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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. 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

  3. Genome-wide study predicts promoter-G4 DNA motifs regulate selective functions in bacteria: radioresistance of D. radiodurans involves G4 DNA-mediated regulation

    PubMed Central

    Beaume, Nicolas; Pathak, Rajiv; Yadav, Vinod Kumar; Kota, Swathi; Misra, Hari S.; Gautam, Hemant K.; Chowdhury, Shantanu

    2013-01-01

    A remarkable number of guanine-rich sequences with potential to adopt non-canonical secondary structures called G-quadruplexes (or G4 DNA) are found within gene promoters. Despite growing interest, regulatory role of quadruplex DNA motifs in intrinsic cellular function remains poorly understood. Herein, we asked whether occurrence of potential G4 (PG4) DNA in promoters is associated with specific function(s) in bacteria. Using a normalized promoter-PG4-content (PG4P) index we analysed >60 000 promoters in 19 well-annotated species for (a) function class(es) and (b) gene(s) with enriched PG4P. Unexpectedly, PG4-associated functional classes were organism specific, suggesting that PG4 motifs may impart specific function to organisms. As a case study, we analysed radioresistance. Interestingly, unsupervised clustering using PG4P of 21 genes, crucial for radioresistance, grouped three radioresistant microorganisms including Deinococcus radiodurans. Based on these predictions we tested and found that in presence of nanomolar amounts of the intracellular quadruplex-binding ligand N-methyl mesoporphyrin (NMM), radioresistance of D. radiodurans was attenuated by ∼60%. In addition, important components of the RecF recombinational repair pathway recA, recF, recO, recR and recQ genes were found to harbour promoter-PG4 motifs and were also down-regulated in presence of NMM. Together these results provide first evidence that radioresistance may involve G4 DNA-mediated regulation and support the rationale that promoter-PG4s influence selective functions. PMID:23161683

  4. Tc-99m diethylenetriamine pentaacetic acid (DTPA) renal function reserve estimation: is it a reliable predictive tool for assessment of preclinical renal involvement in scleroderma patients?

    PubMed

    Amin, Amr; El-Sayed, S; Taher, N; Sedki, M; Nasr, H

    2012-06-01

    Prognosis of systemic sclerosis (SSc) depends on internal organ involvement. We assessed the value of renal function reserve (RFR) for the detection of preclinical nephropathy in scleroderma. Thirty SSc patients with normal serum creatinine and 30 healthy controls were included. Medsger disease severity score, glomerular filtration rate (GFR), and microalbuminuria were measured. Tc-99m DTPA was utilized for GFR measurement at baseline and after oral protein overload (stimulated GFR). RFR was calculated as the percentile increase of stimulated GFR. SSc patients had lower means of baseline GFR (P=0.001), stimulated GFR (P=0.004), RFR (P=0.046), and higher microalbuminuria (P=0.009) than controls. According to baseline GFR, SSc patients showed three categories-normal baseline GFR (n=12), hyperfiltration GFR (n=3), and reduced baseline GFR (n=15). In the former category, RFR was normal in 6/12 patients and abnormal in the remainders (50%). Hyperfiltration patients and those with reduced baseline GFR showed abnormal RFR. A statistically significant negative association was found between microalbuminuria versus stimulated GFR and RFR (r= -0.5, P=0.007 and r= -0.45, P=0.013, respectively). The majority of SSc patients with abnormal RFR had disease duration of ≥48 months (60% vs. 20%, P=0.008). All SSc patients with pulmonary hypertension had abnormal RFR, while reduced baseline GFR was noted in only 60%. A significant negative correlation was found between reduced baseline GFR and cumulative dose of corticosteroids in SSc patients (r= -0.4, P=0.022). RFR estimation could be a useful predictive marker for preclinical renal involvement in SSc patients so that early prophylactic measures and therapy modifications could be considered. PMID:22362258

  5. Fractal calculus involving gauge function

    NASA Astrophysics Data System (ADS)

    Golmankhaneh, Alireza K.; Baleanu, Dumitru

    2016-08-01

    Henstock-Kurzweil integral or gauge integral is the generalization of the Riemann integral. The functions which are not integrable because of singularity in the senses of Lebesgue or Riemann are gauge integrable. In this manuscript, we have generalized Fα-calculus using the gauge integral method for the integrating of the functions on fractal set subset of real-line where they have singularities. The suggested new method leads to the wider class of functions on the fractal subset of real-line that are *Fα-integrable. Using gauge function we define *Fα-derivative of functions their Fα-derivative is not exist. The reported results can be used for generalizing the fundamental theorem of Fα-calculus.

  6. Structural model of ρ1 GABAC receptor based on evolutionary analysis: Testing of predicted protein–protein interactions involved in receptor assembly and function

    PubMed Central

    Adamian, Larisa; Gussin, Hélène A; Tseng, Yan Yuan; Muni, Niraj J; Feng, Feng; Qian, Haohua; Pepperberg, David R; Liang, Jie

    2009-01-01

    The homopentameric ρ1 GABAC receptor is a ligand-gated ion channel with a binding pocket for γ-aminobutyric acid (GABA) at the interfaces of N-terminal extracellular domains. We combined evolutionary analysis, structural modeling, and experimental testing to study determinants of GABAC receptor assembly and channel gating. We estimated the posterior probability of selection pressure at amino acid residue sites measured as ω-values and built a comparative structural model, which identified several polar residues under strong selection pressure at the subunit interfaces that may form intersubunit hydrogen bonds or salt bridges. At three selected sites (R111, T151, and E55), mutations disrupting intersubunit interactions had strong effects on receptor folding, assembly, and function. We next examined the role of a predicted intersubunit salt bridge for residue pair R158–D204. The mutant R158D, where the positively charged residue is replaced by a negatively charged aspartate, yielded a partially degraded receptor and lacked membrane surface expression. The membrane surface expression was rescued by the double mutant R158D–D204R, where positive and negative charges are switched, although the mutant receptor was inactive. The single mutants R158A, D204R, and D204A exhibited diminished activities and altered kinetic profiles with fast recovery kinetics, suggesting that R158–D204 salt bridge perhaps stabilizes the open state of the GABAC receptor. Our results emphasize the functional importance of highly conserved polar residues at the protein–protein interfaces in GABAC ρ1 receptors and demonstrate how the integration of computational and experimental approaches can aid discovery of functionally important interactions. PMID:19768800

  7. Infancy to Age Five: Predicting Fathers' Involvement.

    ERIC Educational Resources Information Center

    Bailey, William T.

    Four years after a study of paternal involvement among intact, middle-class families with an infant, a follow-up was conducted of 26 of the still intact families to determine the stability of paternal involvement and the psychological predictors of fathers' behavior at the time. Paternal involvement was assessed at both times in terms of care,…

  8. Predicting communities from functional traits.

    PubMed

    Cadotte, Marc W; Arnillas, Carlos A; Livingstone, Stuart W; Yasui, Simone-Louise E

    2015-09-01

    Species traits influence where species live and how they interact. While there have been many advances in describing the functional composition and diversity of communities, only recently do researchers have the ability to predict community composition and diversity. This predictive ability can offer fundamental insights into ecosystem resilience and restoration. PMID:26190136

  9. Functional MicroRNA Involved in Endometriosis

    PubMed Central

    Creighton, Chad J.; Han, Derek Y.; Zariff, Azam; Anderson, Matthew L.; Gunaratne, Preethi H.; Matzuk, Martin M.

    2011-01-01

    Endometriosis is a common disease seen by gynecologists. Clinical features involve pelvic pain and unexplained infertility. Although endometriosis is pathologically characterized by endometrial tissue outside the normal uterine location, endometriosis is otherwise not easily explained. Endometriomas, endometriotic cysts of the ovary, typically cause pain and distortion of pelvic anatomy. To begin to understand the pathogenesis of endometriomas, we describe the first transcriptome-microRNAome analysis of endometriomas and eutopic endometrium using next-generation sequencing technology. Using this approach, we generated a total of more than 54 million independent small RNA reads from our 19 clinical samples. At the microRNA level, we found 10 microRNA that were up-regulated (miR-202, 193a-3p, 29c, 708, 509-3-5p, 574-3p, 193a-5p, 485-3p, 100, and 720) and 12 microRNA that were down-regulated (miR-504, 141, 429, 203, 10a, 200b, 873, 200c, 200a, 449b, 375, and 34c-5p) in endometriomas compared with endometrium. Using in silico prediction algorithms, we correlated these microRNA with their corresponding differentially expressed mRNA targets. To validate the functional roles of microRNA, we manipulated levels of miR-29c in an in vitro system of primary cultures of human endometrial stromal fibroblasts. Extracellular matrix genes that were potential targets of miR-29c in silico were significantly down-regulated using this biological in vitro system. In vitro functional studies using luciferase reporter constructs further confirmed that miR-29c directly affects specific extracellular matrix genes that are dysregulated in endometriomas. Thus, miR-29c and other abnormally regulated microRNA appear to play important roles in the pathophysiology of uterine function and dysfunction. PMID:21436257

  10. 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.

  11. [Muscular Dystrophies Involving the Retinal Function].

    PubMed

    Jägle, H

    2016-03-01

    Muscular dystrophies are rare disorders, with an incidence of approx. 20 in 100 000. Some dystrophies also affect retinal or optic nerve function. In such cases, the ophthalmological findings may be critical for differential diagnosis or patient counseling. For example in Duchenne muscular dystrophy, where the alteration in retinal function seems to reflect cerebral involvement. Other important forms are mitochondrial and metabolic disorders, such as the Kearns-Sayre syndrome and the Refsum syndrome. Molecular genetic analysis has become a major tool for differential diagnosis, but may be complex and demanding. This article gives an overview of major muscular dystrophies involving retinal function and their genetic origin, in order to guide differential diagnosis. PMID:27011029

  12. 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.

  13. Vascular function and ocular involvement in sarcoidosis.

    PubMed

    Siasos, Gerasimos; Paraskevopoulos, Theodoros; Gialafos, Elias; Rapti, Aggeliki; Oikonomou, Evangelos; Zaromitidou, Marina; Mourouzis, Konstantinos; Siasou, Georgia; Gouliopoulos, Nikolaos; Tsalamandris, Sotiris; Vlasis, Konstantinos; Stefanadis, Christodoulos; Papavassiliou, Athanasios G; Tousoulis, Dimitris

    2015-07-01

    Ocular involvement occurs in sarcoidosis (Sar) patients mainly in the form of uveitis. This study was designed to determine if uveitis in Sar patients is associated with vascular impairment. We enrolled 82 Sar patients and 77, age and sex matched, control subjects (Cl). Sar patients were divided into those with ocular sarcoidosis (OS) and those without ocular sarcoidosis (WOS). Endothelial function was evaluated by flow-mediated dilation (FMD). Pulse wave velocity (PWV) was measured as an index of aortic stiffness and augmentation index (AIx) as a measure of arterial wave reflections. Although there was no significant difference in sex, age and mean arterial pressure, patients with OS compared to WOS patients and Cl subjects had impaired FMD (p<0.001), increased AIx (p=0.02) and increased PWV (p=0.001). Interestingly, impaired FMD in Sar patients was independently, from possible covariates (age, sex, smoking habits, arterial hypertension, dyslipidemia), associated with increased odds of ocular involvement (odds ratio=1.69, p=0.001). More precisely ROC curve analysis revealed that FMD had a significant diagnostic ability for the detection of OS (AUC=0.77, p<0.001) with a sensitivity of 79% and a specificity of 68% for an FMD value below 6.00%. To conclude in the present study we have shown that ocular involvement in Sar patients is associated with impaired endothelial function and increased arterial stiffness. These results strengthen the vascular theory which considers uveitis a consequence of vascular dysfunction in Sar patients and reveals a possible clinical importance of the use of endothelial function tests. PMID:25937082

  14. 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.

  15. Predicting hand function after hemidisconnection.

    PubMed

    Küpper, Hanna; Kudernatsch, Manfred; Pieper, Tom; Groeschel, Samuel; Tournier, Jacques-Donald; Raffelt, David; Winkler, Peter; Holthausen, Hans; Staudt, Martin

    2016-09-01

    Hemidisconnections (i.e. hemispherectomies or hemispherotomies) invariably lead to contralateral hemiparesis. Many patients with a pre-existing hemiparesis, however, experience no deterioration in motor functions, and some can still grasp with their paretic hand after hemidisconnection. The scope of our study was to predict this phenomenon. Hypothesizing that preserved contralateral grasping ability after hemidisconnection can only occur in patients controlling their paretic hands via ipsilateral corticospinal projections already in the preoperative situation, we analysed the asymmetries of the brainstem (by manual magnetic resonance imaging volumetry) and of the structural connectivity of the corticospinal tracts within the brainstem (by magnetic resonance imaging diffusion tractography), assuming that marked hypoplasia or Wallerian degeneration on the lesioned side in patients who can grasp with their paretic hands indicate ipsilateral control. One hundred and two patients who underwent hemidisconnections between 0.8 and 36 years of age were included. Before the operation, contralateral hand function was normal in 3/102 patients, 47/102 patients showed hemiparetic grasping ability and 52/102 patients could not grasp with their paretic hands. After hemidisconnection, 20/102 patients showed a preserved grasping ability, and 5/102 patients began to grasp with their paretic hands only after the operation. All these 25 patients suffered from pre- or perinatal brain lesions. Thirty of 102 patients lost their grasping ability. This group included all seven patients with a post-neonatally acquired or progressive brain lesion who could grasp before the operation, and also all three patients with a preoperatively normal hand function. The remaining 52/102 patients were unable to grasp pre- and postoperatively. On magnetic resonance imaging, the patients with preserved grasping showed significantly more asymmetric brainstem volumes than the patients who lost their grasping

  16. 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…

  17. 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. ...

  18. Inequalities involving modified Bessel functions of the first kind II

    NASA Astrophysics Data System (ADS)

    Baricz, Arpad; Neuman, Edward

    2007-08-01

    The intrinsic properties, including logarithmic convexity (concavity), of the modified Bessel functions of the first kind and some other related functions are obtained. Several inequalities involving functions under discussion are established.

  19. Theoretical prediction of new Kubas four centre H2 complexes involving dimolybdate clusters

    NASA Astrophysics Data System (ADS)

    Simandiras, Emmanuel D.; Liakos, Dimitrios G.

    2013-09-01

    A new type of Kubas nonclassical molecular hydrogen complex involving two metallic centers is predicted by extensive DFT calculations, using five accurate functionals. The interaction consists of a four centre bond involving two metal atoms and the H2 molecule, the latter retaining a significant part of its molecular nature. [Mo2Cl8(μ-H2)]2- and [Mo2(CO)8(μ-H2)] are two examples that are found to be stable.

  20. 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

  1. 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"…

  2. Quantitative assessment of protein function prediction programs.

    PubMed

    Rodrigues, B N; Steffens, M B R; Raittz, R T; Santos-Weiss, I C R; Marchaukoski, J N

    2015-01-01

    Fast prediction of protein function is essential for high-throughput sequencing analysis. Bioinformatic resources provide cheaper and faster techniques for function prediction and have helped to accelerate the process of protein sequence characterization. In this study, we assessed protein function prediction programs that accept amino acid sequences as input. We analyzed the classification, equality, and similarity between programs, and, additionally, compared program performance. The following programs were selected for our assessment: Blast2GO, InterProScan, PANTHER, Pfam, and ScanProsite. This selection was based on the high number of citations (over 500), fully automatic analysis, and the possibility of returning a single best classification per sequence. We tested these programs using 12 gold standard datasets from four different sources. The gold standard classification of the databases was based on expert analysis, the Protein Data Bank, or the Structure-Function Linkage Database. We found that the miss rate among the programs is globally over 50%. Furthermore, we observed little overlap in the correct predictions from each program. Therefore, a combination of multiple types of sources and methods, including experimental data, protein-protein interaction, and data mining, may be the best way to generate more reliable predictions and decrease the miss rate. PMID:26782400

  3. 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

  4. 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. PMID:26869536

  5. Prediction of Motor Recovery Using Diffusion Tensor Tractography in Supratentorial Stroke Patients With Severe Motor Involvement

    PubMed Central

    Kim, Kang Hee; Kim, Yun-Hee; Kim, Min Su; Park, Chang-hyun; Lee, Ahee

    2015-01-01

    Objective To investigate whether early stage diffusion tensor tractography (DTT) values predict motor function at 3 months after onset in supratentorial stroke patients with severe motor involvement. Methods A retrospective study design was used to analyze medical records and neuroimaging data of 49 supratentorial stroke patients with severe motor involvement. Diffusion tensor imaging was assessed within 3 weeks after stroke in all patients. Three-dimensional tractography of the ipsilateral corticospinal tract (CST) was performed using the fiber assignment of the continuous tracking algorithm. The two-step DTT analysis was used. The first step was classification according to ipsilateral CST visualization. The second step was a quantitative analysis of the visible-CST group parameters. Motor function was assessed at 2 weeks and at 3 months after stroke. Comparative and correlation analyses were performed between DTT-derived measures and motor assessment scores. Results Motor function of the upper extremity at 3 months after stroke was significantly higher in the visible-CST group than that in the nonvisible-CST group (p<0.05). Early stage fractional anisotropy was of DTT correlated significantly with upper extremity motor function at 3 months after stroke in the visible-CST group (p<0.05). Conclusion These results demonstrate that early DTT-derived measures predict motor recovery in the upper extremity at 3 months after onset in supratentorial stroke patients with severe motor involvement. PMID:26361593

  6. Biological cluster evaluation for gene function prediction.

    PubMed

    Klie, Sebastian; Nikoloski, Zoran; Selbig, Joachim

    2014-06-01

    Recent advances in high-throughput omics techniques render it possible to decode the function of genes by using the "guilt-by-association" principle on biologically meaningful clusters of gene expression data. However, the existing frameworks for biological evaluation of gene clusters are hindered by two bottleneck issues: (1) the choice for the number of clusters, and (2) the external measures which do not take in consideration the structure of the analyzed data and the ontology of the existing biological knowledge. Here, we address the identified bottlenecks by developing a novel framework that allows not only for biological evaluation of gene expression clusters based on existing structured knowledge, but also for prediction of putative gene functions. The proposed framework facilitates propagation of statistical significance at each of the following steps: (1) estimating the number of clusters, (2) evaluating the clusters in terms of novel external structural measures, (3) selecting an optimal clustering algorithm, and (4) predicting gene functions. The framework also includes a method for evaluation of gene clusters based on the structure of the employed ontology. Moreover, our method for obtaining a probabilistic range for the number of clusters is demonstrated valid on synthetic data and available gene expression profiles from Saccharomyces cerevisiae. Finally, we propose a network-based approach for gene function prediction which relies on the clustering of optimal score and the employed ontology. Our approach effectively predicts gene function on the Saccharomyces cerevisiae data set and is also employed to obtain putative gene functions for an Arabidopsis thaliana data set. PMID:20059365

  7. 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. PMID:22868650

  8. State public policy issues involved with the Parkfield prediction experiment.

    USGS Publications Warehouse

    Andrews, R.; Goltz, J.

    1988-01-01

    The earthquake-prediction experiment at Parkfield may well be the most important such experiment currently underway worldwide. Its importance, however, extends beyond the scientific data that will be gathered and whether those data that will be gathered and whether those data can provide reliable prediction methods. Important public policy lessons are being learned (and are yet to be learned), and these lessons may be transferable to other parts of California and the nation. Indeed, the Parkfield experiment has captured the interest of numerous Californians, including State officials, emergency managers, the news media, and at least some of the public.

  9. 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.

  10. 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…

  11. 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

  12. 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…

  13. Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining

    PubMed Central

    Hoehndorf, Robert; Martin, Maria J.; Solovyev, Victor

    2016-01-01

    The widening gap between known proteins and their functions has encouraged the development of methods to automatically infer annotations. Automatic functional annotation of proteins is expected to meet the conflicting requirements of maximizing annotation coverage, while minimizing erroneous functional assignments. This trade-off imposes a great challenge in designing intelligent systems to tackle the problem of automatic protein annotation. In this work, we present a system that utilizes rule mining techniques to predict metabolic pathways in prokaryotes. The resulting knowledge represents predictive models that assign pathway involvement to UniProtKB entries. We carried out an evaluation study of our system performance using cross-validation technique. We found that it achieved very promising results in pathway identification with an F1-measure of 0.982 and an AUC of 0.987. Our prediction models were then successfully applied to 6.2 million UniProtKB/TrEMBL reference proteome entries of prokaryotes. As a result, 663,724 entries were covered, where 436,510 of them lacked any previous pathway annotations. PMID:27390860

  14. 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. PMID:26751597

  15. 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

  16. 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. PMID:26935902

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

    PubMed

    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

    2014-08-15

    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. 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

  19. Contrast sensitivity function calibration based on image quality prediction

    NASA Astrophysics Data System (ADS)

    Han, Yu; Cai, Yunze

    2014-11-01

    Contrast sensitivity functions (CSFs) describe visual stimuli based on their spatial frequency. However, CSF calibration is limited by the size of the sample collection and this remains an open issue. In this study, we propose an approach for calibrating CSFs that is based on the hypothesis that a precise CSF model can accurately predict image quality. Thus, CSF calibration is regarded as the inverse problem of image quality prediction according to our hypothesis. A CSF could be calibrated by optimizing the performance of a CSF-based image quality metric using a database containing images with known quality. Compared with the traditional method, this would reduce the work involved in sample collection dramatically. In the present study, we employed three image databases to optimize some existing CSF models. The experimental results showed that the performance of a three-parameter CSF model was better than that of other models. The results of this study may be helpful in CSF and image quality research.

  20. Predicting Head Start parent involvement in an alcohol and other drug prevention program.

    PubMed

    Hahn, E J

    1995-01-01

    This study examined Health Belief Model predictors of parent involvement with preschool children in an alcohol and other drug (AOD) prevention program. Over 300 Head Start parents were invited to participate in BABES (Beginning Alcohol and Addictions Basic Education Studies) with their children once a week for 7 weeks. Two hundred parents completed self-report instruments prior to participation in BABES. Previous classroom involvement, barriers, county, and race predicted high attendance (3 to 7 lessons). AOD use severity, benefits, and role modeling predicted low attendance (1 to 2 lessons). Further research involving manipulation of external cues, parent involvement in nonclassroom settings, and race-homogeneous samples is recommended. PMID:7862545

  1. 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. PMID:24937013

  2. 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.

  3. 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. PMID:26627261

  4. 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

  5. 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

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

    PubMed

    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

  7. Cellular functions of vaults and their involvement in multidrug resistance.

    PubMed

    Steiner, E; Holzmann, K; Elbling, L; Micksche, M; Berger, W

    2006-08-01

    Vaults are evolutionary highly conserved ribonucleoprotein (RNP) particles with a hollow barrel-like structure. They are 41 x 73 nm in size and are composed of multiple copies of three proteins and small untranslated RNA (vRNA). The main component of vaults represents the 110 kDa major vault protein (MVP), whereas the two minor vault proteins comprise the 193 kDa vault poly(ADP-ribose) polymerase (VPARP) and the 240 kDa telomerase-associated protein-1 (TEP1). Vaults are abundantly present in the cytoplasm of eukaryotic cells and they were found to be associated with cytoskeletal elements as well as occasionally with the nuclear envelope. Vaults and MVP have been associated with several cellular processes which are also involved in cancer development like cell motility and differentiation. Due to the over-expression of MVP (also termed lung resistance-related protein or LRP) in several P-glycoprotein (P-gp)-negative chemoresistant cancer cell lines, vaults have been linked to multidrug resistance (MDR). Accordingly, high levels of MVP were found in tissues chronically exposed to xenobiotics. In addition, the expression of MVP correlated with the degree of malignancy in certain cancer types, suggesting a direct involvement in tumor development and/or progression. Based on the finding that MVP binds several phosphatases and kinases including PTEN, SHP-2 as well as Erk, evidence is accumulating that MVP might be involved in the regulation of important cell signalling pathways including the PI3K/Akt and the MAPK pathways. In this review we summarize the current knowledge concerning the vault particle and discuss its possible cellular functions, focusing on the role of vaults in chemotherapy resistance. PMID:16918321

  8. Predicting and exploring network components involved in pathogenesis in the malaria parasite via novel subnetwork alignments

    PubMed Central

    2015-01-01

    Background Malaria is a major health threat, affecting over 40% of the world's population. The latest report released by the World Health Organization estimated about 207 million cases of malaria infection, and about 627,000 deaths in 2012 alone. During the past decade, new therapeutic targets have been identified and are at various stages of characterization, thanks to the emerging omics-based technologies. However, the mechanism of malaria pathogenesis remains largely unknown. In this paper, we employ a novel neighborhood subnetwork alignment approach to identify network components that are potentially involved in pathogenesis. Results Our module-based subnetwork alignment approach identified 24 functional homologs of pathogenesis-related proteins in the malaria parasite P. falciparum, using the protein-protein interaction networks in Escherichia coli as references. Eighteen out of these 24 proteins are associated with 418 other proteins that are related to DNA replication, transcriptional regulation, translation, signaling, metabolism, cell cycle regulation, as well as cytoadherence and entry to the host. Conclusions The subnetwork alignments and subsequent protein-protein association network mining predicted a group of malarial proteins that may be involved in parasite development and parasite-host interaction, opening a new systems-level view of parasite pathogenesis and virulence. PMID:26100579

  9. Predicted vibrational spectra from anharmonic potential functions

    SciTech Connect

    Dunn, K.M.

    1986-01-01

    The dissertation develops a procedure for predicting vibrational spectra of polyatomic molecules from a combination of theoretical and experimental information. Ab initio quantum chemical calculations provide anharmonic force constants including cubics and diagonal quartics. A variational procedure analogous to configuration interaction is then used to compute eigenvalues of the pure vibrational Hamiltonian. The diagonal quadratic force constants are then adjusted until the calculated fundamental frequencies agree with experiment. The resulting theoretical-experimental force field may then be used to predict the energies of vibrationally excited states. The method is applied to three molecules: hydrogen cyanide, ammonia, and methyl fluoride. For hydrogen cyanide, the dissertation presents predicted energies for all of the vibrationally excited states with up to four quanta of excitation distributed among the four modes. The root-mean-square error is 8.7 cm{sup {minus}1} for the states below 11,000 cm{sup {minus}1}. The force constants for ammonia are adjusted to reproduce the fundamental frequencies of ND{sub 3}. The force constants then predict the energies of states below 7000 cm{sup {minus}1} with an rms error of 5.8 cm{sup {minus}1} for ND{sub 3} and 16.7 cm{sup {minus}1} for NH{sub 3}. Finally, the adjusted force constants for methyl fluoride predict the energies of states below 4100 cm{sup {minus}1} with an rms error of 4.3 cm{sup {minus}1}. These force constants are also used to predict the CH stretching overtone region of CH{sub 3}F and the first, second and third overtone regions of CD{sub 2}FH for which experimental information is not available.

  10. Father involvement: Identifying and predicting family members' shared and unique perceptions.

    PubMed

    Dyer, W Justin; Day, Randal D; Harper, James M

    2014-08-01

    Father involvement research has typically not recognized that reports of involvement contain at least two components: 1 reflecting a view of father involvement that is broadly recognized in the family, and another reflecting each reporter's unique perceptions. Using a longitudinal sample of 302 families, this study provides a first examination of shared and unique views of father involvement (engagement and warmth) from the perspectives of fathers, children, and mothers. This study also identifies influences on these shared and unique perspectives. Father involvement reports were obtained when the child was 12 and 14 years old. Mother reports overlapped more with the shared view than father or child reports. This suggests the mother's view may be more in line with broadly recognized father involvement. Regarding antecedents, for fathers' unique view, a compensatory model partially explains results; that is, negative aspects of family life were positively associated with fathers' unique view. Children's unique view of engagement may partially reflect a sentiment override with father antisocial behaviors being predictive. Mothers' unique view of engagement was predicted by father and mother work hours and her unique view of warmth was predicted by depression and maternal gatekeeping. Taken, together finding suggests a far more nuanced view of father involvement should be considered. PMID:25000130

  11. Network-based prediction of protein function

    PubMed Central

    Sharan, Roded; Ulitsky, Igor; Shamir, Ron

    2007-01-01

    Functional annotation of proteins is a fundamental problem in the post-genomic era. The recent availability of protein interaction networks for many model species has spurred on the development of computational methods for interpreting such data in order to elucidate protein function. In this review, we describe the current computational approaches for the task, including direct methods, which propagate functional information through the network, and module-assisted methods, which infer functional modules within the network and use those for the annotation task. Although a broad variety of interesting approaches has been developed, further progress in the field will depend on systematic evaluation of the methods and their dissemination in the biological community. PMID:17353930

  12. 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.

  13. 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.

  14. Predicting the Career Involvement of Women One Year After College Graduation.

    ERIC Educational Resources Information Center

    Lentz, Linda P.

    A 1980 study was conducted to determine those factors (educational background, career plans, family influence, parental background, and career salience) predictive of women's career involvement one year after college graduation. A second analysis further differentiated between the groups on the variable "commitment to working." Participants were…

  15. 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)

  16. 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. PMID:23184588

  17. Probabilistic Protein Function Prediction from Heterogeneous Genome-Wide Data

    PubMed Central

    Nariai, Naoki; Kolaczyk, Eric D.; Kasif, Simon

    2007-01-01

    Dramatic improvements in high throughput sequencing technologies have led to a staggering growth in the number of predicted genes. However, a large fraction of these newly discovered genes do not have a functional assignment. Fortunately, a variety of novel high-throughput genome-wide functional screening technologies provide important clues that shed light on gene function. The integration of heterogeneous data to predict protein function has been shown to improve the accuracy of automated gene annotation systems. In this paper, we propose and evaluate a probabilistic approach for protein function prediction that integrates protein-protein interaction (PPI) data, gene expression data, protein motif information, mutant phenotype data, and protein localization data. First, functional linkage graphs are constructed from PPI data and gene expression data, in which an edge between nodes (proteins) represents evidence for functional similarity. The assumption here is that graph neighbors are more likely to share protein function, compared to proteins that are not neighbors. The functional linkage graph model is then used in concert with protein domain, mutant phenotype and protein localization data to produce a functional prediction. Our method is applied to the functional prediction of Saccharomyces cerevisiae genes, using Gene Ontology (GO) terms as the basis of our annotation. In a cross validation study we show that the integrated model increases recall by 18%, compared to using PPI data alone at the 50% precision. We also show that the integrated predictor is significantly better than each individual predictor. However, the observed improvement vs. PPI depends on both the new source of data and the functional category to be predicted. Surprisingly, in some contexts integration hurts overall prediction accuracy. Lastly, we provide a comprehensive assignment of putative GO terms to 463 proteins that currently have no assigned function. PMID:17396164

  18. Metabolic Syndrome Biomarkers Predict Lung Function Impairment

    PubMed Central

    Naveed, Bushra; Weiden, Michael D.; Kwon, Sophia; Gracely, Edward J.; Comfort, Ashley L.; Ferrier, Natalia; Kasturiarachchi, Kusali J.; Cohen, Hillel W.; Aldrich, Thomas K.; Rom, William N.; Kelly, Kerry; Prezant, David J.

    2012-01-01

    Rationale: Cross-sectional studies demonstrate an association between metabolic syndrome and impaired lung function. Objectives: To define if metabolic syndrome biomarkers are risk factors for loss of lung function after irritant exposure. Methods: A nested case-control study of Fire Department of New York personnel with normal pre–September 11th FEV1 and who presented for subspecialty pulmonary evaluation before March 10, 2008. We correlated metabolic syndrome biomarkers obtained within 6 months of World Trade Center dust exposure with subsequent FEV1. FEV1 at subspecialty pulmonary evaluation within 6.5 years defined disease status; cases had FEV1 less than lower limit of normal, whereas control subjects had FEV1 greater than or equal to lower limit of normal. Measurements and Main Results: Clinical data and serum sampled at the first monitoring examination within 6 months of September 11, 2001, assessed body mass index, heart rate, serum glucose, triglycerides and high-density lipoprotein (HDL), leptin, pancreatic polypeptide, and amylin. Cases and control subjects had significant differences in HDL less than 40 mg/dl with triglycerides greater than or equal to 150 mg/dl, heart rate greater than or equal to 66 bpm, and leptin greater than or equal to 10,300 pg/ml. Each increased the odds of abnormal FEV1 at pulmonary evaluation by more than twofold, whereas amylin greater than or equal to 116 pg/ml decreased the odds by 84%, in a multibiomarker model adjusting for age, race, body mass index, and World Trade Center arrival time. This model had a sensitivity of 41%, a specificity of 86%, and a receiver operating characteristic area under the curve of 0.77. Conclusions: Abnormal triglycerides and HDL and elevated heart rate and leptin are independent risk factors of greater susceptibility to lung function impairment after September 11, 2001, whereas elevated amylin is protective. Metabolic biomarkers are predictors of lung disease, and may be useful for assessing

  19. Functional prediction of hypothetical proteins in human adenoviruses.

    PubMed

    Dorden, Shane; Mahadevan, Padmanabhan

    2015-01-01

    Assigning functional information to hypothetical proteins in virus genomes is crucial for gaining insight into their proteomes. Human adenoviruses are medium sized viruses that cause a range of diseases. Their genomes possess proteins with uncharacterized function known as hypothetical proteins. Using a wide range of protein function prediction servers, functional information was obtained about these hypothetical proteins. A comparison of functional information obtained from these servers revealed that some of them produced functional information, while others provided little functional information about these human adenovirus hypothetical proteins. The PFP, ESG, PSIPRED, 3d2GO, and ProtFun servers produced the most functional information regarding these hypothetical proteins. PMID:26664031

  20. Sexual abuse predicts functional somatic symptoms: an adolescent population study.

    PubMed

    Bonvanie, Irma J; van Gils, Anne; Janssens, Karin A M; Rosmalen, Judith G M

    2015-08-01

    The main aim of this study was to investigate the effect of childhood sexual abuse on medically not well explained or functional somatic symptoms (FSSs) in adolescents. We hypothesized that sexual abuse predicts higher levels of FSSs and that anxiety and depression contribute to this relationship. In addition, we hypothesized that more severe abuse is associated with higher levels of FSSs and that sexual abuse is related to gastrointestinal FSSs in particular. This study was part of the Tracking Adolescents' Individual Lives Survey (TRAILS): a general population cohort which started in 2001 (N=2,230; 50.8% girls, mean age 11.1 years). The current study uses data of 1,680 participants over four assessment waves (75% of baseline, mean duration of follow-up: 8 years). FSSs were measured by the Somatic Complaints subscale of the Youth Self-Report at all waves. Sexual abuse before the age of sixteen was assessed retrospectively with a questionnaire at T4. To test the hypotheses linear mixed models were used adjusted for age, sex, socioeconomic status, anxiety and depression. Sexual abuse predicted higher levels of FSSs after adjustment for age sex and socioeconomic status (B=.06) and after additional adjustment for anxiety and depression (B=.03). While sexual abuse involving physical contact significantly predicted the level of FSSs (assault; B=.08, rape; B=.05), non-contact sexual abuse was not significantly associated with FSSs (B=.04). Sexual abuse was not a stronger predictor of gastrointestinal FSSs (B=.06) than of all FSSs. Further research is needed to clarify possible mechanisms underlying relationship between sexual abuse and FSSs. PMID:26142915

  1. Using search engine technology for protein function prediction.

    PubMed

    Chen, Ziyang; Cai, Zhao; Li, Min; Liu, Binbin

    2011-01-01

    Prediction of protein function is one of the most challenging problems in the post-genomic era. In this paper, we propose a novel algorithm Improved ProteinRank (IPR) for protein function prediction, which is based on the search engine technology and the preferential attachment criteria. In addition, an improved algorithm IPRW is developed from IPR to be used in the weighted protein?protein interaction (PPI) network. The proposed algorithms IPR and IPRW are applied to the PPI network of S.cerevisiae. The experimental results show that both IPR and IPRW outweigh the previous methods for the prediction of protein functions. PMID:21441099

  2. 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

  3. Cerebral Involvement in the Cognitive Functioning of Bilinguals.

    ERIC Educational Resources Information Center

    Vaid, Jyotsna; Lambert, Wallace E.

    The cognitive processing strategies of two groups of French-English bilinguals were studied by means of an auditory Stroop test designed to evaluate cerebral hemispheric involvement. An "early bilingual" group were bilingual before the age of five, and a "late bilingual" group were bilingual after the age of ten. Stimuli were words uttered in…

  4. Rumination prospectively predicts executive functioning impairments in adolescents

    PubMed Central

    Connolly, Samantha L.; Wagner, Clara A.; Shapero, Benjamin G.; Pendergast, Laura L.; Abramson, Lyn Y.; Alloy, Lauren B.

    2014-01-01

    Background and objectives The current study tested the resource allocation hypothesis, examining whether baseline rumination or depressive symptom levels prospectively predicted deficits in executive functioning in an adolescent sample. The alternative to this hypothesis was also evaluated by testing whether lower initial levels of executive functioning predicted increases in rumination or depressive symptoms at follow-up. Methods A community sample of 200 adolescents (ages 12–13) completed measures of depressive symptoms, rumination, and executive functioning at baseline and at a follow-up session approximately 15 months later. Results Adolescents with higher levels of baseline rumination displayed decreases in selective attention and attentional switching at follow-up. Rumination did not predict changes in working memory or sustained and divided attention. Depressive symptoms were not found to predict significant changes in executive functioning scores at follow-up. Baseline executive functioning was not associated with change in rumination or depression over time. Conclusions Findings partially support the resource allocation hypothesis that engaging in ruminative thoughts consumes cognitive resources that would otherwise be allocated towards difficult tests of executive functioning. Support was not found for the alternative hypothesis that lower levels of initial executive functioning would predict increased rumination or depressive symptoms at follow-up. Our study is the first to find support for the resource allocation hypothesis using a longitudinal design and an adolescent sample. Findings highlight the potentially detrimental effects of rumination on executive functioning during early adolescence. PMID:23978629

  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. PMID:25343279

  6. 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

  7. 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

  8. Predicting Pelvic Lymph Node Involvement in Current-Era Prostate Cancer

    SciTech Connect

    Rahman, Sophia; Cosmatos, Harry; Dave, Giatri; Williams, Stephen; Tome, Michael

    2012-02-01

    Purpose: The Roach formula [2/3 Multiplication-Sign prostate-specific antigen + (Gleason score - 6) Multiplication-Sign 10], derived in 1993 during the early prostate specific antigen (PSA) screening era, has been used to predict the risk of pelvic lymph node involvement in patients with prostate cancer. In the current era of widespread PSA screening with a shift to earlier disease stages, there is evidence to suggest that the Roach score overestimates risk of nodal metastasis. This study retrospectively reviews the validity of this formula as a prediction tool. Methods and Materials: We conducted a retrospective institutional review including men with clinical T1c-T3 prostate cancer, with baseline PSA levels and biopsy-obtained Gleason scores who underwent radical prostatectomy with pelvic node dissection from 2001 through 2009 (N = 1,022). The predicted risk of nodal involvement was calculated for each patient using the Roach formula and then compared with actual rates following surgery. Results: The study included 1,022 patients; 99.6% had clinical T1c/T2 disease, with a mean of 10.3 lymph nodes surgically evaluated. Overall, 42 patients (4.1%) had nodal metastasis. For every range of scores, the Roach formula overestimates the risk of nodal involvement. Observed nodal positivity was 1%, 6.3%, 10%, 15.2%, and 16.7% for Roach scores {<=}10%, >10%-20%, >20%-30%, >30%-40%, and >40%, respectively. The Roach score overestimates the risk by approximately 4.5-fold in patients with scores {<=}10%, by 2.5-fold for all scores between 10% and 40%, and by 4-fold for scores >40%. Conclusion: The Roach formula overpredicts the risk of pelvic nodal involvement in current-era prostate cancer patients undergoing regular PSA screening and with mainly T1c/T2 disease. Contemporary patients are much less likely to have nodal involvement for a given PSA and Gleason score.

  9. Identification of chromosomal regions involved in decapentaplegic function in Drosophila.

    PubMed Central

    Nicholls, R E; Gelbart, W M

    1998-01-01

    Signaling molecules of the transforming growth factor beta (TGF-beta) family contribute to numerous developmental processes in a variety of organisms. However, our understanding of the mechanisms which regulate the activity of and mediate the response to TGF-beta family members remains incomplete. The product of the Drosophila decapentaplegic (dpp) locus is a well-characterized member of this family. We have taken a genetic approach to identify factors required for TGF-beta function in Drosophila by testing for genetic interactions between mutant alleles of dpp and a collection of chromosomal deficiencies. Our survey identified two deficiencies that act as maternal enhancers of recessive embryonic lethal alleles of dpp. The enhanced individuals die with weakly ventralized phenotypes. These phenotypes are consistent with a mechanism whereby the deficiencies deplete two maternally provided factors required for dpp's role in embryonic dorsal-ventral pattern formation. One of these deficiencies also appears to delete a factor required for dpp function in wing vein formation. These deficiencies remove material from the 54F-55A and 66B-66C polytene chromosomal regions, respectively. As neither of these regions has been previously implicated in dpp function, we propose that each of the deficiencies removes a novel factor or factors required for dpp function. PMID:9584097

  10. Gene function prediction with knowledge from gene ontology.

    PubMed

    Shen, Ying; Zhang, Lin

    2015-01-01

    Gene function prediction is an important problem in bioinformatics. Due to the inherent noise existing in the gene expression data, the attempt to improve the prediction accuracy resorting to new classification techniques is limited. With the emergence of Gene Ontology (GO), extra knowledge about the gene products can be extracted from GO and facilitates solving the gene function prediction problem. In this paper, we propose a new method which utilises GO information to improve the classifiers' performance in gene function prediction. Specifically, our method learns a distance metric under the supervision of the GO knowledge using the distance learning technique. Compared with the traditional distance metrics, the learned one produces a better performance and consequently classification accuracy can be improved. The effectiveness of our proposed method has been corroborated by the extensive experimental results. PMID:26529907

  11. 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

  12. 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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 ...

  14. Preschool Executive Functioning Abilities Predict Early Mathematics Achievement

    ERIC Educational Resources Information Center

    Clark, Caron A. C.; Pritchard, Verena E.; Woodward, Lianne J.

    2010-01-01

    Impairments in executive function have been documented in school-age children with mathematical learning difficulties. However, the utility and specificity of preschool executive function abilities in predicting later mathematical achievement are poorly understood. This study examined linkages between children's developing executive function…

  15. 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…

  16. 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

  17. STRIPAK Complexes: structure, biological function, and involvement in human diseases

    PubMed Central

    Hwang, Juyeon; Pallas, David C.

    2014-01-01

    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–like complexes in cellular processes of multiple organisms. These studies have identified novel STRIPAK or 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 will explore possible roles of striatin family complexes in disease, especially cerebral cavernous malformation. PMID:24333164

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

    PubMed Central

    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. PMID:26441501

  19. 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

  20. 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. PMID:23353650

  1. Protein Structure and Function Prediction Using I-TASSER

    PubMed Central

    Yang, Jianyi; Zhang, Yang

    2016-01-01

    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. PMID:26678386

  2. Involvement of Local Lamellipodia in Endothelial Barrier Function

    PubMed Central

    Breslin, Jerome W.; Zhang, Xun E.; Worthylake, Rebecca A.; Souza-Smith, Flavia M.

    2015-01-01

    Recently we observed that endothelial cells cultured in tightly confluent monolayers display frequent local lamellipodia, and that thrombin, an agent that increases endothelial permeability, reduces lamellipodia protrusions. This led us to test the hypothesis that local lamellipodia contribute to endothelial barrier function. Movements of subcellular structures containing GFP-actin or VE-cadherin-GFP expressed in endothelial cells were recorded using time-lapse microscopy. Transendothelial electrical resistance (TER) served as an index of endothelial barrier function. Changes in both lamellipodia dynamics and TER were assessed during baseline and after cells were treated with either the barrier-disrupting agent thrombin, or the barrier-stabilizing agent sphingosine-1-phosphate (S1P). The myosin II inhibitor blebbistatin was used to selectively block lamellipodia formation, and was used to test their role in the barrier function of endothelial cell monolayers and isolated, perfused rat mesenteric venules. Myosin light chain (MLC) phosphorylation was assessed by immunofluorescence microscopy. Rac1 and RhoA activation were evaluated using G-LISA assays. The role of Rac1 was tested with the specific inhibitor NSC23766 or by expressing wild-type or dominant negative GFP-Rac1. The results show that thrombin rapidly decreased both TER and the lamellipodia protrusion frequency. S1P rapidly increased TER in association with increased protrusion frequency. Blebbistatin nearly abolished local lamellipodia protrusions while cortical actin fibers and stress fibers remained intact. Blebbistatin also significantly decreased TER of cultured endothelial cells and increased permeability of isolated rat mesenteric venules. Both thrombin and S1P increased MLC phosphorylation and activation of RhoA. However, thrombin and S1P had differential impacts on Rac1, correlating with the changes in TER and lamellipodia protrusion frequency. Overexpression of Rac1 elevated, while NSC23766 and

  3. Involvement of local lamellipodia in endothelial barrier function.

    PubMed

    Breslin, Jerome W; Zhang, Xun E; Worthylake, Rebecca A; Souza-Smith, Flavia M

    2015-01-01

    Recently we observed that endothelial cells cultured in tightly confluent monolayers display frequent local lamellipodia, and that thrombin, an agent that increases endothelial permeability, reduces lamellipodia protrusions. This led us to test the hypothesis that local lamellipodia contribute to endothelial barrier function. Movements of subcellular structures containing GFP-actin or VE-cadherin-GFP expressed in endothelial cells were recorded using time-lapse microscopy. Transendothelial electrical resistance (TER) served as an index of endothelial barrier function. Changes in both lamellipodia dynamics and TER were assessed during baseline and after cells were treated with either the barrier-disrupting agent thrombin, or the barrier-stabilizing agent sphingosine-1-phosphate (S1P). The myosin II inhibitor blebbistatin was used to selectively block lamellipodia formation, and was used to test their role in the barrier function of endothelial cell monolayers and isolated, perfused rat mesenteric venules. Myosin light chain (MLC) phosphorylation was assessed by immunofluorescence microscopy. Rac1 and RhoA activation were evaluated using G-LISA assays. The role of Rac1 was tested with the specific inhibitor NSC23766 or by expressing wild-type or dominant negative GFP-Rac1. The results show that thrombin rapidly decreased both TER and the lamellipodia protrusion frequency. S1P rapidly increased TER in association with increased protrusion frequency. Blebbistatin nearly abolished local lamellipodia protrusions while cortical actin fibers and stress fibers remained intact. Blebbistatin also significantly decreased TER of cultured endothelial cells and increased permeability of isolated rat mesenteric venules. Both thrombin and S1P increased MLC phosphorylation and activation of RhoA. However, thrombin and S1P had differential impacts on Rac1, correlating with the changes in TER and lamellipodia protrusion frequency. Overexpression of Rac1 elevated, while NSC23766 and

  4. Revisiting the prediction of protein function at CASP6.

    PubMed

    Pellegrini-Calace, Marialuisa; Soro, Simonetta; Tramontano, Anna

    2006-07-01

    The ability to predict the function of a protein, given its sequence and/or 3D structure, is an essential requirement for exploiting the wealth of data made available by genomics and structural genomics projects and is therefore raising increasing interest in the computational biology community. To foster developments in the area as well as to establish the state of the art of present methods, a function prediction category was tentatively introduced in the 6th edition of the Critical Assessment of Techniques for Protein Structure Prediction (CASP) worldwide experiment. The assessment of the performance of the methods was made difficult by at least two factors: (a) the experimentally determined function of the targets was not available at the time of assessment; (b) the experiment is run blindly, preventing verification of whether the convergence of different predictions towards the same functional annotation was due to the similarity of the methods or to a genuine signal detectable by different methodologies. In this work, we collected information about the methods used by the various predictors and revisited the results of the experiment by verifying how often and in which cases a convergent prediction was obtained by methods based on different rationale. We propose a method for classifying the type and redundancy of the methods. We also analyzed the cases in which a function for the target protein has become available. Our results show that predictions derived from a consensus of different methods can reach an accuracy as high as 80%. It follows that some of the predictions submitted to CASP6, once reanalyzed taking into account the type of converging methods, can provide very useful information to researchers interested in the function of the target proteins. PMID:16759228

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

    In this paper, we report on the development of a parallel implementation of the coupled-cluster (CC) Green function formulation (GFCC) employing single and double excitations in the cluster operator (GFCCSD). A key aspect of this work is the determination of the frequency dependent self-energy, Σ(ω). The detailed description of the underlying algorithm is provided, including approximations used that preserve the pole structure of the full GFCCSD method, thereby reducing the computational costs while maintaining an accurate character of methodology. Furthermore, for systems with strong local correlation, our formulation reveals a diagonally dominate block structure where as the non-local correlation increases, the block size increases proportionally. To demonstrate the accuracy of our approach, several examples including calculations of ionization potentials for benchmark systems are presented and compared against experiment.

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

    PubMed

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

    2016-04-14

    In this paper, we report on the development of a parallel implementation of the coupled-cluster (CC) Green function formulation (GFCC) employing single and double excitations in the cluster operator (GFCCSD). A key aspect of this work is the determination of the frequency dependent self-energy, Σ(ω). The detailed description of the underlying algorithm is provided, including approximations used that preserve the pole structure of the full GFCCSD method, thereby reducing the computational costs while maintaining an accurate character of methodology. Furthermore, for systems with strong local correlation, our formulation reveals a diagonally dominate block structure where as the non-local correlation increases, the block size increases proportionally. To demonstrate the accuracy of our approach, several examples including calculations of ionization potentials for benchmark systems are presented and compared against experiment. PMID:27083702

  7. Postoperative cognitive dysfunction: Involvement of neuroinflammation and neuronal functioning.

    PubMed

    Hovens, Iris B; Schoemaker, Regien G; van der Zee, Eddy A; Absalom, Anthony R; Heineman, Erik; van Leeuwen, Barbara L

    2014-05-01

    Postoperative cognitive dysfunction (POCD) has been hypothesized to be mediated by surgery-induced inflammatory processes, which may influence neuronal functioning either directly or through modulation of intraneuronal pathways, such as the brain derived neurotrophic factor (BDNF) mediated pathway. To study the time course of post-surgical (neuro)inflammation, changes in the BDNF-pathway and POCD, we subjected 3months old male Wistar rats to abdominal surgery and implanted a jugular vein catheter for timed blood sampling. Cognition, affective behavior and markers for (neuro)inflammation, BDNF and neurogenesis were assessed at 1, 2 and 3weeks following surgery. Rats displayed changes in exploratory activity shortly after surgery, associated with postoperatively elevated IL-6 plasma levels. Spatial learning and memory were temporarily impaired in the first 2weeks following surgery, whereas non-spatial cognitive functions seemed unaffected. Analysis of brain tissue revealed increased neuroinflammation (IL-1B and microgliosis) 7days following surgery, decreased BDNF levels on postoperative day 14 and 21, and decreased neurogenesis until at least 21days following surgery. These findings indicate that in young adult rats only spatial learning and memory is affected by surgery, suggesting hippocampal dependent cognition is especially vulnerable to surgery-induced impairment. The observed differences in time course following surgery and relation to plasma IL-6 suggest cognitive dysfunction and mood changes comprise distinct features of postoperative behavioral impairment. The postoperative changes in neuroinflammation, BDNF and neurogenesis may represent aspects of the underlying mechanism for POCD. Future research should be aimed to elucidate how these players interact. PMID:24517920

  8. Evolution and cellular function of monothiol glutaredoxins: involvement in iron-sulphur cluster assembly.

    PubMed

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

    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

  9. Selenium in the environment, metabolism and involvement in body functions.

    PubMed

    Mehdi, Youcef; Hornick, Jean-Luc; Istasse, Louis; Dufrasne, Isabelle

    2013-01-01

    Selenium (Se³⁴₇₉) is a metalloid which is close to sulfur (S) in terms of properties. The Se concentration in soil varies with type, texture and organic matter content of the soil and with rainfall. Its assimilation by plants is influenced by the physico-chemical properties of the soil (redox status, pH and microbial activity). The presence of Se in the atmosphere is linked to natural and anthropogenic activities. Selenoproteins, in which selenium is present as selenocysteine, present an important role in many body functions, such as antioxidant defense and the formation of thyroid hormones. Some selenoprotein metabolites play a role in cancer prevention. In the immune system, selenium stimulates antibody formation and activity of helper T cells, cytotoxic T cells and Natural Killer (NK) cells. The mechanisms of intestinal absorption of selenium differ depending on the chemical form of the element. Selenium is mainly absorbed in the duodenum and caecum by active transport through a sodium pump. The recommended daily intake of selenium varies from 60 μg/day for women, to 70 μg/day for men. In growing ruminants the requirements are estimated at 100 μg/kg dry matter and 200 μg/Kg for pregnant or lactating females. A deficiency can cause reproductive disorders in humans and animals. PMID:23486107

  10. Structure and function of pseudoknots involved in gene expression control

    PubMed Central

    Peselis, Alla; Serganov, Alexander

    2015-01-01

    Natural RNA molecules can have a high degree of structural complexity but even the most complexly-folded RNAs are assembled from simple structural building blocks. Among the simplest RNA elements are double-stranded helices that participate in the formation of different folding topologies and constitute the major fraction of RNA structures. One common folding motif of RNA is a pseudoknot, defined as a bipartite helical structure formed by base-pairing of the apical loop in the stem-loop structure with an outside sequence. Pseudoknots constitute integral parts of the RNA structures essential for various cellular activities. Among many functions of pseudoknotted RNAs is feedback regulation of gene expression, carried out through specific recognition of various molecules. Pseudoknotted RNAs autoregulate ribosomal and phage protein genes in response to downstream encoded proteins, while many metabolic and transport genes are controlled by cellular metabolites interacting with pseudoknotted RNA elements from the riboswitch family. Modulation of some genes also depends on metabolite-induced mRNA cleavage performed by pseudoknotted ribozymes. Several regulatory pseudoknots have been characterized biochemically and structurally in great detail. These studies have demonstrated a plethora of pseudoknot-based folds and have begun uncovering diverse molecular principles of the ligand-dependent gene expression control. The pseudoknot-mediated mechanisms of gene control and many unexpected and interesting features of the regulatory pseudoknots have significantly advanced our understanding of the genetic circuits and laid the foundation for modulation of their outcomes. PMID:25044223

  11. [Prediction of postoperative visual acuity in retinal detachment with macular involvement].

    PubMed

    Yasukawa, T; Fukuda, T; Kishimoto, M; Ogura, Y

    1995-03-01

    We used laser interferometry (LI) and a potential acuity meter (PAM) to predict visual acuity after surgery for patients with rhegmatogenous retinal detachment with macular involvement. Thirty one eyes of 31 patients with retinal detachment were treated with scleral buckling procedures. Postoperative visual acuity was correlated with preoperative measurements of the LI and PAM, preoperative visual acuity by Landort's ring, and the estimated duration of macular detachment. The correlation between the duration of macular detachment and the postoperative visual acuity was not good (r = 0.55, p < 0.01). Although the preoperative visual acuity showed a relatively good correlation with postoperative visual acuity (r = 0.62, p < 0.01), the results of the LI and PAM provided a better correlation (LI; r = 0.73, PAM; r = 0.71). Our results suggest that the LI and PAM are useful to predict the visual acuity after retinal reattachment in patients with preoperative macular detachment. PMID:7732924

  12. PredictProtein—an open resource for online prediction of protein structural and functional features

    PubMed Central

    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

    2014-01-01

    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. PMID:24799431

  13. Prediction of Postchemotherapy Ovarian Function Using Markers of Ovarian Reserve

    PubMed Central

    Xia, Rong; Schott, Anne F.; McConnell, Daniel; Banerjee, Mousumi; Hayes, Daniel F.

    2014-01-01

    Background. Reproductive-aged women frequently receive both chemotherapy and endocrine therapy as part of their treatment regimen for early stage hormone receptor-positive breast cancer. Chemotherapy results in transient or permanent ovarian failure in the majority of women. The difficulty in determining which patients will recover ovarian function has implications for adjuvant endocrine therapy decision making. We hypothesized that pretreatment serum anti-Müllerian hormone (AMH) and inhibin B concentrations would predict for ovarian function following chemotherapy. Methods. Pre- and perimenopausal women aged 25–50 years with newly diagnosed breast cancer were enrolled. Subjects underwent phlebotomy for assessment of serum AMH, inhibin B, follicle-stimulating hormone, and estradiol prior to chemotherapy and 1 month and 1 year following completion of treatment. Associations among hormone concentrations, clinical factors, and biochemically assessed ovarian function were assessed. Results. Twenty-seven subjects were evaluable for the primary endpoint. Median age was 41. Twenty subjects (74.1%) experienced recovery of ovarian function within 18 months. Of the 26 evaluable subjects assessed prior to chemotherapy, 19 (73.1%) had detectable serum concentrations of AMH. The positive predictive value of a detectable baseline serum AMH concentration for recovery of ovarian function was 94.7%, and the negative predictive value was 85.7%. On univariate analysis, younger age and detectable serum AMH concentration at chemotherapy initiation were predictive of increased likelihood of recovery of ovarian function. Conclusion. Prechemotherapy assessment of serum AMH may be useful for predicting postchemotherapy ovarian function. This finding has implications for decision making about adjuvant endocrine therapy in premenopausal women treated with chemotherapy. PMID:24319018

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

    PubMed Central

    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. PMID:25848497

  15. Predicting real-world functional milestones in schizophrenia.

    PubMed

    Olsson, Anna-Karin; Hjärthag, Fredrik; Helldin, Lars

    2016-08-30

    Schizophrenia is a severe disorder that often causes impairments in major areas of functioning, and most patients do not achieve expected real-world functional milestones. The aim of this study was to identify which variables of demography, illness activity, and functional capacity predict patients' ability to attain real-world functional milestones. Participants were 235 outpatients, 149 men and 86 women, diagnosed with schizophrenia spectrum disorder. Our results showed that younger patients managed to achieve a higher level of functioning in educational level, marital status, and social contacts. Patients' functional capacity was primarily associated with educational level and housing situation. We also found that women needed less support regarding housing and obtained a higher level of marital status as compared with men. Our findings demonstrate the importance of considering current symptoms, especially negative symptoms, and remission stability over time, together with age, duration of illness, gender, educational level, and current functional capacity, when predicting patients' future real-world functioning. We also conclude that there is an advantage in exploring symptoms divided into positive, negative, and general domains considering their probable impact on functional achievements. PMID:27235985

  16. 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. PMID:19406924

  17. Beyond Genotype: Serotonin Transporter Epigenetic Modification Predicts Human Brain Function

    PubMed Central

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

    2014-01-01

    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. PMID:25086606

  18. The rat nucleus accumbens is involved in guiding of instrumental responses by stimuli predicting reward magnitude.

    PubMed

    Giertler, Christian; Bohn, Ines; Hauber, Wolfgang

    2003-10-01

    The present study examined the involvement of N-methyl-d-aspartate (NMDA), alpha-amino-3-hydroxy-5-methyl-4-isoxazolpropionate/kainate (AMPA/KA) and dopamine receptors in the nucleus accumbens (ACB) in influencing reaction times of instrumental responses by the expectancy of reward. A simple reaction time task demanding conditioned lever release was used in which the upcoming reward magnitude was signalled in advance by discriminative cues. After training, in control rats with vehicle infusions (0.5 micro L) into the ACB, reaction times of responses were significantly shorter to the discriminative cue predictive of high reward magnitude. Indirect stimulation of dopamine receptors in the ACB by d-amphetamine (20 micro g/0.5 micro L) decreased reaction times, impaired their guidance by cue-associated reward magnitudes and reduced the accuracy of task performance. Blockade of AMPA/KA receptors in the ACB by 6-cyano-7-nitroquino-xaline-2,3-dione (0.75 and 2.5 micro g/0.5 micro L) or NMDA receptors by d(-)-2-amino-5-phosphonopentanoic acid (5 micro g/0.5 micro L) produced a general increase in reaction times, but left guidance of reaction times by cue-associated reward magnitudes unaffected. Thus, stimulation of intra-ACB ionotropic glutamate receptors is critically involved in modulating the speed of instrumental responding to cues predictive for reward magnitude, but is not required for intact performance of previously learned instrumental behaviour. PMID:14622231

  19. 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

  20. The Prediction of Ego Functioning in Adolescence. Final Report.

    ERIC Educational Resources Information Center

    Taube, Irvin; Vreeland, Rebecca

    The object of this study was to predict ego functioning in college among a group of successful high school graduates. Two hundred and seventy-one graduates of Phillips Exeter Academy who had been admitted to Harvard University during 4 consecutive years were studied. Three types of previously collected data were used: (1) teacher reports on the…

  1. 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.

  2. 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

  3. 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. PMID:24821813

  4. Protein side chain conformation predictions with an MMGBSA energy function.

    PubMed

    Gaillard, Thomas; Panel, Nicolas; Simonson, Thomas

    2016-06-01

    The prediction of protein side chain conformations from backbone coordinates is an important task in structural biology, with applications in structure prediction and protein design. It is a difficult problem due to its combinatorial nature. We study the performance of an "MMGBSA" energy function, implemented in our protein design program Proteus, which combines molecular mechanics terms, a Generalized Born and Surface Area (GBSA) solvent model, with approximations that make the model pairwise additive. Proteus is not a competitor to specialized side chain prediction programs due to its cost, but it allows protein design applications, where side chain prediction is an important step and MMGBSA an effective energy model. We predict the side chain conformations for 18 proteins. The side chains are first predicted individually, with the rest of the protein in its crystallographic conformation. Next, all side chains are predicted together. The contributions of individual energy terms are evaluated and various parameterizations are compared. We find that the GB and SA terms, with an appropriate choice of the dielectric constant and surface energy coefficients, are beneficial for single side chain predictions. For the prediction of all side chains, however, errors due to the pairwise additive approximation overcome the improvement brought by these terms. We also show the crucial contribution of side chain minimization to alleviate the rigid rotamer approximation. Even without GB and SA terms, we obtain accuracies comparable to SCWRL4, a specialized side chain prediction program. In particular, we obtain a better RMSD than SCWRL4 for core residues (at a higher cost), despite our simpler rotamer library. Proteins 2016; 84:803-819. © 2016 Wiley Periodicals, Inc. PMID:26948696

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

    PubMed Central

    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

  6. 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 i ntegrate 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. PMID:26800544

  7. Analysis and Functional Prediction of Reactive Cysteine Residues*

    PubMed Central

    Marino, Stefano M.; Gladyshev, Vadim N.

    2012-01-01

    Cys is much different from other common amino acids in proteins. Being one of the least abundant residues, Cys is often observed in functional sites in proteins. This residue is reactive, polarizable, and redox-active; has high affinity for metals; and is particularly responsive to the local environment. A better understanding of the basic properties of Cys is essential for interpretation of high-throughput data sets and for prediction and classification of functional Cys residues. We provide an overview of approaches used to study Cys residues, from methods for investigation of their basic properties, such as exposure and pKa, to algorithms for functional prediction of different types of Cys in proteins. PMID:22157013

  8. Pattern recognition methods for protein functional site prediction.

    PubMed

    Yang, Zheng Rong; Wang, Lipo; Young, Natasha; Trudgian, Dave; Chou, Kuo-Chen

    2005-10-01

    Protein functional site prediction is closely related to drug design, hence to public health. In order to save the cost and the time spent on identifying the functional sites in sequenced proteins in biology laboratory, computer programs have been widely used for decades. Many of them are implemented using the state-of-the-art pattern recognition algorithms, including decision trees, neural networks and support vector machines. Although the success of this effort has been obvious, advanced and new algorithms are still under development for addressing some difficult issues. This review will go through the major stages in developing pattern recognition algorithms for protein functional site prediction and outline the future research directions in this important area. PMID:16248799

  9. 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

  10. A Prediction Model for Functional Outcomes in Spinal Cord Disorder Patients Using Gaussian Process Regression.

    PubMed

    Lee, Sunghoon Ivan; Mortazavi, Bobak; Hoffman, Haydn A; Lu, Derek S; Li, Charles; Paak, Brian H; Garst, Jordan H; Razaghy, Mehrdad; Espinal, Marie; Park, Eunjeong; Lu, Daniel C; Sarrafzadeh, Majid

    2016-01-01

    Predicting the functional outcomes of spinal cord disorder patients after medical treatments, such as a surgical operation, has always been of great interest. Accurate posttreatment prediction is especially beneficial for clinicians, patients, care givers, and therapists. This paper introduces a prediction method for postoperative functional outcomes by a novel use of Gaussian process regression. The proposed method specifically considers the restricted value range of the target variables by modeling the Gaussian process based on a truncated Normal distribution, which significantly improves the prediction results. The prediction has been made in assistance with target tracking examinations using a highly portable and inexpensive handgrip device, which greatly contributes to the prediction performance. The proposed method has been validated through a dataset collected from a clinical cohort pilot involving 15 patients with cervical spinal cord disorder. The results show that the proposed method can accurately predict postoperative functional outcomes, Oswestry disability index and target tracking scores, based on the patient's preoperative information with a mean absolute error of 0.079 and 0.014 (out of 1.0), respectively. PMID:25423659

  11. 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. PMID:24399338

  12. Scoring functions for prediction of protein-ligand interactions.

    PubMed

    Wang, Jui-Chih; Lin, Jung-Hsin

    2013-01-01

    The scoring functions for protein-ligand interactions plays central roles in computational drug design, virtual screening of chemical libraries for new lead identification, and prediction of possible binding targets of small chemical molecules. An ideal scoring function for protein-ligand interactions is expected to be able to recognize the native binding pose of a ligand on the protein surface among decoy poses, and to accurately predict the binding affinity (or binding free energy) so that the active molecules can be discriminated from the non-active ones. Due to the empirical nature of most, if not all, scoring functions for protein-ligand interactions, the general applicability of empirical scoring functions, especially to domains far outside training sets, is a major concern. In this review article, we will explore the foundations of different classes of scoring functions, their possible limitations, and their suitable application domains. We also provide assessments of several scoring functions on weakly-interacting protein-ligand complexes, which will be useful information in computational fragment-based drug design or virtual screening. PMID:23016847

  13. 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

  14. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function.

    PubMed

    Warde-Farley, David; Donaldson, Sylva L; Comes, Ovi; Zuberi, Khalid; Badrawi, Rashad; Chao, Pauline; Franz, Max; Grouios, Chris; Kazi, Farzana; Lopes, Christian Tannus; Maitland, Anson; Mostafavi, Sara; Montojo, Jason; Shao, Quentin; Wright, George; Bader, Gary D; Morris, Quaid

    2010-07-01

    GeneMANIA (http://www.genemania.org) is a flexible, user-friendly web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Given a query list, GeneMANIA extends the list with functionally similar genes that it identifies using available genomics and proteomics data. GeneMANIA also reports weights that indicate the predictive value of each selected data set for the query. Six organisms are currently supported (Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus, Homo sapiens and Saccharomyces cerevisiae) and hundreds of data sets have been collected from GEO, BioGRID, Pathway Commons and I2D, as well as organism-specific functional genomics data sets. Users can select arbitrary subsets of the data sets associated with an organism to perform their analyses and can upload their own data sets to analyze. The GeneMANIA algorithm performs as well or better than other gene function prediction methods on yeast and mouse benchmarks. The high accuracy of the GeneMANIA prediction algorithm, an intuitive user interface and large database make GeneMANIA a useful tool for any biologist. PMID:20576703

  15. 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

  16. 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

  17. Computational predictions of energy materials using density functional theory

    NASA Astrophysics Data System (ADS)

    Jain, Anubhav; Shin, Yongwoo; Persson, Kristin A.

    2016-01-01

    In the search for new functional materials, quantum mechanics is an exciting starting point. The fundamental laws that govern the behaviour of electrons have the possibility, at the other end of the scale, to predict the performance of a material for a targeted application. In some cases, this is achievable using density functional theory (DFT). In this Review, we highlight DFT studies predicting energy-related materials that were subsequently confirmed experimentally. The attributes and limitations of DFT for the computational design of materials for lithium-ion batteries, hydrogen production and storage materials, superconductors, photovoltaics and thermoelectric materials are discussed. In the future, we expect that the accuracy of DFT-based methods will continue to improve and that growth in computing power will enable millions of materials to be virtually screened for specific applications. Thus, these examples represent a first glimpse of what may become a routine and integral step in materials discovery.

  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. PMID:25599106

  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. Rapid D-Affine Biventricular Cardiac Function with Polar Prediction

    PubMed Central

    Gilbert, Kathleen; Cowan, Brett; Suinesiaputra, Avan; Occleshaw, Christopher; Young, Alistair

    2014-01-01

    Although many solutions have been proposed for left ventricular functional analysis of the heart, right and left (bi-) ventricular function has been problematic due to the complex geometry and large motions. Biventricular function is particularly important in congenital heart disease, the most common type of birth defects. We describe a rapid interactive analysis tool for biventricular function which incorporates 1) a 3D+ time finite element model of biventricular geometry, 2) a fast prediction step which estimates an initial geometry in a polar coordinate system, and 3) a Cartesian update which penalizes deviations from affine transformations (D-Affine) from a prior. Solution times were very rapid, enabling interaction in real time using guide point modeling. The method was applied to 13 patients with congenital heart disease and compared with the clinical gold standard of manual tracing. Results between the methods showed good correlation (R2 > 0.9) and good precision (volume<17ml; mass<11g) for both chambers. PMID:25485422

  1. 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

  2. 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.

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

    PubMed

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

    2016-06-01

    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

  4. 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

  5. Quantitative reactivity profiling predicts functional cysteines in proteomes.

    PubMed

    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

    2010-12-01

    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 profile quantitatively the intrinsic reactivity of cysteine residues en masse directly in native biological systems. Hyper-reactivity was a rare feature among cysteines and it was found to specify a wide range of activities, including nucleophilic and reductive catalysis and sites of oxidative modification. Hyper-reactive 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 is involved in iron-sulphur protein biogenesis. We also demonstrate that quantitative reactivity profiling can 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

  6. Gene Function Prediction from Functional Association Networks Using Kernel Partial Least Squares Regression

    PubMed Central

    Lehtinen, Sonja; Lees, Jon; Bähler, Jürg; Shawe-Taylor, John; Orengo, Christine

    2015-01-01

    With the growing availability of large-scale biological datasets, automated methods of extracting functionally meaningful information from this data are becoming increasingly important. Data relating to functional association between genes or proteins, such as co-expression or functional association, is often represented in terms of gene or protein networks. Several methods of predicting gene function from these networks have been proposed. However, evaluating the relative performance of these algorithms may not be trivial: concerns have been raised over biases in different benchmarking methods and datasets, particularly relating to non-independence of functional association data and test data. In this paper we propose a new network-based gene function prediction algorithm using a commute-time kernel and partial least squares regression (Compass). We compare Compass to GeneMANIA, a leading network-based prediction algorithm, using a number of different benchmarks, and find that Compass outperforms GeneMANIA on these benchmarks. We also explicitly explore problems associated with the non-independence of functional association data and test data. We find that a benchmark based on the Gene Ontology database, which, directly or indirectly, incorporates information from other databases, may considerably overestimate the performance of algorithms exploiting functional association data for prediction. PMID:26288239

  7. 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. PMID:27070016

  8. 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. PMID:25278640

  9. 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

  10. Remote sensing of vegetation ecophysiological function for improved hydrologic prediction

    NASA Astrophysics Data System (ADS)

    Drewry, D.; Ruddell, B. L.

    2014-12-01

    Land surface hydrology in vegetated landscapes is strongly controlled by ecophysiological function. The coupling between photosynthesis, stomatal dynamics and leaf energy balance fundamentally links the hydrologic and carbon cycles, and provides a basis for examining the utility of observations of functional plant traits for hydrologic prediction. Here we explore the potential of solar induced fluorescence (SIF) and thermal infrared (TIR) remote sensing observations to improve the accuracy and reduce the uncertainty in hydrologic prediction. While SIF represents an emission of radiation associated with photosynthesis, TIR provides information on foliage temperature and is related to stomatal function and water stress. A set of remote observing system simulation experiments are conducted to quantify the value of remotely sensed observations of SIF and TIR when assimilated into a detailed vegetation biophysical model. The MLCan model discretizes a dense plant canopy to resolve vertical variation in photosynthesis, water vapor and energy exchange. Here we present extensions to MLCan that allow for direct computation of the canopy emission of both SIF and TIR. The detailed representation of the physical environment and biological functioning of structurally complex canopies makes MLCan an ideal simulation tool for exploring the impact of these two unique, and potentially synergistic observables. This work specifically addresses remote sensing capabilities on both recently launched (OCO-2) and near-term (ECOSTRESS) satellite platforms. We contrast the information gained through the assimilation of SIF and TIR observations to that of the assimilation of data related to physical states such as soil moisture and leaf area index.

  11. 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. PMID:27476848

  12. 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. PMID:25378301

  13. FAST TRACK COMMUNICATION: Solvable nonlinear evolution PDEs in multidimensional space involving trigonometric functions

    NASA Astrophysics Data System (ADS)

    Calogero, F.; Françoise, J.-P.; Sommacal, M.

    2007-05-01

    A solvable nonlinear (system of) evolution PDEs in multidimensional space, involving trigonometric (or hyperbolic) functions, is identified. An isochronous version of this (system of) evolution PDEs in multidimensional space is also reported.

  14. 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 F3(·) 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

  15. 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

  16. Simple topological properties predict functional misannotations in a metabolic network

    PubMed Central

    Liberal, Rodrigo; Pinney, John W.

    2013-01-01

    Motivation: Misannotation in sequence databases is an important obstacle for automated tools for gene function annotation, which rely extensively on comparison with sequences with known function. To improve current annotations and prevent future propagation of errors, sequence-independent tools are, therefore, needed to assist in the identification of misannotated gene products. In the case of enzymatic functions, each functional assignment implies the existence of a reaction within the organism’s metabolic network; a first approximation to a genome-scale metabolic model can be obtained directly from an automated genome annotation. Any obvious problems in the network, such as dead end or disconnected reactions, can, therefore, be strong indications of misannotation. Results: We demonstrate that a machine-learning approach using only network topological features can successfully predict the validity of enzyme annotations. The predictions are tested at three different levels. A random forest using topological features of the metabolic network and trained on curated sets of correct and incorrect enzyme assignments was found to have an accuracy of up to 86% in 5-fold cross-validation experiments. Further cross-validation against unseen enzyme superfamilies indicates that this classifier can successfully extrapolate beyond the classes of enzyme present in the training data. The random forest model was applied to several automated genome annotations, achieving an accuracy of in most cases when validated against recent genome-scale metabolic models. We also observe that when applied to draft metabolic networks for multiple species, a clear negative correlation is observed between predicted annotation quality and phylogenetic distance to the major model organism for biochemistry (Escherichia coli for prokaryotes and Homo sapiens for eukaryotes). Contact: j.pinney@imperial.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID

  17. 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…

  18. 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

  19. "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. PMID:26744417

  20. Electrocortical indices of selective attention predict adolescent executive functioning.

    PubMed

    Lackner, Christine L; Santesso, Diane L; Dywan, Jane; Wade, Terrance J; Segalowitz, Sidney J

    2013-05-01

    Executive functioning is considered a powerful predictor of behavioral and mental health outcomes during adolescence. Our question was whether executive functioning skills, normally considered "top-down" processes, are related to automatic aspects of selective attention. Event-related potentials (ERPs) were recorded from typically-developing 12-14-year-old adolescents as they responded to tones presented in attended and unattended channels in an auditory selective attention task. Examining these ERPs in relation to parental reports on the Behavior Rating Inventory of Executive Function (BRIEF) revealed that an early frontal positivity (EFP) elicited by to-be-ignored/unattended tones was larger in those with poorer executive functions, driven by scores on the BRIEF Metacognition Index. As is traditionally found, N1 amplitudes were more negative for the to-be-attended rather than unattended tones. Additionally, N1 latencies to unattended tones correlated with parent-ratings on the BRIEF Behavior Regulation Index, where shorter latencies predicted better executive functions. Results suggest that the ability to disengage attention from distractor information in the early stages of stimulus processing is associated with adolescent executive functioning skills. PMID:23528784

  1. Motor function predicts parent-reported musculoskeletal pain in children with cerebral palsy

    PubMed Central

    Barney, Chantel C; Krach, Linda E; Rivard, Patrick F; Belew, John L; Symons, Frank J

    2013-01-01

    BACKGROUND: The relationship between pain and motor function is not well understood, especially for children and adolescents with communication and motor impairments associated with cerebral palsy (CP). OBJECTIVES: To determine whether a predictive relationship between motor function and musculoskeletal pain exists in children with CP. METHODS: Following informed consent, caregivers of 34 pediatric patients with CP (mean [± SD] age 9.37±4.49 years; 80.0% male) completed pain- and function-related measures. Parents completed the Dalhousie Pain Interview and the Brief Pain Inventory based on a one-week recall to determine whether pain had been experienced in the past week, its general description, possible cause, duration, frequency, intensity and interference with daily function. The Gross Motor Function Classification System (GMFCS) was used to classify the motor involvement of the child based on their functional ability and their need for assistive devices for mobility. RESULTS: GMFCS level significantly predicted parent-reported musculoskeletal pain frequency (P<0.02), duration (P=0.05) and intensity (P<0.01). Duration of pain was significantly related to interference with activities of daily living (P<0.05). CONCLUSIONS: Children with CP with greater motor involvement, as indexed by GMFCS level, may be at risk for increased pain (intensity, frequency and duration) that interfers with activities of daily living. The clinical index of suspicion should be raised accordingly when evaluating children with developmental disability who cannot self-report reliably. PMID:24308022

  2. [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. PMID:24263862

  3. 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. PMID:25759326

  4. 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

  5. The Evolutionary Legacy of Diversification Predicts Ecosystem Function.

    PubMed

    Yguel, Benjamin; Jactel, Hervé; Pearse, Ian S; Moen, Daniel; Winter, Marten; Hortal, Joaquin; Helmus, Matthew R; Kühn, Ingolf; Pavoine, Sandrine; Purschke, Oliver; Weiher, Evan; Violle, Cyrille; Ozinga, Wim; Brändle, Martin; Bartish, Igor; Prinzing, Andreas

    2016-10-01

    Theory suggests that the structure of evolutionary history represented in a species community may affect its functioning, but phylogenetic diversity metrics do not allow for the identification of major differences in this structure. Here we propose a new metric, ELDERness (for Evolutionary Legacy of DivERsity) to estimate evolutionary branching patterns within communities by fitting a polynomial function to lineage-through-time (LTT) plots. We illustrate how real and simulated community branching patterns can be more correctly described by ELDERness and can successfully predict ecosystem functioning. In particular, the evolutionary history of branching patterns can be encapsulated by the parameters of third-order polynomial functions and further measured through only two parameters, the "ELDERness surfaces." These parameters captured variation in productivity of a grassland community better than existing phylogenetic diversity or diversification metrics and independent of species richness or presence of nitrogen fixers. Specifically, communities with small ELDERness surfaces (constant accumulation of lineages through time in LTT plots) were more productive, consistent with increased productivity resulting from complementary lineages combined with niche filling within lineages. Overall, while existing phylogenetic diversity metrics remain useful in many contexts, we suggest that our ELDERness approach better enables testing hypotheses that relate complex patterns of macroevolutionary history represented in local communities to ecosystem functioning. PMID:27622874

  6. Utility functions predict variance and skewness risk preferences in monkeys

    PubMed Central

    Genest, Wilfried; Stauffer, William R.; Schultz, Wolfram

    2016-01-01

    Utility is the fundamental variable thought to underlie economic choices. In particular, utility functions are believed to reflect preferences toward risk, a key decision variable in many real-life situations. To assess the validity of utility representations, it is therefore important to examine risk preferences. In turn, this approach requires formal definitions of risk. A standard approach is to focus on the variance of reward distributions (variance-risk). In this study, we also examined a form of risk related to the skewness of reward distributions (skewness-risk). Thus, we tested the extent to which empirically derived utility functions predicted preferences for variance-risk and skewness-risk in macaques. The expected utilities calculated for various symmetrical and skewed gambles served to define formally the direction of stochastic dominance between gambles. In direct choices, the animals’ preferences followed both second-order (variance) and third-order (skewness) stochastic dominance. Specifically, for gambles with different variance but identical expected values (EVs), the monkeys preferred high-variance gambles at low EVs and low-variance gambles at high EVs; in gambles with different skewness but identical EVs and variances, the animals preferred positively over symmetrical and negatively skewed gambles in a strongly transitive fashion. Thus, the utility functions predicted the animals’ preferences for variance-risk and skewness-risk. Using these well-defined forms of risk, this study shows that monkeys’ choices conform to the internal reward valuations suggested by their utility functions. This result implies a representation of utility in monkeys that accounts for both variance-risk and skewness-risk preferences. PMID:27402743

  7. Predicting activity approach based on new atoms similarity kernel function.

    PubMed

    Abu El-Atta, Ahmed H; Moussa, M I; Hassanien, Aboul Ella

    2015-07-01

    Drug design is a high cost and long term process. To reduce time and costs for drugs discoveries, new techniques are needed. Chemoinformatics field implements the informational techniques and computer science like machine learning and graph theory to discover the chemical compounds properties, such as toxicity or biological activity. This is done through analyzing their molecular structure (molecular graph). To overcome this problem there is an increasing need for algorithms to analyze and classify graph data to predict the activity of molecules. Kernels methods provide a powerful framework which combines machine learning with graph theory techniques. These kernels methods have led to impressive performance results in many several chemoinformatics problems like biological activity prediction. This paper presents a new approach based on kernel functions to solve activity prediction problem for chemical compounds. First we encode all atoms depending on their neighbors then we use these codes to find a relationship between those atoms each other. Then we use relation between different atoms to find similarity between chemical compounds. The proposed approach was compared with many other classification methods and the results show competitive accuracy with these methods. PMID:26117822

  8. Predicting clinical responses in major depression using intrinsic functional connectivity.

    PubMed

    Qin, Jian; Shen, Hui; Zeng, Ling-Li; Jiang, Weixiong; Liu, Li; Hu, Dewen

    2015-08-19

    There has been increasing interest in multivariate pattern analysis (MVPA) as a means of distinguishing psychiatric patients from healthy controls using brain imaging. However, it remains unclear whether MVPA methods can accurately estimate the medication status of psychiatric patients. This study aims to develop an MVPA approach to accurately predict the antidepressant medication status of individuals with major depression on the basis of whole-brain resting-state functional connectivity MRI (rs-fcMRI). We investigated data from rs-fcMRI of 24 medication-naive depressed patients, 16 out of whom subsequently underwent antidepressant treatment and achieved clinical recovery, and 29 demographically similar controls. By training a linear support vector machine classifier and combining it with principal component analysis, the medication-naive patients were identified from the healthy controls with 100% accuracy. In addition, we found reliable correlations between MVPA prediction scores and clinical symptom severity. Moreover, the most discriminative functional connections were located within or across the cerebellum and default mode, affective, and sensorimotor networks, indicating that these networks may play important roles in major depression. Most importantly, only ∼30% of these discriminative connections were normalized in clinically recovered patients after antidepressant treatment. The current study may not only show the feasibility of estimating medication status by MVPA of whole-brain rs-fcMRI data in major depression but also shed new light on the pathological mechanism of this disorder. PMID:26164454

  9. 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).

  10. 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

  11. Ongoing dynamics in large-scale functional connectivity predict perception

    PubMed Central

    Sadaghiani, Sepideh; Poline, Jean-Baptiste; Kleinschmidt, Andreas; D’Esposito, Mark

    2015-01-01

    Most brain activity occurs in an ongoing manner not directly locked to external events or stimuli. Regional ongoing activity fluctuates in unison with some brain regions but not others, and the degree of long-range coupling is called functional connectivity, often measured with correlation. Strength and spatial distributions of functional connectivity dynamically change in an ongoing manner over seconds to minutes, even when the external environment is held constant. Direct evidence for any behavioral relevance of these continuous large-scale dynamics has been limited. Here, we investigated whether ongoing changes in baseline functional connectivity correlate with perception. In a continuous auditory detection task, participants perceived the target sound in roughly one-half of the trials. Very long (22–40 s) interstimulus intervals permitted investigation of baseline connectivity unaffected by preceding evoked responses. Using multivariate classification, we observed that functional connectivity before the target predicted whether it was heard or missed. Using graph theoretical measures, we characterized the difference in functional connectivity between states that lead to hits vs. misses. Before misses compared with hits and task-free rest, connectivity showed reduced modularity, a measure of integrity of modular network structure. This effect was strongest in the default mode and visual networks and caused by both reduced within-network connectivity and enhanced across-network connections before misses. The relation of behavior to prestimulus connectivity was dissociable from that of prestimulus activity amplitudes. In conclusion, moment to moment dynamic changes in baseline functional connectivity may shape subsequent behavioral performance. A highly modular network structure seems beneficial to perceptual efficiency. PMID:26106164

  12. Intravenous immunoglobulins improve the function and ameliorate joint involvement in systemic sclerosis: a pilot study

    PubMed Central

    Nacci, F; Righi, A; Conforti, M L; Miniati, I; Fiori, G; Martinovic, D; Melchiorre, D; Sapir, T; Blank, M; Shoenfeld, Y; Pignone, A Moggi; Cerinic, M Matucci

    2007-01-01

    Background In systemic sclerosis (SSc), joint involvement may reduce the functional capacity of the hands. Intravenous immunoglobulins have previously been shown to benefit patients with SSc. Aim To verify the efficacy of intravenous immunoglobulins on joint involvement and function in SSc. Patients and methods 7 women with SSc, 5 with limited and 2 with diffuse SSc, with a severe and refractory joint involvement were enrolled in the study. Methotrexate and cyclophosphamide pulse therapy did not ameliorate joint symptoms. Hence, intravenous immunoglobulins therapy was prescribed at a dosage of 2 g/kg body weight during 4 days/month for six consecutive courses. The presence of joint tenderness and swelling, and articular deformities (due to primary joint involvement and not due to skin and subcutaneous changes) were evaluated. Before and after 6 months of treatment, patients were subjected to (1) Ritchie Index (RI) evaluation of joint involvement; (2) Dreiser Algo‐Functional Index (IAFD) evaluation of hand joint function; (3) pain visual analogue scale (VAS) to measure joint pain; (4) Health Assessment Questionnaire (HAQ) to evaluate the limitations in everyday living and physical disability; and (5) modified Rodnan Skin Score for skin involvement. Results After 6 months of intravenous immunoglobulins therapy, joint pain and tenderness, measured with the VAS, decreased significantly (p<0.03), and hand function (IAFD) improved significantly (p<0.02), together with the quality of life (HAQ; p<0.03). All patients significantly improved, except for one. The skin score after 6 months of intravenous immunoglobulins therapy was significantly reduced (p<0.003). Conclusion This pilot study suggests that intravenous immunoglobulins may reduce joint pain and tenderness, with a significant recovery of joint function in patients with SSc with severe and refractory joint involvement. The cost of intravenous immunoglobulins might limit their use only to patients who

  13. 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…

  14. Further results involving a class of generalized Hurwitz-Lerch zeta functions

    NASA Astrophysics Data System (ADS)

    Srivastava, H. M.; Gaboury, S.; Fugère, B.-J.

    2014-10-01

    In this paper, we present several new expansion formulas for a class of generalized Hurwitz-Lerch zeta functions which were introduced by Raina and Chhajed [R. K. Raina and P. K. Chhajed, "Certain Results Involving a Class of Functions Associated with the Hurwitz Zeta Function," Acta Math. Univ. Comenian. 73, 89-100 (2004)] and (more recently) by Srivastava et al. [H. M. Srivastava, M.-J. Luo, and R. K. Raina, "New Results Involving a Class of Generalized Hurwitz-Lerch Zeta Functions and Their Applications," Turkish J. Anal. Number Theory 1, 26-35 (2013)]. These expansion formulas are obtained with the help of some fractional calculus theorems such as the generalized Leibniz rules, the Taylorlike expansions in terms of different functions and the generalized chain rule. Several (known or new) special cases are also considered.

  15. 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

  16. Evolution of the class C GPCR Venus flytrap modules involved positive selected functional divergence

    PubMed Central

    Cao, Jianhua; Huang, Siluo; Qian, Ji; Huang, Jinlin; Jin, Li; Su, Zhixi; Yang, Ji; Liu, Jianfeng

    2009-01-01

    Background Class C G protein-coupled receptors (GPCRs) represent a distinct group of the GPCR family, which structurally possess a characteristically distinct extracellular domain inclusive of the Venus flytrap module (VFTM). The VFTMs of the class C GPCRs is responsible for ligand recognition and binding, and share sequence similarity with bacterial periplasmic amino acid binding proteins (PBPs). An extensive phylogenetic investigation of the VFTMs was conducted by analyzing for functional divergence and testing for positive selection for five typical groups of the class C GPCRs. The altered selective constraints were determined to identify the sites that had undergone functional divergence via positive selection. In order to structurally demonstrate the pattern changes during the evolutionary process, three-dimensional (3D) structures of the GPCR VFTMs were modelled and reconstructed from ancestral VFTMs. Results Our results show that the altered selective constraints in the VFTMs of class C GPCRs are statistically significant. This implies that functional divergence played a key role in characterizing the functions of the VFTMs after gene duplication events. Meanwhile, positive selection is involved in the evolutionary process and drove the functional divergence of the VFTMs. Our results also reveal that three continuous duplication events occurred in order to shape the evolutionary topology of class C GPCRs. The five groups of the class C GPCRs have essentially different sites involved in functional divergence, which would have shaped the specific structures and functions of the VFTMs. Conclusion Taken together, our results show that functional divergence involved positive selection and is partially responsible for the evolutionary patterns of the class C GPCR VFTMs. The sites involved in functional divergence will provide more clues and candidates for further research on structural-function relationships of these modules as well as shedding light on the

  17. Predicting individual brain maturity using dynamic functional connectivity

    PubMed Central

    Qin, Jian; Chen, Shan-Guang; Hu, Dewen; Zeng, Ling-Li; Fan, Yi-Ming; Chen, Xiao-Ping; Shen, Hui

    2015-01-01

    Neuroimaging-based functional connectivity (FC) analyses have revealed significant developmental trends in specific intrinsic connectivity networks linked to cognitive and behavioral maturation. However, knowledge of how brain functional maturation is associated with FC dynamics at rest is limited. Here, we examined age-related differences in the temporal variability of FC dynamics with data publicly released by the Nathan Kline Institute (NKI; n = 183, ages 7–30) and showed that dynamic inter-region interactions can be used to accurately predict individual brain maturity across development. Furthermore, we identified a significant age-dependent trend underlying dynamic inter-network FC, including increasing variability of the connections between the visual network, default mode network (DMN) and cerebellum as well as within the cerebellum and DMN and decreasing variability within the cerebellum and between the cerebellum and DMN as well as the cingulo-opercular network. Overall, the results suggested significant developmental changes in dynamic inter-network interaction, which may shed new light on the functional organization of typical developmental brains. PMID:26236224

  18. Predicting Gene-Regulation Functions: Lessons from Temperate Bacteriophages

    PubMed Central

    Teif, Vladimir B.

    2010-01-01

    Gene-regulation functions (GRF) provide a unique characteristic of a cis-regulatory module (CRM), relating the concentrations of transcription factors (input) to the promoter activities (output). The challenge is to predict GRFs from the sequence. Here we systematically consider the lysogeny-lysis CRMs of different temperate bacteriophages such as the Lactobacillus casei phage A2, Escherichia coli phages λ, and 186 and Lactococcal phage TP901-1. This study allowed explaining a recent experimental puzzle on the role of Cro protein in the lambda switch. Several general conclusions have been drawn: 1), long-range interactions, multilayer assembly and DNA looping may lead to complex GRFs that cannot be described by linear functions of binding site occupancies; 2), in general, GRFs cannot be described by the Boolean logic, whereas a three-state non-Boolean logic suffices for the studied examples; 3), studied CRMs of the intact phages seemed to have a similar GRF topology (the number of plateaus and peaks corresponding to different expression regimes); we hypothesize that functionally equivalent CRMs might have topologically equivalent GRFs for a larger class of genetic systems; and 4) within a given GRF class, a set of mechanistic-to-mathematical transformations has been identified, which allows shaping the GRF before carrying out a system-level analysis. PMID:20371324

  19. 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. PMID:26108101

  20. 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

  1. 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.

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

    DOE PAGESBeta

    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

  3. Predicting stability constants for uranyl complexes using density functional theory.

    PubMed

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

    2015-04-20

    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 use density functional theory (B3LYP) and the integral equation formalism polarizable continuum model (IEF-PCM) to compute aqueous stability constants for UO2(2+) 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 chelating capability to uranyl. PMID:25835578

  4. FunPred-1: protein function prediction from a protein interaction network using neighborhood analysis.

    PubMed

    Saha, Sovan; Chatterjee, Piyali; Basu, Subhadip; Kundu, Mahantapas; Nasipuri, Mita

    2014-12-01

    Proteins are responsible for all biological activities in living organisms. Thanks to genome sequencing projects, large amounts of DNA and protein sequence data are now available, but the biological functions of many proteins are still not annotated in most cases. The unknown function of such non-annotated proteins may be inferred or deduced from their neighbors in a protein interaction network. In this paper, we propose two new methods to predict protein functions based on network neighborhood properties. FunPred 1.1 uses a combination of three simple-yet-effective scoring techniques: the neighborhood ratio, the protein path connectivity and the relative functional similarity. FunPred 1.2 applies a heuristic approach using the edge clustering coefficient to reduce the search space by identifying densely connected neighborhood regions. The overall accuracy achieved in FunPred 1.2 over 8 functional groups involving hetero-interactions in 650 yeast proteins is around 87%, which is higher than the accuracy with FunPred 1.1. It is also higher than the accuracy of many of the state-of-the-art protein function prediction methods described in the literature. The test datasets and the complete source code of the developed software are now freely available at http://code.google.com/p/cmaterbioinfo/ . PMID:25424913

  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. 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…

  7. The Role of Family Involvement in Predicting Student-Teacher Relationships and Academic and Behavioral Outcomes for Children of Immigrants

    ERIC Educational Resources Information Center

    Ryce, Patrice

    2012-01-01

    Using a multi-ethnic, socioeconomically varied sample of children of immigrants attending Islamic and public schools from first through third grade, this dissertation examined the degree to which school-based family involvement predicted teacher perceptions of value differences with parents, teacher expectations, child externalizing behavioral…

  8. 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.

  9. 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

  10. 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…

  11. 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. PMID:20609376

  12. Academic Achievement and School Functioning among Nonincarcerated Youth Involved with the Juvenile Justice System

    ERIC Educational Resources Information Center

    Brown, Jonathan D.; Riley, Anne W.; Walrath, Christine M.; Leaf, Philip J.; Valdez, Carmen

    2008-01-01

    The relationship between academic problems and delinquency is well documented among incarcerated populations but has not been examined among nonincarcerated youth involved with the juvenile justice system. This research examined the school functioning and academic achievement of 157 youth who had brief contact with a state department of juvenile…

  13. 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…

  14. 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…

  15. Sensitivity and specificity of the functional hallux limitus test to predict foot function.

    PubMed

    Payne, Craig; Chuter, Vivienne; Miller, Kathryn

    2002-05-01

    Functional hallux limitus is an underrecognized entity that generally does not produce symptoms but can result in a variety of compensatory mechanisms that can produce symptoms. Clinically, hallux limitus can be determined by assessing the range of motion available at the first metatarsophalangeal joint while the first ray is prevented from plantarflexing. The aim of this study was to determine the sensitivity and specificity of this clinical test to predict abnormal excessive midtarsal joint function during gait. A total of 86 feet were examined for functional hallux limitus and abnormal pronation of the midtarsal joint during late midstance. The test had a sensitivity of 0.72 and a specificity of 0.66, suggesting that clinicians should consider functional hallux limitus when there is late midstance pronation of the midtarsal joint during gait. PMID:12015407

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

    PubMed Central

    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

    2016-01-01

    Background and study aims: 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. Patients and methods: Retrospective multicenter study in which Lewis score (LS) was systematically determined in 190 CE of patients diagnosed with CD between 2003 and 2014. Results: 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). Conclusions: 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. PMID:27556069

  17. The role of family, peers and school perceptions in predicting involvement in youth violence.

    PubMed

    Laufer, Avital; Harel, Yossi

    2003-01-01

    This study explored the relative importance of family, peers and school in predicting youth violence. The analysis was done on a nationally representative sample included 8,394 students from grade 6th-10th in Israel. Measures of youth violence included bullying, physical fights and weapon carrying. The findings suggested that all three social systems had significant relations with youth violence, respectively. Variables found to predict violence were: Family-lack of parental support regarding school; Peers-Lack of social integration or too many evenings out with friends; School-feeling of school alienation, low academic achievement and perceptions of frequent acts of violence in school. School perceptions had the strongest predicting power. Findings emphasized the importance of focusing on improving the daily school experience in reducing youth violence. PMID:12964445

  18. Anatomical Involvement of the Subventricular Zone Predicts Poor Survival Outcome in Low-Grade Astrocytomas

    PubMed Central

    Liu, Shuai; Wang, Yinyan; Fan, Xing; Ma, Jun; Ma, Wenbin; Wang, Renzhi; Jiang, Tao

    2016-01-01

    The subventricular zone (SVZ) has been implicated in the origination, development, and biological behavior of gliomas. Tumor-SVZ contact is also postulated to be a poor prognostic factor in glioblastomas. We aimed to evaluate the prognostic consequence of the anatomical involvement of low-grade gliomas with the SVZ. To that end, we reviewed 143 patients with diffuse astrocytomas, and tumor lesions were manually delineated on magnetic resonance images. We initially investigated the prognostic role of SVZ contact in all patients. Additionally, we investigated the influence of the anatomical proximity of the tumor lesion centroids to the SVZ in the SVZ-involved patient cohorts, as well as location within the SVZ. We found SVZ contact with tumors to be a significant prognostic factor of overall survival in all patients with diffuse astrocytomas (p = 0.027). In the SVZ-involved cohort, a shorter distance from the tumor centroid to the SVZ (≤30 mm) correlated with shorter overall survival (p = 0.022) on univariate analysis. However, there was no significant difference in overall survival with respect to the SVZ region involved with the tumor (p = 0.930). Multivariate analysis showed that a shorter distance between the tumor centroid and the SVZ (p = 0.039) was significantly associated with poor overall survival in SVZ-involved patients. Hence, this study helps establish the prognostic role of the anatomical interaction of tumors with the SVZ in low-grade astrocytomas. PMID:27120204

  19. 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

  20. Prediction of Functional Outcome in Axonal Guillain-Barre Syndrome

    PubMed Central

    2016-01-01

    Objective To identify the factors that could predict the functional outcome in patients with the axonal type of Guillain-Barre syndrome (GBS). Methods Two hundred and two GBS patients admitted to our university hospital between 2003 and 2014 were reviewed retrospectively. We defined a good outcome as being "able to walk independently at 1 month after onset" and a poor outcome as being "unable to walk independently at 1 month after onset". We evaluated the factors that differed between the good and poor outcome groups. Results Twenty-four patients were classified into the acute motor axonal neuropathy type. There was a statistically significant difference between the good and poor outcome groups in terms of the GBS disability score at admission, and GBS disability score and Medical Research Council sum score at 1 month after admission. In an electrophysiologic analysis, the good outcome group showed greater amplitude of median, ulnar, deep peroneal, and posterior tibial nerve compound muscle action potentials (CMAP) and greater amplitude of median, ulnar, and superficial peroneal sensory nerve action potentials (SNAP) than the poor outcome group. Conclusion A lower GBS disability score at admission, high amplitude of median, ulnar, deep peroneal, and posterior tibial CMAPs, and high amplitude of median, ulnar, and superficial peroneal SNAPs were associated with being able to walk at 1 month in patients with axonal GBS. PMID:27446785

  1. Asymmetries involving dihadron fragmentation functions: from DIS to e+ e- annihilation

    SciTech Connect

    Bacchetta, Alessandro; Radici, M.; Mukherjee, Asmita; Ceccopieri, Federico

    2009-01-01

    Using a model calculation of dihadron fragmentation functions, we fit the spin asymmetry recently extracted by HERMES for the semi-inclusive pion pair production in deep-inelastic scattering on a transversely polarized proton target. By evolving the obtained dihadron fragmentation functions, we make predictions for the correlation of the angular distributions of two pion pairs produced in electron-positron annihilations at BELLE kinematics. Our study shows that the combination of two-hadron inclusive deep-inelastic scattering and electron-positron annihilation measurements can provide a valid alternative to Collins effect for the extraction of the quark transversity distribution in the nucleon.

  2. 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,…

  3. How Does Motivational Interviewing Work? Therapist Interpersonal Skill Predicts Client Involvement Within Motivational Interviewing Sessions

    ERIC Educational Resources Information Center

    Moyers, Theresa B.; Miller, William R.; Hendrickson, Stacey M. L.

    2005-01-01

    Although many studies have shown that motivational interviewing (MI) is effective in reducing problem behaviors, few have investigated purported causal mechanisms. Therapist interpersonal skills have been proposed as an influence on client involvement during MI sessions and as a necessary precursor to client commitment language. Using the…

  4. 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…

  5. 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…

  6. 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

  7. 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

  8. 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

  9. 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. PMID:27134523

  10. 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

  11. 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

  12. 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. PMID:27328724

  13. Can a video-based hazard perception test used for driver licensing predict crash involvement?

    PubMed

    Horswill, Mark S; Hill, Andrew; Wetton, Mark

    2015-09-01

    In 2008, the state of Queensland in Australia introduced a video-based hazard perception test as part of the licensing process for new drivers. A key validity check for such a test is whether scores are associated with crash involvement. We present data demonstrating that drivers who failed the hazard perception test (based on a ROC curve-derived pass mark) were 25% [95% confidence interval (CI) 6%, 48%] more likely to be involved in an active crash (defined as a crash occurring while the driver's vehicle was moving but they were not engaged in parking or reversing) during a one year period following the test (controlling for driving exposure, age, and sex). Failing drivers were also 17% (95% CI 6%, 29%) more likely to have been involved in active crashes prior to the test, in the period since obtaining their provisional license. These data support the proposal that the hazard perception test is a valid measure of crash-related driving performance. PMID:26093097

  14. 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

  15. Reduced Cognitive Function Predicts Functional Decline in Patients with Heart Failure over 12 months

    PubMed Central

    Alosco, Michael L.; Spitznagel, Mary Beth; Cohen, Ronald; Sweet, Lawrence H.; Colbert, Lisa H.; Josephson, Richard; Hughes, Joel; Rosneck, Jim; Gunstad, John

    2016-01-01

    Background Impaired activities of daily living (ADL) are common in heart failure (HF) patients and contribute to the elevated mortality and hospitalization rates in this population. Cognitive impairment is also prevalent in HF, though its ability to predict functional decline over time is unknown. Aims This study examined the longitudinal pattern of activities of daily living in HF persons and whether reduced baseline cognitive status predicts functional decline in this population. Methods 110 persons with HF completed the Lawton-Brody Activities of Daily Living Scale and were administered the Modified Mini-Mental Status Examination (3MS) at baseline and a 12-month follow-up. Three composite scores were derived from the Lawton-Brody, including total, instrumental, and basic ADLs. Results HF patients reported high rates of baseline impairments in instrumental ADLs, including shopping, food preparation, housekeeping duties, laundry, among others. Repeated measures analyses showed significant declines in total and instrumental ADLs from baseline to the 12-month follow-up in HF (p < .05). Hierarchical regression analyses showed that poorer baseline performance on the 3MS predicted worse total ADL performance at 12-months (β = .15, p = .049), including greater dependence in shopping, driving, feeding, and physical ambulation (p < .05 for all). Conclusion The current results show that HF patients report significant functional decline over a 12-month period and brief cognitive tests can identify those patients at highest risk for decline. If replicated, such findings encourage the use of cognitive screening measures to identify HF patients most likely to require assistance with ADL tasks. PMID:23754840

  16. 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. PMID:26493392

  17. Recent improvements in prediction of protein structure by global optimization of a potential energy function

    PubMed Central

    Pillardy, Jarosław; Czaplewski, Cezary; Liwo, Adam; Lee, Jooyoung; Ripoll, Daniel R.; Kaźmierkiewicz, Rajmund; Ołdziej, Stanisław; Wedemeyer, William J.; Gibson, Kenneth D.; Arnautova, Yelena A.; Saunders, Jeff; Ye, Yuan-Jie; Scheraga, Harold A.

    2001-01-01

    Recent improvements of a hierarchical ab initio or de novo approach for predicting both α and β structures of proteins are described. The united-residue energy function used in this procedure includes multibody interactions from a cumulant expansion of the free energy of polypeptide chains, with their relative weights determined by Z-score optimization. The critical initial stage of the hierarchical procedure involves a search of conformational space by the conformational space annealing (CSA) method, followed by optimization of an all-atom model. The procedure was assessed in a recent blind test of protein structure prediction (CASP4). The resulting lowest-energy structures of the target proteins (ranging in size from 70 to 244 residues) agreed with the experimental structures in many respects. The entire experimental structure of a cyclic α-helical protein of 70 residues was predicted to within 4.3 Å α-carbon (Cα) rms deviation (rmsd) whereas, for other α-helical proteins, fragments of roughly 60 residues were predicted to within 6.0 Å Cα rmsd. Whereas β structures can now be predicted with the new procedure, the success rate for α/β- and β-proteins is lower than that for α-proteins at present. For the β portions of α/β structures, the Cα rmsd's are less than 6.0 Å for contiguous fragments of 30–40 residues; for one target, three fragments (of length 10, 23, and 28 residues, respectively) formed a compact part of the tertiary structure with a Cα rmsd less than 6.0 Å. Overall, these results constitute an important step toward the ab initio prediction of protein structure solely from the amino acid sequence. PMID:11226239

  18. 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. PMID:25553620

  19. Prediction of functional sites in proteins using conserved functional group analysis.

    PubMed

    Innis, C Axel; Anand, A Prem; Sowdhamini, R

    2004-04-01

    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. PMID:15033369

  20. On the regularization of extremal three-point functions involving giant gravitons

    NASA Astrophysics Data System (ADS)

    Kristjansen, Charlotte; Mori, Stefano; Young, Donovan

    2015-11-01

    In the AdS5 /CFT4 set-up, extremal three-point functions involving two giant 1/2 BPS gravitons and one point-like 1/2 BPS graviton, when calculated using semi-classical string theory methods, match the corresponding three-point functions obtained in the tree-level gauge theory. The string theory computation relies on a certain regularization procedure whose justification is based on the match between gauge and string theory. We revisit the regularization procedure and reformulate it in a way which allows a generalization to the ABJM set-up where three-point functions of 1/2 BPS operators are not protected and where a match between tree-level gauge theory and semi-classical string theory is hence not expected.

  1. Identification of Interphase Functions for the NIMA Kinase Involving Microtubules and the ESCRT Pathway

    PubMed Central

    Govindaraghavan, Meera; McGuire Anglin, Sarah Lea; Shen, Kuo-Fang; Shukla, Nandini; De Souza, Colin P.; Osmani, Stephen A.

    2014-01-01

    The Never in Mitosis A (NIMA) kinase (the founding member of the Nek family of kinases) has been considered a mitotic specific kinase with nuclear restricted roles in the model fungus Aspergillus nidulans. By extending to A. nidulans the results of a synthetic lethal screen performed in Saccharomyces cerevisiae using the NIMA ortholog KIN3, we identified a conserved genetic interaction between nimA and genes encoding proteins of the Endosomal Sorting Complex Required for Transport (ESCRT) pathway. Absence of ESCRT pathway functions in combination with partial NIMA function causes enhanced cell growth defects, including an inability to maintain a single polarized dominant cell tip. These genetic insights suggest NIMA potentially has interphase functions in addition to its established mitotic functions at nuclei. We therefore generated endogenously GFP-tagged NIMA (NIMA-GFP) which was fully functional to follow its interphase locations using live cell spinning disc 4D confocal microscopy. During interphase some NIMA-GFP locates to the tips of rapidly growing cells and, when expressed ectopically, also locates to the tips of cytoplasmic microtubules, suggestive of non-nuclear interphase functions. In support of this, perturbation of NIMA function either by ectopic overexpression or through partial inactivation results in marked cell tip growth defects with excess NIMA-GFP promoting multiple growing cell tips. Ectopic NIMA-GFP was found to locate to the plus ends of microtubules in an EB1 dependent manner, while impairing NIMA function altered the dynamic localization of EB1 and the cytoplasmic microtubule network. Together, our genetic and cell biological analyses reveal novel non-nuclear interphase functions for NIMA involving microtubules and the ESCRT pathway for normal polarized fungal cell tip growth. These insights extend the roles of NIMA both spatially and temporally and indicate that this conserved protein kinase could help integrate cell cycle progression

  2. Oil palm phenolics confer neuroprotective effects involving cognitive and motor functions in mice

    PubMed Central

    Leow, Soon-Sen; Sekaran, Shamala Devi; Tan, YewAi; Sundram, Kalyana; Sambanthamurthi, Ravigadevi

    2013-01-01

    Objectives Phenolics are important phytochemicals which have positive effects on chronic diseases, including neurodegenerative ailments. The oil palm (Elaeis guineensis) is a rich source of water-soluble phenolics. This study was carried out to discover the effects of administering oil palm phenolics (OPP) to mice, with the aim of identifying whether these compounds possess significant neuroprotective properties. Methods OPP was given to BALB/c mice on a normal diet as fluids for 6 weeks while the controls were given distilled water. These animals were tested in a water maze and on a rotarod weekly to assess the effects of OPP on cognitive and motor functions, respectively. Using Illumina microarrays, we further explored the brain gene expression changes caused by OPP in order to determine the molecular mechanisms involved. Real-time quantitative reverse transcription-polymerase chain reaction experiments were then carried out to validate the microarray data. Results We found that mice given OPP showed better cognitive function and spatial learning when tested in a water maze, and their performance also improved when tested on a rotarod, possibly due to better motor function and balance. Microarray gene expression analysis showed that these compounds up-regulated genes involved in brain development and activity, such as those under the regulation of the brain-derived neurotrophic factor. OPP also down-regulated genes involved in inflammation. Discussion These results suggest that the improvement of mouse cognitive and motor functions by OPP is caused by the neuroprotective and anti-inflammatory effects of the extract. PMID:23433062

  3. Proteomic biomarkers predicting lymph node involvement in serum of cervical cancer patients. Limitations of SELDI-TOF MS

    PubMed Central

    2012-01-01

    Background Lymph node status is not part of the staging system for cervical cancer, but provides important information for prognosis and treatment. We investigated whether lymph node status can be predicted with proteomic profiling. Material & methods Serum samples of 60 cervical cancer patients (FIGO I/II) were obtained before primary treatment. Samples were run through a HPLC depletion column, eliminating the 14 most abundant proteins ubiquitously present in serum. Unbound fractions were concentrated with spin filters. Fractions were spotted onto CM10 and IMAC30 surfaces and analyzed with surface-enhanced laser desorption time of flight (SELDI-TOF) mass spectrometry (MS). Unsupervised peak detection and peak clustering was performed using MASDA software. Leave-one-out (LOO) validation for weighted Least Squares Support Vector Machines (LSSVM) was used for prediction of lymph node involvement. Other outcomes were histological type, lymphvascular space involvement (LVSI) and recurrent disease. Results LSSVM models were able to determine LN status with a LOO area under the receiver operating characteristics curve (AUC) of 0.95, based on peaks with m/z values 2,698.9, 3,953.2, and 15,254.8. Furthermore, we were able to predict LVSI (AUC 0.81), to predict recurrence (AUC 0.92), and to differentiate between squamous carcinomas and adenocarcinomas (AUC 0.88), between squamous and adenosquamous carcinomas (AUC 0.85), and between adenocarcinomas and adenosquamous carcinomas (AUC 0.94). Conclusions Potential markers related with lymph node involvement were detected, and protein/peptide profiling support differentiation between various subtypes of cervical cancer. However, identification of the potential biomarkers was hampered by the technical limitations of SELDI-TOF MS. PMID:22694804

  4. Integrative functional genomic delineation of the cascades of transcriptional changes involved in hepatocellular carcinoma progression.

    PubMed

    Ramesh, Vignesh; Ganesan, Kumaresan

    2016-10-01

    Development of targeted therapeutics is still at its early stage for hepatocellular carcinoma (HCC) due to the incomplete understanding of the confounding regulations at signaling pathway level. In this investigation, gene co-expression-based networking and integrative functional genomic modeling of HCC mRNA profiles as signaling processes were employed to understand the complex signaling cascades involved in HCC development toward understanding the avenues for targeted therapeutics. Multiple sets of genes and molecular biological processes involved during HCC development were identified from this integrative analysis: (i) Loss of liver cellular features due to the reduced HNF4A & PPAR signaling in the early stages of HCC, (ii) activated inflammatory and stress signals in the cirrhosis stages and (iii) highly activated cellular proliferation with the activated E2F-MYC oncogenic signaling with the gain of embryonic liver stem cell-like features in the advanced stage tumors. Upon connecting these gene-sets with the established drug sensitivity-related gene signatures, targeted therapeutic strategies for the heterogeneous HCC conditions have been identified. PPAR agonist class of drugs for early stage HCC conditions, anti-inflammatory drugs for cirrhosis and topoisomerase inhibitors for the advanced HCC conditions were inferred. Integrative functional genomic analysis of HCC transcriptome profiles at the context of signaling pathways has defined the key molecular processes involved in HCC development. Further, the study highlights the stage-specific and pathway focused targeted therapeutics for HCC. These findings deserve extensive preclinical explorations toward the establishment of targeted therapeutics. PMID:27194100

  5. 21 CFR 868.1890 - Predictive pulmonary-function value calculator.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Predictive pulmonary-function value calculator. 868.1890 Section 868.1890 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN... pulmonary-function value calculator. (a) Identification. A predictive pulmonary-function value calculator...

  6. 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. PMID:21672959

  7. The functional analysis of MicroRNAs involved in NF-κB signaling.

    PubMed

    Yang, Y; Wang, J-K

    2016-05-01

    Nuclear factor kB (NF-kB) is a transcriptional factor that regulates a large number of genes that controls diverse biological functions, ranging from inflammation, cell proliferation and tumor development to learning and memory. MicroRNAs (miRNAs) are small non-coding RNA molecules involved in most aspects of physiological and pathological processes, including cancer, viral infections, inflammation and autoimmune diseases. miRNAs also play an important role in the regulation of NF-kB signaling pathway, some being inhibitory and others activating. Here, we analyzed the convergence of miRNAs involved in NF-kB signaling regulation and dysregulation of miRNAs and NF-kB activation in human diseases, particularly in cancer. The function of miR-146, miR-125b, miR-21, miR-301a, miR-30b, and miR-199 and their impacts on tumorigenesis are analyzed in this work. miRNAs as one of the most abundant classes of regulatory molecules, deciphering their biological function and pathological contribution in NF-kB dysregulation is essential to understand the complexity of immune systems and to develop therapeutics against cancer. PMID:27212168

  8. Working memory involved in predicting future outcomes based on past experiences.

    PubMed

    Dretsch, Michael N; Tipples, Jason

    2008-02-01

    Deficits in working memory have been shown to contribute to poor performance on the Iowa Gambling Task [IGT: Bechara, A., & Martin, E.M. (2004). Impaired decision making related to working memory deficits in individuals with substance addictions. Neuropsychology, 18, 152-162]. Similarly, a secondary memory load task has been shown to impair task performance [Hinson, J., Jameson, T. & Whitney, P. (2002). Somatic markers, working memory, and decision making. Cognitive, Affective, & Behavioural Neuroscience, 2, 341-353]. In the present study, we investigate whether the latter findings were due to increased random responding [Franco-Watkins, A. M., Pashler, H., & Rickard, T. C. (2006). Does working memory load lead to greater impulsivity? Commentary on Hinson, Jameson, and Whitney's (2003). Journal of Experimental Psychology: Learning, Memory & Cognition, 32, 443-447]. Participants were tested under Low Working Memory (LWM; n=18) or High Working Memory (HWM; n=17) conditions while performing the Reversed IGT in which punishment was immediate and reward delayed [Bechara, A., Dolan, S., & Hindes, A. (2002). Decision making and addiction (part II): Myopia for the future or hypersensitivity to reward? Neuropsychologia, 40, 1690-1705]. In support of a role for working memory in emotional decision making, compared to the LWM condition, participants in the HWM condition made significantly greater number of disadvantageous selections than that predicted by chance. Performance by the HWM group could not be fully explained by random responding. PMID:17628270

  9. 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.

  10. 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

  11. 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. PMID:27303024

  12. 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…

  13. 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

  14. Towards quantifying the role of exact exchange in the prediction hydrogen bond spin-spin coupling constants involving fluorine.

    PubMed

    San Fabián, J; Omar, S; García de la Vega, J M

    2016-08-28

    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. PMID:27586916

  15. The inhomogeneous distribution of liver function: possible impact on the prediction of post-operative remnant liver function

    PubMed Central

    Nilsson, Henrik; Karlgren, Silja; Blomqvist, Lennart; Jonas, Eduard

    2015-01-01

    Background Previous studies have shown that liver function is inhomogeneously distributed in diseased livers, and this uneven distribution cannot be compensated for if a global liver function test is used for the prediction of post-operative remnant liver function. Dynamic Gd-EOB-DTPA-enhanced magnetic resonance imaging (MRI) can assess segmental liver function, thus offering the possibility to overcome this problem. Methods In 10 patients with liver cirrhosis and 10 normal volunteers, the contribution of individual liver segments to total liver function and volume was calculated using dynamic Gd-EOB-DTPA-enhanced MRI. Remnant liver function predictions using a segmental method and global assessment were compared for a simulated left hemihepatectomy. For the prediction based on segmental functional MRI assessment, the estimated function of the remnant liver segments was added. Results Global liver function assessment overestimated the remnant liver function in 9 out of 10 patients by as much as 9.3% [median −3.5% (−9.3–3.5%)]. In the normal volunteers there was a slight underestimation of remnant function in 9 out of 10 cases [median 1.07% (−0.7–2.5%)]. Discussion The present study underlines the necessity of a segmental liver function test able to compensate for the non-homogeneous nature of liver function, if the prediction of post-operative remnant liver function is to be improved. PMID:25297934

  16. 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.

  17. Right Ventricular and Right Atrial Involvement Can Predict Atrial Fibrillation in Patients with Hypertrophic Cardiomyopathy?

    PubMed Central

    Doesch, Christina; Lossnitzer, Dirk; Rudic, Boris; Tueluemen, Erol; Budjan, Johannes; Haubenreisser, Holger; Henzler, Thomas; Schoenberg, Stefan O.; Borggrefe, Martin; Papavassiliu, Theano

    2016-01-01

    Objectives and Background: 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. Methods: 98 Patients with HCM and 30 healthy controls underwent CMR and were followed-up for 6±3 years. Results: 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. Conclusion: 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. PMID:26812947

  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. PMID:23971032

  20. 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. PMID:26400858

  1. Neural networks involved in adolescent reward processing: An activation likelihood estimation meta-analysis of functional neuroimaging studies.

    PubMed

    Silverman, Merav H; Jedd, Kelly; Luciana, Monica

    2015-11-15

    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 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

  2. High-throughput functional testing of ENCODE segmentation predictions

    PubMed Central

    Kwasnieski, Jamie C.; Fiore, Christopher; Chaudhari, Hemangi G.

    2014-01-01

    The histone modification state of genomic regions is hypothesized to reflect the regulatory activity of the underlying genomic DNA. Based on this hypothesis, the ENCODE Project Consortium measured the status of multiple histone modifications across the genome in several cell types and used these data to segment the genome into regions with different predicted regulatory activities. We measured the cis-regulatory activity of more than 2000 of these predictions in the K562 leukemia cell line. We tested genomic segments predicted to be Enhancers, Weak Enhancers, or Repressed elements in K562 cells, along with other sequences predicted to be Enhancers specific to the H1 human embryonic stem cell line (H1-hESC). Both Enhancer and Weak Enhancer sequences in K562 cells were more active than negative controls, although surprisingly, Weak Enhancer segmentations drove expression higher than did Enhancer segmentations. Lower levels of the covalent histone modifications H3K36me3 and H3K27ac, thought to mark active enhancers and transcribed gene bodies, associate with higher expression and partly explain the higher activity of Weak Enhancers over Enhancer predictions. While DNase I hypersensitivity (HS) is a good predictor of active sequences in our assay, transcription factor (TF) binding models need to be included in order to accurately identify highly expressed sequences. Overall, our results show that a significant fraction (∼26%) of the ENCODE enhancer predictions have regulatory activity, suggesting that histone modification states can reflect the cis-regulatory activity of sequences in the genome, but that specific sequence preferences, such as TF-binding sites, are the causal determinants of cis-regulatory activity. PMID:25035418

  3. 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

  4. 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

  5. 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. PMID:24524947

  6. 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

  7. Identification of four novel PCDH19 Mutations and prediction of their functional impact.

    PubMed

    Leonardi, Emanuela; Sartori, Stefano; Vecchi, Marilena; Bettella, Elisa; Polli, Roberta; Palma, Luca De; Boniver, Clementina; Murgia, Alessandra

    2014-11-01

    The PCDH19 gene encodes protocadherin-19, a transmembrane protein with six cadherin (EC) domains, containing adhesive interfaces likely to be involved in neuronal connection. Over a hundred mostly private mutations have been identified in girls with epilepsy, with or without intellectual disability (ID). Furthermore, transmitting hemizygous males are devoid of seizures or ID, making it difficult to establish the pathogenic nature of newly identified variants. Here, we describe an integrated approach to evaluate the pathogenicity of four novel PCDH19 mutations. Segregation analysis has been complemented with an in silico analysis of mutation effects at the protein level. Using sequence information, we compared different computational prediction methods. We used homology modeling to build structural models of two PCDH19 EC-domains, and compared wild-type and mutant models to identify differences in residue interactions or biochemical properties of the model surfaces. Our analysis suggests different molecular effects of the novel mutations in exerting their pathogenic role. Two of them interfere with or alter functional residues predicted to mediate ligand or protein binding, one alters the EC-domain folding stability; the frame-shift mutation produces a truncated protein lacking the intracellular domain. Interestingly, the girl carrying the putative loss of function mutation presents the most severe phenotype. PMID:25227595

  8. 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

  9. Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data

    PubMed Central

    Aßhauer, Kathrin P.; Wemheuer, Bernd; Daniel, Rolf; Meinicke, Peter

    2015-01-01

    Motivation: The characterization of phylogenetic and functional diversity is a key element in the analysis of microbial communities. Amplicon-based sequencing of marker genes, such as 16S rRNA, is a powerful tool for assessing and comparing the structure of microbial communities at a high phylogenetic resolution. Because 16S rRNA sequencing is more cost-effective than whole metagenome shotgun sequencing, marker gene analysis is frequently used for broad studies that involve a large number of different samples. However, in comparison to shotgun sequencing approaches, insights into the functional capabilities of the community get lost when restricting the analysis to taxonomic assignment of 16S rRNA data. Results: Tax4Fun is a software package that predicts the functional capabilities of microbial communities based on 16S rRNA datasets. We evaluated Tax4Fun on a range of paired metagenome/16S rRNA datasets to assess its performance. Our results indicate that Tax4Fun provides a good approximation to functional profiles obtained from metagenomic shotgun sequencing approaches. Availability and implementation: Tax4Fun is an open-source R package and applicable to output as obtained from the SILVAngs web server or the application of QIIME with a SILVA database extension. Tax4Fun is freely available for download at http://tax4fun.gobics.de/. Contact: kasshau@gwdg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25957349

  10. 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. PMID:23797468

  11. Misshapen/NIK-related kinase (MINK1) is involved in platelet function, hemostasis, and thrombus formation.

    PubMed

    Yue, Ming; Luo, Dongjiao; Yu, Shanshan; Liu, Pu; Zhou, Qi; Hu, Mengjiao; Liu, Yangyang; Wang, Shuai; Huang, Qian; Niu, Yuxi; Lu, Linrong; Hu, Hu

    2016-02-18

    The sterile-20 kinase misshapen/Nck-interacting kinase (NIK)-related kinase 1 (MINK1) is involved in many important cellular processes such as growth, cytoskeletal rearrangement, and motility. Here, with MINK1-deficient (MINK1(-/-)) mice, we showed that MINK1 plays an important role in hemostasis and thrombosis via the regulation of platelet functions. In the tail-bleeding assay, MINK1(-/-) mice exhibited a longer bleeding time than wild-type (WT) mice (575.2 ± 59.7 seconds vs 419.6 ± 66.9 seconds). In a model of ferric chloride-induced mesenteric arteriolar thrombosis, vessel occlusion times were twice as long in MINK1(-/-) mice as in WT mice. In an in vitro microfluidic whole-blood perfusion assay, thrombus formation on a collagen matrix under arterial shear conditions was significantly reduced in MINK1(-/-) platelets. Moreover, MINK1(-/-) platelets demonstrated impaired aggregation and secretion in response to low doses of thrombin and collagen. Furthermore, platelet spreading on fibrinogen was largely hampered in MINK1(-/-) platelets. The functional differences of MINK1(-/-) platelets could be attributed to impaired adenosine 5'-diphosphate secretion. Signaling events associated with MINK1 appeared to involve extracellular signal-regulated kinase, p38, and Akt. Hence, MINK1 may be an important signaling molecule that mediates mitogen-activated protein kinase signaling and participates in platelet activation and thrombus formation. PMID:26598717

  12. A Biochemical and Functional Protein Complex Involving Dopamine Synthesis and Transport into Synaptic Vesicles

    PubMed Central

    Cartier, Etienne A.; Parra, Leonardo A.; Baust, Tracy B.; Quiroz, Marisol; Salazar, Gloria; Faundez, Victor; Egaña, Loreto; Torres, Gonzalo E.

    2010-01-01

    Synaptic transmission depends on neurotransmitter pools stored within vesicles that undergo regulated exocytosis. In the brain, the vesicular monoamine transporter-2 (VMAT2) 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 VMAT2 physically and functionally interacts with the enzymes responsible for DA synthesis. In rat striata, TH and AADC co-immunoprecipitate with VMAT2, whereas in PC 12 cells, TH co-immunoprecipitates with the closely related VMAT1 and with overexpressed VMAT2. GST pull-down assays further identified three cytosolic domains of VMAT2 involved in the interaction with TH and AADC. Furthermore, in vitro binding assays demonstrated that TH directly interacts with VMAT2. Additionally, using fractionation and immunoisolation approaches, we demonstrate that TH and AADC associate with VMAT2-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 VMAT2/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 VMAT2-mediated transport into vesicles. PMID:19903816

  13. 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…

  14. 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)…

  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. Motor cortex excitability changes within 8 hours after ischaemic stroke may predict the functional outcome.

    PubMed

    Di Lazzaro, V; Oliviero, A; Profice, P; Saturno, E; Pilato, F; Tonali, P

    1999-06-01

    Motor evoked potentials after magnetic transcranial stimulation and the excitability of the motor cortex to increasing magnetic stimulus intensities were evaluated in six patients with hemiparesis after ischaemic stroke within 8 hours after stroke. The latencies of motor evoked potentials were normal in all patients. After stimulation of the ischaemic hemisphere we obtained responses comparable with the contralateral ones in two patients (mean NIH score 2 (SD 0)) and this group was completely asymptomatic after 15 days (NIH score 0). In four patients the excitability of the motor cortex involved by the ischaemia was reduced and magnetic motor threshold was higher than that of the spared motor cortex. This finding was associated with a poor motor recovery and the NIH score after 15 days was unchanged (NIH score 1.75 (SD 1.5)). The present data suggest that the evaluation of the excitability of motor cortex may offer a mean of predicting functional outcome following stroke. PMID:10461555

  17. 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

  18. Predicting Biological Functions of Compounds Based on Chemical-Chemical Interactions

    PubMed Central

    Huang, Tao; Cai, Yu-Dong; Chou, Kuo-Chen

    2011-01-01

    Given a compound, how can we effectively predict its biological function? It is a fundamentally important problem because the information thus obtained may benefit the understanding of many basic biological processes and provide useful clues for drug design. In this study, based on the information of chemical-chemical interactions, a novel method was developed that can be used to identify which of the following eleven metabolic pathway classes a query compound may be involved with: (1) Carbohydrate Metabolism, (2) Energy Metabolism, (3) Lipid Metabolism, (4) Nucleotide Metabolism, (5) Amino Acid Metabolism, (6) Metabolism of Other Amino Acids, (7) Glycan Biosynthesis and Metabolism, (8) Metabolism of Cofactors and Vitamins, (9) Metabolism of Terpenoids and Polyketides, (10) Biosynthesis of Other Secondary Metabolites, (11) Xenobiotics Biodegradation and Metabolism. It was observed that the overall success rate obtained by the method via the 5-fold cross-validation test on a benchmark dataset consisting of 3,137 compounds was 77.97%, which is much higher than 10.45%, the corresponding success rate obtained by the random guesses. Besides, to deal with the situation that some compounds may be involved with more than one metabolic pathway class, the method presented here is featured by the capacity able to provide a series of potential metabolic pathway classes ranked according to the descending order of their likelihood for each of the query compounds concerned. Furthermore, our method was also applied to predict 5,549 compounds whose metabolic pathway classes are unknown. Interestingly, the results thus obtained are quite consistent with the deductions from the reports by other investigators. It is anticipated that, with the continuous increase of the chemical-chemical interaction data, the current method will be further enhanced in its power and accuracy, so as to become a useful complementary vehicle in annotating uncharacterized compounds for their biological

  19. 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. PMID:27155483

  20. Better prediction of functional effects for sequence variants

    PubMed Central

    2015-01-01

    Elucidating the effects of naturally occurring genetic variation is one of the major challenges for personalized health and personalized medicine. Here, we introduce SNAP2, a novel neural network based classifier that improves over the state-of-the-art in distinguishing between effect and neutral variants. Our method's improved performance results from screening many potentially relevant protein features and from refining our development data sets. Cross-validated on >100k experimentally annotated variants, SNAP2 significantly outperformed other methods, attaining a two-state accuracy (effect/neutral) of 83%. SNAP2 also outperformed combinations of other methods. Performance increased for human variants but much more so for other organisms. Our method's carefully calibrated reliability index informs selection of variants for experimental follow up, with the most strongly predicted half of all effect variants predicted at over 96% accuracy. As expected, the evolutionary information from automatically generated multiple sequence alignments gave the strongest signal for the prediction. However, we also optimized our new method to perform surprisingly well even without alignments. This feature reduces prediction runtime by over two orders of magnitude, enables cross-genome comparisons, and renders our new method as the best solution for the 10-20% of sequence orphans. SNAP2 is available at: https://rostlab.org/services/snap2web Definitions used Delta, input feature that results from computing the difference feature scores for native amino acid and feature scores for variant amino acid; nsSNP, non-synoymous SNP; PMD, Protein Mutant Database; SNAP, Screening for non-acceptable polymorphisms; SNP, single nucleotide polymorphism; variant, any amino acid changing sequence variant. PMID:26110438

  1. 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. PMID:27132070

  2. 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.

  3. A kinome wide screen identifies novel kinases involved in regulation of monoamine transporter function.

    PubMed

    Vuorenpää, Anne; Ammendrup-Johnsen, Ina; Jørgensen, Trine N; Gether, Ulrik

    2016-09-01

    The high affinity transporters for the monoamine neurotransmitters, dopamine, norepinephrine, and serotonin, play a key role in controlling monoaminergic neurotransmission. It is believed that the transporters (DAT, NET and SERT, respectively) are subject to tight regulation by the cellular signaling machinery to maintain monoaminergic homeostasis. Kinases constitute a pivotal role in cellular signaling, however, the regulation of monoamine transporters by the entire ensemble of kinases is unknown. Here, we perform a whole human kinome RNA interference screen to identify novel kinases involved in regulation of monoamine transporter function and surface expression. A primary screen in HEK 293 cells stably expressing DAT or SERT with siRNAs against 573 human kinases revealed 93 kinases putatively regulating transporter function. All 93 hits, which also included kinases previously implicated in monoamine transporter regulation, such as Protein kinase B (Akt) and mitogen-activated protein kinases (MAPK), were validated with a new set of siRNAs in a secondary screen. In this screen we assessed both changes in uptake and surface expression leading to selection of 11 kinases for further evaluation in HEK 293 cells transiently expressing DAT, SERT or NET. Subsequently, three kinases; salt inducible kinase 3 (SIK3), cAMP-dependent protein kinase catalytic subunit alpha (PKA C-α) and protein kinase X-linked (PrKX); were selected for additional exploration in catecholaminergic CATH.a differentiated cells (CAD) and rat chromocytoma (PC12) cells. Whereas SIK3 likely transcriptionally regulated expression of the three transfected transporters, depletion of PKA C-α was shown to decrease SERT function. Depletion of PrKX caused decreased surface expression and function of DAT without changing protein levels, suggesting that PrKX stabilizes the transporter at the cell surface. Summarized, our data provide novel insight into kinome regulation of the monoamine transporters and

  4. Predictive Factors of Social Functioning in Patients with Schizophrenia: Exploration for the Best Combination of Variables Using Data Mining

    PubMed Central

    Bae, Sung-Man; Park, Young-Min; Hyun, Myung-Ho; Yoon, Hiejin

    2010-01-01

    Objective This study aimed to use data mining to explore the significantly contributing variables to good social functioning in schizophrenia patients. Methods The study cohort comprised 67 schizophrenia patients on stable medication. A total of 51 variables (6 demographic data, 3 illness history, 22 social cognition, 16 neurocognition, 4 psychiatric symptoms) were input into a data-mining decision tree using the Answer Tree program to find the pathway for the best social functioning. Results Several contributing factors for good social functioning were found. Continuous attention was the strongest contributing factor. Three variables involving best social functioning included good continuous attention, good theory of mind (TOM), and low sensitivity of disgust emotion. Conclusion Our results confirmed the mediating roles of social cognition between neurocognition and functional outcomes, and suggested that social cognition can significantly predict social functioning in schizophrenia patients. PMID:20577617

  5. Wiggle—Predicting Functionally Flexible Regions from Primary Sequence

    PubMed Central

    Gu, Jenny; Gribskov, Michael; Bourne, Philip E

    2006-01-01

    The Wiggle series are support vector machine–based predictors that identify regions of functional flexibility using only protein sequence information. Functionally flexible regions are defined as regions that can adopt different conformational states and are assumed to be necessary for bioactivity. Many advances have been made in understanding the relationship between protein sequence and structure. This work contributes to those efforts by making strides to understand the relationship between protein sequence and flexibility. A coarse-grained protein dynamic modeling approach was used to generate the dataset required for support vector machine training. We define our regions of interest based on the participation of residues in correlated large-scale fluctuations. Even with this structure-based approach to computationally define regions of functional flexibility, predictors successfully extract sequence-flexibility relationships that have been experimentally confirmed to be functionally important. Thus, a sequence-based tool to identify flexible regions important for protein function has been created. The ability to identify functional flexibility using a sequence based approach complements structure-based definitions and will be especially useful for the large majority of proteins with unknown structures. The methodology offers promise to identify structural genomics targets amenable to crystallization and the possibility to engineer more flexible or rigid regions within proteins to modify their bioactivity. PMID:16839194

  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 only very frequent function words show sensitivity to predictability from the preceding word. The results support the view that content and function words are accessed by different production mechanisms. We argue that words’ form differences due to frequency or repetition stem from their faster or slower lexical access, mediated by a general mechanism that coordinates the pace of higher-level planning and the execution of the articulatory plan.

  7. 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

  8. Functional connectivity classification of autism identifies highly predictive brain features but falls short of biomarker standards

    PubMed Central

    Plitt, Mark; Barnes, Kelly Anne; Martin, Alex

    2014-01-01

    Objectives Autism spectrum disorders (ASD) are diagnosed based on early-manifesting clinical symptoms, including markedly impaired social communication. We assessed the viability of resting-state functional MRI (rs-fMRI) connectivity measures as diagnostic biomarkers for ASD and investigated which connectivity features are predictive of a diagnosis. Methods Rs-fMRI scans from 59 high functioning males with ASD and 59 age- and IQ-matched typically developing (TD) males were used to build a series of machine learning classifiers. Classification features were obtained using 3 sets of brain regions. Another set of classifiers was built from participants' scores on behavioral metrics. An additional age and IQ-matched cohort of 178 individuals (89 ASD; 89 TD) from the Autism Brain Imaging Data Exchange (ABIDE) open-access dataset (http://fcon_1000.projects.nitrc.org/indi/abide/) were included for replication. Results High classification accuracy was achieved through several rs-fMRI methods (peak accuracy 76.67%). However, classification via behavioral measures consistently surpassed rs-fMRI classifiers (peak accuracy 95.19%). The class probability estimates, P(ASD|fMRI data), from brain-based classifiers significantly correlated with scores on a measure of social functioning, the Social Responsiveness Scale (SRS), as did the most informative features from 2 of the 3 sets of brain-based features. The most informative connections predominantly originated from regions strongly associated with social functioning. Conclusions While individuals can be classified as having ASD with statistically significant accuracy from their rs-fMRI scans alone, this method falls short of biomarker standards. Classification methods provided further evidence that ASD functional connectivity is characterized by dysfunction of large-scale functional networks, particularly those involved in social information processing. PMID:25685703

  9. Integrated protein function prediction by mining function associations, sequences, and protein–protein and gene–gene interaction networks

    PubMed Central

    Cao, Renzhi; Cheng, Jianlin

    2016-01-01

    Motivations Protein function prediction is an important and challenging problem in bioinformatics and computational biology. Functionally relevant biological information such as protein sequences, gene expression, and protein–protein interactions has been used mostly separately for protein function prediction. One of the major challenges is how to effectively integrate multiple sources of both traditional and new information such as spatial gene–gene interaction networks generated from chromosomal conformation data together to improve protein function prediction. Results In this work, we developed three different probabilistic scores (MIS, SEQ, and NET score) to combine protein sequence, function associations, and protein–protein interaction and spatial gene–gene interaction networks for protein function prediction. The MIS score is mainly generated from homologous proteins found by PSI-BLAST search, and also association rules between Gene Ontology terms, which are learned by mining the Swiss-Prot database. The SEQ score is generated from protein sequences. The NET score is generated from protein–protein interaction and spatial gene–gene interaction networks. These three scores were combined in a new Statistical Multiple Integrative Scoring System (SMISS) to predict protein function. We tested SMISS on the data set of 2011 Critical Assessment of Function Annotation (CAFA). The method performed substantially better than three base-line methods and an advanced method based on protein profile–sequence comparison, profile–profile comparison, and domain co-occurrence networks according to the maximum F-measure. PMID:26370280

  10. Functional convergence of structurally distinct thioesterases from cyanobacteria and plants involved in phylloquinone biosynthesis.

    PubMed

    Furt, Fabienne; Allen, William J; Widhalm, Joshua R; Madzelan, Peter; Rizzo, Robert C; Basset, Gilles; Wilson, Mark A

    2013-10-01

    The synthesis of phylloquinone (vitamin K1) in photosynthetic organisms requires a thioesterase that hydrolyzes 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA) to release 1,4-dihydroxy-2-naphthoate (DHNA). Cyanobacteria and plants contain distantly related hotdog-fold thioesterases that catalyze this reaction, although the structural basis of these convergent enzymatic activities is unknown. To investigate this, the crystal structures of hotdog-fold DHNA-CoA thioesterases from the cyanobacterium Synechocystis (Slr0204) and the flowering plant Arabidopsis thaliana (AtDHNAT1) were determined. These enzymes form distinct homotetramers and use different active sites to catalyze hydrolysis of DHNA-CoA, similar to the 4-hydroxybenzoyl-CoA (4-HBA-CoA) thioesterases from Pseudomonas and Arthrobacter. Like the 4-HBA-CoA thioesterases, the DHNA-CoA thioesterases contain either an active-site aspartate (Slr0204) or glutamate (AtDHNAT1) that are predicted to be catalytically important. Computational modeling of the substrate-bound forms of both enzymes indicates the residues that are likely to be involved in substrate binding and catalysis. Both enzymes are selective for DHNA-CoA as a substrate, but this selectivity is achieved using divergent predicted binding strategies. The Slr0204 binding pocket is predominantly hydrophobic and closely conforms to DHNA, while that of AtDHNAT1 is more polar and solvent-exposed. Considered in light of the related 4-HBA-CoA thioesterases, these structures indicate that hotdog-fold thioesterases using either an active-site aspartate or glutamate diverged into distinct clades prior to the evolution of strong substrate specificity in these enzymes. PMID:24100308