virulence. For example, certain sugars such as sucrose (saccharose) were utilised only by low virulence strains whereas some sugar derivatives such as D-turanose promoted respiration only in the more virulent strains. Strains with a higher level of virulence also displayed flexibility and metabolic adaptability at two different temperature conditions tested (28 and 37°C). Phenotype microarray data were integrated with the whole-genome sequence data of S. aurantiacum to reconstruct a pathway map for the metabolism of selected substrates to further elucidate differences between the strains. PMID:25811884

  10. Short communication: Cytokine profiles from blood mononuclear cells of dairy cows classified with divergent immune response phenotypes.

    PubMed

    Martin, C E; Paibomesai, M A; Emam, S M; Gallienne, J; Hine, B C; Thompson-Crispi, K A; Mallard, B A

    2016-03-01

    Genetic selection for enhanced immune response has been shown to decrease disease occurrence in dairy cattle. Cows can be classified as high (H), average, or low responders based on antibody-mediated immune response (AMIR), predominated by type-2 cytokine production, and cell-mediated immune response (CMIR) through estimated breeding values for these traits. The purpose of this study was to identify in vitro tests that correlate with in vivo immune response phenotyping in dairy cattle. Blood mononuclear cells (BMC) isolated from cows classified as H-AMIR and H-CMIR through estimated breeding values for immune response traits were stimulated with concanavalin A (ConA; Sigma Aldrich, St. Louis, MO) and gene expression, cytokine production, and cell proliferation was determined at multiple time points. A repeated measures model, which included the effects of immune response group, parity, and stage of lactation, was used to compare differences between immune response phenotype groups. The H-AMIR cows produced more IL-4 protein than H-CMIR cows at 48 h; however, no difference in gene expression of type-2 transcription factor GATA3 or IL4 was noted. The BMC from H-CMIR cows had increased production of IFN-γ protein at 48, 72, and 96 h compared with H-AMIR animals. Further, H-CMIR cows had increased expression of the IFNG gene at 16, 24, and 48 h post-treatment with ConA, although expression of the type-1 transcription factor gene TBX21 did not differ between immune response groups. Although proliferation of BMC increased from 24 to 72 h after ConA stimulation, no differences were found between the immune response groups. Overall, stimulation of H-AMIR and H-CMIR bovine BMC with ConA resulted in distinct cytokine production profiles according to genetically defined groups. These distinct cytokine profiles could be used to define disease resistance phenotypes in dairy cows according to stimulation in vitro; however, other immune response phenotypes should be assessed.

  11. Microbial Forensics: Predicting Phenotypic Characteristics and Environmental Conditions from Large-Scale Gene Expression Profiles

    PubMed Central

    Kim, Minseung; Zorraquino, Violeta; Tagkopoulos, Ilias

    2015-01-01

    A tantalizing question in cellular physiology is whether the cellular state and environmental conditions can be inferred by the expression signature of an organism. To investigate this relationship, we created an extensive normalized gene expression compendium for the bacterium Escherichia coli that was further enriched with meta-information through an iterative learning procedure. We then constructed an ensemble method to predict environmental and cellular state, including strain, growth phase, medium, oxygen level, antibiotic and carbon source presence. Results show that gene expression is an excellent predictor of environmental structure, with multi-class ensemble models achieving balanced accuracy between 70.0% (±3.5%) to 98.3% (±2.3%) for the various characteristics. Interestingly, this performance can be significantly boosted when environmental and strain characteristics are simultaneously considered, as a composite classifier that captures the inter-dependencies of three characteristics (medium, phase and strain) achieved 10.6% (±1.0%) higher performance than any individual models. Contrary to expectations, only 59% of the top informative genes were also identified as differentially expressed under the respective conditions. Functional analysis of the respective genetic signatures implicates a wide spectrum of Gene Ontology terms and KEGG pathways with condition-specific information content, including iron transport, transferases, and enterobactin synthesis. Further experimental phenotypic-to-genotypic mapping that we conducted for knock-out mutants argues for the information content of top-ranked genes. This work demonstrates the degree at which genome-scale transcriptional information can be predictive of latent, heterogeneous and seemingly disparate phenotypic and environmental characteristics, with far-reaching applications. PMID:25774498

  12. Microbial forensics: predicting phenotypic characteristics and environmental conditions from large-scale gene expression profiles.

    PubMed

    Kim, Minseung; Zorraquino, Violeta; Tagkopoulos, Ilias

    2015-03-01

    A tantalizing question in cellular physiology is whether the cellular state and environmental conditions can be inferred by the expression signature of an organism. To investigate this relationship, we created an extensive normalized gene expression compendium for the bacterium Escherichia coli that was further enriched with meta-information through an iterative learning procedure. We then constructed an ensemble method to predict environmental and cellular state, including strain, growth phase, medium, oxygen level, antibiotic and carbon source presence. Results show that gene expression is an excellent predictor of environmental structure, with multi-class ensemble models achieving balanced accuracy between 70.0% (±3.5%) to 98.3% (±2.3%) for the various characteristics. Interestingly, this performance can be significantly boosted when environmental and strain characteristics are simultaneously considered, as a composite classifier that captures the inter-dependencies of three characteristics (medium, phase and strain) achieved 10.6% (±1.0%) higher performance than any individual models. Contrary to expectations, only 59% of the top informative genes were also identified as differentially expressed under the respective conditions. Functional analysis of the respective genetic signatures implicates a wide spectrum of Gene Ontology terms and KEGG pathways with condition-specific information content, including iron transport, transferases, and enterobactin synthesis. Further experimental phenotypic-to-genotypic mapping that we conducted for knock-out mutants argues for the information content of top-ranked genes. This work demonstrates the degree at which genome-scale transcriptional information can be predictive of latent, heterogeneous and seemingly disparate phenotypic and environmental characteristics, with far-reaching applications.

  13. Gene Expression Profiling of H9c2 Myoblast Differentiation towards a Cardiac-Like Phenotype.

    PubMed

    Branco, Ana F; Pereira, Susana P; Gonzalez, Susana; Gusev, Oleg; Rizvanov, Albert A; Oliveira, Paulo J

    2015-01-01

    H9c2 myoblasts are a cell model used as an alternative for cardiomyocytes. H9c2 cells have the ability to differentiate towards a cardiac phenotype when the media serum is reduced in the presence of all-trans-retinoic acid (RA), creating multinucleated cells with low proliferative capacity. In the present study, we performed for the first time a transcriptional analysis of the H9c2 cell line in two differentiation states, i.e. embryonic cells and differentiated cardiac-like cells. The results show that RA-induced H9c2 differentiation increased the expression of genes encoding for cardiac sarcomeric proteins such as troponin T, or calcium transporters and associated machinery, including SERCA2, ryanodine receptor and phospholamban as well as genes associated with mitochondrial energy production including respiratory chain complexes subunits, mitochondrial creatine kinase, carnitine palmitoyltransferase I and uncoupling proteins. Undifferentiated myoblasts showed increased gene expression of pro-survival proteins such as Bcl-2 as well as cell cycle-regulating proteins. The results indicate that the differentiation of H9c2 cells lead to an increase of transcripts and protein levels involved in calcium handling, glycolytic and mitochondrial metabolism, confirming that H9c2 cell differentiation induced by RA towards a more cardiac-like phenotype involves remodeled mitochondrial function. PI3K, PDK1 and p-CREB also appear to be involved on H9c2 differentiation. Furthermore, complex analysis of differently expressed transcripts revealed significant up-regulation of gene expression related to cardiac muscle contraction, dilated cardiomyopathy and other pathways specific for the cardiac tissue. Metabolic and gene expression remodeling impacts cell responses to different stimuli and determine how these cells are used for biochemical assays. PMID:26121149

  14. Stereomicroscopic 3D-pattern profiling of murine and human intestinal inflammation reveals unique structural phenotypes

    PubMed Central

    Rodriguez-Palacios, Alex; Kodani, Tomohiro; Kaydo, Lindsey; Pietropaoli, Davide; Corridoni, Daniele; Howell, Scott; Katz, Jeffry; Xin, Wei; Pizarro, Theresa T.; Cominelli, Fabio

    2015-01-01

    Histology is fundamental to assess two-dimensional intestinal inflammation; however, inflammatory bowel diseases (IBDs) are often indistinguishable microscopically on the basis of mucosal biopsies. Here, we use stereomicroscopy (SM) to rapidly profile the entire intestinal topography and assess inflammation. We examine the mucosal surface of >700 mice (encompassing >16 strains and various IBD-models), create a profiling catalogue of 3D-stereomicroscopic abnormalities and demonstrate that mice with comparable histological scores display unique sub-clusters of 3D-structure-patterns of IBD pathology, which we call 3D-stereoenterotypes, and which are otherwise indiscernible histologically. We show that two ileal IBD-stereoenterotypes (‘cobblestones' versus ‘villous mini-aggregation') cluster separately within two distinct mouse lines of spontaneous ileitis, suggesting that host genetics drive unique and divergent inflammatory 3D-structural patterns in the gut. In humans, stereomicroscopy reveals ‘liquefaction' lesions and hierarchical fistulous complexes, enriched with clostridia/segmented filamentous bacteria, running under healthy mucosa in Crohn's disease. We suggest that stereomicroscopic (3D-SMAPgut) profiling can be easily implemented and enable the comprehensive study of inflammatory 3D structures, genetics and flora in IBD. PMID:26154811

  15. Developing a Predictive Gene Classifier for Autism Spectrum Disorders Based upon Differential Gene Expression Profiles of Phenotypic Subgroups

    PubMed Central

    Hu, Valerie W.; Lai, Yinglei

    2013-01-01

    Autism spectrum disorders (ASD) are neurodevelopmental disorders which are currently diagnosed solely on the basis of abnormal stereotyped behavior as well as observable deficits in communication and social functioning. Although a variety of candidate genes have been identified on the basis of genetic analyses and up to 20% of ASD cases can be collectively associated with a genetic abnormality, no single gene or genetic variant is applicable to more than 1–2 percent of the general ASD population. In this report, we apply class prediction algorithms to gene expression profiles of lymphoblastoid cell lines (LCL) from several phenotypic subgroups of idiopathic autism defined by cluster analyses of behavioral severity scores on the Autism Diagnostic Interview-Revised diagnostic instrument for ASD. We further demonstrate that individuals from these ASD subgroups can be distinguished from nonautistic controls on the basis of limited sets of differentially expressed genes with a predicted classification accuracy of up to 94% and sensitivities and specificities of ~90% or better, based on support vector machine analyses with leave-one-out validation. Validation of a subset of the “classifier” genes by high-throughput quantitative nuclease protection assays with a new set of LCL samples derived from individuals in one of the phenotypic subgroups and from a new set of controls resulted in an overall class prediction accuracy of ~82%, with ~90% sensitivity and 75% specificity. Although additional validation with a larger cohort is needed, and effective clinical translation must include confirmation of the differentially expressed genes in primary cells from cases earlier in development, we suggest that such panels of genes, based on expression analyses of phenotypically more homogeneous subgroups of individuals with ASD, may be useful biomarkers for diagnosis of subtypes of idiopathic autism. PMID:24363828

  16. Selective IgM deficiency in adults: phenotypically and functionally altered profiles of peripheral blood lymphocytes.

    PubMed Central

    Ohno, T; Inaba, M; Kuribayashi, K; Masuda, T; Kanoh, T; Uchino, H

    1987-01-01

    Peripheral blood lymphocytes from four patients with selective IgM deficiency were examined phenotypically and functionally. Although B cell subpopulations determined by surface immunoglobulins were within normal or nearly normal range, T8+ cells were significantly increased and T4/T8 ratios were inverted in three patients. IgM specific hyporesponsiveness in the PWM-driven immunoglobulin production system was observed in all four patients. Ia-like antigen positive T cells were increased in two patients; both had increased Leu2a+ Leu15+ suppressor-effector cells. In addition, Leu3a+ Leu8+ suppressor-inducer cells were increased in one of these two patients. Excessive (either IgM-specific or isotype non-specific) suppressor activity of T cells and IgM specific hyporesponsiveness of non-T cells were observed in these two patients in the recombination plaque assay. Although these results showed the complexity of the pathogenesis of this syndrome, they suggested that suppressor-associated T cells may play a role in some patients with selective IgM deficiency. PMID:2958191

  17. Phenotypic side effects prediction by optimizing correlation with chemical and target profiles of drugs.

    PubMed

    Kanji, Rakesh; Sharma, Abhinav; Bagler, Ganesh

    2015-11-01

    Despite technological progresses and improved understanding of biological systems, discovery of novel drugs is an inefficient, arduous and expensive process. Research and development cost of drugs is unreasonably high, largely attributed to the high attrition rate of candidate drugs due to adverse drug reactions. Computational methods for accurate prediction of drug side effects, rooted in empirical data of drugs, have the potential to enhance the efficacy of the drug discovery process. Identification of features critical for specifying side effects would facilitate efficient computational procedures for their prediction. We devised a generalized ordinary canonical correlation model for prediction of drug side effects based on their chemical properties as well as their target profiles. While the former is based on 2D and 3D chemical features, the latter enumerates a systems-level property of drugs. We find that the model incorporating chemical features outperforms that incorporating target profiles. Furthermore we identified the 2D and 3D chemical properties that yield best results, thereby implying their relevance in specifying adverse drug reactions. PMID:26252576

  18. In Situ Characterizing Membrane Lipid Phenotype of Human Lung Cancer Cell Lines Using Mass Spectrometry Profiling

    PubMed Central

    He, Manwen; Guo, Shuai; Ren, Junling; Li, Zhili

    2016-01-01

    Abnormal lipid metabolisms are closely associated with cancers. In this study, mass spectrometry was employed to in situ investigate the associations of membrane lipid phenotypes of six human lung cancer cell lines (i.e., A549, H1650, H1975 from adenocarcinoma, H157 and H1703 from squamous cell carcinomas, and H460 from a large cell carcinoma) with cancer cell types and finally total 230 lipids were detected. Based these 230 lipids, partial least-square discriminant analysis indicated that fifteen lipids (i.e., PE 18:0_18:1, PI 18:0_20:4, SM 42:2, PE 16:0_20:4, PE 36:2, PC 36:2, SM 34:1, PA 38:3,C18:0, C22:4, PA 34:2, C20:5, C20:2, C18:2, and CerP 36:2) with variable importance in the projection (VIP) value of > 1.0 could be used to differentiate six cancer cell lines with the Predicted Residual Sum of Square (PRESS) score of 0.1974. Positive correlation between polyunsaturated fatty acids (i.e., C20:4, C22:4, C22:5, and C22:6) and polyunsaturated phospholipids (PE 16:0_20:4, PE 38:4, and PI 18:0_20:4) was observed in lung adenocarcinoma cells, especially for H1975 cells. Three adenocarcinoma cell lines (i.e., A549, H1650, and H1975) could be differentiated from other lung cancer cell lines based on the expression of C18:1, C20:1, C20:2, C20:5, and C22:6. PMID:27162539

  19. Gene expression profiles underlying alternative caste phenotypes in a highly eusocial bee, Melipona quadrifasciata.

    PubMed

    Judice, C C; Carazzole, M F; Festa, F; Sogayar, M C; Hartfelder, K; Pereira, G A G

    2006-02-01

    To evaluate caste-biased gene expression in Melipona quadrifasciata, a stingless bee, we generated 1278 ESTs using Representational Difference Analysis. Most annotated sequences were similar to honey bee genes of unknown function. Only few queen-biased sequences had their putative function assigned by sequence comparison, contrasting with the worker-biased ESTs. The expression of six annotated genes connected to caste specificity was validated by real time PCR. Interestingly, queens that were developmentally induced by treatment with a juvenile hormone analogue displayed an expression profile clearly different from natural queens for this set of genes. In summary, this study represents an important first step in applying a comparative genomic approach to queen/worker polyphenism in the bee.

  20. Evaluation of a 7-Gene Genetic Profile for Athletic Endurance Phenotype in Ironman Championship Triathletes

    PubMed Central

    Grealy, Rebecca; Herruer, Jasper; Smith, Carl L. E.; Hiller, Doug; Haseler, Luke J.; Griffiths, Lyn R.

    2015-01-01

    Polygenic profiling has been proposed for elite endurance performance, using an additive model determining the proportion of optimal alleles in endurance athletes. To investigate this model’s utility for elite triathletes, we genotyped seven polymorphisms previously associated with an endurance polygenic profile (ACE Ins/Del, ACTN3 Arg577Ter, AMPD1 Gln12Ter, CKMM 1170bp/985+185bp, HFE His63Asp, GDF8 Lys153Arg and PPARGC1A Gly482Ser) in a cohort of 196 elite athletes who participated in the 2008 Kona Ironman championship triathlon. Mean performance time (PT) was not significantly different in individual marker analysis. Age, sex, and continent of origin had a significant influence on PT and were adjusted for. Only the AMPD1 endurance-optimal Gln allele was found to be significantly associated with an improvement in PT (model p = 5.79 x 10−17, AMPD1 genotype p = 0.01). Individual genotypes were combined into a total genotype score (TGS); TGS distribution ranged from 28.6 to 92.9, concordant with prior studies in endurance athletes (mean±SD: 60.75±12.95). TGS distribution was shifted toward higher TGS in the top 10% of athletes, though the mean TGS was not significantly different (p = 0.164) and not significantly associated with PT even when adjusted for age, sex, and origin. Receiver operating characteristic curve analysis determined that TGS alone could not significantly predict athlete finishing time with discriminating sensitivity and specificity for three outcomes (less than median PT, less than mean PT, or in the top 10%), though models with the age, sex, continent of origin, and either TGS or AMPD1 genotype could. These results suggest three things: that more sophisticated genetic models may be necessary to accurately predict athlete finishing time in endurance events; that non-genetic factors such as training are hugely influential and should be included in genetic analyses to prevent confounding; and that large collaborations may be necessary to obtain

  1. Predictive model for toluene degradation and microbial phenotypic profiles in flat plate vapor phase bioreactor

    SciTech Connect

    Mirpuri, R.; Sharp, W.; Villaverde, S.; Jones, W.; Lewandowski, Z.; Cunningham, A.

    1997-06-01

    A predictive model has been developed to describe degradation of toluene in a flat-plate vapor phase bioreactor (VPBR). The VPBR model incorporates kinetic, stoichiometric, injury, and irreversible loss coefficients from suspended culture studies for toluene degradation by P. putida 54G and measured values of Henry`s law constant and boundary layer thickness at the gas-liquid and liquid-biofilm interface. The model is used to estimate the performance of the reactor with respect to toluene degradation and to predict profiles of toluene concentration and bacterial physiological state within the biofilm. These results have been compared with experimentally determined values from a flat plate VPBR under electron acceptor and electron donor limiting conditions. The model accurately predicts toluene concentrations in the vapor phase and toluene degradation rate by adjusting only three parameters: biomass density and rates of death and endogenous decay. Qualitatively, the model also predicts gradients in the physiological state cells in the biofilm. This model provides a rational design for predicting an upper limit of toluene degradation capability in a VPBR and is currently being tested to assess applications for predicting performance of bench and pilot-scale column reactors.

  2. Characterisation of Phenotypic and Genotypic Antibiotic Resistance Profile of Enterococci from Cheeses in Turkey.

    PubMed

    Kürekci, Cemil; Önen, Sevda Pehlivanlar; Yipel, Mustafa; Aslantaş, Özkan; Gündoğdu, Aycan

    2016-01-01

    The aim of this study was to determine the prevalence of enterococci in cheese samples and to characterize their antimicrobial resistance profiles as well as the associated resistance genes. A total of 139 enterococci were isolated from 99 cheese samples, the isolates were identified as E. faecalis (61.2%), E. faecium (15.1%), E. gallinarum (12.9%), E. durans (5.0%), E. casseliflavis (2.9%) and E. avium (2.9%). The most frequent antimicrobial resistance observed in enterococci isolates was to lincomycin (88.5%), followed by kanamycin (84.2%), gentamycin (low level, 51.1%), rifampin (46.8%) and tetracycline (33.8%). Among the isolates, the frequencies of high level gentamycin and streptomycin resistant enterococci strains were 2.2% and 5.8%, respectively. Apart from the mentioned antibiotics, low levels of resistance to ciprofloxacin, erythromycin and chloramphenicol were found. Moreover no resistance was observed against penicillin and ampicillin. The antimicrobial resistance genes including tetM, tetL, ermB, cat, aph(3')-IIIa, ant(6)-Ia and aac(6')-Ieaph(2")-Ia were found in enterococci from Turkish cheese samples. In the current study, we provided data for antibiotic resistance and the occurrence of resistance genes among enterococci. Regulatory and quality control programs for milk and other dairy products from farms to retail outlets has to be established and strengthened to monitor trends in antimicrobial resistance among emerging food borne pathogens in Turkey. PMID:27433106

  3. Characterisation of Phenotypic and Genotypic Antibiotic Resistance Profile of Enterococci from Cheeses in Turkey

    PubMed Central

    Yipel, Mustafa; Aslantaş, Özkan; Gündoğdu, Aycan

    2016-01-01

    The aim of this study was to determine the prevalence of enterococci in cheese samples and to characterize their antimicrobial resistance profiles as well as the associated resistance genes. A total of 139 enterococci were isolated from 99 cheese samples, the isolates were identified as E. faecalis (61.2%), E. faecium (15.1%), E. gallinarum (12.9%), E. durans (5.0%), E. casseliflavis (2.9%) and E. avium (2.9%). The most frequent antimicrobial resistance observed in enterococci isolates was to lincomycin (88.5%), followed by kanamycin (84.2%), gentamycin (low level, 51.1%), rifampin (46.8%) and tetracycline (33.8%). Among the isolates, the frequencies of high level gentamycin and streptomycin resistant enterococci strains were 2.2% and 5.8%, respectively. Apart from the mentioned antibiotics, low levels of resistance to ciprofloxacin, erythromycin and chloramphenicol were found. Moreover no resistance was observed against penicillin and ampicillin. The antimicrobial resistance genes including tetM, tetL, ermB, cat, aph(3’)-IIIa, ant(6)-Ia and aac(6’)-Ieaph(2”)-Ia were found in enterococci from Turkish cheese samples. In the current study, we provided data for antibiotic resistance and the occurrence of resistance genes among enterococci. Regulatory and quality control programs for milk and other dairy products from farms to retail outlets has to be established and strengthened to monitor trends in antimicrobial resistance among emerging food borne pathogens in Turkey. PMID:27433106

  4. Childhood-onset systemic lupus erythematosus in Singapore: clinical phenotypes, disease activity, damage, and autoantibody profiles.

    PubMed

    Tan, J H T; Hoh, S F; Win, M T M; Chan, Y H; Das, L; Arkachaisri, T

    2015-08-01

    Childhood-onset systemic lupus erythematosus (cSLE) is a multisystem autoimmune disease characterized by immune dysregulation affecting patients less than 18 years old. One-fifth of SLE cases are diagnosed during childhood. cSLE presents differently from adults and has a more severe and aggressive course. We describe the clinical and antibody profiles in our cSLE Singapore cohort. All cSLE patients who satisfied the 1997 American College of Rheumatology diagnostic criteria were captured in our lupus registry from January 2009 to January 2014. Data including demographic, cumulative clinical, serologic data, and damage indices were collected. Adjusted mean SLEDAI-2K (AMS) was used to summarize disease activity over multiple visits. Cluster analysis using non-hierarchical K-means procedure was performed on eight selected antibodies. The 64 patients (female:male ratio 5:1; Chinese 45.3%, Malay 28.1%, Indian 9.4%, and other races 17.2%) had a mean onset age of 11.5 years (range 2.1-16.7) and mean age at diagnosis was 11.9 years (range 2.6-18.0). Our study demonstrated differences in clinical manifestations for which hematologic involvement was the most common manifestation with less renal disease and uncommon neurologic manifestation as compared to other cSLE cohorts reported in our region. Antibody clusters were identified in our cohort but their clinical association/discrimination and outcome prediction required further validation study. Outcomes of our cohort in regard to disease activity after therapy and organ damages were comparable if not better to other cSLE cohorts elsewhere. Steroid-related damage, including symptomatic multifocal avascular necrosis and cataract, were not uncommon locally. Infection remains the major cause of death for the continent. Nevertheless, the five year survival rate of our cohort (98.4%) was high.

  5. Development of a Rapid Microbore Metabolic Profiling Ultraperformance Liquid Chromatography-Mass Spectrometry Approach for High-Throughput Phenotyping Studies.

    PubMed

    Gray, Nicola; Adesina-Georgiadis, Kyrillos; Chekmeneva, Elena; Plumb, Robert S; Wilson, Ian D; Nicholson, Jeremy K

    2016-06-01

    A rapid gradient microbore ultraperformance liquid chromatography-mass spectrometry (UPLC-MS) method has been developed to provide a high-throughput analytical platform for the metabolic phenotyping of urine from large sample cohorts. The rapid microbore metabolic profiling (RAMMP) approach was based on scaling a conventional reversed-phase UPLC-MS method for urinary profiling from 2.1 mm × 100 mm columns to 1 mm × 50 mm columns, increasing the linear velocity of the solvent, and decreasing the gradient time to provide an analysis time of 2.5 min/sample. Comparison showed that conventional UPLC-MS and rapid gradient approaches provided peak capacities of 150 and 50, respectively, with the conventional method detecting approximately 19 000 features compared to the ∼6 000 found using the rapid gradient method. Similar levels of repeatability were seen for both methods. Despite the reduced peak capacity and the reduction in ions detected, the RAMMP method was able to achieve similar levels of group discrimination as conventional UPLC-MS when applied to rat urine samples obtained from investigative studies on the effects of acute 2-bromophenol and chronic acetaminophen administration. When compared to a direct infusion MS method of similar analysis time the RAMMP method provided superior selectivity. The RAMMP approach provides a robust and sensitive method that is well suited to high-throughput metabonomic analysis of complex mixtures such as urine combined with a 5-fold reduction in analysis time compared with the conventional UPLC-MS method. PMID:27116471

  6. Phenotypic and transcriptional profiling in Entamoeba histolytica reveal costs to fitness and adaptive responses associated with metronidazole resistance

    PubMed Central

    Penuliar, Gil M.; Nakada-Tsukui, Kumiko; Nozaki, Tomoyoshi

    2015-01-01

    Antimicrobial chemotherapy is critical in the fight against infectious diseases caused by Entamoeba histolytica. Among the drugs available for the treatment of amebiasis, metronidazole (MTZ) is considered the drug of choice. Recently, in vitro studies have described MTZ resistance and the potential mechanisms involved. Costs to fitness and adaptive responses associated with resistance, however, have not been investigated. In this study we generated an HM-1 derived strain resistant to 12 μM MTZ (MTZR). We examined its phenotypic and transcriptional profile to determine the consequences and mRNA level changes associated with MTZ resistance. Our results indicated increased cell size and granularity, and decreased rates in cell division, adhesion, phagocytosis, cytopathogenicity, and glucose consumption. Transcriptome analysis revealed 142 differentially expressed genes in MTZR. In contrast to other MTZ resistant parasites, MTZR did not down-regulate pyruvate:ferredoxin oxidoreductase, but showed increased expression of genes for a hypothetical protein (HP1) and several iron-sulfur flavoproteins, and downregulation of genes for leucine-rich proteins. Fisher's exact test showed 24 significantly enriched GO terms in MTZR, and a 3-way comparison of modulated genes in MTZR against those of MTZR cultured without MTZ and HM-1 cultured with MTZ, showed that 88 genes were specific to MTZR. Overall, our findings suggested that MTZ resistance is associated with specific transcriptional changes and decreased parasite virulence. PMID:25999919

  7. Isolation and Molecular Profiling of Primary Mouse Retinal Ganglion Cells: Comparison of Phenotypes from Healthy and Glaucomatous Retinas

    PubMed Central

    Chintalapudi, Sumana R.; Djenderedjian, Levon; Stiemke, Andrew B.; Steinle, Jena J.; Jablonski, Monica M.; Morales-Tirado, Vanessa M.

    2016-01-01

    Loss of functional retinal ganglion cells (RGC) is an element of retinal degeneration that is poorly understood. This is in part due to the lack of a reliable and validated protocol for the isolation of primary RGCs. Here we optimize a feasible, reproducible, standardized flow cytometry-based protocol for the isolation and enrichment of homogeneous RGC with the Thy1.2hiCD48negCD15negCD57neg surface phenotype. A three-step validation process was performed by: (1) genomic profiling of 25-genes associated with retinal cells; (2) intracellular labeling of homogeneous sorted cells for the intracellular RGC-markers SNCG, brain-specific homeobox/POU domain protein 3A (BRN3A), TUJ1, and RNA-binding protein with multiple splicing (RBPMS); and (3) by applying the methodology on RGC from a mouse model with elevated intraocular pressure (IOP) and optic nerve damage. Use of primary RGC cultures will allow for future careful assessment of important cell specific pathways in RGC to provide mechanistic insights into the declining of visual acuity in aged populations and those suffering from retinal neurodegenerative diseases. PMID:27242509

  8. Quantification of oxidative stress phenotypes based on high-throughput growth profiling of protein kinase and phosphatase knockouts.

    PubMed

    Altıntaş, Ali; Martini, Jacopo; Mortensen, Uffe H; Workman, Christopher T

    2016-02-01

    Cellular responses to oxidative stress are important for restoring redox balance and ensuring cell survival. Genetic defects in response factors can lead to impaired response to oxidative damage and contribute to disease and aging. In single cell organisms, such as yeasts, the integrity of the oxidative stress response can be observed through its influences on growth characteristics. In this study, we investigated the time-dependent batch growth effects as a function of oxidative stress levels in protein kinase and phosphatase deletion backgrounds of Saccharomyces cerevisiae. In total, 41 different protein kinases and phosphatase mutants were selected for their known activities in oxidative stress or other stress response pathways and were investigated for their dosage-dependent response to hydrogen peroxide. Detailed growth profiles were analyzed after the induction of stress for growth rate, lag time duration and growth efficiency, and by a novel method to identify stress-induced diauxic shift delay. This approach extracts more phenotypic information than traditional plate-based methods due to the assessment of time dynamics in the time scale of minutes. With this approach, we were able to identify surprisingly diverse sensitivity and resistance patterns as a function of gene knockout.

  9. A Molecular Profile of Cocaine Abuse Includes the Differential Expression of Genes that Regulate Transcription, Chromatin, and Dopamine Cell Phenotype

    PubMed Central

    Bannon, Michael J; Johnson, Magen M; Michelhaugh, Sharon K; Hartley, Zachary J; Halter, Steven D; David, James A; Kapatos, Gregory; Schmidt, Carl J

    2014-01-01

    Chronic drug abuse, craving, and relapse are thought to be linked to long-lasting changes in neural gene expression arising through transcriptional and chromatin-related mechanisms. The key contributions of midbrain dopamine (DA)-synthesizing neurons throughout the addiction process provide a compelling rationale for determining the drug-induced molecular changes that occur in these cells. Yet our understanding of these processes remains rudimentary. The postmortem human brain constitutes a unique resource that can be exploited to gain insights into the pathophysiology of complex disorders such as drug addiction. In this study, we analyzed the profiles of midbrain gene expression in chronic cocaine abusers and well-matched drug-free control subjects using microarray and quantitative PCR. A small number of genes exhibited robust differential expression; many of these are involved in the regulation of transcription, chromatin, or DA cell phenotype. Transcript abundances for approximately half of these differentially expressed genes were diagnostic for assigning subjects to the cocaine-abusing vs control cohort. Identification of a molecular signature associated with pathophysiological changes occurring in cocaine abusers' midbrains should contribute to the development of biomarkers and novel therapeutic targets for drug addiction. PMID:24642598

  10. Proteomic and transcriptomic profiling of Staphylococcus aureus surface LPXTG-proteins: correlation with agr genotypes and adherence phenotypes.

    PubMed

    Ythier, Mathilde; Resch, Grégory; Waridel, Patrice; Panchaud, Alexandre; Gfeller, Aurélie; Majcherczyk, Paul; Quadroni, Manfredo; Moreillon, Philippe

    2012-11-01

    Staphylococcus aureus infections involve numerous adhesins and toxins, which expression depends on complex regulatory networks. Adhesins include a family of surface proteins covalently attached to the peptidoglycan via a conserved LPXTG motif. Here we determined the protein and mRNA expression of LPXTG-proteins of S. aureus Newman in time-course experiments, and their relation to fibrinogen adherence in vitro. Experiments were performed with mutants in the global accessory-gene regulator (agr), surface protein A (Spa), and fibrinogen-binding protein A (ClfA), as well as during growth in iron-rich or iron-poor media. Surface proteins were recovered by trypsin-shaving of live bacteria. Released peptides were analyzed by liquid chromatography coupled to tandem mass-spectrometry. To unambiguously identify peptides unique to LPXTG-proteins, the analytical conditions were refined using a reference library of S. aureus LPXTG-proteins heterogeneously expressed in surrogate Lactococcus lactis. Transcriptomes were determined by microarrays. Sixteen of the 18 LPXTG-proteins present in S. aureus Newman were detected by proteomics. Nine LPXTG-proteins showed a bell-shape agr-like expression that was abrogated in agr-negative mutants including Spa, fibronectin-binding protein A (FnBPA), ClfA, iron-binding IsdA, and IsdB, immunomodulator SasH, functionally uncharacterized SasD, biofilm-related SasG and methicillin resistance-related FmtB. However, only Spa and SasH modified their proteomic and mRNA profiles in parallel in the parent and its agr- mutant, whereas all other LPXTG-proteins modified their proteomic profiles independently of their mRNA. Moreover, ClfA became highly transcribed and active in fibrinogen-adherence tests during late growth (24 h), whereas it remained poorly detected by proteomics. On the other hand, iron-regulated IsdA-B-C increased their protein expression by >10-times in iron-poor conditions. Thus, proteomic, transcriptomic, and adherence-phenotype

  11. Proteomic and Transcriptomic Profiling of Staphylococcus aureus Surface LPXTG-proteins: Correlation with agr Genotypes and Adherence Phenotypes*

    PubMed Central

    Ythier, Mathilde; Resch, Grégory; Waridel, Patrice; Panchaud, Alexandre; Gfeller, Aurélie; Majcherczyk, Paul; Quadroni, Manfredo; Moreillon, Philippe

    2012-01-01

    Staphylococcus aureus infections involve numerous adhesins and toxins, which expression depends on complex regulatory networks. Adhesins include a family of surface proteins covalently attached to the peptidoglycan via a conserved LPXTG motif. Here we determined the protein and mRNA expression of LPXTG-proteins of S. aureus Newman in time-course experiments, and their relation to fibrinogen adherence in vitro. Experiments were performed with mutants in the global accessory-gene regulator (agr), surface protein A (Spa), and fibrinogen-binding protein A (ClfA), as well as during growth in iron-rich or iron-poor media. Surface proteins were recovered by trypsin-shaving of live bacteria. Released peptides were analyzed by liquid chromatography coupled to tandem mass-spectrometry. To unambiguously identify peptides unique to LPXTG-proteins, the analytical conditions were refined using a reference library of S. aureus LPXTG-proteins heterogeneously expressed in surrogate Lactococcus lactis. Transcriptomes were determined by microarrays. Sixteen of the 18 LPXTG-proteins present in S. aureus Newman were detected by proteomics. Nine LPXTG-proteins showed a bell-shape agr-like expression that was abrogated in agr-negative mutants including Spa, fibronectin-binding protein A (FnBPA), ClfA, iron-binding IsdA, and IsdB, immunomodulator SasH, functionally uncharacterized SasD, biofilm-related SasG and methicillin resistance-related FmtB. However, only Spa and SasH modified their proteomic and mRNA profiles in parallel in the parent and its agr- mutant, whereas all other LPXTG-proteins modified their proteomic profiles independently of their mRNA. Moreover, ClfA became highly transcribed and active in fibrinogen-adherence tests during late growth (24 h), whereas it remained poorly detected by proteomics. On the other hand, iron-regulated IsdA-B-C increased their protein expression by >10-times in iron-poor conditions. Thus, proteomic, transcriptomic, and adherence-phenotype

  12. Comparative Proteomic Profiling of Divergent Phenotypes for Water Holding Capacity across the Post Mortem Ageing Period in Porcine Muscle Exudate.

    PubMed

    Di Luca, Alessio; Hamill, Ruth M; Mullen, Anne Maria; Slavov, Nikolai; Elia, Giuliano

    2016-01-01

    Two dimensional Difference Gel Electrophoresis (2-D DIGE) and mass spectrometry were applied to investigate the changes in metabolic proteins that occur over a seven day (day 1, 3 and 7) post mortem ageing period in porcine centrifugal exudate from divergent meat quality phenotypes. The objectives of the research were to enhance our understanding of the phenotype (water holding capacity) and search for biomarkers of this economically significant pork quality attribute. Major changes in protein abundance across nine phenotype-by-time conditions were observed. Proteomic patterns were dominated by post mortem ageing timepoint. Using a machine learning algorithm (l1-regularized logistic regression), a model was derived with the ability to discriminate between high drip and low drip phenotypes using a subset of 25 proteins with an accuracy of 63%. Models discriminating between divergent phenotypes with accuracy of 72% and 73% were also derived comparing respectively, high drip plus intermediate phenotype (considered as one phenotype) versus low drip and comparing low drip plus intermediate phenotype (considered as one phenotype) versus high drip. In all comparisons, the general classes of discriminatory proteins identified include metabolic enzymes, stress response, transport and structural proteins. In this research we have enhanced our understanding of the protein related processes underpinning this phenotype and provided strong data to work toward development of protein biomarkers for water holding capacity.

  13. Comparative Proteomic Profiling of Divergent Phenotypes for Water Holding Capacity across the Post Mortem Ageing Period in Porcine Muscle Exudate

    PubMed Central

    Di Luca, Alessio; Hamill, Ruth M.; Mullen, Anne Maria; Slavov, Nikolai; Elia, Giuliano

    2016-01-01

    Two dimensional Difference Gel Electrophoresis (2-D DIGE) and mass spectrometry were applied to investigate the changes in metabolic proteins that occur over a seven day (day 1, 3 and 7) post mortem ageing period in porcine centrifugal exudate from divergent meat quality phenotypes. The objectives of the research were to enhance our understanding of the phenotype (water holding capacity) and search for biomarkers of this economically significant pork quality attribute. Major changes in protein abundance across nine phenotype-by-time conditions were observed. Proteomic patterns were dominated by post mortem ageing timepoint. Using a machine learning algorithm (l1-regularized logistic regression), a model was derived with the ability to discriminate between high drip and low drip phenotypes using a subset of 25 proteins with an accuracy of 63%. Models discriminating between divergent phenotypes with accuracy of 72% and 73% were also derived comparing respectively, high drip plus intermediate phenotype (considered as one phenotype) versus low drip and comparing low drip plus intermediate phenotype (considered as one phenotype) versus high drip. In all comparisons, the general classes of discriminatory proteins identified include metabolic enzymes, stress response, transport and structural proteins. In this research we have enhanced our understanding of the protein related processes underpinning this phenotype and provided strong data to work toward development of protein biomarkers for water holding capacity. PMID:26950297

  14. Comprehensive impurity profiling of nutritional infusion solutions by multidimensional off-line reversed-phase liquid chromatography × hydrophilic interaction chromatography-ion trap mass-spectrometry and charged aerosol detection with universal calibration.

    PubMed

    Schiesel, Simone; Lämmerhofer, Michael; Lindner, Wolfgang

    2012-10-12

    A new analysis strategy was employed for the establishment of a comprehensive qualitative and quantitative impurity profile of a stressed multi-constituent pharmaceutical drug formulation, namely a nutritional infusion solution composed of amino acids and dipeptides. To deal with the highly complex samples a multidimensional analysis approach was developed which made use of an off-line two-dimensional reversed-phase liquid chromatography (RPLC)×hydrophilic interaction chromatography (HILIC) separation and combination of complementary detection involving ion trap mass spectrometry (IT-MS) and a charged aerosol detector (CAD). The CAD is a mass-sensitive universal detector for non-volatile compounds with relatively consistent detector response. A universal calibration function was set up with a set of standards. This universal calibration function was then employed to quantify unknown impurities allowing their classification into those that need to be reported (>0.05% relative to the precursor compound), identified (>0.1%), and quantified (>0.15%). The dilemma of unavailability of authentic standards at this stage of research for quantification could thereby be circumvented. Relevant impurities above the reporting threshold were identified by IT-MS. Impurities detected comprised di-, tri- and tetrapeptides, cyclic dipeptides (diketopiperazines), pyroglutamic acid derivatives and their condensation products. Cross-validation with HPLC-MS/MS methods using synthesized authentic standards confirmed the results obtained by the presented multidimensional analysis assay.

  15. Phenotypic Transition as a Survival Strategy of Glioma

    PubMed Central

    ICHIKAWA, Tomotsugu; OTANI, Yoshihiro; KUROZUMI, Kazuhiko; DATE, Isao

    2016-01-01

    Malignant glioma is characterized by rapid proliferation, invasion into surrounding central nervous system tissues, and aberrant vascularization. There is increasing evidence that shows gliomas are more complex than previously thought, as each tumor comprises considerable intratumoral heterogeneity with mixtures of genetically and phenotypically distinct subclones. Heterogeneity within and across tumors is recognized as a critical factor that limits therapeutic progress for malignant glioma. Recent genotyping and expression profiling of gliomas has allowed for the creation of classification schemes that assign tumors to subtypes based on similarity to defined expression signatures. Also, malignant gliomas frequently shift their biological features upon recurrence and progression. The ability of glioma cells to resist adverse conditions such as hypoxia and metabolic stress is necessary for sustained tumor growth and strongly influences tumor behaviors. In general, glioma cells are in one of two phenotypic categories: higher proliferative activity with angiogenesis, or higher migratory activity with attenuated proliferative ability. Further, they switch phenotypic categories depending on the situation. To date, a multidimensional approach has been employed to clarify the mechanisms of phenotypic shift of glioma. Various molecular and signaling pathways are involved in phenotypic shifts of glioma, possibly with crosstalk between them. In this review, we discuss molecular and phenotypic heterogeneity of glioma cells and mechanisms of phenotypic shifts in regard to the glioma proliferation, angiogenesis, and invasion. A better understanding of the molecular mechanisms that underlie phenotypic shifts of glioma may provide new insights into targeted therapeutic strategies. PMID:27169497

  16. MicroRNA Profiling of Laser-Microdissected Hepatocellular Carcinoma Reveals an Oncogenic Phenotype of the Tumor Capsule123

    PubMed Central

    Peveling-Oberhag, Jan; Seiz, Anna; Döring, Claudia; Hartmann, Sylvia; Köberle, Verena; Liese, Juliane; Zeuzem, Stefan; Hansmann, Martin-Leo; Piiper, Albrecht

    2014-01-01

    Several microRNAs (miRNAs) are associated with the molecular pathogenesis of hepatocellular carcinoma (HCC). However, previous studies analyzing the dysregulation of miRNAs in HCC show heterogeneous results. We hypothesized that part of this heterogeneity might be attributable to variations of miRNA expression deriving from the HCC capsule or the fibrotic septa within the peritumoral tissue used as controls. Tissue from surgically resected hepatitis C–associated HCC from six well-matched patients was microdissected using laser microdissection and pressure catapulting technique. Four distinct histologic compartments were isolated: tumor parenchyma (TP), fibrous capsule of the tumor (TC), tumor-adjacent liver parenchyma (LP), and cirrhotic septa of the tumor-adjacent liver (LC). MiRNA expression profiling analysis of 1105 mature miRNAs and precursors was performed using miRNA microarray. Principal component analysis and consecutive pairwise supervised comparisons demonstrated distinct patterns of expressed miRNAs not only for TP versus LP (e.g., intratumoral down-regulation of miR-214, miR-199a, miR-146a, and miR-125a; P< .05) but also for TC versus LC (including down-regulation within TC of miR-126, miR-99a/100, miR-26a, and miR-125b; P< .05). The tumor capsule therefore demonstrates a tumor-like phenotype with down-regulation of well-known tumor-suppressive miRNAs. Variations of co-analyzed fibrotic tissue within the tumor or in controls may have profound influence on miRNA expression analyses in HCC. Several miRNAs, which are proposed to be HCC specific, may indeed be rather associated to the tumor capsule. As miRNAs evolve to be important biomarkers in liver tumors, the presented data have important translational implications on diagnostics and treatment in patients with HCC. PMID:25500075

  17. Expanding the phenotypic profile of Kleefstra syndrome: A female with low-average intelligence and childhood apraxia of speech.

    PubMed

    Samango-Sprouse, Carole; Lawson, Patrick; Sprouse, Courtney; Stapleton, Emily; Sadeghin, Teresa; Gropman, Andrea

    2016-05-01

    Kleefstra syndrome (KS) is a rare neurogenetic disorder most commonly caused by deletion in the 9q34.3 chromosomal region and is associated with intellectual disabilities, severe speech delay, and motor planning deficits. To our knowledge, this is the first patient (PQ, a 6-year-old female) with a 9q34.3 deletion who has near normal intelligence, and developmental dyspraxia with childhood apraxia of speech (CAS). At 6, the Wechsler Preschool and Primary Intelligence testing (WPPSI-III) revealed a Verbal IQ of 81 and Performance IQ of 79. The Beery Buktenica Test of Visual Motor Integration, 5th Edition (VMI) indicated severe visual motor deficits: VMI = 51; Visual Perception = 48; Motor Coordination < 45. On the Receptive One Word Picture Vocabulary Test-R (ROWPVT-R), she had standard scores of 96 and 99 in contrast to an Expressive One Word Picture Vocabulary-R (EOWPVT-R) standard scores of 73 and 82, revealing a discrepancy in vocabulary domains on both evaluations. Preschool Language Scale-4 (PLS-4) on PQ's first evaluation reveals a significant difference between auditory comprehension and expressive communication with standard scores of 78 and 57, respectively, further supporting the presence of CAS. This patient's near normal intelligence expands the phenotypic profile as well as the prognosis associated with KS. The identification of CAS in this patient provides a novel explanation for the previously reported speech delay and expressive language disorder. Further research is warranted on the impact of CAS on intelligence and behavioral outcome in KS. Therapeutic and prognostic implications are discussed. PMID:26833960

  18. Impact of HIV type 1 drug resistance mutations and phenotypic resistance profile on virologic response to salvage therapy.

    PubMed

    Ross, L; Liao, Q; Gao, H; Pham, S; Tolson, J; Hertogs, K; Larder, B; Saag, M S

    2001-10-10

    This study examines the association between presence of drug resistance mutations and phenotypic resistance at baseline to virologic response to salvage therapy in a community setting. The study population consisted of 58 antiretroviral drug-experienced patients with HIV-1 infection who had recently switched therapy because of virologic failure. Drug resistance mutations in the reverse transcriptase- and protease-coding regions and phenotypic susceptibility to 13 antiretroviral drugs were assessed at baseline. Plasma HIV-1 RNA levels were assessed at baseline and at subsequent clinic visits. Results showed that three variables were significant in predicting virologic response: HIV-1 levels at baseline, number of protease mutations, and phenotypic sensitivity score for the regimen at baseline. For four drugs there was a significant association between the presence of specific drug resistance mutations and >10-fold phenotypic resistance to that drug. With phenotypic resistance defined as >4-fold resistance, the association between specific drug resistance mutations and phenotypic resistance was significant for seven drugs. Overall, these data show that phenotypic susceptibility and absence of drug resistance mutations, particularly protease mutations, are significant predictors of virologic response. For several drugs, specific combinations of drug resistance mutations are associated with decreased phenotypic susceptibility and might provide useful clinical guidelines in selecting therapeutic options.

  19. Levels of alpha-toxin correlate with distinct phenotypic response profiles of blood mononuclear cells and with agr background of community-associated Staphylococcus aureus isolates.

    PubMed

    Mairpady Shambat, Srikanth; Haggar, Axana; Vandenesch, Francois; Lina, Gerard; van Wamel, Willem J B; Arakere, Gayathri; Svensson, Mattias; Norrby-Teglund, Anna

    2014-01-01

    Epidemiological studies of Staphylococcus aureus have shown a relation between certain clones and the presence of specific virulence genes, but how this translates into virulence-associated functional responses is not fully elucidated. Here we addressed this issue by analyses of community-acquired S. aureus strains characterized with respect to antibiotic resistance, ST types, agr types, and virulence gene profiles. Supernatants containing exotoxins were prepared from overnight bacterial cultures, and tested in proliferation assays using human peripheral blood mononuclear cells (PBMC). The strains displayed stable phenotypic response profiles, defined by either a proliferative or cytotoxic response. Although, virtually all strains elicited superantigen-mediated proliferative responses, the strains with a cytotoxic profile induced proliferation only in cultures with the most diluted supernatants. This indicated that the superantigen-response was masked by a cytotoxic effect which was also confirmed by flow cytometry analysis. The cytotoxic supernatants contained significantly higher levels of α-toxin than did the proliferative supernatants. Addition of α-toxin to supernatants characterized as proliferative switched the response into cytotoxic profiles. In contrast, no effect of Panton Valentine Leukocidin, δ-toxin or phenol soluble modulin α-3 was noted in the proliferative assay. Furthermore, a significant association between agr type and phenotypic profile was found, where agrII and agrIII strains had predominantly a proliferative profile whereas agrI and IV strains had a predominantly cytotoxic profile. The differential response profiles associated with specific S. aureus strains with varying toxin production could possibly have an impact on disease manifestations, and as such may reflect specific pathotypes.

  20. Levels of Alpha-Toxin Correlate with Distinct Phenotypic Response Profiles of Blood Mononuclear Cells and with agr Background of Community-Associated Staphylococcus aureus Isolates

    PubMed Central

    Mairpady Shambat, Srikanth; Haggar, Axana; Vandenesch, Francois; Lina, Gerard; van Wamel, Willem J. B.; Arakere, Gayathri; Svensson, Mattias; Norrby-Teglund, Anna

    2014-01-01

    Epidemiological studies of Staphylococcus aureus have shown a relation between certain clones and the presence of specific virulence genes, but how this translates into virulence-associated functional responses is not fully elucidated. Here we addressed this issue by analyses of community-acquired S. aureus strains characterized with respect to antibiotic resistance, ST types, agr types, and virulence gene profiles. Supernatants containing exotoxins were prepared from overnight bacterial cultures, and tested in proliferation assays using human peripheral blood mononuclear cells (PBMC). The strains displayed stable phenotypic response profiles, defined by either a proliferative or cytotoxic response. Although, virtually all strains elicited superantigen-mediated proliferative responses, the strains with a cytotoxic profile induced proliferation only in cultures with the most diluted supernatants. This indicated that the superantigen-response was masked by a cytotoxic effect which was also confirmed by flow cytometry analysis. The cytotoxic supernatants contained significantly higher levels of α-toxin than did the proliferative supernatants. Addition of α-toxin to supernatants characterized as proliferative switched the response into cytotoxic profiles. In contrast, no effect of Panton Valentine Leukocidin, δ-toxin or phenol soluble modulin α-3 was noted in the proliferative assay. Furthermore, a significant association between agr type and phenotypic profile was found, where agrII and agrIII strains had predominantly a proliferative profile whereas agrI and IV strains had a predominantly cytotoxic profile. The differential response profiles associated with specific S. aureus strains with varying toxin production could possibly have an impact on disease manifestations, and as such may reflect specific pathotypes. PMID:25166615

  1. Metabolite profiling of Camellia sinensis by automated sequential, multidimensional gas chromatography/mass spectrometry reveals strong monsoon effects on tea constituents.

    PubMed

    Kowalsick, Amanda; Kfoury, Nicole; Robbat, Albert; Ahmed, Selena; Orians, Colin; Griffin, Timothy; Cash, Sean B; Stepp, John Richard

    2014-11-28

    Seasonal variation in tea (Camellia sinensis (L.) Kuntze; Theaceae) chemistry was investigated using automated sequential, multidimensional gas chromatography/mass spectrometry (GC-GC/MS). Metabolite libraries were produced for teas harvested from the Bulang Mountains in Yunnan, China before and after the onset of the East Asian Monsoon. A total of 201 spring and 196 monsoon metabolites were identified, with 169 common and 59 seasonally unique compounds. An additional 163 metabolites were detected but their identity could not be confirmed. Spectral deconvolution of GC/MS data was used to measure the relative concentrations in the teas. Within each family individual metabolite concentrations increased, decreased and stayed the same. The major constituents in both teas were linalool (28%), geraniol (13%), α-terpineol (10%), hotrienol (4%) and nerol (3%). This work provides the foundation to monitor seasonal variations of tea chemistry.

  2. Metabolic parameters linked by Phenotype MicroArray to acid resistance profiles of poultry-associated Salmonella enterica

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phenotype microarrays were analyzed for 51 datasets derived from Salmonella enterica. The top 4 serovars associated with poultry products and one associated with turkey, respectively Typhimurium, Enteritidis, Heidelberg, Infantis and Senftenberg, were represented. Datasets were clustered into two ...

  3. Metabolic profiling of plant extracts using direct-injection electrospray ionization mass spectrometry allows for high-throughput phenotypic characterization according to genetic and environmental effects.

    PubMed

    García-Flores, Martín; Juárez-Colunga, Sheila; García-Casarrubias, Adrián; Trachsel, Samuel; Winkler, Robert; Tiessen, Axel

    2015-01-28

    In comparison to the exponential increase of genotyping methods, phenotyping strategies are lagging behind in agricultural sciences. Genetic improvement depends upon the abundance of quantitative phenotypic data and the statistical partitioning of variance into environmental, genetic, and random effects. A metabolic phenotyping strategy was adapted to increase sample throughput while saving reagents, reducing cost, and simplifying data analysis. The chemical profiles of stem extracts from maize plants grown under low nitrogen (LN) or control trial (CT) were analyzed using optimized protocols for direct-injection electrospray ionization mass spectrometry (DIESI-MS). Specific ions significantly decreased or increased because of environmental (LN versus CT) or genotypic effects. Biochemical profiling with DIESI-MS had a superior cost-benefit compared to other standard analytical technologies (e.g., ultraviolet, near-infrared reflectance spectroscopy, high-performance liquid chromatography, and gas chromatography with flame ionization detection) routinely used for plant breeding. The method can be successfully applied in maize, strawberry, coffee, and other crop species. PMID:25588121

  4. Bi-content micro-collagen chip provides contractility-based biomechanical readout for phenotypic drug screening with expanded and profiled targets.

    PubMed

    Zhao, Hui; Zhou, Lyu; Zhang, Qiang; Zhou, Xiaoying; Zhang, Yonghui; Chen, Huijun; Du, Yanan

    2015-09-01

    Phenotypic screening has regained momentum in the pharmaceutical industry owing to its success over target-based screening. Most phenotypic screening relies on nonspecific biochemical readouts regarding cellular viability, which hampers the discovery of novel drug mechanisms of action (MOAs). Here we present a Contractility-based bi-Content micro-Collagen Chip (3CChip), which establishes cellular contractility as a biomechanics-related phenotype for drug screening. Bi-content analysis of cell contractility (imaged by iPhone) and viability suggests that the label-free contractility-based analysis exhibits superior sensitivity to compounds targeting contractile elements (e.g. focal adhesion, cytoskeleton), resulting in a enlarged target pool for drug assessment. Six typical readout patterns of drug response are summarized according to the relative positions of the contraction/viability curves, and drug targets are profiled into three categories (biomechanical, biochemical and housekeeping) by 3CChip, which will benefit subsequent target identification. The simple-to-use and effective 3CChip offers a robust platform for micro-tissue-based functional screening and may lead to a new era of mechanism-informed phenotypic drug discovery. PMID:26219255

  5. Multidimensional profiling of CSF1R screening hits and inhibitors: assessing cellular activity, target residence time, and selectivity in a higher throughput way.

    PubMed

    Uitdehaag, Joost C M; Sünnen, Cecile M; van Doornmalen, Antoon M; de Rouw, Nikki; Oubrie, Arthur; Azevedo, Rita; Ziebell, Michael; Nickbarg, Elliott; Karstens, Willem-Jan; Ruygrok, Simone

    2011-10-01

    Over the past years, improvements in high-throughput screening (HTS) technology and compound libraries have resulted in a dramatic increase in the amounts of good-quality screening hits, and there is a growing need for follow-on hit profiling assays with medium throughput to further triage hits. Here the authors present such assays for the colony-stimulating factor 1 receptor (CSF1R, Fms), including tests for cellular activity and a homogeneous assay to measure affinity for inactive CSF1R. They also present a high-throughput assay to measure target residence time, which is based on competitive binding kinetics. To better fit k(off) rates, they present a modified mathematical model for competitive kinetics. In all assays, they profiled eight reference inhibitors (imatinib, sorafenib, sunitinib, tandutinib, dasatinib, GW2580, Ki20227, and J&J's pyrido[2,3-d]pyrimidin-5-one). Using the known biochemical selectivities of these inhibitors, which can be quantified using metrics such as the selectivity entropy, the authors have determined which assay readout best predicts hit selectivity. Their profiling shows surprisingly that imatinib has a preference for the active form of CSF1R and that Ki20227 has an unusually slow target dissociation rate. This confirms that follow-on hit profiling is essential to ensure that the best hits are selected for lead optimization.

  6. Computational Typologies of Multidimensional End-of-Primary-School Performance Profiles from an Educational Perspective of Large-Scale TIMSS and PIRLS Surveys

    ERIC Educational Resources Information Center

    Unlu, Ali; Schurig, Michael

    2015-01-01

    Recently, performance profiles in reading, mathematics and science were created using the data collectively available in the Trends in International Mathematics and Science Study (TIMSS) and the Progress in International Reading Literacy Study (PIRLS) 2011. In addition, a classification of children to the end of their primary school years was…

  7. Multidimensional Risk Analysis: MRISK

    NASA Technical Reports Server (NTRS)

    McCollum, Raymond; Brown, Douglas; O'Shea, Sarah Beth; Reith, William; Rabulan, Jennifer; Melrose, Graeme

    2015-01-01

    Multidimensional Risk (MRISK) calculates the combined multidimensional score using Mahalanobis distance. MRISK accounts for covariance between consequence dimensions, which de-conflicts the interdependencies of consequence dimensions, providing a clearer depiction of risks. Additionally, in the event the dimensions are not correlated, Mahalanobis distance reduces to Euclidean distance normalized by the variance and, therefore, represents the most flexible and optimal method to combine dimensions. MRISK is currently being used in NASA's Environmentally Responsible Aviation (ERA) project o assess risk and prioritize scarce resources.

  8. Peripheral Blood MicroRNA Expression Profiles in Alzheimer's Disease: Screening, Validation, Association with Clinical Phenotype and Implications for Molecular Mechanism.

    PubMed

    Ren, Ru-Jing; Zhang, Yong-Fang; Dammer, Eric B; Zhou, Yi; Wang, Li-Ling; Liu, Xiao-Hong; Feng, Bei-Lei; Jiang, Guo-Xin; Chen, Sheng-Di; Wang, Gang; Cheng, Qi

    2016-10-01

    A series of investigations have been performed regarding microRNA (miRNA, miR) of Alzheimer's disease (AD) patients. However, most of these used microarray with neither validation by PCR nor any follow-up on the biological mechanism implicated by findings. Further, there were rarely any analyses linking clinical phenotype of de novo, drug-naive patients to cellular pathogenic mechanism(s) to date. Microarray screening followed by validation via quantitative PCR (Q-PCR) assays and the relationship between miRNAs and phenotypic indices were evaluated. Additionally, the cellular mechanism of miRNAs through effects of β-site amyloid precursor protein (APP) cleaving enzyme (BACE1) was assessed. We identified 2 specific differentially expressed (DE) miRNAs (miR-339 and miR-425) as potential diagnostic biomarkers for AD and revealed that these DE miRNAs could be involved in modulating the pathogenesis of AD via BACE1 protein inhibition. The findings presented here reveal a detailed snapshot of the profile of peripheral blood mononuclear cells (PBMC) miRNA changes in AD patients, association with clinical phenotype, and potential roles in cellular pathogenesis. PMID:26497032

  9. Low- versus high-baseline epinephrine output shapes opposite innate cytokine profiles: presence of Lewis- and Fischer-like neurohormonal immune phenotypes in humans?

    PubMed

    Elenkov, Ilia J; Kvetnansky, Richard; Hashiramoto, Akira; Bakalov, Vladimir K; Link, Amrey A; Zachman, Keith; Crane, Marianna; Jezova, Daniela; Rovensky, Jozef; Dimitrov, Mariana A; Gold, Philip W; Bonini, Sergio; Fleisher, Thomas; Chrousos, George P; Wilder, Ronald L

    2008-08-01

    Immunogenetic mechanisms operating within the immune system are known to influence cytokine profiles and disease susceptibility. Yet the role of the individual's neurohormonal background in these processes remains undefined. Hormonal imbalances are documented in immune-related diseases, but it is unclear whether this represents a secondary phenomenon or a primary "defect" related to specific neurohormonal immune phenotype(s). We report that in a large subpopulation of healthy humans the baseline epinephrine output (but not cortisol and sex steroid hormones) correlated inversely with proinflammatory and positively with anti-inflammatory cytokine production. Thus, low vs high epinephrine excretors had a 2- to 5-fold higher TNF-alpha and IL-12 production but 2-fold lower IL-10 production induced by LPS ex vivo. In alternative settings, we found low baseline levels and profoundly blunted stress-induced epinephrine responses but high TNF-alpha levels in Lewis vs Fischer inbred rats. Additionally, isoproterenol, a beta adrenoreceptor agonist suppressed LPS-induced TNF-alpha production, with more pronounced effect in Lewis than in Fischer rats. In human monocytes, epinephrine and the beta(2) adrenoreceptor agonist fenoterol potently inhibited LPS-induced TNF-alpha and IL-12, but stimulated IL-10 production. The order of potency for hormones able to inhibit IL-12 production ex vivo was: epinephrine > norepinephrine > or = 1,25-(OH)(2) vitamin D(3) > hydrocortisone. This indicates that baseline epinephrine conditions cytokine responsiveness and through this mechanism intrinsic hypo- or hyperactive adrenal medullas in some individuals may shape opposite cytokine profiles. Since Lewis and Fischer rats have opposite susceptibility to experimental immunological diseases, this suggests that the parallel human phenotypes could be linked to differing responsiveness and susceptibility to infections and immune/inflammatory-related conditions. PMID:18641310

  10. Differences in the phenotype, cytokine gene expression profiles and in vivo alloreactivity of T cells mobilized with plerixafor compared to G-CSF1

    PubMed Central

    Lundqvist, Andreas; Smith, Aleah L.; Takahashi, Yoshiyuki; Wong, Susan; Bahceci, Erkut; Cook, Lisa; Ramos, Catalina; Tawab, Abdul; McCoy, J. Philip; Read, Elizabeth J.; Khuu, Hanh M.; Bolan, Charles D.; Jungnam, Joo; Geller, Nancy; Leitman, Susan F.; Calandra, Gary; Dunbar, Cynthia; Kurlander, Roger; Childs, Richard W.

    2013-01-01

    Plerixafor (Mozobil®) is a CXCR4 antagonist that rapidly mobilizes CD34+ cells into circulation. Recently, plerixafor has been used as a single agent to mobilize peripheral blood stem cells (PBSC) for allogeneic hematopoietic cell transplantation. Although G-CSF mobilization is known to alter the phenotype and cytokine polarization of transplanted T-cells, the effects of plerixafor mobilization on T-cells have not been well characterized. In this study, we show that alterations in the T-cell phenotype and cytokine gene expression profiles characteristic of G-CSF mobilization do not occur following mobilization with plerixafor. Compared to non-mobilized T-cells, plerixafor-mobilized T-cells had similar phenotype, mixed lymphocyte reactivity, FoxP3 gene expression levels in CD4+ T-cells, and did not undergo a change in expression levels of 84 genes associated with Th1/Th2/Th3 pathways. In contrast to plerixafor, G-CSF mobilization decreased CD62L expression on both CD4 and CD8+ T-cells and altered expression levels of 16 cytokine-associated genes in CD3+ T-cells. To assess the clinical relevance of these findings, we explored a murine model of GVHD in which transplant recipients received plerixafor or G-CSF mobilized allograft from MHC-matched, minor histocompatibility mismatched donors; recipients of plerixafor mobilized PBSC had a significantly higher incidence of skin GVHD compared to mice receiving G-CSF mobilized transplants (100% vs. 50% respectively, p=0.02). These preclinical data show plerixafor, in contrast to G-CSF, does not alter the phenotype and cytokine polarization of T-cells, which raises the possibility that T-cell mediated immune sequelae of allogeneic transplantation in humans may differ when donor allografts are mobilized with plerixafor compared to G-CSF. PMID:24244025

  11. Surface modified capillary electrophoresis combined with in solution isoelectric focusing and MALDI-TOF/TOF MS: a gel-free multidimensional electrophoresis approach for proteomic profiling--exemplified on human follicular fluid.

    PubMed

    Hanrieder, Jörg; Zuberovic, Aida; Bergquist, Jonas

    2009-04-24

    Development of miniaturized analytical tools continues to be of great interest to face the challenges in proteomic analysis of complex biological samples such as human body fluids. In the light of these challenges, special emphasis is put on the speed and simplicity of newly designed technological approaches as well as the need for cost efficiency and low sample consumption. In this study, we present an alternative multidimensional bottom-up approach for proteomic profiling for fast, efficient and sensitive protein analysis in complex biological matrices. The presented setup was based on sample pre-fractionation using microscale in solution isoelectric focusing (IEF) followed by tryptic digestion and subsequent capillary electrophoresis (CE) coupled off-line to matrix assisted laser desorption/ionization time of flight tandem mass spectrometry (MALDI TOF MS/MS). For high performance CE-separation, PolyE-323 modified capillaries were applied to minimize analyte-wall interactions. The potential of the analytical setup was demonstrated on human follicular fluid (hFF) representing a typical complex human body fluid with clinical implication. The obtained results show significant identification of 73 unique proteins (identified at 95% significance level), including mostly acute phase proteins but also protein identities that are well known to be extensively involved in follicular development.

  12. Saccular Transcriptome Profiles of the Seasonal Breeding Plainfin Midshipman Fish (Porichthys notatus), a Teleost with Divergent Sexual Phenotypes

    PubMed Central

    Faber-Hammond, Joshua; Samanta, Manoj P.; Whitchurch, Elizabeth A.; Manning, Dustin; Sisneros, Joseph A.; Coffin, Allison B.

    2015-01-01

    Acoustic communication is essential for the reproductive success of the plainfin midshipman fish (Porichthys notatus). During the breeding season, type I males use acoustic cues to advertise nest location to potential mates, creating an audible signal that attracts reproductive females. Type II (sneaker) males also likely use this social acoustic signal to find breeding pairs from which to steal fertilizations. Estrogen-induced changes in the auditory system of breeding females are thought to enhance neural encoding of the advertisement call, and recent anatomical data suggest the saccule (the main auditory end organ) as one possible target for this seasonal modulation. Here we describe saccular transcriptomes from all three sexual phenotypes (females, type I and II males) collected during the breeding season as a first step in understanding the mechanisms underlying sexual phenotype-specific and seasonal differences in auditory function. We used RNA-Seq on the Ion Torrent platform to create a combined transcriptome dataset containing over 79,000 assembled transcripts representing almost 9,000 unique annotated genes. These identified genes include several with known inner ear function and multiple steroid hormone receptors. Transcripts most closely matched to published genomes of nile tilapia and large yellow croaker, inconsistent with the phylogenetic relationship between these species but consistent with the importance of acoustic communication in their life-history strategies. We then compared the RNA-Seq results from the saccules of reproductive females with a separate transcriptome from the non-reproductive female phenotype and found over 700 differentially expressed transcripts, including members of the Wnt and Notch signaling pathways that mediate cell proliferation and hair cell addition in the inner ear. These data constitute a valuable resource for furthering our understanding of the molecular basis for peripheral auditory function as well as a range of

  13. Saccular Transcriptome Profiles of the Seasonal Breeding Plainfin Midshipman Fish (Porichthys notatus), a Teleost with Divergent Sexual Phenotypes.

    PubMed

    Faber-Hammond, Joshua; Samanta, Manoj P; Whitchurch, Elizabeth A; Manning, Dustin; Sisneros, Joseph A; Coffin, Allison B

    2015-01-01

    Acoustic communication is essential for the reproductive success of the plainfin midshipman fish (Porichthys notatus). During the breeding season, type I males use acoustic cues to advertise nest location to potential mates, creating an audible signal that attracts reproductive females. Type II (sneaker) males also likely use this social acoustic signal to find breeding pairs from which to steal fertilizations. Estrogen-induced changes in the auditory system of breeding females are thought to enhance neural encoding of the advertisement call, and recent anatomical data suggest the saccule (the main auditory end organ) as one possible target for this seasonal modulation. Here we describe saccular transcriptomes from all three sexual phenotypes (females, type I and II males) collected during the breeding season as a first step in understanding the mechanisms underlying sexual phenotype-specific and seasonal differences in auditory function. We used RNA-Seq on the Ion Torrent platform to create a combined transcriptome dataset containing over 79,000 assembled transcripts representing almost 9,000 unique annotated genes. These identified genes include several with known inner ear function and multiple steroid hormone receptors. Transcripts most closely matched to published genomes of nile tilapia and large yellow croaker, inconsistent with the phylogenetic relationship between these species but consistent with the importance of acoustic communication in their life-history strategies. We then compared the RNA-Seq results from the saccules of reproductive females with a separate transcriptome from the non-reproductive female phenotype and found over 700 differentially expressed transcripts, including members of the Wnt and Notch signaling pathways that mediate cell proliferation and hair cell addition in the inner ear. These data constitute a valuable resource for furthering our understanding of the molecular basis for peripheral auditory function as well as a range of

  14. Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling.

    PubMed

    Wawer, Mathias J; Li, Kejie; Gustafsdottir, Sigrun M; Ljosa, Vebjorn; Bodycombe, Nicole E; Marton, Melissa A; Sokolnicki, Katherine L; Bray, Mark-Anthony; Kemp, Melissa M; Winchester, Ellen; Taylor, Bradley; Grant, George B; Hon, C Suk-Yee; Duvall, Jeremy R; Wilson, J Anthony; Bittker, Joshua A; Dančík, Vlado; Narayan, Rajiv; Subramanian, Aravind; Winckler, Wendy; Golub, Todd R; Carpenter, Anne E; Shamji, Alykhan F; Schreiber, Stuart L; Clemons, Paul A

    2014-07-29

    High-throughput screening has become a mainstay of small-molecule probe and early drug discovery. The question of how to build and evolve efficient screening collections systematically for cell-based and biochemical screening is still unresolved. It is often assumed that chemical structure diversity leads to diverse biological performance of a library. Here, we confirm earlier results showing that this inference is not always valid and suggest instead using biological measurement diversity derived from multiplexed profiling in the construction of libraries with diverse assay performance patterns for cell-based screens. Rather than using results from tens or hundreds of completed assays, which is resource intensive and not easily extensible, we use high-dimensional image-based cell morphology and gene expression profiles. We piloted this approach using over 30,000 compounds. We show that small-molecule profiling can be used to select compound sets with high rates of activity and diverse biological performance.

  15. Numerical approaches for multidimensional simulations of stellar explosions

    NASA Astrophysics Data System (ADS)

    Chen, Ke-Jung; Heger, Alexander; Almgren, Ann S.

    2013-11-01

    We introduce numerical algorithms for initializing multidimensional simulations of stellar explosions with 1D stellar evolution models. The initial mapping from 1D profiles onto multidimensional grids can generate severe numerical artifacts, one of the most severe of which is the violation of conservation laws for physical quantities. We introduce a numerical scheme for mapping 1D spherically-symmetric data onto multidimensional meshes so that these physical quantities are conserved. We verify our scheme by porting a realistic 1D Lagrangian stellar profile to the new multidimensional Eulerian hydro code CASTRO. Our results show that all important features in the profiles are reproduced on the new grid and that conservation laws are enforced at all resolutions after mapping. We also introduce a numerical scheme for initializing multidimensional supernova simulations with realistic perturbations predicted by 1D stellar evolution models. Instead of seeding 3D stellar profiles with random perturbations, we imprint them with velocity perturbations that reproduce the Kolmogorov energy spectrum expected for highly turbulent convective regions in stars. Our models return Kolmogorov energy spectra and vortex structures like those in turbulent flows before the modes become nonlinear. Finally, we describe approaches to determining the resolution for simulations required to capture fluid instabilities and nuclear burning. Our algorithms are applicable to multidimensional simulations besides stellar explosions that range from astrophysics to cosmology.

  16. Neuropsychological and dimensional behavioral trait profiles in Costa Rican ADHD sib pairs: Potential intermediate phenotypes for genetic studies.

    PubMed

    Peskin, Viviana A; Ordóñez, Anna; Mackin, R Scott; Delucchi, Kevin; Monge, Silvia; McGough, James J; Chavira, Denise A; Berrocal, Monica; Cheung, Erika; Fournier, Eduardo; Badner, Judith A; Herrera, Luis Diego; Mathews, Carol A

    2015-06-01

    Attention deficit hyperactivity disorder (ADHD) is associated with substantial functional impairment in children and in adults. Many individuals with ADHD have clear neurocognitive deficits, including problems with visual attention, processing speed, and set shifting. ADHD is etiologically complex, and although genetic factors play a role in its development, much of the genetic contribution to ADHD remains unidentified. We conducted clinical and neuropsychological assessments of 294 individuals (269 with ADHD) from 163 families (48 multigenerational families created using genealogical reconstruction, 78 affected sib pair families, and 37 trios) from the Central Valley of Costa Rica (CVCR). We used principal components analysis (PCA) to group neurocognitive and behavioral variables using the subscales of the Child Behavior Checklist (CBCL) and 15 neuropsychological measures, and created quantitative traits for heritability analyses. We identified seven cognitive and two behavioral domains. Individuals with ADHD were significantly more impaired than their unaffected siblings on most behavioral and cognitive domains. The verbal IQ domain had the highest heritability (92%), followed by auditory attention (87%), visual processing speed and problem solving (85%), and externalizing symptoms (81%). The quantitative traits identified here have high heritabilities, similar to the reported heritability of ADHD (70-90%), and may represent appropriate alternative phenotypes for genetic studies. The use of multigenerational families from a genetically isolated population may facilitate the identification of ADHD risk genes in the face of phenotypic and genetic heterogeneity. PMID:25832558

  17. Neuropsychological and dimensional behavioral trait profiles in Costa Rican ADHD sib pairs: Potential intermediate phenotypes for genetic studies.

    PubMed

    Peskin, Viviana A; Ordóñez, Anna; Mackin, R Scott; Delucchi, Kevin; Monge, Silvia; McGough, James J; Chavira, Denise A; Berrocal, Monica; Cheung, Erika; Fournier, Eduardo; Badner, Judith A; Herrera, Luis Diego; Mathews, Carol A

    2015-06-01

    Attention deficit hyperactivity disorder (ADHD) is associated with substantial functional impairment in children and in adults. Many individuals with ADHD have clear neurocognitive deficits, including problems with visual attention, processing speed, and set shifting. ADHD is etiologically complex, and although genetic factors play a role in its development, much of the genetic contribution to ADHD remains unidentified. We conducted clinical and neuropsychological assessments of 294 individuals (269 with ADHD) from 163 families (48 multigenerational families created using genealogical reconstruction, 78 affected sib pair families, and 37 trios) from the Central Valley of Costa Rica (CVCR). We used principal components analysis (PCA) to group neurocognitive and behavioral variables using the subscales of the Child Behavior Checklist (CBCL) and 15 neuropsychological measures, and created quantitative traits for heritability analyses. We identified seven cognitive and two behavioral domains. Individuals with ADHD were significantly more impaired than their unaffected siblings on most behavioral and cognitive domains. The verbal IQ domain had the highest heritability (92%), followed by auditory attention (87%), visual processing speed and problem solving (85%), and externalizing symptoms (81%). The quantitative traits identified here have high heritabilities, similar to the reported heritability of ADHD (70-90%), and may represent appropriate alternative phenotypes for genetic studies. The use of multigenerational families from a genetically isolated population may facilitate the identification of ADHD risk genes in the face of phenotypic and genetic heterogeneity.

  18. Multidimensional spectral load balancing

    SciTech Connect

    Hendrickson, B.; Leland, R.

    1993-01-01

    We describe an algorithm for the static load balancing of scientific computations that generalizes and improves upon spectral bisection. Through a novel use of multiple eigenvectors, our new spectral algorithm can divide a computation into 4 or 8 pieces at once. These multidimensional spectral partitioning algorithms generate balanced partitions that have lower communication overhead and are less expensive to compute than those produced by spectral bisection. In addition, they automatically work to minimize message contention on a hypercube or mesh architecture. These spectral partitions are further improved by a multidimensional generalization of the Kernighan-Lin graph partitioning algorithm. Results on several computational grids are given and compared with other popular methods.

  19. CDH23 Mutation and Phenotype Heterogeneity: A Profile of 107 Diverse Families with Usher Syndrome and Nonsyndromic Deafness

    PubMed Central

    Astuto, L. M.; Bork, J. M.; Weston, M. D.; Askew, J. W.; Fields, R. R.; Orten, D. J.; Ohliger, S. J.; Riazuddin, S.; Morell, R. J.; Khan, S.; Riazuddin, S.; Kremer, H.; van Hauwe, P.; Moller, C. G.; Cremers, C. W. R. J.; Ayuso, C.; Heckenlively, J. R.; Rohrschneider, K.; Spandau, U.; Greenberg, J.; Ramesar, R.; Reardon, W.; Bitoun, P.; Millan, J.; Legge, R.; Friedman, T. B.; Kimberling, W. J.

    2002-01-01

    Usher syndrome type I is characterized by congenital hearing loss, retinitis pigmentosa (RP), and variable vestibular areflexia. Usher syndrome type ID, one of seven Usher syndrome type I genetic localizations, have been mapped to a chromosomal interval that overlaps with a nonsyndromic-deafness localization, DFNB12. Mutations in CDH23, a gene that encodes a putative cell-adhesion protein with multiple cadherin-like domains, are responsible for both Usher syndrome and DFNB12 nonsyndromic deafness. Specific CDH23 mutational defects have been identified that differentiate these two phenotypes. Only missense mutations of CDH23 have been observed in families with nonsyndromic deafness, whereas nonsense, frameshift, splice-site, and missense mutations have been identified in families with Usher syndrome. In the present study, a panel of 69 probands with Usher syndrome and 38 probands with recessive nonsyndromic deafness were screened for the presence of mutations in the entire coding region of CDH23, by heteroduplex, single-strand conformation polymorphism, and direct sequence analyses. A total of 36 different CDH23 mutations were detected in 45 families; 33 of these mutations were novel, including 18 missense, 3 nonsense, 5 splicing defects, 5 microdeletions, and 2 insertions. A total of seven mutations were common to more than one family. Numerous exonic and intronic polymorphisms also were detected. Results of ophthalmologic examinations of the patients with nonsyndromic deafness have found asymptomatic RP–like manifestations, indicating that missense mutations may have a subtle effect in the retina. Furthermore, patients with mutations in CDH23 display a wide range of hearing loss and RP phenotypes, differing in severity, age at onset, type, and the presence or absence of vestibular areflexia. PMID:12075507

  20. The effect of novel nitrogen-rich plasma polymer coatings on the phenotypic profile of notochordal cells

    PubMed Central

    Mwale, Fackson; Wang, Hong Tian; Petit, Alain; Girard-Lauriault, Pierre-Luc; Hunter, Christopher J; Ouellet, Jean A; Wertheimer, Michael R; Antoniou, John

    2007-01-01

    Background The loss of the notochordal cells from the nucleus pulposus is associated with ageing and disc degeneration. However, understanding the mechanisms responsible for the loss of these cells has been hampered in part due to the difficulty of culturing and maintaining their phenotype. Furthermore, little is known about the influence of the substratum on the molecular markers of notochordal cells. Methods Notochordal cells were isolated from lumbar spine of non-chondrodystrophoid dogs and cultured on N-rich plasma polymer layers, so-called "PPE:N" (N-doped plasma-polymerised ethylene, containing up to 36% [N]) surfaces, for 3, 7 or 14 days. Gene expression of vimentin (VIM), pleiotrophin (PTN), matrix Gla protein (MGP), cartilage oligomeric matrix protein (COMP), keratin 18 (KRT 18), aggrecan (AGG), collagen type 1 (COL1A2), collagen type 2 (COL2A1) was analyzed through semi-quantitative reverse transcription-polymerase chain reaction (RT-PCR). Results Notochordal cells were maintained in culture on PPE:N for up to 14 days with no loss in cell viability. Except for VIM, gene expression varied depending on the culture periods and [N] concentration of the substratum. Generally, PPE:N surfaces altered gene expression significantly when cells were cultured for 3 or 7 days. Conclusion The present study has shown that notochordal cells from dogs can attach to and grow on PPE:N surfaces. Analysis of the expression of different genes in these cells cultured on different N-functionalized surfaces indicates that cellular behaviour is gene-specific and time-dependent. Further studies are required to better understand the roles of specific surface functionalities on receptor sites, and their effects on cellular phenotypes. PMID:17822560

  1. MicroRNA profiles of t(14;18)–negative follicular lymphoma support a late germinal center B-cell phenotype

    PubMed Central

    Leich, Ellen; Zamo, Alberto; Horn, Heike; Haralambieva, Eugenia; Puppe, Bernhard; Gascoyne, Randy D.; Chan, Wing-Chung; Braziel, Rita M.; Rimsza, Lisa M.; Weisenburger, Dennis D.; Delabie, Jan; Jaffe, Elaine S.; Fitzgibbon, Jude; Staudt, Louis M.; Mueller-Hermelink, Hans-Konrad; Calaminici, Mariarita; Campo, Elias; Ott, German; Hernández, Luis

    2011-01-01

    A total of 90% of follicular lymphomas (FLs) harbor the translocation t(14;18) leading to deregulated BCL2 expression. Conversely, 10% of FLs lack the t(14;18), and the majority of these FLs do not express BCL2. The molecular features of t(14;18)–negative FLs remain largely unknown. We performed microRNA expression analysis in 32 FL grades 1 to 3A, including 17 t(14;18)–positive FLs, 9 t(14;18)–negative FLs without BCL2 expression, and 6 t(14;18)–negative FLs with BCL2 expression. MicroRNA profiles were correlated with corresponding mRNA expression patterns, and potential targets were investigated by quantitative PCR and immunohistochemistry in an independent validation series of 83 FLs. Statistical analysis identified 17 microRNAs that were differentially expressed between t(14;18)–positive FLs and t(14;18)–negative FLs. The down-regulation of miR-16, miR-26a, miR-101, miR-29c, and miR138 in the t(14;18)-negative FL subset was associated with profound mRNA expression changes of potential target genes involving cell cycle control, apoptosis, and B-cell differentiation. miR-16 target CHEK1 showed increased expression in t(14;18)-negative FLs, whereas TCL1A expression was reduced, in line with a partial loss of the germinal center B-cell phenotype in this FL subset. In conclusion, t(14;18)–negative FL have distinct microRNA profiles that are associated with an increased proliferative capacity and a “late” germinal center B-cell phenotype. PMID:21960592

  2. Real-life assessment of the multidimensional nature of dyspnoea in COPD outpatients.

    PubMed

    Morélot-Panzini, Capucine; Gilet, Hélène; Aguilaniu, Bernard; Devillier, Philippe; Didier, Alain; Perez, Thierry; Pignier, Christophe; Arnould, Benoit; Similowski, Thomas

    2016-06-01

    Dyspnoea is a prominent symptom of chronic obstructive pulmonary disease (COPD). Recent multidimensional dyspnoea questionnaires like the Multidimensional Dyspnea Profile (MDP) individualise the sensory and affective dimensions of dyspnoea. We tested the MDP in COPD outpatients based on the hypothesis that the importance of the affective dimension of dyspnoea would vary according to clinical characteristics.A multicentre, prospective, observational, real-life study was conducted in 276 patients. MDP data were compared across various categories of patients (modified Medical Research Council (mMRC) dyspnoea score, COPD Assessment Test (CAT) score, Global Initiative for Chronic Obstructive Lung Disease (GOLD) airflow obstruction categories, GOLD "ABCD" categories, and Hospital Anxiety and Depression Scale (HADS)). Univariate and multivariate regressions were conducted to explore factors influencing the affective dimension of dyspnoea. Cluster analysis was conducted to create homogeneous patient profiles.The MDP identified a more marked affective dimension of dyspnoea with more severe mMRC, CAT, 12-item Short-Form Health Survey mental component, airflow obstruction and HADS. Multivariate analysis identified airflow obstruction, depressive symptoms and physical activity as determinants of the affective dimension of dyspnoea. Patients clustered into an "elderly, ex-smoker, severe disease, no rehabilitation" group exhibited the most marked affective dimension of dyspnoea.An affective/emotional dimension of dyspnoea can be identified in routine clinical practice. It can contribute to the phenotypic description of patients. Studies are needed to determine whether targeted therapeutic interventions can be designed and whether they are useful.

  3. Phenotypically anchored transcriptome profiling of developmental exposure to the antimicrobial agent, triclosan, reveals hepatotoxicity in embryonic zebrafish.

    PubMed

    Haggard, Derik E; Noyes, Pamela D; Waters, Katrina M; Tanguay, Robert L

    2016-10-01

    Triclosan (TCS) is an antimicrobial agent commonly found in a variety of personal care products and cosmetics. TCS readily enters the environment through wastewater and is detected in human plasma, urine, and breast milk due to its widespread use. Studies have implicated TCS as a disruptor of thyroid and estrogen signaling; therefore, research examining the developmental effects of TCS is warranted. In this study, we used embryonic zebrafish to investigate the developmental toxicity and potential mechanism of action of TCS. Embryos were exposed to graded concentrations of TCS from 6 to 120hours post-fertilization (hpf) and the concentration where 80% of the animals had mortality or morbidity at 120hpf (EC80) was calculated. Transcriptomic profiling was conducted on embryos exposed to the EC80 (7.37μM). We identified a total of 922 significant differentially expressed transcripts (FDR adjusted P-value≤0.05; fold change ≥2). Pathway and gene ontology enrichment analyses identified biological networks and transcriptional hubs involving normal liver functioning, suggesting TCS may be hepatotoxic in zebrafish. Tissue-specific gene enrichment analysis further supported the role of the liver as a target organ for TCS toxicity. We also examined the in vitro bioactivity profile of TCS reported by the ToxCast screening program. TCS had a diverse bioactivity profile and was a hit in 217 of the 385 assay endpoints we identified. We observed similarities in gene expression and hepatic steatosis assays; however, hit data for TCS were more concordant with the hypothesized CAR/PXR activity of TCS from rodent and human in vitro studies. PMID:27538710

  4. Bioreactor-engineered cancer tissue-like structures mimic phenotypes, gene expression profiles and drug resistance patterns observed "in vivo".

    PubMed

    Hirt, Christian; Papadimitropoulos, Adam; Muraro, Manuele G; Mele, Valentina; Panopoulos, Evangelos; Cremonesi, Eleonora; Ivanek, Robert; Schultz-Thater, Elke; Droeser, Raoul A; Mengus, Chantal; Heberer, Michael; Oertli, Daniel; Iezzi, Giandomenica; Zajac, Paul; Eppenberger-Castori, Serenella; Tornillo, Luigi; Terracciano, Luigi; Martin, Ivan; Spagnoli, Giulio C

    2015-09-01

    Anticancer compound screening on 2D cell cultures poorly predicts "in vivo" performance, while conventional 3D culture systems are usually characterized by limited cell proliferation, failing to produce tissue-like-structures (TLS) suitable for drug testing. We addressed engineering of TLS by culturing cancer cells in porous scaffolds under perfusion flow. Colorectal cancer (CRC) HT-29 cells were cultured in 2D, on collagen sponges in static conditions or in perfused bioreactors, or injected subcutaneously in immunodeficient mice. Perfused 3D (p3D) cultures resulted in significantly higher (p < 0.0001) cell proliferation than static 3D (s3D) cultures and yielded more homogeneous TLS, with morphology and phenotypes similar to xenografts. Transcriptome analysis revealed a high correlation between xenografts and p3D cultures, particularly for gene clusters regulating apoptotic processes and response to hypoxia. Treatment with 5-Fluorouracil (5-FU), a frequently used but often clinically ineffective chemotherapy drug, induced apoptosis, down-regulation of anti-apoptotic genes (BCL-2, TRAF1, and c-FLIP) and decreased cell numbers in 2D, but only "nucleolar stress" in p3D and xenografts. Conversely, BCL-2 inhibitor ABT-199 induced cytotoxic effects in p3D but not in 2D cultures. Our findings advocate the importance of perfusion flow in 3D cultures of tumor cells to efficiently mimic functional features observed "in vivo" and to test anticancer compounds. PMID:26051518

  5. Cervical Cancer Cell Supernatants Induce a Phenotypic Switch from U937-Derived Macrophage-Activated M1 State into M2-Like Suppressor Phenotype with Change in Toll-Like Receptor Profile

    PubMed Central

    Sánchez-Reyes, Karina; Bravo-Cuellar, Alejandro; Hernández-Flores, Georgina; Lerma-Díaz, José Manuel; Jave-Suárez, Luis Felipe; Gómez-Lomelí, Paulina; de Celis, Ruth; Aguilar-Lemarroy, Adriana; Domínguez-Rodríguez, Jorge Ramiro; Ortiz-Lazareno, Pablo Cesar

    2014-01-01

    Cervical cancer (CC) is the second most common cancer among women worldwide. Infection with human papillomavirus (HPV) is the main risk factor for developing CC. Macrophages are important immune effector cells; they can be differentiated into two phenotypes, identified as M1 (classically activated) and M2 (alternatively activated). Macrophage polarization exerts profound effects on the Toll-like receptor (TLR) profile. In this study, we evaluated whether the supernatant of human CC cells HeLa, SiHa, and C-33A induces a shift of M1 macrophage toward M2 macrophage in U937-derived macrophages. Results. The results showed that soluble factors secreted by CC cells induce a change in the immunophenotype of macrophages from macrophage M1 into macrophage M2. U937-derived macrophages M1 released proinflammatory cytokines and nitric oxide; however, when these cells were treated with the supernatant of CC cell lines, we observed a turnover of M1 toward M2. These cells increased CD163 and IL-10 expression. The expression of TLR-3, -7, and -9 is increased when the macrophages were treated with the supernatant of CC cells. Conclusions. Our result strongly suggests that CC cells may, through the secretion of soluble factors, induce a change of immunophenotype M1 into M2 macrophages. PMID:25309919

  6. Characterization of the phenotypic and lymphokine profile associated with strong CD8+ anti-HIV-1 suppressor activity (CASA)

    PubMed Central

    Wilkinson, J; Zaunders, J J; Carr, A; Guillemin, G; Cooper, D A

    2002-01-01

    A panel of 22 CD8+ T cell lines, with a broad range of CD8+ anti-HIV-1 suppressor activity (CASA) were generated from a single patient with HIV-1 infection. CD8+ T cell lines with either strong or weak CASA were examined and compared for cell surface and intracellular markers, constitutive chemokine and lymphokine mRNA levels and inducible lymphokine expression. Strong CASA significantly correlated with CD8+ T cell lines that highly coexpressed the molecule CD28+ (r = 0·52, P = 0·01) and Ki67+ (r = 0·88, P = 0·02), with strong CASA CD8+ T cell lines demonstrating significantly higher (P < 0·05) expression of CD8+CD28+ and CD8+Ki67+ compared to those with weak activity. No such correlations or findings were observed for the markers CD38, HLA-DR, CD57 or perforin. The Th1 cytokines were expressed at greater levels than the Th2 cytokines, with strong CASA significantly associated with an increased inducible level of IL-2 production (P = 0·05). Constitutive RANTES, IP-10 and I-309 mRNA expression were significantly (P < 0·05) elevated in CD8+ T cell lines exhibiting strong CASA compared to those with weak CASA. There was no significant difference in the mRNA expression of the lymphokines IL-2, 4, 5, 8, 9, 10, 14, 15, or chemokines MIP-1α, MIP-1β, MCP-1, and Ltn. Strong CASA was therefore associated with rapidly replicating CD8+ T cells of the phenotype CD8+CD28+Ki67+ that expressed greater levels of IL-2 and the ligands RANTES and I-309. PMID:11882045

  7. Influence of blood pressure profile on frailty phenotype in community-dwelling elders in Brazil - FIBRA study.

    PubMed

    Fattori, A; Santimaria, M R; Alves, R M A; Guariento, M E; Neri, A L

    2013-01-01

    Frailty is a clinical condition associated with pathological aging and biological vulnerability. In the spectrum of events related to frailty, aging of the cardiocirculatory system and abnormalities in arterial blood pressure (BP) partly explain the changes in tissue perfusion and, potentially, the decrease in physiological reserves. This study investigated the relationship between BP levels, systemic arterial hypertension (SAH) and the frailty phenotype by analyzing frailty criteria in a cross-sectional model into the FIBRA network, a populational sample of community-dwelling elders in Southeastern Brazil. Study participants with ≥65 years were selected by probabilistic sampling of residents in the urban area of the municipality of Campinas (n=900). Considering frailty as a whole and the difference between genders, there was a greater proportion of frail or pre-frail individuals among women than men. Analysis of individual frailty criteria showed that weight loss and fatigue were more common among women (18.3% vs. 12.5%, p=0.034 and 22.5% vs. 11.9%, p<0.001, respectively). Comparison of individuals with or without SAH failed to reveal any differences related to frailty criteria. Nevertheless, averages of diastolic blood pressure (DBP) and mean arterial blood pressure values were lower among elderly individuals with reduced grip strength, physical activity and the frailty classification as a whole (OR 0.986, IC 0.975-0.997) (for every 1 mmHg reduction in MBP values, the likelihood of being frail increased 1.4%). Our findings corroborate the relationship between BP values and frailty in the elderly and contribute to an understanding of the pathophysiological mechanisms of the syndrome.

  8. Sex-Related Cognitive Profile in Autism Spectrum Disorders Diagnosed Late in Life: Implications for the Female Autistic Phenotype.

    PubMed

    Lehnhardt, Fritz-Georg; Falter, Christine Michaela; Gawronski, Astrid; Pfeiffer, Kathleen; Tepest, Ralf; Franklin, Jeremy; Vogeley, Kai

    2016-01-01

    Females with high-functioning ASD are known to camouflage their autistic symptoms better than their male counterparts, making them prone to being under-ascertained and delayed in diagnostic assessment. Thus far the underlying cognitive processes that enable such successful socio-communicative adaptation are not well understood. The current results show sex-related differences in the cognitive profile of ASD individuals, which were diagnosed late in life exclusively. Higher verbal abilities were found in males (n = 69) as opposed to higher processing speed and better executive functions in females with ASD (n = 38). Since both sexes remained unidentified during childhood and adolescence, these results are suggestive for sex-distinctive cognitive strategies as an alternative to typically-developed reciprocal social behavior and social mimicry in high functioning ASD.

  9. Phenotypes and gene expression profiles of Saccharopolyspora erythraea rifampicin-resistant (rif) mutants affected in erythromycin production

    PubMed Central

    Carata, Elisabetta; Peano, Clelia; Tredici, Salvatore M; Ferrari, Francesco; Talà, Adelfia; Corti, Giorgio; Bicciato, Silvio; De Bellis, Gianluca; Alifano, Pietro

    2009-01-01

    Background There is evidence from previous works that bacterial secondary metabolism may be stimulated by genetic manipulation of RNA polymerase (RNAP). In this study we have used rifampicin selection as a strategy to genetically improve the erythromycin producer Saccharopolyspora erythraea. Results Spontaneous rifampicin-resistant (rif) mutants were isolated from the parental strain NRRL2338 and two rif mutations mapping within rpoB, S444F and Q426R, were characterized. With respect to the parental strain, S444F mutants exhibited higher respiratory performance and up to four-fold higher final erythromycin yields; in contrast, Q426R mutants were slow-growing, developmental-defective and severely impaired in erythromycin production. DNA microarray analysis demonstrated that these rif mutations deeply changed the transcriptional profile of S. erythraea. The expression of genes coding for key enzymes of carbon (and energy) and nitrogen central metabolism was dramatically altered in turn affecting the flux of metabolites through erythromycin feeder pathways. In particular, the valine catabolic pathway that supplies propionyl-CoA for biosynthesis of the erythromycin precursor 6-deoxyerythronolide B was strongly up-regulated in the S444F mutants, while the expression of the biosynthetic gene cluster of erythromycin (ery) was not significantly affected. In contrast, the ery cluster was down-regulated (<2-fold) in the Q426R mutants. These strains also exhibited an impressive stimulation of the nitrogen regulon, which may contribute to lower erythromycin yields as erythromycin production was strongly inhibited by ammonium. Conclusion Rifampicin selection is a simple and reliable tool to investigate novel links between primary and secondary metabolism and morphological differentiation in S. erythraea and to improve erythromycin production. At the same time genome-wide analysis of expression profiles using DNA microarrays allowed information to be gained about the mechanisms

  10. Pemetrexed alters folate phenotype and inflammatory profile in EA.hy 926 cells grown under low-folate conditions

    PubMed Central

    Hammons, Andrea L.; Summers, Carolyn M.; Jochems, Jeanine; Arora, Jasbir S.; Zhang, Suhong; Blair, Ian A.; Whitehead, Alexander S.

    2014-01-01

    Elevated homocysteine is a risk marker for several major human pathologies. Emerging evidence suggests that perturbations of folate/homocysteine metabolism can directly modify production of inflammatory mediators. Pemetrexed acts by inhibiting thymidylate synthetase (TYMS), dihydrofolate reductase (DHFR), and glycinamide ribonucleotide formyltransferase (GARFT). EA.hy 926 cells grown under low (“Lo”) and high (“Hi”) folate conditions were treated with pemetrexed. The concentrations of several intracellular folate derivatives were measured using LC-MRM/MS. Lo cells had lower total folate concentrations and a different distribution of the intracellular folate derivatives than Hi cells. Treatment with pemetrexed caused a decrease in individual folate analytes. Microarray analysis showed that several genes were significantly up or down-regulated in pemetrexed treated Lo cells. Several of the significantly up-regulated transcripts were inflammatory. Changes in transcript levels of selected targets, including C3, IL-8, and DHFR, were confirmed by quantitative RT-PCR. C3 and IL-8 transcript levels were increased in pemetrexed-treated Lo cells relative to Lo controls; DHFR transcript levels were decreased. In Lo cells, IL-8 and C3 protein concentrations were increased following pemetrexed treatment. Pemetrexed drug treatment was shown in this study to have effects that lead to an increase in pro-inflammatory mediators in Lo cells. No such changes were observed in Hi cells, suggesting that pemetrexed could not modify the inflammatory profile in the context of cellular folate sufficiency. PMID:22975265

  11. Proteomic and Glycoproteomic Profilings Reveal That Post-translational Modifications of Toxins Contribute to Venom Phenotype in Snakes.

    PubMed

    Andrade-Silva, Débora; Zelanis, André; Kitano, Eduardo S; Junqueira-de-Azevedo, Inácio L M; Reis, Marcelo S; Lopes, Aline S; Serrano, Solange M T

    2016-08-01

    Snake venoms are biological weapon systems composed of secreted proteins and peptides that are used for immobilizing or killing prey. Although post-translational modifications are widely investigated because of their importance in many biological phenomena, we currently still have little understanding of how protein glycosylation impacts the variation and stability of venom proteomes. To address these issues, here we characterized the venom proteomes of seven Bothrops snakes using a shotgun proteomics strategy. Moreover, we compared the electrophoretic profiles of native and deglycosylated venoms and, in order to assess their subproteomes of glycoproteins, we identified the proteins with affinity for three lectins with different saccharide specificities and their putative glycosylation sites. As proteinases are abundant glycosylated toxins, we examined the effect of N-deglycosylation on their catalytic activities and show that the proteinases of the seven venoms were similarly affected by removal of N-glycans. Moreover, we prospected putative glycosylation sites of transcripts of a B. jararaca venom gland data set and detected toxin family related patterns of glycosylation. Based on our global analysis, we report that Bothrops venom proteomes and glycoproteomes contain a core of components that markedly define their composition, which is conserved upon evolution in parallel to other molecular markers that determine their phylogenetic classification. PMID:27297130

  12. Multidimensional spectroscopy of photoreactivity

    PubMed Central

    Ruetzel, Stefan; Diekmann, Meike; Nuernberger, Patrick; Walter, Christof; Engels, Bernd; Brixner, Tobias

    2014-01-01

    Coherent multidimensional electronic spectroscopy is commonly used to investigate photophysical phenomena such as light harvesting in photosynthesis in which the system returns back to its ground state after energy transfer. By contrast, we introduce multidimensional spectroscopy to study ultrafast photochemical processes in which the investigated molecule changes permanently. Exemplarily, the emergence in 2D and 3D spectra of a cross-peak between reactant and product reveals the cis–trans photoisomerization of merocyanine isomers. These compounds have applications in organic photovoltaics and optical data storage. Cross-peak oscillations originate from a vibrational wave packet in the electronically excited state of the photoproduct. This concept isolates the isomerization dynamics along different vibrational coordinates assigned by quantum-chemical calculations, and is applicable to determine chemical dynamics in complex photoreactive networks. PMID:24639540

  13. Multidimensional radar picture

    NASA Astrophysics Data System (ADS)

    Waz, Mariusz

    2010-05-01

    In marine navigation systems, the three-dimensional (3D) visualization is often and often used. Echosonders and sonars working in hydroacustic systems can present pictures in three dimensions. Currently, vector maps also offer 3D presentation. This presentation is used in aviation and underwater navigation. In the nearest future three-dimensional presentation may be obligatory presentation in displays of navigation systems. A part of these systems work with radar and communicates with it transmitting data in a digital form. 3D presentation of radar picture require a new technology to develop. In the first step it is necessary to compile digital form of radar signal. The modern navigation radar do not present data in three-dimensional form. Progress in technology of digital signal processing make it possible to create multidimensional radar pictures. For instance, the RSC (Radar Scan Converter) - digital radar picture recording and transforming tool can be used to create new picture online. Using RSC and techniques of modern computer graphics multidimensional radar pictures can be generated. The radar pictures mentioned should be readable for ECDIS. The paper presents a method for generating multidimensional radar picture from original signal coming from radar receiver.

  14. Differential Phenotypic and Functional Profiles of TcCA-2 -Specific Cytotoxic CD8+ T Cells in the Asymptomatic versus Cardiac Phase in Chagasic Patients

    PubMed Central

    Egui, Adriana; Thomas, M. Carmen; Carrilero, Bartolomé; Segovia, Manuel; Alonso, Carlos; Marañón, Concepción; López, Manuel Carlos

    2015-01-01

    It has been reported that the immune response mediated by T CD8+ lymphocytes plays a critical role in the control of Trypanosoma cruzi infection and that the clinical symptoms of Chagas disease appear to be related to the competence of the CD8+ T immune response against the parasite. Herewith, in silico prediction and binding assays on TAP-deficient T2 cells were used to identify potential HLA-A*02:01 ligands in the T. cruzi TcCA-2 protein. The TcCA-2-specific CD8+ T cells were functionality evaluated by Granzyme B and cytokine production in peripheral blood mononuclear cells (PBMC) from Chagas disease patients stimulated with the identified HLA-A*02:01 peptides. The specific cells were phenotypically characterized by flow cytometry using several surface markers and HLA-A*02:01 APC-labeled dextramer loaded with the peptides. In the T. cruzi TcCA-2 protein four T CD8+ epitopes were identified which are processed and presented during Chagas disease. Interestingly, a differential cellular phenotypic profile could be correlated with the severity of the disease. The TcCA-2-specific T CD8+ cells from patients with cardiac symptoms are mainly effector memory cells (TEM and TEMRA) while, those present in the asymptomatic phase are predominantly naive cells (TNAIVE). Moreover, in patients with cardiac symptoms the percentage of cells with senescence features is significantly higher than in patients at the asymptomatic phase of the disease. We consider that the identification of these new class I-restricted epitopes are helpful for designing biomarkers of sickness pathology as well as the development of immunotherapies against T. cruzi infection. PMID:25816096

  15. Elevated paternal glucocorticoid exposure alters the small noncoding RNA profile in sperm and modifies anxiety and depressive phenotypes in the offspring

    PubMed Central

    Short, A K; Fennell, K A; Perreau, V M; Fox, A; O'Bryan, M K; Kim, J H; Bredy, T W; Pang, T Y; Hannan, A J

    2016-01-01

    Recent studies have suggested that physiological and behavioral traits may be transgenerationally inherited through the paternal lineage, possibly via non-genomic signals derived from the sperm. To investigate how paternal stress might influence offspring behavioral phenotypes, a model of hypothalamic–pituitary–adrenal (HPA) axis dysregulation was used. Male breeders were administered water supplemented with corticosterone (CORT) for 4 weeks before mating with untreated female mice. Female, but not male, F1 offspring of CORT-treated fathers displayed altered fear extinction at 2 weeks of age. Only male F1 offspring exhibited altered patterns of ultrasonic vocalization at postnatal day 3 and, as adults, showed decreased time in open on the elevated-plus maze and time in light on the light–dark apparatus, suggesting a hyperanxiety-like behavioral phenotype due to paternal CORT treatment. Interestingly, expression of the paternally imprinted gene Igf2 was increased in the hippocampus of F1 male offspring but downregulated in female offspring. Male and female F2 offspring displayed increased time spent in the open arm of the elevated-plus maze, suggesting lower levels of anxiety compared with control animals. Only male F2 offspring showed increased immobility time on the forced-swim test and increased latency to feed on the novelty-supressed feeding test, suggesting a depression-like phenotype in these animals. Collectively, these data provide evidence that paternal CORT treatment alters anxiety and depression-related behaviors across multiple generations. Analysis of the small RNA profile in sperm from CORT-treated males revealed marked effects on the expression of small noncoding RNAs. Sperm from CORT-treated males contained elevated levels of three microRNAs, miR-98, miR-144 and miR-190b, which are predicted to interact with multiple growth factors, including Igf2 and Bdnf. Sustained elevation of glucocorticoids is therefore involved in the transmission of

  16. Elevated paternal glucocorticoid exposure alters the small noncoding RNA profile in sperm and modifies anxiety and depressive phenotypes in the offspring.

    PubMed

    Short, A K; Fennell, K A; Perreau, V M; Fox, A; O'Bryan, M K; Kim, J H; Bredy, T W; Pang, T Y; Hannan, A J

    2016-01-01

    Recent studies have suggested that physiological and behavioral traits may be transgenerationally inherited through the paternal lineage, possibly via non-genomic signals derived from the sperm. To investigate how paternal stress might influence offspring behavioral phenotypes, a model of hypothalamic-pituitary-adrenal (HPA) axis dysregulation was used. Male breeders were administered water supplemented with corticosterone (CORT) for 4 weeks before mating with untreated female mice. Female, but not male, F1 offspring of CORT-treated fathers displayed altered fear extinction at 2 weeks of age. Only male F1 offspring exhibited altered patterns of ultrasonic vocalization at postnatal day 3 and, as adults, showed decreased time in open on the elevated-plus maze and time in light on the light-dark apparatus, suggesting a hyperanxiety-like behavioral phenotype due to paternal CORT treatment. Interestingly, expression of the paternally imprinted gene Igf2 was increased in the hippocampus of F1 male offspring but downregulated in female offspring. Male and female F2 offspring displayed increased time spent in the open arm of the elevated-plus maze, suggesting lower levels of anxiety compared with control animals. Only male F2 offspring showed increased immobility time on the forced-swim test and increased latency to feed on the novelty-supressed feeding test, suggesting a depression-like phenotype in these animals. Collectively, these data provide evidence that paternal CORT treatment alters anxiety and depression-related behaviors across multiple generations. Analysis of the small RNA profile in sperm from CORT-treated males revealed marked effects on the expression of small noncoding RNAs. Sperm from CORT-treated males contained elevated levels of three microRNAs, miR-98, miR-144 and miR-190b, which are predicted to interact with multiple growth factors, including Igf2 and Bdnf. Sustained elevation of glucocorticoids is therefore involved in the transmission of paternal

  17. Behavioural and Brain Gene Expression Profiling in Pigs during Tail Biting Outbreaks - Evidence of a Tail Biting Resistant Phenotype.

    PubMed

    Brunberg, Emma; Jensen, Per; Isaksson, Anders; Keeling, Linda J

    2013-01-01

    Abnormal tail biting behaviour is a major welfare problem for pigs receiving the behaviour, as well as an indication of decreased welfare in the pigs performing it. However, not all pigs in a pen perform or receive tail biting behaviour and it has recently been shown that these 'neutral' pigs not only differ in their behaviour, but also in their gene expression compared to performers and receivers of tail biting in the same pen. To investigate whether this difference was linked to the cause or a consequence of them not being involved in the outbreak of tail biting, behaviour and brain gene expression was compared with 'control' pigs housed in pens with no tail biting. It was shown that the pigs housed in control pens performed a wider variety of pig-directed abnormal behaviour (belly nosing 0.95±1.59, tail in mouth 0.31±0.60 and 'other' abnormal 1.53±4.26; mean±S.D) compared to the neutral pigs (belly nosing 0.30±0.62, tail in mouth 0.13±0.50 and "other" abnormal 0.42±1.06). With Affymetrix gene expression arrays, 107 transcripts were identified as differently expressed (p<0.05) between these two categories of pigs. Several of these transcripts had already been shown to be differently expressed in the neutral pigs when they were compared to performers and receivers of tail biting in the same pen in an earlier study. Hence, the different expression of these genes cannot be a consequence of the neutral pigs not being involved in tail biting behaviour, but rather linked to the cause contributing to why they were not involved in tail biting interactions. These neutral pigs seem to have a genetic and behavioural profile that somehow contributes to them being resistant to performing or receiving pig-directed abnormal behaviour, such as tail biting, even when housed in an environment that elicits that behaviour in other pigs. PMID:23824700

  18. Behavioural and Brain Gene Expression Profiling in Pigs during Tail Biting Outbreaks – Evidence of a Tail Biting Resistant Phenotype

    PubMed Central

    Brunberg, Emma; Jensen, Per; Isaksson, Anders; Keeling, Linda J.

    2013-01-01

    Abnormal tail biting behaviour is a major welfare problem for pigs receiving the behaviour, as well as an indication of decreased welfare in the pigs performing it. However, not all pigs in a pen perform or receive tail biting behaviour and it has recently been shown that these ‘neutral’ pigs not only differ in their behaviour, but also in their gene expression compared to performers and receivers of tail biting in the same pen. To investigate whether this difference was linked to the cause or a consequence of them not being involved in the outbreak of tail biting, behaviour and brain gene expression was compared with ‘control’ pigs housed in pens with no tail biting. It was shown that the pigs housed in control pens performed a wider variety of pig-directed abnormal behaviour (belly nosing 0.95±1.59, tail in mouth 0.31±0.60 and ‘other‘ abnormal 1.53±4.26; mean±S.D) compared to the neutral pigs (belly nosing 0.30±0.62, tail in mouth 0.13±0.50 and “other“ abnormal 0.42±1.06). With Affymetrix gene expression arrays, 107 transcripts were identified as differently expressed (p<0.05) between these two categories of pigs. Several of these transcripts had already been shown to be differently expressed in the neutral pigs when they were compared to performers and receivers of tail biting in the same pen in an earlier study. Hence, the different expression of these genes cannot be a consequence of the neutral pigs not being involved in tail biting behaviour, but rather linked to the cause contributing to why they were not involved in tail biting interactions. These neutral pigs seem to have a genetic and behavioural profile that somehow contributes to them being resistant to performing or receiving pig-directed abnormal behaviour, such as tail biting, even when housed in an environment that elicits that behaviour in other pigs. PMID:23824700

  19. Differences and Similarities in the Transcriptional Profile of Peripheral Whole Blood in Early and Late-Onset Preeclampsia: Insights into the Molecular Basis of the Phenotype of Preeclampsia

    PubMed Central

    Chaiworapongsa, Tinnakorn; Romero, Roberto; Whitten, Amy; Tarca, Adi L; Bhatti, Gaurav; Draghici, Sorin; Chaemsaithong, Piya; Miranda, Jezid; Kim, Chong Jai; Hassan, Sonia S

    2014-01-01

    Objective Preeclampsia (PE) has been sub-divided into early- and late-onset phenotypes. The pathogenesis of these two phenotypes has not been elucidated. To gain insight into the mechanisms of disease, the transcriptional profiles of whole blood from women with early- and late-onset PE were examined. Methods A cross-sectional study was conducted to include women with: 1) early-onset PE (diagnosed prior to 34 weeks, n=25); 2) late-onset PE (after 34 weeks, n=47); and 3) uncomplicated pregnancy (n=61). Microarray analysis of mRNA expression in peripheral whole blood was undertaken using Affymetrix microarrays. Differential gene expression was evaluated using a moderated t-test (false discovery rate <0.1 and fold change >1.5), adjusting for maternal WBC count and gestational age. Validation by real-time qRT-PCR was performed in a larger sample size [early PE (n=31), late PE (n=72) and controls (n=99)] in all differentially expressed genes. Gene Ontology analysis and pathway analysis were performed. Results 1) 43 and 28 genes were differentially expressed in early- and late-onset PE compared to the control group respectively; 2) qRT-PCR confirmed the microarray results for early and late-onset PE in 77% (33/43) and 71% (20/28) of genes, respectively; 3) 20 genes that are involved in coagulation (SERPINI2), immune regulation (VSIG4, CD24), developmental process (H19) and inflammation (S100A10) were differentially expressed in early-onset PE alone. In contrast, only seven genes that encoded proteins involved in innate immunity (LTF, ELANE) and cell-to-cell recognition in the nervous system (CNTNAP3) were differentially expressed in late-onset PE alone. Thirteen genes that encode proteins involved in host defense (DEFA4, BPI, CTSG, LCN2), tight junctions in blood-brain barrier (EMP1) and liver regeneration (ECT2) were differentially expressed in both early- and late-onset PE. Conclusion Early- and late-onset PE are characterized by a common signature in the

  20. Multidimensional sexual perfectionism.

    PubMed

    Stoeber, Joachim; Harvey, Laura N; Almeida, Isabel; Lyons, Emma

    2013-11-01

    Perfectionism is a multidimensional personality characteristic that can affect all areas of life. This article presents the first systematic investigation of multidimensional perfectionism in the domain of sexuality exploring the unique relationships that different forms of sexual perfectionism show with positive and negative aspects of sexuality. A sample of 272 university students (52 male, 220 female) completed measures of four forms of sexual perfectionism: self-oriented, partner-oriented, partner-prescribed, and socially prescribed. In addition, they completed measures of sexual esteem, sexual self-efficacy, sexual optimism, sex life satisfaction (capturing positive aspects of sexuality) and sexual problem self-blame, sexual anxiety, sexual depression, and negative sexual perfectionism cognitions during sex (capturing negative aspects). Results showed unique patterns of relationships for the four forms of sexual perfectionism, suggesting that partner-prescribed and socially prescribed sexual perfectionism are maladaptive forms of sexual perfectionism associated with negative aspects of sexuality whereas self-oriented and partner-oriented sexual perfectionism emerged as ambivalent forms associated with positive and negative aspects. PMID:23842783

  1. Theta vocabulary II. Multidimensional case

    NASA Astrophysics Data System (ADS)

    Kharchev, S.; Zabrodin, A.

    2016-06-01

    It is shown that the Jacobi and Riemann identities of degree four for the multidimensional theta functions as well as the Weierstrass identities emerge as algebraic consequences of the fundamental multidimensional binary identities connecting the theta functions with Riemann matrices τ and 2 τ.

  2. Multidimensional Perfectionism and the Self

    ERIC Educational Resources Information Center

    Ward, Andrew M.; Ashby, Jeffrey S.

    2008-01-01

    This study examined multidimensional perfectionism and self-development. Two hundred seventy-one undergraduates completed a measure of multidimensional perfectionism and two Kohutian measures designed to measure aspects of self-development including social connectedness, social assurance, goal instability (idealization), and grandiosity. The…

  3. Linear and Nonlinear Thinking: A Multidimensional Model and Measure

    ERIC Educational Resources Information Center

    Groves, Kevin S.; Vance, Charles M.

    2015-01-01

    Building upon previously developed and more general dual-process models, this paper provides empirical support for a multidimensional thinking style construct comprised of linear thinking and multiple dimensions of nonlinear thinking. A self-report assessment instrument (Linear/Nonlinear Thinking Style Profile; LNTSP) is presented and…

  4. Phenotypic profile of dendritic and T cells in the lymph node of Balb/C mice with breast cancer submitted to dendritic cells immunotherapy.

    PubMed

    da Cunha, Alessandra; Antoniazi Michelin, Marcia; Cândido Murta, Eddie Fernando

    2016-09-01

    Breast cancer (BC) is the most common malignant neoplasm and the cause of death by cancer among women worldwide. Its development influenced by various mutations that occur in the tumor cell and by the immune system's status, which has a direct influence on the tumor microenvironment and, consequently, on interactions with non-tumor cells involved in the immunological response. Strategies using dendritic cells (DCs) or antigen-presenting cells (APCs), therapeutic mode, in cancer have been developed for some time. The proper interaction between DCs and T cells upon antigen presentation is of greatest importance for an antitumor immune response activation. Thus, various receptors on the surface of T cells must be able to recognize ligands that are located on the surface of APCs. However, little is known about the real behavior and interaction forms of CDs and T cells after vaccination. Due to the crucial importance of DCs in an effective anti-tumor immune response activation and the search for compliant results in inducing this response by immunotherapies with DCs, the phenotypic profile of DCs and T cells in lymph nodes obtained from female Balb/C mice with breast cancer induced by 4T1 cells and DCs treated with vaccines was investigated. We evaluated through flow cytometry based on the surface and intracellular molecules marking; as well as the presence of cytokines and chemokines, IL-2, IL-4, IL-10, IL-12, IFN-γ, TNF-α and TGF-β in the supernatant of the culture of Balb/C lymph nodes by ELISA. The results show that the vaccination with DCs, in the maturation parameters used in this study, was able to stimulate the secretion of cytokines such as IFN-γ and IL-12 and inhibit the secretion of TGF-β and IL-10 in nodal lymph infiltrates, as well as co-stimulatory activating (CD86) and adhesion molecules in DCs and T cells LFA-1/ICAM-1 and inhibit the secretion of CTLA-4 present in lymph nodes. Facts that led to aTh1 profile polarization, immuno competent in relation

  5. Phenotypic profile of dendritic and T cells in the lymph node of Balb/C mice with breast cancer submitted to dendritic cells immunotherapy.

    PubMed

    da Cunha, Alessandra; Antoniazi Michelin, Marcia; Cândido Murta, Eddie Fernando

    2016-09-01

    Breast cancer (BC) is the most common malignant neoplasm and the cause of death by cancer among women worldwide. Its development influenced by various mutations that occur in the tumor cell and by the immune system's status, which has a direct influence on the tumor microenvironment and, consequently, on interactions with non-tumor cells involved in the immunological response. Strategies using dendritic cells (DCs) or antigen-presenting cells (APCs), therapeutic mode, in cancer have been developed for some time. The proper interaction between DCs and T cells upon antigen presentation is of greatest importance for an antitumor immune response activation. Thus, various receptors on the surface of T cells must be able to recognize ligands that are located on the surface of APCs. However, little is known about the real behavior and interaction forms of CDs and T cells after vaccination. Due to the crucial importance of DCs in an effective anti-tumor immune response activation and the search for compliant results in inducing this response by immunotherapies with DCs, the phenotypic profile of DCs and T cells in lymph nodes obtained from female Balb/C mice with breast cancer induced by 4T1 cells and DCs treated with vaccines was investigated. We evaluated through flow cytometry based on the surface and intracellular molecules marking; as well as the presence of cytokines and chemokines, IL-2, IL-4, IL-10, IL-12, IFN-γ, TNF-α and TGF-β in the supernatant of the culture of Balb/C lymph nodes by ELISA. The results show that the vaccination with DCs, in the maturation parameters used in this study, was able to stimulate the secretion of cytokines such as IFN-γ and IL-12 and inhibit the secretion of TGF-β and IL-10 in nodal lymph infiltrates, as well as co-stimulatory activating (CD86) and adhesion molecules in DCs and T cells LFA-1/ICAM-1 and inhibit the secretion of CTLA-4 present in lymph nodes. Facts that led to aTh1 profile polarization, immuno competent in relation

  6. Multidimensional persistence in biomolecular data

    PubMed Central

    Xia, Kelin; Wei, Guo-Wei

    2015-01-01

    Persistent homology has emerged as a popular technique for the topological simplification of big data, including biomolecular data. Multidimensional persistence bears considerable promise to bridge the gap between geometry and topology. However, its practical and robust construction has been a challenge. We introduce two families of multidimensional persistence, namely pseudo-multidimensional persistence and multiscale multidimensional persistence. The former is generated via the repeated applications of persistent homology filtration to high dimensional data, such as results from molecular dynamics or partial differential equations. The latter is constructed via isotropic and anisotropic scales that create new simiplicial complexes and associated topological spaces. The utility, robustness and efficiency of the proposed topological methods are demonstrated via protein folding, protein flexibility analysis, the topological denoising of cryo-electron microscopy data, and the scale dependence of nano particles. Topological transition between partial folded and unfolded proteins has been observed in multidimensional persistence. The separation between noise topological signatures and molecular topological fingerprints is achieved by the Laplace-Beltrami flow. The multiscale multidimensional persistent homology reveals relative local features in Betti-0 invariants and the relatively global characteristics of Betti-1 and Betti-2 invariants. PMID:26032339

  7. Comparative Phenotypic and Molecular Genetic Profiling of Wild Lactococcus lactis subsp. lactis Strains of the L. lactis subsp. lactis and L. lactis subsp. cremoris Genotypes, Isolated from Starter-Free Cheeses Made of Raw Milk▿

    PubMed Central

    Fernández, Elena; Alegría, Ángel; Delgado, Susana; Martín, M. Cruz; Mayo, Baltasar

    2011-01-01

    Twenty Lactococcus lactis strains with an L. lactis subsp. lactis phenotype isolated from five traditional cheeses made of raw milk with no added starters belonging to the L. lactis subsp. lactis and L. lactis subsp. cremoris genotypes (lactis and cremoris genotypes, respectively; 10 strains each) were subjected to a series of phenotypic and genetic typing methods, with the aims of determining their phylogenetic relationships and suitability as starters. Pulsed-field gel electrophoresis (PFGE) analysis of intact genomes digested with SalI and SmaI proved that all strains were different except for three isolates of the cremoris genotype, which showed identical PFGE profiles. Multilocus sequence typing (MLST) analysis using internal sequences of seven loci (namely, atpA, rpoA, pheS, pepN, bcaT, pepX, and 16S rRNA gene) revealed considerable intergenotype nucleotide polymorphism, although deduced amino acid changes were scarce. Analysis of the MLST data for the present strains and others from other dairy and nondairy sources showed that all of them clustered into the cremoris or lactis genotype group, by using both independent and combined gene sequences. These two groups of strains also showed distinctive carbohydrate fermentation and enzyme activity profiles, with the strains in the cremoris group showing broader profiles. However, the profiles of resistance/susceptibility to 16 antibiotics were very similar, showing no atypical resistance, except for tetracycline resistance in three identical cremoris genotype isolates. The numbers and concentrations of volatile compounds produced in milk by the strains belonging to these two groups were clearly different, with the cremoris genotype strains producing higher concentrations of more branched-chain, derived compounds. Together, the present results support the idea that the lactis and cremoris genotypes of phenotypic Lactococcus lactis subsp. lactis actually represent true subspecies. Some strains of the two subspecies

  8. Profiling functions of ectomycorrhizal diversity and root structuring in seedlings of Norway spruce (Picea abies) with fast- and slow-growing phenotypes.

    PubMed

    Velmala, Sannakajsa M; Rajala, Tiina; Heinonsalo, Jussi; Taylor, Andy F S; Pennanen, Taina

    2014-01-01

    We studied the role of taxonomical and functional ectomycorrhizal (ECM) fungal diversity in root formation and nutrient uptake by Norway spruce (Picea abies) seedlings with fast- and slow-growing phenotypes. Seedlings were grown with an increasing ECM fungal diversity gradient from one to four species and sampled before aboveground growth differences between the two phenotypes were apparent. ECM fungal colonization patterns were determined and functional diversity was assayed via measurements of potential enzyme activities of eight exoenzymes probably involved in nutrient mobilization. Phenotypes did not vary in their receptiveness to different ECM fungal species. However, seedlings of slow-growing phenotypes had higher fine-root density and thus more condensed root systems than fast-growing seedlings, but the potential enzyme activities of ectomycorrhizas did not differ qualitatively or quantitatively. ECM species richness increased host nutrient acquisition potential by diversifying the exoenzyme palette. Needle nitrogen content correlated positively with high chitinase activity of ectomycorrhizas. Rather than fast- and slow-growing phenotypes exhibiting differing receptiveness to ECM fungi, our results suggest that distinctions in fine-root structuring and in the belowground growth strategy already apparent at early stages of seedling development may explain later growth differences between fast- and slow-growing families.

  9. Multidimensionality in host manipulation mimicked by serotonin injection.

    PubMed

    Perrot-Minnot, Marie-Jeanne; Sanchez-Thirion, Kevin; Cézilly, Frank

    2014-12-01

    Manipulative parasites often alter the phenotype of their hosts along multiple dimensions. 'Multidimensionality' in host manipulation could consist in the simultaneous alteration of several physiological pathways independently of one another, or proceed from the disruption of some key physiological parameter, followed by a cascade of effects. We compared multidimensionality in 'host manipulation' between two closely related amphipods, Gammarus fossarum and Gammarus pulex, naturally and experimentally infected with Pomphorhynchus laevis (Acanthocephala), respectively. To that end, we calculated in each host-parasite association the effect size of the difference between infected and uninfected individuals for six different traits (activity, phototaxis, geotaxis, attraction to conspecifics, refuge use and metabolic rate). The effects sizes were highly correlated between host-parasite associations, providing evidence for a relatively constant 'infection syndrome'. Using the same methodology, we compared the extent of phenotypic alterations induced by an experimental injection of serotonin (5-HT) in uninfected G. pulex to that induced by experimental or natural infection with P. laevis. We observed a significant correlation between effect sizes across the six traits, indicating that injection with 5-HT can faithfully mimic the 'infection syndrome'. This is, to our knowledge, the first experimental evidence that multidimensionality in host manipulation can proceed, at least partly, from the disruption of some major physiological mechanism.

  10. Multidimensionality in host manipulation mimicked by serotonin injection.

    PubMed

    Perrot-Minnot, Marie-Jeanne; Sanchez-Thirion, Kevin; Cézilly, Frank

    2014-12-01

    Manipulative parasites often alter the phenotype of their hosts along multiple dimensions. 'Multidimensionality' in host manipulation could consist in the simultaneous alteration of several physiological pathways independently of one another, or proceed from the disruption of some key physiological parameter, followed by a cascade of effects. We compared multidimensionality in 'host manipulation' between two closely related amphipods, Gammarus fossarum and Gammarus pulex, naturally and experimentally infected with Pomphorhynchus laevis (Acanthocephala), respectively. To that end, we calculated in each host-parasite association the effect size of the difference between infected and uninfected individuals for six different traits (activity, phototaxis, geotaxis, attraction to conspecifics, refuge use and metabolic rate). The effects sizes were highly correlated between host-parasite associations, providing evidence for a relatively constant 'infection syndrome'. Using the same methodology, we compared the extent of phenotypic alterations induced by an experimental injection of serotonin (5-HT) in uninfected G. pulex to that induced by experimental or natural infection with P. laevis. We observed a significant correlation between effect sizes across the six traits, indicating that injection with 5-HT can faithfully mimic the 'infection syndrome'. This is, to our knowledge, the first experimental evidence that multidimensionality in host manipulation can proceed, at least partly, from the disruption of some major physiological mechanism. PMID:25339729

  11. A Multidimensional Partial Credit Model with Associated Item and Test Statistics: An Application to Mixed-Format Tests

    ERIC Educational Resources Information Center

    Yao, Lihua; Schwarz, Richard D.

    2006-01-01

    Multidimensional item response theory (IRT) models have been proposed for better understanding the dimensional structure of data or to define diagnostic profiles of student learning. A compensatory multidimensional two-parameter partial credit model (M-2PPC) for constructed-response items is presented that is a generalization of those proposed to…

  12. Multidimensional persistence in biomolecular data.

    PubMed

    Xia, Kelin; Wei, Guo-Wei

    2015-07-30

    Persistent homology has emerged as a popular technique for the topological simplification of big data, including biomolecular data. Multidimensional persistence bears considerable promise to bridge the gap between geometry and topology. However, its practical and robust construction has been a challenge. We introduce two families of multidimensional persistence, namely pseudomultidimensional persistence and multiscale multidimensional persistence. The former is generated via the repeated applications of persistent homology filtration to high-dimensional data, such as results from molecular dynamics or partial differential equations. The latter is constructed via isotropic and anisotropic scales that create new simiplicial complexes and associated topological spaces. The utility, robustness, and efficiency of the proposed topological methods are demonstrated via protein folding, protein flexibility analysis, the topological denoising of cryoelectron microscopy data, and the scale dependence of nanoparticles. Topological transition between partial folded and unfolded proteins has been observed in multidimensional persistence. The separation between noise topological signatures and molecular topological fingerprints is achieved by the Laplace-Beltrami flow. The multiscale multidimensional persistent homology reveals relative local features in Betti-0 invariants and the relatively global characteristics of Betti-1 and Betti-2 invariants.

  13. Noncommutative accelerated multidimensional universe dominated by quintessence

    NASA Astrophysics Data System (ADS)

    El-Nabulsi, Ahmad Rami

    2010-04-01

    Noncommutative Geometry recently attracted growing interest of cosmologists, mainly after the greatest success of unifying the forces of nature into a single gravitational spectral action in a purely algebraic way, rather than as being an entirely new formalism. In the present work, we discuss a multidimensional Friedmann-Robertson-Walker flat universe in which the perfect fluid has a Gaussian profile in time and depends on a fundamental minimal length sqrt{θ} like ρ= ρ(0)exp (- t 2/4 θ) for some positive constant ρ(0). This special form is motivated by a more recent noncommutative inflationary cosmological model, which was found to be able to drive the universe through a bounce without the need of any scalar field. Furthermore, we conjecture that the generalized equation of state has the special form p= ω a m ρ- ρ,( ω, m)∈ℝ where a( t) is the scale factor. It was found that the expansion of the multidimensional universe accelerates in time and is dominated for very large time by quintessence. Many additional consequences are revealed and discussed in some detail.

  14. Multidimensional Learner Model In Intelligent Learning System

    NASA Astrophysics Data System (ADS)

    Deliyska, B.; Rozeva, A.

    2009-11-01

    The learner model in an intelligent learning system (ILS) has to ensure the personalization (individualization) and the adaptability of e-learning in an online learner-centered environment. ILS is a distributed e-learning system whose modules can be independent and located in different nodes (servers) on the Web. This kind of e-learning is achieved through the resources of the Semantic Web and is designed and developed around a course, group of courses or specialty. An essential part of ILS is learner model database which contains structured data about learner profile and temporal status in the learning process of one or more courses. In the paper a learner model position in ILS is considered and a relational database is designed from learner's domain ontology. Multidimensional modeling agent for the source database is designed and resultant learner data cube is presented. Agent's modules are proposed with corresponding algorithms and procedures. Multidimensional (OLAP) analysis guidelines on the resultant learner module for designing dynamic learning strategy have been highlighted.

  15. Modeling, calculating, and analyzing multidimensional vibrational spectroscopies.

    PubMed

    Tanimura, Yoshitaka; Ishizaki, Akihito

    2009-09-15

    Spectral line shapes in a condensed phase contain information from various dynamic processes that modulate the transition energy, such as microscopic dynamics, inter- and intramolecular couplings, and solvent dynamics. Because nonlinear response functions are sensitive to the complex dynamics of chemical processes, multidimensional vibrational spectroscopies can separate these processes. In multidimensional vibrational spectroscopy, the nonlinear response functions of a molecular dipole or polarizability are measured using ultrashort pulses to monitor inter- and intramolecular vibrational motions. Because a complex profile of such signals depends on the many dynamic and structural aspects of a molecular system, researchers would like to have a theoretical understanding of these phenomena. In this Account, we explore and describe the roles of different physical phenomena that arise from the peculiarities of the system-bath coupling in multidimensional spectra. We also present simple analytical expressions for a weakly coupled multimode Brownian system, which we use to analyze the results obtained by the experiments and simulations. To calculate the nonlinear optical response, researchers commonly use a particular form of a system Hamiltonian fit to the experimental results. The optical responses of molecular vibrational motions have been studied in either an oscillator model or a vibration energy state model. In principle, both models should give the same results as long as the energy states are chosen to be the eigenstates of the oscillator model. The energy state model can provide a simple description of nonlinear optical processes because the diagrammatic Liouville space theory that developed in the electronically resonant spectroscopies can easily handle three or four energy states involved in high-frequency vibrations. However, the energy state model breaks down if we include the thermal excitation and relaxation processes in the dynamics to put the system in a

  16. Generalized multidimensional dynamic allocation method.

    PubMed

    Lebowitsch, Jonathan; Ge, Yan; Young, Benjamin; Hu, Feifang

    2012-12-10

    Dynamic allocation has received considerable attention since it was first proposed in the 1970s as an alternative means of allocating treatments in clinical trials which helps to secure the balance of prognostic factors across treatment groups. The purpose of this paper is to present a generalized multidimensional dynamic allocation method that simultaneously balances treatment assignments at three key levels: within the overall study, within each level of each prognostic factor, and within each stratum, that is, combination of levels of different factors Further it offers capabilities for unbalanced and adaptive designs for trials. The treatment balancing performance of the proposed method is investigated through simulations which compare multidimensional dynamic allocation with traditional stratified block randomization and the Pocock-Simon method. On the basis of these results, we conclude that this generalized multidimensional dynamic allocation method is an improvement over conventional dynamic allocation methods and is flexible enough to be applied for most trial settings including Phases I, II and III trials.

  17. A log-linear multidimensional Rasch model for capture-recapture.

    PubMed

    Pelle, E; Hessen, D J; van der Heijden, P G M

    2016-02-20

    In this paper, a log-linear multidimensional Rasch model is proposed for capture-recapture analysis of registration data. In the model, heterogeneity of capture probabilities is taken into account, and registrations are viewed as dichotomously scored indicators of one or more latent variables that can account for correlations among registrations. It is shown how the probability of a generic capture profile is expressed under the log-linear multidimensional Rasch model and how the parameters of the traditional log-linear model are derived from those of the log-linear multidimensional Rasch model. Finally, an application of the model to neural tube defects data is presented.

  18. On the Need for Multidimensional Stirling Simulations

    NASA Technical Reports Server (NTRS)

    Dyson, Rodger W.; Wilson, Scott D.; Tew, Roy C.; Demko, Rikako

    2005-01-01

    Given the cost and complication of simulating Stirling convertors, do we really need multidimensional modeling when one-dimensional capabilities exist? This paper provides a comprehensive description of when and why multidimensional simulation is needed.

  19. A Multidimensional Software Engineering Course

    ERIC Educational Resources Information Center

    Barzilay, O.; Hazzan, O.; Yehudai, A.

    2009-01-01

    Software engineering (SE) is a multidimensional field that involves activities in various areas and disciplines, such as computer science, project management, and system engineering. Though modern SE curricula include designated courses that address these various subjects, an advanced summary course that synthesizes them is still missing. Such a…

  20. The Variable Responding Scale for Detection of Random Responding on the Multidimensional Pain Inventory.

    ERIC Educational Resources Information Center

    Bruehl, Stephen; Lofland, Kenneth R.; Carlson, Charles R.; Sherman, Jeffrey J.

    1998-01-01

    Developed a scale for detecting random responses on the Multidimensional Pain Inventory using 95 undergraduates, 34 chronic pain patients, and 115 health-care professionals. A variable response scale was developed that discriminated accurately between valid and random profiles in two cross-validation samples, predicting random profiles with 90%…

  1. A combined analysis of the Frost Multidimensional Perfectionism Scale (FMPS), Child and Adolescent Perfectionism Scale (CAPS), and Almost Perfect Scale-Revised (APS-R): Different perfectionist profiles in adolescent high school students.

    PubMed

    Sironic, Amanda; Reeve, Robert A

    2015-12-01

    To investigate differences and similarities in the dimensional constructs of the Frost Multidimensional Perfectionism Scale (FMPS; Frost, Marten, Lahart, & Rosenblate, 1990), Child and Adolescent Perfectionism Scale (CAPS; Flett, Hewitt, Boucher, Davidson, & Munro, 2000), and Almost Perfect Scale-Revised (APS-R; Slaney, Rice, Mobley, Trippi, & Ashby, 2001), 938 high school students completed the 3 perfectionism questionnaires, as well as the Depression Anxiety Stress Scales (DASS; Lovibond & Lovibond, 1995). Preliminary analyses revealed commonly observed factor structures for each perfectionism questionnaire. Exploratory factor analysis of item responses from the questionnaires (combined) yielded a 4-factor solution (factors were labeled High Personal Standards, Concerns, Doubts and Discrepancy, Externally Motivated Perfectionism, and Organization and Order). A latent class analysis of individuals' mean ratings on each of the 4 factors yielded a 6-class solution. Three of the 6 classes represented perfectionist subgroups (labeled adaptive perfectionist, externally motivated maladaptive perfectionist, and mixed maladaptive perfectionist), and 3 represented nonperfectionist subgroups (labeled nonperfectionist A, nonperfectionist B, and order and organization nonperfectionist). Each of the 6 subgroups was meaningfully associated with the DASS. Findings showed that 3 out of 10 students were classified as maladaptive perfectionists, and maladaptive perfectionists were more prevalent than adaptive perfectionists. In sum, it is evident that combined ratings from the FMPS, CAPS, and APS-R offer a meaningful characterization of perfectionism. PMID:25984636

  2. A combined analysis of the Frost Multidimensional Perfectionism Scale (FMPS), Child and Adolescent Perfectionism Scale (CAPS), and Almost Perfect Scale-Revised (APS-R): Different perfectionist profiles in adolescent high school students.

    PubMed

    Sironic, Amanda; Reeve, Robert A

    2015-12-01

    To investigate differences and similarities in the dimensional constructs of the Frost Multidimensional Perfectionism Scale (FMPS; Frost, Marten, Lahart, & Rosenblate, 1990), Child and Adolescent Perfectionism Scale (CAPS; Flett, Hewitt, Boucher, Davidson, & Munro, 2000), and Almost Perfect Scale-Revised (APS-R; Slaney, Rice, Mobley, Trippi, & Ashby, 2001), 938 high school students completed the 3 perfectionism questionnaires, as well as the Depression Anxiety Stress Scales (DASS; Lovibond & Lovibond, 1995). Preliminary analyses revealed commonly observed factor structures for each perfectionism questionnaire. Exploratory factor analysis of item responses from the questionnaires (combined) yielded a 4-factor solution (factors were labeled High Personal Standards, Concerns, Doubts and Discrepancy, Externally Motivated Perfectionism, and Organization and Order). A latent class analysis of individuals' mean ratings on each of the 4 factors yielded a 6-class solution. Three of the 6 classes represented perfectionist subgroups (labeled adaptive perfectionist, externally motivated maladaptive perfectionist, and mixed maladaptive perfectionist), and 3 represented nonperfectionist subgroups (labeled nonperfectionist A, nonperfectionist B, and order and organization nonperfectionist). Each of the 6 subgroups was meaningfully associated with the DASS. Findings showed that 3 out of 10 students were classified as maladaptive perfectionists, and maladaptive perfectionists were more prevalent than adaptive perfectionists. In sum, it is evident that combined ratings from the FMPS, CAPS, and APS-R offer a meaningful characterization of perfectionism.

  3. Deterministic multidimensional nonuniform gap sampling.

    PubMed

    Worley, Bradley; Powers, Robert

    2015-12-01

    Born from empirical observations in nonuniformly sampled multidimensional NMR data relating to gaps between sampled points, the Poisson-gap sampling method has enjoyed widespread use in biomolecular NMR. While the majority of nonuniform sampling schemes are fully randomly drawn from probability densities that vary over a Nyquist grid, the Poisson-gap scheme employs constrained random deviates to minimize the gaps between sampled grid points. We describe a deterministic gap sampling method, based on the average behavior of Poisson-gap sampling, which performs comparably to its random counterpart with the additional benefit of completely deterministic behavior. We also introduce a general algorithm for multidimensional nonuniform sampling based on a gap equation, and apply it to yield a deterministic sampling scheme that combines burst-mode sampling features with those of Poisson-gap schemes. Finally, we derive a relationship between stochastic gap equations and the expectation value of their sampling probability densities.

  4. Deterministic multidimensional nonuniform gap sampling

    NASA Astrophysics Data System (ADS)

    Worley, Bradley; Powers, Robert

    2015-12-01

    Born from empirical observations in nonuniformly sampled multidimensional NMR data relating to gaps between sampled points, the Poisson-gap sampling method has enjoyed widespread use in biomolecular NMR. While the majority of nonuniform sampling schemes are fully randomly drawn from probability densities that vary over a Nyquist grid, the Poisson-gap scheme employs constrained random deviates to minimize the gaps between sampled grid points. We describe a deterministic gap sampling method, based on the average behavior of Poisson-gap sampling, which performs comparably to its random counterpart with the additional benefit of completely deterministic behavior. We also introduce a general algorithm for multidimensional nonuniform sampling based on a gap equation, and apply it to yield a deterministic sampling scheme that combines burst-mode sampling features with those of Poisson-gap schemes. Finally, we derive a relationship between stochastic gap equations and the expectation value of their sampling probability densities.

  5. Multidimensional theory of protein folding

    NASA Astrophysics Data System (ADS)

    Itoh, Kazuhito; Sasai, Masaki

    2009-04-01

    Theory of multidimensional representation of free energy surface of protein folding is developed by adopting structural order parameters of multiple regions in protein as multiple coordinates. Various scenarios of folding are classified in terms of cooperativity within individual regions and interactions among multiple regions and thus obtained classification is used to analyze the folding process of several example proteins. Ribosomal protein S6, src-SH3 domain, CheY, barnase, and BBL domain are analyzed with the two-dimensional representation by using a structure-based Hamiltonian model. The extension to the higher dimensional representation leads to the finer description of the folding process. Barnase, NtrC, and an ankyrin repeat protein are examined with the three-dimensional representation. The multidimensional representation allows us to directly address questions on folding pathways, intermediates, and transition states.

  6. Multidimensional bioseparation with modular microfluidics

    DOEpatents

    Chirica, Gabriela S.; Renzi, Ronald F.

    2013-08-27

    A multidimensional chemical separation and analysis system is described including a prototyping platform and modular microfluidic components capable of rapid and convenient assembly, alteration and disassembly of numerous candidate separation systems. Partial or total computer control of the separation system is possible. Single or multiple alternative processing trains can be tested, optimized and/or run in parallel. Examples related to the separation and analysis of human bodily fluids are given.

  7. Cuba: Multidimensional numerical integration library

    NASA Astrophysics Data System (ADS)

    Hahn, Thomas

    2016-08-01

    The Cuba library offers four independent routines for multidimensional numerical integration: Vegas, Suave, Divonne, and Cuhre. The four algorithms work by very different methods, and can integrate vector integrands and have very similar Fortran, C/C++, and Mathematica interfaces. Their invocation is very similar, making it easy to cross-check by substituting one method by another. For further safeguarding, the output is supplemented by a chi-square probability which quantifies the reliability of the error estimate.

  8. Multidimensionality in host manipulation mimicked by serotonin injection

    PubMed Central

    Perrot-Minnot, Marie-Jeanne; Sanchez-Thirion, Kevin; Cézilly, Frank

    2014-01-01

    Manipulative parasites often alter the phenotype of their hosts along multiple dimensions. ‘Multidimensionality’ in host manipulation could consist in the simultaneous alteration of several physiological pathways independently of one another, or proceed from the disruption of some key physiological parameter, followed by a cascade of effects. We compared multidimensionality in ‘host manipulation’ between two closely related amphipods, Gammarus fossarum and Gammarus pulex, naturally and experimentally infected with Pomphorhynchus laevis (Acanthocephala), respectively. To that end, we calculated in each host–parasite association the effect size of the difference between infected and uninfected individuals for six different traits (activity, phototaxis, geotaxis, attraction to conspecifics, refuge use and metabolic rate). The effects sizes were highly correlated between host–parasite associations, providing evidence for a relatively constant ‘infection syndrome’. Using the same methodology, we compared the extent of phenotypic alterations induced by an experimental injection of serotonin (5-HT) in uninfected G. pulex to that induced by experimental or natural infection with P. laevis. We observed a significant correlation between effect sizes across the six traits, indicating that injection with 5-HT can faithfully mimic the ‘infection syndrome’. This is, to our knowledge, the first experimental evidence that multidimensionality in host manipulation can proceed, at least partly, from the disruption of some major physiological mechanism. PMID:25339729

  9. Molecular phenotype of zebrafish ovarian follicle by serial analysis of gene expression and proteomic profiling, and comparison with the transcriptomes of other animals

    PubMed Central

    Knoll-Gellida, Anja; André, Michèle; Gattegno, Tamar; Forgue, Jean; Admon, Arie; Babin, Patrick J

    2006-01-01

    Background The ability of an oocyte to develop into a viable embryo depends on the accumulation of specific maternal information and molecules, such as RNAs and proteins. A serial analysis of gene expression (SAGE) was carried out in parallel with proteomic analysis on fully-grown ovarian follicles from zebrafish (Danio rerio). The data obtained were compared with ovary/follicle/egg molecular phenotypes of other animals, published or available in public sequence databases. Results Sequencing of 27,486 SAGE tags identified 11,399 different ones, including 3,329 tags with an occurrence superior to one. Fifty-eight genes were expressed at over 0.15% of the total population and represented 17.34% of the mRNA population identified. The three most expressed transcripts were a rhamnose-binding lectin, beta-actin 2, and a transcribed locus similar to the H2B histone family. Comparison with the large-scale expressed sequence tags sequencing approach revealed highly expressed transcripts that were not previously known to be expressed at high levels in fish ovaries, like the short-sized polarized metallothionein 2 transcript. A higher sensitivity for the detection of transcripts with a characterized maternal genetic contribution was also demonstrated compared to large-scale sequencing of cDNA libraries. Ferritin heavy polypeptide 1, heat shock protein 90-beta, lactate dehydrogenase B4, beta-actin isoforms, tubulin beta 2, ATP synthase subunit 9, together with 40 S ribosomal protein S27a, were common highly-expressed transcripts of vertebrate ovary/unfertilized egg. Comparison of transcriptome and proteome data revealed that transcript levels provide little predictive value with respect to the extent of protein abundance. All the proteins identified by proteomic analysis of fully-grown zebrafish follicles had at least one transcript counterpart, with two exceptions: eosinophil chemotactic cytokine and nothepsin. Conclusion This study provides a complete sequence data set of

  10. Outstanding Phenotypic Differences in the Profile of Amyloid-β between Tg2576 and APPswe/PS1dE9 Transgenic Mouse Models of Alzheimer's Disease.

    PubMed

    Allué, José Antonio; Sarasa, Leticia; Izco, María; Pérez-Grijalba, Virginia; Fandos, Noelia; Pascual-Lucas, María; Ogueta, Samuel; Pesini, Pedro; Sarasa, Manuel

    2016-05-30

    APPswe/PS1dE9 and Tg2576 are very common transgenic mouse models of Alzheimer's disease (AD), used in many laboratories as tools to research the mechanistic process leading to the disease. In order to augment our knowledge about the amyloid-β (Aβ) isoforms present in both transgenic mouse models, we have developed two chromatographic methods, one acidic and the other basic, for the characterization of the Aβ species produced in the brains of the two transgenic mouse models. After immunoprecipitation and micro-liquid chromatography-electrospray ionization mass spectrometry/mass spectrometry, 10 species of Aβ, surprisingly all of human origin, were detected in the brain of Tg2576 mouse, whereas 39 species, of both murine and human origin, were detected in the brain of the APP/PS1 mouse. To the best of our knowledge, this is the first study showing the identification of such a high number of Aβ species in the brain of the APP/PS1 transgenic mouse, whereas, in contrast, a much lower number of Aβ species were identified in the Tg2576 mouse. Therefore, this study brings to light a relevant phenotypic difference between these two popular mice models of AD. PMID:27258422

  11. Measures for a multidimensional multiverse

    NASA Astrophysics Data System (ADS)

    Chung, Hyeyoun

    2015-04-01

    We explore the phenomenological implications of generalizing the causal patch and fat geodesic measures to a multidimensional multiverse, where the vacua can have differing numbers of large dimensions. We consider a simple model in which the vacua are nucleated from a D -dimensional parent spacetime through dynamical compactification of the extra dimensions, and compute the geometric contribution to the probability distribution of observations within the multiverse for each measure. We then study how the shape of this probability distribution depends on the time scales for the existence of observers, for vacuum domination, and for curvature domination (tobs,tΛ , and tc, respectively.) In this work we restrict ourselves to bubbles with positive cosmological constant, Λ . We find that in the case of the causal patch cutoff, when the bubble universes have p +1 large spatial dimensions with p ≥2 , the shape of the probability distribution is such that we obtain the coincidence of time scales tobs˜tΛ˜tc . Moreover, the size of the cosmological constant is related to the size of the landscape. However, the exact shape of the probability distribution is different in the case p =2 , compared to p ≥3 . In the case of the fat geodesic measure, the result is even more robust: the shape of the probability distribution is the same for all p ≥2 , and we once again obtain the coincidence tobs˜tΛ˜tc . These results require only very mild conditions on the prior probability of the distribution of vacua in the landscape. Our work shows that the observed double coincidence of time scales is a robust prediction even when the multiverse is generalized to be multidimensional; that this coincidence is not a consequence of our particular Universe being (3 +1 )-dimensional; and that this observable cannot be used to preferentially select one measure over another in a multidimensional multiverse.

  12. Phenotypic, Functional, and Gene Expression Profiling of Peripheral CD45RA+ and CD45RO+ CD4+CD25+CD127low Treg Cells in Patients With Chronic Rheumatoid Arthritis

    PubMed Central

    Walter, Gina J.; Fleskens, Veerle; Frederiksen, Klaus S.; Rajasekhar, Megha; Menon, Bina; Gerwien, Jens G.; Evans, Hayley G.

    2015-01-01

    Objective Conflicting evidence exists regarding the suppressive capacity of Treg cells in the peripheral blood (PB) of patients with rheumatoid arthritis (RA). The aim of this study was to determine whether Treg cells are intrinsically defective in RA. Methods Using a range of assays on PB samples from patients with chronic RA and healthy controls, CD3+CD4+CD25+CD127low Treg cells from the CD45RO+ or CD45RA+ T cell compartments were analyzed for phenotype, cytokine expression (ex vivo and after in vitro stimulation), suppression of Teff cell proliferation and cytokine production, suppression of monocyte‐derived cytokine/chemokine production, and gene expression profiles. Results No differences between RA patients and healthy controls were observed with regard to the frequency of Treg cells, ex vivo phenotype (CD4, CD25, CD127, CD39, or CD161), or proinflammatory cytokine profile (interleukin‐17 [IL‐17], interferon‐γ [IFNγ], or tumor necrosis factor [TNF]). FoxP3 expression was slightly increased in Treg cells from RA patients. The ability of Treg cells to suppress the proliferation of T cells or the production of cytokines (IFNγ or TNF) upon coculture with autologous CD45RO+ Teff cells and monocytes was not significantly different between RA patients and healthy controls. In PB samples from some RA patients, CD45RO+ Treg cells showed an impaired ability to suppress the production of certain cytokines/chemokines (IL‐1β, IL‐1 receptor antagonist, IL‐7, CCL3, or CCL4) by autologous lipopolysaccharide‐activated monocytes. However, this was not observed in all patients, and other cytokines/chemokines (TNF, IL‐6, IL‐8, IL‐12, IL‐15, or CCL5) were generally suppressed. Finally, gene expression profiling of CD45RA+ or CD45RO+ Treg cells from the PB revealed no statistically significant differences between RA patients and healthy controls. Conclusion Our findings indicate that there is no global defect in either CD45RO+ or CD45RA+ Treg cells in

  13. On Compensation in Multidimensional Response Modeling

    ERIC Educational Resources Information Center

    van der Linden, Wim J.

    2012-01-01

    The issue of compensation in multidimensional response modeling is addressed. We show that multidimensional response models are compensatory in their ability parameters if and only if they are monotone. In addition, a minimal set of assumptions is presented under which the MLEs of the ability parameters are also compensatory. In a recent series of…

  14. Multidimensional Scaling of Classroom Interaction Data.

    ERIC Educational Resources Information Center

    Rumery, Robert E.; Hartnett, Barbara M.

    The use of Kruskal's nonmetric multidimensional scaling model for analysis of classroom interaction data is discussed. Four distance models are proposed which lead to multidimensional representation of single sequences, sets of sequences, and behavior categories using symmetric and conditional proximity options of the model. Results of application…

  15. Multidimensional quantum tunneling in the Schwinger effect

    NASA Astrophysics Data System (ADS)

    Dumlu, Cesim K.

    2016-03-01

    We study the Schwinger effect, in which the external field having a spatiotemporal profile creates electron-positron pairs via multidimensional quantum tunneling. Our treatment is based on the trace formula for the QED effective action, whose imaginary part is represented by a sum over complex worldline solutions. The worldlines are multiperiodic, and the periods of motion collectively depend on the strength of spatial and temporal inhomogeneity. We argue that the classical action that leads to the correct tunneling amplitude must take into account both the full period, T ˜ and the first fundamental period, T1. In view of this argument we investigate pair production in an exponentially damped sinusoidal field and find that the initial momenta for multiperiodic trajectories lie on parabolic curves, such that on each curve the ratio T ˜/T1 stays uniform. Evaluation of the tunneling amplitude using these trajectories shows that vacuum decay rate is reduced by an order of magnitude, with respect to the purely time-dependent case, due to the presence of magnetic field.

  16. Differentiation of Shewanella putrefaciens and Shewanella alga on the basis of whole-cell protein profiles, ribotyping, phenotypic characterization, and 16S rRNA gene sequence analysis.

    PubMed Central

    Vogel, B F; Jørgensen, K; Christensen, H; Olsen, J E; Gram, L

    1997-01-01

    Seventy-six presumed Shewanella putrefaciens isolates from fish, oil drillings, and clinical specimens, the type strain of Shewanella putrefaciens (ATCC 8071), the type strain of Shewanella alga (IAM 14159), and the type strain of Shewanella hanedai (ATCC 33224) were compared by several typing methods. Numerical analysis of sodium dodecyl sulfate-polyacrylamide gel electrophoresis of whole-cell protein and ribotyping patterns showed that the strains were separated into two distinct clusters with 56% +/- 10% and 40% +/- 14% similarity for whole-cell protein profiling and ribotyping, respectively. One cluster consisted of 26 isolates with 52 to 55 mol% G + C and included 15 human isolates, mostly clinical specimens, 8 isolates from marine waters, and the type strain of S. alga. This homogeneous cluster of mesophilic, halotolerant strains was by all analyses identical to the recently defined species S. alga (U. Simidu et al., Int. J. Syst. Bacteriol, 40:331-336, 1990). Fifty-two typically psychrotolerant strains formed the other, more heterogeneous major cluster, with 43 to 47 mol% G + C. The type strain of S. putrefaciens was included in this group. The two groups were confirmed by 16S rRNA gene sequence analysis. It is concluded that the isolates must be considered two different species, S. alga and S. putrefaciens, and that most mesophilic isolates formerly identified as S. putrefaciens belong to S. alga. The ecological role and potential pathogenicity of S. alga can be evaluated only if the organism is correctly identified. PMID:9172338

  17. Physical Self-Concept in Adolescence: Generalizability of a Multidimensional, Hierarchical Model Across Gender and Grade

    ERIC Educational Resources Information Center

    Hagger, Martin S.; Biddle, Stuart J. H.; John Wang, C. K.

    2005-01-01

    This study tests the generalizability of the factor pattern, structural parameters, and latent mean structure of a multidimensional, hierarchical model of physical self-concept in adolescents across gender and grade. A children's version of the Physical Self-Perception Profile (C-PSPP) was administered to seventh-, eighth- and ninth-grade high…

  18. Physical Self-Perceptions in Adolescence: Generalizability of a Hierarchical Multidimensional Model across Three Cultures.

    ERIC Educational Resources Information Center

    Hagger, Martin S.; Biddle, Stuart J. H.; Chow, Edward W.; Stambulova, Natalia; Kavussanu, Maria

    2003-01-01

    Examined the generalizability of the form, structural parameters, and latent means of a hierarchical multidimensional model of physical self-perceptions in adolescents from three cultures. A children's version of the physical self-perception profile was administered to British, Hong Kong, and Russian students. Tests of cross-cultural…

  19. Development of a Multidimensional Thinking Styles Scale Based on Theory of Mental Self-Government for Sixth Grade Students

    ERIC Educational Resources Information Center

    Chaiyapornpattana, Niorn; Wongwanich, Suwimon

    2013-01-01

    This study designed 1) to develop a multidimensional thinking styles scale based on theory of mental self-government for sixth grade student 2) to investigate quality of the developed scale 3) to study profile of styles of sixth grade student and a relation of profile of styles of student in each dimension and background of gender and grade with…

  20. Multidimensional Adaptation in MAS Organizations.

    PubMed

    Alberola, Juan M; Julian, Vicente; Garcia-Fornes, Ana

    2013-04-01

    Organization adaptation requires determining the consequences of applying changes not only in terms of the benefits provided but also measuring the adaptation costs as well as the impact that these changes have on all of the components of the organization. In this paper, we provide an approach for adaptation in multiagent systems based on a multidimensional transition deliberation mechanism (MTDM). This approach considers transitions in multiple dimensions and is aimed at obtaining the adaptation with the highest potential for improvement in utility based on the costs of adaptation. The approach provides an accurate measurement of the impact of the adaptation since it determines the organization that is to be transitioned to as well as the changes required to carry out this transition. We show an example of adaptation in a service provider network environment in order to demonstrate that the measurement of the adaptation consequences taken by the MTDM improves the organization performance more than the other approaches.

  1. Finding the target after screening the phenotype.

    PubMed

    Hart, Charles P

    2005-04-01

    Although most screening for new drug leads is being directed at known or emerging molecular targets, there has been a renaissance in screening based on changes in cell or organismal phenotypes. Phenotype-based screening is accompanied by the challenge of identifying the molecular target or targets bound by the drug leads and responsible for their pharmacological activity. A variety of technologies and approaches are being explored for target identification after phenotypic screening. Direct approaches employing affinity chromatography, expression cloning and protein microarrays analyze the compound bound to its target. Indirect approaches are based on comparison of the genome-wide activity profile of the compound with databases of the activity profiles of other compounds with known targets or activity profiles following specific genetic changes. This review will use case studies of target identification efforts and highlight the advantages and disadvantages of the various approaches to target identification after phenotypic screening. PMID:15809197

  2. RNA: State Memory and Mediator of Cellular Phenotype

    PubMed Central

    Kim, Junhyong; Eberwine, James

    2010-01-01

    It has become increasingly clear that the genome is dynamic and exquisitely sensitive, changing expression patterns in response to age, environmental stimuli and pharmacological and physiological manipulations. Similarly, cellular phenotype, traditionally viewed as a stable end-state, should be viewed as versatile and changeable. The phenotype of a cell is better defined as a “homeostatic phenotype” implying plasticity resulting from a dynamically-changing yet characteristic pattern of gene/protein expression. A stable change in phenotype is the result of the movement of a cell between different multi-dimensional identity spaces. Here, we describe a key driver of this transition and the stabilizer of phenotype: the relative abundances of the cellular RNAs. We argue that the quantitative state of RNA can be likened to a state memory, that when transferred between cells, alters the phenotype in a predictable manner. PMID:20382532

  3. Analytical chemistry, multidimensional spectral signatures, and the future of coherent multidimensional spectroscopy

    NASA Astrophysics Data System (ADS)

    Wright, John C.

    2016-10-01

    Spectroscopy is a dominant measurement methodology because it resolves molecular level details over a wide concentration range. Its limitations, however, become challenged when applied to complex materials. Coherent multidimensional spectroscopy (CMDS) is the optical analogue of multidimensional NMR and like NMR, its multidimensionality promises to increase the spectral selectivity of vibrational and electronic spectroscopy. This article explores whether this promise can make CMDS a dominant spectroscopic method throughout the sciences. In order for CMDS to become a dominant methodology, it must create multidimensional spectral fingerprints that provide the selectivity required for probing complex samples. Pump-CMDS probe methods separate the pump's measurement of dynamics from a multidimensional and selective probe. Fully coherent CMDS methods are ideal multidimensional probes because they avoid relaxation effects, spectrally isolate the output signals, and provide unique and invariant spectral signatures using any combination of vibrational and electronic quantum states.

  4. Random Effects Diagonal Metric Multidimensional Scaling Models.

    ERIC Educational Resources Information Center

    Clarkson, Douglas B.; Gonzalez, Richard

    2001-01-01

    Defines a random effects diagonal metric multidimensional scaling model, gives its computational algorithms, describes researchers' experiences with these algorithms, and provides an illustration of the use of the model and algorithms. (Author/SLD)

  5. Systems of Values and Their Multidimensional Representations

    ERIC Educational Resources Information Center

    Jones, Russell A.; And Others

    1978-01-01

    Values were elicited spontaneously from a sample of undergraduates and adults attending college, and were compared to Rokeach's terminal and instrumental values. Multidimensional scaling revealed a simpler structure among spontaneously mentioned values than Rokeach's values. (JKS)

  6. VH-1: Multidimensional ideal compressible hydrodynamics code

    NASA Astrophysics Data System (ADS)

    Hawley, John; Blondin, John; Lindahl, Greg; Lufkin, Eric

    2012-04-01

    VH-1 is a multidimensional ideal compressible hydrodynamics code written in FORTRAN for use on any computing platform, from desktop workstations to supercomputers. It uses a Lagrangian remap version of the Piecewise Parabolic Method developed by Paul Woodward and Phil Colella in their 1984 paper. VH-1 comes in a variety of versions, from a simple one-dimensional serial variant to a multi-dimensional version scalable to thousands of processors.

  7. Multidimensional stochastic approximation Monte Carlo.

    PubMed

    Zablotskiy, Sergey V; Ivanov, Victor A; Paul, Wolfgang

    2016-06-01

    Stochastic Approximation Monte Carlo (SAMC) has been established as a mathematically founded powerful flat-histogram Monte Carlo method, used to determine the density of states, g(E), of a model system. We show here how it can be generalized for the determination of multidimensional probability distributions (or equivalently densities of states) of macroscopic or mesoscopic variables defined on the space of microstates of a statistical mechanical system. This establishes this method as a systematic way for coarse graining a model system, or, in other words, for performing a renormalization group step on a model. We discuss the formulation of the Kadanoff block spin transformation and the coarse-graining procedure for polymer models in this language. We also apply it to a standard case in the literature of two-dimensional densities of states, where two competing energetic effects are present g(E_{1},E_{2}). We show when and why care has to be exercised when obtaining the microcanonical density of states g(E_{1}+E_{2}) from g(E_{1},E_{2}). PMID:27415383

  8. Multidimensionally encoded magnetic resonance imaging.

    PubMed

    Lin, Fa-Hsuan

    2013-07-01

    Magnetic resonance imaging (MRI) typically achieves spatial encoding by measuring the projection of a q-dimensional object over q-dimensional spatial bases created by linear spatial encoding magnetic fields (SEMs). Recently, imaging strategies using nonlinear SEMs have demonstrated potential advantages for reconstructing images with higher spatiotemporal resolution and reducing peripheral nerve stimulation. In practice, nonlinear SEMs and linear SEMs can be used jointly to further improve the image reconstruction performance. Here, we propose the multidimensionally encoded (MDE) MRI to map a q-dimensional object onto a p-dimensional encoding space where p > q. MDE MRI is a theoretical framework linking imaging strategies using linear and nonlinear SEMs. Using a system of eight surface SEM coils with an eight-channel radiofrequency coil array, we demonstrate the five-dimensional MDE MRI for a two-dimensional object as a further generalization of PatLoc imaging and O-space imaging. We also present a method of optimizing spatial bases in MDE MRI. Results show that MDE MRI with a higher dimensional encoding space can reconstruct images more efficiently and with a smaller reconstruction error when the k-space sampling distribution and the number of samples are controlled.

  9. Multidimensional stochastic approximation Monte Carlo

    NASA Astrophysics Data System (ADS)

    Zablotskiy, Sergey V.; Ivanov, Victor A.; Paul, Wolfgang

    2016-06-01

    Stochastic Approximation Monte Carlo (SAMC) has been established as a mathematically founded powerful flat-histogram Monte Carlo method, used to determine the density of states, g (E ) , of a model system. We show here how it can be generalized for the determination of multidimensional probability distributions (or equivalently densities of states) of macroscopic or mesoscopic variables defined on the space of microstates of a statistical mechanical system. This establishes this method as a systematic way for coarse graining a model system, or, in other words, for performing a renormalization group step on a model. We discuss the formulation of the Kadanoff block spin transformation and the coarse-graining procedure for polymer models in this language. We also apply it to a standard case in the literature of two-dimensional densities of states, where two competing energetic effects are present g (E1,E2) . We show when and why care has to be exercised when obtaining the microcanonical density of states g (E1+E2) from g (E1,E2) .

  10. Multidimensional Modeling of Nova Outbursts

    NASA Astrophysics Data System (ADS)

    José, J.

    2014-12-01

    Classical novae repeatedly eject ˜10-4-10-5 M⊙ enriched in nuclear-processed material relative to solar abundances, recurring on intervals of decades to tens of millennia. They are probably the main sources of Galactic 15N, 17O and 13C. The origin of the large enhancements and inhomogeneous distribution of these species observed in high-resolution spectra of ejected nova shells has, however, remained unexplained for almost 50 years. Several mechanisms, including mixing by diffusion, shear or resonant gravity waves, have been proposed in the framework of one-dimensional or two-dimensional simulations, but none has proven successful because convective mixing can only be modeled accurately in three-dimensions. This review focuses on multidimensional modeling of nova explosions, with emphasis on mixing at the core-envelope interface. Examples of buoyant fingering driving vortices from the Kelvin-Helmholtz instability, leading to enrichment of the accreted envelope with material from the outer white dwarf core, will be described. This mixing mechanism naturally accounts for large-scale chemical inhomogeneities. Preliminary simulations of the interaction between the nova ejecta and the secondary star will also be outlined.

  11. Multidimensional Unfolding by Nonmetric Multidimensional Scaling of Spearman Distances in the Extended Permutation Polytope

    ERIC Educational Resources Information Center

    Van Deun, Katrijn; Heiser, Willem J.; Delbeke, Luc

    2007-01-01

    A multidimensional unfolding technique that is not prone to degenerate solutions and is based on multidimensional scaling of a complete data matrix is proposed: distance information about the unfolding data and about the distances both among judges and among objects is included in the complete matrix. The latter information is derived from the…

  12. Improved multidimensional semiclassical tunneling theory.

    PubMed

    Wagner, Albert F

    2013-12-12

    We show that the analytic multidimensional semiclassical tunneling formula of Miller et al. [Miller, W. H.; Hernandez, R.; Handy, N. C.; Jayatilaka, D.; Willets, A. Chem. Phys. Lett. 1990, 172, 62] is qualitatively incorrect for deep tunneling at energies well below the top of the barrier. The origin of this deficiency is that the formula uses an effective barrier weakly related to the true energetics but correctly adjusted to reproduce the harmonic description and anharmonic corrections of the reaction path at the saddle point as determined by second order vibrational perturbation theory. We present an analytic improved semiclassical formula that correctly includes energetic information and allows a qualitatively correct representation of deep tunneling. This is done by constructing a three segment composite Eckart potential that is continuous everywhere in both value and derivative. This composite potential has an analytic barrier penetration integral from which the semiclassical action can be derived and then used to define the semiclassical tunneling probability. The middle segment of the composite potential by itself is superior to the original formula of Miller et al. because it incorporates the asymmetry of the reaction barrier produced by the known reaction exoergicity. Comparison of the semiclassical and exact quantum tunneling probability for the pure Eckart potential suggests a simple threshold multiplicative factor to the improved formula to account for quantum effects very near threshold not represented by semiclassical theory. The deep tunneling limitations of the original formula are echoed in semiclassical high-energy descriptions of bound vibrational states perpendicular to the reaction path at the saddle point. However, typically ab initio energetic information is not available to correct it. The Supporting Information contains a Fortran code, test input, and test output that implements the improved semiclassical tunneling formula. PMID:24224758

  13. Image demodulation using multidimensional energy separation

    NASA Astrophysics Data System (ADS)

    Maragos, Petros; Bovik, Alan C.

    1995-09-01

    Locally narrow-band images can be modeled as two-dimensional (2D) spatial AM-FM signals with several applications in image texture analysis and computer vision. We formulate an image-demodulation problem and present a solution based on the multidimensional energy operator Phi (f)= \\double-vertical-bar \\inverted-Delta-triangle f \\double-vertical-bar 2-f \\inverted-Delta-triangle 2 f . This nonlinear operator is a multidimensional extension of the one-dimensional (1D) energy-tracking operator Psi (f)=( f\\prime)2 -ff\\prime\\prime , which has been found useful for demodulating 1D AM-FM and speech signals. We discuss some interesting properties of the multidimensional operator and develop a multidimensional energy-separation algorithm to estimate the amplitude envelope and instantaneous frequencies of 2D spatially varying AM-FM signals. Experiments are also presented on applying this 2D energy-demodulation algorithm to estimate the instantaneous amplitude contrast and spatial frequencies of image textures bandpass filtered by means of Gabor filters. The attractive features of the multidimensional energy operator and the 2D energy-separation algorithm are their simplicity, efficiency, and ability to track instantaneously varying

  14. Fast adaptive estimation of multidimensional psychometric functions.

    PubMed

    DiMattina, Christopher

    2015-01-01

    Recently in vision science there has been great interest in understanding the perceptual representations of complex multidimensional stimuli. Therefore, it is becoming very important to develop methods for performing psychophysical experiments with multidimensional stimuli and efficiently estimating psychometric models that have multiple free parameters. In this methodological study, I analyze three efficient implementations of the popular Ψ method for adaptive data collection, two of which are novel approaches to psychophysical experiments. Although the standard implementation of the Ψ procedure is intractable in higher dimensions, I demonstrate that my implementations generalize well to complex psychometric models defined in multidimensional stimulus spaces and can be implemented very efficiently on standard laboratory computers. I show that my implementations may be of particular use for experiments studying how subjects combine multiple cues to estimate sensory quantities. I discuss strategies for speeding up experiments and suggest directions for future research in this rapidly growing area at the intersection of cognitive science, neuroscience, and machine learning.

  15. Fast adaptive estimation of multidimensional psychometric functions.

    PubMed

    DiMattina, Christopher

    2015-01-01

    Recently in vision science there has been great interest in understanding the perceptual representations of complex multidimensional stimuli. Therefore, it is becoming very important to develop methods for performing psychophysical experiments with multidimensional stimuli and efficiently estimating psychometric models that have multiple free parameters. In this methodological study, I analyze three efficient implementations of the popular Ψ method for adaptive data collection, two of which are novel approaches to psychophysical experiments. Although the standard implementation of the Ψ procedure is intractable in higher dimensions, I demonstrate that my implementations generalize well to complex psychometric models defined in multidimensional stimulus spaces and can be implemented very efficiently on standard laboratory computers. I show that my implementations may be of particular use for experiments studying how subjects combine multiple cues to estimate sensory quantities. I discuss strategies for speeding up experiments and suggest directions for future research in this rapidly growing area at the intersection of cognitive science, neuroscience, and machine learning. PMID:26200886

  16. Preface: Special Topic on Multidimensional Spectroscopy

    NASA Astrophysics Data System (ADS)

    Mukamel, Shaul; Bakker, Huib J.

    2015-06-01

    Multidimensional signals are generated by subjecting molecules to sequences of short optical pulses and recording correlation plots related to the various controlled delay periods. These techniques which span all the way from the THz to the x-ray regimes provide qualitatively new structural and dynamical molecular information not available from conventional one-dimensional techniques. This issue surveys the recent experimental and theoretical progresses in this rapidly developing 20 year old field which illustrates the novel insights provided by multidimensional techniques into electronic and nuclear motions. It should serve as a valuable source for experts in the field and help introduce newcomers to this exciting and challenging branch of nonlinear spectroscopy.

  17. Preface: Special Topic on Multidimensional Spectroscopy

    SciTech Connect

    Mukamel, Shaul; Bakker, Huib J.

    2015-06-07

    Multidimensional signals are generated by subjecting molecules to sequences of short optical pulses and recording correlation plots related to the various controlled delay periods. These techniques which span all the way from the THz to the x-ray regimes provide qualitatively new structural and dynamical molecular information not available from conventional one-dimensional techniques. This issue surveys the recent experimental and theoretical progresses in this rapidly developing 20 year old field which illustrates the novel insights provided by multidimensional techniques into electronic and nuclear motions. It should serve as a valuable source for experts in the field and help introduce newcomers to this exciting and challenging branch of nonlinear spectroscopy.

  18. Preface: Special Topic on Multidimensional Spectroscopy.

    PubMed

    Mukamel, Shaul; Bakker, Huib J

    2015-06-01

    Multidimensional signals are generated by subjecting molecules to sequences of short optical pulses and recording correlation plots related to the various controlled delay periods. These techniques which span all the way from the THz to the x-ray regimes provide qualitatively new structural and dynamical molecular information not available from conventional one-dimensional techniques. This issue surveys the recent experimental and theoretical progresses in this rapidly developing 20 year old field which illustrates the novel insights provided by multidimensional techniques into electronic and nuclear motions. It should serve as a valuable source for experts in the field and help introduce newcomers to this exciting and challenging branch of nonlinear spectroscopy.

  19. Multidimensional stationary probability distribution for interacting active particles

    PubMed Central

    Maggi, Claudio; Marconi, Umberto Marini Bettolo; Gnan, Nicoletta; Di Leonardo, Roberto

    2015-01-01

    We derive the stationary probability distribution for a non-equilibrium system composed by an arbitrary number of degrees of freedom that are subject to Gaussian colored noise and a conservative potential. This is based on a multidimensional version of the Unified Colored Noise Approximation. By comparing theory with numerical simulations we demonstrate that the theoretical probability density quantitatively describes the accumulation of active particles around repulsive obstacles. In particular, for two particles with repulsive interactions, the probability of close contact decreases when one of the two particle is pinned. Moreover, in the case of isotropic confining potentials, the radial density profile shows a non trivial scaling with radius. Finally we show that the theory well approximates the “pressure” generated by the active particles allowing to derive an equation of state for a system of non-interacting colored noise-driven particles. PMID:26021260

  20. Sex Differences in the Multidimensional Self-Concepts of African American Adolescents: The Mediating Role of Gender Identity

    ERIC Educational Resources Information Center

    Thomson, Nicole Renick; Zand, Debra H.

    2007-01-01

    The present study investigates whether the gender identities of African American adolescents mediate sex differences found in their multidimensional self-concepts. The sample included 174 African American adolescents who completed the 21-item Children's Personal Attributes Questionnaire and the Self-Perception Profile for Adolescents. Results…

  1. Examination of the Structure and Grade-Related Differentiation of Multidimensional Self-Concept Instruments for Children Using ESEM

    ERIC Educational Resources Information Center

    Arens, A. Katrin; Morin, Alexandre J. S.

    2016-01-01

    This study is a substantive-methodological synergy in which exploratory structural equation modeling is applied to investigate the factor structure of multidimensional self-concept instruments. On the basis of a sample of German students (N = 1958) who completed the Self-Description Questionnaire I and the Self-Perception Profile for Children, the…

  2. The Efficacy of Multidimensional Constraint Keys in Database Query Performance

    ERIC Educational Resources Information Center

    Cardwell, Leslie K.

    2012-01-01

    This work is intended to introduce a database design method to resolve the two-dimensional complexities inherent in the relational data model and its resulting performance challenges through abstract multidimensional constructs. A multidimensional constraint is derived and utilized to implement an indexed Multidimensional Key (MK) to abstract a…

  3. Multidimensional Human Dynamics in Mobile Phone Communications

    PubMed Central

    Quadri, Christian; Zignani, Matteo; Capra, Lorenzo; Gaito, Sabrina; Rossi, Gian Paolo

    2014-01-01

    In today's technology-assisted society, social interactions may be expressed through a variety of techno-communication channels, including online social networks, email and mobile phones (calls, text messages). Consequently, a clear grasp of human behavior through the diverse communication media is considered a key factor in understanding the formation of the today's information society. So far, all previous research on user communication behavior has focused on a sole communication activity. In this paper we move forward another step on this research path by performing a multidimensional study of human sociality as an expression of the use of mobile phones. The paper focuses on user temporal communication behavior in the interplay between the two complementary communication media, text messages and phone calls, that represent the bi-dimensional scenario of analysis. Our study provides a theoretical framework for analyzing multidimensional bursts as the most general burst category, that includes one-dimensional bursts as the simplest case, and offers empirical evidence of their nature by following the combined phone call/text message communication patterns of approximately one million people over three-month period. This quantitative approach enables the design of a generative model rooted in the three most significant features of the multidimensional burst - the number of dimensions, prevalence and interleaving degree - able to reproduce the main media usage attitude. The other findings of the paper include a novel multidimensional burst detection algorithm and an insight analysis of the human media selection process. PMID:25068479

  4. Longitudinal Network Analysis Using Multidimensional Scaling.

    ERIC Educational Resources Information Center

    Barnett, George A.; Palmer, Mark T.

    The Galileo System, a variant of metric multidimensional scaling, is used in this paper to analyze over-time changes in social networks. The paper first discusses the theoretical necessity for the use of this procedure and the methodological problems associated with its use. It then examines the air traffic network among 31 major cities in the…

  5. Multidimensional Perspectives on Principal Leadership Effectiveness

    ERIC Educational Resources Information Center

    Beycioglu, Kadir, Ed.; Pashiardis, Petros, Ed.

    2015-01-01

    Exceptional management skills are crucial to success in educational environments. As school leaders, principals are expected to effectively supervise the school system while facing a multitude of issues and demands. "Multidimensional Perspectives on Principal Leadership Effectiveness" combines best practices and the latest approaches in…

  6. Uncertainty of Comparative Judgments and Multidimensional Structure

    ERIC Educational Resources Information Center

    Sjoberg, Lennart

    1975-01-01

    An analysis of preferences with respect to silhouette drawings of nude females is presented. Systematic intransitivities were discovered. The dispersions of differences (comparatal dispersons) were shown to reflect the multidimensional structure of the stimuli, a finding expected on the basis of prior work. (Author)

  7. Bilingual Creativity, Multidimensional Analysis, and World Englishes.

    ERIC Educational Resources Information Center

    Baker, Wendy; Eggington, William G.

    1999-01-01

    Using Biber's multidimensional analysis (1998) to examine a large corpus of world English literatures written in Indian, West African, British, Anglo-American, and Mexican-American varieties of English, examines whether quantitative analyses can also be insightful and useful in the examination of world Englishes literatures in expanding…

  8. Multidimensional human dynamics in mobile phone communications.

    PubMed

    Quadri, Christian; Zignani, Matteo; Capra, Lorenzo; Gaito, Sabrina; Rossi, Gian Paolo

    2014-01-01

    In today's technology-assisted society, social interactions may be expressed through a variety of techno-communication channels, including online social networks, email and mobile phones (calls, text messages). Consequently, a clear grasp of human behavior through the diverse communication media is considered a key factor in understanding the formation of the today's information society. So far, all previous research on user communication behavior has focused on a sole communication activity. In this paper we move forward another step on this research path by performing a multidimensional study of human sociality as an expression of the use of mobile phones. The paper focuses on user temporal communication behavior in the interplay between the two complementary communication media, text messages and phone calls, that represent the bi-dimensional scenario of analysis. Our study provides a theoretical framework for analyzing multidimensional bursts as the most general burst category, that includes one-dimensional bursts as the simplest case, and offers empirical evidence of their nature by following the combined phone call/text message communication patterns of approximately one million people over three-month period. This quantitative approach enables the design of a generative model rooted in the three most significant features of the multidimensional burst - the number of dimensions, prevalence and interleaving degree - able to reproduce the main media usage attitude. The other findings of the paper include a novel multidimensional burst detection algorithm and an insight analysis of the human media selection process. PMID:25068479

  9. Multidimensional human dynamics in mobile phone communications.

    PubMed

    Quadri, Christian; Zignani, Matteo; Capra, Lorenzo; Gaito, Sabrina; Rossi, Gian Paolo

    2014-01-01

    In today's technology-assisted society, social interactions may be expressed through a variety of techno-communication channels, including online social networks, email and mobile phones (calls, text messages). Consequently, a clear grasp of human behavior through the diverse communication media is considered a key factor in understanding the formation of the today's information society. So far, all previous research on user communication behavior has focused on a sole communication activity. In this paper we move forward another step on this research path by performing a multidimensional study of human sociality as an expression of the use of mobile phones. The paper focuses on user temporal communication behavior in the interplay between the two complementary communication media, text messages and phone calls, that represent the bi-dimensional scenario of analysis. Our study provides a theoretical framework for analyzing multidimensional bursts as the most general burst category, that includes one-dimensional bursts as the simplest case, and offers empirical evidence of their nature by following the combined phone call/text message communication patterns of approximately one million people over three-month period. This quantitative approach enables the design of a generative model rooted in the three most significant features of the multidimensional burst - the number of dimensions, prevalence and interleaving degree - able to reproduce the main media usage attitude. The other findings of the paper include a novel multidimensional burst detection algorithm and an insight analysis of the human media selection process.

  10. Multidimensional IRT Models for Composite Scores

    ERIC Educational Resources Information Center

    Yen, Shu Jing; Walker, Leah

    2007-01-01

    Tests of English Language Proficiency are often designed such that each section of the test measures a single latent ability. For instance an English Proficiency Assessment might consist of sections measuring Speaking, Listening, and Reading ability. However, Overall English Proficiency and composite abilities are naturally multidimensional. This…

  11. Determining Factor Structure in a Multidimensional Inventory.

    ERIC Educational Resources Information Center

    Deeter, Thomas E.; Gill, Diane L.

    A two-step procedure is described and used to revise a multidimensional inventory in its developmental stages. First, the latent factors influencing the observed variables on the inventory are determined and justified using the following five methods: Kaiser's criterion, root staring, examination of difference values, examination of root mean…

  12. Stability of Adolescents' Multidimensional Life Satisfaction Reports

    ERIC Educational Resources Information Center

    Antaramian, Susan P.; Huebner, E. Scott

    2009-01-01

    Eighty-four students were administered the Multidimensional Students' Life Satisfaction Scale (MSLSS) on three occasions, 1 year apart (Grades 8, 9, and 10). The 1-year stability coefficients ranged from 0.29 to 0.59, whereas the 2-year stability coefficients ranged from 0.41 to 0.59. MSLSS mean scores were consistent across administrations, with…

  13. A New Heterogeneous Multidimensional Unfolding Procedure

    ERIC Educational Resources Information Center

    Park, Joonwook; Rajagopal, Priyali; DeSarbo, Wayne S.

    2012-01-01

    A variety of joint space multidimensional scaling (MDS) methods have been utilized for the spatial analysis of two- or three-way dominance data involving subjects' preferences, choices, considerations, intentions, etc. so as to provide a parsimonious spatial depiction of the underlying relevant dimensions, attributes, stimuli, and/or subjects'…

  14. Multidimensional NMR spectroscopy in a single scan.

    PubMed

    Gal, Maayan; Frydman, Lucio

    2015-11-01

    Multidimensional NMR has become one of the most widespread spectroscopic tools available to study diverse structural and functional aspects of organic and biomolecules. A main feature of multidimensional NMR is the relatively long acquisition times that these experiments demand. For decades, scientists have been working on a variety of alternatives that would enable NMR to overcome this limitation, and deliver its data in shorter acquisition times. Counting among these methodologies is the so-called ultrafast (UF) NMR approach, which in principle allows one to collect arbitrary multidimensional correlations in a single sub-second transient. By contrast to conventional acquisitions, a main feature of UF NMR is a spatiotemporal manipulation of the spins that imprints the chemical shift and/or J-coupling evolutions being sought, into a spatial pattern. Subsequent gradient-based manipulations enable the reading out of this information and its multidimensional correlation into patterns that are identical to those afforded by conventional techniques. The current review focuses on the fundamental principles of this spatiotemporal UF NMR manipulation, and on a few of the methodological extensions that this form of spectroscopy has undergone during the years. PMID:26249041

  15. A Multidimensional Construct of Self-Esteem

    ERIC Educational Resources Information Center

    Norem-Hebeisen, Ardyth A.

    1976-01-01

    Evidence for construct validity of this multi-dimensional concept of self esteem includes the relative congruence of the factor structure with the theoretical construct, the stability of the structure when subjected to a series of empirical tests, increasingly positive self-referent responses with increasing age, willingness to become more…

  16. The Multidimensional Curriculum Model (MdCM)

    ERIC Educational Resources Information Center

    Vidergor, Hava E.

    2010-01-01

    The multidimensional Curriculum Model (MdCM) helps teachers to better prepare gifted and able students for our changing world, acquiring much needed skills. It is influenced by general learning theory of constructivism, notions of preparing students for 21st century, Teaching the Future Model, and current comprehensive curriculum models for…

  17. Scaling Multidimensional Inference for Structured Gaussian Processes.

    PubMed

    Gilboa, Elad; Saatçi, Yunus; Cunningham, John P

    2013-09-30

    Exact Gaussian process (GP) regression has O(N^3) runtime for data size N, making it intractable for large N. Many algorithms for improving GP scaling approximate the covariance with lower rank matrices. Other work has exploited structure inherent in particular covariance functions, including GPs with implied Markov structure, and inputs on a lattice (both enable O(N) or O(N log N) runtime). However, these GP advances have not been well extended to the multidimensional input setting, despite the preponderance of multidimensional applications. This paper introduces and tests three novel extensions of structured GPs to multidimensional inputs, for models with additive and multiplicative kernels. First we present a new method for inference in additive GPs, showing a novel connection between the classic backfitting method and the Bayesian framework. We extend this model using two advances: a variant of projection pursuit regression, and a Laplace approximation for non-Gaussian observations. Lastly, for multiplicative kernel structure, we present a novel method for GPs with inputs on a multidimensional grid. We illustrate the power of these three advances on several datasets, achieving performance equal to or very close to the naive GP at orders of magnitude less cost.

  18. Scaling Multidimensional Inference for Structured Gaussian Processes.

    PubMed

    Gilboa, Elad; Saatçi, Yunus; Cunningham, John P

    2015-02-01

    Exact Gaussian process (GP) regression has O(N(3)) runtime for data size N, making it intractable for large N . Many algorithms for improving GP scaling approximate the covariance with lower rank matrices. Other work has exploited structure inherent in particular covariance functions, including GPs with implied Markov structure, and inputs on a lattice (both enable O(N) or O(N log N) runtime). However, these GP advances have not been well extended to the multidimensional input setting, despite the preponderance of multidimensional applications. This paper introduces and tests three novel extensions of structured GPs to multidimensional inputs, for models with additive and multiplicative kernels. First we present a new method for inference in additive GPs, showing a novel connection between the classic backfitting method and the Bayesian framework. We extend this model using two advances: a variant of projection pursuit regression, and a Laplace approximation for non-Gaussian observations. Lastly, for multiplicative kernel structure, we present a novel method for GPs with inputs on a multidimensional grid. We illustrate the power of these three advances on several data sets, achieving performance equal to or very close to the naive GP at orders of magnitude less cost.

  19. Multidimensional neural growing networks and computer intelligence

    SciTech Connect

    Yashchenko, V.A.

    1995-03-01

    This paper examines information-computation processes in time and in space and some aspects of computer intelligence using multidimensional matrix neural growing networks. In particular, issues of object-oriented {open_quotes}thinking{close_quotes} of computers are considered.

  20. Multidimensional Treatment of Fear of Death.

    ERIC Educational Resources Information Center

    Hoelter, Jon W.

    1979-01-01

    Presents a multidimensional conception of fear of death and provides subscales for measuring suggested dimensions (fear of the dying process, of the dead, of being destroyed, for significant others, of the unknown, of conscious death, for body after death, and of premature death). Evidence for construct validity is provided. (Author/BEF)

  1. Paradoxical Results in Multidimensional Item Response Theory

    ERIC Educational Resources Information Center

    Hooker, Giles; Finkelman, Matthew; Schwartzman, Armin

    2009-01-01

    In multidimensional item response theory (MIRT), it is possible for the estimate of a subject's ability in some dimension to decrease after they have answered a question correctly. This paper investigates how and when this type of paradoxical result can occur. We demonstrate that many response models and statistical estimates can produce…

  2. Unidimensional Interpretations for Multidimensional Test Items

    ERIC Educational Resources Information Center

    Kahraman, Nilufer

    2013-01-01

    This article considers potential problems that can arise in estimating a unidimensional item response theory (IRT) model when some test items are multidimensional (i.e., show a complex factorial structure). More specifically, this study examines (1) the consequences of model misfit on IRT item parameter estimates due to unintended minor item-level…

  3. Pathway Profiling in Mycobacterium tuberculosis

    PubMed Central

    Thomas, Suzanne T.; VanderVen, Brian C.; Sherman, David R.; Russell, David G.; Sampson, Nicole S.

    2011-01-01

    Mycobacterium tuberculosis, the bacterium that causes tuberculosis, imports and metabolizes host cholesterol during infection. This ability is important in the chronic phase of infection. Here we investigate the role of the intracellular growth operon (igr), which has previously been identified as having a cholesterol-sensitive phenotype in vitro and which is important for intracellular growth of the mycobacteria. We have employed isotopically labeled low density lipoproteins containing either [1,7,15,22,26-14C]cholesterol or [1,7,15,22,26-13C]cholesterol and high resolution LC/MS as tools to profile the cholesterol-derived metabolome of an igr operon-disrupted mutant (Δigr) of M. tuberculosis. A partially metabolized cholesterol species accumulated in the Δigr knock-out strain that was absent in the complemented and parental wild-type strains. Structural elucidation by multidimensional 1H and 13C NMR spectroscopy revealed the accumulated metabolite to be methyl 1β-(2′-propanoate)-3aα-H-4α-(3′-propanoic acid)-7aβ-methylhexahydro-5-indanone. Heterologously expressed and purified FadE28-FadE29, an acyl-CoA dehydrogenase encoded by the igr operon, catalyzes the dehydrogenation of 2′-propanoyl-CoA ester side chains in substrates with structures analogous to the characterized metabolite. Based on the structure of the isolated metabolite, enzyme activity, and bioinformatic annotations, we assign the primary function of the igr operon to be degradation of the 2′-propanoate side chain. Therefore, the igr operon is necessary to completely metabolize the side chain of cholesterol metabolites. PMID:22045806

  4. On the monotonicity of multidimensional finite difference schemes

    NASA Astrophysics Data System (ADS)

    Kovyrkina, O.; Ostapenko, V.

    2016-10-01

    The classical concept of monotonicity, introduced by Godunov for linear one-dimensional difference schemes, is extended to multidimensional case. Necessary and sufficient conditions of monotonicity are obtained for linear multidimensional difference schemes of first order. The constraints on the numerical viscosity are given that ensure the monotonicity of a difference scheme in the multidimensional case. It is proposed a modification of the second order multidimensional CABARET scheme that preserves the monotonicity of one-dimensional discrete solutions and, as a result, ensures higher smoothness in the computation of multidimensional discontinuous solutions. The results of two-dimensional test computations illustrating the advantages of the modified CABARET scheme are presented.

  5. Serum Biochemical Phenotypes in the Domestic Dog.

    PubMed

    Chang, Yu-Mei; Hadox, Erin; Szladovits, Balazs; Garden, Oliver A

    2016-01-01

    The serum or plasma biochemical profile is essential in the diagnosis and monitoring of systemic disease in veterinary medicine, but current reference intervals typically take no account of breed-specific differences. Breed-specific hematological phenotypes have been documented in the domestic dog, but little has been published on serum biochemical phenotypes in this species. Serum biochemical profiles of dogs in which all measurements fell within the existing reference intervals were retrieved from a large veterinary database. Serum biochemical profiles from 3045 dogs were retrieved, of which 1495 had an accompanying normal glucose concentration. Sixty pure breeds plus a mixed breed control group were represented by at least 10 individuals. All analytes, except for sodium, chloride and glucose, showed variation with age. Total protein, globulin, potassium, chloride, creatinine, cholesterol, total bilirubin, ALT, CK, amylase, and lipase varied between sexes. Neutering status significantly impacted all analytes except albumin, sodium, calcium, urea, and glucose. Principal component analysis of serum biochemical data revealed 36 pure breeds with distinctive phenotypes. Furthermore, comparative analysis identified 23 breeds with significant differences from the mixed breed group in all biochemical analytes except urea and glucose. Eighteen breeds were identified by both principal component and comparative analysis. Tentative reference intervals were generated for breeds with a distinctive phenotype identified by comparative analysis and represented by at least 120 individuals. This is the first large-scale analysis of breed-specific serum biochemical phenotypes in the domestic dog and highlights potential genetic components of biochemical traits in this species. PMID:26919479

  6. Serum Biochemical Phenotypes in the Domestic Dog

    PubMed Central

    Chang, Yu-Mei; Hadox, Erin; Szladovits, Balazs; Garden, Oliver A.

    2016-01-01

    The serum or plasma biochemical profile is essential in the diagnosis and monitoring of systemic disease in veterinary medicine, but current reference intervals typically take no account of breed-specific differences. Breed-specific hematological phenotypes have been documented in the domestic dog, but little has been published on serum biochemical phenotypes in this species. Serum biochemical profiles of dogs in which all measurements fell within the existing reference intervals were retrieved from a large veterinary database. Serum biochemical profiles from 3045 dogs were retrieved, of which 1495 had an accompanying normal glucose concentration. Sixty pure breeds plus a mixed breed control group were represented by at least 10 individuals. All analytes, except for sodium, chloride and glucose, showed variation with age. Total protein, globulin, potassium, chloride, creatinine, cholesterol, total bilirubin, ALT, CK, amylase, and lipase varied between sexes. Neutering status significantly impacted all analytes except albumin, sodium, calcium, urea, and glucose. Principal component analysis of serum biochemical data revealed 36 pure breeds with distinctive phenotypes. Furthermore, comparative analysis identified 23 breeds with significant differences from the mixed breed group in all biochemical analytes except urea and glucose. Eighteen breeds were identified by both principal component and comparative analysis. Tentative reference intervals were generated for breeds with a distinctive phenotype identified by comparative analysis and represented by at least 120 individuals. This is the first large-scale analysis of breed-specific serum biochemical phenotypes in the domestic dog and highlights potential genetic components of biochemical traits in this species. PMID:26919479

  7. Framework for analyzing ecological trait-based models in multidimensional niche spaces

    NASA Astrophysics Data System (ADS)

    Biancalani, Tommaso; DeVille, Lee; Goldenfeld, Nigel

    2015-05-01

    We develop a theoretical framework for analyzing ecological models with a multidimensional niche space. Our approach relies on the fact that ecological niches are described by sequences of symbols, which allows us to include multiple phenotypic traits. Ecological drivers, such as competitive exclusion, are modeled by introducing the Hamming distance between two sequences. We show that a suitable transform diagonalizes the community interaction matrix of these models, making it possible to predict the conditions for niche differentiation and, close to the instability onset, the asymptotically long time population distributions of niches. We exemplify our method using the Lotka-Volterra equations with an exponential competition kernel.

  8. Framework for analyzing ecological trait-based models in multidimensional niche spaces.

    PubMed

    Biancalani, Tommaso; DeVille, Lee; Goldenfeld, Nigel

    2015-05-01

    We develop a theoretical framework for analyzing ecological models with a multidimensional niche space. Our approach relies on the fact that ecological niches are described by sequences of symbols, which allows us to include multiple phenotypic traits. Ecological drivers, such as competitive exclusion, are modeled by introducing the Hamming distance between two sequences. We show that a suitable transform diagonalizes the community interaction matrix of these models, making it possible to predict the conditions for niche differentiation and, close to the instability onset, the asymptotically long time population distributions of niches. We exemplify our method using the Lotka-Volterra equations with an exponential competition kernel. PMID:26066119

  9. [Intermediate phenotype of schizophrenia].

    PubMed

    Hashimoto, Ryota

    2013-04-01

    Genes are major contributors to schizophrenia. The intermediate phenotype concept represents a strategy for identifying risk genes for schizophrenia and for characterizing the neural systems affected by risk gene variants to elucidate quantitative, mechanistic aspects of brain function implicated in schizophrenia. Intermediate phenotypes are defined by being heritable, being able to measure quantitatively; being related to the disorder and its symptoms in the general population; being stable over time; showing increased expression in unaffected relatives of probands; and cosegregation with the disorder in families. Intermediate phenotypes in schizophrenia are neurocognition, neuroimaging, neurophysiology, etc. In this review, we present concept, recent work, and future perspective of intermediate phenotype.

  10. Preface: Special Topic on Multidimensional Spectroscopy.

    PubMed

    Mukamel, Shaul; Bakker, Huib J

    2015-06-01

    Multidimensional signals are generated by subjecting molecules to sequences of short optical pulses and recording correlation plots related to the various controlled delay periods. These techniques which span all the way from the THz to the x-ray regimes provide qualitatively new structural and dynamical molecular information not available from conventional one-dimensional techniques. This issue surveys the recent experimental and theoretical progresses in this rapidly developing 20 year old field which illustrates the novel insights provided by multidimensional techniques into electronic and nuclear motions. It should serve as a valuable source for experts in the field and help introduce newcomers to this exciting and challenging branch of nonlinear spectroscopy. PMID:26049418

  11. Multidimensional x-space magnetic particle imaging.

    PubMed

    Goodwill, Patrick W; Conolly, Steven M

    2011-09-01

    Magnetic particle imaging (MPI) is a promising new medical imaging tracer modality with potential applications in human angiography, cancer imaging, in vivo cell tracking, and inflammation imaging. Here we demonstrate both theoretically and experimentally that multidimensional MPI is a linear shift-invariant imaging system with an analytic point spread function. We also introduce a fast image reconstruction method that obtains the intrinsic MPI image with high signal-to-noise ratio via a simple gridding operation in x-space. We also demonstrate a method to reconstruct large field-of-view (FOV) images using partial FOV scanning, despite the loss of first harmonic image information due to direct feedthrough contamination. We conclude with the first experimental test of multidimensional x-space MPI.

  12. Relevance in the science classroom: A multidimensional analysis

    NASA Astrophysics Data System (ADS)

    Hartwell, Matthew F.

    While perceived relevance is considered a fundamental component of adaptive learning, the experience of relevance and its conceptual definition have not been well described. The mixed-methods research presented in this dissertation aimed to clarify the conceptual meaning of relevance by focusing on its phenomenological experience from the students' perspective. Following a critical literature review, I propose an identity-based model of perceived relevance that includes three components: a contextual target, an identity target, and a connection type, or lens. An empirical investigation of this model that consisted of two general phases was implemented in four 9th grade-biology classrooms. Participants in Phase 1 (N = 118) completed a series of four open-ended writing activities focused on eliciting perceived personal connections to academic content. Exploratory qualitative content analysis of a 25% random sample of the student responses was used to identify the main meaning-units of the proposed model as well as different dimensions of student relevance perceptions. These meaning-units and dimensions provided the basis for the construction of a conceptual mapping sentence capturing students' perceived relevance, which was then applied in a confirmatory analysis to all other student responses. Participants in Phase 2 (N = 139) completed a closed survey designed based on the mapping sentence to assess their perceived relevance of a biology unit. The survey also included scales assessing other domain-level motivational processes. Exploratory factor analysis and non-metric multidimensional scaling indicated a coherent conceptual structure, which included a primary interpretive relevance dimension. Comparison of the conceptual structure across various groups (randomly-split sample, gender, academic level, domain-general motivational profiles) provided support for its ubiquity and insight into variation in the experience of perceived relevance among students of different

  13. On the Need for Multidimensional Stirling Analysis

    NASA Technical Reports Server (NTRS)

    Dyson, Rodger; Wilson, Scott; Tew, Roy; Demko, Rikako

    2006-01-01

    Contents include the following: Dual opposed convertors. High efficiency. Low mass space power. One-dimensional analysis. Fast computation. Design optimizations are easily done. Need for multidimensional modeling. Axisymmetric simulation. Flow characteristics. Low mach number. Laminar, transitional, and turbulent flow. Conjugate heat transfer. Third order analysis. Recent whole engine modeling. Regenerator geometry. Turbulence modeling. Flat head heater not 1-D. Empirical coefficients needed. Experiment design. Flow distribution. Sensor placement. Calibration. Validation.

  14. Multidimensional integration in a heterogeneous network environment

    NASA Astrophysics Data System (ADS)

    Veseli, Siniša

    1998-01-01

    We consider several issues related to the multidimensional integration using a network of heterogeneous computers. Based on these considerations, we develop a new general purpose scheme which can significantly reduce the time needed for evaluation of integrals with CPU intensive integrands. This scheme is a parallel version of the well-known adaptive Monte Carlo method (the VEGAS algorithm), and is incorporated into a new integration package which uses the standard set of message-passing routines in the PVM software system.

  15. Multidimensional reaction rate theory with anisotropic diffusion.

    PubMed

    Berezhkovskii, Alexander M; Szabo, Attila; Greives, Nicholas; Zhou, Huan-Xiang

    2014-11-28

    An analytical expression is derived for the rate constant that describes diffusive transitions between two deep wells of a multidimensional potential. The expression, in contrast to the Kramers-Langer formula for the rate constant, is valid even when the diffusion is highly anisotropic. Our approach is based on a variational principle for the reactive flux and uses a trial function for the splitting probability or commitor. The theoretical result is validated by Brownian dynamics simulations.

  16. Multidimensional Homophily in Friendship Networks1

    PubMed Central

    Block, Per; Grund, Thomas

    2014-01-01

    Homophily – the tendency for individuals to associate with similar others – is one of the most persistent findings in social network analysis. Its importance is established along the lines of a multitude of sociologically relevant dimensions, e.g. sex, ethnicity and social class. Existing research, however, mostly focuses on one dimension at a time. But people are inherently multidimensional, have many attributes and are members of multiple groups. In this article, we explore such multidimensionality further in the context of network dynamics. Are friendship ties increasingly likely to emerge and persist when individuals have an increasing number of attributes in common? We analyze eleven friendship networks of adolescents, draw on stochastic actor-oriented network models and focus on the interaction of established homophily effects. Our results indicate that main effects for homophily on various dimensions are positive. At the same time, the interaction of these homophily effects is negative. There seems to be a diminishing effect for having more than one attribute in common. We conclude that studies of homophily and friendship formation need to address such multidimensionality further. PMID:25525503

  17. Phenotype definition in epilepsy.

    PubMed

    Winawer, Melodie R

    2006-05-01

    Phenotype definition consists of the use of epidemiologic, biological, molecular, or computational methods to systematically select features of a disorder that might result from distinct genetic influences. By carefully defining the target phenotype, or dividing the sample by phenotypic characteristics, we can hope to narrow the range of genes that influence risk for the trait in the study population, thereby increasing the likelihood of finding them. In this article, fundamental issues that arise in phenotyping in epilepsy and other disorders are reviewed, and factors complicating genotype-phenotype correlation are discussed. Methods of data collection, analysis, and interpretation are addressed, focusing on epidemiologic studies. With this foundation in place, the epilepsy subtypes and clinical features that appear to have a genetic basis are described, and the epidemiologic studies that have provided evidence for the heritability of these phenotypic characteristics, supporting their use in future genetic investigations, are reviewed. Finally, several molecular approaches to phenotype definition are discussed, in which the molecular defect, rather than the clinical phenotype, is used as a starting point.

  18. Simultaneous in vivo phenotyping of CYP enzymes.

    PubMed

    Ghassabian, Sussan; Murray, Michael

    2013-01-01

    As major determinants of the duration of drug action the CYP enzymes strongly influence drug efficacy and toxicity. In vivo phenotyping for CYP activities using cocktails of well-tolerated CYP-specific substrates may be valuable in the development of personalized medicine protocols, particularly for drugs that have significant toxicity profiles. However, the use of the cocktail approach in the clinic is dependent on the rapid provision of patient-specific information to the clinician. Here we describe the application of liquid chromatography-tandem mass spectrometry (LC-MS-MS) for the simultaneous phenotyping of five major drug-metabolizing CYPs in patients within a 5-min assay.

  19. The Drosophila phenotype ontology

    PubMed Central

    2013-01-01

    Background Phenotype ontologies are queryable classifications of phenotypes. They provide a widely-used means for annotating phenotypes in a form that is human-readable, programatically accessible and that can be used to group annotations in biologically meaningful ways. Accurate manual annotation requires clear textual definitions for terms. Accurate grouping and fruitful programatic usage require high-quality formal definitions that can be used to automate classification. The Drosophila phenotype ontology (DPO) has been used to annotate over 159,000 phenotypes in FlyBase to date, but until recently lacked textual or formal definitions. Results We have composed textual definitions for all DPO terms and formal definitions for 77% of them. Formal definitions reference terms from a range of widely-used ontologies including the Phenotype and Trait Ontology (PATO), the Gene Ontology (GO) and the Cell Ontology (CL). We also describe a generally applicable system, devised for the DPO, for recording and reasoning about the timing of death in populations. As a result of the new formalisations, 85% of classifications in the DPO are now inferred rather than asserted, with much of this classification leveraging the structure of the GO. This work has significantly improved the accuracy and completeness of classification and made further development of the DPO more sustainable. Conclusions The DPO provides a set of well-defined terms for annotating Drosophila phenotypes and for grouping and querying the resulting annotation sets in biologically meaningful ways. Such queries have already resulted in successful function predictions from phenotype annotation. Moreover, such formalisations make extended queries possible, including cross-species queries via the external ontologies used in formal definitions. The DPO is openly available under an open source license in both OBO and OWL formats. There is good potential for it to be used more broadly by the Drosophila

  20. Nuclear Forensic Inferences Using Iterative Multidimensional Statistics

    SciTech Connect

    Robel, M; Kristo, M J; Heller, M A

    2009-06-09

    Nuclear forensics involves the analysis of interdicted nuclear material for specific material characteristics (referred to as 'signatures') that imply specific geographical locations, production processes, culprit intentions, etc. Predictive signatures rely on expert knowledge of physics, chemistry, and engineering to develop inferences from these material characteristics. Comparative signatures, on the other hand, rely on comparison of the material characteristics of the interdicted sample (the 'questioned sample' in FBI parlance) with those of a set of known samples. In the ideal case, the set of known samples would be a comprehensive nuclear forensics database, a database which does not currently exist. In fact, our ability to analyze interdicted samples and produce an extensive list of precise materials characteristics far exceeds our ability to interpret the results. Therefore, as we seek to develop the extensive databases necessary for nuclear forensics, we must also develop the methods necessary to produce the necessary inferences from comparison of our analytical results with these large, multidimensional sets of data. In the work reported here, we used a large, multidimensional dataset of results from quality control analyses of uranium ore concentrate (UOC, sometimes called 'yellowcake'). We have found that traditional multidimensional techniques, such as principal components analysis (PCA), are especially useful for understanding such datasets and drawing relevant conclusions. In particular, we have developed an iterative partial least squares-discriminant analysis (PLS-DA) procedure that has proven especially adept at identifying the production location of unknown UOC samples. By removing classes which fell far outside the initial decision boundary, and then rebuilding the PLS-DA model, we have consistently produced better and more definitive attributions than with a single pass classification approach. Performance of the iterative PLS-DA method

  1. Construct continuity in the presence of multidimensionality

    NASA Astrophysics Data System (ADS)

    Staniewska, Dorota

    Unidimensionality -- a condition, under which only one dominant construct is being measured by the test, is a fundamental assumption of most modern day psychometric models. However, some tests are multidimensional by design. A test, for instance, might measure physics, biology and chemistry subscales combined to measure a "general science" composite. The relative magnitudes of those subscales sometimes shift from administration to administration, which results in an altered composite. This study examined the conditions under which two different forms of a multidimensional test measure the same composite construct to a degree that allows them to be equated, i.e. used interchangeably. IRT true-score equating was used in a simulation study to assess the closeness of the scores on the forms. Conditions examined included the correlations between subscales, varying number of items per subscale form to form, and different subpopulation ability estimates on the subscales. Differences in the equating errors due to generating model (1PL or 3PL) were also examined. A way of calculating a unidimensional composite from a two-dimensional ability was devised and compared to the unidimensional composite obtained from Parscale. It was found that in general, the errors increase with decreasing correlation between traits and increased divergence of the two forms to be equated, with the later being the main predictor of the equating errors. However, the magnitude of those errors was small for the population as a whole especially when all examinee abilities are drawn from the same distribution. It was concluded that IRT true score equating is relatively robust to multidimensionality for the conditions examined, especially if the overall population score is desired. However, when accurate estimate of the equated score for individuals at the extremes of the population is needed, or whenever population abilities are drawn from more than one distribution, the unidimensional true score

  2. A Multidimensional Scaling Approach to Dimensionality Assessment for Measurement Instruments Modeled by Multidimensional Item Response Theory

    ERIC Educational Resources Information Center

    Toro, Maritsa

    2011-01-01

    The statistical assessment of dimensionality provides evidence of the underlying constructs measured by a survey or test instrument. This study focuses on educational measurement, specifically tests comprised of items described as multidimensional. That is, items that require examinee proficiency in multiple content areas and/or multiple cognitive…

  3. Palmprint based multidimensional fuzzy vault scheme.

    PubMed

    Liu, Hailun; Sun, Dongmei; Xiong, Ke; Qiu, Zhengding

    2014-01-01

    Fuzzy vault scheme (FVS) is one of the most popular biometric cryptosystems for biometric template protection. However, error correcting code (ECC) proposed in FVS is not appropriate to deal with real-valued biometric intraclass variances. In this paper, we propose a multidimensional fuzzy vault scheme (MDFVS) in which a general subspace error-tolerant mechanism is designed and embedded into FVS to handle intraclass variances. Palmprint is one of the most important biometrics; to protect palmprint templates; a palmprint based MDFVS implementation is also presented. Experimental results show that the proposed scheme not only can deal with intraclass variances effectively but also could maintain the accuracy and meanwhile enhance security. PMID:24892094

  4. A multidimensional representation model of geographic features

    USGS Publications Warehouse

    Usery, E. Lynn; Timson, George; Coletti, Mark

    2016-01-28

    A multidimensional model of geographic features has been developed and implemented with data from The National Map of the U.S. Geological Survey. The model, programmed in C++ and implemented as a feature library, was tested with data from the National Hydrography Dataset demonstrating the capability to handle changes in feature attributes, such as increases in chlorine concentration in a stream, and feature geometry, such as the changing shoreline of barrier islands over time. Data can be entered directly, from a comma separated file, or features with attributes and relationships can be automatically populated in the model from data in the Spatial Data Transfer Standard format.

  5. A multidimensional representation model of geographic features

    USGS Publications Warehouse

    Usery, E. Lynn; Timson, George; Coletti, Mark

    2016-01-01

    A multidimensional model of geographic features has been developed and implemented with data from The National Map of the U.S. Geological Survey. The model, programmed in C++ and implemented as a feature library, was tested with data from the National Hydrography Dataset demonstrating the capability to handle changes in feature attributes, such as increases in chlorine concentration in a stream, and feature geometry, such as the changing shoreline of barrier islands over time. Data can be entered directly, from a comma separated file, or features with attributes and relationships can be automatically populated in the model from data in the Spatial Data Transfer Standard format.

  6. Multidimensional world, inflation, and modern acceleration

    SciTech Connect

    Bronnikov, K. A.; Rubin, S. G.; Svadkovsky, I. V.

    2010-04-15

    Starting from pure multidimensional gravity with curvature-nonlinear terms but no matter fields in the initial action, we obtain a cosmological model with two effective scalar fields related to the size of two extra factor spaces. The model includes both an early inflationary stage and that of modern accelerated expansion and satisfies the observational data. There are no small parameters; the effective inflaton mass depends on the initial conditions which explain its small value as compared to the Planck mass. At the modern stage, the size of extra dimensions slowly increases, therefore this model predicts drastic changes in the physical laws of our Universe in the remote future.

  7. Multidimensional visualization and browsing for intelligence analysis

    SciTech Connect

    Crow, V.; Pottier, M.; Thomas, J.

    1994-09-01

    Visualization tools have been invaluable in the process of scientific discovery by providing researchers with insights gained through graphical tools and techniques. At PNL, the Multidimensional Visualization and Advanced Browsing (MVAB) project is extending visualization technology to the problems of intelligence analysis of textual documents by creating spatial representations of textual information. By representing an entire corpus of documents as points in a coordinate space of two or more dimensions, the tools developed by the MVAB team give the analyst the ability to quickly browse the entire document base and determine relationships among documents and publication patterns not readily discernible through traditional lexical means.

  8. Evolution of multidimensional flat anisotropic cosmological models

    SciTech Connect

    Beloborodov, A. ); Demianski, M. Nicolaus Copernicus Astronomical Center, Bartycka 18, 00-716 Warsaw International Center for Relativistic Astrophysics , Universita di Roma I, La Sapienza, Rome ); Ivanov, P.; Polnarev, A.G. )

    1993-07-15

    We study the dynamics of a flat multidimensional anisotropic cosmological model filled with an anisotropic fluidlike medium. By an appropriate choice of variables, the dynamical equations reduce to a two-dimensional dynamical system. We present a detailed analysis of the time evolution of this system and the conditions of the existence of spacetime singularities. We investigate the conditions under which violent, exponential, and power-law inflation is possible. We show that dimensional reduction cannot proceed by anti-inflation (rapid contraction of internal space). Our model indicates that it is very difficult to achieve dimensional reduction by classical means.

  9. The Phenotype of Spontaneous Preterm Birth: Application of a Clinical Phenotyping Tool

    PubMed Central

    Manuck, Tracy A.; Esplin, M. Sean; Biggio, Joseph; Bukowski, Radek; Parry, Samuel; Zhang, Heping; Varner, Michael W.; Andrews, William; Saade, George; Sadovsky, Yoel; Reddy, Uma M.; Ilekis, John

    2015-01-01

    Objective Spontaneous preterm birth (SPTB) is a complex condition that is likely a final common pathway with multiple possible etiologies. We hypothesized that a comprehensive classification system could appropriately group women with similar STPB etiologies, and provide an explanation, at least in part, for the disparities in SPTB associated with race and gestational age at delivery. Study Design Planned analysis of a multicenter, prospective study of singleton SPTB. Women with SPTB < 34 weeks were included. We defined 9 potential SPTB phenotypes based on clinical data, including infection/inflammation, maternal stress, decidual hemorrhage, uterine distention, cervical insufficiency, placental dysfunction, premature rupture of the membranes, maternal comorbidities, and familial factors. Each woman was evaluated for each phenotype. Delivery gestational age was compared between those with and without each phenotype. Phenotype profiles were also compared between women with very early (20.0–27.9 weeks) SPTB vs. those with early SPTB (28.0–34.0 weeks), and between African-American and Caucasian women. Statistical analysis was by t-test and chi-square as appropriate. Results The phenotyping tool was applied to 1025 women with SPTB who delivered at a mean 30.0 (+/− 3.2) weeks gestation. Of these, 800 (78%) had ≥2 phenotypes. Only 43 (4.2%) had no phenotypes. The 281 women with early SPTB were more likely to have infection/inflammation, decidual hemorrhage, and cervical insufficiency phenotypes (all p≤0.001). African-American women had more maternal stress and cervical insufficiency but less decidual hemorrhage and placental dysfunction compared to Caucasian women (all p<0.05). Gestational age at delivery decreased as the number of phenotypes present increased. Conclusions Precise SPTB phenotyping classifies women with SPTB and identifies specific differences between very early and early SPTB and between African-Americans and Caucasians. PMID:25687564

  10. The integrated phenotype.

    PubMed

    Murren, Courtney J

    2012-07-01

    Proper functioning of complex phenotypes requires that multiple traits work together. Examination of relationships among traits within and between complex characters and how they interact to function as a whole organism is critical to advancing our understanding of evolutionary developmental plasticity. Phenotypic integration refers to the relationships among multiple characters of a complex phenotype, and their relationships with other functional units (modules) in an organism. In this review, I summarize a brief history of the concept of phenotypic integration in plant and animal biology. Following an introduction of concepts, including modularity, I use an empirical case-study approach to highlight recent advance in clarifying the developmental and genomic basis of integration. I end by highlighting some novel approaches to genomic and epigenetic perturbations that offer promise in further addressing the role of phenotypic integration in evolutionary diversification. In the age of the phenotype, studies that examine the genomic and developmental changes in relationships of traits across environments will shape the next chapter in our quest for understanding the evolution of complex characters.

  11. Multidimensional Modeling of Coronal Rain Dynamics

    NASA Astrophysics Data System (ADS)

    Fang, X.; Xia, C.; Keppens, R.

    2013-07-01

    We present the first multidimensional, magnetohydrodynamic simulations that capture the initial formation and long-term sustainment of the enigmatic coronal rain phenomenon. We demonstrate how thermal instability can induce a spectacular display of in situ forming blob-like condensations which then start their intimate ballet on top of initially linear force-free arcades. Our magnetic arcades host a chromospheric, transition region, and coronal plasma. Following coronal rain dynamics for over 80 minutes of physical time, we collect enough statistics to quantify blob widths, lengths, velocity distributions, and other characteristics which directly match modern observational knowledge. Our virtual coronal rain displays the deformation of blobs into V-shaped features, interactions of blobs due to mostly pressure-mediated levitations, and gives the first views of blobs that evaporate in situ or are siphoned over the apex of the background arcade. Our simulations pave the way for systematic surveys of coronal rain showers in true multidimensional settings to connect parameterized heating prescriptions with rain statistics, ultimately allowing us to quantify the coronal heating input.

  12. Heterogeneous multidimensional scaling for complex networks

    NASA Astrophysics Data System (ADS)

    Xuan, Qi; Ma, Xiaodi; Fu, Chenbo; Dong, Hui; Zhang, Guijun; Yu, Li

    2015-07-01

    Many real-world networks are essentially heterogeneous, where the nodes have different abilities to gain connections. Such networks are difficult to be embedded into low-dimensional Euclidean space if we ignore the heterogeneity and treat all the nodes equally. In this paper, based on a newly defined heterogeneous distance and a generalized network distance under the constraints of network and triangle inequalities, respectively, we propose a new heterogeneous multidimensional scaling method (HMDS) to embed different networks into proper Euclidean spaces. We find that HMDS behaves much better than the traditional multidimensional scaling method (MDS) in embedding different artificial and real-world networks into Euclidean spaces. Besides, we also propose a method to estimate the appropriate dimensions of Euclidean spaces for different networks, and find that the estimated dimensions are quite close to the real dimensions for those geometrical networks under study. These methods thus can help to better understand the evolution of real-world networks, and have practical importance in network visualization, community detection, link prediction and localization of wireless sensors.

  13. Visualizing multidimensional query results using animation

    NASA Astrophysics Data System (ADS)

    Sawant, Amit P.; Healey, Christopher G.

    2008-01-01

    Effective representation of large, complex collections of information (datasets) presents a difficult challenge. Visualization is a solution that uses a visual interface to support efficient analysis and discovery within the data. Our primary goal in this paper is a technique that allows viewers to compare multiple query results representing user-selected subsets of a multidimensional dataset. We present an algorithm that visualizes multidimensional information along a space-filling spiral. Graphical glyphs that vary their position, color, and texture appearance are used to represent attribute values for the data elements in each query result. Guidelines from human perception allow us to construct glyphs that are specifically designed to support exploration, facilitate the discovery of trends and relationships both within and between data elements, and highlight exceptions. A clustering algorithm applied to a user-chosen ranking attribute bundles together similar data elements. This encapsulation is used to show relationships across different queries via animations that morph between query results. We apply our techniques to the MovieLens recommender system, to demonstrate their applicability in a real-world environment, and then conclude with a simple validation experiment to identify the strengths and limitations of our design, compared to a traditional side-by-side visualization.

  14. MULTIDIMENSIONAL MODELING OF CORONAL RAIN DYNAMICS

    SciTech Connect

    Fang, X.; Xia, C.; Keppens, R.

    2013-07-10

    We present the first multidimensional, magnetohydrodynamic simulations that capture the initial formation and long-term sustainment of the enigmatic coronal rain phenomenon. We demonstrate how thermal instability can induce a spectacular display of in situ forming blob-like condensations which then start their intimate ballet on top of initially linear force-free arcades. Our magnetic arcades host a chromospheric, transition region, and coronal plasma. Following coronal rain dynamics for over 80 minutes of physical time, we collect enough statistics to quantify blob widths, lengths, velocity distributions, and other characteristics which directly match modern observational knowledge. Our virtual coronal rain displays the deformation of blobs into V-shaped features, interactions of blobs due to mostly pressure-mediated levitations, and gives the first views of blobs that evaporate in situ or are siphoned over the apex of the background arcade. Our simulations pave the way for systematic surveys of coronal rain showers in true multidimensional settings to connect parameterized heating prescriptions with rain statistics, ultimately allowing us to quantify the coronal heating input.

  15. Multidimensional Conservation Laws and Low Regularity Solutions

    SciTech Connect

    Barbara Lee Keyfitz

    2007-06-16

    This is the concluding report for the project, a continuation of research by Keyfitz and co-workers on multidimensional conservation laws, and applications of nonhyperbolic conservation laws in the two-fluid model for multiphase flow. The multidimensional research project was started with Suncica Canic, at the University of Houston and with Eun Heui Kim, now at California State University Long Beach. Two postdoctoral researchers, Katarina Jegdic and Allen Tesdall, also worked on this research. Jegdic's research was supported (for a total of one year) by this grant. Work on nonhyperbolic models for two-phase flows is being pursued jointly with Michael Sever, Hebrew University. Background for the project is contained in earlier reports. Note that in 2006, the project received a one-year no-cost extension that will end in September, 2007. A new proposal, for continuation of the research and for new projects, will be submitted in the Fall of 2007, with funding requested to begin in the summer of 2008. The reason for the 'funding gap' is Keyfitz's four-year stint as Director of the Fields Institute in Toronto, Canada. The research has continued, but has been supported by Canadian grant funds, as seems appropriate during this period.

  16. Computations of entropy bounds: Multidimensional geometric methods

    SciTech Connect

    Makaruk, H.E.

    1998-02-01

    The entropy bounds for constructive upper bound on the needed number-of-bits for solving a dichotomy is represented by the quotient of two multidimensional solid volumes. For minimization of this upper bound exact calculation of the volume of this quotient is needed. Three methods for exact computing of the volume of a given nD volume are presented: (1) general method for calculation any nD volume by slicing it into volumes of decreasing dimension is presented; (2) a method applying appropriate curvilinear coordinate system is described for volume bounded by symmetrical curvilinear hypersurfaces (spheres, cones, hyperboloids, ellipsoids, cylinders, etc.); and (3) an algorithm for dividing any nD complex into simplices and computing of the volume of the simplices is presented, supplemented by a general formula for calculation of volume of an nD simplex. These mathematical methods enable exact calculation of volume of any complicated multidimensional solids. The methods allow for the calculation of the minimal volume and lead to tighter bounds on the needed number-of-bits.

  17. Quantitative classification and natural clustering of Caenorhabditis elegans behavioral phenotypes.

    PubMed

    Geng, Wei; Cosman, Pamela; Baek, Joong-Hwan; Berry, Charles C; Schafer, William R

    2003-11-01

    Genetic analysis of nervous system function relies on the rigorous description of behavioral phenotypes. However, standard methods for classifying the behavioral patterns of mutant Caenorhabditis elegans rely on human observation and are therefore subjective and imprecise. Here we describe the application of machine learning to quantitatively define and classify the behavioral patterns of C. elegans nervous system mutants. We have used an automated tracking and image processing system to obtain measurements of a wide range of morphological and behavioral features from recordings of representative mutant types. Using principal component analysis, we represented the behavioral patterns of eight mutant types as data clouds distributed in multidimensional feature space. Cluster analysis using the k-means algorithm made it possible to quantitatively assess the relative similarities between different behavioral phenotypes and to identify natural phenotypic clusters among the data. Since the patterns of phenotypic similarity identified in this study closely paralleled the functional similarities of the mutant gene products, the complex phenotypic signatures obtained from these image data appeared to represent an effective diagnostic of the mutants' underlying molecular defects.

  18. ICM: a web server for integrated clustering of multi-dimensional biomedical data.

    PubMed

    He, Song; He, Haochen; Xu, Wenjian; Huang, Xin; Jiang, Shuai; Li, Fei; He, Fuchu; Bo, Xiaochen

    2016-07-01

    Large-scale efforts for parallel acquisition of multi-omics profiling continue to generate extensive amounts of multi-dimensional biomedical data. Thus, integrated clustering of multiple types of omics data is essential for developing individual-based treatments and precision medicine. However, while rapid progress has been made, methods for integrated clustering are lacking an intuitive web interface that facilitates the biomedical researchers without sufficient programming skills. Here, we present a web tool, named Integrated Clustering of Multi-dimensional biomedical data (ICM), that provides an interface from which to fuse, cluster and visualize multi-dimensional biomedical data and knowledge. With ICM, users can explore the heterogeneity of a disease or a biological process by identifying subgroups of patients. The results obtained can then be interactively modified by using an intuitive user interface. Researchers can also exchange the results from ICM with collaborators via a web link containing a Project ID number that will directly pull up the analysis results being shared. ICM also support incremental clustering that allows users to add new sample data into the data of a previous study to obtain a clustering result. Currently, the ICM web server is available with no login requirement and at no cost at http://biotech.bmi.ac.cn/icm/.

  19. ICM: a web server for integrated clustering of multi-dimensional biomedical data

    PubMed Central

    He, Song; He, Haochen; Xu, Wenjian; Huang, Xin; Jiang, Shuai; Li, Fei; He, Fuchu; Bo, Xiaochen

    2016-01-01

    Large-scale efforts for parallel acquisition of multi-omics profiling continue to generate extensive amounts of multi-dimensional biomedical data. Thus, integrated clustering of multiple types of omics data is essential for developing individual-based treatments and precision medicine. However, while rapid progress has been made, methods for integrated clustering are lacking an intuitive web interface that facilitates the biomedical researchers without sufficient programming skills. Here, we present a web tool, named Integrated Clustering of Multi-dimensional biomedical data (ICM), that provides an interface from which to fuse, cluster and visualize multi-dimensional biomedical data and knowledge. With ICM, users can explore the heterogeneity of a disease or a biological process by identifying subgroups of patients. The results obtained can then be interactively modified by using an intuitive user interface. Researchers can also exchange the results from ICM with collaborators via a web link containing a Project ID number that will directly pull up the analysis results being shared. ICM also support incremental clustering that allows users to add new sample data into the data of a previous study to obtain a clustering result. Currently, the ICM web server is available with no login requirement and at no cost at http://biotech.bmi.ac.cn/icm/. PMID:27131784

  20. Heteronuclear Multidimensional Protein NMR in a Teaching Laboratory

    ERIC Educational Resources Information Center

    Wright, Nathan T.

    2016-01-01

    Heteronuclear multidimensional NMR techniques are commonly used to study protein structure, function, and dynamics, yet they are rarely taught at the undergraduate level. Here, we describe a senior undergraduate laboratory where students collect, process, and analyze heteronuclear multidimensional NMR experiments using an unstudied Ig domain (Ig2…

  1. Multidimensional Computerized Adaptive Testing for Indonesia Junior High School Biology

    ERIC Educational Resources Information Center

    Kuo, Bor-Chen; Daud, Muslem; Yang, Chih-Wei

    2015-01-01

    This paper describes a curriculum-based multidimensional computerized adaptive test that was developed for Indonesia junior high school Biology. In adherence to the Indonesian curriculum of different Biology dimensions, 300 items was constructed, and then tested to 2238 students. A multidimensional random coefficients multinomial logit model was…

  2. Multidimensional Linking for Tests with Mixed Item Types

    ERIC Educational Resources Information Center

    Yao, Lihua; Boughton, Keith

    2009-01-01

    Numerous assessments contain a mixture of multiple choice (MC) and constructed response (CR) item types and many have been found to measure more than one trait. Thus, there is a need for multidimensional dichotomous and polytomous item response theory (IRT) modeling solutions, including multidimensional linking software. For example,…

  3. Evaluating Item Fit for Multidimensional Item Response Models

    ERIC Educational Resources Information Center

    Zhang, Bo; Stone, Clement A.

    2008-01-01

    This research examines the utility of the s-x[superscript 2] statistic proposed by Orlando and Thissen (2000) in evaluating item fit for multidimensional item response models. Monte Carlo simulation was conducted to investigate both the Type I error and statistical power of this fit statistic in analyzing two kinds of multidimensional test…

  4. Multidimensional Physical Self-Concept of Athletes with Physical Disabilities

    ERIC Educational Resources Information Center

    Shapiro, Deborah R.; Martin, Jeffrey J.

    2010-01-01

    The purposes of this investigation were first to predict reported PA (physical activity) behavior and self-esteem using a multidimensional physical self-concept model and second to describe perceptions of multidimensional physical self-concept (e.g., strength, endurance, sport competence) among athletes with physical disabilities. Athletes (N =…

  5. The Concept of Aptitude and Multidimensional Validity Revisited.

    ERIC Educational Resources Information Center

    Roeser, Robert W.; Shavelson, Richard J.; Kupermintz, Haggai; Lau, Shun; Ayala, Carlos; Haydel, Angela; Schultz, Susan; Gallagher, Larry; Quihuis, Gisell

    2002-01-01

    Provides an overview of the approach of Richard E. Snow to the concept of aptitude and multidimensional validity and summarizes the studies in this special issue. Overall, studies confirmed the multidimensional structure of science achievement scores, the validity of some key motivational constructs for predicting achievement, and other ideas…

  6. Entropic uncertainty relations in multidimensional position and momentum spaces

    SciTech Connect

    Huang Yichen

    2011-05-15

    Commutator-based entropic uncertainty relations in multidimensional position and momentum spaces are derived, twofold generalizing previous entropic uncertainty relations for one-mode states. They provide optimal lower bounds and imply the multidimensional variance-based uncertainty principle. The article concludes with an open conjecture.

  7. Characterization of systemic metabolic phenotypes associated with subclinical atherosclerosis.

    PubMed

    Würtz, Peter; Soininen, Pasi; Kangas, Antti J; Mäkinen, Ville-Petteri; Groop, Per-Henrik; Savolainen, Markku J; Juonala, Markus; Viikari, Jorma S; Kähönen, Mika; Lehtimäki, Terho; Raitakari, Olli T; Ala-Korpela, Mika

    2011-02-01

    Detailed molecular phenotyping gives insight into disease mechanisms and can individualize medical practice for improved risk assessment and treatment. We show in an epidemiological study (n = 4309) that the multi-metabolic profiles obtained by serum NMR metabonomics inherently associate with the extent of atherosclerosis already in preclinical stages. Data-driven analysis of the spectral profiles of healthy, young adults revealed three distinct metabolic phenotypes associated with high carotid intima-media thickness (IMT), a surrogate marker of cardiovascular disease. The phenotypes were characterized by varying combinations of well-known metabolic disturbances like elevated VLDL and LDL and low HDL levels. Low IMT was also associated with distinct metabolic phenotypes with lipoprotein as well as other biochemical characteristics partly opposing those found for the high IMT phenotypes. Profiles of low-molecular-weight metabolites quantified from the experimentation were also characteristic for the metabolic phenotypes and substantiate developments toward the use of multi-metabolic risk phenotypes. The methodology can be taken as a direct extension for the routine analytics used for the risk assessment of atherosclerosis; quantification of metabolites will complement and might even replace conventional lipid measurements. Serum NMR metabonomics is therefore anticipated as a rational option for comprehensive cardiovascular risk assessment.

  8. Behavioural phenotypes predict disease susceptibility and infectiousness.

    PubMed

    Araujo, Alessandra; Kirschman, Lucas; Warne, Robin W

    2016-08-01

    Behavioural phenotypes may provide a means for identifying individuals that disproportionally contribute to disease spread and epizootic outbreaks. For example, bolder phenotypes may experience greater exposure and susceptibility to pathogenic infection because of distinct interactions with conspecifics and their environment. We tested the value of behavioural phenotypes in larval amphibians for predicting ranavirus transmission in experimental trials. We found that behavioural phenotypes characterized by latency-to-food and swimming profiles were predictive of disease susceptibility and infectiousness defined as the capacity of an infected host to transmit an infection by contacts. While viral shedding rates were positively associated with transmission, we also found an inverse relationship between contacts and infections. Together these results suggest intrinsic traits that influence behaviour and the quantity of pathogens shed during conspecific interactions may be an important contributor to ranavirus transmission. These results suggest that behavioural phenotypes provide a means to identify individuals more likely to spread disease and thus give insights into disease outbreaks that threaten wildlife and humans. PMID:27555652

  9. Multidimensional scaling of musical time estimations.

    PubMed

    Cocenas-Silva, Raquel; Bueno, José Lino Oliveira; Molin, Paul; Bigand, Emmanuel

    2011-06-01

    The aim of this study was to identify the psycho-musical factors that govern time evaluation in Western music from baroque, classic, romantic, and modern repertoires. The excerpts were previously found to represent variability in musical properties and to induce four main categories of emotions. 48 participants (musicians and nonmusicians) freely listened to 16 musical excerpts (lasting 20 sec. each) and grouped those that seemed to have the same duration. Then, participants associated each group of excerpts to one of a set of sine wave tones varying in duration from 16 to 24 sec. Multidimensional scaling analysis generated a two-dimensional solution for these time judgments. Musical excerpts with high arousal produced an overestimation of time, and affective valence had little influence on time perception. The duration was also overestimated when tempo and loudness were higher, and to a lesser extent, timbre density. In contrast, musical tension had little influence. PMID:21853763

  10. AMADA-Analysis of multidimensional astronomical datasets

    NASA Astrophysics Data System (ADS)

    de Souza, R. S.; Ciardi, B.

    2015-09-01

    We present AMADA, an interactive web application to analyze multidimensional datasets. The user uploads a simple ASCII file and AMADA performs a number of exploratory analysis together with contemporary visualizations diagnostics. The package performs a hierarchical clustering in the parameter space, and the user can choose among linear, monotonic or non-linear correlation analysis. AMADA provides a number of clustering visualization diagnostics such as heatmaps, dendrograms, chord diagrams, and graphs. In addition, AMADA has the option to run a standard or robust principal components analysis, displaying the results as polar bar plots. The code is written in R and the web interface was created using the SHINY framework. AMADA source-code is freely available at https://goo.gl/KeSPue, and the shiny-app at http://goo.gl/UTnU7I.

  11. Multidimensional Electronic Spectroscopy of Photochemical Reactions.

    PubMed

    Nuernberger, Patrick; Ruetzel, Stefan; Brixner, Tobias

    2015-09-21

    Coherent multidimensional electronic spectroscopy can be employed to unravel various channels in molecular chemical reactions. This approach is thus not limited to analysis of energy transfer or charge transfer (i.e. processes from photophysics), but can also be employed in situations where the investigated system undergoes permanent structural changes (i.e. in photochemistry). Photochemical model reactions are discussed by using the example of merocyanine/spiropyran-based molecular switches, which show a rich variety of reaction channels, in particular ring opening and ring closing, cis-trans isomerization, coherent vibrational wave-packet motion, radical ion formation, and population relaxation. Using pump-probe, pump-repump-probe, coherent two-dimensional and three-dimensional, triggered-exchange 2D, and quantum-control spectroscopy, we gain intuitive pictures on which product emerges from which reactant and which reactive molecular modes are associated. PMID:26382095

  12. Multidimensional student skills with collaborative filtering

    NASA Astrophysics Data System (ADS)

    Bergner, Yoav; Rayyan, Saif; Seaton, Daniel; Pritchard, David E.

    2013-01-01

    Despite the fact that a physics course typically culminates in one final grade for the student, many instructors and researchers believe that there are multiple skills that students acquire to achieve mastery. Assessment validation and data analysis in general may thus benefit from extension to multidimensional ability. This paper introduces an approach for model determination and dimensionality analysis using collaborative filtering (CF), which is related to factor analysis and item response theory (IRT). Model selection is guided by machine learning perspectives, seeking to maximize the accuracy in predicting which students will answer which items correctly. We apply the CF to response data for the Mechanics Baseline Test and combine the results with prior analysis using unidimensional IRT.

  13. Multidimensional multiphysics simulation of TRISO particle fuel

    NASA Astrophysics Data System (ADS)

    Hales, J. D.; Williamson, R. L.; Novascone, S. R.; Perez, D. M.; Spencer, B. W.; Pastore, G.

    2013-11-01

    Multidimensional multiphysics analysis of TRISO-coated particle fuel using the BISON finite element nuclear fuels code is described. The governing equations and material models applicable to particle fuel and implemented in BISON are outlined. Code verification based on a recent IAEA benchmarking exercise is described, and excellent comparisons are reported. Multiple TRISO-coated particles of increasing geometric complexity are considered. The code's ability to use the same algorithms and models to solve problems of varying dimensionality from 1D through 3D is demonstrated. The code provides rapid solutions of 1D spherically symmetric and 2D axially symmetric models, and its scalable parallel processing capability allows for solutions of large, complex 3D models. Additionally, the flexibility to easily include new physical and material models and straightforward ability to couple to lower length scale simulations makes BISON a powerful tool for simulation of coated-particle fuel. Future code development activities and potential applications are identified.

  14. Multidimensional Multiphysics Simulation of TRISO Particle Fuel

    SciTech Connect

    J. D. Hales; R. L. Williamson; S. R. Novascone; D. M. Perez; B. W. Spencer; G. Pastore

    2013-11-01

    Multidimensional multiphysics analysis of TRISO-coated particle fuel using the BISON finite-element based nuclear fuels code is described. The governing equations and material models applicable to particle fuel and implemented in BISON are outlined. Code verification based on a recent IAEA benchmarking exercise is described, and excellant comparisons are reported. Multiple TRISO-coated particles of increasing geometric complexity are considered. It is shown that the code's ability to perform large-scale parallel computations permits application to complex 3D phenomena while very efficient solutions for either 1D spherically symmetric or 2D axisymmetric geometries are straightforward. Additionally, the flexibility to easily include new physical and material models and uncomplicated ability to couple to lower length scale simulations makes BISON a powerful tool for simulation of coated-particle fuel. Future code development activities and potential applications are identified.

  15. Path integral learning of multidimensional movement trajectories

    NASA Astrophysics Data System (ADS)

    André, João; Santos, Cristina; Costa, Lino

    2013-10-01

    This paper explores the use of Path Integral Methods, particularly several variants of the recent Path Integral Policy Improvement (PI2) algorithm in multidimensional movement parametrized policy learning. We rely on Dynamic Movement Primitives (DMPs) to codify discrete and rhythmic trajectories, and apply the PI2-CMA and PIBB methods in the learning of optimal policy parameters, according to different cost functions that inherently encode movement objectives. Additionally we merge both of these variants and propose the PIBB-CMA algorithm, comparing all of them with the vanilla version of PI2. From the obtained results we conclude that PIBB-CMA surpasses all other methods in terms of convergence speed and iterative final cost, which leads to an increased interest in its application to more complex robotic problems.

  16. Biological evolution in a multidimensional fitness landscape.

    PubMed

    Saakian, David B; Kirakosyan, Zara; Hu, Chin-Kun

    2012-09-01

    We considered a multiblock molecular model of biological evolution, in which fitness is a function of the mean types of alleles located at different parts (blocks) of the genome. We formulated an infinite population model with selection and mutation, and calculated the mean fitness. For the case of recombination, we formulated a model with a multidimensional fitness landscape (the dimension of the space is equal to the number of blocks) and derived a theorem about the dynamics of initially narrow distribution. We also considered the case of lethal mutations. We also formulated the finite population version of the model in the case of lethal mutations. Our models, derived for the virus evolution, are interesting also for the statistical mechanics and the Hamilton-Jacobi equation as well.

  17. Multi-dimensional Liquid Chromatography in Proteomics

    PubMed Central

    Zhang, Xiang; Fang, Aiqin; Riley, Catherine P.; Wang, Mu; Regnier, Fred E.; Buck, Charles

    2010-01-01

    Proteomics is the large-scale study of proteins, particularly their expression, structures and functions. This still-emerging combination of technologies aims to describe and characterize all expressed proteins in a biological system. Because of upper limits on mass detection of mass spectrometers, proteins are usually digested into peptides and the peptides are then separated, identified and quantified from this complex enzymatic digest. The problem in digesting proteins first and then analyzing the peptide cleavage fragments by mass spectrometry is that huge numbers of peptides are generated that overwhelm direct mass spectral analyses. The objective in the liquid chromatography approach to proteomics is to fractionate peptide mixtures to enable and maximize identification and quantification of the component peptides by mass spectrometry. This review will focus on existing multidimensional liquid chromatographic (MDLC) platforms developed for proteomics and their application in combination with other techniques such as stable isotope labeling. We also provide some perspectives on likely future developments. PMID:20363391

  18. Multidimensional Scaling Visualization Using Parametric Entropy

    NASA Astrophysics Data System (ADS)

    Lopes, António M.; Tenreiro Machado, J. A.; Galhano, Alexandra M.

    2015-12-01

    This paper studies complex systems using a generalized multidimensional scaling (MDS) technique. Complex systems are characterized by time-series responses, interpreted as a manifestation of their dynamics. Two types of time-series are analyzed, namely 18 stock markets and the gross domestic product per capita of 18 countries. For constructing the MDS charts, indices based on parametric entropies are adopted. Multiparameter entropies allow the variation of the parameters leading to alternative sets of charts. The final MDS maps are then assembled by means of Procrustes’ method that maximizes the fit between the individual charts. Therefore, the proposed method can be interpreted as a generalization to higher dimensions of the standard technique that represents (and discretizes) items by means of single “points” (i.e. zero-dimensional “objects”). The MDS plots, involving one-, two- and three-dimensional “objects”, reveal a good performance in capturing the correlations between data.

  19. The path decomposition expansion and multidimensional tunneling

    NASA Astrophysics Data System (ADS)

    Auerbach, Assa; Kivelson, S.

    This paper consists of two main topics. (i) The path decomposition expansion: a new path integral technique which allows us to break configuration space into disjoint regions and express the dynamics of the full system in terms of its parts. (ii) The application of the PDX and semiclassical methods for solving quantum-mechanical tunneling problems in multidimensions. The result is a conceptually simple, computationally straightforward method for calculating tunneling effects in complicated multidimensional potentials, even in cases where the nature of the states in the classically allowed regions is nontrivial. Algorithms for computing tunneling effects in general classes of problems are obtained.In addition, we present the detailed solutions to three model problems of a tunneling coordinate coupled to a phonon. This enables us to define various well-controlled approximation schemes, which help to reduce the dimensions of complicated tunneling calculations in real physical systems.

  20. Biological evolution in a multidimensional fitness landscape.

    PubMed

    Saakian, David B; Kirakosyan, Zara; Hu, Chin-Kun

    2012-09-01

    We considered a multiblock molecular model of biological evolution, in which fitness is a function of the mean types of alleles located at different parts (blocks) of the genome. We formulated an infinite population model with selection and mutation, and calculated the mean fitness. For the case of recombination, we formulated a model with a multidimensional fitness landscape (the dimension of the space is equal to the number of blocks) and derived a theorem about the dynamics of initially narrow distribution. We also considered the case of lethal mutations. We also formulated the finite population version of the model in the case of lethal mutations. Our models, derived for the virus evolution, are interesting also for the statistical mechanics and the Hamilton-Jacobi equation as well. PMID:23030957

  1. Multidimensional Langevin Modeling of Nonoverdamped Dynamics

    NASA Astrophysics Data System (ADS)

    Schaudinnus, Norbert; Bastian, Björn; Hegger, Rainer; Stock, Gerhard

    2015-07-01

    Based on a given time series, data-driven Langevin modeling aims to construct a low-dimensional dynamical model of the underlying system. When dealing with physical data as provided by, e.g., all-atom molecular dynamics simulations, effects due to small damping may be important to correctly describe the statistics (e.g., the energy landscape) and the dynamics (e.g., transition times). To include these effects in a dynamical model, an algorithm that propagates a second-order Langevin scheme is derived, which facilitates the treatment of multidimensional data. Adopting extensive molecular dynamics simulations of a peptide helix, a five-dimensional model is constructed that successfully forecasts the complex structural dynamics of the system. Neglect of small damping effects, on the other hand, is shown to lead to significant errors and inconsistencies.

  2. Down Syndrome: Cognitive Phenotype

    ERIC Educational Resources Information Center

    Silverman, Wayne

    2007-01-01

    Down syndrome is the most prevalent cause of intellectual impairment associated with a genetic anomaly, in this case, trisomy of chromosome 21. It affects both physical and cognitive development and produces a characteristic phenotype, although affected individuals vary considerably with respect to severity of specific impairments. Studies…

  3. Outstanding Phenotypic Differences in the Profile of Amyloid-β between Tg2576 and APPswe/PS1dE9 Transgenic Mouse Models of Alzheimer’s Disease

    PubMed Central

    Allué, José Antonio; Sarasa, Leticia; Izco, María; Pérez-Grijalba, Virginia; Fandos, Noelia; Pascual-Lucas, María; Ogueta, Samuel; Pesini, Pedro; Sarasa, Manuel

    2016-01-01

    APPswe/PS1dE9 and Tg2576 are very common transgenic mouse models of Alzheimer’s disease (AD), used in many laboratories as tools to research the mechanistic process leading to the disease. In order to augment our knowledge about the amyloid-β (Aβ) isoforms present in both transgenic mouse models, we have developed two chromatographic methods, one acidic and the other basic, for the characterization of the Aβ species produced in the brains of the two transgenic mouse models. After immunoprecipitation and micro-liquid chromatography-electrospray ionization mass spectrometry/mass spectrometry, 10 species of Aβ, surprisingly all of human origin, were detected in the brain of Tg2576 mouse, whereas 39 species, of both murine and human origin, were detected in the brain of the APP/PS1 mouse. To the best of our knowledge, this is the first study showing the identification of such a high number of Aβ species in the brain of the APP/PS1 transgenic mouse, whereas, in contrast, a much lower number of Aβ species were identified in the Tg2576 mouse. Therefore, this study brings to light a relevant phenotypic difference between these two popular mice models of AD. PMID:27258422

  4. Versatile lipid profiling by liquid chromatography-high resolution mass spectrometry using all ion fragmentation and polarity switching. Preliminary application for serum samples phenotyping related to canine mammary cancer.

    PubMed

    Gallart-Ayala, H; Courant, F; Severe, S; Antignac, J-P; Morio, F; Abadie, J; Le Bizec, B

    2013-09-24

    Lipids represent an extended class of substances characterized by such high variety and complexity that makes their unified analyses by liquid chromatography coupled to either high resolution or tandem mass spectrometry (LC-HRMS or LC-MS/MS) a real challenge. In the present study, a new versatile methodology associating ultra high performance liquid chromatography coupled to high resolution tandem mass spectrometry (UHPLC-HRMS/MS) have been developed for a comprehensive analysis of lipids. The use of polarity switching and "all ion fragmentation" (AIF) have been two action levels particularly exploited to finally permit the detection and identification of a multi-class and multi-analyte extended range of lipids in a single run. For identification purposes, both higher energy collision dissociation (HCD) and in-source CID (collision induced dissociation) fragmentation were evaluated in order to obtain information about the precursor and product ions in the same spectra. This approach provides both class-specific and lipid-specific fragments, enhancing lipid identification. Finally, the developed method was applied for differential phenotyping of serum samples collected from pet dogs developing spontaneous malignant mammary tumors and health controls. A biological signature associated with the presence of cancer was then successfully revealed from this lipidome analysis, which required to be further investigated and confirmed at larger scale.

  5. A study of multidimensional modeling approaches for data warehouse

    NASA Astrophysics Data System (ADS)

    Yusof, Sharmila Mat; Sidi, Fatimah; Ibrahim, Hamidah; Affendey, Lilly Suriani

    2016-08-01

    Data warehouse system is used to support the process of organizational decision making. Hence, the system must extract and integrate information from heterogeneous data sources in order to uncover relevant knowledge suitable for decision making process. However, the development of data warehouse is a difficult and complex process especially in its conceptual design (multidimensional modeling). Thus, there have been various approaches proposed to overcome the difficulty. This study surveys and compares the approaches of multidimensional modeling and highlights the issues, trend and solution proposed to date. The contribution is on the state of the art of the multidimensional modeling design.

  6. Multidimensional displacement vector measurement methods utilizing instantaneous phase.

    PubMed

    Sumi, Chikayoshi

    2005-01-01

    In this report, we propose two new methods for measuring multidimensional displacement vector using instantaneous ultrasound signal phase, i.e., the multidimensional autocorrelation method and the multidimensional Doppler's method. In order to realize high measurement accuracy, respective displacement vector measurement methods are combined with our proposed useful lateral modulation method, i.e., the lateral Gaussian envelop cosine modulation method. We further report measurement accuracy evaluated through simulations. These methods can be applied to tissue strain measurement, blood flow measurement, sonar measurement, etc.

  7. Stem cells isolated from adipose tissue of obese patients show changes in their transcriptomic profile that indicate loss in stemcellness and increased commitment to an adipocyte-like phenotype

    PubMed Central

    2013-01-01

    Background The adipose tissue is an endocrine regulator and a risk factor for atherosclerosis and cardiovascular disease when by excessive accumulation induces obesity. Although the adipose tissue is also a reservoir for stem cells (ASC) their function and “stemcellness” has been questioned. Our aim was to investigate the mechanisms by which obesity affects subcutaneous white adipose tissue (WAT) stem cells. Results Transcriptomics, in silico analysis, real-time polymerase chain reaction (PCR) and western blots were performed on isolated stem cells from subcutaneous abdominal WAT of morbidly obese patients (ASCmo) and of non-obese individuals (ASCn). ASCmo and ASCn gene expression clustered separately from each other. ASCmo showed downregulation of “stemness” genes and upregulation of adipogenic and inflammatory genes with respect to ASCn. Moreover, the application of bioinformatics and Ingenuity Pathway Analysis (IPA) showed that the transcription factor Smad3 was tentatively affected in obese ASCmo. Validation of this target confirmed a significantly reduced Smad3 nuclear translocation in the isolated ASCmo. Conclusions The transcriptomic profile of the stem cells reservoir in obese subcutaneous WAT is highly modified with significant changes in genes regulating stemcellness, lineage commitment and inflammation. In addition to body mass index, cardiovascular risk factor clustering further affect the ASC transcriptomic profile inducing loss of multipotency and, hence, capacity for tissue repair. In summary, the stem cells in the subcutaneous WAT niche of obese patients are already committed to adipocyte differentiation and show an upregulated inflammatory gene expression associated to their loss of stemcellness. PMID:24040759

  8. Phenotypic approaches to drought in cassava: review.

    PubMed

    Okogbenin, Emmanuel; Setter, Tim L; Ferguson, Morag; Mutegi, Rose; Ceballos, Hernan; Olasanmi, Bunmi; Fregene, Martin

    2013-01-01

    Cassava is an important crop in Africa, Asia, Latin America, and the Caribbean. Cassava can be produced adequately in drought conditions making it the ideal food security crop in marginal environments. Although cassava can tolerate drought stress, it can be genetically improved to enhance productivity in such environments. Drought adaptation studies in over three decades in cassava have identified relevant mechanisms which have been explored in conventional breeding. Drought is a quantitative trait and its multigenic nature makes it very challenging to effectively manipulate and combine genes in breeding for rapid genetic gain and selection process. Cassava has a long growth cycle of 12-18 months which invariably contributes to a long breeding scheme for the crop. Modern breeding using advances in genomics and improved genotyping, is facilitating the dissection and genetic analysis of complex traits including drought tolerance, thus helping to better elucidate and understand the genetic basis of such traits. A beneficial goal of new innovative breeding strategies is to shorten the breeding cycle using minimized, efficient or fast phenotyping protocols. While high throughput genotyping have been achieved, this is rarely the case for phenotyping for drought adaptation. Some of the storage root phenotyping in cassava are often done very late in the evaluation cycle making selection process very slow. This paper highlights some modified traits suitable for early-growth phase phenotyping that may be used to reduce drought phenotyping cycle in cassava. Such modified traits can significantly complement the high throughput genotyping procedures to fast track breeding of improved drought tolerant varieties. The need for metabolite profiling, improved phenomics to take advantage of next generation sequencing technologies and high throughput phenotyping are basic steps for future direction to improve genetic gain and maximize speed for drought tolerance breeding.

  9. Phenotypic approaches to drought in cassava: review

    PubMed Central

    Okogbenin, Emmanuel; Setter, Tim L.; Ferguson, Morag; Mutegi, Rose; Ceballos, Hernan; Olasanmi, Bunmi; Fregene, Martin

    2012-01-01

    Cassava is an important crop in Africa, Asia, Latin America, and the Caribbean. Cassava can be produced adequately in drought conditions making it the ideal food security crop in marginal environments. Although cassava can tolerate drought stress, it can be genetically improved to enhance productivity in such environments. Drought adaptation studies in over three decades in cassava have identified relevant mechanisms which have been explored in conventional breeding. Drought is a quantitative trait and its multigenic nature makes it very challenging to effectively manipulate and combine genes in breeding for rapid genetic gain and selection process. Cassava has a long growth cycle of 12–18 months which invariably contributes to a long breeding scheme for the crop. Modern breeding using advances in genomics and improved genotyping, is facilitating the dissection and genetic analysis of complex traits including drought tolerance, thus helping to better elucidate and understand the genetic basis of such traits. A beneficial goal of new innovative breeding strategies is to shorten the breeding cycle using minimized, efficient or fast phenotyping protocols. While high throughput genotyping have been achieved, this is rarely the case for phenotyping for drought adaptation. Some of the storage root phenotyping in cassava are often done very late in the evaluation cycle making selection process very slow. This paper highlights some modified traits suitable for early-growth phase phenotyping that may be used to reduce drought phenotyping cycle in cassava. Such modified traits can significantly complement the high throughput genotyping procedures to fast track breeding of improved drought tolerant varieties. The need for metabolite profiling, improved phenomics to take advantage of next generation sequencing technologies and high throughput phenotyping are basic steps for future direction to improve genetic gain and maximize speed for drought tolerance breeding. PMID

  10. Development and Validation of Triarchic Psychopathy Scales from the Multidimensional Personality Questionnaire

    PubMed Central

    Brislin, Sarah J.; Drislane, Laura E.; Smith, Shannon Toney; Edens, John F.; Patrick, Christopher J.

    2015-01-01

    Psychopathy is conceptualized by the triarchic model as encompassing three distinct phenotypic constructs: boldness, meanness, and disinhibition. In the current study, the Multidimensional Personality Questionnaire (MPQ), a normal-range personality measure, was evaluated for representation of these three constructs. Consensus ratings were used to identify MPQ items most related to each triarchic (Tri) construct. Scale measures were developed from items indicative of each construct, and scores for these scales were evaluated for convergent and discriminant validity in community (N = 176) and incarcerated samples (N = 240). A cross the two samples, MPQ-Tri scale scores demonstrated good internal consistencies and relationships with criterion measures of various types consistent with predictions based on the triarchic model. Findings are discussed in terms of their implications for further investigation of the triarchic model constructs in preexisting datasets that include the MPQ, in particular longitudinal and genetically informative datasets. PMID:25642934

  11. NASA Multidimensional Stirling Convertor Code Developed

    NASA Technical Reports Server (NTRS)

    Tew, Roy C.; Thieme, Lanny G.

    2004-01-01

    A high-efficiency Stirling Radioisotope Generator (SRG) for use on potential NASA Space Science missions is being developed by the Department of Energy, Lockheed Martin, Stirling Technology Company, and the NASA Glenn Research Center. These missions may include providing spacecraft onboard electric power for deep space missions or power for unmanned Mars rovers. Glenn is also developing advanced technology for Stirling convertors, aimed at substantially improving the specific power and efficiency of the convertor and the overall power system. Performance and mass improvement goals have been established for second- and third-generation Stirling radioisotope power systems. Multiple efforts are underway to achieve these goals, both in house at Glenn and under various grants and contracts. These efforts include the development of a multidimensional Stirling computational fluid dynamics code, high-temperature materials, advanced controllers, an end-to-end system dynamics model, low-vibration techniques, advanced regenerators, and a lightweight convertor. Under a NASA grant, Cleveland State University (CSU) and its subcontractors, the University of Minnesota (UMN) and Gedeon Associates, have developed a twodimensional computer simulation of a CSUmod Stirling convertor. The CFD-ACE commercial software developed by CFD Research Corp. of Huntsville, Alabama, is being used. The CSUmod is a scaled version of the Stirling Technology Demonstrator Convertor (TDC), which was designed and fabricated by the Stirling Technology Company and is being tested by NASA. The schematic illustrates the structure of this model. Modeled are the fluid-flow and heat-transfer phenomena that occur in the expansion space, the heater, the regenerator, the cooler, the compression space, the surrounding walls, and the moving piston and displacer. In addition, the overall heat transfer, the indicated power, and the efficiency can be calculated. The CSUmod model is being converted to a two

  12. Phenotype-associated lectin-binding profiles of normal and transformed blood cells: a comparative analysis of mannose- and galactose-binding lectins from plants and human serum/placenta.

    PubMed

    Mann, K K; André, S; Gabius, H J; Sharp, J G

    1994-10-01

    Surface glycoconjugates of normal and transformed blood cells are commonly characterized by plant lectins. To infer physiological significance of protein-carbohydrate interactions, mammalian lectins are obviously preferable as research tools. So far, human serum lectins have not been used to assess their binding to immunophenotyped human normal or transformed blood cells. Thus, our study combines two groups of lectins with different specificity from plant and human sources. Besides concanavalin A (ConA) we have isolated the mannose-binding protein and serum amyloid P component from human serum. Especially the mannose-binding protein is believed to play a role in host defence against bacteria and yeast cells with unknown impact on normal and tumor cells. These three lectins establish the first group. In addition to the immunomodulatory mistletoe lectin, whose binding can elicit enhanced cytokine secretion from mononuclear blood cells, we included the beta-galactoside-binding lectin (14 kDa) from human placenta in the second group. The initial series of measurements was undertaken using two-color flow cytometry to determine the phenotype-associated binding (based on cluster designation; CD) of the lectins to blood and bone marrow cells from normal donors and the cell line CEM (T-lymphoblastoid), KG1-A (primitive myeloid leukemia) and Croco II (B-lymphoblastoid). Heterogeneity was apparent for each lectin in the CD-defined cell populations. Significant differences in binding were noted between Viscum album agglutinin (VAA) and other lectins for CD4+ cells from blood and between mannose-binding protein (MBP) and VAA versus 14 kDa, ConA and serum amyloid P component (SAP) for CD19+ cells from bone marrow.(ABSTRACT TRUNCATED AT 250 WORDS)

  13. Multiple pathways to identification: exploring the multidimensionality of academic identity formation in ethnic minority males.

    PubMed

    Matthews, Jamaal S

    2014-04-01

    Empirical trends denote the academic underachievement of ethnic minority males across various academic domains. Identity-based explanations for this persistent phenomenon describe ethnic minority males as disidentified with academics, alienated, and oppositional. The present work interrogates these theoretical explanations and empirically substantiates a multidimensional lens for discussing academic identity formation within 330 African American and Latino early-adolescent males. Both hierarchical and iterative person-centered methods were utilized and reveal 5 distinct profiles derived from 6 dimensions of academic identity. These profiles predict self-reported classroom grades, mastery orientation, and self-handicapping in meaningful and varied ways. The results demonstrate multiple pathways to motivation and achievement, challenging previous oversimplified stereotypes of marginalized males. This exploratory study triangulates unique interpersonal and intrapersonal attributes for promoting healthy identity development and academic achievement among ethnic minority adolescent males.

  14. Exploring multidimensional free energy surfaces of peptides

    NASA Astrophysics Data System (ADS)

    Wang, Yan; Kuczera, Krzysztof

    1997-03-01

    A new statistical mechanics thermodynamic integration method is presented, enabling exploration of multidimensional conformational free energy surfaces of large flexible molecules. In this approach a single molecular dynamics simulation in which a set of coordinates has been constrained to fixed values yields the free energy gradient with respect to all coordinates in the set. The availability of the multidimensional gradient opens new possibilities for exploration of molecular conformational free energy surfaces, including free energy optimization to locate free energy minima, calculation of higher free energy derivatives, and finding optimal free energy paths between states. Additionally, choosing of all "soft" degrees of freedom as the constrained set leads to accelerated convergence of averages, effectively overcoming the sampling problem of free energy simulations. Two applications of the method are presented: Helical states of model peptides. For model peptides (Ala)n and (Aib)n where n=6,8,10 and Aib is α-methylalanine in vacuum, free energy maps and free energy optimization in φ-ψ space are used to locate free energy minima corresponding to α-, π- and 3_10-helical structures. The stability of the minima is characterized by calculating numerical second derivatives of the free energy. Free energy decomposition is employed to reveal the molecular mechanism for the improved stability of the 3_10h relative to the ah in Aib-containing peptides. DPDPE peptide pre-organization. For the linear form of the opioid peptide DPDPE in aqueous solution, the effective local sampling made possible by fixing all soft degrees of freedom is used to calculate the free energy difference between the open and cyclic-like structures, providing an estimate of the free energy of pre-organizing the peptide for disulfide bond formation. The open structure was found to be more stable by 4.0 ± 0.8 kcal/mol. The cyclic-like conformation was much better solvated than the open

  15. The Measurement of Self-Rated Depression: A Multidimensional Approach.

    ERIC Educational Resources Information Center

    Bolon, Kevin; Barling, Julian

    1980-01-01

    Investigates the capacity of the Zung Self-Rating Depression Scale for providing specific multidimensional descriptors of depressive behavior. Ideational, physiological and behavioral depression factors were evident in data from 96 normal, white university student volunteers. (Author/RH)

  16. Design of Multidimensional Shinnar-Le Roux RF Pulses

    PubMed Central

    Ma, Chao; Liang, Zhi-Pei

    2014-01-01

    Purpose To generalize the conventional Shinnar-Le Roux (SLR) method for the design of multidimensional RF pulses. Methods Using echo-planar gradients, the multidimensional RF pulse design problem was converted into a series of 1D polynomial design problems. Each of the 1D polynomial design problems was solved efficiently. B0 inhomogeneity compensation and design of spatial-spectral pulses were also considered. Results The proposed method was used to design 2D excitation and refocusing pulses. The results were validated through Bloch equation simulation and experiments on a 3.0 T scanner. Large-tip-angle, equiripple-error, multidimensional excitation was achieved with ripple levels closely matching the design specifications. Conclusion The conventional SLR method can be extended to design multidimensional RF pulses. The proposed method achieves almost equiripple excitation errors, allows easy control of the tradeoff among design parameters, and is computationally efficient. PMID:24578212

  17. A multidimensional subdiffusion model: An arbitrage-free market

    NASA Astrophysics Data System (ADS)

    Li, Guo-Hua; Zhang, Hong; Luo, Mao-Kang

    2012-12-01

    To capture the subdiffusive characteristics of financial markets, the subordinated process, directed by the inverse α-stale subordinator Sα(t) for 0 < α < 1, has been employed as the model of asset prices. In this article, we introduce a multidimensional subdiffusion model that has a bond and K correlated stocks. The stock price process is a multidimensional subdiffusion process directed by the inverse α-stable subordinator. This model describes the period of stagnation for each stock and the behavior of the dependency between multiple stocks. Moreover, we derive the multidimensional fractional backward Kolmogorov equation for the subordinated process using the Laplace transform technique. Finally, using a martingale approach, we prove that the multidimensional subdiffusion model is arbitrage-free, and also gives an arbitrage-free pricing rule for contingent claims associated with the martingale measure.

  18. The space transformation in the simulation of multidimensional random fields

    USGS Publications Warehouse

    Christakos, G.

    1987-01-01

    Space transformations are proposed as a mathematically meaningful and practically comprehensive approach to simulate multidimensional random fields. Within this context the turning bands method of simulation is reconsidered and improved in both the space and frequency domains. ?? 1987.

  19. Central Schemes for Multi-Dimensional Hamilton-Jacobi Equations

    NASA Technical Reports Server (NTRS)

    Bryson, Steve; Levy, Doron; Biegel, Bryan (Technical Monitor)

    2002-01-01

    We present new, efficient central schemes for multi-dimensional Hamilton-Jacobi equations. These non-oscillatory, non-staggered schemes are first- and second-order accurate and are designed to scale well with an increasing dimension. Efficiency is obtained by carefully choosing the location of the evolution points and by using a one-dimensional projection step. First-and second-order accuracy is verified for a variety of multi-dimensional, convex and non-convex problems.

  20. Multidimensional Programming Methods for Energy Facility Siting: Alternative Approaches

    NASA Technical Reports Server (NTRS)

    Solomon, B. D.; Haynes, K. E.

    1982-01-01

    The use of multidimensional optimization methods in solving power plant siting problems, which are characterized by several conflicting, noncommensurable objectives is addressed. After a discussion of data requirements and exclusionary site screening methods for bounding the decision space, classes of multiobjective and goal programming models are discussed in the context of finite site selection. Advantages and limitations of these approaches are highlighted and the linkage of multidimensional methods with the subjective, behavioral components of the power plant siting process is emphasized.

  1. Single cell dynamic phenotyping

    PubMed Central

    Patsch, Katherin; Chiu, Chi-Li; Engeln, Mark; Agus, David B.; Mallick, Parag; Mumenthaler, Shannon M.; Ruderman, Daniel

    2016-01-01

    Live cell imaging has improved our ability to measure phenotypic heterogeneity. However, bottlenecks in imaging and image processing often make it difficult to differentiate interesting biological behavior from technical artifact. Thus there is a need for new methods that improve data quality without sacrificing throughput. Here we present a 3-step workflow to improve dynamic phenotype measurements of heterogeneous cell populations. We provide guidelines for image acquisition, phenotype tracking, and data filtering to remove erroneous cell tracks using the novel Tracking Aberration Measure (TrAM). Our workflow is broadly applicable across imaging platforms and analysis software. By applying this workflow to cancer cell assays, we reduced aberrant cell track prevalence from 17% to 2%. The cost of this improvement was removing 15% of the well-tracked cells. This enabled detection of significant motility differences between cell lines. Similarly, we avoided detecting a false change in translocation kinetics by eliminating the true cause: varied proportions of unresponsive cells. Finally, by systematically seeking heterogeneous behaviors, we detected subpopulations that otherwise could have been missed, including early apoptotic events and pre-mitotic cells. We provide optimized protocols for specific applications and step-by-step guidelines for adapting them to a variety of biological systems. PMID:27708391

  2. Correlative visualization techniques for multidimensional data

    NASA Technical Reports Server (NTRS)

    Treinish, Lloyd A.; Goettsche, Craig

    1989-01-01

    Critical to the understanding of data is the ability to provide pictorial or visual representation of those data, particularly in support of correlative data analysis. Despite the advancement of visualization techniques for scientific data over the last several years, there are still significant problems in bringing today's hardware and software technology into the hands of the typical scientist. For example, there are other computer science domains outside of computer graphics that are required to make visualization effective such as data management. Well-defined, flexible mechanisms for data access and management must be combined with rendering algorithms, data transformation, etc. to form a generic visualization pipeline. A generalized approach to data visualization is critical for the correlative analysis of distinct, complex, multidimensional data sets in the space and Earth sciences. Different classes of data representation techniques must be used within such a framework, which can range from simple, static two- and three-dimensional line plots to animation, surface rendering, and volumetric imaging. Static examples of actual data analyses will illustrate the importance of an effective pipeline in data visualization system.

  3. Multi-dimensionally encoded magnetic resonance imaging

    PubMed Central

    Lin, Fa-Hsuan

    2013-01-01

    Magnetic resonance imaging typically achieves spatial encoding by measuring the projection of a q-dimensional object over q-dimensional spatial bases created by linear spatial encoding magnetic fields (SEMs). Recently, imaging strategies using nonlinear SEMs have demonstrated potential advantages for reconstructing images with higher spatiotemporal resolution and reducing peripheral nerve stimulation. In practice, nonlinear SEMs and linear SEMs can be used jointly to further improve the image reconstruction performance. Here we propose the multi-dimensionally encoded (MDE) MRI to map a q-dimensional object onto a p-dimensional encoding space where p > q. MDE MRI is a theoretical framework linking imaging strategies using linear and nonlinear SEMs. Using a system of eight surface SEM coils with an eight-channel RF coil array, we demonstrate the five-dimensional MDE MRI for a two-dimensional object as a further generalization of PatLoc imaging and O-space imaging. We also present a method of optimizing spatial bases in MDE MRI. Results show that MDE MRI with a higher dimensional encoding space can reconstruct images more efficiently and with a smaller reconstruction error when the k-space sampling distribution and the number of samples are controlled. PMID:22926830

  4. Multi-dimensional cosmology and GUP

    SciTech Connect

    Zeynali, K.; Motavalli, H.; Darabi, F. E-mail: f.darabi@azaruniv.edu

    2012-12-01

    We consider a multidimensional cosmological model with FRW type metric having 4-dimensional space-time and d-dimensional Ricci-flat internal space sectors with a higher dimensional cosmological constant. We study the classical cosmology in commutative and GUP cases and obtain the corresponding exact solutions for negative and positive cosmological constants. It is shown that for negative cosmological constant, the commutative and GUP cases result in finite size universes with smaller size and longer ages, and larger size and shorter age, respectively. For positive cosmological constant, the commutative and GUP cases result in infinite size universes having late time accelerating behavior in good agreement with current observations. The accelerating phase starts in the GUP case sooner than the commutative case. In both commutative and GUP cases, and for both negative and positive cosmological constants, the internal space is stabilized to the sub-Planck size, at least within the present age of the universe. Then, we study the quantum cosmology by deriving the Wheeler-DeWitt equation, and obtain the exact solutions in the commutative case and the perturbative solutions in GUP case, to first order in the GUP small parameter, for both negative and positive cosmological constants. It is shown that good correspondence exists between the classical and quantum solutions.

  5. Proposed empirical gas geothermometer using multidimensional approach

    SciTech Connect

    Supranto; Sudjatmiko; Toha, Budianto; Wintolo, Djoko; Alhamid, Idrus

    1996-01-24

    Several formulas of surface gas geothermometer have been developed to utilize in geothermal exploration, i.e. by D'Amore and Panichi (1980) and by Darling and Talbot (1992). This paper presents an empirical gas geothermometer formula using multidimensional approach. The formula was derived from 37 selected chemical data of the 5 production wells from the Awibengkok Geothermal Volcanic Field in West Java. Seven components, i.e., gas volume percentage, CO2, H2S, CH4, H2, N2, and NH3, from these data are utilize to developed three model equations which represent relationship between temperature and gas compositions. These formulas are then tested by several fumarolic chemical data from Sibual-buali Area (North Sumatera) and from Ringgit Area (South Sumatera). Preliminary result indicated that gas volume percentage, H2S and CO2 concentrations have a significant role in term of gas geothermometer. Further verification is currently in progress.

  6. Multidimensional mass spectrometry-based shotgun lipidomics.

    PubMed

    Wang, Miao; Han, Xianlin

    2014-01-01

    Multidimensional mass spectrometry-based shotgun lipidomics (MDMS-SL) has become a foundational analytical technology platform among current lipidomics practices due to its high efficiency, sensitivity, and reproducibility, as well as its broad coverage. This platform has been broadly used to determine the altered content and/or composition of lipid classes, subclasses, and individual molecular species induced by diseases, genetic manipulations, drug treatments, and aging, among others. Herein, we briefly discuss the principles underlying this technology and present a protocol for routine analysis of many of the lipid classes and subclasses covered by MDMS-SL directly from lipid extracts of biological samples. In particular, lipid sample preparation from a variety of biological materials, which is one of the key components of MDMS-SL, is described in detail. The protocol for mass spectrometric analysis can readily be expanded for analysis of other lipid classes not mentioned as long as appropriate sample preparation is conducted, and should aid researchers in the field to better understand and manage the technology for analysis of cellular lipidomes. PMID:25270931

  7. COMMUNITY READINESS AS A MULTIDIMENSIONAL CONSTRUCT

    PubMed Central

    Chilenski, Sarah M.; Greenberg, Mark T.; Feinberg, Mark E.

    2008-01-01

    Both the organizational studies literature and the community psychology literature discuss the importance of readiness when implementing change. Although each area emphasizes different characteristics, several common themes are present within the literature. The current study integrates and applies organizational and community psychology literature in evaluating community readiness in the context of a school–community–university collaborative prevention model. Results demonstrate (a) that there is substantial agreement between members of community prevention teams on the level of readiness of a community; (b) that readiness is a cohesive, but multidimensional, construct related to hypothesized community and individual characteristics; and (c) that there is small to moderate agreement between members of prevention teams and their “agency directors.” These results support the notion that clear “theories of change” need to be formulated before deciding how to assess community readiness, as assessments will vary due to several factors: the type of respondent, the level in which analyses are conducted, and the specific community domain (i.e., school, workplace collaboration, collaboration experience) investigated. PMID:18714368

  8. The Path Decomposition Expansion and Multidimensional Tunneling

    NASA Astrophysics Data System (ADS)

    Auerbach, Assa

    The dissertation consists of two main topics. (a) The Path Decomposition Expansion (PDX): A new path integral technique which allows us to break configuration space into disjoint regions, and express the dynamics of the full system in terms of its parts. (b) The application of the PDX and semiclassical methods for solving quantum -mechanical problems in multidimensions. The result is a conceptually simple, computationally straightforward method for calculating tunneling effects in complicated multidimensional potentials, even in cases where the nature of the states in the classically allowed regions in nontrivial. Algorithms for computing tunneling effects in general classes of problems are obtained. The detailed solutions to several model problems are presented. These enable us to define various well -controlled approximation schemes, which help to reduce the dimensions of complicated tunneling calculations in real physical systems. The dramatic effects of transverse fluctuations on the asymptotic behavior of the groundstate tunnel-splitting are studied also in potentials with non -quadratic minima where standard instanton techniques fail. The power of the PDX is demonstrated by a calculation of the optical absorption coefficient of trans-polyacetylene where large amplitude (non-perturbative) quantum fluctuations of the lattice play an important role in determining the sub-gap absorption tail. Good agreement with experimental data is found, and suggestions for further measurements in this regime are made.

  9. Multidimensional time-correlated single photon counting

    NASA Astrophysics Data System (ADS)

    Becker, Wolfgang; Bergmann, Axel

    2006-10-01

    Time-correlated single photon counting (TCSPC) is based on the detection of single photons of a periodic light signal, measurement of the detection time of the photons, and the build-up of the photon distribution versus the time in the signal period. TCSPC achieves a near ideal counting efficiency and transit-time-spread-limited time resolution for a given detector. The drawback of traditional TCSPC is the low count rate, long acquisition time, and the fact that the technique is one-dimensional, i.e. limited to the recording of the pulse shape of light signals. We present an advanced TCSPC technique featuring multi-dimensional photon acquisition and a count rate close to the capability of currently available detectors. The technique is able to acquire photon distributions versus wavelength, spatial coordinates, and the time on the ps scale, and to record fast changes in the fluorescence lifetime and fluorescence intensity of a sample. Biomedical applications of advanced TCSPC techniques are time-domain optical tomography, recording of transient phenomena in biological systems, spectrally resolved fluorescence lifetime imaging, FRET experiments in living cells, and the investigation of dye-protein complexes by fluorescence correlation spectroscopy. We demonstrate the potential of the technique for selected applications.

  10. Multidimensional In Vivo Hazard Assessment Using Zebrafish

    PubMed Central

    Tanguay, Robert L.

    2014-01-01

    There are tens of thousands of man-made chemicals in the environment; the inherent safety of most of these chemicals is not known. Relevant biological platforms and new computational tools are needed to prioritize testing of chemicals with limited human health hazard information. We describe an experimental design for high-throughput characterization of multidimensional in vivo effects with the power to evaluate trends relating to commonly cited chemical predictors. We evaluated all 1060 unique U.S. EPA ToxCast phase 1 and 2 compounds using the embryonic zebrafish and found that 487 induced significant adverse biological responses. The utilization of 18 simultaneously measured endpoints means that the entire system serves as a robust biological sensor for chemical hazard. The experimental design enabled us to describe global patterns of variation across tested compounds, evaluate the concordance of the available in vitro and in vivo phase 1 data with this study, highlight specific mechanisms/value-added/novel biology related to notochord development, and demonstrate that the developmental zebrafish detects adverse responses that would be missed by less comprehensive testing strategies. PMID:24136191

  11. Multidimensional thermal-chemical cookoff modeling

    SciTech Connect

    Baer, M.R.; Gross, R.J.; Gartling, D.K.; Hobbs, M.L.

    1994-08-01

    Multidimensional thermal/chemical modeling is an essential step in the development of a predictive capability for cookoff of energetic materials in systems subjected to abnormal thermal environments. COYOTE II is a state-of-the-art two- and three-dimensional finite element code for the solution of heat conduction problems including surface-to-surface thermal radiation heat transfer and decomposition chemistry. Multistep finite rate chemistry is incorporated into COYOTE II using an operator-splitting methodology; rate equations are solved element-by-element with a modified matrix-free stiff solver, CHEMEQ. COYOTE II is purposely designed with a user-oriented input structure compatible with the database, the pre-processing mesh generation, and the post-processing tools for data visualization shared with other engineering analysis codes available at Sandia National Laboratories. As demonstrated in a companion paper, decomposition during cookoff in a confined or semi-confined system leads to significant mechanical behavior. Although mechanical effect are not presently considered in COYOTE II, the formalism for including mechanics in multidimensions is under development.

  12. Multidimensional View of the Bacterial Cytoskeleton

    PubMed Central

    Celler, Katherine; Koning, Roman I.; Koster, Abraham J.

    2013-01-01

    The perspective of the cytoskeleton as a feature unique to eukaryotic organisms was overturned when homologs of the eukaryotic cytoskeletal elements were identified in prokaryotes and implicated in major cell functions, including growth, morphogenesis, cell division, DNA partitioning, and cell motility. FtsZ and MreB were the first identified homologs of tubulin and actin, respectively, followed by the discovery of crescentin as an intermediate filament-like protein. In addition, new elements were identified which have no apparent eukaryotic counterparts, such as the deviant Walker A-type ATPases, bactofilins, and several novel elements recently identified in streptomycetes, highlighting the unsuspected complexity of cytostructural components in bacteria. In vivo multidimensional fluorescence microscopy has demonstrated the dynamics of the bacterial intracellular world, and yet we are only starting to understand the role of cytoskeletal elements. Elucidating structure-function relationships remains challenging, because core cytoskeletal protein motifs show remarkable plasticity, with one element often performing various functions and one function being performed by several types of elements. Structural imaging techniques, such as cryo-electron tomography in combination with advanced light microscopy, are providing the missing links and enabling scientists to answer many outstanding questions regarding prokaryotic cellular architecture. Here we review the recent advances made toward understanding the different roles of cytoskeletal proteins in bacteria, with particular emphasis on modern imaging approaches. PMID:23417493

  13. Multidimensional multiphysics simulation of nuclear fuel behavior

    NASA Astrophysics Data System (ADS)

    Williamson, R. L.; Hales, J. D.; Novascone, S. R.; Tonks, M. R.; Gaston, D. R.; Permann, C. J.; Andrs, D.; Martineau, R. C.

    2012-04-01

    Nuclear fuel operates in an environment that induces complex multiphysics phenomena, occurring over distances ranging from inter-atomic spacing to meters, and times scales ranging from microseconds to years. This multiphysics behavior is often tightly coupled and many important aspects are inherently multidimensional. Most current fuel modeling codes employ loose multiphysics coupling and are restricted to 2D axisymmetric or 1.5D approximations. This paper describes a new modeling tool able to simulate coupled multiphysics and multiscale fuel behavior, for either 2D axisymmetric or 3D geometries. Specific fuel analysis capabilities currently implemented in this tool are described, followed by a set of demonstration problems which include a 10-pellet light water reactor fuel rodlet, three-dimensional analysis of pellet clad mechanical interaction in the vicinity of a defective fuel pellet, coupled heat transfer and fission product diffusion in a TRISO-coated fuel particle, a demonstration of the ability to couple to lower-length scale models to account for material property variation with microstructural evolution, and a demonstration of the tool's ability to efficiently solve very large and complex problems using massively-parallel computing. A final section describes an early validation exercise, comparing simulation results to a light water reactor fuel rod experiment.

  14. The gene expression profile of psoralen plus UVA-induced premature senescence in skin fibroblasts resembles a combined DNA-damage and stress-induced cellular senescence response phenotype.

    PubMed

    Borlon, Céline; Debacq-Chainiaux, Florence; Hinrichs, Christina; Scharffetter-Kochanek, Karin; Toussaint, Olivier; Wlaschek, Meinhard

    2007-09-01

    After a finite number of population doublings, normal human cells undergo replicative senescence accompanied by growth arrest. We previously described a model of stress-induced premature senescence by treatment of dermal fibroblasts with psoralen plus UVA, a common photodermatological therapy. Psoralen photoactivation has long been used as a therapy for hyperproliferative skin disorders. The repetitive therapeutical treatment is accompanied by premature aging of the skin. Treatment of fibroblasts in vitro with 8-methoxypsoralen (8-MOP) and subsequent ultraviolet A (UVA) irradiation results in growth arrest with morphological and functional changes reminiscent of replicative senescence. For gene expression profiling in two strains of human skin fibroblasts after PUVA treatment, we used a low-density DNA array representing 240 genes involved in senescence and stress response. Twenty-nine genes were differentially expressed after PUVA treatment in the two strains of human skin fibroblasts. These genes are involved in growth arrest, stress response, modification of the extracellular matrix and senescence. This study contributes further to the elucidation of the PUVA model and its validation as a useful stress-induced premature senescence model aiming to characterize the premature senescence of fibroblasts and to identify biomarkers that could be applied in vivo.

  15. Construction of Multi-dimensional Arterial Health Status Map based on Molecular and Clinical Measurements, Fuzzy System and Data Cubes

    PubMed Central

    Chan, Lawrence W.C.; Benzie, Iris F.F.; Lau, Thomas Y.H.; Zheng, Yongping; Wong, Alex K.S.; Liu, Y.; Chan, Phoebe S.T.

    2008-01-01

    Atherosclerosis results from inflammatory processes involving biomarkers, such as lipid profile, haemoglobin A1C, oxidative stress, coronary artery calcium score and flow-mediated endothelial response through nitric oxide. This paper proposes a health status coefficient, which comprehends molecular and clinical measurements concerning atherosclerosis to provide a measure of arterial health. An arterial health status map is produced to map the multi-dimensional measurements to the health status coefficient. The mapping is modeled by a fuzzy system embedded with the health domain expert knowledge. The measurements obtained from the pilot study are used to tune the fuzzy system. The inferred arterial health coefficients are stored into the data cubes of a multi-dimensional database. Due to this adaptability and transparency of fuzzy system, the health status map can be easily updated when the refinement of fuzzy rule base is needed or new measurements are obtained. PMID:21347120

  16. A multidimensional model of mothers' perceptions of parent alcohol socialization and adolescent alcohol misuse.

    PubMed

    Ennett, Susan T; Jackson, Christine; Cole, Veronica T; Haws, Susan; Foshee, Vangie A; Reyes, Heathe Luz McNaughton; Burns, Alison Reimuller; Cox, Melissa J; Cai, Li

    2016-02-01

    We assessed a multidimensional model of parent alcohol socialization in which key socialization factors were considered simultaneously to identify combinations of factors that increase or decrease risk for development of adolescent alcohol misuse. Of interest was the interplay between putative risk and protective factors, such as whether the typically detrimental effects on youth drinking of parenting practices tolerant of some adolescent alcohol use are mitigated by an effective overall approach to parenting and parental modeling of modest alcohol use. The sample included 1,530 adolescents and their mothers; adolescents' mean age was 13.0 (SD = .99) at the initial assessment. Latent profile analysis was conducted of mothers' reports of their attitude toward teen drinking, alcohol-specific parenting practices, parental alcohol use and problem use, and overall approach to parenting. The profiles were used to predict trajectories of adolescent alcohol misuse from early to middle adolescence. Four profiles were identified: 2 profiles reflected conservative alcohol-specific parenting practices and 2 reflected alcohol-tolerant practices, all in the context of other attributes. Alcohol misuse accelerated more rapidly from Grade 6 through 10 in the 2 alcohol-tolerant compared with conservative profiles. Results suggest that maternal tolerance of some youth alcohol use, even in the presence of dimensions of an effective parenting style and low parental alcohol use and problem use, is not an effective strategy for reducing risky adolescent alcohol use. (PsycINFO Database Record

  17. A Multidimensional Model of Mothers’ Perceptions of Parent Alcohol Socialization and Adolescent Alcohol Misuse

    PubMed Central

    Ennett, Susan T.; Jackson, Christine; Cole, Veronica T.; Haws, Susan; Foshee, Vangie A.; Reyes, Heathe Luz McNaughton; Burns, Alison Reimuller; Cox, Melissa J.; Cai, Li

    2015-01-01

    We assessed a multidimensional model of parent alcohol socialization in which key socialization factors were considered simultaneously to identify combinations of factors that increase or decrease risk for development of adolescent alcohol misuse. Of interest was the interplay between putative risk and protective factors, such as whether the typically detrimental effects on youth drinking of parenting practices tolerant of some adolescent alcohol use are mitigated by an effective overall approach to parenting and parental modeling of modest alcohol use. The sample included 1,530 adolescents and their mothers; adolescents’ mean age was 13.0 (SD = .99) at the initial assessment. Latent profile analysis was conducted of mothers’ reports of their attitude toward teen drinking, alcohol-specific parenting practices, parental alcohol use and problem use, and overall approach to parenting. The profiles were used to predict trajectories of adolescent alcohol misuse from early to middle adolescence. Four profiles were identified: two profiles reflected conservative alcohol-specific parenting practices and two reflected alcohol-tolerant practices, all in the context of other attributes. Alcohol misuse accelerated more rapidly from grade 6 through 10 in the two alcohol-tolerant compared with conservative profiles. Results suggest that maternal tolerance of some youth alcohol use, even in the presence of dimensions of an effective parenting style and low parental alcohol use and problem use, is not an effective strategy for reducing risky adolescent alcohol use. PMID:26415053

  18. [Metabolic profiling of human blood].

    PubMed

    Trifonova, O P; Lokhov, P G; Archakov, A I

    2014-01-01

    Metabolomics is a novel "omics" branch of science intended for studying a comprehensive set of low molecular weight substances (metabolites) of various biological objects. Metabolite profiles represent a molecular phenotype of biological systems and reflect information encoded at the genome level and realized at the transcriptome and proteome levels. Analysis of human blood metabolic profile is universal and promising tool for clinical applications because it is a sensitive measure of both endogenous and exogenous (environmental) factors affected on the patient's organism. Technical implementation of metabolic profiling of blood and statistic analysis of metabolite profiles for effective diagnostics and risk assessments of diseases are discussed in this review.

  19. `Weak A' phenotypes

    PubMed Central

    Cartron, J. P.; Gerbal, A.; Hughes-Jones, N. C.; Salmon, C.

    1974-01-01

    Thirty-five weak A samples including fourteen A3, eight Ax, seven Aend, three Am and three Ae1 were studied in order to determine their A antigen site density, using an IgG anti-A labelled with 125I. The values obtained ranged between 30,000 A antigen sites for A3 individuals, and 700 sites for the Ae1 red cells. The hierarchy of values observed made it possible to establish a quantitative relationship between the red cell agglutinability of these phenotypes measured under standard conditions, and their antigen site density. PMID:4435836

  20. Information theoretic approaches to multidimensional neural computations

    NASA Astrophysics Data System (ADS)

    Fitzgerald, Jeffrey D.

    Many systems in nature process information by transforming inputs from their environments into observable output states. These systems are often difficult to study because they are performing computations on multidimensional inputs with many degrees of freedom using highly nonlinear functions. The work presented in this dissertation deals with some of the issues involved with characterizing real-world input/output systems and understanding the properties of idealized systems using information theoretic methods. Using the principle of maximum entropy, a family of models are created that are consistent with certain measurable correlations from an input/output dataset but are maximally unbiased in all other respects, thereby eliminating all unjustified assumptions about the computation. In certain cases, including spiking neurons, we show that these models also minimize the mutual information. This property gives one the advantage of being able to identify the relevant input/output statistics by calculating their information content. We argue that these maximum entropy models provide a much needed quantitative framework for characterizing and understanding sensory processing neurons that are selective for multiple stimulus features. To demonstrate their usefulness, these ideas are applied to neural recordings from macaque retina and thalamus. These neurons, which primarily respond to two stimulus features, are shown to be well described using only first and second order statistics, indicating that their firing rates encode information about stimulus correlations. In addition to modeling multi-feature computations in the relevant feature space, we also show that maximum entropy models are capable of discovering the relevant feature space themselves. This technique overcomes the disadvantages of two commonly used dimensionality reduction methods and is explored using several simulated neurons, as well as retinal and thalamic recordings. Finally, we ask how neurons in a

  1. Multidimensional coherent spectroscopy of a semiconductor microcavity

    NASA Astrophysics Data System (ADS)

    Wilmer, Brian L.; Passmann, Felix; Gehl, Michael; Khitrova, Galina; Bristow, Alan D.

    2016-03-01

    Multidimensional coherent spectroscopy maps the detuning dependence of the upper (UP) and lower (LP) excitonpolariton branches1 in a wedged microcavity with a single InGaAs quantum well at 5 K. Features on the diagonal correspond to intra-action coherences of the UP and LP branches. Off-diagonal peaks are interaction coherences between the UP and LP branches. With increasing detuning (Δ), all peaks move to higher energy, the exciton-like (EEX) and cavity-like (Eγ) modes swap position and have maximum intensity near the anti-crossing at Δ=0. An isolated biexciton (B) is only seen at Δ<0, separated by a binding energy of approximately 2 meV. For Δ>0, the spectral weight of the off-diagonal features swap, as the LP and B come into resonance. This indicates that the off-diagonal features are sensitive to the interactions including two-quantum contributions and that a situation similar to a Feshbach resonance exists.2 Polarization of two-quantum contributions show spin sensitive two-polariton and new biexciton correlations. The latter likely influence the Feshbach resonance between biexcitons and two-polariton states. The two-quantum signatures also demonstate that biexcitons perturb the light-matter coupling in the microcavity to reduce the mixed two-polariton contributions. Detuning dependence of zero-quantum contributions show Raman-like coherences that are enhanced near zero detuning. Asymmetry of the Raman coherences are indicative of many-body interactions, which also grow stronger as the light-matter interactions are enhanced near zero deuning.

  2. Multidimensional radiative effects in supercritical shocks

    NASA Astrophysics Data System (ADS)

    Leygnac, S.; Lanz, T.; Stehlé, C.; Michaut, C.; Korĉáková, D.

    Recent radiative shocks experiments performed on the LULI laser at Ecole Polytechnique in France (Fleury et al., Lasers and Particle Beams 20, 263, 2002) put in evidence a supercritical shock wave in a xenon gas cell. The structure of these shocks is quite similar to those of accretion shock wave in the case of stellar formation, as indicated in Stehlé and Chieze (SF2A - Paris proceedings, 2002). Some points require further studies like the contribution of the gas excitation/ionization energy to the compression ratio and the understanding of the discrepancy, which was noted between the velocity of the radiative precursor in the experiment and in the 1D simulation. Thus, to understand the physics of the radiative shock waves, the academic case of the stationary shock is particularly interesting. We have thus studied the structure of a radiative shock wave which propagates in an ionized gas. We study the extended Rankine Hugoniot equations in various media with inclusion of radiation pressure and energy and study also the extension of the radiative precursor in the diffusion approximation. We also study the equations of multidimensional radiative transfer for a snapshot of the experimental shock in xenon in order to quantify the radiative losses in the finite experimental cell. This academic approach will help to improve the knowledge of the physical processes which take place in radiative shocks of astrophysical interest, like in the birth and death of stars, and prepare ourselves to define appropriate experiments on future high power lasers like LIL and LMJ in Bordeaux.

  3. Combining multidimensional genomic measurements for predicting cancer prognosis: observations from TCGA

    PubMed Central

    Zhao, Qing; Shi, Xingjie; Xie, Yang; Huang, Jian; Shia, BenChang

    2015-01-01

    With accumulating research on the interconnections among different types of genomic regulations, researchers have found that multidimensional genomic studies outperform one-dimensional studies in multiple aspects. Among many sources of multidimensional genomic data, The Cancer Genome Atlas (TCGA) provides the public with comprehensive profiling data on >30 cancer types, making it an ideal test bed for conducting and comparing different analyses. In this article, the analysis goal is to apply several existing methods and associate multidimensional genomic measurements with cancer outcomes in particular prognosis, with special focus on the predictive power of genomic signatures. We exploit clinical data and four types of genomic measurement including mRNA gene expression, DNA methylation, microRNA and copy number alterations for breast invasive carcinoma, glioblastoma multiforme, acute myeloid leukemia and lung squamous cell carcinoma collected by TCGA. To accommodate the high dimensionality, we extract important features using Principal Component Analysis, Partial Least Squares and Least Absolute Shrinkage and Selection Operator (Lasso), which are representative of dimension reduction and variable selection techniques and have been extensively adopted, and fit Cox survival models with combined important features. We calibrate the predictive power of each type of genomic measurement for the prognosis of four cancer types and find that the results vary across cancers. Our analysis also suggests that for most of the cancers in our study and the adopted methods, there is no substantial improvement in prediction when adding other genomic measurement after gene expression and clinical covariates have been included in the model. This is consistent with the findings that molecular features measured at the transcription level affect clinical outcomes more directly than those measured at the DNA/epigenetic level. PMID:24632304

  4. Limits of detection and quantification in comprehensive multidimensional separations. 1. A theoretical look.

    PubMed

    de la Mata, A Paulina; Harynuk, James J

    2012-08-01

    Comprehensive multidimensional separations (e.g., GC×GC, LC×LC, etc.) are increasingly popular tools for the analysis of complex samples, due to their many advantages, such as vastly increased peak capacity, and improvements in sensitivity. The most well-established of these techniques, GC×GC, has revolutionized analytical separations in fields as diverse as petroleum, environmental research, food and flavors, and metabolic profiling. Using multidimensional approaches, analytes can be quantified at levels substantially lower than those possible by one-dimensional techniques. However, it has also been shown that the modulation process introduces a new source of error to the measurement. In this work, we present the results of a study into the limits of quantification and detection (LOQ and LOD) in comprehensive multidimensional separations using GC×GC and the more popular "two-step" integration algorithm as an example. Simulation of chromatographic data permits precise control of relevant parameters of peak geometry and modulation phase. Results are expressed in terms of the dimensionless parameter of signal-to-noise ratio of the base peak (S/N(BP)) making them transportable to any result where quantification is performed using a two-step algorithm. Based on these results, the LOD is found to depend upon the modulation ratio used for the experiment and vary between a S/N(BP) of 10-17, while the LOQ depends on both the modulation ratio and the phase of the modulation for the peak and ranges from a S/N(BP) of 10 to 50, depending on the circumstances. PMID:22813213

  5. The Phenotype of Loneliness

    PubMed Central

    Cacioppo, John T.; Cacioppo, Stephanie

    2012-01-01

    Goossens’ (in press) review nicely maps the progression of scientific research from its early focus on loneliness as a dysphoric state that results from the discrepancy between a person's ideal and actual social relationships to its current emphasis on the centrality of loneliness to our very nature as a social species, and he argues that developmental science throughout Europe has a great deal to contribute to our understanding of this construct. He concludes that psychologists should care about research on loneliness for five reasons: (i) it is a well-defined phenotype, (ii) it shows both high stability and individual differences in rates of change across years, (iii) it has adaptive value and evolutionary significance, (iv) it has a genetic substrate that is moderated by social environments, and (v) it has self-maintaining features that can lead to adverse mental health outcomes. Goossen's (2012) review is rife with information and ideas. We focus here on two additional important reasons and on the phenotype of loneliness. PMID:23024688

  6. [Predisposition - obesity phenotype].

    PubMed

    Blüher, M

    2014-05-01

    Obesity belongs to the five most important health burdens in modern societies and reaches with ~20 % prevalence in Germany epidemic proportions. Obesity significantly increases the risk of developing metabolic (e. g. type 2 diabetes), cardiovascular, orthopaedic, psychologic and other disorders. Despite the well established epidemiologic relationship between obesity and these co-morbidities, there is a subgroup of metabolically healthy obese patients, which seems to be protected against metabolic and cardiovascular obesity related disorders. Compared to metabolically unhealthy or high risk obese patients, metabolically healthy obese individuals are characterized by preserved insulin sensitivity, lower liver fat content, lower visceral fat mass, as well as normal adipose tissue function. Noteworthy, metabolically healthy obese individuals do not significantly improve their obesity-associated risk for the development of type 2 diabetes and vascular diseases. Therefore, distinction between metabolically healthy from high-risk obese phenotypes will facilitate the identification of the obese person who will benefit the most from early lifestyle, pharmacological or bariatric surgery interventions. A stratified treatment approach considering these different obesity phenotypes should be introduced into clinical management of obese patients.

  7. Distinguishing ichthyoses by protein profiling.

    PubMed

    Rice, Robert H; Bradshaw, Katie M; Durbin-Johnson, Blythe P; Rocke, David M; Eigenheer, Richard A; Phinney, Brett S; Schmuth, Matthias; Gruber, Robert

    2013-01-01

    To explore the usefulness of protein profiling for characterization of ichthyoses, we here determined the profile of human epidermal stratum corneum by shotgun proteomics. Samples were analyzed after collection on tape circles from six anatomic sites (forearm, palm, lower leg, forehead, abdomen, upper back), demonstrating site-specific differences in profiles. Additional samples were collected from the forearms of subjects with ichthyosis vulgaris (filaggrin (FLG) deficiency), recessive X-linked ichthyosis (steroid sulfatase (STS) deficiency) and autosomal recessive congenital ichthyosis type lamellar ichthyosis (transglutaminase 1 (TGM1) deficiency). The ichthyosis protein expression patterns were readily distinguishable from each other and from phenotypically normal epidermis. In general, the degree of departure from normal was lower from ichthyosis vulgaris than from lamellar ichthyosis, parallel to the severity of the phenotype. Analysis of samples from families with ichthyosis vulgaris and concomitant modifying gene mutations (STS deficiency, GJB2 deficiency) permitted correlation of alterations in protein profile with more complex genetic constellations.

  8. Red blood cell phenotype matching for various ethnic groups.

    PubMed

    Badjie, Karafa S W; Tauscher, Craig D; van Buskirk, Camille M; Wong, Clare; Jenkins, Sarah M; Smith, Carin Y; Stubbs, James R

    2011-01-01

    Patients requiring chronic transfusion support are at risk of alloimmunization after red blood cell (RBC) transfusion because of a disparity between donor and recipient antigen profiles. This research explored the probability of obtaining an exact extended phenotype match between blood donors randomly selected from our institution and patients randomly selected from particular ethnic groups. Blood samples from 1,000 blood donors tested by molecular method were evaluated for the predicted phenotype distribution of Rh, Kell, Kidd, Duffy, and MNS. A random subsample of 800 donor phenotypes was then evaluated for the probability of obtaining an exact match with respect to phenotype with a randomly selected patient from a particular ethnic group. Overall, there was a greater than 80 percent probability of finding an exact donor-recipient match for the K/k alleles in the Kell system. The probability ranged from 3 percent to 38 percent, depending on the ethnicity and disparities in phenotypic profiles, for the Rh, Kidd, Duffy, and MNS systems. A significant donor-recipient phenotype mismatch ratio exists with certain blood group antigens such that, with current routine ABO and D matching practices, recipients of certain ethnic groups are predisposed to alloimmunization. PMID:22356481

  9. Red blood cell phenotype matching for various ethnic groups.

    PubMed

    Badjie, Karafa S W; Tauscher, Craig D; van Buskirk, Camille M; Wong, Clare; Jenkins, Sarah M; Smith, Carin Y; Stubbs, James R

    2011-01-01

    Patients requiring chronic transfusion support are at risk of alloimmunization after red blood cell (RBC) transfusion because of a disparity between donor and recipient antigen profiles. This research explored the probability of obtaining an exact extended phenotype match between blood donors randomly selected from our institution and patients randomly selected from particular ethnic groups. Blood samples from 1,000 blood donors tested by molecular method were evaluated for the predicted phenotype distribution of Rh, Kell, Kidd, Duffy, and MNS. A random subsample of 800 donor phenotypes was then evaluated for the probability of obtaining an exact match with respect to phenotype with a randomly selected patient from a particular ethnic group. Overall, there was a greater than 80 percent probability of finding an exact donor-recipient match for the K/k alleles in the Kell system. The probability ranged from 3 percent to 38 percent, depending on the ethnicity and disparities in phenotypic profiles, for the Rh, Kidd, Duffy, and MNS systems. A significant donor-recipient phenotype mismatch ratio exists with certain blood group antigens such that, with current routine ABO and D matching practices, recipients of certain ethnic groups are predisposed to alloimmunization.

  10. Computational models reveal genotype-phenotype associations in Saccharomyces cerevisiae.

    PubMed

    Franco-Duarte, Ricardo; Mendes, Inês; Umek, Lan; Drumonde-Neves, João; Zupan, Blaz; Schuller, Dorit

    2014-07-01

    Genome sequencing is essential to understand individual variation and to study the mechanisms that explain relations between genotype and phenotype. The accumulated knowledge from large-scale genome sequencing projects of Saccharomyces cerevisiae isolates is being used to study the mechanisms that explain such relations. Our objective was to undertake genetic characterization of 172 S. cerevisiae strains from different geographical origins and technological groups, using 11 polymorphic microsatellites, and computationally relate these data with the results of 30 phenotypic tests. Genetic characterization revealed 280 alleles, with the microsatellite ScAAT1 contributing most to intrastrain variability, together with alleles 20, 9 and 16 from the microsatellites ScAAT4, ScAAT5 and ScAAT6. These microsatellite allelic profiles are characteristic for both the phenotype and origin of yeast strains. We confirm the strength of these associations by construction and cross-validation of computational models that can predict the technological application and origin of a strain from the microsatellite allelic profile. Associations between microsatellites and specific phenotypes were scored using information gain ratios, and significant findings were confirmed by permutation tests and estimation of false discovery rates. The phenotypes associated with higher number of alleles were the capacity to resist to sulphur dioxide (tested by the capacity to grow in the presence of potassium bisulphite) and the presence of galactosidase activity. Our study demonstrates the utility of computational modelling to estimate a strain technological group and phenotype from microsatellite allelic combinations as tools for preliminary yeast strain selection.

  11. Multidimensional traction force microscopy reveals out-of-plane rotational moments about focal adhesions.

    PubMed

    Legant, Wesley R; Choi, Colin K; Miller, Jordan S; Shao, Lin; Gao, Liang; Betzig, Eric; Chen, Christopher S

    2013-01-15

    Recent methods have revealed that cells on planar substrates exert both shear (in-plane) and normal (out-of-plane) tractions against the extracellular matrix (ECM). However, the location and origin of the normal tractions with respect to the adhesive and cytoskeletal elements of cells have not been elucidated. We developed a high-spatiotemporal-resolution, multidimensional (2.5D) traction force microscopy to measure and model the full 3D nature of cellular forces on planar 2D surfaces. We show that shear tractions are centered under elongated focal adhesions whereas upward and downward normal tractions are detected on distal (toward the cell edge) and proximal (toward the cell body) ends of adhesions, respectively. Together, these forces produce significant rotational moments about focal adhesions in both protruding and retracting peripheral regions. Temporal 2.5D traction force microscopy analysis of migrating and spreading cells shows that these rotational moments are highly dynamic, propagating outward with the leading edge of the cell. Finally, we developed a finite element model to examine how rotational moments could be generated about focal adhesions in a thin lamella. Our model suggests that rotational moments can be generated largely via shear lag transfer to the underlying ECM from actomyosin contractility applied at the intracellular surface of a rigid adhesion of finite thickness. Together, these data demonstrate and probe the origin of a previously unappreciated multidimensional stress profile associated with adhesions and highlight the importance of new approaches to characterize cellular forces. PMID:23277584

  12. Phenotypic analyses of Agrobacterium.

    PubMed

    Morton, Elise R; Fuqua, Clay

    2012-05-01

    Agrobacterium species are plant-associated relatives of the rhizobia. Several species cause plant diseases such as crown gall and hairy root, although there are also avirulent species. A. tumefaciens is the most intensively studied species and causes crown gall, a neoplastic disease that occurs on a variety of plants. Virulence is specified by large plasmids, and in the case of A. tumefaciens this is called the Ti (tumor-inducing) plasmid. During pathogenesis virulent agrobacteria copy a segment of the Ti plasmid and transfer it to the plant, where it subsequently integrates into the plant genome, and expresses genes that result in the disease symptoms. A. tumefaciens has been used extensively as a plant genetic engineering tool and is also a model microorganism that has been well studied for host-microbe associations, horizontal gene transfer, cell-cell communication, and biofilm formation. This unit describes standard protocols for simple phenotypic characterizations of A. tumefaciens. PMID:22549164

  13. Graphical Representation of Proximity Measures for Multidimensional Data

    PubMed Central

    Zand, Martin S.; Wang, Jiong; Hilchey, Shannon

    2015-01-01

    We describe the use of classical and metric multidimensional scaling methods for graphical representation of the proximity between collections of data consisting of cases characterized by multidimensional attributes. These methods can preserve metric differences between cases, while allowing for dimensional reduction and projection to two or three dimensions ideal for data exploration. We demonstrate these methods with three datasets for: (i) the immunological similarity of influenza proteins measured by a multidimensional assay; (ii) influenza protein sequence similarity; and (iii) reconstruction of airport-relative locations from paired proximity measurements. These examples highlight the use of proximity matrices, eigenvalues, eigenvectors, and linear and nonlinear mappings using numerical minimization methods. Some considerations and caveats for each method are also discussed, and compact Mathematica programs are provided. PMID:26692757

  14. The acquisition of multidimensional NMR spectra within a single scan

    PubMed Central

    Frydman, Lucio; Scherf, Tali; Lupulescu, Adonis

    2002-01-01

    A scheme enabling the complete sampling of multidimensional NMR domains within a single continuous acquisition is introduced and exemplified. Provided that an analyte's signal is sufficiently strong, the acquisition time of multidimensional NMR experiments can thus be shortened by orders of magnitude. This could enable the characterization of transient events such as proteins folding, 2D NMR experiments on samples being chromatographed, bring the duration of higher dimensional experiments (e.g., 4D NMR) into the lifetime of most proteins under physiological conditions, and facilitate the incorporation of spectroscopic 2D sequences into in vivo imaging investigations. The protocol is compatible with existing multidimensional pulse sequences and can be implemented by using conventional hardware; its performance is exemplified here with a variety of homonuclear 2D NMR acquisitions. PMID:12461169

  15. Formalism for Hypercomplex Multidimensional NMR Employing Partial-Component Subsampling

    PubMed Central

    Schuyler, Adam D; Maciejewski, Mark W; Stern, Alan S; Hoch, Jeffrey C

    2012-01-01

    Multidimensional NMR spectroscopy typically employs phase-sensitive detection, which results in hypercomplex data (and spectra) when utilized in more than one dimension. Nonuniform sampling approaches have become commonplace in multidimensional NMR, enabling dramatic reductions in experiment time, increases in sensitivity and/or increases in resolution. In order to utilize nonuniform sampling optimally, it is necessary to characterize the relationship between the spectrum of a uniformly sampled data set and the spectrum of a subsampled data set. In this work we construct an algebra of hypercomplex numbers suitable for representing multidimensional NMR data along with partial-component nonuniform sampling (i.e. the hypercomplex components of data points are subsampled). This formalism leads to a modified DFT–convolution relationship involving a partial-component, hypercomplex point-spread function set. The framework presented here is essential for the continued development and appropriate characterization of partial-component nonuniform sampling. PMID:23246651

  16. Quantum and Multidimensional Explanations in a Neurobiological Context of Mind.

    PubMed

    Korf, Jakob

    2015-08-01

    This article examines the possible relevance of physical-mathematical multidimensional or quantum concepts aiming at understanding the (human) mind in a neurobiological context. Some typical features of the quantum and multidimensional concepts are briefly introduced, including entanglement, superposition, holonomic, and quantum field theories. Next, we consider neurobiological principles, such as the brain and its emerging (physical) mind, evolutionary and ontological origins, entropy, syntropy/neg-entropy, causation, and brain energy metabolism. In many biological processes, including biochemical conversions, protein folding, and sensory perception, the ubiquitous involvement of quantum mechanisms is well recognized. Quantum and multidimensional approaches might be expected to help describe and model both brain and mental processes, but an understanding of their direct involvement in mental activity, that is, without mediation by molecular processes, remains elusive. More work has to be done to bridge the gap between current neurobiological and physical-mathematical concepts with their associated quantum-mind theories.

  17. EHR Big Data Deep Phenotyping

    PubMed Central

    Lenert, L.; Lopez-Campos, G.

    2014-01-01

    Summary Objectives Given the quickening speed of discovery of variant disease drivers from combined patient genotype and phenotype data, the objective is to provide methodology using big data technology to support the definition of deep phenotypes in medical records. Methods As the vast stores of genomic information increase with next generation sequencing, the importance of deep phenotyping increases. The growth of genomic data and adoption of Electronic Health Records (EHR) in medicine provides a unique opportunity to integrate phenotype and genotype data into medical records. The method by which collections of clinical findings and other health related data are leveraged to form meaningful phenotypes is an active area of research. Longitudinal data stored in EHRs provide a wealth of information that can be used to construct phenotypes of patients. We focus on a practical problem around data integration for deep phenotype identification within EHR data. The use of big data approaches are described that enable scalable markup of EHR events that can be used for semantic and temporal similarity analysis to support the identification of phenotype and genotype relationships. Conclusions Stead and colleagues’ 2005 concept of using light standards to increase the productivity of software systems by riding on the wave of hardware/processing power is described as a harbinger for designing future healthcare systems. The big data solution, using flexible markup, provides a route to improved utilization of processing power for organizing patient records in genotype and phenotype research. PMID:25123744

  18. Cognitive Profile of Turner Syndrome

    ERIC Educational Resources Information Center

    Hong, David; Kent, Jamie Scaletta; Kesler, Shelli

    2009-01-01

    Turner syndrome (TS) is a relatively common neurogenetic disorder characterized by complete or partial monosomy-X in a phenotypic female. TS is associated with a cognitive profile that typically includes intact intellectual function and verbal abilities with relative weaknesses in visual-spatial, executive, and social cognitive domains. In this…

  19. Ultrafast Multidimensional Laplace NMR Using a Single-Sided Magnet.

    PubMed

    King, Jared N; Lee, Vanessa J; Ahola, Susanna; Telkki, Ville-Veikko; Meldrum, Tyler

    2016-04-11

    Laplace NMR (LNMR) consists of relaxation and diffusion measurements providing detailed information about molecular motion and interaction. Here we demonstrate that ultrafast single- and multidimensional LNMR experiments, based on spatial encoding, are viable with low-field, single-sided magnets with an inhomogeneous magnetic field. This approach shortens the experiment time by one to two orders of magnitude relative to traditional experiments, and increases the sensitivity per unit time by a factor of three. The reduction of time required to collect multidimensional data opens significant prospects for mobile chemical analysis using NMR. Particularly tantalizing is future use of hyperpolarization to increase sensitivity by orders of magnitude, allowed by single-scan approach.

  20. Gingival Tissue Transcriptomes Identify Distinct Periodontitis Phenotypes

    PubMed Central

    Kebschull, M.; Demmer, R.T.; Grün, B.; Guarnieri, P.; Pavlidis, P.; Papapanou, P.N.

    2014-01-01

    The currently recognized principal forms of periodontitis—chronic and aggressive—lack an unequivocal, pathobiology-based foundation. We explored whether gingival tissue transcriptomes can serve as the basis for an alternative classification of periodontitis. We used cross-sectional whole-genome gene expression data from 241 gingival tissue biopsies obtained from sites with periodontal pathology in 120 systemically healthy nonsmokers with periodontitis, with available data on clinical periodontal status, subgingival microbial profiles, and serum IgG antibodies to periodontal microbiota. Adjusted model-based clustering of transcriptomic data using finite mixtures generated two distinct clusters of patients that did not align with the current classification of chronic and aggressive periodontitis. Differential expression profiles primarily related to cell proliferation in cluster 1 and to lymphocyte activation and unfolded protein responses in cluster 2. Patients in the two clusters did not differ with respect to age but presented with distinct phenotypes (statistically significantly different whole-mouth clinical measures of extent/severity, subgingival microbial burden by several species, and selected serum antibody responses). Patients in cluster 2 showed more extensive/severe disease and were more often male. The findings suggest that distinct gene expression signatures in pathologic gingival tissues translate into phenotypic differences and can provide a basis for a novel classification. PMID:24646639

  1. Racial Identity, Phenotype, and Self-Esteem among Biracial Polynesian/White Individuals

    ERIC Educational Resources Information Center

    Allen, G. E. Kawika; Garriott, Patton O.; Reyes, Carla J.; Hsieh, Catherine

    2013-01-01

    This study examined racial identity, self-esteem, and phenotype among biracial Polynesian/White adults. Eighty-four Polynesian/White persons completed the Biracial Identity Attitude Scale, the Rosenberg Self-Esteem Inventory, and a Polynesian phenotype scale. Profile analyses showed participants identified more with their Polynesian parent. A…

  2. Identification of Pathogenic Rare Yeast Species in Clinical Samples: Comparison between Phenotypical and Molecular Methods▿

    PubMed Central

    Cendejas-Bueno, Emilio; Gomez-Lopez, Alicia; Mellado, Emilia; Rodriguez-Tudela, Juan L.; Cuenca-Estrella, Manuel

    2010-01-01

    Species identification using both phenotypic and molecular methods and antifungal susceptibility tests was carried out with 60 uncommon clinical yeasts. Our data show that phenotypic methods were insufficient for correct identification (only 25%) and that most of the wrongly identified strains showed a resistant antifungal profile. PMID:20237094

  3. Measurement Error, Multidimensionality, and Scale Shrinkage: A Reply to Yen and Burket.

    ERIC Educational Resources Information Center

    Camilli, Gregory

    1999-01-01

    Yen and Burket suggested that shrinkage in vertical equating cannot be understood apart from multidimensionality. Reviews research on reliability, multidimensionality, and scale shrinkage, and explores issues of practical importance to educators. (SLD)

  4. Multi-dimensional, non-contact metrology using trilateration and high resolution FMCW ladar.

    PubMed

    Mateo, Ana Baselga; Barber, Zeb W

    2015-07-01

    Here we propose, describe, and provide experimental proof-of-concept demonstrations of a multidimensional, non-contact-length metrology system design based on high resolution (millimeter to sub-100 micron) frequency modulated continuous wave (FMCW) ladar and trilateration based on length measurements from multiple, optical fiber-connected transmitters. With an accurate FMCW ladar source, the trilateration-based design provides 3D resolution inherently independent of standoff range and allows self-calibration to provide flexible setup of a field system. A proof-of-concept experimental demonstration was performed using a highly stabilized, 2 THz bandwidth chirped laser source, two emitters, and one scanning emitter/receiver providing 1D surface profiles (2D metrology) of diffuse targets. The measured coordinate precision of <200 microns was determined to be limited by laser speckle issues caused by diffuse scattering of the targets. PMID:26193132

  5. Multidimensional structure of employee motivation - Clustering approach

    NASA Astrophysics Data System (ADS)

    Gąsior, Marcin; Skowron, Łukasz; Sak-Skowron, Monika

    2014-12-01

    Employees' motivation along with their satisfaction with work is one of the most significant factors determining functioning and the success of an organization on the market. The purpose of this article is to demonstrate that motivation to work is a phenomenon whose nature is different among subsequent employees not only in terms of its general level, but also internal structure, and checking whether among various possible structures of motivation there is repeatability which could prove the existence of specific regularities and enabling possible classification of employees. Reasoning with regard to internal structure of motivation was conducted on the basis of the designated 14 variables expressing it, which included both internal factors (feelings) and external (actions), both positive and negative in its meaning. The conducted research consisted in segmentation of the surveyed employees using the generalized method of k-means, in order to separate groups with the same subsequent intensity profiles, so designated variables. By way of research, five various groups of employees were found. Each has a unique, different profile of motivation, at the same time, in each of them a different satisfaction level of the employed was observed. The analysis leads to a conclusion that the motivation profile itself is not completely connected with the perceived satisfaction with work. While signs of motivation positive in nature are usually stronger among satisfied employees, and the weaker - among dissatisfied ones, we cannot speak about a similar regularity when it comes to factors of negative nature. Furthermore, the presented research shows that within negative factors, larger intensification can be observed among ones of internal nature, while among these of external nature - it is smaller.

  6. The Broad Autism Phenotype Questionnaire

    ERIC Educational Resources Information Center

    Hurley, Robert S. E.; Losh, Molly; Parlier, Morgan; Reznick, J. Steven; Piven, Joseph

    2007-01-01

    The broad autism phenotype (BAP) is a set of personality and language characteristics that reflect the phenotypic expression of the genetic liability to autism, in non-autistic relatives of autistic individuals. These characteristics are milder but qualitatively similar to the defining features of autism. A new instrument designed to measure the…

  7. Plant Phenotype Characterization System

    SciTech Connect

    Daniel W McDonald; Ronald B Michaels

    2005-09-09

    This report is the final scientific report for the DOE Inventions and Innovations Project: Plant Phenotype Characterization System, DE-FG36-04GO14334. The period of performance was September 30, 2004 through July 15, 2005. The project objective is to demonstrate the viability of a new scientific instrument concept for the study of plant root systems. The root systems of plants are thought to be important in plant yield and thus important to DOE goals in renewable energy sources. The scientific study and understanding of plant root systems is hampered by the difficulty in observing root activity and the inadequacy of existing root study instrumentation options. We have demonstrated a high throughput, non-invasive, high resolution technique for visualizing plant root systems in-situ. Our approach is based upon low-energy x-ray radiography and the use of containers and substrates (artificial soil) which are virtually transparent to x-rays. The system allows us to germinate and grow plant specimens in our containers and substrates and to generate x-ray images of the developing root system over time. The same plant can be imaged at different times in its development. The system can be used for root studies in plant physiology, plant morphology, plant breeding, plant functional genomics and plant genotype screening.

  8. Best Design for Multidimensional Computerized Adaptive Testing with the Bifactor Model

    ERIC Educational Resources Information Center

    Seo, Dong Gi; Weiss, David J.

    2015-01-01

    Most computerized adaptive tests (CATs) have been studied using the framework of unidimensional item response theory. However, many psychological variables are multidimensional and might benefit from using a multidimensional approach to CATs. This study investigated the accuracy, fidelity, and efficiency of a fully multidimensional CAT algorithm…

  9. Multidimensional Measurement of Poverty among Women in Sub-Saharan Africa

    ERIC Educational Resources Information Center

    Batana, Yele Maweki

    2013-01-01

    Since the seminal work of Sen, poverty has been recognized as a multidimensional phenomenon. The recent availability of relevant databases renewed the interest in this approach. This paper estimates multidimensional poverty among women in fourteen Sub-Saharan African countries using the Alkire and Foster multidimensional poverty measures, whose…

  10. A Multidimensional Scaling Analysis of Students' Attitudes about Science Careers

    ERIC Educational Resources Information Center

    Masnick, Amy M.; Valenti, S. Stavros; Cox, Brian D.; Osman, Christopher J.

    2010-01-01

    To encourage students to seek careers in Science, Technology, Engineering and Mathematics (STEM) fields, it is important to gauge students' implicit and explicit attitudes towards scientific professions. We asked high school and college students to rate the similarity of pairs of occupations, and then used multidimensional scaling (MDS) to create…

  11. Turkish Validity Examination of the Multidimensional Students' Life Satisfaction Scale

    ERIC Educational Resources Information Center

    Irmak, Sezgin; Kuruuzum, Ayse

    2009-01-01

    The validation studies of the Multidimensional Students' Life Satisfaction Scale (MSLSS) have been conducted with samples from different nations but mostly from western individualistic cultures. Life satisfaction and its constructs could differ depending on cultural characteristics and life satisfaction scales should be validated in different…

  12. An overview of multidimensional liquid phase separations in food analysis.

    PubMed

    Franco, Maraíssa Silva; Padovan, Rodrigo Nogueira; Fumes, Bruno Henrique; Lanças, Fernando Mauro

    2016-07-01

    Food safety is a priority public health concern that demands analytical methods capable to detect low concentration level of contaminants (e.g. pesticides and antibiotics) in different food matrices. Due to the high complexity of these matrices, a sample preparation step is in most cases mandatory to achieve satisfactory results being usually tedious, lengthy, and prone to the introduction of errors. For this reason, many research groups have focused efforts on the development of online systems capable to do the cleanup, concentration, and separation steps at once through multidimensional separation techniques (MDS). Among several possible setups, the most popular are the multidimensional chromatographic techniques (MDC) that consist in combining more than one mobile and/or stationary phase to provide a satisfactory separation. In the present review, we selected a variety of multidimensional separation systems used for food contaminant analysis in order to discuss the instrumentation aspects, the concept of orthogonality, column approaches used in these systems, and new materials that can be used in these columns. Selected classes of contaminants present in food matrices are introduced and discussed as example of the potential applications of multidimensional liquid phase separation techniques in food safety. PMID:27030380

  13. Multidimensional Scaling: Review and Geographical Applications, Technical Paper No. 10.

    ERIC Educational Resources Information Center

    Golledge, R. G.; Rushton, Gerard

    The purpose of this monograph is to show that sufficient achievements in scaling applications have been made to justify serious study of scaling methodologies, particularly multidimensional scaling (MDS) as a tool for geographers. To be useful research, it was felt that the common methodological and technical problems that specialized researchers…

  14. Multidimensional Scoring of Abilities: The Ordered Polytomous Response Case

    ERIC Educational Resources Information Center

    de la Torre, Jimmy

    2008-01-01

    Recent work has shown that multidimensionally scoring responses from different tests can provide better ability estimates. For educational assessment data, applications of this approach have been limited to binary scores. Of the different variants, the de la Torre and Patz model is considered more general because implementing the scoring procedure…

  15. An overview of multidimensional liquid phase separations in food analysis.

    PubMed

    Franco, Maraíssa Silva; Padovan, Rodrigo Nogueira; Fumes, Bruno Henrique; Lanças, Fernando Mauro

    2016-07-01

    Food safety is a priority public health concern that demands analytical methods capable to detect low concentration level of contaminants (e.g. pesticides and antibiotics) in different food matrices. Due to the high complexity of these matrices, a sample preparation step is in most cases mandatory to achieve satisfactory results being usually tedious, lengthy, and prone to the introduction of errors. For this reason, many research groups have focused efforts on the development of online systems capable to do the cleanup, concentration, and separation steps at once through multidimensional separation techniques (MDS). Among several possible setups, the most popular are the multidimensional chromatographic techniques (MDC) that consist in combining more than one mobile and/or stationary phase to provide a satisfactory separation. In the present review, we selected a variety of multidimensional separation systems used for food contaminant analysis in order to discuss the instrumentation aspects, the concept of orthogonality, column approaches used in these systems, and new materials that can be used in these columns. Selected classes of contaminants present in food matrices are introduced and discussed as example of the potential applications of multidimensional liquid phase separation techniques in food safety.

  16. BMDS: A Collection of R Functions for Bayesian Multidimensional Scaling

    ERIC Educational Resources Information Center

    Okada, Kensuke; Shigemasu, Kazuo

    2009-01-01

    Bayesian multidimensional scaling (MDS) has attracted a great deal of attention because: (1) it provides a better fit than do classical MDS and ALSCAL; (2) it provides estimation errors of the distances; and (3) the Bayesian dimension selection criterion, MDSIC, provides a direct indication of optimal dimensionality. However, Bayesian MDS is not…

  17. A MULTIDIMENSIONAL AND MULTIPHYSICS APPROACH TO NUCLEAR FUEL BEHAVIOR SIMULATION

    SciTech Connect

    R. L. Williamson; J. D. Hales; S. R. Novascone; M. R. Tonks; D. R. Gaston; C. J. Permann; D. Andrs; R. C. Martineau

    2012-04-01

    Important aspects of fuel rod behavior, for example pellet-clad mechanical interaction (PCMI), fuel fracture, oxide formation, non-axisymmetric cooling, and response to fuel manufacturing defects, are inherently multidimensional in addition to being complicated multiphysics problems. Many current modeling tools are strictly 2D axisymmetric or even 1.5D. This paper outlines the capabilities of a new fuel modeling tool able to analyze either 2D axisymmetric or fully 3D models. These capabilities include temperature-dependent thermal conductivity of fuel; swelling and densification; fuel creep; pellet fracture; fission gas release; cladding creep; irradiation growth; and gap mechanics (contact and gap heat transfer). The need for multiphysics, multidimensional modeling is then demonstrated through a discussion of results for a set of example problems. The first, a 10-pellet rodlet, demonstrates the viability of the solution method employed. This example highlights the effect of our smeared cracking model and also shows the multidimensional nature of discrete fuel pellet modeling. The second example relies on our the multidimensional, multiphysics approach to analyze a missing pellet surface problem. As a final example, we show a lower-length-scale simulation coupled to a continuum-scale simulation.

  18. A Multidimensional Latent Trait Model for Measuring Learning and Change.

    ERIC Educational Resources Information Center

    Embretson, Susan E.

    1991-01-01

    A multidimensional model is presented for measuring learning and change based on item response theory. The model specifies a Wiener simplex pattern for involvement of initial ability and one or more modifiabilities in response potential for successive measurement occasions. Properties of the model are explored for several classical issues. (SLD)

  19. Psychometric Properties of the Multidimensional-Multiattributional Causality Scale.

    ERIC Educational Resources Information Center

    Hamilton, Richard J.; Akhter, Selina

    2002-01-01

    Studied the construct validity of the dimensions of the Multidimensional-Multiattributional Causality Scale based on B. Wiener's attribution model (1979) in achievement and affiliation goal domains. Results for 172 New Zealand college students provide evidence that the measure is better used as a goal specific measure than a general measure. (SLD)

  20. Multidimensional Vector Model of Stimulus-Response Compatibility

    ERIC Educational Resources Information Center

    Yamaguchi, Motonori; Proctor, Robert W.

    2012-01-01

    The present study proposes and examines the multidimensional vector (MDV) model framework as a modeling schema for choice response times. MDV extends the Thurstonian model, as well as signal detection theory, to classification tasks by taking into account the influence of response properties on stimulus discrimination. It is capable of accounting…

  1. Assessing Multidimensional Energy Literacy of Secondary Students Using Contextualized Assessment

    ERIC Educational Resources Information Center

    Chen, Kuan-Li; Liu, Shiang-Yao; Chen, Po-Hsi

    2015-01-01

    Energy literacy is multidimensional, comprising broad content knowledge as well as affect and behavior. Our previous study has defined four core dimensions for the assessment framework, including energy concepts, reasoning on energy issues, low-carbon lifestyle, and civic responsibility for a sustainable society. The present study compiled a…

  2. Three-Mode Multidimensional Scaling with Points of View Solutions

    ERIC Educational Resources Information Center

    Tzeng, Oliver C. S.; Landis, Dan

    1978-01-01

    Two popular models for performing multidimensional scaling, Tucker and Messick's points-of-view model, and Tucker's three mode model, are combined into a single analytic procedure, the 3M-POV model. The procedure is described and its strengths are discussed. Carroll and Chang's INDSCAL model is also mentioned. (JKS)

  3. Reporting of Subscores Using Multidimensional Item Response Theory

    ERIC Educational Resources Information Center

    Haberman, Shelby J.; Sinharay, Sandip

    2010-01-01

    Recently, there has been increasing interest in reporting subscores. This paper examines reporting of subscores using multidimensional item response theory (MIRT) models (e.g., Reckase in "Appl. Psychol. Meas." 21:25-36, 1997; C.R. Rao and S. Sinharay (Eds), "Handbook of Statistics, vol. 26," pp. 607-642, North-Holland, Amsterdam, 2007; Beguin &…

  4. A Review of the Brief Multidimensional Students' Life Satisfaction Scale

    ERIC Educational Resources Information Center

    Huebner, E. Scott; Seligson, Julie L.; Valois, Robert F.; Suldo, Shannon M.

    2006-01-01

    There are few psychometrically sound measures of life satisfaction suitable for children and adolescents. The purpose of this paper is to describe the rationale, development, and psychometric properties of a brief multidimensional life satisfaction scale appropriate for use with children of ages 8-18. The paper summarizes extant studies of its…

  5. Generalizations of Paradoxical Results in Multidimensional Item Response Theory

    ERIC Educational Resources Information Center

    Jordan, Pascal; Spiess, Martin

    2012-01-01

    Maximum likelihood and Bayesian ability estimation in multidimensional item response models can lead to paradoxical results as proven by Hooker, Finkelman, and Schwartzman ("Psychometrika" 74(3): 419-442, 2009): Changing a correct response on one item into an incorrect response may produce a higher ability estimate in one dimension. Furthermore,…

  6. Income Tax Preparation Assistance Service Learning Program: A Multidimensional Assessment

    ERIC Educational Resources Information Center

    Aldridge, Richard; Callahan, Richard A.; Chen, Yining; Wade, Stacy R.

    2015-01-01

    The authors present a multidimensional assessment of the outcomes and benefits of an income tax preparation assistance (ITPA) service learning program. They measure the perceived proximate benefits at the delivery of the service program, the actual learning outcome benefits prior to graduation, and the perceived long-term benefits from a…

  7. Individual and Institutional Determinants of Multidimensional Poverty: A European Comparison

    ERIC Educational Resources Information Center

    Dewilde, Caroline

    2008-01-01

    In this article we evaluate to what extent between-country differences in the probability of being "multidimensional" poor can be explained by a range of "domain-specific" indicators of welfare regime arrangements. To this end, a so-called micro-macro model is estimated, testing the "independent" effect of institutions, as opposed to alternative…

  8. Development and Validation of the Multidimensional State Boredom Scale

    ERIC Educational Resources Information Center

    Fahlman, Shelley A.; Mercer-Lynn, Kimberley B.; Flora, David B.; Eastwood, John D.

    2013-01-01

    This article describes the development and validation of the Multidimensional State Boredom Scale (MSBS)--the first and only full-scale measure of state boredom. It was developed based on a theoretically and empirically grounded definition of boredom. A five-factor structure of the scale (Disengagement, High Arousal, Low Arousal, Inattention, and…

  9. Income and beyond: Multidimensional Poverty in Six Latin American Countries

    ERIC Educational Resources Information Center

    Battiston, Diego; Cruces, Guillermo; Lopez-Calva, Luis Felipe; Lugo, Maria Ana; Santos, Maria Emma

    2013-01-01

    This paper studies multidimensional poverty for Argentina, Brazil, Chile, El Salvador, Mexico and Uruguay for the period 1992-2006. The approach overcomes the limitations of the two traditional methods of poverty analysis in Latin America (income-based and unmet basic needs) by combining income with five other dimensions: school attendance for…

  10. The Multi-Dimensional Demands of Reading in the Disciplines

    ERIC Educational Resources Information Center

    Lee, Carol D.

    2014-01-01

    This commentary addresses the complexities of reading comprehension with an explicit focus on reading in the disciplines. The author proposes reading as entailing multi-dimensional demands of the reader and posing complex challenges for teachers. These challenges are intensified by restrictive conceptions of relevant prior knowledge and experience…

  11. Multidimensional Poverty in China: Findings Based on the CHNS

    ERIC Educational Resources Information Center

    Yu, Jiantuo

    2013-01-01

    This paper estimates multidimensional poverty in China by applying the Alkire-Foster methodology to the China Health and Nutrition Survey 2000-2009 data. Five dimensions are included: income, living standard, education, health and social security. Results suggest that rapid economic growth has resulted not only in a reduction in income poverty but…

  12. Multidimensional Item Response Theory Parameter Estimation with Nonsimple Structure Items

    ERIC Educational Resources Information Center

    Finch, Holmes

    2011-01-01

    Estimation of multidimensional item response theory (MIRT) model parameters can be carried out using the normal ogive with unweighted least squares estimation with the normal-ogive harmonic analysis robust method (NOHARM) software. Previous simulation research has demonstrated that this approach does yield accurate and efficient estimates of item…

  13. Five Evils: Multidimensional Poverty and Race in America

    ERIC Educational Resources Information Center

    Reeves, Richard; Rodrigue, Edward; Kneebone, Elizabeth

    2016-01-01

    Poverty is about a lack of money, but it's not only about that. As a lived experience, poverty is also characterized by ill health, insecurity, discomfort, isolation, and more. To put it another way: Poverty is multidimensional, and its dimensions often cluster together to intensify the negative effects of being poor. In this first of a two-part…

  14. The Structure and Validity of the Multidimensional Social Support Questionnaire

    ERIC Educational Resources Information Center

    Hardesty, Patrick H.; Richardson, George B.

    2012-01-01

    The factor structure and concurrent validity of the Multidimensional Social Support Questionnaire, a brief measure of perceived social support for use with adolescents, was examined. Findings suggest that four dimensions of perceived social support may yield more information than assessments of the unitary construct of support. (Contains 8 tables…

  15. The structure of multidimensional strained flames under transcritical conditions

    NASA Astrophysics Data System (ADS)

    Pons, L.; Darabiha, N.; Candel, S.; Schmitt, T.; Cuenot, B.

    2009-06-01

    Strained flames are commonly used to study the structure of reactive layers and describe the local properties of turbulent combustion. This model is attractive because constant strain rate flames only depend on a transverse coordinate and can be treated as a one-dimensional problem. This configuration is considered in a multidimensional context in which the strained flow is obtained by two counterflowing streams of reactants. It is used to examine the structure of transcritical strained flames in which one or two reactants are injected at a high pressure exceeding the critical value while their temperature is below the critical value. Calculations are carried out in a two-dimensional domain to test numerical models developed for multidimensional simulations and test thermodynamic and transport models devised to deal with high pressure real gas effects. Multidimensional strained flame calculations carried out in this study serve to check the validity of a new version of a Navier-Stokes flow solver (AVBP) conceived to deal with transcritical combustion of interest to liquid propellant rocket applications. This article describes the basic elements of such simulations and discusses results of calculations. It is shown that the calculated multidimensional strained flames have the expected features in terms of structure and response to the imposed strain rate. To cite this article: L. Pons et al., C. R. Mecanique 337 (2009).

  16. Multidimensional Model of Trauma and Correlated Antisocial Personality Disorder

    ERIC Educational Resources Information Center

    Martens, Willem H. J.

    2005-01-01

    Many studies have revealed an important relationship between psychosocial trauma and antisocial personality disorder. A multidimensional model is presented which describes the psychopathological route from trauma to antisocial development. A case report is also included that can illustrate the etiological process from trauma to severe antisocial…

  17. Multi-Dimensional Models for Teaching Deaf-Blind Children.

    ERIC Educational Resources Information Center

    Baud, Hank, Ed.; Garrett, Jeff, Ed.

    Presented are five papers on multidimensional teaching models presented at a workshop for professionals serving deaf-blind children. In "Interpretation of Visual Reports", M. Efron discusses procedures for improving visual diagnosis and provides a questionnaire format for an educationally oriented vision report. M. Marshall, in her paper entitled…

  18. Educational Mismatch of Graduates: A Multidimensional and Fuzzy Indicator

    ERIC Educational Resources Information Center

    Betti, Gianni; D'Agostino, Antonella; Neri, Laura

    2011-01-01

    In this paper we attempt to measure the educational mismatch, seen as a problem of overeducation, using a multidimensional and fuzzy methodology. Educational mismatch can be difficult to measure because many factors can converge to its definition and the traditional unidimensional indicators presented in literature can offer a restricted view of…

  19. The Multidimensionality of Calling: Conceptualization, Measurement and a Bicultural Perspective

    ERIC Educational Resources Information Center

    Hagmaier, Tamara; Abele, Andrea E.

    2012-01-01

    The experience of a calling may be seen as the ultimate form of subjective career success that has many positive consequences for individuals and organizations. We are here concerned with the conceptualization of a new multidimensional measure of calling, the MCM. In the first two studies we employed a qualitative approach and came up with five…

  20. Analysis of stock market indices through multidimensional scaling

    NASA Astrophysics Data System (ADS)

    Machado, J. Tenreiro; Duarte, Fernando B.; Duarte, Gonçalo Monteiro

    2011-12-01

    We propose a graphical method to visualize possible time-varying correlations between fifteen stock market values. The method is useful for observing stable or emerging clusters of stock markets with similar behaviour. The graphs, originated from applying multidimensional scaling techniques (MDS), may also guide the construction of multivariate econometric models.

  1. Studying Children's Early Literacy Development: Confirmatory Multidimensional Scaling Growth Modeling

    ERIC Educational Resources Information Center

    Ding, Cody

    2012-01-01

    There has been considerable debate over the ways in which children's early literacy skills develop over time. Using confirmatory multidimensional scaling (MDS) growth analysis, this paper directly tested the hypothesis of a cumulative trajectory versus a compensatory trajectory of development in early literacy skills among a group of 1233…

  2. Examining the Reliability of Student Growth Percentiles Using Multidimensional IRT

    ERIC Educational Resources Information Center

    Monroe, Scott; Cai, Li

    2015-01-01

    Student growth percentiles (SGPs, Betebenner, 2009) are used to locate a student's current score in a conditional distribution based on the student's past scores. Currently, following Betebenner (2009), quantile regression (QR) is most often used operationally to estimate the SGPs. Alternatively, multidimensional item response theory (MIRT) may…

  3. The Relationship between Anxiety and Stuttering: A Multidimensional Approach

    ERIC Educational Resources Information Center

    Ezrati-Vinacour, Ruth; Levin, Iris

    2004-01-01

    The relationship between anxiety and stuttering is equivocal from both clinical and empirical perspectives. This study examined the relationship within the framework of the multidimensional interaction model of anxiety that includes an approach to general anxiety in specific situations [J. Pers. Soc. Psychol. 60 (1991) 919]. Ninety-four males aged…

  4. The Structure of Masculinity-Femininity: Multidimensionality and Gender Differences.

    ERIC Educational Resources Information Center

    Ratliff, Elyse Sutherland; Conley, James

    1981-01-01

    Investigated the structure of sex role self-descriptors. Factor analyzed responses of female and male undergraduates to the Bem Sex Role Inventory. Seven factors emerged: personal warmth, social dominance, autonomy, affect, masculinity-feminity, vulnerability, and responsibility. Results support a multidimensional conception of…

  5. Evaluation of Linking Methods for Multidimensional IRT Calibrations

    ERIC Educational Resources Information Center

    Min, Kyung-Seok

    2007-01-01

    Most researchers agree that psychological/educational tests are sensitive to multiple traits, implying the need for a multidimensional item response theory (MIRT). One limitation of applying a MIRT in practice is the difficulty in establishing equivalent scales of multiple traits. In this study, a new MIRT linking method was proposed and evaluated…

  6. Gender and Attitudes toward People Using Wheelchairs: A Multidimensional Perspective

    ERIC Educational Resources Information Center

    Vilchinsky, Noa; Werner, Shirli; Findler, Liora

    2010-01-01

    This study aims to investigate the effect of observer's gender and target's gender on attitudes toward people who use wheelchairs due to a physical disability. Four hundred four Jewish Israeli students without disabilities completed the "Multidimensional Attitudes Scale Toward Persons With Disabilities" (MAS). Initially, confirmatory factor…

  7. The Multidimensional Structure of Verbal Comprehension Test Items.

    ERIC Educational Resources Information Center

    Peled, Zimra

    1984-01-01

    The multidimensional structure of verbal comprehension test items was investigated. Empirical evidence was provided to support the theory that item tasks are multivariate-multiordered composites of faceted components: language, contextual knowledge, and cognitive operation. Linear and circular properties of cylindrical manifestation were…

  8. A Multidimensional Approach to E-Learning Sustainability

    ERIC Educational Resources Information Center

    Trentin, Guglielmo, Ed.

    2007-01-01

    The aim of the article is to outline the possible key elements related to the sustainability of e-learning. After analyzing trends in e-learning diffusion, a multidimensional model for sustainability of e-learning innovations is presented. The proposed model is characterized by eight dimensions that are closely and mutually interrelated:…

  9. On the Solution of NBVP for Multidimensional Hyperbolic Equations

    PubMed Central

    Ashyralyev, Allaberen

    2014-01-01

    We are interested in studying multidimensional hyperbolic equations with nonlocal integral and Neumann or nonclassical conditions. For the approximate solution of this problem first and second order of accuracy difference schemes are presented. Stability estimates for the solution of these difference schemes are established. Some numerical examples illustrating applicability of these methods to hyperbolic problems are given. PMID:24983006

  10. The Multidimensional Behavior Rating Scale: An Assessment Device for Depression.

    ERIC Educational Resources Information Center

    Rothblum, Esther D.; Green, Leon

    The Multidimensional Behavior Rating Scale (MBRS) was constructed to assess symptoms of depression across seven modalities: behavior, affect, sensation, imagery, cognition, interpersonal relationship, and drugs. Subjects (N=33) were matched by level of depression on the Minnesota Multiphasic Personality Inventory Depression Scale to either a…

  11. Extending Validity Evidence for Multidimensional Measures of Coaching Competency

    ERIC Educational Resources Information Center

    Myers, Nicholas D.; Wolfe, Edward W.; Maier, Kimberly S.; Feltz, Deborah L.; Reckase, Mark D.

    2006-01-01

    This study extended validity evidence for multidimensional measures of coaching competency derived from the Coaching Competency Scale (CCS; Myers, Feltz, Maier, Wolfe, & Reckase, 2006) by examining use of the original rating scale structure and testing how measures related to satisfaction with the head coach within teams and between teams.…

  12. A Framework for Dimensionality Assessment for Multidimensional Item Response Models

    ERIC Educational Resources Information Center

    Svetina, Dubravka; Levy, Roy

    2014-01-01

    A framework is introduced for considering dimensionality assessment procedures for multidimensional item response models. The framework characterizes procedures in terms of their confirmatory or exploratory approach, parametric or nonparametric assumptions, and applicability to dichotomous, polytomous, and missing data. Popular and emerging…

  13. The Multidimensionality of Child Poverty: Evidence from Afghanistan

    ERIC Educational Resources Information Center

    Trani, Jean-Francois; Biggeri, Mario; Mauro, Vincenzo

    2013-01-01

    This paper examines multidimensional poverty among children in Afghanistan using the Alkire-Foster method. Several previous studies have underlined the need to separate children from their adult nexus when studying poverty and treat them according to their own specificities. From the capability approach, child poverty is understood to be the lack…

  14. The Multidimensional Fear of Death Scale: An Independent Analysis.

    ERIC Educational Resources Information Center

    Walkey, Frank H.

    1982-01-01

    Examined the factor structure and subscale reliabilities of an eight-dimensional measure of fear of death (the Multidimensional Fear of Death Scale) using a New Zealand sample. Comparison with the results of a United States study showed that both the subscale reliabilities and the factor structure were almost perfectly reproduced. (Author)

  15. A General Multidimensional Model for the Measurement of Cultural Differences.

    ERIC Educational Resources Information Center

    Olmedo, Esteban L.; Martinez, Sergio R.

    A multidimensional model for measuring cultural differences (MCD) based on factor analytic theory and techniques is proposed. The model assumes that a cultural space may be defined by means of a relatively small number of orthogonal dimensions which are linear combinations of a much larger number of cultural variables. Once a suitable,…

  16. Multidimensional Adaptive Testing with Optimal Design Criteria for Item Selection

    ERIC Educational Resources Information Center

    Mulder, Joris; van der Linden, Wim J.

    2009-01-01

    Several criteria from the optimal design literature are examined for use with item selection in multidimensional adaptive testing. In particular, it is examined what criteria are appropriate for adaptive testing in which all abilities are intentional, some should be considered as a nuisance, or the interest is in the testing of a composite of the…

  17. Positivity-preserving numerical schemes for multidimensional advection

    NASA Technical Reports Server (NTRS)

    Leonard, B. P.; Macvean, M. K.; Lock, A. P.

    1993-01-01

    This report describes the construction of an explicit, single time-step, conservative, finite-volume method for multidimensional advective flow, based on a uniformly third-order polynomial interpolation algorithm (UTOPIA). Particular attention is paid to the problem of flow-to-grid angle-dependent, anisotropic distortion typical of one-dimensional schemes used component-wise. The third-order multidimensional scheme automatically includes certain cross-difference terms that guarantee good isotropy (and stability). However, above first-order, polynomial-based advection schemes do not preserve positivity (the multidimensional analogue of monotonicity). For this reason, a multidimensional generalization of the first author's universal flux-limiter is sought. This is a very challenging problem. A simple flux-limiter can be found; but this introduces strong anisotropic distortion. A more sophisticated technique, limiting part of the flux and then restoring the isotropy-maintaining cross-terms afterwards, gives more satisfactory results. Test cases are confined to two dimensions; three-dimensional extensions are briefly discussed.

  18. Image matrix processor for fast multi-dimensional computations

    DOEpatents

    Roberson, G.P.; Skeate, M.F.

    1996-10-15

    An apparatus for multi-dimensional computation is disclosed which comprises a computation engine, including a plurality of processing modules. The processing modules are configured in parallel and compute respective contributions to a computed multi-dimensional image of respective two dimensional data sets. A high-speed, parallel access storage system is provided which stores the multi-dimensional data sets, and a switching circuit routes the data among the processing modules in the computation engine and the storage system. A data acquisition port receives the two dimensional data sets representing projections through an image, for reconstruction algorithms such as encountered in computerized tomography. The processing modules include a programmable local host, by which they may be configured to execute a plurality of different types of multi-dimensional algorithms. The processing modules thus include an image manipulation processor, which includes a source cache, a target cache, a coefficient table, and control software for executing image transformation routines using data in the source cache and the coefficient table and loading resulting data in the target cache. The local host processor operates to load the source cache with a two dimensional data set, loads the coefficient table, and transfers resulting data out of the target cache to the storage system, or to another destination. 10 figs.

  19. Image matrix processor for fast multi-dimensional computations

    DOEpatents

    Roberson, George P.; Skeate, Michael F.

    1996-01-01

    An apparatus for multi-dimensional computation which comprises a computation engine, including a plurality of processing modules. The processing modules are configured in parallel and compute respective contributions to a computed multi-dimensional image of respective two dimensional data sets. A high-speed, parallel access storage system is provided which stores the multi-dimensional data sets, and a switching circuit routes the data among the processing modules in the computation engine and the storage system. A data acquisition port receives the two dimensional data sets representing projections through an image, for reconstruction algorithms such as encountered in computerized tomography. The processing modules include a programmable local host, by which they may be configured to execute a plurality of different types of multi-dimensional algorithms. The processing modules thus include an image manipulation processor, which includes a source cache, a target cache, a coefficient table, and control software for executing image transformation routines using data in the source cache and the coefficient table and loading resulting data in the target cache. The local host processor operates to load the source cache with a two dimensional data set, loads the coefficient table, and transfers resulting data out of the target cache to the storage system, or to another destination.

  20. Multidimensional representation of objects--The influence of task demands.

    PubMed

    Goldfarb, L; Sabah, K

    2016-04-01

    In our daily life, we often encounter situations in which different features of several multidimensional objects must be perceived simultaneously. There are two types of environments of this kind: environments with multidimensional objects that have unique feature associations, and environments with multidimensional objects that have mixed feature associations. Recently, we (Goldfarb & Treisman, 2013) described the association effect, suggesting that the latter type causes behavioral perception difficulties. In the present study, we investigated this effect further by examining whether the effect is determined via a feedforward visual path or via a high-order task demand component. In order to test this question, in Experiment 1 a set of multidimensional objects were presented while we manipulated the letter case of a target feature, thus creating a visually different but semantically equivalent object, in terms of its identity. Similarly, in Experiment 2 artificial groups with different physical properties were created according to the task demands. The results indicated that the association effect is determined by the task demands, which create the group of reference. The importance of high-order task demand components in the association effect is further discussed, as well as the possible role of the neural synchrony of object files in explaining this effect. PMID:26163190

  1. A Multidimensional Analysis of a Written L2 Spanish Corpus

    ERIC Educational Resources Information Center

    Asencion-Delaney, Yuly; Collentine, Joseph

    2011-01-01

    The present study adds to our understanding of how learners employ lexical and grammatical phenomena to communicate in writing in different types of interlanguage discourse. A multidimensional (factor) analysis of a corpus of L2 Spanish writing (202,241 words) generated by second- and third-year, university-level learners was performed. The…

  2. Multidimensional Collaboration: Reflections on Action Research in a Clinical Context

    ERIC Educational Resources Information Center

    Gregory, Sheila; Poland, Fiona; Spalding, Nicola J.; Sargen, Kevin; McCulloch, Jane; Vicary, Penny

    2011-01-01

    This paper reflects on the challenges and benefits of multidimensional collaboration in an action research study to evaluate and improve preoperative education for patients awaiting colorectal surgery. Three cycles of planning, acting, observing and reflecting were designed to evaluate practice and implement change in this interactive setting,…

  3. Integrable multidimensional gravitational and cosmological models and applications

    NASA Astrophysics Data System (ADS)

    Ivashchuk, V. D.; Melnikov, V. N.

    2016-01-01

    Two families of exact solutions in multidimensional gravity with scalar fields and fields of forms are considered: fluxbrane and black brane ones. A brief overview of main results on billiard approach for cosmological-type models with branes is also presented.

  4. Distinct metabolic network states manifest in the gene expression profiles of pediatric inflammatory bowel disease patients and controls

    NASA Astrophysics Data System (ADS)

    Knecht, Carolin; Fretter, Christoph; Rosenstiel, Philip; Krawczak, Michael; Hütt, Marc-Thorsten

    2016-09-01

    Information on biological networks can greatly facilitate the function-orientated interpretation of high-throughput molecular data. Genome-wide metabolic network models of human cells, in particular, can be employed to contextualize gene expression profiles of patients with the goal of both, a better understanding of individual etiologies and an educated reclassification of (clinically defined) phenotypes. We analyzed publicly available expression profiles of intestinal tissues from treatment-naive pediatric inflammatory bowel disease (IBD) patients and age-matched control individuals, using a reaction-centric metabolic network derived from the Recon2 model. By way of defining a measure of ‘coherence’, we quantified how well individual patterns of expression changes matched the metabolic network. We observed a bimodal distribution of metabolic network coherence in both patients and controls, albeit at notably different mixture probabilities. Multidimensional scaling analysis revealed a bisectional pattern as well that overlapped widely with the metabolic network-based results. Expression differences driving the observed bimodality were related to cellular transport of thiamine and bile acid metabolism, thereby highlighting the crosstalk between metabolism and other vital pathways. We demonstrated how classical data mining and network analysis can jointly identify biologically meaningful patterns in gene expression data.

  5. Distinct metabolic network states manifest in the gene expression profiles of pediatric inflammatory bowel disease patients and controls.

    PubMed

    Knecht, Carolin; Fretter, Christoph; Rosenstiel, Philip; Krawczak, Michael; Hütt, Marc-Thorsten

    2016-09-02

    Information on biological networks can greatly facilitate the function-orientated interpretation of high-throughput molecular data. Genome-wide metabolic network models of human cells, in particular, can be employed to contextualize gene expression profiles of patients with the goal of both, a better understanding of individual etiologies and an educated reclassification of (clinically defined) phenotypes. We analyzed publicly available expression profiles of intestinal tissues from treatment-naive pediatric inflammatory bowel disease (IBD) patients and age-matched control individuals, using a reaction-centric metabolic network derived from the Recon2 model. By way of defining a measure of 'coherence', we quantified how well individual patterns of expression changes matched the metabolic network. We observed a bimodal distribution of metabolic network coherence in both patients and controls, albeit at notably different mixture probabilities. Multidimensional scaling analysis revealed a bisectional pattern as well that overlapped widely with the metabolic network-based results. Expression differences driving the observed bimodality were related to cellular transport of thiamine and bile acid metabolism, thereby highlighting the crosstalk between metabolism and other vital pathways. We demonstrated how classical data mining and network analysis can jointly identify biologically meaningful patterns in gene expression data.

  6. Distinct metabolic network states manifest in the gene expression profiles of pediatric inflammatory bowel disease patients and controls.

    PubMed

    Knecht, Carolin; Fretter, Christoph; Rosenstiel, Philip; Krawczak, Michael; Hütt, Marc-Thorsten

    2016-01-01

    Information on biological networks can greatly facilitate the function-orientated interpretation of high-throughput molecular data. Genome-wide metabolic network models of human cells, in particular, can be employed to contextualize gene expression profiles of patients with the goal of both, a better understanding of individual etiologies and an educated reclassification of (clinically defined) phenotypes. We analyzed publicly available expression profiles of intestinal tissues from treatment-naive pediatric inflammatory bowel disease (IBD) patients and age-matched control individuals, using a reaction-centric metabolic network derived from the Recon2 model. By way of defining a measure of 'coherence', we quantified how well individual patterns of expression changes matched the metabolic network. We observed a bimodal distribution of metabolic network coherence in both patients and controls, albeit at notably different mixture probabilities. Multidimensional scaling analysis revealed a bisectional pattern as well that overlapped widely with the metabolic network-based results. Expression differences driving the observed bimodality were related to cellular transport of thiamine and bile acid metabolism, thereby highlighting the crosstalk between metabolism and other vital pathways. We demonstrated how classical data mining and network analysis can jointly identify biologically meaningful patterns in gene expression data. PMID:27585741

  7. Distinct metabolic network states manifest in the gene expression profiles of pediatric inflammatory bowel disease patients and controls

    PubMed Central

    Knecht, Carolin; Fretter, Christoph; Rosenstiel, Philip; Krawczak, Michael; Hütt, Marc-Thorsten

    2016-01-01

    Information on biological networks can greatly facilitate the function-orientated interpretation of high-throughput molecular data. Genome-wide metabolic network models of human cells, in particular, can be employed to contextualize gene expression profiles of patients with the goal of both, a better understanding of individual etiologies and an educated reclassification of (clinically defined) phenotypes. We analyzed publicly available expression profiles of intestinal tissues from treatment-naive pediatric inflammatory bowel disease (IBD) patients and age-matched control individuals, using a reaction-centric metabolic network derived from the Recon2 model. By way of defining a measure of ‘coherence’, we quantified how well individual patterns of expression changes matched the metabolic network. We observed a bimodal distribution of metabolic network coherence in both patients and controls, albeit at notably different mixture probabilities. Multidimensional scaling analysis revealed a bisectional pattern as well that overlapped widely with the metabolic network-based results. Expression differences driving the observed bimodality were related to cellular transport of thiamine and bile acid metabolism, thereby highlighting the crosstalk between metabolism and other vital pathways. We demonstrated how classical data mining and network analysis can jointly identify biologically meaningful patterns in gene expression data. PMID:27585741

  8. Second order multidimensional sign-preserving remapping for ALE methods

    SciTech Connect

    Hill, Ryan N; Szmelter, J.

    2010-12-15

    A second-order conservative sign-preserving remapping scheme for Arbitrary Lagrangian-Eulerian (ALE) methods is developed utilising concepts of the Multidimensional Positive Definite Advection Transport Algorithm (MPDATA). The algorithm is inherently multidimensional, and so does not introduce splitting errors. The remapping is implemented in a two-dimensional, finite element ALE solver employing staggered quadrilateral meshes. The MPDATA remapping uses a finite volume discretization developed for volume coordinates. It is applied for the remapping of density and internal energy arranged as cell centered, and velocity as nodal, dependent variables. In the paper, the advection of scalar fields is examined first for test cases with prescribed mesh movement. A direct comparison of MPDATA with the performance of the van Leer MUSCL scheme indicates advantages of a multidimensional approach. Furthermore, distinctly different performance between basic MPDATA and the infinite gauge option is illustrated using benchmarks involving transport of a sign changing velocity field. Further development extends the application of MPDATA remapping to the full ALE solver with a staggered mesh arrangement for density, internal energy and momentum using volume coordinates. At present, two options of the algorithm - basic and infinite gauge - are implemented. To ensure a meaningful assessment, an identical Lagrangian solver and computational mesh update routines are used with either MPDATA or van Leer MUSCL remapping. The evaluation places particular focus on the abilities of both schemes to accurately model multidimensional problems. Theoretical considerations are supported with numerical examples. In addition to the prescribed mesh movement cases for advection of scalars, the demonstrations include two-dimensional Eulerian and ALE flow simulations on quadrilateral meshes with both fixed and variable timestep control. The key comparisons include the standard test cases of Sod and Noh

  9. Psychometric Properties of the Frost Multidimensional Perfectionism Scale with Australian Adolescent Girls: Clarification of Multidimensionality and Perfectionist Typology

    ERIC Educational Resources Information Center

    Hawkins, Colleen C.; Watt, Helen M. G.; Sinclair, Kenneth E.

    2006-01-01

    The psychometric properties of the Frost, Marten, Lahart, and Rosenblate Multidimensional Perfectionism Scale (1990) are investigated to determine its usefulness as a measurement of perfectionism with Australian secondary school girls and to find empirical support for the existence of both healthy and unhealthy types of perfectionist students.…

  10. Parasitic manipulation of hosts' phenotype, or how to make a zombie--an introduction to the symposium.

    PubMed

    Weinersmith, Kelly; Faulkes, Zen

    2014-07-01

    Nearly all animals in nature are infected by at least one parasite, and many of those parasites can significantly change the phenotype of their hosts, often in ways that increase the parasite's likelihood of transmission. Hosts' phenotypic changes are multidimensional, and manipulated traits include behavior, neurotransmission, coloration, morphology, and hormone levels. The field of parasitic manipulation of hosts' phenotype has now accrued many examples of systems where parasites manipulate the phenotypes of their hosts and focus has shifted to answering three main questions. First, through what mechanisms do parasites manipulate the hosts' phenotype? Parasites often induce changes in the hosts' phenotypes that neuroscientists are unable to recreate under laboratory conditions, suggesting that parasites may have much to teach us about links between the brain, immune system, and the expression of phenotype. Second, what are the ecological implications of phenotypic manipulation? Manipulated hosts are often abundant, and changes in their phenotype may have important population, community, and ecosystem-level implications. Finally, how did parasitic manipulation of hosts' phenotype evolve? The selective pressures faced by parasites are extremely complex, often with multiple hosts that are actively resisting infection, both in physiological and evolutionary time-scales. Here, we provide an overview of how the work presented in this special issue contributes to tackling these three main questions. Studies on parasites' manipulation of their hosts' phenotype are undertaken largely by parasitologists, and a major goal of this symposium is to recruit researchers from other fields to the study of these phenomena. Our ability to answer the three questions outlined above would be greatly enhanced by participation from individuals trained in the fields of, for example, neurobiology, physiology, immunology, ecology, evolutionary biology, and invertebrate biology. Conversely

  11. Metabolic Phenotypes in Pancreatic Cancer

    PubMed Central

    Yu, Min; Zhou, Quanbo; Zhou, Yu; Fu, Zhiqiang; Tan, Langping; Ye, Xiao; Zeng, Bing; Gao, Wenchao; Zhou, Jiajia; Liu, Yimin; Li, Zhihua; Lin, Ye; Lin, Qing; Chen, Rufu

    2015-01-01

    Introduction The aim of present study was to profile the glucose-dependent and glutamine- dependent metabolism in pancreatic cancer. Methods We performed Immunohistochemical staining of GLUT1, CAIX, BNIP3, p62, LC3, GLUD1, and GOT1. Based on the expression of metabolism-related proteins, the metabolic phenotypes of tumors were classified into two categories, including glucose- and glutamine-dependent metabolism. There were Warburg type, reverse Warburg type, mixed type, and null type in glucose-dependent metabolism, and canonical type, non-canonical type, mixed type, null type in glutamine-dependent metabolism. Results Longer overall survival was associated with high expression of BNIP3 in tumor (p = 0.010). Shorter overall survival was associated with high expression of GLUT1 in tumor (P = 0.002) and GOT1 in tumor (p = 0.030). Warburg type of glucose-dependent metabolism had a highest percentage of tumors with nerve infiltration (P = 0.0003), UICC stage (P = 0.0004), and activated autophagic status in tumor (P = 0.0167). Mixed type of glucose-dependent metabolism comprised the highest percentage of tumors with positive marginal status (P<0.0001), lymphatic invasion (P<0.0001), and activated autophagic status in stroma (P = 0.0002). Mixed type and Warburg type had a significant association with shorter overall survival (P = 0.018). Non-canonical type and mixed type of glutamine-dependent metabolism comprised the highest percentage of tumors with vascular invasion (p = 0.0073), highest percentage of activated autophagy in tumors (P = 0.0034). Moreover, these two types of glutamine-dependent metabolism were significantly associated with shorter overall survival (P<0.001). Further analysis suggested that most of tumors were dependent on both glucose- and glutamine-dependent metabolism. After dividing the tumors according to the number of metabolism, we found that the increasing numbers of metabolism subtypes inversely associated with survival outcome. Conclusion

  12. Finding our way through phenotypes.

    PubMed

    Deans, Andrew R; Lewis, Suzanna E; Huala, Eva; Anzaldo, Salvatore S; Ashburner, Michael; Balhoff, James P; Blackburn, David C; Blake, Judith A; Burleigh, J Gordon; Chanet, Bruno; Cooper, Laurel D; Courtot, Mélanie; Csösz, Sándor; Cui, Hong; Dahdul, Wasila; Das, Sandip; Dececchi, T Alexander; Dettai, Agnes; Diogo, Rui; Druzinsky, Robert E; Dumontier, Michel; Franz, Nico M; Friedrich, Frank; Gkoutos, George V; Haendel, Melissa; Harmon, Luke J; Hayamizu, Terry F; He, Yongqun; Hines, Heather M; Ibrahim, Nizar; Jackson, Laura M; Jaiswal, Pankaj; James-Zorn, Christina; Köhler, Sebastian; Lecointre, Guillaume; Lapp, Hilmar; Lawrence, Carolyn J; Le Novère, Nicolas; Lundberg, John G; Macklin, James; Mast, Austin R; Midford, Peter E; Mikó, István; Mungall, Christopher J; Oellrich, Anika; Osumi-Sutherland, David; Parkinson, Helen; Ramírez, Martín J; Richter, Stefan; Robinson, Peter N; Ruttenberg, Alan; Schulz, Katja S; Segerdell, Erik; Seltmann, Katja C; Sharkey, Michael J; Smith, Aaron D; Smith, Barry; Specht, Chelsea D; Squires, R Burke; Thacker, Robert W; Thessen, Anne; Fernandez-Triana, Jose; Vihinen, Mauno; Vize, Peter D; Vogt, Lars; Wall, Christine E; Walls, Ramona L; Westerfeld, Monte; Wharton, Robert A; Wirkner, Christian S; Woolley, James B; Yoder, Matthew J; Zorn, Aaron M; Mabee, Paula

    2015-01-01

    Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. PMID:25562316

  13. Finding Our Way through Phenotypes

    PubMed Central

    Deans, Andrew R.; Lewis, Suzanna E.; Huala, Eva; Anzaldo, Salvatore S.; Ashburner, Michael; Balhoff, James P.; Blackburn, David C.; Blake, Judith A.; Burleigh, J. Gordon; Chanet, Bruno; Cooper, Laurel D.; Courtot, Mélanie; Csösz, Sándor; Cui, Hong; Dahdul, Wasila; Das, Sandip; Dececchi, T. Alexander; Dettai, Agnes; Diogo, Rui; Druzinsky, Robert E.; Dumontier, Michel; Franz, Nico M.; Friedrich, Frank; Gkoutos, George V.; Haendel, Melissa; Harmon, Luke J.; Hayamizu, Terry F.; He, Yongqun; Hines, Heather M.; Ibrahim, Nizar; Jackson, Laura M.; Jaiswal, Pankaj; James-Zorn, Christina; Köhler, Sebastian; Lecointre, Guillaume; Lapp, Hilmar; Lawrence, Carolyn J.; Le Novère, Nicolas; Lundberg, John G.; Macklin, James; Mast, Austin R.; Midford, Peter E.; Mikó, István; Mungall, Christopher J.; Oellrich, Anika; Osumi-Sutherland, David; Parkinson, Helen; Ramírez, Martín J.; Richter, Stefan; Robinson, Peter N.; Ruttenberg, Alan; Schulz, Katja S.; Segerdell, Erik; Seltmann, Katja C.; Sharkey, Michael J.; Smith, Aaron D.; Smith, Barry; Specht, Chelsea D.; Squires, R. Burke; Thacker, Robert W.; Thessen, Anne; Fernandez-Triana, Jose; Vihinen, Mauno; Vize, Peter D.; Vogt, Lars; Wall, Christine E.; Walls, Ramona L.; Westerfeld, Monte; Wharton, Robert A.; Wirkner, Christian S.; Woolley, James B.; Yoder, Matthew J.; Zorn, Aaron M.; Mabee, Paula

    2015-01-01

    Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. PMID:25562316

  14. Finding our way through phenotypes.

    PubMed

    Deans, Andrew R; Lewis, Suzanna E; Huala, Eva; Anzaldo, Salvatore S; Ashburner, Michael; Balhoff, James P; Blackburn, David C; Blake, Judith A; Burleigh, J Gordon; Chanet, Bruno; Cooper, Laurel D; Courtot, Mélanie; Csösz, Sándor; Cui, Hong; Dahdul, Wasila; Das, Sandip; Dececchi, T Alexander; Dettai, Agnes; Diogo, Rui; Druzinsky, Robert E; Dumontier, Michel; Franz, Nico M; Friedrich, Frank; Gkoutos, George V; Haendel, Melissa; Harmon, Luke J; Hayamizu, Terry F; He, Yongqun; Hines, Heather M; Ibrahim, Nizar; Jackson, Laura M; Jaiswal, Pankaj; James-Zorn, Christina; Köhler, Sebastian; Lecointre, Guillaume; Lapp, Hilmar; Lawrence, Carolyn J; Le Novère, Nicolas; Lundberg, John G; Macklin, James; Mast, Austin R; Midford, Peter E; Mikó, István; Mungall, Christopher J; Oellrich, Anika; Osumi-Sutherland, David; Parkinson, Helen; Ramírez, Martín J; Richter, Stefan; Robinson, Peter N; Ruttenberg, Alan; Schulz, Katja S; Segerdell, Erik; Seltmann, Katja C; Sharkey, Michael J; Smith, Aaron D; Smith, Barry; Specht, Chelsea D; Squires, R Burke; Thacker, Robert W; Thessen, Anne; Fernandez-Triana, Jose; Vihinen, Mauno; Vize, Peter D; Vogt, Lars; Wall, Christine E; Walls, Ramona L; Westerfeld, Monte; Wharton, Robert A; Wirkner, Christian S; Woolley, James B; Yoder, Matthew J; Zorn, Aaron M; Mabee, Paula

    2015-01-01

    Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility.

  15. The digital revolution in phenotyping

    PubMed Central

    Oellrich, Anika; Collier, Nigel; Groza, Tudor; Rebholz-Schuhmann, Dietrich; Shah, Nigam; Bodenreider, Olivier; Boland, Mary Regina; Georgiev, Ivo; Liu, Hongfang; Livingston, Kevin; Luna, Augustin; Mallon, Ann-Marie; Manda, Prashanti; Robinson, Peter N.; Rustici, Gabriella; Simon, Michelle; Wang, Liqin; Winnenburg, Rainer; Dumontier, Michel

    2016-01-01

    Phenotypes have gained increased notoriety in the clinical and biological domain owing to their application in numerous areas such as the discovery of disease genes and drug targets, phylogenetics and pharmacogenomics. Phenotypes, defined as observable characteristics of organisms, can be seen as one of the bridges that lead to a translation of experimental findings into clinical applications and thereby support ‘bench to bedside’ efforts. However, to build this translational bridge, a common and universal understanding of phenotypes is required that goes beyond domain-specific definitions. To achieve this ambitious goal, a digital revolution is ongoing that enables the encoding of data in computer-readable formats and the data storage in specialized repositories, ready for integration, enabling translational research. While phenome research is an ongoing endeavor, the true potential hidden in the currently available data still needs to be unlocked, offering exciting opportunities for the forthcoming years. Here, we provide insights into the state-of-the-art in digital phenotyping, by means of representing, acquiring and analyzing phenotype data. In addition, we provide visions of this field for future research work that could enable better applications of phenotype data. PMID:26420780

  16. Phenotypic Characterization of Chicken Thymic Stromal Elements

    PubMed Central

    Wilson, Trevor J.; Bean, Andrew G.; Ward, Harry A.; Gershwin, M. Eric

    1992-01-01

    Phenotypic profiles of the thymic stromal components provide an excellent approach to elucidating the nature of the microenvironment of this organ. To address this issue in chickens, we have produced an extensive panel of 18 mAb to the thymic stroma. These mAb have been extensively characterized with respect to their phenotypic specificities and reveal that the stromal cells are equally as complex as the T cells whose maturation they direct. They further demonstrate that, in comparison to the mammalian thymus, there is a remarkable degree of conservation in thymic architecture between phylogenetically diverse species. Eleven mAb reacted with thymic epithelial cells: MUI-73 was panepithelium, MUI-54 stained all cortical and medullary epithelium but only a minority of the subcapsule, MUI-52 was specific for isolated stellate cortical epithelial cells, MUI-62, -69, and -71 were specific for the medulla (including Hassall’s corpusclelike structures), MUI-51, -53, -70, and -75 reacted only with the type-I epithelium, or discrete regions therein, lining the subcapsular and perivascular regions and MUI-58 demonstrated the antigenic similarity between the subcapsule and the medulla. Seven other mAb identified distinct isolated stromal cells throughout the cortex and medulla. Large thymocyte-rich regions, which often spanned from the outer cortex to medulla, lacked epithelial cells. These mAb should prove invaluable for determining the functional significance of thymic stromal-cell subsets to thymopoiesis. PMID:1387829

  17. Measurement and inference of profile soil-water dynamics at different hillslope positions in a semi-arid agricultural watershed

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dynamics of profile soil water vary in relation to terrain, soil and plant characteristics. The objectives of this study are to quantify dynamic soil-water content over a range of slope positions, infer soil profile water fluxes, and identify locations most likely influenced by multidimensional flo...

  18. Incompressible limit of solutions of multidimensional steady compressible Euler equations

    NASA Astrophysics Data System (ADS)

    Chen, Gui-Qiang G.; Huang, Feimin; Wang, Tian-Yi; Xiang, Wei

    2016-06-01

    A compactness framework is formulated for the incompressible limit of approximate solutions with weak uniform bounds with respect to the adiabatic exponent for the steady Euler equations for compressible fluids in any dimension. One of our main observations is that the compactness can be achieved by using only natural weak estimates for the mass conservation and the vorticity. Another observation is that the incompressibility of the limit for the homentropic Euler flow is directly from the continuity equation, while the incompressibility of the limit for the full Euler flow is from a combination of all the Euler equations. As direct applications of the compactness framework, we establish two incompressible limit theorems for multidimensional steady Euler flows through infinitely long nozzles, which lead to two new existence theorems for the corresponding problems for multidimensional steady incompressible Euler equations.

  19. A Multidimensional Data Warehouse for Community Health Centers.

    PubMed

    Kunjan, Kislaya; Toscos, Tammy; Turkcan, Ayten; Doebbeling, Brad N

    2015-01-01

    Community health centers (CHCs) play a pivotal role in healthcare delivery to vulnerable populations, but have not yet benefited from a data warehouse that can support improvements in clinical and financial outcomes across the practice. We have developed a multidimensional clinic data warehouse (CDW) by working with 7 CHCs across the state of Indiana and integrating their operational, financial and electronic patient records to support ongoing delivery of care. We describe in detail the rationale for the project, the data architecture employed, the content of the data warehouse, along with a description of the challenges experienced and strategies used in the development of this repository that may help other researchers, managers and leaders in health informatics. The resulting multidimensional data warehouse is highly practical and is designed to provide a foundation for wide-ranging healthcare data analytics over time and across the community health research enterprise.

  20. Ultrafast Multidimensional Laplace NMR Using a Single-Sided Magnet.

    PubMed

    King, Jared N; Lee, Vanessa J; Ahola, Susanna; Telkki, Ville-Veikko; Meldrum, Tyler

    2016-04-11

    Laplace NMR (LNMR) consists of relaxation and diffusion measurements providing detailed information about molecular motion and interaction. Here we demonstrate that ultrafast single- and multidimensional LNMR experiments, based on spatial encoding, are viable with low-field, single-sided magnets with an inhomogeneous magnetic field. This approach shortens the experiment time by one to two orders of magnitude relative to traditional experiments, and increases the sensitivity per unit time by a factor of three. The reduction of time required to collect multidimensional data opens significant prospects for mobile chemical analysis using NMR. Particularly tantalizing is future use of hyperpolarization to increase sensitivity by orders of magnitude, allowed by single-scan approach. PMID:26960011

  1. Advanced numerics for multi-dimensional fluid flow calculations

    SciTech Connect

    Vanka, S.P.

    1984-04-01

    In recent years, there has been a growing interest in the development and use of mathematical models for the simulation of fluid flow, heat transfer and combustion processes in engineering equipment. The equations representing the multi-dimensional transport of mass, momenta and species are numerically solved by finite-difference or finite-element techniques. However despite the multiude of differencing schemes and solution algorithms, and the advancement of computing power, the calculation of multi-dimensional flows, especially three-dimensional flows, remains a mammoth task. The following discussion is concerned with the author's recent work on the construction of accurate discretization schemes for the partial derivatives, and the efficient solution of the set of nonlinear algebraic equations resulting after discretization. The present work has been jointly supported by the Ramjet Engine Division of the Wright Patterson Air Force Base, Ohio, and the NASA Lewis Research Center.

  2. The West Haven-Yale Multidimensional Pain Inventory (WHYMPI).

    PubMed

    Kerns, R D; Turk, D C; Rudy, T E

    1985-12-01

    The complexity of chronic pain has represented a major dilemma for clinical researchers interested in the reliable and valid assessment of the problem and the evaluation of treatment approaches. The West Haven-Yale Multidimensional Pain Inventory (WHYMPI) was developed in order to fill a widely recognized void in the assessment of clinical pain. Assets of the inventory are its brevity and clarity, its foundation in contemporary psychological theory, its multidimensional focus, and its strong psychometric properties. Three parts of the inventory, comprised of 12 scales, examine the impact of pain on the patients' lives, the responses of others to the patients' communications of pain, and the extent to which patients participate in common daily activities. The instrument is recommended for use in conjunction with behavioral and psychophysiological assessment strategies in the evaluation of chronic pain patients in clinical settings. The utility of the WHYMPI in empirical investigations of chronic pain is also discussed.

  3. Multidimensional nanomaterials for the control of stem cell fate

    NASA Astrophysics Data System (ADS)

    Chueng, Sy-Tsong Dean; Yang, Letao; Zhang, Yixiao; Lee, Ki-Bum

    2016-09-01

    Current stem cell therapy suffers low efficiency in giving rise to differentiated cell lineages, which can replace the original damaged cells. Nanomaterials, on the other hand, provide unique physical size, surface chemistry, conductivity, and topographical microenvironment to regulate stem cell differentiation through multidimensional approaches to facilitate gene delivery, cell-cell, and cell-ECM interactions. In this review, nanomaterials are demonstrated to work both alone and synergistically to guide selective stem cell differentiation. From three different nanotechnology families, three approaches are shown: (1) soluble microenvironmental factors; (2) insoluble physical microenvironment; and (3) nano-topographical features. As regenerative medicine is heavily invested in effective stem cell therapy, this review is inspired to generate discussions in the potential clinical applications of multi-dimensional nanomaterials.

  4. Optimized Linear Prediction for Radial Sampled Multidimensional NMR Experiments

    PubMed Central

    Gledhill, John M.; Kasinath, Vignesh; Wand, A. Joshua

    2011-01-01

    Radial sampling in multidimensional NMR experiments offers greatly decreased acquisition times while also providing an avenue for increased sensitivity. Digital resolution remains concern and depends strongly upon the extent of sampling of individual radial angles. Truncated time domain data leads to spurious peaks (artifacts) upon FT and 2D FT. Linear prediction is commonly employed to improve resolution in Cartesian sampled NMR experiments. Here, we adapt the linear prediction method to radial sampling. Significantly more accurate estimates of linear prediction coefficients are obtained by combining quadrature frequency components from the multiple angle spectra. This approach results in significant improvement in both resolution and removal of spurious peaks as compared to traditional linear prediction methods applied to radial sampled data. The ‘averaging linear prediction’ (ALP) method is demonstrated as a general tool for resolution improvement in multidimensional radial sampled experiments. PMID:21767968

  5. Advanced numerics for multi-dimensional fluid flow calculations

    NASA Technical Reports Server (NTRS)

    Vanka, S. P.

    1984-01-01

    In recent years, there has been a growing interest in the development and use of mathematical models for the simulation of fluid flow, heat transfer and combustion processes in engineering equipment. The equations representing the multi-dimensional transport of mass, momenta and species are numerically solved by finite-difference or finite-element techniques. However despite the multiude of differencing schemes and solution algorithms, and the advancement of computing power, the calculation of multi-dimensional flows, especially three-dimensional flows, remains a mammoth task. The following discussion is concerned with the author's recent work on the construction of accurate discretization schemes for the partial derivatives, and the efficient solution of the set of nonlinear algebraic equations resulting after discretization. The present work has been jointly supported by the Ramjet Engine Division of the Wright Patterson Air Force Base, Ohio, and the NASA Lewis Research Center.

  6. Analyzing stochastic dependence of cognitive processes in multidimensional source recognition.

    PubMed

    Meiser, Thorsten

    2014-01-01

    Stochastic dependence among cognitive processes can be modeled in different ways, and the family of multinomial processing tree models provides a flexible framework for analyzing stochastic dependence among discrete cognitive states. This article presents a multinomial model of multidimensional source recognition that specifies stochastic dependence by a parameter for the joint retrieval of multiple source attributes together with parameters for stochastically independent retrieval. The new model is equivalent to a previous multinomial model of multidimensional source memory for a subset of the parameter space. An empirical application illustrates the advantages of the new multinomial model of joint source recognition. The new model allows for a direct comparison of joint source retrieval across conditions, it avoids statistical problems due to inflated confidence intervals and does not imply a conceptual imbalance between source dimensions. Model selection criteria that take model complexity into account corroborate the new model of joint source recognition.

  7. Coherent multidimensional optical spectra measured using incoherent light

    NASA Astrophysics Data System (ADS)

    Turner, Daniel B.; Arpin, Paul C.; McClure, Scott D.; Ulness, Darin J.; Scholes, Gregory D.

    2013-08-01

    Four-wave mixing measurements can reveal spectral and dynamics information that is hidden in linear spectra by the interactions among light-absorbing molecules and with their environment. Coherent multidimensional optical spectroscopy is an important variant of four-wave mixing because it resolves a map of interactions and correlations between absorption bands. Previous coherent multidimensional optical spectroscopy measurements have used femtosecond pulses with great success, and it may seem that femtosecond pulses are necessary for such measurements. Here we present coherent two-dimensional electronic spectra measured using incoherent light. The spectra of model molecular systems using broadband spectrally incoherent light are similar but not identical to those expected from measurements using femtosecond pulses. Specifically, the spectra show particular sensitivity to long-lived intermediates such as photoisomers. The results will motivate the design of similar experiments in spectral ranges where femtosecond pulses are difficult to produce.

  8. Multidimensional Analysis of Quenching: Comparison of Inverse Techniques

    SciTech Connect

    Dowding, K.J.

    1998-11-18

    Understanding the surface heat transfer during quenching can be beneficial. Analysis to estimate the surface heat transfer from internal temperature measurements is referred to as the inverse heat conduction problem (IHCP). Function specification and gradient adjoint methods, which use a gradient search method coupled with an adjoint operator, are widely u led methods to solve the IHCP. In this paper the two methods are presented for the multidimensional case. The focus is not a rigorous comparison of numerical results. Instead after formulating the multidimensional solutions, issues associated with the numerical implementation and practical application of the methods are discussed. In addition, an experiment that measured the surface heat flux and temperatures for a transient experimental case is analyzed. Transient temperatures are used to estimate the surface heat flux, which is compared to the measured values. The estimated surface fluxes are comparable for the two methods.

  9. An object-oriented multidimensional model for data warehouse

    NASA Astrophysics Data System (ADS)

    Gosain, Anjana; Mann, Suman

    2011-12-01

    Organizations, to have a competitive edge upon each other, resort to business intelligence which refers to information available for enterprise to make strategic decisions. Data warehouse being the repository of data provides the backend for achieving business intelligence. The design of data warehouse, thereby, forms the key, to extract and obtain the relevant information facilitating to make strategic decisions. The initial focus for the design had been upon the conceptual models but now object oriented multidimensional modelling has emerged as the foundation for the designing of data warehouse. Several proposals have been put forth for object oriented multidimensional modelling, each incorporating some or other features, but not all. This paper consolidates all the features previously introduced and the new introduced, thus, proposing a new model having features to be incorporated while designing the data warehouse.

  10. Multidimensional and Multimodal Separations by HPTLC in Phytochemistry

    NASA Astrophysics Data System (ADS)

    Ciesla, Lukasz; Waksmundzka-Hajnos, Monika

    HPTLC is one of the most widely applied methods in phytochemical analysis. It is due to its numerous advantages, e.g., it is the only chromatographic method offering the option of presenting the results as an image. Other advantages include simplicity, low costs, parallel analysis of samples, high sample capacity, rapidly obtained results, and possibility of multiple detection. HPTLC provides identification as well as quantitative results. It also enables the identification of adulterants. In case of complex samples, the resolving power of traditional one-dimensional chromatography is usually inadequate, hence special modes of development are required. Multidimensional and multimodal HPTLC techniques include those realized in one direction (UMD, IMD, GMD, BMD, AMD) as well as typical two-dimensional methods realized on mono- or bi-layers. In this manuscript, an overview on variable multidimensional and multimodal methods, applied in the analysis of phytochemical samples, is presented.

  11. Counting multidimensional objects: implications for the neural-synchrony theory.

    PubMed

    Goldfarb, Liat; Treisman, Anne

    2013-03-01

    It has been suggested that a neural instantiation of the temporary multidimensional representations of objects might be synchrony of firing between the neurons representing the features that co-occur in a given location. In this article, we direct attention to a logical problem that arises when certain synchrony assumptions are applied to real situations in which multiple multidimensional objects are presented. We demonstrate a new behavioral effect that shows that this logical problem coincides with a genuine behavioral problem. Even when a display contains only a small number of objects characterized by features on two dimensions, the representation of the display becomes difficult when, according to our described assumptions, the object representations cannot be simultaneously synchronized on both features. This article outlines a new principle that governs object representation, and the experimental results might be unique behavioral evidence for a neural-based theory of feature binding. PMID:23334446

  12. A Multidimensional Data Warehouse for Community Health Centers

    PubMed Central

    Kunjan, Kislaya; Toscos, Tammy; Turkcan, Ayten; Doebbeling, Brad N.

    2015-01-01

    Community health centers (CHCs) play a pivotal role in healthcare delivery to vulnerable populations, but have not yet benefited from a data warehouse that can support improvements in clinical and financial outcomes across the practice. We have developed a multidimensional clinic data warehouse (CDW) by working with 7 CHCs across the state of Indiana and integrating their operational, financial and electronic patient records to support ongoing delivery of care. We describe in detail the rationale for the project, the data architecture employed, the content of the data warehouse, along with a description of the challenges experienced and strategies used in the development of this repository that may help other researchers, managers and leaders in health informatics. The resulting multidimensional data warehouse is highly practical and is designed to provide a foundation for wide-ranging healthcare data analytics over time and across the community health research enterprise. PMID:26958297

  13. Psychometric precision in phenotype definition is a useful step in molecular genetic investigation of psychiatric disorders

    PubMed Central

    Xu, M K; Gaysina, D; Barnett, J H; Scoriels, L; van de Lagemaat, L N; Wong, A; Richards, M; Croudace, T J; Jones, P B

    2015-01-01

    Affective disorders are highly heritable, but few genetic risk variants have been consistently replicated in molecular genetic association studies. The common method of defining psychiatric phenotypes in molecular genetic research is either a summation of symptom scores or binary threshold score representing the risk of diagnosis. Psychometric latent variable methods can improve the precision of psychiatric phenotypes, especially when the data structure is not straightforward. Using data from the British 1946 birth cohort, we compared summary scores with psychometric modeling based on the General Health Questionnaire (GHQ-28) scale for affective symptoms in an association analysis of 27 candidate genes (249 single-nucleotide polymorphisms (SNPs)). The psychometric method utilized a bi-factor model that partitioned the phenotype variances into five orthogonal latent variable factors, in accordance with the multidimensional data structure of the GHQ-28 involving somatic, social, anxiety and depression domains. Results showed that, compared with the summation approach, the affective symptoms defined by the bi-factor psychometric model had a higher number of associated SNPs of larger effect sizes. These results suggest that psychometrically defined mental health phenotypes can reflect the dimensions of complex phenotypes better than summation scores, and therefore offer a useful approach in genetic association investigations. PMID:26125156

  14. Analysis of self-similar solutions of multidimensional conservation laws

    SciTech Connect

    Keyfitz, Barbara

    2014-02-15

    This project focused on analysis of multidimensional conservation laws, specifically on extensions to the study of self-siminar solutions, a project initiated by the PI. In addition, progress was made on an approach to studying conservation laws of very low regularity; in this research, the context was a novel problem in chromatography. Two graduate students in mathematics were supported during the grant period, and have almost completed their thesis research.

  15. Probes for multidimensional nanospectroscopic imaging and methods of fabrication thereof

    DOEpatents

    Weber-Bargioni, Alexander; Cabrini, Stefano; Bao, Wei; Melli, Mauro; Yablonovitch, Eli; Schuck, Peter J

    2015-03-17

    This disclosure provides systems, methods, and apparatus related to probes for multidimensional nanospectroscopic imaging. In one aspect, a method includes providing a transparent tip comprising a dielectric material. A four-sided pyramidal-shaped structure is formed at an apex of the transparent tip using a focused ion beam. Metal layers are deposited over two opposing sides of the four-sided pyramidal-shaped structure.

  16. Unveiling Bacterial Interactions through Multidimensional Scaling and Dynamics Modeling

    PubMed Central

    Dorado-Morales, Pedro; Vilanova, Cristina; P. Garay, Carlos; Martí, Jose Manuel; Porcar, Manuel

    2015-01-01

    We propose a new strategy to identify and visualize bacterial consortia by conducting replicated culturing of environmental samples coupled with high-throughput sequencing and multidimensional scaling analysis, followed by identification of bacteria-bacteria correlations and interactions. We conducted a proof of concept assay with pine-tree resin-based media in ten replicates, which allowed detecting and visualizing dynamical bacterial associations in the form of statistically significant and yet biologically relevant bacterial consortia. PMID:26671778

  17. Multidimensional signal modulation and/or demodulation for data communications

    DOEpatents

    Smith, Stephen F.; Dress, William B.

    2008-03-04

    Systems and methods are described for multidimensional signal modulation and/or demodulation for data communications. A method includes modulating a carrier signal in a first domain selected from the group consisting of phase, frequency, amplitude, polarization and spread; modulating the carrier signal in a second domain selected from the group consisting of phase, frequency, amplitude, polarization and spread; and modulating the carrier signal in a third domain selected from the group consisting of phase, frequency, amplitude, polarization and spread.

  18. Application of Multidimensional Spectrum Analysis for Analytical Chemistry

    SciTech Connect

    Hatsukawa, Yuichi; Hayakawa, Takehito; Toh, Yosuke; Shinohara, Nobuo; Oshima, Masumi

    1999-12-31

    Feasibility of application of the multidimensional {gamma} ray spectroscopy for analytical chemistry was examined. Two reference igneous rock (JP-1, JB-1a) samples issued by the Geological Survey of Japan (GSJ) were irradiated at a research reactor with thermal neutrons, and {gamma} rays from the radioisotopes produced by neutron capture reactions were measured using a {gamma}-ray detector array. Simultaneously 27 elements were observed with no chemical separation.

  19. Multidimensional, multiphysics simulations of core-collapse supernovae

    SciTech Connect

    Messer, Bronson; Mezzacappa, Anthony; Blondin, J. M.; Bruenn, S. W.; Hix, William Raphael

    2008-01-01

    CHIMERA is a multi-dimensional radiation hydrodynamics code designed to study core-collapse supernovae. The code is made up of three essentially independent parts: a hydrodynamics module, a nuclear burning module, and a neutrino transport solver combined within an operator-split approach. We review the code s architecture and some recently improved implementations used in the code. We also briefly discuss preliminary results obtained with the code in three spatial dimensions.

  20. Multidimensional, multiphysics simulations of core-collapse supernovae

    SciTech Connect

    Messer, Bronson; Mezzacappa, Anthony; Blondin, J. M.; Bruenn, S. W.; Hix, William Raphael

    2008-01-01

    CHIMERA is a multi-dimensional radiation hydrodynamics code designed to study core-collapse supernovae. The code is made up of three essentially independent parts: a hydrodynamics module, a nuclear burning module, and a neutrino transport solver combined within an operator-split approach. We review the code's architecture and some recently improved implementations used in the code. We also briefly discuss preliminary results obtained with the code in three spatial dimensions.

  1. POLARIZED LINE FORMATION IN MULTI-DIMENSIONAL MEDIA. III. HANLE EFFECT WITH PARTIAL FREQUENCY REDISTRIBUTION

    SciTech Connect

    Anusha, L. S.; Nagendra, K. N.

    2011-09-01

    In two previous papers, we solved the polarized radiative transfer (RT) equation in multi-dimensional (multi-D) geometries with partial frequency redistribution as the scattering mechanism. We assumed Rayleigh scattering as the only source of linear polarization (Q/I, U/I) in both these papers. In this paper, we extend these previous works to include the effect of weak oriented magnetic fields (Hanle effect) on line scattering. We generalize the technique of Stokes vector decomposition in terms of the irreducible spherical tensors T{sup K}{sub Q}, developed by Anusha and Nagendra, to the case of RT with Hanle effect. A fast iterative method of solution (based on the Stabilized Preconditioned Bi-Conjugate-Gradient technique), developed by Anusha et al., is now generalized to the case of RT in magnetized three-dimensional media. We use the efficient short-characteristics formal solution method for multi-D media, generalized appropriately to the present context. The main results of this paper are the following: (1) a comparison of emergent (I, Q/I, U/I) profiles formed in one-dimensional (1D) media, with the corresponding emergent, spatially averaged profiles formed in multi-D media, shows that in the spatially resolved structures, the assumption of 1D may lead to large errors in linear polarization, especially in the line wings. (2) The multi-D RT in semi-infinite non-magnetic media causes a strong spatial variation of the emergent (Q/I, U/I) profiles, which is more pronounced in the line wings. (3) The presence of a weak magnetic field modifies the spatial variation of the emergent (Q/I, U/I) profiles in the line core, by producing significant changes in their magnitudes.

  2. Multidimensional colorimetric sensor array for discrimination of proteins.

    PubMed

    Mao, Jinpeng; Lu, Yuexiang; Chang, Ning; Yang, Jiaoe; Zhang, Sichun; Liu, Yueying

    2016-12-15

    An extensible multidimensional colorimetric sensor array for the detection of protein is developed based on DNA functionalized gold nanoparticles (DNA-AuNPs) as receptors. In the presence of different proteins, the aggregation behavior of DNA-AuNPs was regulated by the high concentrations of salt and caused different color change; while DNA-AuNPs grew induced by the reduction of HAuCl4 and NH2OH as a reductant on the surface of nanoparticles exhibited different morphologies and color appearance for different proteins. The transducers based on AuNPs modified by specific and nonspecific DNA enables naked-eye discrimination of the target analytes. This extensible sensing platform with only two receptors could simultaneously discriminate ten native proteins and their thermally denatured conformations using hierarchical cluster analysis (HCA) at the concentration of 50nM with 100% accuracy. This opens up the possibility of the sensor array to investigate the different conformational changes of biomacromolecules, and it gives a new direction of developing multidimensional transduction principles based on plasmonic nanoparticle conjugates. Furthermore, the sensing system could discriminate proteins at the concentration of 500nM in the presence of 50% human urine, which indicated this sensor array has great potential ability in analyzing real biological fluids. In addition, the multidimensional colorimetric sensor array is suitable for analysis of target analytes in the resource-restricted regions because of rapid, simple, low cost, and in-field detection with the naked eye. PMID:27322936

  3. Interdisciplinary hospice team processes and multidimensional pain: a qualitative study.

    PubMed

    Dugan Day, Michele

    2012-01-01

    Hospice teams may address multidimensional pain through the synergistic interaction of team members from various professional disciplines during regularly scheduled team meetings. However, the occurrence of that critical exchange has not been adequately described or documented. The purpose of this qualitative study was to explore two processes in team pain palliation: communication and collaboration. Data were gathered through individual interviews and a 1-year observation of team members from two hospices (physicians, nurses, aides, chaplains, social workers). Utilizing constant comparison, 14 final thematic categories were discovered. Use of biopsychosocial/spiritual terms by all team members meant that the team had the common language needed to communicate about multidimensional pain. Interviews and observation revealed a gap in translating multidisciplinary communication in team meetings into collaborative acts for pain treatment. In addition, structural influences inhibited creativity in pain palliation. There was no mutual understanding of the purpose for team meetings, no recognition of the need to reflect on team process, or common definition of leadership. Social work roles in hospice should include leadership that moves teams toward interdisciplinary care for multidimensional pain.

  4. Multidimensional EEMD filter bank for geophysical data processing

    NASA Astrophysics Data System (ADS)

    Jeng, Yih; Chen, Chih-Sung; Lee, Chao-Shing

    2014-05-01

    The ensemble empirical mode decomposition (EEMD) algorithm is a noise-assisted data-driven nonlinear analysis method evolved from its original version, the empirical mode decomposition (EMD) method. The advantage of using EEMD is mainly to alleviate mode mixing problem of the EMD filter bank. The EMD and EEMD techniques have been widely applied to many fields of scientific and engineering studies in the last decade but just a few to the geophysical exploration data analysis probably due to the multidimensional feature of exploration data. Several 2D EMD based data analysis algorithms have been developed lately; however, the difficulty of sifting 2D data and the mode mixing problem inherited from EMD algorithm hindered their further developments. To deal with the stated issues, we modify a newer technique, the multidimensional ensemble empirical mode decomposition (MDEEMD) algorithm, to achieve a 2D EEMD filter bank for exploration data signal enhancement. With the data reconstructed by using significant components of the filter bank, the signal embedded in the original data can be retrieved successfully. Furthermore, we compare the performance of MDEEMD with that of logarithmic transformed multidimensional empirical mode decomposition (NLT MDEMD) to find a solution for compromising computation cost. A controlled model study along with a set of real exploration data example are provided to demonstrate the robustness of the proposed method.

  5. An Improved Multidimensional MPA Procedure for Bidirectional Earthquake Excitations

    PubMed Central

    Wang, Feng; Sun, Jian-Gang; Zhang, Ning

    2014-01-01

    Presently, the modal pushover analysis procedure is extended to multidimensional analysis of structures subjected to multidimensional earthquake excitations. an improved multidimensional modal pushover analysis (IMMPA) method is presented in the paper in order to estimate the response demands of structures subjected to bidirectional earthquake excitations, in which the unidirectional earthquake excitation applied on equivalent SDOF system is replaced by the direct superposition of two components earthquake excitations, and independent analysis in each direction is not required and the application of simplified superposition formulas is avoided. The strength reduction factor spectra based on superposition of earthquake excitations are discussed and compared with the traditional strength reduction factor spectra. The step-by-step procedure is proposed to estimate seismic demands of structures. Two examples are implemented to verify the accuracy of the method, and the results of the examples show that (1) the IMMPA method can be used to estimate the responses of structure subjected to bidirectional earthquake excitations. (2) Along with increase of peak of earthquake acceleration, structural response deviation estimated with the IMMPA method may also increase. (3) Along with increase of the number of total floors of structures, structural response deviation estimated with the IMMPA method may also increase. PMID:25140333

  6. An improved multidimensional MPA procedure for bidirectional earthquake excitations.

    PubMed

    Wang, Feng; Sun, Jian-Gang; Zhang, Ning

    2014-01-01

    Presently, the modal pushover analysis procedure is extended to multidimensional analysis of structures subjected to multidimensional earthquake excitations. an improved multidimensional modal pushover analysis (IMMPA) method is presented in the paper in order to estimate the response demands of structures subjected to bidirectional earthquake excitations, in which the unidirectional earthquake excitation applied on equivalent SDOF system is replaced by the direct superposition of two components earthquake excitations, and independent analysis in each direction is not required and the application of simplified superposition formulas is avoided. The strength reduction factor spectra based on superposition of earthquake excitations are discussed and compared with the traditional strength reduction factor spectra. The step-by-step procedure is proposed to estimate seismic demands of structures. Two examples are implemented to verify the accuracy of the method, and the results of the examples show that (1) the IMMPA method can be used to estimate the responses of structure subjected to bidirectional earthquake excitations. (2) Along with increase of peak of earthquake acceleration, structural response deviation estimated with the IMMPA method may also increase. (3) Along with increase of the number of total floors of structures, structural response deviation estimated with the IMMPA method may also increase. PMID:25140333

  7. Igloo-Plot: a tool for visualization of multidimensional datasets.

    PubMed

    Kuntal, Bhusan K; Ghosh, Tarini Shankar; Mande, Sharmila S

    2014-01-01

    Advances in science and technology have resulted in an exponential growth of multivariate (or multi-dimensional) datasets which are being generated from various research areas especially in the domain of biological sciences. Visualization and analysis of such data (with the objective of uncovering the hidden patterns therein) is an important and challenging task. We present a tool, called Igloo-Plot, for efficient visualization of multidimensional datasets. The tool addresses some of the key limitations of contemporary multivariate visualization and analysis tools. The visualization layout, not only facilitates an easy identification of clusters of data-points having similar feature compositions, but also the 'marker features' specific to each of these clusters. The applicability of the various functionalities implemented herein is demonstrated using several well studied multi-dimensional datasets. Igloo-Plot is expected to be a valuable resource for researchers working in multivariate data mining studies. Igloo-Plot is available for download from: http://metagenomics.atc.tcs.com/IglooPlot/.

  8. Theme section: Multi-dimensional modelling, analysis and visualization

    NASA Astrophysics Data System (ADS)

    Guilbert, Éric; Çöltekin, Arzu; Castro, Francesc Antón; Pettit, Chris

    2016-07-01

    Spatial data are now collected and processed in larger amounts, and used by larger populations than ever before. While most geospatial data have traditionally been recorded as two-dimensional data, the evolution of data collection methods and user demands have led to data beyond the two dimensions describing complex multidimensional phenomena. An example of the relevance of multidimensional modelling is seen with the development of urban modelling where several dimensions have been added to the traditional 2D map representation (Sester et al., 2011). These include obviously the third spatial dimension (Biljecki et al., 2015) as well as the temporal, but also the scale dimension (Van Oosterom and Stoter, 2010) or, as mentioned by (Lu et al., 2016), multi-spectral and multi-sensor data. Such a view provides an organisation of multidimensional data around these different axes and it is time to explore each axis as the availability of unprecedented amounts of new data demands new solutions. The availability of such large amounts of data induces an acute need for developing new approaches to assist with their dissemination, visualisation, and analysis by end users. Several issues need to be considered in order to provide a meaningful representation and assist in data visualisation and mining, modelling and analysis; such as data structures allowing representation at different scales or in different contexts of thematic information.

  9. An Economical High-Throughput Protocol for Multidimensional Fractionation of Proteins

    PubMed Central

    Tooth, David John; Gopala Krishna, Varun; Layfield, Robert

    2012-01-01

    A sequential protocol of multidimensional fractionation was optimised to enable the comparative profiling of fractions of proteomes from cultured human cells. Differential detergent fractionation was employed as a first step to obtain fractions enriched for cytosolic, membrane/organelle, nuclear, and cytoskeletal proteins. Following buffer exchange using gel-permeation chromatography, cytosolic proteins were further fractionated by 2-dimensional chromatography employing anion-exchange followed by reversed-phase steps. Chromatographic fractions were shown to be readily compatible with 1- and 2-dimensional gel electrophoresis or with direct analysis by mass spectrometry using linear-MALDI-TOF-MS. Precision of extraction was confirmed by reproducible SDS-PAGE profiles, MALDI-TOF-MS spectra, and quantitation of trypsinolytic peptides using LC-MS/MS (MRM) analyses. Solid phases were immobilised in disposable cartridges and mobile-phase flow was achieved using a combination of centrifugation and vacuum pumping. These approaches yielded parallel sample handling which was limited only by the capacities of the employed devices and which enabled both high-throughput and experimentally precise procedures, as demonstrated by the processing of experimental replicates. Protocols were employed at 10 mg scale of extracted cell protein, but these approaches would be directly applicable to both smaller and larger quantities merely by adjusting the employed solid- and mobile-phase volumes. Additional potential applications of the fractionation protocol are briefly described. PMID:23008771

  10. Genomics: moving behavioural ecology beyond the phenotypic gambit

    PubMed Central

    Rittschof, Clare C.; Robinson, Gene E.

    2014-01-01

    Researchers studying the adaptive significance of behaviour typically assume that genetic mechanisms will not inhibit evolutionary trajectories, an assumption commonly known as the ‘phenotypic gambit’. Although the phenotypic gambit continues to be a useful heuristic for behavioural ecology, here we discuss how genomic methods provide new tools and conceptual approaches that are relevant to behavioural ecology. We first describe how the concept of a genetic toolkit for behaviour can allow behavioural ecologists to synthesize both genomic and ecological information when assessing behavioural adaptation. Then we show how gene expression profiles can be viewed as complex phenotypic measurements, used to (1) predict behaviour, (2) evaluate phenotypic plasticity and (3) devise methods to manipulate behaviour in order to test adaptive hypotheses. We propose that advances in genomics and bioinformatics may allow researchers to overcome some of the logistical obstacles that motivated the inception of the phenotypic gambit. Behavioural ecology and genomics are mutually informative, providing potential synergy that could lead to powerful advances in the field of animal behaviour. PMID:24954950

  11. In pursuit of taste phenotypes.

    PubMed

    Green, Barry G

    2013-05-01

    Notable progress has been made relating individual differences in bitter taste sensitivity to specific alleles and TAS2R receptors, but psychophysical evidence of reliable phenotypes for other tastes has been more elusive. In this issue, Wise and Breslin report a study of individual differences in threshold sensitivity to sour and salty taste, which, though failing to find clear phenotypes, exemplifies the type of approach and analysis necessary to disentangle sources of variance inherent in the psychophysical measures applied from those attributable to true differences in sensitivity. Methodological and theoretical lessons that can be taken from this work are discussed in the context of the early and dramatic evidence of chemosensory phenotypes that belied the complexity of taste receptor genetics and focused attention solely on peripheral determinants of sensitivity.

  12. Optofluidic Detection for Cellular Phenotyping

    PubMed Central

    Tung, Yi-Chung; Huang, Nien-Tsu; Oh, Bo-Ram; Patra, Bishnubrata; Pan, Chi-Chun; Qiu, Teng; Paul, K. Chu; Zhang, Wenjun; Kurabayashi, Katsuo

    2012-01-01

    Quantitative analysis of the output of processes and molecular interactions within a single cell is highly critical to the advancement of accurate disease screening and personalized medicine. Optical detection is one of the most broadly adapted measurement methods in biological and clinical assays and serves cellular phenotyping. Recently, microfluidics has obtained increasing attention due to several advantages, such as small sample and reagent volumes, very high throughput, and accurate flow control in the spatial and temporal domains. Optofluidics, which is the attempt to integrate optics with microfluidic, shows great promise to enable on-chip phenotypic measurements with high precision, sensitivity, specificity, and simplicity. This paper reviews the most recent developments of optofluidic technologies for cellular phenotyping optical detection. PMID:22854915

  13. Phenotypic MicroRNA Microarrays

    PubMed Central

    Kwon, Yong-Jun; Heo, Jin Yeong; Kim, Hi Chul; Kim, Jin Yeop; Liuzzi, Michel; Soloveva, Veronica

    2013-01-01

    Microarray technology has become a very popular approach in cases where multiple experiments need to be conducted repeatedly or done with a variety of samples. In our lab, we are applying our high density spots microarray approach to microscopy visualization of the effects of transiently introduced siRNA or cDNA on cellular morphology or phenotype. In this publication, we are discussing the possibility of using this micro-scale high throughput process to study the role of microRNAs in the biology of selected cellular models. After reverse-transfection of microRNAs and siRNA, the cellular phenotype generated by microRNAs regulated NF-κB expression comparably to the siRNA. The ability to print microRNA molecules for reverse transfection into cells is opening up the wide horizon for the phenotypic high content screening of microRNA libraries using cellular disease models.

  14. Profile Analysis via Multidimensional Scaling for the "Revised Two-Factor Learning Process Questionnaire"

    ERIC Educational Resources Information Center

    Socha, Alan; Sigler, Ellen A.

    2011-01-01

    The "Revised Learning Process Questionnaire" has been part of the development of a conceptual understanding of how students learn and what motivates them to engage in particular tasks. We obtained responses from 329 student volunteers at a mid-sized public university in the southeast United States. While looking at the psychometric properties of…

  15. Kinetic and multidimensional profiling of accelerated degradation of oil sludge by biostimulation.

    PubMed

    Dong, Yijie; Lang, Zhe; Kong, Xian; Lu, Diannan; Liu, Zheng

    2015-04-01

    Biostimulation, which employs nutrients to enhance the proliferation of indigenous microorganisms and therefore the degradation of contaminants, is an effective tool for treatment of oil-contaminated soil. However, the evolution of microbial ecology, which responds directly to stimulation procedures and intrinsically determines the degradation of oil contaminants, has rarely been explored, particularly in the context of biostimulation. In this study, the effects of biostimulation procedures including the regulation of the C : N : P ratio, as well as application of surfactants and electron acceptors in the degradation of crude oil contaminants and the evolution of the microbial community were examined simultaneously to provide ecological insights into the biostimulation. The real-time PCR showed that biostimulation promoted the proliferation of bacteria, with Gammaproteobacteria showing the greatest increase. However, the proliferation of fungi was inhibited by the accumulation of the degradation products. The degradation of polar compounds of crude oil contaminants was characterized by negative-ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (negative-ion ESI FT-ICR MS), showing a biased increase in the relative abundance of naphthenic acids. Principal component analysis (PCA) showed that different species in oil sludge have different degradation rates during biostimulation. The addition of fertilizers with surfactants and electron acceptors profoundly stimulated the indigenous microorganisms with N1, O1 and O2 species as substrates while those with O3 and O4 species were little affected. An enriched abundance of alkB genes was observed during the degradation of saturated hydrocarbons. Monitoring the kinetics of the microbial community, functional genes and degradation offers a comprehensive view for the understanding and optimization of the biostimulation process.

  16. From Career Decision-Making Styles to Career Decision-Making Profiles: A Multidimensional Approach

    ERIC Educational Resources Information Center

    Gati, Itamar; Landman, Shiri; Davidovitch, Shlomit; Asulin-Peretz, Lisa; Gadassi, Reuma

    2010-01-01

    Previous research on individual differences in career decision-making processes has often focused on classifying individuals into a few types of decision-making "styles" based on the most dominant trait or characteristic of their approach to the decision process (e.g., rational, intuitive, dependent; Harren, 1979). In this research, an alternative…

  17. Combining Human Disease Genetics and Mouse Model Phenotypes towards Drug Repositioning for Parkinson's disease.

    PubMed

    Chen, Yang; Cai, Xiaoshu; Xu, Rong

    2015-01-01

    Parkinson's disease (PD) is a severe neurodegenerative disorder without effective treatments. Here, we present a novel drug repositioning approach to predict new drugs for PD leveraging both disease genetics and large amounts of mouse model phenotypes. First, we identified PD-specific mouse phenotypes using well-studied human disease genes. Then we searched all FDA-approved drugs for candidates that share similar mouse phenotype profiles with PD. We demonstrated the validity of our approach using drugs that have been approved for PD: 10 approved PD drugs were ranked within top 10% among 1197 candidates. In predicting novel PD drugs, our approach achieved a mean average precision of 0.24, which is significantly higher (pphenotype data. Comparison of gene expression profiles between PD and top-ranked drug candidates indicates that quetiapine has the potential to treat PD.

  18. Seismic interferometry by multidimensional deconvolution without wavefield separation

    NASA Astrophysics Data System (ADS)

    Ravasi, Matteo; Meles, Giovanni; Curtis, Andrew; Rawlinson, Zara; Yikuo, Liu

    2015-07-01

    Seismic interferometry comprises a suite of methods to redatum recorded wavefields to those that would have been recorded if different sources (so-called virtual sources) had been activated. Seismic interferometry by cross-correlation has been formulated using either two-way (for full wavefields) or one-way (for directionally decomposed wavefields) representation theorems. To obtain improved Green's function estimates, the cross-correlation result can be deconvolved by a quantity that identifies the smearing of the virtual source in space and time, the so-called point-spread function. This type of interferometry, known as interferometry by multidimensional deconvolution (MDD), has so far been applied only to one-way directionally decomposed fields, requiring accurate wavefield decomposition from dual (e.g. pressure and velocity) recordings. Here we propose a form of interferometry by multidimensional deconvolution that uses full wavefields with two-way representations, and simultaneously invert for pressure and (normal) velocity Green's functions, rather than only velocity responses as for its one-way counterpart. Tests on synthetic data show that two-way MDD improves on results of interferometry by cross-correlation, and generally produces estimates of similar quality to those obtained by one-way MDD, suggesting that the preliminary decomposition into up- and downgoing components of the pressure field is not required if pressure and velocity data are jointly used in the deconvolution. We also show that constraints on the directionality of the Green's functions sought can be added directly into the MDD inversion process to further improve two-way multidimensional deconvolution. Finally, as a by-product of having pressure and particle velocity measurements, we adapt one- and two-way representation theorems to convert any particle velocity receiver into its corresponding virtual dipole/gradient source by means of MDD. Thus data recorded from standard monopolar (e

  19. A kernel machine method for detecting effects of interaction between multidimensional variable sets: an imaging genetics application.

    PubMed

    Ge, Tian; Nichols, Thomas E; Ghosh, Debashis; Mormino, Elizabeth C; Smoller, Jordan W; Sabuncu, Mert R

    2015-04-01

    Measurements derived from neuroimaging data can serve as markers of disease and/or healthy development, are largely heritable, and have been increasingly utilized as (intermediate) phenotypes in genetic association studies. To date, imaging genetic studies have mostly focused on discovering isolated genetic effects, typically ignoring potential interactions with non-genetic variables such as disease risk factors, environmental exposures, and epigenetic markers. However, identifying significant interaction effects is critical for revealing the true relationship between genetic and phenotypic variables, and shedding light on disease mechanisms. In this paper, we present a general kernel machine based method for detecting effects of the interaction between multidimensional variable sets. This method can model the joint and epistatic effect of a collection of single nucleotide polymorphisms (SNPs), accommodate multiple factors that potentially moderate genetic influences, and test for nonlinear interactions between sets of variables in a flexible framework. As a demonstration of application, we applied the method to the data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) to detect the effects of the interactions between candidate Alzheimer's disease (AD) risk genes and a collection of cardiovascular disease (CVD) risk factors, on hippocampal volume measurements derived from structural brain magnetic resonance imaging (MRI) scans. Our method identified that two genes, CR1 and EPHA1, demonstrate significant interactions with CVD risk factors on hippocampal volume, suggesting that CR1 and EPHA1 may play a role in influencing AD-related neurodegeneration in the presence of CVD risks. PMID:25600633

  20. Enhancing Privacy in Participatory Sensing Applications with Multidimensional Data

    SciTech Connect

    Forrest, Stephanie; He, Wenbo; Groat, Michael; Edwards, Benjamin; Horey, James L

    2013-01-01

    Participatory sensing applications rely on individuals to share personal data to produce aggregated models and knowledge. In this setting, privacy concerns can discourage widespread adoption of new applications. We present a privacy-preserving participatory sensing scheme based on negative surveys for both continuous and multivariate categorical data. Without relying on encryption, our algorithms enhance the privacy of sensed data in an energy and computation efficient manner. Simulations and implementation on Android smart phones illustrate how multidimensional data can be aggregated in a useful and privacy-enhancing manner.