Science.gov

Sample records for function prediction involved

  1. Predicting the Academic Functioning of Youth Involved in Residential Care

    ERIC Educational Resources Information Center

    Griffith, Annette K.; Trout, Alexandra L.; Epstein, Michael H.; Garbin, Calvin P.; Pick, Robert; Wright, Tanya

    2010-01-01

    Youth involved in residential care programs present with significant difficulties across behavioral and mental health domains. Although this is a group that is also at considerable risk for academic failure, very little research has been done to understand the academic functioning of this population. The current study sought to expand what is…

  2. Molecular clock is involved in predictive circadian adjustment of renal function

    PubMed Central

    Zuber, Annie Mercier; Centeno, Gabriel; Pradervand, Sylvain; Nikolaeva, Svetlana; Maquelin, Lionel; Cardinaux, Léonard; Bonny, Olivier; Firsov, Dmitri

    2009-01-01

    Renal excretion of water and major electrolytes exhibits a significant circadian rhythm. This functional periodicity is believed to result, at least in part, from circadian changes in secretion/reabsorption capacities of the distal nephron and collecting ducts. Here, we studied the molecular mechanisms underlying circadian rhythms in the distal nephron segments, i.e., distal convoluted tubule (DCT) and connecting tubule (CNT) and the cortical collecting duct (CCD). Temporal expression analysis performed on microdissected mouse DCT/CNT or CCD revealed a marked circadian rhythmicity in the expression of a large number of genes crucially involved in various homeostatic functions of the kidney. This analysis also revealed that both DCT/CNT and CCD possess an intrinsic circadian timing system characterized by robust oscillations in the expression of circadian core clock genes (clock, bma11, npas2, per, cry, nr1d1) and clock-controlled Par bZip transcriptional factors dbp, hlf, and tef. The clock knockout mice or mice devoid of dbp/hlf/tef (triple knockout) exhibit significant changes in renal expression of several key regulators of water or sodium balance (vasopressin V2 receptor, aquaporin-2, aquaporin-4, αENaC). Functionally, the loss of clock leads to a complex phenotype characterized by partial diabetes insipidus, dysregulation of sodium excretion rhythms, and a significant decrease in blood pressure. Collectively, this study uncovers a major role of molecular clock in renal function. PMID:19805330

  3. Molecular clock is involved in predictive circadian adjustment of renal function.

    PubMed

    Zuber, Annie Mercier; Centeno, Gabriel; Pradervand, Sylvain; Nikolaeva, Svetlana; Maquelin, Lionel; Cardinaux, Léonard; Bonny, Olivier; Firsov, Dmitri

    2009-09-22

    Renal excretion of water and major electrolytes exhibits a significant circadian rhythm. This functional periodicity is believed to result, at least in part, from circadian changes in secretion/reabsorption capacities of the distal nephron and collecting ducts. Here, we studied the molecular mechanisms underlying circadian rhythms in the distal nephron segments, i.e., distal convoluted tubule (DCT) and connecting tubule (CNT) and the cortical collecting duct (CCD). Temporal expression analysis performed on microdissected mouse DCT/CNT or CCD revealed a marked circadian rhythmicity in the expression of a large number of genes crucially involved in various homeostatic functions of the kidney. This analysis also revealed that both DCT/CNT and CCD possess an intrinsic circadian timing system characterized by robust oscillations in the expression of circadian core clock genes (clock, bma11, npas2, per, cry, nr1d1) and clock-controlled Par bZip transcriptional factors dbp, hlf, and tef. The clock knockout mice or mice devoid of dbp/hlf/tef (triple knockout) exhibit significant changes in renal expression of several key regulators of water or sodium balance (vasopressin V2 receptor, aquaporin-2, aquaporin-4, alphaENaC). Functionally, the loss of clock leads to a complex phenotype characterized by partial diabetes insipidus, dysregulation of sodium excretion rhythms, and a significant decrease in blood pressure. Collectively, this study uncovers a major role of molecular clock in renal function.

  4. The involvement of proline-rich protein Mus musculus predicted gene 4736 in ocular surface functions.

    PubMed

    Qi, Xia; Ren, Sheng-Wei; Zhang, Feng; Wang, Yi-Qiang

    2016-01-01

    To research the two homologous predicted proline-rich protein genes, Mus musculus predicted gene 4736 (MP4) and proline-rich protein BstNI subfamily 1 (Prb1) which were significantly upregulated in cultured corneal organs when encountering fungal pathogen preparations. This study was to confirm the expression and potential functions of these two genes in ocular surface. A Pseudomonas aeruginosa keratitis model was established in Balb/c mice. One day post infection, mRNA level of MP4 was measured using real-time polymerase chain reaction (PCR), and MP4 protein detected by immunohistochemistry (IHC) or Western blot using a customized polyclonal anti-MP4 antibody preparation. Lacrimal glands from normal mice were also subjected to IHC staining for MP4. An online bioinformatics program, BioGPS, was utilized to screen public data to determine other potential locations of MP4. One day after keratitis induction, MP4 was upregulated in the corneas at both mRNA level as measured using real-time PCR and protein levels as measured using Western blot and IHC. BioGPS analysis of public data suggested that the MP4 gene was most abundantly expressed in the lacrimal glands, and IHC revealed that normal murine lacrimal glands were positive for MP4 staining. MP4 and Prb1 are closely related with the physiology and pathological processes of the ocular surface. Considering the significance of ocular surface abnormalities like dry eye, we propose that MP4 and Prb1 contribute to homeostasis of ocular surface, and deserve more extensive functional and disease correlation studies.

  5. The involvement of proline-rich protein Mus musculus predicted gene 4736 in ocular surface functions

    PubMed Central

    Qi, Xia; Ren, Sheng-Wei; Zhang, Feng; Wang, Yi-Qiang

    2016-01-01

    AIM To research the two homologous predicted proline-rich protein genes, Mus musculus predicted gene 4736 (MP4) and proline-rich protein BstNI subfamily 1 (Prb1) which were significantly upregulated in cultured corneal organs when encountering fungal pathogen preparations. This study was to confirm the expression and potential functions of these two genes in ocular surface. METHODS A Pseudomonas aeruginosa keratitis model was established in Balb/c mice. One day post infection, mRNA level of MP4 was measured using real-time polymerase chain reaction (PCR), and MP4 protein detected by immunohistochemistry (IHC) or Western blot using a customized polyclonal anti-MP4 antibody preparation. Lacrimal glands from normal mice were also subjected to IHC staining for MP4. An online bioinformatics program, BioGPS, was utilized to screen public data to determine other potential locations of MP4. RESULTS One day after keratitis induction, MP4 was upregulated in the corneas at both mRNA level as measured using real-time PCR and protein levels as measured using Western blot and IHC. BioGPS analysis of public data suggested that the MP4 gene was most abundantly expressed in the lacrimal glands, and IHC revealed that normal murine lacrimal glands were positive for MP4 staining. CONCLUSION MP4 and Prb1 are closely related with the physiology and pathological processes of the ocular surface. Considering the significance of ocular surface abnormalities like dry eye, we propose that MP4 and Prb1 contribute to homeostasis of ocular surface, and deserve more extensive functional and disease correlation studies. PMID:27588265

  6. Predicting Social Functioning in Schizotypy

    PubMed Central

    McCleery, Amanda; Divilbiss, Marielle; St-Hilaire, Annie; Aakre, Jennifer M.; Seghers, James P.; Bell, Emily K.; Docherty, Nancy M.

    2015-01-01

    Theory of mind (ToM) is an aspect of social cognition that refers to the ability to make inferences about the thoughts, feelings, and intentions of other people. It is believed to be related to social functioning. Previous investigations of ToM in schizotypy have yielded mixed results. Using a correlational approach, the present study explored the relationship between schizotypal traits, ToM, neurocognition, depressed mood, and social functioning in a sample of 50 undergraduate students. Schizotypy was related to poor social functioning. Contrary to predictions, schizotypal traits were not associated with impaired ToM. In fact, schizotypal traits were associated with enhanced performance on a ToM task that involved detection of ironic statements. However, strong relationships emerged among schizotypy, depressed mood, and social functioning, highlighting the need to also examine depression when assessing the relations between elevated schizotypy and poor social functioning. PMID:22297312

  7. Anatomic Location of Tumor Predicts the Accuracy of Motor Function Localization in Diffuse Lower-Grade Gliomas Involving the Hand Knob Area.

    PubMed

    Fang, S; Liang, J; Qian, T; Wang, Y; Liu, X; Fan, X; Li, S; Wang, Y; Jiang, T

    2017-08-24

    The accuracy of preoperative blood oxygen level-dependent fMRI remains controversial. This study assessed the association between the anatomic location of a tumor and the accuracy of fMRI-based motor function mapping in diffuse lower-grade gliomas. Thirty-five patients with lower-grade gliomas involving motor areas underwent preoperative blood oxygen level-dependent fMRI scans with grasping tasks and received intraoperative direct cortical stimulation. Patients were classified into an overlapping group and a nonoverlapping group, depending on the extent to which blood oxygen level-dependent fMRI and direct cortical stimulation results concurred. Tumor location was quantitatively measured, including the shortest distance from the tumor to the hand knob and the deviation distance of the midpoint of the hand knob in the lesion hemisphere relative to the midline compared with the normal contralateral hemisphere. A 4-mm shortest distance from the tumor to the hand knob value was identified as optimal for differentiating the overlapping and nonoverlapping group with the receiver operating characteristic curve (sensitivity, 84.6%; specificity, 77.8%). The shortest distances from the tumor to the hand knob of ≤4 mm were associated with inaccurate fMRI-based localizations of the hand motor cortex. The shortest distances from the tumor to the hand knob were larger (P = .002), and the deviation distances for the midpoint of the hand knob in the lesion hemisphere were smaller (P = .003) in the overlapping group than in the nonoverlapping group. This study suggests that the shortest distance from the tumor to the hand knob and the deviation distance for the midpoint of the hand knob on the lesion hemisphere are predictive of the accuracy of blood oxygen level-dependent fMRI results. Smaller shortest distances from the tumor to the hand knob and larger deviation distances for the midpoint of hand knob on the lesion hemisphere are associated with less accuracy of motor cortex

  8. Predicting cancer involvement of genes from heterogeneous data

    PubMed Central

    Aragues, Ramon; Sander, Chris; Oliva, Baldo

    2008-01-01

    Background Systematic approaches for identifying proteins involved in different types of cancer are needed. Experimental techniques such as microarrays are being used to characterize cancer, but validating their results can be a laborious task. Computational approaches are used to prioritize between genes putatively involved in cancer, usually based on further analyzing experimental data. Results We implemented a systematic method using the PIANA software that predicts cancer involvement of genes by integrating heterogeneous datasets. Specifically, we produced lists of genes likely to be involved in cancer by relying on: (i) protein-protein interactions; (ii) differential expression data; and (iii) structural and functional properties of cancer genes. The integrative approach that combines multiple sources of data obtained positive predictive values ranging from 23% (on a list of 811 genes) to 73% (on a list of 22 genes), outperforming the use of any of the data sources alone. We analyze a list of 20 cancer gene predictions, finding that most of them have been recently linked to cancer in literature. Conclusion Our approach to identifying and prioritizing candidate cancer genes can be used to produce lists of genes likely to be involved in cancer. Our results suggest that differential expression studies yielding high numbers of candidate cancer genes can be filtered using protein interaction networks. PMID:18371197

  9. Serotonin involvement in pituitary-adrenal function

    NASA Technical Reports Server (NTRS)

    Vernikos-Danellis, J.; Kellar, K. J.; Kent, D.; Gonzales, C.; Berger, P. A.; Barchas, J. D.

    1977-01-01

    Experiments clarifying the effects of serotonin (5-HT) in the regulation of the hypothalamic-pituitary-adrenocortical system are surveyed. Lesion experiments which seek to determine functional maps of serotonergic input to areas involved in regulation are reported. Investigations of the effects of 5-HT levels on the plasma ACTH response to stress and the diurnal variation in basal plasma corticosterone are summarized, and the question of whether serotonergic transmission is involved in the regulation of all aspects of pituitary-adrenal function is considered with attention to the stimulatory and inhibitory action of 5-HT.

  10. Year 2 Report: Protein Function Prediction Platform

    SciTech Connect

    Zhou, C E

    2012-04-27

    Upon completion of our second year of development in a 3-year development cycle, we have completed a prototype protein structure-function annotation and function prediction system: Protein Function Prediction (PFP) platform (v.0.5). We have met our milestones for Years 1 and 2 and are positioned to continue development in completion of our original statement of work, or a reasonable modification thereof, in service to DTRA Programs involved in diagnostics and medical countermeasures research and development. The PFP platform is a multi-scale computational modeling system for protein structure-function annotation and function prediction. As of this writing, PFP is the only existing fully automated, high-throughput, multi-scale modeling, whole-proteome annotation platform, and represents a significant advance in the field of genome annotation (Fig. 1). PFP modules perform protein functional annotations at the sequence, systems biology, protein structure, and atomistic levels of biological complexity (Fig. 2). Because these approaches provide orthogonal means of characterizing proteins and suggesting protein function, PFP processing maximizes the protein functional information that can currently be gained by computational means. Comprehensive annotation of pathogen genomes is essential for bio-defense applications in pathogen characterization, threat assessment, and medical countermeasure design and development in that it can short-cut the time and effort required to select and characterize protein biomarkers.

  11. Some completely monotonic functions involving polygamma functions and an application

    NASA Astrophysics Data System (ADS)

    Qi, Feng; Cui, Run-Qing; Chen, Chao-Ping; Guo, Bai-Ni

    2005-10-01

    By using the first Binet's formula the strictly completely monotonic properties of functions involving the psi and polygamma functions are obtainedE As direct consequences, two inequalities are proved. As an application, the best lower and upper bounds of the nth harmonic number are established.

  12. Multiple behavioural impulsivity tasks predict prospective alcohol involvement in adolescents

    PubMed Central

    Fernie, Gordon; Peeters, Margot; Gullo, Matthew J; Christiansen, Paul; Cole, Jon C; Sumnall, Harry; Field, Matt

    2013-01-01

    Aims We investigated reciprocal prospective relationships between multiple behavioural impulsivity tasks (assessing delay discounting, risk-taking and disinhibition) and alcohol involvement (consumption, drunkenness and problems) among adolescents. We hypothesized that performance on the tasks would predict subsequent alcohol involvement, and that alcohol involvement would lead to increases in behavioural impulsivity over time. Design Cross-lagged prospective design in which impulsivity and alcohol involvement were assessed five times over 2 years (once every 6 months, on average). Setting Classrooms in secondary schools in North West England. Participants Two hundred and eighty-seven adolescents (51.2% male) who were aged 12 or 13 years at study enrolment. Measurements Participants reported their alcohol involvement and completed computerized tasks of disinhibition, delay discounting and risk-taking at each assessment. Cross-sectional and prospective relationships between the variables of interest were investigated using cross-lagged analyses. Findings All behavioural impulsivity tasks predicted a composite index of alcohol involvement 6 months later (all Ps < 0.01), and these prospective relationships were reliable across the majority of time-points. Importantly, we did not observe the converse relationship across time: alcohol involvement did not predict performance on behavioural impulsivity tasks at any subsequent time point. Conclusions Several measures of impulsivity predict escalation in alcohol involvement in young adolescents, but alcohol use does not appear to alter impulsivity. PMID:23795646

  13. Fusion excitation functions involving transitional nuclei

    SciTech Connect

    Rehm, K.E.; Jiang, C.L.; Esbensen, H.

    1995-08-01

    Measurements of fusion excitation functions involving transitional nuclei {sup 78}Kr and {sup 100}Mo showed a different behavior at low energies, if compared to measurements with {sup 86}Kr and {sup 92}Mo. This points to a possible influence of nuclear structure on the fusion process. One way to characterize the structure of vibrational nuclei is via their restoring force parameters C{sub 2} which can be calculated from the energy of the lowest 2{sup +} state and the corresponding B(E2) value. A survey of the even-even nuclei between A = 28-150 shows strong variations in C{sub 2} values spanning two orders of magnitude. The lowest values for C{sub 2} are observed for {sup 78}Kr, {sup 104}Ru and {sup 124}Xe followed by {sup 74,76}Ge, {sup 74,76}Se, {sup 100}Mo and {sup 110}Pd. In order to learn more about the influence of {open_quotes}softness{close_quotes} on the sub-barrier fusion enhancement, we measured cross sections for evaporation residue production for the systems {sup 78}Kr + {sup 104}Ru and {sup 78}Kr + {sup 76}Ge with the gas-filled magnet technique. For both systems, fusion excitation functions involving the closed neutron shell nucleus {sup 86}Kr were measured previously. The data are presently being analyzed.

  14. Functional brain networks involved in reality monitoring.

    PubMed

    Metzak, Paul D; Lavigne, Katie M; Woodward, Todd S

    2015-08-01

    Source monitoring refers to the recollection of variables that specify the context and conditions in which a memory episode was encoded. This process involves using the qualitative and quantitative features of a memory trace to distinguish its source. One specific class of source monitoring is reality monitoring, which involves distinguishing internally generated from externally generated information, that is, memories of imagined events from real events. The purpose of the present study was to identify functional brain networks that underlie reality monitoring, using an alternative type of source monitoring as a control condition. On the basis of previous studies on self-referential thinking, it was expected that a medial prefrontal cortex (mPFC) based network would be more active during reality monitoring than the control condition, due to the requirement to focus on a comparison of internal (self) and external (other) source information. Two functional brain networks emerged from this analysis, one reflecting increasing task-related activity, and one reflecting decreasing task-related activity. The second network was mPFC based, and was characterized by task-related deactivations in areas resembling the default-mode network; namely, the mPFC, middle temporal gyri, lateral parietal regions, and the precuneus, and these deactivations were diminished during reality monitoring relative to source monitoring, resulting in higher activity during reality monitoring. This result supports previous research suggesting that self-referential thinking involves the mPFC, but extends this to a network-level interpretation of reality monitoring. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. Prediction of Research Self-Efficacy and Future Research Involvement.

    ERIC Educational Resources Information Center

    Bishop, Rosean M.; And Others

    Although graduate programs hope that their students will be committed to research in their careers, most students express ambivalence towards research. Identifying the variables that predict involvement in research thus seems crucial. In this study 136 doctoral students from a wide range of disciplines completed the Research Self-Efficacy Scale…

  16. Predictive value of pedicle involvement with MRI in spine metastases

    PubMed Central

    Bian, Chong; Liang, Yun; Jiang, Libo; Qian, Chen; Dong, Jian

    2016-01-01

    Objectives The study aimed to retrospectively evaluate the accuracy and value of magnetic resonance imaging (MRI) in predicting pedicle involvement for patients with spine metastases. Methods Forty-five patients with a vertebral metastasis encroaching at least one pedicle were studied using MRI before surgery and regularly after surgery. Patients were categorized on the basis of their numbers of pedicle involvement (Group 1: one pedicle was involved, n = 23; Group 2: two pedicles were involved, n = 22). The diagnostic accuracy was calculated, and comparisons of intraoperative blood loss and recurrence rate between the two groups were performed. Results The overall performance of MRI in predicting the pedicle involvement was as follows: accuracy, 94.4%; sensitivity, 95.5%; and specificity, 91.3%. Less intraoperative blood loss was observed for Group 1 compared with Group 2 (1,661 ± 672 ml and 2,173 ± 790 ml, respectively, P = 0.024). Tumor relapse occurred in 8.7% (2/23) of Group 1 and in 22.7% (5/22) of Group 2 with median recurrence free survival time 14 and 9 months, respectively. Conclusions MRI is a reliable approach to assess pedicle involvement. It has potential for use in the evaluation of the clinical characteristics of patients with spine metastases. PMID:27486876

  17. Can Coronary Artery Involvement in Kawasaki Disease be Predicted?

    PubMed

    Ghelani, Sunil J; Kwatra, Neha S; Spurney, Christopher F

    2013-03-26

    Coronary artery involvement is seen in approximately 15-20% of children with Kawasaki disease. There is conflicting literature regarding the clinical and laboratory findings associated with coronary artery involvement. In this retrospective study, we attempt identification of predictive factors for coronary artery involvement at our institute and review the existing literature. A review of 203 patients (65% males) with Kawasaki disease was performed, of whom 33 (16.3%) had coronary artery involvement. High erythrocyte sedimentation rate, high platelet count, low hematocrit, low albumin levels, and refractory Kawasaki disease showed significant association with coronary artery involvement. High erythrocyte sedimentation rate and refractory Kawasaki disease were found to be independent predictors of coronary artery involvement. Review of literature suggested a wide range of coronary involvement (<5% to >60%), and highly conflicting clinical and laboratory associations. It remains difficult to accurately determine risk of coronary artery involvement, although some laboratory markers may provide information that is helpful for parental counseling and clinical follow up. Future identification of novel biomarkers and host predispositions may further our understanding of coronary artery risks and help personalize therapy for Kawasaki disease.

  18. Parental alcohol involvement and adolescent alcohol expectancies predict alcohol involvement in male adolescents.

    PubMed

    Cranford, James A; Zucker, Robert A; Jester, Jennifer M; Puttler, Leon I; Fitzgerald, Hiram E

    2010-09-01

    Current models of adolescent drinking behavior hypothesize that alcohol expectancies mediate the effects of other proximal and distal risk factors. This longitudinal study tested the hypothesis that the effects of parental alcohol involvement on their children's drinking behavior in mid-adolescence are mediated by the children's alcohol expectancies in early adolescence. A sample of 148 initially 9-11 year old boys and their parents from a high-risk population and a contrast group of community families completed measures of drinking behavior and alcohol expectancies over a 6-year interval. We analyzed data from middle childhood (M age = 10.4 years), early adolescence (M age = 13.5 years), and mid-adolescence (M age = 16.5 years). The sample was restricted only to adolescents who had begun to drink by mid-adolescence. Results from zero-inflated Poisson regression analyses showed that 1) maternal drinking during their children's middle childhood predicted number of drinking days in middle adolescence; 2) negative and positive alcohol expectancies in early adolescence predicted odds of any intoxication in middle adolescence; and 3) paternal alcoholism during their children's middle childhood and adolescents' alcohol expectancies in early adolescence predicted frequency of intoxication in middle adolescence. Contrary to predictions, child alcohol expectancies did not mediate the effects of parental alcohol involvement in this high-risk sample. Different aspects of parental alcohol involvement, along with early adolescent alcohol expectancies, independently predicted adolescent drinking behavior in middle adolescence. Alternative pathways for the influence of maternal and paternal alcohol involvement and implications for expectancy models of adolescent drinking behavior were discussed.

  19. An iterative approach of protein function prediction

    PubMed Central

    2011-01-01

    Background Current approaches of predicting protein functions from a protein-protein interaction (PPI) dataset are based on an assumption that the available functions of the proteins (a.k.a. annotated proteins) will determine the functions of the proteins whose functions are unknown yet at the moment (a.k.a. un-annotated proteins). Therefore, the protein function prediction is a mono-directed and one-off procedure, i.e. from annotated proteins to un-annotated proteins. However, the interactions between proteins are mutual rather than static and mono-directed, although functions of some proteins are unknown for some reasons at present. That means when we use the similarity-based approach to predict functions of un-annotated proteins, the un-annotated proteins, once their functions are predicted, will affect the similarities between proteins, which in turn will affect the prediction results. In other words, the function prediction is a dynamic and mutual procedure. This dynamic feature of protein interactions, however, was not considered in the existing prediction algorithms. Results In this paper, we propose a new prediction approach that predicts protein functions iteratively. This iterative approach incorporates the dynamic and mutual features of PPI interactions, as well as the local and global semantic influence of protein functions, into the prediction. To guarantee predicting functions iteratively, we propose a new protein similarity from protein functions. We adapt new evaluation metrics to evaluate the prediction quality of our algorithm and other similar algorithms. Experiments on real PPI datasets were conducted to evaluate the effectiveness of the proposed approach in predicting unknown protein functions. Conclusions The iterative approach is more likely to reflect the real biological nature between proteins when predicting functions. A proper definition of protein similarity from protein functions is the key to predicting functions iteratively. The

  20. Nicotinic involvement in memory function in zebrafish.

    PubMed

    Levin, Edward D; Chen, Elaine

    2004-01-01

    Zebrafish are an emerging model for the study of the molecular mechanisms of brain function. To conduct studies of the neural bases of behavior in zebrafish, we must understand the behavioral function of zebrafish and how it is altered by perturbations of brain function. This study determined nicotine actions on memory function in zebrafish. With the methods that we have developed to assess memory in zebrafish using delayed spatial alternation (DSA), we determined the dose effect function of acute nicotine on memory function in zebrafish. As in rodents and primates, low nicotine doses improve memory in zebrafish, while high nicotine doses have diminished effect and can impair memory. This study shows that nicotine affects memory function in zebrafish much like in rats, mice, monkeys and humans. Now, zebrafish can be used to help understand the molecular mechanisms crucial to nicotine effects on memory.

  1. Predicted structures of two proteins involved in human diseases.

    PubMed

    Zhou, H X; Wang, G

    2001-01-01

    Structures of 79 proteins involved in human diseases were predicted by sequence alignments with structural templates. The predicted structures for ALDP and CSA, proteins responsible for adrenoleukodystrophy and the Cockayne syndrome, respectively, were analyzed to elucidate the molecular basis of disease mutations. In particular we positioned residue P484 of ALDP in the homodimer interface. This positioning is consistent with a recent experimental finding that the mutation P484R significantly decreases the self-interaction of ALDP and suggests that the disease mechanism of this mutation lies in the impaired ALDP dimerization. We identified two new WD repeats in CSA and suggest that one of these forms part of the interaction surface with other proteins.

  2. PREDICTION OF NONLINEAR SPATIAL FUNCTIONALS. (R827257)

    EPA Science Inventory

    Spatial statistical methodology can be useful in the arena of environmental regulation. Some regulatory questions may be addressed by predicting linear functionals of the underlying signal, but other questions may require the prediction of nonlinear functionals of the signal. ...

  3. Protein Function Prediction: Problems and Pitfalls.

    PubMed

    Pearson, William R

    2015-09-03

    The characterization of new genomes based on their protein sets has been revolutionized by new sequencing technologies, but biologists seeking to exploit new sequence information are often frustrated by the challenges associated with accurately assigning biological functions to newly identified proteins. Here, we highlight some of the challenges in functional inference from sequence similarity. Investigators can improve the accuracy of function prediction by (1) being conservative about the evolutionary distance to a protein of known function; (2) considering the ambiguous meaning of "functional similarity," and (3) being aware of the limitations of annotations in functional databases. Protein function prediction does not offer "one-size-fits-all" solutions. Prediction strategies work better when the idiosyncrasies of function and functional annotation are better understood.

  4. Hierarchical Ensemble Methods for Protein Function Prediction

    PubMed Central

    2014-01-01

    Protein function prediction is a complex multiclass multilabel classification problem, characterized by multiple issues such as the incompleteness of the available annotations, the integration of multiple sources of high dimensional biomolecular data, the unbalance of several functional classes, and the difficulty of univocally determining negative examples. Moreover, the hierarchical relationships between functional classes that characterize both the Gene Ontology and FunCat taxonomies motivate the development of hierarchy-aware prediction methods that showed significantly better performances than hierarchical-unaware “flat” prediction methods. In this paper, we provide a comprehensive review of hierarchical methods for protein function prediction based on ensembles of learning machines. According to this general approach, a separate learning machine is trained to learn a specific functional term and then the resulting predictions are assembled in a “consensus” ensemble decision, taking into account the hierarchical relationships between classes. The main hierarchical ensemble methods proposed in the literature are discussed in the context of existing computational methods for protein function prediction, highlighting their characteristics, advantages, and limitations. Open problems of this exciting research area of computational biology are finally considered, outlining novel perspectives for future research. PMID:25937954

  5. Hierarchical ensemble methods for protein function prediction.

    PubMed

    Valentini, Giorgio

    2014-01-01

    Protein function prediction is a complex multiclass multilabel classification problem, characterized by multiple issues such as the incompleteness of the available annotations, the integration of multiple sources of high dimensional biomolecular data, the unbalance of several functional classes, and the difficulty of univocally determining negative examples. Moreover, the hierarchical relationships between functional classes that characterize both the Gene Ontology and FunCat taxonomies motivate the development of hierarchy-aware prediction methods that showed significantly better performances than hierarchical-unaware "flat" prediction methods. In this paper, we provide a comprehensive review of hierarchical methods for protein function prediction based on ensembles of learning machines. According to this general approach, a separate learning machine is trained to learn a specific functional term and then the resulting predictions are assembled in a "consensus" ensemble decision, taking into account the hierarchical relationships between classes. The main hierarchical ensemble methods proposed in the literature are discussed in the context of existing computational methods for protein function prediction, highlighting their characteristics, advantages, and limitations. Open problems of this exciting research area of computational biology are finally considered, outlining novel perspectives for future research.

  6. Predicting network functions with nested patterns

    NASA Astrophysics Data System (ADS)

    Ganter, Mathias; Kaltenbach, Hans-Michael; Stelling, Jörg

    2014-01-01

    Identifying suitable patterns in complex biological interaction networks helps understanding network functions and allows for predictions at the pattern level: by recognizing a known pattern, one can assign its previously established function. However, current approaches fail for previously unseen patterns, when patterns overlap and when they are embedded into a new network context. Here we show how to conceptually extend pattern-based approaches. We define metabolite patterns in metabolic networks that formalize co-occurrences of metabolites. Our probabilistic framework decodes the implicit information in the networks’ metabolite patterns to predict metabolic functions. We demonstrate the predictive power by identifying ‘indicator patterns’, for instance, for enzyme classification, by predicting directions of novel reactions and of known reactions in new network contexts, and by ranking candidate network extensions for gap filling. Beyond their use in improving genome annotations and metabolic network models, we expect that the concepts transfer to other network types.

  7. Does sociability predict civic involvement and political participation?

    PubMed

    Foschi, Renato; Lauriola, Marco

    2014-02-01

    In contemporary history as well as in political science, a strong associational life known as sociability is thought to explain the roots of modern democracy by establishing a link between the increasing availability of free time to the middle classes, increasing willingness to gather with others in circles or associations, and increasing social capital. In personality psychology, sociability is related to prosocial behavior (i.e., the need for affiliation, agreeableness, openness, and extraversion), whose importance in different political behaviors is increasingly recognized. In the present article, we carried out 5 studies (N = 1,429) that showed that political and associative sociability (a) can be reliably assessed, can have cross-cultural validity, and are properly associated with general social interest measures and personality domains and facets in the five-factor model; (b) do not overlap with similar concepts used in political psychology to account for political participation (political expertise, political interest, political self-efficacy); and (c) predicted political and nonpolitical group membership as well as observable choices in decision-making tasks with political and nonpolitical outcomes. The results are discussed, taking into consideration the extent to which specific facets of sociability can mediate between general personality traits and measures of civic involvement and political participation in a holistic model of political behavior. PsycINFO Database Record (c) 2014 APA, all rights reserved.

  8. Monotonicity and Logarithmic Concavity of Two Functions Involving Exponential Function

    ERIC Educational Resources Information Center

    Liu, Ai-Qi; Li, Guo-Fu; Guo, Bai-Ni; Qi, Feng

    2008-01-01

    The function 1 divided by "x"[superscript 2] minus "e"[superscript"-x"] divided by (1 minus "e"[superscript"-x"])[superscript 2] for "x" greater than 0 is proved to be strictly decreasing. As an application of this monotonicity, the logarithmic concavity of the function "t" divided by "e"[superscript "at"] minus "e"[superscript"(a-1)""t"] for "a"…

  9. Genetic Ancestry in Lung-Function Predictions

    PubMed Central

    Kumar, Rajesh; Seibold, Max A.; Aldrich, Melinda C.; Williams, L. Keoki; Reiner, Alex P.; Colangelo, Laura; Galanter, Joshua; Gignoux, Christopher; Hu, Donglei; Sen, Saunak; Choudhry, Shweta; Peterson, Edward L.; Rodriguez-Santana, Jose; Rodriguez-Cintron, William; Nalls, Michael A.; Leak, Tennille S.; O’Meara, Ellen; Meibohm, Bernd; Kritchevsky, Stephen B.; Li, Rongling; Harris, Tamara B.; Nickerson, Deborah A.; Fornage, Myriam; Enright, Paul; Ziv, Elad; Smith, Lewis J.; Liu, Kiang; Burchard, Esteban González

    2010-01-01

    BACKGROUND Self-identified race or ethnic group is used to determine normal reference standards in the prediction of pulmonary function. We conducted a study to determine whether the genetically determined percentage of African ancestry is associated with lung function and whether its use could improve predictions of lung function among persons who identified themselves as African American. METHODS We assessed the ancestry of 777 participants self-identified as African American in the Coronary Artery Risk Development in Young Adults (CARDIA) study and evaluated the relation between pulmonary function and ancestry by means of linear regression. We performed similar analyses of data for two independent cohorts of subjects identifying themselves as African American: 813 participants in the Health, Aging, and Body Composition (HABC) study and 579 participants in the Cardiovascular Health Study (CHS). We compared the fit of two types of models to lung-function measurements: models based on the covariates used in standard prediction equations and models incorporating ancestry. We also evaluated the effect of the ancestry-based models on the classification of disease severity in two asthma-study populations. RESULTS African ancestry was inversely related to forced expiratory volume in 1 second (FEV1) and forced vital capacity in the CARDIA cohort. These relations were also seen in the HABC and CHS cohorts. In predicting lung function, the ancestry-based model fit the data better than standard models. Ancestry-based models resulted in the reclassification of asthma severity (based on the percentage of the predicted FEV1) in 4 to 5% of participants. CONCLUSIONS Current predictive equations, which rely on self-identified race alone, may misestimate lung function among subjects who identify themselves as African American. Incorporating ancestry into normative equations may improve lung-function estimates and more accurately categorize disease severity. (Funded by the National

  10. Prediction processes during multiple object tracking (MOT): involvement of dorsal and ventral premotor cortices

    PubMed Central

    Atmaca, Silke; Stadler, Waltraud; Keitel, Anne; Ott, Derek V M; Lepsien, Jöran; Prinz, Wolfgang

    2013-01-01

    Background The multiple object tracking (MOT) paradigm is a cognitive task that requires parallel tracking of several identical, moving objects following nongoal-directed, arbitrary motion trajectories. Aims The current study aimed to investigate the employment of prediction processes during MOT. As an indicator for the involvement of prediction processes, we targeted the human premotor cortex (PM). The PM has been repeatedly implicated to serve the internal modeling of future actions and action effects, as well as purely perceptual events, by means of predictive feedforward functions. Materials and methods Using functional magnetic resonance imaging (fMRI), BOLD activations recorded during MOT were contrasted with those recorded during the execution of a cognitive control task that used an identical stimulus display and demanded similar attentional load. A particular effort was made to identify and exclude previously found activation in the PM-adjacent frontal eye fields (FEF). Results We replicated prior results, revealing occipitotemporal, parietal, and frontal areas to be engaged in MOT. Discussion The activation in frontal areas is interpreted to originate from dorsal and ventral premotor cortices. The results are discussed in light of our assumption that MOT engages prediction processes. Conclusion We propose that our results provide first clues that MOT does not only involve visuospatial perception and attention processes, but prediction processes as well. PMID:24363971

  11. Involvement of functional autoantibodies against vascular receptors in systemic sclerosis.

    PubMed

    Riemekasten, Gabriela; Philippe, Aurélie; Näther, Melanie; Slowinski, Torsten; Müller, Dominik N; Heidecke, Harald; Matucci-Cerinic, Marco; Czirják, László; Lukitsch, Ivo; Becker, Mike; Kill, Angela; van Laar, Jacob M; Catar, Rusan; Luft, Friedrich C; Burmester, Gerd R; Hegner, Björn; Dragun, Duska

    2011-03-01

    Systemic sclerosis (SSc) features autoimmunity, vasculopathy and tissue fibrosis. The renin-angiotensin and endothelin systems have been implicated in vasculopathy and fibrosis. A role for autoantibody-mediated receptor stimulation is hypothesised, linking three major pathophysiological features consistent with SSc. Serum samples from 478 patients with SSc (298 in the study cohort and 180 from two further independent cohorts), 372 healthy subjects and 311 control-disease subjects were tested for antibodies against angiotensin II type 1 receptor (AT(1)R) and endothelin-1 type A receptor (ET(A)R) by solid phase assay. Binding specificities were tested by immunoprecipitation. The biological effects of autoantibodies in microvascular endothelial cells in vitro were also determined, as well as the quantitative differences in autoantibody levels on specific organ involvements and their predictive value for SSc-related mortality. Anti-AT(1)R and anti-ET(A)R autoantibodies were detected in most patients with SSc. Autoantibodies specifically bound to respective receptors on endothelial cells. Higher levels of both autoantibodies were associated with more severe disease manifestations and predicted SSc-related mortality. Both autoantibodies exert biological effects as they induced extracellular signal-regulated kinase 1/2 phosphorylation and increased transforming growth factor β gene expression in endothelial cells which could be blocked with specific receptor antagonists. Functional autoimmunity directed at AT(1)R and ET(A)R is common in patients with SSc. AT(1)R and ET(A)R autoantibodies could contribute to disease pathogenesis and may serve as biomarkers for risk assessment of disease progression.

  12. Improved network community structure improves function prediction

    PubMed Central

    Lee, Juyong; Gross, Steven P.; Lee, Jooyoung

    2013-01-01

    We are overwhelmed by experimental data, and need better ways to understand large interaction datasets. While clustering related nodes in such networks—known as community detection—appears a promising approach, detecting such communities is computationally difficult. Further, how to best use such community information has not been determined. Here, within the context of protein function prediction, we address both issues. First, we apply a novel method that generates improved modularity solutions than the current state of the art. Second, we develop a better method to use this community information to predict proteins' functions. We discuss when and why this community information is important. Our results should be useful for two distinct scientific communities: first, those using various cost functions to detect community structure, where our new optimization approach will improve solutions, and second, those working to extract novel functional information about individual nodes from large interaction datasets. PMID:23852097

  13. Protein function prediction based on data fusion and functional interrelationship.

    PubMed

    Meng, Jun; Wekesa, Jael-Sanyanda; Shi, Guan-Li; Luan, Yu-Shi

    2016-04-01

    One of the challenging tasks of bioinformatics is to predict more accurate and confident protein functions from genomics and proteomics datasets. Computational approaches use a variety of high throughput experimental data, such as protein-protein interaction (PPI), protein sequences and phylogenetic profiles, to predict protein functions. This paper presents a method that uses transductive multi-label learning algorithm by integrating multiple data sources for classification. Multiple proteomics datasets are integrated to make inferences about functions of unknown proteins and use a directed bi-relational graph to assign labels to unannotated proteins. Our method, bi-relational graph based transductive multi-label function annotation (Bi-TMF) uses functional correlation and topological PPI network properties on both the training and testing datasets to predict protein functions through data fusion of the individual kernel result. The main purpose of our proposed method is to enhance the performance of classifier integration for protein function prediction algorithms. Experimental results demonstrate the effectiveness and efficiency of Bi-TMF on multi-sources datasets in yeast, human and mouse benchmarks. Bi-TMF outperforms other recently proposed methods.

  14. Functional association prediction by community profiling.

    PubMed

    Jiao, Dazhi; Han, Wontack; Ye, Yuzhen

    2017-04-26

    Recent years have witnessed unprecedented accumulation of DNA sequences and therefore protein sequences (predicted from DNA sequences), due to the advances of sequencing technology. One of the major sources of the hypothetical proteins is the metagenomics research. Current annotation of metagenomes (collections of short metagenomic sequences or assemblies) relies on similarity searches against known gene/protein families, based on which functional profiles of microbial communities can be built. This practice, however, leaves out the hypothetical proteins, which may outnumber the known proteins for many microbial communities. On the other hand, we may ask: what can we gain from the large number of metagenomes made available by the metagenomic studies, for the annotation of metagenomic sequences as well as functional annotation of hypothetical proteins in general? Here we propose a community profiling approach for predicting functional associations between proteins: two proteins are predicted to be associated if they share similar presence and absence profiles (called community profiles) across microbial communities. Community profiling is conceptually similar to the phylogenetic profiling approach to functional prediction, however with fundamental differences. We tested different profile construction methods, the selection of reference metagenomes, and correlation metrics, among others, to optimize the performance of this new approach. We demonstrated that the community profiling approach alone slightly outperforms the phylogenetic profiling approach for associating proteins in species that are well represented by sequenced genomes, and combining phylogenetic and community profiling further improves (though only marginally) the prediction of functional association. Further we showed that community profiling method significantly outperforms phylogenetic profiling, revealing more functional associations, when applied to a more recently sequenced bacterial genome

  15. Prediction of Chemical Function: Model Development and ...

    EPA Pesticide Factsheets

    The United States Environmental Protection Agency’s Exposure Forecaster (ExpoCast) project is developing both statistical and mechanism-based computational models for predicting exposures to thousands of chemicals, including those in consumer products. The high-throughput (HT) screening-level exposures developed under ExpoCast can be combined with HT screening (HTS) bioactivity data for the risk-based prioritization of chemicals for further evaluation. The functional role (e.g. solvent, plasticizer, fragrance) that a chemical performs can drive both the types of products in which it is found and the concentration in which it is present and therefore impacting exposure potential. However, critical chemical use information (including functional role) is lacking for the majority of commercial chemicals for which exposure estimates are needed. A suite of machine-learning based models for classifying chemicals in terms of their likely functional roles in products based on structure were developed. This effort required collection, curation, and harmonization of publically-available data sources of chemical functional use information from government and industry bodies. Physicochemical and structure descriptor data were generated for chemicals with function data. Machine-learning classifier models for function were then built in a cross-validated manner from the descriptor/function data using the method of random forests. The models were applied to: 1) predict chemi

  16. Prediction of Chemical Function: Model Development and ...

    EPA Pesticide Factsheets

    The United States Environmental Protection Agency’s Exposure Forecaster (ExpoCast) project is developing both statistical and mechanism-based computational models for predicting exposures to thousands of chemicals, including those in consumer products. The high-throughput (HT) screening-level exposures developed under ExpoCast can be combined with HT screening (HTS) bioactivity data for the risk-based prioritization of chemicals for further evaluation. The functional role (e.g. solvent, plasticizer, fragrance) that a chemical performs can drive both the types of products in which it is found and the concentration in which it is present and therefore impacting exposure potential. However, critical chemical use information (including functional role) is lacking for the majority of commercial chemicals for which exposure estimates are needed. A suite of machine-learning based models for classifying chemicals in terms of their likely functional roles in products based on structure were developed. This effort required collection, curation, and harmonization of publically-available data sources of chemical functional use information from government and industry bodies. Physicochemical and structure descriptor data were generated for chemicals with function data. Machine-learning classifier models for function were then built in a cross-validated manner from the descriptor/function data using the method of random forests. The models were applied to: 1) predict chemi

  17. Predictable convergence in hemoglobin function has unpredictable molecular underpinnings.

    PubMed

    Natarajan, Chandrasekhar; Hoffmann, Federico G; Weber, Roy E; Fago, Angela; Witt, Christopher C; Storz, Jay F

    2016-10-21

    To investigate the predictability of genetic adaptation, we examined the molecular basis of convergence in hemoglobin function in comparisons involving 56 avian taxa that have contrasting altitudinal range limits. Convergent increases in hemoglobin-oxygen affinity were pervasive among high-altitude taxa, but few such changes were attributable to parallel amino acid substitutions at key residues. Thus, predictable changes in biochemical phenotype do not have a predictable molecular basis. Experiments involving resurrected ancestral proteins revealed that historical substitutions have context-dependent effects, indicating that possible adaptive solutions are contingent on prior history. Mutations that produce an adaptive change in one species may represent precluded possibilities in other species because of differences in genetic background. Copyright © 2016, American Association for the Advancement of Science.

  18. Computations involving differential operators and their actions on functions

    NASA Technical Reports Server (NTRS)

    Crouch, Peter E.; Grossman, Robert; Larson, Richard

    1991-01-01

    The algorithms derived by Grossmann and Larson (1989) are further developed for rewriting expressions involving differential operators. The differential operators involved arise in the local analysis of nonlinear dynamical systems. These algorithms are extended in two different directions: the algorithms are generalized so that they apply to differential operators on groups and the data structures and algorithms are developed to compute symbolically the action of differential operators on functions. Both of these generalizations are needed for applications.

  19. Optimizing nondecomposable loss functions in structured prediction.

    PubMed

    Ranjbar, Mani; Lan, Tian; Wang, Yang; Robinovitch, Steven N; Li, Ze-Nian; Mori, Greg

    2013-04-01

    We develop an algorithm for structured prediction with nondecomposable performance measures. The algorithm learns parameters of Markov Random Fields (MRFs) and can be applied to multivariate performance measures. Examples include performance measures such as Fβ score (natural language processing), intersection over union (object category segmentation), Precision/Recall at k (search engines), and ROC area (binary classifiers). We attack this optimization problem by approximating the loss function with a piecewise linear function. The loss augmented inference forms a Quadratic Program (QP), which we solve using LP relaxation. We apply this approach to two tasks: object class-specific segmentation and human action retrieval from videos. We show significant improvement over baseline approaches that either use simple loss functions or simple scoring functions on the PASCAL VOC and H3D Segmentation datasets, and a nursing home action recognition dataset.

  20. Parental education predicts corticostriatal functionality in adulthood.

    PubMed

    Gianaros, Peter J; Manuck, Stephen B; Sheu, Lei K; Kuan, Dora C H; Votruba-Drzal, Elizabeth; Craig, Anna E; Hariri, Ahmad R

    2011-04-01

    Socioeconomic disadvantage experienced in early development predicts ill health in adulthood. However, the neurobiological pathways linking early disadvantage to adult health remain unclear. Lower parental education-a presumptive indicator of early socioeconomic disadvantage-predicts health-impairing adult behaviors, including tobacco and alcohol dependencies. These behaviors depend, in part, on the functionality of corticostriatal brain systems that 1) show developmental plasticity and early vulnerability, 2) process reward-related information, and 3) regulate impulsive decisions and actions. Hence, corticostriatal functionality in adulthood may covary directly with indicators of early socioeconomic disadvantage, particularly lower parental education. Here, we tested the covariation between parental education and corticostriatal activation and connectivity in 76 adults without confounding clinical syndromes. Corticostriatal activation and connectivity were assessed during the processing of stimuli signaling monetary gains (positive feedback [PF]) and losses (negative feedback). After accounting for participants' own education and other explanatory factors, lower parental education predicted reduced activation in anterior cingulate and dorsomedial prefrontal cortices during PF, along with reduced connectivity between these cortices and orbitofrontal and striatal areas implicated in reward processing and impulse regulation. In speculation, adult alterations in corticostriatal functionality may represent facets of a neurobiological endophenotype linked to socioeconomic conditions of early development.

  1. Parental Education Predicts Corticostriatal Functionality in Adulthood

    PubMed Central

    Manuck, Stephen B.; Sheu, Lei K.; Kuan, Dora C. H.; Votruba-Drzal, Elizabeth; Craig, Anna E.; Hariri, Ahmad R.

    2011-01-01

    Socioeconomic disadvantage experienced in early development predicts ill health in adulthood. However, the neurobiological pathways linking early disadvantage to adult health remain unclear. Lower parental education—a presumptive indicator of early socioeconomic disadvantage—predicts health-impairing adult behaviors, including tobacco and alcohol dependencies. These behaviors depend, in part, on the functionality of corticostriatal brain systems that 1) show developmental plasticity and early vulnerability, 2) process reward-related information, and 3) regulate impulsive decisions and actions. Hence, corticostriatal functionality in adulthood may covary directly with indicators of early socioeconomic disadvantage, particularly lower parental education. Here, we tested the covariation between parental education and corticostriatal activation and connectivity in 76 adults without confounding clinical syndromes. Corticostriatal activation and connectivity were assessed during the processing of stimuli signaling monetary gains (positive feedback [PF]) and losses (negative feedback). After accounting for participants’ own education and other explanatory factors, lower parental education predicted reduced activation in anterior cingulate and dorsomedial prefrontal cortices during PF, along with reduced connectivity between these cortices and orbitofrontal and striatal areas implicated in reward processing and impulse regulation. In speculation, adult alterations in corticostriatal functionality may represent facets of a neurobiological endophenotype linked to socioeconomic conditions of early development. PMID:20810623

  2. Teachers' Self-Efficacy vs. Parental Involvement: Prediction and Implementation

    ERIC Educational Resources Information Center

    Fisher, Yael; Kostelitz, Yifat

    2015-01-01

    This research examines the influence of teachers' views regarding parental involvement on their perception of self-efficacy. Data were collected from a sample of 319 Israeli elementary schools teachers. A path analysis procedure was employed to test the mediating effect of personal background and organizational variables and perceived parental…

  3. Mining phenotypes for gene function prediction

    PubMed Central

    Groth, Philip; Weiss, Bertram; Pohlenz, Hans-Dieter; Leser, Ulf

    2008-01-01

    Background Health and disease of organisms are reflected in their phenotypes. Often, a genetic component to a disease is discovered only after clearly defining its phenotype. In the past years, many technologies to systematically generate phenotypes in a high-throughput manner, such as RNA interference or gene knock-out, have been developed and used to decipher functions for genes. However, there have been relatively few efforts to make use of phenotype data beyond the single genotype-phenotype relationships. Results We present results on a study where we use a large set of phenotype data – in textual form – to predict gene annotation. To this end, we use text clustering to group genes based on their phenotype descriptions. We show that these clusters correlate well with several indicators for biological coherence in gene groups, such as functional annotations from the Gene Ontology (GO) and protein-protein interactions. We exploit these clusters for predicting gene function by carrying over annotations from well-annotated genes to other, less-characterized genes in the same cluster. For a subset of groups selected by applying objective criteria, we can predict GO-term annotations from the biological process sub-ontology with up to 72.6% precision and 16.7% recall, as evaluated by cross-validation. We manually verified some of these clusters and found them to exhibit high biological coherence, e.g. a group containing all available antennal Drosophila odorant receptors despite inconsistent GO-annotations. Conclusion The intrinsic nature of phenotypes to visibly reflect genetic activity underlines their usefulness in inferring new gene functions. Thus, systematically analyzing these data on a large scale offers many possibilities for inferring functional annotation of genes. We show that text clustering can play an important role in this process. PMID:18315868

  4. Characterization and Prediction of Chemical Functions and ...

    EPA Pesticide Factsheets

    Assessing exposures from the thousands of chemicals in commerce requires quantitative information on the chemical constituents of consumer products. Unfortunately, gaps in available composition data prevent assessment of exposure to chemicals in many products. Here we propose filling these gaps via consideration of chemical functional role. We obtained function information for thousands of chemicals from public sources and used a clustering algorithm to assign chemicals into 35 harmonized function categories (e.g., plasticizers, antimicrobials, solvents). We combined these functions with weight fraction data for 4115 personal care products (PCPs) to characterize the composition of 66 different product categories (e.g., shampoos). We analyzed the combined weight fraction/function dataset using machine learning techniques to develop quantitative structure property relationship (QSPR) classifier models for 22 functions and for weight fraction, based on chemical-specific descriptors (including chemical properties). We applied these classifier models to a library of 10196 data-poor chemicals. Our predictions of chemical function and composition will inform exposure-based screening of chemicals in PCPs for combination with hazard data in risk-based evaluation frameworks. As new information becomes available, this approach can be applied to other classes of products and the chemicals they contain in order to provide essential consumer product data for use in exposure-b

  5. SitesIdentify: a protein functional site prediction tool

    PubMed Central

    2009-01-01

    Background The rate of protein structures being deposited in the Protein Data Bank surpasses the capacity to experimentally characterise them and therefore computational methods to analyse these structures have become increasingly important. Identifying the region of the protein most likely to be involved in function is useful in order to gain information about its potential role. There are many available approaches to predict functional site, but many are not made available via a publicly-accessible application. Results Here we present a functional site prediction tool (SitesIdentify), based on combining sequence conservation information with geometry-based cleft identification, that is freely available via a web-server. We have shown that SitesIdentify compares favourably to other functional site prediction tools in a comparison of seven methods on a non-redundant set of 237 enzymes with annotated active sites. Conclusion SitesIdentify is able to produce comparable accuracy in predicting functional sites to its closest available counterpart, but in addition achieves improved accuracy for proteins with few characterised homologues. SitesIdentify is available via a webserver at http://www.manchester.ac.uk/bioinformatics/sitesidentify/ PMID:19922660

  6. Children on the Autism Spectrum: Grandmother Involvement and Family Functioning

    ERIC Educational Resources Information Center

    Sullivan, Alison; Winograd, Greta; Verkuilen, Jay; Fish, Marian C.

    2012-01-01

    Background: This study investigated associations between the presence of a child with autism or Asperger's disorder in the family, family functioning and grandmother experiences with the goal of better understanding grandparent involvement in the lives of grandchildren on the autism spectrum and their families. Methods: Mothers and grandmothers of…

  7. Children on the Autism Spectrum: Grandmother Involvement and Family Functioning

    ERIC Educational Resources Information Center

    Sullivan, Alison; Winograd, Greta; Verkuilen, Jay; Fish, Marian C.

    2012-01-01

    Background: This study investigated associations between the presence of a child with autism or Asperger's disorder in the family, family functioning and grandmother experiences with the goal of better understanding grandparent involvement in the lives of grandchildren on the autism spectrum and their families. Methods: Mothers and grandmothers of…

  8. Graph pyramids for protein function prediction

    PubMed Central

    2015-01-01

    Background Uncovering the hidden organizational characteristics and regularities among biological sequences is the key issue for detailed understanding of an underlying biological phenomenon. Thus pattern recognition from nucleic acid sequences is an important affair for protein function prediction. As proteins from the same family exhibit similar characteristics, homology based approaches predict protein functions via protein classification. But conventional classification approaches mostly rely on the global features by considering only strong protein similarity matches. This leads to significant loss of prediction accuracy. Methods Here we construct the Protein-Protein Similarity (PPS) network, which captures the subtle properties of protein families. The proposed method considers the local as well as the global features, by examining the interactions among 'weakly interacting proteins' in the PPS network and by using hierarchical graph analysis via the graph pyramid. Different underlying properties of the protein families are uncovered by operating the proposed graph based features at various pyramid levels. Results Experimental results on benchmark data sets show that the proposed hierarchical voting algorithm using graph pyramid helps to improve computational efficiency as well the protein classification accuracy. Quantitatively, among 14,086 test sequences, on an average the proposed method misclassified only 21.1 sequences whereas baseline BLAST score based global feature matching method misclassified 362.9 sequences. With each correctly classified test sequence, the fast incremental learning ability of the proposed method further enhances the training model. Thus it has achieved more than 96% protein classification accuracy using only 20% per class training data. PMID:26044522

  9. Graph pyramids for protein function prediction.

    PubMed

    Sandhan, Tushar; Yoo, Youngjun; Choi, Jin; Kim, Sun

    2015-01-01

    Uncovering the hidden organizational characteristics and regularities among biological sequences is the key issue for detailed understanding of an underlying biological phenomenon. Thus pattern recognition from nucleic acid sequences is an important affair for protein function prediction. As proteins from the same family exhibit similar characteristics, homology based approaches predict protein functions via protein classification. But conventional classification approaches mostly rely on the global features by considering only strong protein similarity matches. This leads to significant loss of prediction accuracy. Here we construct the Protein-Protein Similarity (PPS) network, which captures the subtle properties of protein families. The proposed method considers the local as well as the global features, by examining the interactions among 'weakly interacting proteins' in the PPS network and by using hierarchical graph analysis via the graph pyramid. Different underlying properties of the protein families are uncovered by operating the proposed graph based features at various pyramid levels. Experimental results on benchmark data sets show that the proposed hierarchical voting algorithm using graph pyramid helps to improve computational efficiency as well the protein classification accuracy. Quantitatively, among 14,086 test sequences, on an average the proposed method misclassified only 21.1 sequences whereas baseline BLAST score based global feature matching method misclassified 362.9 sequences. With each correctly classified test sequence, the fast incremental learning ability of the proposed method further enhances the training model. Thus it has achieved more than 96% protein classification accuracy using only 20% per class training data.

  10. Prediction of protein function from protein sequence and structure.

    PubMed

    Whisstock, James C; Lesk, Arthur M

    2003-08-01

    The sequence of a genome contains the plans of the possible life of an organism, but implementation of genetic information depends on the functions of the proteins and nucleic acids that it encodes. Many individual proteins of known sequence and structure present challenges to the understanding of their function. In particular, a number of genes responsible for diseases have been identified but their specific functions are unknown. Whole-genome sequencing projects are a major source of proteins of unknown function. Annotation of a genome involves assignment of functions to gene products, in most cases on the basis of amino-acid sequence alone. 3D structure can aid the assignment of function, motivating the challenge of structural genomics projects to make structural information available for novel uncharacterized proteins. Structure-based identification of homologues often succeeds where sequence-alone-based methods fail, because in many cases evolution retains the folding pattern long after sequence similarity becomes undetectable. Nevertheless, prediction of protein function from sequence and structure is a difficult problem, because homologous proteins often have different functions. Many methods of function prediction rely on identifying similarity in sequence and/or structure between a protein of unknown function and one or more well-understood proteins. Alternative methods include inferring conservation patterns in members of a functionally uncharacterized family for which many sequences and structures are known. However, these inferences are tenuous. Such methods provide reasonable guesses at function, but are far from foolproof. It is therefore fortunate that the development of whole-organism approaches and comparative genomics permits other approaches to function prediction when the data are available. These include the use of protein-protein interaction patterns, and correlations between occurrences of related proteins in different organisms, as

  11. STRING: a database of predicted functional associations between proteins.

    PubMed

    von Mering, Christian; Huynen, Martijn; Jaeggi, Daniel; Schmidt, Steffen; Bork, Peer; Snel, Berend

    2003-01-01

    Functional links between proteins can often be inferred from genomic associations between the genes that encode them: groups of genes that are required for the same function tend to show similar species coverage, are often located in close proximity on the genome (in prokaryotes), and tend to be involved in gene-fusion events. The database STRING is a precomputed global resource for the exploration and analysis of these associations. Since the three types of evidence differ conceptually, and the number of predicted interactions is very large, it is essential to be able to assess and compare the significance of individual predictions. Thus, STRING contains a unique scoring-framework based on benchmarks of the different types of associations against a common reference set, integrated in a single confidence score per prediction. The graphical representation of the network of inferred, weighted protein interactions provides a high-level view of functional linkage, facilitating the analysis of modularity in biological processes. STRING is updated continuously, and currently contains 261 033 orthologs in 89 fully sequenced genomes. The database predicts functional interactions at an expected level of accuracy of at least 80% for more than half of the genes; it is online at http://www.bork.embl-heidelberg.de/STRING/.

  12. Predictive Factors Involved in Development of Postoperative Pulmonary Complications.

    PubMed

    Saraçoğlu, Ayten; Yavru, Ayşen; Küçükgöncü, Semra; Tüzüner, Filiz; Karadeniz, Meltem; Başaran, Burcu; Şentürk, Nüzhet Mert

    2014-12-01

    In the present study, we applied the method of the multi-center Prospective Evaluation of a Risk Score for postoperative pulmonary Complications in Europe (PERISCOPE) study, which was designed to predict postoperative complications and funded by the European Society of Anaesthesiology, to patients in our institution with the aim of prospectively analyzing the postoperative risk factors of pulmonary complications. One hundred patients over 18 years of age who had emergency or elective non-thoracic or non-obstetric surgery under general anaesthesia or neuraxial blocks were included in the study. Collected data regarding the preoperative and postoperative period were filled in separate forms for all patients. A total of 11 patients developed pulmonary complications. We observed respiratory failure in 8 patients, pleural effusion in 3 patients, atelectasis in 5 patients, bronchospasm in 3 patients, and pneumothorax in 1 patient. In the univariate logistic regression model, patient age, gender, weight, rate of preoperative respiratory symptoms, cough test results, American Society of Anesthesiology (ASA) score, and the duration of surgery did not significantly increase the complication risk (p>0.05). However, in the univariate logistic regression model, the presence of respiratory symptoms increased the risk for complications approximately 5.34-fold (p=0.014). There was an increase in the possibility of complications in parallel with the increase in the duration of postoperative hospital stay (p=0.012). More respiratory symptoms (p=0.019) and longer hospital stay (6.5 vs. 3.5 days respectively, p=0.029) were recorded in patients with postoperative pulmonary complications. Considering patients undergoing non-thoracic or non-obstetric surgery, the prevalence of postoperative pulmonary complications is higher in patients diagnosed with respiratory symptoms in the preoperative period. These complications significantly extend the length of hospital stay.

  13. Executive functions predict conceptual learning of science.

    PubMed

    Rhodes, Sinéad M; Booth, Josephine N; Palmer, Lorna Elise; Blythe, Richard A; Delibegovic, Mirela; Wheate, Nial J

    2016-06-01

    We examined the relationship between executive functions and both factual and conceptual learning of science, specifically chemistry, in early adolescence. Sixty-three pupils in their second year of secondary school (aged 12-13 years) participated. Pupils completed tasks of working memory (Spatial Working Memory), inhibition (Stop-Signal), attention set-shifting (ID/ED), and planning (Stockings of Cambridge), from the CANTAB. They also participated in a chemistry teaching session, practical, and assessment on the topic of acids and alkalis designed specifically for this study. Executive function data were related to (1) the chemistry assessment which included aspects of factual and conceptual learning and (2) a recent school science exam. Correlational analyses between executive functions and both the chemistry assessment and science grades revealed that science achievements were significantly correlated with working memory. Linear regression analysis revealed that visuospatial working memory ability was predictive of chemistry performance. Interestingly, this relationship was observed solely in relation to the conceptual learning condition of the assessment highlighting the role of executive functions in understanding and applying knowledge about what is learned within science teaching.

  14. Interspecies gene function prediction using semantic similarity.

    PubMed

    Yu, Guoxian; Luo, Wei; Fu, Guangyuan; Wang, Jun

    2016-12-23

    Gene Ontology (GO) is a collaborative project that maintains and develops controlled vocabulary (or terms) to describe the molecular function, biological roles and cellular location of gene products in a hierarchical ontology. GO also provides GO annotations that associate genes with GO terms. GO consortium independently and collaboratively annotate terms to gene products, mainly from model organisms (or species) they are interested in. Due to experiment ethics, research interests of biologists and resources limitations, homologous genes from different species currently are annotated with different terms. These differences can be more attributed to incomplete annotations of genes than to functional difference between them. Semantic similarity between genes is derived from GO hierarchy and annotations of genes. It is positively correlated with the similarity derived from various types of biological data and has been applied to predict gene function. In this paper, we investigate whether it is possible to replenish annotations of incompletely annotated genes by using semantic similarity between genes from two species with homology. For this investigation, we utilize three representative semantic similarity metrics to compute similarity between genes from two species. Next, we determine the k nearest neighborhood genes from the two species based on the chosen metric and then use terms annotated to k neighbors of a gene to replenish annotations of that gene. We perform experiments on archived (from Jan-2014 to Jan-2016) GO annotations of four species (Human, Mouse, Danio rerio and Arabidopsis thaliana) to assess the contribution of semantic similarity between genes from different species. The experimental results demonstrate that: (1) semantic similarity between genes from homologous species contributes much more on the improved accuracy (by 53.22%) than genes from single species alone, and genes from two species with low homology; (2) GO annotations of genes from

  15. Identification of Resting State Networks Involved in Executive Function.

    PubMed

    Connolly, Joanna; McNulty, Jonathan P; Boran, Lorraine; Roche, Richard A P; Delany, David; Bokde, Arun L W

    2016-06-01

    The structural networks in the human brain are consistent across subjects, and this is reflected also in that functional networks across subjects are relatively consistent. These findings are not only present during performance of a goal oriented task but there are also consistent functional networks during resting state. It suggests that goal oriented activation patterns may be a function of component networks identified using resting state. The current study examines the relationship between resting state networks measured and patterns of neural activation elicited during a Stroop task. The association between the Stroop-activated networks and the resting state networks was quantified using spatial linear regression. In addition, we investigated if the degree of spatial association of resting state networks with the Stroop task may predict performance on the Stroop task. The results of this investigation demonstrated that the Stroop activated network can be decomposed into a number of resting state networks, which were primarily associated with attention, executive function, visual perception, and the default mode network. The close spatial correspondence between the functional organization of the resting brain and task-evoked patterns supports the relevance of resting state networks in cognitive function.

  16. Functional limitations due to foot involvement in spondyloarthritis

    PubMed Central

    Ozaras, Nihal; Havan, Nuri; Poyraz, Emine; Rezvanı, Aylin; Aydın, Teoman

    2016-01-01

    [Purpose] Spondyloarthritis is a major inflammatory disease followed-up in the rheumatology clinics, foot involvement in spodyloarthritis is common. The functional states of patients with spondyloarthritis are usually evaluated globally. The aim of this study was to assess the foot involvement-related functional limitations in patients with spondyloarthritis. [Subjects and Methods] Patients with ankylosing spondylitis and psoriatic arthritis with foot pain more than 4 weeks who underwent anteroposterior and lateral feet radiography were enrolled into the study. A “clinical findings score” was calculated by assigning 1 point for every finding of swelling, redness, and tenderness. C-reactive protein and erythrocyte sedimentation rate were used as serum markers for disease activity. Foot radiograms were evaluated using the spondyloarthropathy tarsal radiographic index and the foot-related functional state of patients was determined by the Turkish version of the Foot and Ankle Outcome Score. [Results] There were no relationships between Foot and Ankle Outcome Score subscales and clinical findings score, serum markers, or radiologic score. Pain and symptoms subscale scores were result positively correlated with activity of daily living, sport and recreation, and quality of life subscale scores. [Conclusion] Pain and symptoms are the main determinants of foot-related functional limitations in spondyloarthritis. PMID:27512252

  17. Integration of biological data by kernels on graph nodes allows prediction of new genes involved in mitotic chromosome condensation

    PubMed Central

    Hériché, Jean-Karim; Lees, Jon G.; Morilla, Ian; Walter, Thomas; Petrova, Boryana; Roberti, M. Julia; Hossain, M. Julius; Adler, Priit; Fernández, José M.; Krallinger, Martin; Haering, Christian H.; Vilo, Jaak; Valencia, Alfonso; Ranea, Juan A.; Orengo, Christine; Ellenberg, Jan

    2014-01-01

    The advent of genome-wide RNA interference (RNAi)–based screens puts us in the position to identify genes for all functions human cells carry out. However, for many functions, assay complexity and cost make genome-scale knockdown experiments impossible. Methods to predict genes required for cell functions are therefore needed to focus RNAi screens from the whole genome on the most likely candidates. Although different bioinformatics tools for gene function prediction exist, they lack experimental validation and are therefore rarely used by experimentalists. To address this, we developed an effective computational gene selection strategy that represents public data about genes as graphs and then analyzes these graphs using kernels on graph nodes to predict functional relationships. To demonstrate its performance, we predicted human genes required for a poorly understood cellular function—mitotic chromosome condensation—and experimentally validated the top 100 candidates with a focused RNAi screen by automated microscopy. Quantitative analysis of the images demonstrated that the candidates were indeed strongly enriched in condensation genes, including the discovery of several new factors. By combining bioinformatics prediction with experimental validation, our study shows that kernels on graph nodes are powerful tools to integrate public biological data and predict genes involved in cellular functions of interest. PMID:24943848

  18. Predicting involvement in prison gang activity: street gang membership, social and psychological factors.

    PubMed

    Wood, Jane L; Alleyne, Emma; Mozova, Katarina; James, Mark

    2014-06-01

    The aim of this study was to examine whether street gang membership, psychological factors, and social factors such as preprison experiences could predict young offenders' involvement in prison gang activity. Data were collected via individual interviews with 188 young offenders held in a Young Offenders Institution in the United Kingdom. Results showed that psychological factors such as the value individuals attached to social status, a social dominance orientation, and antiauthority attitudes were important in predicting young offenders' involvement in prison gang activity. Further important predictors included preimprisonment events such as levels of threat, levels of individual delinquency, and levels of involvement in group crime. Longer current sentences also predicted involvement in prison gang activity. However, street gang membership was not an important predictor of involvement in prison gang activity. These findings have implications for identifying prisoners involved in prison gang activity and for considering the role of psychological factors and group processes in gang research.

  19. Community-Wide Evaluation of Computational Function Prediction.

    PubMed

    Friedberg, Iddo; Radivojac, Predrag

    2017-01-01

    A biological experiment is the most reliable way of assigning function to a protein. However, in the era of high-throughput sequencing, scientists are unable to carry out experiments to determine the function of every single gene product. Therefore, to gain insights into the activity of these molecules and guide experiments, we must rely on computational means to functionally annotate the majority of sequence data. To understand how well these algorithms perform, we have established a challenge involving a broad scientific community in which we evaluate different annotation methods according to their ability to predict the associations between previously unannotated protein sequences and Gene Ontology terms. Here we discuss the rationale, benefits, and issues associated with evaluating computational methods in an ongoing community-wide challenge.

  20. Identification of autosomal regions involved in Drosophila Raf function.

    PubMed Central

    Li, W; Noll, E; Perrimon, N

    2000-01-01

    Raf is an essential downstream effector of activated p21(Ras) (Ras) in transducing proliferation or differentiation signals. Following binding to Ras, Raf is translocated to the plasma membrane, where it is activated by a yet unidentified "Raf activator." In an attempt to identify the Raf activator or additional molecules involved in the Raf signaling pathway, we conducted a genetic screen to identify genomic regions that are required for the biological function of Drosophila Raf (Draf). We tested a collection of chromosomal deficiencies representing approximately 70% of the autosomal euchromatic genomic regions for their abilities to enhance the lethality associated with a hypomorphic viable allele of Draf, Draf(Su2). Of the 148 autosomal deficiencies tested, 23 behaved as dominant enhancers of Draf(Su2), causing lethality in Draf(Su2) hemizygous males. Four of these deficiencies identified genes known to be involved in the Drosophila Ras/Raf (Ras1/Draf) pathway: Ras1, rolled (rl, encoding a MAPK), 14-3-3epsilon, and bowel (bowl). Two additional deficiencies removed the Drosophila Tec and Src homologs, Tec29A and Src64B. We demonstrate that Src64B interacts genetically with Draf and that an activated form of Src64B, when overexpressed in early embryos, causes ectopic expression of the Torso (Tor) receptor tyrosine kinase-target gene tailless. In addition, we show that a mutation in Tec29A partially suppresses a gain-of-function mutation in tor. These results suggest that Tec29A and Src64B are involved in Tor signaling, raising the possibility that they function to activate Draf. Finally, we discovered a genetic interaction between Draf(Su2) and Df(3L)vin5 that revealed a novel role of Draf in limb development. We find that loss of Draf activity causes limb defects, including pattern duplications, consistent with a role for Draf in regulation of engrailed (en) expression in imaginal discs. PMID:11014822

  1. Lenticulostriate Artery Involvement is Predictive of Poor Outcomes in Superficial Middle Cerebral Artery Territory Infarction

    PubMed Central

    Lee, Kijeong; Kim, Eun Hye; Song, Dongbeom; Kim, Young Dae; Nam, Hyo Suk; Lee, Hye Sun

    2017-01-01

    Purpose Patients with superficial middle cerebral artery (MCA) territory infarction may have concomitant lenticulostriate artery (LSA) territory infarction. We investigated the mechanisms thereof and the outcomes of patients with superficial MCA territory infarction according to the presence or absence of LSA involvement. Materials and Methods Consecutive patients with first-ever infarction in the unilateral superficial MCA territory were included in this study. They were divided into the superficial MCA only (SM) group and the superficial MCA plus LSA (SM+L) group. Results Of the 398 patients, 84 patients (21.1%) had LSA involvement (SM+L group). The SM+L group more frequently had significant stenosis of the proximal MCA or carotid artery and high-risk cardioembolic sources. Stroke severity and outcomes were remarkably different between the groups. The SM+L group showed more severe neurologic deficits (National Institute of Health Stroke Scale score 10.8±7.1 vs. 4.0±5.0, p<0.001) and larger infarct in the superficial MCA territory (40.8±62.6 cm3 vs. 10.8±21.8 cm3, p<0.001) than the SM group. A poor functional outcome (mRS >2) at 3 months was more common in the SM+L group (64.3% vs. 15.9%, p<0.001). During a mean follow-up of 26 months, 67 patients died. All-cause (hazard ratio, 2.246) and stroke (hazard ratio, 9.193) mortalities were higher in the SM+L group than the SM group. In multivariate analyses, LSA involvement was an independent predictor of poor functional outcomes and stroke mortality. Conclusion LSA territory involvement is predictive of poor long-term outcomes in patients with superficial MCA territory infarction. PMID:27873504

  2. Dynamic functional brain networks involved in simple visual discrimination learning.

    PubMed

    Fidalgo, Camino; Conejo, Nélida María; González-Pardo, Héctor; Arias, Jorge Luis

    2014-10-01

    Visual discrimination tasks have been widely used to evaluate many types of learning and memory processes. However, little is known about the brain regions involved at different stages of visual discrimination learning. We used cytochrome c oxidase histochemistry to evaluate changes in regional brain oxidative metabolism during visual discrimination learning in a water-T maze at different time points during training. As compared with control groups, the results of the present study reveal the gradual activation of cortical (prefrontal and temporal cortices) and subcortical brain regions (including the striatum and the hippocampus) associated to the mastery of a simple visual discrimination task. On the other hand, the brain regions involved and their functional interactions changed progressively over days of training. Regions associated with novelty, emotion, visuo-spatial orientation and motor aspects of the behavioral task seem to be relevant during the earlier phase of training, whereas a brain network comprising the prefrontal cortex was found along the whole learning process. This study highlights the relevance of functional interactions among brain regions to investigate learning and memory processes. Copyright © 2014 Elsevier Inc. All rights reserved.

  3. Resting state functional connectivity predicts neurofeedback response

    PubMed Central

    Scheinost, Dustin; Stoica, Teodora; Wasylink, Suzanne; Gruner, Patricia; Saksa, John; Pittenger, Christopher; Hampson, Michelle

    2014-01-01

    Tailoring treatments to the specific needs and biology of individual patients—personalized medicine—requires delineation of reliable predictors of response. Unfortunately, these have been slow to emerge, especially in neuropsychiatric disorders. We have recently described a real-time functional magnetic resonance imaging (rt-fMRI) neurofeedback protocol that can reduce contamination-related anxiety, a prominent symptom of many cases of obsessive-compulsive disorder (OCD). Individual response to this intervention is variable. Here we used patterns of brain functional connectivity, as measured by baseline resting-state fMRI (rs-fMRI), to predict improvements in contamination anxiety after neurofeedback training. Activity of a region of the orbitofrontal cortex (OFC) and anterior prefrontal cortex, Brodmann area (BA) 10, associated with contamination anxiety in each subject was measured in real time and presented as a neurofeedback signal, permitting subjects to learn to modulate this target brain region. We have previously reported both enhanced OFC/BA 10 control and improved anxiety in a group of subclinically anxious subjects after neurofeedback. Five individuals with contamination-related OCD who underwent the same protocol also showed improved clinical symptomatology. In both groups, these behavioral improvements were strongly correlated with baseline whole-brain connectivity in the OFC/BA 10, computed from rs-fMRI collected several days prior to neurofeedback training. These pilot data suggest that rs-fMRI can be used to identify individuals likely to benefit from rt-fMRI neurofeedback training to control contamination anxiety. PMID:25309375

  4. Origin and Functional Prediction of Pollen Allergens in Plants.

    PubMed

    Chen, Miaolin; Xu, Jie; Devis, Deborah; Shi, Jianxin; Ren, Kang; Searle, Iain; Zhang, Dabing

    2016-09-01

    Pollen allergies have long been a major pandemic health problem for human. However, the evolutionary events and biological function of pollen allergens in plants remain largely unknown. Here, we report the genome-wide prediction of pollen allergens and their biological function in the dicotyledonous model plant Arabidopsis (Arabidopsis thaliana) and the monocotyledonous model plant rice (Oryza sativa). In total, 145 and 107 pollen allergens were predicted from rice and Arabidopsis, respectively. These pollen allergens are putatively involved in stress responses and metabolic processes such as cell wall metabolism during pollen development. Interestingly, these putative pollen allergen genes were derived from large gene families and became diversified during evolution. Sequence analysis across 25 plant species from green alga to angiosperms suggest that about 40% of putative pollen allergenic proteins existed in both lower and higher plants, while other allergens emerged during evolution. Although a high proportion of gene duplication has been observed among allergen-coding genes, our data show that these genes might have undergone purifying selection during evolution. We also observed that epitopes of an allergen might have a biological function, as revealed by comprehensive analysis of two known allergens, expansin and profilin. This implies a crucial role of conserved amino acid residues in both in planta biological function and allergenicity. Finally, a model explaining how pollen allergens were generated and maintained in plants is proposed. Prediction and systematic analysis of pollen allergens in model plants suggest that pollen allergens were evolved by gene duplication and then functional specification. This study provides insight into the phylogenetic and evolutionary scenario of pollen allergens that will be helpful to future characterization and epitope screening of pollen allergens. © 2016 American Society of Plant Biologists. All rights reserved.

  5. Functional involvement of human discs large tumor suppressor in cytokinesis

    SciTech Connect

    Unno, Kenji; Hanada, Toshihiko; Chishti, Athar H.

    2008-10-15

    Cytokinesis is the final step of cell division that completes the separation of two daughter cells. We found that the human discs large (hDlg) tumor suppressor homologue is functionally involved in cytokinesis. The guanylate kinase (GUK) domain of hDlg mediates the localization of hDlg to the midbody during cytokinesis, and over-expression of the GUK domain in U2OS and HeLa cells impaired cytokinesis. Mouse embryonic fibroblasts (MEFs) derived from dlg mutant mice contained an increased number of multinucleated cells and showed reduced proliferation in culture. A kinesin-like motor protein, GAKIN, which binds directly to the GUK domain of hDlg, exhibited a similar intracellular distribution pattern with hDlg throughout mitosis and localized to the midbody during cytokinesis. However, the targeting of hDlg and GAKIN to the midbody appeared to be independent of each other. The midbody localization of GAKIN required its functional kinesin-motor domain. Treatment of cells with the siRNA specific for hDlg and GAKIN caused formation of multinucleated cells and delayed cytokinesis. Together, these results suggest that hDlg and GAKIN play functional roles in the maintenance of midbody architecture during cytokinesis.

  6. Stably Expressed Genes Involved in Basic Cellular Functions.

    PubMed

    Wang, Kejian; Vijay, Vikrant; Fuscoe, James C

    2017-01-01

    Stably Expressed Genes (SEGs) whose expression varies within a narrow range may be involved in core cellular processes necessary for basic functions. To identify such genes, we re-analyzed existing RNA-Seq gene expression profiles across 11 organs at 4 developmental stages (from immature to old age) in both sexes of F344 rats (n = 4/group; 320 samples). Expression changes (calculated as the maximum expression / minimum expression for each gene) of >19000 genes across organs, ages, and sexes ranged from 2.35 to >109-fold, with a median of 165-fold. The expression of 278 SEGs was found to vary ≤4-fold and these genes were significantly involved in protein catabolism (proteasome and ubiquitination), RNA transport, protein processing, and the spliceosome. Such stability of expression was further validated in human samples where the expression variability of the homologous human SEGs was significantly lower than that of other genes in the human genome. It was also found that the homologous human SEGs were generally less subject to non-synonymous mutation than other genes, as would be expected of stably expressed genes. We also found that knockout of SEG homologs in mouse models was more likely to cause complete preweaning lethality than non-SEG homologs, corroborating the fundamental roles played by SEGs in biological development. Such stably expressed genes and pathways across life-stages suggest that tight control of these processes is important in basic cellular functions and that perturbation by endogenous (e.g., genetics) or exogenous agents (e.g., drugs, environmental factors) may cause serious adverse effects.

  7. Stably Expressed Genes Involved in Basic Cellular Functions

    PubMed Central

    Wang, Kejian; Fuscoe, James C.

    2017-01-01

    Stably Expressed Genes (SEGs) whose expression varies within a narrow range may be involved in core cellular processes necessary for basic functions. To identify such genes, we re-analyzed existing RNA-Seq gene expression profiles across 11 organs at 4 developmental stages (from immature to old age) in both sexes of F344 rats (n = 4/group; 320 samples). Expression changes (calculated as the maximum expression / minimum expression for each gene) of >19000 genes across organs, ages, and sexes ranged from 2.35 to >109-fold, with a median of 165-fold. The expression of 278 SEGs was found to vary ≤4-fold and these genes were significantly involved in protein catabolism (proteasome and ubiquitination), RNA transport, protein processing, and the spliceosome. Such stability of expression was further validated in human samples where the expression variability of the homologous human SEGs was significantly lower than that of other genes in the human genome. It was also found that the homologous human SEGs were generally less subject to non-synonymous mutation than other genes, as would be expected of stably expressed genes. We also found that knockout of SEG homologs in mouse models was more likely to cause complete preweaning lethality than non-SEG homologs, corroborating the fundamental roles played by SEGs in biological development. Such stably expressed genes and pathways across life-stages suggest that tight control of these processes is important in basic cellular functions and that perturbation by endogenous (e.g., genetics) or exogenous agents (e.g., drugs, environmental factors) may cause serious adverse effects. PMID:28125669

  8. Resting-state functional connectivity predicts longitudinal change in autistic traits and adaptive functioning in autism.

    PubMed

    Plitt, Mark; Barnes, Kelly Anne; Wallace, Gregory L; Kenworthy, Lauren; Martin, Alex

    2015-12-01

    Although typically identified in early childhood, the social communication symptoms and adaptive behavior deficits that are characteristic of autism spectrum disorder (ASD) persist throughout the lifespan. Despite this persistence, even individuals without cooccurring intellectual disability show substantial heterogeneity in outcomes. Previous studies have found various behavioral assessments [such as intelligence quotient (IQ), early language ability, and baseline autistic traits and adaptive behavior scores] to be predictive of outcome, but most of the variance in functioning remains unexplained by such factors. In this study, we investigated to what extent functional brain connectivity measures obtained from resting-state functional connectivity MRI (rs-fcMRI) could predict the variance left unexplained by age and behavior (follow-up latency and baseline autistic traits and adaptive behavior scores) in two measures of outcome--adaptive behaviors and autistic traits at least 1 y postscan (mean follow-up latency = 2 y, 10 mo). We found that connectivity involving the so-called salience network (SN), default-mode network (DMN), and frontoparietal task control network (FPTCN) was highly predictive of future autistic traits and the change in autistic traits and adaptive behavior over the same time period. Furthermore, functional connectivity involving the SN, which is predominantly composed of the anterior insula and the dorsal anterior cingulate, predicted reliable improvement in adaptive behaviors with 100% sensitivity and 70.59% precision. From rs-fcMRI data, our study successfully predicted heterogeneity in outcomes for individuals with ASD that was unaccounted for by simple behavioral metrics and provides unique evidence for networks underlying long-term symptom abatement.

  9. Resting-state functional connectivity predicts longitudinal change in autistic traits and adaptive functioning in autism

    PubMed Central

    Plitt, Mark; Barnes, Kelly Anne; Wallace, Gregory L.; Kenworthy, Lauren; Martin, Alex

    2015-01-01

    Although typically identified in early childhood, the social communication symptoms and adaptive behavior deficits that are characteristic of autism spectrum disorder (ASD) persist throughout the lifespan. Despite this persistence, even individuals without cooccurring intellectual disability show substantial heterogeneity in outcomes. Previous studies have found various behavioral assessments [such as intelligence quotient (IQ), early language ability, and baseline autistic traits and adaptive behavior scores] to be predictive of outcome, but most of the variance in functioning remains unexplained by such factors. In this study, we investigated to what extent functional brain connectivity measures obtained from resting-state functional connectivity MRI (rs-fcMRI) could predict the variance left unexplained by age and behavior (follow-up latency and baseline autistic traits and adaptive behavior scores) in two measures of outcome—adaptive behaviors and autistic traits at least 1 y postscan (mean follow-up latency = 2 y, 10 mo). We found that connectivity involving the so-called salience network (SN), default-mode network (DMN), and frontoparietal task control network (FPTCN) was highly predictive of future autistic traits and the change in autistic traits and adaptive behavior over the same time period. Furthermore, functional connectivity involving the SN, which is predominantly composed of the anterior insula and the dorsal anterior cingulate, predicted reliable improvement in adaptive behaviors with 100% sensitivity and 70.59% precision. From rs-fcMRI data, our study successfully predicted heterogeneity in outcomes for individuals with ASD that was unaccounted for by simple behavioral metrics and provides unique evidence for networks underlying long-term symptom abatement. PMID:26627261

  10. Text Mining Improves Prediction of Protein Functional Sites

    PubMed Central

    Cohn, Judith D.; Ravikumar, Komandur E.

    2012-01-01

    We present an approach that integrates protein structure analysis and text mining for protein functional site prediction, called LEAP-FS (Literature Enhanced Automated Prediction of Functional Sites). The structure analysis was carried out using Dynamics Perturbation Analysis (DPA), which predicts functional sites at control points where interactions greatly perturb protein vibrations. The text mining extracts mentions of residues in the literature, and predicts that residues mentioned are functionally important. We assessed the significance of each of these methods by analyzing their performance in finding known functional sites (specifically, small-molecule binding sites and catalytic sites) in about 100,000 publicly available protein structures. The DPA predictions recapitulated many of the functional site annotations and preferentially recovered binding sites annotated as biologically relevant vs. those annotated as potentially spurious. The text-based predictions were also substantially supported by the functional site annotations: compared to other residues, residues mentioned in text were roughly six times more likely to be found in a functional site. The overlap of predictions with annotations improved when the text-based and structure-based methods agreed. Our analysis also yielded new high-quality predictions of many functional site residues that were not catalogued in the curated data sources we inspected. We conclude that both DPA and text mining independently provide valuable high-throughput protein functional site predictions, and that integrating the two methods using LEAP-FS further improves the quality of these predictions. PMID:22393388

  11. A Prediction Model of the Capillary Pressure J-Function

    PubMed Central

    Xu, W. S.; Luo, P. Y.; Sun, L.; Lin, N.

    2016-01-01

    The capillary pressure J-function is a dimensionless measure of the capillary pressure of a fluid in a porous medium. The function was derived based on a capillary bundle model. However, the dependence of the J-function on the saturation Sw is not well understood. A prediction model for it is presented based on capillary pressure model, and the J-function prediction model is a power function instead of an exponential or polynomial function. Relative permeability is calculated with the J-function prediction model, resulting in an easier calculation and results that are more representative. PMID:27603701

  12. Internalization of isolated functional mitochondria: involvement of macropinocytosis

    PubMed Central

    Kitani, Tomoya; Kami, Daisuke; Matoba, Satoaki; Gojo, Satoshi

    2014-01-01

    In eukaryotic cells, mitochondrial dysfunction is associated with a variety of human diseases. Delivery of exogenous functional mitochondria into damaged cells has been proposed as a mechanism of cell transplant and physiological repair for damaged tissue. We here demonstrated that isolated mitochondria can be transferred into homogeneic and xenogeneic cells by simple co-incubation using genetically labelled mitochondria, and elucidated the mechanism and the effect of direct mitochondrial transfer. Intracellular localization of exogenous mitochondria was confirmed by PCR, real-time PCR, live fluorescence imaging, three-dimensional reconstruction imaging, continuous time-lapse microscopic observation, flow cytometric analysis and immunoelectron microscopy. Isolated homogeneic mitochondria were transferred into human uterine endometrial gland-derived mesenchymal cells in a dose-dependent manner. Moreover, mitochondrial transfer rescued the mitochondrial respiratory function and improved the cellular viability in mitochondrial DNA-depleted cells and these effects lasted several days. Finally, we discovered that mitochondrial internalization involves macropinocytosis. In conclusion, these data support direct transfer of exogenous mitochondria as a promising approach for the treatment of various diseases. PMID:24912369

  13. Functional type 1 secretion system involved in Legionella pneumophila virulence.

    PubMed

    Fuche, Fabien; Vianney, Anne; Andrea, Claire; Doublet, Patricia; Gilbert, Christophe

    2015-02-01

    Legionella pneumophila is a Gram-negative pathogen found mainly in water, either in a free-living form or within infected protozoans, where it replicates. This bacterium can also infect humans by inhalation of contaminated aerosols, causing a severe form of pneumonia called legionellosis or Legionnaires' disease. The involvement of type II and IV secretion systems in the virulence of L. pneumophila is now well documented. Despite bioinformatic studies showing that a type I secretion system (T1SS) could be present in this pathogen, the functionality of this system based on the LssB, LssD, and TolC proteins has never been established. Here, we report the demonstration of the functionality of the T1SS, as well as its role in the infectious cycle of L. pneumophila. Using deletion mutants and fusion proteins, we demonstrated that the repeats-in-toxin protein RtxA is secreted through an LssB-LssD-TolC-dependent mechanism. Moreover, fluorescence monitoring and confocal microscopy showed that this T1SS is required for entry into the host cell, although it seems dispensable to the intracellular cycle. Together, these results underline the active participation of L. pneumophila, via its T1SS, in its internalization into host cells.

  14. Internalization of isolated functional mitochondria: involvement of macropinocytosis.

    PubMed

    Kitani, Tomoya; Kami, Daisuke; Matoba, Satoaki; Gojo, Satoshi

    2014-08-01

    In eukaryotic cells, mitochondrial dysfunction is associated with a variety of human diseases. Delivery of exogenous functional mitochondria into damaged cells has been proposed as a mechanism of cell transplant and physiological repair for damaged tissue. We here demonstrated that isolated mitochondria can be transferred into homogeneic and xenogeneic cells by simple co-incubation using genetically labelled mitochondria, and elucidated the mechanism and the effect of direct mitochondrial transfer. Intracellular localization of exogenous mitochondria was confirmed by PCR, real-time PCR, live fluorescence imaging, three-dimensional reconstruction imaging, continuous time-lapse microscopic observation, flow cytometric analysis and immunoelectron microscopy. Isolated homogeneic mitochondria were transferred into human uterine endometrial gland-derived mesenchymal cells in a dose-dependent manner. Moreover, mitochondrial transfer rescued the mitochondrial respiratory function and improved the cellular viability in mitochondrial DNA-depleted cells and these effects lasted several days. Finally, we discovered that mitochondrial internalization involves macropinocytosis. In conclusion, these data support direct transfer of exogenous mitochondria as a promising approach for the treatment of various diseases.

  15. CombFunc: predicting protein function using heterogeneous data sources.

    PubMed

    Wass, Mark N; Barton, Geraint; Sternberg, Michael J E

    2012-07-01

    Only a small fraction of known proteins have been functionally characterized, making protein function prediction essential to propose annotations for uncharacterized proteins. In recent years many function prediction methods have been developed using various sources of biological data from protein sequence and structure to gene expression data. Here we present the CombFunc web server, which makes Gene Ontology (GO)-based protein function predictions. CombFunc incorporates ConFunc, our existing function prediction method, with other approaches for function prediction that use protein sequence, gene expression and protein-protein interaction data. In benchmarking on a set of 1686 proteins CombFunc obtains precision and recall of 0.71 and 0.64 respectively for gene ontology molecular function terms. For biological process GO terms precision of 0.74 and recall of 0.41 is obtained. CombFunc is available at http://www.sbg.bio.ic.ac.uk/combfunc.

  16. Which Working Memory Functions Predict Intelligence?

    ERIC Educational Resources Information Center

    Oberauer, Klaus; Sub, Heinz-Martin; Wilhelm, Oliver; Wittmann, Werner W.

    2008-01-01

    Investigates the relationship between three factors of working memory (storage and processing, relational integration, and supervision) and four factors of intelligence (reasoning, speed, memory, and creativity) using structural equation models. Relational integration predicted reasoning ability at least as well as the storage-and-processing…

  17. Protein Function Prediction: Towards Integration of Similarity Metrics

    PubMed Central

    Erdin, Serkan; Lisewski, Andreas Martin; Lichtarge, Olivier

    2011-01-01

    Summary Genomics centers discover increasingly many protein sequences and structures, but not necessarily their full biological functions. Thus, currently, fewer than one percent of proteins have experimentally verified biochemical activities. To fill this gap, function prediction algorithms apply metrics of similarity between proteins on the premise that those sufficiently alike in sequence, or structure, will perform identical functions. Although high sensitivity is elusive, network analyses that integrate these metrics together hold the promise of rapid gains in function prediction specificity. PMID:21353529

  18. Functional brain network efficiency predicts intelligence.

    PubMed

    Langer, Nicolas; Pedroni, Andreas; Gianotti, Lorena R R; Hänggi, Jürgen; Knoch, Daria; Jäncke, Lutz

    2012-06-01

    The neuronal causes of individual differences in mental abilities such as intelligence are complex and profoundly important. Understanding these abilities has the potential to facilitate their enhancement. The purpose of this study was to identify the functional brain network characteristics and their relation to psychometric intelligence. In particular, we examined whether the functional network exhibits efficient small-world network attributes (high clustering and short path length) and whether these small-world network parameters are associated with intellectual performance. High-density resting state electroencephalography (EEG) was recorded in 74 healthy subjects to analyze graph-theoretical functional network characteristics at an intracortical level. Ravens advanced progressive matrices were used to assess intelligence. We found that the clustering coefficient and path length of the functional network are strongly related to intelligence. Thus, the more intelligent the subjects are the more the functional brain network resembles a small-world network. We further identified the parietal cortex as a main hub of this resting state network as indicated by increased degree centrality that is associated with higher intelligence. Taken together, this is the first study that substantiates the neural efficiency hypothesis as well as the Parieto-Frontal Integration Theory (P-FIT) of intelligence in the context of functional brain network characteristics. These theories are currently the most established intelligence theories in neuroscience. Our findings revealed robust evidence of an efficiently organized resting state functional brain network for highly productive cognitions.

  19. Extracurricular Activity and Parental Involvement Predict Positive Outcomes in Elementary School Children

    ERIC Educational Resources Information Center

    Lagace-Seguin, Daniel G.; Case, Emily

    2010-01-01

    The main goal of this study was to explore if parental involvement and extracurricular activity participation could predict well-being and academic competence in elementary school children. Seventy-two children (mean age = 10.9 years, SD = 0.85) and their parents participated. Results revealed that parental pressure and support, when paired with…

  20. No Parent Left Behind: Predicting Parental Involvement in Adolescents' Education within a Sociodemographically Diverse Population

    ERIC Educational Resources Information Center

    Park, Sira; Holloway, Susan D.

    2013-01-01

    Numerous studies have investigated the utility of the Hoover-Dempsey and Sandler (HDS) model for predicting parents' involvement in students' education. Yet, the model has yet to be thoroughly evaluated with respect to youth who are (a) in high school and (b) from sociodemographically diverse families. Using a nationally representative sample of…

  1. Magnetic resonance imaging cannot predict histological tumour involvement of a circumferential surgical margin in rectal cancer.

    PubMed

    Dent, O F; Chapuis, P H; Haboubi, N; Bokey, L

    2011-09-01

    Several recent studies have attempted to evaluate the accuracy of preoperative magnetic resonance imaging (MRI) in predicting the likelihood of tumour involvement of the postoperative circumferential resection margin (CRM) in rectal cancer with the intention of selecting patients who might benefit from neoadjuvant therapy and as a guide to surgery. The aim of this study was to assess whether such studies can provide a valid answer as to whether preoperative MRI can accurately predict CRM involvement by tumour. The study design and methodology of studies on this topic were critically examined. Features identified as affecting the efficacy of these studies were: representativeness of patients, definition of the margin assessed by MRI and by histology, lack of blinding of surgeons and pathologists to MRI results, effect of neoadjuvant treatment, and number of patients studied. Because of methodological inadequacies in studies completed to date, there is insufficient evidence of the ability of a positive MRI result to predict an involved CRM. Although MRI may be able to identify a tumour that has extended to the mesorectal fascia and/or intersphincteric plane, logically, it cannot indicate where the surgical boundary of the resection will ultimately lie, and therefore cannot validly predict an involved CRM and should not be relied upon for this purpose. © 2011 The Authors. Colorectal Disease © 2011 The Association of Coloproctology of Great Britain and Ireland.

  2. The Factorial and Predictive Validities of a Revised Measure of Zaichkowsky's Personal Involvement Inventory.

    ERIC Educational Resources Information Center

    Munson, J. Michael; McQuarrie, Edward F.

    1987-01-01

    A shortened version of Zaichkowsky's 20-item Personal Involvement Inventory was created, removing four items which might be difficult to understand for noncollege-educated populations. The 16-item modified version had acceptable internal consistency; test-retest reliability; and factorial and predictive validity. (Author/GDC)

  3. No Parent Left Behind: Predicting Parental Involvement in Adolescents' Education within a Sociodemographically Diverse Population

    ERIC Educational Resources Information Center

    Park, Sira; Holloway, Susan D.

    2013-01-01

    Numerous studies have investigated the utility of the Hoover-Dempsey and Sandler (HDS) model for predicting parents' involvement in students' education. Yet, the model has yet to be thoroughly evaluated with respect to youth who are (a) in high school and (b) from sociodemographically diverse families. Using a nationally representative sample of…

  4. Pulmonary involvement in diffuse cutaneous systemic sclerosis: broncheoalveolar fluid granulocytosis predicts progression of fibrosing alveolitis

    PubMed Central

    Witt, C.; Borges, A.; John, M.; Fietze, I.; Baumann, G.; Krause, A.

    1999-01-01

    OBJECTIVE—The clinical course of fibrosing alveolitis (FA) in patients with systemic sclerosis (SSc) may vary considerably from stable condition for years to continuous fatal progression. This prospective study aimed at identifying the prognostic value of bronchoalveolar lavage fluid (BALF) analysis in FASSc.
METHODS—Seventy three consecutive patients with SSc and clinical signs of pulmonary involvement were enrolled. Every patient underwent clinical examination, lung function tests, computed tomography (CT), gallium scan, echocardiography, and bronchoalveolar lavage (BAL). Forty nine patients, 26 with pathological and 23 with normal BALF findings were prospectively followed up for two years and re-evaluated annually.
RESULTS—At baseline, 51 subjects (70%) showed radiological signs of lung fibrosis and/or alveolitis by CT and diffusion capacity for carbon monoxide (DLco) was decreased in 47 patients (64%). Thirty five patients (48%) had pathological BALF findings. BALF differential counts included BALF granulocytosis in 18, BALF lymphocytosis in 12, and a mixed increase of both granulocytes and lymphocytes in five patients. On follow up, a progression of FA with a significant decrease of DLco was only observed in patients with BALF granulocytosis. In contrast, patients with BALF lymphocytosis or normal BALF cell count had stable lung funtion parameters during the study period. In none of our patients echocardiography showed evidence of pulmonary hypertension.
CONCLUSION—BALF granulocytosis predicts progression of FA with deterioration of lung function, which is most sensitively monitored by DLco. Immunosuppressive treatment is recommended in patients with granulocytic FASSc.

 PMID:10491363

  5. MASS FUNCTION PREDICTIONS BEYOND {Lambda}CDM

    SciTech Connect

    Bhattacharya, Suman; Lukic, Zarija; Habib, Salman; Heitmann, Katrin; White, Martin; Wagner, Christian

    2011-05-10

    The statistics of dark matter halos is an essential component of precision cosmology. The mass distribution of halos, as specified by the halo mass function, is a key input for several cosmological probes. The sizes of N-body simulations are now such that, for the most part, results need no longer be statistics-limited, but are still subject to various systematic uncertainties. Discrepancies in the results of simulation campaigns for the halo mass function remain in excess of statistical uncertainties and of roughly the same size as the error limits set by near-future observations; we investigate and discuss some of the reasons for these differences. Quantifying error sources and compensating for them as appropriate, we carry out a high-statistics study of dark matter halos from 67 N-body simulations to investigate the mass function and its evolution for a reference {Lambda}CDM cosmology and for a set of wCDM cosmologies. For the reference {Lambda}CDM cosmology (close to WMAP5), we quantify the breaking of universality in the form of the mass function as a function of redshift, finding an evolution of as much as 10% away from the universal form between redshifts z = 0 and z = 2. For cosmologies very close to this reference we provide a fitting formula to our results for the (evolving) {Lambda}CDM mass function over a mass range of 6 x 10{sup 11}-3 x 10{sup 15} M{sub sun} to an estimated accuracy of about 2%. The set of wCDM cosmologies is taken from the Coyote Universe simulation suite. The mass functions from this suite (which includes a {Lambda}CDM cosmology and others with w {approx_equal} -1) are described by the fitting formula for the reference {Lambda}CDM case at an accuracy level of 10%, but with clear systematic deviations. We argue that, as a consequence, fitting formulae based on a universal form for the mass function may have limited utility in high-precision cosmological applications.

  6. Mass Function Predictions Beyond ΛCDM

    NASA Astrophysics Data System (ADS)

    Bhattacharya, Suman; Heitmann, Katrin; White, Martin; Lukić, Zarija; Wagner, Christian; Habib, Salman

    2011-05-01

    The statistics of dark matter halos is an essential component of precision cosmology. The mass distribution of halos, as specified by the halo mass function, is a key input for several cosmological probes. The sizes of N-body simulations are now such that, for the most part, results need no longer be statistics-limited, but are still subject to various systematic uncertainties. Discrepancies in the results of simulation campaigns for the halo mass function remain in excess of statistical uncertainties and of roughly the same size as the error limits set by near-future observations; we investigate and discuss some of the reasons for these differences. Quantifying error sources and compensating for them as appropriate, we carry out a high-statistics study of dark matter halos from 67 N-body simulations to investigate the mass function and its evolution for a reference ΛCDM cosmology and for a set of wCDM cosmologies. For the reference ΛCDM cosmology (close to WMAP5), we quantify the breaking of universality in the form of the mass function as a function of redshift, finding an evolution of as much as 10% away from the universal form between redshifts z = 0 and z = 2. For cosmologies very close to this reference we provide a fitting formula to our results for the (evolving) ΛCDM mass function over a mass range of 6 × 1011-3 × 1015 M sun to an estimated accuracy of about 2%. The set of wCDM cosmologies is taken from the Coyote Universe simulation suite. The mass functions from this suite (which includes a ΛCDM cosmology and others with w ~= -1) are described by the fitting formula for the reference ΛCDM case at an accuracy level of 10%, but with clear systematic deviations. We argue that, as a consequence, fitting formulae based on a universal form for the mass function may have limited utility in high-precision cosmological applications.

  7. Early executive function predicts reasoning development.

    PubMed

    Richland, Lindsey E; Burchinal, Margaret R

    2013-01-01

    Analogical reasoning is a core cognitive skill that distinguishes humans from all other species and contributes to general fluid intelligence, creativity, and adaptive learning capacities. Yet its origins are not well understood. In the study reported here, we analyzed large-scale longitudinal data from the Study of Early Child Care and Youth Development to test predictors of growth in analogical-reasoning skill from third grade to adolescence. Our results suggest an integrative resolution to the theoretical debate regarding contributory factors arising from smaller-scale, cross-sectional experiments on analogy development. Children with greater executive-function skills (both composite and inhibitory control) and vocabulary knowledge in early elementary school displayed higher scores on a verbal analogies task at age 15 years, even after adjusting for key covariates. We posit that knowledge is a prerequisite to analogy performance, but strong executive-functioning resources during early childhood are related to long-term gains in fundamental reasoning skills.

  8. Do optimism and pessimism predict physical functioning?

    PubMed

    Brenes, Gretchen A; Rapp, Stephen R; Rejeski, W Jack; Miller, Michael E

    2002-06-01

    Dispositional optimism has been shown to be related to self-report measures of health and well-being, yet little research has examined the relationship between optimism and more objective measures of functioning. The purpose of this study was to examine the relationship between optimism and pessimism and objective physical functioning. Four hundred eighty community-dwelling older adults with knee pain completed a measure of optimism and pessimism and were observed performing four daily activities (walking, lifting an object, climbing stairs, and getting into and out of a car). Results indicated that pessimism was significantly related to performance on all four tasks (p < .001), while optimism was related to performance only on the walking task (p < .05), after controlling for demographic and health variables.

  9. Development of a predictive model of Crohn's disease proximal small bowel involvement in capsule endoscopy evaluation.

    PubMed

    Rodrigues-Pinto, Eduardo; Cardoso, Helder; Rosa, Bruno; Santos-Antunes, João; Rodrigues, Susana; Marques, Margarida; Lopes, Susana; Albuquerque, Andreia; Carvalho, Pedro; Moreira, Maria; Cotter, José; Macedo, Guilherme

    2016-06-01

    One of the indications for capsule endoscopy (CE) is the detection of proximal small bowel (SB) involvement in Crohn's disease (CD) patients. Our aim was to assess clinical, laboratory and endoscopic predictors associated with proximal SB involvement in CD patients submitted to CE. Retrospective multicenter study in which Lewis score (LS) was systematically determined in 190 CE of patients diagnosed with CD between 2003 and 2014. Significant inflammatory activity (LS > 135) was present in 23 % of the patients in the first tertile and in 31 % of the patients in the second tertile. Albumin, haemoglobin, and total proteins were significantly lower in patients with a LS > 790 compared to patients with a LS < 135, while white blood cell counts and C-reactive protein were significantly higher. In the univariable analysis, a higher risk for proximal SB involvement at CE was associated with ileal involvement at ileocolonoscopy (OR 2.858, P = 0.006), higher platelets levels (OR 1.005, P = 0.004) and significant weight loss (OR 2.450, P = 0.006). In logistic regression, ileal involvement at ileocolonoscopy (OR 6.817, P = 0.003), stricturing behavior (OR 8.653, P = 0.011) and significant weight loss (OR 3.629, P = 0.028) were independently associated with proximal SB involvement at CE. Considering the ROC curve of this model, a cut-off > 0.249 predicts proximal SB involvement with 90 % sensitivity and 40 % specificity (AUROC 0.732). One-third of patients had proximal SB involvement. Predictive factors were significant weight loss, stricturing behaviour, and ileal involvement at ileocolonoscopy. These data help to select CD patients that benefit the most from performing a CE.

  10. Improving structure-based function prediction using molecular dynamics

    PubMed Central

    Glazer, Dariya S.; Radmer, Randall J.; Altman, Russ B.

    2009-01-01

    Summary The number of molecules with solved three-dimensional structure but unknown function is increasing rapidly. Particularly problematic are novel folds with little detectable similarity to molecules of known function. Experimental assays can determine the functions of such molecules, but are time-consuming and expensive. Computational approaches can identify potential functional sites; however, these approaches generally rely on single static structures and do not use information about dynamics. In fact, structural dynamics can enhance function prediction: we coupled molecular dynamics simulations with structure-based function prediction algorithms that identify Ca2+ binding sites. When applied to 11 challenging proteins, both methods showed substantial improvement in performance, revealing 22 more sites in one case and 12 more in the other, with a modest increase in apparent false positives. Thus, we show that treating molecules as dynamic entities improves the performance of structure-based function prediction methods. PMID:19604472

  11. A generating function for certain coefficients involving several complex variables.

    PubMed

    Srivastava, H M

    1970-10-01

    In an attempt to unify a number of generating functions for certain classes of generalized hypergeometric polynomials, Lagrange's expansion formula is applied to prove a generating relation for an n-dimensional polynomial with arbitrary coefficients. It is also shown how these coefficients can be specialized to obtain the generalized Lauricella function as a generating function for a class of generalized hypergeometric polynomials of several complex variables.

  12. A predictive index of axillary nodal involvement in operable breast cancer.

    PubMed Central

    De Laurentiis, M.; Gallo, C.; De Placido, S.; Perrone, F.; Pettinato, G.; Petrella, G.; Carlomagno, C.; Panico, L.; Delrio, P.; Bianco, A. R.

    1996-01-01

    We investigated the association between pathological characteristics of primary breast cancer and degree of axillary nodal involvement and obtained a predictive index of the latter from the former. In 2076 cases, 17 histological features, including primary tumour and local invasion variables, were recorded. The whole sample was randomly split in a training (75% of cases) and a test sample. Simple and multiple correspondence analysis were used to select the variables to enter in a multinomial logit model to build an index predictive of the degree of nodal involvement. The response variable was axillary nodal status coded in four classes (N0, N1-3, N4-9, N > or = 10). The predictive index was then evaluated by testing goodness-of-fit and classification accuracy. Covariates significantly associated with nodal status were tumour size (P < 0.0001), tumour type (P < 0.0001), type of border (P = 0.048), multicentricity (P = 0.003), invasion of lymphatic and blood vessels (P < 0.0001) and nipple invasion (P = 0.006). Goodness-of-fit was validated by high concordance between observed and expected number of cases in each decile of predicted probability in both training and test samples. Classification accuracy analysis showed that true node-positive cases were well recognised (84.5%), but there was no clear distinction among the classes of node-positive cases. However, 10 year survival analysis showed a superimposible prognostic behaviour between predicted and observed nodal classes. Moreover, misclassified node-negative patients (i.e. those who are predicted positive) showed an outcome closer to patients with 1-3 metastatic nodes than to node-negative ones. In conclusion, the index cannot completely substitute for axillary node information, but it is a predictor of prognosis as accurate as nodal involvement and identifies a subgroup of node-negative patients with unfavourable prognosis. PMID:8630286

  13. Gene function prediction using labeled and unlabeled data

    PubMed Central

    Zhao, Xing-Ming; Wang, Yong; Chen, Luonan; Aihara, Kazuyuki

    2008-01-01

    Background In general, gene function prediction can be formalized as a classification problem based on machine learning technique. Usually, both labeled positive and negative samples are needed to train the classifier. For the problem of gene function prediction, however, the available information is only about positive samples. In other words, we know which genes have the function of interested, while it is generally unclear which genes do not have the function, i.e. the negative samples. If all the genes outside of the target functional family are seen as negative samples, the imbalanced problem will arise because there are only a relatively small number of genes annotated in each family. Furthermore, the classifier may be degraded by the false negatives in the heuristically generated negative samples. Results In this paper, we present a new technique, namely Annotating Genes with Positive Samples (AGPS), for defining negative samples in gene function prediction. With the defined negative samples, it is straightforward to predict the functions of unknown genes. In addition, the AGPS algorithm is able to integrate various kinds of data sources to predict gene functions in a reliable and accurate manner. With the one-class and two-class Support Vector Machines as the core learning algorithm, the AGPS algorithm shows good performances for function prediction on yeast genes. Conclusion We proposed a new method for defining negative samples in gene function prediction. Experimental results on yeast genes show that AGPS yields good performances on both training and test sets. In addition, the overlapping between prediction results and GO annotations on unknown genes also demonstrates the effectiveness of the proposed method. PMID:18221567

  14. Accurate sperm morphology assessment predicts sperm function.

    PubMed

    Abu Hassan Abu, D; Franken, D R; Hoffman, B; Henkel, R

    2012-05-01

    Sperm morphology has been associated with in vitro as well as in vivo fertilisation. The study aimed to evaluate the possible relation between the percentage of spermatozoa with normal morphology and the following sperm functional assays: (i) zona-induced acrosome reaction (ZIAR); (ii) DNA integrity; (iii) chromatin condensation; (iv) sperm apoptosis; and (v) fertilisation rates. Regression analysis was employed to calculate the association between morphology and different functional tests. Normal sperm morphology correlated significantly with the percentages of live acrosome-reacted spermatozoa in the ZIAR (r = 0.518; P < 0.0001; n = 92), DNA integrity (r = -0.515; P = 0.0018; n = 34), CMA(3) -positive spermatozoa (r = -0.745; P < 0.0001; n = 92), sperm apoptosis (r = -0.395; P = 0.0206; n = 34) and necrosis (r = -0.545; P = 0.0009; n = 34). Negative correlations existed between for the acrosome reaction, and DNA integrity, while negative associations were recorded with the percentages of CMA(3) -positive spermatozoa, apoptotic and necrotic spermatozoa. Sperm morphology is related to sperm dysfunction such as poor chromatin condensation, acrosome reaction and DNA integrity. Negative and significant correlations existed between normal sperm morphology and chromatin condensation, the percentage of spermatozoa with abnormal DNA and spermatozoa with apoptotic activity. The authors do not regard sperm morphology as the only test for the diagnosis of male fertility, but sperm morphology can serve as a valuable indicator of underlying dysfunction.

  15. Taper Functions for Predicting Product Volumes in Natural Shortleaf Pines

    Treesearch

    Robert M. Farrar; Paul A. Murphy

    1987-01-01

    Taper (stem-profile) functions are presented for natural shortleaf pine (Pinus echinata Mill.) trees growing in the West Gulf area. These functions, when integrated, permit the prediction of volume between any two heights on a stem and, conversely by iteration, the volume between any two diameters on a stem. Examples are given of use of the functions...

  16. Motivational functionalism and urban conservation stewardship: implications for volunteer involvement

    Treesearch

    Stanley T. Asah; Dale J. Blahna

    2012-01-01

    Conservation in urban areas faces growing financial challenges and inadequate stakeholder involvement. Conservation psychology can mitigate these challenges in many ways. One way is through conservation volunteerism, if we attend to and capitalize on volunteers' motivations. Conservation volunteerism significantly contributes to ecological knowledge acquisition,...

  17. Dopamine neurons share common response function for reward prediction error

    PubMed Central

    Eshel, Neir; Tian, Ju; Bukwich, Michael; Uchida, Naoshige

    2016-01-01

    Dopamine neurons are thought to signal reward prediction error, or the difference between actual and predicted reward. How dopamine neurons jointly encode this information, however, remains unclear. One possibility is that different neurons specialize in different aspects of prediction error; another is that each neuron calculates prediction error in the same way. We recorded from optogenetically-identified dopamine neurons in the lateral ventral tegmental area (VTA) while mice performed classical conditioning tasks. Our tasks allowed us to determine the full prediction error functions of dopamine neurons and compare them to each other. We found striking homogeneity among individual dopamine neurons: their responses to both unexpected and expected rewards followed the same function, just scaled up or down. As a result, we could describe both individual and population responses using just two parameters. Such uniformity ensures robust information coding, allowing each dopamine neuron to contribute fully to the prediction error signal. PMID:26854803

  18. Early involvement in friendships predicts later plasma concentrations of oxytocin and vasopressin in juvenile rhesus macaques (Macaca mulatta)

    PubMed Central

    Weinstein, Tamara A. R.; Bales, Karen L.; Maninger, Nicole; Hostetler, Caroline M.; Capitanio, John P.

    2014-01-01

    The neuropeptides oxytocin (OT) and arginine vasopressin (AVP) are involved in social bonding in attachment relationships, but their role in friendship is poorly understood. We investigated whether rhesus macaques’ (Macaca mulatta) friendships at age one predicted plasma OT and AVP at two later time points. Subjects were 54 rhesus macaques at the California National Primate Research Center (CNPRC). Blood was drawn during a brief capture-and-release in the home cage, and plasma assayed for OT and AVP using an enzyme immunoassay (EIA). Separate linear mixed models for each sex tested the effects of dominance rank, age, sampling time point, housing condition, parturition status, two blood draw timing measures, and five friendship types: proximity friendships, play friendships, reciprocal friendships (a preference for a peer that also preferred the subject), multiplex friendships (friendships displayed in more than one behavioral domain), and total number of friendships. Females’ number of reciprocal and play friendships at age one significantly predicted later OT; additionally, these two friendship types interacted with rank, such that high-ranking females with the fewest friendships had the highest OT concentrations. Friendship did not predict later OT levels in males, however proximity, play, reciprocal, and total number of friendships predicted males’ plasma AVP. Play and total number of friendships also tended to predict AVP in females. Our results show that peripheral measures of neuroendocrine functioning in juvenile rhesus monkeys are influenced by early involvement in friendships. Friendships have an especially strong impact on an individual’s psychosocial development, and our data suggest OT and AVP as potential underlying mechanisms. Moreover, sex differences in the functioning of the OT and AVP systems, and their relation to friendship, may have important clinical implications for the use of OT as a therapeutic, as well as informing the social

  19. Multicentre validation of different predictive tools of non-sentinel lymph node involvement in breast cancer.

    PubMed

    Cserni, G; Boross, G; Maráz, R; Leidenius, M H K; Meretoja, T J; Heikkila, P S; Regitnig, P; Luschin-Ebengreuth, G; Zgajnar, J; Perhavec, A; Gazic, B; Lázár, G; Takács, T; Vörös, A; Audisio, R A

    2012-06-01

    Sentinel lymph node (SN) biopsy offers the possibility of selective axillary treatment for breast cancer patients, but there are only limited means for the selective treatment of SN-positive patients. Eight predictive models assessing the risk of non-SN involvement in patients with SN metastasis were tested in a multi-institutional setting. Data of 200 consecutive patients with metastatic SNs and axillary lymph node dissection from each of the 5 participating centres were entered into the selected non-SN metastasis predictive tools. There were significant differences between centres in the distribution of most parameters used in the predictive models, including tumour size, type, grade, oestrogen receptor positivity, rate of lymphovascular invasion, proportion of micrometastatic cases and the presence of extracapsular extension of SN metastasis. There were also significant differences in the proportion of cases classified as having low risk of non-SN metastasis. Despite these differences, there were practically no such differences in the sensitivities, specificities and false reassurance rates of the predictive tools. Each predictive tool used in clinical practice for patient and physician decision on further axillary treatment of SN-positive patients may require individual institutional validation; such validation may reveal different predictive tools to be the best in different institutions.

  20. Analysis of molecular markers as predictive factors of lymph node involvement in breast carcinoma

    PubMed Central

    Paula, Luciana Marques; De Moraes, Luis Henrique Ferreira; Do Canto, Abaeté Leite; Dos Santos, Laurita; Martin, Airton Abrahão; Rogatto, Silvia Regina; De Azevedo Canevari, Renata

    2017-01-01

    Nodal status is the most significant independent prognostic factor in breast cancer. Identification of molecular markers would allow stratification of patients who require surgical assessment of lymph nodes from the large numbers of patients for whom this surgical procedure is unnecessary, thus leading to a more accurate prognosis. However, up to now, the reported studies are preliminary and controversial, and although hundreds of markers have been assessed, few of them have been used in clinical practice for treatment or prognosis in breast cancer. The purpose of the present study was to determine whether protein phosphatase Mg2+/Mn2+ dependent 1D, β-1,3-N-acetylglucosaminyltransferase, neural precursor cell expressed, developmentally down-regulated 9, prohibitin, phosphoinositide-3-kinase regulatory subunit 5 (PIK3R5), phosphatidylinositol-5-phosphate 4-kinase type IIα, TRF1-interacting ankyrin-related ADP-ribose polymerase 2, BCL2 associated agonist of cell death, G2 and S-phase expressed 1 and PAX interacting protein 1 genes, described as prognostic markers in breast cancer in a previous microarray study, are also predictors of lymph node involvement in breast carcinoma Reverse transcription-quantitative polymerase chain reaction analysis was performed on primary breast tumor tissues from women with negative lymph node involvement (n=27) compared with primary tumor tissues from women with positive lymph node involvement (n=23), and was also performed on primary tumors and paired lymph node metastases (n=11). For all genes analyzed, only the PIK3R5 gene exhibited differential expression in samples of primary tumors with positive lymph node involvement compared with primary tumors with negative lymph node involvement (P=0.0347). These results demonstrate that the PIK3R5 gene may be considered predictive of lymph node involvement in breast carcinoma. Although the other genes evaluated in the present study have been previously characterized to be involved with

  1. Analysis of molecular markers as predictive factors of lymph node involvement in breast carcinoma.

    PubMed

    Paula, Luciana Marques; De Moraes, Luis Henrique Ferreira; Do Canto, Abaeté Leite; Dos Santos, Laurita; Martin, Airton Abrahão; Rogatto, Silvia Regina; De Azevedo Canevari, Renata

    2017-01-01

    Nodal status is the most significant independent prognostic factor in breast cancer. Identification of molecular markers would allow stratification of patients who require surgical assessment of lymph nodes from the large numbers of patients for whom this surgical procedure is unnecessary, thus leading to a more accurate prognosis. However, up to now, the reported studies are preliminary and controversial, and although hundreds of markers have been assessed, few of them have been used in clinical practice for treatment or prognosis in breast cancer. The purpose of the present study was to determine whether protein phosphatase Mg2+/Mn2+ dependent 1D, β-1,3-N-acetylglucosaminyltransferase, neural precursor cell expressed, developmentally down-regulated 9, prohibitin, phosphoinositide-3-kinase regulatory subunit 5 (PIK3R5), phosphatidylinositol-5-phosphate 4-kinase type IIα, TRF1-interacting ankyrin-related ADP-ribose polymerase 2, BCL2 associated agonist of cell death, G2 and S-phase expressed 1 and PAX interacting protein 1 genes, described as prognostic markers in breast cancer in a previous microarray study, are also predictors of lymph node involvement in breast carcinoma Reverse transcription-quantitative polymerase chain reaction analysis was performed on primary breast tumor tissues from women with negative lymph node involvement (n=27) compared with primary tumor tissues from women with positive lymph node involvement (n=23), and was also performed on primary tumors and paired lymph node metastases (n=11). For all genes analyzed, only the PIK3R5 gene exhibited differential expression in samples of primary tumors with positive lymph node involvement compared with primary tumors with negative lymph node involvement (P=0.0347). These results demonstrate that the PIK3R5 gene may be considered predictive of lymph node involvement in breast carcinoma. Although the other genes evaluated in the present study have been previously characterized to be involved with

  2. Karyopherins: potential biological elements involved in the delayed graft function in renal transplant recipients

    PubMed Central

    2014-01-01

    Background Immediately after renal transplantation, patients experience rapid and significant improvement of their clinical conditions and undergo considerable systemic and cellular modifications. However, some patients present a slow recovery of the renal function commonly defined as delayed graft function (DGF). Although clinically well characterized, the molecular mechanisms underlying this condition are not totally defined, thus, we are currently missing specific clinical markers to predict and to make early diagnosis of this event. Methods We investigated, using a pathway analysis approach, the transcriptomic profile of peripheral blood mononuclear cells (PBMC) from renal transplant recipients with DGF and with early graft function (EGF), before (T0) and 24 hours (T24) after transplantation. Results Bioinformatics/statistical analysis showed that 15 pathways (8 up-regulated and 7 down-regulated) and 11 pathways (5 up-regulated and 6 down-regulated) were able to identify DGF patients at T0 and T24, respectively. Interestingly, the most up-regulated pathway at both time points was NLS-bearing substrate import into nucleus, which includes genes encoding for several subtypes of karyopherins, a group of proteins involved in nucleocytoplasmic transport. Signal transducers and activators of transcription (STAT) utilize karyopherins-alpha (KPNA) for their passage from cytoplasm into the nucleus. In vitro functional analysis demonstrated that in PBMCs of DGF patients, there was a significant KPNA-mediated nuclear translocation of the phosphorylated form of STAT3 (pSTAT3) after short-time stimulation (2 and 5 minutes) with interleukin-6. Conclusions Our study suggests the involvement, immediately before transplantation, of karyopherin-mediated nuclear transport in the onset and development of DGF. Additionally, it reveals that karyopherins could be good candidates as potential DGF predictive clinical biomarkers and targets for pharmacological interventions in renal

  3. Religious Involvement and Health over Time: Predictive Effects in a National Sample of African Americans

    PubMed Central

    Roth, David L.; Usher, Therri; Clark, Eddie M.; Holt, Cheryl L.

    2016-01-01

    In this study, two telephone interviews that assessed both religious involvement and health-related quality of life were conducted approximately 2.5 years apart in a national sample of 290 African Americans. Religious involvement was assessed with an instrument that measured both personal religious beliefs (e.g., having a personal relationship with God) and more public religious behaviors (e.g., attending church services). Health-related quality of life was measured with version 2 of the Medical Outcomes Study 12-item short form (SF-12v2). Structural equation models indicated that higher religious beliefs at baseline predicted better physical and mental health 2.5 years later. Higher religious behaviors at baseline contributed smaller, complementary suppression effects. Physical and mental health indicators from the SF-12v2 at baseline did not predict changes in either religious beliefs or religious behaviors over time. These findings indicate that, for African Americans, personal religious beliefs lead to beneficial health effects over time, whereas individual differences in health do not appear to predict changes in religious involvement. PMID:28502992

  4. Positive symptoms and duration of illness predict functional laterality and attention modulation in schizophrenia.

    PubMed

    Løberg, E-M; Jørgensen, H A; Green, M F; Rund, B R; Lund, A; Diseth, A; Oie, M; Hugdahl, K

    2006-04-01

    Dichotic listening (DL) performance in schizophrenia, reflecting hemispheric asymmetry and the functional integrity of the left temporal lobe, can vary with clinical characteristics. Previous studies have not taken the co-linearity of clinical variables into account. The aim of the present study was to evaluate the roles of positive symptoms and duration of illness in DL through Structural Equation Modeling (SEM), thus allowing for complex relationships between the variables. We pooled patients from four previous DL studies to create a heterogeneous group of 129 schizophrenic patients, all tested with a consonant-vowel syllables DL procedure that included attentional instructions. A model where positive symptoms predicted a laterality component and duration of illness predicted an attention component in DL was confirmed. Positive symptoms predicted reduced functional laterality, suggesting involvement of left temporal lobe language processing. Duration of illness predicted impaired attention modulation, possibly reflecting the involvement of frontotemporal networks.

  5. A new protein structure representation for efficient protein function prediction.

    PubMed

    Maghawry, Huda A; Mostafa, Mostafa G M; Gharib, Tarek F

    2014-12-01

    One of the challenging problems in bioinformatics is the prediction of protein function. Protein function is the main key that can be used to classify different proteins. Protein function can be inferred experimentally with very small throughput or computationally with very high throughput. Computational methods are sequence based or structure based. Structure-based methods produce more accurate protein function prediction. In this article, we propose a new protein structure representation for efficient protein function prediction. The representation is based on three-dimensional patterns of protein residues. In the analysis, we used protein function based on enzyme activity through six mechanistically diverse enzyme superfamilies: amidohydrolase, crotonase, haloacid dehalogenase, isoprenoid synthase type I, and vicinal oxygen chelate. We applied three different classification methods, naïve Bayes, k-nearest neighbors, and random forest, to predict the enzyme superfamily of a given protein. The prediction accuracy using the proposed representation outperforms a recently introduced representation method that is based only on the distance patterns. The results show that the proposed representation achieved prediction accuracy up to 98%, with improvement of about 10% on average.

  6. Thyroid Gland Involvement in Carcinoma Larynx and Hypopharynx-Predictive Factors and Prognostic Significance.

    PubMed

    Iype, Elizabeth Mathew; Jagad, Vijay; Nochikattil, Santhosh Kumar; Varghese, Bipin T; Sebastian, Paul

    2016-02-01

    Intraoperative management of thyroid gland in laryngeal and hypopharyngeal cancer is controversial. The objectives of this study were to determine the incidence of thyroid gland invasion in patients undergoing surgery for laryngeal or hypopharyngeal carcinoma, to assess predictive factors and to assess the prognosis in patients with and without thyroid gland invasion. One hundred and thirty-three patients who underwent surgery for carcinoma larynx and hypopharynx from 2006 to 2010 were reviewed retrospectively. Surgical specimens were examined to determine the incidence of thyroid gland invasion and predictive factors were analysed. The recurrence rate and the survival in patients with and without thyroid gland invasion were also analysed. Out of the 133 patients with carcinoma larynx and hypopharynx who underwent surgery, histological thyroid gland invasion was observed in 28/133 (21%) patients. Significant relationship was found between histological thyroid gland invasion and preoperative evidence of thyroid cartilage erosion by CT scan and also when gross thyroid gland involvement observed during surgery. There is significant association between thyroid gland invasion when there is upper oesophageal or subglottic involvement. After analysing the retrospective data from our study, we would like to suggest that thyroid gland need not be removed routinely in all laryngectomies, unless there is advanced disease with thyroid cartilage erosion and gross thyroid gland involvement or disease with significant subglottic or oesophageal involvement.

  7. Thyroid Gland Involvement in Carcinoma Larynx and Hypopharynx-Predictive Factors and Prognostic Significance

    PubMed Central

    Iype, Elizabeth Mathew; Jagad, Vijay; Varghese, Bipin T.; Sebastian, Paul

    2016-01-01

    Introduction Intraoperative management of thyroid gland in laryngeal and hypopharyngeal cancer is controversial. Aim The objectives of this study were to determine the incidence of thyroid gland invasion in patients undergoing surgery for laryngeal or hypopharyngeal carcinoma, to assess predictive factors and to assess the prognosis in patients with and without thyroid gland invasion. Materials and Methods One hundred and thirty-three patients who underwent surgery for carcinoma larynx and hypopharynx from 2006 to 2010 were reviewed retrospectively. Surgical specimens were examined to determine the incidence of thyroid gland invasion and predictive factors were analysed. The recurrence rate and the survival in patients with and without thyroid gland invasion were also analysed. Results Out of the 133 patients with carcinoma larynx and hypopharynx who underwent surgery, histological thyroid gland invasion was observed in 28/133 (21%) patients. Significant relationship was found between histological thyroid gland invasion and preoperative evidence of thyroid cartilage erosion by CT scan and also when gross thyroid gland involvement observed during surgery. There is significant association between thyroid gland invasion when there is upper oesophageal or subglottic involvement. Conclusion After analysing the retrospective data from our study, we would like to suggest that thyroid gland need not be removed routinely in all laryngectomies, unless there is advanced disease with thyroid cartilage erosion and gross thyroid gland involvement or disease with significant subglottic or oesophageal involvement. PMID:27042568

  8. Dimensions and predictions of professional involvement in self-help groups: a view from within.

    PubMed

    Ben-Ari, Adital Tirosh

    2002-05-01

    This article focuses on an analysis of how members of self-help groups perceived professional involvement and what they defined as the dimensions of such involvement. Models to predict these identified dimensions are also suggested. The instrument developed for the study consisted of two parts: (1) demographic question and (2) 12 statements concerning self-help group members' attitudes toward professional involvement. Based on responses from 183 members of self-help groups, three categories were identfied according to their main focus: groups dealing with health issues, groups dealing with alternative lifestyles, and groups based on the 12-step model. Analysis yielded two conceptually different constructs influencing group members' attitudes: collaboration and duality.

  9. Adaptive bandwidth measurements of importance functions for speech intelligibility prediction.

    PubMed

    Whitmal, Nathaniel A; DeRoy, Kristina

    2011-12-01

    The Articulation Index (AI) and Speech Intelligibility Index (SII) predict intelligibility scores from measurements of speech and hearing parameters. One component in the prediction is the "importance function," a weighting function that characterizes contributions of particular spectral regions of speech to speech intelligibility. Previous work with SII predictions for hearing-impaired subjects suggests that prediction accuracy might improve if importance functions for individual subjects were available. Unfortunately, previous importance function measurements have required extensive intelligibility testing with groups of subjects, using speech processed by various fixed-bandwidth low-pass and high-pass filters. A more efficient approach appropriate to individual subjects is desired. The purpose of this study was to evaluate the feasibility of measuring importance functions for individual subjects with adaptive-bandwidth filters. In two experiments, ten subjects with normal-hearing listened to vowel-consonant-vowel (VCV) nonsense words processed by low-pass and high-pass filters whose bandwidths were varied adaptively to produce specified performance levels in accordance with the transformed up-down rules of Levitt [(1971). J. Acoust. Soc. Am. 49, 467-477]. Local linear psychometric functions were fit to resulting data and used to generate an importance function for VCV words. Results indicate that the adaptive method is reliable and efficient, and produces importance function data consistent with that of the corresponding AI/SII importance function.

  10. Adaptive bandwidth measurements of importance functions for speech intelligibility prediction

    PubMed Central

    Whitmal, Nathaniel A.; DeRoy, Kristina

    2011-01-01

    The Articulation Index (AI) and Speech Intelligibility Index (SII) predict intelligibility scores from measurements of speech and hearing parameters. One component in the prediction is the “importance function,” a weighting function that characterizes contributions of particular spectral regions of speech to speech intelligibility. Previous work with SII predictions for hearing-impaired subjects suggests that prediction accuracy might improve if importance functions for individual subjects were available. Unfortunately, previous importance function measurements have required extensive intelligibility testing with groups of subjects, using speech processed by various fixed-bandwidth low-pass and high-pass filters. A more efficient approach appropriate to individual subjects is desired. The purpose of this study was to evaluate the feasibility of measuring importance functions for individual subjects with adaptive-bandwidth filters. In two experiments, ten subjects with normal-hearing listened to vowel-consonant-vowel (VCV) nonsense words processed by low-pass and high-pass filters whose bandwidths were varied adaptively to produce specified performance levels in accordance with the transformed up-down rules of Levitt [(1971). J. Acoust. Soc. Am. 49, 467–477]. Local linear psychometric functions were fit to resulting data and used to generate an importance function for VCV words. Results indicate that the adaptive method is reliable and efficient, and produces importance function data consistent with that of the corresponding AI/SII importance function. PMID:22225057

  11. Molecular and functional characterization of mulberry EST encoding remorin (MiREM) involved in abiotic stress.

    PubMed

    Checker, Vibha G; Khurana, Paramjit

    2013-11-01

    Group1 remorins may help the plants to optimize their growth under adverse conditions by their involvement in mediating osmotic stress responses in plants. Mulberry (Morus indica), a deciduous woody tree, serves as the cardinal component of the sericulture industry. Genomic endeavors in sequencing of mulberry ESTs provided clues to stress-specific clones, but their functional relevance remains fragmentary. Therefore in this study, we assessed the functional significance of a remorin gene family member that was identified in leaf ESTs. Remorins represent a large, plant-specific multigene family gaining importance in recent times with respect to their role in plant-microbe interactions, although their role in response to environmental stresses remains speculative as in vivo functions of remorin genes are limited. Mulberry remorin (MiREM) localizes to plasma membrane and is ubiquitously present in all plant organs. Expression analysis of MiREM by northern analysis reveals that its transcript increases under different abiotic stress conditions especially during dehydration and salt stress, implicating it in regulation of stress signaling pathways. Concomitantly, transgenic Arabidopsis plants overexpressing heterologous remorin show tolerance to dehydration and salinity at the germination and seedling stages as revealed by percentage germination, root inhibition assays, fresh weight and activity of photosystem II. This study predicts the possible function of group 1 remorin gene in mediating osmotic stress thus bringing novel perspectives in understanding the function of remorins in plant abiotic stress responses.

  12. Reelin and its complex involvement in brain development and function.

    PubMed

    Lakatosova, Silvia; Ostatnikova, Daniela

    2012-09-01

    Reelin is a neuroprotein with crucial role during neurodevelopment and also in postnatal period. It regulates neuronal migration and positioning in developing neocortex and cerebellar cortex. Postnatally it participates in regulation of dendritic and axonal growth, synaptogenesis, neurotransmission and it contribute to synaptic plasticity necessary for learning and memory functions. Role of Reelin seems to be rather complex, profound research gradually uncovers its further functions. Deficits of Reelin were detected in neuropsychiatric disorders such as schizophrenia, bipolar disorder and autism. Pathogenesis of these disorders is far from being clearly understood. Reelin contribution to these diseases seems to be vital, since genetic variants of Reelin were associated with these diseases and often influence symptom severity. Reelin is a promising candidate molecule with potential future use in diagnostics and therapy, however further detailed research is essential. Copyright © 2012 Elsevier Ltd. All rights reserved.

  13. STRIPAK complexes: structure, biological function, and involvement in human diseases.

    PubMed

    Hwang, Juyeon; Pallas, David C

    2014-02-01

    The mammalian striatin family consists of three proteins, striatin, S/G2 nuclear autoantigen, and zinedin. Striatin family members have no intrinsic catalytic activity, but rather function as scaffolding proteins. Remarkably, they organize multiple diverse, large signaling complexes that participate in a variety of cellular processes. Moreover, they appear to be regulatory/targeting subunits for the major eukaryotic serine/threonine protein phosphatase 2A. In addition, striatin family members associate with germinal center kinase III kinases as well as other novel components, earning these assemblies the name striatin-interacting phosphatase and kinase (STRIPAK) complexes. Recently, there has been a great increase in functional and mechanistic studies aimed at identifying and understanding the roles of STRIPAK and STRIPAK-like complexes in cellular processes of multiple organisms. These studies have identified novel STRIPAK and STRIPAK-like complexes and have explored their roles in specific signaling pathways. Together, the results of these studies have sparked increased interest in striatin family complexes because they have revealed roles in signaling, cell cycle control, apoptosis, vesicular trafficking, Golgi assembly, cell polarity, cell migration, neural and vascular development, and cardiac function. Moreover, STRIPAK complexes have been connected to clinical conditions, including cardiac disease, diabetes, autism, and cerebral cavernous malformation. In this review, we discuss the expression, localization, and protein domain structure of striatin family members. Then we consider the diverse complexes these proteins and their homologs form in various organisms, emphasizing what is known regarding function and regulation. Finally, we explore possible roles of striatin family complexes in disease, especially cerebral cavernous malformation.

  14. A Survey of Computational Intelligence Techniques in Protein Function Prediction

    PubMed Central

    Tiwari, Arvind Kumar; Srivastava, Rajeev

    2014-01-01

    During the past, there was a massive growth of knowledge of unknown proteins with the advancement of high throughput microarray technologies. Protein function prediction is the most challenging problem in bioinformatics. In the past, the homology based approaches were used to predict the protein function, but they failed when a new protein was different from the previous one. Therefore, to alleviate the problems associated with homology based traditional approaches, numerous computational intelligence techniques have been proposed in the recent past. This paper presents a state-of-the-art comprehensive review of various computational intelligence techniques for protein function predictions using sequence, structure, protein-protein interaction network, and gene expression data used in wide areas of applications such as prediction of DNA and RNA binding sites, subcellular localization, enzyme functions, signal peptides, catalytic residues, nuclear/G-protein coupled receptors, membrane proteins, and pathway analysis from gene expression datasets. This paper also summarizes the result obtained by many researchers to solve these problems by using computational intelligence techniques with appropriate datasets to improve the prediction performance. The summary shows that ensemble classifiers and integration of multiple heterogeneous data are useful for protein function prediction. PMID:25574395

  15. A survey of computational intelligence techniques in protein function prediction.

    PubMed

    Tiwari, Arvind Kumar; Srivastava, Rajeev

    2014-01-01

    During the past, there was a massive growth of knowledge of unknown proteins with the advancement of high throughput microarray technologies. Protein function prediction is the most challenging problem in bioinformatics. In the past, the homology based approaches were used to predict the protein function, but they failed when a new protein was different from the previous one. Therefore, to alleviate the problems associated with homology based traditional approaches, numerous computational intelligence techniques have been proposed in the recent past. This paper presents a state-of-the-art comprehensive review of various computational intelligence techniques for protein function predictions using sequence, structure, protein-protein interaction network, and gene expression data used in wide areas of applications such as prediction of DNA and RNA binding sites, subcellular localization, enzyme functions, signal peptides, catalytic residues, nuclear/G-protein coupled receptors, membrane proteins, and pathway analysis from gene expression datasets. This paper also summarizes the result obtained by many researchers to solve these problems by using computational intelligence techniques with appropriate datasets to improve the prediction performance. The summary shows that ensemble classifiers and integration of multiple heterogeneous data are useful for protein function prediction.

  16. Enhanced functional connectivity involving the ventromedial hypothalamus following methamphetamine exposure.

    PubMed

    Zuloaga, Damian G; Iancu, Ovidiu D; Weber, Sydney; Etzel, Desiree; Marzulla, Tessa; Stewart, Blair; Allen, Charles N; Raber, Jacob

    2015-01-01

    Methamphetamine (MA) consumption causes disruption of many biological rhythms including the sleep-wake cycle. This circadian effect is seen shortly following MA exposure and later in life following developmental MA exposure. MA phase shifts, entrains the circadian clock and can also alter the entraining effect of light by currently unknown mechanisms. We analyzed and compared immunoreactivity of the immediate early gene c-Fos, a marker of neuronal activity, to assess neuronal activation 2 h following MA exposure in the light and dark phases. We used network analyses of correlation patterns derived from global brain immunoreactivity patterns of c-Fos, to infer functional connectivity between brain regions. There were five distinct patterns of neuronal activation. In several brain areas, neuronal activation following exposure to MA was stronger in the light than the dark phase, highlighting the importance of considering circadian periods of increased effects of MA in defining experimental conditions and understanding the mechanisms underlying detrimental effects of MA exposure to brain function. Functional connectivity between the ventromedial hypothalamus (VMH) and other brain areas, including the paraventricular nucleus of the hypothalamus and basolateral and medial amygdala, was enhanced following MA exposure, suggesting a role for the VMH in the effects of MA on the brain.

  17. Empirical sediment transport function predicting seepage erosion undercutting for cohesive bank failure prediction

    USDA-ARS?s Scientific Manuscript database

    Seepage erosion is an important factor in hillslope instability and failure. However, predicting erosion by subsurface flow or seepage and incorporating its effects into stability models remains a challenge. Limitations exist with all existing seepage erosion sediment transport functions, including ...

  18. INTEGRATING COMPUTATIONAL PROTEIN FUNCTION PREDICTION INTO DRUG DISCOVERY INITIATIVES

    PubMed Central

    Grant, Marianne A.

    2014-01-01

    Pharmaceutical researchers must evaluate vast numbers of protein sequences and formulate innovative strategies for identifying valid targets and discovering leads against them as a way of accelerating drug discovery. The ever increasing number and diversity of novel protein sequences identified by genomic sequencing projects and the success of worldwide structural genomics initiatives have spurred great interest and impetus in the development of methods for accurate, computationally empowered protein function prediction and active site identification. Previously, in the absence of direct experimental evidence, homology-based protein function annotation remained the gold-standard for in silico analysis and prediction of protein function. However, with the continued exponential expansion of sequence databases, this approach is not always applicable, as fewer query protein sequences demonstrate significant homology to protein gene products of known function. As a result, several non-homology based methods for protein function prediction that are based on sequence features, structure, evolution, biochemical and genetic knowledge have emerged. Herein, we review current bioinformatic programs and approaches for protein function prediction/annotation and discuss their integration into drug discovery initiatives. The development of such methods to annotate protein functional sites and their application to large protein functional families is crucial to successfully utilizing the vast amounts of genomic sequence information available to drug discovery and development processes. PMID:25530654

  19. A Unitary Executive Function Predicts Intelligence in Children

    ERIC Educational Resources Information Center

    Brydges, Christopher R.; Reid, Corinne L.; Fox, Allison M.; Anderson, Mike

    2012-01-01

    Executive functions (EF) and intelligence are of critical importance to success in many everyday tasks. Working memory, or updating, which is one latent variable identified in confirmatory factor analytic models of executive functions, predicts intelligence (both fluid and crystallised) in adults, but inhibition and shifting do not (Friedman et…

  20. A Unitary Executive Function Predicts Intelligence in Children

    ERIC Educational Resources Information Center

    Brydges, Christopher R.; Reid, Corinne L.; Fox, Allison M.; Anderson, Mike

    2012-01-01

    Executive functions (EF) and intelligence are of critical importance to success in many everyday tasks. Working memory, or updating, which is one latent variable identified in confirmatory factor analytic models of executive functions, predicts intelligence (both fluid and crystallised) in adults, but inhibition and shifting do not (Friedman et…

  1. Rapid Catalytic Template Searching as an Enzyme Function Prediction Procedure

    PubMed Central

    Nilmeier, Jerome P.; Kirshner, Daniel A.; Wong, Sergio E.; Lightstone, Felice C.

    2013-01-01

    We present an enzyme protein function identification algorithm, Catalytic Site Identification (CatSId), based on identification of catalytic residues. The method is optimized for highly accurate template identification across a diverse template library and is also very efficient in regards to time and scalability of comparisons. The algorithm matches three-dimensional residue arrangements in a query protein to a library of manually annotated, catalytic residues – The Catalytic Site Atlas (CSA). Two main processes are involved. The first process is a rapid protein-to-template matching algorithm that scales quadratically with target protein size and linearly with template size. The second process incorporates a number of physical descriptors, including binding site predictions, in a logistic scoring procedure to re-score matches found in Process 1. This approach shows very good performance overall, with a Receiver-Operator-Characteristic Area Under Curve (AUC) of 0.971 for the training set evaluated. The procedure is able to process cofactors, ions, nonstandard residues, and point substitutions for residues and ions in a robust and integrated fashion. Sites with only two critical (catalytic) residues are challenging cases, resulting in AUCs of 0.9411 and 0.5413 for the training and test sets, respectively. The remaining sites show excellent performance with AUCs greater than 0.90 for both the training and test data on templates of size greater than two critical (catalytic) residues. The procedure has considerable promise for larger scale searches. PMID:23675414

  2. β1-Integrin Cytoplasmic Subdomains Involved in Dominant Negative Function

    PubMed Central

    Retta, S. Francesco; Balzac, Fiorella; Ferraris, Piercarlo; Belkin, Alexey M.; Fässler, Reinhard; Humphries, Martin J.; De Leo, Giacomo; Silengo, Lorenzo; Tarone, Guido

    1998-01-01

    The β1-integrin cytoplasmic domain consists of a membrane proximal subdomain common to the four known isoforms (“common” region) and a distal subdomain specific for each isoform (“variable” region). To investigate in detail the role of these subdomains in integrin-dependent cellular functions, we used β1A and β1B isoforms as well as four mutants lacking the entire cytoplasmic domain (β1TR), the variable region (β1COM), or the common region (β1ΔCOM-B and β1ΔCOM-A). By expressing these constructs in Chinese hamster ovary and β1 integrin-deficient GD25 cells (Wennerberg et al., J Cell Biol 132, 227–238, 1996), we show that β1B, β1COM, β1ΔCOM-B, and β1ΔCOM-A molecules are unable to support efficient cell adhesion to matrix proteins. On exposure to Mn++ ions, however, β1B, but none of the mutants, can mediate cell adhesion, indicating specific functional properties of this isoform. Analysis of adhesive functions of transfected cells shows that β1B interferes in a dominant negative manner with β1A and β3/β5 integrins in cell spreading, focal adhesion formation, focal adhesion kinase tyrosine phosphorylation, and fibronectin matrix assembly. None of the β1 mutants tested shows this property, indicating that the dominant negative effect depends on the specific combination of common and B subdomains, rather than from the absence of the A subdomain in the β1B isoform. PMID:9529373

  3. beta1-integrin cytoplasmic subdomains involved in dominant negative function.

    PubMed

    Retta, S F; Balzac, F; Ferraris, P; Belkin, A M; Fässler, R; Humphries, M J; De Leo, G; Silengo, L; Tarone, G

    1998-04-01

    The beta1-integrin cytoplasmic domain consists of a membrane proximal subdomain common to the four known isoforms ("common" region) and a distal subdomain specific for each isoform ("variable" region). To investigate in detail the role of these subdomains in integrin-dependent cellular functions, we used beta1A and beta1B isoforms as well as four mutants lacking the entire cytoplasmic domain (beta1TR), the variable region (beta1COM), or the common region (beta1 deltaCOM-B and beta1 deltaCOM-A). By expressing these constructs in Chinese hamster ovary and beta1 integrin-deficient GD25 cells (Wennerberg et al., J Cell Biol 132, 227-238, 1996), we show that beta1B, beta1COM, beta1 deltaCOM-B, and beta1 deltaCOM-A molecules are unable to support efficient cell adhesion to matrix proteins. On exposure to Mn++ ions, however, beta1B, but none of the mutants, can mediate cell adhesion, indicating specific functional properties of this isoform. Analysis of adhesive functions of transfected cells shows that beta1B interferes in a dominant negative manner with beta1A and beta3/beta5 integrins in cell spreading, focal adhesion formation, focal adhesion kinase tyrosine phosphorylation, and fibronectin matrix assembly. None of the beta1 mutants tested shows this property, indicating that the dominant negative effect depends on the specific combination of common and B subdomains, rather than from the absence of the A subdomain in the beta1B isoform.

  4. A large-scale evaluation of computational protein function prediction.

    PubMed

    Radivojac, Predrag; Clark, Wyatt T; Oron, Tal Ronnen; Schnoes, Alexandra M; Wittkop, Tobias; Sokolov, Artem; Graim, Kiley; Funk, Christopher; Verspoor, Karin; Ben-Hur, Asa; Pandey, Gaurav; Yunes, Jeffrey M; Talwalkar, Ameet S; Repo, Susanna; Souza, Michael L; Piovesan, Damiano; Casadio, Rita; Wang, Zheng; Cheng, Jianlin; Fang, Hai; Gough, Julian; Koskinen, Patrik; Törönen, Petri; Nokso-Koivisto, Jussi; Holm, Liisa; Cozzetto, Domenico; Buchan, Daniel W A; Bryson, Kevin; Jones, David T; Limaye, Bhakti; Inamdar, Harshal; Datta, Avik; Manjari, Sunitha K; Joshi, Rajendra; Chitale, Meghana; Kihara, Daisuke; Lisewski, Andreas M; Erdin, Serkan; Venner, Eric; Lichtarge, Olivier; Rentzsch, Robert; Yang, Haixuan; Romero, Alfonso E; Bhat, Prajwal; Paccanaro, Alberto; Hamp, Tobias; Kaßner, Rebecca; Seemayer, Stefan; Vicedo, Esmeralda; Schaefer, Christian; Achten, Dominik; Auer, Florian; Boehm, Ariane; Braun, Tatjana; Hecht, Maximilian; Heron, Mark; Hönigschmid, Peter; Hopf, Thomas A; Kaufmann, Stefanie; Kiening, Michael; Krompass, Denis; Landerer, Cedric; Mahlich, Yannick; Roos, Manfred; Björne, Jari; Salakoski, Tapio; Wong, Andrew; Shatkay, Hagit; Gatzmann, Fanny; Sommer, Ingolf; Wass, Mark N; Sternberg, Michael J E; Škunca, Nives; Supek, Fran; Bošnjak, Matko; Panov, Panče; Džeroski, Sašo; Šmuc, Tomislav; Kourmpetis, Yiannis A I; van Dijk, Aalt D J; ter Braak, Cajo J F; Zhou, Yuanpeng; Gong, Qingtian; Dong, Xinran; Tian, Weidong; Falda, Marco; Fontana, Paolo; Lavezzo, Enrico; Di Camillo, Barbara; Toppo, Stefano; Lan, Liang; Djuric, Nemanja; Guo, Yuhong; Vucetic, Slobodan; Bairoch, Amos; Linial, Michal; Babbitt, Patricia C; Brenner, Steven E; Orengo, Christine; Rost, Burkhard; Mooney, Sean D; Friedberg, Iddo

    2013-03-01

    Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale community-based critical assessment of protein function annotation (CAFA) experiment. Fifty-four methods representing the state of the art for protein function prediction were evaluated on a target set of 866 proteins from 11 organisms. Two findings stand out: (i) today's best protein function prediction algorithms substantially outperform widely used first-generation methods, with large gains on all types of targets; and (ii) although the top methods perform well enough to guide experiments, there is considerable need for improvement of currently available tools.

  5. Protein Structure and Function Prediction Using I-TASSER.

    PubMed

    Yang, Jianyi; Zhang, Yang

    2015-12-17

    I-TASSER is a hierarchical protocol for automated protein structure prediction and structure-based function annotation. Starting from the amino acid sequence of target proteins, I-TASSER first generates full-length atomic structural models from multiple threading alignments and iterative structural assembly simulations followed by atomic-level structure refinement. The biological functions of the protein, including ligand-binding sites, enzyme commission number, and gene ontology terms, are then inferred from known protein function databases based on sequence and structure profile comparisons. I-TASSER is freely available as both an on-line server and a stand-alone package. This unit describes how to use the I-TASSER protocol to generate structure and function prediction and how to interpret the prediction results, as well as alternative approaches for further improving the I-TASSER modeling quality for distant-homologous and multi-domain protein targets. Copyright © 2015 John Wiley & Sons, Inc.

  6. A large-scale evaluation of computational protein function prediction

    PubMed Central

    Radivojac, Predrag; Clark, Wyatt T; Ronnen Oron, Tal; Schnoes, Alexandra M; Wittkop, Tobias; Sokolov, Artem; Graim, Kiley; Funk, Christopher; Verspoor, Karin; Ben-Hur, Asa; Pandey, Gaurav; Yunes, Jeffrey M; Talwalkar, Ameet S; Repo, Susanna; Souza, Michael L; Piovesan, Damiano; Casadio, Rita; Wang, Zheng; Cheng, Jianlin; Fang, Hai; Gough, Julian; Koskinen, Patrik; Törönen, Petri; Nokso-Koivisto, Jussi; Holm, Liisa; Cozzetto, Domenico; Buchan, Daniel W A; Bryson, Kevin; Jones, David T; Limaye, Bhakti; Inamdar, Harshal; Datta, Avik; Manjari, Sunitha K; Joshi, Rajendra; Chitale, Meghana; Kihara, Daisuke; Lisewski, Andreas M; Erdin, Serkan; Venner, Eric; Lichtarge, Olivier; Rentzsch, Robert; Yang, Haixuan; Romero, Alfonso E; Bhat, Prajwal; Paccanaro, Alberto; Hamp, Tobias; Kassner, Rebecca; Seemayer, Stefan; Vicedo, Esmeralda; Schaefer, Christian; Achten, Dominik; Auer, Florian; Böhm, Ariane; Braun, Tatjana; Hecht, Maximilian; Heron, Mark; Hönigschmid, Peter; Hopf, Thomas; Kaufmann, Stefanie; Kiening, Michael; Krompass, Denis; Landerer, Cedric; Mahlich, Yannick; Roos, Manfred; Björne, Jari; Salakoski, Tapio; Wong, Andrew; Shatkay, Hagit; Gatzmann, Fanny; Sommer, Ingolf; Wass, Mark N; Sternberg, Michael J E; Škunca, Nives; Supek, Fran; Bošnjak, Matko; Panov, Panče; Džeroski, Sašo; Šmuc, Tomislav; Kourmpetis, Yiannis A I; van Dijk, Aalt D J; ter Braak, Cajo J F; Zhou, Yuanpeng; Gong, Qingtian; Dong, Xinran; Tian, Weidong; Falda, Marco; Fontana, Paolo; Lavezzo, Enrico; Di Camillo, Barbara; Toppo, Stefano; Lan, Liang; Djuric, Nemanja; Guo, Yuhong; Vucetic, Slobodan; Bairoch, Amos; Linial, Michal; Babbitt, Patricia C; Brenner, Steven E; Orengo, Christine; Rost, Burkhard; Mooney, Sean D; Friedberg, Iddo

    2013-01-01

    Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale community-based Critical Assessment of protein Function Annotation (CAFA) experiment. Fifty-four methods representing the state-of-the-art for protein function prediction were evaluated on a target set of 866 proteins from eleven organisms. Two findings stand out: (i) today’s best protein function prediction algorithms significantly outperformed widely-used first-generation methods, with large gains on all types of targets; and (ii) although the top methods perform well enough to guide experiments, there is significant need for improvement of currently available tools. PMID:23353650

  7. Involvement of autophagy in NK cell development and function.

    PubMed

    López-Soto, Alejandro; Bravo-San Pedro, José Manuel; Kroemer, Guido; Galluzzi, Lorenzo; Gonzalez, Segundo

    2017-03-04

    Natural killer (NK) cells are the prototypical members of the recently identified family of innate lymphoid cells (ILCs). Thanks to their cytotoxic and secretory functions, NK cells play a key role in the immune response to cells experiencing various forms of stress, including viral infection and malignant transformation. Autophagy is a highly conserved network of degradative pathways that participate in the maintenance of cellular and organismal homeostasis as they promote adaptation to adverse microenvironmental conditions. The relevance of autophagy in the development and functionality of cellular components of the adaptive immune system is well established. Conversely, whether autophagy also plays an important role in the biology of ILC populations such as NK cells has long remained elusive. Recent experimental evidence shows that ablating Atg5 (autophagy-related 5, an essential component of the autophagic machinery) in NK cells and other specific ILC populations results in progressive mitochondrial damage, reactive oxygen species (ROS) overgeneration, and regulated cell death, hence interrupting ILC development. Moreover, disrupting the interaction of ATG7 with phosphorylated FOXO1 (forkhead box O1) in the cytosol of immature NK cells prevents autophagic responses that are essential for NK cell maturation. These findings suggest that activating autophagy may support the maturation of NK cells and other ILCs that manifest antiviral and anticancer activity.

  8. Spindle function in Xenopus oocytes involves possible nanodomain calcium signaling

    PubMed Central

    Li, Ruizhen; Leblanc, Julie; He, Kevin; Liu, X. Johné

    2016-01-01

    Intracellular calcium transients are a universal phenomenon at fertilization and are required for egg activation, but the exact role of Ca2+ in second-polar-body emission remains unknown. On the other hand, similar calcium transients have not been demonstrated during oocyte maturation, and yet, manipulating intracellular calcium levels interferes with first-polar-body emission in mice and frogs. To determine the precise role of calcium signaling in polar body formation, we used live-cell imaging coupled with temporally precise intracellular calcium buffering. We found that BAPTA-based calcium chelators cause immediate depolymerization of spindle microtubules in meiosis I and meiosis II. Surprisingly, EGTA at similar or higher intracellular concentrations had no effect on spindle function or polar body emission. Using two calcium probes containing permutated GFP and the calcium sensor calmodulin (Lck-GCaMP3 and GCaMP3), we demonstrated enrichment of the probes at the spindle but failed to detect calcium increase during oocyte maturation at the spindle or elsewhere. Finally, endogenous calmodulin was found to colocalize with spindle microtubules throughout all stages of meiosis. Our results—most important, the different sensitivities of the spindle to BAPTA and EGTA—suggest that meiotic spindle function in frog oocytes requires highly localized, or nanodomain, calcium signaling. PMID:27582389

  9. Roles for text mining in protein function prediction.

    PubMed

    Verspoor, Karin M

    2014-01-01

    The Human Genome Project has provided science with a hugely valuable resource: the blueprints for life; the specification of all of the genes that make up a human. While the genes have all been identified and deciphered, it is proteins that are the workhorses of the human body: they are essential to virtually all cell functions and are the primary mechanism through which biological function is carried out. Hence in order to fully understand what happens at a molecular level in biological organisms, and eventually to enable development of treatments for diseases where some aspect of a biological system goes awry, we must understand the functions of proteins. However, experimental characterization of protein function cannot scale to the vast amount of DNA sequence data now available. Computational protein function prediction has therefore emerged as a problem at the forefront of modern biology (Radivojac et al., Nat Methods 10(13):221-227, 2013).Within the varied approaches to computational protein function prediction that have been explored, there are several that make use of biomedical literature mining. These methods take advantage of information in the published literature to associate specific proteins with specific protein functions. In this chapter, we introduce two main strategies for doing this: association of function terms, represented as Gene Ontology terms (Ashburner et al., Nat Genet 25(1):25-29, 2000), to proteins based on information in published articles, and a paradigm called LEAP-FS (Literature-Enhanced Automated Prediction of Functional Sites) in which literature mining is used to validate the predictions of an orthogonal computational protein function prediction method.

  10. Functions of genes and enzymes involved in phenalinolactone biosynthesis.

    PubMed

    Daum, Martina; Schnell, Hans-Jörg; Herrmann, Simone; Günther, Andreas; Murillo, Renato; Müller, Rolf; Bisel, Philippe; Müller, Michael; Bechthold, Andreas

    2010-07-05

    Phenalinolactones are novel terpene glycoside antibiotics produced by Streptomyces sp. Tü6071. Inactivation of three oxygenase genes (plaO2, plaO3 and plaO5), two dehydrogenase genes (plaU, plaZ) and one putative acetyltransferase gene (plaV) led to the production of novel phenalinolactone derivatives (PL HS6, PL HS7, PL HS2 and PL X1). Furthermore, the exact biosynthetic functions of two enzymes were determined, and their in vitro activities were demonstrated. PlaO1, an Fe(II)/alpha-ketoglutarate-dependent dioxygenase, is responsible for the key step in gamma-butyrolactone formation, whereas PlaO5, a cytochrome P450-dependent monooxygenase, catalyses the 1-C-hydroxylation of phenalinolactone D. In addition, stable isotope feeding experiments with biosynthetic precursors shed light on the origin of the carbons in the gamma-butyrolactone moiety.

  11. Coupled cluster Green function: Model involving single and double excitations

    SciTech Connect

    Bhaskaran-Nair, Kiran; Kowalski, Karol; Shelton, William A.

    2016-04-14

    In this paper we report on the parallel implementation of the coupled-cluster (CC) Green function formulation (GF-CC) employing single and double excitations in the cluster operator (GF-CCSD). The detailed description of the underlying algorithm is provided, including the structure of ionization-potential- and electron-affinity-type intermediate tensors which enable to formulate GF-CC approach in a computationally feasible form. Several examples including calculations of ionization-potentials and electron a*ffinities for benchmark systems, which are juxtaposed against the experimental values, provide an illustration of the accuracies attainable in the GFCCSD simulations. We also discuss the structure of the CCSD self energies and discuss approximation that are geared to reduce the computational cost while maintaining the pole structure of the full GF-CCSD approach.

  12. On the application of the genetic algorithm to the predictability problems involving "on-off" switches

    NASA Astrophysics Data System (ADS)

    Zheng, Q.

    2011-12-01

    On the application of the genetic algorithm to the predictability problems involving "on-off" switches ZHENG Qin(1,2), DAI Yi(1), ZHANG Lu(1)and LU Xiaoqing(1) (1)Institute of Science, PLA University of Science and Technology, Nanjing 211101, China; (2)State Key Laboratory of Numerical Modeling for Atmospheric Sciences and Geophysical Fluid Dynamics (LASG), Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing 100029, China Abstract The lower bound of maximum predictable time can be formulated into a constrained nonlinear optimization problem, and the traditional solution to this problem is the filtering method and the conditional nonlinear optimal perturbation (CNOP) method. Usually, the CNOP method is implemented with the help of a gradient descent algorithm based on the adjoint method, which is named as the ADJ-CNOP, hereinafter. However, with the increasing improvement of actual prediction models, more and more physical processes are taken into consideration in models in the form of parameterization, thus giving rise to the "on-off" switch problem, which affects tremendously the effectiveness of the conventional gradient descent algorithm based on the adjoint method. This paper attempts to apply a genetic algorithm (GA) to the CNOP method, named as the GA-CNOP, to solve the predictability problems involving the "on-off" switches. As the precision of the filtering method depends uniquely on the division of the constraint region, its results are taken as benchmarks and a series of comparisons between the ADJ-CNOP and the GA-CNOP are performed. It is revealed that the GA-CNOP can always figure out the accurate lower bound of maximum predictable time even in discontinuous cases, while the ADJ-CNOP, owing to the effect of "on-off" switches, often yields the incorrect lower bound of maximum predictable time. This would suggest that in non-smooth cases, using a GA to solve the predictability problems is more effective than using the conventional

  13. Evolution and Cellular Function of Monothiol Glutaredoxins: Involvement in Iron-Sulphur Cluster Assembly

    PubMed Central

    Vilella, Felipe; Alves, Rui; Rodríguez-Manzaneque, María Teresa; Bellí, Gemma; Swaminathan, Swarna; Sunnerhagen, Per

    2004-01-01

    A number of bacterial species, mostly proteobacteria, possess monothiol glutaredoxins homologous to the Saccharomyces cerevisiae mitochondrial protein Grx5, which is involved in iron–sulphur cluster synthesis. Phylogenetic profiling is used to predict that bacterial monothiol glutaredoxins also participate in the iron–sulphur cluster (ISC) assembly machinery, because their phylogenetic profiles are similar to the profiles of the bacterial homologues of yeast ISC proteins. High evolutionary co-occurrence is observed between the Grx5 homologues and the homologues of the Yah1 ferredoxin, the scaffold proteins Isa1 and Isa2, the frataxin protein Yfh1 and the Nfu1 protein. This suggests that a specific functional interaction exists between these ISC machinery proteins. Physical interaction analyses using low-definition protein docking predict the formation of strong and specific complexes between Grx5 and several components of the yeast ISC machinery. Two-hybrid analysis has confirmed the in vivo interaction between Grx5 and Isa1. Sequence comparison techniques and cladistics indicate that the other two monothiol glutaredoxins of S. cerevisiae, Grx3 and Grx4, have evolved from the fusion of a thioredoxin gene with a monothiol glutaredoxin gene early in the eukaryotic lineage, leading to differential functional specialization. While bacteria do not contain these chimaeric glutaredoxins, in many eukaryotic species Grx5 and Grx3/4-type monothiol glutaredoxins coexist in the cell. PMID:18629168

  14. Predicting individual brain functional connectivity using a Bayesian hierarchical model.

    PubMed

    Dai, Tian; Guo, Ying

    2017-02-15

    Network-oriented analysis of functional magnetic resonance imaging (fMRI), especially resting-state fMRI, has revealed important association between abnormal connectivity and brain disorders such as schizophrenia, major depression and Alzheimer's disease. Imaging-based brain connectivity measures have become a useful tool for investigating the pathophysiology, progression and treatment response of psychiatric disorders and neurodegenerative diseases. Recent studies have started to explore the possibility of using functional neuroimaging to help predict disease progression and guide treatment selection for individual patients. These studies provide the impetus to develop statistical methodology that would help provide predictive information on disease progression-related or treatment-related changes in neural connectivity. To this end, we propose a prediction method based on Bayesian hierarchical model that uses individual's baseline fMRI scans, coupled with relevant subject characteristics, to predict the individual's future functional connectivity. A key advantage of the proposed method is that it can improve the accuracy of individualized prediction of connectivity by combining information from both group-level connectivity patterns that are common to subjects with similar characteristics as well as individual-level connectivity features that are particular to the specific subject. Furthermore, our method also offers statistical inference tools such as predictive intervals that help quantify the uncertainty or variability of the predicted outcomes. The proposed prediction method could be a useful approach to predict the changes in individual patient's brain connectivity with the progression of a disease. It can also be used to predict a patient's post-treatment brain connectivity after a specified treatment regimen. Another utility of the proposed method is that it can be applied to test-retest imaging data to develop a more reliable estimator for individual

  15. Simple criteria to predict margin involvement after chemoradiotherapy and sphincter-sparing for low rectal cancer.

    PubMed

    Dumont, F; Tilly, C; Dartigues, P; Goéré, D; Honoré, C; Elias, D

    2015-09-01

    Low rectal cancers carry a high risk of circumferential margin involvement (CRM+). The anatomy of the lower part of the rectum and a long course of chemoradiotherapy (CRT) limit the accuracy of imaging to predict the CRM+. Additional criteria are required. Eighty six patients undergoing rectal resection with a sphincter-sparing procedure after CRT for low rectal cancer between 2000 and 2013 were retrospectively reviewed. Risk factors of CRM+ and the cut-off number of risk factors required to accurately predict the CRM+ were analyzed. The CRM+ rate was 9.3% and in the multivariate analysis, the significant risk factors were a tumor size exceeding 3 cm, poor response to CRT and a fixed tumor. The best cut-off to predict CRM+ was the presence of 2 risk factors. Patients with 0-1 and 2-3 risk factors had a CRM+ respectively in 1.3% and 50% of cases and a 3-year recurrence rate of 7% and 35% after a median follow-up of 50 months. Poor response, a residual tumor greater than 3 cm and a fixed tumor are predictive of CRM+. Sphincter sparing is an oncological safety procedure for patients with 0-1 criteria but not for patients with 2-3 criteria. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. Functional involvement of cerebral cortex in adult sleepwalking.

    PubMed

    Oliviero, A; Della Marca, G; Tonali, P A; Pilato, F; Saturno, E; Dileone, M; Rubino, M; Di Lazzaro, V

    2007-08-01

    The pathophysiology of adult sleepwalking is still poorly understood. However, it is widely accepted that sleepwalking is a disorder of arousal. Arousal circuits widely project to the cortex, including motor cortex. We hypothesized that functional abnormality of these circuits could lead to changes in cortical excitability in sleepwalkers, even during wakefulness. We used transcranial magnetic stimulation (TMS) to examine the excitability of the human motor cortex during wakefulness in a group of adult sleepwalkers. When compared with the healthy control group, short interval intracortical inhibition (SICI), cortical silent period (CSP) duration, and short latency afferent inhibition (SAI) were reduced in adult sleepwalkers during wakefulness. Mean CSP duration was shorter in patients than in controls (80.9 +/- 41 ms vs. 139.4 +/- 37 ms; p = 0.0040). Mean SICI was significantly reduced in patients than in controls (73.5 +/- 38.4% vs. 36.7 +/- 13.1%; p = 0.0061). Mean SAI was also significantly reduced in patients than in controls (65.8 +/- 14.2% vs. 42.8 +/- 16.9%; p = 0.0053). This neurophysiological study suggests that there are alterations in sleepwalkers consistent with an impaired efficiency of inhibitory circuits during wakefulness. This inhibitory impairment could represent the neurophysiological correlate of brain "abnormalities" of sleepwalkers like "immaturity" of some neural circuits, synapses, or receptors.

  17. BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins.

    PubMed

    Kankainen, Matti; Ojala, Teija; Holm, Liisa

    2012-02-15

    Automated function prediction has played a central role in determining the biological functions of bacterial proteins. Typically, protein function annotation relies on homology, and function is inferred from other proteins with similar sequences. This approach has become popular in bacterial genomics because it is one of the few methods that is practical for large datasets and because it does not require additional functional genomics experiments. However, the existing solutions produce erroneous predictions in many cases, especially when query sequences have low levels of identity with the annotated source protein. This problem has created a pressing need for improvements in homology-based annotation. We present an automated method for the functional annotation of bacterial protein sequences. Based on sequence similarity searches, BLANNOTATOR accurately annotates query sequences with one-line summary descriptions of protein function. It groups sequences identified by BLAST into subsets according to their annotation and bases its prediction on a set of sequences with consistent functional information. We show the results of BLANNOTATOR's performance in sets of bacterial proteins with known functions. We simulated the annotation process for 3090 SWISS-PROT proteins using a database in its state preceding the functional characterisation of the query protein. For this dataset, our method outperformed the five others that we tested, and the improved performance was maintained even in the absence of highly related sequence hits. We further demonstrate the value of our tool by analysing the putative proteome of Lactobacillus crispatus strain ST1. BLANNOTATOR is an accurate method for bacterial protein function prediction. It is practical for genome-scale data and does not require pre-existing sequence clustering; thus, this method suits the needs of bacterial genome and metagenome researchers. The method and a web-server are available at http://ekhidna.biocenter.helsinki.fi/poxo/blannotator/.

  18. MicroRNA: biogenetic and functional mechanisms and involvements in cell differentiation and cancer.

    PubMed

    Tsuchiya, Soken; Okuno, Yasushi; Tsujimoto, Gozoh

    2006-08-01

    MicroRNAs (miRNAs) are endogenous small noncoding RNAs (20-23 nucleotides) that negatively regulate the gene expressions at the posttranscriptional level by base pairing to the 3' untranslated region of target messenger RNAs. Hundreds of miRNAs have been identified in humans and evolutionarily conserved from plants to animals. It is revealed that miRNAs regulate various physiological and pathological pathways such as cell differentiation, cell proliferation, and tumoriogenesis. By the computational analysis, it is predicted that 30% of protein-encoding genes are regulated by miRNAs. In this review, we discuss recent remarkable advances in the miRNA biogenetic and functional mechanisms and the involvements of miRNAs in cell differentiation, especially in hematopoietic lineages, and cancer. These evidences offer the possibility that miRNAs would be potentially useful for drug discovery.

  19. PRISM offers a comprehensive genomic approach to transcription factor function prediction.

    PubMed

    Wenger, Aaron M; Clarke, Shoa L; Guturu, Harendra; Chen, Jenny; Schaar, Bruce T; McLean, Cory Y; Bejerano, Gill

    2013-05-01

    The human genome encodes 1500-2000 different transcription factors (TFs). ChIP-seq is revealing the global binding profiles of a fraction of TFs in a fraction of their biological contexts. These data show that the majority of TFs bind directly next to a large number of context-relevant target genes, that most binding is distal, and that binding is context specific. Because of the effort and cost involved, ChIP-seq is seldom used in search of novel TF function. Such exploration is instead done using expression perturbation and genetic screens. Here we propose a comprehensive computational framework for transcription factor function prediction. We curate 332 high-quality nonredundant TF binding motifs that represent all major DNA binding domains, and improve cross-species conserved binding site prediction to obtain 3.3 million conserved, mostly distal, binding site predictions. We combine these with 2.4 million facts about all human and mouse gene functions, in a novel statistical framework, in search of enrichments of particular motifs next to groups of target genes of particular functions. Rigorous parameter tuning and a harsh null are used to minimize false positives. Our novel PRISM (predicting regulatory information from single motifs) approach obtains 2543 TF function predictions in a large variety of contexts, at a false discovery rate of 16%. The predictions are highly enriched for validated TF roles, and 45 of 67 (67%) tested binding site regions in five different contexts act as enhancers in functionally matched cells.

  20. PRISM offers a comprehensive genomic approach to transcription factor function prediction

    PubMed Central

    Wenger, Aaron M.; Clarke, Shoa L.; Guturu, Harendra; Chen, Jenny; Schaar, Bruce T.; McLean, Cory Y.; Bejerano, Gill

    2013-01-01

    The human genome encodes 1500–2000 different transcription factors (TFs). ChIP-seq is revealing the global binding profiles of a fraction of TFs in a fraction of their biological contexts. These data show that the majority of TFs bind directly next to a large number of context-relevant target genes, that most binding is distal, and that binding is context specific. Because of the effort and cost involved, ChIP-seq is seldom used in search of novel TF function. Such exploration is instead done using expression perturbation and genetic screens. Here we propose a comprehensive computational framework for transcription factor function prediction. We curate 332 high-quality nonredundant TF binding motifs that represent all major DNA binding domains, and improve cross-species conserved binding site prediction to obtain 3.3 million conserved, mostly distal, binding site predictions. We combine these with 2.4 million facts about all human and mouse gene functions, in a novel statistical framework, in search of enrichments of particular motifs next to groups of target genes of particular functions. Rigorous parameter tuning and a harsh null are used to minimize false positives. Our novel PRISM (predicting regulatory information from single motifs) approach obtains 2543 TF function predictions in a large variety of contexts, at a false discovery rate of 16%. The predictions are highly enriched for validated TF roles, and 45 of 67 (67%) tested binding site regions in five different contexts act as enhancers in functionally matched cells. PMID:23382538

  1. Prediction of Erectile Function Following Treatment for Prostate Cancer

    PubMed Central

    Alemozaffar, Mehrdad; Regan, Meredith M.; Cooperberg, Matthew R.; Wei, John T.; Michalski, Jeff M.; Sandler, Howard M.; Hembroff, Larry; Sadetsky, Natalia; Saigal, Christopher S.; Litwin, Mark S.; Klein, Eric; Kibel, Adam S.; Hamstra, Daniel A.; Pisters, Louis L.; Kuban, Deborah A.; Kaplan, Irving D.; Wood, David P.; Ciezki, Jay; Dunn, Rodney L.; Carroll, Peter R.; Sanda, Martin G.

    2013-01-01

    Context Sexual function is the health-related quality of life (HRQOL) domain most commonly impaired after prostate cancer treatment; however, validated tools to enable personalized prediction of erectile dysfunction after prostate cancer treatment are lacking. Objective To predict long-term erectile function following prostate cancer treatment based on individual patient and treatment characteristics. Design Pretreatment patient characteristics, sexual HRQOL, and treatment details measured in a longitudinal academic multicenter cohort (Prostate Cancer Outcomes and Satisfaction With Treatment Quality Assessment; enrolled from 2003 through 2006), were used to develop models predicting erectile function 2 years after treatment. A community-based cohort (community-based Cancer of the Prostate Strategic Urologic Research Endeavor [CaPSURE]; enrolled 1995 through 2007) externally validated model performance. Patients in US academic and community-based practices whose HRQOL was measured pretreatment (N = 1201) underwent follow-up after prostatectomy, external radiotherapy, or brachytherapy for prostate cancer. Sexual outcomes among men completing 2 years’ follow-up (n = 1027) were used to develop models predicting erectile function that were externally validated among 1913 patients in a community-based cohort. Main Outcome Measures Patient-reported functional erections suitable for intercourse 2 years following prostate cancer treatment. Results Two years after prostate cancer treatment, 368 (37% [95% CI, 34%–40%]) of all patients and 335 (48% [95% CI, 45%–52%]) of those with functional erections prior to treatment reported functional erections; 531 (53% [95% CI, 50%–56%]) of patients without penile prostheses reported use of medications or other devices for erectile dysfunction. Pretreatment sexual HRQOL score, age, serum prostate-specific antigen level, race/ethnicity, body mass index, and intended treatment details were associated with functional erections 2

  2. An overview of in silico protein function prediction.

    PubMed

    Sleator, Roy D; Walsh, Paul

    2010-03-01

    As the protein databases continue to expand at an exponential rate, fed by daily uploads from multiple large scale genomic and metagenomic projects, the problem of assigning a function to each new protein has become the focus of significant research interest in recent times. Herein, we review the most recent advances in the field of automated function prediction (AFP). We begin by defining what is meant by biological "function" and the means of describing such functions using standardised machine readable ontologies. We then focus on the various function-prediction programs available, both sequence and structure based, and outline their associated strengths and weaknesses. Finally, we conclude with a brief overview of the future challenges and outstanding questions in the field, which still remain unanswered.

  3. Prediction of margin involvement and local recurrence after skin-sparing and simple mastectomy.

    PubMed

    Al-Himdani, S; Timbrell, S; Tan, K T; Morris, J; Bundred, N J

    2016-07-01

    Skin-sparing mastectomy (SSM) facilitates immediate breast reconstruction. We investigated locoregional recurrence rates after SSM compared with simple mastectomy and the factors predicting oncological failure. Patients with early breast cancer that underwent mastectomy between 2000 and 2005 at a single institution were studied to ascertain local and systemic recurrence rates between groups. Kaplan-Meier curves and log-rank test were used to evaluate disease-free survival. Patients (n = 577) underwent simple mastectomy (80%) or SSM (20%). Median follow up was 80 months. Patients undergoing SSM were of younger average age, less often had involved lymph nodes (22% vs 44%, p < 0.001), more often had DCIS present (79% vs 53%, p < 0.001) and involved margins (29% vs 15%, p = 0.001). Involved surgical margins were associated with large size (p = 0.001). The 8-year local recurrence (LR) rates were 7.9% for SSM and 5% for simple mastectomy respectively (p = 0.35). Predictors of locoregional recurrence were lymph node involvement (HR 8.0, for >4 nodes, p < 0.001) and involved surgical margins (HR 3.3, p = 0.002). In node negative patients, SSM was a predictor of locoregional recurrence (HR 4.8 [1.1, 19.9], p = 0.033). Delayed reconstruction is more appropriate for node positive early breast cancer after post-mastectomy radiotherapy. Re-excision of involved margins is essential to prevent local recurrence after mastectomy. Copyright © 2016 Elsevier Ltd, BASO ~ the Association for Cancer Surgery, and the European Society of Surgical Oncology. All rights reserved.

  4. Elementary inequalities that involve two nonnegative vectors or functions

    PubMed Central

    Cohen, Joel E.; Kemperman, J. H. B.; Zbăganu, Gheorghe

    2004-01-01

    obtained from the first by replacing both outer summations by products, min by ×, × by +, and the nonnegative vectors a and b by nonnegative measurable functions f and g. The proofs of these inequalities are mysteriously diverse. PMID:15452346

  5. Cortical thickness in frontoparietal and cingulo-opercular networks predicts executive function performance in older adults.

    PubMed

    Schmidt, Erica L; Burge, Wesley; Visscher, Kristina M; Ross, Lesley A

    2016-03-01

    This study examined the relationship between cortical thickness in executive control networks and neuropsychological measures of executive function. Forty-one community-dwelling older adults completed an MRI scan and a neuropsychological battery including 5 measures of executive function. Factor analysis of executive function measures revealed 2 distinct factors: (a) Complex Attention Control (CAC), comprised of tasks that required immediate response to stimuli and involved subtle performance feedback; and (b) Sustained Executive Control (SEC), comprised of tasks that involved maintenance and manipulation of information over time. Neural networks of interest were the frontoparietal network (F-P) and cingulo-opercular network (C-O), which have previously been hypothesized to relate to different components of executive function, based on functional MRI studies, but not neuropsychological factors. Linear regression models revealed that greater cortical thickness in the F-P network, but not the C-O network, predicted better performance on the CAC factor, whereas greater cortical thickness in the C-O network, but not the F-P network, predicted better performance on the SEC factor. The relationship between cortical thickness and performance on executive function measures was characterized by a double dissociation between the thickness of cortical regions hypothesized to be involved in executive control and distinct executive processes. Results indicate that fundamentally different executive processes may be predicted by cortical thickness in distinct brain networks. (c) 2016 APA, all rights reserved).

  6. Predicting protein function by frequent functional association pattern mining in protein interaction networks.

    PubMed

    Cho, Young-Rae; Zhang, Aidong

    2010-01-01

    Predicting protein function from protein interaction networks has been challenging because of the complexity of functional relationships among proteins. Most previous function prediction methods depend on the neighborhood of or the connected paths to known proteins. However, their accuracy has been limited due to the functional inconsistency of interacting proteins. In this paper, we propose a novel approach for function prediction by identifying frequent patterns of functional associations in a protein interaction network. A set of functions that a protein performs is assigned into the corresponding node as a label. A functional association pattern is then represented as a labeled subgraph. Our frequent labeled subgraph mining algorithm efficiently searches the functional association patterns that occur frequently in the network. It iteratively increases the size of frequent patterns by one node at a time by selective joining, and simplifies the network by a priori pruning. Using the yeast protein interaction network, our algorithm found more than 1400 frequent functional association patterns. The function prediction is performed by matching the subgraph, including the unknown protein, with the frequent patterns analogous to it. By leave-one-out cross validation, we show that our approach has better performance than previous link-based methods in terms of prediction accuracy. The frequent functional association patterns generated in this study might become the foundations of advanced analysis for functional behaviors of proteins in a system level.

  7. Predicting functional brain ROIs via fiber shape models.

    PubMed

    Zhang, Tuo; Guo, Lei; Li, Kaiming; Zhu, Dajing; Cui, Guangbin; Liu, Tianming

    2011-01-01

    Study of structural and functional connectivities of the human brain has received significant interest and effort recently. A fundamental question arises when attempting to measure the structural and/or functional connectivities of specific brain networks: how to best identify possible Regions of Interests (ROIs)? In this paper, we present a novel ROI prediction framework that localizes ROIs in individual brains based on learned fiber shape models from multimodal task-based fMRI and diffusion tensor imaging (DTI) data. In the training stage, ROIs are identified as activation peaks in task-based fMRI data. Then, shape models of white matter fibers emanating from these functional ROIs are learned. In addition, ROIs' location distribution model is learned to be used as an anatomical constraint. In the prediction stage, functional ROIs are predicted in individual brains based on DTI data. The ROI prediction is formulated and solved as an energy minimization problem, in which the two learned models are used as energy terms. Our experiment results show that the average ROI prediction error is 3.45 mm, in comparison with the benchmark data provided by working memory task-based fMRI. Promising results were also obtained on the ADNI-2 longitudinal DTI dataset.

  8. Discontinuous unilateral involvement of 12 part core biopsies by adenocarcinoma predicts bilateral involvement of subsequent radical prostatectomy.

    PubMed

    Lowenthal, Brett Matthew; Liao, Xiaoyan; Wen, Fang; Bagherzadeh, Nader; Mahooti, Sepi

    2016-08-01

    At our institution, percent tumor burden in prostate core biopsies is quantified using variations of one of two methods. Measurement by the Aggregate method reports only adenocarcinoma and omits intervening stroma and benign prostatic glands while the Discontinuous method includes the intervening stroma and benign glands between distinct foci of adenocarcinoma. In this study, we selected cases with 12-part core biopsies that were followed by a radical prostatectomy within two years. Interestingly, we found that when adenocarcinoma involved prostate 12-part core biopsies and subsequent resection unilaterally, there is no significant difference in absolute percentage of tumor using either measuring method (P = 0.4). In contrast, when adenocarcinoma involved the biopsies unilaterally and subsequent prostatectomy bilaterally, the two measurement methods had a statistically significant difference in percentage scores (P = 0.002). In the study cohort, other factors including Gleason score (P = 0.88) and total number of adenocarcinoma-involved cores (P = 0.27) did not introduce any significant correlation with bilateral involvement. In this study, we found that biopsies that discontinuously and unilaterally involve half of a prostate are much more likely to involve both lobes than those that are unilateral and present in nodular aggregates.

  9. PredictProtein--an open resource for online prediction of protein structural and functional features.

    PubMed

    Yachdav, Guy; Kloppmann, Edda; Kajan, Laszlo; Hecht, Maximilian; Goldberg, Tatyana; Hamp, Tobias; Hönigschmid, Peter; Schafferhans, Andrea; Roos, Manfred; Bernhofer, Michael; Richter, Lothar; Ashkenazy, Haim; Punta, Marco; Schlessinger, Avner; Bromberg, Yana; Schneider, Reinhard; Vriend, Gerrit; Sander, Chris; Ben-Tal, Nir; Rost, Burkhard

    2014-07-01

    PredictProtein is a meta-service for sequence analysis that has been predicting structural and functional features of proteins since 1992. Queried with a protein sequence it returns: multiple sequence alignments, predicted aspects of structure (secondary structure, solvent accessibility, transmembrane helices (TMSEG) and strands, coiled-coil regions, disulfide bonds and disordered regions) and function. The service incorporates analysis methods for the identification of functional regions (ConSurf), homology-based inference of Gene Ontology terms (metastudent), comprehensive subcellular localization prediction (LocTree3), protein-protein binding sites (ISIS2), protein-polynucleotide binding sites (SomeNA) and predictions of the effect of point mutations (non-synonymous SNPs) on protein function (SNAP2). Our goal has always been to develop a system optimized to meet the demands of experimentalists not highly experienced in bioinformatics. To this end, the PredictProtein results are presented as both text and a series of intuitive, interactive and visually appealing figures. The web server and sources are available at http://ppopen.rostlab.org. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  10. White matter predicts functional connectivity in premanifest Huntington's disease.

    PubMed

    McColgan, Peter; Gregory, Sarah; Razi, Adeel; Seunarine, Kiran K; Gargouri, Fatma; Durr, Alexandra; Roos, Raymund A C; Leavitt, Blair R; Scahill, Rachael I; Clark, Chris A; Tabrizi, Sarah J; Rees, Geraint; Coleman, A; Decolongon, J; Fan, M; Petkau, T; Jauffret, C; Justo, D; Lehericy, S; Nigaud, K; Valabrègue, R; Choonderbeek, A; Hart, E P T; Hensman Moss, D J; Crawford, H; Johnson, E; Papoutsi, M; Berna, C; Reilmann, R; Weber, N; Stout, J; Labuschagne, I; Landwehrmeyer, B; Orth, M; Johnson, H

    2017-02-01

    The distribution of pathology in neurodegenerative disease can be predicted by the organizational characteristics of white matter in healthy brains. However, we have very little evidence for the impact these pathological changes have on brain function. Understanding any such link between structure and function is critical for understanding how underlying brain pathology influences the progressive behavioral changes associated with neurodegeneration. Here, we demonstrate such a link between structure and function in individuals with premanifest Huntington's. Using diffusion tractography and resting state functional magnetic resonance imaging to characterize white matter organization and functional connectivity, we investigate whether characteristic patterns of white matter organization in the healthy human brain shape the changes in functional coupling between brain regions in premanifest Huntington's disease. We find changes in functional connectivity in premanifest Huntington's disease that link directly to underlying patterns of white matter organization in healthy brains. Specifically, brain areas with strong structural connectivity show decreases in functional connectivity in premanifest Huntington's disease relative to controls, while regions with weak structural connectivity show increases in functional connectivity. Furthermore, we identify a pattern of dissociation in the strongest functional connections between anterior and posterior brain regions such that anterior functional connectivity increases in strength in premanifest Huntington's disease, while posterior functional connectivity decreases. Our findings demonstrate that organizational principles of white matter underlie changes in functional connectivity in premanifest Huntington's disease. Furthermore, we demonstrate functional antero-posterior dissociation that is in keeping with the caudo-rostral gradient of striatal pathology in HD.

  11. Executive function processes predict mobility outcomes in older adults.

    PubMed

    Gothe, Neha P; Fanning, Jason; Awick, Elizabeth; Chung, David; Wójcicki, Thomas R; Olson, Erin A; Mullen, Sean P; Voss, Michelle; Erickson, Kirk I; Kramer, Arthur F; McAuley, Edward

    2014-02-01

    To examine the relationship between performance on executive function measures and subsequent mobility outcomes in community-dwelling older adults. Randomized controlled clinical trial. Champaign-Urbana, Illinois. Community-dwelling older adults (N = 179; mean age 66.4). A 12-month exercise trial with two arms: an aerobic exercise group and a stretching and strengthening group. Established cognitive tests of executive function (flanker task, task switching, and a dual-task paradigm) and the Wisconsin card sort test. Mobility was assessed using the timed 8-foot up and go test and times to climb up and down a flight of stairs. Participants completed the cognitive tests at baseline and the mobility measures at baseline and after 12 months of the intervention. Multiple regression analyses were conducted to determine whether baseline executive function predicted postintervention functional performance after controlling for age, sex, education, cardiorespiratory fitness, and baseline mobility levels. Selective baseline executive function measurements, particularly performance on the flanker task (β = 0.15-0.17) and the Wisconsin card sort test (β = 0.11-0.16) consistently predicted mobility outcomes at 12 months. The estimates were in the expected direction, such that better baseline performance on the executive function measures predicted better performance on the timed mobility tests independent of intervention. Executive functions of inhibitory control, mental set shifting, and attentional flexibility were predictive of functional mobility. Given the literature associating mobility limitations with disability, morbidity, and mortality, these results are important for understanding the antecedents to poor mobility function that well-designed interventions to improve cognitive performance can attenuate. © 2014, Copyright the Authors Journal compilation © 2014, The American Geriatrics Society.

  12. DIANA-microT web server: elucidating microRNA functions through target prediction.

    PubMed

    Maragkakis, M; Reczko, M; Simossis, V A; Alexiou, P; Papadopoulos, G L; Dalamagas, T; Giannopoulos, G; Goumas, G; Koukis, E; Kourtis, K; Vergoulis, T; Koziris, N; Sellis, T; Tsanakas, P; Hatzigeorgiou, A G

    2009-07-01

    Computational microRNA (miRNA) target prediction is one of the key means for deciphering the role of miRNAs in development and disease. Here, we present the DIANA-microT web server as the user interface to the DIANA-microT 3.0 miRNA target prediction algorithm. The web server provides extensive information for predicted miRNA:target gene interactions with a user-friendly interface, providing extensive connectivity to online biological resources. Target gene and miRNA functions may be elucidated through automated bibliographic searches and functional information is accessible through Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The web server offers links to nomenclature, sequence and protein databases, and users are facilitated by being able to search for targeted genes using different nomenclatures or functional features, such as the genes possible involvement in biological pathways. The target prediction algorithm supports parameters calculated individually for each miRNA:target gene interaction and provides a signal-to-noise ratio and a precision score that helps in the evaluation of the significance of the predicted results. Using a set of miRNA targets recently identified through the pSILAC method, the performance of several computational target prediction programs was assessed. DIANA-microT 3.0 achieved there with 66% the highest ratio of correctly predicted targets over all predicted targets. The DIANA-microT web server is freely available at www.microrna.gr/microT.

  13. Do parents' exercise habits predict 13-18-year-old adolescents' involvement in sport?

    PubMed

    Sukys, Saulius; Majauskienė, Daiva; Cesnaitiene, Vida J; Karanauskiene, Diana

    2014-09-01

    This study examined links between parents' exercise habits and adolescents' participation in sports activities, considering the aspects of gender and age. It was hypothesized that regular exercise by both parents would be related to children's involvement in sport regardless of their gender and age. Moreover, it was hypothesized that children's sports activities would be more strongly related to their father's exercise activities. The study also examined the links between parents' exercise habits and children's motivation for sports. It was hypothesized that competition motives would be more important for children whose parents exercised regularly. The research sample included 2335 students from the seventh (n = 857), ninth (n = 960) and eleventh (n = 518) grades of various Lithuanian schools. The study used a questionnaire survey method, which revealed the links between parents' exercise habits and their children's participation in sport. Assessment of data for girls and boys showed that daughters' participation in sport could be predicted by both their fathers' and mothers' exercise habits, but sons' sports activities could be predicted only by the regular physical activities of their fathers. The assessment of children's sporting activities according to age revealed links between parental exercising and the engagement of older (15-16 years old), but not younger adolescents (13-14 years old). Analysis of sports motivation showed that competition motives were more important for boys than for girls. Fitness, well-being and appearance motives were more important for older adolescents (15-18 years old), while competition motives were more important for younger adolescents (13-14 years old). Research revealed the relationship between children's sport motives and fathers' exercise habits, while examination of mothers' exercise revealed no difference. Key pointsParental exercising significantly predicts adolescents' engagement in sport. Daughter's engagement in sport is

  14. Do Parents’ Exercise Habits Predict 13–18-Year-Old Adolescents’ Involvement in Sport?

    PubMed Central

    Sukys, Saulius; Majauskienė, Daiva; Cesnaitiene, Vida J.; Karanauskiene, Diana

    2014-01-01

    This study examined links between parents’ exercise habits and adolescents’ participation in sports activities, considering the aspects of gender and age. It was hypothesized that regular exercise by both parents would be related to children’s involvement in sport regardless of their gender and age. Moreover, it was hypothesized that children’s sports activities would be more strongly related to their father’s exercise activities. The study also examined the links between parents’ exercise habits and children’s motivation for sports. It was hypothesized that competition motives would be more important for children whose parents exercised regularly. The research sample included 2335 students from the seventh (n = 857), ninth (n = 960) and eleventh (n = 518) grades of various Lithuanian schools. The study used a questionnaire survey method, which revealed the links between parents’ exercise habits and their children’s participation in sport. Assessment of data for girls and boys showed that daughters’ participation in sport could be predicted by both their fathers’ and mothers’ exercise habits, but sons’ sports activities could be predicted only by the regular physical activities of their fathers. The assessment of children’s sporting activities according to age revealed links between parental exercising and the engagement of older (15–16 years old), but not younger adolescents (13–14 years old). Analysis of sports motivation showed that competition motives were more important for boys than for girls. Fitness, well-being and appearance motives were more important for older adolescents (15–18 years old), while competition motives were more important for younger adolescents (13–14 years old). Research revealed the relationship between children’s sport motives and fathers’ exercise habits, while examination of mothers’ exercise revealed no difference. Key points Parental exercising significantly predicts adolescents

  15. Biochemical functional predictions for protein structures of unknown or uncertain function.

    PubMed

    Mills, Caitlyn L; Beuning, Penny J; Ondrechen, Mary Jo

    2015-01-01

    With the exponential growth in the determination of protein sequences and structures via genome sequencing and structural genomics efforts, there is a growing need for reliable computational methods to determine the biochemical function of these proteins. This paper reviews the efforts to address the challenge of annotating the function at the molecular level of uncharacterized proteins. While sequence- and three-dimensional-structure-based methods for protein function prediction have been reviewed previously, the recent trends in local structure-based methods have received less attention. These local structure-based methods are the primary focus of this review. Computational methods have been developed to predict the residues important for catalysis and the local spatial arrangements of these residues can be used to identify protein function. In addition, the combination of different types of methods can help obtain more information and better predictions of function for proteins of unknown function. Global initiatives, including the Enzyme Function Initiative (EFI), COMputational BRidges to EXperiments (COMBREX), and the Critical Assessment of Function Annotation (CAFA), are evaluating and testing the different approaches to predicting the function of proteins of unknown function. These initiatives and global collaborations will increase the capability and reliability of methods to predict biochemical function computationally and will add substantial value to the current volume of structural genomics data by reducing the number of absent or inaccurate functional annotations.

  16. Cerebellar Neural Circuits Involving Executive Control Network Predict Response to Group Cognitive Behavior Therapy in Social Anxiety Disorder.

    PubMed

    MinlanYuan; Meng, Yajing; Zhang, Yan; Nie, Xiaojing; Ren, Zhengjia; Zhu, Hongru; Li, Yuchen; Lui, Su; Gong, Qiyong; Qiu, Changjian; Zhang, Wei

    2017-06-01

    Some intrinsic connectivity networks including the default mode network (DMN) and executive control network (ECN) may underlie social anxiety disorder (SAD). Although the cerebellum has been implicated in the pathophysiology of SAD and several networks relevant to higher-order cognition, it remains unknown whether cerebellar areas involved in DMN and ECN exhibit altered resting-state functional connectivity (rsFC) with cortical networks in SAD. Forty-six patients with SAD and 64 healthy controls (HC) were included and submitted to the baseline resting-state functional magnetic resonance imaging (fMRI). Seventeen SAD patients who completed post-treatment clinical assessments were included after group cognitive behavior therapy (CBT). RsFC of three cerebellar subregions in both groups was assessed respectively in a voxel-wise way, and these rsFC maps were compared by two-sample t tests between groups. Whole-brain voxel-wise regression was performed to examine whether cerebellar connectivity networks can predict response to CBT. Lower rsFC circuits of cerebellar subregions compared with HC at baseline (p < 0.05, corrected by false discovery rate) were revealed. The left Crus I rsFC with dorsal medial prefrontal cortex was negatively correlated with symptom severity. The clinical assessments in SAD patients were significantly decreased after CBT. Higher pretreatment cerebellar rsFC with angular gyrus and dorsal lateral frontal cortex corresponded with greater symptom improvement following CBT. Cerebellar rsFC circuits involving DMN and ECN are possible neuropathologic mechanisms of SAD. Stronger pretreatment cerebellar rsFC circuits involving ECN suggest potential neural markers to predict CBT response.

  17. The Predictive Role of Maternal Parenting and Stress on Pupils' Bullying involvement.

    PubMed

    Alizadeh Maralani, Fatemeh; Mirnasab, Mirmahmoud; Hashemi, Touraj

    2016-10-03

    The link between inappropriate parenting style and both bullying and victimization is well documented. However, it is not clear as to which kind of parenting style is associated with victimization. Furthermore, no studies have yet been conducted regarding the role of parental stress in bullying and victimization. This study aimed to examine the role of parenting styles and maternal stress in pupils' bullying and victimization. A total of 300 primary school pupils, enrolled in fourth and fifth grades, participated in the study. Initially, 100 noninvolved pupils were randomly selected using a multistage cluster sampling method. Then using a screening method, 100 bully pupils and 100 victimized peers were selected. Olweus Bullying Scale and teacher nomination were administered for screening these pupils. Baumrind Parenting Style Questionnaire and revised version of Abidin Parental Stress Index (short form) were also applied to all pupils in the study. Data were analyzed using discriminant function analysis. The findings showed that (a) with regard to parenting styles, significant differences were found among groups. Authoritarian parenting style could significantly predict pupils' bullying behavior, whereas victimization was predictable in families with permissive parenting style. In addition, noninvolved pupils were predicted to have authoritative parenting style. (b) Considering maternal stress, significant differences were observed across groups. Parents of bullies and victims were predicted to have higher maternal stress than noninvolved pupils. The implications of the study in relation to the role of mothers in bullying and victimization are discussed. © The Author(s) 2016.

  18. Predicting species establishment using absent species and functional neighborhoods.

    PubMed

    Bennett, Jonathan A; Pärtel, Meelis

    2017-04-01

    Species establishment within a community depends on their interactions with the local environment and resident community. Such environmental and biotic filtering is frequently inferred from functional trait and phylogenetic patterns within communities; these patterns may also predict which additional species can establish. However, differentiating between environmental and biotic filtering can be challenging, which may complicate establishment predictions. Creating a habitat-specific species pool by identifying which absent species within the region can establish in the focal habitat allows us to isolate biotic filtering by modeling dissimilarity between the observed and biotically excluded species able to pass environmental filters. Similarly, modeling the dissimilarity between the habitat-specific species pool and the environmentally excluded species within the region can isolate local environmental filters. Combined, these models identify potentially successful phenotypes and why certain phenotypes were unsuccessful. Here, we present a framework that uses the functional dissimilarity among these groups in logistic models to predict establishment of additional species. This approach can use multivariate trait distances and phylogenetic information, but is most powerful when using individual traits and their interactions. It also requires an appropriate distance-based dissimilarity measure, yet the two most commonly used indices, nearest neighbor (one species) and mean pairwise (all species) distances, may inaccurately predict establishment. By iteratively increasing the number of species used to measure dissimilarity, a functional neighborhood can be chosen that maximizes the detection of underlying trait patterns. We tested this framework using two seed addition experiments in calcareous grasslands. Although the functional neighborhood size that best fits the community's trait structure depended on the type of filtering considered, selecting these functional

  19. Childhood bullying involvement predicts low-grade systemic inflammation into adulthood

    PubMed Central

    Copeland, William E.; Wolke, Dieter; Lereya, Suzet Tanya; Shanahan, Lilly; Worthman, Carol; Costello, E. Jane

    2014-01-01

    Bullying is a common childhood experience that involves repeated mistreatment to improve or maintain one’s status. Victims display long-term social, psychological, and health consequences, whereas bullies display minimal ill effects. The aim of this study is to test how this adverse social experience is biologically embedded to affect short- or long-term levels of C-reactive protein (CRP), a marker of low-grade systemic inflammation. The prospective population-based Great Smoky Mountains Study (n = 1,420), with up to nine waves of data per subject, was used, covering childhood/adolescence (ages 9–16) and young adulthood (ages 19 and 21). Structured interviews were used to assess bullying involvement and relevant covariates at all childhood/adolescent observations. Blood spots were collected at each observation and assayed for CRP levels. During childhood and adolescence, the number of waves at which the child was bullied predicted increasing levels of CRP. Although CRP levels rose for all participants from childhood into adulthood, being bullied predicted greater increases in CRP levels, whereas bullying others predicted lower increases in CRP compared with those uninvolved in bullying. This pattern was robust, controlling for body mass index, substance use, physical and mental health status, and exposures to other childhood psychosocial adversities. A child’s role in bullying may serve as either a risk or a protective factor for adult low-grade inflammation, independent of other factors. Inflammation is a physiological response that mediates the effects of both social adversity and dominance on decreases in health. PMID:24821813

  20. Childhood bullying involvement predicts low-grade systemic inflammation into adulthood.

    PubMed

    Copeland, William E; Wolke, Dieter; Lereya, Suzet Tanya; Shanahan, Lilly; Worthman, Carol; Costello, E Jane

    2014-05-27

    Bullying is a common childhood experience that involves repeated mistreatment to improve or maintain one's status. Victims display long-term social, psychological, and health consequences, whereas bullies display minimal ill effects. The aim of this study is to test how this adverse social experience is biologically embedded to affect short- or long-term levels of C-reactive protein (CRP), a marker of low-grade systemic inflammation. The prospective population-based Great Smoky Mountains Study (n = 1,420), with up to nine waves of data per subject, was used, covering childhood/adolescence (ages 9-16) and young adulthood (ages 19 and 21). Structured interviews were used to assess bullying involvement and relevant covariates at all childhood/adolescent observations. Blood spots were collected at each observation and assayed for CRP levels. During childhood and adolescence, the number of waves at which the child was bullied predicted increasing levels of CRP. Although CRP levels rose for all participants from childhood into adulthood, being bullied predicted greater increases in CRP levels, whereas bullying others predicted lower increases in CRP compared with those uninvolved in bullying. This pattern was robust, controlling for body mass index, substance use, physical and mental health status, and exposures to other childhood psychosocial adversities. A child's role in bullying may serve as either a risk or a protective factor for adult low-grade inflammation, independent of other factors. Inflammation is a physiological response that mediates the effects of both social adversity and dominance on decreases in health.

  1. Tumor Budding Is Independently Predictive for Lymph Node Involvement in Early Gastric Cancer.

    PubMed

    Gulluoglu, Mine; Yegen, Gulcin; Ozluk, Yasemin; Keskin, Metin; Dogan, Serap; Gundogdu, Gökçen; Onder, Semen; Balik, Emre

    2015-08-01

    The most important prognostic factor for early gastric cancer (EGC) is the lymph node status. It is important to predict early lesions without lymph node metastasis (LNM) before proceeding to radical surgery in locally excised lesions. Tumor budding is a feature known to be related to aggressive tumor behavior in several solid tumors. We aimed to assess the predictive value of tumor budding for LNM in pT1a and pT1b gastric cancer. We retrospectively investigated radical gastrectomy specimens for of 126 EGC patients and assess the possible relation between the clinicopathologic features, including age, gender, tumor location, tumor size, macroscopic tumor type, histologic differentiation, depth and width of submucosal invasion, lymphovascular invasion, and tumor budding with lymph node involvement. Among the 126 EGCs, 38 were stages as pT1a and 88 as pT1b. LNM rate in pT1a tumors was 13% whereas it was 33% in pT1b tumors. Tumor budding was the only factor significantly and independently related to LNM in pT1a patients. Female gender and tumor budding were found to be independent risk factors in pT1b group. Other clinicopathologic features were not related to LNM. Based on these results, we suggest that budding is a promising parameter to assess for prediction of LNM in EGC removed by endoscopic surgery, and to decide on the appropriate surgical approach. © The Author(s) 2015.

  2. Polymorphisms in genes involved in EGFR-turnover are predictive for cetuximab efficacy in colorectal cancer

    PubMed Central

    Stintzing, Sebastian; Zhang, Wu; Heinemann, Volker; Neureiter, Daniel; Kemmerling, Ralf; Kirchner, Thomas; Jung, Andreas; Folwaczny, Matthias; Yang, Dongyun; Ning, Yan; Sebio, Ana; Stremitzer, Stefan; Sunakawa, Yu; Matsusaka, Satoshi; Yamauchi, Shinichi; Loupakis, Fotios; Cremolini, Chiara; Falcone, Alfredo; Lenz, Heinz-Josef

    2015-01-01

    Transmembrane receptors such as the epidermal growth factor receptor (EGFR) are regulated by their turnover, which is dependent on the ubiquitin-proteasome-system (UPS). We tested in two independent study cohorts whether single nucleotide polymorphisms (SNPs) in genes involved in EGFR turnover predict clinical outcome in cetuximab treated metastatic colorectal cancer patients. The following SNPs involved in EGFR degradation were analyzed in a screening cohort of 108 patients treated with cetuximab in the chemorefractory setting: c-CBL (rs7105971; rs4938637; rs4938638; rs251837), EPS15 (rs17567; rs7308; rs1065754), NAE1 (rs363169; rs363170; rs363172); SH3KBP1 (rs7051590; rs5955820; rs1017874; rs11795873); SGIP1 (rs604737; rs6570808; rs7526812); UBE2M (rs895364; rs895374); UBE2L3 (rs5754216). SNPs showing an association with response or survival were analyzed in BRAF and RAS wild-type samples from the FIRE-3 study. 153 FOLFIRI plus cetuximab treated patients served as validation set, 168 patients of the FOLFIRI plus bevacizumab arm served as controls. EGFR FISH was done in 138 samples to test whether significant SNPs were associated with EGFR expression. UBE2M rs895374 was significantly associated with PFS (logrank-p = 0.005; HR 0.60) within cetuximab treated patients. No association with bevacizumab treated patients (n=168) could be established (p= 0.56, HR: 0.90). rs895374 genotype did not affect EGFR FISH measurements. EGFR recycling is an interesting mechanism of secondary resistance to cetuximab in mCRC. This is the first report suggesting that germline polymorphisms in the degradation process predict efficacy of cetuximab in patients with mCRC. Genes involved in EGFR turnover may be new targets in the treatment of mCRC. PMID:26206335

  3. 3D-Fun: predicting enzyme function from structure.

    PubMed

    von Grotthuss, Marcin; Plewczynski, Dariusz; Vriend, Gert; Rychlewski, Leszek

    2008-07-01

    The 'omics' revolution is causing a flurry of data that all needs to be annotated for it to become useful. Sequences of proteins of unknown function can be annotated with a putative function by comparing them with proteins of known function. This form of annotation is typically performed with BLAST or similar software. Structural genomics is nowadays also bringing us three dimensional structures of proteins with unknown function. We present here software that can be used when sequence comparisons fail to determine the function of a protein with known structure but unknown function. The software, called 3D-Fun, is implemented as a server that runs at several European institutes and is freely available for everybody at all these sites. The 3D-Fun servers accept protein coordinates in the standard PDB format and compare them with all known protein structures by 3D structural superposition using the 3D-Hit software. If structural hits are found with proteins with known function, these are listed together with their function and some vital comparison statistics. This is conceptually very similar in 3D to what BLAST does in 1D. Additionally, the superposition results are displayed using interactive graphics facilities. Currently, the 3D-Fun system only predicts enzyme function but an expanded version with Gene Ontology predictions will be available soon. The server can be accessed at http://3dfun.bioinfo.pl/ or at http://3dfun.cmbi.ru.nl/.

  4. Beyond genotype: serotonin transporter epigenetic modification predicts human brain function.

    PubMed

    Nikolova, Yuliya S; Koenen, Karestan C; Galea, Sandro; Wang, Chiou-Miin; Seney, Marianne L; Sibille, Etienne; Williamson, Douglas E; Hariri, Ahmad R

    2014-09-01

    We examined epigenetic regulation in regards to behaviorally and clinically relevant human brain function. Specifically, we found that increased promoter methylation of the serotonin transporter gene predicted increased threat-related amygdala reactivity and decreased mRNA expression in postmortem amygdala tissue. These patterns were independent of functional genetic variation in the same region. Furthermore, the association with amygdala reactivity was replicated in a second cohort and was robust to both sampling methods and age.

  5. Predictability of Genetic Interactions from Functional Gene Modules

    PubMed Central

    Young, Jonathan H.; Marcotte, Edward M.

    2016-01-01

    Characterizing genetic interactions is crucial to understanding cellular and organismal response to gene-level perturbations. Such knowledge can inform the selection of candidate disease therapy targets, yet experimentally determining whether genes interact is technically nontrivial and time-consuming. High-fidelity prediction of different classes of genetic interactions in multiple organisms would substantially alleviate this experimental burden. Under the hypothesis that functionally related genes tend to share common genetic interaction partners, we evaluate a computational approach to predict genetic interactions in Homo sapiens, Drosophila melanogaster, and Saccharomyces cerevisiae. By leveraging knowledge of functional relationships between genes, we cross-validate predictions on known genetic interactions and observe high predictive power of multiple classes of genetic interactions in all three organisms. Additionally, our method suggests high-confidence candidate interaction pairs that can be directly experimentally tested. A web application is provided for users to query genes for predicted novel genetic interaction partners. Finally, by subsampling the known yeast genetic interaction network, we found that novel genetic interactions are predictable even when knowledge of currently known interactions is minimal. PMID:28007839

  6. The Prediction of Key Cytoskeleton Components Involved in Glomerular Diseases Based on a Protein-Protein Interaction Network.

    PubMed

    Ding, Fangrui; Tan, Aidi; Ju, Wenjun; Li, Xuejuan; Li, Shao; Ding, Jie

    2016-01-01

    Maintenance of the physiological morphologies of different types of cells and tissues is essential for the normal functioning of each system in the human body. Dynamic variations in cell and tissue morphologies depend on accurate adjustments of the cytoskeletal system. The cytoskeletal system in the glomerulus plays a key role in the normal process of kidney filtration. To enhance the understanding of the possible roles of the cytoskeleton in glomerular diseases, we constructed the Glomerular Cytoskeleton Network (GCNet), which shows the protein-protein interaction network in the glomerulus, and identified several possible key cytoskeletal components involved in glomerular diseases. In this study, genes/proteins annotated to the cytoskeleton were detected by Gene Ontology analysis, and glomerulus-enriched genes were selected from nine available glomerular expression datasets. Then, the GCNet was generated by combining these two sets of information. To predict the possible key cytoskeleton components in glomerular diseases, we then examined the common regulation of the genes in GCNet in the context of five glomerular diseases based on their transcriptomic data. As a result, twenty-one cytoskeleton components as potential candidate were highlighted for consistently down- or up-regulating in all five glomerular diseases. And then, these candidates were examined in relation to existing known glomerular diseases and genes to determine their possible functions and interactions. In addition, the mRNA levels of these candidates were also validated in a puromycin aminonucleoside(PAN) induced rat nephropathy model and were also matched with existing Diabetic Nephropathy (DN) transcriptomic data. As a result, there are 15 of 21 candidates in PAN induced nephropathy model were consistent with our predication and also 12 of 21 candidates were matched with differentially expressed genes in the DN transcriptomic data. By providing a novel interaction network and prediction, GCNet

  7. Predicting enzymatic function from global binding site descriptors.

    PubMed

    Volkamer, Andrea; Kuhn, Daniel; Rippmann, Friedrich; Rarey, Matthias

    2013-03-01

    Due to the rising number of solved protein structures, computer-based techniques for automatic protein functional annotation and classification into families are of high scientific interest. DoGSiteScorer automatically calculates global descriptors for self-predicted pockets based on the 3D structure of a protein. Protein function predictors on three levels with increasing granularity are built by use of a support vector machine (SVM), based on descriptors of 26632 pockets from enzymes with known structure and enzyme classification. The SVM models represent a generalization of the available descriptor space for each enzyme class, subclass, and substrate-specific sub-subclass. Cross-validation studies show accuracies of 68.2% for predicting the correct main class and accuracies between 62.8% and 80.9% for the six subclasses. Substrate-specific recall rates for a kinase subset are 53.8%. Furthermore, application studies show the ability of the method for predicting the function of unknown proteins and gaining valuable information for the function prediction field. Copyright © 2012 Wiley Periodicals, Inc.

  8. Prediction of First Grade Social-Emotional and Intellectual Functioning.

    ERIC Educational Resources Information Center

    Kohn, Martin; And Others

    In order to determine the longitudinal persistence of two major personality dimensions, namely Apathy-Withdrawal versus Interest-Participation (Factor 1) and Anger-Defiance versus Conformity-Compliance (Factor 2), and to test the hypothesis that the social-emotional functioning of the preschool child is predictive of later intellectual-academic…

  9. Exploring Function Prediction in Protein Interaction Networks via Clustering Methods

    PubMed Central

    Trivodaliev, Kire; Bogojeska, Aleksandra; Kocarev, Ljupco

    2014-01-01

    Complex networks have recently become the focus of research in many fields. Their structure reveals crucial information for the nodes, how they connect and share information. In our work we analyze protein interaction networks as complex networks for their functional modular structure and later use that information in the functional annotation of proteins within the network. We propose several graph representations for the protein interaction network, each having different level of complexity and inclusion of the annotation information within the graph. We aim to explore what the benefits and the drawbacks of these proposed graphs are, when they are used in the function prediction process via clustering methods. For making this cluster based prediction, we adopt well established approaches for cluster detection in complex networks using most recent representative algorithms that have been proven as efficient in the task at hand. The experiments are performed using a purified and reliable Saccharomyces cerevisiae protein interaction network, which is then used to generate the different graph representations. Each of the graph representations is later analysed in combination with each of the clustering algorithms, which have been possibly modified and implemented to fit the specific graph. We evaluate results in regards of biological validity and function prediction performance. Our results indicate that the novel ways of presenting the complex graph improve the prediction process, although the computational complexity should be taken into account when deciding on a particular approach. PMID:24972109

  10. Human transfer functions used to predict system performance parameters

    NASA Technical Reports Server (NTRS)

    1966-01-01

    Automatic, parameter-tracking, model-matching technique compares the responses of a human operator with those of an analog computer model of a human operator to predict and analyze the performance of mechanical or electromechanical systems prior to construction. Transfer functions represent the input-output relation of an operator controlling a closed-loop system.

  11. Ontology-Based Prediction and Prioritization of Gene Functional Annotations.

    PubMed

    Chicco, Davide; Masseroli, Marco

    2016-01-01

    Genes and their protein products are essential molecular units of a living organism. The knowledge of their functions is key for the understanding of physiological and pathological biological processes, as well as in the development of new drugs and therapies. The association of a gene or protein with its functions, described by controlled terms of biomolecular terminologies or ontologies, is named gene functional annotation. Very many and valuable gene annotations expressed through terminologies and ontologies are available. Nevertheless, they might include some erroneous information, since only a subset of annotations are reviewed by curators. Furthermore, they are incomplete by definition, given the rapidly evolving pace of biomolecular knowledge. In this scenario, computational methods that are able to quicken the annotation curation process and reliably suggest new annotations are very important. Here, we first propose a computational pipeline that uses different semantic and machine learning methods to predict novel ontology-based gene functional annotations; then, we introduce a new semantic prioritization rule to categorize the predicted annotations by their likelihood of being correct. Our tests and validations proved the effectiveness of our pipeline and prioritization of predicted annotations, by selecting as most likely manifold predicted annotations that were later confirmed.

  12. Nailfold capillaroscopy for prediction of novel future severe organ involvement in systemic sclerosis.

    PubMed

    Smith, Vanessa; Riccieri, Valeria; Pizzorni, Carmen; Decuman, Saskia; Deschepper, Ellen; Bonroy, Carolien; Sulli, Alberto; Piette, Yves; De Keyser, Filip; Cutolo, Maurizio

    2013-12-01

    Assessment of associations of nailfold videocapillaroscopy (NVC) scleroderma (systemic sclerosis; SSc) ("early," "active," and "late") with novel future severe clinical involvement in 2 independent cohorts. Sixty-six consecutive Belgian and 82 Italian patients with SSc underwent NVC at baseline. Images were blindly assessed and classified into normal, early, active, or late NVC pattern. Clinical evaluation was performed for 9 organ systems (general, peripheral vascular, skin, joint, muscle, gastrointestinal tract, lung, heart, and kidney) according to the Medsger disease severity scale (DSS) at baseline and in the future (18-24 months of followup). Severe clinical involvement was defined as category 2 to 4 per organ of the DSS. Logistic regression analysis (continuous NVC predictor variable) was performed. The OR to develop novel future severe organ involvement was stronger according to more severe NVC patterns and similar in both cohorts. In simple logistic regression analysis the OR in the Belgian/Italian cohort was 2.16 (95% CI 1.19-4.47, p = 0.010)/2.33 (95% CI 1.36-4.22, p = 0.002) for the early NVC SSc pattern, 4.68/5.42 for the active pattern, and 10.14/12.63 for the late pattern versus the normal pattern. In multiple logistic regression analysis, adjusting for disease duration, subset, and vasoactive medication, the OR was 2.99 (95% CI 1.31-8.82, p = 0.007)/1.88 (95% CI 1.00-3.71, p = 0.050) for the early NVC SSc pattern, 8.93/3.54 for the active pattern, and 26.69/6.66 for the late pattern versus the normal pattern. Capillaroscopy may be predictive of novel future severe organ involvement in SSc, as attested by 2 independent cohorts.

  13. Disorganized symptoms and executive functioning predict impaired social functioning in subjects at risk for psychosis.

    PubMed

    Eslami, Ali; Jahshan, Carol; Cadenhead, Kristin S

    2011-01-01

    Predictors of social functioning deficits were assessed in 22 individuals "at risk" for psychosis. Disorganized symptoms and executive functioning predicted social functioning at follow-up. Early intervention efforts that focus on social and cognitive skills are indicated in this vulnerable population.

  14. Protein function prediction using guilty by association from interaction networks.

    PubMed

    Piovesan, Damiano; Giollo, Manuel; Ferrari, Carlo; Tosatto, Silvio C E

    2015-12-01

    Protein function prediction from sequence using the Gene Ontology (GO) classification is useful in many biological problems. It has recently attracted increasing interest, thanks in part to the Critical Assessment of Function Annotation (CAFA) challenge. In this paper, we introduce Guilty by Association on STRING (GAS), a tool to predict protein function exploiting protein-protein interaction networks without sequence similarity. The assumption is that whenever a protein interacts with other proteins, it is part of the same biological process and located in the same cellular compartment. GAS retrieves interaction partners of a query protein from the STRING database and measures enrichment of the associated functional annotations to generate a sorted list of putative functions. A performance evaluation based on CAFA metrics and a fair comparison with optimized BLAST similarity searches is provided. The consensus of GAS and BLAST is shown to improve overall performance. The PPI approach is shown to outperform similarity searches for biological process and cellular compartment GO predictions. Moreover, an analysis of the best practices to exploit protein-protein interaction networks is also provided.

  15. Predicting Protein Function via Semantic Integration of Multiple Networks.

    PubMed

    Yu, Guoxian; Fu, Guangyuan; Wang, Jun; Zhu, Hailong

    2016-01-01

    Determining the biological functions of proteins is one of the key challenges in the post-genomic era. The rapidly accumulated large volumes of proteomic and genomic data drives to develop computational models for automatically predicting protein function in large scale. Recent approaches focus on integrating multiple heterogeneous data sources and they often get better results than methods that use single data source alone. In this paper, we investigate how to integrate multiple biological data sources with the biological knowledge, i.e., Gene Ontology (GO), for protein function prediction. We propose a method, called SimNet, to Semantically integrate multiple functional association Networks derived from heterogenous data sources. SimNet firstly utilizes GO annotations of proteins to capture the semantic similarity between proteins and introduces a semantic kernel based on the similarity. Next, SimNet constructs a composite network, obtained as a weighted summation of individual networks, and aligns the network with the kernel to get the weights assigned to individual networks. Then, it applies a network-based classifier on the composite network to predict protein function. Experiment results on heterogenous proteomic data sources of Yeast, Human, Mouse, and Fly show that, SimNet not only achieves better (or comparable) results than other related competitive approaches, but also takes much less time. The Matlab codes of SimNet are available at https://sites.google.com/site/guoxian85/simnet.

  16. Predicting transfer performance: a comparison of competing function learning models.

    PubMed

    McDaniel, Mark A; Dimperio, Eric; Griego, Jacqueline A; Busemeyer, Jerome R

    2009-01-01

    The population of linear experts (POLE) model suggests that function learning and transfer are mediated by activation of a set of prestored linear functions that together approximate the given function (Kalish, Lewandowsky, & Kruschke, 2004). In the extrapolation-association (EXAM) model, an exemplar-based architecture associates trained input values with their paired output values. Transfer incorporates a linear rule-based response mechanism (McDaniel & Busemeyer, 2005). Learners were trained on a functional relationship defined by 2 linear-function segments with mirror slopes. In Experiment 1, 1 segment was densely trained and 1 was sparsely trained; in Experiment 2, both segments were trained equally, but the 2 segments were widely separated. Transfer to new input values was tested. For each model, training performance for each individual participant was fit, and transfer predictions were generated. POLE generally better fit the training data than did EXAM, but EXAM was more accurate at predicting (and fitting) transfer behaviors. It was especially telling that in Experiment 2 the transfer pattern was more consistent with EXAM's but not POLE's predictions, even though the presentation of salient linear segments during training dovetailed with POLE's approach.

  17. Structure-based Methods for Computational Protein Functional Site Prediction

    PubMed Central

    Dukka, B KC

    2013-01-01

    Due to the advent of high throughput sequencing techniques and structural genomic projects, the number of gene and protein sequences has been ever increasing. Computational methods to annotate these genes and proteins are even more indispensable. Proteins are important macromolecules and study of the function of proteins is an important problem in structural bioinformatics. This paper discusses a number of methods to predict protein functional site especially focusing on protein ligand binding site prediction. Initially, a short overview is presented on recent advances in methods for selection of homologous sequences. Furthermore, a few recent structural based approaches and sequence-and-structure based approaches for protein functional sites are discussed in details. PMID:24688745

  18. Protein Function Prediction Using Deep Restricted Boltzmann Machines

    PubMed Central

    Zou, Xianchun; Wang, Guijun

    2017-01-01

    Accurately annotating biological functions of proteins is one of the key tasks in the postgenome era. Many machine learning based methods have been applied to predict functional annotations of proteins, but this task is rarely solved by deep learning techniques. Deep learning techniques recently have been successfully applied to a wide range of problems, such as video, images, and nature language processing. Inspired by these successful applications, we investigate deep restricted Boltzmann machines (DRBM), a representative deep learning technique, to predict the missing functional annotations of partially annotated proteins. Experimental results on Homo sapiens, Saccharomyces cerevisiae, Mus musculus, and Drosophila show that DRBM achieves better performance than other related methods across different evaluation metrics, and it also runs faster than these comparing methods. PMID:28744460

  19. Hallucinogen use predicts reduced recidivism among substance-involved offenders under community corrections supervision.

    PubMed

    Hendricks, Peter S; Clark, C Brendan; Johnson, Matthew W; Fontaine, Kevin R; Cropsey, Karen L

    2014-01-01

    Hallucinogen-based interventions may benefit substance use populations, but contemporary data informing the impact of hallucinogens on addictive behavior are scarce. Given that many individuals in the criminal justice system engage in problematic patterns of substance use, hallucinogen treatments also may benefit criminal justice populations. However, the relationship between hallucinogen use and criminal recidivism is unknown. In this longitudinal study, we examined the relationship between naturalistic hallucinogen use and recidivism among individuals under community corrections supervision with a history of substance involvement (n=25,622). We found that hallucinogen use predicted a reduced likelihood of supervision failure (e.g. noncompliance with legal requirements including alcohol and other drug use) while controlling for an array of potential confounding factors (odds ratio (OR)=0.60 (0.46, 0.79)). Our results suggest that hallucinogens may promote alcohol and other drug abstinence and prosocial behavior in a population with high rates of recidivism.

  20. A review of protein function prediction under machine learning perspective.

    PubMed

    Bernardes, Juliana S; Pedreira, Carlos E

    2013-08-01

    Protein function prediction is one of the most challenging problems in the post-genomic era. The number of newly identified proteins has been exponentially increasing with the advances of the high-throughput techniques. However, the functional characterization of these new proteins was not incremented in the same proportion. To fill this gap, a large number of computational methods have been proposed in the literature. Early approaches have explored homology relationships to associate known functions to the newly discovered proteins. Nevertheless, these approaches tend to fail when a new protein is considerably different (divergent) from previously known ones. Accordingly, more accurate approaches, that use expressive data representation and explore sophisticate computational techniques are required. Regarding these points, this review provides a comprehensible description of machine learning approaches that are currently applied to protein function prediction problems. We start by defining several problems enrolled in understanding protein function aspects, and describing how machine learning can be applied to these problems. We aim to expose, in a systematical framework, the role of these techniques in protein function inference, sometimes difficult to follow up due to the rapid evolvement of the field. With this purpose in mind, we highlight the most representative contributions, the recent advancements, and provide an insightful categorization and classification of machine learning methods in functional proteomics.

  1. Automated protein function prediction--the genomic challenge.

    PubMed

    Friedberg, Iddo

    2006-09-01

    Overwhelmed with genomic data, biologists are facing the first big post-genomic question--what do all genes do? First, not only is the volume of pure sequence and structure data growing, but its diversity is growing as well, leading to a disproportionate growth in the number of uncharacterized gene products. Consequently, established methods of gene and protein annotation, such as homology-based transfer, are annotating less data and in many cases are amplifying existing erroneous annotation. Second, there is a need for a functional annotation which is standardized and machine readable so that function prediction programs could be incorporated into larger workflows. This is problematic due to the subjective and contextual definition of protein function. Third, there is a need to assess the quality of function predictors. Again, the subjectivity of the term 'function' and the various aspects of biological function make this a challenging effort. This article briefly outlines the history of automated protein function prediction and surveys the latest innovations in all three topics.

  2. Predicting plants -modeling traits as a function of environment

    NASA Astrophysics Data System (ADS)

    Franklin, Oskar

    2016-04-01

    A central problem in understanding and modeling vegetation dynamics is how to represent the variation in plant properties and function across different environments. Addressing this problem there is a strong trend towards trait-based approaches, where vegetation properties are functions of the distributions of functional traits rather than of species. Recently there has been enormous progress in in quantifying trait variability and its drivers and effects (Van Bodegom et al. 2012; Adier et al. 2014; Kunstler et al. 2015) based on wide ranging datasets on a small number of easily measured traits, such as specific leaf area (SLA), wood density and maximum plant height. However, plant function depends on many other traits and while the commonly measured trait data are valuable, they are not sufficient for driving predictive and mechanistic models of vegetation dynamics -especially under novel climate or management conditions. For this purpose we need a model to predict functional traits, also those not easily measured, and how they depend on the plants' environment. Here I present such a mechanistic model based on fitness concepts and focused on traits related to water and light limitation of trees, including: wood density, drought response, allocation to defense, and leaf traits. The model is able to predict observed patterns of variability in these traits in relation to growth and mortality, and their responses to a gradient of water limitation. The results demonstrate that it is possible to mechanistically predict plant traits as a function of the environment based on an eco-physiological model of plant fitness. References Adier, P.B., Salguero-Gómez, R., Compagnoni, A., Hsu, J.S., Ray-Mukherjee, J., Mbeau-Ache, C. et al. (2014). Functional traits explain variation in plant lifehistory strategies. Proc. Natl. Acad. Sci. U. S. A., 111, 740-745. Kunstler, G., Falster, D., Coomes, D.A., Hui, F., Kooyman, R.M., Laughlin, D.C. et al. (2015). Plant functional traits

  3. Optical coherence tomography predicts visual outcome in macula-involving rhegmatogenous retinal detachment

    PubMed Central

    Cho, Minhee; Witmer, Matthew T; Favarone, Guilleherme; Chan, RV Paul; D’Amico, Donald J; Kiss, Szilárd

    2012-01-01

    Purpose Visual recovery after rhegmatogenous retinal detachment (RRD) repair depends upon various anatomical factors. We investigated spectral-domain optical coherence tomography (SD-OCT) abnormalities, pre- and postoperatively, in patients with nontraumatic RRD and correlated these findings with visual outcome. Methods The medical records of all patients presenting to Weill Cornell Medical College with nontraumatic macula-involving RRD from August 2010 to September 2011 were retrospectively reviewed in this single-center, consecutive case series. All patients underwent pre- and postoperative visual acuity (VA) testing, slit-lamp biomicroscopy, and dilated fundus examination. Spectral domain optical coherence tomography was obtained preoperatively in twelve patients and postoperatively in ten patients. Results Twelve patients (12 eyes) were included in the final analysis. Preoperative optical coherence tomography revealed that the inner segment/outer segment (IS/OS) junction was disrupted in 10/12 eyes (83%), the external limiting membrane (ELM) was disrupted in 9/12 (75%) eyes, cystoid macular edema (CME) was present in 10/12 (83%) eyes, an epiretinal membrane (ERM) was present in 2/12 eyes (17%) and outer retinal corrugation was present in 7/12 (58%) eyes. In postoperative imaging of 10 eyes, the IS/OS junction was disrupted in 4/10 (40%), the ELM was disrupted in 3/10 (30%) eyes, CME was present in 2/10 (20%), and an ERM in 1/10 (10%). All retinas were attached postoperatively. Outer retinal corrugation was the most predictive of worse preoperative (P = 0.0016) and 1-month postoperative visual acuity (P = 0.05). Conclusion Preoperative SD-OCT demonstrating outer retinal corrugation in macula involving RRD predicts poor visual acuity outcome in nontraumatic RRD. Such findings may have implications for the urgency for these eyes to undergo surgical repair. PMID:22275812

  4. Predicting functional decline and survival in amyotrophic lateral sclerosis.

    PubMed

    Ong, Mei-Lyn; Tan, Pei Fang; Holbrook, Joanna D

    2017-01-01

    Better predictors of amyotrophic lateral sclerosis disease course could enable smaller and more targeted clinical trials. Partially to address this aim, the Prize for Life foundation collected de-identified records from amyotrophic lateral sclerosis sufferers who participated in clinical trials of investigational drugs and made them available to researchers in the PRO-ACT database. In this study, time series data from PRO-ACT subjects were fitted to exponential models. Binary classes for decline in the total score of amyotrophic lateral sclerosis functional rating scale revised (ALSFRS-R) (fast/slow progression) and survival (high/low death risk) were derived. Data was segregated into training and test sets via cross validation. Learning algorithms were applied to the demographic, clinical and laboratory parameters in the training set to predict ALSFRS-R decline and the derived fast/slow progression and high/low death risk categories. The performance of predictive models was assessed by cross-validation in the test set using Receiver Operator Curves and root mean squared errors. A model created using a boosting algorithm containing the decline in four parameters (weight, alkaline phosphatase, albumin and creatine kinase) post baseline, was able to predict functional decline class (fast or slow) with fair accuracy (AUC = 0.82). However similar approaches to build a predictive model for decline class by baseline subject characteristics were not successful. In contrast, baseline values of total bilirubin, gamma glutamyltransferase, urine specific gravity and ALSFRS-R item score-climbing stairs were sufficient to predict survival class. Using combinations of small numbers of variables it was possible to predict classes of functional decline and survival across the 1-2 year timeframe available in PRO-ACT. These findings may have utility for design of future ALS clinical trials.

  5. Predicting functional decline and survival in amyotrophic lateral sclerosis

    PubMed Central

    Ong, Mei-Lyn; Tan, Pei Fang

    2017-01-01

    Background Better predictors of amyotrophic lateral sclerosis disease course could enable smaller and more targeted clinical trials. Partially to address this aim, the Prize for Life foundation collected de-identified records from amyotrophic lateral sclerosis sufferers who participated in clinical trials of investigational drugs and made them available to researchers in the PRO-ACT database. Methods In this study, time series data from PRO-ACT subjects were fitted to exponential models. Binary classes for decline in the total score of amyotrophic lateral sclerosis functional rating scale revised (ALSFRS-R) (fast/slow progression) and survival (high/low death risk) were derived. Data was segregated into training and test sets via cross validation. Learning algorithms were applied to the demographic, clinical and laboratory parameters in the training set to predict ALSFRS-R decline and the derived fast/slow progression and high/low death risk categories. The performance of predictive models was assessed by cross-validation in the test set using Receiver Operator Curves and root mean squared errors. Results A model created using a boosting algorithm containing the decline in four parameters (weight, alkaline phosphatase, albumin and creatine kinase) post baseline, was able to predict functional decline class (fast or slow) with fair accuracy (AUC = 0.82). However similar approaches to build a predictive model for decline class by baseline subject characteristics were not successful. In contrast, baseline values of total bilirubin, gamma glutamyltransferase, urine specific gravity and ALSFRS-R item score—climbing stairs were sufficient to predict survival class. Conclusions Using combinations of small numbers of variables it was possible to predict classes of functional decline and survival across the 1–2 year timeframe available in PRO-ACT. These findings may have utility for design of future ALS clinical trials. PMID:28406915

  6. BioFuelDB: a database and prediction server of enzymes involved in biofuels production.

    PubMed

    Chaudhary, Nikhil; Gupta, Ankit; Gupta, Sudheer; Sharma, Vineet K

    2017-01-01

    In light of the rapid decrease in fossils fuel reserves and an increasing demand for energy, novel methods are required to explore alternative biofuel production processes to alleviate these pressures. A wide variety of molecules which can either be used as biofuels or as biofuel precursors are produced using microbial enzymes. However, the common challenges in the industrial implementation of enzyme catalysis for biofuel production are the unavailability of a comprehensive biofuel enzyme resource, low efficiency of known enzymes, and limited availability of enzymes which can function under extreme conditions in the industrial processes. We have developed a comprehensive database of known enzymes with proven or potential applications in biofuel production through text mining of PubMed abstracts and other publicly available information. A total of 131 enzymes with a role in biofuel production were identified and classified into six enzyme classes and four broad application categories namely 'Alcohol production', 'Biodiesel production', 'Fuel Cell' and 'Alternate biofuels'. A prediction tool 'Benz' was developed to identify and classify novel homologues of the known biofuel enzyme sequences from sequenced genomes and metagenomes. 'Benz' employs a hybrid approach incorporating HMMER 3.0 and RAPSearch2 programs to provide high accuracy and high speed for prediction. Using the Benz tool, 153,754 novel homologues of biofuel enzymes were identified from 23 diverse metagenomic sources. The comprehensive data of curated biofuel enzymes, their novel homologs identified from diverse metagenomes, and the hybrid prediction tool Benz are presented as a web server which can be used for the prediction of biofuel enzymes from genomic and metagenomic datasets. The database and the Benz tool is publicly available at http://metabiosys.iiserb.ac.in/biofueldb& http://metagenomics.iiserb.ac.in/biofueldb.

  7. BioFuelDB: a database and prediction server of enzymes involved in biofuels production

    PubMed Central

    Gupta, Sudheer

    2017-01-01

    Background In light of the rapid decrease in fossils fuel reserves and an increasing demand for energy, novel methods are required to explore alternative biofuel production processes to alleviate these pressures. A wide variety of molecules which can either be used as biofuels or as biofuel precursors are produced using microbial enzymes. However, the common challenges in the industrial implementation of enzyme catalysis for biofuel production are the unavailability of a comprehensive biofuel enzyme resource, low efficiency of known enzymes, and limited availability of enzymes which can function under extreme conditions in the industrial processes. Methods We have developed a comprehensive database of known enzymes with proven or potential applications in biofuel production through text mining of PubMed abstracts and other publicly available information. A total of 131 enzymes with a role in biofuel production were identified and classified into six enzyme classes and four broad application categories namely ‘Alcohol production’, ‘Biodiesel production’, ‘Fuel Cell’ and ‘Alternate biofuels’. A prediction tool ‘Benz’ was developed to identify and classify novel homologues of the known biofuel enzyme sequences from sequenced genomes and metagenomes. ‘Benz’ employs a hybrid approach incorporating HMMER 3.0 and RAPSearch2 programs to provide high accuracy and high speed for prediction. Results Using the Benz tool, 153,754 novel homologues of biofuel enzymes were identified from 23 diverse metagenomic sources. The comprehensive data of curated biofuel enzymes, their novel homologs identified from diverse metagenomes, and the hybrid prediction tool Benz are presented as a web server which can be used for the prediction of biofuel enzymes from genomic and metagenomic datasets. The database and the Benz tool is publicly available at http://metabiosys.iiserb.ac.in/biofueldb& http://metagenomics.iiserb.ac.in/biofueldb. PMID:28875065

  8. Predicting the functions of long noncoding RNAs using RNA-seq based on Bayesian network.

    PubMed

    Xiao, Yun; Lv, Yanling; Zhao, Hongying; Gong, Yonghui; Hu, Jing; Li, Feng; Xu, Jinyuan; Bai, Jing; Yu, Fulong; Li, Xia

    2015-01-01

    Long noncoding RNAs (lncRNAs) have been shown to play key roles in various biological processes. However, functions of most lncRNAs are poorly characterized. Here, we represent a framework to predict functions of lncRNAs through construction of a regulatory network between lncRNAs and protein-coding genes. Using RNA-seq data, the transcript profiles of lncRNAs and protein-coding genes are constructed. Using the Bayesian network method, a regulatory network, which implies dependency relations between lncRNAs and protein-coding genes, was built. In combining protein interaction network, highly connected coding genes linked by a given lncRNA were subsequently used to predict functions of the lncRNA through functional enrichment. Application of our method to prostate RNA-seq data showed that 762 lncRNAs in the constructed regulatory network were assigned functions. We found that lncRNAs are involved in diverse biological processes, such as tissue development or embryo development (e.g., nervous system development and mesoderm development). By comparison with functions inferred using the neighboring gene-based method and functions determined using lncRNA knockdown experiments, our method can provide comparable predicted functions of lncRNAs. Overall, our method can be applied to emerging RNA-seq data, which will help researchers identify complex relations between lncRNAs and coding genes and reveal important functions of lncRNAs.

  9. Procalcitonin for the early prediction of renal parenchymal involvement in children with UTI: preliminary results.

    PubMed

    Kotoula, Aggeliki; Gardikis, Stefanos; Tsalkidis, Aggelos; Mantadakis, Elpis; Zissimopoulos, Athanassios; Kambouri, Katerina; Deftereos, Savvas; Tripsianis, Gregorios; Manolas, Konstantinos; Chatzimichael, Athanassios; Vaos, George

    2009-01-01

    In order to establish the most reliable marker for distinguishing urinary tract infections (UTI) with and without renal parenchymal involvement (RPI), we recorded the clinical features and admission leukocyte count, erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), and serum procalcitonin (PCT) in 57 children (including 43 girls) aged 2-108 months admitted with a first episode of UTI. RPI was evaluated by Tc-99m dimercaptosuccinic acid (DMSA) scintigraphy within 7 days of admission. To establish cut-off points for ESR, CRP, and PCT, we used receiver operating characteristics curves and compared the area under the curve for ESR, CRP, and PCT. Twenty-seven children were diagnosed as having RPI based on positive renal scintigraphy. A body temperature of >38 degrees C, a history of diarrhea, and poor oral intake were more common in patients with RPI. ESR, CRP, and PCT, but not leukocyte count, were significantly higher in patients with RPI (P < 0.001). PCT was more sensitive and specific for the diagnosis of upper versus lower UTI than ESR and CRP. Using a cut-off value of 0.85 ng/ml, PCT had the best performance, with sensitivity, specificity, and positive and negative predictive values of 89%, 97%, 96%, and 91% respectively. Serum PCT is a better marker than ESR, CRP, and leukocyte count for the early prediction of RPI in children with a first episode of UTI.

  10. Expression and functional studies of genes involved in transport and metabolism of glycerol in Pachysolen tannophilus

    PubMed Central

    2013-01-01

    Background Pachysolen tannophilus is a non-conventional yeast, which can metabolize many of the carbon sources found in low cost feedstocks including glycerol and xylose. The xylose utilisation pathways have been extensively studied in this organism. However, the mechanism behind glycerol metabolism is poorly understood. Using the recently published genome sequence of P. tannophilus CBS4044, we searched for genes with functions in glycerol transport and metabolism by performing a BLAST search using the sequences of the relevant genes from Saccharomyces cerevisiae as queries. Results Quantitative real-time PCR was performed to unveil the expression patterns of these genes during growth of P. tannophilus on glycerol and glucose as sole carbon sources. The genes predicted to be involved in glycerol transport in P. tannophilus were expressed in S. cerevisiae to validate their function. The S. cerevisiae strains transformed with heterologous genes showed improved growth and glycerol consumption rates with glycerol as the sole carbon source. Conclusions P. tannophilus has characteristics relevant for a microbial cell factory to be applied in a biorefinery setting, i.e. its ability to utilise the carbon sources such as xylose and glycerol. However, the strain is not currently amenable to genetic modification and transformation. Heterologous expression of the glycerol transporters from P. tannophilus, which has a relatively high growth rate on glycerol, could be used as an approach for improving the efficiency of glycerol assimilation in other well characterized and applied cell factories such as S. cerevisiae. PMID:23514356

  11. The function and catalysis of 2-oxoglutarate-dependent oxygenases involved in plant flavonoid biosynthesis.

    PubMed

    Cheng, Ai-Xia; Han, Xiao-Juan; Wu, Yi-Feng; Lou, Hong-Xiang

    2014-01-15

    Flavonoids are secondary metabolites derived from phenylalanine and acetate metabolism. They fulfil a variety of functions in plants and have health benefits for humans. During the synthesis of the tricyclic flavonoid natural products in plants, oxidative modifications to the central C ring are catalyzed by four of FeII and 2-oxoglutarate dependent (2-ODD) oxygenases, namely flavone synthase I (FNS I), flavonol synthase (FLS), anthocyanidin synthase (ANS) and flavanone 3β-hydroxylase (FHT). FNS I, FLS and ANS are involved in desaturation of C2-C3 of flavonoids and FHT in hydroxylation of C3. FNS I, which is restricted to the Apiaceae species and in rice, is predicted to have evolved from FHT by duplication. Due to their sequence similarity and substrate specificity, FLS and ANS, which interact with the α surface of the substrate, belong to a group of dioxygenases having a broad substrate specificity, while FNS I and FHT are more selective, and interact with the naringenin β surface. Here, we summarize recent findings regarding the function of the four 2-ODD oxygenases and the relationship between their catalytic activity, their polypeptide sequence and their tertiary structure.

  12. Predicting protein function and other biomedical characteristics with heterogeneous ensembles

    PubMed Central

    Whalen, Sean; Pandey, Om Prakash

    2015-01-01

    Prediction problems in biomedical sciences, including protein function prediction (PFP), are generally quite difficult. This is due in part to incomplete knowledge of the cellular phenomenon of interest, the appropriateness and data quality of the variables and measurements used for prediction, as well as a lack of consensus regarding the ideal predictor for specific problems. In such scenarios, a powerful approach to improving prediction performance is to construct heterogeneous ensemble predictors that combine the output of diverse individual predictors that capture complementary aspects of the problems and/or datasets. In this paper, we demonstrate the potential of such heterogeneous ensembles, derived from stacking and ensemble selection methods, for addressing PFP and other similar biomedical prediction problems. Deeper analysis of these results shows that the superior predictive ability of these methods, especially stacking, can be attributed to their attention to the following aspects of the ensemble learning process: (i) better balance of diversity and performance, (ii) more effective calibration of outputs and (iii) more robust incorporation of additional base predictors. Finally, to make the effective application of heterogeneous ensembles to large complex datasets (big data) feasible, we present DataSink, a distributed ensemble learning framework, and demonstrate its sound scalability using the examined datasets. DataSink is publicly available from https://github.com/shwhalen/datasink. PMID:26342255

  13. Protein function prediction using local 3D templates.

    PubMed

    Laskowski, Roman A; Watson, James D; Thornton, Janet M

    2005-08-19

    The prediction of a protein's function from its 3D structure is becoming more and more important as the worldwide structural genomics initiatives gather pace and continue to solve 3D structures, many of which are of proteins of unknown function. Here, we present a methodology for predicting function from structure that shows great promise. It is based on 3D templates that are defined as specific 3D conformations of small numbers of residues. We use four types of template, covering enzyme active sites, ligand-binding residues, DNA-binding residues and reverse templates. The latter are templates generated from the target structure itself and scanned against a representative subset of all known protein structures. Together, the templates provide a fairly thorough coverage of the known structures and ensure that if there is a match to a known structure it is unlikely to be missed. A new scoring scheme provides a highly sensitive means of discriminating between true positive and false positive template matches. In all, the methodology provides a powerful new tool for function prediction to complement those already in use.

  14. Quantitative assessment of protein function prediction from metagenomics shotgun sequences.

    PubMed

    Harrington, E D; Singh, A H; Doerks, T; Letunic, I; von Mering, C; Jensen, L J; Raes, J; Bork, P

    2007-08-28

    To assess the potential of protein function prediction in environmental genomics data, we analyzed shotgun sequences from four diverse and complex habitats. Using homology searches as well as customized gene neighborhood methods that incorporate intergenic and evolutionary distances, we inferred specific functions for 76% of the 1.4 million predicted ORFs in these samples (83% when nonspecific functions are considered). Surprisingly, these fractions are only slightly smaller than the corresponding ones in completely sequenced genomes (83% and 86%, respectively, by using the same methodology) and considerably higher than previously thought. For as many as 75,448 ORFs (5% of the total), only neighborhood methods can assign functions, illustrated here by a previously undescribed gene associated with the well characterized heme biosynthesis operon and a potential transcription factor that might regulate a coupling between fatty acid biosynthesis and degradation. Our results further suggest that, although functions can be inferred for most proteins on earth, many functions remain to be discovered in numerous small, rare protein families.

  15. Postpartum Sexual Functioning and Its Predicting Factors among Iranian Women

    PubMed Central

    Rezaei, Nazanin; Azadi, Arman; Sayehmiri, Kourosh; Valizadeh, Reza

    2017-01-01

    Background Many women experience sexual dysfunction following childbirth but this has not been well investigated in Iran. The aim of this study was to evaluate women’s sexual function in the postpartum period in Iran. It also sought to determine predicting factors associated with their sexual function. Methods This was a cross-sectional study among 380 postpartum women attending 10 urban health centers in Ilam province in southwestern Iran. Participants were selected using random cluster sampling. Data was collected using the female sexual function index (FSFI) and a checklist of socio-demographic and maternal status for each of the women. Sexual dysfunction was classified according to an FSFI score of ≤ 28. Data were analysed using SPSS version 22. Results The majority of participants (76.3%) had sexual dysfunction. Primiparity (adjusted odds ratio (aOR): 1.78 (95% Confidence Interval (CI): 1.11, 2.94); P = 0.006) and exclusive breastfeeding (aOR: 2.47 (95% CI: 1.21, 5.03); P = 0.012) were associated with increased odds of experiencing sexual dysfunction in the postpartum period. Other factors such as age, type of delivery, education, time since delivery and family income did not predict women’s postpartum sexual function. Conclusion This study confirmed findings of previous studies on factors that may have an adverse effect on new mothers’ sexual function in the postpartum period. However the effect of type of delivery on postpartum sexual function remains unclear. PMID:28381932

  16. Gender as a Moderator in Predicting Re-arrest Among Treated Drug-Involved Offenders

    PubMed Central

    Yang, Y.; Knight, K.; Joe, G.W.; Rowan, G.A.; Lehman, W. E.K.; Flynn, P.M.

    2016-01-01

    The primary aim of the current study is to explore gender differences on the relationships of pre-treatment risk factors (i.e., substance use severity and criminal history) and psychosocial functioning (i.e., decision making, risk taking, self-esteem, social support, and peer support) with time to re-arrest following termination from prison. With gender as a moderator variable, survival analysis was used to model time to re-arrest in terms of pre-treatment risk factors and psychosocial functioning. The sample consisted of 697 participants (384 males and 313 females) who were admitted to four prison-based substance abuse treatment programs. Female inmates experienced a longer time to re-arrest than male inmates. Better decision making and more peer support were associated with lower levels of re-arrest for males. Males with higher self-esteem were more likely to be re-arrested than their counterparts. Females with more self-reported criminal involvements had a higher rate of re-arrest than those with less criminal involvement. In contrast to males, females with relatively high self-reported self-esteem had a lower rate of re-arrest than their counterparts. Clinical implications include the importance of enhancing decision-making ability and peer support for males and self-esteem for females. PMID:25216813

  17. Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network

    PubMed Central

    Hwang, Sohyun; Rhee, Seung Y; Marcotte, Edward M; Lee, Insuk

    2012-01-01

    AraNet is a functional gene network for the reference plant Arabidopsis and has been constructed in order to identify new genes associated with plant traits. It is highly predictive for diverse biological pathways and can be used to prioritize genes for functional screens. Moreover, AraNet provides a web-based tool with which plant biologists can efficiently discover novel functions of Arabidopsis genes (http://www.functionalnet.org/aranet/). This protocol explains how to conduct network-based prediction of gene functions using AraNet and how to interpret the prediction results. Functional discovery in plant biology is facilitated by combining candidate prioritization by AraNet with focused experimental tests. PMID:21886106

  18. Plant functional traits predict green roof ecosystem services.

    PubMed

    Lundholm, Jeremy; Tran, Stephanie; Gebert, Luke

    2015-02-17

    Plants make important contributions to the services provided by engineered ecosystems such as green roofs. Ecologists use plant species traits as generic predictors of geographical distribution, interactions with other species, and ecosystem functioning, but this approach has been little used to optimize engineered ecosystems. Four plant species traits (height, individual leaf area, specific leaf area, and leaf dry matter content) were evaluated as predictors of ecosystem properties and services in a modular green roof system planted with 21 species. Six indicators of ecosystem services, incorporating thermal, hydrological, water quality, and carbon sequestration functions, were predicted by the four plant traits directly or indirectly via their effects on aggregate ecosystem properties, including canopy density and albedo. Species average height and specific leaf area were the most useful traits, predicting several services via effects on canopy density or growth rate. This study demonstrates that easily measured plant traits can be used to select species to optimize green roof performance across multiple key services.

  19. Optimizing Non-Decomposable Loss Functions in Structured Prediction

    PubMed Central

    Ranjbar, Mani; Lan, Tian; Wang, Yang; Robinovitch, Steven N.; Li, Ze-Nian; Mori, Greg

    2012-01-01

    We develop an algorithm for structured prediction with non-decomposable performance measures. The algorithm learns parameters of Markov random fields and can be applied to multivariate performance measures. Examples include performance measures such as Fβ score (natural language processing), intersection over union (object category segmentation), Precision/Recall at k (search engines) and ROC area (binary classifiers). We attack this optimization problem by approximating the loss function with a piecewise linear function. The loss augmented inference forms a quadratic program (QP), which we solve using LP relaxation. We apply this approach to two tasks: object class-specific segmentation and human action retrieval from videos. We show significant improvement over baseline approaches that either use simple loss functions or simple scoring functions on the PASCAL VOC and H3D Segmentation datasets, and a nursing home action recognition dataset. PMID:22868650

  20. Predicting taxonomic and functional structure of microbial communities in acid mine drainage

    PubMed Central

    Kuang, Jialiang; Huang, Linan; He, Zhili; Chen, Linxing; Hua, Zhengshuang; Jia, Pu; Li, Shengjin; Liu, Jun; Li, Jintian; Zhou, Jizhong; Shu, Wensheng

    2016-01-01

    Predicting the dynamics of community composition and functional attributes responding to environmental changes is an essential goal in community ecology but remains a major challenge, particularly in microbial ecology. Here, by targeting a model system with low species richness, we explore the spatial distribution of taxonomic and functional structure of 40 acid mine drainage (AMD) microbial communities across Southeast China profiled by 16S ribosomal RNA pyrosequencing and a comprehensive microarray (GeoChip). Similar environmentally dependent patterns of dominant microbial lineages and key functional genes were observed regardless of the large-scale geographical isolation. Functional and phylogenetic β-diversities were significantly correlated, whereas functional metabolic potentials were strongly influenced by environmental conditions and community taxonomic structure. Using advanced modeling approaches based on artificial neural networks, we successfully predicted the taxonomic and functional dynamics with significantly higher prediction accuracies of metabolic potentials (average Bray–Curtis similarity 87.8) as compared with relative microbial abundances (similarity 66.8), implying that natural AMD microbial assemblages may be better predicted at the functional genes level rather than at taxonomic level. Furthermore, relative metabolic potentials of genes involved in many key ecological functions (for example, nitrogen and phosphate utilization, metals resistance and stress response) were extrapolated to increase under more acidic and metal-rich conditions, indicating a critical strategy of stress adaptation in these extraordinary communities. Collectively, our findings indicate that natural selection rather than geographic distance has a more crucial role in shaping the taxonomic and functional patterns of AMD microbial community that readily predicted by modeling methods and suggest that the model-based approach is essential to better understand natural

  1. Ferromagnetic elements by epitaxial growth: A density functional prediction

    NASA Astrophysics Data System (ADS)

    Schönecker, Stephan; Richter, Manuel; Koepernik, Klaus; Eschrig, Helmut

    2012-01-01

    The periodic table contains only six natural elements with a ferromagnetic ground state. For example, the metal uranium, which is magnetically ordered in many compounds, is paramagnetic in all its known elemental bulk phases. Also, the iron-group elements ruthenium and osmium are known to be bulk paramagnets. We predict by means of density functional calculations that epitaxial growth of uranium, ruthenium, or osmium on suitable substrates may allow stabilization of bulklike films with tetragonal structures showing ferromagnetic order.

  2. High Precision Prediction of Functional Sites in Protein Structures

    PubMed Central

    Buturovic, Ljubomir; Wong, Mike; Tang, Grace W.; Altman, Russ B.; Petkovic, Dragutin

    2014-01-01

    We address the problem of assigning biological function to solved protein structures. Computational tools play a critical role in identifying potential active sites and informing screening decisions for further lab analysis. A critical parameter in the practical application of computational methods is the precision, or positive predictive value. Precision measures the level of confidence the user should have in a particular computed functional assignment. Low precision annotations lead to futile laboratory investigations and waste scarce research resources. In this paper we describe an advanced version of the protein function annotation system FEATURE, which achieved 99% precision and average recall of 95% across 20 representative functional sites. The system uses a Support Vector Machine classifier operating on the microenvironment of physicochemical features around an amino acid. We also compared performance of our method with state-of-the-art sequence-level annotator Pfam in terms of precision, recall and localization. To our knowledge, no other functional site annotator has been rigorously evaluated against these key criteria. The software and predictive models are incorporated into the WebFEATURE service at http://feature.stanford.edu/wf4.0-beta. PMID:24632601

  3. Intelligence, creativity, and cognitive control: The common and differential involvement of executive functions in intelligence and creativity

    PubMed Central

    Benedek, Mathias; Jauk, Emanuel; Sommer, Markus; Arendasy, Martin; Neubauer, Aljoscha C.

    2014-01-01

    Intelligence and creativity are known to be correlated constructs suggesting that they share a common cognitive basis. The present study assessed three specific executive abilities – updating, shifting, and inhibition – and examined their common and differential relations to fluid intelligence and creativity (i.e., divergent thinking ability) within a latent variable model approach. Additionally, it was tested whether the correlation of fluid intelligence and creativity can be explained by a common executive involvement. As expected, fluid intelligence was strongly predicted by updating, but not by shifting or inhibition. Creativity was predicted by updating and inhibition, but not by shifting. Moreover, updating (and the personality factor openness) was found to explain a relevant part of the shared variance between intelligence and creativity. The findings provide direct support for the executive involvement in creative thought and shed further light on the functional relationship between intelligence and creativity. PMID:25278640

  4. Intelligence, creativity, and cognitive control: The common and differential involvement of executive functions in intelligence and creativity.

    PubMed

    Benedek, Mathias; Jauk, Emanuel; Sommer, Markus; Arendasy, Martin; Neubauer, Aljoscha C

    2014-09-01

    Intelligence and creativity are known to be correlated constructs suggesting that they share a common cognitive basis. The present study assessed three specific executive abilities - updating, shifting, and inhibition - and examined their common and differential relations to fluid intelligence and creativity (i.e., divergent thinking ability) within a latent variable model approach. Additionally, it was tested whether the correlation of fluid intelligence and creativity can be explained by a common executive involvement. As expected, fluid intelligence was strongly predicted by updating, but not by shifting or inhibition. Creativity was predicted by updating and inhibition, but not by shifting. Moreover, updating (and the personality factor openness) was found to explain a relevant part of the shared variance between intelligence and creativity. The findings provide direct support for the executive involvement in creative thought and shed further light on the functional relationship between intelligence and creativity.

  5. Predictions of Geospace Drivers By the Probability Distribution Function Model

    NASA Astrophysics Data System (ADS)

    Bussy-Virat, C.; Ridley, A. J.

    2014-12-01

    Geospace drivers like the solar wind speed, interplanetary magnetic field (IMF), and solar irradiance have a strong influence on the density of the thermosphere and the near-Earth space environment. This has important consequences on the drag on satellites that are in low orbit and therefore on their position. One of the basic problems with space weather prediction is that these drivers can only be measured about one hour before they affect the environment. In order to allow for adequate planning for some members of the commercial, military, or civilian communities, reliable long-term space weather forecasts are needed. The study presents a model for predicting geospace drivers up to five days in advance. This model uses the same general technique to predict the solar wind speed, the three components of the IMF, and the solar irradiance F10.7. For instance, it uses Probability distribution functions (PDFs) to relate the current solar wind speed and slope to the future solar wind speed, as well as the solar wind speed to the solar wind speed one solar rotation in the future. The PDF Model has been compared to other models for predictions of the speed. It has been found that it is better than using the current solar wind speed (i.e., persistence), and better than the Wang-Sheeley-Arge Model for prediction horizons of 24 hours. Once the drivers are predicted, and the uncertainty on the drivers are specified, the density in the thermosphere can be derived using various models of the thermosphere, such as the Global Ionosphere Thermosphere Model. In addition, uncertainties on the densities can be estimated, based on ensembles of simulations. From the density and uncertainty predictions, satellite positions, as well as the uncertainty in those positions can be estimated. These can assist operators in determining the probability of collisions between objects in low Earth orbit.

  6. Simplified analytical model for sound level prediction at shielded urban locations involving multiple diffraction and reflections.

    PubMed

    Wei, Weigang; Van Renterghem, Timothy; Botteldooren, Dick

    2015-11-01

    Accurate and efficient prediction of the sound field in shadow zones behind obstacles is a challenging task but essential to produce urban noise maps. A simplified method is presented to predict sound levels at shielded urban locations, including multi-edge diffraction over successive buildings and multiple reflections between parallel façades. The model is essentially based on Pierce's diffraction theory, where the Fresnel Integral is approximated by trigonometric functions for efficient evaluation, and parameterized for urban environments. The model has been validated for idealized urban configurations by comparing to the results of Pierce's theory and a full-wave numerical method. In case of multi-edge diffraction over buildings in absence of a source or receiver canyon, deviations from the full-wave simulations are smaller than 2 dB for the octave bands with central frequencies ranging from 125 to 1000 Hz. However, larger errors are made when receivers are close to the extension line from the diffraction edge closest to the receiver. In case of combining the simplified multi-edge diffraction model with an efficient approach for including the series of mirror sources and mirror receivers, based on the Hurwitz-Lerch transcendent, this same accuracy is obtained.

  7. Quantitative reactivity profiling predicts functional cysteines in proteomes

    PubMed Central

    Weerapana, Eranthie; Wang, Chu; Simon, Gabriel M.; Richter, Florian; Khare, Sagar; Dillon, Myles B.D.; Bachovchin, Daniel A.; Mowen, Kerri; Baker, David; Cravatt, Benjamin F.

    2010-01-01

    Cysteine is the most intrinsically nucleophilic amino acid in proteins, where its reactivity is tuned to perform diverse biochemical functions. The absence of a consensus sequence that defines functional cysteines in proteins has hindered their discovery and characterization. Here, we describe a proteomics method to quantitatively profile the intrinsic reactivity of cysteine residues en masse directly in native biological systems. Hyperreactivity was a rare feature among cysteines and found to specify a wide range of activities, including nucleophilic and reductive catalysis and sites of oxidative modification. Hyperreactive cysteines were identified in several proteins of uncharacterized function, including a residue conserved across eukaryotic phylogeny that we show is required for yeast viability and involved in iron-sulfur protein biogenesis. Finally, we demonstrate that quantitative reactivity profiling can also form the basis for screening and functional assignment of cysteines in computationally designed proteins, where it discriminated catalytically active from inactive cysteine hydrolase designs. PMID:21085121

  8. Certain fractional integral formulas involving the product of generalized Bessel functions.

    PubMed

    Baleanu, D; Agarwal, P; Purohit, S D

    2013-01-01

    We apply generalized operators of fractional integration involving Appell's function F 3(·) due to Marichev-Saigo-Maeda, to the product of the generalized Bessel function of the first kind due to Baricz. The results are expressed in terms of the multivariable generalized Lauricella functions. Corresponding assertions in terms of Saigo, Erdélyi-Kober, Riemann-Liouville, and Weyl type of fractional integrals are also presented. Some interesting special cases of our two main results are presented. We also point out that the results presented here, being of general character, are easily reducible to yield many diverse new and known integral formulas involving simpler functions.

  9. Certain Fractional Integral Formulas Involving the Product of Generalized Bessel Functions

    PubMed Central

    Baleanu, D.; Agarwal, P.; Purohit, S. D.

    2013-01-01

    We apply generalized operators of fractional integration involving Appell's function F 3(·) due to Marichev-Saigo-Maeda, to the product of the generalized Bessel function of the first kind due to Baricz. The results are expressed in terms of the multivariable generalized Lauricella functions. Corresponding assertions in terms of Saigo, Erdélyi-Kober, Riemann-Liouville, and Weyl type of fractional integrals are also presented. Some interesting special cases of our two main results are presented. We also point out that the results presented here, being of general character, are easily reducible to yield many diverse new and known integral formulas involving simpler functions. PMID:24379745

  10. Multitrophic functional diversity predicts ecosystem functioning in experimental assemblages of estuarine consumers.

    PubMed

    Lefcheck, Jonathan S; Duffy, J Emmett

    2015-11-01

    The use of functional traits to explain how biodiversity affects ecosystem functioning has attracted intense interest, yet few studies have a priori altered functional diversity, especially in multitrophic communities. Here, we manipulated multivariate functional diversity of estuarine grazers and predators within multiple levels of species richness to test how species richness and functional diversity predicted ecosystem functioning in a multitrophic food web. Community functional diversity was a better predictor than species richness for the majority of ecosystem properties, based on generalized linear mixed-effects models. Combining inferences from eight traits into a single multivariate index increased prediction accuracy of these models relative to any individual trait. Structural equation modeling revealed that functional diversity of both grazers and predators was important in driving final biomass within trophic levels, with stronger effects observed for predators. We also show that different species drove different ecosystem responses, with evidence for both sampling effects and complementarity. Our study extends experimental investigations of functional trait diversity to a multilevel food web, and demonstrates that functional diversity can be more accurate and effective than species richness in predicting community biomass in a food web context.

  11. Conserved Functional Motifs and Homology Modeling to Predict Hidden Moonlighting Functional Sites

    PubMed Central

    Wong, Aloysius; Gehring, Chris; Irving, Helen R.

    2015-01-01

    Moonlighting functional centers within proteins can provide them with hitherto unrecognized functions. Here, we review how hidden moonlighting functional centers, which we define as binding sites that have catalytic activity or regulate protein function in a novel manner, can be identified using targeted bioinformatic searches. Functional motifs used in such searches include amino acid residues that are conserved across species and many of which have been assigned functional roles based on experimental evidence. Molecules that were identified in this manner seeking cyclic mononucleotide cyclases in plants are used as examples. The strength of this computational approach is enhanced when good homology models can be developed to test the functionality of the predicted centers in silico, which, in turn, increases confidence in the ability of the identified candidates to perform the predicted functions. Computational characterization of moonlighting functional centers is not diagnostic for catalysis but serves as a rapid screening method, and highlights testable targets from a potentially large pool of candidates for subsequent in vitro and in vivo experiments required to confirm the functionality of the predicted moonlighting centers. PMID:26106597

  12. Quality of Parental Homework Involvement: Predictors and Reciprocal Relations with Academic Functioning in the Reading Domain

    ERIC Educational Resources Information Center

    Dumont, Hanna; Trautwein, Ulrich; Nagy, Gabriel; Nagengast, Benjamin

    2014-01-01

    This study examined predictors of the quality of parental homework involvement and reciprocal relations between the quality of parental homework involvement and students' reading achievement and academic functioning in a reading-intensive subject (German). Data from 2,830 students in nonacademic tracks and their parents who were surveyed in both…

  13. Quality of Parental Homework Involvement: Predictors and Reciprocal Relations with Academic Functioning in the Reading Domain

    ERIC Educational Resources Information Center

    Dumont, Hanna; Trautwein, Ulrich; Nagy, Gabriel; Nagengast, Benjamin

    2014-01-01

    This study examined predictors of the quality of parental homework involvement and reciprocal relations between the quality of parental homework involvement and students' reading achievement and academic functioning in a reading-intensive subject (German). Data from 2,830 students in nonacademic tracks and their parents who were surveyed in both…

  14. miRDB: an online resource for microRNA target prediction and functional annotations.

    PubMed

    Wong, Nathan; Wang, Xiaowei

    2015-01-01

    MicroRNAs (miRNAs) are small non-coding RNAs that are extensively involved in many physiological and disease processes. One major challenge in miRNA studies is the identification of genes regulated by miRNAs. To this end, we have developed an online resource, miRDB (http://mirdb.org), for miRNA target prediction and functional annotations. Here, we describe recently updated features of miRDB, including 2.1 million predicted gene targets regulated by 6709 miRNAs. In addition to presenting precompiled prediction data, a new feature is the web server interface that allows submission of user-provided sequences for miRNA target prediction. In this way, users have the flexibility to study any custom miRNAs or target genes of interest. Another major update of miRDB is related to functional miRNA annotations. Although thousands of miRNAs have been identified, many of the reported miRNAs are not likely to play active functional roles or may even have been falsely identified as miRNAs from high-throughput studies. To address this issue, we have performed combined computational analyses and literature mining, and identified 568 and 452 functional miRNAs in humans and mice, respectively. These miRNAs, as well as associated functional annotations, are presented in the FuncMir Collection in miRDB.

  15. Molecular integrals involving hulthén-type functions ( n = l STO) in relativistic quantum chemistry

    NASA Astrophysics Data System (ADS)

    Malli, Gulzari

    1981-03-01

    Dirac-Fock-Roothaan (DFR) treatment of molecules (with STO as basis) leads to molecular integrals involving n = l STOs which are known in nuclear physics as Hulthén-type functions (HTFs) It is pointed out. that with minor modifications, the existing non-relativistic molecular integral programs which use STO as basis can be used to evaluate molecular integrals involving Hulthén-type functions

  16. Spinal meningiomas: clinicoradiological factors predicting recurrence and functional outcome.

    PubMed

    Maiti, Tanmoy K; Bir, Shyamal C; Patra, Devi Prasad; Kalakoti, Piyush; Guthikonda, Bharat; Nanda, Anil

    2016-08-01

    OBJECTIVE Spinal meningiomas are benign tumors with a wide spectrum of clinical and radiological features at presentation. The authors analyzed multiple clinicoradiological factors to predict recurrence and functional outcome in a cohort with a mean follow-up of more than 4 years. The authors also discuss the results of clinical studies regarding spinal meningiomas in the last 15 years. METHODS The authors retrospectively reviewed the clinical and radiological details of patients who underwent surgery for spinal tumors between 2001 and 2015 that were histopathologically confirmed as meningiomas. Demographic parameters, such as age, sex, race, and association with neurofibromatosis Type 2, were considered. Radiological parameters, such as tumor size, signal changes of spinal cord, spinal level, number of levels, location of tumor attachment, shape of tumor, and presence of dural tail/calcification, were noted. These factors were analyzed to predict recurrence and functional outcome. Furthermore, a pooled analysis was performed from 13 reports of spinal meningiomas in the last 15 years. RESULTS A total of 38 patients were included in this study. Male sex and tumors with radiological evidence of a dural tail were associated with an increased risk of recurrence at a mean follow-up of 51.2 months. Ventral or ventrolateral location, large tumors, T2 cord signal changes, and poor preoperative functional status were associated with poor functional outcome at 1-year follow-up. CONCLUSIONS Spine surgeons must be aware of the natural history and risk factors of spinal meningiomas to establish a prognosis for their patients.

  17. Predicting Cognitive Function from Clinical Measures of Physical Function and Health Status in Older Adults

    PubMed Central

    Bolandzadeh, Niousha; Kording, Konrad; Salowitz, Nicole; Davis, Jennifer C.; Hsu, Liang; Chan, Alison; Sharma, Devika; Blohm, Gunnar; Liu-Ambrose, Teresa

    2015-01-01

    Introduction Current research suggests that the neuropathology of dementia—including brain changes leading to memory impairment and cognitive decline—is evident years before the onset of this disease. Older adults with cognitive decline have reduced functional independence and quality of life, and are at greater risk for developing dementia. Therefore, identifying biomarkers that can be easily assessed within the clinical setting and predict cognitive decline is important. Early recognition of cognitive decline could promote timely implementation of preventive strategies. Methods We included 89 community-dwelling adults aged 70 years and older in our study, and collected 32 measures of physical function, health status and cognitive function at baseline. We utilized an L1–L2 regularized regression model (elastic net) to identify which of the 32 baseline measures were strongly predictive of cognitive function after one year. We built three linear regression models: 1) based on baseline cognitive function, 2) based on variables consistently selected in every cross-validation loop, and 3) a full model based on all the 32 variables. Each of these models was carefully tested with nested cross-validation. Results Our model with the six variables consistently selected in every cross-validation loop had a mean squared prediction error of 7.47. This number was smaller than that of the full model (115.33) and the model with baseline cognitive function (7.98). Our model explained 47% of the variance in cognitive function after one year. Discussion We built a parsimonious model based on a selected set of six physical function and health status measures strongly predictive of cognitive function after one year. In addition to reducing the complexity of the model without changing the model significantly, our model with the top variables improved the mean prediction error and R-squared. These six physical function and health status measures can be easily implemented in a

  18. [Chronic diseases, functional ability, social involvement and satisfaction in community-dwelling elderly: the Fibra study].

    PubMed

    Pinto, Juliana Martins; Neri, Anita Liberalesso

    2013-12-01

    The scope of this article is to describe variations in the measurement of chronic diseases, functional ability, social involvement and satisfaction with respect to memory, problem solving, social relationships, environment, health services and transportation. This is done according to gender, age and income. It analyzes correlations between social involvement and functional ability in independent community dwelling-elderly aged 65 and above. 2,472 seniors without cognitive deficit, from probabilistic samples of seven Brazilian locations, were submitted to self-reported measurement concerning all variables, with the exception of grip strength and gait speed assessed by objective tests. Mean age was 72.2 ± 5.5 years and mean income was 3.9 ± 4.9 MW; 65.7% were women, who had more diseases, worse functional performance and greater social involvement than men; those aged 80 and above and the poorest participants had worse functional performance and less social involvement. Correlations were observed between functional ability and social involvement. Level of income was related to satisfaction concerning memory, problem solving, health and transport services. Health, functionality and satisfaction interact in old age, influencing patterns of activity and social involvement.

  19. Predicting re-involvement for children adopted out of a public child welfare system.

    PubMed

    Orsi, Rebecca

    2015-01-01

    Some of the approximately 400,000 children currently placed out-of-home in a public child welfare system will not reunify with their family of origin. They may instead be adopted into a new family. Adoption placements can be characterized by poor adjustment for children; some such placements even result in disruption or dissolution. We conducted a stratified Cox regression of 4,016 children from the Colorado public child welfare system. All of the children had a finalized adoption during the years 2002 through 2006. The two outcomes analyzed were new child protection and youth-in-conflict referrals and assessments for these previously adopted children. New child welfare referrals and assessments may be early indicators of poor adjustment for adopted children within the adoptive family. Study results indicate that older children and Hispanic children had higher rates of referral and assessment. Children with a pre-adoption history including longer time out-of-home or a larger number of out-of-home placements also experienced higher referral and assessment rates. Additional factors which predicted subsequent system re-involvement included presence of paid adoption assistance, adoption by a non-relative foster parent and younger adoptive parent age. Several study results were moderated by the presence or absence of an ethnic match between the child and the adoptive parents. We provide an overview of the statistical model used for analysis and we discuss implications of the study results for child welfare practice.

  20. Models for predicting objective function weights in prostate cancer IMRT

    SciTech Connect

    Boutilier, Justin J. Lee, Taewoo; Craig, Tim; Sharpe, Michael B.; Chan, Timothy C. Y.

    2015-04-15

    Purpose: To develop and evaluate the clinical applicability of advanced machine learning models that simultaneously predict multiple optimization objective function weights from patient geometry for intensity-modulated radiation therapy of prostate cancer. Methods: A previously developed inverse optimization method was applied retrospectively to determine optimal objective function weights for 315 treated patients. The authors used an overlap volume ratio (OV) of bladder and rectum for different PTV expansions and overlap volume histogram slopes (OVSR and OVSB for the rectum and bladder, respectively) as explanatory variables that quantify patient geometry. Using the optimal weights as ground truth, the authors trained and applied three prediction models: logistic regression (LR), multinomial logistic regression (MLR), and weighted K-nearest neighbor (KNN). The population average of the optimal objective function weights was also calculated. Results: The OV at 0.4 cm and OVSR at 0.1 cm features were found to be the most predictive of the weights. The authors observed comparable performance (i.e., no statistically significant difference) between LR, MLR, and KNN methodologies, with LR appearing to perform the best. All three machine learning models outperformed the population average by a statistically significant amount over a range of clinical metrics including bladder/rectum V53Gy, bladder/rectum V70Gy, and dose to the bladder, rectum, CTV, and PTV. When comparing the weights directly, the LR model predicted bladder and rectum weights that had, on average, a 73% and 74% relative improvement over the population average weights, respectively. The treatment plans resulting from the LR weights had, on average, a rectum V70Gy that was 35% closer to the clinical plan and a bladder V70Gy that was 29% closer, compared to the population average weights. Similar results were observed for all other clinical metrics. Conclusions: The authors demonstrated that the KNN and MLR

  1. Variability in Cumulative Habitual Sleep Duration Predicts Waking Functional Connectivity.

    PubMed

    Khalsa, Sakh; Mayhew, Stephen D; Przezdzik, Izabela; Wilson, Rebecca; Hale, Joanne; Goldstone, Aimee; Bagary, Manny; Bagshaw, Andrew P

    2016-01-01

    We examined whether interindividual differences in habitual sleep patterns, quantified as the cumulative habitual total sleep time (cTST) over a 2-w period, were reflected in waking measurements of intranetwork and internetwork functional connectivity (FC) between major nodes of three intrinsically connected networks (ICNs): default mode network (DMN), salience network (SN), and central executive network (CEN). Resting state functional magnetic resonance imaging (fMRI) study using seed-based FC analysis combined with 14-d wrist actigraphy, sleep diaries, and subjective questionnaires (N = 33 healthy adults, mean age 34.3, standard deviation ± 11.6 y). Data were statistically analyzed using multiple linear regression. Fourteen consecutive days of wrist actigraphy in participant's home environment and fMRI scanning on day 14 at the Birmingham University Imaging Centre. Seed-based FC analysis on ICNs from resting-state fMRI data and multiple linear regression analysis performed for each ICN seed and target. cTST was used to predict FC (controlling for age). cTST was specific predictor of intranetwork FC when the mesial prefrontal cortex (MPFC) region of the DMN was used as a seed for FC, with a positive correlation between FC and cTST observed. No significant relationship between FC and cTST was seen for any pair of nodes not including the MPFC. Internetwork FC between the DMN (MPFC) and SN (right anterior insula) was also predicted by cTST, with a negative correlation observed between FC and cTST. This study improves understanding of the relationship between intranetwork and internetwork functional connectivity of intrinsically connected networks (ICNs) in relation to habitual sleep quality and duration. The cumulative amount of sleep that participants achieved over a 14-d period was significantly predictive of intranetwork and inter-network functional connectivity of ICNs, an observation that may underlie the link between sleep status and cognitive performance.

  2. Marijuana Use Predicts Cognitive Performance on Tasks of Executive Function

    PubMed Central

    Dahlgren, Mary Kathryn; Sagar, Kelly A.; Racine, Megan T.; Dreman, Meredith W.; Gruber, Staci A.

    2016-01-01

    Objective: Despite growing evidence that chronic marijuana use is associated with cognitive impairment, particularly when use is initiated at an early age, national trends demonstrate significant decreases in the perceived risk of marijuana corresponding with increased use, especially among youth. The current study assessed the impact of marijuana use on executive function and whether patterns of marijuana use, including earlier age at onset, higher frequency, and increased magnitude of use, predict impairment. Method: Forty-four chronic, heavy marijuana smokers (37 male, 7 female) and 32 healthy, nonsmoking control participants (20 male, 12 female) recruited from the Greater Boston area completed two assessments of executive function: the Stroop Color Word Test and Wisconsin Card Sorting Test (WCST). Results: Marijuana smokers had poorer executive function relative to control participants, a between-group difference that was primarily driven by individuals with early onset of marijuana use (before age 16; n = 21); significance remained even when controlling for frequency and magnitude of use. Further, earlier age at marijuana onset and increased marijuana use predicted poorer neurocognitive performance, and perseverative errors on the WCST significantly predicted marijuana group membership. Conclusions: These findings underscore the impact of early onset of marijuana use on executive function impairment independent of increased frequency and magnitude of use. In addition, poorer performance on the WCST may serve as a neuropsychological marker for heavy marijuana users. These results highlight the need for additional research to identify predictors associated with early marijuana use, as exposure to marijuana during a period of developmental vulnerability may result in negative cognitive consequences. PMID:26997188

  3. Brain natriuretic peptide predicts functional outcome in ischemic stroke

    PubMed Central

    Rost, Natalia S; Biffi, Alessandro; Cloonan, Lisa; Chorba, John; Kelly, Peter; Greer, David; Ellinor, Patrick; Furie, Karen L

    2011-01-01

    Background Elevated serum levels of brain natriuretic peptide (BNP) have been associated with cardioembolic (CE) stroke and increased post-stroke mortality. We sought to determine whether BNP levels were associated with functional outcome after ischemic stroke. Methods We measured BNP in consecutive patients aged ≥18 years admitted to our Stroke Unit between 2002–2005. BNP quintiles were used for analysis. Stroke subtypes were assigned using TOAST criteria. Outcomes were measured as 6-month modified Rankin Scale score (“good outcome” = 0–2 vs. “poor”) as well as mortality. Multivariate logistic regression was used to assess association between the quintiles of BNP and outcomes. Predictive performance of BNP as compared to clinical model alone was assessed by comparing ROC curves. Results Of 569 ischemic stroke patients, 46% were female; mean age was 67.9 ± 15 years. In age- and gender-adjusted analysis, elevated BNP was associated with lower ejection fraction (p<0.0001) and left atrial dilatation (p<0.001). In multivariate analysis, elevated BNP decreased the odds of good functional outcome (OR 0.64, 95%CI 0.41–0.98) and increased the odds of death (OR 1.75, 95%CI 1.36–2.24) in these patients. Addition of BNP to multivariate models increased their predictive performance for functional outcome (p=0.013) and mortality (p<0.03) after CE stroke. Conclusions Serum BNP levels are strongly associated with CE stroke and functional outcome at 6 months after ischemic stroke. Inclusion of BNP improved prediction of mortality in patients with CE stroke. PMID:22116811

  4. An empirical propellant response function for combustion stability predictions

    NASA Technical Reports Server (NTRS)

    Hessler, R. O.

    1980-01-01

    An empirical response function model was developed for ammonium perchlorate propellants to supplant T-burner testing at the preliminary design stage. The model was developed by fitting a limited T-burner data base, in terms of oxidizer size and concentration, to an analytical two parameter response function expression. Multiple peaks are predicted, but the primary effect is of a single peak for most formulations, with notable bulges for the various AP size fractions. The model was extended to velocity coupling with the assumption that dynamic response was controlled primarily by the solid phase described by the two parameter model. The magnitude of velocity coupling was then scaled using an erosive burning law. Routine use of the model for stability predictions on a number of propulsion units indicates that the model tends to overpredict propellant response. It is concluded that the model represents a generally conservative prediction tool, suited especially for the preliminary design stage when T-burner data may not be readily available. The model work included development of a rigorous summation technique for pseudopropellant properties and of a concept for modeling ordered packing of particulates.

  5. Integrating phenotype and gene expression data for predicting gene function.

    PubMed

    Malone, Brandon M; Perkins, Andy D; Bridges, Susan M

    2009-10-08

    This paper presents a framework for integrating disparate data sets to predict gene function. The algorithm constructs a graph, called an integrated similarity graph, by computing similarities based upon both gene expression and textual phenotype data. This integrated graph is then used to make predictions about whether individual genes should be assigned a particular annotation from the Gene Ontology. A combined graph was generated from publicly-available gene expression data and phenotypic information from Saccharomyces cerevisiae. This graph was used to assign annotations to genes, as were graphs constructed from gene expression data and textual phenotype information alone. While the F-measure appeared similar for all three methods, annotations based upon the integrated similarity graph exhibited a better overall precision than gene expression or phenotype information alone can generate. The integrated approach was also able to assign almost as many annotations as the gene expression method alone, and generated significantly more total and correct assignments than the phenotype information could provide. These results suggest that augmenting standard gene expression data sets with publicly-available textual phenotype data can help generate more precise functional annotation predictions while mitigating the weaknesses of a standard textual phenotype approach.

  6. "Reverse Genomics" Predicts Function of Human Conserved Noncoding Elements.

    PubMed

    Marcovitz, Amir; Jia, Robin; Bejerano, Gill

    2016-05-01

    Evolutionary changes in cis-regulatory elements are thought to play a key role in morphological and physiological diversity across animals. Many conserved noncoding elements (CNEs) function as cis-regulatory elements, controlling gene expression levels in different biological contexts. However, determining specific associations between CNEs and related phenotypes is a challenging task. Here, we present a computational "reverse genomics" approach that predicts the phenotypic functions of human CNEs. We identify thousands of human CNEs that were lost in at least two independent mammalian lineages (IL-CNEs), and match their evolutionary profiles against a diverse set of phenotypes recently annotated across multiple mammalian species. We identify 2,759 compelling associations between human CNEs and a diverse set of mammalian phenotypes. We discuss multiple CNEs, including a predicted ear element near BMP7, a pelvic CNE in FBN1, a brain morphology element in UBE4B, and an aquatic adaptation forelimb CNE near EGR2, and provide a full list of our predictions. As more genomes are sequenced and more traits are annotated across species, we expect our method to facilitate the interpretation of noncoding mutations in human disease and expedite the discovery of individual CNEs that play key roles in human evolution and development. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  7. Platelet Serotonin Transporter Function Predicts Default-Mode Network Activity

    PubMed Central

    Kasess, Christian H.; Meyer, Bernhard M.; Hofmaier, Tina; Diers, Kersten; Bartova, Lucie; Pail, Gerald; Huf, Wolfgang; Uzelac, Zeljko; Hartinger, Beate; Kalcher, Klaudius; Perkmann, Thomas; Haslacher, Helmuth; Meyer-Lindenberg, Andreas; Kasper, Siegfried; Freissmuth, Michael; Windischberger, Christian; Willeit, Matthäus; Lanzenberger, Rupert; Esterbauer, Harald; Brocke, Burkhard; Moser, Ewald; Sitte, Harald H.; Pezawas, Lukas

    2014-01-01

    Background The serotonin transporter (5-HTT) is abundantly expressed in humans by the serotonin transporter gene SLC6A4 and removes serotonin (5-HT) from extracellular space. A blood-brain relationship between platelet and synaptosomal 5-HT reuptake has been suggested, but it is unknown today, if platelet 5-HT uptake can predict neural activation of human brain networks that are known to be under serotonergic influence. Methods A functional magnetic resonance study was performed in 48 healthy subjects and maximal 5-HT uptake velocity (Vmax) was assessed in blood platelets. We used a mixed-effects multilevel analysis technique (MEMA) to test for linear relationships between whole-brain, blood-oxygen-level dependent (BOLD) activity and platelet Vmax. Results The present study demonstrates that increases in platelet Vmax significantly predict default-mode network (DMN) suppression in healthy subjects independent of genetic variation within SLC6A4. Furthermore, functional connectivity analyses indicate that platelet Vmax is related to global DMN activation and not intrinsic DMN connectivity. Conclusion This study provides evidence that platelet Vmax predicts global DMN activation changes in healthy subjects. Given previous reports on platelet-synaptosomal Vmax coupling, results further suggest an important role of neuronal 5-HT reuptake in DMN regulation. PMID:24667541

  8. Predictive computation of genomic logic processing functions in embryonic development

    PubMed Central

    Peter, Isabelle S.; Faure, Emmanuel; Davidson, Eric H.

    2012-01-01

    Gene regulatory networks (GRNs) control the dynamic spatial patterns of regulatory gene expression in development. Thus, in principle, GRN models may provide system-level, causal explanations of developmental process. To test this assertion, we have transformed a relatively well-established GRN model into a predictive, dynamic Boolean computational model. This Boolean model computes spatial and temporal gene expression according to the regulatory logic and gene interactions specified in a GRN model for embryonic development in the sea urchin. Additional information input into the model included the progressive embryonic geometry and gene expression kinetics. The resulting model predicted gene expression patterns for a large number of individual regulatory genes each hour up to gastrulation (30 h) in four different spatial domains of the embryo. Direct comparison with experimental observations showed that the model predictively computed these patterns with remarkable spatial and temporal accuracy. In addition, we used this model to carry out in silico perturbations of regulatory functions and of embryonic spatial organization. The model computationally reproduced the altered developmental functions observed experimentally. Two major conclusions are that the starting GRN model contains sufficiently complete regulatory information to permit explanation of a complex developmental process of gene expression solely in terms of genomic regulatory code, and that the Boolean model provides a tool with which to test in silico regulatory circuitry and developmental perturbations. PMID:22927416

  9. Multiscale prediction of patient-specific platelet function under flow.

    PubMed

    Flamm, Matthew H; Colace, Thomas V; Chatterjee, Manash S; Jing, Huiyan; Zhou, Songtao; Jaeger, Daniel; Brass, Lawrence F; Sinno, Talid; Diamond, Scott L

    2012-07-05

    During thrombotic or hemostatic episodes, platelets bind collagen and release ADP and thromboxane A(2), recruiting additional platelets to a growing deposit that distorts the flow field. Prediction of clotting function under hemodynamic conditions for a patient's platelet phenotype remains a challenge. A platelet signaling phenotype was obtained for 3 healthy donors using pairwise agonist scanning, in which calcium dye-loaded platelets were exposed to pairwise combinations of ADP, U46619, and convulxin to activate the P2Y(1)/P2Y(12), TP, and GPVI receptors, respectively, with and without the prostacyclin receptor agonist iloprost. A neural network model was trained on each donor's pairwise agonist scanning experiment and then embedded into a multiscale Monte Carlo simulation of donor-specific platelet deposition under flow. The simulations were compared directly with microfluidic experiments of whole blood flowing over collagen at 200 and 1000/s wall shear rate. The simulations predicted the ranked order of drug sensitivity for indomethacin, aspirin, MRS-2179 (a P2Y(1) inhibitor), and iloprost. Consistent with measurement and simulation, one donor displayed larger clots and another presented with indomethacin resistance (revealing a novel heterozygote TP-V241G mutation). In silico representations of a subject's platelet phenotype allowed prediction of blood function under flow, essential for identifying patient-specific risks, drug responses, and novel genotypes.

  10. Premotor functional connectivity predicts impulsivity in juvenile offenders.

    PubMed

    Shannon, Benjamin J; Raichle, Marcus E; Snyder, Abraham Z; Fair, Damien A; Mills, Kathryn L; Zhang, Dongyang; Bache, Kevin; Calhoun, Vince D; Nigg, Joel T; Nagel, Bonnie J; Stevens, Alexander A; Kiehl, Kent A

    2011-07-05

    Teenagers are often impulsive. In some cases this is a phase of normal development; in other cases impulsivity contributes to criminal behavior. Using functional magnetic resonance imaging, we examined resting-state functional connectivity among brain systems and behavioral measures of impulsivity in 107 juveniles incarcerated in a high-security facility. In less-impulsive juveniles and normal controls, motor planning regions were correlated with brain networks associated with spatial attention and executive control. In more-impulsive juveniles, these same regions correlated with the default-mode network, a constellation of brain areas associated with spontaneous, unconstrained, self-referential cognition. The strength of these brain-behavior relationships was sufficient to predict impulsivity scores at the individual level. Our data suggest that increased functional connectivity of motor-planning regions with networks subserving unconstrained, self-referential cognition, rather than those subserving executive control, heightens the predisposition to impulsive behavior in juvenile offenders. To further explore the relationship between impulsivity and neural development, we studied functional connectivity in the same motor-planning regions in 95 typically developing individuals across a wide age span. The change in functional connectivity with age mirrored that of impulsivity: younger subjects tended to exhibit functional connectivity similar to the more-impulsive incarcerated juveniles, whereas older subjects exhibited a less-impulsive pattern. This observation suggests that impulsivity in the offender population is a consequence of a delay in typical development, rather than a distinct abnormality.

  11. Premotor functional connectivity predicts impulsivity in juvenile offenders

    PubMed Central

    Shannon, Benjamin J.; Raichle, Marcus E.; Snyder, Abraham Z.; Fair, Damien A.; Mills, Kathryn L.; Zhang, Dongyang; Bache, Kevin; Calhoun, Vince D.; Nigg, Joel T.; Nagel, Bonnie J.; Stevens, Alexander A.; Kiehl, Kent A.

    2011-01-01

    Teenagers are often impulsive. In some cases this is a phase of normal development; in other cases impulsivity contributes to criminal behavior. Using functional magnetic resonance imaging, we examined resting-state functional connectivity among brain systems and behavioral measures of impulsivity in 107 juveniles incarcerated in a high-security facility. In less-impulsive juveniles and normal controls, motor planning regions were correlated with brain networks associated with spatial attention and executive control. In more-impulsive juveniles, these same regions correlated with the default-mode network, a constellation of brain areas associated with spontaneous, unconstrained, self-referential cognition. The strength of these brain–behavior relationships was sufficient to predict impulsivity scores at the individual level. Our data suggest that increased functional connectivity of motor-planning regions with networks subserving unconstrained, self-referential cognition, rather than those subserving executive control, heightens the predisposition to impulsive behavior in juvenile offenders. To further explore the relationship between impulsivity and neural development, we studied functional connectivity in the same motor-planning regions in 95 typically developing individuals across a wide age span. The change in functional connectivity with age mirrored that of impulsivity: younger subjects tended to exhibit functional connectivity similar to the more-impulsive incarcerated juveniles, whereas older subjects exhibited a less-impulsive pattern. This observation suggests that impulsivity in the offender population is a consequence of a delay in typical development, rather than a distinct abnormality. PMID:21709236

  12. The predictability of molecular evolution during functional innovation.

    PubMed

    Blank, Diana; Wolf, Luise; Ackermann, Martin; Silander, Olin K

    2014-02-25

    Determining the molecular changes that give rise to functional innovations is a major unresolved problem in biology. The paucity of examples has served as a significant hindrance in furthering our understanding of this process. Here we used experimental evolution with the bacterium Escherichia coli to quantify the molecular changes underlying functional innovation in 68 independent instances ranging over 22 different metabolic functions. Using whole-genome sequencing, we show that the relative contribution of regulatory and structural mutations depends on the cellular context of the metabolic function. In addition, we find that regulatory mutations affect genes that act in pathways relevant to the novel function, whereas structural mutations affect genes that act in unrelated pathways. Finally, we use population genetic modeling to show that the relative contributions of regulatory and structural mutations during functional innovation may be affected by population size. These results provide a predictive framework for the molecular basis of evolutionary innovation, which is essential for anticipating future evolutionary trajectories in the face of rapid environmental change.

  13. Predicting athletes' functional and dysfunctional emotions: The role of the motivational climate and motivation regulations.

    PubMed

    Ruiz, Montse C; Haapanen, Saara; Tolvanen, Asko; Robazza, Claudio; Duda, Joan L

    2016-08-26

    This study examined the relationships between perceptions of the motivational climate, motivation regulations, and the intensity and functionality levels of athletes' pleasant and unpleasant emotional states. Specifically, we examined the hypothesised mediational role of motivation regulations in the climate-emotion relationship. We also tested a sequence in which emotions were assumed to be predicted by the motivational climate dimensions and then served as antecedents to variability in motivation regulations. Participants (N = 494) completed a multi-section questionnaire assessing targeted variables. Structural equation modelling (SEM) revealed that a perceived task-involving climate was a positive predictor of autonomous motivation and of the impact of functional anger, and a negative predictor of the intensity of anxiety and dysfunctional anger. Autonomous motivation was a partial mediator of perceptions of a task-involving climate and the impact of functional anger. An ego-involving climate was a positive predictor of controlled motivation, and of the intensity and impact of functional anger and the intensity of dysfunctional anger. Controlled motivation partially mediated the relationship between an ego-involving climate and the intensity of dysfunctional anger. Good fit to the data also emerged for the motivational climate, emotional states, and motivation regulations sequence. Findings provide support for the consideration of hedonic tone and functionality distinctions in the assessment of athletes' emotional states.

  14. Variability in Cumulative Habitual Sleep Duration Predicts Waking Functional Connectivity

    PubMed Central

    Khalsa, Sakh; Mayhew, Stephen D.; Przezdzik, Izabela; Wilson, Rebecca; Hale, Joanne; Goldstone, Aimee; Bagary, Manny; Bagshaw, Andrew P.

    2016-01-01

    Study Objectives: We examined whether interindividual differences in habitual sleep patterns, quantified as the cumulative habitual total sleep time (cTST) over a 2-w period, were reflected in waking measurements of intranetwork and internetwork functional connectivity (FC) between major nodes of three intrinsically connected networks (ICNs): default mode network (DMN), salience network (SN), and central executive network (CEN). Methods: Resting state functional magnetic resonance imaging (fMRI) study using seed-based FC analysis combined with 14-d wrist actigraphy, sleep diaries, and subjective questionnaires (N = 33 healthy adults, mean age 34.3, standard deviation ± 11.6 y). Data were statistically analyzed using multiple linear regression. Fourteen consecutive days of wrist actigraphy in participant's home environment and fMRI scanning on day 14 at the Birmingham University Imaging Centre. Seed-based FC analysis on ICNs from resting-state fMRI data and multiple linear regression analysis performed for each ICN seed and target. cTST was used to predict FC (controlling for age). Results: cTST was specific predictor of intranetwork FC when the mesial prefrontal cortex (MPFC) region of the DMN was used as a seed for FC, with a positive correlation between FC and cTST observed. No significant relationship between FC and cTST was seen for any pair of nodes not including the MPFC. Internetwork FC between the DMN (MPFC) and SN (right anterior insula) was also predicted by cTST, with a negative correlation observed between FC and cTST. Conclusions: This study improves understanding of the relationship between intranetwork and internetwork functional connectivity of intrinsically connected networks (ICNs) in relation to habitual sleep quality and duration. The cumulative amount of sleep that participants achieved over a 14-d period was significantly predictive of intranetwork and inter-network functional connectivity of ICNs, an observation that may underlie the link

  15. Predicting effects of climate change on the composition and function of soil microbial communities

    NASA Astrophysics Data System (ADS)

    Dubinsky, E.; Brodie, E.; Myint, C.; Ackerly, D.; van Nostrand, J.; Bird, J.; Zhou, J.; Andersen, G.; Firestone, M.

    2008-12-01

    of these predictable changes in community composition were measured with functional arrays that detect genes involved in the metabolism of carbon, nitrogen and other elements. The response of soil microbial communities to altered precipitation can be predicted from the distribution of microbial taxa across moisture gradients.

  16. Confronting species distribution model predictions with species functional traits.

    PubMed

    Wittmann, Marion E; Barnes, Matthew A; Jerde, Christopher L; Jones, Lisa A; Lodge, David M

    2016-02-01

    Species distribution models are valuable tools in studies of biogeography, ecology, and climate change and have been used to inform conservation and ecosystem management. However, species distribution models typically incorporate only climatic variables and species presence data. Model development or validation rarely considers functional components of species traits or other types of biological data. We implemented a species distribution model (Maxent) to predict global climate habitat suitability for Grass Carp (Ctenopharyngodon idella). We then tested the relationship between the degree of climate habitat suitability predicted by Maxent and the individual growth rates of both wild (N = 17) and stocked (N = 51) Grass Carp populations using correlation analysis. The Grass Carp Maxent model accurately reflected the global occurrence data (AUC = 0.904). Observations of Grass Carp growth rate covered six continents and ranged from 0.19 to 20.1 g day(-1). Species distribution model predictions were correlated (r = 0.5, 95% CI (0.03, 0.79)) with observed growth rates for wild Grass Carp populations but were not correlated (r = -0.26, 95% CI (-0.5, 0.012)) with stocked populations. Further, a review of the literature indicates that the few studies for other species that have previously assessed the relationship between the degree of predicted climate habitat suitability and species functional traits have also discovered significant relationships. Thus, species distribution models may provide inferences beyond just where a species may occur, providing a useful tool to understand the linkage between species distributions and underlying biological mechanisms.

  17. Prediction of functional residues in water channels and related proteins.

    PubMed Central

    Froger, A.; Tallur, B.; Thomas, D.; Delamarche, C.

    1998-01-01

    In this paper, we present an updated classification of the ubiquitous MIP (Major Intrinsic Protein) family proteins, including 153 fully or partially sequenced members available in public databases. Presently, about 30 of these proteins have been functionally characterized, exhibiting essentially two distinct types of channel properties: (1) specific water transport by the aquaporins, and (2) small neutral solutes transport, such as glycerol by the glycerol facilitators. Sequence alignments were used to predict amino acids and motifs discriminant in channel specificity. The protein sequences were also analyzed using statistical tools (comparisons of means and correspondence analysis). Five key positions were clearly identified where the residues are specific for each functional subgroup and exhibit high dissimilar physico-chemical properties. Moreover, we have found that the putative channels for small neutral solutes clearly differ from the aquaporins by the amino acid content and the length of predicted loop regions, suggesting a substrate filter function for these loops. From these results, we propose a signature pattern for water transport. PMID:9655351

  18. Structure and function predictions of the Msa protein in Staphylococcus aureus.

    PubMed

    Nagarajan, Vijayaraj; Elasri, Mohamed O

    2007-11-01

    Staphylococcus aureus is a human pathogen that causes a wide variety of life-threatening infections using a large number of virulence factors. One of the major global regulators used by S. aureus is the staphylococcal accessory regulator (sarA). We have identified and characterized a new gene (modulator of sarA: msa) that modulates the expression of sarA. Genetic and functional analysis shows that msa has a global effect on gene expression in S. aureus. However, the mechanism of Msa function is still unknown. Function predictions of Msa are complicated by the fact that it does not have a homologous partner in any other organism. This work aims at predicting the structure and function of the Msa protein. Preliminary sequence analysis showed that Msa is a putative membrane protein. It would therefore be very difficult to purify and crystallize Msa in order to acquire structure information about this protein. We have used several computational tools to predict the physico-chemical properties, secondary structural features, topology, 3D tertiary structure, binding sites, motifs/patterns/domains and cellular location. We have built a consensus that is derived from analysis using different algorithms to predict several structural features. We confirm that Msa is a putative membrane protein with three transmembrane regions. We also predict that Msa has phosphorylation sites and binding sites suggesting functions in signal transduction. Based on our predictions we hypothesise that Msa is a novel signal transducer that might be involved in the interaction of the S. aureus with its environment.

  19. Prediction of Dislocation Cores in Aluminum from Density Functional Theory

    NASA Astrophysics Data System (ADS)

    Woodward, C.; Trinkle, D. R.; Hector, L. G., Jr.; Olmsted, D. L.

    2008-02-01

    The strain field of isolated screw and edge dislocation cores in aluminum are calculated using density-functional theory and a flexible boundary condition method. Nye tensor density contours and differential displacement fields are used to accurately bound Shockley partial separation distances. Our results of 5 7.5 Å (screw) and 7.0 9.5 Å (edge) eliminate uncertainties resulting from the wide range of previous results based on Peierls-Nabarro and atomistic methods. Favorable agreement of the predicted cores with limited experimental measurements demonstrates the need for quantum mechanical treatment of dislocation cores.

  20. Pediatric brain injury: Can DTI scalars predict functional outcome?

    PubMed Central

    Xu, Duan; Mukherjee, Pratik; Barkovich, A James

    2013-01-01

    Diffusion imaging has made significant inroads into the clinical diagnosis of a variety of diseases by inferring changes in microstructure, namely cell membranes, myelin sheath and other structures that inhibit water diffusion. This review discusses recent progress in the use of diffusion parameters in predicting functional outcome. Studies in the literature using only scalar parameters from diffusion measurements, such as apparent diffusion coefficient (ADC) and fractional anisotropy (FA), are summarized. Other more complex mathematical models and post-processing uses are also discussed briefly. PMID:23288477

  1. Prediction of functional rehabilitation outcomes in clients with stroke.

    PubMed

    Man, David Wai-Kwong; Tam, Sing Fai; Hui-Chan, Christina

    2006-02-01

    To evaluate the validity of the Neurobehavioral Cognitive Status Examination (NCSE or Cognistat) and to determine its effects in order to estimate the functional outcomes of survivors with stroke. The present study first studied the factor structure NCSE in 148 Chinese survivors with stroke (aged 45-91 years). They were admitted to hospital consecutively and recruited prospectively. The relationship of NCSE with Functional Independence Measures (FIM), a set of measures commonly adopted as an indicator of the outcome of rehabilitation, was studied. One hundred and forty-eight patients with stroke (49.3% male, 50.7% female), with a mean age of 70.38 and an average number of years of education of 3.50 years joined the study. A two-factor NCSE structure was obtained, namely verbal-spatial and integrated cognition, accounting for 62.77% of the variance. A significant relationship between NCSE factors and the functional status of clients with stroke on admission and upon discharge, as well as age, years of education and length of hospital stay were indicated. This study supports a systematic relationship between cognitive factors and functional outcome in Chinese patients with stroke. Similarities and differences in the NCSE factor structure between the population with stroke and general neurological populations were discussed and the utility of NCSE in stroke rehabilitation, such as its predictive validity in functional independence is suggested.

  2. Prediction of microRNAs involved in immune system diseases through network based features.

    PubMed

    Prabahar, Archana; Natarajan, Jeyakumar

    2017-01-01

    MicroRNAs are a class of small non-coding regulatory RNA molecules that modulate the expression of several genes at post-transcriptional level and play a vital role in disease pathogenesis. Recent research shows that a range of miRNAs are involved in the regulation of immunity and its deregulation results in immune mediated diseases such as cancer, inflammation and autoimmune diseases. Computational discovery of these immune miRNAs using a set of specific features is highly desirable. In the current investigation, we present a SVM based classification system which uses a set of novel network based topological and motif features in addition to the baseline sequential and structural features to predict immune specific miRNAs from other non-immune miRNAs. The classifier was trained and tested on a balanced set of equal number of positive and negative examples to show the discriminative power of our network features. Experimental results show that our approach achieves an accuracy of 90.2% and outperforms the classification accuracy of 63.2% reported using the traditional miRNA sequential and structural features. The proposed classifier was further validated with two immune disease sub-class datasets related to multiple sclerosis microarray data and psoriasis RNA-seq data with higher accuracy. These results indicate that our classifier which uses network and motif features along with sequential and structural features will lead to significant improvement in classifying immune miRNAs and hence can be applied to identify other specific classes of miRNAs as an extensible miRNA classification system.

  3. Loss of anterior concavity of the first sacrum can predict spinal involvement in ankylosing spondylitis.

    PubMed

    Kim, Ji Young; Lee, Seunghun; Joo, Kyung Bin; Song, Yoonah; Joo, Young Bin; Kim, Tae-Hwan

    2016-01-01

    In this study, we evaluated the frequency of squaring of the first sacrum (S1), defined as the loss of anterior concavity, in patients with ankylosing spondylitis (AS). We also determined the interobserver reliability in the assessment of S1 squaring and the relationships of S1 squaring with MRI findings and the modified Stoke Ankylosing Spondylitis Spinal Score (mSASSS). To this end, we performed a retrospective study of 100 patients with AS (mean age 33.2 years; range 19-57 years) and 100 control patients (mean age 35.6 years; range 19-50 years). Four experienced radiologists independently assessed the presence of S1 squaring in the AS and control groups. The frequencies of S1 squaring as scored by the four observers were 47, 48, 46, and 42 in the AS group and 3, 6, 4, and 6 in the control group. The interobserver agreement among the four observers with respect to S1 squaring was excellent (κ value 0.80) in the AS group and fair to good (κ value 0.61) in the control group. In patients with AS, the presence of S1 squaring showed fair to good agreement with the MRI changes (κ value 0.74). Moreover, the mSASSSs of patients with versus without S1 squaring were significantly different (mean 23.9 vs 7.0, p < 0.001). In conclusion, S1 squaring is relatively common in patients with AS. Moreover, S1 squaring is closely correlated with MRI changes and significantly associated with the mSASSS. Assessment of S1 squaring could be a simple method that is potentially useful for predicting early spinal structural involvement in patients with AS.

  4. Defining Predictive Probability Functions for Species Sampling Models.

    PubMed

    Lee, Jaeyong; Quintana, Fernando A; Müller, Peter; Trippa, Lorenzo

    2013-01-01

    We review the class of species sampling models (SSM). In particular, we investigate the relation between the exchangeable partition probability function (EPPF) and the predictive probability function (PPF). It is straightforward to define a PPF from an EPPF, but the converse is not necessarily true. In this paper we introduce the notion of putative PPFs and show novel conditions for a putative PPF to define an EPPF. We show that all possible PPFs in a certain class have to define (unnormalized) probabilities for cluster membership that are linear in cluster size. We give a new necessary and sufficient condition for arbitrary putative PPFs to define an EPPF. Finally, we show posterior inference for a large class of SSMs with a PPF that is not linear in cluster size and discuss a numerical method to derive its PPF.

  5. Predicting Infrared Spectra of Nerve Agents Using Density Functional Theory

    NASA Astrophysics Data System (ADS)

    Zhang, Y.-P.; Wang, H.-T.; Zheng, W.-P.; Sun, C.; Bai, Y.; Guo, X.-D.; Sun, H.

    2016-09-01

    Vibration frequencies of four nerve agents and two simulators are calculated using B3LYP coupled with ten basis sets. To evaluate the accuracy of calculated spectra, root mean square error (RMSE) and weighted cross-correlation average (WCCA) are considered. The evaluation shows that B3LYP/6-311+g(d,p) performs best in predicting infrared spectra, and polarization functions are found to be more important than diffusion functions in spectra simulation. Moreover, B3LYP calculation underestimates frequencies related to the P atom. The WCCA metric derives 1.008 as a unique scaling factor for calculated frequencies. The results indicate that the WCCA metric can identify six agents based on calculated spectra.

  6. Predicting Parental Home and School Involvement in High School African American Adolescents

    ERIC Educational Resources Information Center

    Hayes, DeMarquis

    2011-01-01

    Predictors of parental home and school involvement for high school adolescents were examined within two groups of urban African American parents from various socioeconomic levels. Home involvement was defined as parent-adolescent communication about school and learning, while school involvement was defined in terms of parent attendance and…

  7. Graphlet kernels for prediction of functional residues in protein structures.

    PubMed

    Vacic, Vladimir; Iakoucheva, Lilia M; Lonardi, Stefano; Radivojac, Predrag

    2010-01-01

    We introduce a novel graph-based kernel method for annotating functional residues in protein structures. A structure is first modeled as a protein contact graph, where nodes correspond to residues and edges connect spatially neighboring residues. Each vertex in the graph is then represented as a vector of counts of labeled non-isomorphic subgraphs (graphlets), centered on the vertex of interest. A similarity measure between two vertices is expressed as the inner product of their respective count vectors and is used in a supervised learning framework to classify protein residues. We evaluated our method on two function prediction problems: identification of catalytic residues in proteins, which is a well-studied problem suitable for benchmarking, and a much less explored problem of predicting phosphorylation sites in protein structures. The performance of the graphlet kernel approach was then compared against two alternative methods, a sequence-based predictor and our implementation of the FEATURE framework. On both tasks, the graphlet kernel performed favorably; however, the margin of difference was considerably higher on the problem of phosphorylation site prediction. While there is data that phosphorylation sites are preferentially positioned in intrinsically disordered regions, we provide evidence that for the sites that are located in structured regions, neither the surface accessibility alone nor the averaged measures calculated from the residue microenvironments utilized by FEATURE were sufficient to achieve high accuracy. The key benefit of the graphlet representation is its ability to capture neighborhood similarities in protein structures via enumerating the patterns of local connectivity in the corresponding labeled graphs.

  8. Functional Embedding Predicts the Variability of Neural Activity

    PubMed Central

    Mišić, Bratislav; Vakorin, Vasily A.; Paus, Tomáš; McIntosh, Anthony R.

    2011-01-01

    Neural activity is irregular and unpredictable, yet little is known about why this is the case and how this property relates to the functional architecture of the brain. Here we show that the variability of a region’s activity systematically varies according to its topological role in functional networks. We recorded the resting-state electroencephalogram (EEG) and constructed undirected graphs of functional networks. We measured the centrality of each node in terms of the number of connections it makes (degree), the ease with which the node can be reached from other nodes in the network (efficiency) and the tendency of the node to occupy a position on the shortest paths between other pairs of nodes in the network (betweenness). As a proxy for variability, we estimated the information content of neural activity using multiscale entropy analysis. We found that the rate at which information was generated was largely predicted by centrality. Namely, nodes with greater degree, betweenness, and efficiency were more likely to have high information content, while peripheral nodes had relatively low information content. These results suggest that the variability of regional activity reflects functional embedding. PMID:22164135

  9. Risk prediction for myocardial infarction via generalized functional regression models.

    PubMed

    Ieva, Francesca; Paganoni, Anna M

    2016-08-01

    In this paper, we propose a generalized functional linear regression model for a binary outcome indicating the presence/absence of a cardiac disease with multivariate functional data among the relevant predictors. In particular, the motivating aim is the analysis of electrocardiographic traces of patients whose pre-hospital electrocardiogram (ECG) has been sent to 118 Dispatch Center of Milan (the Italian free-toll number for emergencies) by life support personnel of the basic rescue units. The statistical analysis starts with a preprocessing of ECGs treated as multivariate functional data. The signals are reconstructed from noisy observations. The biological variability is then removed by a nonlinear registration procedure based on landmarks. Thus, in order to perform a data-driven dimensional reduction, a multivariate functional principal component analysis is carried out on the variance-covariance matrix of the reconstructed and registered ECGs and their first derivatives. We use the scores of the Principal Components decomposition as covariates in a generalized linear model to predict the presence of the disease in a new patient. Hence, a new semi-automatic diagnostic procedure is proposed to estimate the risk of infarction (in the case of interest, the probability of being affected by Left Bundle Brunch Block). The performance of this classification method is evaluated and compared with other methods proposed in literature. Finally, the robustness of the procedure is checked via leave-j-out techniques.

  10. Habitual fat intake predicts memory function in younger women.

    PubMed

    Gibson, E Leigh; Barr, Suzanne; Jeanes, Yvonne M

    2013-01-01

    High intakes of fat have been linked to greater cognitive decline in old age, but such associations may already occur in younger adults. We tested memory and learning in 38 women (25 to 45 years old), recruited for a larger observational study in women with polycystic ovary syndrome. These women varied in health status, though not significantly between cases (n = 23) and controls (n = 15). Performance on tests sensitive to medial temporal lobe function (CANTABeclipse, Cambridge Cognition Ltd, Cambridge, UK), i.e., verbal memory, visuo-spatial learning, and delayed pattern matching (DMS), were compared with intakes of macronutrients from 7-day diet diaries and physiological indices of metabolic syndrome. Partial correlations were adjusted for age, activity, and verbal IQ (National Adult Reading Test). Greater intakes of saturated and trans fats, and higher saturated to unsaturated fat ratio (Sat:UFA), were associated with more errors on the visuo-spatial task and with poorer word recall and recognition. Unexpectedly, higher UFA intake predicted poorer performance on the word recall and recognition measures. Fasting insulin was positively correlated with poorer word recognition only, whereas higher blood total cholesterol was associated only with visuo-spatial learning errors. None of these variables predicted performance on a DMS test. The significant nutrient-cognition relationships were tested for mediation by total energy intake: saturated and trans fat intakes, and Sat:UFA, remained significant predictors specifically of visuo-spatial learning errors, whereas total fat and UFA intakes now predicted only poorer word recall. Examination of associations separately for monounsaturated (MUFA) and polyunsaturated fats suggested that only MUFA intake was predictive of poorer word recall. Saturated and trans fats, and fasting insulin, may already be associated with cognitive deficits in younger women. The findings need extending but may have important implications for

  11. Prediction of functional aerobic capacity without exercise testing

    NASA Technical Reports Server (NTRS)

    Jackson, A. S.; Blair, S. N.; Mahar, M. T.; Wier, L. T.; Ross, R. M.; Stuteville, J. E.

    1990-01-01

    The purpose of this study was to develop functional aerobic capacity prediction models without using exercise tests (N-Ex) and to compare the accuracy with Astrand single-stage submaximal prediction methods. The data of 2,009 subjects (9.7% female) were randomly divided into validation (N = 1,543) and cross-validation (N = 466) samples. The validation sample was used to develop two N-Ex models to estimate VO2peak. Gender, age, body composition, and self-report activity were used to develop two N-Ex prediction models. One model estimated percent fat from skinfolds (N-Ex %fat) and the other used body mass index (N-Ex BMI) to represent body composition. The multiple correlations for the developed models were R = 0.81 (SE = 5.3 ml.kg-1.min-1) and R = 0.78 (SE = 5.6 ml.kg-1.min-1). This accuracy was confirmed when applied to the cross-validation sample. The N-Ex models were more accurate than what was obtained from VO2peak estimated from the Astrand prediction models. The SEs of the Astrand models ranged from 5.5-9.7 ml.kg-1.min-1. The N-Ex models were cross-validated on 59 men on hypertensive medication and 71 men who were found to have a positive exercise ECG. The SEs of the N-Ex models ranged from 4.6-5.4 ml.kg-1.min-1 with these subjects.(ABSTRACT TRUNCATED AT 250 WORDS).

  12. Habitual fat intake predicts memory function in younger women

    PubMed Central

    Gibson, E. Leigh; Barr, Suzanne; Jeanes, Yvonne M.

    2013-01-01

    High intakes of fat have been linked to greater cognitive decline in old age, but such associations may already occur in younger adults. We tested memory and learning in 38 women (25 to 45 years old), recruited for a larger observational study in women with polycystic ovary syndrome. These women varied in health status, though not significantly between cases (n = 23) and controls (n = 15). Performance on tests sensitive to medial temporal lobe function (CANTABeclipse, Cambridge Cognition Ltd, Cambridge, UK), i.e., verbal memory, visuo-spatial learning, and delayed pattern matching (DMS), were compared with intakes of macronutrients from 7-day diet diaries and physiological indices of metabolic syndrome. Partial correlations were adjusted for age, activity, and verbal IQ (National Adult Reading Test). Greater intakes of saturated and trans fats, and higher saturated to unsaturated fat ratio (Sat:UFA), were associated with more errors on the visuo-spatial task and with poorer word recall and recognition. Unexpectedly, higher UFA intake predicted poorer performance on the word recall and recognition measures. Fasting insulin was positively correlated with poorer word recognition only, whereas higher blood total cholesterol was associated only with visuo-spatial learning errors. None of these variables predicted performance on a DMS test. The significant nutrient–cognition relationships were tested for mediation by total energy intake: saturated and trans fat intakes, and Sat:UFA, remained significant predictors specifically of visuo-spatial learning errors, whereas total fat and UFA intakes now predicted only poorer word recall. Examination of associations separately for monounsaturated (MUFA) and polyunsaturated fats suggested that only MUFA intake was predictive of poorer word recall. Saturated and trans fats, and fasting insulin, may already be associated with cognitive deficits in younger women. The findings need extending but may have important implications for

  13. Prediction of functional aerobic capacity without exercise testing

    NASA Technical Reports Server (NTRS)

    Jackson, A. S.; Blair, S. N.; Mahar, M. T.; Wier, L. T.; Ross, R. M.; Stuteville, J. E.

    1990-01-01

    The purpose of this study was to develop functional aerobic capacity prediction models without using exercise tests (N-Ex) and to compare the accuracy with Astrand single-stage submaximal prediction methods. The data of 2,009 subjects (9.7% female) were randomly divided into validation (N = 1,543) and cross-validation (N = 466) samples. The validation sample was used to develop two N-Ex models to estimate VO2peak. Gender, age, body composition, and self-report activity were used to develop two N-Ex prediction models. One model estimated percent fat from skinfolds (N-Ex %fat) and the other used body mass index (N-Ex BMI) to represent body composition. The multiple correlations for the developed models were R = 0.81 (SE = 5.3 ml.kg-1.min-1) and R = 0.78 (SE = 5.6 ml.kg-1.min-1). This accuracy was confirmed when applied to the cross-validation sample. The N-Ex models were more accurate than what was obtained from VO2peak estimated from the Astrand prediction models. The SEs of the Astrand models ranged from 5.5-9.7 ml.kg-1.min-1. The N-Ex models were cross-validated on 59 men on hypertensive medication and 71 men who were found to have a positive exercise ECG. The SEs of the N-Ex models ranged from 4.6-5.4 ml.kg-1.min-1 with these subjects.(ABSTRACT TRUNCATED AT 250 WORDS).

  14. Predicting functional associations from metabolism using bi-partite network algorithms.

    PubMed

    Veeramani, Balaji; Bader, Joel S

    2010-07-14

    Metabolic reconstructions contain detailed information about metabolic enzymes and their reactants and products. These networks can be used to infer functional associations between metabolic enzymes. Many methods are based on the number of metabolites shared by two enzymes, or the shortest path between two enzymes. Metabolite sharing can miss associations between non-consecutive enzymes in a serial pathway, and shortest-path algorithms are sensitive to high-degree metabolites such as water and ATP that create connections between enzymes with little functional similarity. We present new, fast methods to infer functional associations in metabolic networks. A local method, the degree-corrected Poisson score, is based only on the metabolites shared by two enzymes, but uses the known metabolite degree distribution. A global method, based on graph diffusion kernels, predicts associations between enzymes that do not share metabolites. Both methods are robust to high-degree metabolites. They out-perform previous methods in predicting shared Gene Ontology (GO) annotations and in predicting experimentally observed synthetic lethal genetic interactions. Including cellular compartment information improves GO annotation predictions but degrades synthetic lethal interaction prediction. These new methods perform nearly as well as computationally demanding methods based on flux balance analysis. We present fast, accurate methods to predict functional associations from metabolic networks. Biological significance is demonstrated by identifying enzymes whose strong metabolic correlations are missed by conventional annotations in GO, most often enzymes involved in transport vs. synthesis of the same metabolite or other enzyme pairs that share a metabolite but are separated by conventional pathway boundaries. More generally, the methods described here may be valuable for analyzing other types of networks with long-tailed degree distributions and high-degree hubs.

  15. A regression-based K nearest neighbor algorithm for gene function prediction from heterogeneous data.

    PubMed

    Yao, Zizhen; Ruzzo, Walter L

    2006-03-20

    As a variety of functional genomic and proteomic techniques become available, there is an increasing need for functional analysis methodologies that integrate heterogeneous data sources. In this paper, we address this issue by proposing a general framework for gene function prediction based on the k-nearest-neighbor (KNN) algorithm. The choice of KNN is motivated by its simplicity, flexibility to incorporate different data types and adaptability to irregular feature spaces. A weakness of traditional KNN methods, especially when handling heterogeneous data, is that performance is subject to the often ad hoc choice of similarity metric. To address this weakness, we apply regression methods to infer a similarity metric as a weighted combination of a set of base similarity measures, which helps to locate the neighbors that are most likely to be in the same class as the target gene. We also suggest a novel voting scheme to generate confidence scores that estimate the accuracy of predictions. The method gracefully extends to multi-way classification problems. We apply this technique to gene function prediction according to three well-known Escherichia coli classification schemes suggested by biologists, using information derived from microarray and genome sequencing data. We demonstrate that our algorithm dramatically outperforms the naive KNN methods and is competitive with support vector machine (SVM) algorithms for integrating heterogenous data. We also show that by combining different data sources, prediction accuracy can improve significantly Our extension of KNN with automatic feature weighting, multi-class prediction, and probabilistic inference, enhance prediction accuracy significantly while remaining efficient, intuitive and flexible. This general framework can also be applied to similar classification problems involving heterogeneous datasets.

  16. Emotion Regulation Predicts Pain and Functioning in Children With Juvenile Idiopathic Arthritis: An Electronic Diary Study

    PubMed Central

    Bromberg, Maggie H.; Anthony, Kelly K.; Gil, Karen M.; Franks, Lindsey; Schanberg, Laura E.

    2012-01-01

    Objectives This study utilized e-diaries to evaluate whether components of emotion regulation predict daily pain and function in children with juvenile idiopathic arthritis (JIA). Methods 43 children ages 8–17 years and their caregivers provided baseline reports of child emotion regulation. Children then completed thrice daily e-diary assessments of emotion, pain, and activity involvement for 28 days. E-diary ratings of negative and positive emotions were used to calculate emotion variability and to infer adaptive emotion modulation following periods of high or low emotion intensity. Hierarchical linear models were used to evaluate how emotion regulation related to pain and function. Results The attenuation of negative emotion following a period of high negative emotion predicted reduced pain; greater variability of negative emotion predicted higher pain and increased activity limitation. Indices of positive emotion regulation also significantly predicted pain. Conclusions Components of emotion regulation as captured by e-diaries predict important health outcomes in children with JIA. PMID:22037006

  17. Cutaneous Functional Units Predict Shoulder Range of Motion Recovery in Children Receiving Rehabilitation.

    PubMed

    Parry, Ingrid; Sen, Soman; Sattler-Petrocchi, Kelly; Greenhalgh, David; Palmieri, Tina

    Cutaneous functional units (CFUs) are fields of skin that functionally contribute to range of motion (ROM) at an associated joint. When replaced with scar tissue, the skin is less extensible and may result in loss of movement at the joint. Consideration of the amount of CFU affected by burn injury is increasingly being used to predict the development of burn scar contracture (BSC) in burn survivors. Previous work established that, in adults, burn rehabilitation time per CFU was the greatest predictor of preventing BSC. Our study aimed to examine the direct relationship between percent involvement of CFU and ROM achieved in children with BSC who received 6 months of rehabilitation therapy services. ROM was measured at baseline and throughout the study period using traditional methods of goniometry as well as three-dimensional motion capture during the performance of functional tasks. Burn extent and distribution were mapped using an electronic diagram to calculate the percentage of CFU affected by scarring or skin grafts. Pearson's correlations and multivariate linear regression analyses were performed to determine associations between variables. Results showed that percent CFU involvement was negatively correlated with maximal goniometric and functional shoulder ROM achieved. That is, the amount of a given CFU scarred was predictive of less ROM achieved in the associated area. Percentage of CFU involved did not significantly correlate with baseline shoulder ROM, suggesting that other factors may be associated with initial limitations in ROM. Evaluation of the percentage of CFU scarred is useful for predicting shoulder ROM recovery with rehabilitation and may be used to help guide clinical decision making and allocation of time and resource for therapy services.

  18. Variability in functional brain networks predicts expertise during action observation.

    PubMed

    Amoruso, Lucía; Ibáñez, Agustín; Fonseca, Bruno; Gadea, Sebastián; Sedeño, Lucas; Sigman, Mariano; García, Adolfo M; Fraiman, Ricardo; Fraiman, Daniel

    2017-02-01

    Observing an action performed by another individual activates, in the observer, similar circuits as those involved in the actual execution of that action. This activation is modulated by prior experience; indeed, sustained training in a particular motor domain leads to structural and functional changes in critical brain areas. Here, we capitalized on a novel graph-theory approach to electroencephalographic data (Fraiman et al., 2016) to test whether variability in functional brain networks implicated in Tango observation can discriminate between groups differing in their level of expertise. We found that experts and beginners significantly differed in the functional organization of task-relevant networks. Specifically, networks in expert Tango dancers exhibited less variability and a more robust functional architecture. Notably, these expertise-dependent effects were captured within networks derived from electrophysiological brain activity recorded in a very short time window (2s). In brief, variability in the organization of task-related networks seems to be a highly sensitive indicator of long-lasting training effects. This finding opens new methodological and theoretical windows to explore the impact of domain-specific expertise on brain plasticity, while highlighting variability as a fruitful measure in neuroimaging research. Copyright © 2016 Elsevier Inc. All rights reserved.

  19. Functional Characterization of Cucurbitadienol Synthase and Triterpene Glycosyltransferase Involved in Biosynthesis of Mogrosides from Siraitia grosvenorii.

    PubMed

    Dai, Longhai; Liu, Can; Zhu, Yueming; Zhang, Jiangsheng; Men, Yan; Zeng, Yan; Sun, Yuanxia

    2015-06-01

    Mogrosides, the major bioactive components isolated from the fruits of Siraitia grosvenorii, are a family of cucurbitane-type tetracyclic triterpenoid saponins that are used worldwide as high-potency sweeteners and possess a variety of notable pharmacological activities. Mogrosides are synthesized from 2,3-oxidosqualene via a series of reactions catalyzed by cucurbitadienol synthase (CbQ), Cyt P450s (P450s) and UDP glycosyltransferases (UGTs) in vivo. However, the relevant genes have not been characterized to date. In this study, we report successful identification of SgCbQ and UGT74AC1, which were previously predicted via RNA-sequencing (RNA-seq) and digital gene expression (DGE) profile analysis of the fruits of S. grosvenorii. SgCbQ was functionally characterized by expression in the lanosterol synthase-deficient yeast strain GIL77 and was found to accumulate cucurbitadienol as the sole product. UGT74AC1 was heterologously expressed in Escherichia coli as a His-tag protein and it showed specificity for mogrol by transfer of a glucose moiety to the C-3 hydroxyl to form mogroside IE by in vitro enzymatic activity assays. This study reports the identification of CbQ and glycosyltransferase from S. grosvenorii for the first time. The results also suggest that RNA-seq, combined with DGE profile analysis, is a promising approach for discovery of candidate genes involved in biosynthesis of triterpene saponins. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  20. Critical Motor Involvement in Prediction of Human and Non-biological Motion Trajectories

    PubMed Central

    de Wit, Matthieu M.; Buxbaum, Laurel J.

    2017-01-01

    Objectives Adaptive interaction with the environment requires the ability to predict both human and non-biological motion trajectories. Prior accounts of the neurocognitive basis for prediction of these two motion classes may generally be divided into those that posit that non-biological motion trajectories are predicted using the same motor planning and/or simulation mechanisms used for human actions, and those that posit distinct mechanisms for each. Using brain lesion patients and healthy controls, this study examined critical neural substrates and behavioral correlates of human and non-biological motion prediction. Methods Twenty-seven left hemisphere stroke patients and 13 neurologically intact controls performed a visual occlusion task requiring prediction of pantomimed tool use, real tool use, and non-biological motion videos. Patients were also assessed with measures of motor strength and speed, praxis, and action recognition. Results Prediction impairment for both human and non-biological motion was associated with limb apraxia and, weakly, with the severity of motor production deficits, but not with action recognition ability. Furthermore, impairment for human and non-biological motion prediction was equivalently associated with lesions in the left inferior parietal cortex, left dorsal frontal cortex, and the left insula. Conclusions These data suggest that motor planning mechanisms associated with specific loci in the sensorimotor network are critical for prediction of spatiotemporal trajectory information characteristic of both human and non-biological motions. PMID:28205497

  1. Do knowledge and cultural perceptions of modern female contraceptives predict male involvement in Ayete, Nigeria?

    PubMed

    Sanusi, A; Akinyemi, Oluwaseun O; Onoviran, Oghemetega O

    2014-12-01

    Male involvement is crucial to female contraceptive use. This study examined how male knowledge and cultural perceptions of modern female contraceptives influence involvement in contraceptive use. A cross-sectional survey of 389 men from Ayete, Nigeria was used to regress a continuous male involvement score on demographic variables, knowledge of at least one method of modern female contraception and a scored male perception variable using Ordinary Least Squares regression. Controlling for perception, the knowledge of at least one method of modern female contraception was not significantly associated with a change in male involvement (p=0.264). Increasing positive perception was associated with higher male involvement scores (p=0.001). Higher educated males, those with a current desire to have children and males whose partners were currently using a method had greater male involvement scores (p<0.05). Policy and intervention efforts should be focused on changing cultural perceptions, in addition to providing in-depth knowledge of contraceptive methods.

  2. Predictive factors of functional capacity and real-world functioning in patients with schizophrenia.

    PubMed

    Menendez-Miranda, I; Garcia-Portilla, M P; Garcia-Alvarez, L; Arrojo, M; Sanchez, P; Sarramea, F; Gomar, J; Bobes-Bascaran, M T; Sierra, P; Saiz, P A; Bobes, J

    2015-07-01

    This study was performed to identify the predictive factors of functional capacity assessed by the Spanish University of California Performance Skills Assessment (Sp-UPSA) and real-world functioning assessed by the Spanish Personal and Social Performance scale (PSP) in outpatients with schizophrenia. Naturalistic, 6-month follow-up, multicentre, validation study. Here, we report data on 139 patients with schizophrenia at their baseline visit. Positive and Negative Syndrome Scale (PANSS), Clinical Global Impression-Severity (CGI-S), Sp-UPSA and PSP. Pearson's correlation coefficient (r) was used to determine the relationships between variables, and multivariable stepwise linear regression analyses to identify predictive variables of Sp-UPSA and PSP total scores. Functional capacity: scores on the PSP and PANSS-GP entered first and second at P<0.0001 and accounted for 21% of variance (R(2)=0.208, model df=2, F=15.724, P<0.0001). Real-world functioning: scores on the CGI-S (B=-5.406), PANSS-N (B=-0.657) and Sp-UPSA (B=0.230) entered first, second and third, and accounted for 51% of variance (model df=3, F=37.741, P<0.0001). In patients with schizophrenia, functional capacity and real-world functioning are two related but different constructs. Each one predicts the other along with other factors; general psychopathology for functional capacity, and severity of the illness and negative symptoms for real-world functioning. These findings have important clinical implications: (1) both types of functioning should be assessed in patients with schizophrenia and (2) strategies for improving them should be different. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

  3. Predictive models of control strategies involved in containing indoor airborne infections.

    PubMed

    Chen, S-C; Chang, C-F; Liao, C-M

    2006-12-01

    Recently developed control measure modeling approaches for containing airborne infections, including engineering controls with respiratory protection and public health interventions, are readily amenable to an integrated-scale analysis. Here we show that such models can be derived from an integrated-scale analysis generated from three different types of functional relationship: Wells-Riley mathematical model, competing-risks model, and Von Foerster equation, both of the key epidemiological determinants involved and of the functional connections between them. We examine mathematically the impact of engineering control measures such as enhanced air exchange and air filtration rates with personal masking combined with public health interventions such as vaccination, isolation, and contact tracing in containing the spread of indoor airborne infections including influenza, chickenpox, measles, and severe acute respiratory syndrome (SARS). If enhanced engineering controls could reduce the basic reproductive number (R0) below 1.60 for chickenpox and 3 for measles, our simulations show that in such a prepared response with public health interventions would have a high probability of containing the indoor airborne infections. Combinations of engineering control measures and public health interventions could moderately contain influenza strains with an R0 as high as 4. Our analysis indicates that effective isolation of symptomatic patients with low-efficacy contact tracing is sufficient to control a SARS outbreak. We suggest that a valuable added dimension to public health inventions could be provided by systematically quantifying transmissibility and proportion of asymptomatic infection of indoor airborne infection. Practical Implications We have developed a flexible mathematical model that can help determine the best intervention strategies for containing indoor airborne infections. The approach presented here is scalable and can be extended to include additional control

  4. Striatal structure and function predict individual biases in learning to avoid pain.

    PubMed

    Eldar, Eran; Hauser, Tobias U; Dayan, Peter; Dolan, Raymond J

    2016-04-26

    Pain is an elemental inducer of avoidance. Here, we demonstrate that people differ in how they learn to avoid pain, with some individuals refraining from actions that resulted in painful outcomes, whereas others favor actions that helped prevent pain. These individual biases were best explained by differences in learning from outcome prediction errors and were associated with distinct forms of striatal responses to painful outcomes. Specifically, striatal responses to pain were modulated in a manner consistent with an aversive prediction error in individuals who learned predominantly from pain, whereas in individuals who learned predominantly from success in preventing pain, modulation was consistent with an appetitive prediction error. In contrast, striatal responses to success in preventing pain were consistent with an appetitive prediction error in both groups. Furthermore, variation in striatal structure, encompassing the region where pain prediction errors were expressed, predicted participants' predominant mode of learning, suggesting the observed learning biases may reflect stable individual traits. These results reveal functional and structural neural components underlying individual differences in avoidance learning, which may be important contributors to psychiatric disorders involving pathological harm avoidance behavior.

  5. Striatal structure and function predict individual biases in learning to avoid pain

    PubMed Central

    Eldar, Eran; Hauser, Tobias U.; Dayan, Peter; Dolan, Raymond J.

    2016-01-01

    Pain is an elemental inducer of avoidance. Here, we demonstrate that people differ in how they learn to avoid pain, with some individuals refraining from actions that resulted in painful outcomes, whereas others favor actions that helped prevent pain. These individual biases were best explained by differences in learning from outcome prediction errors and were associated with distinct forms of striatal responses to painful outcomes. Specifically, striatal responses to pain were modulated in a manner consistent with an aversive prediction error in individuals who learned predominantly from pain, whereas in individuals who learned predominantly from success in preventing pain, modulation was consistent with an appetitive prediction error. In contrast, striatal responses to success in preventing pain were consistent with an appetitive prediction error in both groups. Furthermore, variation in striatal structure, encompassing the region where pain prediction errors were expressed, predicted participants’ predominant mode of learning, suggesting the observed learning biases may reflect stable individual traits. These results reveal functional and structural neural components underlying individual differences in avoidance learning, which may be important contributors to psychiatric disorders involving pathological harm avoidance behavior. PMID:27071092

  6. Functional network architecture predicts psychologically mediated analgesia related to treatment in chronic knee pain patients.

    PubMed

    Hashmi, Javeria Ali; Kong, Jian; Spaeth, Rosa; Khan, Sheraz; Kaptchuk, Ted J; Gollub, Randy L

    2014-03-12

    Placebo analgesia is an indicator of how efficiently the brain translates psychological signals conveyed by a treatment procedure into pain relief. It has been demonstrated that functional connectivity between distributed brain regions predicts placebo analgesia in chronic back pain patients. Greater network efficiency in baseline brain networks may allow better information transfer and facilitate adaptive physiological responses to psychological aspects of treatment. Here, we theorized that topological network alignments in resting state scans predict psychologically conditioned analgesic responses to acupuncture treatment in chronic knee osteoarthritis pain patients (n = 45). Analgesia was induced by building positive expectations toward acupuncture treatment with verbal suggestion and heat pain conditioning on a test site of the arm. This procedure induced significantly more analgesia after sham or real acupuncture on the test site than in a control site. The psychologically conditioned analgesia was invariant to sham versus real treatment. Efficiency of information transfer within local networks calculated with graph-theoretic measures (local efficiency and clustering coefficients) significantly predicted conditioned analgesia. Clustering coefficients in regions associated with memory, motivation, and pain modulation were closely involved in predicting analgesia. Moreover, women showed higher clustering coefficients and marginally greater pain reduction than men. Overall, analgesic response to placebo cues can be predicted from a priori resting state data by observing local network topology. Such low-cost synchronizations may represent preparatory resources that facilitate subsequent performance of brain circuits in responding to adaptive environmental cues. This suggests a potential utility of network measures in predicting placebo response for clinical use.

  7. Individual differences in common factors of emotional traits and executive functions predict functional connectivity of the amygdala.

    PubMed

    Rohr, C S; Dreyer, F R; Aderka, I M; Margulies, D S; Frisch, S; Villringer, A; Okon-Singer, H

    2015-10-15

    Evidence suggests that individual differences in emotion control are associated with frontoparietal-limbic networks and linked to emotional traits and executive functions. In a first attempt to directly target the link between emotional traits and executive functions using resting-state fMRI analysis, 43 healthy adults completed a test battery including executive tasks and emotional trait self-assessments that were subjected to a principal component analysis. Of the three factors detected, two explained 40.4% of the variance and were further investigated. Both factors suggest a relation between emotional traits and executive functions. Specifically, the first factor consisted of measures related to inhibitory control and negative affect, and the second factor was related to reward and positive affect. To investigate whether this interplay between emotional traits and executive functions is reflected in neural connectivity, we used resting-state fMRI to explore the functional connectivity of the amygdala as a starting point, and progressed to other seed-based analyses based on the initial findings. We found that the first factor predicted the strength of connectivity between brain regions known to be involved in the cognitive control of emotion, including the amygdala and the dorsolateral prefrontal cortex, whereas the second factor predicted the strength of connectivity between brain regions known to be involved in reward and attention, including the amygdala, the caudate and the thalamus. These findings suggest that individual differences in the ability to inhibit negative affect are mediated by prefrontal-limbic pathways, while the ability to be positive and use rewarding information is mediated by a network that includes the amygdala and thalamostriatal regions.

  8. Does preoperative cross-sectional imaging accurately predict main duct involvement in intraductal papillary mucinous neoplasm?

    PubMed

    Barron, M R; Roch, A M; Waters, J A; Parikh, J A; DeWitt, J M; Al-Haddad, M A; Ceppa, E P; House, M G; Zyromski, N J; Nakeeb, A; Pitt, H A; Schmidt, C Max

    2014-03-01

    Main pancreatic duct (MPD) involvement is a well-demonstrated risk factor for malignancy in intraductal papillary mucinous neoplasm (IPMN). Preoperative radiographic determination of IPMN type is heavily relied upon in oncologic risk stratification. We hypothesized that radiographic assessment of MPD involvement in IPMN is an accurate predictor of pathological MPD involvement. Data regarding all patients undergoing resection for IPMN at a single academic institution between 1992 and 2012 were gathered prospectively. Retrospective analysis of imaging and pathologic data was undertaken. Preoperative classification of IPMN type was based on cross-sectional imaging (MRI/magnetic resonance cholangiopancreatography (MRCP) and/or CT). Three hundred sixty-two patients underwent resection for IPMN. Of these, 334 had complete data for analysis. Of 164 suspected branch duct (BD) IPMN, 34 (20.7%) demonstrated MPD involvement on final pathology. Of 170 patients with suspicion of MPD involvement, 50 (29.4%) demonstrated no MPD involvement. Of 34 patients with suspected BD-IPMN who were found to have MPD involvement on pathology, 10 (29.4%) had invasive carcinoma. Alternatively, 2/50 (4%) of the patients with suspected MPD involvement who ultimately had isolated BD-IPMN demonstrated invasive carcinoma. Preoperative radiographic IPMN type did not correlate with final pathology in 25% of the patients. In addition, risk of invasive carcinoma correlates with pathologic presence of MPD involvement.

  9. Does subsequent criminal justice involvement predict foster care and termination of parental rights for children born to incarcerated women?

    PubMed

    Kubiak, Sheryl Pimlott; Kasiborski, Natalie; Karim, Nidal; Schmittel, Emily

    2012-01-01

    This longitudinal study of 83 incarcerated women, who gave birth during incarceration and retained their parental rights through brief sentences, examines the intersection between subsequent criminal justice involvement postrelease and child welfare outcomes. Ten years of multiple state-level administrative data sets are used to determine if arrest or conviction predict foster care and/or termination of parental rights. Findings indicate that only felony arrest is a significant predictor of foster care involvement. Additionally, 69% of mothers retained legal custody, despite subsequent criminal involvement for many, suggesting supportive parenting programs and resources need to be available to these women throughout and after incarceration.

  10. Does obesity predict functional outcome in the dysvascular amputee?

    PubMed

    Kalbaugh, Corey A; Taylor, Spence M; Kalbaugh, Brooke A; Halliday, Matthew; Daniel, Grace; Cass, Anna L; Blackhurst, Dawn W; Cull, David L; Langan, Eugene M; Carsten, Christopher G; York, John W; Snyder, Bruce A; Youkey, Jerry R

    2006-08-01

    Limited information is available concerning the effects of obesity on the functional outcomes of patients requiring major lower limb amputation because of peripheral arterial disease (PAD). The purpose of this study was to examine the predictive ability of body mass index (BMI) to determine functional outcome in the dysvascular amputee. To do this, 434 consecutive patients (mean age, 65.8 +/- 13.3, 59% male, 71.4% diabetic) undergoing major limb amputation (225 below-knee amputation, 27 through-knee amputation, 132 above-knee amputation, and 50 bilateral) as a complication of PAD from January 1998 through May 2004 were analyzed according to preoperative BMI. BMI was classified according to the four-group Center for Disease Control system: underweight, 0 to 18.4 kg/m2; normal, 18.5 to 24.9 kg/m2; overweight, 25 to 29.9 kg/m2; and obese, > or = 30 kg/m2. Outcome parameters measured included prosthetic usage, maintenance of ambulation, survival, and maintenance of independent living status. The chi2 test for association was used to examine prosthesis wear. Kaplan-Meier curves were constructed to assess maintenance of ambulation, survival, and maintenance of independent living status. Multivariate analysis using the multiple logistic regression model and a Cox proportional hazards model were used to predict variables independently associated with prosthetic use and ambulation, survival, and independence, respectively. Overall prosthetic usage and 36-month ambulation, survival, and independent living status for the entire cohort was 48.6 per cent, 42.8 per cent, 48.1 per cent, 72.3 per cent, and for patients with normal BMI was 41.5 per cent, 37.4 per cent, 45.6 per cent, and 69.5 per cent, respectively. There was no statistically significant difference in outcomes for overweight patients (59.2%, 50.7%, 52.5%, and 75%) or obese patients (51.8%, 46.2%, 49.7%, and 75%) when compared with normal patients. Although there were significantly poorer outcomes for underweight

  11. Predictive Factors in Undergraduates' Involvement in Campus Secret Cults in Public Universities in Edo State of Nigeria

    ERIC Educational Resources Information Center

    Azetta Arhedo, Philip; Aluede, Oyaziwo; Adomeh, Ilu O. C.

    2011-01-01

    This study examined the predictive factors in undergraduates' involvement in campus secret cults in public universities in Edo State of Nigeria. The study employed the descriptive method, specifically the survey format. A random sample of three hundred and eighty (380) undergraduates was drawn from the two public universities. Data were elicited…

  12. Predictive Factors in Undergraduates' Involvement in Campus Secret Cults in Public Universities in Edo State of Nigeria

    ERIC Educational Resources Information Center

    Azetta Arhedo, Philip; Aluede, Oyaziwo; Adomeh, Ilu O. C.

    2011-01-01

    This study examined the predictive factors in undergraduates' involvement in campus secret cults in public universities in Edo State of Nigeria. The study employed the descriptive method, specifically the survey format. A random sample of three hundred and eighty (380) undergraduates was drawn from the two public universities. Data were elicited…

  13. Probability-based prediction of activity in multiple arm muscles: implications for functional electrical stimulation.

    PubMed

    Anderson, Chad V; Fuglevand, Andrew J

    2008-07-01

    Functional electrical stimulation (FES) involves artificial activation of muscles with implanted electrodes to restore motor function in paralyzed individuals. The range of motor behaviors that can be generated by FES, however, is limited to a small set of preprogrammed movements such as hand grasp and release. A broader range of movements has not been implemented because of the substantial difficulty associated with identifying the patterns of muscle stimulation needed to elicit specified movements. To overcome this limitation in controlling FES systems, we used probabilistic methods to estimate the levels of muscle activity in the human arm during a wide range of free movements based on kinematic information of the upper limb. Conditional probability distributions were generated based on hand kinematics and associated surface electromyographic (EMG) signals from 12 arm muscles recorded during a training task involving random movements of the arm in one subject. These distributions were then used to predict in four other subjects the patterns of muscle activity associated with eight different movement tasks. On average, about 40% of the variance in the actual EMG signals could be accounted for in the predicted EMG signals. These results suggest that probabilistic methods ultimately might be used to predict the patterns of muscle stimulation needed to produce a wide array of desired movements in paralyzed individuals with FES.

  14. Dimensions and Predictions of Professional Involvement in Self-Help Groups: A View from Within.

    ERIC Educational Resources Information Center

    Ben-Ari, Adital Tirosh

    2002-01-01

    Discusses analysis of how members of self-help groups perceived professional involvement and dimensions of such involvement. Three categories were identified according to their main focus: groups dealing with health issues, groups dealing with alternative lifestyles, and groups based on the 12-step model. Analysis yielded two conceptually…

  15. Salience Network Functional Connectivity Predicts Placebo Effects in Major Depression

    PubMed Central

    Sikora, Magdalena; Heffernan, Joseph; Avery, Erich T.; Mickey, Brian J.; Zubieta, Jon-Kar; Peciña, Marta

    2015-01-01

    Background Recent neuroimaging studies have demonstrated resting-state functional connectivity (rsFC) abnormalities among intrinsic brain networks in Major Depressive Disorder (MDD); however, their role as predictors of treatment response has not yet been explored. Here, we investigate whether network-based rsFC predicts antidepressant and placebo effects in MDD. Methods We performed a randomized controlled trial of two weeklong, identical placebos (described as having either “active” fast-acting, antidepressant effects or as “inactive”) followed by a ten-week open-label antidepressant medication treatment. Twenty-nine participants underwent a rsFC fMRI scan at the completion of each placebo condition. Networks were isolated from resting-state blood-oxygen-level-dependent signal fluctuations using independent component analysis. Baseline and placebo-induced changes in rsFC within the default-mode, salience, and executive networks were examined for associations with placebo and antidepressant treatment response. Results Increased baseline rsFC in the rostral anterior cingulate (rACC) within the salience network, a region classically implicated in the formation of placebo analgesia and the prediction of treatment response in MDD, was associated with greater response to one week of active placebo and ten weeks of antidepressant treatment. Machine learning further demonstrated that increased salience network rsFC, mainly within the rACC, significantly predicts individual responses to placebo administration. Conclusions These data demonstrate that baseline rsFC within the salience network is linked to clinical placebo responses. This information could be employed to identify patients who would benefit from lower doses of antidepressant medication or non-pharmacological approaches, or to develop biomarkers of placebo effects in clinical trials. PMID:26709390

  16. Predicted equations for ventilatory function among Kuching (Sarawak, Malaysia) population.

    PubMed

    Djojodibroto, R D; Pratibha, G; Kamaluddin, B; Manjit, S S; Sumitabha, G; Kumar, A Deva; Hashami, B

    2009-12-01

    Spirometry data of 869 individuals (males and females) between the ages of 10 to 60 years were analyzed. The analysis yielded the following conclusions: 1. The pattern of Forced Vital Capacity (FVC) and Forced Expiratory Volume in One Second (FEV1) for the selected subgroups seems to be gender dependant: in males, the highest values were seen in the Chinese, followed by the Malay, and then the Dayak; in females, the highest values were seen in the Chinese, followed by the Dayak, and then the Malay. 2. Smoking that did not produce respiratory symptom was not associated with a decline in lung function, in fact we noted higher values in smokers as compared to nonsmokers. 3. Prediction formulae (54 in total) are worked out for FVC & FEV1 for the respective gender and each of the selected subgroups.

  17. Link prediction boosted psychiatry disorder classification for functional connectivity network

    NASA Astrophysics Data System (ADS)

    Li, Weiwei; Mei, Xue; Wang, Hao; Zhou, Yu; Huang, Jiashuang

    2017-02-01

    Functional connectivity network (FCN) is an effective tool in psychiatry disorders classification, and represents cross-correlation of the regional blood oxygenation level dependent signal. However, FCN is often incomplete for suffering from missing and spurious edges. To accurate classify psychiatry disorders and health control with the incomplete FCN, we first `repair' the FCN with link prediction, and then exact the clustering coefficients as features to build a weak classifier for every FCN. Finally, we apply a boosting algorithm to combine these weak classifiers for improving classification accuracy. Our method tested by three datasets of psychiatry disorder, including Alzheimer's Disease, Schizophrenia and Attention Deficit Hyperactivity Disorder. The experimental results show our method not only significantly improves the classification accuracy, but also efficiently reconstructs the incomplete FCN.

  18. Application of Functional Use Predictions to Aid in Structure ...

    EPA Pesticide Factsheets

    Humans are potentially exposed to thousands of anthropogenic chemicals in commerce. Recent work has shown that the bulk of this exposure may occur in near-field indoor environments (e.g., home, school, work, etc.). Advances in suspect screening analyses (SSA) now allow an improved understanding of the chemicals present in these environments. However, due to the nature of suspect screening techniques, investigators are often left with chemical formula predictions, with the possibility of many chemical structures matching to each formula. Here, newly developed quantitative structure-use relationship (QSUR) models are used to identify potential exposure sources for candidate structures. Previously, a suspect screening workflow was introduced and applied to house dust samples collected from the U.S. Department of Housing and Urban Development’s American Healthy Homes Survey (AHHS) [Rager, et al., Env. Int. 88 (2016)]. This workflow utilized the US EPA’s Distributed Structure-Searchable Toxicity (DSSTox) Database to link identified molecular features to molecular formulas, and ultimately chemical structures. Multiple QSUR models were applied to support the evaluation of candidate structures. These QSURs predict the likelihood of a chemical having a functional use commonly associated with consumer products having near-field use. For 3,228 structures identified as possible chemicals in AHHS house dust samples, we were able to obtain the required descriptors to appl

  19. A Prediction for the 4-Loop beta Function in QCD

    SciTech Connect

    Samuel, Mark A.

    2003-05-14

    We predict that the four-loop contribution {beta}{sub 3} to the QCD {beta} function in the {ovr MS} prescription is given by {beta}{sub 3} {approx_equal} 23,600(900) - 6,400(200) N{sub f} + 350(70)N{sub f}{sup 2} + 1.5 N{sub f}{sup 3}, where N{sub f} is the number of flavours and the coefficient of N{sub f}{sup 3} is an exact result from large-N{sub f} expansion. In the phenomenologically-interesting case N{sub f} = 3, we estimate {beta}{sub 3} = (7.6 {+-} 0.1) x 10{sup 3}. We discuss our estimates of the errors in these QCD predictions, basing them on the demonstrated accuracy of our method in test applications to the O(N) {Phi}{sup 4} theory, and on variations in the details of our estimation method, which goes beyond conventional Pade approximants by estimating and correcting for subasymptotic deviations from exact results.

  20. Predicting Stability Constants for Uranyl Complexes Using Density Functional Theory

    DOE PAGES

    Vukovic, Sinisa; Hay, Benjamin P.; Bryantsev, Vyacheslav S.

    2015-04-02

    The ability to predict the equilibrium constants for the formation of 1:1 uranyl:ligand complexes (log K1 values) provides the essential foundation for the rational design of ligands with enhanced uranyl affinity and selectivity. We also use density functional theory (B3LYP) and the IEFPCM continuum solvation model to compute aqueous stability constants for UO22+ complexes with 18 donor ligands. Theoretical calculations permit reasonably good estimates of relative binding strengths, while the absolute log K1 values are significantly overestimated. Accurate predictions of the absolute log K1 values (root mean square deviation from experiment < 1.0 for log K1 values ranging from 0more » to 16.8) can be obtained by fitting the experimental data for two groups of mono and divalent negative oxygen donor ligands. The utility of correlations is demonstrated for amidoxime and imide dioxime ligands, providing a useful means of screening for new ligands with strong chelate capability to uranyl.« less

  1. A yeast functional screen predicts new candidate ALS disease genes

    PubMed Central

    Couthouis, Julien; Hart, Michael P.; Shorter, James; DeJesus-Hernandez, Mariely; Erion, Renske; Oristano, Rachel; Liu, Annie X.; Ramos, Daniel; Jethava, Niti; Hosangadi, Divya; Epstein, James; Chiang, Ashley; Diaz, Zamia; Nakaya, Tadashi; Ibrahim, Fadia; Kim, Hyung-Jun; Solski, Jennifer A.; Williams, Kelly L.; Mojsilovic-Petrovic, Jelena; Ingre, Caroline; Boylan, Kevin; Graff-Radford, Neill R.; Dickson, Dennis W.; Clay-Falcone, Dana; Elman, Lauren; McCluskey, Leo; Greene, Robert; Kalb, Robert G.; Lee, Virginia M.-Y.; Trojanowski, John Q.; Ludolph, Albert; Robberecht, Wim; Andersen, Peter M.; Nicholson, Garth A.; Blair, Ian P.; King, Oliver D.; Bonini, Nancy M.; Van Deerlin, Vivianna; Rademakers, Rosa; Mourelatos, Zissimos; Gitler, Aaron D.

    2011-01-01

    Amyotrophic lateral sclerosis (ALS) is a devastating and universally fatal neurodegenerative disease. Mutations in two related RNA-binding proteins, TDP-43 and FUS, that harbor prion-like domains, cause some forms of ALS. There are at least 213 human proteins harboring RNA recognition motifs, including FUS and TDP-43, raising the possibility that additional RNA-binding proteins might contribute to ALS pathogenesis. We performed a systematic survey of these proteins to find additional candidates similar to TDP-43 and FUS, followed by bioinformatics to predict prion-like domains in a subset of them. We sequenced one of these genes, TAF15, in patients with ALS and identified missense variants, which were absent in a large number of healthy controls. These disease-associated variants of TAF15 caused formation of cytoplasmic foci when expressed in primary cultures of spinal cord neurons. Very similar to TDP-43 and FUS, TAF15 aggregated in vitro and conferred neurodegeneration in Drosophila, with the ALS-linked variants having a more severe effect than wild type. Immunohistochemistry of postmortem spinal cord tissue revealed mislocalization of TAF15 in motor neurons of patients with ALS. We propose that aggregation-prone RNA-binding proteins might contribute very broadly to ALS pathogenesis and the genes identified in our yeast functional screen, coupled with prion-like domain prediction analysis, now provide a powerful resource to facilitate ALS disease gene discovery. PMID:22065782

  2. Application of Functional Use Predictions to Aid in Structure ...

    EPA Pesticide Factsheets

    Humans are potentially exposed to thousands of anthropogenic chemicals in commerce. Recent work has shown that the bulk of this exposure may occur in near-field indoor environments (e.g., home, school, work, etc.). Advances in suspect screening analyses (SSA) now allow an improved understanding of the chemicals present in these environments. However, due to the nature of suspect screening techniques, investigators are often left with chemical formula predictions, with the possibility of many chemical structures matching to each formula. Here, newly developed quantitative structure-use relationship (QSUR) models are used to identify potential exposure sources for candidate structures. Previously, a suspect screening workflow was introduced and applied to house dust samples collected from the U.S. Department of Housing and Urban Development’s American Healthy Homes Survey (AHHS) [Rager, et al., Env. Int. 88 (2016)]. This workflow utilized the US EPA’s Distributed Structure-Searchable Toxicity (DSSTox) Database to link identified molecular features to molecular formulas, and ultimately chemical structures. Multiple QSUR models were applied to support the evaluation of candidate structures. These QSURs predict the likelihood of a chemical having a functional use commonly associated with consumer products having near-field use. For 3,228 structures identified as possible chemicals in AHHS house dust samples, we were able to obtain the required descriptors to appl

  3. Predicting biomedical document access as a function of past use.

    PubMed

    Goodwin, J Caleb; Johnson, Todd R; Cohen, Trevor; Herskovic, Jorge R; Bernstam, Elmer V

    2012-01-01

    To determine whether past access to biomedical documents can predict future document access. The authors used 394 days of query log (August 1, 2009 to August 29, 2010) from PubMed users in the Texas Medical Center, which is the largest medical center in the world. The authors evaluated two document access models based on the work of Anderson and Schooler. The first is based on how frequently a document was accessed. The second is based on both frequency and recency. The model based only on frequency of past access was highly correlated with the empirical data (R²=0.932), whereas the model based on frequency and recency had a much lower correlation (R²=0.668). The frequency-only model accurately predicted whether a document will be accessed based on past use. Modeling accesses as a function of frequency requires storing only the number of accesses and the creation date for the document. This model requires low storage overheads and is computationally efficient, making it scalable to large corpora such as MEDLINE. It is feasible to accurately model the probability of a document being accessed in the future based on past accesses.

  4. Predicting Stability Constants for Uranyl Complexes Using Density Functional Theory

    SciTech Connect

    Vukovic, Sinisa; Hay, Benjamin P.; Bryantsev, Vyacheslav S.

    2015-04-02

    The ability to predict the equilibrium constants for the formation of 1:1 uranyl:ligand complexes (log K1 values) provides the essential foundation for the rational design of ligands with enhanced uranyl affinity and selectivity. We also use density functional theory (B3LYP) and the IEFPCM continuum solvation model to compute aqueous stability constants for UO22+ complexes with 18 donor ligands. Theoretical calculations permit reasonably good estimates of relative binding strengths, while the absolute log K1 values are significantly overestimated. Accurate predictions of the absolute log K1 values (root mean square deviation from experiment < 1.0 for log K1 values ranging from 0 to 16.8) can be obtained by fitting the experimental data for two groups of mono and divalent negative oxygen donor ligands. The utility of correlations is demonstrated for amidoxime and imide dioxime ligands, providing a useful means of screening for new ligands with strong chelate capability to uranyl.

  5. Prediction of glass durability as a function of environmental conditions

    SciTech Connect

    Jantzen, C M

    1988-01-01

    A thermodynamic model of glass durability is applied to natural, ancient, and nuclear waste glasses. The durabilities of over 150 different natural and man-made glasses, including actual ancient Roman and Islamic glasses (Jalame ca. 350 AD, Nishapur 10-11th century AD and Gorgon 9-11th century AD), are compared. Glass durability is a function of the thermodynamic hydration free energy, ..delta..G/sub hyd/, which can be calculated from glass composition and solution pH. The durability of the most durable nuclear waste glasses examined was /approximately/10/sup 6/ years. The least durable waste glass formulations were comparable in durability to the most durable simulated medieval window glasses of /approximately/10/sup 3/ years. In this manner, the durability of nuclear waste glasses has been interpolated to be /approximately/10/sup 6/ years and no less than 10/sup 3/ years. Hydration thermodynamics have been shown to be applicable to the dissolution of glass in various natural environments. Groundwater-glass interactions relative to geologic disposal of nuclear waste, hydration rind dating of obsidians, andor other archeological studies can be modeled, e.g., the relative durabilities of six simulated medieval window glasses have been correctly predicted for both laboratory (one month) and burial (5 years) experiments. Effects of solution pH on glass dissolution has been determined experimentally for the 150 different glasses and can be predicted theoretically by hydration thermodynamics. The effects of solution redox on dissolution of glass matrix elements such as SI and B have shown to be minimal. The combined effects of solution pH and Eh have been described and unified by construction of thermodynamically calculated Pourbaix (pH-Eh) diagrams for glass dissolution. The Pourbaix diagrams have been quantified to describe glass dissolution as a function of environmental conditions by use of the data derived from hydration thermodynamics. 56 refs., 7 figs.

  6. Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids.

    PubMed

    Iyer, Lakshminarayan M; Tahiliani, Mamta; Rao, Anjana; Aravind, L

    2009-06-01

    Modified bases in nucleic acids present a layer of information that directs biological function over and beyond the coding capacity of the conventional bases. While a large number of modified bases have been identified, many of the enzymes generating them still remain to be discovered. Recently, members of the 2-oxoglutarate- and iron(II)-dependent dioxygenase super-family, which modify diverse substrates from small molecules to biopolymers, were predicted and subsequently confirmed to catalyze oxidative modification of bases in nucleic acids. Of these, two distinct families, namely the AlkB and the kinetoplastid base J binding proteins (JBP) catalyze in situ hydroxylation of bases in nucleic acids. Using sensitive computational analysis of sequences, structures and contextual information from genomic structure and protein domain architectures, we report five distinct families of 2-oxoglutarate- and iron(II)-dependent dioxygenase that we predict to be involved in nucleic acid modifications. Among the DNA-modifying families, we show that the dioxygenase domains of the kinetoplastid base J-binding proteins belong to a larger family that includes the Tet proteins, prototyped by the human oncogene Tet1, and proteins from basidiomycete fungi, chlorophyte algae, heterolobosean amoeboflagellates and bacteriophages. We present evidence that some of these proteins are likely to be involved in oxidative modification of the 5-methyl group of cytosine leading to the formation of 5-hydroxymethylcytosine. The Tet/JBP homologs from basidiomycete fungi such as Laccaria and Coprinopsis show large lineage-specific expansions and a tight linkage with genes encoding a novel and distinct family of predicted transposases, and a member of the Maelstrom-like HMG family. We propose that these fungal members are part of a mobile transposon. To the best of our knowledge, this is the first report of a eukaryotic transposable element that encodes its own DNA-modification enzyme with a

  7. Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids

    PubMed Central

    Iyer, Lakshminarayan M.; Tahiliani, Mamta; Rao, Anjana; Aravind, L.

    2010-01-01

    Modified bases in nucleic acids present a layer of information that directs biological function over and beyond the coding capacity of the conventional bases. While a large number of modified bases have been identified, many of the enzymes generating them still remain to be discovered. Recently, members of the 2-oxoglutarate- and iron(II)-dependent dioxygenase superfamily, which modify diverse substrates from small molecules to biopolymers, were predicted and subsequently confirmed to catalyze oxidative modification of bases in nucleic acids. Of these, two distinct families, namely the AlkB and the kinetoplastid base J binding proteins (JBP) catalyze in situ hydroxylation of bases in nucleic acids. Using sensitive computational analysis of sequences, structures and contextual information from genomic structure and protein domain architectures, we report five distinct families of 2-oxoglutarate- and iron(II)-dependent dioxygenase that we predict to be involved in nucleic acid modifications. Among the DNA-modifying families, we show that the dioxygenase domains of the kinetoplastid base J-binding proteins belong to a larger family that includes the Tet proteins, prototyped by the human oncogene Tet1, and proteins from basidiomycete fungi, chlorophyte algae, heterolobosean amoeboflagellates and bacteriophages. We present evidence that some of these proteins are likely to be involved in oxidative modification of the 5-methyl group of cytosine leading to the formation of 5-hydroxymethyl-cytosine. The Tet/JBP homologs from basidiomycete fungi such as Laccaria and Coprinopsis show large lineage-specific expansions and a tight linkage with genes encoding a novel and distinct family of predicted transposases, and a member of the Maelstrom-like HMG family. We propose that these fungal members are part of a mobile transposon. To the best of our knowledge, this is the first report of a eukaryotic transposable element that encodes its own DNA-modification enzyme with a

  8. Relationship between involvement and functional milk desserts intention to purchase. Influence on attitude towards packaging characteristics.

    PubMed

    Ares, Gastón; Besio, Mariángela; Giménez, Ana; Deliza, Rosires

    2010-10-01

    Consumers perceive functional foods as member of the particular food category to which they belong. In this context, apart from health and sensory characteristics, non-sensory factors such as packaging might have a key role on determining consumers' purchase decisions regarding functional foods. The aims of the present work were to study the influence of different package attributes on consumer willingness to purchase regular and functional chocolate milk desserts; and to assess if the influence of these attributes was affected by consumers' level of involvement with the product. A conjoint analysis task was carried out with 107 regular milk desserts consumers, who were asked to score their willingness to purchase of 16 milk dessert package concepts varying in five features of the package, and to complete a personal involvement inventory questionnaire. Consumers' level of involvement with the product affected their interest in the evaluated products and their reaction towards the considered conjoint variables, suggesting that it could be a useful segmentation tool during food development. Package colour and the presence of a picture on the label were the variables with the highest relative importance, regardless of consumers' involvement with the product. The importance of these variables was higher than the type of dessert indicating that packaging may play an important role in consumers' perception and purchase intention of functional foods.

  9. Self-Determination and Student Involvement in Functional Assessment: Innovative Practices

    ERIC Educational Resources Information Center

    Wehmeyer, Michael L.; Baker, Daniel J.; Blumberg, Richard; Harrison, Richard

    2004-01-01

    The fundamental feature that distinguishes positive behavior support (PBS) from previous generations of applied behavior analysis is its focus on the remediation of deficient contexts that are determined to be the source of the problem. Determining this source involves conducting a functional assessment. This innovative practices article presents…

  10. On a fractional integral equation of periodic functions involving Weyl-Riesz operator in Banach algebras

    NASA Astrophysics Data System (ADS)

    Momani, Shaher; Ibrahim, Rabha W.

    2008-03-01

    In this paper, we study the existence of periodic solutions for a nonlinear integral equation of periodic functions involving Weyl-Riesz fractional integral operator under the mixed generalized Lipschitz, Carathéodory and monotonicity conditions. The fixed point theorems due to Dhage are the main tool in carrying out our proofs.

  11. Can Parents' Involvement in Children's Education Offset the Effects of Early Insensitivity on Academic Functioning?

    ERIC Educational Resources Information Center

    Monti, Jennifer D.; Pomerantz, Eva M.; Roisman, Glenn I.

    2014-01-01

    Data from the National Institute of Child Health and Human Development Study of Early Child Care and Youth Development (N = 1,312) were analyzed to examine whether the adverse effects of early insensitive parenting on children's academic functioning can be offset by parents' later involvement in children's education. Observations of mothers' early…

  12. Homework Involvement and Functions: Perceptions of Hong Kong Chinese Primary School Students and Parents

    ERIC Educational Resources Information Center

    Tam, Vicky C. W.; Chan, Raymond M. C.

    2011-01-01

    This study examines the perceptions of Chinese students and parents in Hong Kong on homework involvement, assignment type and homework functions. The relationships of homework perceptions to student and parent attributes are also assessed. The sample includes 1393 pairs of students and their parents from 36 primary schools in Hong Kong. Findings…

  13. Can Parents' Involvement in Children's Education Offset the Effects of Early Insensitivity on Academic Functioning?

    ERIC Educational Resources Information Center

    Monti, Jennifer D.; Pomerantz, Eva M.; Roisman, Glenn I.

    2014-01-01

    Data from the National Institute of Child Health and Human Development Study of Early Child Care and Youth Development (N = 1,312) were analyzed to examine whether the adverse effects of early insensitive parenting on children's academic functioning can be offset by parents' later involvement in children's education. Observations of mothers' early…

  14. Transcriptome profiling to identify genes involved in peroxisome assembly and function

    PubMed Central

    Smith, Jennifer J.; Marelli, Marcello; Christmas, Rowan H.; Vizeacoumar, Franco J.; Dilworth, David J.; Ideker, Trey; Galitski, Timothy; Dimitrov, Krassen; Rachubinski, Richard A.; Aitchison, John D.

    2002-01-01

    Yeast cells were induced to proliferate peroxisomes, and microarray transcriptional profiling was used to identify PEX genes encoding peroxins involved in peroxisome assembly and genes involved in peroxisome function. Clustering algorithms identified 224 genes with expression profiles similar to those of genes encoding peroxisomal proteins and genes involved in peroxisome biogenesis. Several previously uncharacterized genes were identified, two of which, YPL112c and YOR084w, encode proteins of the peroxisomal membrane and matrix, respectively. Ypl112p, renamed Pex25p, is a novel peroxin required for the regulation of peroxisome size and maintenance. These studies demonstrate the utility of comparative gene profiling as an alternative to functional assays to identify genes with roles in peroxisome biogenesis. PMID:12135984

  15. A continuous function model for path prediction of entities

    NASA Astrophysics Data System (ADS)

    Nanda, S.; Pray, R.

    2007-04-01

    As militaries across the world continue to evolve, the roles of humans in various theatres of operation are being increasingly targeted by military planners for substitution with automation. Forward observation and direction of supporting arms to neutralize threats from dynamic adversaries is one such example. However, contemporary tracking and targeting systems are incapable of serving autonomously for they do not embody the sophisticated algorithms necessary to predict the future positions of adversaries with the accuracy offered by the cognitive and analytical abilities of human operators. The need for these systems to incorporate methods characterizing such intelligence is therefore compelling. In this paper, we present a novel technique to achieve this goal by modeling the path of an entity as a continuous polynomial function of multiple variables expressed as a Taylor series with a finite number of terms. We demonstrate the method for evaluating the coefficient of each term to define this function unambiguously for any given entity, and illustrate its use to determine the entity's position at any point in time in the future.

  16. Local functional descriptors for surface comparison based binding prediction

    PubMed Central

    2012-01-01

    Background Molecular recognition in proteins occurs due to appropriate arrangements of physical, chemical, and geometric properties of an atomic surface. Similar surface regions should create similar binding interfaces. Effective methods for comparing surface regions can be used in identifying similar regions, and to predict interactions without regard to the underlying structural scaffold that creates the surface. Results We present a new descriptor for protein functional surfaces and algorithms for using these descriptors to compare protein surface regions to identify ligand binding interfaces. Our approach uses descriptors of local regions of the surface, and assembles collections of matches to compare larger regions. Our approach uses a variety of physical, chemical, and geometric properties, adaptively weighting these properties as appropriate for different regions of the interface. Our approach builds a classifier based on a training corpus of examples of binding sites of the target ligand. The constructed classifiers can be applied to a query protein providing a probability for each position on the protein that the position is part of a binding interface. We demonstrate the effectiveness of the approach on a number of benchmarks, demonstrating performance that is comparable to the state-of-the-art, with an approach with more generality than these prior methods. Conclusions Local functional descriptors offer a new method for protein surface comparison that is sufficiently flexible to serve in a variety of applications. PMID:23176080

  17. Parental food involvement predicts parent and child intakes of fruits and vegetables.

    PubMed

    Ohly, Heather; Pealing, Juliet; Hayter, Arabella K M; Pettinger, Clare; Pikhart, Hynek; Watt, Richard G; Rees, Gail

    2013-10-01

    In order to develop successful interventions to improve children's diets, the factors influencing food choice need to be understood. Parental food involvement - the level of importance of food in a person's life - may be one of many important factors. The aim of this study was to determine whether parental food involvement is associated with parents' and children's diet quality. As part of an intervention study, 394 parents with children aged between 18 months and 5 years were recruited from children's centres in Cornwall and Islington, UK. Questionnaires were used to collect data on socio-demographic characteristics, parents' diets, and attitudes towards food including food involvement. Children's diets were assessed using the multiple pass 24 h recall method. Parents reported low intakes of fruits and vegetables and high intakes of sugary items for themselves and their young children. Parental food involvement was strongly correlated with consumption of fruits and vegetables (amount and diversity) for both parents and children. Correlations with consumption of sugary drinks and snacks/foods were not significant. These findings indicate that parental food involvement may influence consumption of fruits and vegetables, more so than sugary items. Further research is needed to investigate how parental food involvement could mediate dietary changes. Copyright © 2013 Elsevier Ltd. All rights reserved.

  18. Nonseparable exchange–correlation functional for molecules, including homogeneous catalysis involving transition metals

    SciTech Connect

    Yu, Haoyu S.; Zhang, Wenjing; Verma, Pragya; He, Xiao; Truhlar, Donald G.

    2015-01-01

    The goal of this work is to develop a gradient approximation to the exchange–correlation functional of Kohn–Sham density functional theory for treating molecular problems with a special emphasis on the prediction of quantities important for homogeneous catalysis and other molecular energetics. Our training and validation of exchange–correlation functionals is organized in terms of databases and subdatabases. The key properties required for homogeneous catalysis are main group bond energies (database MGBE137), transition metal bond energies (database TMBE32), reaction barrier heights (database BH76), and molecular structures (database MS10). We also consider 26 other databases, most of which are subdatabases of a newly extended broad database called Database 2015, which is presented in the present article and in its ESI. Based on the mathematical form of a nonseparable gradient approximation (NGA), as first employed in the N12 functional, we design a new functional by using Database 2015 and by adding smoothness constraints to the optimization of the functional. The resulting functional is called the gradient approximation for molecules, or GAM. The GAM functional gives better results for MGBE137, TMBE32, and BH76 than any available generalized gradient approximation (GGA) or than N12. The GAM functional also gives reasonable results for MS10 with an MUE of 0.018 Å. The GAM functional provides good results both within the training sets and outside the training sets. The convergence tests and the smooth curves of exchange–correlation enhancement factor as a function of the reduced density gradient show that the GAM functional is a smooth functional that should not lead to extra expense or instability in optimizations. NGAs, like GGAs, have the advantage over meta-GGAs and hybrid GGAs of respectively smaller grid-size requirements for integrations and lower costs for extended systems. These computational advantages combined with the relatively high accuracy

  19. Nonseparable exchange-correlation functional for molecules, including homogeneous catalysis involving transition metals.

    PubMed

    Yu, Haoyu S; Zhang, Wenjing; Verma, Pragya; He, Xiao; Truhlar, Donald G

    2015-05-14

    The goal of this work is to develop a gradient approximation to the exchange-correlation functional of Kohn-Sham density functional theory for treating molecular problems with a special emphasis on the prediction of quantities important for homogeneous catalysis and other molecular energetics. Our training and validation of exchange-correlation functionals is organized in terms of databases and subdatabases. The key properties required for homogeneous catalysis are main group bond energies (database MGBE137), transition metal bond energies (database TMBE32), reaction barrier heights (database BH76), and molecular structures (database MS10). We also consider 26 other databases, most of which are subdatabases of a newly extended broad database called Database 2015, which is presented in the present article and in its ESI. Based on the mathematical form of a nonseparable gradient approximation (NGA), as first employed in the N12 functional, we design a new functional by using Database 2015 and by adding smoothness constraints to the optimization of the functional. The resulting functional is called the gradient approximation for molecules, or GAM. The GAM functional gives better results for MGBE137, TMBE32, and BH76 than any available generalized gradient approximation (GGA) or than N12. The GAM functional also gives reasonable results for MS10 with an MUE of 0.018 Å. The GAM functional provides good results both within the training sets and outside the training sets. The convergence tests and the smooth curves of exchange-correlation enhancement factor as a function of the reduced density gradient show that the GAM functional is a smooth functional that should not lead to extra expense or instability in optimizations. NGAs, like GGAs, have the advantage over meta-GGAs and hybrid GGAs of respectively smaller grid-size requirements for integrations and lower costs for extended systems. These computational advantages combined with the relatively high accuracy for all

  20. Intermediate CD14(++)CD16(+) monocyte predicts severe coronary stenosis and extensive plaque involvement in asymptomatic individuals.

    PubMed

    Lo, Shyh-Chyi; Lee, Wen-Jeng; Chen, Ching-Yi; Lee, Bai-Chin

    2017-02-26

    Circulating leukocyte subtypes and monocyte subsets are independent predictors of cardiovascular events. We hypothesized that an increased leukocyte subtype would predict severe coronary stenosis and extensive plaque involvement. We retrospectively analyzed clinical, laboratory, and coronary CT data in a total of 588 asymptomatic adults (69% men; mean age, 57 ± 9 years) undergoing a general health check-up. Intermediate CD14(++)CD16(+) monocyte count had the strongest association with mixed and calcified plaque scores, whereas the numbers of neutrophils and classical CD14(++)CD16(-) monocytes were significantly associated with non-calcified plaque score. Only high CD14(++)CD16(+) monocyte count (>12 cells/μL) significantly predicted extensive plaque involvement [odds ratio 3.16 (95% confidence interval 1.84-5.43), P < 0.001; quartile 4 vs. 1-3] and severe coronary stenosis [3.67 (1.84-7.33), P < 0.001; quartile 4 vs. 1-3] after adjustments for Framingham Risk Score (FRS), metabolic syndrome, and C-reactive protein. The CD14(++)CD16(+) monocyte count, when added to FRS, significantly reclassified 30.4 and 26.7% of the overall and 50.2 and 36.2% of the intermediate-risk population (FRS 6-20%) for predicting extensive plaque involvement and severe coronary stenosis, respectively. Thus, in asymptomatic individuals, intermediate CD14(++)CD16(+) monocyte could independently predict severe CAD and improve risk stratification.

  1. Nursing students' prosocial motivation: does it predict professional commitment and involvement in the job?

    PubMed

    Nesje, Kjersti

    2015-01-01

    This study investigated how prosocial motivation reported by nursing students in their final year of academic studies relates to career commitment and job involvement three years after graduation. Most studies investigating nurses' prosocial motivation for choosing the nursing profession examine only their prosocial motivation for entering nursing training; they do not investigate whether this motivation is associated with job involvement or commitment to the profession. A longitudinal survey design was used. The present longitudinal study included 160 nurses. In their final academic year of spring 2007, the nurses received a questionnaire about their motivation for entering nursing. Three years after graduation, spring 2010, they received another questionnaire about their level of job involvement and career commitment. The results showed that prosocial motivation measured in their last academic year was related to career commitment three years after graduation, but unrelated to job involvement. The results indicated that prosocial motivation is important in identifying with the profession but not necessarily for personal involvement in the job. The study gives important knowledge on how a commonly reported motivation for entering nursing relates to the nurses' attitudes about their work life. © 2014 John Wiley & Sons Ltd.

  2. Genetic Adaptation to Climate in White Spruce Involves Small to Moderate Allele Frequency Shifts in Functionally Diverse Genes

    PubMed Central

    Hornoy, Benjamin; Pavy, Nathalie; Gérardi, Sébastien; Beaulieu, Jean; Bousquet, Jean

    2015-01-01

    Understanding the genetic basis of adaptation to climate is of paramount importance for preserving and managing genetic diversity in plants in a context of climate change. Yet, this objective has been addressed mainly in short-lived model species. Thus, expanding knowledge to nonmodel species with contrasting life histories, such as forest trees, appears necessary. To uncover the genetic basis of adaptation to climate in the widely distributed boreal conifer white spruce (Picea glauca), an environmental association study was conducted using 11,085 single nucleotide polymorphisms representing 7,819 genes, that is, approximately a quarter of the transcriptome. Linear and quadratic regressions controlling for isolation-by-distance, and the Random Forest algorithm, identified several dozen genes putatively under selection, among which 43 showed strongest signals along temperature and precipitation gradients. Most of them were related to temperature. Small to moderate shifts in allele frequencies were observed. Genes involved encompassed a wide variety of functions and processes, some of them being likely important for plant survival under biotic and abiotic environmental stresses according to expression data. Literature mining and sequence comparison also highlighted conserved sequences and functions with angiosperm homologs. Our results are consistent with theoretical predictions that local adaptation involves genes with small frequency shifts when selection is recent and gene flow among populations is high. Accordingly, genetic adaptation to climate in P. glauca appears to be complex, involving many independent and interacting gene functions, biochemical pathways, and processes. From an applied perspective, these results shall lead to specific functional/association studies in conifers and to the development of markers useful for the conservation of genetic resources. PMID:26560341

  3. Genetic Adaptation to Climate in White Spruce Involves Small to Moderate Allele Frequency Shifts in Functionally Diverse Genes.

    PubMed

    Hornoy, Benjamin; Pavy, Nathalie; Gérardi, Sébastien; Beaulieu, Jean; Bousquet, Jean

    2015-11-11

    Understanding the genetic basis of adaptation to climate is of paramount importance for preserving and managing genetic diversity in plants in a context of climate change. Yet, this objective has been addressed mainly in short-lived model species. Thus, expanding knowledge to nonmodel species with contrasting life histories, such as forest trees, appears necessary. To uncover the genetic basis of adaptation to climate in the widely distributed boreal conifer white spruce (Picea glauca), an environmental association study was conducted using 11,085 single nucleotide polymorphisms representing 7,819 genes, that is, approximately a quarter of the transcriptome.Linear and quadratic regressions controlling for isolation-by-distance, and the Random Forest algorithm, identified several dozen genes putatively under selection, among which 43 showed strongest signals along temperature and precipitation gradients. Most of them were related to temperature. Small to moderate shifts in allele frequencies were observed. Genes involved encompassed a wide variety of functions and processes, some of them being likely important for plant survival under biotic and abiotic environmental stresses according to expression data. Literature mining and sequence comparison also highlighted conserved sequences and functions with angiosperm homologs.Our results are consistent with theoretical predictions that local adaptation involves genes with small frequency shifts when selection is recent and gene flow among populations is high. Accordingly, genetic adaptation to climate in P. glauca appears to be complex, involving many independent and interacting gene functions, biochemical pathways, and processes. From an applied perspective, these results shall lead to specific functional/association studies in conifers and to the development of markers useful for the conservation of genetic resources. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular

  4. Predicting Preschoolers' Attachment Security from Fathers' Involvement, Internal Working Models, and Use of Social Support

    ERIC Educational Resources Information Center

    Newland, Lisa A.; Coyl, Diana D.; Freeman, Harry

    2008-01-01

    Associations between preschoolers' attachment security, fathers' involvement (i.e. parenting behaviors and consistency) and fathering context (i.e. fathers' internal working models (IWMs) and use of social support) were examined in a subsample of 102 fathers, taken from a larger sample of 235 culturally diverse US families. The authors predicted…

  5. Parental Involvement in Middle School Predicting College Attendance for First-Generation Students

    ERIC Educational Resources Information Center

    Bui, Khanh; Rush, Ryan A.

    2016-01-01

    Using data from the National Education Longitudinal Study, this report examined the relationship between parental involvement in eighth grade and college attendance by eight years after high school for students whose parents have no college education (i.e., first-generation students; n = 1,358) in comparison to students whose parents have some…

  6. Arts Involvement Predicts Academic Achievement Only When the Child Has a Musical Instrument

    ERIC Educational Resources Information Center

    Young, Laura N.; Cordes, Sara; Winner, Ellen

    2014-01-01

    We examined the associations between academic achievement and arts involvement (access to a musical instrument for the child at home, participation in unspecified after-school arts activities) in a sample of 2339 11-12-year-olds surveyed in the USA between 1998 and 2008. We compared the contributions of these variables to other kinds of cognitive…

  7. High School Drinker Typologies Predict Alcohol Involvement and Psychosocial Adjustment during Acclimation to College

    ERIC Educational Resources Information Center

    Hersh, Matthew A.; Hussong, Andrea M.

    2006-01-01

    This study examined differences among distinct types of high school drinkers on their alcohol involvement and psychosocial adjustment during the first semester of college. Participants were 147 college freshmen (66% female; 86% Caucasian) from a large Southeastern public university who reported on high school drinking and college stress, affect,…

  8. Arts Involvement Predicts Academic Achievement Only When the Child Has a Musical Instrument

    ERIC Educational Resources Information Center

    Young, Laura N.; Cordes, Sara; Winner, Ellen

    2014-01-01

    We examined the associations between academic achievement and arts involvement (access to a musical instrument for the child at home, participation in unspecified after-school arts activities) in a sample of 2339 11-12-year-olds surveyed in the USA between 1998 and 2008. We compared the contributions of these variables to other kinds of cognitive…

  9. Parental Involvement in Middle School Predicting College Attendance for First-Generation Students

    ERIC Educational Resources Information Center

    Bui, Khanh; Rush, Ryan A.

    2016-01-01

    Using data from the National Education Longitudinal Study, this report examined the relationship between parental involvement in eighth grade and college attendance by eight years after high school for students whose parents have no college education (i.e., first-generation students; n = 1,358) in comparison to students whose parents have some…

  10. Predicting Preschoolers' Attachment Security from Fathers' Involvement, Internal Working Models, and Use of Social Support

    ERIC Educational Resources Information Center

    Newland, Lisa A.; Coyl, Diana D.; Freeman, Harry

    2008-01-01

    Associations between preschoolers' attachment security, fathers' involvement (i.e. parenting behaviors and consistency) and fathering context (i.e. fathers' internal working models (IWMs) and use of social support) were examined in a subsample of 102 fathers, taken from a larger sample of 235 culturally diverse US families. The authors predicted…

  11. Parental Involvement in Predicting School Motivation: Similar and Differential Effects across Ethnic Groups

    ERIC Educational Resources Information Center

    Fan, Weihua; Williams, Cathy M.; Wolters, Christopher A.

    2012-01-01

    The authors investigated how different dimensions of parental involvement similarly or differentially linked to various constructs of school motivation (academic self-efficacy in mathematics and English, intrinsic motivation toward mathematics and English, and engagement) across ethnic groups of Caucasian, African American, Asian American, and…

  12. Functional identity and diversity of animals predict ecosystem functioning better than species-based indices.

    PubMed

    Gagic, Vesna; Bartomeus, Ignasi; Jonsson, Tomas; Taylor, Astrid; Winqvist, Camilla; Fischer, Christina; Slade, Eleanor M; Steffan-Dewenter, Ingolf; Emmerson, Mark; Potts, Simon G; Tscharntke, Teja; Weisser, Wolfgang; Bommarco, Riccardo

    2015-02-22

    Drastic biodiversity declines have raised concerns about the deterioration of ecosystem functions and have motivated much recent research on the relationship between species diversity and ecosystem functioning. A functional trait framework has been proposed to improve the mechanistic understanding of this relationship, but this has rarely been tested for organisms other than plants. We analysed eight datasets, including five animal groups, to examine how well a trait-based approach, compared with a more traditional taxonomic approach, predicts seven ecosystem functions below- and above-ground. Trait-based indices consistently provided greater explanatory power than species richness or abundance. The frequency distributions of single or multiple traits in the community were the best predictors of ecosystem functioning. This implies that the ecosystem functions we investigated were underpinned by the combination of trait identities (i.e. single-trait indices) and trait complementarity (i.e. multi-trait indices) in the communities. Our study provides new insights into the general mechanisms that link biodiversity to ecosystem functioning in natural animal communities and suggests that the observed responses were due to the identity and dominance patterns of the trait composition rather than the number or abundance of species per se. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  13. Functional identity and diversity of animals predict ecosystem functioning better than species-based indices

    PubMed Central

    Gagic, Vesna; Bartomeus, Ignasi; Jonsson, Tomas; Taylor, Astrid; Winqvist, Camilla; Fischer, Christina; Slade, Eleanor M.; Steffan-Dewenter, Ingolf; Emmerson, Mark; Potts, Simon G.; Tscharntke, Teja; Weisser, Wolfgang; Bommarco, Riccardo

    2015-01-01

    Drastic biodiversity declines have raised concerns about the deterioration of ecosystem functions and have motivated much recent research on the relationship between species diversity and ecosystem functioning. A functional trait framework has been proposed to improve the mechanistic understanding of this relationship, but this has rarely been tested for organisms other than plants. We analysed eight datasets, including five animal groups, to examine how well a trait-based approach, compared with a more traditional taxonomic approach, predicts seven ecosystem functions below- and above-ground. Trait-based indices consistently provided greater explanatory power than species richness or abundance. The frequency distributions of single or multiple traits in the community were the best predictors of ecosystem functioning. This implies that the ecosystem functions we investigated were underpinned by the combination of trait identities (i.e. single-trait indices) and trait complementarity (i.e. multi-trait indices) in the communities. Our study provides new insights into the general mechanisms that link biodiversity to ecosystem functioning in natural animal communities and suggests that the observed responses were due to the identity and dominance patterns of the trait composition rather than the number or abundance of species per se. PMID:25567651

  14. Lung function indices for predicting mortality in COPD

    PubMed Central

    Boutou, Afroditi K.; Shrikrishna, Dinesh; Tanner, Rebecca J.; Smith, Cayley; Kelly, Julia L.; Ward, Simon P.; Polkey, Michael I.; Hopkinson, Nicholas S.

    2013-01-01

    Chronic obstructive pulmonary disease (COPD) is characterised by high morbidity and mortality. It remains unknown which aspect of lung function carries the most prognostic information and if simple spirometry is sufficient. Survival was assessed in COPD outpatients whose data had been added prospectively to a clinical audit database from the point of first full lung function testing including spirometry, lung volumes, gas transfer and arterial blood gases. Variables univariately associated with survival were entered into a multivariate Cox proportional hazard model. 604 patients were included (mean±sd age 61.9±9.7 years; forced expiratory volume in 1 s 37±18.1% predicted; 62.9% males); 229 (37.9%) died during a median follow-up of 83 months. Median survival was 91.9 (95% CI 80.8–103) months with survival rates at 3 and 5 years 0.83 and 0.66, respectively. Carbon monoxide transfer factor % pred quartiles (best quartile (>51%): HR 0.33, 95% CI 0.172–0.639; and second quartile (51–37.3%): HR 0.52, 95% CI 0.322–0.825; versus lowest quartile (<27.9%)), age (HR 1.04, 95% CI 1.02–1.06) and arterial oxygen partial pressure (HR 0.85, 95% CI 0.77–0.94) were the only parameters independently associated with mortality. Measurement of gas transfer provides additional prognostic information compared to spirometry in patients under hospital follow-up and could be considered routinely. PMID:23349449

  15. Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction

    SciTech Connect

    Wang, Jing; Ma, Zihao; Carr, Steven A.; Mertins, Philipp; Zhang, Hui; Zhang, Zhen; Chan, Daniel W.; Ellis, Matthew J. C.; Townsend, R. Reid; Smith, Richard D.; McDermott, Jason E.; Chen, Xian; Paulovich, Amanda G.; Boja, Emily S.; Mesri, Mehdi; Kinsinger, Christopher R.; Rodriguez, Henry; Rodland, Karin D.; Liebler, Daniel C.; Zhang, Bing

    2016-11-11

    Coexpression of mRNAs under multiple conditions is commonly used to infer cofunctionality of their gene products despite well-known limitations of this “guilt-by-association” (GBA) approach. Recent advancements in mass spectrometry-based proteomic technologies have enabled global expression profiling at the protein level; however, whether proteome profiling data can outperform transcriptome profiling data for coexpression based gene function prediction has not been systematically investigated. Here, we address this question by constructing and analyzing mRNA and protein coexpression networks for three cancer types with matched mRNA and protein profiling data from The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC). Our analyses revealed a marked difference in wiring between the mRNA and protein coexpression networks. Whereas protein coexpression was driven primarily by functional similarity between coexpressed genes, mRNA coexpression was driven by both cofunction and chromosomal colocalization of the genes. Functionally coherent mRNA modules were more likely to have their edges preserved in corresponding protein networks than functionally incoherent mRNA modules. Proteomic data strengthened the link between gene expression and function for at least 75% of Gene Ontology (GO) biological processes and 90% of KEGG pathways. A web application Gene2Net (http://cptac.gene2net.org) developed based on the three protein coexpression networks revealed novel gene-function relationships, such as linking ERBB2 (HER2) to lipid biosynthetic process in breast cancer, identifying PLG as a new gene involved in complement activation, and identifying AEBP1 as a new epithelial-mesenchymal transition (EMT) marker. Our results demonstrate that proteome profiling outperforms transcriptome profiling for coexpression based gene function prediction. Proteomics should be integrated if not preferred in gene function and human disease studies

  16. Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction.

    PubMed

    Wang, Jing; Ma, Zihao; Carr, Steven A; Mertins, Philipp; Zhang, Hui; Zhang, Zhen; Chan, Daniel W; Ellis, Matthew J C; Townsend, R Reid; Smith, Richard D; McDermott, Jason E; Chen, Xian; Paulovich, Amanda G; Boja, Emily S; Mesri, Mehdi; Kinsinger, Christopher R; Rodriguez, Henry; Rodland, Karin D; Liebler, Daniel C; Zhang, Bing

    2017-01-01

    Coexpression of mRNAs under multiple conditions is commonly used to infer cofunctionality of their gene products despite well-known limitations of this "guilt-by-association" (GBA) approach. Recent advancements in mass spectrometry-based proteomic technologies have enabled global expression profiling at the protein level; however, whether proteome profiling data can outperform transcriptome profiling data for coexpression based gene function prediction has not been systematically investigated. Here, we address this question by constructing and analyzing mRNA and protein coexpression networks for three cancer types with matched mRNA and protein profiling data from The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC). Our analyses revealed a marked difference in wiring between the mRNA and protein coexpression networks. Whereas protein coexpression was driven primarily by functional similarity between coexpressed genes, mRNA coexpression was driven by both cofunction and chromosomal colocalization of the genes. Functionally coherent mRNA modules were more likely to have their edges preserved in corresponding protein networks than functionally incoherent mRNA modules. Proteomic data strengthened the link between gene expression and function for at least 75% of Gene Ontology (GO) biological processes and 90% of KEGG pathways. A web application Gene2Net (http://cptac.gene2net.org) developed based on the three protein coexpression networks revealed novel gene-function relationships, such as linking ERBB2 (HER2) to lipid biosynthetic process in breast cancer, identifying PLG as a new gene involved in complement activation, and identifying AEBP1 as a new epithelial-mesenchymal transition (EMT) marker. Our results demonstrate that proteome profiling outperforms transcriptome profiling for coexpression based gene function prediction. Proteomics should be integrated if not preferred in gene function and human disease studies. © 2017 by

  17. Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction*

    PubMed Central

    Wang, Jing; Ma, Zihao; Carr, Steven A.; Mertins, Philipp; Zhang, Hui; Zhang, Zhen; Chan, Daniel W.; Ellis, Matthew J. C.; Townsend, R. Reid; Smith, Richard D.; McDermott, Jason E.; Chen, Xian; Paulovich, Amanda G.; Boja, Emily S.; Mesri, Mehdi; Kinsinger, Christopher R.; Rodriguez, Henry; Rodland, Karin D.; Liebler, Daniel C.; Zhang, Bing

    2017-01-01

    Coexpression of mRNAs under multiple conditions is commonly used to infer cofunctionality of their gene products despite well-known limitations of this “guilt-by-association” (GBA) approach. Recent advancements in mass spectrometry-based proteomic technologies have enabled global expression profiling at the protein level; however, whether proteome profiling data can outperform transcriptome profiling data for coexpression based gene function prediction has not been systematically investigated. Here, we address this question by constructing and analyzing mRNA and protein coexpression networks for three cancer types with matched mRNA and protein profiling data from The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC). Our analyses revealed a marked difference in wiring between the mRNA and protein coexpression networks. Whereas protein coexpression was driven primarily by functional similarity between coexpressed genes, mRNA coexpression was driven by both cofunction and chromosomal colocalization of the genes. Functionally coherent mRNA modules were more likely to have their edges preserved in corresponding protein networks than functionally incoherent mRNA modules. Proteomic data strengthened the link between gene expression and function for at least 75% of Gene Ontology (GO) biological processes and 90% of KEGG pathways. A web application Gene2Net (http://cptac.gene2net.org) developed based on the three protein coexpression networks revealed novel gene-function relationships, such as linking ERBB2 (HER2) to lipid biosynthetic process in breast cancer, identifying PLG as a new gene involved in complement activation, and identifying AEBP1 as a new epithelial-mesenchymal transition (EMT) marker. Our results demonstrate that proteome profiling outperforms transcriptome profiling for coexpression based gene function prediction. Proteomics should be integrated if not preferred in gene function and human disease studies. PMID

  18. Error estimates for density-functional theory predictions of surface energy and work function

    NASA Astrophysics Data System (ADS)

    De Waele, Sam; Lejaeghere, Kurt; Sluydts, Michael; Cottenier, Stefaan

    2016-12-01

    Density-functional theory (DFT) predictions of materials properties are becoming ever more widespread. With increased use comes the demand for estimates of the accuracy of DFT results. In view of the importance of reliable surface properties, this work calculates surface energies and work functions for a large and diverse test set of crystalline solids. They are compared to experimental values by performing a linear regression, which results in a measure of the predictable and material-specific error of the theoretical result. Two of the most prevalent functionals, the local density approximation (LDA) and the Perdew-Burke-Ernzerhof parametrization of the generalized gradient approximation (PBE-GGA), are evaluated and compared. Both LDA and GGA-PBE are found to yield accurate work functions with error bars below 0.3 eV, rivaling the experimental precision. LDA also provides satisfactory estimates for the surface energy with error bars smaller than 10%, but GGA-PBE significantly underestimates the surface energy for materials with a large correlation energy.

  19. Gene function prediction based on the Gene Ontology hierarchical structure.

    PubMed

    Cheng, Liangxi; Lin, Hongfei; Hu, Yuncui; Wang, Jian; Yang, Zhihao

    2014-01-01

    The information of the Gene Ontology annotation is helpful in the explanation of life science phenomena, and can provide great support for the research of the biomedical field. The use of the Gene Ontology is gradually affecting the way people store and understand bioinformatic data. To facilitate the prediction of gene functions with the aid of text mining methods and existing resources, we transform it into a multi-label top-down classification problem and develop a method that uses the hierarchical relationships in the Gene Ontology structure to relieve the quantitative imbalance of positive and negative training samples. Meanwhile the method enhances the discriminating ability of classifiers by retaining and highlighting the key training samples. Additionally, the top-down classifier based on a tree structure takes the relationship of target classes into consideration and thus solves the incompatibility between the classification results and the Gene Ontology structure. Our experiment on the Gene Ontology annotation corpus achieves an F-value performance of 50.7% (precision: 52.7% recall: 48.9%). The experimental results demonstrate that when the size of training set is small, it can be expanded via topological propagation of associated documents between the parent and child nodes in the tree structure. The top-down classification model applies to the set of texts in an ontology structure or with a hierarchical relationship.

  20. Predicting regional neurodegeneration from the healthy brain functional connectome.

    PubMed

    Zhou, Juan; Gennatas, Efstathios D; Kramer, Joel H; Miller, Bruce L; Seeley, William W

    2012-03-22

    Neurodegenerative diseases target large-scale neural networks. Four competing mechanistic hypotheses have been proposed to explain network-based disease patterning: nodal stress, transneuronal spread, trophic failure, and shared vulnerability. Here, we used task-free fMRI to derive the healthy intrinsic connectivity patterns seeded by brain regions vulnerable to any of five distinct neurodegenerative diseases. These data enabled us to investigate how intrinsic connectivity in health predicts region-by-region vulnerability to disease. For each illness, specific regions emerged as critical network "epicenters" whose normal connectivity profiles most resembled the disease-associated atrophy pattern. Graph theoretical analyses in healthy subjects revealed that regions with higher total connectional flow and, more consistently, shorter functional paths to the epicenters, showed greater disease-related vulnerability. These findings best fit a transneuronal spread model of network-based vulnerability. Molecular pathological approaches may help clarify what makes each epicenter vulnerable to its targeting disease and how toxic protein species travel between networked brain structures.

  1. Phylogenomic analysis of the Chlamydomonas genome unmasks proteins potentially involved in photosynthetic function and regulation

    PubMed Central

    Karpowicz, Steven J.; Heinnickel, Mark; Dewez, David; Hamel, Blaise; Dent, Rachel; Niyogi, Krishna K.; Johnson, Xenie; Alric, Jean; Wollman, Francis-André; Li, Huiying; Merchant, Sabeeha S.

    2010-01-01

    Chlamydomonas reinhardtii, a unicellular green alga, has been exploited as a reference organism for identifying proteins and activities associated with the photosynthetic apparatus and the functioning of chloroplasts. Recently, the full genome sequence of Chlamydomonas was generated and a set of gene models, representing all genes on the genome, was developed. Using these gene models, and gene models developed for the genomes of other organisms, a phylogenomic, comparative analysis was performed to identify proteins encoded on the Chlamydomonas genome which were likely involved in chloroplast functions (or specifically associated with the green algal lineage); this set of proteins has been designated the GreenCut. Further analyses of those GreenCut proteins with uncharacterized functions and the generation of mutant strains aberrant for these proteins are beginning to unmask new layers of functionality/regulation that are integrated into the workings of the photosynthetic apparatus. PMID:20490922

  2. How to Develop, Validate, and Compare Clinical Prediction Models Involving Radiological Parameters: Study Design and Statistical Methods.

    PubMed

    Han, Kyunghwa; Song, Kijun; Choi, Byoung Wook

    2016-01-01

    Clinical prediction models are developed to calculate estimates of the probability of the presence/occurrence or future course of a particular prognostic or diagnostic outcome from multiple clinical or non-clinical parameters. Radiologic imaging techniques are being developed for accurate detection and early diagnosis of disease, which will eventually affect patient outcomes. Hence, results obtained by radiological means, especially diagnostic imaging, are frequently incorporated into a clinical prediction model as important predictive parameters, and the performance of the prediction model may improve in both diagnostic and prognostic settings. This article explains in a conceptual manner the overall process of developing and validating a clinical prediction model involving radiological parameters in relation to the study design and statistical methods. Collection of a raw dataset; selection of an appropriate statistical model; predictor selection; evaluation of model performance using a calibration plot, Hosmer-Lemeshow test and c-index; internal and external validation; comparison of different models using c-index, net reclassification improvement, and integrated discrimination improvement; and a method to create an easy-to-use prediction score system will be addressed. This article may serve as a practical methodological reference for clinical researchers.

  3. How to Develop, Validate, and Compare Clinical Prediction Models Involving Radiological Parameters: Study Design and Statistical Methods

    PubMed Central

    Han, Kyunghwa; Choi, Byoung Wook

    2016-01-01

    Clinical prediction models are developed to calculate estimates of the probability of the presence/occurrence or future course of a particular prognostic or diagnostic outcome from multiple clinical or non-clinical parameters. Radiologic imaging techniques are being developed for accurate detection and early diagnosis of disease, which will eventually affect patient outcomes. Hence, results obtained by radiological means, especially diagnostic imaging, are frequently incorporated into a clinical prediction model as important predictive parameters, and the performance of the prediction model may improve in both diagnostic and prognostic settings. This article explains in a conceptual manner the overall process of developing and validating a clinical prediction model involving radiological parameters in relation to the study design and statistical methods. Collection of a raw dataset; selection of an appropriate statistical model; predictor selection; evaluation of model performance using a calibration plot, Hosmer-Lemeshow test and c-index; internal and external validation; comparison of different models using c-index, net reclassification improvement, and integrated discrimination improvement; and a method to create an easy-to-use prediction score system will be addressed. This article may serve as a practical methodological reference for clinical researchers. PMID:27134523

  4. Separate cortical networks involved in music perception: preliminary functional MRI evidence for modularity of music processing.

    PubMed

    Schmithorst, Vincent J

    2005-04-01

    Music perception is a quite complex cognitive task, involving the perception and integration of various elements including melody, harmony, pitch, rhythm, and timbre. A preliminary functional MRI investigation of music perception was performed, using a simplified passive listening task. Group independent component analysis (ICA) was used to separate out various components involved in music processing, as the hemodynamic responses are not known a priori. Various components consistent with auditory processing, expressive language, syntactic processing, and visual association were found. The results are discussed in light of various hypotheses regarding modularity of music processing and its overlap with language processing. The results suggest that, while some networks overlap with ones used for language processing, music processing may involve its own domain-specific processing subsystems.

  5. Discriminative local subspaces in gene expression data for effective gene function prediction

    PubMed Central

    Gutiérrez, Rodrigo A.; Soto, Alvaro

    2012-01-01

    Motivation: Massive amounts of genome-wide gene expression data have become available, motivating the development of computational approaches that leverage this information to predict gene function. Among successful approaches, supervised machine learning methods, such as Support Vector Machines (SVMs), have shown superior prediction accuracy. However, these methods lack the simple biological intuition provided by co-expression networks (CNs), limiting their practical usefulness. Results: In this work, we present Discriminative Local Subspaces (DLS), a novel method that combines supervised machine learning and co-expression techniques with the goal of systematically predict genes involved in specific biological processes of interest. Unlike traditional CNs, DLS uses the knowledge available in Gene Ontology (GO) to generate informative training sets that guide the discovery of expression signatures: expression patterns that are discriminative for genes involved in the biological process of interest. By linking genes co-expressed with these signatures, DLS is able to construct a discriminative CN that links both, known and previously uncharacterized genes, for the selected biological process. This article focuses on the algorithm behind DLS and shows its predictive power using an Arabidopsis thaliana dataset and a representative set of 101 GO terms from the Biological Process Ontology. Our results show that DLS has a superior average accuracy than both SVMs and CNs. Thus, DLS is able to provide the prediction accuracy of supervised learning methods while maintaining the intuitive understanding of CNs. Availability: A MATLAB® implementation of DLS is available at http://virtualplant.bio.puc.cl/cgi-bin/Lab/tools.cgi Contact: tfpuelma@uc.cl Supplementary Information: Supplementary data are available at http://bioinformatics.mpimp-golm.mpg.de/. PMID:22820203

  6. Distinct Functional Connectivities Predict Clinical Response with Emotion Regulation Therapy.

    PubMed

    Fresco, David M; Roy, Amy K; Adelsberg, Samantha; Seeley, Saren; García-Lesy, Emmanuel; Liston, Conor; Mennin, Douglas S

    2017-01-01

    Despite the success of available medical and psychosocial treatments, a sizable subgroup of individuals with commonly co-occurring disorders, generalized anxiety disorder (GAD) and major depressive disorder (MDD), fail to make sufficient treatment gains thereby prolonging their deficits in life functioning and satisfaction. Clinically, these patients often display temperamental features reflecting heightened sensitivity to underlying motivational systems related to threat/safety and reward/loss (e.g., somatic anxiety) as well as inordinate negative self-referential processing (e.g., worry, rumination). This profile may reflect disruption in two important neural networks associated with emotional/motivational salience (e.g., salience network) and self-referentiality (e.g., default network, DN). Emotion Regulation Therapy (ERT) was developed to target this hypothesized profile and its neurobehavioral markers. In the present study, 22 GAD patients (with and without MDD) completed resting state MRI scans before receiving 16 sessions of ERT. To test study these hypotheses, we examined the associations between baseline patterns of intrinsic functional connectivity (iFC) of the insula and of hubs within the DN (anterior and dorsal medial prefrontal cortex [MPFC] and posterior cingulate cortex [PCC]) and treatment-related changes in worry, somatic anxiety symptoms and decentering. Results suggest that greater treatment linked reductions in worry were associated with iFC clusters in both the insular and parietal cortices. Greater treatment linked gains in decentering, a metacognitive process that involves the capacity to observe items that arise in the mind with healthy psychological distance that is targeted by ERT, was associated with iFC clusters in the anterior and posterior DN. The current study adds to the growing body of research implicating disruptions in the default and salience networks as promising targets of treatment for GAD with and without co-occurring MDD.

  7. Distinct Functional Connectivities Predict Clinical Response with Emotion Regulation Therapy

    PubMed Central

    Fresco, David M.; Roy, Amy K.; Adelsberg, Samantha; Seeley, Saren; García-Lesy, Emmanuel; Liston, Conor; Mennin, Douglas S.

    2017-01-01

    Despite the success of available medical and psychosocial treatments, a sizable subgroup of individuals with commonly co-occurring disorders, generalized anxiety disorder (GAD) and major depressive disorder (MDD), fail to make sufficient treatment gains thereby prolonging their deficits in life functioning and satisfaction. Clinically, these patients often display temperamental features reflecting heightened sensitivity to underlying motivational systems related to threat/safety and reward/loss (e.g., somatic anxiety) as well as inordinate negative self-referential processing (e.g., worry, rumination). This profile may reflect disruption in two important neural networks associated with emotional/motivational salience (e.g., salience network) and self-referentiality (e.g., default network, DN). Emotion Regulation Therapy (ERT) was developed to target this hypothesized profile and its neurobehavioral markers. In the present study, 22 GAD patients (with and without MDD) completed resting state MRI scans before receiving 16 sessions of ERT. To test study these hypotheses, we examined the associations between baseline patterns of intrinsic functional connectivity (iFC) of the insula and of hubs within the DN (anterior and dorsal medial prefrontal cortex [MPFC] and posterior cingulate cortex [PCC]) and treatment-related changes in worry, somatic anxiety symptoms and decentering. Results suggest that greater treatment linked reductions in worry were associated with iFC clusters in both the insular and parietal cortices. Greater treatment linked gains in decentering, a metacognitive process that involves the capacity to observe items that arise in the mind with healthy psychological distance that is targeted by ERT, was associated with iFC clusters in the anterior and posterior DN. The current study adds to the growing body of research implicating disruptions in the default and salience networks as promising targets of treatment for GAD with and without co-occurring MDD

  8. Functional imaging of the cerebellum and basal ganglia during predictive motor timing in early Parkinson's disease.

    PubMed

    Husárová, Ivica; Lungu, Ovidiu V; Mareček, Radek; Mikl, Michal; Gescheidt, Tomáš; Krupa, Petr; Bareš, Martin

    2014-01-01

    The basal ganglia and the cerebellum have both emerged as important structures involved in the processing of temporal information. We examined the roles of the cerebellum and striatum in predictive motor timing during a target interception task in healthy individuals (HC group; n = 21) and in patients with early Parkinson's disease (early stage PD group; n = 20) using functional magnetic resonance imaging. Despite having similar hit ratios, the PD failed more often than the HC to postpone their actions until the right moment and to adapt their behavior from one trial to the next. We found more activation in the right cerebellar lobule VI in HC than in early stage PD during successful trials. Successful trial-by-trial adjustments were associated with higher activity in the right putamen and lobule VI of the cerebellum in HC. We conclude that both the cerebellum and striatum are involved in predictive motor timing tasks. The cerebellar activity is associated exclusively with the postponement of action until the right moment, whereas both the cerebellum and striatum are needed for successful adaptation of motor actions from one trial to the next. We found a general ''hypoactivation'' of basal ganglia and cerebellum in early stage PD relative to HC, indicating that even in early stages of the PD there could be functional perturbations in the motor system beyond striatum. Copyright © 2011 by the American Society of Neuroimaging.

  9. Expert Involvement Predicts mHealth App Downloads: Multivariate Regression Analysis of Urology Apps.

    PubMed

    Pereira-Azevedo, Nuno; Osório, Luís; Cavadas, Vitor; Fraga, Avelino; Carrasquinho, Eduardo; Cardoso de Oliveira, Eduardo; Castelo-Branco, Miguel; Roobol, Monique J

    2016-07-15

    Urological mobile medical (mHealth) apps are gaining popularity with both clinicians and patients. mHealth is a rapidly evolving and heterogeneous field, with some urology apps being downloaded over 10,000 times and others not at all. The factors that contribute to medical app downloads have yet to be identified, including the hypothetical influence of expert involvement in app development. The objective of our study was to identify predictors of the number of urology app downloads. We reviewed urology apps available in the Google Play Store and collected publicly available data. Multivariate ordinal logistic regression evaluated the effect of publicly available app variables on the number of apps being downloaded. Of 129 urology apps eligible for study, only 2 (1.6%) had >10,000 downloads, with half having ≤100 downloads and 4 (3.1%) having none at all. Apps developed with expert urologist involvement (P=.003), optional in-app purchases (P=.01), higher user rating (P<.001), and more user reviews (P<.001) were more likely to be installed. App cost was inversely related to the number of downloads (P<.001). Only data from the Google Play Store and the developers' websites, but not other platforms, were publicly available for analysis, and the level and nature of expert involvement was not documented. The explicit participation of urologists in app development is likely to enhance its chances to have a higher number of downloads. This finding should help in the design of better apps and further promote urologist involvement in mHealth. Official certification processes are required to ensure app quality and user safety.

  10. Expert Involvement Predicts mHealth App Downloads: Multivariate Regression Analysis of Urology Apps

    PubMed Central

    Osório, Luís; Cavadas, Vitor; Fraga, Avelino; Carrasquinho, Eduardo; Cardoso de Oliveira, Eduardo; Castelo-Branco, Miguel; Roobol, Monique J

    2016-01-01

    Background Urological mobile medical (mHealth) apps are gaining popularity with both clinicians and patients. mHealth is a rapidly evolving and heterogeneous field, with some urology apps being downloaded over 10,000 times and others not at all. The factors that contribute to medical app downloads have yet to be identified, including the hypothetical influence of expert involvement in app development. Objective The objective of our study was to identify predictors of the number of urology app downloads. Methods We reviewed urology apps available in the Google Play Store and collected publicly available data. Multivariate ordinal logistic regression evaluated the effect of publicly available app variables on the number of apps being downloaded. Results Of 129 urology apps eligible for study, only 2 (1.6%) had >10,000 downloads, with half having ≤100 downloads and 4 (3.1%) having none at all. Apps developed with expert urologist involvement (P=.003), optional in-app purchases (P=.01), higher user rating (P<.001), and more user reviews (P<.001) were more likely to be installed. App cost was inversely related to the number of downloads (P<.001). Only data from the Google Play Store and the developers’ websites, but not other platforms, were publicly available for analysis, and the level and nature of expert involvement was not documented. Conclusions The explicit participation of urologists in app development is likely to enhance its chances to have a higher number of downloads. This finding should help in the design of better apps and further promote urologist involvement in mHealth. Official certification processes are required to ensure app quality and user safety. PMID:27421338

  11. Physical characteristics that predict involvement with the ball in recreational youth soccer.

    PubMed

    Ré, Alessandro H Nicolai; Cattuzzo, Maria Teresa; Henrique, Rafael Dos Santos; Stodden, David F

    2016-09-01

    This study examined the relative contribution of age, stage of puberty, anthropometric characteristics, health-related fitness, soccer-specific tests and match-related technical performance to variance in involvements with the ball during recreational 5-a-side small-sided (32 × 15 m) soccer matches. Using a cross-sectional design, 80 healthy male students (14.6 ± 0.5 years of age; range 13.6-15.4) who played soccer recreationally were randomly divided into 10 teams and played against each other. Measurements included height, body mass, pubertal status, health-related fitness (12-min walk/run test, standing long jump, 15-m sprint and sit-ups in 30 s), soccer-specific tests (kicking for speed, passing for accuracy and agility run with and without a ball), match-related technical performance (kicks, passes and dribbles) and involvements with the ball during matches. Forward multiple regression analysis revealed that cardiorespiratory fitness (12-min walk/run test) accounted for 36% of the variance in involvements with the ball. When agility with the ball (zigzag running) and power (standing long jump) were included among the predictors, the total explained variance increased to 62%. In conclusion, recreational adolescent players, regardless of their soccer-specific skills, may increase participation in soccer matches most through physical activities that promote improvement in cardiorespiratory fitness, muscle power and agility.

  12. Contribution of Neuro-Imaging for Prediction of Functional Recovery after Ischemic Stroke.

    PubMed

    Heiss, Wolf-Dieter

    2017-09-05

    Prediction measures of recovery and outcome after stroke perform with only modest levels of accuracy if based only on clinical data. Prediction scores can be improved by including morphologic imaging data, where size, location, and development of the ischemic lesion is best documented by magnetic resonance imaging. In addition to the primary lesion, the involvement of fiber tracts contributes to prognosis, and consequently the use of diffusion tensor imaging (DTI) to assess primary and secondary pathways improves the prediction of outcome and of therapeutic effects. The recovery of ischemic tissue and the progression of damage are dependent on the quality of blood supply. Therefore, the status of the supplying arteries and of the collateral flow is not only crucial for determining eligibility for acute interventions, but also has an impact on the potential to integrate areas surrounding the lesion that are not typically part of a functional network into the recovery process. The changes in these functional networks after a localized lesion are assessed by functional imaging methods, which additionally show altered pathways and activated secondary centers related to residual functions and demonstrate changes in activation patterns within these networks with improved performance. These strategies in some instances record activation in secondary centers of a network, for example, also in homolog contralateral areas, which might be inhibitory to the recovery of primary centers. Such findings might have therapeutic consequences, for example, image-guided inhibitory stimulation of these areas. In the future, a combination of morphological imaging including DTI of fiber tracts and activation studies during specific tasks might yield the best information on residual function, reserve capacity, and prospects for recovery after ischemic stroke. © 2017 S. Karger AG, Basel.

  13. Origin and Functional Prediction of Pollen Allergens in Plants1[OPEN

    PubMed Central

    Chen, Miaolin; Xu, Jie; Ren, Kang; Searle, Iain

    2016-01-01

    Pollen allergies have long been a major pandemic health problem for human. However, the evolutionary events and biological function of pollen allergens in plants remain largely unknown. Here, we report the genome-wide prediction of pollen allergens and their biological function in the dicotyledonous model plant Arabidopsis (Arabidopsis thaliana) and the monocotyledonous model plant rice (Oryza sativa). In total, 145 and 107 pollen allergens were predicted from rice and Arabidopsis, respectively. These pollen allergens are putatively involved in stress responses and metabolic processes such as cell wall metabolism during pollen development. Interestingly, these putative pollen allergen genes were derived from large gene families and became diversified during evolution. Sequence analysis across 25 plant species from green alga to angiosperms suggest that about 40% of putative pollen allergenic proteins existed in both lower and higher plants, while other allergens emerged during evolution. Although a high proportion of gene duplication has been observed among allergen-coding genes, our data show that these genes might have undergone purifying selection during evolution. We also observed that epitopes of an allergen might have a biological function, as revealed by comprehensive analysis of two known allergens, expansin and profilin. This implies a crucial role of conserved amino acid residues in both in planta biological function and allergenicity. Finally, a model explaining how pollen allergens were generated and maintained in plants is proposed. Prediction and systematic analysis of pollen allergens in model plants suggest that pollen allergens were evolved by gene duplication and then functional specification. This study provides insight into the phylogenetic and evolutionary scenario of pollen allergens that will be helpful to future characterization and epitope screening of pollen allergens. PMID:27436829

  14. Structure and function of a novel LD-carboxypeptidase a involved in peptidoglycan recycling.

    PubMed

    Das, Debanu; Hervé, Mireille; Elsliger, Marc-André; Kadam, Rameshwar U; Grant, Joanna C; Chiu, Hsiu-Ju; Knuth, Mark W; Klock, Heath E; Miller, Mitchell D; Godzik, Adam; Lesley, Scott A; Deacon, Ashley M; Mengin-Lecreulx, Dominique; Wilson, Ian A

    2013-12-01

    Approximately 50% of cell wall peptidoglycan in Gram-negative bacteria is recycled with each generation. The primary substrates used for peptidoglycan biosynthesis and recycling in the cytoplasm are GlcNAc-MurNAc(anhydro)-tetrapeptide and its degradation product, the free tetrapeptide. This complex process involves ∼15 proteins, among which the cytoplasmic enzyme ld-carboxypeptidase A (LdcA) catabolizes the bond between the last two l- and d-amino acid residues in the tetrapeptide to form the tripeptide, which is then utilized as a substrate by murein peptide ligase (Mpl). LdcA has been proposed as an antibacterial target. The crystal structure of Novosphingobium aromaticivorans DSM 12444 LdcA (NaLdcA) was determined at 1.89-Å resolution. The enzyme was biochemically characterized and its interactions with the substrate modeled, identifying residues potentially involved in substrate binding. Unaccounted electron density at the dimer interface in the crystal suggested a potential site for disrupting protein-protein interactions should a dimer be required to perform its function in bacteria. Our analysis extends the identification of functional residues to several other homologs, which include enzymes from bacteria that are involved in hydrocarbon degradation and destruction of coral reefs. The NaLdcA crystal structure provides an alternate system for investigating the structure-function relationships of LdcA and increases the structural coverage of the protagonists in bacterial cell wall recycling.

  15. Structure and Function of a Novel ld-Carboxypeptidase A Involved in Peptidoglycan Recycling

    PubMed Central

    Das, Debanu; Hervé, Mireille; Elsliger, Marc-André; Kadam, Rameshwar U.; Grant, Joanna C.; Chiu, Hsiu-Ju; Knuth, Mark W.; Klock, Heath E.; Miller, Mitchell D.; Godzik, Adam; Lesley, Scott A.; Deacon, Ashley M.

    2013-01-01

    Approximately 50% of cell wall peptidoglycan in Gram-negative bacteria is recycled with each generation. The primary substrates used for peptidoglycan biosynthesis and recycling in the cytoplasm are GlcNAc-MurNAc(anhydro)-tetrapeptide and its degradation product, the free tetrapeptide. This complex process involves ∼15 proteins, among which the cytoplasmic enzyme ld-carboxypeptidase A (LdcA) catabolizes the bond between the last two l- and d-amino acid residues in the tetrapeptide to form the tripeptide, which is then utilized as a substrate by murein peptide ligase (Mpl). LdcA has been proposed as an antibacterial target. The crystal structure of Novosphingobium aromaticivorans DSM 12444 LdcA (NaLdcA) was determined at 1.89-Å resolution. The enzyme was biochemically characterized and its interactions with the substrate modeled, identifying residues potentially involved in substrate binding. Unaccounted electron density at the dimer interface in the crystal suggested a potential site for disrupting protein-protein interactions should a dimer be required to perform its function in bacteria. Our analysis extends the identification of functional residues to several other homologs, which include enzymes from bacteria that are involved in hydrocarbon degradation and destruction of coral reefs. The NaLdcA crystal structure provides an alternate system for investigating the structure-function relationships of LdcA and increases the structural coverage of the protagonists in bacterial cell wall recycling. PMID:24123814

  16. Comparative analysis of grapevine whole-genome gene predictions, functional annotation, categorization and integration of the predicted gene sequences

    PubMed Central

    2012-01-01

    Background The first draft assembly and gene prediction of the grapevine genome (8X base coverage) was made available to the scientific community in 2007, and functional annotation was developed on this gene prediction. Since then additional Sanger sequences were added to the 8X sequences pool and a new version of the genomic sequence with superior base coverage (12X) was produced. Results In order to more efficiently annotate the function of the genes predicted in the new assembly, it is important to build on as much of the previous work as possible, by transferring 8X annotation of the genome to the 12X version. The 8X and 12X assemblies and gene predictions of the grapevine genome were compared to answer the question, “Can we uniquely map 8X predicted genes to 12X predicted genes?” The results show that while the assemblies and gene structure predictions are too different to make a complete mapping between them, most genes (18,725) showed a one-to-one relationship between 8X predicted genes and the last version of 12X predicted genes. In addition, reshuffled genomic sequence structures appeared. These highlight regions of the genome where the gene predictions need to be taken with caution. Based on the new grapevine gene functional annotation and in-depth functional categorization, twenty eight new molecular networks have been created for VitisNet while the existing networks were updated. Conclusions The outcomes of this study provide a functional annotation of the 12X genes, an update of VitisNet, the system of the grapevine molecular networks, and a new functional categorization of genes. Data are available at the VitisNet website (http://www.sdstate.edu/ps/research/vitis/pathways.cfm). PMID:22554261

  17. Relating Phylogenetic and Functional Diversity among Denitrifiers and Quantifying their Capacity to Predict Community Functioning.

    PubMed

    Salles, Joana Falcão; Le Roux, Xavier; Poly, Franck

    2012-01-01

    Genetic diversity of phylogenetic or functional markers is widely used as a proxy of microbial diversity. However, it remains unclear to what extent functional diversity (FD), gene sequence diversity and community functioning are linked. For a range of denitrifying bacteria, we analyzed the relationships between (i) the similarity of functional traits evaluated from metabolic profiles (BIOLOG plates) or from N(2)O accumulation patterns on different carbon sources and (ii) the similarity of phylogenetic (16S rRNA gene) or functional (nir gene) markers. We also calculated different proxies for the diversity of denitrifier community based on taxa richness, phylogenetic (16S rRNA gene) or functional similarities (based either on metabolic profiles or N(2)O accumulation patterns), and evaluated their performance in inferring the functioning of assembled denitrifying communities. For individual strains, the variation in the 16S rRNA gene sequence was weakly correlated with the variation in metabolic patterns (ρ = 0.35) and was not related to N(2)O accumulation. The latter was correlated with the similarity of nitrite reductase residues. When nir genes were analyzed separately, the similarity in amino acids coded by the nirS genes was highly correlated with the observed patterns of N(2)O accumulation (ρ = 0.62), whereas nirK amino acid residues were unrelated to N(2)O accumulation. For bacterial assemblages, phylogenetic diversity (average similarity among species in a community) and mean community dissimilarity (average distance between species) calculated using 16S rRNA gene sequences, and FD measures associated with metabolic profiles, poorly predicted the variation in the functioning of assembled communities (≤15%). In contrast, the proxies of FD based on N(2)O accumulation patterns performed better and explained from 23 to 42% of the variation in denitrification. Amongst those, community niche was the best metric, indicating the importance of

  18. Relating Phylogenetic and Functional Diversity among Denitrifiers and Quantifying their Capacity to Predict Community Functioning

    PubMed Central

    Salles, Joana Falcão; Le Roux, Xavier; Poly, Franck

    2012-01-01

    Genetic diversity of phylogenetic or functional markers is widely used as a proxy of microbial diversity. However, it remains unclear to what extent functional diversity (FD), gene sequence diversity and community functioning are linked. For a range of denitrifying bacteria, we analyzed the relationships between (i) the similarity of functional traits evaluated from metabolic profiles (BIOLOG plates) or from N2O accumulation patterns on different carbon sources and (ii) the similarity of phylogenetic (16S rRNA gene) or functional (nir gene) markers. We also calculated different proxies for the diversity of denitrifier community based on taxa richness, phylogenetic (16S rRNA gene) or functional similarities (based either on metabolic profiles or N2O accumulation patterns), and evaluated their performance in inferring the functioning of assembled denitrifying communities. For individual strains, the variation in the 16S rRNA gene sequence was weakly correlated with the variation in metabolic patterns (ρ = 0.35) and was not related to N2O accumulation. The latter was correlated with the similarity of nitrite reductase residues. When nir genes were analyzed separately, the similarity in amino acids coded by the nirS genes was highly correlated with the observed patterns of N2O accumulation (ρ = 0.62), whereas nirK amino acid residues were unrelated to N2O accumulation. For bacterial assemblages, phylogenetic diversity (average similarity among species in a community) and mean community dissimilarity (average distance between species) calculated using 16S rRNA gene sequences, and FD measures associated with metabolic profiles, poorly predicted the variation in the functioning of assembled communities (≤15%). In contrast, the proxies of FD based on N2O accumulation patterns performed better and explained from 23 to 42% of the variation in denitrification. Amongst those, community niche was the best metric, indicating the importance of complementarity for

  19. Exploring patient involvement in healthcare decision making across different education and functional health literacy groups.

    PubMed

    Smith, Sian K; Dixon, Ann; Trevena, Lyndal; Nutbeam, Don; McCaffery, Kirsten J

    2009-12-01

    Education and health literacy potentially limit a person's ability to be involved in decisions about their health. Few studies, however, have explored understandings and experiences of involvement in decision making among patients varying in education and health literacy. This paper reports on a qualitative interview study of 73 men and women living in Sydney, Australia, with varying education and functional health literacy levels. Participants were recruited from a community sample with lower educational attainment, plus an educated sample of University of Sydney alumni. The transcripts were analysed using the 'Framework' approach, a matrix-based method of thematic analysis. We found that participants with different education conceptualised their involvement in decision making in diverse ways. Participants with higher education appeared to conceive their involvement as sharing the responsibility with the doctor throughout the decision-making process. This entailed verifying the credibility of the information and exploring options beyond those presented in the consultation. They also viewed themselves as helping others in their health decisions and acting as information resources. In contrast, participants with lower education appeared to conceive their involvement in terms of consenting to an option recommended by the doctor, and having responsibility for the ultimate decision, to agree or disagree with the recommendation. They also described how relatives and friends sought information on their behalf and played a key role in their decisions. Both education groups described how aspects of the patient-practitioner relationship (e.g. continuity, negotiation, trust) and the practitioner's interpersonal communication skills influenced their involvement. Health information served a variety of needs for all groups (e.g. supporting psychosocial, practical and decision support needs). These findings have practical implications for how to involve patients with different

  20. Impairment in Occupational Functioning and Adult ADHD: The Predictive Utility of Executive Function (EF) Ratings Versus EF Tests

    PubMed Central

    Barkley, Russell A.; Murphy, Kevin R.

    2010-01-01

    Attention deficit hyperactivity disorder (ADHD) is associated with deficits in executive functioning (EF). ADHD in adults is also associated with impairments in major life activities, particularly occupational functioning. We investigated the extent to which EF deficits assessed by both tests and self-ratings contributed to the degree of impairment in 11 measures involving self-reported occupational problems, employer reported workplace adjustment, and clinician rated occupational adjustment. Three groups of adults were recruited as a function of their severity of ADHD: ADHD diagnosis (n = 146), clinical controls self-referring for ADHD but not diagnosed with it (n = 97), and community controls (n = 109). Groups were combined and regression analyses revealed that self-ratings of EF were significantly predictive of impairments in all 11 measures of occupational adjustment. Although several tests of EF also did so, they contributed substantially less than did the EF ratings, particularly when analyzed jointly with the ratings. We conclude that EF deficits contribute to the impairments in occupational functioning that occur in conjunction with adult ADHD. Ratings of EF in daily life contribute more to such impairments than do EF tests, perhaps because, as we hypothesize, each assesses a different level in the hierarchical organization of EF as a meta-construct. PMID:20197297

  1. Diurnal rhythmicity in biological processes involved in bioavailability of functional food factors.

    PubMed

    Tsurusaki, Takashi; Sakakibara, Hiroyuki; Aoshima, Yoshiki; Yamazaki, Shunsuke; Sakono, Masanobu; Shimoi, Kayoko

    2013-05-01

    In the past few decades, many types of functional factors have been identified in dietary foods; for example, flavonoids are major groups widely distributed in the plant kingdom. However, the absorption rates of the functional food factors are usually low, and many of these are difficult to be absorbed in the intact forms because of metabolization by biological processes during absorption. To gain adequate beneficial effects, it is therefore mandatory to know whether functional food factors are absorbed in sufficient quantity, and then reach target organs while maintaining beneficial effects. These are the reasons why the bioavailability of functional food factors has been well investigated using rodent models. Recently, many of the biological processes have been reported to follow diurnal rhythms recurring every 24 h. Therefore, absorption and metabolism of functional food factors influenced by the biological processes may vary with time of day. Consequently, the evaluation of the bioavailability of functional food factors using rodent models should take into consideration the timing of consumption. In this review, we provide a perspective overview of the diurnal rhythm of biological processes involved in the bioavailability of functional food factors, particularly flavonoids.

  2. Diurnal rhythmicity in biological processes involved in bioavailability of functional food factors

    PubMed Central

    Tsurusaki, Takashi; Sakakibara, Hiroyuki; Aoshima, Yoshiki; Yamazaki, Shunsuke; Sakono, Masanobu; Shimoi, Kayoko

    2013-01-01

    In the past few decades, many types of functional factors have been identified in dietary foods; for example, flavonoids are major groups widely distributed in the plant kingdom. However, the absorption rates of the functional food factors are usually low, and many of these are difficult to be absorbed in the intact forms because of metabolization by biological processes during absorption. To gain adequate beneficial effects, it is therefore mandatory to know whether functional food factors are absorbed in sufficient quantity, and then reach target organs while maintaining beneficial effects. These are the reasons why the bioavailability of functional food factors has been well investigated using rodent models. Recently, many of the biological processes have been reported to follow diurnal rhythms recurring every 24 h. Therefore, absorption and metabolism of functional food factors influenced by the biological processes may vary with time of day. Consequently, the evaluation of the bioavailability of functional food factors using rodent models should take into consideration the timing of consumption. In this review, we provide a perspective overview of the diurnal rhythm of biological processes involved in the bioavailability of functional food factors, particularly flavonoids. PMID:23704810

  3. Parental Involvement in Infant Sleep Routines Predicts Differential Sleep Patterns in Children With and Without Anxiety Disorders.

    PubMed

    Cowie, Jennifer; Palmer, Cara A; Hussain, Hira; Alfano, Candice A

    2016-08-01

    This study compared parents' retrospective reports of their involvement in infant settling strategies and their relation to current sleep patterns among children (N = 84, ages 7-11) with generalized anxiety disorder (GAD) and healthy controls. Parents of children with GAD were significantly more likely to report rocking their infants to sleep and putting infants down when they were already asleep than parents of healthy controls, even when accounting for infant health-related factors and parental anxiety. Greater involvement in infant sleep routines also predicted sleep patterns (measured via actigraphy) during childhood, though opposite relationships were observed in the two groups. Early involvement was related to poorer sleep in control children but better sleep for children with GAD even after controlling for current parenting practices. Findings suggest differential effects of early sleep-related parenting for children with and without later anxiety disorders with possible implications for early intervention.

  4. Anomalies in Network Bridges Involved in Bile Acid Metabolism Predict Outcomes of Colorectal Cancer Patients

    PubMed Central

    Yoon, Seyeol; Lee, Jae W.; Lee, Doheon

    2014-01-01

    Biomarkers prognostic for colorectal cancer (CRC) would be highly desirable in clinical practice. Proteins that regulate bile acid (BA) homeostasis, by linking metabolic sensors and metabolic enzymes, also called bridge proteins, may be reliable prognostic biomarkers for CRC. Based on a devised metric, “bridgeness,” we identified bridge proteins involved in the regulation of BA homeostasis and identified their prognostic potentials. The expression patterns of these bridge proteins could distinguish between normal and diseased tissues, suggesting that these proteins are associated with CRC pathogenesis. Using a supervised classification system, we found that these bridge proteins were reproducibly prognostic, with high prognostic ability compared to other known markers. PMID:25259881

  5. A selective involvement of putamen functional connectivity in youth with internet gaming disorder.

    PubMed

    Hong, Soon-Beom; Harrison, Ben J; Dandash, Orwa; Choi, Eun-Jung; Kim, Seong-Chan; Kim, Ho-Hyun; Shim, Do-Hyun; Kim, Chang-Dai; Kim, Jae-Won; Yi, Soon-Hyung

    2015-03-30

    Brain cortico-striatal circuits have consistently been implicated in the pathology of addiction related disorders. We applied a reliable seed-based analysis of the resting-state brain activity to comprehensively delineate the subdivisions of striatal functional connectivity implicated in internet gaming disorder. Among twelve right-handed male adolescents with internet gaming disorder and 11 right-handed and gender-matched healthy controls, we examined group differences in the functional connectivity of dorsal and ventral subdivisions of the caudate nucleus and putamen, as well as the association of these connectivity indices with behavioral measures of internet use. Adolescents with internet gaming disorder showed significantly reduced dorsal putamen functional connectivity with the posterior insula-parietal operculum. More time spent playing online games predicted significantly greater functional connectivity between the dorsal putamen and bilateral primary somatosensory cortices in adolescents with internet gaming disorder, and significantly lower functional connectivity between the dorsal putamen and bilateral sensorimotor cortices in healthy controls. The dorsal putamen functional connectivity was significantly and specifically different in adolescents with internet gaming disorder. The findings suggest a possible biomarker of internet gaming disorder.

  6. Prediction of functionally important residues in globular proteins from unusual central distances of amino acids

    PubMed Central

    2011-01-01

    Background Well-performing automated protein function recognition approaches usually comprise several complementary techniques. Beside constructing better consensus, their predictive power can be improved by either adding or refining independent modules that explore orthogonal features of proteins. In this work, we demonstrated how the exploration of global atomic distributions can be used to indicate functionally important residues. Results Using a set of carefully selected globular proteins, we parametrized continuous probability density functions describing preferred central distances of individual protein atoms. Relative preferred burials were estimated using mixture models of radial density functions dependent on the amino acid composition of a protein under consideration. The unexpectedness of extraordinary locations of atoms was evaluated in the information-theoretic manner and used directly for the identification of key amino acids. In the validation study, we tested capabilities of a tool built upon our approach, called SurpResi, by searching for binding sites interacting with ligands. The tool indicated multiple candidate sites achieving success rates comparable to several geometric methods. We also showed that the unexpectedness is a property of regions involved in protein-protein interactions, and thus can be used for the ranking of protein docking predictions. The computational approach implemented in this work is freely available via a Web interface at http://www.bioinformatics.org/surpresi. Conclusions Probabilistic analysis of atomic central distances in globular proteins is capable of capturing distinct orientational preferences of amino acids as resulting from different sizes, charges and hydrophobic characters of their side chains. When idealized spatial preferences can be inferred from the sole amino acid composition of a protein, residues located in hydrophobically unfavorable environments can be easily detected. Such residues turn out to be

  7. Structure activity relationships: their function in biological prediction

    SciTech Connect

    Schultz, T.W.

    1982-01-01

    Quantitative structure activity relationships provide a means of ranking or predicting biological effects based on chemical structure. For each compound used to formulate a structure activity model two kinds of quantitative information are required: (1) biological activity and (2) molecular properties. Molecular properties are of three types: (1) molecular shape, (2) physiochemical parameters, and (3) abstract quantitations of molecular structure. Currently the two best descriptors are the hydrophobic parameter, log 1-octanol/water partition coefficient (log P), and the /sup 1/X/sup v/(one-chi-v) molecular connectivity index. Biological responses can be divided into three main categories: (1) non-specific effects due to membrane perturbation, (2) non-specific effects due to interaction with functional groups of proteins, and (3) specific effects due to interaction with receptors. Twenty-six synthetic fossil fuel-related nitrogen-containing aromatic compounds were examined to determine the quantitative correlation between log P and /sup 1/X/sup v/ and population growth impairment of Tetrahymena pyriformis. Nitro-containing compounds are the most active, followed by amino-containing compounds and azaarenes. Within each analog series activity increases with alkyl substitution and ring addition. The planar model log BR = 0.5564 log P + 0.3000 /sup 1/X/sup v/ -2.0138 was determined using mono-nitrogen substituted compounds. Attempts to extrapolate this model to dinitrogen-containing molecules were, for the most part, unsuccessful because of a change in mode of action from membrane perturbation to uncoupling of oxidative phosphoralation.

  8. Is the use of diffuse functions essential for the properly description of noncovalent interactions involving anions?

    PubMed

    Bauzá, Antonio; Quiñonero, David; Deyà, Pere M; Frontera, Antonio

    2013-03-28

    It is commonly assumed that theoretical DFT or ab initio calculations involving anions require the utilization of diffuse functions in order to obtain reliable results. In large systems, the use of diffuse functions in the calculations increases the computational cost and, more importantly, sometimes provokes self-consistent-field (SCF) convergence problems, especially in open shell systems. Nowadays, the popular and often used bases for studying noncovalent interactions are the correlation-consistent polarized basis sets of Dunning and co-workers, denoted as cc-pVXZ (X = D, T, etc.), and the Turbomole def2 basis set family (def2-SVP and def2-TZVP). In this paper we study the effect of the utilization of diffuse functions on the energetic and geometric features of several noncovalent complexes, including hydrogen, halogen, and pnicogen bonding, lithium bonds, anion-π interactions, and van der Waals interactions.

  9. Predictive Accuracy of Urinary neutrophil gelatinase associated lipocalin (NGAL) for renal parenchymal involvement in Children with Acute Pyelonephritis

    PubMed Central

    Ghasemi, Kambiz; Esteghamati, Maryam; Borzoo, Sara; Parvaneh, Erfan; Borzoo, Samira

    2016-01-01

    Introduction Urinary tract infections (UTIs) are among the most prevalent infections in children and infants. Early and accurate detection of renal parenchymal involvement in UTI is necessary for decision making and determining treatment strategies. The aim of this study was to determine the predictive accuracy of urinary neutrophil gelatinase-associated lipocalin (NGAL) for renal parenchymal involvement in children with acute pyelonephritis. Methods This descriptive, cross-sectional study was conducted in 2014 on children who had been diagnosed with UTI. Children who were admitted to Koodakan Hospital in Bandar Abbas, Hormozgan Province, Iran, and whose ages ranged from two months to 14 years were enrolled in the study. Urine samples were taken to conduct urinary NGAL tests, urine cultures, and urinalyses. In addition, some blood samples were collected for the purpose of determining leukocyte count and C-reactive protein (CRP) and to conduct erythrocyte sedimentation rate (ESR) tests. All patients underwent a dimercaptosuccinic acid (DMSA) scan. SPSS software was used to analyze the data. Results Among the participants in the study, 29 were male (32%), and 60 were female (68%). The mean age of the children who participated in the study was 2.99 ± 2.94 years. The results of the Kruskal-Wallis test showed a significant increase in the urinary NGAL level, an increase in the CRP level, and higher DMSA scan grades (p < 0.001). The cutoff point amounted to > 5 mg/l, having the negative predictive value (NPV) of 76.3%, the specificity of 97.83%, the positive predictive value (PPV) of 96.7%, and the sensitivity of 67.4%. Conclusion Urinary NGAL is not sensitive enough for the prediction of renal parenchymal involvement, but it is a specific marker. PMID:27053998

  10. Executive function plays a role in coordinating different perspectives, particularly when one's own perspective is involved.

    PubMed

    Fizke, Ella; Barthel, Dana; Peters, Thomas; Rakoczy, Hannes

    2014-03-01

    While developmental experiments with children and elderly subjects, work with neuropsychological patients and adult experimental studies have consistently found close relations between executive function and theory of mind, the foundation of this relation still remains somewhat unclear. One prominent account holds that executive function is specifically involved in ascribing such mental states, paradigmatically beliefs, that aim at representing the world truly because ascribing such states requires inhibition of normative defaults (beliefs being true) (e.g. Sabbagh, Moses, & Shiverick, 2006). The present studies systematically tested for the role of executive function in different forms of mental state ascription as a function of the type of state ascribed (beliefs or desires) and the first person involvement of the ascriber (whether she herself has an attitude conflicting with one to be ascribed to someone else) in young children. The results reveal that (i) executive function is related not only to belief ascription but equally to desire ascription when both are matched in terms of logical complexity (such that two subjective attitudes have to be ascribed to two agents that are incompatible with each other). (ii) Both for desires and for beliefs, these relations are strongest in such tasks where the ascriber herself is one of the two agents, i.e. has a belief or desire herself that stands in contrast to that to be ascribed to someone else. All in all, these findings suggest that executive function figures in coordinating perspectives more generally, not only epistemic ones, and in particular in coordinating others' and one's own conflicting perspectives.

  11. Adolescent abortion and parental notification: evidence for the importance of family functioning on the perceived quality of parental involvement in U.S. families.

    PubMed

    Griffin-Carlson, M S; Schwanenflugel, P J

    1998-05-01

    This study was an investigation of the relationship between family variables and the perceived quality of parental involvement following parental notification of an adolescent's decision to have an abortion. Demographics, family religiosity, and family functioning variables were examined. Pregnant adolescent clients from seven abortion clinics in three states completed a survey assessing their perception of the quality of parental involvement and the family variables. Only family functioning variables were significantly related to the perceived quality of parental involvement. Family adaptability (the family's ability to change its power structure, role relationships, and relationship rules in response to situational and developmental stress) was the most predictive. Adolescents from adaptable families had a more positive experience with parental involvement than adolescents from less adaptable families.

  12. Prediction of biological functions on glycosylation site migrations in human influenza H1N1 viruses.

    PubMed

    Sun, Shisheng; Wang, Qinzhe; Zhao, Fei; Chen, Wentian; Li, Zheng

    2012-01-01

    Protein glycosylation alteration is typically employed by various viruses for escaping immune pressures from their hosts. Our previous work had shown that not only the increase of glycosylation sites (glycosites) numbers, but also glycosite migration might be involved in the evolution of human seasonal influenza H1N1 viruses. More importantly, glycosite migration was likely a more effectively alteration way for the host adaption of human influenza H1N1 viruses. In this study, we provided more bioinformatics and statistic evidences for further predicting the significant biological functions of glycosite migration in the host adaptation of human influenza H1N1 viruses, by employing homology modeling and in silico protein glycosylation of representative HA and NA proteins as well as amino acid variability analysis at antigenic sites of HA and NA. The results showed that glycosite migrations in human influenza viruses have at least five possible functions: to more effectively mask the antigenic sites, to more effectively protect the enzymatic cleavage sites of neuraminidase (NA), to stabilize the polymeric structures, to regulate the receptor binding and catalytic activities and to balance the binding activity of hemagglutinin (HA) with the release activity of NA. The information here can provide some constructive suggestions for the function research related to protein glycosylation of influenza viruses, although these predictions still need to be supported by experimental data.

  13. Homology modeling and functional sites prediction of azoreductase enzyme from the cyanobacterium Nostoc sp. PCC7120.

    PubMed

    Devi, Philem Priyadarshini; Adhikari, Samrat

    2012-12-01

    Industrial dyes such as azodyes are potential environmental pollutants causing deleterious health hazards complications. These dyes are potentially degraded by azoreductase enzyme which is widely distributed in bacteria and also cyanobacteria. The azoreductase enzymes from cyanobacteria have not been explored in detail. Hence this enzyme from Nostoc sp. PCC 7120 has been addressed in detail in the present study considering to explore the physico-chemical properties, evolutionary relationships, functional sites and structural properties using various bioinformatics tools. Four conserved regions were obtained from the multiple sequence analysis. The multiple sequence alignment showed conserved regions at different stretches from 1-11, 40-57, 82-120 and 161-177 amino acid residues. These regions could be used for designing degenerate primers or probes for PCR-based amplification or hybridization-based detection of azoreductase sequences from different source organisms. Domain analysis and functional site prediction showed the presence of functional sites and domain such as flavodoxin like fold responsible for enzyme activity. 3D model was constructed and the best model was selected and validated. Superimposition of the final structure and the template showed variations in certain regions which might be involved in the accommodation of various dyes. Our results may be helpful for further investigations like docking studies as well as in vivo and in vitro conditions although these predictions still need to be studied.

  14. Prediction of functional sites in proteins using conserved functional group analysis.

    PubMed

    Innis, C Axel; Anand, A Prem; Sowdhamini, R

    2004-04-02

    A detailed knowledge of a protein's functional site is an absolute prerequisite for understanding its mode of action at the molecular level. However, the rapid pace at which sequence and structural information is being accumulated for proteins greatly exceeds our ability to determine their biochemical roles experimentally. As a result, computational methods are required which allow for the efficient processing of the evolutionary information contained in this wealth of data, in particular that related to the nature and location of functionally important sites and residues. The method presented here, referred to as conserved functional group (CFG) analysis, relies on a simplified representation of the chemical groups found in amino acid side-chains to identify functional sites from a single protein structure and a number of its sequence homologues. We show that CFG analysis can fully or partially predict the location of functional sites in approximately 96% of the 470 cases tested and that, unlike other methods available, it is able to tolerate wide variations in sequence identity. In addition, we discuss its potential in a structural genomics context, where automation, scalability and efficiency are critical, and an increasing number of protein structures are determined with no prior knowledge of function. This is exemplified by our analysis of the hypothetical protein Ydde_Ecoli, whose structure was recently solved by members of the North East Structural Genomics consortium. Although the proposed active site for this protein needs to be validated experimentally, this example illustrates the scope of CFG analysis as a general tool for the identification of residues likely to play an important role in a protein's biochemical function. Thus, our method offers a convenient solution to rapidly and automatically process the vast amounts of data that are beginning to emerge from structural genomics projects.

  15. Prediction of additional lymph node involvement in breast cancer patients with positive sentinel lymph nodes.

    PubMed

    Pohlodek, K; Bozikova, S; Meciarova, I; Mucha, V; Bartova, M; Ondrias, F

    2016-01-01

    Axillary lymph node dissection (ALND) has traditionally been the principal method for evaluating axillary lymph node status in breast cancer patients. In the past decades sentinel lymph nodes biopsy after lymphatic mapping has been used to stage the disease. The majority of sentinel lymph nodes (SLN) positive patients do not have additional metastases in non-sentinel nodes (non-SLN) after additional ALND. These patients are exposed to the morbidity of ALND without any benefit from additional axillary clearence. In the present study we would like to asses the criteria for selecting those patients, who have high risk for non-SLN metastases in the axilla in cases of positive SLN. In this retrospective analysis, clinical and pathologic data from 163 patients who underwent SLN biopsy followed by ALND were collected. Following clinical and pathological characteristics were analyzed to predict the likehood of non-SLN metastases: age, staging, histologic type and grading of the tumors, hormonal receptor status, HER-2 receptor status and Ki-67 protein, angioinvasion, metastases in SLN and non-SLN. Relative frequencies of individual characteristics between sample groups were statistically tested by Chi-square test at significance level p=0.5, when sample sizes in groups were small (≤5) by Fisher´s exact test. Metastasis in SLN were present in 67 (41%) of patients, 48 patients (29,4%) had metastasis also in non-SLN. The ratio between non-SLN positive / non-SLN negative lymph nodes in patients with positive SLN increases with the stage of the disease, the difference between values for the pT1c and pT2 stadium was statistically significant (p = 0.0296). The same applies to grading, but the differences were not significant (p>0.05). We could not find significant differences for angioinvasion of the tumor, probably for small number of patients with angioinvasion (p>0.05).Only the stage of the tumor was shown to be significant in predicting the metastasis in non-SLN in our

  16. Right Ventricular and Right Atrial Involvement Can Predict Atrial Fibrillation in Patients with Hypertrophic Cardiomyopathy?

    PubMed

    Doesch, Christina; Lossnitzer, Dirk; Rudic, Boris; Tueluemen, Erol; Budjan, Johannes; Haubenreisser, Holger; Henzler, Thomas; Schoenberg, Stefan O; Borggrefe, Martin; Papavassiliu, Theano

    2016-01-01

    Atrial fibrillation (AF) is associated with clinical deterioration, stroke and disability in patients with hypertrophic cardiomyopathy (HCM). Therefore, the objective of this study was to evaluated cardiac magnetic resonance (CMR)-derived determinants for the occurrence of AF in patients with HCM. 98 Patients with HCM and 30 healthy controls underwent CMR and were followed-up for 6 ± 3 years. 19 (19.4%) patients presented with AF at initial diagnosis, 19 (19.4%) developed AF during follow-up and 60 (61.2%) remained in sinus rhythm (SR). Compared to healthy controls, patients with HCM who remained in SR presented with significantly increased left ventricular mass, an elevated left ventricular remodeling index, enlarged left atrial volumes and reduced septal mitral annular plane systolic excursion (MAPSE) compared to healthy controls. Whereas HCM patients who presented with AF at initial diagnosis and those who developed AF during follow-up additionally presented with reduced tricuspid annular plane systolic excursion (TAPSE) and right atrial (RA) dilatation. Receiver-operator curve analysis indicated good predictive performance of TAPSE, RA diameter and septal MAPSE (AUC 0.73, 0.69 and 0.71, respectively) to detect patients at risk of developing AF. Reduced MAPSE measurements and enlarged LA volumes seems to be a common feature in patients with HCM, whereas reduced TAPSE and RA dilatation only seem to be altered in patients with history of AF and those developing AF. Therefore, they could serve as easy determinable markers of AF in patients with HCM.

  17. Prediction and validation of potential pathogenic microRNAs involved in Phytophthora infestans infection.

    PubMed

    Cui, Juanjuan; Luan, Yushi; Wang, Weichen; Zhai, Junmiao

    2014-03-01

    Being one kind of approximately 22nt long small RNA, miRNA has shown its roles in host-pathogen interaction, providing one possible way for pathogen infection. Though Phytophthora infestans is a major pathogen that causes devastating late blight of potato, tomato and so on, so far there have not been any systematic researches on miRNAs and even pathogenic miRNAs in P. infestans. Here, for the first time we comprehensively predicted and identified pathogenic miRNAs that may exist in P. infestans. First, a total of 128 putative miRNAs belonging to 66 miRNA family were identified by bioinformatic approaches. Then, 33 vital pathogenic miRNAs were screened by constructing miRNA-miRNA relationship networks. Finally, four potential pathogenic miRNAs were chosen for detection, two of which are chosen for validation. The expression quantity of pi-miR466 and pi-miR1918 changed dramatically during incubation of tomato leaves, implying that they are potential pathogenic miRNAs.

  18. Comparison of Nodal Risk Formula and MR Lymphography for Predicting Lymph Node Involvement in Prostate Cancer

    SciTech Connect

    Deserno, Willem M.L.L.G.; Debats, Oscar A.; Rozema, Tom; Fortuin, Ansje S.; Heesakkers, Roel A.M.; Hoogeveen, Yvonne; Peer, Petronella G.M.; Barentsz, Jelle O.; Lin, Emile N.J.T. van

    2011-09-01

    Purpose: To compare the nodal risk formula (NRF) as a predictor for lymph node (LN) metastasis in patients with prostate cancer with magnetic resonance lymphography (MRL) using Ultrasmall Super-Paramagnetic particles of Iron Oxide (USPIO) and with histology as gold standard. Methods and Materials: Logistic regression analysis was performed with the results of histopathological evaluation of the LN as dependent variable and the nodal risk according to the NRF and the result of MRL as independent input variables. Receiver operating characteristic (ROC) analysis was performed to assess the performance of the models. Results: The analysis included 375 patients. In the single-predictor regression models, the NRF and MRL results were both significantly (p <0.001) predictive of the presence of LN metastasis. In the models with both predictors included, NRF was nonsignificant (p = 0.126), but MRL remained significant (p <0.001). For NRF, sensitivity was 0.79 and specificity was 0.38; for MRL, sensitivity was 0.82 and specificity was 0.93. After a negative MRL result, the probability of LN metastasis is 4% regardless of the NRF result. After a positive MRL, the probability of having LN metastasis is 68%. Conclusions: MRL is a better predictor of the presence of LN metastasis than NRF. Using only the NRF can lead to a significant overtreatment on the pelvic LN by radiation therapy. When the MRL result is available, the NRF is no longer of added value.

  19. Living alongside more affluent neighbors predicts greater involvement in antisocial behavior among low-income boys

    PubMed Central

    Odgers, Candice L.; Donley, Sachiko; Caspi, Avshalom; Bates, Christopher J.; Moffitt, Terrie E.

    2016-01-01

    Background The creation of economically mixed communities has been proposed as one way to improve the life outcomes of children growing up in poverty. However, whether low-income children benefit from living alongside more affluent neighbors is unknown. Method Prospectively gathered data on over 1,600 children from the Environmental Risk (E-Risk) Longitudinal Twin Study living in urban environments is used to test whether living alongside more affluent neighbors (measured via high-resolution geo-spatial indices) predicts low-income children’s antisocial behavior (reported by mothers and teachers at the ages of 5, 7, 10, and 12). Results Results indicated that low-income boys (but not girls) surrounded by more affluent neighbors had higher levels of antisocial behavior than their peers embedded in concentrated poverty. The negative effect of growing up alongside more affluent neighbors on low-income boys’ antisocial behavior held across childhood and after controlling for key neighborhood and family-level factors. Conclusions Findings suggest that efforts to create more economically mixed communities for children, if not properly supported, may have iatrogenic effects on boys’ antisocial behavior. PMID:25611118

  20. Living alongside more affluent neighbors predicts greater involvement in antisocial behavior among low-income boys.

    PubMed

    Odgers, Candice L; Donley, Sachiko; Caspi, Avshalom; Bates, Christopher J; Moffitt, Terrie E

    2015-10-01

    The creation of economically mixed communities has been proposed as one way to improve the life outcomes of children growing up in poverty. However, whether low-income children benefit from living alongside more affluent neighbors is unknown. Prospectively gathered data on over 1,600 children from the Environmental Risk (E-Risk) Longitudinal Twin Study living in urban environments is used to test whether living alongside more affluent neighbors (measured via high-resolution geo-spatial indices) predicts low-income children's antisocial behavior (reported by mothers and teachers at the ages of 5, 7, 10, and 12). Results indicated that low-income boys (but not girls) surrounded by more affluent neighbors had higher levels of antisocial behavior than their peers embedded in concentrated poverty. The negative effect of growing up alongside more affluent neighbors on low-income boys' antisocial behavior held across childhood and after controlling for key neighborhood and family-level factors. Findings suggest that efforts to create more economically mixed communities for children, if not properly supported, may have iatrogenic effects on boys' antisocial behavior. © 2015 Association for Child and Adolescent Mental Health.

  1. Task Performance Modulates Functional Connectivity Involving the Dorsolateral Prefrontal Cortex in Patients with Schizophrenia.

    PubMed

    Wu, Shihao; Wang, Huiling; Chen, Cheng; Zou, Jilin; Huang, Huan; Li, Peifu; Zhao, Yilin; Xu, Qizhong; Zhang, Liang; Wang, Hesheng; Pandit, Sanjib; Dahal, Subodh; Chen, Jun; Zhou, Yuan; Jiang, Tianzi; Wang, Gaohua

    2017-01-01

    Previous studies have suggested that patients with schizophrenia and healthy controls exhibit differential activation of and connectivity involving the dorsolateral prefrontal cortex (DLPFC) during working memory tasks, though their findings remain inconsistent. The functional integration perspective further suggests that working memory performance also modulates differences in functional interactions of the DLPFC between patients and controls. To explore this possibility, 45 healthy controls and 45 patients with schizophrenia were recruited to perform a 2-back task during functional magnetic resonance imaging (fMRI). Each group was further divided into two subgroups based on task performance to examine the modulatory effect of performance on functional interactions of the DLPFC, as measured via psychophysiological interaction (PPI) analyses. We observed that, in patients with schizophrenia who exhibited impaired working memory capacity and decreased brain activation/deactivation, functional interactions between the right/left DLPFC and angular cortex were decreased relative to those of healthy controls. Furthermore, we observed an interaction effect of working memory performance and diagnosis on functional connectivity between the right/left DLPFC seed region and posterior regions such as the angular cortex, fusiform gyrus, and middle occipital gyrus. This interaction effect was mainly driven by the negative correlation between functional connectivity and performance in healthy controls, and by the positive correlation in patients with schizophrenia. These results demonstrate the effects of inter-individual differences in working memory performance on functional interactions between the DLPFC and posterior regions in patients with schizophrenia as well as healthy controls, which may shed new light on the neural basis of working memory.

  2. Task Performance Modulates Functional Connectivity Involving the Dorsolateral Prefrontal Cortex in Patients with Schizophrenia

    PubMed Central

    Wu, Shihao; Wang, Huiling; Chen, Cheng; Zou, Jilin; Huang, Huan; Li, Peifu; Zhao, Yilin; Xu, Qizhong; Zhang, Liang; Wang, Hesheng; Pandit, Sanjib; Dahal, Subodh; Chen, Jun; Zhou, Yuan; Jiang, Tianzi; Wang, Gaohua

    2017-01-01

    Previous studies have suggested that patients with schizophrenia and healthy controls exhibit differential activation of and connectivity involving the dorsolateral prefrontal cortex (DLPFC) during working memory tasks, though their findings remain inconsistent. The functional integration perspective further suggests that working memory performance also modulates differences in functional interactions of the DLPFC between patients and controls. To explore this possibility, 45 healthy controls and 45 patients with schizophrenia were recruited to perform a 2-back task during functional magnetic resonance imaging (fMRI). Each group was further divided into two subgroups based on task performance to examine the modulatory effect of performance on functional interactions of the DLPFC, as measured via psychophysiological interaction (PPI) analyses. We observed that, in patients with schizophrenia who exhibited impaired working memory capacity and decreased brain activation/deactivation, functional interactions between the right/left DLPFC and angular cortex were decreased relative to those of healthy controls. Furthermore, we observed an interaction effect of working memory performance and diagnosis on functional connectivity between the right/left DLPFC seed region and posterior regions such as the angular cortex, fusiform gyrus, and middle occipital gyrus. This interaction effect was mainly driven by the negative correlation between functional connectivity and performance in healthy controls, and by the positive correlation in patients with schizophrenia. These results demonstrate the effects of inter-individual differences in working memory performance on functional interactions between the DLPFC and posterior regions in patients with schizophrenia as well as healthy controls, which may shed new light on the neural basis of working memory. PMID:28289394

  3. Functional analysis of genes involved in the biosynthesis of isoprene in Bacillus subtilis

    PubMed Central

    Julsing, Mattijs K.; Rijpkema, Michael; Woerdenbag, Herman J.; Quax, Wim J.

    2007-01-01

    In comparison to other bacteria Bacillus subtilis emits the volatile compound isoprene in high concentrations. Isoprene is the smallest representative of the natural product group of terpenoids. A search in the genome of B. subtilis resulted in a set of genes with yet unknown function, but putatively involved in the methylerythritol phosphate (MEP) pathway to isoprene. Further identification of these genes would give the possibility to engineer B. subtilis as a host cell for the production of terpenoids like the valuable plant-produced drugs artemisinin and paclitaxel. Conditional knock-out strains of putative genes were analyzed for the amount of isoprene emitted. Differences in isoprene emission were used to identify the function of the enzymes and of the corresponding selected genes in the MEP pathway. We give proof on a biochemical level that several of these selected genes from this species are involved in isoprene biosynthesis. This opens the possibilities to investigate the physiological function of isoprene emission and to increase the endogenous flux to the terpenoid precursors, isopentenyl diphosphate and dimethylallyl diphosphate, for the heterologous production of more complex terpenoids in B. subtilis. PMID:17458547

  4. Communication abnormalities predict functional outcomes in chronic schizophrenia: differential associations with social and adaptive functions.

    PubMed

    Bowie, Christopher R; Harvey, Philip D

    2008-08-01

    Communication abnormalities are hallmark features of schizophrenia. Despite the prevalence and persistence of these symptoms, little is known about their functional implications. In this study, we examined, in a sample of chronically institutionalized schizophrenia patients (N=317), whether two types of communication abnormalities (i.e., verbal underproductivity and disconnected speech) had differential relationships with social and adaptive outcomes. Baseline ratings of verbal underproductivity, disconnected speech, global cognitive performance, and clinical symptoms, were entered into stepwise regression analyses to examine their relationship with 2.5 year social and adaptive outcomes. At baseline, disconnected speech was significantly associated with socially impolite behavior, while verbal underproductivity was associated with social disengagement and impaired friendships. Both types of communication abnormalities were significantly associated with other types of social skills. Verbal underproductivity predicted follow-up social skills, social engagement, and friendships, accounting for more variance than. cognition or symptoms. In contrast to social outcomes, adaptive outcomes were predicted by baseline neurocognition and clinical symptoms, but not communication abnormalities. These findings provide evidence for specific relationships of communication disorder subtypes with diverse impairments in social functions. In this chronically institutionalized sample, communication disorder was a stronger predictor of social, but not adaptive, outcomes than neurocognition or clinical symptoms.

  5. Communication Abnormalities Predict Functional Outcomes in Chronic Schizophrenia: Differential Associations with Social and Adaptive Functions

    PubMed Central

    Bowie, Christopher R.; Harvey, Philip D.

    2014-01-01

    Communication abnormalities are hallmark features of schizophrenia. Despite the prevalence and persistence of these symptoms, little is known about their functional implications. In this study, we examined, in a sample of chronically institutionalized schizophrenia patients (N=317), whether two types of communication abnormalities (i.e., verbal underproductivity and disconnected speech) had differential relationships with social and adaptive outcomes. Baseline ratings of verbal underproductivity, disconnected speech, global cognitive performance, and clinical symptoms, were entered into stepwise regression analyses to examine their relationship with 2.5 year social and adaptive outcomes. At baseline, disconnected speech was significantly associated with socially impolite behavior, while verbal underproductivity was associated with social disengagement and impaired friendships. Both types of communication abnormalities were significantly associated with other types of social skills. Verbal underproductivity predicted follow-up social skills, social engagement, and friendships, accounting for more variance than cognition or symptoms. In contrast to social outcomes, adaptive outcomes were predicted by baseline neurocognition and clinical symptoms, but not communication abnormalities. These findings provide evidence for specific relationships of communication disorder subtypes with diverse impairments in social functions. In this chronically institutionalized sample, communication disorder was a stronger predictor of social, but not adaptive, outcomes than neurocognition or clinical symptoms. PMID:18571378

  6. Molecular Evolution and Functional Characterization of a Bifunctional Decarboxylase Involved in Lycopodium Alkaloid Biosynthesis.

    PubMed

    Bunsupa, Somnuk; Hanada, Kousuke; Maruyama, Akira; Aoyagi, Kaori; Komatsu, Kana; Ueno, Hideki; Yamashita, Madoka; Sasaki, Ryosuke; Oikawa, Akira; Saito, Kazuki; Yamazaki, Mami

    2016-08-01

    Lycopodium alkaloids (LAs) are derived from lysine (Lys) and are found mainly in Huperziaceae and Lycopodiaceae. LAs are potentially useful against Alzheimer's disease, schizophrenia, and myasthenia gravis. Here, we cloned the bifunctional lysine/ornithine decarboxylase (L/ODC), the first gene involved in LA biosynthesis, from the LA-producing plants Lycopodium clavatum and Huperzia serrata We describe the in vitro and in vivo functional characterization of the L. clavatum L/ODC (LcL/ODC). The recombinant LcL/ODC preferentially catalyzed the decarboxylation of l-Lys over l-ornithine (l-Orn) by about 5 times. Transient expression of LcL/ODC fused with the amino or carboxyl terminus of green fluorescent protein, in onion (Allium cepa) epidermal cells and Nicotiana benthamiana leaves, showed LcL/ODC localization in the cytosol. Transgenic tobacco (Nicotiana tabacum) hairy roots and Arabidopsis (Arabidopsis thaliana) plants expressing LcL/ODC enhanced the production of a Lys-derived alkaloid, anabasine, and cadaverine, respectively, thus, confirming the function of LcL/ODC in plants. In addition, we present an example of the convergent evolution of plant Lys decarboxylase that resulted in the production of Lys-derived alkaloids in Leguminosae (legumes) and Lycopodiaceae (clubmosses). This convergent evolution event probably occurred via the promiscuous functions of the ancestral Orn decarboxylase, which is an enzyme involved in the primary metabolism of polyamine. The positive selection sites were detected by statistical analyses using phylogenetic trees and were confirmed by site-directed mutagenesis, suggesting the importance of those sites in granting the promiscuous function to Lys decarboxylase while retaining the ancestral Orn decarboxylase function. This study contributes to a better understanding of LA biosynthesis and the molecular evolution of plant Lys decarboxylase. © 2016 American Society of Plant Biologists. All Rights Reserved.

  7. Molecular Evolution and Functional Characterization of a Bifunctional Decarboxylase Involved in Lycopodium Alkaloid Biosynthesis1[OPEN

    PubMed Central

    Bunsupa, Somnuk; Hanada, Kousuke; Maruyama, Akira; Aoyagi, Kaori; Komatsu, Kana; Ueno, Hideki; Yamashita, Madoka; Sasaki, Ryosuke; Oikawa, Akira; Yamazaki, Mami

    2016-01-01

    Lycopodium alkaloids (LAs) are derived from lysine (Lys) and are found mainly in Huperziaceae and Lycopodiaceae. LAs are potentially useful against Alzheimer’s disease, schizophrenia, and myasthenia gravis. Here, we cloned the bifunctional lysine/ornithine decarboxylase (L/ODC), the first gene involved in LA biosynthesis, from the LA-producing plants Lycopodium clavatum and Huperzia serrata. We describe the in vitro and in vivo functional characterization of the L. clavatum L/ODC (LcL/ODC). The recombinant LcL/ODC preferentially catalyzed the decarboxylation of l-Lys over l-ornithine (l-Orn) by about 5 times. Transient expression of LcL/ODC fused with the amino or carboxyl terminus of green fluorescent protein, in onion (Allium cepa) epidermal cells and Nicotiana benthamiana leaves, showed LcL/ODC localization in the cytosol. Transgenic tobacco (Nicotiana tabacum) hairy roots and Arabidopsis (Arabidopsis thaliana) plants expressing LcL/ODC enhanced the production of a Lys-derived alkaloid, anabasine, and cadaverine, respectively, thus, confirming the function of LcL/ODC in plants. In addition, we present an example of the convergent evolution of plant Lys decarboxylase that resulted in the production of Lys-derived alkaloids in Leguminosae (legumes) and Lycopodiaceae (clubmosses). This convergent evolution event probably occurred via the promiscuous functions of the ancestral Orn decarboxylase, which is an enzyme involved in the primary metabolism of polyamine. The positive selection sites were detected by statistical analyses using phylogenetic trees and were confirmed by site-directed mutagenesis, suggesting the importance of those sites in granting the promiscuous function to Lys decarboxylase while retaining the ancestral Orn decarboxylase function. This study contributes to a better understanding of LA biosynthesis and the molecular evolution of plant Lys decarboxylase. PMID:27303024

  8. Does cost-benefit analysis or self-control predict involvement in two forms of aggression?

    PubMed

    Archer, John; Fernández-Fuertes, Andrés A; Thanzami, Van Lal

    2010-01-01

    The main aim of this research was to assess the relative association between physical aggression and (1) self-control and (2) cost-benefit assessment, these variables representing the operation of impulsive and reflective processes. Study 1 involved direct and indirect aggression among young Indian men, and Study 2 physical aggression to dating partners among Spanish adolescents. In Study 1, perceived benefits and costs but not self-control were associated with direct aggression at other men, and the association remained when their close association with indirect aggression was controlled. In Study 2, benefits and self-control showed significant and independent associations (positive for benefits, negative for self-control) with physical aggression at other-sex partners. Although being victimized was also correlated in the same direction with self-control and benefits, perpetration and being victimized were highly correlated, and there was no association between being victimized and these variables when perpetration was controlled. These results support the theory that reflective (cost-benefit analyses) processes and impulsive (self-control) processes operate in parallel in affecting aggression. The finding that male adolescents perceived more costs and fewer benefits from physical aggression to a partner than female adolescents did is consistent with findings indicating greater social disapproval of men hitting women than vice versa, rather than with the view that male violence to women is facilitated by internalized patriarchal values. (c) 2010 Wiley-Liss, Inc.

  9. Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map.

    PubMed

    Collins, Sean R; Miller, Kyle M; Maas, Nancy L; Roguev, Assen; Fillingham, Jeffrey; Chu, Clement S; Schuldiner, Maya; Gebbia, Marinella; Recht, Judith; Shales, Michael; Ding, Huiming; Xu, Hong; Han, Junhong; Ingvarsdottir, Kristin; Cheng, Benjamin; Andrews, Brenda; Boone, Charles; Berger, Shelley L; Hieter, Phil; Zhang, Zhiguo; Brown, Grant W; Ingles, C James; Emili, Andrew; Allis, C David; Toczyski, David P; Weissman, Jonathan S; Greenblatt, Jack F; Krogan, Nevan J

    2007-04-12

    Defining the functional relationships between proteins is critical for understanding virtually all aspects of cell biology. Large-scale identification of protein complexes has provided one important step towards this goal; however, even knowledge of the stoichiometry, affinity and lifetime of every protein-protein interaction would not reveal the functional relationships between and within such complexes. Genetic interactions can provide functional information that is largely invisible to protein-protein interaction data sets. Here we present an epistatic miniarray profile (E-MAP) consisting of quantitative pairwise measurements of the genetic interactions between 743 Saccharomyces cerevisiae genes involved in various aspects of chromosome biology (including DNA replication/repair, chromatid segregation and transcriptional regulation). This E-MAP reveals that physical interactions fall into two well-represented classes distinguished by whether or not the individual proteins act coherently to carry out a common function. Thus, genetic interaction data make it possible to dissect functionally multi-protein complexes, including Mediator, and to organize distinct protein complexes into pathways. In one pathway defined here, we show that Rtt109 is the founding member of a novel class of histone acetyltransferases responsible for Asf1-dependent acetylation of histone H3 on lysine 56. This modification, in turn, enables a ubiquitin ligase complex containing the cullin Rtt101 to ensure genomic integrity during DNA replication.

  10. Prediction of Chemical Function: Model Development and Application

    EPA Science Inventory

    The United States Environmental Protection Agency’s Exposure Forecaster (ExpoCast) project is developing both statistical and mechanism-based computational models for predicting exposures to thousands of chemicals, including those in consumer products. The high-throughput (...

  11. firestar—advances in the prediction of functionally important residues

    PubMed Central

    Lopez, Gonzalo; Maietta, Paolo; Rodriguez, Jose Manuel; Valencia, Alfonso; Tress, Michael L.

    2011-01-01

    firestar is a server for predicting catalytic and ligand-binding residues in protein sequences. Here, we present the important developments since the first release of firestar. Previous versions of the server required human interpretation of the results; the server is now fully automatized. firestar has been implemented as a web service and can now be run in high-throughput mode. Prediction coverage has been greatly improved with the extension of the FireDB database and the addition of alignments generated by HHsearch. Ligands in FireDB are now classified for biological relevance. Many of the changes have been motivated by the critical assessment of techniques for protein structure prediction (CASP) ligand-binding prediction experiment, which provided us with a framework to test the performance of firestar. URL: http://firedb.bioinfo.cnio.es/Php/FireStar.php. PMID:21672959

  12. firestar--advances in the prediction of functionally important residues.

    PubMed

    Lopez, Gonzalo; Maietta, Paolo; Rodriguez, Jose Manuel; Valencia, Alfonso; Tress, Michael L

    2011-07-01

    firestar is a server for predicting catalytic and ligand-binding residues in protein sequences. Here, we present the important developments since the first release of firestar. Previous versions of the server required human interpretation of the results; the server is now fully automatized. firestar has been implemented as a web service and can now be run in high-throughput mode. Prediction coverage has been greatly improved with the extension of the FireDB database and the addition of alignments generated by HHsearch. Ligands in FireDB are now classified for biological relevance. Many of the changes have been motivated by the critical assessment of techniques for protein structure prediction (CASP) ligand-binding prediction experiment, which provided us with a framework to test the performance of firestar. URL: http://firedb.bioinfo.cnio.es/Php/FireStar.php.

  13. Prediction of Chemical Function: Model Development and Application

    EPA Science Inventory

    The United States Environmental Protection Agency’s Exposure Forecaster (ExpoCast) project is developing both statistical and mechanism-based computational models for predicting exposures to thousands of chemicals, including those in consumer products. The high-throughput (...

  14. Modularity in the gain and loss of genes: applications for function prediction.

    PubMed

    Ettema, T; van der Oost, J; Huynen, M

    2001-09-01

    Genes that are clustered on multiple genomes and are likely to functionally interact tend to be gained or lost together during genome evolution. Here, we demonstrate that exceptions to this pattern indicate relatively distant functional interactions between the encoded proteins. Hence, this can be used to divide predicted clusters of functionally interacting proteins into sub-clusters, and as such, to refine the prediction of their function and functional interactions.

  15. Clinicopathologic features predicting involvement of non- sentinel axillary lymph nodes in Iranian women with breast cancer.

    PubMed

    Moosavi, Seyed Alireza; Abdirad, Afshin; Omranipour, Ramesh; Hadji, Maryam; Razavi, Amirnader Emami; Najafi, Massoome

    2014-01-01

    Almost half of the breast cancer patients with positive sentinel lymph nodes have no additional disease in the remaining axillary lymph nodes. This group of patients do not benefit from complete axillary lymph node dissection. This study was designed to assess the clinicopathologic factors that predict non-sentinel lymph node metastasis in Iranian breast cancer patients with positive sentinel lymph nodes. The records of patients who underwent sentinel lymph node biopsy, between 2003 and 2012, were reviewed. Patients with at least one positive sentinel lymph node who underwent completion axillary lymph node dissection were enrolled in the present study. Demographic and clinicopathologic characteristics including age, primary tumor size, histological and nuclear grade, lymphovascular invasion, perineural invasion, extracapsular invasion, and number of harvested lymph nodes, were evaluated. The data of 167 patients were analyzed. A total of 92 (55.1%) had non-sentinel lymph node metastasis. Univariate analysis of data revealed that age, primary tumor size, histological grade, lymphovascular invasion, perineural invasion, extracapsular invasion, and the number of positive sentinel lymph nodes to the total number of harvested sentinel lymph nodes ratio, were associated with non-sentinel lymph node metastasis. After logistic regression analysis, age (OR=0.13; 95% CI, 0.02-0.8), primary tumor size (OR=7.7; 95% CI, 1.4-42.2), lymphovascular invasion (OR=19.4; 95% CI, 1.4- 268.6), extracapsular invasion (OR=13.3; 95% CI, 2.3-76), and the number of positive sentinel lymph nodes to the total number of harvested sentinel lymph nodes ratio (OR=20.2; 95% CI, 3.4-121.9), were significantly associated with non-sentinel lymph node metastasis. According to this study, age, primary tumor size, lymphovascular invasion, extracapsular invasion, and the ratio of positive sentinel lymph nodes to the total number of harvested sentinel lymph nodes, were found to be independent predictors of

  16. Predicting extracapsular involvement in prostate cancer through the tumor contact length and the apparent diffusion coefficient.

    PubMed

    Granja, M F; Pedraza, C M; Flórez, D C; Romero, J A; Palau, M A; Aguirre, D A

    To evaluate the diagnostic performance of the length of the tumor contact with the capsule (LTC) and the apparent diffusion coefficient (ADC) map in the prediction of microscopic extracapsular extension in patients with prostate cancer who are candidates for radical prostatectomy. We used receiver operating curves to retrospectively study the diagnostic performance of the ADC map and the LTC as predictors of microscopic extracapsular extension in 92 patients with prostate cancer and moderate to high risk who were examined between May 2011 and December 2013. The optimal cutoff for the ADC map was 0.87× 10(-3) mm(2)/s, which yielded an area under the ROC curve of 72% (95% CI: 57%-86%), corresponding to a sensitivity of 83% and a specificity of 61%. The optimal cutoff for the LTC was 17.5mm, which yielded an area under the ROC curve of 74% (95% CI: 61%-87%), corresponding to a sensitivity of 91% and a specificity of 57%. Combining the two criteria improved the diagnostic performance, yielding an area under the ROC curve of 77% (95% CI: 62%-92%), corresponding to a sensitivity of 77% and a specificity of 61%. We elaborated a logistic regression model, obtaining an area under the ROC curve of 82% (95% CI: 73%-93%). Using quantitative measures improves the diagnostic accuracy of multiparametric magnetic resonance imaging in the staging of prostate cancer. The values of the ADC and LTC were predictors of microscopic extracapsular extension, and the best results were obtained when both values were used in combination. Copyright © 2017 SERAM. Publicado por Elsevier España, S.L.U. All rights reserved.

  17. Predicting the Risk of Pelvic Node Involvement Among Men With Prostate Cancer in the Contemporary Era

    SciTech Connect

    Nguyen, Paul L. Chen, M.-H.; Hoffman, Karen E.; Katz, Matthew S.; D'Amico, Anthony V.

    2009-05-01

    Purpose: The 'Roach formula' for the risk of pelvic lymph node metastases [(2/3) * PSA + (Gleason score - 6) * 10] was developed in the early prostate-specific antigen (PSA) era. We examined the accuracy of this formula in contemporary patients. Methods: We included men in the Surveillance, Epidemiology, and End Results Registry with a diagnosis of clinical T1c-T4 prostate cancer in 2004 who had a surgical lymph node evaluation, Gleason score (typically from prostatectomy), and baseline PSA level (n = 9,387). Expected and observed rates of node positivity were compared. Results: Ninety-eight percent were clinical T1c/T2, and 97% underwent prostatectomy. Overall, 309 patients (3.29%) had positive lymph nodes. Roach scores overestimated the actual rate of positive lymph nodes in the derivation set by 16-fold for patients with Roach score less than or equal to 10%, by 7-fold for scores greater than 10-20%, and by approximately 2.5-fold for scores greater than 20%. Applying these adjustment factors to Roach scores in the validation data set yielded accurate predictions of risk. For those with Roach score less than or equal to 10%, adjusted expected risk was 0.2% and observed risk was 0.2%. For Roach score greater than 10-20%, adjusted expected risk was 2.0% and observed risk was 2.1%. For Roach score greater than 20-30%, adjusted expected risk was 9.7% and observed risk was 6.5%. For Roach score greater than 30-40%, adjusted expected risk was 13.9% and observed risk was 13.9%. Conclusion: Applied to contemporary patients with mainly T1c/T2 disease, the Roach formula appears to overestimate pelvic lymph node risk. The adjustment factors presented here should be validated by using biopsy Gleason scores and extended lymphadenectomies.

  18. Towards quantifying the role of exact exchange in the prediction hydrogen bond spin-spin coupling constants involving fluorine

    NASA Astrophysics Data System (ADS)

    San Fabián, J.; Omar, S.; García de la Vega, J. M.

    2016-08-01

    The effect of a fraction of Hartree-Fock exchange on the calculated spin-spin coupling constants involving fluorine through a hydrogen bond is analyzed in detail. Coupling constants calculated using wavefunction methods are revisited in order to get high-level calculations using the same basis set. Accurate MCSCF results are obtained using an additive approach. These constants and their contributions are used as a reference for density functional calculations. Within the density functional theory, the Hartree-Fock exchange functional is split in short- and long-range using a modified version of the Coulomb-attenuating method with the SLYP functional as well as with the original B3LYP. Results support the difficulties for calculating hydrogen bond coupling constants using density functional methods when fluorine nuclei are involved. Coupling constants are very sensitive to the Hartree-Fock exchange and it seems that, contrary to other properties, it is important to include this exchange for short-range interactions. Best functionals are tested in two different groups of complexes: those related with anionic clusters of type [F(HF)n]- and those formed by difluoroacetylene and either one or two hydrogen fluoride molecules.

  19. Dominant bacterial phyla in caves and their predicted functional roles in C and N cycle.

    PubMed

    De Mandal, Surajit; Chatterjee, Raghunath; Kumar, Nachimuthu Senthil

    2017-04-11

    Bacteria present in cave often survive by modifying their metabolic pathway or other mechanism. Understanding these adopted bacteria and their survival strategy inside the cave is an important aspect of microbial ecology. Present study focuses on the bacterial community and geochemistry in five caves of Mizoram, Northeast India. The objective of this study was to explore the taxonomic composition and presumed functional diversity of cave sediment metagenomes using paired end Illumina sequencing using V3 region of 16S rRNA gene and bioinformatics pipeline. Actinobacteria, Proteobacteria, Verrucomicrobia and Acidobacteria were the major phyla in all the five cave sediment samples. Among the five caves the highest diversity is found in Lamsialpuk with a Shannon index 12.5 and the lowest in Bukpuk (Shannon index 8.22). In addition, imputed metagenomic approach was used to predict the functional role of microbial community in biogeochemical cycling in the cave environments. Functional module showed high representation of genes involved in Amino Acid Metabolism in (20.9%) and Carbohydrate Metabolism (20.4%) in the KEGG pathways. Genes responsible for carbon degradation, carbon fixation, methane metabolism, nitrification, nitrate reduction and ammonia assimilation were also predicted in the present study. The cave sediments of the biodiversity hotspot region possessing a oligotrophic environment harbours high phylogenetic diversity dominated by Actinobacteria and Proteobacteria. Among the geochemical factors, ferric oxide was correlated with increased microbial diversity. In-silico analysis detected genes involved in carbon, nitrogen, methane metabolism and complex metabolic pathways responsible for the survival of the bacterial community in nutrient limited cave environments. Present study with Paired end Illumina sequencing along with bioinformatics analysis revealed the essential ecological role of the cave bacterial communities. These results will be useful in

  20. Neural Networks Involved in Adolescent Reward Processing: An Activation Likelihood Estimation Meta-Analysis of Functional Neuroimaging Studies

    PubMed Central

    Silverman, Merav H.; Jedd, Kelly; Luciana, Monica

    2015-01-01

    Behavioral responses to, and the neural processing of, rewards change dramatically during adolescence and may contribute to observed increases in risk-taking during this developmental period. Functional MRI (fMRI) studies suggest differences between adolescents and adults in neural activation during reward processing, but findings are contradictory, and effects have been found in non-predicted directions. The current study uses an activation likelihood estimation (ALE) approach for quantitative meta-analysis of functional neuroimaging studies to: 1) confirm the network of brain regions involved in adolescents’ reward processing, 2) identify regions involved in specific stages (anticipation, outcome) and valence (positive, negative) of reward processing, and 3) identify differences in activation likelihood between adolescent and adult reward-related brain activation. Results reveal a subcortical network of brain regions involved in adolescent reward processing similar to that found in adults with major hubs including the ventral and dorsal striatum, insula, and posterior cingulate cortex (PCC). Contrast analyses find that adolescents exhibit greater likelihood of activation in the insula while processing anticipation relative to outcome and greater likelihood of activation in the putamen and amygdala during outcome relative to anticipation. While processing positive compared to negative valence, adolescents show increased likelihood for activation in the posterior cingulate cortex (PCC) and ventral striatum. Contrasting adolescent reward processing with the existing ALE of adult reward processing (Liu et al., 2011) reveals increased likelihood for activation in limbic, frontolimbic, and striatal regions in adolescents compared with adults. Unlike adolescents, adults also activate executive control regions of the frontal and parietal lobes. These findings support hypothesized elevations in motivated activity during adolescence. PMID:26254587

  1. Variations in pelvic dimensions do not predict the risk of circumferential resection margin (CRM) involvement in rectal cancer.

    PubMed

    Salerno, G; Daniels, I R; Brown, G; Norman, A R; Moran, B J; Heald, R J

    2007-06-01

    The objective of this study was to assess the value of preoperative pelvimetry, using magnetic resonance imaging (MRI), in predicting the risk of an involved circumferential resection margin (CRM) in a group of patients with operable rectal cancer. A cohort of 186 patients from the MERCURY study was selected. These patients' histological CRM status was compared against 14 pelvimetry parameters measured from the preoperative MRI. These measurements were taken by one of the investigators (G.S.), who was blinded to the final CRM status. There was no correlation between the pelvimetry and the CRM status. However, there was a difference in the height of the rectal cancer and the positive CRM rate (p = 0.011). Of 61 patients with low rectal cancer, 10 had positive CRM at histology (16.4% with CI 8.2%-22.1%) compared with 5 of 110 patients with mid/upper rectal cancers (4.5% with CI 0.7%-8.4%). Magnetic resonance imaging can predict clear margins in most cases of rectal cancer. Circumferential resection margin positivity cannot be predicted from pelvimetry in patients with rectal cancer selected for curative surgery. The only predictive factor for a positive CRM in the patients studied was tumor height.

  2. Exploring the Use of a Participative Design in the Early Development of a Predictive Test: The Importance of Physician Involvement.

    PubMed

    Veilleux, Sophie; Villeneuve, Maude; Lachapelle, Nathalie; Kohen, Rita; Vachon, Luc; White Guay, Brian; Rioux, John D; Bitton, Alain

    2017-08-17

    In this study, we contribute to the personalized medicine and health care management literature by developing and testing a new participative design approach. We propose that involving gastroenterologists in the development of a predictive test to assist them in their clinical decision-making process for the treatment of inflammatory bowel diseases will increase the likelihood of their acceptance of the innovation. Based on data obtained from 6 focus groups across Canada from a total of 28 physicians, analyses reveal that current tools do not enable discriminating between treatment options to find the best fit for each patient. Physicians expect a new predictive tool to have the capability of showing clear reliability and significant benefits for the patient, while being accessible in a timely manner that facilitates clinical decisions. Physicians also insist on their key role in the implementation process, hence confirming the relevance and importance of participative designs in personalized medicine. © 2017 S. Karger AG, Basel.

  3. On-scene factors that predict severe injury of patients involved in frontal crashes of passenger cars.

    PubMed

    Kim, S C; Lee, K H; Choi, H Y; Noble, J; Lee, K; Jeon, H J

    2016-07-28

    We sought to determine on-scene factors that predict severe injury to the occupants of passenger cars involved in frontal crashes. From January 2011 to December 2014, we collected data from patients who were taken to two emergency centres following a frontal motor vehicle crash. Binomial logistic regression was used to model the effects of occupant characteristics (sex, age, body mass index), vehicle damage (according to the collision deformation classification code), and safety devices on severe injuries (injury severity score >15). Of 344 subjects, 75 (21.8 %) had severe injuries. Sex, seat belt status, extent of vertical crash, intrusion, and deformation extent (DE) were significantly different between severe and non-severe injuries. After adjusting for confounders, non-use of seat belt tripled the odds of severe injury [odds ratio (OR) 2.7, 95 % confidence interval (CI) 1.461-5.105]. DE ≥4 and intrusion increased the risk of severe injury (OR 2.4, 95 % CI 1.120-5.204 and OR 5.2, 95 % CI 2.525-10.780, respectively). A combination model to predict severe injury using intrusion, seat belt use, and DE ≥4 demonstrated 56.0 % sensitivity, 88.9 % specificity, and 58.4 % positive predictive value (AUC = 0.781, 95 % CI 0.734-0.824). For passenger cars involved in a frontal crash, intrusion, unbelted status, and DE ≥4 are good predictors of severe injury. Sequential criteria using vehicle DE, seat belt use, and intrusion can be used by first responders to triage patients involved in a frontal collision.

  4. Metataxonomic profiling and prediction of functional behaviour of wheat straw degrading microbial consortia.

    PubMed

    Jiménez, Diego Javier; Dini-Andreote, Francisco; van Elsas, Jan Dirk

    2014-01-01

    Mixed microbial cultures, in which bacteria and fungi interact, have been proposed as an efficient way to deconstruct plant waste. The characterization of specific microbial consortia could be the starting point for novel biotechnological applications related to the efficient conversion of lignocellulose to cello-oligosaccharides, plastics and/or biofuels. Here, the diversity, composition and predicted functional profiles of novel bacterial-fungal consortia are reported, on the basis of replicated aerobic wheat straw enrichment cultures. In order to set up biodegradative microcosms, microbial communities were retrieved from a forest soil and introduced into a mineral salt medium containing 1% of (un)treated wheat straw. Following each incubation step, sequential transfers were carried out using 1 to 1,000 dilutions. The microbial source next to three sequential batch cultures (transfers 1, 3 and 10) were analyzed by bacterial 16S rRNA gene and fungal ITS1 pyrosequencing. Faith's phylogenetic diversity values became progressively smaller from the inoculum to the sequential batch cultures. Moreover, increases in the relative abundances of Enterobacteriales, Pseudomonadales, Flavobacteriales and Sphingobacteriales were noted along the enrichment process. Operational taxonomic units affiliated with Acinetobacter johnsonii, Pseudomonas putida and Sphingobacterium faecium were abundant and the underlying strains were successfully isolated. Interestingly, Klebsiella variicola (OTU1062) was found to dominate in both consortia, whereas K. variicola-affiliated strains retrieved from untreated wheat straw consortia showed endoglucanase/xylanase activities. Among the fungal players with high biotechnological relevance, we recovered members of the genera Penicillium, Acremonium, Coniochaeta and Trichosporon. Remarkably, the presence of peroxidases, alpha-L-fucosidases, beta-xylosidases, beta-mannases and beta-glucosidases, involved in lignocellulose degradation, was indicated

  5. Metataxonomic profiling and prediction of functional behaviour of wheat straw degrading microbial consortia

    PubMed Central

    2014-01-01

    Background Mixed microbial cultures, in which bacteria and fungi interact, have been proposed as an efficient way to deconstruct plant waste. The characterization of specific microbial consortia could be the starting point for novel biotechnological applications related to the efficient conversion of lignocellulose to cello-oligosaccharides, plastics and/or biofuels. Here, the diversity, composition and predicted functional profiles of novel bacterial-fungal consortia are reported, on the basis of replicated aerobic wheat straw enrichment cultures. Results In order to set up biodegradative microcosms, microbial communities were retrieved from a forest soil and introduced into a mineral salt medium containing 1% of (un)treated wheat straw. Following each incubation step, sequential transfers were carried out using 1 to 1,000 dilutions. The microbial source next to three sequential batch cultures (transfers 1, 3 and 10) were analyzed by bacterial 16S rRNA gene and fungal ITS1 pyrosequencing. Faith’s phylogenetic diversity values became progressively smaller from the inoculum to the sequential batch cultures. Moreover, increases in the relative abundances of Enterobacteriales, Pseudomonadales, Flavobacteriales and Sphingobacteriales were noted along the enrichment process. Operational taxonomic units affiliated with Acinetobacter johnsonii, Pseudomonas putida and Sphingobacterium faecium were abundant and the underlying strains were successfully isolated. Interestingly, Klebsiella variicola (OTU1062) was found to dominate in both consortia, whereas K. variicola-affiliated strains retrieved from untreated wheat straw consortia showed endoglucanase/xylanase activities. Among the fungal players with high biotechnological relevance, we recovered members of the genera Penicillium, Acremonium, Coniochaeta and Trichosporon. Remarkably, the presence of peroxidases, alpha-L-fucosidases, beta-xylosidases, beta-mannases and beta-glucosidases, involved in lignocellulose

  6. Involvement of brain serotonergic function in lidocaine-induced convulsions in mice.

    PubMed

    Endo, K; Morita, K; Uchiyama, Y; Takada, K; Tsujimoto, A; Dohi, T

    1993-07-01

    Influences of drug-induced manipulations of central serotonergic function on lidocaine- and pentylenetetrazol (PTZ)-induced convulsions were examined in mice. Agents that suppressed serotonergic transmission increased, whereas drugs that facilitated serotonin (5-HT) function decreased the incidence of lidocaine-induced convulsions. These treatments had similar influences on the incidence of PTZ-induced convulsions. Lidocaine (10(-5)-10(-3) M) reduced the stimulation evoked [3H]5-HT release from cortical slices, followed with an increased spontaneous [3H] overflow at higher concentrations. These results may suggest that brain 5-HT neurons are causally involved as inhibitory neurons in lidocaine-induced convulsions as in the case of PTZ-induced convulsions.

  7. Exercise Influence on Hippocampal Function: Possible Involvement of Orexin-A

    PubMed Central

    Chieffi, Sergio; Messina, Giovanni; Villano, Ines; Messina, Antonietta; Esposito, Maria; Monda, Vincenzo; Valenzano, Anna; Moscatelli, Fiorenzo; Esposito, Teresa; Carotenuto, Marco; Viggiano, Andrea; Cibelli, Giuseppe; Monda, Marcellino

    2017-01-01

    In the present article, we provide a brief review of current knowledge regarding the effects induced by physical exercise on hippocampus. Research involving animals and humans supports the view that physical exercise, enhancing hippocampal neurogenesis and function, improves cognition, and regulates mood. These beneficial effects depend on the contribute of more factors including the enhancement of vascularization and upregulation of growth factors. Among these, the BDNF seems to play a significant role. Another putative factor that might contribute to beneficial effects of exercise is the orexin-A. In support of this hypothesis there are the following observations: (1) orexin-A enhances hippocampal neurogenesis and function and (2) the levels of orexin-A increase with physical exercise. The beneficial effects of exercise may represent an important resource to hinder the cognitive decline associated with the aging-related hippocampal deterioration and ameliorate depressive symptoms. PMID:28261108

  8. Predicting Transfer Performance: A Comparison of Competing Function Learning Models

    ERIC Educational Resources Information Center

    McDaniel, Mark A.; Dimperio, Eric; Griego, Jacqueline A.; Busemeyer, Jerome R.

    2009-01-01

    The population of linear experts (POLE) model suggests that function learning and transfer are mediated by activation of a set of prestored linear functions that together approximate the given function (Kalish, Lewandowsky, & Kruschke, 2004). In the extrapolation-association (EXAM) model, an exemplar-based architecture associates trained input…

  9. Predicting Transfer Performance: A Comparison of Competing Function Learning Models

    ERIC Educational Resources Information Center

    McDaniel, Mark A.; Dimperio, Eric; Griego, Jacqueline A.; Busemeyer, Jerome R.

    2009-01-01

    The population of linear experts (POLE) model suggests that function learning and transfer are mediated by activation of a set of prestored linear functions that together approximate the given function (Kalish, Lewandowsky, & Kruschke, 2004). In the extrapolation-association (EXAM) model, an exemplar-based architecture associates trained input…

  10. Functional connectivity between brain regions involved in learning words of a new language.

    PubMed

    Veroude, Kim; Norris, David G; Shumskaya, Elena; Gullberg, Marianne; Indefrey, Peter

    2010-04-01

    Previous studies have identified several brain regions that appear to be involved in the acquisition of novel word forms. Standard word-by-word presentation is often used although exposure to a new language normally occurs in a natural, real world situation. In the current experiment we investigated naturalistic language exposure and applied a model-free analysis for hemodynamic-response data. Functional connectivity, temporal correlations between hemodynamic activity of different areas, was assessed during rest before and after presentation of a movie of a weather report in Mandarin Chinese to Dutch participants. We hypothesized that learning of novel words might be associated with stronger functional connectivity of regions that are involved in phonological processing. Participants were divided into two groups, learners and non-learners, based on the scores on a post hoc word recognition task. The learners were able to recognize Chinese target words from the weather report, while the non-learners were not. In the first resting state period, before presentation of the movie, stronger functional connectivity was observed for the learners compared to the non-learners between the left supplementary motor area and the left precentral gyrus as well as the left insula and the left rolandic operculum, regions that are important for phonological rehearsal. After exposure to the weather report, functional connectivity between the left and right supramarginal gyrus was stronger for learners than for non-learners. This is consistent with a role of the left supramarginal gyrus in the storage of phonological forms. These results suggest both pre-existing and learning-induced differences between the two groups.

  11. Aquaporin-Mediated Water and Hydrogen Peroxide Transport Is Involved in Normal Human Spermatozoa Functioning.

    PubMed

    Laforenza, Umberto; Pellavio, Giorgia; Marchetti, Anna Lisa; Omes, Claudia; Todaro, Federica; Gastaldi, Giulia

    2016-12-30

    Different aquaporins (AQPs) are expressed in human sperm cells and with a different localization. Their function has been related to cell volume control in response to the osmotic changes encountered passing from the epididymal fluid to the cervical mucus or involved in the end stage of cytoplasm removal during sperm maturation. Recently, AQPs have also shown hydrogen peroxide (H₂O₂) permeability properties. Here, we investigate the expression, localization and functioning of AQPs in human sperm cells with particular attention to their role as peroxiporins in reactive oxygen species (ROS) scavenging in both normospermic and sub-fertile human subjects. Western blotting and immunocytochemistry were used to confirm and clarify the AQPs expression and localization. Water and H₂O₂ permeability was tested by stopped flow light scattering method and by the CM-H2DCFDA (5-(and-6)-chloromethyl-2',7'-dichlorodihydro-fluorescein diacetate, acetyl ester) H₂O₂ fluorescence probe, respectively. AQP3, -7, -8, and -11 proteins were found in human sperm cells and localized in the head (AQP7), in the middle piece (AQP8) and in the tail (AQP3 and -11) in both the plasma membrane and in intracellular structures. Sperm cells showed water and H₂O₂ permeability which was reversibly inhibited by H₂O₂, heat stress and the AQP inhibitor HgCl₂. Reduced functionality was observed in patients with compromised basal semen parameters. Present findings suggest that AQPs are involved in both volume regulation and ROS elimination. The relationship between sperm number and motility and AQP functioning was also demonstrated.

  12. Circadian misalignment, reward-related brain function, and adolescent alcohol involvement.

    PubMed

    Hasler, Brant P; Clark, Duncan B

    2013-04-01

    Developmental changes in sleep and circadian rhythms that occur during adolescence may contribute to reward-related brain dysfunction, and consequently increase the risk of alcohol use disorders (AUDs). This review (i) describes marked changes in circadian rhythms, reward-related behavior and brain function, and alcohol involvement that occur during adolescence, (ii) offers evidence that these parallel developmental changes are associated, and (iii) posits a conceptual model by which misalignment between sleep-wake timing and endogenous circadian timing may increase the risk of adolescent AUDs by altering reward-related brain function. The timing of sleep shifts later throughout adolescence, in part due to developmental changes in endogenous circadian rhythms, which tend to become more delayed. This tendency for delayed sleep and circadian rhythms is at odds with early school start times during secondary education, leading to misalignment between many adolescents' sleep-wake schedules and their internal circadian timing. Circadian misalignment is associated with increased alcohol use and other risk-taking behaviors, as well as sleep loss and sleep disturbance. Growing evidence indicates that circadian rhythms modulate the reward system, suggesting that circadian misalignment may impact adolescent alcohol involvement by altering reward-related brain function. Neurocognitive function is also subject to sleep and circadian influence, and thus circadian misalignment may also impair inhibitory control and other cognitive processes relevant to alcohol use. Specifically, circadian misalignment may further exacerbate the cortical-subcortical imbalance within the reward circuit, an imbalance thought to explain increased risk-taking and sensation-seeking during adolescence. Adolescent alcohol use is highly contextualized, however, and thus studies testing this model will also need to consider factors that may influence both circadian misalignment and alcohol use. This review

  13. Aquaporin-Mediated Water and Hydrogen Peroxide Transport Is Involved in Normal Human Spermatozoa Functioning

    PubMed Central

    Laforenza, Umberto; Pellavio, Giorgia; Marchetti, Anna Lisa; Omes, Claudia; Todaro, Federica; Gastaldi, Giulia

    2016-01-01

    Different aquaporins (AQPs) are expressed in human sperm cells and with a different localization. Their function has been related to cell volume control in response to the osmotic changes encountered passing from the epididymal fluid to the cervical mucus or involved in the end stage of cytoplasm removal during sperm maturation. Recently, AQPs have also shown hydrogen peroxide (H2O2) permeability properties. Here, we investigate the expression, localization and functioning of AQPs in human sperm cells with particular attention to their role as peroxiporins in reactive oxygen species (ROS) scavenging in both normospermic and sub-fertile human subjects. Western blotting and immunocytochemistry were used to confirm and clarify the AQPs expression and localization. Water and H2O2 permeability was tested by stopped flow light scattering method and by the CM-H2DCFDA (5-(and-6)-chloromethyl-2′,7′-dichlorodihydro-fluorescein diacetate, acetyl ester) H2O2 fluorescence probe, respectively. AQP3, -7, -8, and -11 proteins were found in human sperm cells and localized in the head (AQP7), in the middle piece (AQP8) and in the tail (AQP3 and -11) in both the plasma membrane and in intracellular structures. Sperm cells showed water and H2O2 permeability which was reversibly inhibited by H2O2, heat stress and the AQP inhibitor HgCl2. Reduced functionality was observed in patients with compromised basal semen parameters. Present findings suggest that AQPs are involved in both volume regulation and ROS elimination. The relationship between sperm number and motility and AQP functioning was also demonstrated. PMID:28042826

  14. Circadian Misalignment, Reward-Related Brain Function, and Adolescent Alcohol Involvement

    PubMed Central

    Hasler, Brant P.; Clark, Duncan B.

    2013-01-01

    Background Developmental changes in sleep and circadian rhythms that occur during adolescence may contribute to reward-related brain dysfunction, and consequently increase the risk of alcohol use disorders (AUDs). Methods This review (a) describes marked changes in circadian rhythms, reward-related behavior and brain function, and alcohol involvement that occur during adolescence, (b) offers evidence that these parallel developmental changes are associated, and (c) posits a conceptual model by which misalignment between sleep-wake timing and endogenous circadian timing may increase the risk of adolescent AUDs by altering reward-related brain function. Results The timing of sleep shifts later throughout adolescence, in part due to developmental changes in endogenous circadian rhythms, which tend to become more delayed. This tendency for delayed sleep and circadian rhythms is at odds with early school start times during secondary education, leading to misalignment between many adolescents’ sleep-wake schedules and their internal circadian timing. Circadian misalignment is associated with increased alcohol use and other risk-taking behaviors, as well as sleep loss and sleep disturbance. Growing evidence indicates that circadian rhythms modulate the reward system, suggesting that circadian misalignment may impact adolescent alcohol involvement by altering reward-related brain function. Neurocognitive function is also subject to sleep and circadian influence, and thus circadian misalignment may also impair inhibitory control and other cognitive processes relevant to alcohol use. Specifically, circadian misalignment may further exacerbate the cortical-subcortical imbalance within the reward circuit, an imbalance thought to explain increased risk-taking and sensation-seeking during adolescence. Adolescent alcohol use is highly contexualized, however, and thus studies testing this model will also need to consider factors that may influence both circadian misalignment and

  15. Obesity is marked by distinct functional connectivity in brain networks involved in food reward and salience.

    PubMed

    Wijngaarden, M A; Veer, I M; Rombouts, S A R B; van Buchem, M A; Willems van Dijk, K; Pijl, H; van der Grond, J

    2015-01-01

    We hypothesized that brain circuits involved in reward and salience respond differently to fasting in obese versus lean individuals. We compared functional connectivity networks related to food reward and saliency after an overnight fast (baseline) and after a prolonged fast of 48 h in lean versus obese subjects. We included 13 obese (2 males, 11 females, BMI 35.4 ± 1.2 kg/m(2), age 31 ± 3 years) and 11 lean subjects (2 males, 9 females, BMI 23.2 ± 0.5 kg/m(2), age 28 ± 3 years). Resting-state functional magnetic resonance imaging scans were made after an overnight fast (baseline) and after a prolonged 48 h fast. Functional connectivity of the amygdala, hypothalamus and posterior cingulate cortex (default-mode) networks was assessed using seed-based correlations. At baseline, we found a stronger connectivity between hypothalamus and left insula in the obese subjects. This effect diminished upon the prolonged fast. After prolonged fasting, connectivity of the hypothalamus with the dorsal anterior cingulate cortex (dACC) increased in lean subjects and decreased in obese subjects. Amygdala connectivity with the ventromedial prefrontal cortex was stronger in lean subjects at baseline, which did not change upon the prolonged fast. No differences in posterior cingulate cortex connectivity were observed. In conclusion, obesity is marked by alterations in functional connectivity networks involved in food reward and salience. Prolonged fasting differentially affected hypothalamic connections with the dACC and the insula between obese and lean subjects. Our data support the idea that food reward and nutrient deprivation are differently perceived and/or processed in obesity.

  16. Involvement of S6K1 in mitochondria function and structure in HeLa cells.

    PubMed

    Park, Jisoo; Tran, Quangdon; Mun, Kisun; Masuda, Kouhei; Kwon, So Hee; Kim, Seon-Hwan; Kim, Dong-Hoon; Thomas, George; Park, Jongsun

    2016-12-01

    The major biological function of mitochondria is to generate cellular energy through oxidative phosphorylation. Apart from cellular respiration, mitochondria also play a key role in signaling processes, including aging and cancer metabolism. It has been shown that S6K1-knockout mice are resistant to obesity due to enhanced beta-oxidation, with an increased number of large mitochondria. Therefore, in this report, the possible involvement of S6K1 in regulating mitochondria dynamics and function has been investigated in stable lenti-shS6K1-HeLa cells. Interestingly, S6K1-stably depleted HeLa cells showed phenotypical changes in mitochondria morphology. This observation was further confirmed by detailed image analysis of mitochondria shape. Corresponding molecular changes were also observed in these cells, such as the induction of mitochondrial fission proteins (Drp1 and Fis1). Oxygen consumption is elevated in S6K1-depeleted HeLa cells and FL5.12 cells. In addition, S6K1 depletion leads to enhancement of ATP production in cytoplasm and mitochondria. However, the relative ratio of mitochondrial ATP to cytoplasmic ATP is actually decreased in lenti-shS6K1-HeLa cells compared to control cells. Lastly, induction of mitophagy was found in lenti-shS6K1-HeLa cells with corresponding changes of mitochondria shape on electron microscope analysis. Taken together, our results indicate that S6K1 is involved in the regulation of mitochondria morphology and function in HeLa cells. This study will provide novel insights into S6K1 function in mitochondria-mediated cellular signaling.

  17. Increased involvement of the parahippocampal gyri in a sad mood predicts future depressive symptoms

    PubMed Central

    Huffziger, Silke; Ebner-Priemer, Ulrich; Kuehner, Christine; Kirsch, Peter

    2014-01-01

    Behavioral studies suggest a relationship between autobiographical memory, rumination and depression. The objective of this study was to determine whether remitted depressed patients show alterations in connectivity of the posterior cingulate cortex (PCC, a node in the default mode network) with the parahippocampal gyri (PHG, a region associated with autobiographical memory) while intensively recalling negative memories and whether this is related to daily life symptoms and to the further course of depression. Sad mood was induced with keywords of personal negative life events in participants with remitted depression (n = 29) and matched healthy controls (n = 29) during functional magnetic resonance imaging. Additionally, daily life assessments of mood and rumination and a 6-month follow-up were conducted. Remitted depressed participants showed greater connectivity than healthy controls of the PCC with the PHG, which was even stronger in patients with more previous episodes. Furthermore, patients with increased PCC–PHG connectivity showed a sadder mood and more rumination in daily life and a worsening of rumination and depression scores during follow-up. A relationship of negative autobiographical memory processing, rumination, sad mood and depression on a neural level seems likely. The identified increased connectivity probably indicates a ‘scar’ of recurrent depression and may represent a prognostic factor for future depression. PMID:24493842

  18. Cloud Prediction of Protein Structure and Function with PredictProtein for Debian

    PubMed Central

    Kaján, László; Yachdav, Guy; Vicedo, Esmeralda; Steinegger, Martin; Mirdita, Milot; Angermüller, Christof; Böhm, Ariane; Domke, Simon; Ertl, Julia; Mertes, Christian; Reisinger, Eva; Rost, Burkhard

    2013-01-01

    We report the release of PredictProtein for the Debian operating system and derivatives, such as Ubuntu, Bio-Linux, and Cloud BioLinux. The PredictProtein suite is available as a standard set of open source Debian packages. The release covers the most popular prediction methods from the Rost Lab, including methods for the prediction of secondary structure and solvent accessibility (profphd), nuclear localization signals (predictnls), and intrinsically disordered regions (norsnet). We also present two case studies that successfully utilize PredictProtein packages for high performance computing in the cloud: the first analyzes protein disorder for whole organisms, and the second analyzes the effect of all possible single sequence variants in protein coding regions of the human genome. PMID:23971032

  19. Cloud prediction of protein structure and function with PredictProtein for Debian.

    PubMed

    Kaján, László; Yachdav, Guy; Vicedo, Esmeralda; Steinegger, Martin; Mirdita, Milot; Angermüller, Christof; Böhm, Ariane; Domke, Simon; Ertl, Julia; Mertes, Christian; Reisinger, Eva; Staniewski, Cedric; Rost, Burkhard

    2013-01-01

    We report the release of PredictProtein for the Debian operating system and derivatives, such as Ubuntu, Bio-Linux, and Cloud BioLinux. The PredictProtein suite is available as a standard set of open source Debian packages. The release covers the most popular prediction methods from the Rost Lab, including methods for the prediction of secondary structure and solvent accessibility (profphd), nuclear localization signals (predictnls), and intrinsically disordered regions (norsnet). We also present two case studies that successfully utilize PredictProtein packages for high performance computing in the cloud: the first analyzes protein disorder for whole organisms, and the second analyzes the effect of all possible single sequence variants in protein coding regions of the human genome.

  20. FLOCK cluster analysis of plasma cell flow cytometry data predicts bone marrow involvement by plasma cell neoplasia.

    PubMed

    Dorfman, David M; LaPlante, Charlotte D; Li, Betty

    2016-09-01

    We analyzed plasma cell populations in bone marrow samples from 353 patients with possible bone marrow involvement by a plasma cell neoplasm, using FLOCK (FLOw Clustering without K), an unbiased, automated, computational approach to identify cell subsets in multidimensional flow cytometry data. FLOCK identified discrete plasma cell populations in the majority of bone marrow specimens found by standard histologic and immunophenotypic criteria to be involved by a plasma cell neoplasm (202/208 cases; 97%), including 34 cases that were negative by standard flow cytometric analysis that included clonality assessment. FLOCK identified discrete plasma cell populations in only a minority of cases negative for involvement by a plasma cell neoplasm by standard histologic and immunophenotypic criteria (38/145 cases; 26%). Interestingly, 55% of the cases negative by standard analysis, but containing a FLOCK-identified discrete plasma cell population, were positive for monoclonal gammopathy by serum protein electrophoresis and immunofixation. FLOCK-identified and quantitated plasma cell populations accounted for 3.05% of total cells on average in cases positive for involvement by a plasma cell neoplasm by standard histologic and immunophenotypic criteria, and 0.27% of total cells on average in cases negative for involvement by a plasma cell neoplasm by standard histologic and immunophenotypic criteria (p<0.0001; area under the curve by ROC analysis=0.96). The presence of a FLOCK-identified discrete plasma cell population was predictive of the presence of plasma cell neoplasia with a sensitivity of 97%, compared with only 81% for standard flow cytometric analysis, and had specificity of 74%, PPV of 84% and NPV of 95%. FLOCK analysis, which has been shown to provide useful diagnostic information for evaluating patients with suspected systemic mastocytosis, is able to identify neoplastic plasma cell populations analyzed by flow cytometry, and may be helpful in the diagnostic

  1. The prediction of EEG signals using a feedback-structured adaptive rational function filter.

    PubMed

    Kim, H S; Kim, T S; Choi, Y H; Park, S H

    2000-08-01

    In this article, we present a feedback-structured adaptive rational function filter based on a recursive modified Gram-Schmidt algorithm and apply it to the prediction of an EEG signal that has nonlinear and nonstationary characteristics. For the evaluation of the prediction performance, the proposed filter is compared with other methods, where a single-step prediction and a multi-step prediction are considered for a short-term prediction, and the prediction performance is assessed in normalized mean square error. The experimental results show that the proposed filter shows better performance than other methods considered for the short-term prediction of EEG signals.

  2. Functional brain imaging predicts public health campaign success.

    PubMed

    Falk, Emily B; O'Donnell, Matthew Brook; Tompson, Steven; Gonzalez, Richard; Dal Cin, Sonya; Strecher, Victor; Cummings, Kenneth Michael; An, Lawrence

    2016-02-01

    Mass media can powerfully affect health decision-making. Pre-testing through focus groups or surveys is a standard, though inconsistent, predictor of effectiveness. Converging evidence demonstrates that activity within brain systems associated with self-related processing can predict individual behavior in response to health messages. Preliminary evidence also suggests that neural activity in small groups can forecast population-level campaign outcomes. Less is known about the psychological processes that link neural activity and population-level outcomes, or how these predictions are affected by message content. We exposed 50 smokers to antismoking messages and used their aggregated neural activity within a 'self-localizer' defined region of medial prefrontal cortex to predict the success of the same campaign messages at the population level (n = 400,000 emails). Results demonstrate that: (i) independently localized neural activity during health message exposure complements existing self-report data in predicting population-level campaign responses (model combined R(2) up to 0.65) and (ii) this relationship depends on message content-self-related neural processing predicts outcomes in response to strong negative arguments against smoking and not in response to compositionally similar neutral images. These data advance understanding of the psychological link between brain and large-scale behavior and may aid the construction of more effective media health campaigns.

  3. Functional brain imaging predicts public health campaign success

    PubMed Central

    O’Donnell, Matthew Brook; Tompson, Steven; Gonzalez, Richard; Dal Cin, Sonya; Strecher, Victor; Cummings, Kenneth Michael; An, Lawrence

    2016-01-01

    Mass media can powerfully affect health decision-making. Pre-testing through focus groups or surveys is a standard, though inconsistent, predictor of effectiveness. Converging evidence demonstrates that activity within brain systems associated with self-related processing can predict individual behavior in response to health messages. Preliminary evidence also suggests that neural activity in small groups can forecast population-level campaign outcomes. Less is known about the psychological processes that link neural activity and population-level outcomes, or how these predictions are affected by message content. We exposed 50 smokers to antismoking messages and used their aggregated neural activity within a ‘self-localizer’ defined region of medial prefrontal cortex to predict the success of the same campaign messages at the population level (n = 400 000 emails). Results demonstrate that: (i) independently localized neural activity during health message exposure complements existing self-report data in predicting population-level campaign responses (model combined R2 up to 0.65) and (ii) this relationship depends on message content—self-related neural processing predicts outcomes in response to strong negative arguments against smoking and not in response to compositionally similar neutral images. These data advance understanding of the psychological link between brain and large-scale behavior and may aid the construction of more effective media health campaigns. PMID:26400858

  4. Nuclear pore proteins are involved in the biogenesis of functional tRNA.

    PubMed Central

    Simos, G; Tekotte, H; Grosjean, H; Segref, A; Sharma, K; Tollervey, D; Hurt, E C

    1996-01-01

    Los1p and Pus1p, which are involved in tRNA biogenesis, were found in a genetic screen for components interacting with the nuclear pore protein Nsp1p. LOS1, PUS1 and NSP1 interact functionally, since the combination of mutations in the three genes causes synthetic lethality. Pus1p is an intranuclear protein which exhibits a nucleotide-specific and intron-dependent tRNA pseudouridine synthase activity. Los1p was shown previously to be required for efficient pre-tRNA splicing; we report here that Los1p localizes to the nuclear pores and is linked functionally to several components of the tRNA biogenesis machinery including Pus1p and Tfc4p. When the formation of functional tRNA was analyzed by an in vivo assay, the los1(-) pus1(-) double mutant, as well as several thermosensitive nucleoporin mutants including nsp1, nup116, nup133 and nup85, exhibited loss of suppressor tRNA activity even at permissive temperatures. These data suggest that nuclear pore proteins are required for the biogenesis of functional tRNA. Images PMID:8641292

  5. The Ku70 DNA-repair protein is involved in centromere function in a grasshopper species.

    PubMed

    Cabrero, Josefa; Bakkali, Mohammed; Navarro-Domínguez, Beatriz; Ruíz-Ruano, Francisco J; Martín-Blázquez, Rubén; López-León, María Dolores; Camacho, Juan Pedro M

    2013-06-25

    The Ku70 protein is involved in numerous cell functions, the nonhomologous end joining (NHEJ) DNA repair pathway being the best known. Here, we report a novel function for this protein in the grasshopper Eyprepocnemis plorans. We observed the presence of large Ku70 foci on the centromeres of meiotic and mitotic chromosomes during the cell cycle stages showing the highest centromeric activity (i.e., metaphase and anaphase). The fact that colchicine treatment prevented centromeric location of Ku70, suggests a microtubule-dependent centromeric function for Ku70. Likewise, the absence of Ku70 at metaphase-anaphase centromeres from three males whose Ku70 gene had been knocked down using interference RNA, and the dramatic increase in the frequency of polyploid spermatids observed in these males, suggest that the centromeric presence of Ku70 is required for normal cytokinesis in this species. The centromeric function of Ku70 was not observed in 14 other grasshopper and locust species, or in the mouse, thus suggesting that it is an autapomorphy in E. plorans.

  6. Person perception involves functional integration between the extrastriate body area and temporal pole.

    PubMed

    Greven, Inez M; Ramsey, Richard

    2017-02-01

    The majority of human neuroscience research has focussed on understanding functional organisation within segregated patches of cortex. The ventral visual stream has been associated with the detection of physical features such as faces and body parts, whereas the theory-of-mind network has been associated with making inferences about mental states and underlying character, such as whether someone is friendly, selfish, or generous. To date, however, it is largely unknown how such distinct processing components integrate neural signals. Using functional magnetic resonance imaging and connectivity analyses, we investigated the contribution of functional integration to social perception. During scanning, participants observed bodies that had previously been associated with trait-based or neutral information. Additionally, we independently localised the body perception and theory-of-mind networks. We demonstrate that when observing someone who cues the recall of stored social knowledge compared to non-social knowledge, a node in the ventral visual stream (extrastriate body area) shows greater coupling with part of the theory-of-mind network (temporal pole). These results show that functional connections provide an interface between perceptual and inferential processing components, thus providing neurobiological evidence that supports the view that understanding the visual environment involves interplay between conceptual knowledge and perceptual processing.

  7. A biochemical and functional protein complex involving dopamine synthesis and transport into synaptic vesicles.

    PubMed

    Cartier, Etienne A; Parra, Leonardo A; Baust, Tracy B; Quiroz, Marisol; Salazar, Gloria; Faundez, Victor; Egaña, Loreto; Torres, Gonzalo E

    2010-01-15

    Synaptic transmission depends on neurotransmitter pools stored within vesicles that undergo regulated exocytosis. In the brain, the vesicular monoamine transporter-2 (VMAT(2)) is responsible for the loading of dopamine (DA) and other monoamines into synaptic vesicles. Prior to storage within vesicles, DA synthesis occurs at the synaptic terminal in a two-step enzymatic process. First, the rate-limiting enzyme tyrosine hydroxylase (TH) converts tyrosine to di-OH-phenylalanine. Aromatic amino acid decarboxylase (AADC) then converts di-OH-phenylalanine into DA. Here, we provide evidence that VMAT(2) physically and functionally interacts with the enzymes responsible for DA synthesis. In rat striata, TH and AADC co-immunoprecipitate with VMAT(2), whereas in PC 12 cells, TH co-immunoprecipitates with the closely related VMAT(1) and with overexpressed VMAT(2). GST pull-down assays further identified three cytosolic domains of VMAT(2) involved in the interaction with TH and AADC. Furthermore, in vitro binding assays demonstrated that TH directly interacts with VMAT(2). Additionally, using fractionation and immunoisolation approaches, we demonstrate that TH and AADC associate with VMAT(2)-containing synaptic vesicles from rat brain. These vesicles exhibited specific TH activity. Finally, the coupling between synthesis and transport of DA into vesicles was impaired in the presence of fragments involved in the VMAT(2)/TH/AADC interaction. Taken together, our results indicate that DA synthesis can occur at the synaptic vesicle membrane, where it is physically and functionally coupled to VMAT(2)-mediated transport into vesicles.

  8. Effect of ethylic alcohol on attentive functions involved in driving abilities.

    PubMed

    Bivona, Umberto; Garbarino, Sergio; Rigon, Jessica; Buzzi, Maria Gabriella; Onder, Graziano; Matteis, Maria; Catani, Sheila; Giustini, Marco; Mancardi, Giovanni Luigi; Formisano, Rita

    2015-01-01

    The burden of injuries due to drunk drivers has been estimated only indirectly. Indeed, alcohol is considered one of the most important contributing cause of car crash injuries and its effect on cognitive functions needs to be better elucidated. Aims of the study were i) to examine the effect of alcohol on attentive abilities involved while driving, and ii) to investigate whether Italian law limits for safe driving are sufficiently accurate to prevent risky behaviours and car crash risk while driving. We conducted a cross-over study at IRCCS Fondazione Santa Lucia Rehabilitation Hospital in Rome. Thirty-two healthy subjects were enrolled in this experiment. Participants were submitted to an attentive test battery assessing attention before taking Ethylic Alcohol (EA-) and after taking EA (EA+). In the EA+ condition subjects drank enough wine until the blood alcohol concentration, measured by means of Breath Analyzer, was equal to or higher than 0.5 g/l. Data analysis revealed that after alcohol assumption, tonic and phasic alertness, selective, divided attention and vigilance were significantly impaired when BAC level was at least 0.5 g/l. These data reveal that alcohol has a negative effect on attentive functions which are primarily involved in driving skills and that Italian law limits are adequate to prevent risky driving behaviour.

  9. Possible involvement of the cerebellum in motor-function impairment in progranulin-deficient mice.

    PubMed

    Matsuwaki, Takashi; Kobayashi, Akira; Mase, Kanade; Nakamura, Katsuyuki; Nakano, Shin-Ichi; Miyoshi, Takahiro; Yamanouchi, Keitaro; Nishihara, Masugi

    2015-09-30

    Progranulin (PGRN) is a multifunctional growth factor involved in many physiological and pathological processes in the brain such as sexual differentiation, neurogenesis, neuroinflammation, and neurodegeneration. Previously, we showed that PGRN was expressed broadly in the brain and the Purkinje cells in the cerebellum were one of the regions with the highest expression level of PGRN. Thus, in the present study, we investigated the possible roles of PGRN in the cerebellum by comparing wild-type (WT) and PGRN-deficient (KO) mice with immunohistochemical staining for calbindin, a marker of Purkinje cells. The results showed that the density of Purkinje cell dendrites in the molecular layer of the cerebellum was significantly higher in KO mice than in WT mice, although the number of cell bodies was comparable between the genotypes. Subsequently, as the cerebellum is the center of the motor function, we performed a rotarod test and found that KO mice remained on the rotating rod for significantly shorter periods than WT mice. However, KO and WT mice did not differ significantly with respect to the diameter of myofibers in a skeletal muscle. These results suggest that PGRN is involved in the development and/or maturation of neuronal networks comprising Purkinje cells in the cerebellum, which may be a prerequisite to normal motor function.

  10. Functional involvement of RFVT3/SLC52A3 in intestinal riboflavin absorption.

    PubMed

    Yoshimatsu, Hiroki; Yonezawa, Atsushi; Yao, Yoshiaki; Sugano, Kumiko; Nakagawa, Shunsaku; Omura, Tomohiro; Matsubara, Kazuo

    2014-01-01

    Riboflavin, also known as vitamin B2, is transported across the biological membrane into various organs by transport systems. Riboflavin transporter RFVT3 is expressed in the small intestine and has been suggested to localize in the apical membranes of the intestinal epithelial cells. In this study, we investigated the functional involvement of RFVT3 in riboflavin absorption using intestinal epithelial T84 cells and mouse small intestine. T84 cells expressed RFVT3 and conserved unidirectional riboflavin transport corresponding to intestinal absorption. Apical [(3)H]riboflavin uptake was pH-dependent in T84 cells. This uptake was not affected by Na(+) depletion at apical pH 6.0, although it was significantly decreased at apical pH 7.4. The [(3)H]riboflavin uptake from the apical side of T84 cells was prominently inhibited by the RFVT3 selective inhibitor methylene blue and significantly decreased by transfection of RFVT3-small-interfering RNA. In the gastrointestinal tract, RFVT3 was expressed in the jejunum and ileum. Mouse jejunal and ileal permeabilities of [(3)H]riboflavin were measured by the in situ closed-loop method and were significantly reduced by methylene blue. These results strongly suggest that RFVT3 would functionally be involved in riboflavin absorption in the apical membranes of intestinal epithelial cells.

  11. Microarray Technology Reveals Potentially Novel Genes and Pathways Involved in Non-Functioning Pituitary Adenomas

    PubMed Central

    Qiao, X; Wang, H; Wang, X; Zhao, B; Liu, J

    2016-01-01

    Abstract Microarray data of non-functioning pituitary adenomas (NFPAs) were analyzed to disclose novel genes and pathways involved in NFPA tumorigenesis. Raw microarray data were downloaded from Gene Expression Omnibus. Data pre-treatment and differential analysis were conducted using packages in R. Functional and pathway enrichment analyses were performed using package GOs-tats. A protein-protein interaction (PPI) network was constructed using server STRING and Cytoscape. Known genes involved in pituitary adenomas (PAs), were obtained from the Comparative Toxicogenomics Database. A total of 604 differentially expressed genes (DEGs) were identifed between NFPAs and controls, including 177 up- and 427 down-regulated genes. Jak-STAT and p53 signaling pathways were significantly enriched by DEGs. The PPI network of DEGs was constructed, containing 99 up- and 288 down-regulated known disease genes (e.g. EGFR and ESR1) as well as 16 up- and 17 down-regulated potential novel NFPAs-related genes (e.g. COL4A5, LHX3, MSN, and GHSR). Genes like COL4A5, LHX3, MSN, and GHSR and pathways such as p53 signaling and Jak-STAT signaling, might participate in NFPA development. Although further validations are required, these findings might provide guidance for future basic and therapy researches. PMID:28289583

  12. In vitro gene regulatory networks predict in vivo function of liver

    PubMed Central

    2010-01-01

    Background Evolution of toxicity testing is predicated upon using in vitro cell based systems to rapidly screen and predict how a chemical might cause toxicity to an organ in vivo. However, the degree to which we can extend in vitro results to in vivo activity and possible mechanisms of action remains to be fully addressed. Results Here we use the nitroaromatic 2,4,6-trinitrotoluene (TNT) as a model chemical to compare and determine how we might extrapolate from in vitro data to in vivo effects. We found 341 transcripts differentially expressed in common among in vitro and in vivo assays in response to TNT. The major functional term corresponding to these transcripts was cell cycle. Similarly modulated common pathways were identified between in vitro and in vivo. Furthermore, we uncovered the conserved common transcriptional gene regulatory networks between in vitro and in vivo cellular liver systems that responded to TNT exposure, which mainly contain 2 subnetwork modules: PTTG1 and PIR centered networks. Interestingly, all 7 genes in the PTTG1 module were involved in cell cycle and downregulated by TNT both in vitro and in vivo. Conclusions The results of our investigation of TNT effects on gene expression in liver suggest that gene regulatory networks obtained from an in vitro system can predict in vivo function and mechanisms. Inhibiting PTTG1 and its targeted cell cyle related genes could be key machanism for TNT induced liver toxicity. PMID:21073692

  13. Functions of Parental Involvement and Effects of School Climate on Bullying Behaviors among South Korean Middle School Students

    ERIC Educational Resources Information Center

    Lee, Chang-Hun; Song, Juyoung

    2012-01-01

    This study uses an ecological systems theory to understand bullying behavior. Emphasis is given to overcome limitations found in the literature, such as very little empirical research on functions of parental involvement and the impacts of school climate on bullying as an outcome variable. Two functions of parental involvement investigated are (a)…

  14. Does cognitive functioning predict chronic pain? Results from a prospective surgical cohort.

    PubMed

    Attal, Nadine; Masselin-Dubois, Anne; Martinez, Valéria; Jayr, Christian; Albi, Aline; Fermanian, Jacques; Bouhassira, Didier; Baudic, Sophie

    2014-03-01

    It is well established that chronic pain impairs cognition, particularly memory, attention and mental flexibility. Overlaps have been found between the brain regions involved in pain modulation and cognition, including in particular the prefrontal cortex and the anterior cingulate cortex, which are involved in executive function, attention and memory. However, whether cognitive function may predict chronic pain has not been investigated. We addressed this question in surgical patients, because such patients can be followed prospectively and may have no pain before surgery. In this prospective longitudinal study, we investigated the links between executive function, visual memory and attention, as assessed by clinical measurements and the development of chronic pain, its severity and neuropathic symptoms (based on the 'Douleur Neuropathique 4' questionnaire), 6 and 12 months after surgery (total knee arthroplasty for osteoarthritis or breast surgery for cancer). Neuropsychological tests included the Trail-Making Test A and B, and the Rey-Osterrieth Complex Figure copy and immediate recall, which assess cognitive flexibility, visuospatial processing and visual memory. Anxiety, depression and coping strategies were also evaluated. In total, we investigated 189 patients before surgery: 96% were re-evaluated at 6 months, and 88% at 12 months. Multivariate logistic regression (stepwise selection) for the total group of patients indicated that the presence of clinical meaningful pain at 6 and 12 months (pain intensity ≥ 3/10) was predicted by poorer cognitive performance in the Trail Making Test B (P = 0.0009 and 0.02 for pain at 6 and 12 months, respectively), Rey-Osterrieth Complex Figure copy (P = 0.015 and 0.006 for pain at 6 and 12 months, respectively) and recall (P = 0.016 for pain at 12 months), independently of affective variables. Linear regression analyses indicated that impaired scores on these tests predicted pain intensity (P < 0.01) and neuropathic

  15. Baseline Religion Involvement Predicts Subsequent Salivary Cortisol Levels Among Male But not Female Black Youth

    PubMed Central

    Assari, Shervin; Moghani Lankarani, Maryam; Malekahmadi, Mohammad Reza; Caldwell, Cleopatra Howard; Zimmerman, Marc

    2015-01-01

    race, sex, religiosity, chronic stress, coping, and function of hypothalamo-pituitary-adrenal (HPA). It is not known whether male Black youth who are and those who are not religious differently cope with stress associated with daily discrimination and living in disadvantaged neighborhoods. PMID:26633983

  16. Molecular pathways involved in loss of kidney graft function with tubular atrophy and interstitial fibrosis.

    PubMed

    Maluf, Daniel G; Mas, Valeria R; Archer, Kellie J; Yanek, Kenneth; Gibney, Eric M; King, Anne L; Cotterell, Adrian; Fisher, Robert A; Posner, Marc P

    2008-01-01

    Loss of kidney graft function with tubular atrophy (TA) and interstitial fibrosis (IF) causes most kidney allograft losses. We aimed to identify the molecular pathways involved in IF/TA progression. Kidney biopsies from normal kidneys (n = 24), normal allografts (n = 6), and allografts with IF/TA (n = 17) were analyzed using high-density oligonucleotide microarray. Probe set level tests of hypotheses tests were conducted to identify genes with a significant trend in gene expression across the three groups using Jonckheere-Terpstra test for trend. Interaction networks and functional analysis were used. An unsupervised hierarchical clustering analysis showed that all the IF/TA samples were associated with high correlation. Gene ontology classified the differentially expressed genes as related to immune response, inflammation, and matrix deposition. Chemokines (CX), CX receptor (for example, CCL5 and CXCR4), interleukin, and interleukin receptor (for example, IL-8 and IL10RA) genes were overexpressed in IF/TA samples compared with normal allografts and normal kidneys. Genes involved in apoptosis (for example, CASP4 and CASP5) were importantly overexpressed in IF/TA. Genes related to angiogenesis (for example, ANGPTL3, ANGPT2, and VEGF) were downregulated in IF/TA. Genes related to matrix production-deposition were upregulated in IF/TA. A distinctive gene expression pattern was observed in IF/TA samples compared with normal allografts and normal kidneys. We were able to establish a trend in gene expression for genes involved in different pathways among the studied groups. The top-scored networks were related to immune response, inflammation, and cell-to-cell interaction, showing the importance of chronic inflammation in progressive graft deterioration.

  17. Replication Protein A Presents Canonical Functions and Is Also Involved in the Differentiation Capacity of Trypanosoma cruzi.

    PubMed

    Pavani, Raphael Souza; da Silva, Marcelo Santos; Fernandes, Carlos Alexandre Henrique; Morini, Flavia Souza; Araujo, Christiane Bezerra; Fontes, Marcos Roberto de Mattos; Sant'Anna, Osvaldo Augusto; Machado, Carlos Renato; Cano, Maria Isabel; Fragoso, Stenio Perdigão; Elias, Maria Carolina

    2016-12-01

    Replication Protein A (RPA), the major single stranded DNA binding protein in eukaryotes, is composed of three subunits and is a fundamental player in DNA metabolism, participating in replication, transcription, repair, and the DNA damage response. In human pathogenic trypanosomatids, only limited studies have been performed on RPA-1 from Leishmania. Here, we performed in silico, in vitro and in vivo analysis of Trypanosoma cruzi RPA-1 and RPA-2 subunits. Although computational analysis suggests similarities in DNA binding and Ob-fold structures of RPA from T. cruzi compared with mammalian and fungi RPA, the predicted tridimensional structures of T. cruzi RPA-1 and RPA-2 indicated that these molecules present a more flexible tertiary structure, suggesting that T. cruzi RPA could be involved in additional responses. Here, we demonstrate experimentally that the T. cruzi RPA complex interacts with DNA via RPA-1 and is directly related to canonical functions, such as DNA replication and DNA damage response. Accordingly, a reduction of TcRPA-2 expression by generating heterozygous knockout cells impaired cell growth, slowing down S-phase progression. Moreover, heterozygous knockout cells presented a better efficiency in differentiation from epimastigote to metacyclic trypomastigote forms and metacyclic trypomastigote infection. Taken together, these findings indicate the involvement of TcRPA in the metacyclogenesis process and suggest that a delay in cell cycle progression could be linked with differentiation in T. cruzi.

  18. Replication Protein A Presents Canonical Functions and Is Also Involved in the Differentiation Capacity of Trypanosoma cruzi

    PubMed Central

    Pavani, Raphael Souza; da Silva, Marcelo Santos; Fernandes, Carlos Alexandre Henrique; Morini, Flavia Souza; Araujo, Christiane Bezerra; Fontes, Marcos Roberto de Mattos; Sant’Anna, Osvaldo Augusto; Machado, Carlos Renato; Cano, Maria Isabel; Fragoso, Stenio Perdigão; Elias, Maria Carolina

    2016-01-01

    Replication Protein A (RPA), the major single stranded DNA binding protein in eukaryotes, is composed of three subunits and is a fundamental player in DNA metabolism, participating in replication, transcription, repair, and the DNA damage response. In human pathogenic trypanosomatids, only limited studies have been performed on RPA-1 from Leishmania. Here, we performed in silico, in vitro and in vivo analysis of Trypanosoma cruzi RPA-1 and RPA-2 subunits. Although computational analysis suggests similarities in DNA binding and Ob-fold structures of RPA from T. cruzi compared with mammalian and fungi RPA, the predicted tridimensional structures of T. cruzi RPA-1 and RPA-2 indicated that these molecules present a more flexible tertiary structure, suggesting that T. cruzi RPA could be involved in additional responses. Here, we demonstrate experimentally that the T. cruzi RPA complex interacts with DNA via RPA-1 and is directly related to canonical functions, such as DNA replication and DNA damage response. Accordingly, a reduction of TcRPA-2 expression by generating heterozygous knockout cells impaired cell growth, slowing down S-phase progression. Moreover, heterozygous knockout cells presented a better efficiency in differentiation from epimastigote to metacyclic trypomastigote forms and metacyclic trypomastigote infection. Taken together, these findings indicate the involvement of TcRPA in the metacyclogenesis process and suggest that a delay in cell cycle progression could be linked with differentiation in T. cruzi. PMID:27984589

  19. Accurate perception of negative emotions predicts functional capacity in schizophrenia.

    PubMed

    Abram, Samantha V; Karpouzian, Tatiana M; Reilly, James L; Derntl, Birgit; Habel, Ute; Smith, Matthew J

    2014-04-30

    Several studies suggest facial affect perception (FAP) deficits in schizophrenia are linked to poorer social functioning. However, whether reduced functioning is associated with inaccurate perception of specific emotional valence or a global FAP impairment remains unclear. The present study examined whether impairment in the perception of specific emotional valences (positive, negative) and neutrality were uniquely associated with social functioning, using a multimodal social functioning battery. A sample of 59 individuals with schizophrenia and 41 controls completed a computerized FAP task, and measures of functional capacity, social competence, and social attainment. Participants also underwent neuropsychological testing and symptom assessment. Regression analyses revealed that only accurately perceiving negative emotions explained significant variance (7.9%) in functional capacity after accounting for neurocognitive function and symptoms. Partial correlations indicated that accurately perceiving anger, in particular, was positively correlated with functional capacity. FAP for positive, negative, or neutral emotions were not related to social competence or social attainment. Our findings were consistent with prior literature suggesting negative emotions are related to functional capacity in schizophrenia. Furthermore, the observed relationship between perceiving anger and performance of everyday living skills is novel and warrants further exploration.

  20. Predicted Risk of Radiation-Induced Cancers After Involved Field and Involved Node Radiotherapy With or Without Intensity Modulation for Early-Stage Hodgkin Lymphoma in Female Patients

    SciTech Connect

    Weber, Damien C.; Johanson, Safora; Peguret, Nicolas; Cozzi, Luca; Olsen, Dag R.

    2011-10-01

    Purpose: To assess the excess relative risk (ERR) of radiation-induced cancers (RIC) in female patients with Hodgkin lymphoma (HL) female patients treated with conformal (3DCRT), intensity modulated (IMRT), or volumetric modulated arc (RA) radiation therapy. Methods and Materials: Plans for 10 early-stage HL female patients were computed for 3DCRT, IMRT, and RA with involved field RT (IFRT) and involvednode RT (INRT) radiation fields. Organs at risk dose--volume histograms were computed and inter-compared for IFRT vs. INRT and 3DCRT vs. IMRT/RA, respectively. The ERR for cancer induction in breasts, lungs, and thyroid was estimated using both linear and nonlinear models. Results: The mean estimated ERR for breast, lung, and thyroid were significantly lower (p < 0.01) with INRT than with IFRT planning, regardless of the radiation delivery technique used, assuming a linear dose-risk relationship. We found that using the nonlinear model, the mean ERR values were significantly (p < 0.01) increased with IMRT or RA compared to those with 3DCRT planning for the breast, lung, and thyroid, using an IFRT paradigm. After INRT planning, IMRT or RA increased the risk of RIC for lung and thyroid only. Conclusions: In this comparative planning study, using a nonlinear dose--risk model, IMRT or RA increased the estimated risk of RIC for breast, lung, and thyroid for HL female patients. This study also suggests that INRT planning, compared to IFRT planning, may reduce the ERR of RIC when risk is predicted using a linear model. Observing the opposite effect, with a nonlinear model, however, questions the validity of these biologically parameterized models.

  1. Functional MRI in Awake Dogs Predicts Suitability for Assistance Work

    NASA Astrophysics Data System (ADS)

    Berns, Gregory S.; Brooks, Andrew M.; Spivak, Mark; Levy, Kerinne

    2017-03-01

    The overall goal of this work was to measure the efficacy of fMRI for predicting whether a dog would be a successful service dog. The training and imaging were performed in 49 dogs entering service training at 17-21 months of age. 33 dogs completed service training and were matched with a person, while 10 were released for behavioral reasons (4 were selected as breeders and 2 were released for medical reasons.) After 2 months of training, fMRI responses were measured while each dog observed hand signals indicating either reward or no reward and given by both a familiar handler and a stranger. Using anatomically defined ROIs in the caudate, amygdala, and visual cortex, we developed a classifier based on the dogs’ subsequent training outcomes. The classifier had a positive predictive value of 94% and a negative predictive value of 67%. The area under the ROC curve was 0.91 (0.80 with 4-fold cross-validation, P = 0.01), indicating a significant predictive capability. The magnitude of response in the caudate was positively correlated with a successful outcome, while the response in the amygdala depended on the interaction with the visual cortex during the stranger condition and was negatively correlated with outcome (higher being associated with failure). These results suggest that, as indexed by caudate activity, successful service dogs generalize associations to hand signals regardless who gives them but without excessive arousal as measured in the amygdala.

  2. Functional MRI in Awake Dogs Predicts Suitability for Assistance Work

    PubMed Central

    Berns, Gregory S.; Brooks, Andrew M.; Spivak, Mark; Levy, Kerinne

    2017-01-01

    The overall goal of this work was to measure the efficacy of fMRI for predicting whether a dog would be a successful service dog. The training and imaging were performed in 49 dogs entering service training at 17–21 months of age. 33 dogs completed service training and were matched with a person, while 10 were released for behavioral reasons (4 were selected as breeders and 2 were released for medical reasons.) After 2 months of training, fMRI responses were measured while each dog observed hand signals indicating either reward or no reward and given by both a familiar handler and a stranger. Using anatomically defined ROIs in the caudate, amygdala, and visual cortex, we developed a classifier based on the dogs’ subsequent training outcomes. The classifier had a positive predictive value of 94% and a negative predictive value of 67%. The area under the ROC curve was 0.91 (0.80 with 4-fold cross-validation, P = 0.01), indicating a significant predictive capability. The magnitude of response in the caudate was positively correlated with a successful outcome, while the response in the amygdala depended on the interaction with the visual cortex during the stranger condition and was negatively correlated with outcome (higher being associated with failure). These results suggest that, as indexed by caudate activity, successful service dogs generalize associations to hand signals regardless who gives them but without excessive arousal as measured in the amygdala. PMID:28266550

  3. Functional MRI in Awake Dogs Predicts Suitability for Assistance Work.

    PubMed

    Berns, Gregory S; Brooks, Andrew M; Spivak, Mark; Levy, Kerinne

    2017-03-07

    The overall goal of this work was to measure the efficacy of fMRI for predicting whether a dog would be a successful service dog. The training and imaging were performed in 49 dogs entering service training at 17-21 months of age. 33 dogs completed service training and were matched with a person, while 10 were released for behavioral reasons (4 were selected as breeders and 2 were released for medical reasons.) After 2 months of training, fMRI responses were measured while each dog observed hand signals indicating either reward or no reward and given by both a familiar handler and a stranger. Using anatomically defined ROIs in the caudate, amygdala, and visual cortex, we developed a classifier based on the dogs' subsequent training outcomes. The classifier had a positive predictive value of 94% and a negative predictive value of 67%. The area under the ROC curve was 0.91 (0.80 with 4-fold cross-validation, P = 0.01), indicating a significant predictive capability. The magnitude of response in the caudate was positively correlated with a successful outcome, while the response in the amygdala depended on the interaction with the visual cortex during the stranger condition and was negatively correlated with outcome (higher being associated with failure). These results suggest that, as indexed by caudate activity, successful service dogs generalize associations to hand signals regardless who gives them but without excessive arousal as measured in the amygdala.

  4. Functional characterization of an α-esterase gene involving malathion detoxification in Bactrocera dorsalis (Hendel).

    PubMed

    Wang, Luo-Luo; Lu, Xue-Ping; Meng, Li-Wei; Huang, Yong; Wei, Dong; Jiang, Hong-Bo; Smagghe, Guy; Wang, Jin-Jun

    2016-06-01

    Extensive use of insecticides in many orchards has prompted resistance development in the oriental fruit fly, Bactrocera dorsalis (Hendel). In this study, a laboratory selected strain of B. dorsalis (MR) with a 21-fold higher resistance to malathion was used to examine the resistance mechanisms to this organophosphate insecticide. Carboxylesterase (CarE) was found to be involved in malathion resistance in B. dorsalis from the synergism bioassay by CarE-specific inhibitor triphenylphosphate (TPP). Molecular studies further identified a previously uncharacterized α-esterase gene, BdCarE2, that may function in the development of malathion resistance in B. dorsalis via gene upregulation. This gene is predominantly expressed in the Malpighian tubules, a key insect tissue for detoxification. The transcript levels of BdCarE2 were also compared between the MR and a malathion-susceptible (MS) strain of B. dorsalis, and it was significantly more abundant in the MR strain. No sequence mutation or gene copy changes were detected between the two strains. Functional studies using RNA interference (RNAi)-mediated knockdown of BdCarE2 significantly increased the malathion susceptibility in the adult files. Furthermore, heterologous expression of BdCarE2 combined with cytotoxicity assay in Sf9 cells demonstrated that BdCarE2 could probably detoxify malathion. Taken together, the current study bring new molecular evidence supporting the involvement of CarE-mediated metabolism in resistance development against malathion in B. dorsalis and also provide bases on functional analysis of insect α-esterase associated with insecticide resistance. Copyright © 2015 Elsevier Inc. All rights reserved.

  5. Motor functioning differentially predicts mortality in men and women.

    PubMed

    Bravell, Marie Ernsth; Finkel, Deborah; Dahl Aslan, Anna; Reynolds, Chandra A; Hallgren, Jenny; Pedersen, Nancy L

    2017-09-01

    Research indicates gender differences in functional performance at advanced ages, but little is known about their impact on longevity for men and women. To derive a set of motor function factors from a battery of functional performance measures and examine their associations with mortality, incorporating possible gender interactions. Analyses were performed on the longitudinal Swedish Adoption/Twin Study of Aging (SATSA) including twenty-four assessments of motor function up to six times over a 19-year period. Three motor factors were derived from several factor analyses; fine motor, balance/upper strength, and flexibility. A latent growth curve model was used to capture longitudinal age changes in the motor factors and generated estimates of intercept at age 70 (I), rates of change before (S1) and after age 70 (S2) for each factor. Cox regression models were used to determine how gender in interaction with the motor factors was related to mortality. Females demonstrated lower functional performance in all motor functions relative to men. Cox regression survival analyses demonstrated that both balance/upper strength, and fine motor function were significantly related to mortality. Gender specific analyses revealed that this was true for women only. For men, none of the motor factors were related to mortality. Women demonstrated more difficulties in all functioning facets, and only among women were motor functioning (balance/upper strength and fine motor function) associated with mortality. These results provide evidence for the importance of considering motor functioning, and foremost observed gender differences when planning for individualized treatment and rehabilitation. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Prediction of Functional Outcome in Individuals at Clinical High Risk for Psychosis

    PubMed Central

    Carrión, Ricardo E.; McLaughlin, Danielle; Goldberg, Terry E.; Auther, Andrea M.; Olsen, Ruth H.; Olvet, Doreen M.; Correll, Christoph U.; Cornblatt, Barbara A.

    2014-01-01

    Importance A major public health concern associated with schizophrenia and psychotic disorders is the long-term disability that involves impaired cognition, lack of social support, and an inability to function independently in the community. A critical goal of early detection and intervention studies in psychosis is therefore to understand the factors leading to this often profound impairment. Objective To develop a predictive model of functional (social and role) outcome in a clinical high-risk sample for psychosis. Design Prospective, naturalistic, longitudinal 3- to 5-year follow-up study. Setting The Recognition and Prevention Program in New York, a research clinic located in the Zucker Hillside Hospital in New York. Participants One hundred one treatment-seeking patients at clinical high risk for psychosis. Ninety-two (91%) were followed up prospectively for a mean (SD) of 3 (1.6) years. Intervention Neurocognitive and clinical assessment. Main Outcomes and Measures The primary outcome variables were social and role functioning at the last follow-up visit. Results Poor social outcome was predicted by reduced processing speed (odds ratio [OR], 1.38; 95% CI, 1.050-1.823; P = .02), impaired social functioning at baseline (OR, 1.85; 95% CI, 1.258-2.732; P = .002), and total disorganized symptoms (OR, 5.06; 95% CI, 1.548-16.527; P = .007). Reduced performance on tests for verbal memory (OR, 1.74; 95% CI, 1.169-2.594; P = .006), role functioning at baseline (OR, 1.34; 95% CI, 1.053-1.711; P = .02), and motor disturbances (OR, 1.77; 95% CI, 1.060-2.969; P = .03) predicted role outcome. The areas under the curve for the social and role prediction models were 0.824 (95% CI, 0.736-0.913; P < .001) and 0.77 (95% CI, 0.68-0.87; P < .001), respectively, demonstrating a high discriminative ability. In addition, poor functional outcomes were not entirely dependent on the development of psychosis, because 40.3% and 45.5% of nonconverters at clinical high risk had poor social

  7. Predicting future forests: Understanding diverse phenological responses within a community and functional trait framework

    NASA Astrophysics Data System (ADS)

    Wolkovich, E. M.; Flynn, D. F. B.

    2016-12-01

    In recent years increasing attention has focused on plant phenology as an important indicator of the biological impacts of climate change, as many plants have shifted their leafing and flowering earlier with increasing temperatures. As data have accumulated, researchers have found a link between phenological responses to warming and plant performance and invasions. Such work suggests phenology may not only be a major impact of warming, but a critical predictor of future plant performance. Yet alongside this increasing interest in phenology, important issues remain unanswered: responses to warming for species at the same site or in the same genus vary often by weeks or more and the explanatory power of phenology for performance and invasions when analyzed across diverse datasets remains low. We propose progress can come from explicitly considering phenology within a community context and as a critical plant trait correlated with other major plant functional traits. Here, we lay out a framework for our proposal: specifically we review how we expect phenology and phenological cues of different species within a community to vary and what other functional traits are predicted to co-vary with phenological traits. Much research currently suggests phenology is a critical functional trait that is shaped strongly by the environment. Plants are expected to adjust their phenologies to avoid periods of high abiotic risk and/or high competition. Thus we may expect phenology to correlate strongly to other traits involved in mitigating risk and high competition. Results from recent meta-analyses as well as experimental and observational research from 28 species in northeastern North American temperate forests suggest that species within a community show the predicted diversified set of phenological cues. We review early work on links to other functional traits and in closing review how these correlations may in turn determine the diversity of phenological responses observed for

  8. Involvement of fission yeast Pdc2 in RNA degradation and P-body function.

    PubMed

    Wang, Chun-Yu; Wang, Yi-Ting; Hsiao, Wan-Yi; Wang, Shao-Win

    2017-04-01

    In this study we identified Pdc2, the fission yeast ortholog of human Pat1b protein, which forms a complex with Lsm1-7 and plays a role in coupling deadenylation and decapping. The involvement of Pdc2 in RNA degradation and P-body function was also determined. We found that Pdc2 interacts with Dcp2 and is required for decapping in vivo. Although not absolutely essential for P-body assembly, overexpression of Pdc2 enhanced P-body formation even in the absence of Pdc1, the fission yeast functional homolog of human Edc4 protein, indicating that Pdc2 also plays a role in P-body formation. Intriguingly, in the absence of Pdc2, Lsm1 was found to accumulate in the nucleus, suggesting that Pdc2 shuttling between nucleus and cytoplasm plays a role in decreasing the nuclear concentration of Lsm1 to increase Lsm1 in the cytoplasm. Furthermore, unlike other components of P-bodies, the deadenylase Ccr4 did not accumulate in P-bodies in cells growing under favorable conditions and was only recruited to P-bodies after deprivation of glucose in a Pdc2-Lsm1-dependent manner, indicating a function of Pdc2 in cellular response to environmental stress. In supporting this idea, pdc2 mutants are defective in recovery from glucose starvation with a much longer time to re-enter the cell cycle. In keeping with the notion that Pat1 is a nucleocytoplasmic protein, functioning also in the nucleus, we found that Pdc2 physically and genetically interacts with the nuclear 5'-3' exonuclease Dhp1. A function of Pdc2-Lsm1, in concert with Dhp1, regulating RNA by promoting its decapping/destruction in the nucleus was suggested.

  9. Executive Function Predicts Artificial Language Learning in Children and Adults

    ERIC Educational Resources Information Center

    Kapa, Leah Lynn

    2013-01-01

    Prior research has established an executive function advantage among bilinguals as compared to monolingual peers. These non-linguistic cognitive advantages are largely assumed to result from the experience of managing two linguistic systems. However, the possibility remains that the relationship between bilingualism and executive function is…

  10. Prospective Prediction of Functional Difficulties among Recently Separated Veterans

    DTIC Science & Technology

    2014-01-01

    military, posttraumatic stress disorder, prospective, PTSD, reintegration , risk factors, Veterans , work functioning. INTRODUCTION Studies suggest that Iraq...2010) documented the prevalence and types of community reintegration problems among 754 post-9/11 combat Veterans receiving Department of Veter- ans...understand factors that place recently separated Veterans at risk for functional difficulties and more broadly at risk for difficulty reintegrating

  11. Executive Function Predicts Artificial Language Learning in Children and Adults

    ERIC Educational Resources Information Center

    Kapa, Leah Lynn

    2013-01-01

    Prior research has established an executive function advantage among bilinguals as compared to monolingual peers. These non-linguistic cognitive advantages are largely assumed to result from the experience of managing two linguistic systems. However, the possibility remains that the relationship between bilingualism and executive function is…

  12. In silico prediction of structure and functions for some proteins of male-specific region of the human Y chromosome.

    PubMed

    Saha, Chinmoy; Polash, Ahsan Habib; Islam, Md Tariqul; Shafrin, Farhana

    2013-12-01

    Male-specific region of the human Y chromosome (MSY) comprises 95% of its length that is functionally active. This portion inherits in block from father to male offspring. Most of the genes in the MSY region are involved in male-specific function, such as sex determination and spermatogenesis; also contains genes probably involved in other cellular functions. However, a detailed characterization of numerous MSY-encoded proteins still remains to be done. In this study, 12 uncharacterized proteins of MSY were analyzed through bioinformatics tools for structural and functional characterization. Within these 12 proteins, a total of 55 domains were found, with DnaJ domain signature corresponding to be the highest (11%) followed by both FAD-dependent pyridine nucleotide reductase signature and fumarate lyase superfamily signature (9%). The 3D structures of our selected proteins were built up using homology modeling and the protein threading approaches. These predicted structures confirmed in detail the stereochemistry; indicating reasonably good quality model. Furthermore the predicted functions and the proteins with whom they interact established their biological role and their mechanism of action at molecular level. The results of these structure-functional annotations provide a comprehensive view of the proteins encoded by MSY, which sheds light on their biological functions and molecular mechanisms. The data presented in this study may assist in future prognosis of several human diseases such as Turner syndrome, gonadal sex reversal, spermatogenic failure, and gonadoblastoma.

  13. Fitness Costs Predict Inbreeding Aversion Irrespective of Self-Involvement: Support for Hypotheses Derived from Evolutionary Theory

    PubMed Central

    Antfolk, Jan; Lieberman, Debra; Santtila, Pekka

    2012-01-01

    It is expected that in humans, the lowered fitness of inbred offspring has produced a sexual aversion between close relatives. Generally, the strength of this aversion depends on the degree of relatedness between two individuals, with closer relatives inciting greater aversion than more distant relatives. Individuals are also expected to oppose acts of inbreeding that do not include the self, as inbreeding between two individuals posits fitness costs not only to the individuals involved in the sexual act, but also to their biological relatives. Thus, the strength of inbreeding aversion should be predicted by the fitness costs an inbred child posits to a given individual, irrespective of this individual’s actual involvement in the sexual act. To test this prediction, we obtained information about the family structures of 663 participants, who reported the number of same-sex siblings, opposite-sex siblings, opposite-sex half siblings and opposite-sex cousins. Each participant was presented with three different types of inbreeding scenarios: 1) Participant descriptions, in which participants themselves were described as having sex with an actual opposite-sex relative (sibling, half sibling, or cousin); 2) Related third-party descriptions, in which participants’ actual same-sex siblings were described as having sex with their actual opposite-sex relatives; 3) Unrelated third-party descriptions, in which individuals of the same sex as the participants but unrelated to them were described as having sex with opposite-sex relatives. Participants rated each description on the strength of sexual aversion (i.e., disgust-reaction). We found that unrelated third-party descriptions elicited less disgust than related third-party and participant descriptions. Related third-party and participant descriptions elicited similar levels of disgust suggesting that the strength of inbreeding aversion is predicted by inclusive fitness costs. Further, in the related and unrelated

  14. The FlbA-regulated predicted transcription factor Fum21 of Aspergillus niger is involved in fumonisin production.

    PubMed

    Aerts, David; Hauer, Esther E; Ohm, Robin A; Arentshorst, Mark; Teertstra, Wieke R; Phippen, Christopher; Ram, Arthur F J; Frisvad, Jens C; Wösten, Han A B

    2017-09-30

    Aspergillus niger secretes proteins throughout the colony except for the zone that forms asexual spores called conidia. Inactivation of flbA that encodes a regulator of G-protein signaling results in colonies that are unable to reproduce asexually and that secrete proteins throughout the mycelium. In addition, the ΔflbA strain shows cell lysis and has thinner cell walls. Expression analysis showed that 38 predicted transcription factor genes are differentially expressed in strain ΔflbA. Here, the most down-regulated predicted transcription factor gene, called fum21, was inactivated. Growth, conidiation, and protein secretion were not affected in strain Δfum21. Whole genome expression analysis revealed that 63 and 11 genes were down- and up-regulated in Δfum21, respectively, when compared to the wild-type strain. Notably, 24 genes predicted to be involved in secondary metabolism were down-regulated in Δfum21, including 10 out of 12 genes of the fumonisin cluster. This was accompanied by absence of fumonisin production in the deletion strain and a 25% reduction in production of pyranonigrin A. Together, these results link FlbA-mediated sporulation-inhibited secretion with mycotoxin production.

  15. Timing Correlations in Proteins Predict Functional Modules and Dynamic Allostery.

    PubMed

    Lin, Milo M

    2016-04-20

    How protein structure encodes functionality is not fully understood. For example, long-range intraprotein communication can occur without measurable conformational change and is often not captured by existing structural correlation functions. It is shown here that important functional information is encoded in the timing of protein motions, rather than motion itself. I introduce the conditional activity function to quantify such timing correlations among the degrees of freedom within proteins. For three proteins, the conditional activities between side-chain dihedral angles were computed using the output of microseconds-long atomistic simulations. The new approach demonstrates that a sparse fraction of side-chain pairs are dynamically correlated over long distances (spanning protein lengths up to 7 nm), in sharp contrast to structural correlations, which are short-ranged (<1 nm). Regions of high self- and inter-side-chain dynamical correlations are found, corresponding to experimentally determined functional modules and allosteric connections, respectively.

  16. Chemistry-based functional proteomics to identify novel deubiquitylating enzymes involved in viral infection.

    PubMed

    Lei, Yunlong; Xie, Ke; Huang, Kai; Wu, Hong; Huang, Canhua

    2012-05-01

    Ubiquitylation is a reversible post-translational modification pathway that regulates a variety of cellular processes including protein degradation and trafficking, intracellular localization, DNA repair, immune response and cellcycle progression. Deubiquitylating enzymes (DUBs) can remove the ubiquitin from the modified proteins and reverse the ubiquitylation-induced biological processes; hence it isn't hard to understand that viral pathogens take advantage of the host cell ubiquitin system through disturbing DUBs, for infection and replication. Although accumulated virus-related DUBs have been defined, but how viruses regulate their expression and activities is poor understand because of limitation of technologies. Recently, chemistry-based functional proteomics, which can not only monitor the alteration of abundance but also changes in activity of enzymes, was used to study the function of DUBs involved in virus infection and held much promise. Theses works suggest that chemistry-based functional proteomics is a potent strategy for high throughput screening of virus-related DUBs and exploring their roles in virus infection.

  17. Hal2p functions in Bdf1p-involved salt stress response in Saccharomyces cerevisiae.

    PubMed

    Chen, Lei; Liu, Liangyu; Wang, Mingpeng; Fu, Jiafang; Zhang, Zhaojie; Hou, Jin; Bao, Xiaoming

    2013-01-01

    The Saccharomyces cerevisiae Bdf1p associates with the basal transcription complexes TFIID and acts as a transcriptional regulator. Lack of Bdf1p is salt sensitive and displays abnormal mitochondrial function. The nucleotidase Hal2p detoxifies the toxic compound 3' -phosphoadenosine-5'-phosphate (pAp), which blocks the biosynthesis of methionine. Hal2p is also a target of high concentration of Na(+). Here, we reported that HAL2 overexpression recovered the salt stress sensitivity of bdf1Δ. Further evidence demonstrated that HAL2 expression was regulated indirectly by Bdf1p. The salt stress response mechanisms mediated by Bdf1p and Hal2p were different. Unlike hal2Δ, high Na(+) or Li(+) stress did not cause pAp accumulation in bdf1Δ and methionine supplementation did not recover its salt sensitivity. HAL2 overexpression in bdf1Δ reduced ROS level and improved mitochondrial function, but not respiration. Further analyses suggested that autophagy was apparently defective in bdf1Δ, and autophagy stimulated by Hal2p may play an important role in recovering mitochondrial functions and Na(+) sensitivity of bdf1Δ. Our findings shed new light towards our understanding about the molecular mechanism of Bdf1p-involved salt stress response in budding yeast.

  18. Recognition of nontrivial remote homology relationships involving proteins of Helicobacter pylori: implications for function recognition.

    PubMed

    Tyagi, Nidhi; Srinivasan, Narayanaswamy

    2013-01-01

    This chapter explains techniques for recognition of nontrivial remote homology relationships involving proteins of Helicobacter pylori and their implications for function recognition. Using the remote homology detection method, employing multiple-profile representations for every protein domain family, remotely related domain family information has been assigned for the 122, 77, and 95 protein sequences of 26695, and J99, and HPAG1 strains of H. pylori, respectively. Relationships for some of the H. pylori protein sequences with Pfam domain families are reported for the first time. In publicly available domain databases such as Pfam, for some of the H. pylori protein sequences functional domain information is associated only with part(s) of the proteins. In the current study other parts of such proteins have been shown to be remotely related to known domain families, raising the possibility of identifying functions for parts of the proteins that do not yet have domains assigned. Further, homologues of enzymes that potentially catalyze step(s) in various metabolic processes in H. pylori have been identified for the first time.

  19. Involvement of endogenous CCK and CCK1 receptors in colonic motor function

    PubMed Central

    Varga, Gábor; Bálint, András; Burghardt, Beáta; D'Amato, Massimo

    2004-01-01

    Cholecystokinin (CCK) is a brain-gut peptide; it functions both as a neuropeptide and as a gut hormone. Although the pancreas and the gallbladder were long thought to be the principal peripheral targets of CCK, CCK receptors are found throughout the gut. It is likely that CCK has a physiological role not only in the stimulation of pancreatic and biliary secretions but also in the regulation of gastrointestinal motility. The motor effects of CCK include postprandial inhibition of gastric emptying and inhibition of colonic transit. It is now evident that at least two different receptors, CCK1 and CCK2 (formerly CCK-A and CCK-B, respectively), mediate the actions of CCK. Both localization and functional studies suggest that the motor effects of CCK are mediated by CCK1 receptors in humans. Since CCK is involved in sensory and motor responses to distension in the intestinal tract, it may contribute to the symptoms of constipation, bloating and abdominal pain that are often characteristic of functional gastrointestinal disorders in general and irritable bowel syndrome (IBS), in particular. CCK1 receptor antagonists are therefore currently under development for the treatment of constipation-predominant IBS. Clinical studies suggest that CCK1 receptor antagonists are effective facilitators of gastric emptying and inhibitors of gallbladder contraction and can accelerate colonic transit time in healthy volunteers and patients with IBS. These drugs are therefore potentially of great value in the treatment of motility disorders such as constipation and constipation-predominant IBS. PMID:15100163

  20. Association between functional polymorphisms in genes involved in the MAPK signaling pathways and cutaneous melanoma risk

    PubMed Central

    Wei, Qingyi

    2013-01-01

    Genome-wide association studies (GWASs) have mainly focused on top significant single nucleotide polymorphisms (SNPs), most of which did not have clear biological functions but were just surrogates for unknown causal variants. Studying SNPs with modest association and putative functions in biologically plausible pathways has become one complementary approach to GWASs. To unravel the key roles of mitogen-activated protein kinase (MAPK) pathways in cutaneous melanoma (CM) risk, we re-evaluated the associations between 47 818 SNPs in 280 MAPK genes and CM risk using our published GWAS dataset with 1804 CM cases and 1026 controls. We initially found 105 SNPs with P ≤ 0.001, more than expected by chance, 26 of which were predicted to be putatively functional SNPs. The risk associations with 16 SNPs around DUSP14 (rs1051849) and a previous reported melanoma locus MAFF/PLA2G6 (proxy SNP rs4608623) were replicated in the GenoMEL dataset (P < 0.01) but failed in the Australian dataset. Meta-analysis showed that rs1051849 in the 3ʹ untranslated regions of DUSP14 was associated with a reduced risk of melanoma (odds ratio = 0.89, 95% confidence interval: 0.82–0.96, P = 0.003, false discovery rate = 0.056). Further genotype–phenotype correlation analysis using the 90 HapMap lymphoblastoid cell lines from Caucasians showed significant correlations between two SNPs (rs1051849 and rs4608623) and messenger RNA expression levels of DUSP14 and MAFF (P = 0.025 and P = 0.010, respectively). Gene-based tests also revealed significant SNPs were over-represented in MAFF, PLA2G6, DUSP14 and other 16 genes. Our results suggest that functional SNPs in MAPK pathways may contribute to CM risk. Further studies are warranted to validate our findings. PMID:23291271

  1. Predicting Future Years of Life, Health, and Functional Ability

    PubMed Central

    Diehr, Paula; Diehr, Michael; Arnold, Alice; Yee, Laura M.; Odden, Michelle C.; Hirsch, Calvin H; Thielke, Stephen; Psaty, Bruce M.; Johnson, W. Craig; Kizer, MD, Jorge R.; Newman, Anne

    2015-01-01

    Objective: To create personalized estimates of future health and ability status for older adults. Method: Data came from the Cardiovascular Health Study (CHS), a large longitudinal study. Outcomes included years of life, years of healthy life (based on self-rated health), years of able life (based on activities of daily living), and years of healthy and able life. We developed regression estimates using the demographic and health characteristics that best predicted the four outcomes. Internal and external validity were assessed. Results: A prediction equation based on 11 variables accounted for about 40% of the variability for each outcome. Internal validity was excellent, and external validity was satisfactory. The resulting CHS Healthy Life Calculator (CHSHLC) is available at http://healthylifecalculator.org. Conclusion: CHSHLC provides a well-documented estimate of future years of healthy and able life for older adults, who may use it in planning for the future. PMID:28138467

  2. A Meta-Analysis Based Method for Prioritizing Candidate Genes Involved in a Pre-specific Function

    PubMed Central

    Zhai, Jingjing; Tang, Yunjia; Yuan, Hao; Wang, Longteng; Shang, Haoli; Ma, Chuang

    2016-01-01

    The identification of genes associated with a given biological function in plants remains a challenge, although network-based gene prioritization algorithms have been developed for Arabidopsis thaliana and many non-model plant species. Nevertheless, these network-based gene prioritization algorithms have encountered several problems; one in particular is that of unsatisfactory prediction accuracy due to limited network coverage, varying link quality, and/or uncertain network connectivity. Thus, a model that integrates complementary biological data may be expected to increase the prediction accuracy of gene prioritization. Toward this goal, we developed a novel gene prioritization method named RafSee, to rank candidate genes using a random forest algorithm that integrates sequence, evolutionary, and epigenetic features of plants. Subsequently, we proposed an integrative approach named RAP (Rank Aggregation-based data fusion for gene Prioritization), in which an order statistics-based meta-analysis was used to aggregate the rank of the network-based gene prioritization method and RafSee, for accurately prioritizing candidate genes involved in a pre-specific biological function. Finally, we showcased the utility of RAP by prioritizing 380 flowering-time genes in Arabidopsis. The “leave-one-out” cross-validation experiment showed that RafSee could work as a complement to a current state-of-art network-based gene prioritization system (AraNet v2). Moreover, RAP ranked 53.68% (204/380) flowering-time genes higher than AraNet v2, resulting in an 39.46% improvement in term of the first quartile rank. Further evaluations also showed that RAP was effective in prioritizing genes-related to different abiotic stresses. To enhance the usability of RAP for Arabidopsis and non-model plant species, an R package implementing the method is freely available at http://bioinfo.nwafu.edu.cn/software. PMID:28018423

  3. Intrinsic functional connectivity predicts individual differences in distractibility.

    PubMed

    Poole, Victoria N; Robinson, Meghan E; Singleton, Omar; DeGutis, Joseph; Milberg, William P; McGlinchey, Regina E; Salat, David H; Esterman, Michael

    2016-06-01

    Distractor suppression, the ability to filter and ignore task-irrelevant information, is critical for efficient task performance. While successful distractor suppression relies on a balance of activity in neural networks responsible for attention maintenance (dorsal attention network; DAN), reorientation (ventral attention network; VAN), and internal thought (default mode network, DMN), the degree to which intrinsic connectivity within and between these networks contributes to individual differences in distractor suppression ability is not well-characterized. For the purposes of understanding these interactions, the current study collected resting-state fMRI data from 32 Veterans and, several months later (7±5 months apart), performance on the additional singleton paradigm, a measure of distractor suppression. Using multivariate support vector regression models composed of resting state connectivity between regions of the DAN, VAN, and DMN, and a leave-one-subject-out cross-validation procedure, we were able to predict an individual's task performance, yielding a significant correlation between the actual and predicted distractor suppression (r=0.48, p=0.0053). Network-level analyses revealed that greater within-network DMN connectivity was predictive of better distractor suppression, while greater connectivity between the DMN and attention networks was predictive of poorer distractor suppression. The strongest connection hubs were determined to be the right frontal eye field and temporoparietal junction of the DAN and VAN, respectively, and medial (ventromedial prefrontal and posterior cingulate cortices) and bilateral prefrontal regions of the DMN. These results are amongst a small but growing number of studies demonstrating that resting state connectivity is related to stable individual differences in cognitive ability, and suggest that greater integrity and independence of the DMN is related to better attentional ability.

  4. Predicting functional capacity during treadmill testing independent of exercise protocol.

    PubMed

    Foster, C; Crowe, A J; Daines, E; Dumit, M; Green, M A; Lettau, S; Thompson, N N; Weymier, J

    1996-06-01

    Clinically useful estimates of VO2max from treadmill tests (GXT) may be made using protocol-specific equations. In many cases, GXT may proceed more effectively if the clinician is free to adjust speed and grade independent of a specific protocol. We sought to determine whether VO2max could be predicted from the estimated steady-state VO2 of the terminal exercise stage. Seventy clinically stable individuals performed GXT with direct measurement of VO2. Exercise was incremented each minute to optimize clinical examination. Measured VO2max was compared to the estimated steady-state VO2 of the terminal stage based on ACSM equations. Equations for walking or running were used based on the patient's observed method of ambulation. The measured VO2max was always less than the ACSM estimate, with a regular relationship between measured and estimated VO2max. No handrail support: VO2max = 0.869.ACSM -0.07; R2 = 0.955, SEE = 4.8 ml.min-1.kg-1 (N = 30). With handrail support: VO2max = 0.694.ACSM + 3.33; R2 = 0.833, SEE = 4.4 ml.min-1.kg-1 (N = 40). The equations were cross-validated with 20 patients. The correlation between predicted and observed values was r = 0.98 and 0.97 without and with handrail support, respectively. The mean absolute prediction error (3.1 and 4.1 ml.min-1.kg-1) were similar to protocol-specific equations. We conclude that VO2max can be predicted independent of treadmill protocol with approximately the same error as protocol-specific equations.

  5. MicroRNAs of Toxocara canis and their predicted functional roles.

    PubMed

    Ma, Guangxu; Luo, Yongfang; Zhu, Honghong; Luo, Yongli; Korhonen, Pasi K; Young, Neil D; Gasser, Robin B; Zhou, Rongqiong

    2016-04-23

    Toxocara canis is the causative agent of toxocariasis of humans and other animals. This parasitic nematode (roundworm) has a complex life cycle, in which substantial developmental changes and switches occur. As small non-coding RNAs (sRNAs) are key regulators of gene expression in a wide range of organisms, we explored these RNAs in T. canis to provide a basis for future studies of its developmental biology as well as host interactions and disease at the molecular level. We conducted high-throughput RNA sequencing and bioinformatic analyses to define sRNAs in individual male and female adults of T. canis. Apart from snRNA and snoRNA, 560 and 619 microRNAs (miRNAs), including 5 and 2 novel miRNAs, were identified in male and female worms, respectively, without piRNAs being detected in either sex. An analysis of transcriptional profiles showed that, of 564 miRNAs predicted as being differentially transcribed between male and female individuals of T. canis, 218 miRNAs were transcribed exclusively in male and 277 in female worms. Functional enrichment analysis predicted that both male and female miRNAs were mainly involved in regulating embryonic morphogenesis, hemidesmosome assembly and genetic information processing. The miRNAs differentially transcribed between the sexes were predicted to be associated with sex determination, embryonic morphogenesis and nematode larval development. The roles of miRNAs were predicted based on gene ontology (GO) and KEGG pathway annotations. The miRNAs Tc-miR-2305 and Tc-miR-6090 are proposed to have roles in reproduction, embryo development and larval development, and Tc-let-7-5p, Tc-miR-34 and Tc-miR-100 appear to be involved in host-parasite interactions. Together with published information from previous studies, some miRNAs (such as Tc-miR-2861, Tc-miR-2881 and Tc-miR-5126) are predicted to represent drug targets and/or associated with drug resistance. This is the first exploration of miRNAs in T. canis, which could provide a

  6. Predictability Effects on Durations of Content and Function Words in Conversational English

    SciTech Connect

    Bell, Alan; Brenier, Jason; Gregory, Michelle L.; girand, cynthia; Jurafsky, Daniel

    2009-01-01

    Content and function word duration are affected differently by their frequency and predictability. Regression analyses of conversational speech show that content words are shorter when they are more frequent, but function words are not. Repeated content words are shorter, but function words are not. Furthermore, function words have shorter pronunciations, after controlling for frequency and predictability. both content and function words are strongly affected by predictability from the word following them, and on