Does the use of orthoses improve self-reported pain and function measures in patients with plantar fasciitis? A meta-analysis.

PubMed

Lee, Sae Yong; McKeon, Patrick; Hertel, Jay

2009-02-01

To perform a meta-analysis examining the effects of foot orthoses on self-reported pain and function in patients with plantar fasciitis. MEDLINE, SPORTDiscus, and CINAHL were searched from their inception until December 2007 using the terms "foot", "plantar fascia", "arch", "orthotic", "orthoses" and "plantar fasciitis". Original research studies which met these criteria were included: (1) randomised controlled trials or prospective cohort designs, (2) the patients had to be suffering from plantar fasciitis at the time of recruitment, (3) evaluated the efficacy of foot orthoses with self-reported pain and/or function, (4) means, standard deviations, and sample size of each group had to be reported. We utilised the Roos, Engstrom, and Soderberg (Roos, E., Engstrom, M., & Soderberg, B. (2006). Foot orthoses for the treatment of plantar fasciitis. Foot and Ankle International, 8, 606-611) night splint condition to compare our pooled orthoses results. The meta-analysis results showed significant reductions in pain after orthotic intervention. The Roos et al.' (Roos, E., Engstrom, M., & Soderberg, B. (2006). Foot orthoses for the treatment of plantar fasciitis. Foot and Ankle International, 8, 606-611) study also showed significant reduction in pain after night splint treatment. The meta-analysis results also showed significant increases in function after orthotic use. In contrast, the Roos et al.' (Roos, E., Engstrom, M., & Soderberg, B. (2006). Foot orthoses for the treatment of plantar fasciitis. Foot and Ankle International, 8, 606-611) study did not show a significant increase in function after night splinting for 12 weeks. The use of foot orthoses in patients with plantar fasciitis appears to be associated with reduced pain and increased function.

Research of the Dispersity of the Functional Sericite/Methylphenyl- Silicone Resin

PubMed Central

Jiang, B.; Zhu, C. C.; Huang, Y. D.

2015-01-01

In order to improve the homogeneity and dispersity of the sericite in methylphenyl-silicone resin, the agglomerate state of the sericites was controlled effectively. The dispersive model of the sericite in methylphenyl-silicone resin was designed also. First, the modified sericite was prepared using hexadecyl trimethyl ammonium bromide as the intercalating agent. Then, functional sericite was incorporated into methylphenyl-silicone by terminal hydroxyl. The structure and dispersive performance of the hybrid polymers was charactered by analytical instruments. Scanning electron microscopy and Transmission electron microscope, Laser scanning confocal microscope and X-ray diffraction analysis showed that functional sericite was dispersed homogeneously in methylphenyl-silicone resin matrix. X-ray photoelectron spectroscopy analysis showed that the absorption peaks of the Si-OH band of methylphenyl-silicone resin were decreased and the Si-O-Si band was increased. This change evidently showed a significant role to enhance the reaction degree of the functional sericite in methylphenyl-silicone resin. PMID:26061002

A systematic analysis of the PARP protein family identifies new functions critical for cell physiology

PubMed Central

Vyas, Sejal; Chesarone-Cataldo, Melissa; Todorova, Tanya; Huang, Yun-Han; Chang, Paul

2013-01-01

The poly(ADP-ribose) polymerase (PARP) family of proteins use NAD+ as their substrate to modify acceptor proteins with adenosine diphosphate-ribose (ADPr) modifications. The function of most PARPs under physiological conditions is unknown. Here, to better understand this protein family, we systematically analyze the cell cycle localization of each PARP and of poly(ADP-ribose), a product of PARP activity, then identify the knock-down phenotype of each protein and perform secondary assays to elucidate function. We show that most PARPs are cytoplasmic, identify cell cycle differences in the ratio of nuclear to cytoplasmic poly(ADP-ribose), and identify four phenotypic classes of PARP function. These include the regulation of membrane structures, cell viability, cell division, and the actin cytoskeleton. Further analysis of PARP14 shows that it is a component of focal adhesion complexes required for proper cell motility and focal adhesion function. In total, we show that PARP proteins are critical regulators of eukaryotic physiology. PMID:23917125

Quantum computation and analysis of Wigner and Husimi functions: toward a quantum image treatment.

PubMed

Terraneo, M; Georgeot, B; Shepelyansky, D L

2005-06-01

We study the efficiency of quantum algorithms which aim at obtaining phase-space distribution functions of quantum systems. Wigner and Husimi functions are considered. Different quantum algorithms are envisioned to build these functions, and compared with the classical computation. Different procedures to extract more efficiently information from the final wave function of these algorithms are studied, including coarse-grained measurements, amplitude amplification, and measure of wavelet-transformed wave function. The algorithms are analyzed and numerically tested on a complex quantum system showing different behavior depending on parameters: namely, the kicked rotator. The results for the Wigner function show in particular that the use of the quantum wavelet transform gives a polynomial gain over classical computation. For the Husimi distribution, the gain is much larger than for the Wigner function and is larger with the help of amplitude amplification and wavelet transforms. We discuss the generalization of these results to the simulation of other quantum systems. We also apply the same set of techniques to the analysis of real images. The results show that the use of the quantum wavelet transform allows one to lower dramatically the number of measurements needed, but at the cost of a large loss of information.

Reorganization of brain function after a short-term behavioral intervention for stuttering.

PubMed

Lu, Chunming; Zheng, Lifen; Long, Yuhang; Yan, Qian; Ding, Guosheng; Liu, Li; Peng, Danling; Howell, Peter

2017-05-01

This study investigated changes in brain function that occurred over a 7-day behavioral intervention for adults who stutter (AWS). Thirteen AWS received the intervention (AWS+), and 13 AWS did not receive the intervention (AWS-). There were 13 fluent controls (FC-). All participants were scanned before and after the intervention. Whole-brain analysis pre-intervention showed significant differences in task-related brain activation between AWS and FC- in the right inferior frontal cortex (IFC) and left middle temporal cortex, but there were no differences between the two AWS groups. Across the 7-day period of the intervention, AWS+ alone showed a significant increase of brain activation in the left ventral IFC/insula. There were no changes in brain function for the other two groups. Further analysis revealed that the change did not correlate with resting-state functional connectivity (RSFC) that AWS showed in the cerebellum (Lu et al., 2012). However, both changes in task-related brain function and RSFC correlated with changes in speech fluency level. Together, these findings suggest that functional reorganization in a brain region close to the left IFC that shows anomalous function in AWS, occurs after a short-term behavioral intervention for stuttering. Copyright © 2017 Elsevier Inc. All rights reserved.

Relative contributions of three descriptive methods: implications for behavioral assessment.

PubMed

Pence, Sacha T; Roscoe, Eileen M; Bourret, Jason C; Ahearn, William H

2009-01-01

This study compared the outcomes of three descriptive analysis methods-the ABC method, the conditional probability method, and the conditional and background probability method-to each other and to the results obtained from functional analyses. Six individuals who had been diagnosed with developmental delays and exhibited problem behavior participated. Functional analyses indicated that participants' problem behavior was maintained by social positive reinforcement (n = 2), social negative reinforcement (n = 2), or automatic reinforcement (n = 2). Results showed that for all but 1 participant, descriptive analysis outcomes were similar across methods. In addition, for all but 1 participant, the descriptive analysis outcome differed substantially from the functional analysis outcome. This supports the general finding that descriptive analysis is a poor means of determining functional relations.

Development of Activity-based Cost Functions for Cellulase, Invertase, and Other Enzymes

NASA Astrophysics Data System (ADS)

Stowers, Chris C.; Ferguson, Elizabeth M.; Tanner, Robert D.

As enzyme chemistry plays an increasingly important role in the chemical industry, cost analysis of these enzymes becomes a necessity. In this paper, we examine the aspects that affect the cost of enzymes based upon enzyme activity. The basis for this study stems from a previously developed objective function that quantifies the tradeoffs in enzyme purification via the foam fractionation process (Cherry et al., Braz J Chem Eng 17:233-238, 2000). A generalized cost function is developed from our results that could be used to aid in both industrial and lab scale chemical processing. The generalized cost function shows several nonobvious results that could lead to significant savings. Additionally, the parameters involved in the operation and scaling up of enzyme processing could be optimized to minimize costs. We show that there are typically three regimes in the enzyme cost analysis function: the low activity prelinear region, the moderate activity linear region, and high activity power-law region. The overall form of the cost analysis function appears to robustly fit the power law form.

Distinct Aging Effects on Functional Networks in Good and Poor Cognitive Performers

PubMed Central

Lee, Annie; Tan, Mingzhen; Qiu, Anqi

2016-01-01

Brain network hubs are susceptible to normal aging processes and disruptions of their functional connectivity are detrimental to decline in cognitive functions in older adults. However, it remains unclear how the functional connectivity of network hubs cope with cognitive heterogeneity in an aging population. This study utilized cognitive and resting-state functional magnetic resonance imaging data, cluster analysis, and graph network analysis to examine age-related alterations in the network hubs’ functional connectivity of good and poor cognitive performers. Our results revealed that poor cognitive performers showed age-dependent disruptions in the functional connectivity of the right insula and posterior cingulate cortex (PCC), while good cognitive performers showed age-related disruptions in the functional connectivity of the left insula and PCC. Additionally, the left PCC had age-related declines in the functional connectivity with the left medial prefrontal cortex (mPFC) and anterior cingulate cortex (ACC). Most interestingly, good cognitive performers showed age-related declines in the functional connectivity of the left insula and PCC with their right homotopic structures. These results may provide insights of neuronal correlates for understanding individual differences in aging. In particular, our study suggests prominent protection roles of the left insula and PCC and bilateral ACC in good performers. PMID:27667972

Energy Response Function of CALET Gamma Ray Burst Monitor

NASA Astrophysics Data System (ADS)

Yamada, Y.; Sakamoto, T.; Yoshida, A.; Calet Collaboration

2016-10-01

We will explain the development of the CGBM energy response function. We will also show the spectral analysis results of CGBM using our developed energy response function for simultaneously detected bright GRBs by other GRB detectors.

Flocking of the Motsch-Tadmor Model with a Cut-Off Interaction Function

NASA Astrophysics Data System (ADS)

Jin, Chunyin

2018-04-01

In this paper, we study the flocking behavior of the Motsch-Tadmor model with a cut-off interaction function. Our analysis shows that connectedness is important for flocking of this kind of model. Fortunately, we get a sufficient condition imposed only on the model parameters and initial data to guarantee the connectedness of the neighbor graph associated with the system. Then we present a theoretical analysis for flocking, and show that the system achieves consensus at an exponential rate.

The Effect of Group Therapy With Transactional Analysis Approach on Emotional Intelligence, Executive Functions and Drug Dependency.

PubMed

Forghani, Masoomeh; Ghanbari Hashem Abadi, Bahram Ali

2016-06-01

The aim of the present study was to evaluate the effect of group psychotherapy with transactional analysis (TA) approach on emotional intelligence (EI), executive functions and substance dependency among drug-addicts at rehabilitation centers in Mashhad city, Iran, in 2013. In this quasi-experimental study with pretest, posttest, case- control stages, 30 patients were selected from a rehabilitation center and randomly divided into two groups. The case group received 12 sessions of group psychotherapy with transactional analysis approach. Then the effects of independent variable (group psychotherapy with TA approach) on EI, executive function and drug dependency were assessed. The Bar-on test was used for EI, Stroop test for measuring executive function and morphine test, meth-amphetamines and B2 test for evaluating drug dependency. Data were analyzed using multifactorial covariance analysis, Levenes' analysis, MANCOVA, t-student and Pearson correlation coefficient tests t with SPSS software. Our results showed that group psychotherapy with the TA approach was effective in improving EI, executive functions and decreasing drug dependency (P < 0.05). The result of this study showed that group psychotherapy with TA approach has significant effects on addicts and prevents addiction recurrence by improving the coping capabilities and some mental functions of the subjects. However, there are some limitations regarding this study including follow-up duration and sample size.

Dark Energy Survey Year 1 Results: Methodology and Projections for Joint Analysis of Galaxy Clustering, Galaxy Lensing, and CMB Lensing Two-point Functions

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

Giannantonio, T.; et al.

Optical imaging surveys measure both the galaxy density and the gravitational lensing-induced shear fields across the sky. Recently, the Dark Energy Survey (DES) collaboration used a joint fit to two-point correlations between these observables to place tight constraints on cosmology (DES Collaboration et al. 2017). In this work, we develop the methodology to extend the DES Collaboration et al. (2017) analysis to include cross-correlations of the optical survey observables with gravitational lensing of the cosmic microwave background (CMB) as measured by the South Pole Telescope (SPT) and Planck. Using simulated analyses, we show how the resulting set of five two-pointmore » functions increases the robustness of the cosmological constraints to systematic errors in galaxy lensing shear calibration. Additionally, we show that contamination of the SPT+Planck CMB lensing map by the thermal Sunyaev-Zel'dovich effect is a potentially large source of systematic error for two-point function analyses, but show that it can be reduced to acceptable levels in our analysis by masking clusters of galaxies and imposing angular scale cuts on the two-point functions. The methodology developed here will be applied to the analysis of data from the DES, the SPT, and Planck in a companion work.« less

Acute toxicity of functionalized single wall carbon nanotubes: A biochemical, histopathologic and proteomics approach.

PubMed

Ahmadi, Homa; Ramezani, Mohammad; Yazdian-Robati, Rezvan; Behnam, Behzad; Razavi Azarkhiavi, Kamal; Hashem Nia, Azadeh; Mokhtarzadeh, Ahad; Matbou Riahi, Maryam; Razavi, Bibi Marjan; Abnous, Khalil

2017-09-25

Recently carbon nanotubes (CNTs) showed promising potentials in different biomedical applications but their safe use in humans and probable toxicities are still challenging. The aim of this study was to determine the acute toxicity of functionalized single walled carbon nanotubes (SWCNTs). In this project, PEGylated and Tween functionalized SWCNTs were prepared. BALB/c mice were randomly divided into nine groups, including PEGylated SWCNTs (75,150μg/mouse) and PEG, Tween80 suspended SWCNTs, Tween 80 and a control group (intact mice). One or 7 days after intravenous injection, the mice were killed and serum and livers were collected. The oxidative stress markers, biochemical and histopathological changes were studied. Subsequently, proteomics approach was used to investigate the alterations of protein expression profiles in the liver. Results showed that there were not any significant differences in malondealdehyde (MDA), glutathione (GSH) levels and biochemical enzymes (ALT and AST) between groups, while the histopathological observations of livers showed some injuries. The results of proteomics analysis revealed indolethylamine N-Methyltransferase (INMT), glycine N-Methyltransferase (GNMT), selenium binding protein (Selenbp), thioredoxin peroxidase (TPx), TNF receptor associated protein 1(Trap1), peroxiredoxin-6 (Prdx6), electron transport flavoprotein (Etf-α), regucalcin (Rgn) and ATP5b proteins were differentially expressed in functionalized SWCNTs groups. Western blot analyses confirmed that the changes in Prdx6 were consistent with 2-DE gel analysis. In summary, acute toxicological study on two functionalized SWCNTs did not show any significant toxicity at selected doses. Proteomics analysis also showed that following exposure to functionalized SWCNTs, the expression of some proteins with antioxidant activity and detoxifying properties were increased in liver tissue. Copyright © 2017 Elsevier B.V. All rights reserved.

Idiopathic Pulmonary Fibrosis: Data-driven Textural Analysis of Extent of Fibrosis at Baseline and 15-Month Follow-up.

PubMed

Humphries, Stephen M; Yagihashi, Kunihiro; Huckleberry, Jason; Rho, Byung-Hak; Schroeder, Joyce D; Strand, Matthew; Schwarz, Marvin I; Flaherty, Kevin R; Kazerooni, Ella A; van Beek, Edwin J R; Lynch, David A

2017-10-01

Purpose To evaluate associations between pulmonary function and both quantitative analysis and visual assessment of thin-section computed tomography (CT) images at baseline and at 15-month follow-up in subjects with idiopathic pulmonary fibrosis (IPF). Materials and Methods This retrospective analysis of preexisting anonymized data, collected prospectively between 2007 and 2013 in a HIPAA-compliant study, was exempt from additional institutional review board approval. The extent of lung fibrosis at baseline inspiratory chest CT in 280 subjects enrolled in the IPF Network was evaluated. Visual analysis was performed by using a semiquantitative scoring system. Computer-based quantitative analysis included CT histogram-based measurements and a data-driven textural analysis (DTA). Follow-up CT images in 72 of these subjects were also analyzed. Univariate comparisons were performed by using Spearman rank correlation. Multivariate and longitudinal analyses were performed by using a linear mixed model approach, in which models were compared by using asymptotic χ 2 tests. Results At baseline, all CT-derived measures showed moderate significant correlation (P < .001) with pulmonary function. At follow-up CT, changes in DTA scores showed significant correlation with changes in both forced vital capacity percentage predicted (ρ = -0.41, P < .001) and diffusing capacity for carbon monoxide percentage predicted (ρ = -0.40, P < .001). Asymptotic χ 2 tests showed that inclusion of DTA score significantly improved fit of both baseline and longitudinal linear mixed models in the prediction of pulmonary function (P < .001 for both). Conclusion When compared with semiquantitative visual assessment and CT histogram-based measurements, DTA score provides additional information that can be used to predict diminished function. Automatic quantification of lung fibrosis at CT yields an index of severity that correlates with visual assessment and functional change in subjects with IPF. © RSNA, 2017.

Rasch analysis of the Italian Lower Extremity Functional Scale: insights on dimensionality and suggestions for an improved 15-item version.

PubMed

Bravini, Elisabetta; Giordano, Andrea; Sartorio, Francesco; Ferriero, Giorgio; Vercelli, Stefano

2017-04-01

To investigate dimensionality and the measurement properties of the Italian Lower Extremity Functional Scale using both classical test theory and Rasch analysis methods, and to provide insights for an improved version of the questionnaire. Rasch analysis of individual patient data. Rehabilitation centre. A total of 135 patients with musculoskeletal diseases of the lower limb. Patients were assessed with the Lower Extremity Functional Scale before and after the rehabilitation. Rasch analysis showed some problems related to rating scale category functioning, items fit, and items redundancy. After an iterative process, which resulted in the reduction of rating scale categories from 5 to 4, and in the deletion of 5 items, the psychometric properties of the Italian Lower Extremity Functional Scale improved. The retained 15 items with a 4-level response format fitted the Rasch model (internal construct validity), and demonstrated unidimensionality and good reliability indices (person-separation reliability 0.92; Cronbach's alpha 0.94). Then, the analysis showed differential item functioning for six of the retained items. The sensitivity to change of the Italian 15-item Lower Extremity Functional Scale was nearly equal to the one of the original version (effect size: 0.93 and 0.98; standardized response mean: 1.20 and 1.28, respectively for the 15-item and 20-item versions). The Italian Lower Extremity Functional Scale had unsatisfactory measurement properties. However, removing five items and simplifying the scoring from 5 to 4 levels resulted in a more valid measure with good reliability and sensitivity to change.

Directed proteomic analysis of the human nucleolus.

PubMed

Andersen, Jens S; Lyon, Carol E; Fox, Archa H; Leung, Anthony K L; Lam, Yun Wah; Steen, Hanno; Mann, Matthias; Lamond, Angus I

2002-01-08

The nucleolus is a subnuclear organelle containing the ribosomal RNA gene clusters and ribosome biogenesis factors. Recent studies suggest it may also have roles in RNA transport, RNA modification, and cell cycle regulation. Despite over 150 years of research into nucleoli, many aspects of their structure and function remain uncharacterized. We report a proteomic analysis of human nucleoli. Using a combination of mass spectrometry (MS) and sequence database searches, including online analysis of the draft human genome sequence, 271 proteins were identified. Over 30% of the nucleolar proteins were encoded by novel or uncharacterized genes, while the known proteins included several unexpected factors with no previously known nucleolar functions. MS analysis of nucleoli isolated from HeLa cells in which transcription had been inhibited showed that a subset of proteins was enriched. These data highlight the dynamic nature of the nucleolar proteome and show that proteins can either associate with nucleoli transiently or accumulate only under specific metabolic conditions. This extensive proteomic analysis shows that nucleoli have a surprisingly large protein complexity. The many novel factors and separate classes of proteins identified support the view that the nucleolus may perform additional functions beyond its known role in ribosome subunit biogenesis. The data also show that the protein composition of nucleoli is not static and can alter significantly in response to the metabolic state of the cell.

Analysis of the relationships between evolvability, thermodynamics, and the functions of intrinsically disordered proteins/regions.

PubMed

Huang, He; Sarai, Akinori

2012-12-01

The evolvability of proteins is not only restricted by functional and structural importance, but also by other factors such as gene duplication, protein stability, and an organism's robustness. Recently, intrinsically disordered proteins (IDPs)/regions (IDRs) have been suggested to play a role in facilitating protein evolution. However, the mechanisms by which this occurs remain largely unknown. To address this, we have systematically analyzed the relationship between the evolvability, stability, and function of IDPs/IDRs. Evolutionary analysis shows that more recently emerged IDRs have higher evolutionary rates with more functional constraints relaxed (or experiencing more positive selection), and that this may have caused accelerated evolution in the flanking regions and in the whole protein. A systematic analysis of observed stability changes due to single amino acid mutations in IDRs and ordered regions shows that while most mutations induce a destabilizing effect in proteins, mutations in IDRs cause smaller stability changes than in ordered regions. The weaker impact of mutations in IDRs on protein stability may have advantages for protein evolvability in the gain of new functions. Interestingly, however, an analysis of functional motifs in the PROSITE and ELM databases showed that motifs in IDRs are more conserved, characterized by smaller entropy and lower evolutionary rate, than in ordered regions. This apparently opposing evolutionary effect may be partly due to the flexible nature of motifs in IDRs, which require some key amino acid residues to engage in tighter interactions with other molecules. Our study suggests that the unique conformational and thermodynamic characteristics of IDPs/IDRs play an important role in the evolvability of proteins to gain new functions. Copyright © 2012 Elsevier Ltd. All rights reserved.

RELATIVE CONTRIBUTIONS OF THREE DESCRIPTIVE METHODS: IMPLICATIONS FOR BEHAVIORAL ASSESSMENT

PubMed Central

Pence, Sacha T; Roscoe, Eileen M; Bourret, Jason C; Ahearn, William H

2009-01-01

This study compared the outcomes of three descriptive analysis methods—the ABC method, the conditional probability method, and the conditional and background probability method—to each other and to the results obtained from functional analyses. Six individuals who had been diagnosed with developmental delays and exhibited problem behavior participated. Functional analyses indicated that participants' problem behavior was maintained by social positive reinforcement (n  =  2), social negative reinforcement (n  =  2), or automatic reinforcement (n  =  2). Results showed that for all but 1 participant, descriptive analysis outcomes were similar across methods. In addition, for all but 1 participant, the descriptive analysis outcome differed substantially from the functional analysis outcome. This supports the general finding that descriptive analysis is a poor means of determining functional relations. PMID:19949536

Wavefront analysis from its slope data

NASA Astrophysics Data System (ADS)

Mahajan, Virendra N.; Acosta, Eva

2017-08-01

In the aberration analysis of a wavefront over a certain domain, the polynomials that are orthogonal over and represent balanced wave aberrations for this domain are used. For example, Zernike circle polynomials are used for the analysis of a circular wavefront. Similarly, the annular polynomials are used to analyze the annular wavefronts for systems with annular pupils, as in a rotationally symmetric two-mirror system, such as the Hubble space telescope. However, when the data available for analysis are the slopes of a wavefront, as, for example, in a Shack- Hartmann sensor, we can integrate the slope data to obtain the wavefront data, and then use the orthogonal polynomials to obtain the aberration coefficients. An alternative is to find vector functions that are orthogonal to the gradients of the wavefront polynomials, and obtain the aberration coefficients directly as the inner products of these functions with the slope data. In this paper, we show that an infinite number of vector functions can be obtained in this manner. We show further that the vector functions that are irrotational are unique and propagate minimum uncorrelated additive random noise from the slope data to the aberration coefficients.

Differential item functioning in the Cambridge Mental Disorders in the Elderly (CAMDEX) Depression Scale across middle age and late life.

PubMed

Estabrook, Ryne; Sadler, Michael E; McGue, Matt

2015-12-01

A long-standing and critical problem in the study of aging and depression is the comparability of measurement across age groups. While psychological measures of depression typically show increased incidence of symptoms with increasing age, rates of depression diagnosis do not show the same age trend. This analysis presents tests of differential item functioning on the depression section of the CAMDEX interview schedule, using factor analysis-derived affective and somatic subscales (McGue & Christensen, 1997). Results for the affective subscale show significant differences in item functioning in the majority of the affective items as a function of age (items "Happy Life," "Lonely," "Nervous" "Worthless," and "Future": χ6(2) = [30.193, 255.971] across items, all p < .0001). Analyses for the somatic subscale show differential item functioning is limited to a single item relating to coping (χ6(2) = 180.754, p < .0001). These results indicate that differences in depression symptoms across age groups are not entirely consistent with a unidimensional depression trait, and that the measurement structure of depression varies over the life span. (c) 2015 APA, all rights reserved).

MaxEnt, second variation, and generalized statistics

NASA Astrophysics Data System (ADS)

Plastino, A.; Rocca, M. C.

2015-10-01

There are two kinds of Tsallis-probability distributions: heavy tail ones and compact support distributions. We show here, by appeal to functional analysis' tools, that for lower bound Hamiltonians, the second variation's analysis of the entropic functional guarantees that the heavy tail q-distribution constitutes a maximum of Tsallis' entropy. On the other hand, in the compact support instance, a case by case analysis is necessary in order to tackle the issue.

USP17 is upregulated in osteosarcoma and promotes cell proliferation, metastasis, and epithelial-mesenchymal transition through stabilizing SMAD4.

PubMed

Song, Chenyang; Liu, Wenge; Li, Jiandong

2017-07-01

USP17 is upregulated in several cancers, indicating that USP17 might play essential functions in tumor development. However, the function of USP17 in osteosarcoma is still unknown. Our work aimed to investigate the function of USP17 in osteosarcoma. We found that the expression of USP17 was upregulated in osteosarcoma tissues and cell lines, including MG-63 and U2OS. Several functional experiments, such as colony formation analysis, Cell Counting Kit-8 assay, wound healing analysis, and transwell assay, showed that USP17 promoted cell proliferation, migration, and invasion. Moreover, we found that USP17 facilitated migration and invasion through promoting epithelial-mesenchymal transition. SMAD4 has been found to regulate epithelial-mesenchymal transition, co-immunopurification, and glutathione S-transferase pull-down analysis demonstrated that USP17 interacted with SMAD4. Furthermore, USP17 stabilized SMAD4 through its deubiquitinase activity. In conclusion, this study shows that USP17 enhances osteosarcoma cell proliferation and invasion through stabilizing SMAD4.

Traumatic brain injury impairs small-world topology

PubMed Central

Pandit, Anand S.; Expert, Paul; Lambiotte, Renaud; Bonnelle, Valerie; Leech, Robert; Turkheimer, Federico E.

2013-01-01

Objective: We test the hypothesis that brain networks associated with cognitive function shift away from a “small-world” organization following traumatic brain injury (TBI). Methods: We investigated 20 TBI patients and 21 age-matched controls. Resting-state functional MRI was used to study functional connectivity. Graph theoretical analysis was then applied to partial correlation matrices derived from these data. The presence of white matter damage was quantified using diffusion tensor imaging. Results: Patients showed characteristic cognitive impairments as well as evidence of damage to white matter tracts. Compared to controls, the graph analysis showed reduced overall connectivity, longer average path lengths, and reduced network efficiency. A particular impact of TBI is seen on a major network hub, the posterior cingulate cortex. Taken together, these results confirm that a network critical to cognitive function shows a shift away from small-world characteristics. Conclusions: We provide evidence that key brain networks involved in supporting cognitive function become less small-world in their organization after TBI. This is likely to be the result of diffuse white matter damage, and may be an important factor in producing cognitive impairment after TBI. PMID:23596068

Integrative analysis of environmental sequences using MEGAN4.

PubMed

Huson, Daniel H; Mitra, Suparna; Ruscheweyh, Hans-Joachim; Weber, Nico; Schuster, Stephan C

2011-09-01

A major challenge in the analysis of environmental sequences is data integration. The question is how to analyze different types of data in a unified approach, addressing both the taxonomic and functional aspects. To facilitate such analyses, we have substantially extended MEGAN, a widely used taxonomic analysis program. The new program, MEGAN4, provides an integrated approach to the taxonomic and functional analysis of metagenomic, metatranscriptomic, metaproteomic, and rRNA data. While taxonomic analysis is performed based on the NCBI taxonomy, functional analysis is performed using the SEED classification of subsystems and functional roles or the KEGG classification of pathways and enzymes. A number of examples illustrate how such analyses can be performed, and show that one can also import and compare classification results obtained using others' tools. MEGAN4 is freely available for academic purposes, and installers for all three major operating systems can be downloaded from www-ab.informatik.uni-tuebingen.de/software/megan.

Discriminant analysis of functional optical topography for schizophrenia diagnosis

NASA Astrophysics Data System (ADS)

Chuang, Ching-Cheng; Nakagome, Kazuyuki; Pu, Shenghong; Lan, Tsuo-Hung; Lee, Chia-Yen; Sun, Chia-Wei

2014-01-01

Abnormal prefrontal function plays a central role in the cognition deficits of schizophrenic patients; however, the character of the relationship between discriminant analysis and prefrontal activation remains undetermined. Recently, evidence of low prefrontal cortex (PFC) activation in individuals with schizophrenia has also been found during verbal fluency tests (VFT) and other cognitive tests with several neuroimaging methods. The purpose of this study is to assess the hemodynamic changes of the PFC and discriminant analysis between schizophrenia patients and healthy controls during VFT task by utilizing functional optical topography. A total of 99 subjects including 53 schizophrenic patients and 46 age- and gender-matched healthy controls were studied. The results showed that the healthy group had larger activation in the right and left PFC than in the middle PFC. Besides, the schizophrenic group showed weaker task performance and lower activation in the whole PFC than the healthy group. The result of the discriminant analysis showed a significant difference with P value <0.001 in six channels (CH 23, 29, 31, 40, 42, 52) between the schizophrenic and healthy groups. Finally, 68.69% and 71.72% of subjects are correctly classified as being schizophrenic or healthy with all 52 channels and six significantly different channels, respectively. Our findings suggest that the left PFC can be a feature region for discriminant analysis of schizophrenic diagnosis.

Identification and activity of a lower eukaryotic serine proteinase inhibitor (serpin) from Cyanea capillata: analysis of a jellyfish serpin, jellypin.

PubMed

Cole, Elisabeth B; Miller, David; Rometo, David; Greenberg, Robert M; Brömme, Dieter; Cataltepe, Sule; Pak, Stephen C; Mills, David R; Silverman, Gary A; Luke, Cliff J

2004-09-21

Delineating the phylogenetic relationships among members of a protein family can provide a high degree of insight into the evolution of domain structure and function relationships. To identify an early metazoan member of the high molecular weight serine proteinase inhibitor (serpin) superfamily, we initiated a cDNA library screen of the cnidarian, Cyanea capillata. We identified one serpin cDNA encoding for a full-length serpin, jellypin. Phylogenetic analysis using the deduced amino acid sequence showed that jellypin was most similar to the platyhelminthe Echinococcus multiocularis serpin and the clade P serpins, suggesting that this serpin evolved approximately 1000 million years ago (MYA). Modeling of jellypin showed that it contained all the functional elements of an inhibitory serpin. In vitro biochemical analysis confirmed that jellypin was an inhibitor of the S1 clan SA family of serine proteinases. Analysis of the interactions between the human serine proteinases, chymotrypsin, cathepsin G, and elastase, showed that jellypin inhibited these enzymes in the classical serpin manner, forming a SDS stable enzyme/inhibitor complex. These data suggest that the coevolution of serpin structure and inhibitory function date back to at least early metazoan evolution, approximately 1000 MYA.

Development of Welding Fumes Health Index (WFHI) for Welding Workplace's Safety and Health Assessment.

PubMed

Hariri, Azian; Paiman, Nuur Azreen; Leman, Abdul Mutalib; Md Yusof, Mohammad Zainal

2014-08-01

This study aimed to develop an index that can rank welding workplace that associate well with possible health risk of welders. Welding Fumes Health Index (WFHI) were developed based on data from case studies conducted in Plant 1 and Plant 2. Personal sampling of welding fumes to assess the concentration of metal constituents along with series of lung function tests was conducted. Fifteen metal constituents were investigated in each case study. Index values were derived from aggregation analysis of metal constituent concentration while significant lung functions were recognized through statistical analysis in each plant. The results showed none of the metal constituent concentration was exceeding the permissible exposure limit (PEL) for all plants. However, statistical analysis showed significant mean differences of lung functions between welders and non-welders. The index was then applied to one of the welding industry (Plant 3) for verification purpose. The developed index showed its promising ability to rank welding workplace, according to the multiple constituent concentrations of welding fumes that associates well with lung functions of the investigated welders. There was possibility that some of the metal constituents were below the detection limit leading to '0' value of sub index, thus the multiplicative form of aggregation model was not suitable for analysis. On the other hand, maximum or minimum operator forms suffer from compensation issues and were not considered in this study.

Compensation through Functional Hyperconnectivity: A Longitudinal Connectome Assessment of Mild Traumatic Brain Injury

PubMed Central

Iraji, Armin; Chen, Hanbo; Wiseman, Natalie; Welch, Robert D.; O'Neil, Brian J.; Haacke, E. Mark; Liu, Tianming; Kou, Zhifeng

2016-01-01

Mild traumatic brain injury (mTBI) is a major public health concern. Functional MRI has reported alterations in several brain networks following mTBI. However, the connectome-scale brain network changes are still unknown. In this study, sixteen mTBI patients were prospectively recruited from an emergency department and followed up at 4–6 weeks after injury. Twenty-four healthy controls were also scanned twice with the same time interval. Three hundred fifty-eight brain landmarks that preserve structural and functional correspondence of brain networks across individuals were used to investigate longitudinal brain connectivity. Network-based statistic (NBS) analysis did not find significant difference in the group-by-time interaction and time effects. However, 258 functional pairs show group differences in which mTBI patients have higher functional connectivity. Meta-analysis showed that “Action” and “Cognition” are the most affected functional domains. Categorization of connectomic signatures using multiview group-wise cluster analysis identified two patterns of functional hyperconnectivity among mTBI patients: (I) between the posterior cingulate cortex and the association areas of the brain and (II) between the occipital and the frontal lobes of the brain. Our results demonstrate that brain concussion renders connectome-scale brain network connectivity changes, and the brain tends to be hyperactivated to compensate the pathophysiological disturbances. PMID:26819765

Compensation through Functional Hyperconnectivity: A Longitudinal Connectome Assessment of Mild Traumatic Brain Injury.

PubMed

Iraji, Armin; Chen, Hanbo; Wiseman, Natalie; Welch, Robert D; O'Neil, Brian J; Haacke, E Mark; Liu, Tianming; Kou, Zhifeng

2016-01-01

Mild traumatic brain injury (mTBI) is a major public health concern. Functional MRI has reported alterations in several brain networks following mTBI. However, the connectome-scale brain network changes are still unknown. In this study, sixteen mTBI patients were prospectively recruited from an emergency department and followed up at 4-6 weeks after injury. Twenty-four healthy controls were also scanned twice with the same time interval. Three hundred fifty-eight brain landmarks that preserve structural and functional correspondence of brain networks across individuals were used to investigate longitudinal brain connectivity. Network-based statistic (NBS) analysis did not find significant difference in the group-by-time interaction and time effects. However, 258 functional pairs show group differences in which mTBI patients have higher functional connectivity. Meta-analysis showed that "Action" and "Cognition" are the most affected functional domains. Categorization of connectomic signatures using multiview group-wise cluster analysis identified two patterns of functional hyperconnectivity among mTBI patients: (I) between the posterior cingulate cortex and the association areas of the brain and (II) between the occipital and the frontal lobes of the brain. Our results demonstrate that brain concussion renders connectome-scale brain network connectivity changes, and the brain tends to be hyperactivated to compensate the pathophysiological disturbances.

Functional diversity of fish in tropical estuaries: A traits-based approach of communities in Pernambuco, Brazil

NASA Astrophysics Data System (ADS)

Silva-Júnior, C. A. B.; Mérigot, B.; Lucena-Frédou, F.; Ferreira, B. P.; Coxey, M. S.; Rezende, S. M.; Frédou, T.

2017-11-01

Environmental changes and human activities may have strong impacts on biodiversity and ecosystem functioning. While biodiversity is traditionally based on species richness and composition, there is a growing concern to take into account functional diversity to assess and manage species communities. In spite of their economic importance, functional diversity quantified by a traits-based approach is still poorly documented in tropical estuaries. In this study, the functional diversity of fishes was investigated within four estuaries in Pernambuco state, northeast of Brazil. These areas are subject to different levels of human impact (e.g. mangrove deforestation, shrimp farming, fishing etc.) and environmental conditions. Fishes were collected during 34 scientific surveys. A total of 122 species were identified and 12 functional traits were quantified describing two main functions: food acquisition and locomotion. Fish abundance and functional dissimilarities data were combined into a multivariate analysis, the Double Principal Coordinate Analysis, to identify the functional typology of fish assemblages according to the estuary. Results showed that Itapissuma, the largest estuary with a wider mangrove forest area, differs from the other three estuaries, showing higher mean values per samples of species richness S and quadratic entropy Q. Similarly, it presented a different functional typology (the first two axes of the DPCoA account for 68.7% of total inertia, while those of a traditional PCA based solely on species abundances provided only 17.4%). Conversely, Suape, Sirinhaém, and to a lower extent Rio Formoso, showed more similarity in their diversity. This result was attributed to their predominantly marine influenced hydrological features, and similar levels of species abundances and in morphological traits. Overall, this study, combining diversity indices and a recent multivariate analysis to access species contribution to functional typology, allows to deepen diversity assessment by providing additional information regarding the functional pattern of fish assemblages.

Clinicians' adherence to clinical practice guidelines for cardiac function monitoring during antipsychotic treatment: a retrospective report on 434 patients with severe mental illness.

PubMed

Manchia, Mirko; Firinu, Giorgio; Carpiniello, Bernardo; Pinna, Federica

2017-03-31

Severe mental illness (SMI) has considerable excess morbidity and mortality, a proportion of which is explained by cardiovascular diseases, caused in part by antipsychotic (AP) induced QT-related arrhythmias and sudden death by Torsade de Point (TdP). The implementation of evidence-based recommendations for cardiac function monitoring might reduce the incidence of these AP-related adverse events. To investigate clinicians' adherence to cardiac function monitoring before and after starting AP, we performed a retrospective assessment of 434 AP-treated SMI patients longitudinally followed-up for 5 years at an academic community mental health center. We classified antipsychotics according to their risk of inducing QT-related arrhythmias and TdP (Center for Research on Therapeutics, University of Arizona). We used univariate tests and multinomial or binary logistic regression model for data analysis. Univariate and multinomial regression analysis showed that psychiatrists were more likely to perform pre-treatment electrocardiogram (ECG) and electrolyte testing with AP carrying higher cardiovascular risk, but not on the basis of AP pharmacological class. Univariate and binomial regression analysis showed that cardiac function parameters (ECG and electrolyte balance) were more frequently monitored during treatment with second generation AP than with first generation AP. Our data show the presence of weaknesses in the cardiac function monitoring of AP-treated SMI patients, and might guide future interventions to tackle them.

Identification of visual evoked response parameters sensitive to pilot mental state

NASA Technical Reports Server (NTRS)

Zacharias, G. L.

1988-01-01

Systems analysis techniques were developed and demonstrated for modeling the electroencephalographic (EEG) steady state visual evoked response (ssVER), for use in EEG data compression and as an indicator of mental workload. The study focused on steady state frequency domain stimulation and response analysis, implemented with a sum-of-sines (SOS) stimulus generator and an off-line describing function response analyzer. Three major tasks were conducted: (1) VER related systems identification material was reviewed; (2) Software for experiment control and data analysis was developed and implemented; and (3) ssVER identification and modeling was demonstrated, via a mental loading experiment. It was found that a systems approach to ssVER functional modeling can serve as the basis for eventual development of a mental workload indicator. The review showed how transient visual evoked response (tVER) and ssVER research are related at the functional level, the software development showed how systems techniques can be used for ssVER characterization, and the pilot experiment showed how a simple model can be used to capture the basic dynamic response of the ssVER, under varying loads.

Effects of Heterogeniety on Spatial Pattern Analysis of Wild Pistachio Trees in Zagros Woodlands, Iran

NASA Astrophysics Data System (ADS)

Erfanifard, Y.; Rezayan, F.

2014-10-01

Vegetation heterogeneity biases second-order summary statistics, e.g., Ripley's K-function, applied for spatial pattern analysis in ecology. Second-order investigation based on Ripley's K-function and related statistics (i.e., L- and pair correlation function g) is widely used in ecology to develop hypothesis on underlying processes by characterizing spatial patterns of vegetation. The aim of this study was to demonstrate effects of underlying heterogeneity of wild pistachio (Pistacia atlantica Desf.) trees on the second-order summary statistics of point pattern analysis in a part of Zagros woodlands, Iran. The spatial distribution of 431 wild pistachio trees was accurately mapped in a 40 ha stand in the Wild Pistachio & Almond Research Site, Fars province, Iran. Three commonly used second-order summary statistics (i.e., K-, L-, and g-functions) were applied to analyse their spatial pattern. The two-sample Kolmogorov-Smirnov goodness-of-fit test showed that the observed pattern significantly followed an inhomogeneous Poisson process null model in the study region. The results also showed that heterogeneous pattern of wild pistachio trees biased the homogeneous form of K-, L-, and g-functions, demonstrating a stronger aggregation of the trees at the scales of 0-50 m than actually existed and an aggregation at scales of 150-200 m, while regularly distributed. Consequently, we showed that heterogeneity of point patterns may bias the results of homogeneous second-order summary statistics and we also suggested applying inhomogeneous summary statistics with related null models for spatial pattern analysis of heterogeneous vegetations.

The Multiple Correspondence Analysis Method and Brain Functional Connectivity: Its Application to the Study of the Non-linear Relationships of Motor Cortex and Basal Ganglia.

PubMed

Rodriguez-Sabate, Clara; Morales, Ingrid; Sanchez, Alberto; Rodriguez, Manuel

2017-01-01

The complexity of basal ganglia (BG) interactions is often condensed into simple models mainly based on animal data and that present BG in closed-loop cortico-subcortical circuits of excitatory/inhibitory pathways which analyze the incoming cortical data and return the processed information to the cortex. This study was aimed at identifying functional relationships in the BG motor-loop of 24 healthy-subjects who provided written, informed consent and whose BOLD-activity was recorded by MRI methods. The analysis of the functional interaction between these centers by correlation techniques and multiple linear regression showed non-linear relationships which cannot be suitably addressed with these methods. The multiple correspondence analysis (MCA), an unsupervised multivariable procedure which can identify non-linear interactions, was used to study the functional connectivity of BG when subjects were at rest. Linear methods showed different functional interactions expected according to current BG models. MCA showed additional functional interactions which were not evident when using lineal methods. Seven functional configurations of BG were identified with MCA, two involving the primary motor and somatosensory cortex, one involving the deepest BG (external-internal globus pallidum, subthalamic nucleus and substantia nigral), one with the input-output BG centers (putamen and motor thalamus), two linking the input-output centers with other BG (external pallidum and subthalamic nucleus), and one linking the external pallidum and the substantia nigral. The results provide evidence that the non-linear MCA and linear methods are complementary and should be best used in conjunction to more fully understand the nature of functional connectivity of brain centers.

Functional Analysis and Treatment of Rumination Using Fixed-Time Delivery of a Flavor Spray

ERIC Educational Resources Information Center

Wilder, David A.; Register, Martisa; Register, Stanley; Bajagic, Vedrana; Neidert, Pamela L.

2009-01-01

A functional analysis suggested that rumination exhibited by an adult with autism was maintained by automatic reinforcement. Next, a preference assessment with three flavor sprays (i.e., flavored sprays used by dieters) showed that apple pie spray was most preferred. Finally, the effects of fixed-time delivery of the apple pie spray on levels of…

Nanoscale functionalization and characterization of surfaces with hydrogel patterns and biomolecules

NASA Astrophysics Data System (ADS)

Dinakar, Hariharasudhan Chirra

The advent of numerous tools, ease of techniques, and concepts related to nanotechnology, in combination with functionalization via simple chemistry has made gold important for various biomedical applications. In this dissertation, the development and characterization of planar gold surfaces with responsive hydrogel patterns for rapid point of care sensing and the functionalization of gold nanoparticles for drug delivery are highlighted. Biomedical micro- and nanoscale devices that are spatially functionalized with intelligent hydrogels are typically fabricated using conventional UV-lithography. Herein, precise 3-D hydrogel patterns made up of temperature responsive crosslinked poly(N-isopropylacrylamide) over gold were synthesized. The XY control of the hydrogel was achieved using microcontact printing, while thickness control was achieved using atom transfer radical polymerization (ATRP). Atomic force microscopy analysis showed that to the ATRP reaction time governed the pattern growth. The temperature dependent swelling ratio was tailored by tuning the mesh size of the hydrogel. While nanopatterns exhibited a broad lower critical solution temperature (LCST) transition, surface roughness showed a sharp LCST transition. Quartz crystal microbalance with dissipation showed rapid response behavior of the thin films, which makes them applicable as functional components in biomedical devices. The easy synthesis, relative biocompatibility, inertness, and easy functionalization of gold nanoparticles (GNPs) have made them useful for various biomedical applications. Although ATRP can be successfully carried out over GNPs, the yield of stable solution based GNPs for biomedical applications prove to be low. As an alternative approach, a novel method of ISOlating, FUnctionalizing, and REleasing nanoparticles (ISOFURE) was proposed. Biodegradable poly(beta-amino ester) hydrogels were used to synthesize ISOFURE-GNP composites. ATRP was performed inside the composite, and the final hydrogel coated GNPs were released via matrix degradation. Response analysis confirmed that the ISOFURE method led to the increased stability and yield of the hydrogel coated ISOFURE-GNPs. The ISOFURE protocol was also utilized in functionalizing GNPs with enzyme catalase in the absence of a stabilizing reagent. Biotin-streptavidin affinity was used as the bioconjugation method. Activity analysis of the conjugated enzyme showed that the ISOFURE-GNPs showed enhanced biomolecular loading relative to solution based stabilizing reagent passivated GNPs. KEYWORDS: Hydrogel, Gold nanoparticle, ISOFURE, Atom transfer radical polymerization, Microcontact printing

Molecular cloning and expression analysis of WRKY transcription factor genes in Salvia miltiorrhiza.

PubMed

Li, Caili; Li, Dongqiao; Shao, Fenjuan; Lu, Shanfa

2015-03-17

WRKY proteins comprise a large family of transcription factors and play important regulatory roles in plant development and defense response. The WRKY gene family in Salvia miltiorrhiza has not been characterized. A total of 61 SmWRKYs were cloned from S. miltiorrhiza. Multiple sequence alignment showed that SmWRKYs could be classified into 3 groups and 8 subgroups. Sequence features, the WRKY domain and other motifs of SmWRKYs are largely conserved with Arabidopsis AtWRKYs. Each group of WRKY domains contains characteristic conserved sequences, and group-specific motifs might attribute to functional divergence of WRKYs. A total of 17 pairs of orthologous SmWRKY and AtWRKY genes and 21 pairs of paralogous SmWRKY genes were identified. Maximum likelihood analysis showed that SmWRKYs had undergone strong selective pressure for adaptive evolution. Functional divergence analysis suggested that the SmWRKY subgroup genes and many paralogous SmWRKY gene pairs were divergent in functions. Various critical amino acids contributed to functional divergence among subgroups were detected. Of the 61 SmWRKYs, 22, 13, 4 and 1 were predominantly expressed in roots, stems, leaves, and flowers, respectively. The other 21 were mainly expressed in at least two tissues analyzed. In S. miltiorrhiza roots treated with MeJA, significant changes of gene expression were observed for 49 SmWRKYs, of which 26 were up-regulated, 18 were down-regulated, while the other 5 were either up-regulated or down-regulated at different time-points of treatment. Analysis of published RNA-seq data showed that 42 of the 61 identified SmWRKYs were yeast extract and Ag(+)-responsive. Through a systematic analysis, SmWRKYs potentially involved in tanshinone biosynthesis were predicted. These results provide insights into functional conservation and diversification of SmWRKYs and are useful information for further elucidating SmWRKY functions.

Effects of Body Mass Index on Lung Function Index of Chinese Population

NASA Astrophysics Data System (ADS)

Guo, Qiao; Ye, Jun; Yang, Jian; Zhu, Changan; Sheng, Lei; Zhang, Yongliang

2018-01-01

To study the effect of body mass index (BMI) on lung function indexes in Chinese population. A cross-sectional study was performed on 10, 592 participants. The linear relationship between lung function and BMI was evaluated by multivariate linear regression analysis, and the correlation between BMI and lung function was assessed by Pearson correlation analysis. Correlation analysis showed that BMI was positively related with the decreasing of forced vital capacity (FVC), forced expiratory volume in one second (FEV1) and FEV1/FVC (P <0.05), the increasing of FVC% predicted value (FVC%pre) and FEV1% predicted value (FEV1%pre). These suggested that Chinese people can restrain the decline of lung function to prevent the occurrence and development of COPD by the control of BMI.

Microarray characterization of gene expression changes in blood during acute ethanol exposure

PubMed Central

2013-01-01

Background As part of the civil aviation safety program to define the adverse effects of ethanol on flying performance, we performed a DNA microarray analysis of human whole blood samples from a five-time point study of subjects administered ethanol orally, followed by breathalyzer analysis, to monitor blood alcohol concentration (BAC) to discover significant gene expression changes in response to the ethanol exposure. Methods Subjects were administered either orange juice or orange juice with ethanol. Blood samples were taken based on BAC and total RNA was isolated from PaxGene™ blood tubes. The amplified cDNA was used in microarray and quantitative real-time polymerase chain reaction (RT-qPCR) analyses to evaluate differential gene expression. Microarray data was analyzed in a pipeline fashion to summarize and normalize and the results evaluated for relative expression across time points with multiple methods. Candidate genes showing distinctive expression patterns in response to ethanol were clustered by pattern and further analyzed for related function, pathway membership and common transcription factor binding within and across clusters. RT-qPCR was used with representative genes to confirm relative transcript levels across time to those detected in microarrays. Results Microarray analysis of samples representing 0%, 0.04%, 0.08%, return to 0.04%, and 0.02% wt/vol BAC showed that changes in gene expression could be detected across the time course. The expression changes were verified by qRT-PCR. The candidate genes of interest (GOI) identified from the microarray analysis and clustered by expression pattern across the five BAC points showed seven coordinately expressed groups. Analysis showed function-based networks, shared transcription factor binding sites and signaling pathways for members of the clusters. These include hematological functions, innate immunity and inflammation functions, metabolic functions expected of ethanol metabolism, and pancreatic and hepatic function. Five of the seven clusters showed links to the p38 MAPK pathway. Conclusions The results of this study provide a first look at changing gene expression patterns in human blood during an acute rise in blood ethanol concentration and its depletion because of metabolism and excretion, and demonstrate that it is possible to detect changes in gene expression using total RNA isolated from whole blood. The analysis approach for this study serves as a workflow to investigate the biology linked to expression changes across a time course and from these changes, to identify target genes that could serve as biomarkers linked to pilot performance. PMID:23883607

[Resting-state functional magnetic resonance study of brain function changes after TIPS operation in patients with liver cirrhosis].

PubMed

Liu, C; Wang, H B; Yu, Y Q; Wang, M Q; Zhang, G B; Xu, L Y; Wu, J M

2016-12-20

Objective: To investigate the brain function changes in cirrhosis patients after transjugular intrahepatic portosystemic shunt (TIPS), resting-state functional MRI (rs-fMRI) performed and fractional amplitude of low frequency fluctuation (fALFF) was analyzed. Methods: From January 2014 to February 2016, a total of 96 cirrhotic patients from invasive technology department and infection department in the First Affiliated Hospital of Anhui Medical University were selected , the blood ammonia data of 96 cirrhotic patients with TIPS operation in four groups were collected after 1, 3, 6 and 12 month, and all subjects performed rs-fMRI scans. The rs-fMRI data processed with DPARSF and SPM12 softwares, whole-brain fALFF values were calculated, and One-Way analysis of variance , multiple comparison analysis and correlation analysis were performed. Results: There were brain regions with significant function changes in four groups patients with TIPS operation after 1, 3, 6 and 12 month, including bilateral superior temporal gyrus, right middle temportal gyrus , right hippocampus, right island of inferior frontal gyrus, left fusiform gyrus, left olfactory cortex, left orbital superior frontal gyrus (all P <0.005). Multiple comparison analysis showed that compared with patients in the 1-month follow-up, patients in the 3-month follow-up showed that brain function areas increased in left olfactory cortex, left inferior temporal gyrus, left fusiform gyrus, left orbital middle frontal gyrus, left putamen, left cerebelum, and decreased in left lingual gyrus; patients in the 6-month follow-up showed that brain function areas increased in left middle temportal gyrus, right supramarginal gyrus, right temporal pole, right central operculum, and decreased in left top edge of angular gyrus, left postcentral gyrus; patients in the 12-month follow-up showed that brain function areas increased in right hippocampus, right middle cingulate gyrus, and decreased in right middle temportal gyrus.Compared with patients in the 3-month follow-up, patients in the 6-month follow-up showed that brain function areas increased in left superior temporal gyrus, left middle temporal gyrus, right temporal pole, right island of inferior frontal gyrus, and decreased in left cerebelum, left orbital inferior frontal gyrus; patients in the 12-month follow-up showed that there were no obvious increase and decrease brain function areas.Compared with patients in the 6-month follow-up, patients in the 12-month follow-up showed that there were no obvious increase brain function areas , but brain function areas decreased in bilateral middle temportal gyrus( P <0.001). Brain regions were positively related to blood ammonia in right middle cingulate gyrus, right central operculum, left parahippocampal gyrus, while as brain regions were negatively related to blood ammonia in bilateral medial prefrontal lobe, anterior cingulate and paracingulate gyrus, right top edge of angular gyrus, right middle temportal gyrus, left anterior central gyrus, left posterior central gyrus (all P <0.005). Conclusion: The resting state brain function increased or decreased with course of disease in cirrhosis patients after TIPS operation. The brain activity of limbic system and sensorimotor system all had significant correlation with blood ammonia levels. The blood ammonia level and the function of relative brain regions after 6-month with TIPS operation can be gradually improved.

Improving information retrieval in functional analysis.

PubMed

Rodriguez, Juan C; González, Germán A; Fresno, Cristóbal; Llera, Andrea S; Fernández, Elmer A

2016-12-01

Transcriptome analysis is essential to understand the mechanisms regulating key biological processes and functions. The first step usually consists of identifying candidate genes; to find out which pathways are affected by those genes, however, functional analysis (FA) is mandatory. The most frequently used strategies for this purpose are Gene Set and Singular Enrichment Analysis (GSEA and SEA) over Gene Ontology. Several statistical methods have been developed and compared in terms of computational efficiency and/or statistical appropriateness. However, whether their results are similar or complementary, the sensitivity to parameter settings, or possible bias in the analyzed terms has not been addressed so far. Here, two GSEA and four SEA methods and their parameter combinations were evaluated in six datasets by comparing two breast cancer subtypes with well-known differences in genetic background and patient outcomes. We show that GSEA and SEA lead to different results depending on the chosen statistic, model and/or parameters. Both approaches provide complementary results from a biological perspective. Hence, an Integrative Functional Analysis (IFA) tool is proposed to improve information retrieval in FA. It provides a common gene expression analytic framework that grants a comprehensive and coherent analysis. Only a minimal user parameter setting is required, since the best SEA/GSEA alternatives are integrated. IFA utility was demonstrated by evaluating four prostate cancer and the TCGA breast cancer microarray datasets, which showed its biological generalization capabilities. Copyright © 2016 Elsevier Ltd. All rights reserved.

Feasibility study analysis for multi-function dual energy oven (case study: tapioca crackers small medium enterprise)

NASA Astrophysics Data System (ADS)

Soraya, N. W.; El Hadi, R. M.; Chumaidiyah, E.; Tripiawan, W.

2017-12-01

Conventional drying process is constrained by weather (cloudy / rainy), and requires wide drying area, and provides low-quality product. Multi-function dual energy oven is the appropriate technology to solve these problems. The oven uses solar thermal or gas heat for drying various type of products, including tapioca crackers. Investment analysis in technical, operational, and financial aspects show that the multi-function dual energy oven is feasible to be implemented for small medium enterprise (SME) processing tapioca crackers.

Structural and Functional Analysis of HIV-1 Coreceptors: Roles of Charged Residues and Posttranslational Modifications on Coreceptor Activity

DTIC Science & Technology

2000-01-01

to sites of inflammation. They may have additional functions. For example analysis of CXCR4 knockout mice show that CXCR4, which is chemotactic for... mice had similar phenotypes (195). Homozygous knockout of CXCR4 or SDF-1 results in embyonic lethality. Though CCR5 appears to be dispensable, other...chemokine receptors have vital functions. CXCR5 knockout mice have B-cell homing defects (118), and CXCR2 knockout mice overproduce B-cells and

Structural and Functional Analysis of HIV-1 Coreceptors: Roles of Charged Residues and Posttranslational Modifications on Coreceptor Activity

DTIC Science & Technology

2000-01-01

various organs and to sites of inflammation. They may have additional functions. For example analysis of CXCR4 knockout mice show that CXCR4, which...SDF-1 knockout mice had similar phenotypes (195). Homozygous knockout of CXCR4 or SDF-1 results in embyonic lethality. Though CCR5 appears to be...dispensable, other chemokine receptors have vital functions. CXCR5 knockout mice have B-cell homing defects (118), and CXCR2 knockout mice

The use of regression analysis in determining reference intervals for low hematocrit and thrombocyte count in multiple electrode aggregometry and platelet function analyzer 100 testing of platelet function.

PubMed

Kuiper, Gerhardus J A J M; Houben, Rik; Wetzels, Rick J H; Verhezen, Paul W M; Oerle, Rene van; Ten Cate, Hugo; Henskens, Yvonne M C; Lancé, Marcus D

2017-11-01

Low platelet counts and hematocrit levels hinder whole blood point-of-care testing of platelet function. Thus far, no reference ranges for MEA (multiple electrode aggregometry) and PFA-100 (platelet function analyzer 100) devices exist for low ranges. Through dilution methods of volunteer whole blood, platelet function at low ranges of platelet count and hematocrit levels was assessed on MEA for four agonists and for PFA-100 in two cartridges. Using (multiple) regression analysis, 95% reference intervals were computed for these low ranges. Low platelet counts affected MEA in a positive correlation (all agonists showed r 2 ≥ 0.75) and PFA-100 in an inverse correlation (closure times were prolonged with lower platelet counts). Lowered hematocrit did not affect MEA testing, except for arachidonic acid activation (ASPI), which showed a weak positive correlation (r 2 = 0.14). Closure time on PFA-100 testing was inversely correlated with hematocrit for both cartridges. Regression analysis revealed different 95% reference intervals in comparison with originally established intervals for both MEA and PFA-100 in low platelet or hematocrit conditions. Multiple regression analysis of ASPI and both tests on the PFA-100 for combined low platelet and hematocrit conditions revealed that only PFA-100 testing should be adjusted for both thrombocytopenia and anemia. 95% reference intervals were calculated using multiple regression analysis. However, coefficients of determination of PFA-100 were poor, and some variance remained unexplained. Thus, in this pilot study using (multiple) regression analysis, we could establish reference intervals of platelet function in anemia and thrombocytopenia conditions on PFA-100 and in thrombocytopenia conditions on MEA.

Variational Methods in Sensitivity Analysis and Optimization for Aerodynamic Applications

NASA Technical Reports Server (NTRS)

Ibrahim, A. H.; Hou, G. J.-W.; Tiwari, S. N. (Principal Investigator)

1996-01-01

Variational methods (VM) sensitivity analysis, which is the continuous alternative to the discrete sensitivity analysis, is employed to derive the costate (adjoint) equations, the transversality conditions, and the functional sensitivity derivatives. In the derivation of the sensitivity equations, the variational methods use the generalized calculus of variations, in which the variable boundary is considered as the design function. The converged solution of the state equations together with the converged solution of the costate equations are integrated along the domain boundary to uniquely determine the functional sensitivity derivatives with respect to the design function. The determination of the sensitivity derivatives of the performance index or functional entails the coupled solutions of the state and costate equations. As the stable and converged numerical solution of the costate equations with their boundary conditions are a priori unknown, numerical stability analysis is performed on both the state and costate equations. Thereafter, based on the amplification factors obtained by solving the generalized eigenvalue equations, the stability behavior of the costate equations is discussed and compared with the state (Euler) equations. The stability analysis of the costate equations suggests that the converged and stable solution of the costate equation is possible only if the computational domain of the costate equations is transformed to take into account the reverse flow nature of the costate equations. The application of the variational methods to aerodynamic shape optimization problems is demonstrated for internal flow problems at supersonic Mach number range. The study shows, that while maintaining the accuracy of the functional sensitivity derivatives within the reasonable range for engineering prediction purposes, the variational methods show a substantial gain in computational efficiency, i.e., computer time and memory, when compared with the finite difference sensitivity analysis.

A Demonstration of Individual Preference for Novel Mands during Functional Communication Training

ERIC Educational Resources Information Center

Winborn-Kemmerer, Lisa; Ringdahl, Joel E.; Wacker, David P.; Kitsukawa, Kana

2009-01-01

Preference for mand topography was evaluated for 2 individuals with developmental disabilities who exhibited problem behavior. The results of a functional analysis showed that each participant's problem behavior was maintained by social reinforcement. Participants were taught two novel mand topographies for the same functional reinforcer, and each…

Scenario-Based Case Study Method and the Functionality of the Section Called "From Production to Consumption" from the Perspective of Primary School Students

ERIC Educational Resources Information Center

Taneri, Ahu

2018-01-01

In this research, the aim was showing the evaluation of students on scenario-based case study method and showing the functionality of the studied section called "from production to consumption". Qualitative research method and content analysis were used to reveal participants' experiences and reveal meaningful relations regarding…

The analysis of mathematics teachers' learning on algebra function limit material based on teaching experience difference

NASA Astrophysics Data System (ADS)

Ma'rufi, Budayasa, I. Ketut; Juniati, Dwi

2017-08-01

The aim of this study was to describe the analysis of mathematics teachers' learning on algebra function limit material based on teaching experience difference. The purpose of this study is to describe the analysis of mathematics teacher's learning on limit algebraic functions in terms of the differences of teaching experience. Learning analysis focused on Pedagogical Content Knowledge (PCK) of teachers in mathematics on limit algebraic functions related to the knowledge of pedagogy. PCK of teachers on limit algebraic function is a type of specialized knowledge for teachers on how to teach limit algebraic function that can be understood by students. Subjects are two high school mathematics teacher who has difference of teaching experience they are one Novice Teacher (NP) and one Experienced Teacher (ET). Data are collected through observation of learning in the class, videos of learning, and then analyzed using qualitative analysis. Teacher's knowledge of Pedagogic defined as a knowledge and understanding of teacher about planning and organizing of learning, and application of learning strategy. The research results showed that the Knowledge of Pedagogy on subject NT in mathematics learning on the material of limit function algebra showed that the subject NT tended to describe procedurally, without explaining the reasons why such steps were used, asking questions which tended to be monotonous not be guiding and digging deeper, and less varied in the use of learning strategies while subject ET gave limited guidance and opportunities to the students to find their own answers, exploit the potential of students to answer questions, provide an opportunity for students to interact and work in groups, and subject ET tended to combine conceptual and procedural explanation.

Genome-wide analysis of the Dof transcription factor gene family reveals soybean-specific duplicable and functional characteristics.

PubMed

Guo, Yong; Qiu, Li-Juan

2013-01-01

The Dof domain protein family is a classic plant-specific zinc-finger transcription factor family involved in a variety of biological processes. There is great diversity in the number of Dof genes in different plants. However, there are only very limited reports on the characterization of Dof transcription factors in soybean (Glycine max). In the present study, 78 putative Dof genes were identified from the whole-genome sequence of soybean. The predicted GmDof genes were non-randomly distributed within and across 19 out of 20 chromosomes and 97.4% (38 pairs) were preferentially retained duplicate paralogous genes located in duplicated regions of the genome. Soybean-specific segmental duplications contributed significantly to the expansion of the soybean Dof gene family. These Dof proteins were phylogenetically clustered into nine distinct subgroups among which the gene structure and motif compositions were considerably conserved. Comparative phylogenetic analysis of these Dof proteins revealed four major groups, similar to those reported for Arabidopsis and rice. Most of the GmDofs showed specific expression patterns based on RNA-seq data analyses. The expression patterns of some duplicate genes were partially redundant while others showed functional diversity, suggesting the occurrence of sub-functionalization during subsequent evolution. Comprehensive expression profile analysis also provided insights into the soybean-specific functional divergence among members of the Dof gene family. Cis-regulatory element analysis of these GmDof genes suggested diverse functions associated with different processes. Taken together, our results provide useful information for the functional characterization of soybean Dof genes by combining phylogenetic analysis with global gene-expression profiling.

Using normalization 3D model for automatic clinical brain quantative analysis and evaluation

NASA Astrophysics Data System (ADS)

Lin, Hong-Dun; Yao, Wei-Jen; Hwang, Wen-Ju; Chung, Being-Tau; Lin, Kang-Ping

2003-05-01

Functional medical imaging, such as PET or SPECT, is capable of revealing physiological functions of the brain, and has been broadly used in diagnosing brain disorders by clinically quantitative analysis for many years. In routine procedures, physicians manually select desired ROIs from structural MR images and then obtain physiological information from correspondent functional PET or SPECT images. The accuracy of quantitative analysis thus relies on that of the subjectively selected ROIs. Therefore, standardizing the analysis procedure is fundamental and important in improving the analysis outcome. In this paper, we propose and evaluate a normalization procedure with a standard 3D-brain model to achieve precise quantitative analysis. In the normalization process, the mutual information registration technique was applied for realigning functional medical images to standard structural medical images. Then, the standard 3D-brain model that shows well-defined brain regions was used, replacing the manual ROIs in the objective clinical analysis. To validate the performance, twenty cases of I-123 IBZM SPECT images were used in practical clinical evaluation. The results show that the quantitative analysis outcomes obtained from this automated method are in agreement with the clinical diagnosis evaluation score with less than 3% error in average. To sum up, the method takes advantage of obtaining precise VOIs, information automatically by well-defined standard 3-D brain model, sparing manually drawn ROIs slice by slice from structural medical images in traditional procedure. That is, the method not only can provide precise analysis results, but also improve the process rate for mass medical images in clinical.

Surface interaction of H2S, SO2, and SO3 on fullerene-like gallium nitride (GaN) nanostructure semiconductor

NASA Astrophysics Data System (ADS)

Salimifard, M.; Rad, A. Shokuhi; Mahanpoor, K.

2017-10-01

Density functional theory (DFT) using MPW1PW91 and B3LYP hybrid functionals was utilized for quantum-based investigations of three major sulfur compounds (H2S, SO2, and SO3) adsorption onto fullerene-like Ga12N12 nanocluster. All chemicals showed high chemisorption with the order of SO3>SO2>>H2S. Results of charge analysis showed that during adsorption, transfer of charge is from H2S to nanocluster while reverse direction of charge transfer is found for SO2 and SO3 molecules. Partial dissociation is found for adsorbates especially for SO2 and SO3 molecules. Results of thermochemistry analysis show negative values for enthalpy and Gibbs free energy of adsorption, confirming exothermic spontaneous process. Analysis of frontier molecular orbital (FMO) showed important role of orbital hybridizing towards formation of new bonds upon adsorption. As a result, we introduce Ga12N12 nanocluster as a strong adsorbent for sulfur compounds.

Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam

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

Chai, Juanjuan; Kora, Guruprasad; Ahn, Tae-Hyuk

2014-10-09

To supply some background, phylogenetic studies have provided detailed knowledge on the evolutionary mechanisms of genes and species in Bacteria and Archaea. However, the evolution of cellular functions, represented by metabolic pathways and biological processes, has not been systematically characterized. Many clades in the prokaryotic tree of life have now been covered by sequenced genomes in GenBank. This enables a large-scale functional phylogenomics study of many computationally inferred cellular functions across all sequenced prokaryotes. Our results show a total of 14,727 GenBank prokaryotic genomes were re-annotated using a new protein family database, UniFam, to obtain consistent functional annotations for accuratemore » comparison. The functional profile of a genome was represented by the biological process Gene Ontology (GO) terms in its annotation. The GO term enrichment analysis differentiated the functional profiles between selected archaeal taxa. 706 prokaryotic metabolic pathways were inferred from these genomes using Pathway Tools and MetaCyc. The consistency between the distribution of metabolic pathways in the genomes and the phylogenetic tree of the genomes was measured using parsimony scores and retention indices. The ancestral functional profiles at the internal nodes of the phylogenetic tree were reconstructed to track the gains and losses of metabolic pathways in evolutionary history. In conclusion, our functional phylogenomics analysis shows divergent functional profiles of taxa and clades. Such function-phylogeny correlation stems from a set of clade-specific cellular functions with low parsimony scores. On the other hand, many cellular functions are sparsely dispersed across many clades with high parsimony scores. These different types of cellular functions have distinct evolutionary patterns reconstructed from the prokaryotic tree.« less

Repolarization of hepatocytes in culture.

PubMed

Talamini, M A; Kappus, B; Hubbard, A

1997-01-01

We have evaluated the biochemical, morphological, and functional redevelopment of polarity in freshly isolated hepatocytes cultured using a double layer collagen gel sandwich technique. Western blot analysis showed increased cellular levels of the cell adhesion protein uvomorulin as cultured hepatocytes repolarized. Immunofluorescence studies using antibodies against domain-specific membrane proteins showed polarity as early as 48 hours, although the pattern of the polymeric Immunoglobulin-A receptor (pIgA-R) differed from in vivo liver. Electron microscopy showed developing bile canaliculi at 1 day. However, the functional presence of tight junctions was absent at 1 day, but present at 5 days. We further showed functional polarity to be present at 4 days by documenting the ability of cultured hepatocytes to metabolize and excrete fluorescein diacetate into visible bile canaliculi. We conclude that hepatocytes cultured appropriately develop morphological and functional polarity. Hepatocyte culture is therefore a useful tool for the study of mechanisms responsible for the development of polarized function.

Financing public health: diminished funding for core needs and state-by-state variation in support.

PubMed

Levi, Jeffrey; Juliano, Chrissie; Richardson, Maxwell

2007-01-01

This article documents the instability and variation in public financing of public health functions at the federal and state levels. Trust for America's Health has charted federal funding for the Centers of Disease Control and Prevention, which in turn provides a major portion of financing for state and local public health departments, and has compiled information about state-generated revenue commitments to public health activities nationwide. The federal-level analysis shows that funding has been marked by diminished support for "core" public health functions. The state-level analysis shows tremendous variation in use of state revenues to support public health functions. The combination of these factors results in very different public health capacities across the country, potentially leaving some states more vulnerable, while simultaneously posing a general threat to the nation since public health problems do not honor state borders. On the basis of this analysis, the authors suggest changes in the financing arrangements for public health, designed to assure a more stable funding stream for core public health functions and a more consistent approach to financing public health activities across the country.

[Effects of plateau zokor disturbance and restoration years on soil nutrients and microbial functional diversity in alpine meadow].

PubMed

Hu, Lei; Ade, Lu-ji; Zi, Hong-biao; Wang, Chang-ting

2015-09-01

To explore the dynamic process of restoration succession in degraded alpine meadow that had been disturbed by plateau zokors in the eastern Tibetan Plateau, we examined soil nutrients and microbial functional diversity using conventional laboratory analysis and the Biolog-ECO microplate method. Our study showed that: 1) The zokors disturbance significantly reduced soil organic matter, total nitrogen, available nitrogen and phosphorus contents, but had no significant effects on soil total phosphorus and potassium contents; 2) Soil microbial carbon utilization efficiency, values of Shannon, Pielou and McIntosh indexes increased with alpine meadow restoration years; 3) Principal component analysis (PCA) showed that carbohydrates and amino acids were the main carbon sources for maintaining soil microbial community; 4) Redundancy analysis ( RDA) indicated that soil pH, soil organic matter, total nitrogen, available nitrogen, and total potassium were the main factors influencing the metabolic rate of soil microbial community and microbial functional diversity. In summary, variations in soil microbial functional diversity at different recovery stages reflected the microbial response to aboveground vegetation, soil microbial composition and soil nutrients.

Identification of key genes associated with the effect of estrogen on ovarian cancer using microarray analysis.

PubMed

Zhang, Shi-tao; Zuo, Chao; Li, Wan-nan; Fu, Xue-qi; Xing, Shu; Zhang, Xiao-ping

2016-02-01

To identify key genes related to the effect of estrogen on ovarian cancer. Microarray data (GSE22600) were downloaded from Gene Expression Omnibus. Eight estrogen and seven placebo treatment samples were obtained using a 2 × 2 factorial designs, which contained 2 cell lines (PEO4 and 2008) and 2 treatments (estrogen and placebo). Differentially expressed genes were identified by Bayesian methods, and the genes with P < 0.05 and |log2FC (fold change)| ≥0.5 were chosen as cut-off criterion. Differentially co-expressed genes (DCGs) and differentially regulated genes (DRGs) were, respectively, identified by DCe function and DRsort function in DCGL package. Topological structure analysis was performed on the important transcriptional factors (TFs) and genes in transcriptional regulatory network using tYNA. Functional enrichment analysis was, respectively, performed for DEGs and the important genes using Gene Ontology and KEGG databases. In total, 465 DEGs were identified. Functional enrichment analysis of DEGs indicated that ACVR2B, LTBP1, BMP7 and MYC involved in TGF-beta signaling pathway. The 2285 DCG pairs and 357 DRGs were identified. Topological structure analysis showed that 52 important TFs and 65 important genes were identified. Functional enrichment analysis of the important genes showed that TP53 and MLH1 participated in DNA damage response and the genes (ACVR2B, LTBP1, BMP7 and MYC) involved in TGF-beta signaling pathway. TP53, MLH1, ACVR2B, LTBP1 and BMP7 might participate in the pathogenesis of ovarian cancer.

Positive effects of combined cognitive and physical exercise training on cognitive function in older adults with mild cognitive impairment or dementia: A meta-analysis.

PubMed

Karssemeijer, Esther G A; Aaronson, Justine A; Bossers, Willem J; Smits, Tara; Olde Rikkert, Marcel G M; Kessels, Roy P C

2017-11-01

Combined cognitive and physical exercise interventions have potential to elicit cognitive benefits in older adults with mild cognitive impairment (MCI) or dementia. This meta-analysis aims to quantify the overall effect of these interventions on global cognitive functioning in older adults with MCI or dementia. Ten randomized controlled trials that applied a combined cognitive-physical intervention with cognitive function as an outcome measure were included. For each study effect sizes were computed (i.e., post-intervention standardized mean difference (SMD) scores) and pooled, using a random-effects meta-analysis. The primary analysis showed a small-to-medium positive effect of combined cognitive-physical interventions on global cognitive function in older adults with MCI or dementia (SMD[95% confidence interval]=0.32[0.17;0.47], p<0.00). A combined intervention was equally beneficial in patients with dementia (SMD=0.36[0.12;0.60], p<0.00) and MCI (SMD=0.39[0.15;0.63], p<0.05). In addition, the analysis showed a moderate-to-large positive effect after combined cognitive-physical interventions for activities of daily living (ADL) (SMD=0.65[0.09;1.21], p<0.01)and a small-to-medium positive effect for mood (SMD=0.27[0.04;0.50], p<0.01). These functional benefits emphasize the clinical relevance of combined cognitive and physical training strategies. Copyright © 2017 Elsevier B.V. All rights reserved.

Existence and stability of dispersive solutions to the Kadomtsev-Petviashvili equation in the presence of dispersion effect

NASA Astrophysics Data System (ADS)

Das, Amiya; Ganguly, Asish

2017-07-01

The paper deals with Kadomtsev-Petviashvili (KP) equation in presence of a small dispersion effect. The nature of solutions are examined under the dispersion effect by using Lyapunov function and dynamical system theory. We prove that when dispersion is added to the KP equation, in certain regions, yet there exist bounded traveling wave solutions in the form of solitary waves, periodic and elliptic functions. The general solution of the equation with or without the dispersion effect are obtained in terms of Weirstrass ℘ functions and Jacobi elliptic functions. New form of kink-type solutions are established by exploring a new technique based on factorization method, use of functional transformation and the Abel's first order nonlinear equation. Furthermore, the stability analysis of the dispersive solutions are examined which shows that the traveling wave velocity is a bifurcation parameter which governs between different classes of waves. We use the phase plane analysis and show that at a critical velocity, the solution has a transcritical bifurcation.

Interconnection of Key Microbial Functional Genes for Enhanced Benzo[a]pyrene Biodegradation in Sediments by Microbial Electrochemistry.

PubMed

Yan, Zaisheng; He, Yuhong; Cai, Haiyuan; Van Nostrand, Joy D; He, Zhili; Zhou, Jizhong; Krumholz, Lee R; Jiang, He-Long

2017-08-01

Sediment microbial fuel cells (SMFCs) can stimulate the degradation of polycyclic aromatic hydrocarbons in sediments, but the mechanism of this process is poorly understood at the microbial functional gene level. Here, the use of SMFC resulted in 92% benzo[a]pyrene (BaP) removal over 970 days relative to 54% in the controls. Sediment functions, microbial community structure, and network interactions were dramatically altered by the SMFC employment. Functional gene analysis showed that c-type cytochrome genes for electron transfer, aromatic degradation genes, and extracellular ligninolytic enzymes involved in lignin degradation were significantly enriched in bulk sediments during SMFC operation. Correspondingly, chemical analysis of the system showed that these genetic changes resulted in increases in the levels of easily oxidizable organic carbon and humic acids which may have resulted in increased BaP bioavailability and increased degradation rates. Tracking microbial functional genes and corresponding organic matter responses should aid mechanistic understanding of BaP enhanced biodegradation by microbial electrochemistry and development of sustainable bioremediation strategies.

Functional Evolution of PLP-dependent Enzymes based on Active-Site Structural Similarities

PubMed Central

Catazaro, Jonathan; Caprez, Adam; Guru, Ashu; Swanson, David; Powers, Robert

2014-01-01

Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5’-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the Comparison of Protein Active Site Structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can be used to infer evolutionary relationships based on functional similarity. The enzymes successfully clustered together based on substrate specificity, function, and three-dimensional fold. This study demonstrates the value of using active site structures for functional evolutionary analysis and the effectiveness of CPASS. PMID:24920327

Functional evolution of PLP-dependent enzymes based on active-site structural similarities.

PubMed

Catazaro, Jonathan; Caprez, Adam; Guru, Ashu; Swanson, David; Powers, Robert

2014-10-01

Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5'-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the comparison of protein active site structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can be used to infer evolutionary relationships based on functional similarity. The enzymes successfully clustered together based on substrate specificity, function, and three-dimensional-fold. This study demonstrates the value of using active site structures for functional evolutionary analysis and the effectiveness of CPASS. © 2014 Wiley Periodicals, Inc.

Characterizing Bonding Patterns in Diradicals and Triradicals by Density-Based Wave Function Analysis: A Uniform Approach.

PubMed

Orms, Natalie; Rehn, Dirk R; Dreuw, Andreas; Krylov, Anna I

2018-02-13

Density-based wave function analysis enables unambiguous comparisons of the electronic structure computed by different methods and removes ambiguity of orbital choices. We use this tool to investigate the performance of different spin-flip methods for several prototypical diradicals and triradicals. In contrast to previous calibration studies that focused on energy gaps between high- and low spin-states, we focus on the properties of the underlying wave functions, such as the number of effectively unpaired electrons. Comparison of different density functional and wave function theory results provides insight into the performance of the different methods when applied to strongly correlated systems such as polyradicals. We show that canonical molecular orbitals for species like large copper-containing diradicals fail to correctly represent the underlying electronic structure due to highly non-Koopmans character, while density-based analysis of the same wave function delivers a clear picture of the bonding pattern.

Development of Welding Fumes Health Index (WFHI) for Welding Workplace’s Safety and Health Assessment

PubMed Central

HARIRI, Azian; PAIMAN, Nuur Azreen; LEMAN, Abdul Mutalib; MD. YUSOF, Mohammad Zainal

2014-01-01

Abstract Background This study aimed to develop an index that can rank welding workplace that associate well with possible health risk of welders. Methods Welding Fumes Health Index (WFHI) were developed based on data from case studies conducted in Plant 1 and Plant 2. Personal sampling of welding fumes to assess the concentration of metal constituents along with series of lung function tests was conducted. Fifteen metal constituents were investigated in each case study. Index values were derived from aggregation analysis of metal constituent concentration while significant lung functions were recognized through statistical analysis in each plant. Results The results showed none of the metal constituent concentration was exceeding the permissible exposure limit (PEL) for all plants. However, statistical analysis showed significant mean differences of lung functions between welders and non-welders. The index was then applied to one of the welding industry (Plant 3) for verification purpose. The developed index showed its promising ability to rank welding workplace, according to the multiple constituent concentrations of welding fumes that associates well with lung functions of the investigated welders. Conclusion There was possibility that some of the metal constituents were below the detection limit leading to ‘0’ value of sub index, thus the multiplicative form of aggregation model was not suitable for analysis. On the other hand, maximum or minimum operator forms suffer from compensation issues and were not considered in this study. PMID:25927034

Network analysis of functional brain connectivity in borderline personality disorder using resting-state fMRI

PubMed Central

Xu, Tingting; Cullen, Kathryn R.; Mueller, Bryon; Schreiner, Mindy W.; Lim, Kelvin O.; Schulz, S. Charles; Parhi, Keshab K.

2016-01-01

Borderline personality disorder (BPD) is associated with symptoms such as affect dysregulation, impaired sense of self, and self-harm behaviors. Neuroimaging research on BPD has revealed structural and functional abnormalities in specific brain regions and connections. However, little is known about the topological organizations of brain networks in BPD. We collected resting-state functional magnetic resonance imaging (fMRI) data from 20 patients with BPD and 10 healthy controls, and constructed frequency-specific functional brain networks by correlating wavelet-filtered fMRI signals from 82 cortical and subcortical regions. We employed graph-theory based complex network analysis to investigate the topological properties of the brain networks, and employed network-based statistic to identify functional dysconnections in patients. In the 0.03–0.06 Hz frequency band, compared to controls, patients with BPD showed significantly larger measures of global network topology, including the size of largest connected graph component, clustering coefficient, small-worldness, and local efficiency, indicating increased local cliquishness of the functional brain network. Compared to controls, patients showed lower nodal centrality at several hub nodes but greater centrality at several non-hub nodes in the network. Furthermore, an interconnected subnetwork in 0.03–0.06 Hz frequency band was identified that showed significantly lower connectivity in patients. The links in the subnetwork were mainly long-distance connections between regions located at different lobes; and the mean connectivity of this subnetwork was negatively correlated with the increased global topology measures. Lastly, the key network measures showed high correlations with several clinical symptom scores, and classified BPD patients against healthy controls with high accuracy based on linear discriminant analysis. The abnormal topological properties and connectivity found in this study may add new knowledge to the current understanding of functional brain networks in BPD. However, due to limitation of small sample sizes, the results of the current study should be viewed as exploratory and need to be validated on large samples in future works. PMID:26977400

Network analysis of functional brain connectivity in borderline personality disorder using resting-state fMRI.

PubMed

Xu, Tingting; Cullen, Kathryn R; Mueller, Bryon; Schreiner, Mindy W; Lim, Kelvin O; Schulz, S Charles; Parhi, Keshab K

2016-01-01

Borderline personality disorder (BPD) is associated with symptoms such as affect dysregulation, impaired sense of self, and self-harm behaviors. Neuroimaging research on BPD has revealed structural and functional abnormalities in specific brain regions and connections. However, little is known about the topological organizations of brain networks in BPD. We collected resting-state functional magnetic resonance imaging (fMRI) data from 20 patients with BPD and 10 healthy controls, and constructed frequency-specific functional brain networks by correlating wavelet-filtered fMRI signals from 82 cortical and subcortical regions. We employed graph-theory based complex network analysis to investigate the topological properties of the brain networks, and employed network-based statistic to identify functional dysconnections in patients. In the 0.03-0.06 Hz frequency band, compared to controls, patients with BPD showed significantly larger measures of global network topology, including the size of largest connected graph component, clustering coefficient, small-worldness, and local efficiency, indicating increased local cliquishness of the functional brain network. Compared to controls, patients showed lower nodal centrality at several hub nodes but greater centrality at several non-hub nodes in the network. Furthermore, an interconnected subnetwork in 0.03-0.06 Hz frequency band was identified that showed significantly lower connectivity in patients. The links in the subnetwork were mainly long-distance connections between regions located at different lobes; and the mean connectivity of this subnetwork was negatively correlated with the increased global topology measures. Lastly, the key network measures showed high correlations with several clinical symptom scores, and classified BPD patients against healthy controls with high accuracy based on linear discriminant analysis. The abnormal topological properties and connectivity found in this study may add new knowledge to the current understanding of functional brain networks in BPD. However, due to limitation of small sample sizes, the results of the current study should be viewed as exploratory and need to be validated on large samples in future works.

Development of large-scale functional brain networks in children.

PubMed

Supekar, Kaustubh; Musen, Mark; Menon, Vinod

2009-07-01

The ontogeny of large-scale functional organization of the human brain is not well understood. Here we use network analysis of intrinsic functional connectivity to characterize the organization of brain networks in 23 children (ages 7-9 y) and 22 young-adults (ages 19-22 y). Comparison of network properties, including path-length, clustering-coefficient, hierarchy, and regional connectivity, revealed that although children and young-adults' brains have similar "small-world" organization at the global level, they differ significantly in hierarchical organization and interregional connectivity. We found that subcortical areas were more strongly connected with primary sensory, association, and paralimbic areas in children, whereas young-adults showed stronger cortico-cortical connectivity between paralimbic, limbic, and association areas. Further, combined analysis of functional connectivity with wiring distance measures derived from white-matter fiber tracking revealed that the development of large-scale brain networks is characterized by weakening of short-range functional connectivity and strengthening of long-range functional connectivity. Importantly, our findings show that the dynamic process of over-connectivity followed by pruning, which rewires connectivity at the neuronal level, also operates at the systems level, helping to reconfigure and rebalance subcortical and paralimbic connectivity in the developing brain. Our study demonstrates the usefulness of network analysis of brain connectivity to elucidate key principles underlying functional brain maturation, paving the way for novel studies of disrupted brain connectivity in neurodevelopmental disorders such as autism.

Development of Large-Scale Functional Brain Networks in Children

PubMed Central

Supekar, Kaustubh; Musen, Mark; Menon, Vinod

2009-01-01

The ontogeny of large-scale functional organization of the human brain is not well understood. Here we use network analysis of intrinsic functional connectivity to characterize the organization of brain networks in 23 children (ages 7–9 y) and 22 young-adults (ages 19–22 y). Comparison of network properties, including path-length, clustering-coefficient, hierarchy, and regional connectivity, revealed that although children and young-adults' brains have similar “small-world” organization at the global level, they differ significantly in hierarchical organization and interregional connectivity. We found that subcortical areas were more strongly connected with primary sensory, association, and paralimbic areas in children, whereas young-adults showed stronger cortico-cortical connectivity between paralimbic, limbic, and association areas. Further, combined analysis of functional connectivity with wiring distance measures derived from white-matter fiber tracking revealed that the development of large-scale brain networks is characterized by weakening of short-range functional connectivity and strengthening of long-range functional connectivity. Importantly, our findings show that the dynamic process of over-connectivity followed by pruning, which rewires connectivity at the neuronal level, also operates at the systems level, helping to reconfigure and rebalance subcortical and paralimbic connectivity in the developing brain. Our study demonstrates the usefulness of network analysis of brain connectivity to elucidate key principles underlying functional brain maturation, paving the way for novel studies of disrupted brain connectivity in neurodevelopmental disorders such as autism. PMID:19621066

Task modulated brain connectivity of the amygdala: a meta-analysis of psychophysiological interactions.

PubMed

Di, Xin; Huang, Jia; Biswal, Bharat B

2017-01-01

Understanding functional connectivity of the amygdala with other brain regions, especially task modulated connectivity, is a critical step toward understanding the role of the amygdala in emotional processes and the interactions between emotion and cognition. The present study performed coordinate-based meta-analysis on studies of task modulated connectivity of the amygdala which used psychophysiological interaction (PPI) analysis. We first analyzed 49 PPI studies on different types of tasks using activation likelihood estimation (ALE) meta-analysis. Widespread cortical and subcortical regions showed consistent task modulated connectivity with the amygdala, including the medial frontal cortex, bilateral insula, anterior cingulate, fusiform gyrus, parahippocampal gyrus, thalamus, and basal ganglia. These regions were in general overlapped with those showed coactivations with the amygdala, suggesting that these regions and amygdala are not only activated together, but also show different levels of interactions during tasks. Further analyses with subsets of PPI studies revealed task specific functional connectivities with the amygdala that were modulated by fear processing, face processing, and emotion regulation. These results suggest a dynamic modulation of connectivity upon task demands, and provide new insights on the functions of the amygdala in different affective and cognitive processes. The meta-analytic approach on PPI studies may offer a framework toward systematical examinations of task modulated connectivity.

Stochastic resonance energy harvesting for a rotating shaft subject to random and periodic vibrations: influence of potential function asymmetry and frequency sweep

NASA Astrophysics Data System (ADS)

Kim, Hongjip; Che Tai, Wei; Zhou, Shengxi; Zuo, Lei

2017-11-01

Stochastic resonance is referred to as a physical phenomenon that is manifest in nonlinear systems whereby a weak periodic signal can be significantly amplified with the aid of inherent noise or vice versa. In this paper, stochastic resonance is considered to harvest energy from two typical vibrations in rotating shafts: random whirl vibration and periodic stick-slip vibration. Stick-slip vibrations impose a constant offset in centrifugal force and distort the potential function of the harvester, leading to potential function asymmetry. A numerical analysis based on a finite element method was conducted to investigate stochastic resonance with potential function asymmetry. Simulation results revealed that a harvester with symmetric potential function generates seven times higher power than that with asymmetric potential function. Furthermore, a frequency-sweep analysis also showed that stochastic resonance has hysteretic behavior, resulting in frequency difference between up-sweep and down-sweep excitations. An electromagnetic energy harvesting system was constructed to experimentally verify the numerical analysis. In contrast to traditional stochastic resonance harvesters, the proposed harvester uses magnetic force to compensate the offset in the centrifugal force. System identification was performed to obtain the parameters needed in the numerical analysis. With the identified parameters, the numerical simulations showed good agreement with the experiment results with around 10% error, which verified the effect of potential function asymmetry and frequency sweep excitation condition on stochastic resonance. Finally, attributed to compensating the centrifugal force offset, the proposed harvester generated nearly three times more open-circuit output voltage than its traditional counterpart.

Structural and functional plasticity specific to musical training with wind instruments.

PubMed

Choi, Uk-Su; Sung, Yul-Wan; Hong, Sujin; Chung, Jun-Young; Ogawa, Seiji

2015-01-01

Numerous neuroimaging studies have shown structural and functional changes resulting from musical training. Among these studies, changes in primary sensory areas are mostly related to motor functions. In this study, we looked for some similar functional and structural changes in other functional modalities, such as somatosensory function, by examining the effects of musical training with wind instruments. We found significant changes in two aspects of neuroplasticity, cortical thickness, and resting-state neuronal networks. A group of subjects with several years of continuous musical training and who are currently playing in university wind ensembles showed differences in cortical thickness in lip- and tongue-related brain areas vs. non-music playing subjects. Cortical thickness in lip-related brain areas was significantly thicker and that in tongue-related areas was significantly thinner in the music playing group compared with that in the non-music playing group. Association analysis of lip-related areas in the music playing group showed that the increase in cortical thickness was caused by musical training. In addition, seed-based correlation analysis showed differential activation in the precentral gyrus and supplementary motor areas (SMA) between the music and non-music playing groups. These results suggest that high-intensity training with specific musical instruments could induce structural changes in related anatomical areas and could also generate a new functional neuronal network in the brain.

Structural and functional plasticity specific to musical training with wind instruments

PubMed Central

Choi, Uk-Su; Sung, Yul-Wan; Hong, Sujin; Chung, Jun-Young; Ogawa, Seiji

2015-01-01

Numerous neuroimaging studies have shown structural and functional changes resulting from musical training. Among these studies, changes in primary sensory areas are mostly related to motor functions. In this study, we looked for some similar functional and structural changes in other functional modalities, such as somatosensory function, by examining the effects of musical training with wind instruments. We found significant changes in two aspects of neuroplasticity, cortical thickness, and resting-state neuronal networks. A group of subjects with several years of continuous musical training and who are currently playing in university wind ensembles showed differences in cortical thickness in lip- and tongue-related brain areas vs. non-music playing subjects. Cortical thickness in lip-related brain areas was significantly thicker and that in tongue-related areas was significantly thinner in the music playing group compared with that in the non-music playing group. Association analysis of lip-related areas in the music playing group showed that the increase in cortical thickness was caused by musical training. In addition, seed-based correlation analysis showed differential activation in the precentral gyrus and supplementary motor areas (SMA) between the music and non-music playing groups. These results suggest that high-intensity training with specific musical instruments could induce structural changes in related anatomical areas and could also generate a new functional neuronal network in the brain. PMID:26578939

Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?

PubMed

Lovelock, Paul K; Spurdle, Amanda B; Mok, Myth T S; Farrugia, Daniel J; Lakhani, Sunil R; Healey, Sue; Arnold, Stephen; Buchanan, Daniel; Couch, Fergus J; Henderson, Beric R; Goldgar, David E; Tavtigian, Sean V; Chenevix-Trench, Georgia; Brown, Melissa A

2007-01-01

Many of the DNA sequence variants identified in the breast cancer susceptibility gene BRCA1 remain unclassified in terms of their potential pathogenicity. Both multifactorial likelihood analysis and functional approaches have been proposed as a means to elucidate likely clinical significance of such variants, but analysis of the comparative value of these methods for classifying all sequence variants has been limited. We have compared the results from multifactorial likelihood analysis with those from several functional analyses for the four BRCA1 sequence variants A1708E, G1738R, R1699Q, and A1708V. Our results show that multifactorial likelihood analysis, which incorporates sequence conservation, co-inheritance, segregation, and tumour immunohistochemical analysis, may improve classification of variants. For A1708E, previously shown to be functionally compromised, analysis of oestrogen receptor, cytokeratin 5/6, and cytokeratin 14 tumour expression data significantly strengthened the prediction of pathogenicity, giving a posterior probability of pathogenicity of 99%. For G1738R, shown to be functionally defective in this study, immunohistochemistry analysis confirmed previous findings of inconsistent 'BRCA1-like' phenotypes for the two tumours studied, and the posterior probability for this variant was 96%. The posterior probabilities of R1699Q and A1708V were 54% and 69%, respectively, only moderately suggestive of increased risk. Interestingly, results from functional analyses suggest that both of these variants have only partial functional activity. R1699Q was defective in foci formation in response to DNA damage and displayed intermediate transcriptional transactivation activity but showed no evidence for centrosome amplification. In contrast, A1708V displayed an intermediate transcriptional transactivation activity and a normal foci formation response in response to DNA damage but induced centrosome amplification. These data highlight the need for a range of functional studies to be performed in order to identify variants with partially compromised function. The results also raise the possibility that A1708V and R1699Q may be associated with a low or moderate risk of cancer. While data pooling strategies may provide more information for multifactorial analysis to improve the interpretation of the clinical significance of these variants, it is likely that the development of current multifactorial likelihood approaches and the consideration of alternative statistical approaches will be needed to determine whether these individually rare variants do confer a low or moderate risk of breast cancer.

An advanced probabilistic structural analysis method for implicit performance functions

NASA Technical Reports Server (NTRS)

Wu, Y.-T.; Millwater, H. R.; Cruse, T. A.

1989-01-01

In probabilistic structural analysis, the performance or response functions usually are implicitly defined and must be solved by numerical analysis methods such as finite element methods. In such cases, the most commonly used probabilistic analysis tool is the mean-based, second-moment method which provides only the first two statistical moments. This paper presents a generalized advanced mean value (AMV) method which is capable of establishing the distributions to provide additional information for reliability design. The method requires slightly more computations than the second-moment method but is highly efficient relative to the other alternative methods. In particular, the examples show that the AMV method can be used to solve problems involving non-monotonic functions that result in truncated distributions.

Do Items that Measure Self-Perceived Physical Appearance Function Differentially across Gender Groups? An Application of the MACS Model

ERIC Educational Resources Information Center

Gonzalez-Roma, Vicente; Tomas, Ines; Ferreres, Doris; Hernandez, Ana

2005-01-01

The aims of this study were to investigate whether the 6 items of the Physical Appearance Scale (Marsh, Richards, Johnson, Roche, & Tremayne, 1994) show differential item functioning (DIF) across gender groups of adolescents, and to show how this can be done using the multigroup mean and covariance structure (MG-MACS) analysis model. Two samples…

Quantification of endocytosis using a folate functionalized silica hollow nanoshell platform

PubMed Central

Sandoval, Sergio; Mendez, Natalie; Alfaro, Jesus G.; Yang, Jian; Aschemeyer, Sharraya; Liberman, Alex; Trogler, William C.; Kummel, Andrew C.

2015-01-01

Abstract. A quantification method to measure endocytosis was designed to assess cellular uptake and specificity of a targeting nanoparticle platform. A simple N-hydroxysuccinimide ester conjugation technique to functionalize 100-nm hollow silica nanoshell particles with fluorescent reporter fluorescein isothiocyanate and folate or polyethylene glycol (PEG) was developed. Functionalized nanoshells were characterized using scanning electron microscopy and transmission electron microscopy and the maximum amount of folate functionalized on nanoshell surfaces was quantified with UV-Vis spectroscopy. The extent of endocytosis by HeLa cervical cancer cells and human foreskin fibroblast (HFF-1) cells was investigated in vitro using fluorescence and confocal microscopy. A simple fluorescence ratio analysis was developed to quantify endocytosis versus surface adhesion. Nanoshells functionalized with folate showed enhanced endocytosis by cancer cells when compared to PEG functionalized nanoshells. Fluorescence ratio analyses showed that 95% of folate functionalized silica nanoshells which adhered to cancer cells were endocytosed, while only 27% of PEG functionalized nanoshells adhered to the cell surface and underwent endocytosis when functionalized with 200 and 900  μg, respectively. Additionally, the endocytosis of folate functionalized nanoshells proved to be cancer cell selective while sparing normal cells. The developed fluorescence ratio analysis is a simple and rapid verification/validation method to quantify cellular uptake between datasets by using an internal control for normalization. PMID:26315280

[Prematurity: longitudinal analysis of executive functions].

PubMed

Sastre-Riba, S

2009-02-27

Understanding cognitive development requires an interdisciplinary and neuropsychological approach. Executive functions facilitates cognitive activity and they are related to progressive cerebral configuration during pregnancy and infancy. One of the aims of the actual neuropsychology is the ontogeny of executive functions and their capacity to explain differential and normative developmental trends, specially because of its consequences on mental flexibility, monitoring, planning and cognitive control; they are also essential for good performance at school. The incidence of developmental risk factors as prematurity could affect long-term executive functioning expressed in learning difficulties or behavioral control. We studied, comparatively and longitudinally, the individual activity on objects displayed by typical babies (n = 25), and preterm babies (n = 10) from 1.5 to 2 years-old. Applying systematic observational methodology, spontaneous babies' activity is registered. Double intra and inter-group analysis compare the data from the resolution of a non-verbal task through a multifaceted design. Results obtained show us differential pattern of early executive functioning among the groups studied. The growth of executive functioning is showed, too, through the ages studied for every group.

FGWAS: Functional genome wide association analysis.

PubMed

Huang, Chao; Thompson, Paul; Wang, Yalin; Yu, Yang; Zhang, Jingwen; Kong, Dehan; Colen, Rivka R; Knickmeyer, Rebecca C; Zhu, Hongtu

2017-10-01

Functional phenotypes (e.g., subcortical surface representation), which commonly arise in imaging genetic studies, have been used to detect putative genes for complexly inherited neuropsychiatric and neurodegenerative disorders. However, existing statistical methods largely ignore the functional features (e.g., functional smoothness and correlation). The aim of this paper is to develop a functional genome-wide association analysis (FGWAS) framework to efficiently carry out whole-genome analyses of functional phenotypes. FGWAS consists of three components: a multivariate varying coefficient model, a global sure independence screening procedure, and a test procedure. Compared with the standard multivariate regression model, the multivariate varying coefficient model explicitly models the functional features of functional phenotypes through the integration of smooth coefficient functions and functional principal component analysis. Statistically, compared with existing methods for genome-wide association studies (GWAS), FGWAS can substantially boost the detection power for discovering important genetic variants influencing brain structure and function. Simulation studies show that FGWAS outperforms existing GWAS methods for searching sparse signals in an extremely large search space, while controlling for the family-wise error rate. We have successfully applied FGWAS to large-scale analysis of data from the Alzheimer's Disease Neuroimaging Initiative for 708 subjects, 30,000 vertices on the left and right hippocampal surfaces, and 501,584 SNPs. Copyright © 2017 Elsevier Inc. All rights reserved.

Production Functions for Water Delivery Systems: Analysis and Estimation Using Dual Cost Function and Implicit Price Specifications

NASA Astrophysics Data System (ADS)

Teeples, Ronald; Glyer, David

1987-05-01

Both policy and technical analysis of water delivery systems have been based on cost functions that are inconsistent with or are incomplete representations of the neoclassical production functions of economics. We present a full-featured production function model of water delivery which can be estimated from a multiproduct, dual cost function. The model features implicit prices for own-water inputs and is implemented as a jointly estimated system of input share equations and a translog cost function. Likelihood ratio tests are performed showing that a minimally constrained, full-featured production function is a necessary specification of the water delivery operations in our sample. This, plus the model's highly efficient and economically correct parameter estimates, confirms the usefulness of a production function approach to modeling the economic activities of water delivery systems.

Physical activity domains and cognitive function over three years in older adults with subjective memory complaints: Secondary analysis from the MAPT trial.

PubMed

de Souto Barreto, Philipe; Andrieu, Sandrine; Rolland, Yves; Vellas, Bruno

2018-01-01

We aimed to examine the associations of physical activity (PA) domains (i.e., PA in leisure-time (LTPA), for housework (HPA), or for gardening (GPA)) with cognitive function in older adults with subjective memory complaints (no-dementia) and to investigate if those associations were dependent on the status of apolipoprotein E allele 4 (APOE4), omega-3 levels and mild cognitive impairment (MCI). Observational prospective secondary analysis using longitudinal data from a randomized controlled trial. Participants were 420 French community-dwelling people (aged 75.6±4.4; 66.4% women) randomized into the placebo group. They were assessed at baseline, 6-, 12-, 24- and 36-month using a battery of neuropsychological tests; a composite cognitive Z score was elaborated for all time points. Data on PA come from baseline and was obtained using a self-reported questionnaire. In time-adjusted analysis, LTPA significantly predicted cognitive function over three years for almost all tests and the composite Z score, with higher LTPA associated with better function; multivariate analysis showed a significant association only for verbal fluency. HPA was not associated to cognitive function, whereas GPA had mixed results. The magnitude of the PA-cognition associations was very weak, being the strongest for LTPA. Stratified analyses showed that the associations between PA and cognitive function were stronger for MCI, people with normal omega-3 index levels, and APOE4 non-carriers. PA domain is an important aspect to take into account when examining the associations between PA and cognitive function. Biomarkers of cognitive function may modulate the PA-cognition associations. Copyright © 2017 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

Accuracy of Presurgical Functional MR Imaging for Language Mapping of Brain Tumors: A Systematic Review and Meta-Analysis.

PubMed

Weng, Hsu-Huei; Noll, Kyle R; Johnson, Jason M; Prabhu, Sujit S; Tsai, Yuan-Hsiung; Chang, Sheng-Wei; Huang, Yen-Chu; Lee, Jiann-Der; Yang, Jen-Tsung; Yang, Cheng-Ta; Tsai, Ying-Huang; Yang, Chun-Yuh; Hazle, John D; Schomer, Donald F; Liu, Ho-Ling

2018-02-01

Purpose To compare functional magnetic resonance (MR) imaging for language mapping (hereafter, language functional MR imaging) with direct cortical stimulation (DCS) in patients with brain tumors and to assess factors associated with its accuracy. Materials and Methods PubMed/MEDLINE and related databases were searched for research articles published between January 2000 and September 2016. Findings were pooled by using bivariate random-effects and hierarchic summary receiver operating characteristic curve models. Meta-regression and subgroup analyses were performed to evaluate whether publication year, functional MR imaging paradigm, magnetic field strength, statistical threshold, and analysis software affected classification accuracy. Results Ten articles with a total of 214 patients were included in the analysis. On a per-patient basis, the pooled sensitivity and specificity of functional MR imaging was 44% (95% confidence interval [CI]: 14%, 78%) and 80% (95% CI: 54%, 93%), respectively. On a per-tag basis (ie, each DCS stimulation site or "tag" was considered a separate data point across all patients), the pooled sensitivity and specificity were 67% (95% CI: 51%, 80%) and 55% (95% CI: 25%, 82%), respectively. The per-tag analysis showed significantly higher sensitivity for studies with shorter functional MR imaging session times (P = .03) and relaxed statistical threshold (P = .05). Significantly higher specificity was found when expressive language task (P = .02), longer functional MR imaging session times (P < .01), visual presentation of stimuli (P = .04), and stringent statistical threshold (P = .01) were used. Conclusion Results of this study showed moderate accuracy of language functional MR imaging when compared with intraoperative DCS, and the included studies displayed significant methodologic heterogeneity. © RSNA, 2017 Online supplemental material is available for this article.

An Analysis of Vocal Stereotypy and Therapist Fading

ERIC Educational Resources Information Center

Athens, Elizabeth S.; Vollmer, Timothy R.; Sloman, Kimberly N.; Pipkin, Claire St. Peter

2008-01-01

A functional analysis for a boy with Down syndrome and autism suggested that vocal stereotypy was maintained by automatic reinforcement. The analysis also showed that instructions and noncontingent attention suppressed vocal stereotypy. A treatment package consisting of noncontingent attention, contingent demands, and response cost effectively…

Comparative analysis of short - term functional outcomes and quality of life in a prospective series of brachytherapy and Da Vinci robotic prostatectomy

PubMed Central

García-Sánchez, Cristina; Román Martín, Ana A.; Conde-Sánchez, J. Manuel; Congregado-Ruíz, C. Belén; Osman-García, Ignacio; Medina-López, Rafael A.

2017-01-01

ABSTRACT Introduction There is a growing interest in achieving higher survival rates with the lowest morbidity in localized prostate cancer (PC) treatment. Consequently, minimally invasive techniques such as low-dose rate brachytherapy (BT) and robotic-assisted prostatectomy (RALP) have been developed and improved. Comparative analysis of functional outcomes and quality of life in a prospective series of 51BT and 42Da Vinci prostatectomies DV Materials and Methods Comparative analysis of functional outcomes and quality of life in a prospective series of 93 patients with low-risk localized PC diagnosed in 2011. 51patients underwent low-dose rate BT and the other 42 patients RALP. IIEF to assess erectile function, ICIQ to evaluate continence and SF36 test to quality of life wee employed. Results ICIQ at the first revision shows significant differences which favour the BT group, 79% present with continence or mild incontinence, whereas in the DV group 45% show these positive results. Differences disappear after 6 months, with 45 patients (89%) presenting with continence or mild incontinence in the BT group vs. 30 (71%) in the DV group. 65% of patients are potent in the first revision following BT and 39% following DV. Such differences are not significant and cannot be observed after 6 months. No significant differences were found in the comparative analysis of quality of life. Conclusions ICIQ after surgery shows significant differences in favour of BT, which disappear after 6 months. Both procedures have a serious impact on erectile function, being even greater in the DV group. Differences between groups disappear after 6 months. PMID:28128908

Association Between Blood Glucose and Functional Outcome in Intracerebral Hemorrhage: A Systematic Review and Meta-Analysis.

PubMed

Zheng, Jun; Yu, Zhiyuan; Ma, Lu; Guo, Rui; Lin, Sen; You, Chao; Li, Hao

2018-03-16

Intracerebral hemorrhage (ICH) is a devastating subtype of stroke. Patients with ICH have poor functional outcomes. The association between blood glucose level and functional outcome in ICH remains unclear. This systematic review and meta-analysis aimed to investigate the association between blood glucose level and functional outcomes in patients with ICH. Literature was searched systemically in PubMed, EMBASE, Web of Science, and Cochrane Library. Published cohort studies evaluating the association between blood glucose and functional outcome in patients with ICH were included. This meta-analysis was performed using odds ratios (ORs) and 95% confidence intervals (CIs). A total of 16 studies were included in our meta-analysis. Our data show that hyperglycemia defined by cutoff values was significantly associated with unfavorable functional outcome (OR, 1.80; 95% CI, 1.36-2.39; P < 0.001). Our analysis also suggested a significant association between increased blood glucose levels and functional outcomes (OR, 1.05; 95% CI, 1.03-1.07; P < 0.001). High blood glucose level is significantly associated with poor functional outcome in ICH. Further studies with larger sample sizes, more time points, and longer follow-up times are necessary to confirm this association. Copyright © 2018 Elsevier Inc. All rights reserved.

Peak finding using biorthogonal wavelets

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

Tan, C.Y.

2000-02-01

The authors show in this paper how they can find the peaks in the input data if the underlying signal is a sum of Lorentzians. In order to project the data into a space of Lorentzian like functions, they show explicitly the construction of scaling functions which look like Lorentzians. From this construction, they can calculate the biorthogonal filter coefficients for both the analysis and synthesis functions. They then compare their biorthogonal wavelets to the FBI (Federal Bureau of Investigations) wavelets when used for peak finding in noisy data. They will show that in this instance, their filters perform muchmore » better than the FBI wavelets.« less

Learning Time-Varying Coverage Functions

PubMed Central

Du, Nan; Liang, Yingyu; Balcan, Maria-Florina; Song, Le

2015-01-01

Coverage functions are an important class of discrete functions that capture the law of diminishing returns arising naturally from applications in social network analysis, machine learning, and algorithmic game theory. In this paper, we propose a new problem of learning time-varying coverage functions, and develop a novel parametrization of these functions using random features. Based on the connection between time-varying coverage functions and counting processes, we also propose an efficient parameter learning algorithm based on likelihood maximization, and provide a sample complexity analysis. We applied our algorithm to the influence function estimation problem in information diffusion in social networks, and show that with few assumptions about the diffusion processes, our algorithm is able to estimate influence significantly more accurately than existing approaches on both synthetic and real world data. PMID:25960624

Learning Time-Varying Coverage Functions.

PubMed

Du, Nan; Liang, Yingyu; Balcan, Maria-Florina; Song, Le

2014-12-08

Coverage functions are an important class of discrete functions that capture the law of diminishing returns arising naturally from applications in social network analysis, machine learning, and algorithmic game theory. In this paper, we propose a new problem of learning time-varying coverage functions, and develop a novel parametrization of these functions using random features. Based on the connection between time-varying coverage functions and counting processes, we also propose an efficient parameter learning algorithm based on likelihood maximization, and provide a sample complexity analysis. We applied our algorithm to the influence function estimation problem in information diffusion in social networks, and show that with few assumptions about the diffusion processes, our algorithm is able to estimate influence significantly more accurately than existing approaches on both synthetic and real world data.

A Meta-Analysis of Differences in IQ Profiles between Individuals with Asperger's Disorder and High-Functioning Autism

ERIC Educational Resources Information Center

Chiang, Hsu-Min; Tsai, Luke Y.; Cheung, Ying Kuen; Brown, Alice; Li, Huacheng

2014-01-01

A meta-analysis was performed to examine differences in IQ profiles between individuals with Asperger's disorder (AspD) and high-functioning autism (HFA). Fifty-two studies were included for this study. The results showed that (a) individuals with AspD had significantly higher full-scale IQ, verbal IQ (VIQ), and performance IQ (PIQ) than did…

Noncoding sequence classification based on wavelet transform analysis: part II

NASA Astrophysics Data System (ADS)

Paredes, O.; Strojnik, M.; Romo-Vázquez, R.; Vélez-Pérez, H.; Ranta, R.; Garcia-Torales, G.; Scholl, M. K.; Morales, J. A.

2017-09-01

DNA sequences in human genome can be divided into the coding and noncoding ones. We hypothesize that the characteristic periodicities of the noncoding sequences are related to their function. We describe the procedure to identify these characteristic periodicities using the wavelet analysis. Our results show that three groups of noncoding sequences, each one with different biological function, may be differentiated by their wavelet coefficients within specific frequency range.

Comprehensive proteome analysis of lysosomes reveals the diverse function of macrophages in immune responses.

PubMed

Gao, Yanpan; Chen, Yanyu; Zhan, Shaohua; Zhang, Wenhao; Xiong, Feng; Ge, Wei

2017-01-31

Phagocytosis and autophagy in macrophages have been shown to be essential to both innate and adaptive immunity. Lysosomes are the main catabolic subcellular organelles responsible for degradation and recycling of both extracellular and intracellular material, which are the final steps in phagocytosis and autophagy. However, the molecular mechanisms underlying lysosomal functions after infection remain obscure. In this study, we conducted a quantitative proteomics analysis of the changes in constitution and glycosylation of proteins in lysosomes derived from murine RAW 264.7 macrophage cells treated with different types of pathogens comprising examples of bacteria (Listeria monocytogenes, L. m), DNA viruses (herpes simplex virus type-1, HSV-1) and RNA viruses (vesicular stomatitis virus, VSV). In total, 3,704 lysosome-related proteins and 300 potential glycosylation sites on 193 proteins were identified. Comparative analysis showed that the aforementioned pathogens induced distinct alterations in the proteome of the lysosome, which is closely associated with the immune functions of macrophages, such as toll-like receptor activation, inflammation and antigen-presentation. The most significant changes in proteins and fluctuations in glycosylation were also determined. Furthermore, Western blot analysis showed that the changes in expression of these proteins were undetectable at the whole cell level. Thus, our study provides unique insights into the function of lysosomes in macrophage activation and immune responses.

Nonparametric functional data estimation applied to ozone data: prediction and extreme value analysis.

PubMed

Quintela-del-Río, Alejandro; Francisco-Fernández, Mario

2011-02-01

The study of extreme values and prediction of ozone data is an important topic of research when dealing with environmental problems. Classical extreme value theory is usually used in air-pollution studies. It consists in fitting a parametric generalised extreme value (GEV) distribution to a data set of extreme values, and using the estimated distribution to compute return levels and other quantities of interest. Here, we propose to estimate these values using nonparametric functional data methods. Functional data analysis is a relatively new statistical methodology that generally deals with data consisting of curves or multi-dimensional variables. In this paper, we use this technique, jointly with nonparametric curve estimation, to provide alternatives to the usual parametric statistical tools. The nonparametric estimators are applied to real samples of maximum ozone values obtained from several monitoring stations belonging to the Automatic Urban and Rural Network (AURN) in the UK. The results show that nonparametric estimators work satisfactorily, outperforming the behaviour of classical parametric estimators. Functional data analysis is also used to predict stratospheric ozone concentrations. We show an application, using the data set of mean monthly ozone concentrations in Arosa, Switzerland, and the results are compared with those obtained by classical time series (ARIMA) analysis. Copyright © 2010 Elsevier Ltd. All rights reserved.

Knee Extensor Strength and Risk of Structural, Symptomatic, and Functional Decline in Knee Osteoarthritis: A Systematic Review and Meta-Analysis.

PubMed

Culvenor, Adam G; Ruhdorfer, Anja; Juhl, Carsten; Eckstein, Felix; Øiestad, Britt Elin

2017-05-01

To perform a systematic review and meta-analysis on the association between knee extensor strength and the risk of structural, symptomatic, or functional deterioration in individuals with or at risk of knee osteoarthritis (KOA). We systematically identified and methodologically appraised all longitudinal studies (≥1-year followup) reporting an association between knee extensor strength and structural (tibiofemoral, patellofemoral), symptomatic (self-reported, knee replacement), or functional (subjective, objective) decline in individuals with or at risk of radiographic or symptomatic KOA. Results were pooled for each of the above associations using meta-analysis, or if necessary, summarized according to a best-evidence synthesis. Fifteen studies were included, evaluating >8,000 participants (51% female), with a followup time between 1.5 and 8 years. Meta-analysis revealed that lower knee extensor strength was associated with an increased risk of symptomatic (Western Ontario and McMaster Universities Osteoarthritis Index [WOMAC] pain: odds ratio [OR] 1.35, 95% confidence interval [95% CI] 1.10-1.67) and functional decline (WOMAC function: OR 1.38, 95% CI 1.00-1.89, and chair-stand task: OR 1.03, 95% CI 1.03-1.04), but not increased risk of radiographic tibiofemoral joint space narrowing (JSN) (OR 1.15, 95% CI 0.84-1.56). No trend in risk was observed for KOA status (present versus absent). Best-evidence synthesis showed inconclusive evidence for lower knee extensor strength being associated with increased risk of patellofemoral deterioration. Meta-analysis showed that lower knee extensor strength is associated with an increased risk of symptomatic and functional deterioration, but not tibiofemoral JSN. The risk of patellofemoral deterioration in the presence of knee extensor strength deficits is inconclusive. © 2016, American College of Rheumatology.

Functional analysis and treatment of the diurnal bruxism of a 16-year-old girl with autism.

PubMed

Armstrong, Amy; Knapp, Vicki Madaus; McAdam, David B

2014-01-01

Bruxism is defined as the clenching and grinding of teeth. This study used a functional analysis to examine whether the bruxism of a 16-year-old girl with autism was maintained by automatic reinforcement or social consequences. A subsequent component analysis of the intervention package described by Barnoy, Najdowski, Tarbox, Wilke, and Nollet (2009) showed that a vocal reprimand (e.g., "stop grinding") effectively reduced the participant's bruxism. Results were maintained across time, and effects extended to novel staff members. © Society for the Experimental Analysis of Behavior.

Projection-based motion estimation for cardiac functional analysis with high temporal resolution: a proof-of-concept study with digital phantom experiment

NASA Astrophysics Data System (ADS)

Suzuki, Yuki; Fung, George S. K.; Shen, Zeyang; Otake, Yoshito; Lee, Okkyun; Ciuffo, Luisa; Ashikaga, Hiroshi; Sato, Yoshinobu; Taguchi, Katsuyuki

2017-03-01

Cardiac motion (or functional) analysis has shown promise not only for non-invasive diagnosis of cardiovascular diseases but also for prediction of cardiac future events. Current imaging modalities has limitations that could degrade the accuracy of the analysis indices. In this paper, we present a projection-based motion estimation method for x-ray CT that estimates cardiac motion with high spatio-temporal resolution using projection data and a reference 3D volume image. The experiment using a synthesized digital phantom showed promising results for motion analysis.

Deletion of the transcriptional coactivator PGC1α in skeletal muscles is associated with reduced expression of genes related to oxidative muscle function

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

Hatazawa, Yukino; Research Fellow of Japan Society for the Promotion of Science, Tokyo; Minami, Kimiko

The expression of the transcriptional coactivator PGC1α is increased in skeletal muscles during exercise. Previously, we showed that increased PGC1α leads to prolonged exercise performance (the duration for which running can be continued) and, at the same time, increases the expression of branched-chain amino acid (BCAA) metabolism-related enzymes and genes that are involved in supplying substrates for the TCA cycle. We recently created mice with PGC1α knockout specifically in the skeletal muscles (PGC1α KO mice), which show decreased mitochondrial content. In this study, global gene expression (microarray) analysis was performed in the skeletal muscles of PGC1α KO mice compared withmore » that of wild-type control mice. As a result, decreased expression of genes involved in the TCA cycle, oxidative phosphorylation, and BCAA metabolism were observed. Compared with previously obtained microarray data on PGC1α-overexpressing transgenic mice, each gene showed the completely opposite direction of expression change. Bioinformatic analysis of the promoter region of genes with decreased expression in PGC1α KO mice predicted the involvement of several transcription factors, including a nuclear receptor, ERR, in their regulation. As PGC1α KO microarray data in this study show opposing findings to the PGC1α transgenic data, a loss-of-function experiment, as well as a gain-of-function experiment, revealed PGC1α’s function in the oxidative energy metabolism of skeletal muscles. - Highlights: • Microarray analysis was performed in the skeletal muscle of PGC1α KO mice. • Expression of genes in the oxidative energy metabolism was decreased. • Bioinformatic analysis of promoter region of the genes predicted involvement of ERR. • PGC1α KO microarray data in this study show the mirror image of transgenic data.« less

An Investigation of Document Partitions.

ERIC Educational Resources Information Center

Shaw, W. M., Jr.

1986-01-01

Empirical significance of document partitions is investigated as a function of index term-weight and similarity thresholds. Results show the same empirically preferred partitions can be detected by two independent strategies: an analysis of cluster-based retrieval analysis and an analysis of regularities in the underlying structure of the document…

The Information Content of Discrete Functions and Their Application in Genetic Data Analysis.

PubMed

Sakhanenko, Nikita A; Kunert-Graf, James; Galas, David J

2017-12-01

The complex of central problems in data analysis consists of three components: (1) detecting the dependence of variables using quantitative measures, (2) defining the significance of these dependence measures, and (3) inferring the functional relationships among dependent variables. We have argued previously that an information theory approach allows separation of the detection problem from the inference of functional form problem. We approach here the third component of inferring functional forms based on information encoded in the functions. We present here a direct method for classifying the functional forms of discrete functions of three variables represented in data sets. Discrete variables are frequently encountered in data analysis, both as the result of inherently categorical variables and from the binning of continuous numerical variables into discrete alphabets of values. The fundamental question of how much information is contained in a given function is answered for these discrete functions, and their surprisingly complex relationships are illustrated. The all-important effect of noise on the inference of function classes is found to be highly heterogeneous and reveals some unexpected patterns. We apply this classification approach to an important area of biological data analysis-that of inference of genetic interactions. Genetic analysis provides a rich source of real and complex biological data analysis problems, and our general methods provide an analytical basis and tools for characterizing genetic problems and for analyzing genetic data. We illustrate the functional description and the classes of a number of common genetic interaction modes and also show how different modes vary widely in their sensitivity to noise.

Microbial functional diversity plays an important role in the degradation of polyhydroxybutyrate (PHB) in soil.

PubMed

Dey, Samrat; Tribedi, Prosun

2018-03-01

Towards bioremediation of recalcitrant materials like synthetic polymer, soil has been recognized as a traditional site for disposal and subsequent degradation as some microorganisms in soil can degrade the polymer in a non-toxic, cost-effective, and environment friendly way. Microbial functional diversity is a constituent of biodiversity that includes wide range of metabolic activities that can influence numerous aspects of ecosystem functioning like ecosystem stability, nutrient availability, ecosystem dynamics, etc. Thus, in the current study, we assumed that microbial functional diversity could play an important role in polymer degradation in soil. To verify this hypothesis, we isolated soil from five different sites of landfill and examined several microbiological parameters wherein we observed a significant variation in heterotrophic microbial count as well as microbial activities among the soil microcosms tested. Multivariate analysis (principle component analysis) based on the carbon sources utilization pattern revealed that soil microcosms showed different metabolic patterns suggesting the variable distribution of microorganisms among the soil microcosms tested. Since microbial functional diversity depends on both microbial richness and evenness, Shannon diversity index was determined to measure microbial richness and Gini coefficient was determined to measure microbial evenness. The tested soil microcosms exhibited variation in both microbial richness and evenness suggesting the considerable difference in microbial functional diversity among the tested microcosms. We then measured polyhydroxybutyrate (PHB) degradation in soil microcosms after desired period of incubation of PHB in soil wherein we found that soil microcosms having higher functional diversity showed enhanced PHB degradation and soil microcosms having lower functional diversity showed reduced PHB degradation. We also noticed that all the tested soil microcosms showed similar pattern in both microbial functional diversity and PHB degradation suggesting a strong positive correlation ( r  = 0.95) between microbial functional diversity and PHB degradation. Thus, the results demonstrate that microbial functional diversity plays an important role in PHB degradation in soil by exhibiting versatile microbial metabolic potentials that lead to the enhanced degradation of PHB.

Functional Connectivity Parcellation of the Human Thalamus by Independent Component Analysis.

PubMed

Zhang, Sheng; Li, Chiang-Shan R

2017-11-01

As a key structure to relay and integrate information, the thalamus supports multiple cognitive and affective functions through the connectivity between its subnuclei and cortical and subcortical regions. Although extant studies have largely described thalamic regional functions in anatomical terms, evidence accumulates to suggest a more complex picture of subareal activities and connectivities of the thalamus. In this study, we aimed to parcellate the thalamus and examine whole-brain connectivity of its functional clusters. With resting state functional magnetic resonance imaging data from 96 adults, we used independent component analysis (ICA) to parcellate the thalamus into 10 components. On the basis of the independence assumption, ICA helps to identify how subclusters overlap spatially. Whole brain functional connectivity of each subdivision was computed for independent component's time course (ICtc), which is a unique time series to represent an IC. For comparison, we computed seed-region-based functional connectivity using the averaged time course across all voxels within a thalamic subdivision. The results showed that, at p < 10 -6 , corrected, 49% of voxels on average overlapped among subdivisions. Compared with seed-region analysis, ICtc analysis revealed patterns of connectivity that were more distinguished between thalamic clusters. ICtc analysis demonstrated thalamic connectivity to the primary motor cortex, which has eluded the analysis as well as previous studies based on averaged time series, and clarified thalamic connectivity to the hippocampus, caudate nucleus, and precuneus. The new findings elucidate functional organization of the thalamus and suggest that ICA clustering in combination with ICtc rather than seed-region analysis better distinguishes whole-brain connectivities among functional clusters of a brain region.

Alternations of functional connectivity in amblyopia patients: a resting-state fMRI study

NASA Astrophysics Data System (ADS)

Wang, Jieqiong; Hu, Ling; Li, Wenjing; Xian, Junfang; Ai, Likun; He, Huiguang

2014-03-01

Amblyopia is a common yet hard-to-cure disease in children and results in poor or blurred vision. Some efforts such as voxel-based analysis, cortical thickness analysis have been tried to reveal the pathogenesis of amblyopia. However, few studies focused on alterations of the functional connectivity (FC) in amblyopia. In this study, we analyzed the abnormalities of amblyopia patients by both the seed-based FC with the left/right primary visual cortex and the network constructed throughout the whole brain. Experiments showed the following results: (1)As for the seed-based FC analysis, FC between superior occipital gyrus and the primary visual cortex was found to significantly decrease in both sides. The abnormalities were also found in lingual gyrus. The results may reflect functional deficits both in dorsal stream and ventral stream. (2)Two increased functional connectivities and 64 decreased functional connectivities were found in the whole brain network analysis. The decreased functional connectivities most concentrate in the temporal cortex. The results suggest that amblyopia may be caused by the deficits in the visual information transmission.

Meta-analysis of neuropsychological measures of executive functioning in children and adolescents with high-functioning autism spectrum disorder.

PubMed

Lai, Chun Lun Eric; Lau, Zoe; Lui, Simon S Y; Lok, Eugenia; Tam, Venus; Chan, Quinney; Cheng, Koi Man; Lam, Siu Man; Cheung, Eric F C

2017-05-01

Existing literature on the profile of executive dysfunction in autism spectrum disorder showed inconsistent results. Age, comorbid attention-deficit/hyperactivity disorder (ADHD) and cognitive abilities appeared to play a role in confounding the picture. Previous meta-analyses have focused on a few components of executive functions. This meta-analysis attempted to delineate the profile of deficit in several components of executive functioning in children and adolescents with high-functioning autism spectrum disorder (HFASD). Ninety-eight English published case-control studies comparing children and adolescents with HFASD with typically developing controls using well-known neuropsychological measures to assess executive functions were included. Results showed that children and adolescents with HFASD were moderately impaired in verbal working memory (g = 0.67), spatial working memory (g = 0.58), flexibility (g = 0.59), planning (g = 0.62), and generativity (g = 0.60) except for inhibition (g = 0.41). Subgroup analysis showed that impairments were still significant for flexibility (g = 0.57-0.61), generativity (g = 0.52-0.68), and working memory (g = 0.49-0.56) in a sample of autism spectrum disorder (ASD) subjects without comorbid ADHD or when the cognitive abilities of the ASD group and the control group were comparable. This meta-analysis confirmed the presence of executive dysfunction in children and adolescents with HFASD. These deficits are not solely accounted for by the effect of comorbid ADHD and the general cognitive abilities. Our results support the executive dysfunction hypothesis and contribute to the clinical understanding and possible development of interventions to alleviate these deficits in children and adolescents with HFASD. Autism Res 2017, 10: 911-939. © 2016 International Society for Autism Research, Wiley Periodicals, Inc. © 2016 International Society for Autism Research, Wiley Periodicals, Inc.

Specific cognitive functions and depressive symptoms as predictors of activities of daily living in older adults with heterogeneous cognitive backgrounds

PubMed Central

de Paula, Jonas J.; Diniz, Breno S.; Bicalho, Maria A.; Albuquerque, Maicon Rodrigues; Nicolato, Rodrigo; de Moraes, Edgar N.; Romano-Silva, Marco A.; Malloy-Diniz, Leandro F.

2015-01-01

Cognitive functioning influences activities of daily living (ADL). However, studies reporting the association between ADL and neuropsychological performance show inconsistent results regarding what specific cognitive domains are related to each specific functional domains. Additionally, whether depressive symptoms are associated with a worse functional performance in older adults is still under explored. We investigated if specific cognitive domains and depressive symptoms would affect different aspects of ADL. Participants were 274 older adults (96 normal aging participants, 85 patients with mild cognitive impairment, and 93 patients probable with mild Alzheimer’s disease dementia) with low formal education (∼4 years). Measures of ADL included three complexity levels: Self-care, Instrumental-Domestic, and Instrumental-Complex. The specific cognitive functions were evaluated through a factorial strategy resulting in four cognitive domains: Executive Functions, Language/Semantic Memory, Episodic Memory, and Visuospatial Abilities. The Geriatric Depression Scale measured depressive symptoms. Multiple linear regression analysis showed executive functions and episodic memory as significant predictors of Instrumental-Domestic ADL, and executive functions, episodic memory and language/semantic memory as predictors of Instrumental-Complex ADL (22 and 28% of explained variance, respectively). Ordinal regression analysis showed the influence of specific cognitive functions and depressive symptoms on each one of the instrumental ADL. We observed a heterogeneous pattern of association with explained variance ranging from 22 to 38%. Different instrumental ADL had specific cognitive predictors and depressive symptoms were predictive of ADL involving social contact. Our results suggest a specific pattern of influence depending on the specific instrumental daily living activity. PMID:26257644

Differential reward network functional connectivity in cannabis dependent and non-dependent users☆

PubMed Central

Filbey, Francesca M.; Dunlop, Joseph

2015-01-01

Background Emergent studies show that similar to other substances of abuse, cue-reactivity to cannabis is also associated with neural response in the brain’s reward pathway (Filbey et al., 2009). However, the inter-relatedness of brain regions during cue-reactivity in cannabis users remains unknown. Methods In this study, we conducted a series of investigations to determine functional connectivity during cue-reactivity in 71 cannabis users. First, we used psychophysiological interaction (PPI) analysis to examine coherent neural response to cannabis cues. Second, we evaluated whether these patterns of network functional connectivity differentiated dependent and non-dependent users. Finally, as an exploratory analysis, we determined the directionality of these connections via Granger connectivity analyses. Results PPI analyses showed reward network functional connectivity with the nucleus accumbens (NAc) seed region during cue exposure. Between-group contrasts found differential effects of dependence status. Dependent users (N = 31) had greater functional connectivity with amygdala and anterior cingulate gyrus (ACG) seeds while the non-dependent users (N = 24) had greater functional connectivity with the NAc, orbitofrontal cortex (OFC) and hippocampus seeds. Granger analyses showed that hippocampal and ACG activation preceded neural response in reward areas. Conclusions Both PPI and Granger analyses demonstrated strong functional coherence in reward regions during exposure to cannabis cues in current cannabis users. Functional connectivity (but not regional activation) in the reward network differentiated dependent from non-dependent cannabis users. Our findings suggest that repeated cannabis exposure causes observable changes in functional connectivity in the reward network and should be considered in intervention strategies. PMID:24838032

Advances in the quantification of mitochondrial function in primary human immune cells through extracellular flux analysis.

PubMed

Nicholas, Dequina; Proctor, Elizabeth A; Raval, Forum M; Ip, Blanche C; Habib, Chloe; Ritou, Eleni; Grammatopoulos, Tom N; Steenkamp, Devin; Dooms, Hans; Apovian, Caroline M; Lauffenburger, Douglas A; Nikolajczyk, Barbara S

2017-01-01

Numerous studies show that mitochondrial energy generation determines the effectiveness of immune responses. Furthermore, changes in mitochondrial function may regulate lymphocyte function in inflammatory diseases like type 2 diabetes. Analysis of lymphocyte mitochondrial function has been facilitated by introduction of 96-well format extracellular flux (XF96) analyzers, but the technology remains imperfect for analysis of human lymphocytes. Limitations in XF technology include the lack of practical protocols for analysis of archived human cells, and inadequate data analysis tools that require manual quality checks. Current analysis tools for XF outcomes are also unable to automatically assess data quality and delete untenable data from the relatively high number of biological replicates needed to power complex human cell studies. The objectives of work presented herein are to test the impact of common cellular manipulations on XF outcomes, and to develop and validate a new automated tool that objectively analyzes a virtually unlimited number of samples to quantitate mitochondrial function in immune cells. We present significant improvements on previous XF analyses of primary human cells that will be absolutely essential to test the prediction that changes in immune cell mitochondrial function and fuel sources support immune dysfunction in chronic inflammatory diseases like type 2 diabetes.

Characterization of bioplastic based from cassava crisp home industrial waste incorporated with chitosan and liquid smoke

NASA Astrophysics Data System (ADS)

Fathanah, U.; Lubis, M. R.; Nasution, F.; Masyawi, M. S.

2018-03-01

Cassava peel (Manihot utilissima) is waste of agricultural result that is much potential as raw material of bioplastic making. This research focuses on bioplastic making from cassava peel. It aims to characterize the resulted bioplastic (mechanical and physical properties, SEM analysis, FTIR analysis and time test of bioplastic degradation). The bioplastic preparation takes place by mixing starch of cassava peel and chitosan (20, 30, 40 and 50% w/w), glycerol 30% w/w as plasticizer, and liquid smoke (0, 1 and 2 mL) as antimicrobial agent. The research result shows the highest value of tensile strength is 96.04 MPa, the highest elongation at break is 52.27%, and the value of water-resistant test is 22.68%. Morphology analysis by using SEM shows uneven surface and there is fracture in its cross-section. The analysis of functional group by FTIR shows the presence of functional groups of O–H (hydroxyl), N–H (amine), dan CH3–O (ether). The fastest complete degradation of bioplastic occurs in 45 days, and the longest occurs in 57 days.

A novel method for calculating relative free energy of similar molecules in two environments

NASA Astrophysics Data System (ADS)

Farhi, Asaf; Singh, Bipin

2017-03-01

Calculating relative free energies is a topic of substantial interest and has many applications including solvation and binding free energies, which are used in computational drug discovery. However, there remain the challenges of accuracy, simple implementation, robustness and efficiency, which prevent the calculations from being automated and limit their use. Here we present an exact and complete decoupling analysis in which the partition functions of the compared systems decompose into the partition functions of the common and different subsystems. This decoupling analysis is applicable to submolecules with coupled degrees of freedom such as the methyl group and to any potential function (including the typical dihedral potentials), enabling to remove less terms in the transformation which results in a more efficient calculation. Then we show mathematically, in the context of partition function decoupling, that the two compared systems can be simulated separately, eliminating the need to design a composite system. We demonstrate the decoupling analysis and the separate transformations in a relative free energy calculation using MD simulations for a general force field and compare to another calculation and to experimental results. We present a unified soft-core technique that ensures the monotonicity of the numerically integrated function (analytical proof) which is important for the selection of intermediates. We show mathematically that in this soft-core technique the numerically integrated function can be non-steep only when we transform the systems separately, which can simplify the numerical integration. Finally, we show that when the systems have rugged energy landscape they can be equilibrated without introducing another sampling dimension which can also enable to use the simulation results for other free energy calculations.

Evaluation of RNAi and CRISPR technologies by large-scale gene expression profiling in the Connectivity Map.

PubMed

Smith, Ian; Greenside, Peyton G; Natoli, Ted; Lahr, David L; Wadden, David; Tirosh, Itay; Narayan, Rajiv; Root, David E; Golub, Todd R; Subramanian, Aravind; Doench, John G

2017-11-01

The application of RNA interference (RNAi) to mammalian cells has provided the means to perform phenotypic screens to determine the functions of genes. Although RNAi has revolutionized loss-of-function genetic experiments, it has been difficult to systematically assess the prevalence and consequences of off-target effects. The Connectivity Map (CMAP) represents an unprecedented resource to study the gene expression consequences of expressing short hairpin RNAs (shRNAs). Analysis of signatures for over 13,000 shRNAs applied in 9 cell lines revealed that microRNA (miRNA)-like off-target effects of RNAi are far stronger and more pervasive than generally appreciated. We show that mitigating off-target effects is feasible in these datasets via computational methodologies to produce a consensus gene signature (CGS). In addition, we compared RNAi technology to clustered regularly interspaced short palindromic repeat (CRISPR)-based knockout by analysis of 373 single guide RNAs (sgRNAs) in 6 cells lines and show that the on-target efficacies are comparable, but CRISPR technology is far less susceptible to systematic off-target effects. These results will help guide the proper use and analysis of loss-of-function reagents for the determination of gene function.

Identification and functional analysis of two alternatively spliced transcripts of ABSCISIC ACID INSENSITIVE3 (ABI3) in linseed flax (Linum usitatissimum L.).

PubMed

Wang, Yanyan; Zhang, Tianbao; Song, Xiaxia; Zhang, Jianping; Dang, Zhanhai; Pei, Xinwu; Long, Yan

2018-01-01

Alternative splicing is a popular phenomenon in different types of plants. It can produce alternative spliced transcripts that encode proteins with altered functions. Previous studies have shown that one transcription factor, ABSCISIC ACID INSENSITIVE3 (ABI3), which encodes an important component in abscisic acid (ABA) signaling, is subjected to alternative splicing in both mono- and dicotyledons. In the current study, we identified two homologs of ABI3 in the genome of linseed flax. We screened two alternatively spliced flax LuABI3 transcripts, LuABI3-2 and LuABI3-3, and one normal flax LuABI3 transcript, LuABI3-1. Sequence analysis revealed that one of the alternatively spliced transcripts, LuABI3-3, retained a 6 bp intron. RNA accumulation analysis showed that all three transcripts were expressed during seed development, while subcellular localization and transgene experiments showed that LuABI3-3 had no biological function. The two normal transcripts, LuABI3-1 and LuABI3-2, are the important functional isoforms in flax and play significant roles in the ABA regulatory pathway during seed development, germination, and maturation.

Visual target modulation of functional connectivity networks revealed by self-organizing group ICA.

PubMed

van de Ven, Vincent; Bledowski, Christoph; Prvulovic, David; Goebel, Rainer; Formisano, Elia; Di Salle, Francesco; Linden, David E J; Esposito, Fabrizio

2008-12-01

We applied a data-driven analysis based on self-organizing group independent component analysis (sogICA) to fMRI data from a three-stimulus visual oddball task. SogICA is particularly suited to the investigation of the underlying functional connectivity and does not rely on a predefined model of the experiment, which overcomes some of the limitations of hypothesis-driven analysis. Unlike most previous applications of ICA in functional imaging, our approach allows the analysis of the data at the group level, which is of particular interest in high order cognitive studies. SogICA is based on the hierarchical clustering of spatially similar independent components, derived from single subject decompositions. We identified four main clusters of components, centered on the posterior cingulate, bilateral insula, bilateral prefrontal cortex, and right posterior parietal and prefrontal cortex, consistently across all participants. Post hoc comparison of time courses revealed that insula, prefrontal cortex and right fronto-parietal components showed higher activity for targets than for distractors. Activation for distractors was higher in the posterior cingulate cortex, where deactivation was observed for targets. While our results conform to previous neuroimaging studies, they also complement conventional results by showing functional connectivity networks with unique contributions to the task that were consistent across subjects. SogICA can thus be used to probe functional networks of active cognitive tasks at the group-level and can provide additional insights to generate new hypotheses for further study. Copyright 2007 Wiley-Liss, Inc.

The Representation of Object-Directed Action and Function Knowledge in the Human Brain

PubMed Central

Chen, Quanjing; Garcea, Frank E.; Mahon, Bradford Z.

2016-01-01

The appropriate use of everyday objects requires the integration of action and function knowledge. Previous research suggests that action knowledge is represented in frontoparietal areas while function knowledge is represented in temporal lobe regions. Here we used multivoxel pattern analysis to investigate the representation of object-directed action and function knowledge while participants executed pantomimes of familiar tool actions. A novel approach for decoding object knowledge was used in which classifiers were trained on one pair of objects and then tested on a distinct pair; this permitted a measurement of classification accuracy over and above object-specific information. Region of interest (ROI) analyses showed that object-directed actions could be decoded in tool-preferring regions of both parietal and temporal cortex, while no independently defined tool-preferring ROI showed successful decoding of object function. However, a whole-brain searchlight analysis revealed that while frontoparietal motor and peri-motor regions are engaged in the representation of object-directed actions, medial temporal lobe areas in the left hemisphere are involved in the representation of function knowledge. These results indicate that both action and function knowledge are represented in a topographically coherent manner that is amenable to study with multivariate approaches, and that the left medial temporal cortex represents knowledge of object function. PMID:25595179

On the Power of Abstract Interpretation

NASA Technical Reports Server (NTRS)

Reddy, Uday S.; Kamin, Samuel N.

1991-01-01

Increasingly sophisticated applications of static analysis place increased burden on the reliability of the analysis techniques. Often, the failure of the analysis technique to detect some information my mean that the time or space complexity of the generated code would be altered. Thus, it is important to precisely characterize the power of static analysis techniques. We follow the approach of Selur et. al. who studied the power of strictness analysis techniques. Their result can be summarized by saying 'strictness analysis is perfect up to variations in constants.' In other words, strictness analysis is as good as it could be, short of actually distinguishing between concrete values. We use this approach to characterize a broad class of analysis techniques based on abstract interpretation including, but not limited to, strictness analysis. For the first-order case, we consider abstract interpretations where the abstract domain for data values is totally ordered. This condition is satisfied by Mycroft's strictness analysis that of Sekar et. al. and Wadler's analysis of list-strictness. For such abstract interpretations, we show that the analysis is complete in the sense that, short of actually distinguishing between concrete values with the same abstraction, it gives the best possible information. We further generalize these results to typed lambda calculus with pairs and higher-order functions. Note that products and function spaces over totally ordered domains are not totally ordered. In fact, the notion of completeness used in the first-order case fails if product domains or function spaces are added. We formulate a weaker notion of completeness based on observability of values. Two values (including pairs and functions) are considered indistinguishable if their observable components are indistinguishable. We show that abstract interpretation of typed lambda calculus programs is complete up to this notion of indistinguishability. We use denotationally-oriented arguments instead of the detailed operational arguments used by Selur et. al.. Hence, our proofs are much simpler. They should be useful for further future improvements.

Beyond Zipf's Law: The Lavalette Rank Function and Its Properties.

PubMed

Fontanelli, Oscar; Miramontes, Pedro; Yang, Yaning; Cocho, Germinal; Li, Wentian

Although Zipf's law is widespread in natural and social data, one often encounters situations where one or both ends of the ranked data deviate from the power-law function. Previously we proposed the Beta rank function to improve the fitting of data which does not follow a perfect Zipf's law. Here we show that when the two parameters in the Beta rank function have the same value, the Lavalette rank function, the probability density function can be derived analytically. We also show both computationally and analytically that Lavalette distribution is approximately equal, though not identical, to the lognormal distribution. We illustrate the utility of Lavalette rank function in several datasets. We also address three analysis issues on the statistical testing of Lavalette fitting function, comparison between Zipf's law and lognormal distribution through Lavalette function, and comparison between lognormal distribution and Lavalette distribution.

Macroevolutionary trends of atomic composition and related functional group proportion in eukaryotic and prokaryotic proteins.

PubMed

Zhang, Yu-Juan; Yang, Chun-Lin; Hao, You-Jin; Li, Ying; Chen, Bin; Wen, Jian-Fan

2014-01-25

To fully explore the trends of atomic composition during the macroevolution from prokaryote to eukaryote, five atoms (oxygen, sulfur, nitrogen, carbon, hydrogen) and related functional groups in prokaryotic and eukaryotic proteins were surveyed and compared. Genome-wide analysis showed that eukaryotic proteins have more oxygen, sulfur and nitrogen atoms than prokaryotes do. Clusters of Orthologous Groups (COG) analysis revealed that oxygen, sulfur, carbon and hydrogen frequencies are higher in eukaryotic proteins than in their prokaryotic orthologs. Furthermore, functional group analysis demonstrated that eukaryotic proteins tend to have higher proportions of sulfhydryl, hydroxyl and acylamino, but lower of sulfide and carboxyl. Taken together, an apparent trend of increase was observed for oxygen and sulfur atoms in the macroevolution; the variation of oxygen and sulfur compositions and their related functional groups in macroevolution made eukaryotic proteins carry more useful functional groups. These results will be helpful for better understanding the functional significances of atomic composition evolution. Copyright © 2013 Elsevier B.V. All rights reserved.

Characterizing bonding patterns in diradicals and triradicals by density-based wave function analysis: A uniform approach

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

Orms, Natalie; Rehn, Dirk; Dreuw, Andreas

Density-based wave function analysis enables unambiguous comparisons of electronic structure computed by different methods and removes ambiguity of orbital choices. Here, we use this tool to investigate the performance of different spin-flip methods for several prototypical diradicals and triradicals. In contrast to previous calibration studies that focused on energy gaps between high and low spin-states, we focus on the properties of the underlying wave functions, such as the number of effectively unpaired electrons. Comparison of different density functional and wave function theory results provides insight into the performance of the different methods when applied to strongly correlated systems such asmore » polyradicals. We also show that canonical molecular orbitals for species like large copper-containing diradicals fail to correctly represent the underlying electronic structure due to highly non-Koopmans character, while density-based analysis of the same wave function delivers a clear picture of bonding pattern.« less

Characterizing bonding patterns in diradicals and triradicals by density-based wave function analysis: A uniform approach

DOE PAGES

Orms, Natalie; Rehn, Dirk; Dreuw, Andreas; ...

2017-12-21

Density-based wave function analysis enables unambiguous comparisons of electronic structure computed by different methods and removes ambiguity of orbital choices. Here, we use this tool to investigate the performance of different spin-flip methods for several prototypical diradicals and triradicals. In contrast to previous calibration studies that focused on energy gaps between high and low spin-states, we focus on the properties of the underlying wave functions, such as the number of effectively unpaired electrons. Comparison of different density functional and wave function theory results provides insight into the performance of the different methods when applied to strongly correlated systems such asmore » polyradicals. We also show that canonical molecular orbitals for species like large copper-containing diradicals fail to correctly represent the underlying electronic structure due to highly non-Koopmans character, while density-based analysis of the same wave function delivers a clear picture of bonding pattern.« less

Functional approach in estimation of cultural ecosystem services of recreational areas

NASA Astrophysics Data System (ADS)

Sautkin, I. S.; Rogova, T. V.

2018-01-01

The article is devoted to the identification and analysis of cultural ecosystem services of recreational areas from the different forest plant functional groups in the suburbs of Kazan. The study explored two cultural ecosystem services supplied by forest plants by linking these services to different plant functional traits. Information on the functional traits of 76 plants occurring in the forest ecosystems of the investigated area was collected from reference books on the biological characteristics of plant species. Analysis of these species and traits with the Ward clustering method yielded four functional groups with different potentials for delivering ecosystem services. The results show that the contribution of species diversity to services can be characterized through the functional traits of plants. This proves that there is a stable relationship between biodiversity and the quality and quantity of ecosystem services. The proposed method can be extended to other types of services (regulating and supporting). The analysis can be used in the socio-economic assessment of natural ecosystems for recreation and other uses.

Using the Oxford Foot Model to determine the association between objective measures of foot function and results of the AOFAS Ankle-Hindfoot Scale and the Foot Function Index: a prospective gait analysis study in Germany

PubMed Central

Kostuj, Tanja; Stief, Felix; Hartmann, Kirsten Anna; Schaper, Katharina; Arabmotlagh, Mohammad; Baums, Mike H; Meurer, Andrea; Krummenauer, Frank; Lieske, Sebastian

2018-01-01

Objective After cross-cultural adaption for the German translation of the Ankle-Hindfoot Scale of the American Orthopaedic Foot and Ankle Society (AOFAS-AHS) and agreement analysis with the Foot Function Index (FFI-D), the following gait analysis study using the Oxford Foot Model (OFM) was carried out to show which of the two scores better correlates with objective gait dysfunction. Design and participants Results of the AOFAS-AHS and FFI-D, as well as data from three-dimensional gait analysis were collected from 20 patients with mild to severe ankle and hindfoot pathologies. Kinematic and kinetic gait data were correlated with the results of the total AOFAS scale and FFI-D as well as the results of those items representing hindfoot function in the AOFAS-AHS assessment. With respect to the foot disorders in our patients (osteoarthritis and prearthritic conditions), we correlated the total range of motion (ROM) in the ankle and subtalar joints as identified by the OFM with values identified during clinical examination ‘translated’ into score values. Furthermore, reduced walking speed, reduced step length and reduced maximum ankle power generation during push-off were taken into account and correlated to gait abnormalities described in the scores. An analysis of correlations with CIs between the FFI-D and the AOFAS-AHS items and the gait parameters was performed by means of the Jonckheere-Terpstra test; furthermore, exploratory factor analysis was applied to identify common information structures and thereby redundancy in the FFI-D and the AOFAS-AHS items. Results Objective findings for hindfoot disorders, namely a reduced ROM, in the ankle and subtalar joints, respectively, as well as reduced ankle power generation during push-off, showed a better correlation with the AOFAS-AHS total score—as well as AOFAS-AHS items representing ROM in the ankle, subtalar joints and gait function—compared with the FFI-D score. Factor analysis, however, could not identify FFI-D items consistently related to these three indicator parameters (pain, disability and function) found in the AOFAS-AHS. Furthermore, factor analysis did not support stratification of the FFI-D into two subscales. Conclusions The AOFAS-AHS showed a good agreement with objective gait parameters and is therefore better suited to evaluate disability and functional limitations of patients suffering from foot and ankle pathologies compared with the FFI-D. PMID:29626046

Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome.

PubMed

Manor, Ohad; Borenstein, Elhanan

2017-02-08

Comparative analyses of the human microbiome have identified both taxonomic and functional shifts that are associated with numerous diseases. To date, however, microbiome taxonomy and function have mostly been studied independently and the taxonomic drivers of functional imbalances have not been systematically identified. Here, we present FishTaco, an analytical and computational framework that integrates taxonomic and functional comparative analyses to accurately quantify taxon-level contributions to disease-associated functional shifts. Applying FishTaco to several large-scale metagenomic cohorts, we show that shifts in the microbiome's functional capacity can be traced back to specific taxa. Furthermore, the set of taxa driving functional shifts and their contribution levels vary markedly between functions. We additionally find that similar functional imbalances in different diseases are driven by both disease-specific and shared taxa. Such integrated analysis of microbiome ecological and functional dynamics can inform future microbiome-based therapy, pinpointing putative intervention targets for manipulating the microbiome's functional capacity. Copyright © 2017 Elsevier Inc. All rights reserved.

Assessment of triglyceride and cholesterol in overweight people based on multiple linear regression and artificial intelligence model.

PubMed

Ma, Jing; Yu, Jiong; Hao, Guangshu; Wang, Dan; Sun, Yanni; Lu, Jianxin; Cao, Hongcui; Lin, Feiyan

2017-02-20

The prevalence of high hyperlipemia is increasing around the world. Our aims are to analyze the relationship of triglyceride (TG) and cholesterol (TC) with indexes of liver function and kidney function, and to develop a prediction model of TG, TC in overweight people. A total of 302 adult healthy subjects and 273 overweight subjects were enrolled in this study. The levels of fasting indexes of TG (fs-TG), TC (fs-TC), blood glucose, liver function, and kidney function were measured and analyzed by correlation analysis and multiple linear regression (MRL). The back propagation artificial neural network (BP-ANN) was applied to develop prediction models of fs-TG and fs-TC. The results showed there was significant difference in biochemical indexes between healthy people and overweight people. The correlation analysis showed fs-TG was related to weight, height, blood glucose, and indexes of liver and kidney function; while fs-TC was correlated with age, indexes of liver function (P < 0.01). The MRL analysis indicated regression equations of fs-TG and fs-TC both had statistic significant (P < 0.01) when included independent indexes. The BP-ANN model of fs-TG reached training goal at 59 epoch, while fs-TC model achieved high prediction accuracy after training 1000 epoch. In conclusions, there was high relationship of fs-TG and fs-TC with weight, height, age, blood glucose, indexes of liver function and kidney function. Based on related variables, the indexes of fs-TG and fs-TC can be predicted by BP-ANN models in overweight people.

A new methodology based on functional principal component analysis to study postural stability post-stroke.

PubMed

Sánchez-Sánchez, M Luz; Belda-Lois, Juan-Manuel; Mena-Del Horno, Silvia; Viosca-Herrero, Enrique; Igual-Camacho, Celedonia; Gisbert-Morant, Beatriz

2018-05-05

A major goal in stroke rehabilitation is the establishment of more effective physical therapy techniques to recover postural stability. Functional Principal Component Analysis provides greater insight into recovery trends. However, when missing values exist, obtaining functional data presents some difficulties. The purpose of this study was to reveal an alternative technique for obtaining the Functional Principal Components without requiring the conversion to functional data beforehand and to investigate this methodology to determine the effect of specific physical therapy techniques in balance recovery trends in elderly subjects with hemiplegia post-stroke. A randomized controlled pilot trial was developed. Thirty inpatients post-stroke were included. Control and target groups were treated with the same conventional physical therapy protocol based on functional criteria, but specific techniques were added to the target group depending on the subjects' functional level. Postural stability during standing was quantified by posturography. The assessments were performed once a month from the moment the participants were able to stand up to six months post-stroke. The target group showed a significant improvement in postural control recovery trend six months after stroke that was not present in the control group. Some of the assessed parameters revealed significant differences between treatment groups (P < 0.05). The proposed methodology allows Functional Principal Component Analysis to be performed when data is scarce. Moreover, it allowed the dynamics of recovery of two different treatment groups to be determined, showing that the techniques added in the target group increased postural stability compared to the base protocol. Copyright © 2018 Elsevier Ltd. All rights reserved.

Normative Data for an Instrumental Assessment of the Upper-Limb Functionality.

PubMed

Caimmi, Marco; Guanziroli, Eleonora; Malosio, Matteo; Pedrocchi, Nicola; Vicentini, Federico; Molinari Tosatti, Lorenzo; Molteni, Franco

2015-01-01

Upper-limb movement analysis is important to monitor objectively rehabilitation interventions, contributing to improving the overall treatments outcomes. Simple, fast, easy-to-use, and applicable methods are required to allow routinely functional evaluation of patients with different pathologies and clinical conditions. This paper describes the Reaching and Hand-to-Mouth Evaluation Method, a fast procedure to assess the upper-limb motor control and functional ability, providing a set of normative data from 42 healthy subjects of different ages, evaluated for both the dominant and the nondominant limb motor performance. Sixteen of them were reevaluated after two weeks to perform test-retest reliability analysis. Data were clustered into three subgroups of different ages to test the method sensitivity to motor control differences. Experimental data show notable test-retest reliability in all tasks. Data from older and younger subjects show significant differences in the measures related to the ability for coordination thus showing the high sensitivity of the method to motor control differences. The presented method, provided with control data from healthy subjects, appears to be a suitable and reliable tool for the upper-limb functional assessment in the clinical environment.

Normative Data for an Instrumental Assessment of the Upper-Limb Functionality

PubMed Central

Caimmi, Marco; Guanziroli, Eleonora; Malosio, Matteo; Pedrocchi, Nicola; Vicentini, Federico; Molinari Tosatti, Lorenzo; Molteni, Franco

2015-01-01

Upper-limb movement analysis is important to monitor objectively rehabilitation interventions, contributing to improving the overall treatments outcomes. Simple, fast, easy-to-use, and applicable methods are required to allow routinely functional evaluation of patients with different pathologies and clinical conditions. This paper describes the Reaching and Hand-to-Mouth Evaluation Method, a fast procedure to assess the upper-limb motor control and functional ability, providing a set of normative data from 42 healthy subjects of different ages, evaluated for both the dominant and the nondominant limb motor performance. Sixteen of them were reevaluated after two weeks to perform test-retest reliability analysis. Data were clustered into three subgroups of different ages to test the method sensitivity to motor control differences. Experimental data show notable test-retest reliability in all tasks. Data from older and younger subjects show significant differences in the measures related to the ability for coordination thus showing the high sensitivity of the method to motor control differences. The presented method, provided with control data from healthy subjects, appears to be a suitable and reliable tool for the upper-limb functional assessment in the clinical environment. PMID:26539500

Aberrant functional connectivity in Papez circuit correlates with memory performance in cognitively intact middle-aged APOE4 carriers.

PubMed

Li, Wenjun; Antuono, Piero G; Xie, Chunming; Chen, Gang; Jones, Jennifer L; Ward, B Douglas; Singh, Suraj P; Franczak, Malgorzata B; Goveas, Joseph S; Li, Shi-Jiang

2014-08-01

The main objective of this study is to detect the early changes in resting-state Papez circuit functional connectivity using the hippocampus as the seed, and to determine the associations between altered functional connectivity (FC) and the episodic memory performance in cognitively intact middle-aged apolipoprotein E4 (APOE4) carriers who are at risk of Alzheimer's disease (AD). Forty-six cognitively intact, middle-aged participants, including 20 APOE4 carriers and 26 age-, sex-, and education-matched noncarriers were studied. The resting-state FC of the hippocampus (HFC) was compared between APOE4 carriers and noncarriers. APOE4 carriers showed significantly decreased FC in brain areas that involve learning and memory functions, including the frontal, cingulate, thalamus and basal ganglia regions. Multiple linear regression analysis showed significant correlations between HFC and the episodic memory performance. Conjunction analysis between neural correlates of memory and altered HFC showed the overlapping regions, especially the subcortical regions such as thalamus, caudate nucleus, and cingulate cortices involved in the Papez circuit. Thus, changes in connectivity in the Papez circuit may be used as an early risk detection for AD. Copyright © 2014. Published by Elsevier Ltd.

Analysis of barosensitive mechanisms in yeast for Pressure Regulated Fermentation

NASA Astrophysics Data System (ADS)

Nomura, Kazuki; Iwahashi, Hitoshi; Iguchi, Akinori; Shigematsu, Toru

2013-06-01

Introduction: We are intending to develop a novel food processing technology, Pressure Regulated Fermentation (PReF), using pressure sensitive (barosensitive) fermentation microorganisms. Objectives of our study are to clarify barosensitive mechanisms for application to PReF technology. We isolated Saccharomyces cerevisiae barosensitive mutant a924E1 that was derived from the parent KA31a. Methods: Gene expression levels were analyzed by DNA microarray. The altered genes of expression levels were classified according to the gene function. Mutated genes were estimated by mating and producing diploid strains and confirmed by PCR of mitochondrial DNA (mtDNA). Results and Discussion: Gene expression profiles showed that genes of `Energy' function and that of encoding protein localized in ``Mitochondria'' were significantly down regulated in the mutant. These results suggest the respiratory deficiency and relationship between barosensitivity and respiratory deficiency. Since the respiratory functions of diploids showed non Mendelian inheritance, the respiratory deficiency was indicated to be due to mtDNA mutation. PCR analysis showed that the region of COX1 locus was deleted. COX1 gene encodes the subunit 1 of cytochrome c oxidase. For this reason, barosensitivity is strongly correlated with mitochondrial functions.

Elisabeth Kubler-Ross and the Tradition of the Private Sphere: An Analysis of Symbols.

ERIC Educational Resources Information Center

Klass, Dennis

1981-01-01

Shows how Kubler-Ross' schema functions as a symbol system. Analyzes the symbol "acceptance." Shows how that symbol is part of a strong American tradition of symbols of the private sphere. (Author/JAC)

Gene Network Construction from Microarray Data Identifies a Key Network Module and Several Candidate Hub Genes in Age-Associated Spatial Learning Impairment

PubMed Central

Uddin, Raihan; Singh, Shiva M.

2017-01-01

As humans age many suffer from a decrease in normal brain functions including spatial learning impairments. This study aimed to better understand the molecular mechanisms in age-associated spatial learning impairment (ASLI). We used a mathematical modeling approach implemented in Weighted Gene Co-expression Network Analysis (WGCNA) to create and compare gene network models of young (learning unimpaired) and aged (predominantly learning impaired) brains from a set of exploratory datasets in rats in the context of ASLI. The major goal was to overcome some of the limitations previously observed in the traditional meta- and pathway analysis using these data, and identify novel ASLI related genes and their networks based on co-expression relationship of genes. This analysis identified a set of network modules in the young, each of which is highly enriched with genes functioning in broad but distinct GO functional categories or biological pathways. Interestingly, the analysis pointed to a single module that was highly enriched with genes functioning in “learning and memory” related functions and pathways. Subsequent differential network analysis of this “learning and memory” module in the aged (predominantly learning impaired) rats compared to the young learning unimpaired rats allowed us to identify a set of novel ASLI candidate hub genes. Some of these genes show significant repeatability in networks generated from independent young and aged validation datasets. These hub genes are highly co-expressed with other genes in the network, which not only show differential expression but also differential co-expression and differential connectivity across age and learning impairment. The known function of these hub genes indicate that they play key roles in critical pathways, including kinase and phosphatase signaling, in functions related to various ion channels, and in maintaining neuronal integrity relating to synaptic plasticity and memory formation. Taken together, they provide a new insight and generate new hypotheses into the molecular mechanisms responsible for age associated learning impairment, including spatial learning. PMID:29066959

Gene Network Construction from Microarray Data Identifies a Key Network Module and Several Candidate Hub Genes in Age-Associated Spatial Learning Impairment.

PubMed

Uddin, Raihan; Singh, Shiva M

2017-01-01

As humans age many suffer from a decrease in normal brain functions including spatial learning impairments. This study aimed to better understand the molecular mechanisms in age-associated spatial learning impairment (ASLI). We used a mathematical modeling approach implemented in Weighted Gene Co-expression Network Analysis (WGCNA) to create and compare gene network models of young (learning unimpaired) and aged (predominantly learning impaired) brains from a set of exploratory datasets in rats in the context of ASLI. The major goal was to overcome some of the limitations previously observed in the traditional meta- and pathway analysis using these data, and identify novel ASLI related genes and their networks based on co-expression relationship of genes. This analysis identified a set of network modules in the young, each of which is highly enriched with genes functioning in broad but distinct GO functional categories or biological pathways. Interestingly, the analysis pointed to a single module that was highly enriched with genes functioning in "learning and memory" related functions and pathways. Subsequent differential network analysis of this "learning and memory" module in the aged (predominantly learning impaired) rats compared to the young learning unimpaired rats allowed us to identify a set of novel ASLI candidate hub genes. Some of these genes show significant repeatability in networks generated from independent young and aged validation datasets. These hub genes are highly co-expressed with other genes in the network, which not only show differential expression but also differential co-expression and differential connectivity across age and learning impairment. The known function of these hub genes indicate that they play key roles in critical pathways, including kinase and phosphatase signaling, in functions related to various ion channels, and in maintaining neuronal integrity relating to synaptic plasticity and memory formation. Taken together, they provide a new insight and generate new hypotheses into the molecular mechanisms responsible for age associated learning impairment, including spatial learning.

Using the Oxford Foot Model to determine the association between objective measures of foot function and results of the AOFAS Ankle-Hindfoot Scale and the Foot Function Index: a prospective gait analysis study in Germany.

PubMed

Kostuj, Tanja; Stief, Felix; Hartmann, Kirsten Anna; Schaper, Katharina; Arabmotlagh, Mohammad; Baums, Mike H; Meurer, Andrea; Krummenauer, Frank; Lieske, Sebastian

2018-04-05

After cross-cultural adaption for the German translation of the Ankle-Hindfoot Scale of the American Orthopaedic Foot and Ankle Society (AOFAS-AHS) and agreement analysis with the Foot Function Index (FFI-D), the following gait analysis study using the Oxford Foot Model (OFM) was carried out to show which of the two scores better correlates with objective gait dysfunction. Results of the AOFAS-AHS and FFI-D, as well as data from three-dimensional gait analysis were collected from 20 patients with mild to severe ankle and hindfoot pathologies.Kinematic and kinetic gait data were correlated with the results of the total AOFAS scale and FFI-D as well as the results of those items representing hindfoot function in the AOFAS-AHS assessment. With respect to the foot disorders in our patients (osteoarthritis and prearthritic conditions), we correlated the total range of motion (ROM) in the ankle and subtalar joints as identified by the OFM with values identified during clinical examination 'translated' into score values. Furthermore, reduced walking speed, reduced step length and reduced maximum ankle power generation during push-off were taken into account and correlated to gait abnormalities described in the scores. An analysis of correlations with CIs between the FFI-D and the AOFAS-AHS items and the gait parameters was performed by means of the Jonckheere-Terpstra test; furthermore, exploratory factor analysis was applied to identify common information structures and thereby redundancy in the FFI-D and the AOFAS-AHS items. Objective findings for hindfoot disorders, namely a reduced ROM, in the ankle and subtalar joints, respectively, as well as reduced ankle power generation during push-off, showed a better correlation with the AOFAS-AHS total score-as well as AOFAS-AHS items representing ROM in the ankle, subtalar joints and gait function-compared with the FFI-D score.Factor analysis, however, could not identify FFI-D items consistently related to these three indicator parameters (pain, disability and function) found in the AOFAS-AHS. Furthermore, factor analysis did not support stratification of the FFI-D into two subscales. The AOFAS-AHS showed a good agreement with objective gait parameters and is therefore better suited to evaluate disability and functional limitations of patients suffering from foot and ankle pathologies compared with the FFI-D. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Psychological and functional effect of different primary treatments for prostate cancer: A comparative prospective analysis.

PubMed

Sciarra, Alessandro; Gentilucci, Alessandro; Salciccia, Stefano; Von Heland, Magnus; Ricciuti, Giam Piero; Marzio, Vittorio; Pierella, Federico; Musio, Daniela; Tombolini, Vincenzo; Frantellizzi, Viviana; Pasquini, Massimo; Maraone, Annalisa; Guandalini, Alessio; Maggi, Martina

2018-04-26

The aim of the study was to comparatively evaluate the psychological and functional effect of different primary treatments in patients with prostate cancer. We conducted a single-center prospective non randomized study in a real-life setting using functional and psychological questionnaires in prostate cancer cases submitted to radical prostatectomy, external radiotherapy, or active surveillance. Totally, 220 cases were evaluated at baseline and during the follow-up at 1-, 3-, 6-, and 12-month interval after therapy. Patients self-completed questionnaires on urinary symptoms and incontinence, erectile and bowel function, psychological distress (PD), anxiety, and depression. Several significant differences among the three groups of treatment were found regarding the total score of the functional questionnaires. Regarding PD, cases submitted to radical prostatectomy showed stable scores during all the 12 months of follow-up whereas cases submitted to radiotherapy showed a rapid significant worsening of scores at 1-month interval and persistent also at 6- and 12-month interval. Cases submitted to active surveillance showed a slight and slow worsening of scores only at 12-month interval. PD and depression resulted to be more associated with urinary symptoms than sexual function worsening whereas anxiety resulted to be associated either with urinary symptoms or sexual function worsening. The results of our comparative and prospective analysis could be used to better inform treatment decision-making. Patients and their teams might wish to know how functional and psychological aspects may differently be influenced by treatment choice. Copyright © 2018 Elsevier Inc. All rights reserved.

Simple procedure for phase-space measurement and entanglement validation

NASA Astrophysics Data System (ADS)

Rundle, R. P.; Mills, P. W.; Tilma, Todd; Samson, J. H.; Everitt, M. J.

2017-08-01

It has recently been shown that it is possible to represent the complete quantum state of any system as a phase-space quasiprobability distribution (Wigner function) [Phys. Rev. Lett. 117, 180401 (2016), 10.1103/PhysRevLett.117.180401]. Such functions take the form of expectation values of an observable that has a direct analogy to displaced parity operators. In this work we give a procedure for the measurement of the Wigner function that should be applicable to any quantum system. We have applied our procedure to IBM's Quantum Experience five-qubit quantum processor to demonstrate that we can measure and generate the Wigner functions of two different Bell states as well as the five-qubit Greenberger-Horne-Zeilinger state. Because Wigner functions for spin systems are not unique, we define, compare, and contrast two distinct examples. We show how the use of these Wigner functions leads to an optimal method for quantum state analysis especially in the situation where specific characteristic features are of particular interest (such as for spin Schrödinger cat states). Furthermore we show that this analysis leads to straightforward, and potentially very efficient, entanglement test and state characterization methods.

Further Insights into the Allan-Herndon-Dudley Syndrome: Clinical and Functional Characterization of a Novel MCT8 Mutation.

PubMed

Armour, Christine M; Kersseboom, Simone; Yoon, Grace; Visser, Theo J

2015-01-01

Mutations in the thyroid hormone (TH) transporter MCT8 have been identified as the cause for Allan-Herndon-Dudley Syndrome (AHDS), characterized by severe psychomotor retardation and altered TH serum levels. Here we report a novel MCT8 mutation identified in 4 generations of one family, and its functional characterization. Proband and family members were screened for 60 genes involved in X-linked cognitive impairment and the MCT8 mutation was confirmed. Functional consequences of MCT8 mutations were studied by analysis of [125I]TH transport in fibroblasts and transiently transfected JEG3 and COS1 cells, and by subcellular localization of the transporter. The proband and a male cousin demonstrated clinical findings characteristic of AHDS. Serum analysis showed high T3, low rT3, and normal T4 and TSH levels in the proband. A MCT8 mutation (c.869C>T; p.S290F) was identified in the proband, his cousin, and several female carriers. Functional analysis of the S290F mutant showed decreased TH transport, metabolism and protein expression in the three cell types, whereas the S290A mutation had no effect. Interestingly, both uptake and efflux of T3 and T4 was impaired in fibroblasts of the proband, compared to his healthy brother. However, no effect of the S290F mutation was observed on TH efflux from COS1 and JEG3 cells. Immunocytochemistry showed plasma membrane localization of wild-type MCT8 and the S290A and S290F mutants in JEG3 cells. We describe a novel MCT8 mutation (S290F) in 4 generations of a family with Allan-Herndon-Dudley Syndrome. Functional analysis demonstrates loss-of-function of the MCT8 transporter. Furthermore, our results indicate that the function of the S290F mutant is dependent on cell context. Comparison of the S290F and S290A mutants indicates that it is not the loss of Ser but its substitution with Phe, which leads to S290F dysfunction.

Further Insights into the Allan-Herndon-Dudley Syndrome: Clinical and Functional Characterization of a Novel MCT8 Mutation

PubMed Central

Yoon, Grace; Visser, Theo J.

2015-01-01

Background Mutations in the thyroid hormone (TH) transporter MCT8 have been identified as the cause for Allan-Herndon-Dudley Syndrome (AHDS), characterized by severe psychomotor retardation and altered TH serum levels. Here we report a novel MCT8 mutation identified in 4 generations of one family, and its functional characterization. Methods Proband and family members were screened for 60 genes involved in X-linked cognitive impairment and the MCT8 mutation was confirmed. Functional consequences of MCT8 mutations were studied by analysis of [125I]TH transport in fibroblasts and transiently transfected JEG3 and COS1 cells, and by subcellular localization of the transporter. Results The proband and a male cousin demonstrated clinical findings characteristic of AHDS. Serum analysis showed high T3, low rT3, and normal T4 and TSH levels in the proband. A MCT8 mutation (c.869C>T; p.S290F) was identified in the proband, his cousin, and several female carriers. Functional analysis of the S290F mutant showed decreased TH transport, metabolism and protein expression in the three cell types, whereas the S290A mutation had no effect. Interestingly, both uptake and efflux of T3 and T4 was impaired in fibroblasts of the proband, compared to his healthy brother. However, no effect of the S290F mutation was observed on TH efflux from COS1 and JEG3 cells. Immunocytochemistry showed plasma membrane localization of wild-type MCT8 and the S290A and S290F mutants in JEG3 cells. Conclusions We describe a novel MCT8 mutation (S290F) in 4 generations of a family with Allan-Herndon-Dudley Syndrome. Functional analysis demonstrates loss-of-function of the MCT8 transporter. Furthermore, our results indicate that the function of the S290F mutant is dependent on cell context. Comparison of the S290F and S290A mutants indicates that it is not the loss of Ser but its substitution with Phe, which leads to S290F dysfunction. PMID:26426690

Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?

PubMed Central

Lovelock, Paul K; Spurdle, Amanda B; Mok, Myth TS; Farrugia, Daniel J; Lakhani, Sunil R; Healey, Sue; Arnold, Stephen; Buchanan, Daniel; Investigators, kConFab; Couch, Fergus J; Henderson, Beric R; Goldgar, David E; Tavtigian, Sean V; Chenevix-Trench, Georgia; Brown, Melissa A

2007-01-01

Introduction Many of the DNA sequence variants identified in the breast cancer susceptibility gene BRCA1 remain unclassified in terms of their potential pathogenicity. Both multifactorial likelihood analysis and functional approaches have been proposed as a means to elucidate likely clinical significance of such variants, but analysis of the comparative value of these methods for classifying all sequence variants has been limited. Methods We have compared the results from multifactorial likelihood analysis with those from several functional analyses for the four BRCA1 sequence variants A1708E, G1738R, R1699Q, and A1708V. Results Our results show that multifactorial likelihood analysis, which incorporates sequence conservation, co-inheritance, segregation, and tumour immunohistochemical analysis, may improve classification of variants. For A1708E, previously shown to be functionally compromised, analysis of oestrogen receptor, cytokeratin 5/6, and cytokeratin 14 tumour expression data significantly strengthened the prediction of pathogenicity, giving a posterior probability of pathogenicity of 99%. For G1738R, shown to be functionally defective in this study, immunohistochemistry analysis confirmed previous findings of inconsistent 'BRCA1-like' phenotypes for the two tumours studied, and the posterior probability for this variant was 96%. The posterior probabilities of R1699Q and A1708V were 54% and 69%, respectively, only moderately suggestive of increased risk. Interestingly, results from functional analyses suggest that both of these variants have only partial functional activity. R1699Q was defective in foci formation in response to DNA damage and displayed intermediate transcriptional transactivation activity but showed no evidence for centrosome amplification. In contrast, A1708V displayed an intermediate transcriptional transactivation activity and a normal foci formation response in response to DNA damage but induced centrosome amplification. Conclusion These data highlight the need for a range of functional studies to be performed in order to identify variants with partially compromised function. The results also raise the possibility that A1708V and R1699Q may be associated with a low or moderate risk of cancer. While data pooling strategies may provide more information for multifactorial analysis to improve the interpretation of the clinical significance of these variants, it is likely that the development of current multifactorial likelihood approaches and the consideration of alternative statistical approaches will be needed to determine whether these individually rare variants do confer a low or moderate risk of breast cancer. PMID:18036263

EMD-WVD time-frequency distribution for analysis of multi-component signals

NASA Astrophysics Data System (ADS)

Chai, Yunzi; Zhang, Xudong

2016-10-01

Time-frequency distribution (TFD) is two-dimensional function that indicates the time-varying frequency content of one-dimensional signals. And The Wigner-Ville distribution (WVD) is an important and effective time-frequency analysis method. The WVD can efficiently show the characteristic of a mono-component signal. However, a major drawback is the extra cross-terms when multi-component signals are analyzed by WVD. In order to eliminating the cross-terms, we decompose signals into single frequency components - Intrinsic Mode Function (IMF) - by using the Empirical Mode decomposition (EMD) first, then use WVD to analyze each single IMF. In this paper, we define this new time-frequency distribution as EMD-WVD. And the experiment results show that the proposed time-frequency method can solve the cross-terms problem effectively and improve the accuracy of WVD time-frequency analysis.

Functional analysis of pathogenicity proteins of the potato cyst nematode Globodera rostochiensis using RNAi.

PubMed

Chen, Qing; Rehman, S; Smant, G; Jones, John T

2005-07-01

RNA interference (RNAi) has been used widely as a tool for examining gene function and a method that allows its use with plant-parasitic nematodes recently has been described. Here, we use a modified method to analyze the function of secreted beta-1,4, endoglucanases of the potato cyst nematode Globodera rostochiensis, the first in vivo functional analysis of a pathogenicity protein of a plant-parasitic nematode. Knockout of the beta-1,4, endoglucanases reduced the ability of the nematodes to invade roots. We also use RNAi to show that gr-ams-1, a secreted protein of the main sense organs (the amphids), is essential for host location.

Intraoperative factors associated with delayed recovery of liver function after hepatectomy: analysis of 1969 living donors.

PubMed

Choi, S-S; Cho, S-S; Ha, T-Y; Hwang, S; Lee, S-G; Kim, Y-K

2016-02-01

The safety of healthy living donors who are undergoing hepatic resection is a primary concern. We aimed to identify intraoperative anaesthetic and surgical factors associated with delayed recovery of liver function after hepatectomy in living donors. We retrospectively analysed 1969 living donors who underwent hepatectomy for living donor liver transplantation. Delayed recovery of hepatic function was defined by increases in international normalised ratio of prothrombin time and concomitant hyperbilirubinaemia on or after post-operative day 5. Univariate and multivariate logistic regression analyses were performed to determine the factors associated with delayed recovery of hepatic function after living donor hepatectomy. Delayed recovery of liver function after donor hepatectomy was observed in 213 (10.8%) donors. Univariate logistic regression analysis showed that sevoflurane anaesthesia, synthetic colloid, donor age, body mass index, fatty change and remnant liver volume were significant factors for prediction of delayed recovery of hepatic function. Multivariate logistic regression analysis showed that independent factors significantly associated with delayed recovery of liver function after donor hepatectomy were sevoflurane anaesthesia (odds ratio = 3.514, P < 0.001), synthetic colloid (odds ratio = 1.045, P = 0.033), donor age (odds ratio = 0.970, P = 0.003), female gender (odds ratio = 1.512, P = 0.014) and remnant liver volume (odds ratio = 0.963, P < 0.001). Anaesthesia with sevoflurane was an independent factor in predicting delayed recovery of hepatic function after donor hepatectomy. Although synthetic colloid may be associated with delayed recovery of hepatic function after donor hepatectomy, further study is required. These results can provide useful information on perioperative management of living liver donors. © 2015 The Acta Anaesthesiologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

The Information Content of Discrete Functions and Their Application in Genetic Data Analysis

DOE PAGES

Sakhanenko, Nikita A.; Kunert-Graf, James; Galas, David J.

2017-10-13

The complex of central problems in data analysis consists of three components: (1) detecting the dependence of variables using quantitative measures, (2) defining the significance of these dependence measures, and (3) inferring the functional relationships among dependent variables. We have argued previously that an information theory approach allows separation of the detection problem from the inference of functional form problem. We approach here the third component of inferring functional forms based on information encoded in the functions. Here, we present here a direct method for classifying the functional forms of discrete functions of three variables represented in data sets. Discretemore » variables are frequently encountered in data analysis, both as the result of inherently categorical variables and from the binning of continuous numerical variables into discrete alphabets of values. The fundamental question of how much information is contained in a given function is answered for these discrete functions, and their surprisingly complex relationships are illustrated. The all-important effect of noise on the inference of function classes is found to be highly heterogeneous and reveals some unexpected patterns. We apply this classification approach to an important area of biological data analysis—that of inference of genetic interactions. Genetic analysis provides a rich source of real and complex biological data analysis problems, and our general methods provide an analytical basis and tools for characterizing genetic problems and for analyzing genetic data. Finally, we illustrate the functional description and the classes of a number of common genetic interaction modes and also show how different modes vary widely in their sensitivity to noise.« less

The Information Content of Discrete Functions and Their Application in Genetic Data Analysis

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

Sakhanenko, Nikita A.; Kunert-Graf, James; Galas, David J.

The complex of central problems in data analysis consists of three components: (1) detecting the dependence of variables using quantitative measures, (2) defining the significance of these dependence measures, and (3) inferring the functional relationships among dependent variables. We have argued previously that an information theory approach allows separation of the detection problem from the inference of functional form problem. We approach here the third component of inferring functional forms based on information encoded in the functions. Here, we present here a direct method for classifying the functional forms of discrete functions of three variables represented in data sets. Discretemore » variables are frequently encountered in data analysis, both as the result of inherently categorical variables and from the binning of continuous numerical variables into discrete alphabets of values. The fundamental question of how much information is contained in a given function is answered for these discrete functions, and their surprisingly complex relationships are illustrated. The all-important effect of noise on the inference of function classes is found to be highly heterogeneous and reveals some unexpected patterns. We apply this classification approach to an important area of biological data analysis—that of inference of genetic interactions. Genetic analysis provides a rich source of real and complex biological data analysis problems, and our general methods provide an analytical basis and tools for characterizing genetic problems and for analyzing genetic data. Finally, we illustrate the functional description and the classes of a number of common genetic interaction modes and also show how different modes vary widely in their sensitivity to noise.« less

Comprehensive proteome analysis of lysosomes reveals the diverse function of macrophages in immune responses

PubMed Central

Zhan, Shaohua; Zhang, Wenhao; Xiong, Feng; Ge, Wei

2017-01-01

Phagocytosis and autophagy in macrophages have been shown to be essential to both innate and adaptive immunity. Lysosomes are the main catabolic subcellular organelles responsible for degradation and recycling of both extracellular and intracellular material, which are the final steps in phagocytosis and autophagy. However, the molecular mechanisms underlying lysosomal functions after infection remain obscure. In this study, we conducted a quantitative proteomics analysis of the changes in constitution and glycosylation of proteins in lysosomes derived from murine RAW 264.7 macrophage cells treated with different types of pathogens comprising examples of bacteria (Listeria monocytogenes, L. m), DNA viruses (herpes simplex virus type-1, HSV-1) and RNA viruses (vesicular stomatitis virus, VSV). In total, 3,704 lysosome-related proteins and 300 potential glycosylation sites on 193 proteins were identified. Comparative analysis showed that the aforementioned pathogens induced distinct alterations in the proteome of the lysosome, which is closely associated with the immune functions of macrophages, such as toll-like receptor activation, inflammation and antigen-presentation. The most significant changes in proteins and fluctuations in glycosylation were also determined. Furthermore, Western blot analysis showed that the changes in expression of these proteins were undetectable at the whole cell level. Thus, our study provides unique insights into the function of lysosomes in macrophage activation and immune responses. PMID:28088779

Individual and institutional factors associated with functional disability in nursing home residents: An observational study with multilevel analysis.

PubMed

Serrano-Urrea, Ramón; Gómez-Rubio, Virgilio; Palacios-Ceña, Domingo; Fernández-de-Las-Peñas, César; García-Meseguer, María José

2017-01-01

High prevalence of functional limitations has been previously observed in nursing homes. Disability may depend not only on the characteristics of the residents but also on the facility characteristics. The aims of this study were: 1, to describe the prevalence of functional disability in older people living in Spanish nursing homes; and 2, to analyze the relationships between individual and nursing home characteristics and residents' functional disability. A cross-sectional study with data collected from 895 residents in 34 nursing homes in the province of Albacete (Spain) was conducted. Functional status was assessed by the Barthel Index. Taking into account both levels of data (individual and institutional characteristics) we resorted to a multilevel analysis in order to take different sources of variability in the data. The prevalence of functional disability of the total sample was 79.8%. The best fitting multilevel model showed that female gender, older age, negative self-perception of health, and living in private nursing homes were factors significantly associated with functional disability. After separating individual and institutional effects, the institutions showed significant differences. In line with previous findings, our study found high levels of functional dependence among institutionalized elders. Gender, age, self-perception of health, and institution ownership were associated with functional status. Disentangling individual and institutional effects by means of multilevel models can help evaluate the quality of the residences.

Transcriptome Analysis of a Premature Leaf Senescence Mutant of Common Wheat (Triticum aestivum L.)

PubMed Central

Xia, Chuan; Zhang, Lichao; Dong, Chunhao; Liu, Xu; Kong, Xiuying

2018-01-01

Leaf senescence is an important agronomic trait that affects both crop yield and quality. In this study, we characterized a premature leaf senescence mutant of wheat (Triticum aestivum L.) obtained by ethylmethane sulfonate (EMS) mutagenesis, named m68. Genetic analysis showed that the leaf senescence phenotype of m68 is controlled by a single recessive nuclear gene. We compared the transcriptome of wheat leaves between the wild type (WT) and the m68 mutant at four time points. Differentially expressed gene (DEG) analysis revealed many genes that were closely related to senescence genes. Gene Ontology (GO) enrichment analysis suggested that transcription factors and protein transport genes might function in the beginning of leaf senescence, while genes that were associated with chlorophyll and carbon metabolism might function in the later stage. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the genes that are involved in plant hormone signal transduction were significantly enriched. Through expression pattern clustering of DEGs, we identified 1012 genes that were induced during senescence, and we found that the WRKY family and zinc finger transcription factors might be more important than other transcription factors in the early stage of leaf senescence. These results will not only support further gene cloning and functional analysis of m68, but also facilitate the study of leaf senescence in wheat. PMID:29534430

End-to-end automated microfluidic platform for synthetic biology: from design to functional analysis

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

Linshiz, Gregory; Jensen, Erik; Stawski, Nina

Synthetic biology aims to engineer biological systems for desired behaviors. The construction of these systems can be complex, often requiring genetic reprogramming, extensive de novo DNA synthesis, and functional screening. Here, we present a programmable, multipurpose microfluidic platform and associated software and apply the platform to major steps of the synthetic biology research cycle: design, construction, testing, and analysis. We show the platform’s capabilities for multiple automated DNA assembly methods, including a new method for Isothermal Hierarchical DNA Construction, and for Escherichia coli and Saccharomyces cerevisiae transformation. The platform enables the automated control of cellular growth, gene expression induction, andmore » proteogenic and metabolic output analysis. Finally, taken together, we demonstrate the microfluidic platform’s potential to provide end-to-end solutions for synthetic biology research, from design to functional analysis.« less

End-to-end automated microfluidic platform for synthetic biology: from design to functional analysis

DOE PAGES

Linshiz, Gregory; Jensen, Erik; Stawski, Nina; ...

2016-02-02

Synthetic biology aims to engineer biological systems for desired behaviors. The construction of these systems can be complex, often requiring genetic reprogramming, extensive de novo DNA synthesis, and functional screening. Here, we present a programmable, multipurpose microfluidic platform and associated software and apply the platform to major steps of the synthetic biology research cycle: design, construction, testing, and analysis. We show the platform’s capabilities for multiple automated DNA assembly methods, including a new method for Isothermal Hierarchical DNA Construction, and for Escherichia coli and Saccharomyces cerevisiae transformation. The platform enables the automated control of cellular growth, gene expression induction, andmore » proteogenic and metabolic output analysis. Finally, taken together, we demonstrate the microfluidic platform’s potential to provide end-to-end solutions for synthetic biology research, from design to functional analysis.« less

A Genome-Wide RNAi Screen for Modifiers of the Circadian Clock in Human Cells

PubMed Central

Zhang, Eric E.; Liu, Andrew C.; Hirota, Tsuyoshi; Miraglia, Loren J.; Welch, Genevieve; Pongsawakul, Pagkapol Y.; Liu, Xianzhong; Atwood, Ann; Huss, Jon W.; Janes, Jeff; Su, Andrew I.; Hogenesch, John B.; Kay, Steve A.

2009-01-01

Summary Two decades of research identified more than a dozen clock genes and defined a biochemical feedback mechanism of circadian oscillator function. To identify additional clock genes and modifiers, we conducted a genome-wide siRNA screen in a human cellular clock model. Knockdown of nearly a thousand genes reduced rhythm amplitude. Potent effects on period length or increased amplitude were less frequent; we found hundreds of these and confirmed them in secondary screens. Characterization of a subset of these genes demonstrated a dosage-dependent effect on oscillator function. Protein interaction network analysis showed that dozens of gene products directly or indirectly associate with known clock components. Pathway analysis revealed these genes are overrepresented for components of insulin and hedgehog signaling, the cell cycle, and the folate metabolism. Coupled with data showing many of these pathways are clock-regulated, we conclude the clock is interconnected with many aspects of cellular function. PMID:19765810

Error analysis of the Golay3 optical imaging system.

PubMed

Wu, Quanying; Fan, Junliu; Wu, Feng; Zhao, Jun; Qian, Lin

2013-05-01

We use aberration theory to derive a generalized pupil function of the Golay3 imaging system when astigmatisms exist in its submirrors. Theoretical analysis and numerical simulation using ZEMAX show that the point spread function (PSF) and the modulation transfer function (MTF) of the Golay3 sparse aperture system have a periodic change when there are piston errors. When the peak-valley value of the wavefront (PV(tilt)) due to the tilt error increases from zero to λ, the PSF and the MTF change significantly, and the change direction is determined by the location of the submirror with the tilt error. When PV(tilt) becomes larger than λ, the PSF and the MTF remain unvaried. We calculate the peaks of the signal-to-noise ratio (PSNR) resulting from the piston and tilt errors according to the Strehl ratio, and show that the PSNR decreases when the errors increase.

Computational gene expression profiling under salt stress reveals patterns of co-expression

PubMed Central

Sanchita; Sharma, Ashok

2016-01-01

Plants respond differently to environmental conditions. Among various abiotic stresses, salt stress is a condition where excess salt in soil causes inhibition of plant growth. To understand the response of plants to the stress conditions, identification of the responsible genes is required. Clustering is a data mining technique used to group the genes with similar expression. The genes of a cluster show similar expression and function. We applied clustering algorithms on gene expression data of Solanum tuberosum showing differential expression in Capsicum annuum under salt stress. The clusters, which were common in multiple algorithms were taken further for analysis. Principal component analysis (PCA) further validated the findings of other cluster algorithms by visualizing their clusters in three-dimensional space. Functional annotation results revealed that most of the genes were involved in stress related responses. Our findings suggest that these algorithms may be helpful in the prediction of the function of co-expressed genes. PMID:26981411

Genome-Wide Comparative Analysis of the Phospholipase D Gene Families among Allotetraploid Cotton and Its Diploid Progenitors

PubMed Central

Tang, Kai; Dong, Chun-Juan; Liu, Jin-Yuan

2016-01-01

In this study, 40 phospholipase D (PLD) genes were identified from allotetraploid cotton Gossypium hirsutum, and 20 PLD genes were examined in diploid cotton Gossypium raimondii. Combining with 19 previously identified Gossypium arboreum PLD genes, a comparative analysis was performed among the PLD gene families among allotetraploid and two diploid cottons. Based on the orthologous relationships, we found that almost each G. hirsutum PLD had a corresponding homolog in the G. arboreum and G. raimondii genomes, except for GhPLDβ3A, whose homolog GaPLDβ3 may have been lost during the evolution of G. arboreum after the interspecific hybridization. Phylogenetic analysis showed that all of the cotton PLDs were unevenly classified into six numbered subgroups: α, β/γ, δ, ε, ζ and φ. An N-terminal C2 domain was found in the α, β/γ, δ and ε subgroups, while phox homology (PX) and pleckstrin homology (PH) domains were identified in the ζ subgroup. The subgroup φ possessed a single peptide instead of a functional domain. In each phylogenetic subgroup, the PLDs showed high conservation in gene structure and amino acid sequences in functional domains. The expansion of GhPLD and GrPLD gene families were mainly attributed to segmental duplication and partly attributed to tandem duplication. Furthermore, purifying selection played a critical role in the evolution of PLD genes in cotton. Quantitative RT-PCR documented that allotetraploid cotton PLD genes were broadly expressed and each had a unique spatial and developmental expression pattern, indicating their functional diversification in cotton growth and development. Further analysis of cis-regulatory elements elucidated transcriptional regulations and potential functions. Our comparative analysis provided valuable information for understanding the putative functions of the PLD genes in cotton fiber. PMID:27213891

Effect of oral isoflavone supplementation on vascular endothelial function in postmenopausal women: a meta-analysis of randomized placebo-controlled trials.

PubMed

Li, Shao-Hua; Liu, Xu-Xia; Bai, Yong-Yi; Wang, Xiao-Jian; Sun, Kai; Chen, Jing-Zhou; Hui, Ru-Tai

2010-02-01

The effect of isoflavone on endothelial function in postmenopausal women is controversial. The objective of this study was to evaluate the effect of oral isoflavone supplementation on endothelial function, as measured by flow-mediated dilation (FMD), in postmenopausal women. A meta-analysis of randomized placebo-controlled trials was conducted to evaluate the effect of oral isoflavone supplementation on endothelial function in postmenopausal women. Trials were searched in PubMed, Embase, the Cochrane Library database, and reviews and reference lists of relevant articles. Summary estimates of weighted mean differences (WMDs) and 95% CIs were obtained by using random-effects models. Meta-regression and subgroup analyses were performed to identify the source of heterogeneity. A total of 9 trials were reviewed in the present meta-analysis. Overall, the results of the 9 trials showed that isoflavone significantly increased FMD (WMD: 1.75%; 95% CI: 0.83%, 2.67%; P = 0.0002). Meta-regression analysis indicated that the age-adjusted baseline FMD was inversely related to effect size. Subgroup analysis showed that oral supplementation of isoflavone had no influence on FMD if the age-adjusted baseline FMD was > or = 5.2% (4 trials; WMD: 0.24%; 95% CI: -0.94%, 1.42%; P = 0.69). This improvement seemed to be significant when the age-adjusted baseline FMD levels were <5.2% (5 trials; WMD: 2.22%; 95% CI: 1.15%, 3.30%; P < 0.0001), although significant heterogeneity was still detected in this low-baseline-FMD subgroup. Oral isoflavone supplementation does not improve endothelial function in postmenopausal women with high baseline FMD levels but leads to significant improvement in women with low baseline FMD levels.

Using scale and feather traits for module construction provides a functional approach to chicken epidermal development.

PubMed

Bao, Weier; Greenwold, Matthew J; Sawyer, Roger H

2017-11-01

Gene co-expression network analysis has been a research method widely used in systematically exploring gene function and interaction. Using the Weighted Gene Co-expression Network Analysis (WGCNA) approach to construct a gene co-expression network using data from a customized 44K microarray transcriptome of chicken epidermal embryogenesis, we have identified two distinct modules that are highly correlated with scale or feather development traits. Signaling pathways related to feather development were enriched in the traditional KEGG pathway analysis and functional terms relating specifically to embryonic epidermal development were also enriched in the Gene Ontology analysis. Significant enrichment annotations were discovered from customized enrichment tools such as Modular Single-Set Enrichment Test (MSET) and Medical Subject Headings (MeSH). Hub genes in both trait-correlated modules showed strong specific functional enrichment toward epidermal development. Also, regulatory elements, such as transcription factors and miRNAs, were targeted in the significant enrichment result. This work highlights the advantage of this methodology for functional prediction of genes not previously associated with scale- and feather trait-related modules.

Resting State Network Topology of the Ferret Brain

PubMed Central

Zhou, Zhe Charles; Salzwedel, Andrew P.; Radtke-Schuller, Susanne; Li, Yuhui; Sellers, Kristin K.; Gilmore, John H.; Shih, Yen-Yu Ian; Fröhlich, Flavio; Gao, Wei

2016-01-01

Resting state functional magnetic resonance imaging (rsfMRI) has emerged as a versatile tool for non-invasive measurement of functional connectivity patterns in the brain. RsfMRI brain dynamics in rodents, non-human primates, and humans share similar properties; however, little is known about the resting state functional connectivity patterns in the ferret, an animal model with high potential for developmental and cognitive translational study. To address this knowledge-gap, we performed rsfMRI on anesthetized ferrets using a 9.4 tesla MRI scanner, and subsequently performed group-level independent component analysis (gICA) to identify functionally connected brain networks. Group-level ICA analysis revealed distributed sensory, motor, and higher-order networks in the ferret brain. Subsequent connectivity analysis showed interconnected higher-order networks that constituted a putative default mode network (DMN), a network that exhibits altered connectivity in neuropsychiatric disorders. Finally, we assessed ferret brain topological efficiency using graph theory analysis and found that the ferret brain exhibits small-world properties. Overall, these results provide additional evidence for pan-species resting-state networks, further supporting ferret-based studies of sensory and cognitive function. PMID:27596024

Time-domain representation of frequency-dependent foundation impedance functions

USGS Publications Warehouse

Safak, E.

2006-01-01

Foundation impedance functions provide a simple means to account for soil-structure interaction (SSI) when studying seismic response of structures. Impedance functions represent the dynamic stiffness of the soil media surrounding the foundation. The fact that impedance functions are frequency dependent makes it difficult to incorporate SSI in standard time-history analysis software. This paper introduces a simple method to convert frequency-dependent impedance functions into time-domain filters. The method is based on the least-squares approximation of impedance functions by ratios of two complex polynomials. Such ratios are equivalent, in the time-domain, to discrete-time recursive filters, which are simple finite-difference equations giving the relationship between foundation forces and displacements. These filters can easily be incorporated into standard time-history analysis programs. Three examples are presented to show the applications of the method.

Assessment of macrovascular endothelial function using pulse wave analysis and its association with microvascular reactivity in healthy subjects.

PubMed

Ibrahim, N N I N; Rasool, A H G

2017-08-01

Pulse wave analysis (PWA) and laser Doppler fluximetry (LDF) are non-invasive methods of assessing macrovascular endothelial function and microvascular reactivity respectively. The aim of this study was to assess the correlation between macrovascular endothelial function assessed by PWA and microvascular reactivity assessed by LDF. 297 healthy and non-smoking subjects (159 females, mean age (±SD) 23.56 ± 4.54 years) underwent microvascular reactivity assessment using LDF followed by macrovascular endothelial function assessments using PWA. Pearson's correlation showed no correlation between macrovascular endothelial function and microvascular reactivity (r = -0.10, P = 0.12). There was no significant correlation between macrovascular endothelial function assessed by PWA and microvascular reactivity assessed by LDF in healthy subjects. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

A single preovulatory administration of ulipristal acetate affects the decidualization process of the human endometrium during the receptive period of the menstrual cycle.

PubMed

Lira-Albarrán, Saúl; Durand, Marta; Barrera, David; Vega, Claudia; Becerra, Rocio García; Díaz, Lorenza; García-Quiroz, Janice; Rangel, Claudia; Larrea, Fernando

2018-04-27

In order to get further information on the effects of ulipristal acetate (UPA) upon the process of decidualization of endometrium, a functional analysis of the differentially expressed genes in endometrium (DEG) from UPA treated-versus control-cycles of normal ovulatory women was performed. A list of 1183 endometrial DEG, from a previously published study by our group, was submitted to gene ontology, gene enrichment and ingenuity pathway analyses (IPA). This functional analysis showed that decidualization was a biological process overrepresented. Gene set enrichment analysis identified LIF, PRL, IL15 and STAT3 among the most down-regulated genes within the JAK STAT canonical pathway. IPA showed that decidualization of uterus was a bio-function predicted as inhibited by UPA. The results demonstrated that this selective progesterone receptor modulator, when administered during the periovulatory phase of the menstrual cycle, may affect the molecular mechanisms leading to endometrial decidualization in response to progesterone during the period of maximum embryo receptivity. Copyright © 2018 Elsevier B.V. All rights reserved.

Studying hemispheric lateralization during a Stroop task through near-infrared spectroscopy-based connectivity

NASA Astrophysics Data System (ADS)

Zhang, Lei; Sun, Jinyan; Sun, Bailei; Luo, Qingming; Gong, Hui

2014-05-01

Near-infrared spectroscopy (NIRS) is a developing and promising functional brain imaging technology. Developing data analysis methods to effectively extract meaningful information from collected data is the major bottleneck in popularizing this technology. In this study, we measured hemodynamic activity of the prefrontal cortex (PFC) during a color-word matching Stroop task using NIRS. Hemispheric lateralization was examined by employing traditional activation and novel NIRS-based connectivity analyses simultaneously. Wavelet transform coherence was used to assess intrahemispheric functional connectivity. Spearman correlation analysis was used to examine the relationship between behavioral performance and activation/functional connectivity, respectively. In agreement with activation analysis, functional connectivity analysis revealed leftward lateralization for the Stroop effect and correlation with behavioral performance. However, functional connectivity was more sensitive than activation for identifying hemispheric lateralization. Granger causality was used to evaluate the effective connectivity between hemispheres. The results showed increased information flow from the left to the right hemispheres for the incongruent versus the neutral task, indicating a leading role of the left PFC. This study demonstrates that the NIRS-based connectivity can reveal the functional architecture of the brain more comprehensively than traditional activation, helping to better utilize the advantages of NIRS.

Does Gender-Specific Differential Item Functioning Affect the Structure in Vocational Interest Inventories?

ERIC Educational Resources Information Center

Beinicke, Andrea; Pässler, Katja; Hell, Benedikt

2014-01-01

The study investigates consequences of eliminating items showing gender-specific differential item functioning (DIF) on the psychometric structure of a standard RIASEC interest inventory. Holland's hexagonal model was tested for structural invariance using a confirmatory methodological approach (confirmatory factor analysis and randomization…

The Analysis of Spontaneous Processes Using Equilibrium Thermodynamics

ERIC Educational Resources Information Center

Honig, J. M.; Ben-Amotz, Dor

2006-01-01

The derivations based on the use of deficit functions provide a simple means of demonstrating the extremism conditions that are applicable to various thermodynamics function. The method shows that the maximum quantity of work is available from a system only when the processes are carried out reversibly since irreversible (spontaneous)…

A time-frequency analysis method to obtain stable estimates of magnetotelluric response function based on Hilbert-Huang transform

NASA Astrophysics Data System (ADS)

Cai, Jianhua

2017-05-01

The time-frequency analysis method represents signal as a function of time and frequency, and it is considered a powerful tool for handling arbitrary non-stationary time series by using instantaneous frequency and instantaneous amplitude. It also provides a possible alternative to the analysis of the non-stationary magnetotelluric (MT) signal. Based on the Hilbert-Huang transform (HHT), a time-frequency analysis method is proposed to obtain stable estimates of the magnetotelluric response function. In contrast to conventional methods, the response function estimation is performed in the time-frequency domain using instantaneous spectra rather than in the frequency domain, which allows for imaging the response parameter content as a function of time and frequency. The theory of the method is presented and the mathematical model and calculation procedure, which are used to estimate response function based on HHT time-frequency spectrum, are discussed. To evaluate the results, response function estimates are compared with estimates from a standard MT data processing method based on the Fourier transform. All results show that apparent resistivities and phases, which are calculated from the HHT time-frequency method, are generally more stable and reliable than those determined from the simple Fourier analysis. The proposed method overcomes the drawbacks of the traditional Fourier methods, and the resulting parameter minimises the estimation bias caused by the non-stationary characteristics of the MT data.

Strategies for the generation of parametric images of [11C]PIB with plasma input functions considering discriminations and reproducibility.

PubMed

Edison, Paul; Brooks, David J; Turkheimer, Federico E; Archer, Hilary A; Hinz, Rainer

2009-11-01

Pittsburgh compound B or [11C]PIB is an amyloid imaging agent which shows a clear differentiation between subjects with Alzheimer's disease (AD) and controls. However the observed signal difference in other forms of dementia such as dementia with Lewy bodies (DLB) is smaller, and mild cognitively impaired (MCI) subjects and some healthy elderly normals may show intermediate levels of [11C]PIB binding. The cerebellum, a commonly used reference region for non-specific tracer uptake in [11C]PIB studies in AD may not be valid in Prion disorders or monogenic forms of AD. The aim of this work was to: 1-compare methods for generating parametric maps of [11C]PIB retention in tissue using a plasma input function in respect of their ability to discriminate between AD subjects and controls and 2-estimate the test-retest reproducibility in AD subjects. 12 AD subjects (5 of which underwent a repeat scan within 6 weeks) and 10 control subjects had 90 minute [11C]PIB dynamic PET scans, and arterial plasma input functions were measured. Parametric maps were generated with graphical analysis of reversible binding (Logan plot), irreversible binding (Patlak plot), and spectral analysis. Between group differentiation was calculated using Student's t-test and comparisons between different methods were made using p values. Reproducibility was assessed by intraclass correlation coefficients (ICC). We found that the 75 min value of the impulse response function showed the best group differentiation and had a higher ICC than volume of distribution maps generated from Logan and spectral analysis. Patlak analysis of [11C]PIB binding was the least reproducible.

DFT calculations on molecular structure, spectral analysis, multiple interactions, reactivity, NLO property and molecular docking study of flavanol-2,4-dinitrophenylhydrazone

NASA Astrophysics Data System (ADS)

Singh, Ravindra Kumar; Singh, Ashok Kumar

2017-02-01

A new flavanol-2,4-dinitrophenylhydrazone (FDNP) was synthesized and its structure was confirmed by FT-IR, FT-Raman, 1H NMR, mass spectrometry and elemental analysis. All quantum chemical calculations were carried out at level of density functional theory (DFT) with B3LYP functional using 6-311++ G (d,p) basis atomic set. UV-Vis absorption spectra for the singlet-singlet transition computed for fully optimized ground state geometry using Time-Dependent-Density Functional Theory (TD-DFT) with CAM-B3LYP functional was found to be in consistent with that of experimental findings. Analysis of vibrational (FT-IR and FT-Raman) spectrum and their assignments has been done by computing Potential Energy Distribution (PED) using Gar2ped. HOMO-LUMO analysis was performed and reactivity descriptors were calculated. Calculated global electrophilicity index (ω = 7.986 eV) shows molecule to be a strong electrophile. 1H NMR chemical shift calculated with the help of gauge-including atomic orbital (GIAO) approach shows agreement with experimental data. Various intramolecular interactions were analysed by AIM approach. DFT computed total first static hyperpolarizability (β0 = 189.03 × 10-30 esu) indicates that title molecule can be used as attractive future NLO material. Solvent induced effects on the NLO properties studied by using self-consistent reaction field (SCRF) method shows that β0 value increases with increase in solvent polarity. To study the thermal behaviour of title molecule, thermodynamic properties such as heat capacity, entropy and enthalpy change at various temperatures have been calculated and reported. Molecular docking results suggests title molecule to be a potential kinase inhibitor and might be used in future for designing of new anticancer drug.

Research Review: Neural response to threat in children, adolescents, and adults after child maltreatment - a quantitative meta-analysis.

PubMed

Hein, Tyler C; Monk, Christopher S

2017-03-01

Child maltreatment is common and has long-term consequences for affective function. Investigations of neural consequences of maltreatment have focused on the amygdala. However, developmental neuroscience indicates that other brain regions are also likely to be affected by child maltreatment, particularly in the social information processing network (SIPN). We conducted a quantitative meta-analysis to: confirm that maltreatment is related to greater bilateral amygdala activation in a large sample that was pooled across studies; investigate other SIPN structures that are likely candidates for altered function; and conduct a data-driven examination to identify additional regions that show altered activation in maltreated children, teens, and adults. We conducted an activation likelihood estimation analysis with 1,733 participants across 20 studies of emotion processing in maltreated individuals. Maltreatment is associated with increased bilateral amygdala activation to emotional faces. One SIPN structure is altered: superior temporal gyrus, of the detection node, is hyperactive in maltreated individuals. The results of the whole-brain corrected analysis also show hyperactivation of the parahippocampal gyrus and insula in maltreated individuals. The meta-analysis confirms that maltreatment is related to increased bilateral amygdala reactivity and also shows that maltreatment affects multiple additional structures in the brain that have received little attention in the literature. Thus, although the majority of studies examining maltreatment and brain function have focused on the amygdala, these findings indicate that the neural consequences of child maltreatment involve a broader network of structures. © 2016 Association for Child and Adolescent Mental Health.

Self-Organizing Maps and Parton Distribution Functions

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

K. Holcomb, Simonetta Liuti, D. Z. Perry

2011-05-01

We present a new method to extract parton distribution functions from high energy experimental data based on a specific type of neural networks, the Self-Organizing Maps. We illustrate the features of our new procedure that are particularly useful for an anaysis directed at extracting generalized parton distributions from data. We show quantitative results of our initial analysis of the parton distribution functions from inclusive deep inelastic scattering.

Performance of bed load transport equations in mountain gravel-bed rivers: A re-analysis

Treesearch

Jeffrey J. Barry; John M. Buffington; John G. King; Peter Goodwin

2006-01-01

Our recent examination of bed load transport data from mountain gravel-bed rivers in the western United States shows that the data can be fit by a simple power function of discharge, with the coefficient being a function of drainage area (a surrogate for basin sediment supply) and the exponent being a function of supply-related channel armoring (transport capacity in...

A quadratically regularized functional canonical correlation analysis for identifying the global structure of pleiotropy with NGS data

PubMed Central

Zhu, Yun; Fan, Ruzong; Xiong, Momiao

2017-01-01

Investigating the pleiotropic effects of genetic variants can increase statistical power, provide important information to achieve deep understanding of the complex genetic structures of disease, and offer powerful tools for designing effective treatments with fewer side effects. However, the current multiple phenotype association analysis paradigm lacks breadth (number of phenotypes and genetic variants jointly analyzed at the same time) and depth (hierarchical structure of phenotype and genotypes). A key issue for high dimensional pleiotropic analysis is to effectively extract informative internal representation and features from high dimensional genotype and phenotype data. To explore correlation information of genetic variants, effectively reduce data dimensions, and overcome critical barriers in advancing the development of novel statistical methods and computational algorithms for genetic pleiotropic analysis, we proposed a new statistic method referred to as a quadratically regularized functional CCA (QRFCCA) for association analysis which combines three approaches: (1) quadratically regularized matrix factorization, (2) functional data analysis and (3) canonical correlation analysis (CCA). Large-scale simulations show that the QRFCCA has a much higher power than that of the ten competing statistics while retaining the appropriate type 1 errors. To further evaluate performance, the QRFCCA and ten other statistics are applied to the whole genome sequencing dataset from the TwinsUK study. We identify a total of 79 genes with rare variants and 67 genes with common variants significantly associated with the 46 traits using QRFCCA. The results show that the QRFCCA substantially outperforms the ten other statistics. PMID:29040274

Relationship between Speech Production and Perception in People Who Stutter.

PubMed

Lu, Chunming; Long, Yuhang; Zheng, Lifen; Shi, Guang; Liu, Li; Ding, Guosheng; Howell, Peter

2016-01-01

Speech production difficulties are apparent in people who stutter (PWS). PWS also have difficulties in speech perception compared to controls. It is unclear whether the speech perception difficulties in PWS are independent of, or related to, their speech production difficulties. To investigate this issue, functional MRI data were collected on 13 PWS and 13 controls whilst the participants performed a speech production task and a speech perception task. PWS performed poorer than controls in the perception task and the poorer performance was associated with a functional activity difference in the left anterior insula (part of the speech motor area) compared to controls. PWS also showed a functional activity difference in this and the surrounding area [left inferior frontal cortex (IFC)/anterior insula] in the production task compared to controls. Conjunction analysis showed that the functional activity differences between PWS and controls in the left IFC/anterior insula coincided across the perception and production tasks. Furthermore, Granger Causality Analysis on the resting-state fMRI data of the participants showed that the causal connection from the left IFC/anterior insula to an area in the left primary auditory cortex (Heschl's gyrus) differed significantly between PWS and controls. The strength of this connection correlated significantly with performance in the perception task. These results suggest that speech perception difficulties in PWS are associated with anomalous functional activity in the speech motor area, and the altered functional connectivity from this area to the auditory area plays a role in the speech perception difficulties of PWS.

Polysaccharide with antioxidant, α-amylase inhibitory and ACE inhibitory activities from Momordica charantia.

PubMed

Tan, Hwee-Feng; Gan, Chee-Yuen

2016-04-01

Functional polysaccharide was isolated from Momordica charantia, with a yield of 36% (w/w). M. charantia bioactive polysaccharide (MCBP) was an acidic and branched heteropolysaccharide with a molecular weight of 92 kDa. Fourier transform infrared spectroscopic analysis indicated that MCBP was a pectin-like polysaccharide with an esterification degree of 53% and it contains numerous monosaccharides, predominantly glucose, galactose, and galaturonic acid. The results also showed that MCBP exhibited free radical scavenging activity (31.9%), ferric reducing antioxidant power (0.95 mM), α-amylase inhibition (89.1%), and angiotensin-converting enzyme inhibition (94.1%). In the terms of functionality, MCBP showed a lower water-holding capacity but higher in oil-holding capacity, emulsifying activity and foaming capacity compared to citrus pectin. Scanning electron microscopy images demonstrated that MCBP formed gels with a porous structure, and flow analysis showed that the gel solution exhibited pseudoplastic shear-thinning behavior. These findings indicated that MCBP is a promising functional macromolecular carbohydrate for the food and nutraceutical industries. Copyright © 2016 Elsevier B.V. All rights reserved.

Partial correlation-based functional connectivity analysis for functional near-infrared spectroscopy signals

NASA Astrophysics Data System (ADS)

Akın, Ata

2017-12-01

A theoretical framework, a partial correlation-based functional connectivity (PC-FC) analysis to functional near-infrared spectroscopy (fNIRS) data, is proposed. This is based on generating a common background signal from a high passed version of fNIRS data averaged over all channels as the regressor in computing the PC between pairs of channels. This approach has been employed to real data collected during a Stroop task. The results show a strong significance in the global efficiency (GE) metric computed by the PC-FC analysis for neutral, congruent, and incongruent stimuli (NS, CS, IcS; GEN=0.10±0.009, GEC=0.11±0.01, GEIC=0.13±0.015, p=0.0073). A positive correlation (r=0.729 and p=0.0259) is observed between the interference of reaction times (incongruent-neutral) and interference of GE values (GEIC-GEN) computed from [HbO] signals.

Resting-state theta band connectivity and graph analysis in generalized social anxiety disorder.

PubMed

Xing, Mengqi; Tadayonnejad, Reza; MacNamara, Annmarie; Ajilore, Olusola; DiGangi, Julia; Phan, K Luan; Leow, Alex; Klumpp, Heide

2017-01-01

Functional magnetic resonance imaging (fMRI) resting-state studies show generalized social anxiety disorder (gSAD) is associated with disturbances in networks involved in emotion regulation, emotion processing, and perceptual functions, suggesting a network framework is integral to elucidating the pathophysiology of gSAD. However, fMRI does not measure the fast dynamic interconnections of functional networks. Therefore, we examined whole-brain functional connectomics with electroencephalogram (EEG) during resting-state. Resting-state EEG data was recorded for 32 patients with gSAD and 32 demographically-matched healthy controls (HC). Sensor-level connectivity analysis was applied on EEG data by using Weighted Phase Lag Index (WPLI) and graph analysis based on WPLI was used to determine clustering coefficient and characteristic path length to estimate local integration and global segregation of networks. WPLI results showed increased oscillatory midline coherence in the theta frequency band indicating higher connectivity in the gSAD relative to HC group during rest. Additionally, WPLI values positively correlated with state anxiety levels within the gSAD group but not the HC group. Our graph theory based connectomics analysis demonstrated increased clustering coefficient and decreased characteristic path length in theta-based whole brain functional organization in subjects with gSAD compared to HC. Theta-dependent interconnectivity was associated with state anxiety in gSAD and an increase in information processing efficiency in gSAD (compared to controls). Results may represent enhanced baseline self-focused attention, which is consistent with cognitive models of gSAD and fMRI studies implicating emotion dysregulation and disturbances in task negative networks (e.g., default mode network) in gSAD.

Linear and nonlinear ARMA model parameter estimation using an artificial neural network

NASA Technical Reports Server (NTRS)

Chon, K. H.; Cohen, R. J.

1997-01-01

This paper addresses parametric system identification of linear and nonlinear dynamic systems by analysis of the input and output signals. Specifically, we investigate the relationship between estimation of the system using a feedforward neural network model and estimation of the system by use of linear and nonlinear autoregressive moving-average (ARMA) models. By utilizing a neural network model incorporating a polynomial activation function, we show the equivalence of the artificial neural network to the linear and nonlinear ARMA models. We compare the parameterization of the estimated system using the neural network and ARMA approaches by utilizing data generated by means of computer simulations. Specifically, we show that the parameters of a simulated ARMA system can be obtained from the neural network analysis of the simulated data or by conventional least squares ARMA analysis. The feasibility of applying neural networks with polynomial activation functions to the analysis of experimental data is explored by application to measurements of heart rate (HR) and instantaneous lung volume (ILV) fluctuations.

Can Automated Facial Expression Analysis Show Differences Between Autism and Typical Functioning?

PubMed

Borsos, Zsófia; Gyori, Miklos

2017-01-01

Exploratory analyses of emotional expressions using a commercially available facial expression recognition software are reported, from the context of a serious game for screening purposes. Our results are based on a comparative analysis of two matched groups of kindergarten-age children (high-functioning children with autism spectrum condition: n=13; typically developing children: n=13). Results indicate that this technology has the potential to identify autism-specific emotion expression features, and may play a role in affective diagnostic and assistive technologies.

Comparison of clinician-predicted to measured low vision outcomes.

PubMed

Chan, Tiffany L; Goldstein, Judith E; Massof, Robert W

2013-08-01

To compare low-vision rehabilitation (LVR) clinicians' predictions of the probability of success of LVR with patients' self-reported outcomes after provision of usual outpatient LVR services and to determine if patients' traits influence clinician ratings. The Activity Inventory (AI), a self-report visual function questionnaire, was administered pre-and post-LVR to 316 low-vision patients served by 28 LVR centers that participated in a collaborative observational study. The physical component of the Short Form-36, Geriatric Depression Scale, and Telephone Interview for Cognitive Status were also administered pre-LVR to measure physical capability, depression, and cognitive status. After patient evaluation, 38 LVR clinicians estimated the probability of outcome success (POS) using their own criteria. The POS ratings and change in functional ability were used to assess the effects of patients' baseline traits on predicted outcomes. A regression analysis with a hierarchical random-effects model showed no relationship between LVR physician POS estimates and AI-based outcomes. In another analysis, kappa statistics were calculated to determine the probability of agreement between POS and AI-based outcomes for different outcome criteria. Across all comparisons, none of the kappa values were significantly different from 0, which indicates that the rate of agreement is equivalent to chance. In an exploratory analysis, hierarchical mixed-effects regression models show that POS ratings are associated with information about the patient's cognitive functioning and the combination of visual acuity and functional ability, as opposed to visual acuity or functional ability alone. Clinicians' predictions of LVR outcomes seem to be influenced by knowledge of patients' cognitive functioning and the combination of visual acuity and functional ability-information clinicians acquire from the patient's history and examination. However, clinicians' predictions do not agree with observed changes in functional ability from the patient's perspective; they are no better than chance.

Graph Theoretical Analysis of Functional Brain Networks: Test-Retest Evaluation on Short- and Long-Term Resting-State Functional MRI Data

PubMed Central

Wang, Jin-Hui; Zuo, Xi-Nian; Gohel, Suril; Milham, Michael P.; Biswal, Bharat B.; He, Yong

2011-01-01

Graph-based computational network analysis has proven a powerful tool to quantitatively characterize functional architectures of the brain. However, the test-retest (TRT) reliability of graph metrics of functional networks has not been systematically examined. Here, we investigated TRT reliability of topological metrics of functional brain networks derived from resting-state functional magnetic resonance imaging data. Specifically, we evaluated both short-term (<1 hour apart) and long-term (>5 months apart) TRT reliability for 12 global and 6 local nodal network metrics. We found that reliability of global network metrics was overall low, threshold-sensitive and dependent on several factors of scanning time interval (TI, long-term>short-term), network membership (NM, networks excluding negative correlations>networks including negative correlations) and network type (NT, binarized networks>weighted networks). The dependence was modulated by another factor of node definition (ND) strategy. The local nodal reliability exhibited large variability across nodal metrics and a spatially heterogeneous distribution. Nodal degree was the most reliable metric and varied the least across the factors above. Hub regions in association and limbic/paralimbic cortices showed moderate TRT reliability. Importantly, nodal reliability was robust to above-mentioned four factors. Simulation analysis revealed that global network metrics were extremely sensitive (but varying degrees) to noise in functional connectivity and weighted networks generated numerically more reliable results in compared with binarized networks. For nodal network metrics, they showed high resistance to noise in functional connectivity and no NT related differences were found in the resistance. These findings provide important implications on how to choose reliable analytical schemes and network metrics of interest. PMID:21818285

Generating linear regression model to predict motor functions by use of laser range finder during TUG.

PubMed

Adachi, Daiki; Nishiguchi, Shu; Fukutani, Naoto; Hotta, Takayuki; Tashiro, Yuto; Morino, Saori; Shirooka, Hidehiko; Nozaki, Yuma; Hirata, Hinako; Yamaguchi, Moe; Yorozu, Ayanori; Takahashi, Masaki; Aoyama, Tomoki

2017-05-01

The purpose of this study was to investigate which spatial and temporal parameters of the Timed Up and Go (TUG) test are associated with motor function in elderly individuals. This study included 99 community-dwelling women aged 72.9 ± 6.3 years. Step length, step width, single support time, variability of the aforementioned parameters, gait velocity, cadence, reaction time from starting signal to first step, and minimum distance between the foot and a marker placed to 3 in front of the chair were measured using our analysis system. The 10-m walk test, five times sit-to-stand (FTSTS) test, and one-leg standing (OLS) test were used to assess motor function. Stepwise multivariate linear regression analysis was used to determine which TUG test parameters were associated with each motor function test. Finally, we calculated a predictive model for each motor function test using each regression coefficient. In stepwise linear regression analysis, step length and cadence were significantly associated with the 10-m walk test, FTSTS and OLS test. Reaction time was associated with the FTSTS test, and step width was associated with the OLS test. Each predictive model showed a strong correlation with the 10-m walk test and OLS test (P < 0.01), which was not significant higher correlation than TUG test time. We showed which TUG test parameters were associated with each motor function test. Moreover, the TUG test time regarded as the lower extremity function and mobility has strong predictive ability in each motor function test. Copyright © 2017 The Japanese Orthopaedic Association. Published by Elsevier B.V. All rights reserved.

Comparative Transcriptome Analysis between the Cytoplasmic Male Sterile Line NJCMS1A and Its Maintainer NJCMS1B in Soybean (Glycine max (L.) Merr.)

PubMed Central

Li, Jiajia; Han, Shaohuai; Ding, Xianlong; He, Tingting; Dai, Jinying; Yang, Shouping; Gai, Junyi

2015-01-01

Background The utilization of soybean heterosis is probably one of the potential approaches in future yield breakthrough as was the situation in rice breeding in China. Cytoplasmic male sterility (CMS) plays an important role in the production of hybrid seeds. However, the molecular mechanism of CMS in soybean remains unclear. Results The comparative transcriptome analysis between cytoplasmic male sterile line NJCMS1A and its near-isogenic maintainer NJCMS1B in soybean was conducted using Illumina sequencing technology. A total of 88,643 transcripts were produced in Illumina sequencing. Then 56,044 genes were obtained matching soybean reference genome. Three hundred and sixty five differentially expressed genes (DEGs) between NJCMS1A and NJCMS1B were screened by threshold, among which, 339 down-regulated and 26 up-regulated in NJCMS1A compared to in NJCMS1B. Gene Ontology (GO) annotation showed that 242 DEGs were annotated to 19 functional categories. Clusters of Orthologous Groups of proteins (COG) annotation showed that 265 DEGs were classified into 19 categories. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that 46 DEGs were assigned to 33 metabolic pathways. According to functional and metabolic pathway analysis combined with reported literatures, the relations between some key DEGs and the male sterility of NJCMS1A were discussed. qRT-PCR analysis validated that the gene expression pattern in RNA-Seq was reliable. Finally, enzyme activity assay showed that energy supply was decreased in NJCMS1A compared to in NJCMS1B. Conclusions We concluded that the male sterility of NJCMS1A might be related to the disturbed functions and metabolism pathways of some key DEGs, such as DEGs involved in carbohydrate and energy metabolism, transcription factors, regulation of pollen development, elimination of reactive oxygen species (ROS), cellular signal transduction, and programmed cell death (PCD) etc. Future research will focus on cloning and transgenic function validation of possible candidate genes associated with soybean CMS. PMID:25985300

Functionalization and characterization of pyrolyzed polymer based carbon microstructures for bionanoelectronics platforms

NASA Astrophysics Data System (ADS)

Hirabayashi, Mieko; Mehta, Beejal; Vahidi, Nasim W.; Khosla, Ajit; Kassegne, Sam

2013-11-01

In this study, the investigation of surface-treatment of chemically inert graphitic carbon microelectrodes (derived from pyrolyzed photoresist polymer) for improving their attachment chemistry with DNA molecular wires and ropes as part of a bionanoelectronics platform is reported. Polymer microelectrodes were fabricated on a silicon wafer using standard negative lithography procedures with negative-tone photoresist. These microelectrode structures were then pyrolyzed and converted to a form of conductive carbon that is referred to as PP (pyrolyzed polymer) carbon throughout this paper. Functionalization of the resulting pyrolyzed structures was done using nitric, sulfuric, 4-amino benzoic acids (4-ABA), and oxygen plasma etching and the surface modifications confirmed with Fourier transform infrared spectroscopy (FTIR), Raman spectroscopy, and electron dispersion x-ray spectroscopy (EDS). Post surface-treatment analysis of microelectrodes with FTIR and Raman spectroscopy showed signature peaks characteristics of carboxyl functional groups while EDS showed an increase in oxygen content in the surface-treatment procedures (except 4-ABA) indicating an increase in carboxyl functional group. These functional groups form the basis for peptide bond with aminated oligonucleotides that in turn could be used as molecular wires and interconnects in a bionanoelectronics platform. Post-pyrolysis analysis using EDS showed relatively higher oxygen concentrations at the edges and location of defects compared to other locations on these microelectrodes. In addition, electrochemical impedance measurements showed metal-like behavior of PP carbon with high conductivity (|Z| <1 KΩ) and no detectable detrimental effect of oxygen plasma surface-treatment on electrical characteristic. In general, characterization results—taken together—indicated that oxygen plasma surface-treatment produced more reliable, less damaging, and consistently repeatable generation of carboxyl functional groups than diazonium salt and strong acid treatments.

The Representation of Object-Directed Action and Function Knowledge in the Human Brain.

PubMed

Chen, Quanjing; Garcea, Frank E; Mahon, Bradford Z

2016-04-01

The appropriate use of everyday objects requires the integration of action and function knowledge. Previous research suggests that action knowledge is represented in frontoparietal areas while function knowledge is represented in temporal lobe regions. Here we used multivoxel pattern analysis to investigate the representation of object-directed action and function knowledge while participants executed pantomimes of familiar tool actions. A novel approach for decoding object knowledge was used in which classifiers were trained on one pair of objects and then tested on a distinct pair; this permitted a measurement of classification accuracy over and above object-specific information. Region of interest (ROI) analyses showed that object-directed actions could be decoded in tool-preferring regions of both parietal and temporal cortex, while no independently defined tool-preferring ROI showed successful decoding of object function. However, a whole-brain searchlight analysis revealed that while frontoparietal motor and peri-motor regions are engaged in the representation of object-directed actions, medial temporal lobe areas in the left hemisphere are involved in the representation of function knowledge. These results indicate that both action and function knowledge are represented in a topographically coherent manner that is amenable to study with multivariate approaches, and that the left medial temporal cortex represents knowledge of object function. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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

PubMed

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

2013-12-01

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

Analysis of functional redundancies within the Arabidopsis TCP transcription factor family

PubMed Central

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

2013-01-01

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

Genome-wide analysis of alternative splicing during human heart development

NASA Astrophysics Data System (ADS)

Wang, He; Chen, Yanmei; Li, Xinzhong; Chen, Guojun; Zhong, Lintao; Chen, Gangbing; Liao, Yulin; Liao, Wangjun; Bin, Jianping

2016-10-01

Alternative splicing (AS) drives determinative changes during mouse heart development. Recent high-throughput technological advancements have facilitated genome-wide AS, while its analysis in human foetal heart transition to the adult stage has not been reported. Here, we present a high-resolution global analysis of AS transitions between human foetal and adult hearts. RNA-sequencing data showed extensive AS transitions occurred between human foetal and adult hearts, and AS events occurred more frequently in protein-coding genes than in long non-coding RNA (lncRNA). A significant difference of AS patterns was found between foetal and adult hearts. The predicted difference in AS events was further confirmed using quantitative reverse transcription-polymerase chain reaction analysis of human heart samples. Functional foetal-specific AS event analysis showed enrichment associated with cell proliferation-related pathways including cell cycle, whereas adult-specific AS events were associated with protein synthesis. Furthermore, 42.6% of foetal-specific AS events showed significant changes in gene expression levels between foetal and adult hearts. Genes exhibiting both foetal-specific AS and differential expression were highly enriched in cell cycle-associated functions. In conclusion, we provided a genome-wide profiling of AS transitions between foetal and adult hearts and proposed that AS transitions and deferential gene expression may play determinative roles in human heart development.

In vivo microvascular and macrovascular endothelial function is not associated with circulating dimethylarginines in patients with rheumatoid arthritis: a prospective analysis of the DRACCO cohort.

PubMed

Dimitroulas, Theodoros; Sandoo, Aamer; Hodson, James; Smith, Jacqueline P; Kitas, George D

2016-07-01

To examine associations between asymmetric (ADMA), symmetric dimethylarginine (SDMA) and ADMA:SDMA ratio with assessments of endothelial function and coronary artery perfusion in RA patients. ADMA and SDMA levels were measured in 197 RA individuals [144 (77.4%) females, median age: 66 years (quartiles: 59-73)]. Patients underwent assessments of microvascular endothelium-dependent and endothelium-independent function, macrovascular endothelium-dependent and endothelium-independent function and vascular morphology (pulse wave analysis, carotid intima-media thickness (cIMT), and carotid plaque). Coronary perfusion was assessed by subendocardial viability ratio (SEVR). SEVR correlated with SDMA (r = 0.172, p = 0.026) and ADMA:SDMA (r = -0.160, p = 0.041) in univariable analysis, but not in multivariable analysis accounting for confounding factors. Neither ADMA:SDMA ratio nor SDMA were significantly correlated with microvascular or macrovascular endothelial function, or with arterial stiffness and cIMT. Within subgroup of patients (n = 26) with high inflammatory markers, a post-hoc analysis showed that SDMA and the ADMA:SDMA ratio were significantly associated with endothelium-dependent microvascular function in univariable analysis, with Pearson's r correlation coefficients of -0.440 (p = 0.031) and 0.511 (p = 0.011), respectively. Similar finding were established between ADMA:SDMA ratio and arterial stiffness in univariable analysis, with Pearson's r of 0.493, (p = 0.024). Dimethylarginines were not found to be significantly associated with several assessments of vascular function and morphology in patients with RA, however, post-hoc analysis indicates that there may be associations in patients with raised inflammatory markers. Our results suggest that dysregulated NO metabolism may not be the sole mechanism for the development of preclinical atherosclerosis in RA.

Application of argon atmospheric cold plasma for indium tin oxide (ITO) based diodes

NASA Astrophysics Data System (ADS)

Akbari Nia, S.; Jalili, Y. Seyed; Salar Elahi, A.

2017-09-01

Transparent Conductive Oxide (TCO) layers due to transparency, high conductivity and hole injection capability have attracted a lot of attention. One of these layers is Indium Tin Oxide (ITO). ITO due to low resistance, transparency in the visible spectrum and its proper work function is widely used in the manufacture of organic light emitting diodes and solar cells. One way for improving the ITO surface is plasma treatment. In this paper, changes in surface morphology, by applying argon atmospheric pressure cold plasma, was studied through Atomic Force Microscopic (AFM) image analysis and Fourier Transform Infrared Spectroscopy (FTIR) analysis. FTIR analysis showed functional groups were not added or removed, but chemical bond angle and bonds strength on the surface were changed and also AFM images showed that surface roughness was increased. These factors lead to the production of diodes with enhanced Ohmic contact and injection mechanism which are more appropriate in industrial applications.

Functional and bioinformatics analysis of an exopolysaccharide-related gene (epsN) from Lactobacillus kefiranofaciens ZW3.

PubMed

Wang, Jingrui; Tang, Wei; Zheng, Yongna; Xing, Zhuqing; Wang, Yanping

2016-09-01

A novel lactic acid bacteria strain Lactobacillus kefiranofaciens ZW3 exhibited the characteristics of high production of exopolysaccharide (EPS). The epsN gene, located in the eps gene cluster of this strain, is associated with EPS biosynthesis. Bioinformatics analysis of this gene was performed. The conserved domain analysis showed that the EpsN protein contained MATE-Wzx-like domains. Then the epsN gene was amplified to construct the recombinant expression vector pMG36e-epsN. The results showed that the EPS yields of the recombinants were significantly improved. By determining the yields of EPS and intracellular polysaccharide, it was considered that epsN gene could play its Wzx flippase role in the EPS biosynthesis. This is the first time to prove the effect of EpsN on L. kefiranofaciens EPS biosynthesis and further prove its functional property.

Reduction of Interhemispheric Functional Brain Connectivity in Early Blindness: A Resting-State fMRI Study

PubMed Central

2017-01-01

Objective The purpose of this study was to investigate the resting-state interhemispheric functional connectivity in early blindness by using voxel-mirrored homotopic connectivity (VMHC). Materials and Methods Sixteen early blind patients (EB group) and sixteen age- and gender-matched sighted control volunteers (SC group) were recruited in this study. We used VMHC to identify brain areas with significant differences in functional connectivity between different groups and used voxel-based morphometry (VBM) to calculate the individual gray matter volume (GMV). Results VMHC analysis showed a significantly lower connectivity in primary visual cortex, visual association cortex, and somatosensory association cortex in EB group compared to sighted controls. Additionally, VBM analysis revealed that GMV was reduced in the left lateral calcarine cortices in EB group compared to sighted controls, while it was increased in the left lateral middle occipital gyri. Statistical analysis showed the duration of blindness negatively correlated with VMHC in the bilateral middle frontal gyri, middle temporal gyri, and inferior temporal gyri. Conclusions Our findings help elucidate the pathophysiological mechanisms of EB. The interhemispheric functional connectivity was impaired in EB patients. Additionally, the middle frontal gyri, middle temporal gyri, and inferior temporal gyri may be potential target regions for rehabilitation. PMID:28656145

Estimate of uncertainties in polarized parton distributions

NASA Astrophysics Data System (ADS)

Miyama, M.; Goto, Y.; Hirai, M.; Kobayashi, H.; Kumano, S.; Morii, T.; Saito, N.; Shibata, T.-A.; Yamanishi, T.

2001-10-01

From \\chi^2 analysis of polarized deep inelastic scattering data, we determined polarized parton distribution functions (Y. Goto et al. (AAC), Phys. Rev. D 62, 34017 (2000).). In order to clarify the reliability of the obtained distributions, we should estimate uncertainties of the distributions. In this talk, we discuss the pol-PDF uncertainties by using a Hessian method. A Hessian matrix H_ij is given by second derivatives of the \\chi^2, and the error matrix \\varepsilon_ij is defined as the inverse matrix of H_ij. Using the error matrix, we calculate the error of a function F by (δ F)^2 = sum_i,j fracpartial Fpartial ai \\varepsilon_ij fracpartial Fpartial aj , where a_i,j are the parameters in the \\chi^2 analysis. Using this method, we show the uncertainties of the pol-PDF, structure functions g_1, and spin asymmetries A_1. Furthermore, we show a role of future experiments such as the RHIC-Spin. An important purpose of planned experiments in the near future is to determine the polarized gluon distribution function Δ g (x) in detail. We reanalyze the pol-PDF uncertainties including the gluon fake data which are expected to be given by the upcoming experiments. From this analysis, we discuss how much the uncertainties of Δ g (x) can be improved by such measurements.

Evaluation of measurement equivalence of the Family Satisfaction with the End-of-Life Care in an ethnically diverse cohort: Tests of differential item functioning

PubMed Central

Teresi, Jeanne A; Ocepek-Welikson, Katja; Ramirez, Mildred; Kleinman, Marjorie; Ornstein, Katherine; Siu, Albert

2016-01-01

Background The Family Satisfaction with End-of-Life Care is an internationally used measure of satisfaction with cancer care. However, the Family Satisfaction with End-of-Life Care has not been studied for equivalence of item endorsement across different socio-demographic groups using differential item functioning. Aims The aims of this secondary data analysis were (1) to examine potential differential item functioning in the family satisfaction item set with respect to type of caregiver, race, and patient age, gender, and education and (2) to provide parameters and documentation of differential item functioning for an item bank. Design A mixed qualitative and quantitative analysis was conducted. A priori hypotheses regarding potential group differences in item response were established. Item response theory and Wald tests were used for the analyses of differential item functioning, accompanied by magnitude and impact measures. Results Very little significant differential item functioning was observed for patient's age and gender. For race, 13 items showed differential item functioning after multiple comparison adjustment, 10 with non-uniform differential item functioning. No items evidenced differential item functioning of high magnitude, and the impact was negligible. For education, 5 items evidenced uniform differential item functioning after adjustment, none of high magnitude. Differential item functioning impact was trivial. One item evidenced differential item functioning for the caregiver relationship variable. Conclusion Differential item functioning was observed primarily for race and education. No differential item functioning of high magnitude was observed for any item, and the overall impact of differential item functioning was negligible. One item, satisfaction with “the patient's pain relief,” might be singled out for further study, given that this item was both hypothesized and observed to show differential item functioning for race and education. PMID:25160692

Isolation and in silico analysis of a novel H+-pyrophosphatase gene orthologue from the halophytic grass Leptochloa fusca

NASA Astrophysics Data System (ADS)

Rauf, Muhammad; Saeed, Nasir A.; Habib, Imran; Ahmed, Moddassir; Shahzad, Khurram; Mansoor, Shahid; Ali, Rashid

2017-02-01

Structure prediction can provide information about function and active sites of protein which helps to design new functional proteins. H+-pyrophosphatase is transmembrane protein involved in establishing proton motive force for active transport of Na+ across membrane by Na+/H+ antiporters. A full length novel H+-pyrophosphatase gene was isolated from halophytic grass Leptochloa fusca using RT-PCR and RACE method. Full length LfVP1 gene sequence of 2292 nucleotides encodes protein of 764 amino acids. DNA and protein sequences were used for characterization using bioinformatics tools. Various important potential sites were predicted by PROSITE webserver. Primary structural analysis showed LfVP1 as stable protein and Grand average hydropathy (GRAVY) indicated that LfVP1 protein has good hydrosolubility. Secondary structure analysis showed that LfVP1 protein sequence contains significant proportion of alpha helix and random coil. Protein membrane topology suggested the presence of 14 transmembrane domains and presence of catalytic domain in TM3. Three dimensional structure from LfVP1 protein sequence also indicated the presence of 14 transmembrane domains and hydrophobicity surface model showed amino acid hydrophobicity. Ramachandran plot showed that 98% amino acid residues were predicted in the favored region.

A Secure and Robust User Authenticated Key Agreement Scheme for Hierarchical Multi-medical Server Environment in TMIS.

PubMed

Das, Ashok Kumar; Odelu, Vanga; Goswami, Adrijit

2015-09-01

The telecare medicine information system (TMIS) helps the patients to gain the health monitoring facility at home and access medical services over the Internet of mobile networks. Recently, Amin and Biswas presented a smart card based user authentication and key agreement security protocol usable for TMIS system using the cryptographic one-way hash function and biohashing function, and claimed that their scheme is secure against all possible attacks. Though their scheme is efficient due to usage of one-way hash function, we show that their scheme has several security pitfalls and design flaws, such as (1) it fails to protect privileged-insider attack, (2) it fails to protect strong replay attack, (3) it fails to protect strong man-in-the-middle attack, (4) it has design flaw in user registration phase, (5) it has design flaw in login phase, (6) it has design flaw in password change phase, (7) it lacks of supporting biometric update phase, and (8) it has flaws in formal security analysis. In order to withstand these security pitfalls and design flaws, we aim to propose a secure and robust user authenticated key agreement scheme for the hierarchical multi-server environment suitable in TMIS using the cryptographic one-way hash function and fuzzy extractor. Through the rigorous security analysis including the formal security analysis using the widely-accepted Burrows-Abadi-Needham (BAN) logic, the formal security analysis under the random oracle model and the informal security analysis, we show that our scheme is secure against possible known attacks. Furthermore, we simulate our scheme using the most-widely accepted and used Automated Validation of Internet Security Protocols and Applications (AVISPA) tool. The simulation results show that our scheme is also secure. Our scheme is more efficient in computation and communication as compared to Amin-Biswas's scheme and other related schemes. In addition, our scheme supports extra functionality features as compared to other related schemes. As a result, our scheme is very appropriate for practical applications in TMIS.

Duration of untreated psychosis and clinical outcomes of first episode psychosis: An observational and an instrumental variables analysis.

PubMed

Sullivan, Sarah A; Carroll, Robert; Peters, Tim J; Amos, Tim; Jones, Peter B; Marshall, Max; Birchwood, Max; Fowler, David; Johnson, Sonia; Fisher, Helen L; Major, Barnaby; Rahaman, Nikola; Joyce, John; Chamberlain-Kent, Nick; Lawrence, Jo; Moran, Paul; Tilling, Kate

2018-04-26

Duration of untreated psychosis (DUP) is considered as a key prognostic variable in psychosis. Yet, it is unclear whether a longer DUP causes worse outcomes or whether reported associations have alternative explanations. Data from 2 cohorts of patients with first episode psychosis were used (n = 2134). Measures of DUP were assessed at baseline and outcomes at 12 months. Regression models were used to investigate the associations between DUP and outcomes. We also investigated whether any associations were replicated using instrumental variables (IV) analysis to reduce the effect of residual confounding and measurement bias. There were associations between DUP per 1-year increase and positive psychotic symptoms (7.0% in symptom score increase 95% confidence interval (CI) 4.0%, 10.0%, P < .001), worse recovery (risk difference [RD] 0.78, 95%, CI 0.68, 0.83, P < .001) and worse global functioning (0.62 decrease in functioning score 95% CI -1.19, -0.04, P = .035). There was no evidence of an association with negative psychotic symptoms (1.0%, 95%, CI -2.0%, 5.0%, P = .455). The IV analysis showed weaker evidence of associations in the same direction between DUP per 1-year increase and positive psychotic symptoms, recovery and global functioning. However, there was evidence of an inverse association with negative psychotic symptoms (decrease of 15.0% in symptom score 95% CI -26.0%, -3.0%, P = .016). We have confirmed previous findings of a positive association between positive psychotic symptoms, global functioning and recovery and DUP using regression analysis. IV analysis shows some support for these findings. Future investigation using IV analysis should be repeated in large data sets. © 2018 John Wiley & Sons Australia, Ltd.

Effects of stimulants on brain function in attention-deficit/hyperactivity disorder: a systematic review and meta-analysis.

PubMed

Rubia, Katya; Alegria, Analucia A; Cubillo, Ana I; Smith, Anna B; Brammer, Michael J; Radua, Joaquim

2014-10-15

Psychostimulant medication, most commonly the catecholamine agonist methylphenidate, is the most effective treatment for attention-deficit/hyperactivity disorder (ADHD). However, relatively little is known on the mechanisms of action. Acute effects on brain function can elucidate underlying neurocognitive effects. We tested methylphenidate effects relative to placebo in functional magnetic resonance imaging (fMRI) during three disorder-relevant tasks in medication-naïve ADHD adolescents. In addition, we conducted a systematic review and meta-analysis of the fMRI findings of acute stimulant effects on ADHD brain function. The fMRI study compared 20 adolescents with ADHD under either placebo or methylphenidate in a randomized controlled trial while performing stop, working memory, and time discrimination tasks. The meta-analysis was conducted searching PubMed, ScienceDirect, Web of Knowledge, Google Scholar, and Scopus databases. Peak coordinates of clusters of significant effects of stimulant medication relative to placebo or off medication were extracted for each study. The fMRI analysis showed that methylphenidate significantly enhanced activation in bilateral inferior frontal cortex (IFC)/insula during inhibition and time discrimination but had no effect on working memory networks. The meta-analysis, including 14 fMRI datasets and 212 children with ADHD, showed that stimulants most consistently enhanced right IFC/insula activation, which also remained for a subgroup analysis of methylphenidate effects alone. A more lenient threshold also revealed increased putamen activation. Psychostimulants most consistently increase right IFC/insula activation, which are key areas of cognitive control and also the most replicated neurocognitive dysfunction in ADHD. These neurocognitive effects may underlie their positive clinical effects. © 2013 Society of Biological Psychiatry Published by Society of Biological Psychiatry All rights reserved.

[ICF-Checklist to Evaluate Inclusion of Elderlies with Intellectual Disability - Psychometric Properties].

PubMed

Queri, Silvia; Eggart, Michael; Wendel, Maren; Peter, Ulrike

2017-11-28

Background An instrument should have been developed to measure participation as one possible criterion to evaluate inclusion of elderly people with intellectual disability. The ICF was utilized, because participation is one part of health related functioning, respectively disability. Furthermore ICF includes environmental factors (contextual factors) and attaches them an essentially influence on health related functioning, in particular on participation. Thus ICF Checklist additionally identifies environmental barriers for elimination. Methodology A linking process with VINELAND-II yielded 138 ICF items for the Checklist. The sample consists of 50 persons with a light or moderate intellectual disability. Two-thirds are female and the average age is 68. They were directly asked about their perceived quality of life. Additionally, proxy interviews were carried out with responsible staff members concerning necessary support and behavioral deviances. The ICF Checklist was administered twice, once (t2) the current staff member should rate health related functioning at the given time and in addition, a staff member who knows the person at least 10 years before (t1) should rate the former functioning. Content validity was investigated with factor analysis and criterion validity with correlational analysis related to supports need, behavioral deviances and perceived quality of life. Quantitative analysis was validated by qualitative content analysis of patient documentation. Results Factor analysis shows logical variable clusters across the extracted factors but neither interpretable factors. The Checklist is reliable, valid related to the chosen criterions and shows the expected age-related shifts. Qualitative analysis corresponds with quantitative data. Consequences/Conclusion ICF Checklist is appropriate to manage and evaluate patient-centered care. © Georg Thieme Verlag KG Stuttgart · New York.

Effects of Stimulants on Brain Function in Attention-Deficit/Hyperactivity Disorder: A Systematic Review and Meta-Analysis

PubMed Central

Rubia, Katya; Alegria, Analucia A.; Cubillo, Ana I.; Smith, Anna B.; Brammer, Michael J.; Radua, Joaquim

2014-01-01

Background Psychostimulant medication, most commonly the catecholamine agonist methylphenidate, is the most effective treatment for attention-deficit/hyperactivity disorder (ADHD). However, relatively little is known on the mechanisms of action. Acute effects on brain function can elucidate underlying neurocognitive effects. We tested methylphenidate effects relative to placebo in functional magnetic resonance imaging (fMRI) during three disorder-relevant tasks in medication-naïve ADHD adolescents. In addition, we conducted a systematic review and meta-analysis of the fMRI findings of acute stimulant effects on ADHD brain function. Methods The fMRI study compared 20 adolescents with ADHD under either placebo or methylphenidate in a randomized controlled trial while performing stop, working memory, and time discrimination tasks. The meta-analysis was conducted searching PubMed, ScienceDirect, Web of Knowledge, Google Scholar, and Scopus databases. Peak coordinates of clusters of significant effects of stimulant medication relative to placebo or off medication were extracted for each study. Results The fMRI analysis showed that methylphenidate significantly enhanced activation in bilateral inferior frontal cortex (IFC)/insula during inhibition and time discrimination but had no effect on working memory networks. The meta-analysis, including 14 fMRI datasets and 212 children with ADHD, showed that stimulants most consistently enhanced right IFC/insula activation, which also remained for a subgroup analysis of methylphenidate effects alone. A more lenient threshold also revealed increased putamen activation. Conclusions Psychostimulants most consistently increase right IFC/insula activation, which are key areas of cognitive control and also the most replicated neurocognitive dysfunction in ADHD. These neurocognitive effects may underlie their positive clinical effects. PMID:24314347

The complicated substrates enhance the microbial diversity and zinc leaching efficiency in sphalerite bioleaching system.

PubMed

Xiao, Yunhua; Xu, YongDong; Dong, Weiling; Liang, Yili; Fan, Fenliang; Zhang, Xiaoxia; Zhang, Xian; Niu, Jiaojiao; Ma, Liyuan; She, Siyuan; He, Zhili; Liu, Xueduan; Yin, Huaqun

2015-12-01

This study used an artificial enrichment microbial consortium to examine the effects of different substrate conditions on microbial diversity, composition, and function (e.g., zinc leaching efficiency) through adding pyrite (SP group), chalcopyrite (SC group), or both (SPC group) in sphalerite bioleaching systems. 16S rRNA gene sequencing analysis showed that microbial community structures and compositions dramatically changed with additions of pyrite or chalcopyrite during the sphalerite bioleaching process. Shannon diversity index showed a significantly increase in the SP (1.460), SC (1.476), and SPC (1.341) groups compared with control (sphalerite group, 0.624) on day 30, meanwhile, zinc leaching efficiencies were enhanced by about 13.4, 2.9, and 13.2%, respectively. Also, additions of pyrite or chalcopyrite could increase electric potential (ORP) and the concentrations of Fe3+ and H+, which were the main factors shaping microbial community structures by Mantel test analysis. Linear regression analysis showed that ORP, Fe3+ concentration, and pH were significantly correlated to zinc leaching efficiency and microbial diversity. In addition, we found that leaching efficiency showed a positive and significant relationship with microbial diversity. In conclusion, our results showed that the complicated substrates could significantly enhance microbial diversity and activity of function.

Molecular mechanism of G1 arrest and cellular senescence induced by LEE011, a novel CDK4/CDK6 inhibitor, in leukemia cells.

PubMed

Tao, Yan-Fang; Wang, Na-Na; Xu, Li-Xiao; Li, Zhi-Heng; Li, Xiao-Lu; Xu, Yun-Yun; Fang, Fang; Li, Mei; Qian, Guang-Hui; Li, Yan-Hong; Li, Yi-Ping; Wu, Yi; Ren, Jun-Li; Du, Wei-Wei; Lu, Jun; Feng, Xing; Wang, Jian; He, Wei-Qi; Hu, Shao-Yan; Pan, Jian

2017-01-01

Overexpression of cyclin D1 dependent kinases 4 and 6 (CDK4/6) is a common feature of many human cancers including leukemia. LEE011 is a novel inhibitor of both CDK4 and 6. To date, the molecular function of LEE011 in leukemia remains unclear. Leukemia cell growth and apoptosis following LEE011 treatment was assessed through CCK-8 and annexin V/propidium iodide staining assays. Cell senescence was assessed by β-galactosidase staining and p16 INK4a expression analysis. Gene expression profiles of LEE011 treated HL-60 cells were investigated using an Arraystar Human LncRNA array. Gene ontology and KEGG pathway analysis were then used to analyze the differentially expressed genes from the cluster analysis. Our studies demonstrated that LEE011 inhibited proliferation of leukemia cells and could induce apoptosis. Hoechst 33,342 staining analysis showed DNA fragmentation and distortion of nuclear structures following LEE011 treatment. Cell cycle analysis showed LEE011 significantly induced cell cycle G 1 arrest in seven of eight acute leukemia cells lines, the exception being THP-1 cells. β-Galactosidase staining analysis and p16 INK4a expression analysis showed that LEE011 treatment can induce cell senescence of leukemia cells. LncRNA microarray analysis showed 2083 differentially expressed mRNAs and 3224 differentially expressed lncRNAs in LEE011-treated HL-60 cells compared with controls. Molecular function analysis showed that LEE011 induced senescence in leukemia cells partially through downregulation of the transcriptional expression of MYBL2. We demonstrate for the first time that LEE011 treatment results in inhibition of cell proliferation and induction of G 1 arrest and cellular senescence in leukemia cells. LncRNA microarray analysis showed differentially expressed mRNAs and lncRNAs in LEE011-treated HL-60 cells and we demonstrated that LEE011 induces cellular senescence partially through downregulation of the expression of MYBL2. These results may open new lines of investigation regarding the molecular mechanism of LEE011 induced cellular senescence.

Structural and functional analysis of 5S rRNA in Saccharomyces cerevisiae

PubMed Central

Kiparisov, S.; Sergiev, P. V.; Dontsova, O. A.; Petrov, A.; Meskauskas, A.; Dinman, J. D.

2005-01-01

5S rRNA extends from the central protuberance of the large ribosomal subunit, through the A-site finger, and down to the GTPase-associated center. Here, we present a structure-function analysis of seven 5S rRNA alleles which are sufficient for viability in the yeast Saccharomyces cerevisiae when expressed in the absence of wild-type 5S rRNAs, and extend this analysis using a large bank of mutant alleles that show semidominant phenotypes in the presence of wild-type 5S rRNA. This analysis supports the hypothesis that 5S rRNA serves to link together several different functional centers of the ribosome. Data are also presented which suggest that in eukaryotic genomes selection has favored the maintenance of multiple alleles of 5S rRNA, and that these may provide cells with a mechanism to post-transcriptionally regulate gene expression. PMID:16047201

Comparisons of synthesized and individual reinforcement contingencies during functional analysis.

PubMed

Fisher, Wayne W; Greer, Brian D; Romani, Patrick W; Zangrillo, Amanda N; Owen, Todd M

2016-09-01

Researchers typically modify individual functional analysis (FA) conditions after results are inconclusive (Hanley, Iwata, & McCord, 2003). Hanley, Jin, Vanselow, and Hanratty (2014) introduced a marked departure from this practice, using an interview-informed synthesized contingency analysis (IISCA). In the test condition, they delivered multiple contingencies simultaneously (e.g., attention and escape) after each occurrence of problem behavior; in the control condition, they delivered those same reinforcers noncontingently and continuously. In the current investigation, we compared the results of the IISCA with a more traditional FA in which we evaluated each putative reinforcer individually. Four of 5 participants displayed destructive behavior that was sensitive to the individual contingencies evaluated in the traditional FA. By contrast, none of the participants showed a response pattern consistent with the assumption of the IISCA. We discuss the implications of these findings on the development of accurate and efficient functional analyses. © 2016 Society for the Experimental Analysis of Behavior.

[Effects of acupuncture at left and right Hegu (LI 4) for cerebral function laterality].

PubMed

Wang, Linying; Xu, Chunsheng; Zhu, Yifang; Li, Chuanfu; Yang, Jun

2015-08-01

To explore the cerebral function laterality of acupuncture at left and right Hegu (LI 4) by using functional magnetic resonance imaging (fMRI) and provide objective evidences for side selection of Hegu (LI 4) in the clinical application. Eighty healthy volunteers were randomly divided into a left-acupoint group and a right-acupoint group, and they were treated with acupuncture at left Hegu (LI 4) and right Hegu (LI 4) respectively. After the arrival of qi, the task-state fMRI data in both groups was collected, and analysis of functional neuroimages (AFNI) software was used to perform intra-group and between-group comparisons. After acupuncture, acupuncture feelings were recorded and MGH acupuncture sensation scale (MASS) was recorded. The difference of MASS between the two groups was not significant (P>0. 05). The result of left-acupoint group showed an increased signal on right cerebral hemisphere, while the right-acupoint group showed extensive signal changes in both cerebral hemispheres. The analysis between left-acupoint group and retroflex right-acupoint group showed differences in brain areas. The central effect of acupuncture at left and right Hegu (LI 4) is dissymmetry, indicating right hemisphere laterality. The right lobus insularis and cingulate gyrus may be the key regions in the acupuncture at Hegu (LI 4).

Crystal Structure Analysis and the Identification of Distinctive Functional Regions of the Protein Elicitor Mohrip2.

PubMed

Liu, Mengjie; Duan, Liangwei; Wang, Meifang; Zeng, Hongmei; Liu, Xinqi; Qiu, Dewen

2016-01-01

The protein elicitor MoHrip2, which was extracted from Magnaporthe oryzae as an exocrine protein, triggers the tobacco immune system and enhances blast resistance in rice. However, the detailed mechanisms by which MoHrip2 acts as an elicitor remain unclear. Here, we investigated the structure of MoHrip2 to elucidate its functions based on molecular structure. The three-dimensional structure of MoHrip2 was obtained. Overall, the crystal structure formed a β-barrel structure and showed high similarity to the pathogenesis-related (PR) thaumatin superfamily protein thaumatin-like xylanase inhibitor (TL-XI). To investigate the functional regions responsible for MoHrip2 elicitor activities, the full length and eight truncated proteins were expressed in Escherichia coli and were evaluated for elicitor activity in tobacco. Biological function analysis showed that MoHrip2 triggered the defense system against Botrytis cinerea in tobacco. Moreover, only MoHrip2M14 and other fragments containing the 14 amino acids residues in the middle region of the protein showed the elicitor activity of inducing a hypersensitive response and resistance related pathways, which were similar to that of full-length MoHrip2. These results revealed that the central 14 amino acid residues were essential for anti-pathogenic activity.

Differential impairments underlying decision making in anorexia nervosa and bulimia nervosa: a cognitive modeling analysis.

PubMed

Chan, Trista Wai Sze; Ahn, Woo-Young; Bates, John E; Busemeyer, Jerome R; Guillaume, Sebastien; Redgrave, Graham W; Danner, Unna N; Courtet, Philippe

2014-03-01

This study examined the underlying processes of decision-making impairments in individuals with anorexia nervosa (AN) and bulimia nervosa (BN). We deconstructed their performance on the widely used decision task, the Iowa Gambling Task (IGT) into cognitive, motivational, and response processes using cognitive modeling analysis. We hypothesized that IGT performance would be characterized by impaired memory functions and heightened punishment sensitivity in AN, and by elevated sensitivity to reward as opposed to punishment in BN. We analyzed trial-by-trial data of IGT obtained from 224 individuals: 94 individuals with AN, 63 with BN, and 67 healthy comparison individuals (HC). The prospect valence learning model was used to assess cognitive, motivational, and response processes underlying IGT performance. Individuals with AN showed marginally impaired IGT performance compared to HC. Their performance was characterized by impairments in memory functions. Individuals with BN showed significantly impaired IGT performance compared to HC. They showed greater relative sensitivity to gains as opposed to losses than HC. Memory functions in AN were positively correlated with body mass index. This study identified differential impairments underlying IGT performance in AN and BN. Findings suggest that impaired decision making in AN might involve impaired memory functions. Impaired decision making in BN might involve altered reward and punishment sensitivity. Copyright © 2013 Wiley Periodicals, Inc.

On convergence of differential evolution over a class of continuous functions with unique global optimum.

PubMed

Ghosh, Sayan; Das, Swagatam; Vasilakos, Athanasios V; Suresh, Kaushik

2012-02-01

Differential evolution (DE) is arguably one of the most powerful stochastic real-parameter optimization algorithms of current interest. Since its inception in the mid 1990s, DE has been finding many successful applications in real-world optimization problems from diverse domains of science and engineering. This paper takes a first significant step toward the convergence analysis of a canonical DE (DE/rand/1/bin) algorithm. It first deduces a time-recursive relationship for the probability density function (PDF) of the trial solutions, taking into consideration the DE-type mutation, crossover, and selection mechanisms. Then, by applying the concepts of Lyapunov stability theorems, it shows that as time approaches infinity, the PDF of the trial solutions concentrates narrowly around the global optimum of the objective function, assuming the shape of a Dirac delta distribution. Asymptotic convergence behavior of the population PDF is established by constructing a Lyapunov functional based on the PDF and showing that it monotonically decreases with time. The analysis is applicable to a class of continuous and real-valued objective functions that possesses a unique global optimum (but may have multiple local optima). Theoretical results have been substantiated with relevant computer simulations.

Dynamic functional connectivity analysis reveals transient states of dysconnectivity in schizophrenia.

PubMed

Damaraju, E; Allen, E A; Belger, A; Ford, J M; McEwen, S; Mathalon, D H; Mueller, B A; Pearlson, G D; Potkin, S G; Preda, A; Turner, J A; Vaidya, J G; van Erp, T G; Calhoun, V D

2014-01-01

Schizophrenia is a psychotic disorder characterized by functional dysconnectivity or abnormal integration between distant brain regions. Recent functional imaging studies have implicated large-scale thalamo-cortical connectivity as being disrupted in patients. However, observed connectivity differences in schizophrenia have been inconsistent between studies, with reports of hyperconnectivity and hypoconnectivity between the same brain regions. Using resting state eyes-closed functional imaging and independent component analysis on a multi-site data that included 151 schizophrenia patients and 163 age- and gender matched healthy controls, we decomposed the functional brain data into 100 components and identified 47 as functionally relevant intrinsic connectivity networks. We subsequently evaluated group differences in functional network connectivity, both in a static sense, computed as the pairwise Pearson correlations between the full network time courses (5.4 minutes in length), and a dynamic sense, computed using sliding windows (44 s in length) and k-means clustering to characterize five discrete functional connectivity states. Static connectivity analysis revealed that compared to healthy controls, patients show significantly stronger connectivity, i.e., hyperconnectivity, between the thalamus and sensory networks (auditory, motor and visual), as well as reduced connectivity (hypoconnectivity) between sensory networks from all modalities. Dynamic analysis suggests that (1), on average, schizophrenia patients spend much less time than healthy controls in states typified by strong, large-scale connectivity, and (2), that abnormal connectivity patterns are more pronounced during these connectivity states. In particular, states exhibiting cortical-subcortical antagonism (anti-correlations) and strong positive connectivity between sensory networks are those that show the group differences of thalamic hyperconnectivity and sensory hypoconnectivity. Group differences are weak or absent during other connectivity states. Dynamic analysis also revealed hypoconnectivity between the putamen and sensory networks during the same states of thalamic hyperconnectivity; notably, this finding cannot be observed in the static connectivity analysis. Finally, in post-hoc analyses we observed that the relationships between sub-cortical low frequency power and connectivity with sensory networks is altered in patients, suggesting different functional interactions between sub-cortical nuclei and sensorimotor cortex during specific connectivity states. While important differences between patients with schizophrenia and healthy controls have been identified, one should interpret the results with caution given the history of medication in patients. Taken together, our results support and expand current knowledge regarding dysconnectivity in schizophrenia, and strongly advocate the use of dynamic analyses to better account for and understand functional connectivity differences.

Dynamic functional connectivity analysis reveals transient states of dysconnectivity in schizophrenia

PubMed Central

Damaraju, E.; Allen, E.A.; Belger, A.; Ford, J.M.; McEwen, S.; Mathalon, D.H.; Mueller, B.A.; Pearlson, G.D.; Potkin, S.G.; Preda, A.; Turner, J.A.; Vaidya, J.G.; van Erp, T.G.; Calhoun, V.D.

2014-01-01

Schizophrenia is a psychotic disorder characterized by functional dysconnectivity or abnormal integration between distant brain regions. Recent functional imaging studies have implicated large-scale thalamo-cortical connectivity as being disrupted in patients. However, observed connectivity differences in schizophrenia have been inconsistent between studies, with reports of hyperconnectivity and hypoconnectivity between the same brain regions. Using resting state eyes-closed functional imaging and independent component analysis on a multi-site data that included 151 schizophrenia patients and 163 age- and gender matched healthy controls, we decomposed the functional brain data into 100 components and identified 47 as functionally relevant intrinsic connectivity networks. We subsequently evaluated group differences in functional network connectivity, both in a static sense, computed as the pairwise Pearson correlations between the full network time courses (5.4 minutes in length), and a dynamic sense, computed using sliding windows (44 s in length) and k-means clustering to characterize five discrete functional connectivity states. Static connectivity analysis revealed that compared to healthy controls, patients show significantly stronger connectivity, i.e., hyperconnectivity, between the thalamus and sensory networks (auditory, motor and visual), as well as reduced connectivity (hypoconnectivity) between sensory networks from all modalities. Dynamic analysis suggests that (1), on average, schizophrenia patients spend much less time than healthy controls in states typified by strong, large-scale connectivity, and (2), that abnormal connectivity patterns are more pronounced during these connectivity states. In particular, states exhibiting cortical–subcortical antagonism (anti-correlations) and strong positive connectivity between sensory networks are those that show the group differences of thalamic hyperconnectivity and sensory hypoconnectivity. Group differences are weak or absent during other connectivity states. Dynamic analysis also revealed hypoconnectivity between the putamen and sensory networks during the same states of thalamic hyperconnectivity; notably, this finding cannot be observed in the static connectivity analysis. Finally, in post-hoc analyses we observed that the relationships between sub-cortical low frequency power and connectivity with sensory networks is altered in patients, suggesting different functional interactions between sub-cortical nuclei and sensorimotor cortex during specific connectivity states. While important differences between patients with schizophrenia and healthy controls have been identified, one should interpret the results with caution given the history of medication in patients. Taken together, our results support and expand current knowledge regarding dysconnectivity in schizophrenia, and strongly advocate the use of dynamic analyses to better account for and understand functional connectivity differences. PMID:25161896

Cognitive and physical functions related to the level of supervision and dependence in the toileting of stroke patients.

PubMed

Sato, Atsushi; Okuda, Yutaka; Fujita, Takaaki; Kimura, Norihiko; Hoshina, Noriyuki; Kato, Sayaka; Tanaka, Shigenari

2016-01-01

This study aimed to clarify which cognitive and physical factors are associated with the need for toileting assistance in stroke patients and to calculate cut-off values for discriminating between independent supervision and dependent toileting ability. This cross-sectional study included 163 first-stroke patients in nine convalescent rehabilitation wards. Based on their FIM Ⓡ instrument score for toileting, the patients were divided into an independent-supervision group and a dependent group. Multiple logistic regression analysis and receiver operating characteristic analysis were performed to identify factors related to toileting performance. The Minimental State Examination (MMSE); the Stroke Impairment Assessment Set (SIAS) score for the affected lower limb, speech, and visuospatial functions; and the Functional Assessment for Control of Trunk (FACT) were analyzed as independent variables. The multiple logistic regression analysis showed that the FIM Ⓡ instrument score for toileting was associated with the SIAS score for the affected lower limb function, MMSE, and FACT. On receiver operating characteristic analysis, the SIAS score for the affected lower limb function cut-off value was 8/7 points, the MMSE cut-off value was 25/24 points, and the FACT cut-off value was 14/13 points. Affected lower limb function, cognitive function, and trunk function were related with the need for toileting assistance. These cut-off values may be useful for judging whether toileting assistance is needed in stroke patients.

The convergence of the order sequence and the solution function sequence on fractional partial differential equation

NASA Astrophysics Data System (ADS)

Rusyaman, E.; Parmikanti, K.; Chaerani, D.; Asefan; Irianingsih, I.

2018-03-01

One of the application of fractional ordinary differential equation is related to the viscoelasticity, i.e., a correlation between the viscosity of fluids and the elasticity of solids. If the solution function develops into function with two or more variables, then its differential equation must be changed into fractional partial differential equation. As the preliminary study for two variables viscoelasticity problem, this paper discusses about convergence analysis of function sequence which is the solution of the homogenous fractional partial differential equation. The method used to solve the problem is Homotopy Analysis Method. The results show that if given two real number sequences (αn) and (βn) which converge to α and β respectively, then the solution function sequences of fractional partial differential equation with order (αn, βn) will also converge to the solution function of fractional partial differential equation with order (α, β).

The Generality of Interview-Informed Functional Analyses: Systematic Replications in School and Home

ERIC Educational Resources Information Center

Santiago, Joana L.; Hanley, Gregory P.; Moore, Keira; Jin, C. Sandy

2016-01-01

Behavioral interventions preceded by a functional analysis have been proven efficacious in treating severe problem behavior associated with autism. There is, however, a lack of research showing socially validated outcomes when assessment and treatment procedures are conducted by ecologically relevant individuals in typical settings. In this study,…

Is the Derivative a Function? If So, How Do We Teach It?

ERIC Educational Resources Information Center

Park, Jungeun

2015-01-01

This study investigated features of instructors' classroom discourse on the derivative with the commognitive lens. The analysis focused on how three calculus instructors addressed the derivative as a point-specific value and as a function in the beginning lessons about the derivative. The results show that (a) the instructors frequently used…

Student Distractor Choices on the Mathematics Virginia Standards of Learning Middle School Assessments

ERIC Educational Resources Information Center

Lewis, Virginia Vimpeny

2011-01-01

Number Concepts; Measurement; Geometry; Probability; Statistics; and Patterns, Functions and Algebra. Procedural Errors were further categorized into the following content categories: Computation; Measurement; Statistics; and Patterns, Functions, and Algebra. The results of the analysis showed the main sources of error for 6th, 7th, and 8th…

Informatic and genomic analysis of melanocyte cDNA libraries as a resource for the study of melanocyte development and function.

PubMed

Baxter, Laura L; Hsu, Benjamin J; Umayam, Lowell; Wolfsberg, Tyra G; Larson, Denise M; Frith, Martin C; Kawai, Jun; Hayashizaki, Yoshihide; Carninci, Piero; Pavan, William J

2007-06-01

As part of the RIKEN mouse encyclopedia project, two cDNA libraries were prepared from melanocyte-derived cell lines, using techniques of full-length clone selection and subtraction/normalization to enrich for rare transcripts. End sequencing showed that these libraries display over 83% complete coding sequence at the 5' end and 96-97% complete coding sequence at the 3' end. Evaluation of the libraries, derived from B16F10Y tumor cells and melan-c cells, revealed that they contain clones for a majority of the genes previously demonstrated to function in melanocyte biology. Analysis of genomic locations for transcripts revealed that the distribution of melanocyte genes is non-random throughout the genome. Three genomic regions identified that showed significant clustering of melanocyte-expressed genes contain one or more genes previously shown to regulate melanocyte development or function. A catalog of genes expressed in these libraries is presented, providing a valuable resource of cDNA clones and sequence information that can be used for identification of new genes important for melanocyte development, function, and disease.

Correlation between the structure modification and conductivity of 3 MeV Si ion-irradiated polyimide

NASA Astrophysics Data System (ADS)

Sun, Youmei; Zhu, Zhiyong; Li, Changlin

2002-05-01

The surface modification of the polyimide (PI/Kapton) films was carried out by 3 MeV Si + implantation to fluences ranging from 1×10 12 to 1.25×10 15 ions/cm 2. Fourier transform infrared (FTIR), Raman and ultraviolet/visible (UV/Vis) spectroscopes were employed to investigate the chemical degradation of function groups in the irradiated layer. FTIR results show that the absorbance of typical function group decreases exponentially as a function of fluence. The damage cross-section of typical bonds of PI was evaluated from the FTIR spectra. Raman analysis shows the absorbed dose for destruction of all function groups is above 218 MGy. The red shifting of the absorption edge from UV to visible reveals the band gap closing which results from increase of the cluster size. The production efficiency of the chromophores was discussed according to UV/Vis analysis. Irradiation dramatically enhances the electrical conductivity and the sheet resistivity in our experiment descends nearly 10 orders of magnitude compared with its intrinsic value.

AIRE is a critical spindle-associated protein in embryonic stem cells

PubMed Central

Gu, Bin; Lambert, Jean-Philippe; Cockburn, Katie; Gingras, Anne-Claude; Rossant, Janet

2017-01-01

Embryonic stem (ES) cells go though embryo-like cell cycles regulated by specialized molecular mechanisms. However, it is not known whether there are ES cell-specific mechanisms regulating mitotic fidelity. Here we showed that Autoimmune Regulator (Aire), a transcription coordinator involved in immune tolerance processes, is a critical spindle-associated protein in mouse ES(mES) cells. BioID analysis showed that AIRE associates with spindle-associated proteins in mES cells. Loss of function analysis revealed that Aire was important for centrosome number regulation and spindle pole integrity specifically in mES cells. We also identified the c-terminal LESLL motif as a critical motif for AIRE’s mitotic function. Combined maternal and zygotic knockout further revealed Aire’s critical functions for spindle assembly in preimplantation embryos. These results uncovered a previously unappreciated function for Aire and provide new insights into the biology of stem cell proliferation and potential new angles to understand fertility defects in humans carrying Aire mutations. DOI: http://dx.doi.org/10.7554/eLife.28131.001 PMID:28742026

Computational screening of functional groups for capture of toxic industrial chemicals in porous materials.

PubMed

Kim, Ki Chul; Fairen-Jimenez, David; Snurr, Randall Q

2017-12-06

A thermodynamic analysis using quantum chemical methods was carried out to identify optimal functional group candidates that can be included in metal-organic frameworks and activated carbons for the selective capture of toxic industrial chemicals (TICs) in humid air. We calculated the binding energies of 14 critical TICs plus water with a series of 10 functional groups attached to a naphthalene ring model. Using vibrational calculations, the free energies of adsorption were calculated in addition to the binding energies. Our results show that, in these systems, the binding energies and free energies follow similar trends. We identified copper(i) carboxylate as the optimal functional group (among those studied) for the selective binding of the majority of the TICs in humid air, and this functional group exhibits especially strong binding for sulfuric acid. Further thermodynamic analysis shows that the presence of water weakens the binding strength of sulfuric acid with the copper carboxylate group. Our calculations predict that functionalization of aromatic rings would be detrimental to selective capture of COCl 2 , CO 2 , and Cl 2 under humid conditions. Finally, we found that forming an ionic complex, H 3 O + HSO 4 - , between H 2 SO 4 and H 2 O via proton transfer is not favorable on copper carboxylate.

Loss of Intrinsic Organization of Cerebellar Networks in Spinocerebellar Ataxia Type 1: Correlates with Disease Severity and Duration

PubMed Central

Peri, Eitan; Chen, E. Elinor; Ben-Jacob, Eshel; Gomez, Christopher M.

2011-01-01

The spinocerebellar ataxias (SCAs) are a genetically heterogeneous group of cerebellar degenerative disorders, characterized by progressive gait unsteadiness, hand incoordination, and dysarthria. The mutational mechanism in SCA1, a dominantly inherited form of SCA, consists of an expanded trinucleotide CAG repeat. In SCA1, there is loss of Purkinje cells, neuronal loss in dentate nucleus, olives, and pontine nuclei. In the present study, we sought to apply intrinsic functional connectivity analysis combined with diffusion tensor imaging to define the state of cerebellar connectivity in SCA1. Our results on the intrinsic functional connectivity in lateral cerebellum and thalamus showed progressive organizational changes in SCA1 noted as a progressive increase in the absolute value of the correlation coefficients. In the lateral cerebellum, the anatomical organization of functional clusters seen as parasagittal bands in controls is lost, changing to a patchy appearance in SCA1. Lastly, only fractional anisotropy in the superior peduncle and changes in functional organization in thalamus showed a linear dependence to duration and severity of disease. The present pilot work represents an initial effort describing connectivity biomarkers of disease progression in SCA1. The functional changes detected with intrinsic functional analysis and diffusion tensor imaging suggest that disease progression can be analyzed as a disconnection syndrome. PMID:20886327

Altered brain functional networks in people with Internet gaming disorder: Evidence from resting-state fMRI.

PubMed

Wang, Lingxiao; Wu, Lingdan; Lin, Xiao; Zhang, Yifen; Zhou, Hongli; Du, Xiaoxia; Dong, Guangheng

2016-08-30

Although numerous neuroimaging studies have detected structural and functional abnormality in specific brain regions and connections in subjects with Internet gaming disorder (IGD), the topological organization of the whole-brain network in IGD remain unclear. In this study, we applied graph theoretical analysis to explore the intrinsic topological properties of brain networks in Internet gaming disorder (IGD). 37 IGD subjects and 35 matched healthy control (HC) subjects underwent a resting-state functional magnetic resonance imaging scan. The functional networks were constructed by thresholding partial correlation matrices of 90 brain regions. Then we applied graph-based approaches to analysis their topological attributes, including small-worldness, nodal metrics, and efficiency. Both IGD and HC subjects show efficient and economic brain network, and small-world topology. Although there was no significant group difference in global topology metrics, the IGD subjects showed reduced regional centralities in the prefrontal cortex, left posterior cingulate cortex, right amygdala, and bilateral lingual gyrus, and increased functional connectivity in sensory-motor-related brain networks compared to the HC subjects. These results imply that people with IGD may be associated with functional network dysfunction, including impaired executive control and emotional management, but enhanced coordination among visual, sensorimotor, auditory and visuospatial systems. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

The interval testing procedure: A general framework for inference in functional data analysis.

PubMed

Pini, Alessia; Vantini, Simone

2016-09-01

We introduce in this work the Interval Testing Procedure (ITP), a novel inferential technique for functional data. The procedure can be used to test different functional hypotheses, e.g., distributional equality between two or more functional populations, equality of mean function of a functional population to a reference. ITP involves three steps: (i) the representation of data on a (possibly high-dimensional) functional basis; (ii) the test of each possible set of consecutive basis coefficients; (iii) the computation of the adjusted p-values associated to each basis component, by means of a new strategy here proposed. We define a new type of error control, the interval-wise control of the family wise error rate, particularly suited for functional data. We show that ITP is provided with such a control. A simulation study comparing ITP with other testing procedures is reported. ITP is then applied to the analysis of hemodynamical features involved with cerebral aneurysm pathology. ITP is implemented in the fdatest R package. © 2016, The International Biometric Society.

Functional Regression Models for Epistasis Analysis of Multiple Quantitative Traits.

PubMed

Zhang, Futao; Xie, Dan; Liang, Meimei; Xiong, Momiao

2016-04-01

To date, most genetic analyses of phenotypes have focused on analyzing single traits or analyzing each phenotype independently. However, joint epistasis analysis of multiple complementary traits will increase statistical power and improve our understanding of the complicated genetic structure of the complex diseases. Despite their importance in uncovering the genetic structure of complex traits, the statistical methods for identifying epistasis in multiple phenotypes remains fundamentally unexplored. To fill this gap, we formulate a test for interaction between two genes in multiple quantitative trait analysis as a multiple functional regression (MFRG) in which the genotype functions (genetic variant profiles) are defined as a function of the genomic position of the genetic variants. We use large-scale simulations to calculate Type I error rates for testing interaction between two genes with multiple phenotypes and to compare the power with multivariate pairwise interaction analysis and single trait interaction analysis by a single variate functional regression model. To further evaluate performance, the MFRG for epistasis analysis is applied to five phenotypes of exome sequence data from the NHLBI's Exome Sequencing Project (ESP) to detect pleiotropic epistasis. A total of 267 pairs of genes that formed a genetic interaction network showed significant evidence of epistasis influencing five traits. The results demonstrate that the joint interaction analysis of multiple phenotypes has a much higher power to detect interaction than the interaction analysis of a single trait and may open a new direction to fully uncovering the genetic structure of multiple phenotypes.

Effect of Finite Computational Domain on Turbulence Scaling Law in Both Physical and Spectral Spaces

NASA Technical Reports Server (NTRS)

Hou, Thomas Y.; Wu, Xiao-Hui; Chen, Shiyi; Zhou, Ye

1998-01-01

The well-known translation between the power law of energy spectrum and that of the correlation function or the second order structure function has been widely used in analyzing random data. Here, we show that the translation is valid only in proper scaling regimes. The regimes of valid translation are different for the correlation function and the structure function. Indeed, they do not overlap. Furthermore, in practice, the power laws exist only for a finite range of scales. We show that this finite range makes the translation inexact even in the proper scaling regime. The error depends on the scaling exponent. The current findings are applicable to data analysis in fluid turbulence and other stochastic systems.

Integrated Analysis and Visualization of Group Differences in Structural and Functional Brain Connectivity: Applications in Typical Ageing and Schizophrenia.

PubMed

Langen, Carolyn D; White, Tonya; Ikram, M Arfan; Vernooij, Meike W; Niessen, Wiro J

2015-01-01

Structural and functional brain connectivity are increasingly used to identify and analyze group differences in studies of brain disease. This study presents methods to analyze uni- and bi-modal brain connectivity and evaluate their ability to identify differences. Novel visualizations of significantly different connections comparing multiple metrics are presented. On the global level, "bi-modal comparison plots" show the distribution of uni- and bi-modal group differences and the relationship between structure and function. Differences between brain lobes are visualized using "worm plots". Group differences in connections are examined with an existing visualization, the "connectogram". These visualizations were evaluated in two proof-of-concept studies: (1) middle-aged versus elderly subjects; and (2) patients with schizophrenia versus controls. Each included two measures derived from diffusion weighted images and two from functional magnetic resonance images. The structural measures were minimum cost path between two anatomical regions according to the "Statistical Analysis of Minimum cost path based Structural Connectivity" method and the average fractional anisotropy along the fiber. The functional measures were Pearson's correlation and partial correlation of mean regional time series. The relationship between structure and function was similar in both studies. Uni-modal group differences varied greatly between connectivity types. Group differences were identified in both studies globally, within brain lobes and between regions. In the aging study, minimum cost path was highly effective in identifying group differences on all levels; fractional anisotropy and mean correlation showed smaller differences on the brain lobe and regional levels. In the schizophrenia study, minimum cost path and fractional anisotropy showed differences on the global level and within brain lobes; mean correlation showed small differences on the lobe level. Only fractional anisotropy and mean correlation showed regional differences. The presented visualizations were helpful in comparing and evaluating connectivity measures on multiple levels in both studies.

Computational biomechanics changes our view on insect head evolution.

PubMed

Blanke, Alexander; Watson, Peter J; Holbrey, Richard; Fagan, Michael J

2017-02-08

Despite large-scale molecular attempts, the relationships of the basal winged insect lineages dragonflies, mayflies and neopterans, are still unresolved. Other data sources, such as morphology, suffer from unclear functional dependencies of the structures considered, which might mislead phylogenetic inference. Here, we assess this problem by combining for the first time biomechanics with phylogenetics using two advanced engineering techniques, multibody dynamics analysis and finite-element analysis, to objectively identify functional linkages in insect head structures which have been used traditionally to argue basal winged insect relationships. With a biomechanical model of unprecedented detail, we are able to investigate the mechanics of morphological characters under biologically realistic load, i.e. biting. We show that a range of head characters, mainly ridges, endoskeletal elements and joints, are indeed mechanically linked to each other. An analysis of character state correlation in a morphological data matrix focused on head characters shows highly significant correlation of these mechanically linked structures. Phylogenetic tree reconstruction under different data exclusion schemes based on the correlation analysis unambiguously supports a sistergroup relationship of dragonflies and mayflies. The combination of biomechanics and phylogenetics as it is proposed here could be a promising approach to assess functional dependencies in many organisms to increase our understanding of phenotypic evolution. © 2017 The Author(s).

Functional and Structural Changes in a Canine Model of Hereditary Primary Angle-Closure Glaucoma

PubMed Central

Kecova, Helga; Harper, Matthew M.; Nilaweera, Wijitha; Kuehn, Markus H.; Kardon, Randy H.

2010-01-01

Purpose. To characterize functional and structural changes in a canine model of hereditary primary angle-closure glaucoma. Methods. Intraocular pressure (IOP) was evaluated with tonometry in a colony of glaucomatous dogs at 8, 15, 18, 20, and 30 months of age. Retinal function was evaluated using electroretinography (scotopic, photopic, and pattern). Examination of anterior segment structures was performed using gonioscopy and high-frequency ultrasonography (HFU). Results. A gradual rise in IOP was observed with an increase in age: 8 months, 14 mm Hg (median value); 15 months, 15.5 mm Hg; 18 months, 17.5 mm Hg; 20 months, 24 mm Hg; 30 months, 36 mm Hg. Provocative testing with mydriatic agents (tropicamide and atropine 1%) caused significant increases in IOP (35% and 50%, respectively). HFU analysis showed complete collapse of iridocorneal angles by 20 months of age. Scotopic and photopic ERG analysis did not reveal significant deficits, but pattern ERG analysis showed significantly reduced amplitudes in glaucomatous dogs (glaucoma, 3.5 ± 0.4 μV; control, 6.2 ± 0.3 μV; P = 0.004; Student's t-test). Histologic analysis revealed collapse of the iridocorneal angle, posterior bowing of the lamina cribrosa, swelling and loss of large retinal ganglion cells, increased glial reactivity, and increased thickening of the lamina cribrosa. Conclusions. Canine hereditary angle-closure glaucoma is characterized by a progressive increase in intraocular pressure, loss of optic nerve function, and retinal ganglion cell loss. PMID:19661222

Time-Frequency Based Instantaneous Frequency Estimation of Sparse Signals from an Incomplete Set of Samples

DTIC Science & Technology

2014-06-17

100 0 2 4 Wigner distribution 0 50 100 0 0.5 1 Auto-correlation function 0 50 100 0 2 4 L- Wigner distribution 0 50 100 0 0.5 1 Auto-correlation function ...bilinear or higher order autocorrelation functions will increase the number of missing samples, the analysis shows that accurate instantaneous...frequency estimation can be achieved even if we deal with only few samples, as long as the auto-correlation function is properly chosen to coincide with

Functional annotation of the vlinc class of non-coding RNAs using systems biology approach

PubMed Central

Laurent, Georges St.; Vyatkin, Yuri; Antonets, Denis; Ri, Maxim; Qi, Yao; Saik, Olga; Shtokalo, Dmitry; de Hoon, Michiel J.L.; Kawaji, Hideya; Itoh, Masayoshi; Lassmann, Timo; Arner, Erik; Forrest, Alistair R.R.; Nicolas, Estelle; McCaffrey, Timothy A.; Carninci, Piero; Hayashizaki, Yoshihide; Wahlestedt, Claes; Kapranov, Philipp

2016-01-01

Functionality of the non-coding transcripts encoded by the human genome is the coveted goal of the modern genomics research. While commonly relied on the classical methods of forward genetics, integration of different genomics datasets in a global Systems Biology fashion presents a more productive avenue of achieving this very complex aim. Here we report application of a Systems Biology-based approach to dissect functionality of a newly identified vast class of very long intergenic non-coding (vlinc) RNAs. Using highly quantitative FANTOM5 CAGE dataset, we show that these RNAs could be grouped into 1542 novel human genes based on analysis of insulators that we show here indeed function as genomic barrier elements. We show that vlincRNAs genes likely function in cis to activate nearby genes. This effect while most pronounced in closely spaced vlincRNA–gene pairs can be detected over relatively large genomic distances. Furthermore, we identified 101 vlincRNA genes likely involved in early embryogenesis based on patterns of their expression and regulation. We also found another 109 such genes potentially involved in cellular functions also happening at early stages of development such as proliferation, migration and apoptosis. Overall, we show that Systems Biology-based methods have great promise for functional annotation of non-coding RNAs. PMID:27001520

Image analysis for the automated estimation of clonal growth and its application to the growth of smooth muscle cells.

PubMed

Gavino, V C; Milo, G E; Cornwell, D G

1982-03-01

Image analysis was used for the automated measurement of colony frequency (f) and colony diameter (d) in cultures of smooth muscle cells, Initial studies with the inverted microscope showed that number of cells (N) in a colony varied directly with d: log N = 1.98 log d - 3.469 Image analysis generated the complement of a cumulative distribution for f as a function of d. The number of cells in each segment of the distribution function was calculated by multiplying f and the average N for the segment. These data were displayed as a cumulative distribution function. The total number of colonies (fT) and the total number of cells (NT) were used to calculate the average colony size (NA). Population doublings (PD) were then expressed as log2 NA. Image analysis confirmed previous studies in which colonies were sized and counted with an inverted microscope. Thus, image analysis is a rapid and automated technique for the measurement of clonal growth.

The Researches on Damage Detection Method for Truss Structures

NASA Astrophysics Data System (ADS)

Wang, Meng Hong; Cao, Xiao Nan

2018-06-01

This paper presents an effective method to detect damage in truss structures. Numerical simulation and experimental analysis were carried out on a damaged truss structure under instantaneous excitation. The ideal excitation point and appropriate hammering method were determined to extract time domain signals under two working conditions. The frequency response function and principal component analysis were used for data processing, and the angle between the frequency response function vectors was selected as a damage index to ascertain the location of a damaged bar in the truss structure. In the numerical simulation, the time domain signal of all nodes was extracted to determine the location of the damaged bar. In the experimental analysis, the time domain signal of a portion of the nodes was extracted on the basis of an optimal sensor placement method based on the node strain energy coefficient. The results of the numerical simulation and experimental analysis showed that the damage detection method based on the frequency response function and principal component analysis could locate the damaged bar accurately.

Nonstandard Analysis and Shock Wave Jump Conditions in a One-Dimensional Compressible Gas

NASA Technical Reports Server (NTRS)

Baty, Roy S.; Farassat, Fereidoun; Hargreaves, John

2007-01-01

Nonstandard analysis is a relatively new area of mathematics in which infinitesimal numbers can be defined and manipulated rigorously like real numbers. This report presents a fairly comprehensive tutorial on nonstandard analysis for physicists and engineers with many examples applicable to generalized functions. To demonstrate the power of the subject, the problem of shock wave jump conditions is studied for a one-dimensional compressible gas. It is assumed that the shock thickness occurs on an infinitesimal interval and the jump functions in the thermodynamic and fluid dynamic parameters occur smoothly across this interval. To use conservations laws, smooth pre-distributions of the Dirac delta measure are applied whose supports are contained within the shock thickness. Furthermore, smooth pre-distributions of the Heaviside function are applied which vary from zero to one across the shock wave. It is shown that if the equations of motion are expressed in nonconservative form then the relationships between the jump functions for the flow parameters may be found unambiguously. The analysis yields the classical Rankine-Hugoniot jump conditions for an inviscid shock wave. Moreover, non-monotonic entropy jump conditions are obtained for both inviscid and viscous flows. The report shows that products of generalized functions may be defined consistently using nonstandard analysis; however, physically meaningful products of generalized functions must be determined from the physics of the problem and not the mathematical form of the governing equations.

Sectorial technetium-99m-dimercaptosuccinic acid scintigraphy for monitoring the effect of extracorporeal piezoelectric lithotripsy for calyceal calculi on regional renal function.

PubMed

Al-Tawheed, A; Al-Awadi, K A; Kehinde, E O; Loutfi, I; Abdul-Haleem, H; Al-Mohannadi, S

2003-01-01

To apply a semiquantitative method for analysis of technetium-99m-dimercaptosuccinic acid ((99m)Tc-DMSA) renal scintigraphy for monitoring the effect of extracorporeal piezoelectric lithotripsy (EPL) in patients with calyceal stones on regional kidney function and to check whether EPL had caused any deleterious effect on the target calyceal renal parenchymal function. Forty patients (mean age 35 years) suffering from calyceal stones documented by abdominal plain radiography, intravenous urogram or abdominal ultrasound were studied. All patients were treated by EPL. (99m)Tc-DMSA scan was performed before and 4 weeks after EPL. Sector analysis involved calculation of the relative function of the target calyx to the function of the ipsilateral kidney and the relative function of the treated kidney to global renal function. The stone sizes were 6-11 mm in diameter and 11 were located in the upper, 13 in the middle and 16 in the lower calyx. After EPL, the overall stone clearance rate was 85% (100% for calculi in the upper and middle calyces, 62% for lower calyces). The sector analysis did not show statistically significant change of the relative regional (calyceal) or whole kidney function between the pre- and post-EPL (99m)Tc-DMSA scans. Using sector analysis, EPL appeared to be a safe modality and its usage was not associated with any untoward effect on calyceal or whole kidney function. Sector analysis of (99m)Tc-DMSA renal scan is a simple semiquantitative method for monitoring regional changes of kidney function after EPL for treatment of calyceal stone. Copyright 2003 S. Karger AG, Basel

Unified Sequence-Based Association Tests Allowing for Multiple Functional Annotations and Meta-analysis of Noncoding Variation in Metabochip Data.

PubMed

He, Zihuai; Xu, Bin; Lee, Seunggeun; Ionita-Laza, Iuliana

2017-09-07

Substantial progress has been made in the functional annotation of genetic variation in the human genome. Integrative analysis that incorporates such functional annotations into sequencing studies can aid the discovery of disease-associated genetic variants, especially those with unknown function and located outside protein-coding regions. Direct incorporation of one functional annotation as weight in existing dispersion and burden tests can suffer substantial loss of power when the functional annotation is not predictive of the risk status of a variant. Here, we have developed unified tests that can utilize multiple functional annotations simultaneously for integrative association analysis with efficient computational techniques. We show that the proposed tests significantly improve power when variant risk status can be predicted by functional annotations. Importantly, when functional annotations are not predictive of risk status, the proposed tests incur only minimal loss of power in relation to existing dispersion and burden tests, and under certain circumstances they can even have improved power by learning a weight that better approximates the underlying disease model in a data-adaptive manner. The tests can be constructed with summary statistics of existing dispersion and burden tests for sequencing data, therefore allowing meta-analysis of multiple studies without sharing individual-level data. We applied the proposed tests to a meta-analysis of noncoding rare variants in Metabochip data on 12,281 individuals from eight studies for lipid traits. By incorporating the Eigen functional score, we detected significant associations between noncoding rare variants in SLC22A3 and low-density lipoprotein and total cholesterol, associations that are missed by standard dispersion and burden tests. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Spectral analysis of the structure of ultradispersed diamonds

NASA Astrophysics Data System (ADS)

Uglov, V. V.; Shimanski, V. I.; Rusalsky, D. P.; Samtsov, M. P.

2008-07-01

The structure of ultradispersed diamonds (UDD) is studied by spectral methods. The presence of diamond crystal phase in the UDD is found based on x-ray analysis and Raman spectra. The Raman spectra also show sp2-and sp3-hybridized carbon. Analysis of IR absorption spectra suggests that the composition of functional groups present in the particles changes during the treatment.

A novel analysis method for near infrared spectroscopy based on Hilbert-Huang transform

NASA Astrophysics Data System (ADS)

Zhou, Zhenyu; Yang, Hongyu; Liu, Yun; Ruan, Zongcai; Luo, Qingming; Gong, Hui; Lu, Zuhong

2007-05-01

Near Infrared Imager (NIRI) has been widely used to access the brain functional activity non-invasively. We use a portable, multi-channel and continuous-wave NIR topography instrument to measure the concentration changes of each hemoglobin species and map cerebral cortex functional activation. By extracting some essential features from the BOLD signals, optical tomography is able to be a new way of neuropsychological studies. Fourier spectral analysis provides a common framework for examining the distribution of global energy in the frequency domain. However, this method assumes that the signal should be stationary, which limits its application in non-stationary system. The hemoglobin species concentration changes are of such kind. In this work we develop a new signal processing method using Hilbert-Huang transform to perform spectral analysis of the functional NIRI signals. Compared with wavelet based multi-resolution analysis (MRA), we demonstrated the extraction of task related signal for observation of activation in the prefrontal cortex (PFC) in vision stimulation experiment. This method provides a new analysis tool for functional NIRI signals. Our experimental results show that the proposed approach provides the unique method for reconstructing target signal without losing original information and enables us to understand the episode of functional NIRI more precisely.

Functionalized mesoporous silica nanoparticles for oral delivery of budesonide

NASA Astrophysics Data System (ADS)

Yoncheva, K.; Popova, M.; Szegedi, A.; Mihaly, J.; Tzankov, B.; Lambov, N.; Konstantinov, S.; Tzankova, V.; Pessina, F.; Valoti, M.

2014-03-01

Non-functionalized and amino-functionalized mesoporous silica nanoparticle were loaded with anti-inflammatory drug budesonide and additionally post-coated with bioadhesive polymer (carbopol). TEM images showed spherical shape of the nanoparticles and slightly higher polydispersity after coating with carbopol. Nitrogen physisorption and thermogravimetic analysis revealed that more efficient loading and incorporation into the pores of nanoparticles was achieved with the amino-functionalized silica carrier. Infrared spectra indicated that the post-coating of these nanoparticles with carbopol led to the formation of bond between amino groups of the functionalized carrier and carboxyl groups of carbopol. The combination of amino-functionalization of the carrier with the post-coating of the nanoparticles sustained budesonide release. Further, an in vitro model of inflammatory bowel disease showed that the cytoprotective effect of budesonide loaded in the post-coated silica nanoparticles on damaged HT-29 cells was more pronounced compared to the cytoprotection obtained with pure budesonide.

Functional analysis of Paracoccidioides brasiliensis 14-3-3 adhesin expressed in Saccharomyces cerevisiae.

PubMed

Assato, Patricia Akemi; da Silva, Julhiany de Fátima; de Oliveira, Haroldo Cesar; Marcos, Caroline Maria; Rossi, Danuza; Valentini, Sandro Roberto; Mendes-Giannini, Maria José Soares; Zanelli, Cleslei Fernando; Fusco-Almeida, Ana Marisa

2015-11-04

14-3-3 proteins comprise a family of eukaryotic multifunctional proteins involved in several cellular processes. The Pb14-3-3 of Paracoccidioides brasiliensis seems to play an important role in the Paracoccidioides-host interaction. Paracoccidioides brasiliensis is an etiological agent of paracoccidioidomycosis, which is a systemic mycosis that is endemic in Latin America. In the initial steps of the infection, Paracoccidioides spp. synthetizes adhesins that allow it to adhere and invade host cells. Therefore, the aim of this work was to perform a functional analysis of Pb14-3-3 using Saccharomyces cerevisiae as a model. The functional analysis of Pb14-3-3 was performed in S. cerevisiae, and it was found that Pb14-3-3 partially complemented S. cerevisiae proteins Bmh1p and Bmh2p, which are recognized as two yeast 14-3-3 homologues. When we evaluated the adhesion profile of S. cerevisiae transformants, Pb14-3-3 acted as an adhesin in S. cerevisiae; however, Bmh1p did not show this function. The influence of Pb14-3-3 in S. cerevisiae ergosterol pathway was also evaluated and our results showed that Pb14-3-3 up-regulates genes involved in ergosterol biosynthesis. Our data showed that Pb14-3-3 was able to partially complement Bmh1p and Bmh2p proteins in S. cerevisiae; however, we suggest that Pb14-3-3 has a differential role as an adhesin. In addition, Pb-14-3-3 may be involved in Paracoccidioides spp. ergosterol biosynthesis which makes it an interest as a therapeutic target.

Pituitary gland volumes in bipolar disorder.

PubMed

Clark, Ian A; Mackay, Clare E; Goodwin, Guy M

2014-12-01

Bipolar disorder has been associated with increased Hypothalamic-Pituitary-Adrenal axis function. The mechanism is not well understood, but there may be associated increases in pituitary gland volume (PGV) and these small increases may be functionally significant. However, research investigating PGV in bipolar disorder reports mixed results. The aim of the current study was twofold. First, to assess PGV in two novel samples of patients with bipolar disorder and matched healthy controls. Second, to perform a meta-analysis comparing PGV across a larger sample of patients and matched controls. Sample 1 consisted of 23 established patients and 32 matched controls. Sample 2 consisted of 39 medication-naïve patients and 42 matched controls. PGV was measured on structural MRI scans. Seven further studies were identified comparing PGV between patients and matched controls (total n; 244 patients, 308 controls). Both novel samples showed a small (approximately 20mm(3) or 4%), but non-significant, increase in PGV in patients. Combining the two novel samples showed a significant association of age and PGV. Meta-analysis showed a trend towards a larger pituitary gland in patients (effect size: .23, CI: -.14, .59). While results suggest a possible small difference in pituitary gland volume between patients and matched controls, larger mega-analyses with sample sizes greater even than those used in the current meta-analysis are still required. There is a small but potentially functionally significant increase in PGV in patients with bipolar disorder compared to controls. Results demonstrate the difficulty of finding potentially important but small effects in functional brain disorders. Copyright © 2014 Elsevier B.V. All rights reserved.

A toolbox to visually explore cerebellar shape changes in cerebellar disease and dysfunction.

PubMed

Abulnaga, S Mazdak; Yang, Zhen; Carass, Aaron; Kansal, Kalyani; Jedynak, Bruno M; Onyike, Chiadi U; Ying, Sarah H; Prince, Jerry L

2016-02-27

The cerebellum plays an important role in motor control and is also involved in cognitive processes. Cerebellar function is specialized by location, although the exact topographic functional relationship is not fully understood. The spinocerebellar ataxias are a group of neurodegenerative diseases that cause regional atrophy in the cerebellum, yielding distinct motor and cognitive problems. The ability to study the region-specific atrophy patterns can provide insight into the problem of relating cerebellar function to location. In an effort to study these structural change patterns, we developed a toolbox in MATLAB to provide researchers a unique way to visually explore the correlation between cerebellar lobule shape changes and function loss, with a rich set of visualization and analysis modules. In this paper, we outline the functions and highlight the utility of the toolbox. The toolbox takes as input landmark shape representations of subjects' cerebellar substructures. A principal component analysis is used for dimension reduction. Following this, a linear discriminant analysis and a regression analysis can be performed to find the discriminant direction associated with a specific disease type, or the regression line of a specific functional measure can be generated. The characteristic structural change pattern of a disease type or of a functional score is visualized by sampling points on the discriminant or regression line. The sampled points are used to reconstruct synthetic cerebellar lobule shapes. We showed a few case studies highlighting the utility of the toolbox and we compare the analysis results with the literature.

A toolbox to visually explore cerebellar shape changes in cerebellar disease and dysfunction

NASA Astrophysics Data System (ADS)

Abulnaga, S. Mazdak; Yang, Zhen; Carass, Aaron; Kansal, Kalyani; Jedynak, Bruno M.; Onyike, Chiadi U.; Ying, Sarah H.; Prince, Jerry L.

2016-03-01

The cerebellum plays an important role in motor control and is also involved in cognitive processes. Cerebellar function is specialized by location, although the exact topographic functional relationship is not fully understood. The spinocerebellar ataxias are a group of neurodegenerative diseases that cause regional atrophy in the cerebellum, yielding distinct motor and cognitive problems. The ability to study the region-specific atrophy patterns can provide insight into the problem of relating cerebellar function to location. In an effort to study these structural change patterns, we developed a toolbox in MATLAB to provide researchers a unique way to visually explore the correlation between cerebellar lobule shape changes and function loss, with a rich set of visualization and analysis modules. In this paper, we outline the functions and highlight the utility of the toolbox. The toolbox takes as input landmark shape representations of subjects' cerebellar substructures. A principal component analysis is used for dimension reduction. Following this, a linear discriminant analysis and a regression analysis can be performed to find the discriminant direction associated with a specific disease type, or the regression line of a specific functional measure can be generated. The characteristic structural change pattern of a disease type or of a functional score is visualized by sampling points on the discriminant or regression line. The sampled points are used to reconstruct synthetic cerebellar lobule shapes. We showed a few case studies highlighting the utility of the toolbox and we compare the analysis results with the literature.

Amide I vibrational circular dichroism of dipeptide: Conformation dependence and fragment analysis

NASA Astrophysics Data System (ADS)

Choi, Jun-Ho; Cho, Minhaeng

2004-03-01

The amide I vibrational circular dichroic response of alanine dipeptide analog (ADA) was theoretically investigated and the density functional theory calculation and fragment analysis results are presented. A variety of vibrational spectroscopic properties, local and normal mode frequencies, coupling constant, dipole, and rotational strengths, are calculated by varying two dihedral angles determining the three-dimensional ADA conformation. Considering two monopeptide fragments separately, we show that the amide I vibrational circular dichroism of the ADA can be quantitatively predicted. For several representative conformations of the model ADA, vibrational circular dichroism spectra are calculated by using both the density functional theory calculation and fragment analysis methods.

Does the use of Nintendo Wii SportsTM improve arm function? Trial of WiiTM in Stroke: a randomized controlled trial and economics analysis.

PubMed

Adie, Katja; Schofield, Christine; Berrow, Margie; Wingham, Jennifer; Humfryes, John; Pritchard, Colin; James, Martin; Allison, Rhoda

2017-02-01

The Trial of Wii™ in Stroke investigated the efficacy of using the Nintendo Wii Sports™ (Wii TM ) to improve affected arm function after stroke. Multicentre, pragmatic, parallel group, randomized controlled trial. Home-based rehabilitation. A total of 240 participants aged 24-90 years with arm weakness following a stroke within the previous six months. Participants were randomly assigned to exercise daily for six weeks using the Wii TM or arm exercises at home. Primary outcome was change in the affected arm function at six weeks follow-up using the Action Research Arm Test. Secondary outcomes included occupational performance, quality of life, arm function at six months and a cost effectiveness analysis. The study was completed by 209 participants (87.1%). There was no significant difference in the primary outcome of affected arm function at six weeks follow-up (mean difference -1.7, 95% CI -3.9 to 0.5, p = 0.12) and no significant difference in secondary outcomes, including occupational performance, quality of life or arm function at six months, between the two groups. No serious adverse events related to the study treatment were reported. The cost effectiveness analysis showed that the Wii TM was more expensive than arm exercises £1106 (SD 1656) vs. £730 (SD 829) (probability 0.866). The trial showed that the Wii TM was not superior to arm exercises in home-based rehabilitation for stroke survivors with arm weakness. The Wii TM was well tolerated but more expensive than arm exercises.

Elliptic supersymmetric integrable model and multivariable elliptic functions

NASA Astrophysics Data System (ADS)

Motegi, Kohei

2017-12-01

We investigate the elliptic integrable model introduced by Deguchi and Martin [Int. J. Mod. Phys. A 7, Suppl. 1A, 165 (1992)], which is an elliptic extension of the Perk-Schultz model. We introduce and study a class of partition functions of the elliptic model by using the Izergin-Korepin analysis. We show that the partition functions are expressed as a product of elliptic factors and elliptic Schur-type symmetric functions. This result resembles recent work by number theorists in which the correspondence between the partition functions of trigonometric models and the product of the deformed Vandermonde determinant and Schur functions were established.

Structure-Based Phylogenetic Analysis of the Lipocalin Superfamily.

PubMed

Lakshmi, Balasubramanian; Mishra, Madhulika; Srinivasan, Narayanaswamy; Archunan, Govindaraju

2015-01-01

Lipocalins constitute a superfamily of extracellular proteins that are found in all three kingdoms of life. Although very divergent in their sequences and functions, they show remarkable similarity in 3-D structures. Lipocalins bind and transport small hydrophobic molecules. Earlier sequence-based phylogenetic studies of lipocalins highlighted that they have a long evolutionary history. However the molecular and structural basis of their functional diversity is not completely understood. The main objective of the present study is to understand functional diversity of the lipocalins using a structure-based phylogenetic approach. The present study with 39 protein domains from the lipocalin superfamily suggests that the clusters of lipocalins obtained by structure-based phylogeny correspond well with the functional diversity. The detailed analysis on each of the clusters and sub-clusters reveals that the 39 lipocalin domains cluster based on their mode of ligand binding though the clustering was performed on the basis of gross domain structure. The outliers in the phylogenetic tree are often from single member families. Also structure-based phylogenetic approach has provided pointers to assign putative function for the domains of unknown function in lipocalin family. The approach employed in the present study can be used in the future for the functional identification of new lipocalin proteins and may be extended to other protein families where members show poor sequence similarity but high structural similarity.

Large-scale genome-wide analysis identifies genetic variants associated with cardiac structure and function

PubMed Central

Wild, Philipp S.; Felix, Janine F.; Schillert, Arne; Chen, Ming-Huei; Leening, Maarten J.G.; Völker, Uwe; Großmann, Vera; Brody, Jennifer A.; Irvin, Marguerite R.; Shah, Sanjiv J.; Pramana, Setia; Lieb, Wolfgang; Schmidt, Reinhold; Stanton, Alice V.; Malzahn, Dörthe; Lyytikäinen, Leo-Pekka; Tiller, Daniel; Smith, J. Gustav; Di Tullio, Marco R.; Musani, Solomon K.; Morrison, Alanna C.; Pers, Tune H.; Morley, Michael; Kleber, Marcus E.; Aragam, Jayashri; Bis, Joshua C.; Bisping, Egbert; Broeckel, Ulrich; Cheng, Susan; Deckers, Jaap W.; Del Greco M, Fabiola; Edelmann, Frank; Fornage, Myriam; Franke, Lude; Friedrich, Nele; Harris, Tamara B.; Hofer, Edith; Hofman, Albert; Huang, Jie; Hughes, Alun D.; Kähönen, Mika; investigators, KNHI; Kruppa, Jochen; Lackner, Karl J.; Lannfelt, Lars; Laskowski, Rafael; Launer, Lenore J.; Lindgren, Cecilia M.; Loley, Christina; Mayet, Jamil; Medenwald, Daniel; Morris, Andrew P.; Müller, Christian; Müller-Nurasyid, Martina; Nappo, Stefania; Nilsson, Peter M.; Nuding, Sebastian; Nutile, Teresa; Peters, Annette; Pfeufer, Arne; Pietzner, Diana; Pramstaller, Peter P.; Raitakari, Olli T.; Rice, Kenneth M.; Rotter, Jerome I.; Ruohonen, Saku T.; Sacco, Ralph L.; Samdarshi, Tandaw E.; Sharp, Andrew S.P.; Shields, Denis C.; Sorice, Rossella; Sotoodehnia, Nona; Stricker, Bruno H.; Surendran, Praveen; Töglhofer, Anna M.; Uitterlinden, André G.; Völzke, Henry; Ziegler, Andreas; Münzel, Thomas; März, Winfried; Cappola, Thomas P.; Hirschhorn, Joel N.; Mitchell, Gary F.; Smith, Nicholas L.; Fox, Ervin R.; Dueker, Nicole D.; Jaddoe, Vincent W.V.; Melander, Olle; Lehtimäki, Terho; Ciullo, Marina; Hicks, Andrew A.; Lind, Lars; Gudnason, Vilmundur; Pieske, Burkert; Barron, Anthony J.; Zweiker, Robert; Schunkert, Heribert; Ingelsson, Erik; Liu, Kiang; Arnett, Donna K.; Psaty, Bruce M.; Blankenberg, Stefan; Larson, Martin G.; Felix, Stephan B.; Franco, Oscar H.; Zeller, Tanja; Vasan, Ramachandran S.; Dörr, Marcus

2017-01-01

BACKGROUND. Understanding the genetic architecture of cardiac structure and function may help to prevent and treat heart disease. This investigation sought to identify common genetic variations associated with inter-individual variability in cardiac structure and function. METHODS. A GWAS meta-analysis of echocardiographic traits was performed, including 46,533 individuals from 30 studies (EchoGen consortium). The analysis included 16 traits of left ventricular (LV) structure, and systolic and diastolic function. RESULTS. The discovery analysis included 21 cohorts for structural and systolic function traits (n = 32,212) and 17 cohorts for diastolic function traits (n = 21,852). Replication was performed in 5 cohorts (n = 14,321) and 6 cohorts (n = 16,308), respectively. Besides 5 previously reported loci, the combined meta-analysis identified 10 additional genome-wide significant SNPs: rs12541595 near MTSS1 and rs10774625 in ATXN2 for LV end-diastolic internal dimension; rs806322 near KCNRG, rs4765663 in CACNA1C, rs6702619 near PALMD, rs7127129 in TMEM16A, rs11207426 near FGGY, rs17608766 in GOSR2, and rs17696696 in CFDP1 for aortic root diameter; and rs12440869 in IQCH for Doppler transmitral A-wave peak velocity. Findings were in part validated in other cohorts and in GWAS of related disease traits. The genetic loci showed associations with putative signaling pathways, and with gene expression in whole blood, monocytes, and myocardial tissue. CONCLUSION. The additional genetic loci identified in this large meta-analysis of cardiac structure and function provide insights into the underlying genetic architecture of cardiac structure and warrant follow-up in future functional studies. FUNDING. For detailed information per study, see Acknowledgments. PMID:28394258

Meta-analysis of executive functioning in ecstasy/polydrug users.

PubMed

Roberts, C A; Jones, A; Montgomery, C

2016-06-01

Ecstasy/3,4-methylenedioxymethamphetamine (MDMA) use is proposed to cause damage to serotonergic (5-HT) axons in humans. Therefore, users should show deficits in cognitive processes that rely on serotonin-rich, prefrontal areas of the brain. However, there is inconsistency in findings to support this hypothesis. The aim of the current study was to examine deficits in executive functioning in ecstasy users compared with controls using meta-analysis. We identified k = 39 studies, contributing 89 effect sizes, investigating executive functioning in ecstasy users and polydrug-using controls. We compared function-specific task performance in 1221 current ecstasy users and 1242 drug-using controls, from tasks tapping the executive functions - updating, switching, inhibition and access to long-term memory. The significant main effect demonstrated overall executive dysfunction in ecstasy users [standardized mean difference (SMD) = -0.18, 95% confidence interval (CI) -0.26 to -0.11, Z = 5.05, p < 0.001, I 2 = 82%], with a significant subgroup effect (χ 2 = 22.06, degrees of freedom = 3, p < 0.001, I 2 = 86.4%) demonstrating differential effects across executive functions. Ecstasy users showed significant performance deficits in access (SMD = -0.33, 95% CI -0.46 to -0.19, Z = 4.72, p < 0.001, I 2 = 74%), switching (SMD = -0.19, 95% CI -0.36 to -0.02, Z = 2.16, p < 0.05, I 2 = 85%) and updating (SMD = -0.26, 95% CI -0.37 to -0.15, Z = 4.49, p < 0.001, I 2 = 82%). No differences were observed in inhibitory control. We conclude that this is the most comprehensive analysis of executive function in ecstasy users to date and provides a behavioural correlate of potential serotonergic neurotoxicity.

Antithrombotic drug therapy for IgA nephropathy: a meta analysis of randomized controlled trials.

PubMed

Liu, Xiu-Juan; Geng, Yan-Qiu; Xin, Shao-Nan; Huang, Guo-Ming; Tu, Xiao-Wen; Ding, Zhong-Ru; Chen, Xiang-Mei

2011-01-01

Antithrombotic agents, including antiplatelet agents, anticoagulants and thrombolysis agents, have been widely used in the management of immunoglobulin A (IgA) nephropathy in Chinese and Japanese populations. To systematically evaluate the effects of antithrombotic agents for IgA nephropathy. Data sources consisted of MEDLINE, EMBASE, the Cochrane Library, Chinese Biomedical Literature Database (CBM), Chinese Science and Technology Periodicals Databases (CNKI) and Japana Centra Revuo Medicina (http://www.jamas.gr.jp) up to April 5, 2011. The quality of the studies was evaluated from the intention to treat analysis and allocation concealment, as well as by the Jadad method. Meta-analyses were performed on the outcomes of proteinuria and renal function. Six articles met the predetermined inclusion criteria. Antithrombotic agents showed statistically significant effects on proteinuria (p<0.0001) but not on the protection of renal function (p=0.07). The pooled risk ratio for proteinuria was 0.53, [95% confidence intervals (CI): 0.41-0.68; I(2)=0%] and for renal function it was 0.42 (95% CI 0.17-1.06; I(2)=72%). Subgroup analysis showed that dipyridamole was beneficial for proteinuria (p=0.0003) but had no significant effects on protecting renal function. Urokinase had statistically significant effects both on the reduction of proteinuria (p=0.0005) and protecting renal function (p<0.00001) when compared with the control group. Antithrombotic agents had statistically significant effects on the reduction of proteinuria but not on the protection of renal function in patients with IgAN. Urokinase had statistically significant effects both on the reduction of proteinuria and on protecting renal function. Urokinase was shown to be a promising medication and should be investigated further.

On the subsystem formulation of linear-response time-dependent DFT.

PubMed

Pavanello, Michele

2013-05-28

A new and thorough derivation of linear-response subsystem time-dependent density functional theory (TD-DFT) is presented and analyzed in detail. Two equivalent derivations are presented and naturally yield self-consistent subsystem TD-DFT equations. One reduces to the subsystem TD-DFT formalism of Neugebauer [J. Chem. Phys. 126, 134116 (2007)]. The other yields Dyson type equations involving three types of subsystem response functions: coupled, uncoupled, and Kohn-Sham. The Dyson type equations for subsystem TD-DFT are derived here for the first time. The response function formalism reveals previously hidden qualities and complications of subsystem TD-DFT compared with the regular TD-DFT of the supersystem. For example, analysis of the pole structure of the subsystem response functions shows that each function contains information about the electronic spectrum of the entire supersystem. In addition, comparison of the subsystem and supersystem response functions shows that, while the correlated response is subsystem additive, the Kohn-Sham response is not. Comparison with the non-subjective partition DFT theory shows that this non-additivity is largely an artifact introduced by the subjective nature of the density partitioning in subsystem DFT.

Developmentally distinct MYB genes encode functionally equivalent proteins in Arabidopsis.

PubMed

Lee, M M; Schiefelbein, J

2001-05-01

The duplication and divergence of developmental control genes is thought to have driven morphological diversification during the evolution of multicellular organisms. To examine the molecular basis of this process, we analyzed the functional relationship between two paralogous MYB transcription factor genes, WEREWOLF (WER) and GLABROUS1 (GL1), in Arabidopsis. The WER and GL1 genes specify distinct cell types and exhibit non-overlapping expression patterns during Arabidopsis development. Nevertheless, reciprocal complementation experiments with a series of gene fusions showed that WER and GL1 encode functionally equivalent proteins, and their unique roles in plant development are entirely due to differences in their cis-regulatory sequences. Similar experiments with a distantly related MYB gene (MYB2) showed that its product cannot functionally substitute for WER or GL1. Furthermore, an analysis of the WER and GL1 proteins shows that conserved sequences correspond to specific functional domains. These results provide new insights into the evolution of the MYB gene family in Arabidopsis, and, more generally, they demonstrate that novel developmental gene function may arise solely by the modification of cis-regulatory sequences.

Accelerated recovery of sensorimotor function in a dog submitted to quasi-total transection of the cervical spinal cord and treated with PEG.

PubMed

Kim, C-Yoon; Hwang, In-Kyu; Kim, Hana; Jang, Se-Woong; Kim, Hong Seog; Lee, Won-Young

2016-01-01

A case report on observing the recovery of sensory-motor function after cervical spinal cord transection. Laminectomy and transection of cervical spinal cord (C5) was performed on a male beagle weighing 3.5 kg. After applying polyethylene glycol (PEG) on the severed part, reconstruction of cervical spinal cord was confirmed by the restoration of sensorimotor function. Tetraplegia was observed immediately after operation, however, the dog showed stable respiration and survival without any complication. The dog showed fast recovery after 1 week, and recovered approximately 90% of normal sensorimotor function 3 weeks after the operation, although urinary disorder was still present. All recovery stages were recorded by video camera twice a week for behavioral analysis. While current belief holds that functional recovery is impossible after a section greater than 50% at C5-6 in the canine model, this case study shows the possibility of cervical spinal cord reconstruction after near-total transection. Furthermore, this case study also confirms that PEG can truly expedite the recovery of sensorimotor function after cervical spinal cord sections in dogs.

Rasch analysis of the participation scale (P-scale): usefulness of the P-scale to a rehabilitation services network.

PubMed

Souza, Mariana Angélica Peixoto; Coster, Wendy Jane; Mancini, Marisa Cotta; Dutra, Fabiana Caetano Martins Silva; Kramer, Jessica; Sampaio, Rosana Ferreira

2017-12-08

A person's participation is acknowledged as an important outcome of the rehabilitation process. The Participation Scale (P-Scale) is an instrument that was designed to assess the participation of individuals with a health condition or disability. The scale was developed in an effort to better describe the participation of people living in middle-income and low-income countries. The aim of this study was to use Rasch analysis to examine whether the Participation Scale is suitable to assess the perceived ability to take part in participation situations by patients with diverse levels of function. The sample was comprised by 302 patients from a public rehabilitation services network. Participants had orthopaedic or neurological health conditions, were at least 18 years old, and completed the Participation Scale. Rasch analysis was conducted using the Winsteps software. The mean age of all participants was 45.5 years (standard deviation = 14.4), 52% were male, 86% had orthopaedic conditions, and 52% had chronic symptoms. Rasch analysis was performed using a dichotomous rating scale, and only one item showed misfit. Dimensionality analysis supported the existence of only one Rasch dimension. The person separation index was 1.51, and the item separation index was 6.38. Items N2 and N14 showed Differential Item Functioning between men and women. Items N6 and N12 showed Differential Item Functioning between acute and chronic conditions. The item difficulty range was -1.78 to 2.09 logits, while the sample ability range was -2.41 to 4.61 logits. The P-Scale was found to be useful as a screening tool for participation problems reported by patients in a rehabilitation context, despite some issues that should be addressed to further improve the scale.

The hOGG1 Ser326Cys Gene Polymorphism and Breast Cancer Risk in Saudi Population.

PubMed

Alanazi, Mohammed; Pathan, Akbar Ali Khan; Shaik, Jilani P; Alhadheq, Abdullah; Khan, Zahid; Khan, Wajahatullah; Al Naeem, Abdulrahman; Parine, Narasimha Reddy

2017-07-01

The purpose of this study was to test the association between human 8-oxoguanine glycosylase 1 (hOGG1) gene polymorphisms and susceptibility to breast cancer in Saudi population. We have also aimed to screen the hOGG1 Ser326Cys polymorphism effect on structural and functional properties of the hOGG1 protein using in silico tools. We have analyzed four SNPs of hOGG1 gene among Saudi breast cancer patients along with healthy controls. Genotypes were screened using TaqMan SNP genotype analysis method. Experimental data was analyzed using Chi-square, t test and logistic regression analysis using SPSS software (v.16). In silco analysis was conducted using discovery studio and HOPE program. Genotypic analysis showed that hOGG1 rs1052133 (Ser326Cys) is significantly associated with breast cancer samples in Saudi population, however rs293795 (T >C), rs2072668 (C>G) and rs2075747 (G >A) did not show any association with breast cancer. The hOGG1 SNP rs1052133 (Ser326Cys) minor allele T showed a significant association with breast cancer samples (OR = 1.78, χ2 = 7.86, p = 0.02024). In silico structural analysis was carried out to compare the wild type (Ser326) and mutant (Cys326) protein structures. The structural prediction studies revealed that Ser326Cys variant may destabilize the protein structure and it may disturb the hOGG1 function. Taken together this is the first In silico study report to confirm Ser326Cys variant effect on structural and functional properties of hOGG1 gene and Ser326Cys role in breast cancer susceptibility in Saudi population.

Growth Type and Functional Trajectories: An Empirical Study of Urban Expansion in Nanjing, China

PubMed Central

Yuan, Feng

2016-01-01

Drawing upon the Landsat satellite images of Nanjing from 1985, 1995, 2001, 2007, and 2013, this paper integrates the convex hull analysis and common edge analysis at double scales, and develops a comprehensive matrix analysis to distinguish the different types of urban land expansion. The results show that Nanjing experienced rapid urban expansion, dominated by a mix of residential and manufacturing land from 1985 to 2013, which in turn has promoted Nanjing’s shift from a compact mononuclear city to a polycentric one. Spatial patterns of three specific types of growth, namely infilling, extension, and enclave were quite different in four consecutive periods. These patterns result primarily from the existing topographic constraints, as well as government-oriented urban planning and policies. By intersecting the function maps, we also reveal the functional evolution of newly-developed urban land. Moreover, both self-enhancing and mutual promotion of the newly developed functions are surveyed over the last decade. Our study confirms that the integration of a multi-scale method and multi-perspective analysis, such as the spatiotemporal patterns and functional evolution, helps us to better understand the rapid urban growth in China. PMID:26845155

Resting state network topology of the ferret brain.

PubMed

Zhou, Zhe Charles; Salzwedel, Andrew P; Radtke-Schuller, Susanne; Li, Yuhui; Sellers, Kristin K; Gilmore, John H; Shih, Yen-Yu Ian; Fröhlich, Flavio; Gao, Wei

2016-12-01

Resting state functional magnetic resonance imaging (rsfMRI) has emerged as a versatile tool for non-invasive measurement of functional connectivity patterns in the brain. RsfMRI brain dynamics in rodents, non-human primates, and humans share similar properties; however, little is known about the resting state functional connectivity patterns in the ferret, an animal model with high potential for developmental and cognitive translational study. To address this knowledge-gap, we performed rsfMRI on anesthetized ferrets using a 9.4T MRI scanner, and subsequently performed group-level independent component analysis (gICA) to identify functionally connected brain networks. Group-level ICA analysis revealed distributed sensory, motor, and higher-order networks in the ferret brain. Subsequent connectivity analysis showed interconnected higher-order networks that constituted a putative default mode network (DMN), a network that exhibits altered connectivity in neuropsychiatric disorders. Finally, we assessed ferret brain topological efficiency using graph theory analysis and found that the ferret brain exhibits small-world properties. Overall, these results provide additional evidence for pan-species resting-state networks, further supporting ferret-based studies of sensory and cognitive function. Copyright © 2016 Elsevier Inc. All rights reserved.

Patient characteristics as predictors of clinical outcome of distraction in treatment of severe ankle osteoarthritis.

PubMed

Marijnissen, A C A; Hoekstra, M C L; Pré, B C du; van Roermund, P M; van Melkebeek, J; Amendola, A; Maathuis, P; Lafeber, F P J G; Welsing, P M J

2014-01-01

Osteoarthritis (OA) is a slowly progressive joint disease. Joint distraction can be a treatment of choice in case of severe OA. Prediction of failure will facilitate implementation of joint distraction in clinical practice. Patients with severe ankle OA, who underwent joint distraction were included. Survival analysis was performed over 12 years (n = 25 after 12 years). Regression analyses were used to predict failures and clinical benefit at 2 years after joint distraction (n = 111). Survival analysis showed that 44% of the patients failed, 17% within 2 years and 37% within 5 years after joint distraction (n = 48 after 5 years). Survival analysis in subgroups showed that the percentage failure was only different in women (30% after 2 years) versus men (after 11 years still no 30% failure). In the multivariate analyses female gender was predictive for failure 2 years after joint distraction. Gender and functional disability at baseline predicted more pain. Functional disability and pain at baseline were associated with more functional disability. Joint distraction shows a long-term clinical beneficial outcome. However, failure rate is considerable over the years. Female patients have a higher chance of failure during follow-up. Unfortunately, not all potential predictors could be investigated and other clinically significant predictors were not found. © 2013 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

Evidence for Functional Networks within the Human Brain's White Matter.

PubMed

Peer, Michael; Nitzan, Mor; Bick, Atira S; Levin, Netta; Arzy, Shahar

2017-07-05

Investigation of the functional macro-scale organization of the human cortex is fundamental in modern neuroscience. Although numerous studies have identified networks of interacting functional modules in the gray-matter, limited research was directed to the functional organization of the white-matter. Recent studies have demonstrated that the white-matter exhibits blood oxygen level-dependent signal fluctuations similar to those of the gray-matter. Here we used these signal fluctuations to investigate whether the white-matter is organized as functional networks by applying a clustering analysis on resting-state functional MRI (RSfMRI) data from white-matter voxels, in 176 subjects (of both sexes). This analysis indicated the existence of 12 symmetrical white-matter functional networks, corresponding to combinations of white-matter tracts identified by diffusion tensor imaging. Six of the networks included interhemispheric commissural bridges traversing the corpus callosum. Signals in white-matter networks correlated with signals from functional gray-matter networks, providing missing knowledge on how these distributed networks communicate across large distances. These findings were replicated in an independent subject group and were corroborated by seed-based analysis in small groups and individual subjects. The identified white-matter functional atlases and analysis codes are available at http://mind.huji.ac.il/white-matter.aspx Our results demonstrate that the white-matter manifests an intrinsic functional organization as interacting networks of functional modules, similarly to the gray-matter, which can be investigated using RSfMRI. The discovery of functional networks within the white-matter may open new avenues of research in cognitive neuroscience and clinical neuropsychiatry. SIGNIFICANCE STATEMENT In recent years, functional MRI (fMRI) has revolutionized all fields of neuroscience, enabling identifications of functional modules and networks in the human brain. However, most fMRI studies ignored a major part of the brain, the white-matter, discarding signals from it as arising from noise. Here we use resting-state fMRI data from 176 subjects to show that signals from the human white-matter contain meaningful information. We identify 12 functional networks composed of interacting long-distance white-matter tracts. Moreover, we show that these networks are highly correlated to resting-state gray-matter networks, highlighting their functional role. Our findings enable reinterpretation of many existing fMRI datasets, and suggest a new way to explore the white-matter role in cognition and its disturbances in neuropsychiatric disorders. Copyright © 2017 the authors 0270-6474/17/376394-14$15.00/0.

Spirituality and sexual orientation: relationship to mental well-being and functional health status.

PubMed

Coleman, Christopher L

2003-09-01

Research has shown that spirituality has a positive effect on physical and mental health; however, few studies have explored the influence of spirituality and sexuality on mental well-being and functional health status in people with human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS). This descriptive cross-sectional study was designed to examine the relationships among spirituality, sexual orientation, mental well-being and aspects of functional health status (physical, role, social and cognitive functioning) in a sample of 117 African-American men and women living with HIV/AIDS. Spirituality was measured using the Spiritual Well-Being Scale. A demographic questionnaire gathered data on sexual orientation, age and gender. The Medical Outcomes Study Questionnaire-30 assessed aspects of functional health status and mental well-being. The HIV Symptom Checklist for Persons With HIV disease was used to collect data on HIV symptoms. The data were collected in 1996. The findings indicate that spirituality had a direct relationship with cognitive and social functioning and was inversely related to HIV symptoms. Sexual orientation had direct relationships with mental well-being, cognitive, physical, social and role functioning. t-Tests showed that heterosexual participants reported poorer mental well-being and functional health status compared with homosexual participants. Regression analysis showed that spirituality, sexual orientation, age and HIV symptoms contributed significantly to mental well-being and functional health status. The regression analysis showed that spirituality, sexual orientation, age and HIV symptoms contributed significantly to mental well-being and functional health status. Further research is needed to explore the various ways that sexual orientation influences health status findings in those with HIV disease in certain segments of the population. The findings support the inclusion of spirituality as a variable when examining mental well-being and physical health. Finally, given the limitations of the design, more rigorous methods should be employed to understand further the contribution of spirituality to the health status of African-Americans living with HIV, because of its social importance to this particular community.

Grey matter abnormalities in methcathinone abusers with a Parkinsonian syndrome.

PubMed

Juurmaa, Julius; Menke, Ricarda A L; Vila, Pierre; Müürsepp, Andreas; Tomberg, Tiiu; Ilves, Pilvi; Nigul, Mait; Johansen-Berg, Heidi; Donaghy, Michael; Stagg, Charlotte J; Stepens, Ainārs; Taba, Pille

2016-11-01

A permanent Parkinsonian syndrome occurs in intravenous abusers of the designer psychostimulant methcathinone (ephedrone). It is attributed to deposition of contaminant manganese, as reflected by characteristic globus pallidus hyperintensity on T1-weighted MRI. We have investigated brain structure and function in methcathinone abusers ( n  = 12) compared to matched control subjects ( n  = 12) using T1-weighted structural and resting-state functional MRI. Segmentation analysis revealed significant ( p  < .05) subcortical grey matter atrophy in methcathinone abusers within putamen and thalamus bilaterally, and the left caudate nucleus. The volume of the caudate nuclei correlated inversely with duration of methcathinone abuse. Voxel-based morphometry showed patients to have significant grey matter loss ( p  < .05) bilaterally in the putamina and caudate nucleus. Surface-based analysis demonstrated nine clusters of cerebral cortical thinning in methcathinone abusers, with relative sparing of prefrontal, parieto-occipital, and temporal regions. Resting-state functional MRI analysis showed increased functional connectivity within the motor network of patients ( p  < .05), particularly within the right primary motor cortex. Taken together, these results suggest that the manganese exposure associated with prolonged methcathinone abuse results in widespread structural and functional changes affecting both subcortical and cortical grey matter and their connections. Underlying the distinctive movement disorder caused by methcathinone abuse, there is a more widespread pattern of brain involvement than is evident from the hyperintensity restricted to the basal ganglia as shown by T1-weighted structural MRI.

Microarray RNA expression analysis of cerebral white matter lesions reveals changes in multiple functional pathways.

PubMed

Simpson, Julie E; Hosny, Ola; Wharton, Stephen B; Heath, Paul R; Holden, Hazel; Fernando, Malee S; Matthews, Fiona; Forster, Gill; O'Brien, John T; Barber, Robert; Kalaria, Raj N; Brayne, Carol; Shaw, Pamela J; Lewis, Claire E; Ince, Paul G

2009-02-01

White matter lesions (WML) in brain aging are linked to dementia and depression. Ischemia contributes to their pathogenesis but other mechanisms may contribute. We used RNA microarray analysis with functional pathway grouping as an unbiased approach to investigate evidence for additional pathogenetic mechanisms. WML were identified by MRI and pathology in brains donated to the Medical Research Council Cognitive Function and Ageing Study Cognitive Function and Aging Study. RNA was extracted to compare WML with nonlesional white matter samples from cases with lesions (WM[L]), and from cases with no lesions (WM[C]) using RNA microarray and pathway analysis. Functional pathways were validated for selected genes by quantitative real-time polymerase chain reaction and immunocytochemistry. We identified 8 major pathways in which multiple genes showed altered RNA transcription (immune regulation, cell cycle, apoptosis, proteolysis, ion transport, cell structure, electron transport, metabolism) among 502 genes that were differentially expressed in WML compared to WM[C]. In WM[L], 409 genes were altered involving the same pathways. Genes selected to validate this microarray data all showed the expected changes in RNA levels and immunohistochemical expression of protein. WML represent areas with a complex molecular phenotype. From this and previous evidence, WML may arise through tissue ischemia but may also reflect the contribution of additional factors like blood-brain barrier dysfunction. Differential expression of genes in WM[L] compared to WM[C] indicate a "field effect" in the seemingly normal surrounding white matter.

CCS52A2/FZR1, a cell cycle regulator, is an essential factor for shoot apical meristem maintenance in Arabidopsis thaliana.

PubMed

Liu, Yajie; Ye, Wei; Li, Beibei; Zhou, Xiaojing; Cui, Yuhai; Running, Mark P; Liu, Kede

2012-08-08

Cell division and cell fate decisions regulate organ formation and function in plant growth and development. It is still unclear how specific meristematic regulatory networks operate with the cell cycle machinery to translate stem cell identity and maintenance into cellular behavior. In this study, we address these questions by analysis of a shoot apex defective mutant, namely xcm9. Phenotypic analysis of the xcm9 mutant reveals concomitant premature termination of floral shoots with frequent bifurcation of the shoot apices, stems, and flowers. Microscopic observations show irregular cell organization in shoot apical meristems of xcm9. Positional cloning revealed that xcm9 is a loss of function allele of the CCS52A2/FZR1 gene, which has previously been implicated in root development. Expression analysis demonstrated that CCS52A2 maintains a higher transcriptional expression level in actively dividing tissue. Genetic studies indicated that the CCS52A2 gene functions together with WUSCHEL (WUS) and CLAVATA3 (CLV3) in regulating the development of the shoot meristem, and also contributes to this regulation together with the chromatin remodeling pathway. In addition, fewer xcm9 cells express CYCLIN B1:1, showing that cell cycle progression is disrupted in the mutant. We propose that the CCS52A2 gene is a mediator that functions together with meristematic genes to regulate meristem organization, and cross-functions with chromatin regulators in cell cycle progression during shoot apical meristem development.

The relation between insulin-like growth factor I levels and cognition in healthy elderly: a meta-analysis.

PubMed

Arwert, L I; Deijen, J B; Drent, M L

2005-12-01

Insulin-like growth factor I (IGF-I) levels and cognitive functioning decrease with aging. Several studies report positive correlations between IGF-I levels and cognitive functioning in healthy elderly. However, because of controversial data no definitive conclusions can be drawn concerning the relation between IGF-I and cognition. Therefore, we carried out a meta-analysis on studies that report on the relation between IGF-I and cognition in healthy elderly. We searched the electronic databases for articles about IGF-I and cognition. Studies from 1985 to January 2005 are included. Two reviewers independently extracted data on study design and cognitive outcomes. Thirteen studies on IGF-I and cognition in elderly, with a total number of 1981 subjects, met the inclusion criteria. On the data from these studies meta-analyses were carried out by means of the program Comprehensive Meta-analysis using a random effects model. Pooled effects show that IGF-I levels in healthy elderly have a positive correlation with cognitive functioning, which appeared to be mainly measured with the mini mental state examination (MMSE). The effect size is 0.6, which indicates the presence of a large positive relationship between IGF and cognition in healthy elderly. These meta-analyses showed an overall relationship between IGF-I levels and cognitive functioning in healthy elderly. Further studies should be performed to clarify the role of IGF-I substitution in preserving cognitive functions with aging.

Meta-analysis of chicken--salmonella infection experiments.

PubMed

Te Pas, Marinus F W; Hulsegge, Ina; Schokker, Dirkjan; Smits, Mari A; Fife, Mark; Zoorob, Rima; Endale, Marie-Laure; Rebel, Johanna M J

2012-04-24

Chicken meat and eggs can be a source of human zoonotic pathogens, especially Salmonella species. These food items contain a potential hazard for humans. Chickens lines differ in susceptibility for Salmonella and can harbor Salmonella pathogens without showing clinical signs of illness. Many investigations including genomic studies have examined the mechanisms how chickens react to infection. Apart from the innate immune response, many physiological mechanisms and pathways are reported to be involved in the chicken host response to Salmonella infection. The objective of this study was to perform a meta-analysis of diverse experiments to identify general and host specific mechanisms to the Salmonella challenge. Diverse chicken lines differing in susceptibility to Salmonella infection were challenged with different Salmonella serovars at several time points. Various tissues were sampled at different time points post-infection, and resulting host transcriptional differences investigated using different microarray platforms. The meta-analysis was performed with the R-package metaMA to create lists of differentially regulated genes. These gene lists showed many similarities for different chicken breeds and tissues, and also for different Salmonella serovars measured at different times post infection. Functional biological analysis of these differentially expressed gene lists revealed several common mechanisms for the chicken host response to Salmonella infection. The meta-analysis-specific genes (i.e. genes found differentially expressed only in the meta-analysis) confirmed and expanded the biological functional mechanisms. The meta-analysis combination of heterogeneous expression profiling data provided useful insights into the common metabolic pathways and functions of different chicken lines infected with different Salmonella serovars.

Meta-analysis of Chicken – Salmonella infection experiments

PubMed Central

2012-01-01

Background Chicken meat and eggs can be a source of human zoonotic pathogens, especially Salmonella species. These food items contain a potential hazard for humans. Chickens lines differ in susceptibility for Salmonella and can harbor Salmonella pathogens without showing clinical signs of illness. Many investigations including genomic studies have examined the mechanisms how chickens react to infection. Apart from the innate immune response, many physiological mechanisms and pathways are reported to be involved in the chicken host response to Salmonella infection. The objective of this study was to perform a meta-analysis of diverse experiments to identify general and host specific mechanisms to the Salmonella challenge. Results Diverse chicken lines differing in susceptibility to Salmonella infection were challenged with different Salmonella serovars at several time points. Various tissues were sampled at different time points post-infection, and resulting host transcriptional differences investigated using different microarray platforms. The meta-analysis was performed with the R-package metaMA to create lists of differentially regulated genes. These gene lists showed many similarities for different chicken breeds and tissues, and also for different Salmonella serovars measured at different times post infection. Functional biological analysis of these differentially expressed gene lists revealed several common mechanisms for the chicken host response to Salmonella infection. The meta-analysis-specific genes (i.e. genes found differentially expressed only in the meta-analysis) confirmed and expanded the biological functional mechanisms. Conclusions The meta-analysis combination of heterogeneous expression profiling data provided useful insights into the common metabolic pathways and functions of different chicken lines infected with different Salmonella serovars. PMID:22531008

Correlation between brain circuit segregation and obesity.

PubMed

Chao, Seh-Huang; Liao, Yin-To; Chen, Vincent Chin-Hung; Li, Cheng-Jui; McIntyre, Roger S; Lee, Yena; Weng, Jun-Cheng

2018-01-30

Obesity is a major public health problem. Herein, we aim to identify the correlation between brain circuit segregation and obesity using multimodal functional magnetic resonance imaging (fMRI) techniques and analysis. Twenty obese patients (BMI=37.66±5.07) and 30 healthy controls (BMI=22.64±3.45) were compared using neuroimaging and assessed for symptoms of anxiety and depression using the Hospital Anxiety and Depression Scale (HADS). All participants underwent resting-state fMRI (rs-fMRI) and T1-weighted imaging using a 1.5T MRI. Multimodal MRI techniques and analyses were used to assess obese patients, including the functional connectivity (FC), amplitude of low-frequency fluctuations (ALFF), regional homogeneity (ReHo), graph theoretical analysis (GTA), and voxel-based morphometry (VBM). Correlations between brain circuit segregation and obesity were also calculated. In the VBM, obese patients showed altered gray matter volumes in the amygdala, thalamus and putamen. In the FC, the obesity group showed increased functional connectivity in the bilateral anterior cingulate cortex and decreased functional connectivity in the frontal gyrus of default mode network. The obesity group also exhibited altered ALFF and ReHo in the prefrontal cortex and precuneus. In the GTA, the obese patients showed a significant decrease in local segregation and a significant increase in global integration, suggesting a shift toward randomization in their functional networks. Our results may provide additional evidence for potential structural and functional imaging markers for clinical diagnosis and future research, and they may improve our understanding of the underlying pathophysiology of obesity. Copyright © 2017 Elsevier B.V. All rights reserved.

Relationship between Speech Production and Perception in People Who Stutter

PubMed Central

Lu, Chunming; Long, Yuhang; Zheng, Lifen; Shi, Guang; Liu, Li; Ding, Guosheng; Howell, Peter

2016-01-01

Speech production difficulties are apparent in people who stutter (PWS). PWS also have difficulties in speech perception compared to controls. It is unclear whether the speech perception difficulties in PWS are independent of, or related to, their speech production difficulties. To investigate this issue, functional MRI data were collected on 13 PWS and 13 controls whilst the participants performed a speech production task and a speech perception task. PWS performed poorer than controls in the perception task and the poorer performance was associated with a functional activity difference in the left anterior insula (part of the speech motor area) compared to controls. PWS also showed a functional activity difference in this and the surrounding area [left inferior frontal cortex (IFC)/anterior insula] in the production task compared to controls. Conjunction analysis showed that the functional activity differences between PWS and controls in the left IFC/anterior insula coincided across the perception and production tasks. Furthermore, Granger Causality Analysis on the resting-state fMRI data of the participants showed that the causal connection from the left IFC/anterior insula to an area in the left primary auditory cortex (Heschl’s gyrus) differed significantly between PWS and controls. The strength of this connection correlated significantly with performance in the perception task. These results suggest that speech perception difficulties in PWS are associated with anomalous functional activity in the speech motor area, and the altered functional connectivity from this area to the auditory area plays a role in the speech perception difficulties of PWS. PMID:27242487

Female Sexual Function Following Surgical Treatment of Stress Urinary Incontinence: Systematic Review and Meta-Analysis.

PubMed

Bicudo-Fürst, Maria Cláudia; Borba Leite, Pedro Henrique; Araújo Glina, Felipe Placco; Baccaglini, Willy; de Carvalho Fürst, Rafael Vilhena; Bezerra, Carlos Alberto; Glina, Sidney

2018-04-01

The impact of surgery for stress urinary incontinence (SUI) on female sexual function has received attention in the medical literature, but not in a structured manner. To assess the most recent evidence on the impact of surgical management for female SUI on female sexual function. The review and meta-analysis of available articles published in Medline, Cochrane, LILACS, SCOPUS, Web of Science, CINHAL, and EMBASE included prospective randomized and non-randomized studies that assessed patients who underwent surgical treatment for UI through 2 validated questionnaires: the Pelvic Organ Prolapse Urinary Incontinence Sexual Questionnaire (PISQ-12) and the Female Sexual Function Index (FSFI). The following terms were searched: (urinary incontinence OR female OR woman OR women) AND (suburethral slings OR transobturator tape* OR transobturator suburethral tape OR trans-obturator tape* OR urethral sling* OR midurethral sling* OR mid-urethral sling* OR "standard midurethral slings" OR tensionless vaginal tape* OR mini sling* OR Burch* OR "Burch colposuspension" OR "urologic surgical procedures" OR "tension-free vaginal tape" OR pubovaginal sling) AND (sexual behavior OR "Female Sexual Function Index" OR FSFI OR sexual function OR "Pelvic Organ Prolapse/Urinary Incontinence Sexual Questionnaire" OR PISQ-12). 1,043 articles were retrieved; 9 studies were included for qualitative analysis and 4 were included for meta-analysis. 25 articles were excluded because they used questionnaires other than the FSFI and PISQ-12. Meta-analysis of 2 studies composed of 411 women who underwent to retropubic and transobturator sling intervention and completed the PISQ-12 questionnaire showed an increase in sexual function of 2.40 points after transobturator compared with retropubic sling intervention (95% CI = -2.48 to -2.32; I 2  = 35%, P < .00001). However, 2 other studies composed of 183 women comparing the same techniques, but using the FSFI, did not show a statistically significant difference (95% CI = -1.77 to 3.78; I 2  = 0%, P = .48). The impact of UI surgery on sexual function is uncertain because of the imprecision of the effect and inconsistency among studies. Only limited evidence on the impact of the transobturator vs the retropubic sling was found. Bicudo-Fürst MC, Borba Leite PH, Araújo Glina FP, et al. Female Sexual Function Following Surgical Treatment of Stress Urinary Incontinence: Systematic Review and Meta-Analysis. Sex Med Rev 2018;6:224-233. Copyright © 2017. Published by Elsevier Inc.

Behavioral analysis of Drosophila transformants expressing human taste receptor genes in the gustatory receptor neurons.

PubMed

Adachi, Ryota; Sasaki, Yuko; Morita, Hiromi; Komai, Michio; Shirakawa, Hitoshi; Goto, Tomoko; Furuyama, Akira; Isono, Kunio

2012-06-01

Transgenic Drosophila expressing human T2R4 and T2R38 bitter-taste receptors or PKD2L1 sour-taste receptor in the fly gustatory receptor neurons and other tissues were prepared using conventional Gal4/UAS binary system. Molecular analysis showed that the transgene mRNAs are expressed according to the tissue specificity of the Gal4 drivers. Transformants expressing the transgene taste receptors in the fly taste neurons were then studied by a behavioral assay to analyze whether transgene chemoreceptors are functional and coupled to the cell response. Since wild-type flies show strong aversion against the T2R ligands as in mammals, the authors analyzed the transformants where the transgenes are expressed in the fly sugar receptor neurons so that they promote feeding ligand-dependently if they are functional and activate the neurons. Although the feeding preference varied considerably among different strains and individuals, statistical analysis using large numbers of transformants indicated that transformants expressing T2R4 showed a small but significant increase in the preference for denatonium and quinine, the T2R4 ligands, as compared to the control flies, whereas transformants expressing T2R38 did not. Similarly, transformants expressing T2R38 and PKD2L1 also showed a similar preference increase for T2R38-specific ligand phenylthiocarbamide (PTC) and a sour-taste ligand, citric acid, respectively. Taken together, the transformants expressing mammalian taste receptors showed a small but significant increase in the feeding preference that is taste receptor and also ligand dependent. Although future improvements are required to attain performance comparable to the endogenous robust response, Drosophila taste neurons may serve as a potential in vivo heterologous expression system for analyzing chemoreceptor function.

GPU accelerated dynamic functional connectivity analysis for functional MRI data.

PubMed

Akgün, Devrim; Sakoğlu, Ünal; Esquivel, Johnny; Adinoff, Bryon; Mete, Mutlu

2015-07-01

Recent advances in multi-core processors and graphics card based computational technologies have paved the way for an improved and dynamic utilization of parallel computing techniques. Numerous applications have been implemented for the acceleration of computationally-intensive problems in various computational science fields including bioinformatics, in which big data problems are prevalent. In neuroimaging, dynamic functional connectivity (DFC) analysis is a computationally demanding method used to investigate dynamic functional interactions among different brain regions or networks identified with functional magnetic resonance imaging (fMRI) data. In this study, we implemented and analyzed a parallel DFC algorithm based on thread-based and block-based approaches. The thread-based approach was designed to parallelize DFC computations and was implemented in both Open Multi-Processing (OpenMP) and Compute Unified Device Architecture (CUDA) programming platforms. Another approach developed in this study to better utilize CUDA architecture is the block-based approach, where parallelization involves smaller parts of fMRI time-courses obtained by sliding-windows. Experimental results showed that the proposed parallel design solutions enabled by the GPUs significantly reduce the computation time for DFC analysis. Multicore implementation using OpenMP on 8-core processor provides up to 7.7× speed-up. GPU implementation using CUDA yielded substantial accelerations ranging from 18.5× to 157× speed-up once thread-based and block-based approaches were combined in the analysis. Proposed parallel programming solutions showed that multi-core processor and CUDA-supported GPU implementations accelerated the DFC analyses significantly. Developed algorithms make the DFC analyses more practical for multi-subject studies with more dynamic analyses. Copyright © 2015 Elsevier Ltd. All rights reserved.

Resting-state functional magnetic resonance imaging: the impact of regression analysis.

PubMed

Yeh, Chia-Jung; Tseng, Yu-Sheng; Lin, Yi-Ru; Tsai, Shang-Yueh; Huang, Teng-Yi

2015-01-01

To investigate the impact of regression methods on resting-state functional magnetic resonance imaging (rsfMRI). During rsfMRI preprocessing, regression analysis is considered effective for reducing the interference of physiological noise on the signal time course. However, it is unclear whether the regression method benefits rsfMRI analysis. Twenty volunteers (10 men and 10 women; aged 23.4 ± 1.5 years) participated in the experiments. We used node analysis and functional connectivity mapping to assess the brain default mode network by using five combinations of regression methods. The results show that regressing the global mean plays a major role in the preprocessing steps. When a global regression method is applied, the values of functional connectivity are significantly lower (P ≤ .01) than those calculated without a global regression. This step increases inter-subject variation and produces anticorrelated brain areas. rsfMRI data processed using regression should be interpreted carefully. The significance of the anticorrelated brain areas produced by global signal removal is unclear. Copyright © 2014 by the American Society of Neuroimaging.

Fracture mechanics analysis of cracked structures using weight function and neural network method

NASA Astrophysics Data System (ADS)

Chen, J. G.; Zang, F. G.; Yang, Y.; Shi, K. K.; Fu, X. L.

2018-06-01

Stress intensity factors(SIFs) due to thermal-mechanical load has been established by using weight function method. Two reference stress states sere used to determine the coefficients in the weight function. Results were evaluated by using data from literature and show a good agreement between them. So, the SIFs can be determined quickly using the weight function obtained when cracks subjected to arbitrary loads, and presented method can be used for probabilistic fracture mechanics analysis. A probabilistic methodology considering Monte-Carlo with neural network (MCNN) has been developed. The results indicate that an accurate probabilistic characteristic of the KI can be obtained by using the developed method. The probability of failure increases with the increasing of loads, and the relationship between is nonlinear.

Functional relevance for type 1 diabetes mellitus-associated genetic variants by using integrative analyses.

PubMed

Qiu, Ying-Hua; Deng, Fei-Yan; Tang, Zai-Xiang; Jiang, Zhen-Huan; Lei, Shu-Feng

2015-10-01

Type 1 diabetes mellitus (type 1 DM) is an autoimmune disease. Although genome-wide association studies (GWAS) and meta-analyses have successfully identified numerous type 1 DM-associated susceptibility loci, the underlying mechanisms for these susceptibility loci are currently largely unclear. Based on publicly available datasets, we performed integrative analyses (i.e., integrated gene relationships among implicated loci, differential gene expression analysis, functional prediction and functional annotation clustering analysis) and combined with expression quantitative trait loci (eQTL) results to further explore function mechanisms underlying the associations between genetic variants and type 1 DM. Among a total of 183 type 1 DM-associated SNPs, eQTL analysis showed that 17 SNPs with cis-regulated eQTL effects on 9 genes. All the 9 eQTL genes enrich in immune-related pathways or Gene Ontology (GO) terms. Functional prediction analysis identified 5 SNPs located in transcription factor (TF) binding sites. Of the 9 eQTL genes, 6 (TAP2, HLA-DOB, HLA-DQB1, HLA-DQA1, HLA-DRB5 and CTSH) were differentially expressed in type 1 DM-associated related cells. Especially, rs3825932 in CTSH has integrative functional evidence supporting the association with type 1 DM. These findings indicated that integrative analyses can yield important functional information to link genetic variants and type 1 DM. Copyright © 2015 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

Receiver Functions From Regional and Near-Teleseismic P Waves

NASA Astrophysics Data System (ADS)

Park, J.; Levin, V.

2001-05-01

P waves from regional-distance earthquakes are complex and reverberatory, as would be expected from a combination of head waves, post-critical crustal reflections and shallow-incident P from the upper mantle. Although developed to analyze steeply-incident teleseismic P waves, receiver function analysis can also retrieve information about crustal structure from regional and near-teleseismic P. Using a new method to estimate receiver functions, based on multiple-taper spectral analysis, regional-distance RFs for GSN stations RAYN and ANTO show broad agreement with teleseismic RFs. At RAYN the moveout of the Moho-converted Ps phase, relative to direct P, follows well the predictions of the IASP91 earth model. The Moho-converted Ps phase shows complexity associated with the transition-zone triplication near Δ =20o and constant delay (zero moveout) as Δ -> 0, consistent with conversion from Pn. Similar behavior is seen for ANTO for events that arrive from the west. For eastern backazimuths the ANTO RFs show features whose moveout is negative as Δ -> 0. This moveout is poorly fit by reverberations in flat layers or by direct scattering from a dipping interface, but is consistent with a topographic scatterer 20--30 km eastward of the ANTO site. Regional receiver functions may therefore be useful in judging whether teleseismic RFs at a particular station are suitable candidates for a 1-D velocity structure inversion. Synthetic seismograms of regional P phases, computed with a locked-mode reflectivity approach, confirm broad features of the RAYN and ANTO regional receiver functions.

Cognitive performance and psychosocial functioning in patients with bipolar disorder, unaffected siblings, and healthy controls.

PubMed

Vasconcelos-Moreno, Mirela P; Bücker, Joana; Bürke, Kelen P; Czepielewski, Leticia; Santos, Barbara T; Fijtman, Adam; Passos, Ives C; Kunz, Mauricio; Bonnín, Caterina Del Mar; Vieta, Eduard; Kapczinski, Flavio; Rosa, Adriane R; Kauer-Sant'Anna, Marcia

2016-01-01

To assess cognitive performance and psychosocial functioning in patients with bipolar disorder (BD), in unaffected siblings, and in healthy controls. Subjects were patients with BD (n=36), unaffected siblings (n=35), and healthy controls (n=44). Psychosocial functioning was accessed using the Functioning Assessment Short Test (FAST). A sub-group of patients with BD (n=21), unaffected siblings (n=14), and healthy controls (n=22) also underwent a battery of neuropsychological tests: California Verbal Learning Test (CVLT), Stroop Color and Word Test, and Wisconsin Card Sorting Test (WCST). Clinical and sociodemographic characteristics were analyzed using one-way analysis of variance or the chi-square test; multivariate analysis of covariance was used to examine differences in neuropsychological variables. Patients with BD showed higher FAST total scores (23.90±11.35) than healthy controls (5.86±5.47; p < 0.001) and siblings (12.60±11.83; p 0.001). Siblings and healthy controls also showed statistically significant differences in FAST total scores (p = 0.008). Patients performed worse than healthy controls on all CVLT sub-tests (p < 0.030) and in the number of correctly completed categories on WCST (p = 0.030). Siblings did not differ from healthy controls in cognitive tests. Unaffected siblings of patients with BD may show poorer functional performance compared to healthy controls. FAST scores may contribute to the development of markers of vulnerability and endophenotypic traits in at-risk populations.

Relation between respiratory function and arterial stiffness assessed using brachial-ankle pulse wave velocity in healthy workers.

PubMed

Inomoto, Atsushi; Fukuda, Rika; Deguchi, Junko; Toyonaga, Toshihiro

2017-09-01

[Purpose] Current studies report that patients with chronic obstructive pulmonary disease (COPD) may also have arteriosclerosis. This study aimed to investigate the relationship between respiratory function and arterial stiffness in healthy workers using the brachial-ankle pulse wave velocity (baPWV). [Subjects and Methods] This study included 104 male Japanese workers without COPD. We collected participant information and measured hemodynamics, body composition, and respiratory function. [Results] In the correlation analysis, baPWV showed a significant positive correlation with age, smoking index, systolic blood pressure, diastolic blood pressure, and heart rate, and a significant negative correlation with height, fat free mass, lower limb muscle mass, forced vital capacity (FVC), and forced expiratory volume in one second (FEV1). In multiple regression analysis using factors other than baPWV and respiratory function as adjustment variables, both FVC and FEV1 showed a significant negative relationship with baPWV (p=0.009 and p=0.027, respectively). FEV1/FVC was not significantly related to baPWV (p=0.704). [Conclusion] The results of this study indicated that FEV1/FVC and the proportion of FEV1 predicted, which are indicators of airflow limitation, are not predictors of baPWV in workers without airflow limitation. However, since baPWV showed a significant negative relationship with FVC and FEV 1, the reduction in respiratory function that does not cause airflow limitation, such as FVC or FEV1 decline, may be related to an increase in the risk of arterial stiffness.

Influence of personality and neuropsychological ability on social functioning and self-management in bipolar disorder.

PubMed

Vierck, Esther; Joyce, Peter R

2015-10-30

A majority of bipolar patients (BD) show functional difficulties even in remission. In recent years cognitive functions and personality characteristics have been associated with occupational and psychosocial outcomes, but findings are not consistent. We assessed personality and cognitive functioning through a range of tests in BD and control participants. Three cognitive domains-verbal memory, facial-executive, and spatial memory-were extracted by principal component analysis. These factors and selected personality dimensions were included in hierarchical regression analysis to predict psychosocial functioning and the use of self-management strategies while controlling for mood status. The best determinants of good psychosocial functioning were good verbal memory and high self-directedness. The use of self-management techniques was associated with a low level of harm-avoidance. Our findings indicate that strategies to improve memory and self-directedness may be useful for increasing functioning in individuals with bipolar disorder. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Quantitative trait nucleotide analysis using Bayesian model selection.

PubMed

Blangero, John; Goring, Harald H H; Kent, Jack W; Williams, Jeff T; Peterson, Charles P; Almasy, Laura; Dyer, Thomas D

2005-10-01

Although much attention has been given to statistical genetic methods for the initial localization and fine mapping of quantitative trait loci (QTLs), little methodological work has been done to date on the problem of statistically identifying the most likely functional polymorphisms using sequence data. In this paper we provide a general statistical genetic framework, called Bayesian quantitative trait nucleotide (BQTN) analysis, for assessing the likely functional status of genetic variants. The approach requires the initial enumeration of all genetic variants in a set of resequenced individuals. These polymorphisms are then typed in a large number of individuals (potentially in families), and marker variation is related to quantitative phenotypic variation using Bayesian model selection and averaging. For each sequence variant a posterior probability of effect is obtained and can be used to prioritize additional molecular functional experiments. An example of this quantitative nucleotide analysis is provided using the GAW12 simulated data. The results show that the BQTN method may be useful for choosing the most likely functional variants within a gene (or set of genes). We also include instructions on how to use our computer program, SOLAR, for association analysis and BQTN analysis.

Binary partition tree analysis based on region evolution and its application to tree simplification.

PubMed

Lu, Huihai; Woods, John C; Ghanbari, Mohammed

2007-04-01

Pyramid image representations via tree structures are recognized methods for region-based image analysis. Binary partition trees can be applied which document the merging process with small details found at the bottom levels and larger ones close to the root. Hindsight of the merging process is stored within the tree structure and provides the change histories of an image property from the leaf to the root node. In this work, the change histories are modelled by evolvement functions and their second order statistics are analyzed by using a knee function. Knee values show the reluctancy of each merge. We have systematically formulated these findings to provide a novel framework for binary partition tree analysis, where tree simplification is demonstrated. Based on an evolvement function, for each upward path in a tree, the tree node associated with the first reluctant merge is considered as a pruning candidate. The result is a simplified version providing a reduced solution space and still complying with the definition of a binary tree. The experiments show that image details are preserved whilst the number of nodes is dramatically reduced. An image filtering tool also results which preserves object boundaries and has applications for segmentation.

Rhodium clustering process on defective (8,0) SWCNT: Analysis of chemical and physical properties using density functional theory

NASA Astrophysics Data System (ADS)

Ambrusi, Ruben E.; Luna, C. Romina; Sandoval, Mario G.; Bechthold, Pablo; Pronsato, M. Estela; Juan, Alfredo

2017-12-01

The Spin-polarized density functional theory is used to study the effect of a single vacancy in a (8,0) single-walled carbon nanotube (SWCNT) on the Rh clustering process. The vacancy is considered oxygenated and non-oxygenated and, in each case, different Rhn cluster sizes (n = 1-4) are taken into account. For the analysis of these systems some physical and chemical properties are calculated, such as binding energy (Eb), work function (WF), magnetic moment, charge transfer, bond length, band gap (Eg), and density of state (DOS). From this analysis it can be concluded that: a single Rh atom and Rh2 dimer are adsorbed on vacancy without oxygen, whereas Rh3 and Rh4 clusters prefer to be adsorbed on oxygenated vacancy. In all cases, Rh adsorption induces a magnetic moment. When the Rh atom and Rh2 dimer are bonded to the defective SWCNT, it has been found that they show a semiconductor behavior that could be interesting to use in the spintronic area. In the case of Rh3 and Rh4 clusters our results show a metallic behavior suggesting that these systems are good candidates for nanotube contact.

Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes.

PubMed

Osato, Naoki

2018-01-19

Transcriptional target genes show functional enrichment of genes. However, how many and how significantly transcriptional target genes include functional enrichments are still unclear. To address these issues, I predicted human transcriptional target genes using open chromatin regions, ChIP-seq data and DNA binding sequences of transcription factors in databases, and examined functional enrichment and gene expression level of putative transcriptional target genes. Gene Ontology annotations showed four times larger numbers of functional enrichments in putative transcriptional target genes than gene expression information alone, independent of transcriptional target genes. To compare the number of functional enrichments of putative transcriptional target genes between cells or search conditions, I normalized the number of functional enrichment by calculating its ratios in the total number of transcriptional target genes. With this analysis, native putative transcriptional target genes showed the largest normalized number of functional enrichments, compared with target genes including 5-60% of randomly selected genes. The normalized number of functional enrichments was changed according to the criteria of enhancer-promoter interactions such as distance from transcriptional start sites and orientation of CTCF-binding sites. Forward-reverse orientation of CTCF-binding sites showed significantly higher normalized number of functional enrichments than the other orientations. Journal papers showed that the top five frequent functional enrichments were related to the cellular functions in the three cell types. The median expression level of transcriptional target genes changed according to the criteria of enhancer-promoter assignments (i.e. interactions) and was correlated with the changes of the normalized number of functional enrichments of transcriptional target genes. Human putative transcriptional target genes showed significant functional enrichments. Functional enrichments were related to the cellular functions. The normalized number of functional enrichments of human putative transcriptional target genes changed according to the criteria of enhancer-promoter assignments and correlated with the median expression level of the target genes. These analyses and characters of human putative transcriptional target genes would be useful to examine the criteria of enhancer-promoter assignments and to predict the novel mechanisms and factors such as DNA binding proteins and DNA sequences of enhancer-promoter interactions.

Analysis of Water Use Efficiency derived from MODIS satellite image in Northeast Asia

NASA Astrophysics Data System (ADS)

Park, J.; Jang, K.; Kang, S.

2014-12-01

Water Use Efficiency (WUE) is defined as ratio of evapotranspriation (ET) to gross primary productivity (GPP). It can detect the changes of ecosystem properties due to the variability of enviromental condition, and provide a chance to understand the linkage between carbon and water processes in terrestrial ecosystem. In a changing climate, the understanding of ecosystem functional responses to climate variability is crucial for evaluating effect. However, continental or sub-continental scale WUE analysis is were rare. In this study, WUE was estimated in the Northeast Asia using satellite data from 2003 to 2010. ET and GPP were estimated using various MODIS products. The estimated ET and GPP showed favorable agreements with flux tower observations. WUE in the study domain showed considerable variations according to the plant functional types and climatic and elevational gradients. The results produced in this study indicate that satellite remote sensing provides a useful tool for monitoring variability of terrestrial ecosystem functions.

Uncertainty in flood damage estimates and its potential effect on investment decisions

NASA Astrophysics Data System (ADS)

Wagenaar, D. J.; de Bruijn, K. M.; Bouwer, L. M.; de Moel, H.

2016-01-01

This paper addresses the large differences that are found between damage estimates of different flood damage models. It explains how implicit assumptions in flood damage functions and maximum damages can have large effects on flood damage estimates. This explanation is then used to quantify the uncertainty in the damage estimates with a Monte Carlo analysis. The Monte Carlo analysis uses a damage function library with 272 functions from seven different flood damage models. The paper shows that the resulting uncertainties in estimated damages are in the order of magnitude of a factor of 2 to 5. The uncertainty is typically larger for flood events with small water depths and for smaller flood events. The implications of the uncertainty in damage estimates for flood risk management are illustrated by a case study in which the economic optimal investment strategy for a dike segment in the Netherlands is determined. The case study shows that the uncertainty in flood damage estimates can lead to significant over- or under-investments.

Experimental assessment and analysis of super-resolution in fluorescence microscopy based on multiple-point spread function fitting of spectrally demultiplexed images

NASA Astrophysics Data System (ADS)

Nishimura, Takahiro; Kimura, Hitoshi; Ogura, Yusuke; Tanida, Jun

2018-06-01

This paper presents an experimental assessment and analysis of super-resolution microscopy based on multiple-point spread function fitting of spectrally demultiplexed images using a designed DNA structure as a test target. For the purpose, a DNA structure was designed to have binding sites at a certain interval that is smaller than the diffraction limit. The structure was labeled with several types of quantum dots (QDs) to acquire their spatial information as spectrally encoded images. The obtained images are analyzed with a point spread function multifitting algorithm to determine the QD locations that indicate the binding site positions. The experimental results show that the labeled locations can be observed beyond the diffraction-limited resolution using three-colored fluorescence images that were obtained with a confocal fluorescence microscope. Numerical simulations show that labeling with eight types of QDs enables the positions aligned at 27.2-nm pitches on the DNA structure to be resolved with high accuracy.

Structure-function analysis of the extracellular domain of the pneumococcal cell division site positioning protein MapZ

NASA Astrophysics Data System (ADS)

Manuse, Sylvie; Jean, Nicolas L.; Guinot, Mégane; Lavergne, Jean-Pierre; Laguri, Cédric; Bougault, Catherine M.; Vannieuwenhze, Michael S.; Grangeasse, Christophe; Simorre, Jean-Pierre

2016-06-01

Accurate placement of the bacterial division site is a prerequisite for the generation of two viable and identical daughter cells. In Streptococcus pneumoniae, the positive regulatory mechanism involving the membrane protein MapZ positions precisely the conserved cell division protein FtsZ at the cell centre. Here we characterize the structure of the extracellular domain of MapZ and show that it displays a bi-modular structure composed of two subdomains separated by a flexible serine-rich linker. We further demonstrate in vivo that the N-terminal subdomain serves as a pedestal for the C-terminal subdomain, which determines the ability of MapZ to mark the division site. The C-terminal subdomain displays a patch of conserved amino acids and we show that this patch defines a structural motif crucial for MapZ function. Altogether, this structure-function analysis of MapZ provides the first molecular characterization of a positive regulatory process of bacterial cell division.

Metric for evaluation of filter efficiency in spectral cameras.

PubMed

Nahavandi, Alireza Mahmoudi; Tehran, Mohammad Amani

2016-11-10

Although metric functions that show the performance of a colorimetric imaging device have been investigated, a metric for performance analysis of a set of filters in wideband filter-based spectral cameras has rarely been studied. Based on a generalization of Vora's Measure of Goodness (MOG) and the spanning theorem, a single function metric that estimates the effectiveness of a filter set is introduced. The improved metric, named MMOG, varies between one, for a perfect, and zero, for the worst possible set of filters. Results showed that MMOG exhibits a trend that is more similar to the mean square of spectral reflectance reconstruction errors than does Vora's MOG index, and it is robust to noise in the imaging system. MMOG as a single metric could be exploited for further analysis of manufacturing errors.

Molecular structure and vibrational spectra of three substituted 4-thioflavones by density functional theory and ab initio Hartree-Fock calculations

NASA Astrophysics Data System (ADS)

Li, Xiao-Hong; Liu, Xiang-Ru; Zhang, Xian-Zhou

2011-01-01

The vibrational frequencies of three substituted 4-thioflavones in the ground state have been calculated using the Hartree-Fock and density functional method (B3LYP) with 6-31G* and 6-31+G** basis sets. The structural analysis shows that there exists H-bonding in the selected compounds and the hydrogen bond lengths increase with the augment of the conjugate parameters of the substituent group on the benzene ring. A complete vibrational assignment aided by the theoretical harmonic wavenumber analysis was proposed. The theoretical spectrograms for FT-IR spectra of the title compounds have been constructed. In addition, it is noted that the selected compounds show significant activity against Shigella flexniri. Several electronic properties and thermodynamic parameters were also calculated.

Research of GIS-services applicability for solution of spatial analysis tasks.

NASA Astrophysics Data System (ADS)

Terekhin, D. A.; Botygin, I. A.; Sherstneva, A. I.; Sherstnev, V. S.

2017-01-01

Experiments for working out the areas of applying various gis-services in the tasks of spatial analysis are discussed in this paper. Google Maps, Yandex Maps, Microsoft SQL Server are used as services of spatial analysis. All services have shown a comparable speed of analyzing the spatial data when carrying out elemental spatial requests (building up the buffer zone of a point object) as well as the preferences of Microsoft SQL Server in operating with more complicated spatial requests. When building up elemental spatial requests, internet-services show higher efficiency due to cliental data handling with JavaScript-subprograms. A weak point of public internet-services is an impossibility to handle data on a server side and a barren variety of spatial analysis functions. Microsoft SQL Server offers a large variety of functions needed for spatial analysis on the server side. The authors conclude that when solving practical problems, the capabilities of internet-services used in building up routes and completing other functions with spatial analysis with Microsoft SQL Server should be involved.

Temporal Drivers of Liking Based on Functional Data Analysis and Non-Additive Models for Multi-Attribute Time-Intensity Data of Fruit Chews.

PubMed

Kuesten, Carla; Bi, Jian

2018-06-03

Conventional drivers of liking analysis was extended with a time dimension into temporal drivers of liking (TDOL) based on functional data analysis methodology and non-additive models for multiple-attribute time-intensity (MATI) data. The non-additive models, which consider both direct effects and interaction effects of attributes to consumer overall liking, include Choquet integral and fuzzy measure in the multi-criteria decision-making, and linear regression based on variance decomposition. Dynamics of TDOL, i.e., the derivatives of the relative importance functional curves were also explored. Well-established R packages 'fda', 'kappalab' and 'relaimpo' were used in the paper for developing TDOL. Applied use of these methods shows that the relative importance of MATI curves offers insights for understanding the temporal aspects of consumer liking for fruit chews.

A Paradoxical Effect of Presession Attention on Stereotypy: Antecedent Attention as an Establishing, Not an Abolishing, Operation

ERIC Educational Resources Information Center

Roantree, Christina F.; Kennedy, Craig H.

2006-01-01

Previous studies have shown that presession attention for problem behavior can serve as an abolishing operation when attention functions as a positive reinforcer. In the current study, we show that the stereotypy of a child with severe disabilities was undifferentiated during standard analogue functional analysis conditions. However, when…

A Model for Teaching Literary Analysis Using Systemic Functional Grammar

ERIC Educational Resources Information Center

McCrocklin, Shannon; Slater, Tammy

2017-01-01

This article introduces an approach that middle-school teachers can follow to help their students carry out linguistic-based literary analyses. As an example, it draws on Systemic Functional Grammar (SFG) to show how J.K. Rowling used language to characterize Hermione as an intelligent female in "Harry Potter and the Deathly Hallows."…

Multifractal analysis with the probability density function at the three-dimensional anderson transition.

PubMed

Rodriguez, Alberto; Vasquez, Louella J; Römer, Rudolf A

2009-03-13

The probability density function (PDF) for critical wave function amplitudes is studied in the three-dimensional Anderson model. We present a formal expression between the PDF and the multifractal spectrum f(alpha) in which the role of finite-size corrections is properly analyzed. We show the non-Gaussian nature and the existence of a symmetry relation in the PDF. From the PDF, we extract information about f(alpha) at criticality such as the presence of negative fractal dimensions and the possible existence of termination points. A PDF-based multifractal analysis is shown to be a valid alternative to the standard approach based on the scaling of inverse participation ratios.

Hyperspectral functional imaging of the human brain

NASA Astrophysics Data System (ADS)

Toronov, Vladislav; Schelkanova, Irina

2013-03-01

We performed the independent component analysis of the hyperspectral functional near-infrared data acquired on humans during exercise and rest. We found that the hyperspectral functional data acquired on the human brain requires only two physiologically meaningful components to cover more than 50% o the temporal variance in hundreds of wavelengths. The analysis of the spectra of independent components showed that these components could be interpreted as results of changes in the cerebral blood volume and blood flow. Also, we found significant contributions of water and cytochrome c oxydase into changes associated with the independent components. Another remarkable effect of ICA was its good performance in terms of the filtering of the data noise.

Sampling with poling-based flux balance analysis: optimal versus sub-optimal flux space analysis of Actinobacillus succinogenes.

PubMed

Binns, Michael; de Atauri, Pedro; Vlysidis, Anestis; Cascante, Marta; Theodoropoulos, Constantinos

2015-02-18

Flux balance analysis is traditionally implemented to identify the maximum theoretical flux for some specified reaction and a single distribution of flux values for all the reactions present which achieve this maximum value. However it is well known that the uncertainty in reaction networks due to branches, cycles and experimental errors results in a large number of combinations of internal reaction fluxes which can achieve the same optimal flux value. In this work, we have modified the applied linear objective of flux balance analysis to include a poling penalty function, which pushes each new set of reaction fluxes away from previous solutions generated. Repeated poling-based flux balance analysis generates a sample of different solutions (a characteristic set), which represents all the possible functionality of the reaction network. Compared to existing sampling methods, for the purpose of generating a relatively "small" characteristic set, our new method is shown to obtain a higher coverage than competing methods under most conditions. The influence of the linear objective function on the sampling (the linear bias) constrains optimisation results to a subspace of optimal solutions all producing the same maximal fluxes. Visualisation of reaction fluxes plotted against each other in 2 dimensions with and without the linear bias indicates the existence of correlations between fluxes. This method of sampling is applied to the organism Actinobacillus succinogenes for the production of succinic acid from glycerol. A new method of sampling for the generation of different flux distributions (sets of individual fluxes satisfying constraints on the steady-state mass balances of intermediates) has been developed using a relatively simple modification of flux balance analysis to include a poling penalty function inside the resulting optimisation objective function. This new methodology can achieve a high coverage of the possible flux space and can be used with and without linear bias to show optimal versus sub-optimal solution spaces. Basic analysis of the Actinobacillus succinogenes system using sampling shows that in order to achieve the maximal succinic acid production CO₂ must be taken into the system. Solutions involving release of CO₂ all give sub-optimal succinic acid production.

Towards tests of quark-hadron duality with functional analysis and spectral function data

NASA Astrophysics Data System (ADS)

Boito, Diogo; Caprini, Irinel

2017-04-01

The presence of terms that violate quark-hadron duality in the expansion of QCD Green's functions is a generally accepted fact. Recently, a new approach was proposed for the study of duality violations (DVs), which exploits the existence of a rigorous lower bound on the functional distance, measured in a certain norm, between a "true" correlator and its approximant calculated theoretically along a contour in the complex energy plane. In the present paper, we pursue the investigation of functional-analysis-based tests towards their application to real spectral function data. We derive a closed analytic expression for the minimal functional distance based on the general weighted L2 norm and discuss its relation with the distance measured in the L∞ norm. Using fake data sets obtained from a realistic toy model in which we allow for covariances inspired from the publicly available ALEPH spectral functions, we obtain, by Monte Carlo simulations, the statistical distribution of the strength parameter that measures the magnitude of the DV term added to the usual operator product expansion. The results show that, if the region with large errors near the end point of the spectrum in τ decays is excluded, the functional-analysis-based tests using either L2 or L∞ norms are able to detect, in a statistically significant way, the presence of DVs in realistic spectral function pseudodata.

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

Wendler, J. J., E-mail: johann.wendler@med.ovgu.de; Porsch, M.; Huehne, S.

Irreversible electroporation (IRE) is a novel nonthermal tissue ablation technique by high current application leading to apoptosis without affecting extracellular matrix. Previous results of renal IRE shall be supplemented by functional MRI and differentiated histological analysis of renal parenchyma in a chronic treatment setting. Three swine were treated with two to three multifocal percutaneous IRE of the right kidney. MRI was performed before, 30 min (immediate-term), 7 days (short-term), and 28 days (mid-term) after IRE. A statistical analysis of the lesion surrounded renal parenchyma intensities was made to analyze functional differences depending on renal part, side and posttreatment time. Histologicalmore » follow-up of cortex and medulla was performed after 28 days. A total of eight ablations were created. MRI showed no collateral damage of surrounded tissue. The highest visual contrast between lesions and normal parenchyma was obtained by T2-HR-SPIR-TSE-w sequence of DCE-MRI. Ablation zones showed inhomogeneous necroses with small perifocal edema in the short-term and sharp delimitable scars in the mid-term. MRI showed no significant differences between adjoined renal parenchyma around ablations and parenchyma of untreated kidney. Histological analysis demonstrated complete destruction of cortical glomeruli and tubules, while collecting ducts, renal calyxes, and pelvis of medulla were preserved. Adjoined kidney parenchyma around IRE lesions showed no qualitative differences to normal parenchyma of untreated kidney. This porcine IRE study reveals a multifocal renal ablation, while protecting surrounded renal parenchyma and collecting system over a mid-term period. That offers prevention of renal function ablating centrally located or multifocal renal masses.« less

Quantum mechanical study and spectroscopic (FT-IR, FT-Raman, 13C, 1H) study, first order hyperpolarizability, NBO analysis, HOMO and LUMO analysis of 2-acetoxybenzoic acid by density functional methods

NASA Astrophysics Data System (ADS)

Bhavani, K.; Renuga, S.; Muthu, S.; Sankara narayanan, K.

2015-02-01

In this work, colorless crystals of 2-acetoxybenzoic acid were grown by slow evaporation method and the FT-IR and FT-Raman spectra of the sample were recorded in the region 4000-500 cm-1 and 4000-100 cm-1 respectively. Molecular structure is optimized with the help of density functional theory method (B3LYP) with 6-31+G(d,p), 6-311++G(d,p) basis sets. Stability of the molecule arising from hyperconjugation and charge delocalization is confirmed by the natural bond orbital analysis (NBO). The results show that electron density (ED) in the σ∗ antibonding orbitals and E(2) energies confirms the occurrence of intramolecular charge transfer (ICT) within the molecule. The assignments of the vibrational spectra have been carried out with the help of normal coordinate analysis following the scaled quantum mechanical force field (SQMFF) methodology. The results of the calculations were applied to simulated spectra of the title compound, which show excellent agreement with observed spectra. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by GIAO method. Mulliken population analysis on atomic charges is also calculated. The calculated HOMO and LUMO energy gap shows that charge transfer occurs within the molecule.

Evaluation and integration of functional annotation pipelines for newly sequenced organisms: the potato genome as a test case.

PubMed

Amar, David; Frades, Itziar; Danek, Agnieszka; Goldberg, Tatyana; Sharma, Sanjeev K; Hedley, Pete E; Proux-Wera, Estelle; Andreasson, Erik; Shamir, Ron; Tzfadia, Oren; Alexandersson, Erik

2014-12-05

For most organisms, even if their genome sequence is available, little functional information about individual genes or proteins exists. Several annotation pipelines have been developed for functional analysis based on sequence, 'omics', and literature data. However, researchers encounter little guidance on how well they perform. Here, we used the recently sequenced potato genome as a case study. The potato genome was selected since its genome is newly sequenced and it is a non-model plant even if there is relatively ample information on individual potato genes, and multiple gene expression profiles are available. We show that the automatic gene annotations of potato have low accuracy when compared to a "gold standard" based on experimentally validated potato genes. Furthermore, we evaluate six state-of-the-art annotation pipelines and show that their predictions are markedly dissimilar (Jaccard similarity coefficient of 0.27 between pipelines on average). To overcome this discrepancy, we introduce a simple GO structure-based algorithm that reconciles the predictions of the different pipelines. We show that the integrated annotation covers more genes, increases by over 50% the number of highly co-expressed GO processes, and obtains much higher agreement with the gold standard. We find that different annotation pipelines produce different results, and show how to integrate them into a unified annotation that is of higher quality than each single pipeline. We offer an improved functional annotation of both PGSC and ITAG potato gene models, as well as tools that can be applied to additional pipelines and improve annotation in other organisms. This will greatly aid future functional analysis of '-omics' datasets from potato and other organisms with newly sequenced genomes. The new potato annotations are available with this paper.

Urea functionalized surface-bonded sol-gel coating for on-line hyphenation of capillary microextraction with high-performance liquid chromatography.

PubMed

Jillani, Shehzada Muhammad Sajid; Alhooshani, Khalid

2018-03-30

Sol-gel urea functionalized-[bis(hydroxyethyl)amine] terminated polydimethylsiloxane coating was developed for capillary microextraction-high performance liquid chromatographic analysis from aqueous samples. A fused silica capillary is coated from the inside with surface bonded coating material and is created through in-situ sol-gel reaction. The urea-functionalized coating was immobilized to the inner surface of the capillary by the condensation reaction of silanol groups of capillary and sol-solution. The characterization of the coating material was successfully done by using X-ray photoelectron spectroscopy, thermogravimetric analysis, field emission scanning electron microscope, and energy dispersive X-ray spectrometer. To make a setup of online capillary microextraction-high performance liquid chromatography, the urea functionalized capillary was installed in the HPLC manual injection port. The analytes of interest were pre-concentrated in the coated sampling loop, desorbed by the mobile phase, chromatographically separated on C-18 column, and analyzed by UV detector. Sol-gel coated capillaries were used for online extraction and high-performance liquid chromatographic analysis of phenols, ketones, aldehydes, and polyaromatic hydrocarbons. This newly developed coating showed excellent extraction for a variety of analytes ranging from highly polar to non-polar in nature. The analysis using sol-gel coating showed excellent overall sensitivity in terms of lower detection limits (S/N = 3) for the analytes (0.10 ng mL -1 -14.29 ng mL -1 ) with acceptable reproducibility that is less than 12.0%RSD (n = 3). Moreover, the capillary to capillary reproducibility of the analysis was also tested by changing the capillary of the same size. This provided excellent%RSD of less than 10.0% (n = 3). Copyright © 2018 Elsevier B.V. All rights reserved.

Surface analysis of gold nanoparticles functionalized with thiol-modified glucose SAMs for biosensor applications.

NASA Astrophysics Data System (ADS)

Spampinato, Valentina; Parracino, Mariaantonietta; La Spina, Rita; Rossi, Francois; Ceccone, Giacomo

2016-02-01

In this work, Time of Flight Secondary Ion Mass Spectrometry (ToF-SIMS), Principal Component Analysis (PCA) and X-ray Photoelectron Spectroscopy (XPS) have been used to characterize the surface chemistry of gold substrates before and after functionalization with thiol-modified glucose self-assembled monolayers and subsequent biochemical specific recognition of maltose binding protein (MBP). The results indicate that the surface functionalization is achieved both on flat and nanoparticles gold substrates thus showing the potential of the developed system as biodetection platform. Moreover, the method presented here has been found to be a sound and valid approach to characterize the surface chemistry of nanoparticles functionalized with large molecules. Both techniques were proved to be very useful tools for monitoring all the functionalization steps, including the investigation of the biological behaviour of the glucose-modified particles in presence of the maltose binding protein.

Surface Analysis of Gold Nanoparticles Functionalized with Thiol-Modified Glucose SAMs for Biosensor Applications

PubMed Central

Spampinato, Valentina; Parracino, Maria Antonietta; La Spina, Rita; Rossi, Francois; Ceccone, Giacomo

2016-01-01

In this work, Time of Flight Secondary Ion Mass Spectrometry (ToF-SIMS), Principal Component Analysis (PCA) and X-ray Photoelectron Spectroscopy (XPS) have been used to characterize the surface chemistry of gold substrates before and after functionalization with thiol-modified glucose self-assembled monolayers and subsequent biochemical specific recognition of maltose binding protein (MBP). The results indicate that the surface functionalization is achieved both on flat and nanoparticles gold substrates thus showing the potential of the developed system as biodetection platform. Moreover, the method presented here has been found to be a sound and valid approach to characterize the surface chemistry of nanoparticles functionalized with large molecules. Both techniques were proved to be very useful tools for monitoring all the functionalization steps, including the investigation of the biological behavior of the glucose-modified particles in the presence of the maltose binding protein. PMID:26973830

[Relationships between soil and rocky desertification in typical karst mountain area based on redundancy analysis].

PubMed

Long, Jian; Liao, Hong-Kai; Li, Juan; Chen, Cai-Yun

2012-06-01

Redundancy analysis (RDA) was employed to reveal the relationships between soil and rocky desertification through vegetation investigation and analysis of soil samples collected in typical karst mountain area of southwest Guizhou Province. The results showed that except TP, TK and ACa, all other variables including SOC, TN, MBC, ROC, DOC, available nutrients and basal respiration showed significant downward trends during the rocky desertification process. RDA results showed significant correlations between different types of desertification and soil variables, described as non-degraded > potential desertification > light desertification > moderate desertification > severe desertification. Moreover, RDA showed that using SOC, TN, AN, and BD as soil indicators, 74.4% of the variance information on soil and rocky desertification could be explained. Furthermore, the results of correlation analysis showed that soil variables were significantly affected by surface vegetation. Considering the ecological function of the aboveground vegetation and the soil quality, Zanthoxylum would be a good choice for restoration of local vegetation in karst mountain area.

Proteomic Analysis of the Arabidopsis Nucleolus Suggests Novel Nucleolar FunctionsD⃞

PubMed Central

Pendle, Alison F.; Clark, Gillian P.; Boon, Reinier; Lewandowska, Dominika; Lam, Yun Wah; Andersen, Jens; Mann, Matthias; Lamond, Angus I.; Brown, John W. S.; Shaw, Peter J.

2005-01-01

The eukaryotic nucleolus is involved in ribosome biogenesis and a wide range of other RNA metabolism and cellular functions. An important step in the functional analysis of the nucleolus is to determine the complement of proteins of this nuclear compartment. Here, we describe the first proteomic analysis of plant (Arabidopsis thaliana) nucleoli, in which we have identified 217 proteins. This allows a direct comparison of the proteomes of an important nuclear structure between two widely divergent species: human and Arabidopsis. The comparison identified many common proteins, plant-specific proteins, proteins of unknown function found in both proteomes, and proteins that were nucleolar in plants but nonnucleolar in human. Seventy-two proteins were expressed as GFP fusions and 87% showed nucleolar or nucleolar-associated localization. In a striking and unexpected finding, we have identified six components of the postsplicing exon-junction complex (EJC) involved in mRNA export and nonsense-mediated decay (NMD)/mRNA surveillance. This association was confirmed by GFP-fusion protein localization. These results raise the possibility that in plants, nucleoli may have additional functions in mRNA export or surveillance. PMID:15496452

Evaluation of nutritional value, characteristics, functional properties of Cymodocea nodosa and its benefits on health diseases.

PubMed

Kolsi, Rihab Ben Abdallah; Salah, Hichem Ben; Saidi, Saber Abdelkader; Allouche, Noureddine; Belghith, Hafedh; Belghith, Karima

2017-12-08

Nutritional fact study has prime importance to make the species edible and commercially viable to the food consumers. This is the first report that indicates the chemical characterization, functional, antioxidant and antihypertensive properties of Cymodocea nodosa to evaluate its nutritional status. Physico-chemical determination was determined by colorimetric and spectroscopic analysis. The functional and texture properties were evaluated since a desirable texture should be retained. Bioactive substances were determined by liquid chromatography-high resolution electrospray ionization mass spectrometry HPLC-DAD-ESI/MS2 analysis. Health benefit of this plant was highlighting by the antioxidant and antihypertensive potentials. Results showed that the seagrass powder was characterized by a high content of fibers (56.4%), the fatty acids profile was dominated by the oleic acid, which represents about 62.0% of the total fatty acids and the functional properties proved important values of swelling capacity (6.71 ± 0.2) and water holding capacity (12.26 ± 0.25), that were comparable to those of some foodstuffs. Finally, the physico-chemical analysis shows the wealth in phenolic compounds, that could be explained by the high antioxidant and antihypertensive ability which was concentration dependent. The results from this study suggested that this marine plant could be utilized as a healthy food item for human consumption.

Biodegradable nasal stents (MgF2 -coated Mg-2 wt %Nd alloy)-A long-term in vivo study.

PubMed

Durisin, Martin; Reifenrath, Janin; Weber, Constantin M; Eifler, Rainer; Maier, Hans J; Lenarz, Thomas; Seitz, Jan-Marten

2017-02-01

Despite innovative surgical techniques and use of current frontal sinus stents from different materials, the problem of treatment failure with consecutive reoperation remains present. The aim of our study is to investigate biocompatibility, degradation kinetics, and functionality of a newly developed fluoride-coated magnesium-based nasal stent. A minipig anatomy of frontal sinus adapted design and an external surgical approach were developed and established. The functionality of the stents was evaluated endoscopically. The stent-tissue blocks were analysed after 90 and 180 days using microcomputed tomography (µ-CT), histology, scanning electron microscopy (SEM), and energy-dispersive X-ray spectroscopy (EDS). Functional evaluation revealed an unobstructed stent lumen in all cases. Histological analysis showed moderate mucosal hyperplasia with a mild, nonspecific inflammatory response, and nonosteoconductive effect. Rejection reactions or necrosis did not occur. The volumetric analysis of the stents showed 51% volume loss after 180 days. The EDS analysis did not detect any neodymium (Nd) in the mucosa or bone. The Mg-2 wt % Nd stents are a promising option when treating the narrow passages following paranasal sinus surgery. In particular, its good biocompatibility and good functionality facilitate the re-epithelization of these constricted passages. © 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 105B: 350-365, 2017. © 2015 Wiley Periodicals, Inc.

Subgrouping Automata: automatic sequence subgrouping using phylogenetic tree-based optimum subgrouping algorithm.

PubMed

Seo, Joo-Hyun; Park, Jihyang; Kim, Eun-Mi; Kim, Juhan; Joo, Keehyoung; Lee, Jooyoung; Kim, Byung-Gee

2014-02-01

Sequence subgrouping for a given sequence set can enable various informative tasks such as the functional discrimination of sequence subsets and the functional inference of unknown sequences. Because an identity threshold for sequence subgrouping may vary according to the given sequence set, it is highly desirable to construct a robust subgrouping algorithm which automatically identifies an optimal identity threshold and generates subgroups for a given sequence set. To meet this end, an automatic sequence subgrouping method, named 'Subgrouping Automata' was constructed. Firstly, tree analysis module analyzes the structure of tree and calculates the all possible subgroups in each node. Sequence similarity analysis module calculates average sequence similarity for all subgroups in each node. Representative sequence generation module finds a representative sequence using profile analysis and self-scoring for each subgroup. For all nodes, average sequence similarities are calculated and 'Subgrouping Automata' searches a node showing statistically maximum sequence similarity increase using Student's t-value. A node showing the maximum t-value, which gives the most significant differences in average sequence similarity between two adjacent nodes, is determined as an optimum subgrouping node in the phylogenetic tree. Further analysis showed that the optimum subgrouping node from SA prevents under-subgrouping and over-subgrouping. Copyright © 2013. Published by Elsevier Ltd.

Characterization of functional brain activity and connectivity using EEG and fMRI in patients with sickle cell disease.

PubMed

Case, Michelle; Zhang, Huishi; Mundahl, John; Datta, Yvonne; Nelson, Stephen; Gupta, Kalpna; He, Bin

2017-01-01

Sickle cell disease (SCD) is a red blood cell disorder that causes many complications including life-long pain. Treatment of pain remains challenging due to a poor understanding of the mechanisms and limitations to characterize and quantify pain. In the present study, we examined simultaneously recording functional MRI (fMRI) and electroencephalogram (EEG) to better understand neural connectivity as a consequence of chronic pain in SCD patients. We performed independent component analysis and seed-based connectivity on fMRI data. Spontaneous power and microstate analysis was performed on EEG-fMRI data. ICA analysis showed that patients lacked activity in the default mode network (DMN) and executive control network compared to controls. EEG-fMRI data revealed that the insula cortex's role in salience increases with age in patients. EEG microstate analysis showed patients had increased activity in pain processing regions. The cerebellum in patients showed a stronger connection to the periaqueductal gray matter (involved in pain inhibition), and negative connections to pain processing areas. These results suggest that patients have reduced activity of DMN and increased activity in pain processing regions during rest. The present findings suggest resting state connectivity differences between patients and controls can be used as novel biomarkers of SCD pain.

Local linear regression for function learning: an analysis based on sample discrepancy.

PubMed

Cervellera, Cristiano; Macciò, Danilo

2014-11-01

Local linear regression models, a kind of nonparametric structures that locally perform a linear estimation of the target function, are analyzed in the context of empirical risk minimization (ERM) for function learning. The analysis is carried out with emphasis on geometric properties of the available data. In particular, the discrepancy of the observation points used both to build the local regression models and compute the empirical risk is considered. This allows to treat indifferently the case in which the samples come from a random external source and the one in which the input space can be freely explored. Both consistency of the ERM procedure and approximating capabilities of the estimator are analyzed, proving conditions to ensure convergence. Since the theoretical analysis shows that the estimation improves as the discrepancy of the observation points becomes smaller, low-discrepancy sequences, a family of sampling methods commonly employed for efficient numerical integration, are also analyzed. Simulation results involving two different examples of function learning are provided.

Minnesota Computer Aided Library System (MCALS); University of Minnesota Subsystem Cost/Benefits Analysis.

ERIC Educational Resources Information Center

Lourey, Eugene D., Comp.

The Minnesota Computer Aided Library System (MCALS) provides a basis of unification for library service program development in Minnesota for eventual linkage to the national information network. A prototype plan for communications functions is illustrated. A cost/benefits analysis was made to show the cost/effectiveness potential for MCALS. System…

Three-dimensional thermal analysis of a high-level waste repository

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

Altenbach, T.J.

1979-04-01

The analysis used the TRUMP computer code to evaluate the thermal fields for six repository scenarios that studied the effects of room ventilation, room backfill, and repository thermal diffusivity. The results for selected nodes are presented as plots showing the effect of temperature as a function of time. 15 figures, 6 tables.

Standardized residual as response function for order identification of multi input intervention analysis

NASA Astrophysics Data System (ADS)

Suhartono, Lee, Muhammad Hisyam; Rezeki, Sri

2017-05-01

Intervention analysis is a statistical model in the group of time series analysis which is widely used to describe the effect of an intervention caused by external or internal factors. An example of external factors that often occurs in Indonesia is a disaster, both natural or man-made disaster. The main purpose of this paper is to provide the results of theoretical studies on identification step for determining the order of multi inputs intervention analysis for evaluating the magnitude and duration of the impact of interventions on time series data. The theoretical result showed that the standardized residuals could be used properly as response function for determining the order of multi inputs intervention model. Then, these results are applied for evaluating the impact of a disaster on a real case in Indonesia, i.e. the magnitude and duration of the impact of the Lapindo mud on the volume of vehicles on the highway. Moreover, the empirical results showed that the multi inputs intervention model can describe and explain accurately the magnitude and duration of the impact of disasters on a time series data.

A stock market forecasting model combining two-directional two-dimensional principal component analysis and radial basis function neural network.

PubMed

Guo, Zhiqiang; Wang, Huaiqing; Yang, Jie; Miller, David J

2015-01-01

In this paper, we propose and implement a hybrid model combining two-directional two-dimensional principal component analysis ((2D)2PCA) and a Radial Basis Function Neural Network (RBFNN) to forecast stock market behavior. First, 36 stock market technical variables are selected as the input features, and a sliding window is used to obtain the input data of the model. Next, (2D)2PCA is utilized to reduce the dimension of the data and extract its intrinsic features. Finally, an RBFNN accepts the data processed by (2D)2PCA to forecast the next day's stock price or movement. The proposed model is used on the Shanghai stock market index, and the experiments show that the model achieves a good level of fitness. The proposed model is then compared with one that uses the traditional dimension reduction method principal component analysis (PCA) and independent component analysis (ICA). The empirical results show that the proposed model outperforms the PCA-based model, as well as alternative models based on ICA and on the multilayer perceptron.

A Stock Market Forecasting Model Combining Two-Directional Two-Dimensional Principal Component Analysis and Radial Basis Function Neural Network

PubMed Central

Guo, Zhiqiang; Wang, Huaiqing; Yang, Jie; Miller, David J.

2015-01-01

In this paper, we propose and implement a hybrid model combining two-directional two-dimensional principal component analysis ((2D)2PCA) and a Radial Basis Function Neural Network (RBFNN) to forecast stock market behavior. First, 36 stock market technical variables are selected as the input features, and a sliding window is used to obtain the input data of the model. Next, (2D)2PCA is utilized to reduce the dimension of the data and extract its intrinsic features. Finally, an RBFNN accepts the data processed by (2D)2PCA to forecast the next day's stock price or movement. The proposed model is used on the Shanghai stock market index, and the experiments show that the model achieves a good level of fitness. The proposed model is then compared with one that uses the traditional dimension reduction method principal component analysis (PCA) and independent component analysis (ICA). The empirical results show that the proposed model outperforms the PCA-based model, as well as alternative models based on ICA and on the multilayer perceptron. PMID:25849483

Identification and Characterization of Bioactive Peptides of Fermented Goat Milk as a Sources of Antioxidant as a Therapeutic Natural Product

NASA Astrophysics Data System (ADS)

Mahdi, Chanif; Untari, Handayu; Cendrakasih Padaga, Masdiana

2018-01-01

The increasing of functional food is rising in line with public awareness for healthy food consumption. Provision of functional food source is developed through enhanced bioactive that has a regulatory function for body. Bioactive peptides in milk is known have variety of beneficial function of the body such as immunomodulator, immunostimulatory, anti-hypertension, anti-hyper cholesterol, as well as a variety of other beneficial function. The aim of this study is to obtain fermentation methods to product functional dairy product contain bioactive peptides and beneficial of fermented goat milk. The result of this study showed that goat milk fermented using 3 % commercial starter able to produce the best yoghurt than using local yoghurt starter. Analysis of protein content showed that the fermentation processing increased the amount of protein in goat milk sample. Using SDS-PAGE showed that the breakdown of protein into fraction of fermented goat milk greater than unfermented goat milk. The result of fractional protein was analyzed by LC MS/MS and showed that there were three kind bioactive sequences of bioactive peptides. Each of which consist of 16 amino acids that safely protected from gastrointestinal animal model that fed by dietary treatment of hypercholesterolemia.

Genome-Wide Analysis of the NADK Gene Family in Plants

PubMed Central

Li, Wen-Yan; Wang, Xiang; Li, Ri; Li, Wen-Qiang; Chen, Kun-Ming

2014-01-01

Background NAD(H) kinase (NADK) is the key enzyme that catalyzes de novo synthesis of NADP(H) from NAD(H) for NADP(H)-based metabolic pathways. In plants, NADKs form functional subfamilies. Studies of these families in Arabidopsis thaliana indicate that they have undergone considerable evolutionary selection; however, the detailed evolutionary history and functions of the various NADKs in plants are not clearly understood. Principal Findings We performed a comparative genomic analysis that identified 74 NADK gene homologs from 24 species representing the eight major plant lineages within the supergroup Plantae: glaucophytes, rhodophytes, chlorophytes, bryophytes, lycophytes, gymnosperms, monocots and eudicots. Phylogenetic and structural analysis classified these NADK genes into four well-conserved subfamilies with considerable variety in the domain organization and gene structure among subfamily members. In addition to the typical NAD_kinase domain, additional domains, such as adenylate kinase, dual-specificity phosphatase, and protein tyrosine phosphatase catalytic domains, were found in subfamily II. Interestingly, NADKs in subfamily III exhibited low sequence similarity (∼30%) in the kinase domain within the subfamily and with the other subfamilies. These observations suggest that gene fusion and exon shuffling may have occurred after gene duplication, leading to specific domain organization seen in subfamilies II and III, respectively. Further analysis of the exon/intron structures showed that single intron loss and gain had occurred, yielding the diversified gene structures, during the process of structural evolution of NADK family genes. Finally, both available global microarray data analysis and qRT-RCR experiments revealed that the NADK genes in Arabidopsis and Oryza sativa show different expression patterns in different developmental stages and under several different abiotic/biotic stresses and hormone treatments, underscoring the functional diversity and functional divergence of the NADK family in plants. Conclusions These findings will facilitate further studies of the NADK family and provide valuable information for functional validation of this family in plants. PMID:24968225

How can we explain the frontal presentation of insular lobe epilepsy? The impact of non-linear analysis of insular seizures.

PubMed

Hagiwara, Koichi; Jung, Julien; Bouet, Romain; Abdallah, Chifaou; Guénot, Marc; Garcia-Larrea, Luis; Mauguière, François; Rheims, Sylvain; Isnard, Jean

2017-05-01

For a decade it has been known that the insular lobe epilepsy can mimic frontal lobe epilepsy. We aimed to clarify the pattern of functional coupling occurring during the frontal presentation. We analyzed five insular lobe epilepsy patients. Frontal semiology was predominant for three of them, whereas insular semiology was predominant for the two others. We applied the non-linear regression analysis to stereoelectroencephalography-recorded seizures. A directed functional coupling index was calculated during clonic discharge periods that were accompanied either with frontal or insular semiology. We found significant functional coupling between the insula and mesial frontal/cingulate regions, with the former being a leader region for seizures propagation. Extra-insular regions showed significantly less or even no coupling with the mesial hemispheric regions. The three patients with frontal semiology showed strong couplings with the mesial frontal as well as cingulate regions, including the medial orbitofrontal cortex, pre-SMA/SMA, and the anterior to posterior cingulate. The two patients with the insular semiology only showed couplings between the insula and cingulate regions. The frontal semiology was expressed by strong functional couplings between the insula and mesial frontal regions. The insular origin of seizure should be considered in cryptogenic mesial frontal epilepsies. Copyright © 2017 International Federation of Clinical Neurophysiology. Published by Elsevier B.V. All rights reserved.

Seizure-Related Regulation of GABAA Receptors in Spontaneously Epileptic Rats

PubMed Central

González, Marco I.; Grabenstatter, Heidi L.; del Rio, Christian Cea; Del Angel, Yasmin Cruz; Carlsen, Jessica; Laoprasert, Rick; White, Andrew M.; Huntsman, Molly M.; Brooks-Kayal, Amy

2015-01-01

In this study, we analyzed the impact that spontaneous seizures might have on the plasma membrane expression, composition and function of GABAA receptors (GABAARs). For this, tissue of chronically epileptic rats was collected within 3 hours of seizure occurrence (≤3 hours group) or at least 24 hours after seizure occurrence (≥24 hours group). A retrospective analysis of seizure frequency revealed that selecting animals on the bases of seizure proximity also grouped animals in terms of overall seizure burden with a higher seizure burden observed in the ≤3 hours group. A biochemical analysis showed that although animals with more frequent/recent seizures (≤3 hours group) had similar levels of GABAAR at the plasma membrane they showed deficits in inhibitory neurotransmission. In contrast, tissue obtained from animals experiencing infrequent seizures (≥24 hours group) had increased plasma membrane levels of GABAAR and showed no deficit in inhibitory function. Together, our findings offer an initial insight into the molecular changes that might help to explain how alterations in GABAAR function can be associated with differential seizure burden. Our findings also suggest that increased plasma membrane levels of GABAAR might act as a compensatory mechanism to more effectively maintain inhibitory function, repress hyperexcitability and reduce seizure burden. This study is an initial step towards a fuller characterization of the molecular events that trigger alterations in GABAergic neurotransmission during chronic epilepsy. PMID:25769812

Two dimensional eye tracking: Sampling rate of forcing function

NASA Technical Reports Server (NTRS)

Hornseth, J. P.; Monk, D. L.; Porterfield, J. L.; Mcmurry, R. L.

1978-01-01

A study was conducted to determine the minimum update rate of a forcing function display required for the operator to approximate the tracking performance obtained on a continuous display. In this study, frequency analysis was used to determine whether there was an associated change in the transfer function characteristics of the operator. It was expected that as the forcing function display update rate was reduced, from 120 to 15 samples per second, the operator's response to the high frequency components of the forcing function would show a decrease in gain, an increase in phase lag, and a decrease in coherence.

Comparison of dose response functions for EBT3 model GafChromic™ film dosimetry system.

PubMed

Aldelaijan, Saad; Devic, Slobodan

2018-05-01

Different dose response functions of EBT3 model GafChromic™ film dosimetry system have been compared in terms of sensitivity as well as uncertainty vs. error analysis. We also made an assessment of the necessity of scanning film pieces before and after irradiation. Pieces of EBT3 film model were irradiated to different dose values in Solid Water (SW) phantom. Based on images scanned in both reflection and transmission mode before and after irradiation, twelve different response functions were calculated. For every response function, a reference radiochromic film dosimetry system was established by generating calibration curve and by performing the error vs. uncertainty analysis. Response functions using pixel values from the green channel demonstrated the highest sensitivity in both transmission and reflection mode. All functions were successfully fitted with rational functional form, and provided an overall one-sigma uncertainty of better than 2% for doses above 2 Gy. Use of pre-scanned images to calculate response functions resulted in negligible improvement in dose measurement accuracy. Although reflection scanning mode provides higher sensitivity and could lead to a more widespread use of radiochromic film dosimetry, it has fairly limited dose range and slightly increased uncertainty when compared to transmission scan based response functions. Double-scanning technique, either in transmission or reflection mode, shows negligible improvement in dose accuracy as well as a negligible increase in dose uncertainty. Normalized pixel value of the images scanned in transmission mode shows linear response in a dose range of up to 11 Gy. Copyright © 2018 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

A "footprint" of plant carbon fixation cycle functions during the development of a heterotrophic fungus.

PubMed

Lyu, Xueliang; Shen, Cuicui; Xie, Jiatao; Fu, Yanping; Jiang, Daohong; Hu, Zijin; Tang, Lihua; Tang, Liguang; Ding, Feng; Li, Kunfei; Wu, Song; Hu, Yanping; Luo, Lilian; Li, Yuanhao; Wang, Qihua; Li, Guoqing; Cheng, Jiasen

2015-08-11

Carbon fixation pathway of plants (CFPP) in photosynthesis converts solar energy to biomass, bio-products and biofuel. Intriguingly, a large number of heterotrophic fungi also possess enzymes functionally associated with CFPP, raising the questions about their roles in fungal development and in evolution. Here, we report on the presence of 17 CFPP associated enzymes (ten in Calvin-Benson-Basham reductive pentose phosphate pathway and seven in C4-dicarboxylic acid cycle) in the genome of Sclerotinia sclerotiorum, a heterotrophic phytopathogenic fungus, and only two unique enzymes: ribulose-1, 5-bisphosphate carboxylase-oxygenase (Rubisco) and phosphoribulokinase (PRK) were absent. This data suggested an incomplete CFPP-like pathway (CLP) in fungi. Functional profile analysis demonstrated that the activity of the incomplete CLP was dramatically regulated during different developmental stages of S. sclerotiorum. Subsequent experiments confirmed that many of them were essential to the virulence and/or sclerotial formation. Most of the CLP associated genes are conserved in fungi. Phylogenetic analysis showed that many of them have undergone gene duplication, gene acquisition or loss and functional diversification in evolutionary history. These findings showed an evolutionary links in the carbon fixation processes of autotrophs and heterotrophs and implicated the functions of related genes were in course of continuous change in different organisms in evolution.

Discovering transnosological molecular basis of human brain diseases using biclustering analysis of integrated gene expression data.

PubMed

Cha, Kihoon; Hwang, Taeho; Oh, Kimin; Yi, Gwan-Su

2015-01-01

It has been reported that several brain diseases can be treated as transnosological manner implicating possible common molecular basis under those diseases. However, molecular level commonality among those brain diseases has been largely unexplored. Gene expression analyses of human brain have been used to find genes associated with brain diseases but most of those studies were restricted either to an individual disease or to a couple of diseases. In addition, identifying significant genes in such brain diseases mostly failed when it used typical methods depending on differentially expressed genes. In this study, we used a correlation-based biclustering approach to find coexpressed gene sets in five neurodegenerative diseases and three psychiatric disorders. By using biclustering analysis, we could efficiently and fairly identified various gene sets expressed specifically in both single and multiple brain diseases. We could find 4,307 gene sets correlatively expressed in multiple brain diseases and 3,409 gene sets exclusively specified in individual brain diseases. The function enrichment analysis of those gene sets showed many new possible functional bases as well as neurological processes that are common or specific for those eight diseases. This study introduces possible common molecular bases for several brain diseases, which open the opportunity to clarify the transnosological perspective assumed in brain diseases. It also showed the advantages of correlation-based biclustering analysis and accompanying function enrichment analysis for gene expression data in this type of investigation.

Discovering transnosological molecular basis of human brain diseases using biclustering analysis of integrated gene expression data

PubMed Central

2015-01-01

Background It has been reported that several brain diseases can be treated as transnosological manner implicating possible common molecular basis under those diseases. However, molecular level commonality among those brain diseases has been largely unexplored. Gene expression analyses of human brain have been used to find genes associated with brain diseases but most of those studies were restricted either to an individual disease or to a couple of diseases. In addition, identifying significant genes in such brain diseases mostly failed when it used typical methods depending on differentially expressed genes. Results In this study, we used a correlation-based biclustering approach to find coexpressed gene sets in five neurodegenerative diseases and three psychiatric disorders. By using biclustering analysis, we could efficiently and fairly identified various gene sets expressed specifically in both single and multiple brain diseases. We could find 4,307 gene sets correlatively expressed in multiple brain diseases and 3,409 gene sets exclusively specified in individual brain diseases. The function enrichment analysis of those gene sets showed many new possible functional bases as well as neurological processes that are common or specific for those eight diseases. Conclusions This study introduces possible common molecular bases for several brain diseases, which open the opportunity to clarify the transnosological perspective assumed in brain diseases. It also showed the advantages of correlation-based biclustering analysis and accompanying function enrichment analysis for gene expression data in this type of investigation. PMID:26043779

Functional Techniques for Data Analysis

NASA Technical Reports Server (NTRS)

Tomlinson, John R.

1997-01-01

This dissertation develops a new general method of solving Prony's problem. Two special cases of this new method have been developed previously. They are the Matrix Pencil and the Osculatory Interpolation. The dissertation shows that they are instances of a more general solution type which allows a wide ranging class of linear functional to be used in the solution of the problem. This class provides a continuum of functionals which provide new methods that can be used to solve Prony's problem.

Instrumental resolution of the chopper spectrometer 4SEASONS evaluated by Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Kajimoto, Ryoichi; Sato, Kentaro; Inamura, Yasuhiro; Fujita, Masaki

2018-05-01

We performed simulations of the resolution function of the 4SEASONS spectrometer at J-PARC by using the Monte Carlo simulation package McStas. The simulations showed reasonably good agreement with analytical calculations of energy and momentum resolutions by using a simplified description. We implemented new functionalities in Utsusemi, the standard data analysis tool used in 4SEASONS, to enable visualization of the simulated resolution function and predict its shape for specific experimental configurations.

Functional Role of Tyr12 in the Catalytic Activity of Novel Zeta-like Glutathione S-transferase from Acidovorax sp. KKS102.

PubMed

Shehu, Dayyabu; Alias, Zazali

2018-05-19

Glutathione S-transferases (GSTs) are a family of enzymes that function in the detoxification of variety of electrophilic substrates. In the present work, we report a novel zeta-like GST (designated as KKSG9) from the biphenyl/polychlorobiphenyl degrading organism Acidovorax sp. KKS102. KKSG9 possessed low sequence similarity but similar biochemical properties to zeta class GSTs. Functional analysis showed that the enzyme exhibits wider substrate specificity compared to most zeta class GSTs by reacting with 1-chloro-2,4-dinitrobenzene (CDNB), p-nitrobenzyl chloride (NBC), ethacrynic acid (EA), hydrogen peroxide, and cumene hydroperoxide. The enzyme also displayed dehalogenation function against dichloroacetate, permethrin, and dieldrin. The functional role of Tyr12 was also investigated by site-directed mutagenesis. The mutant (Y12C) displayed low catalytic activity and dehalogenation function against all the substrates when compared with the wild type. Kinetic analysis using NBC and GSH as substrates showed that the mutant (Y12C) displayed a higher affinity for NBC when compared with the wild type, however, no significant change in GSH affinity was observed. These findings suggest that the presence of tyrosine residue in the motif might represent an evolutionary trend toward improving the catalytic activity of the enzyme. The enzyme as well could be useful in the bioremediation of various types of organochlorine pollutants.

Timed function tests, motor function measure, and quantitative thigh muscle MRI in ambulant children with Duchenne muscular dystrophy: A cross-sectional analysis.

PubMed

Schmidt, Simone; Hafner, Patricia; Klein, Andrea; Rubino-Nacht, Daniela; Gocheva, Vanya; Schroeder, Jonas; Naduvilekoot Devasia, Arjith; Zuesli, Stephanie; Bernert, Guenther; Laugel, Vincent; Bloetzer, Clemens; Steinlin, Maja; Capone, Andrea; Gloor, Monika; Tobler, Patrick; Haas, Tanja; Bieri, Oliver; Zumbrunn, Thomas; Fischer, Dirk; Bonati, Ulrike

2018-01-01

The development of new therapeutic agents for the treatment of Duchenne muscular dystrophy has put a focus on defining outcome measures most sensitive to capture treatment effects. This cross-sectional analysis investigates the relation between validated clinical assessments such as the 6-minute walk test, motor function measure and quantitative muscle MRI of thigh muscles in ambulant Duchenne muscular dystrophy patients, aged 6.5 to 10.8 years (mean 8.2, SD 1.1). Quantitative muscle MRI included the mean fat fraction using a 2-point Dixon technique, and transverse relaxation time (T2) measurements. All clinical assessments were highly significantly inter-correlated with p < 0.001. The strongest correlation with the motor function measure and its D1-subscore was shown by the 6-minute walk test. Clinical assessments showed no correlation with age. Importantly, quantitative muscle MRI values significantly correlated with all clinical assessments with the extensors showing the strongest correlation. In contrast to the clinical assessments, quantitative muscle MRI values were highly significantly correlated with age. In conclusion, the motor function measure and timed function tests measure disease severity in a highly comparable fashion and all tests correlated with quantitative muscle MRI values quantifying fatty muscle degeneration. Copyright © 2017 Elsevier B.V. All rights reserved.

Do motifs reflect evolved function?--No convergent evolution of genetic regulatory network subgraph topologies.

PubMed

Knabe, Johannes F; Nehaniv, Chrystopher L; Schilstra, Maria J

2008-01-01

Methods that analyse the topological structure of networks have recently become quite popular. Whether motifs (subgraph patterns that occur more often than in randomized networks) have specific functions as elementary computational circuits has been cause for debate. As the question is difficult to resolve with currently available biological data, we approach the issue using networks that abstractly model natural genetic regulatory networks (GRNs) which are evolved to show dynamical behaviors. Specifically one group of networks was evolved to be capable of exhibiting two different behaviors ("differentiation") in contrast to a group with a single target behavior. In both groups we find motif distribution differences within the groups to be larger than differences between them, indicating that evolutionary niches (target functions) do not necessarily mold network structure uniquely. These results show that variability operators can have a stronger influence on network topologies than selection pressures, especially when many topologies can create similar dynamics. Moreover, analysis of motif functional relevance by lesioning did not suggest that motifs were of greater importance to the functioning of the network than arbitrary subgraph patterns. Only when drastically restricting network size, so that one motif corresponds to a whole functionally evolved network, was preference for particular connection patterns found. This suggests that in non-restricted, bigger networks, entanglement with the rest of the network hinders topological subgraph analysis.

Extending bicluster analysis to annotate unclassified ORFs and predict novel functional modules using expression data

PubMed Central

Bryan, Kenneth; Cunningham, Pádraig

2008-01-01

Background Microarrays have the capacity to measure the expressions of thousands of genes in parallel over many experimental samples. The unsupervised classification technique of bicluster analysis has been employed previously to uncover gene expression correlations over subsets of samples with the aim of providing a more accurate model of the natural gene functional classes. This approach also has the potential to aid functional annotation of unclassified open reading frames (ORFs). Until now this aspect of biclustering has been under-explored. In this work we illustrate how bicluster analysis may be extended into a 'semi-supervised' ORF annotation approach referred to as BALBOA. Results The efficacy of the BALBOA ORF classification technique is first assessed via cross validation and compared to a multi-class k-Nearest Neighbour (kNN) benchmark across three independent gene expression datasets. BALBOA is then used to assign putative functional annotations to unclassified yeast ORFs. These predictions are evaluated using existing experimental and protein sequence information. Lastly, we employ a related semi-supervised method to predict the presence of novel functional modules within yeast. Conclusion In this paper we demonstrate how unsupervised classification methods, such as bicluster analysis, may be extended using of available annotations to form semi-supervised approaches within the gene expression analysis domain. We show that such methods have the potential to improve upon supervised approaches and shed new light on the functions of unclassified ORFs and their co-regulation. PMID:18831786

Systematic inference of functional phosphorylation events in yeast metabolism.

PubMed

Chen, Yu; Wang, Yonghong; Nielsen, Jens

2017-07-01

Protein phosphorylation is a post-translational modification that affects proteins by changing their structure and conformation in a rapid and reversible way, and it is an important mechanism for metabolic regulation in cells. Phosphoproteomics enables high-throughput identification of phosphorylation events on metabolic enzymes, but identifying functional phosphorylation events still requires more detailed biochemical characterization. Therefore, development of computational methods for investigating unknown functions of a large number of phosphorylation events identified by phosphoproteomics has received increased attention. We developed a mathematical framework that describes the relationship between phosphorylation level of a metabolic enzyme and the corresponding flux through the enzyme. Using this framework, it is possible to quantitatively estimate contribution of phosphorylation events to flux changes. We showed that phosphorylation regulation analysis, combined with a systematic workflow and correlation analysis, can be used for inference of functional phosphorylation events in steady and dynamic conditions, respectively. Using this analysis, we assigned functionality to phosphorylation events of 17 metabolic enzymes in the yeast Saccharomyces cerevisiae , among which 10 are novel. Phosphorylation regulation analysis cannot only be extended for inference of other functional post-translational modifications but also be a promising scaffold for multi-omics data integration in systems biology. Matlab codes for flux balance analysis in this study are available in Supplementary material. yhwang@ecust.edu.cn or nielsenj@chalmers.se. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Hybrid function projective synchronization in complex dynamical networks

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

Wei, Qiang; Wang, Xing-yuan, E-mail: wangxy@dlut.edu.cn; Hu, Xiao-peng

2014-02-15

This paper investigates hybrid function projective synchronization in complex dynamical networks. When the complex dynamical networks could be synchronized up to an equilibrium or periodic orbit, a hybrid feedback controller is designed to realize the different component of vector of node could be synchronized up to different desired scaling function in complex dynamical networks with time delay. Hybrid function projective synchronization (HFPS) in complex dynamical networks with constant delay and HFPS in complex dynamical networks with time-varying coupling delay are researched, respectively. Finally, the numerical simulations show the effectiveness of theoretical analysis.

Distinctive time-lagged resting-state networks revealed by simultaneous EEG-fMRI.

PubMed

Feige, Bernd; Spiegelhalder, Kai; Kiemen, Andrea; Bosch, Oliver G; Tebartz van Elst, Ludger; Hennig, Jürgen; Seifritz, Erich; Riemann, Dieter

2017-01-15

Functional activation as evidenced by blood oxygen level-dependent (BOLD) functional MRI changes or event-related EEG is known to closely follow patterns of stimulation or self-paced action. Any lags are compatible with axonal conduction velocities and neural integration times. The important analysis of resting state networks is generally based on the assumption that these principles also hold for spontaneous fluctuations in brain activity. Previous observations using simultaneous EEG and fMRI indicate that slower processes, with delays in the seconds range, determine at least part of the relationship between spontaneous EEG and fMRI. To assess this relationship systematically, we used deconvolution analysis of EEG-fMRI during the resting state, assessing the relationship between EEG frequency bands and fMRI BOLD across the whole brain while allowing for time lags of up to 10.5s. Cluster analysis, identifying similar BOLD time courses in relation to EEG band power peaks, showed a clear segregation of functional subsystems of the brain. Our analysis shows that fMRI BOLD increases commonly precede EEG power increases by seconds. Most zero-lag correlations, on the other hand, were negative. This indicates two main distinct neuromodulatory mechanisms: an "idling" mechanism of simultaneous electric and metabolic network anticorrelation and a "regulatory" mechanism in which metabolic network activity precedes increased EEG power by some seconds. This has to be taken into consideration in further studies which address the causal and functional relationship of metabolic and electric brain activity patterns. Copyright © 2016 Elsevier Inc. All rights reserved.

Item Response Theory analysis of Fagerström Test for Cigarette Dependence.

PubMed

Svicher, Andrea; Cosci, Fiammetta; Giannini, Marco; Pistelli, Francesco; Fagerström, Karl

2018-02-01

The Fagerström Test for Cigarette Dependence (FTCD) and the Heaviness of Smoking Index (HSI) are the gold standard measures to assess cigarette dependence. However, FTCD reliability and factor structure have been questioned and HSI psychometric properties are in need of further investigations. The present study examined the psychometrics properties of the FTCD and the HSI via the Item Response Theory. The study was a secondary analysis of data collected in 862 Italian daily smokers. Confirmatory factor analysis was run to evaluate the dimensionality of FTCD. A Grade Response Model was applied to FTCD and HSI to verify the fit to the data. Both item and test functioning were analyzed and item statistics, Test Information Function, and scale reliabilities were calculated. Mokken Scale Analysis was applied to estimate homogeneity and Loevinger's coefficients were calculated. The FTCD showed unidimensionality and homogeneity for most of the items and for the total score. It also showed high sensitivity and good reliability from medium to high levels of cigarette dependence, although problems related to some items (i.e., items 3 and 5) were evident. HSI had good homogeneity, adequate item functioning, and high reliability from medium to high levels of cigarette dependence. Significant Differential Item Functioning was found for items 1, 4, 5 of the FTCD and for both items of HSI. HSI seems highly recommended in clinical settings addressed to heavy smokers while FTCD would be better used in smokers with a level of cigarette dependence ranging between low and high. Copyright © 2017 Elsevier Ltd. All rights reserved.

Multilayer motif analysis of brain networks

NASA Astrophysics Data System (ADS)

Battiston, Federico; Nicosia, Vincenzo; Chavez, Mario; Latora, Vito

2017-04-01

In the last decade, network science has shed new light both on the structural (anatomical) and on the functional (correlations in the activity) connectivity among the different areas of the human brain. The analysis of brain networks has made possible to detect the central areas of a neural system and to identify its building blocks by looking at overabundant small subgraphs, known as motifs. However, network analysis of the brain has so far mainly focused on anatomical and functional networks as separate entities. The recently developed mathematical framework of multi-layer networks allows us to perform an analysis of the human brain where the structural and functional layers are considered together. In this work, we describe how to classify the subgraphs of a multiplex network, and we extend the motif analysis to networks with an arbitrary number of layers. We then extract multi-layer motifs in brain networks of healthy subjects by considering networks with two layers, anatomical and functional, respectively, obtained from diffusion and functional magnetic resonance imaging. Results indicate that subgraphs in which the presence of a physical connection between brain areas (links at the structural layer) coexists with a non-trivial positive correlation in their activities are statistically overabundant. Finally, we investigate the existence of a reinforcement mechanism between the two layers by looking at how the probability to find a link in one layer depends on the intensity of the connection in the other one. Showing that functional connectivity is non-trivially constrained by the underlying anatomical network, our work contributes to a better understanding of the interplay between the structure and function in the human brain.

Functional annotation of the vlinc class of non-coding RNAs using systems biology approach.

PubMed

St Laurent, Georges; Vyatkin, Yuri; Antonets, Denis; Ri, Maxim; Qi, Yao; Saik, Olga; Shtokalo, Dmitry; de Hoon, Michiel J L; Kawaji, Hideya; Itoh, Masayoshi; Lassmann, Timo; Arner, Erik; Forrest, Alistair R R; Nicolas, Estelle; McCaffrey, Timothy A; Carninci, Piero; Hayashizaki, Yoshihide; Wahlestedt, Claes; Kapranov, Philipp

2016-04-20

Functionality of the non-coding transcripts encoded by the human genome is the coveted goal of the modern genomics research. While commonly relied on the classical methods of forward genetics, integration of different genomics datasets in a global Systems Biology fashion presents a more productive avenue of achieving this very complex aim. Here we report application of a Systems Biology-based approach to dissect functionality of a newly identified vast class of very long intergenic non-coding (vlinc) RNAs. Using highly quantitative FANTOM5 CAGE dataset, we show that these RNAs could be grouped into 1542 novel human genes based on analysis of insulators that we show here indeed function as genomic barrier elements. We show that vlinc RNAs genes likely function in cisto activate nearby genes. This effect while most pronounced in closely spaced vlinc RNA-gene pairs can be detected over relatively large genomic distances. Furthermore, we identified 101 vlinc RNA genes likely involved in early embryogenesis based on patterns of their expression and regulation. We also found another 109 such genes potentially involved in cellular functions also happening at early stages of development such as proliferation, migration and apoptosis. Overall, we show that Systems Biology-based methods have great promise for functional annotation of non-coding RNAs. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

ABERRANT RESTING-STATE BRAIN ACTIVITY IN POSTTRAUMATIC STRESS DISORDER: A META-ANALYSIS AND SYSTEMATIC REVIEW.

PubMed

Koch, Saskia B J; van Zuiden, Mirjam; Nawijn, Laura; Frijling, Jessie L; Veltman, Dick J; Olff, Miranda

2016-07-01

About 10% of trauma-exposed individuals develop PTSD. Although a growing number of studies have investigated resting-state abnormalities in PTSD, inconsistent results suggest a need for a meta-analysis and a systematic review. We conducted a systematic literature search in four online databases using keywords for PTSD, functional neuroimaging, and resting-state. In total, 23 studies matched our eligibility criteria. For the meta-analysis, we included 14 whole-brain resting-state studies, reporting data on 663 participants (298 PTSD patients and 365 controls). We used the activation likelihood estimation approach to identify concurrence of whole-brain hypo- and hyperactivations in PTSD patients during rest. Seed-based studies could not be included in the quantitative meta-analysis. Therefore, a separate qualitative systematic review was conducted on nine seed-based functional connectivity studies. The meta-analysis showed consistent hyperactivity in the ventral anterior cingulate cortex and the parahippocampus/amygdala, but hypoactivity in the (posterior) insula, cerebellar pyramis and middle frontal gyrus in PTSD patients, compared to healthy controls. Partly concordant with these findings, the systematic review on seed-based functional connectivity studies showed enhanced salience network (SN) connectivity, but decreased default mode network (DMN) connectivity in PTSD. Combined, these altered resting-state connectivity and activity patterns could represent neurobiological correlates of increased salience processing and hypervigilance (SN), at the cost of awareness of internal thoughts and autobiographical memory (DMN) in PTSD. However, several discrepancies between findings of the meta-analysis and systematic review were observed, stressing the need for future studies on resting-state abnormalities in PTSD patients. © 2016 Wiley Periodicals, Inc.

Phylogenetic analysis of IDD gene family and characterization of its expression in response to flower induction in Malus.

PubMed

Fan, Sheng; Zhang, Dong; Xing, Libo; Qi, Siyan; Du, Lisha; Wu, Haiqin; Shao, Hongxia; Li, Youmei; Ma, Juanjuan; Han, Mingyu

2017-08-01

Although INDETERMINATE DOMAIN (IDD) genes encoding specific plant transcription factors have important roles in plant growth and development, little is known about apple IDD (MdIDD) genes and their potential functions in the flower induction. In this study, we identified 20 putative IDD genes in apple and named them according to their chromosomal locations. All identified MdIDD genes shared a conserved IDD domain. A phylogenetic analysis separated MdIDDs and other plant IDD genes into four groups. Bioinformatic analysis of chemical characteristics, gene structure, and prediction of protein-protein interactions demonstrated the functional and structural diversity of MdIDD genes. To further uncover their potential functions, we performed analysis of tandem, synteny, and gene duplications, which indicated several paired homologs of IDD genes between apple and Arabidopsis. Additionally, genome duplications also promoted the expansion and evolution of the MdIDD genes. Quantitative real-time PCR revealed that all the MdIDD genes showed distinct expression levels in five different tissues (stems, leaves, buds, flowers, and fruits). Furthermore, the expression levels of candidate MdIDD genes were also investigated in response to various circumstances, including GA treatment (decreased the flowering rate), sugar treatment (increased the flowering rate), alternate-bearing conditions, and two varieties with different-flowering intensities. Parts of them were affected by exogenous treatments and showed different expression patterns. Additionally, changes in response to alternate-bearing and different-flowering varieties of apple trees indicated that they were also responsive to flower induction. Taken together, our comprehensive analysis provided valuable information for further analysis of IDD genes aiming at flower induction.

Embryotoxic and pharmacologic potency ranking of six azoles in the rat whole embryo culture by morphological and transcriptomic analysis

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

Dimopoulou, Myrto, E-mail: myrto.dimopoulou@wur.nl

Differential gene expression analysis in the rat whole embryo culture (WEC) assay provides mechanistic insight into the embryotoxicity of test compounds. In our study, we hypothesized that comparative analysis of the transcriptomes of rat embryos exposed to six azoles (flusilazole, triadimefon, ketoconazole, miconazole, difenoconazole and prothioconazole) could lead to a better mechanism-based understanding of their embryotoxicity and pharmacological action. For evaluating embryotoxicity, we applied the total morphological scoring system (TMS) in embryos exposed for 48 h. The compounds tested showed embryotoxicity in a dose-response fashion. Functional analysis of differential gene expression after 4 h exposure at the ID{sub 10} (effectivemore » dose for 10% decreased TMS), revealed the sterol biosynthesis pathway and embryonic development genes, dominated by genes in the retinoic acid (RA) pathway, albeit in a differential way. Flusilazole, ketoconazole and triadimefon were the most potent compounds affecting the RA pathway, while in terms of regulation of sterol function, difenoconazole and ketoconazole showed the most pronounced effects. Dose-dependent analysis of the effects of flusilazole revealed that the RA pathway related genes were already differentially expressed at low dose levels while the sterol pathway showed strong regulation at higher embryotoxic doses, suggesting that this pathway is less predictive for the observed embryotoxicity. A similar analysis at the 24-hour time point indicated an additional time-dependent difference in the aforementioned pathways regulated by flusilazole. In summary, the rat WEC assay in combination with transcriptomics could add a mechanistic insight into the embryotoxic potency ranking and pharmacological mode of action of the tested compounds. - Highlights: • Embryonic exposure to azoles revealed concentration-dependent malformations. • Transcriptomics could enhance the mechanistic knowledge of embryotoxicants. • Retinoic acid gene set identifies early embryotoxic responses to azoles. • Toxic versus pharmacologic potency determines functional efficacy.« less

Staircase and fractional part functions

NASA Astrophysics Data System (ADS)

Amram, Meirav; Dagan, Miriam; Ioshpe, Michael; Satianov, Pavel

2016-10-01

The staircase and fractional part functions are basic examples of real functions. They can be applied in several parts of mathematics, such as analysis, number theory, formulas for primes, and so on; in computer programming, the floor and ceiling functions are provided by a significant number of programming languages - they have some basic uses in various programming tasks. In this paper, we view the staircase and fractional part functions as a classical example of non-continuous real functions. We introduce some of their basic properties, present some interesting constructions concerning them, and explore some intriguing interpretations of such functions. Throughout the paper, we use these functions in order to explain basic concepts in a first calculus course, such as domain of definition, discontinuity, and oddness of functions. We also explain in detail how, after researching the properties of such functions, one can draw their graph; this is a crucial part in the process of understanding their nature. In the paper, we present some subjects that the first-year student in the exact sciences may not encounter. We try to clarify those subjects and show that such ideas are important in the understanding of non-continuous functions, as a part of studying analysis in general.

Virtual reality 3D echocardiography in the assessment of tricuspid valve function after surgical closure of ventricular septal defect.

PubMed

Bol Raap, Goris; Koning, Anton H J; Scohy, Thierry V; ten Harkel, A Derk-Jan; Meijboom, Folkert J; Kappetein, A Pieter; van der Spek, Peter J; Bogers, Ad J J C

2007-02-16

This study was done to investigate the potential additional role of virtual reality, using three-dimensional (3D) echocardiographic holograms, in the postoperative assessment of tricuspid valve function after surgical closure of ventricular septal defect (VSD). 12 data sets from intraoperative epicardial echocardiographic studies in 5 operations (patient age at operation 3 weeks to 4 years and bodyweight at operation 3.8 to 17.2 kg) after surgical closure of VSD were included in the study. The data sets were analysed as two-dimensional (2D) images on the screen of the ultrasound system as well as holograms in an I-space virtual reality (VR) system. The 2D images were assessed for tricuspid valve function. In the I-Space, a 6 degrees-of-freedom controller was used to create the necessary projectory positions and cutting planes in the hologram. The holograms were used for additional assessment of tricuspid valve leaflet mobility. All data sets could be used for 2D as well as holographic analysis. In all data sets the area of interest could be identified. The 2D analysis showed no tricuspid valve stenosis or regurgitation. Leaflet mobility was considered normal. In the virtual reality of the I-Space, all data sets allowed to assess the tricuspid leaflet level in a single holographic representation. In 3 holograms the septal leaflet showed restricted mobility that was not appreciated in the 2D echocardiogram. In 4 data sets the posterior leaflet and the tricuspid papillary apparatus were not completely included. This report shows that dynamic holographic imaging of intraoperative postoperative echocardiographic data regarding tricuspid valve function after VSD closure is feasible. Holographic analysis allows for additional tricuspid valve leaflet mobility analysis. The large size of the probe, in relation to small size of the patient, may preclude a complete data set. At the moment the requirement of an I-Space VR system limits the applicability in virtual reality 3D echocardiography in clinical practice.

The Use of Functional Data Analysis to Evaluate Activity in a Spontaneous Model of Degenerative Joint Disease Associated Pain in Cats

PubMed Central

Gruen, Margaret E.; Alfaro-Córdoba, Marcela; Thomson, Andrea E.; Worth, Alicia C.; Staicu, Ana-Maria; Lascelles, B. Duncan X.

2017-01-01

Introduction and objectives Accelerometry is used as an objective measure of physical activity in humans and veterinary species. In cats, one important use of accelerometry is in the study of therapeutics designed to treat degenerative joint disease (DJD) associated pain, where it serves as the most widely applied objective outcome measure. These analyses have commonly used summary measures, calculating the mean activity per-minute over days and comparing between treatment periods. While this technique has been effective, information about the pattern of activity in cats is lost. In this study, functional data analysis was applied to activity data from client-owned cats with (n = 83) and without (n = 15) DJD. Functional data analysis retains information about the pattern of activity over the 24-hour day, providing insight into activity over time. We hypothesized that 1) cats without DJD would have higher activity counts and intensity of activity than cats with DJD; 2) that activity counts and intensity of activity in cats with DJD would be inversely correlated with total radiographic DJD burden and total orthopedic pain score; and 3) that activity counts and intensity would have a different pattern on weekends versus weekdays. Results and conclusions Results showed marked inter-cat variability in activity. Cats exhibited a bimodal pattern of activity with a sharp peak in the morning and broader peak in the evening. Results further showed that this pattern was different on weekends than weekdays, with the morning peak being shifted to the right (later). Cats with DJD showed different patterns of activity from cats without DJD, though activity and intensity were not always lower; instead both the peaks and troughs of activity were less extreme than those of the cats without DJD. Functional data analysis provides insight into the pattern of activity in cats, and an alternative method for analyzing accelerometry data that incorporates fluctuations in activity across the day. PMID:28099449

A novel mutation in the FGB: c.1105C>T turns the codon for amino acid Bβ Q339 into a stop codon causing hypofibrinogenemia.

PubMed

Marchi, Rita; Brennan, Stephen; Meyer, Michael; Rojas, Héctor; Kanzler, Daniela; De Agrela, Marisela; Ruiz-Saez, Arlette

2013-03-01

Routine coagulation tests on a 14year-old male with frequent epistaxis showed a prolonged thrombin time together with diminished functional (162mg/dl) and gravimetric (122mg/dl) fibrinogen concentrations. His father showed similar aberrant results and sequencing of the three fibrinogen genes revealed a novel heterozygous nonsense mutation in the FGB gene c.1105C>T, which converts the codon for residue Bβ 339Q to stop, causing deletion of Bβ chain residues 339-461. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and RP-HPLC (reverse-phase high-pressure liquid chromatography) of purified fibrinogen showed only normal Aα, Bβ, and γ chains, indicating that molecules with the truncated 37,990Da β chain were not secreted into plasma. Functional analysis showed impaired fibrin polymerization, fibrin porosity, and elasticity compared to controls. By laser scanning confocal microscopy the patient's fibers were slightly thinner than normal. Electrospray ionization mass spectrometry (ESI MS) presented normal sialylation of the oligosaccharide chains, and liver function tests showed no evidence of liver dysfunction that might explain the functional abnormalities. Copyright © 2012 Elsevier Inc. All rights reserved.

Evaluation of autonomic functions of patients with multiple system atrophy and Parkinson's disease by head-up tilt test.

PubMed

Watano, Chikako; Shiota, Yuri; Onoda, Keiichi; Sheikh, Abdullah Md; Mishima, Seiji; Nitta, Eri; Yano, Shozo; Yamaguchi, Shuhei; Nagai, Atsushi

2018-02-01

The aim of this study was to evaluate the autonomic neural function in Parkinson's disease (PD) and multiple system atrophy (MSA) with head-up tilt test and spectral analysis of cardiovascular parameters. This study included 15 patients with MSA, 15 patients with PD, and 29 healthy control (HC) subjects. High frequency power of the RR interval (RR-HF), the ratio of low frequency power of RR interval to RR-HF (RR-LF/HF) and LF power of systolic BP were used to evaluate parasympathetic, cardiac sympathetic and vasomotor sympathetic functions, respectively. Both patients with PD and MSA showed orthostatic hypotension and lower parasympathetic function (RR-HF) at tilt position as compared to HC subjects. Cardiac sympathetic function (RR-LF/HF) was significantly high in patients with PD than MSA at supine position. RR-LF/HF tended to increase in MSA and HC, but decreased in PD by tilting. Consequently, the change of the ratio due to tilting (ΔRR-LF/HF) was significantly lower in patients with PD than in HC subjects. Further analysis showed that compared to mild stage of PD, RR-LF/HF at the supine position was significantly higher in advanced stage. By tilting, it was increased in mild stage and decreased in the advanced stage of PD, causing ΔRR-LF/HF to decrease significantly in the advanced stage. Thus, we demonstrated that spectral analysis of cardiovascular parameters is useful to identify sympathetic and parasympathetic disorders in MSA and PD. High cardiac sympathetic function at the supine position, and its reduction by tilting might be a characteristic feature of PD, especially in the advanced stage.

Functional identification and regulatory analysis of Δ6-fatty acid desaturase from the oleaginous fungus Mucor sp. EIM-10.

PubMed

Jiang, Xianzhang; Liu, Hongjiao; Niu, Yongchao; Qi, Feng; Zhang, Mingliang; Huang, Jianzhong

2017-03-01

To enlarge the diversity of the desaturases associated with PUFA biosynthesis and to better understand the transcriptional regulation of desaturases, a Δ 6 -desaturase gene (Md6) from Mucor sp. and its 5'-upstream sequence was functionally identified in Saccharomyces cerevisiae. Expression of the Δ 6 -fatty acid desaturase (Md6) in S. cerevisiae showed that Md6 could convert linolenic acid to γ-linolenic acid. Computational analysis of the promoter of Md6 suggested it contains several eukaryotic fundamental transcription regulatory elements. In vivo functional analysis of the promoter showed the 5'-upstream sequence of Md6 could initiate expression of GFP and Md6 itself in S. cerevisiae. A series deletion analysis of the promoter suggested that sequence between -919 to -784 bp (relative to start site) named as eMd6 is the key factor for high activity of Δ 6 -desaturase. The activity of Δ 6 -desaturase was increased by 2.8-fold and 2.5-fold when the eMd6 sequence was placed upstream of -434 with forward or reverse orientations respectively. To our best knowledge, the native promoter of Md6 from Mucor is the strongest promoter for Δ 6 -desaturase reported so far and the sequence between -919 to -784 bp is an enhancer for Δ 6 -desaturase activity.

The Preoperative Composite Physiologic Index May Predict Mortality in Lung Cancer Patients with Combined Pulmonary Fibrosis and Emphysema.

PubMed

Ueno, Fumika; Kitaguchi, Yoshiaki; Shiina, Takayuki; Asaka, Shiho; Miura, Kentaro; Yasuo, Masanori; Wada, Yosuke; Yoshizawa, Akihiko; Hanaoka, Masayuki

2017-01-01

It remains unclear whether the preoperative pulmonary function parameters and prognostic indices that are indicative of nutritional and immunological status are associated with prognosis in lung cancer patients with combined pulmonary fibrosis and emphysema (CPFE) who have undergone surgery. The aim of this study is to identify prognostic determinants in these patients. The medical records of all patients with lung cancer associated with CPFE who had undergone surgery at Shinshu University Hospital were retrospectively reviewed to obtain clinical data, including the results of preoperative pulmonary function tests and laboratory examinations, chest high-resolution computed tomography (HRCT), and survival. Univariate Cox proportional hazards regression analysis showed that a high pathological stage of the lung cancer, a higher preoperative serum carcinoembryonic antigen level, and a higher preoperative composite physiologic index (CPI) were associated with a high risk of death. Multivariate analysis showed that a high pathological stage of the lung cancer (HR: 1.579; p = 0.0305) and a higher preoperative CPI (HR: 1.034; p = 0.0174) were independently associated with a high risk of death. In contrast, the severity of fibrosis or emphysema on chest HRCT, the individual pulmonary function parameters, the prognostic nutritional index, the neutrophil-to-lymphocyte ratio, and the platelet-to-lymphocyte ratio were not associated with prognosis. In the Kaplan-Meier analysis, the log-rank test showed significant differences in survival between the high-CPI and the low-CPI group (p = 0.0234). The preoperative CPI may predict mortality and provide more powerful prognostic information than individual pulmonary function parameters in lung cancer patients with CPFE who have undergone surgery. © 2017 S. Karger AG, Basel.

Overexpressed HDAC8 in cervical cancer cells shows functional redundancy of tubulin deacetylation with HDAC6.

PubMed

Vanaja, G R; Ramulu, Hemalatha Golaconda; Kalle, Arunasree M

2018-05-02

Histone deacetylases (HDACs) are involved in epigenetic gene regulation via deacetylation of acetylated lysine residues of both histone and non-histone proteins. Among the 18 HDACs identified in humans, HDAC8, a class I HDAC, is best understood structurally and enzymatically. However, its precise subcellular location, function in normal cellular physiology, its protein partners and substrates still remain elusive. The subcellular localization of HDAC8 was studied using immunofluorescence and confocal imaging. The binding parterns were identified employing immunoprecipitation (IP) followed by MALDI-TOF analysis and confirmed using in-silico protein-protein interaction studies, HPLC-based in vitro deacetylation assay, intrinsic fluorescence spectrophotometric analysis, Circular dichroism (CD) and Surface Plasmon Resonance (SPR). Functional characterization of the binding was carried out using immunoblot and knockdown by siRNA. Using one way ANOVA statistical significance (n = 3) was determined. Here, we show that HDAC8 and its phosphorylated form (pHDAC8) localized predominantly in the cytoplasm in cancerous, HeLa, and non-cancerous (normal), HEK293T, cells, although nucleolar localization was observed in HeLa cells. The study identified Alpha tubulin as a novel interacting partner of HDAC8. Further, the results indicated binding and deacetylation of tubulin at ac-lys40 by HDAC8. Knockdown of HDAC8 by siRNA, inhibition of HDAC8 and/or HDAC6 by PCI-34051 and tubastatin respectively, cell-migration, cell morphology and cell cycle analysis clearly explained HDAC8 as tubulin deacetylase in HeLa cells and HDAC6 in HEK 293 T cells. HDAC8 shows functional redundancy with HDAC6 when overexpressed in cervical cancer cells, HeLa, and deacetylaes ac-lys40 of alpha tubulin leading to cervical cancer proliferation and progression.

Evolutionary tradeoffs in cellular composition across diverse bacteria

PubMed Central

Kempes, Christopher P; Wang, Lawrence; Amend, Jan P; Doyle, John; Hoehler, Tori

2016-01-01

One of the most important classic and contemporary interests in biology is the connection between cellular composition and physiological function. Decades of research have allowed us to understand the detailed relationship between various cellular components and processes for individual species, and have uncovered common functionality across diverse species. However, there still remains the need for frameworks that can mechanistically predict the tradeoffs between cellular functions and elucidate and interpret average trends across species. Here we provide a comprehensive analysis of how cellular composition changes across the diversity of bacteria as connected with physiological function and metabolism, spanning five orders of magnitude in body size. We present an analysis of the trends with cell volume that covers shifts in genomic, protein, cellular envelope, RNA and ribosomal content. We show that trends in protein content are more complex than a simple proportionality with the overall genome size, and that the number of ribosomes is simply explained by cross-species shifts in biosynthesis requirements. Furthermore, we show that the largest and smallest bacteria are limited by physical space requirements. At the lower end of size, cell volume is dominated by DNA and protein content—the requirement for which predicts a lower limit on cell size that is in good agreement with the smallest observed bacteria. At the upper end of bacterial size, we have identified a point at which the number of ribosomes required for biosynthesis exceeds available cell volume. Between these limits we are able to discuss systematic and dramatic shifts in cellular composition. Much of our analysis is connected with the basic energetics of cells where we show that the scaling of metabolic rate is surprisingly superlinear with all cellular components. PMID:27046336

A Reverse-Genetics Mutational Analysis of the Barley HvDWARF Gene Results in Identification of a Series of Alleles and Mutants with Short Stature of Various Degree and Disturbance in BR Biosynthesis Allowing a New Insight into the Process.

PubMed

Gruszka, Damian; Gorniak, Malgorzata; Glodowska, Ewelina; Wierus, Ewa; Oklestkova, Jana; Janeczko, Anna; Maluszynski, Miroslaw; Szarejko, Iwona

2016-04-22

Brassinosteroids (BRs) are plant steroid hormones, regulating a broad range of physiological processes. The largest amount of data related with BR biosynthesis has been gathered in Arabidopsis thaliana, however understanding of this process is far less elucidated in monocot crops. Up to now, only four barley genes implicated in BR biosynthesis have been identified. Two of them, HvDWARF and HvBRD, encode BR-6-oxidases catalyzing biosynthesis of castasterone, but their relation is not yet understood. In the present study, the identification of the HvDWARF genomic sequence, its mutational and functional analysis and characterization of new mutants are reported. Various types of mutations located in different positions within functional domains were identified and characterized. Analysis of their impact on phenotype of the mutants was performed. The identified homozygous mutants show reduced height of various degree and disrupted skotomorphogenesis. Mutational analysis of the HvDWARF gene with the "reverse genetics" approach allowed for its detailed functional analysis at the level of protein functional domains. The HvDWARF gene function and mutants' phenotypes were also validated by measurement of endogenous BR concentration. These results allowed a new insight into the BR biosynthesis in barley.

Probing the pH sensitivity of R-phycoerythrin: investigations of active conformational and functional variation.

PubMed

Liu, Lu-Ning; Su, Hai-Nan; Yan, Shi-Gan; Shao, Si-Mi; Xie, Bin-Bin; Chen, Xiu-Lan; Zhang, Xi-Ying; Zhou, Bai-Cheng; Zhang, Yu-Zhong

2009-07-01

Crystal structures of phycobiliproteins have provided valuable information regarding the conformations and amino acid organizations of peptides and chromophores, and enable us to investigate their structural and functional relationships with respect to environmental variations. In this work, we explored the pH-induced conformational and functional dynamics of R-phycoerythrin (R-PE) by means of absorption, fluorescence and circular dichroism spectra, together with analysis of its crystal structure. R-PE presents stronger functional stability in the pH range of 3.5-10 compared to the structural stability. Beyond this range, pronounced functional and structural changes occur. Crystal structure analysis shows that the tertiary structure of R-PE is fixed by several key anchoring points of the protein. With this specific association, the fundamental structure of R-PE is stabilized to present physiological spectroscopic properties, while local variations in protein peptides are also allowed in response to environmental disturbances. The functional stability and relative structural sensitivity of R-PE allow environmental adaptation.

A multicriteria decision analysis of augmentative treatment of upper limbs in persons with tetraplegia.

PubMed

Hummel, J M Marjan; Snoek, Govert J; van Til, Janine A; van Rossum, Wouter; Ijzerman, Maarten J

2005-01-01

This study supported the evaluation by a rehabilitation team of the performance of two treatment options that improve the arm-hand function in subjects with sixth cervical vertebra (C6) level Motor Group 2 tetraplegia. The analytic hierarchy process, a technique for multicriteria decision analysis, was used by a rehabilitation team and potential recipients to quantitatively compare a new technology, Functional Elec trical Stimulation (FES), with conventional surgery. Perform-ance was measured by functional improvement, treatment load, risks, user-friendliness, and social outcomes. Functional improvement after FES was considered better than that after conventional surgery. However, the rehabilitation team's overall rating for conventional surgery was slightly higher than that for FES (57% vs 44%). Compared with the rehabilitation team, potential recipients gave greater weight to burden of treatment and less weight to functional improvement. This study shows that evaluation of new technology must be more comprehensive than the evaluation of functional improvement alone, and that patient preferences may differ from those of the rehabilitation team.

Stability of individual loudness functions obtained by magnitude estimation and production

NASA Technical Reports Server (NTRS)

Hellman, R. P.

1981-01-01

A correlational analysis of individual magnitude estimation and production exponents at the same frequency is performed, as is an analysis of individual exponents produced in different sessions by the same procedure across frequency (250, 1000, and 3000 Hz). Taken as a whole, the results show that individual exponent differences do not decrease by counterbalancing magnitude estimation with magnitude production and that individual exponent differences remain stable over time despite changes in stimulus frequency. Further results show that although individual magnitude estimation and production exponents do not necessarily obey the .6 power law, it is possible to predict the slope of an equal-sensation function averaged for a group of listeners from individual magnitude estimation and production data. On the assumption that individual listeners with sensorineural hearing also produce stable and reliable magnitude functions, it is also shown that the slope of the loudness-recruitment function measured by magnitude estimation and production can be predicted for individuals with bilateral losses of long duration. Results obtained in normal and pathological ears thus suggest that individual listeners can produce loudness judgements that reveal, although indirectly, the input-output characteristic of the auditory system.

Single-walled carbon nanotubes-ciprofloxacin nanoantibiotic: strategy to improve ciprofloxacin antibacterial activity.

PubMed

Assali, Mohyeddin; Zaid, Abdel Naser; Abdallah, Farah; Almasri, Motasem; Khayyat, Rasha

2017-01-01

As infectious diseases continue to be one of the greatest health challenges worldwide, the demand toward alternative agents is continuously increasing. Recent advancement in nanotechnology has expanded our ability to design and construct nanomaterials to treat bacterial infections. Carbon nanotubes are one among these nanomaterials. Herein, we describe the covalent functionalization of the single-walled carbon nanotubes (SWCNTs) with multiple molecules of ciprofloxacin. The prepared nanoantibiotics were characterized using different techniques, including transmission electron microscopy, Raman spectroscopy, and thermogravimetric analysis. The characterization of the nanoantibiotics confirmed the successful covalent functionalization of the SWCNTs with 55% of functionalization as has been observed by thermogravimetric analysis. The release profile revealed that 90% of the loaded ciprofloxacin was released within 2.5 h at pH 7.4 showing a first-order release profile with R 2 >0.99. Interestingly, the results of the antibacterial activity indicated that the functionalized SWCNTs have significant increase in the antibacterial activity against the three strains of bacteria - by 16-fold for Staphylococcus aureus and Pseudomonas aeruginosa and by 8-fold for Escherichia coli - in comparison to the ciprofloxacin free drug. Moreover, the synthesized nanoantibiotic showed high hemocompatibility and cytocompatibility over a wide concentration range.

The use of functional data analysis to study variability in childrens speech: Further data

NASA Astrophysics Data System (ADS)

Koenig, Laura L.; Lucero, Jorge C.

2002-05-01

Much previous research has reported increased token-to-token variability in children relative to adults, but the sources and implications of this variability remain matters of debate. Recently, functional data analysis has been used as a tool to gain greater insight into the nature of variability in children's and adults' speech data. In FDA, signals are time-normalized using a smooth function of time. The magnitude of the time-warping function provides an index of phasing (temporal) variability, and a separate index of amplitude variability is calculated from the time-normalized signal. Here, oral airflow data are analyzed from 5-year-olds, 10-year-olds, and adult women producing laryngeal and oral fricatives (/h, s, z/). The preliminary FDA results show that children generally have higher temporal and amplitude indices than adults, suggesting greater variability both in gestural timing and magnitude. However, individual patterns are evident in the relative magnitude of the two indices, and in which consonants show the highest values. The time-varying patterns of flow variability over time in /s/ are also explored as a method of inferring relative variability among laryngeal and oral gestures. [Work supported by NIH and CNPq, Brazil.

Extension of the Contingency Naming Test to adult assessment: psychometric analysis in a college student sample.

PubMed

Riddle, Tara; Suhr, Julie

2012-01-01

The Contingency Naming Test (CNT; Taylor, Albo, Phebus, Sachs, & Bierl, 1987) was initially designed to assess aspects of executive functioning, such as processing speed and response inhibition, in children. The measure has shown initial utility in identifying differences in executive function among child clinical groups; however, there is an absence of adequate psychometric data for use with adults. The current study expanded psychometric data upward for use with a college student sample and explored the measure's test-retest reliability and factor structure. Performance in the adult sample showed continued improvement above child norms, consistent with theories of executive function development. Exploratory factor analysis showed that the CNT is most closely related to measures of processing speed, as well as elements of response inhibition within the latter trials. Overall, results from the current study provide added support for the utility of the CNT as a measure of executive functioning in young adults. However, more research is needed to determine patterns of performance among adult clinical groups, as well as to better understand how performance patterns may change in a broader age range, including middle and older adulthood.

Age-Related Differences and Heterogeneity in Executive Functions: Analysis of NAB Executive Functions Module Scores.

PubMed

Buczylowska, Dorota; Petermann, Franz

2016-05-01

Normative data from the German adaptation of the Neuropsychological Assessment Battery were used to examine age-related differences in 6 executive function tasks. A multivariate analysis of variance was employed to investigate the differences in performance in 484 participants aged 18-99 years. The coefficient of variation was calculated to compare the heterogeneity of scores between 10 age groups. Analyses showed an increase in the dispersion of scores with age, varying from 7% to 289%, in all subtests. Furthermore, age-dependent heterogeneity appeared to be associated with age-dependent decline because the subtests with the greatest increase in dispersion (i.e., Mazes, Planning, and Categories) also exhibited the greatest decrease in mean scores. In contrast, scores for the subtests Letter Fluency, Word Generation, and Judgment had the lowest increase in dispersion with the lowest decrease in mean scores. Consequently, the results presented here show a pattern of age-related differences in executive functioning that is consistent with the concept of crystallized and fluid intelligence. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Single-walled carbon nanotubes-ciprofloxacin nanoantibiotic: strategy to improve ciprofloxacin antibacterial activity

PubMed Central

Assali, Mohyeddin; Zaid, Abdel Naser; Abdallah, Farah; Almasri, Motasem; Khayyat, Rasha

2017-01-01

As infectious diseases continue to be one of the greatest health challenges worldwide, the demand toward alternative agents is continuously increasing. Recent advancement in nanotechnology has expanded our ability to design and construct nanomaterials to treat bacterial infections. Carbon nanotubes are one among these nanomaterials. Herein, we describe the covalent functionalization of the single-walled carbon nanotubes (SWCNTs) with multiple molecules of ciprofloxacin. The prepared nanoantibiotics were characterized using different techniques, including transmission electron microscopy, Raman spectroscopy, and thermogravimetric analysis. The characterization of the nanoantibiotics confirmed the successful covalent functionalization of the SWCNTs with 55% of functionalization as has been observed by thermogravimetric analysis. The release profile revealed that 90% of the loaded ciprofloxacin was released within 2.5 h at pH 7.4 showing a first-order release profile with R2>0.99. Interestingly, the results of the antibacterial activity indicated that the functionalized SWCNTs have significant increase in the antibacterial activity against the three strains of bacteria – by 16-fold for Staphylococcus aureus and Pseudomonas aeruginosa and by 8-fold for Escherichia coli – in comparison to the ciprofloxacin free drug. Moreover, the synthesized nanoantibiotic showed high hemocompatibility and cytocompatibility over a wide concentration range. PMID:28924348

Dynamic Analysis of Kidney Function and Its Correlation with Nutritional Indicators in a Large Sample of Hospitalized Elderly Patients.

PubMed

Qingping, Li; Ribao, Wei; Yang, Wang; Tingyu, Su; Xi, Yang; Mengjie, Huang; Hui, Miao; Xiangmei, Chen

2017-04-23

BACKGROUND The aim of this study was to analyze changes in kidney function and its correlation with nutritional metabolism indicators in hospitalized elderly patients in a large medical center over the past 7 years. MATERIAL AND METHODS The renal function of patients over 60 years old in the Chinese PLA General Hospital in 2008, 2011, and 2014 were comparatively analyzed. The hemoglobin, serum albumin, triglycerides, cholesterol, uric acid, and urea nitrogen data were collected and used as the nutritional metabolism indicators. In addition, the correlation between these indicators and the eGFR was analyzed. RESULTS The numbers of patients who received kidney function assessments in the 3 years were 15 752, 23 539, and 49 828; their mean ages were 69.97±6.99, 69.51±7.11, and 69.45±7.74 years. The median values of serum creatinine were 75.4, 76.5, and 77.5 μmol/L in the men and 59.6, 60.7, and 62.1 μmol/L in the women. The eGFR in both sexes demonstrated a gradual decreasing trend over the 3 years. According to the CKD staging method, analysis of the different percentages of eGFR intervals in the patients showed that the percentages of the 3 groups with an eGFR lower than 60 mL/min/1.73 m² exhibited a rising trend annually. Correlational analysis of the nutritional indicators showed that the correlations between Hb, ALB, TG, TC, Ur, and BUN with an eGFR lower than 60 mL/min/1.73 m² were 0.582, 0.780, 1.219, 1.364, 2.180, and 3.677, respectively. CONCLUSIONS Serum creatinine showed a gradually increasing trend over the 3 study years. The CKD-EPI equation calculation results showed that the eGFR in elderly people of both sexes gradually decreased. Reduction of hemoglobin and albumin was a risk factor for decreased kidney function, while increases in uric acid and blood lipids affected the progression of renal insufficiency.

Toward a general theory of conical intersections in systems of identical nuclei

NASA Astrophysics Data System (ADS)

Keating, Sean P.; Mead, C. Alden

1987-02-01

It has been shown previously that the Herzberg-Longuet-Higgins sign change produced in Born-Oppenheimer electronic wave functions when the nuclei traverse a closed path around a conical intersection has implications for the symmetry of wave functions under permutations of identical nuclei. For systems of three or four identical nuclei, there are special features present which have facilitated the detailed analysis. The present paper reports progress toward a general theory for systems of n nuclei. For n=3 or 4, the two key functions which locate conical intersections and define compensating phase factors can conveniently be defined so as to transform under permutations according to a two-dimensional irreducible representation of the permutation group. Since such representations do not exist for n>4, we have chosen to develop a formalism in terms of lab-fixed electronic basis functions, and we show how to define the two key functions in principle. The functions so defined both turn out to be totally symmetric under permutations. We show how they can be used to define compensating phase factors so that all modified electronic wave functions are either totally symmetric or totally antisymmetric under permutations. A detailed analysis is made to cyclic permutations in the neighborhood of Dnh symmetry, which can be extended by continuity arguments to more general configurations, and criteria are obtained for sign changes. There is a qualitative discussion of the treatment of more general permutations.

Comparison of Physician-Predicted to Measured Low Vision Outcomes

PubMed Central

Chan, Tiffany L.; Goldstein, Judith E.; Massof, Robert W.

2013-01-01

Purpose To compare low vision rehabilitation (LVR) physicians’ predictions of the probability of success of LVR to patients’ self-reported outcomes after provision of usual outpatient LVR services; and to determine if patients’ traits influence physician ratings. Methods The Activity Inventory (AI), a self-report visual function questionnaire, was administered pre and post-LVR to 316 low vision patients served by 28 LVR centers that participated in a collaborative observational study. The physical component of the Short Form-36, Geriatric Depression Scale, and Telephone Interview for Cognitive Status were also administered pre-LVR to measure physical capability, depression and cognitive status. Following patient evaluation, 38 LVR physicians estimated the probability of outcome success (POS), using their own criteria. The POS ratings and change in functional ability were used to assess the effects of patients’ baseline traits on predicted outcomes. Results A regression analysis with a hierarchical random effects model showed no relationship between LVR physician POS estimates and AI-based outcomes. In another analysis, Kappa statistics were calculated to determine the probability of agreement between POS and AI-based outcomes for different outcome criteria. Across all comparisons, none of the kappa values were significantly different from 0, which indicates the rate of agreement is equivalent to chance. In an exploratory analysis, hierarchical mixed effects regression models show that POS ratings are associated with information about the patient’s cognitive functioning and the combination of visual acuity and functional ability, as opposed to visual acuity or functional ability alone. Conclusions Physicians’ predictions of LVR outcomes appear to be influenced by knowledge of patients’ cognitive functioning and the combination of visual acuity and functional ability - information physicians acquire from the patient’s history and examination. However, physicians’ predictions do not agree with observed changes in functional ability from the patient’s perspective; they are no better than chance. PMID:23873036

The usefulness of videomanometry for studying pediatric esophageal motor disease.

PubMed

Kawahara, Hisayoshi; Kubota, Akio; Okuyama, Hiroomi; Oue, Takaharu; Tazuke, Yuko; Okada, Akira

2004-12-01

Abnormalities in esophageal motor function underlie various symptoms in the pediatric population. Manometry remains an important tool for studying esophageal motor function, whereas its analyses have been conducted with considerable subjective interpretation. The usefulness of videomanometry with topographic analysis was examined in the current study. Videomanometry was conducted in 5 patients with primary gastroesophageal reflux disease (GERD), 4 with postoperative esophageal atresia (EA), 1 with congenital esophageal stenosis (CES), and 1 with diffuse esophageal spasms (DES). Digitized videofluoroscopic images were recorded synchronously with manometric digital data in a personal computer. Manometric analysis was conducted with a view of concurrent esophageal contour and bolus transit. Primary GERD patients showed esophageal flow proceeding into the stomach during peristaltic contractions recorded manometrically, whereas patients with EA/CES frequently showed impaired esophageal transit during defective esophageal peristaltic contractions. A characteristic corkscrew appearance and esophageal flow in a to-and-fro fashion were seen with high-amplitude synchronous esophageal contractions in a DES patient. The topographic analysis showed distinctive images characteristic of each pathological condition. Videomanometry is helpful in interpreting manometric data by analyzing concurrent fluoroscopic images. Topographic analyses provide characteristic images reflecting motor abnormalities in pediatric esophageal disease.

Likelihood ratio meta-analysis: New motivation and approach for an old method.

PubMed

Dormuth, Colin R; Filion, Kristian B; Platt, Robert W

2016-03-01

A 95% confidence interval (CI) in an updated meta-analysis may not have the expected 95% coverage. If a meta-analysis is simply updated with additional data, then the resulting 95% CI will be wrong because it will not have accounted for the fact that the earlier meta-analysis failed or succeeded to exclude the null. This situation can be avoided by using the likelihood ratio (LR) as a measure of evidence that does not depend on type-1 error. We show how an LR-based approach, first advanced by Goodman, can be used in a meta-analysis to pool data from separate studies to quantitatively assess where the total evidence points. The method works by estimating the log-likelihood ratio (LogLR) function from each study. Those functions are then summed to obtain a combined function, which is then used to retrieve the total effect estimate, and a corresponding 'intrinsic' confidence interval. Using as illustrations the CAPRIE trial of clopidogrel versus aspirin in the prevention of ischemic events, and our own meta-analysis of higher potency statins and the risk of acute kidney injury, we show that the LR-based method yields the same point estimate as the traditional analysis, but with an intrinsic confidence interval that is appropriately wider than the traditional 95% CI. The LR-based method can be used to conduct both fixed effect and random effects meta-analyses, it can be applied to old and new meta-analyses alike, and results can be presented in a format that is familiar to a meta-analytic audience. Copyright © 2016 Elsevier Inc. All rights reserved.

Examining the effectiveness of discriminant function analysis and cluster analysis in species identification of male field crickets based on their calling songs.

PubMed

Jaiswara, Ranjana; Nandi, Diptarup; Balakrishnan, Rohini

2013-01-01

Traditional taxonomy based on morphology has often failed in accurate species identification owing to the occurrence of cryptic species, which are reproductively isolated but morphologically identical. Molecular data have thus been used to complement morphology in species identification. The sexual advertisement calls in several groups of acoustically communicating animals are species-specific and can thus complement molecular data as non-invasive tools for identification. Several statistical tools and automated identifier algorithms have been used to investigate the efficiency of acoustic signals in species identification. Despite a plethora of such methods, there is a general lack of knowledge regarding the appropriate usage of these methods in specific taxa. In this study, we investigated the performance of two commonly used statistical methods, discriminant function analysis (DFA) and cluster analysis, in identification and classification based on acoustic signals of field cricket species belonging to the subfamily Gryllinae. Using a comparative approach we evaluated the optimal number of species and calling song characteristics for both the methods that lead to most accurate classification and identification. The accuracy of classification using DFA was high and was not affected by the number of taxa used. However, a constraint in using discriminant function analysis is the need for a priori classification of songs. Accuracy of classification using cluster analysis, which does not require a priori knowledge, was maximum for 6-7 taxa and decreased significantly when more than ten taxa were analysed together. We also investigated the efficacy of two novel derived acoustic features in improving the accuracy of identification. Our results show that DFA is a reliable statistical tool for species identification using acoustic signals. Our results also show that cluster analysis of acoustic signals in crickets works effectively for species classification and identification.

ERP Energy and Cognitive Activity Correlates

NASA Astrophysics Data System (ADS)

Schillaci, Michael Jay; Vendemia, Jennifer M. C.

2014-03-01

We propose a novel analysis approach for high-density event related scalp potential (ERP) data where the integrated channel-power is used to attain an energy density functional state for channel-clusters of neurophysiological significance. The method is applied to data recorded during a two-stimulus, directed lie paradigm and shows that deceptive responses emit between 8% and 10% less power. A time course analysis of these cognitive activity measures over posterior and anterior regions of the cortex suggests that neocortical interactions, reflecting the differing workload demands during executive and semantic processes, take about 50% longer for the case of deception. These results suggest that the proposed method may provide a useful tool for the analysis of ERP correlates of high-order cognitive functioning. We also report on a possible equivalence between the energy functional distribution and near-infrared signatures that have been measured with other modalities.

Impact of ontology evolution on functional analyses.

PubMed

Groß, Anika; Hartung, Michael; Prüfer, Kay; Kelso, Janet; Rahm, Erhard

2012-10-15

Ontologies are used in the annotation and analysis of biological data. As knowledge accumulates, ontologies and annotation undergo constant modifications to reflect this new knowledge. These modifications may influence the results of statistical applications such as functional enrichment analyses that describe experimental data in terms of ontological groupings. Here, we investigate to what degree modifications of the Gene Ontology (GO) impact these statistical analyses for both experimental and simulated data. The analysis is based on new measures for the stability of result sets and considers different ontology and annotation changes. Our results show that past changes in the GO are non-uniformly distributed over different branches of the ontology. Considering the semantic relatedness of significant categories in analysis results allows a more realistic stability assessment for functional enrichment studies. We observe that the results of term-enrichment analyses tend to be surprisingly stable despite changes in ontology and annotation.

Pyrcca: Regularized Kernel Canonical Correlation Analysis in Python and Its Applications to Neuroimaging.

PubMed

Bilenko, Natalia Y; Gallant, Jack L

2016-01-01

In this article we introduce Pyrcca, an open-source Python package for performing canonical correlation analysis (CCA). CCA is a multivariate analysis method for identifying relationships between sets of variables. Pyrcca supports CCA with or without regularization, and with or without linear, polynomial, or Gaussian kernelization. We first use an abstract example to describe Pyrcca functionality. We then demonstrate how Pyrcca can be used to analyze neuroimaging data. Specifically, we use Pyrcca to implement cross-subject comparison in a natural movie functional magnetic resonance imaging (fMRI) experiment by finding a data-driven set of functional response patterns that are similar across individuals. We validate this cross-subject comparison method in Pyrcca by predicting responses to novel natural movies across subjects. Finally, we show how Pyrcca can reveal retinotopic organization in brain responses to natural movies without the need for an explicit model.

Pyrcca: Regularized Kernel Canonical Correlation Analysis in Python and Its Applications to Neuroimaging

PubMed Central

Bilenko, Natalia Y.; Gallant, Jack L.

2016-01-01

In this article we introduce Pyrcca, an open-source Python package for performing canonical correlation analysis (CCA). CCA is a multivariate analysis method for identifying relationships between sets of variables. Pyrcca supports CCA with or without regularization, and with or without linear, polynomial, or Gaussian kernelization. We first use an abstract example to describe Pyrcca functionality. We then demonstrate how Pyrcca can be used to analyze neuroimaging data. Specifically, we use Pyrcca to implement cross-subject comparison in a natural movie functional magnetic resonance imaging (fMRI) experiment by finding a data-driven set of functional response patterns that are similar across individuals. We validate this cross-subject comparison method in Pyrcca by predicting responses to novel natural movies across subjects. Finally, we show how Pyrcca can reveal retinotopic organization in brain responses to natural movies without the need for an explicit model. PMID:27920675

Tract-based Spatial Statistics and fMRI Analysis in Patients with Small Cell Lung Cancer before Prophylactic Cranial Irradiation

NASA Astrophysics Data System (ADS)

Benezi, S.; Bromis, K.; Karavasilis, E.; Karanasiou, I. S.; Koutsoupidou, M.; Matsopoulos, G.; Ventouras, E.; Uzunoglu, N.; Kouloulias, V.; Papathanasiou, M.; Foteineas, A.; Efstathopoulos, E.; Kelekis, N.; Kelekis, D.

2015-09-01

Prophylactic cranial irradiation (PCI) is known to increase life expectancy to a significant degree in Small Cell Lung Cancer (SCLC) patients. The overall scope of this research is to investigate changes in structural and functional connectivity between SCLC patients and controls before and after PCI treatment. In the current study specifically we use diffusion tensor imaging (DTI) and functional Magnetic Resonance (fMRI) to identify potential alterations in white matter structure and brain function respectively, in SCLC patients before PCI compared to healthy participants. The results in DTI analysis have showed lower fractional anisotropy (FA) and higher eigenvalues in white matter regions in the patient group. Similarly, in fMRI analysis a lower level of activation in the primary somatosensory cortex was reported. The results presented herein are subject to further investigation with larger patient and control groups.

Evaluation of statistical distributions to analyze the pollution of Cd and Pb in urban runoff.

PubMed

Toranjian, Amin; Marofi, Safar

2017-05-01

Heavy metal pollution in urban runoff causes severe environmental damage. Identification of these pollutants and their statistical analysis is necessary to provide management guidelines. In this study, 45 continuous probability distribution functions were selected to fit the Cd and Pb data in the runoff events of an urban area during October 2014-May 2015. The sampling was conducted from the outlet of the city basin during seven precipitation events. For evaluation and ranking of the functions, we used the goodness of fit Kolmogorov-Smirnov and Anderson-Darling tests. The results of Cd analysis showed that Hyperbolic Secant, Wakeby and Log-Pearson 3 are suitable for frequency analysis of the event mean concentration (EMC), the instantaneous concentration series (ICS) and instantaneous concentration of each event (ICEE), respectively. In addition, the LP3, Wakeby and Generalized Extreme Value functions were chosen for the EMC, ICS and ICEE related to Pb contamination.

Grain size statistics and depositional pattern of the Ecca Group sandstones, Karoo Supergroup in the Eastern Cape Province, South Africa

NASA Astrophysics Data System (ADS)

Baiyegunhi, Christopher; Liu, Kuiwu; Gwavava, Oswald

2017-11-01

Grain size analysis is a vital sedimentological tool used to unravel the hydrodynamic conditions, mode of transportation and deposition of detrital sediments. In this study, detailed grain-size analysis was carried out on thirty-five sandstone samples from the Ecca Group in the Eastern Cape Province of South Africa. Grain-size statistical parameters, bivariate analysis, linear discriminate functions, Passega diagrams and log-probability curves were used to reveal the depositional processes, sedimentation mechanisms, hydrodynamic energy conditions and to discriminate different depositional environments. The grain-size parameters show that most of the sandstones are very fine to fine grained, moderately well sorted, mostly near-symmetrical and mesokurtic in nature. The abundance of very fine to fine grained sandstones indicate the dominance of low energy environment. The bivariate plots show that the samples are mostly grouped, except for the Prince Albert samples that show scattered trend, which is due to the either mixture of two modes in equal proportion in bimodal sediments or good sorting in unimodal sediments. The linear discriminant function analysis is dominantly indicative of turbidity current deposits under shallow marine environments for samples from the Prince Albert, Collingham and Ripon Formations, while those samples from the Fort Brown Formation are lacustrine or deltaic deposits. The C-M plots indicated that the sediments were deposited mainly by suspension and saltation, and graded suspension. Visher diagrams show that saltation is the major process of transportation, followed by suspension.

Functional status, physical activity level, and exercise regularity in patients with fibromyalgia after Multidisciplinary treatment: retrospective analysis of a randomized controlled trial.

PubMed

Salvat, I; Zaldivar, P; Monterde, S; Montull, S; Miralles, I; Castel, A

2017-03-01

Multidisciplinary treatments have shown to be effective for fibromyalgia. We report detailed functional outcomes of patients with fibromyalgia who attended a 3-month Multidisciplinary treatment program. The hypothesis was that patients would have increased functional status, physical activity level, and exercise regularity after attending this program. We performed a retrospective analysis of a randomized, simple blinded clinical trial. The inclusion criteria consisted of female sex, a diagnosis of fibromyalgia, age 18-60  and 3-8 years of schooling. Measures from the Fibromyalgia Impact Questionnaire (FIQ) and the COOP/WONCA Functional Health Assessment Charts (WONCA) were obtained before and at the end of the treatment and at 3-, 6-, and 12-month follow-ups. Patients recorded their number of steps per day with pedometers. They performed the six-minute walk test (6 MW) before and after treatment. In total, 155 women participated in the study. Their median (interquartile interval) FIQ score was 68.0 (53.0-77.0) at the beginning of the treatment, and the difference between the Multidisciplinary and Control groups was statistically and clinically significant in all of the measures (except the 6-month follow-up). The WONCA charts showed significant clinical improvements in the Multidisciplinary group, with physical fitness in the normal range across almost all values. In that group, steps/day showed more regularity, and the 6 MW results showed improvement of -33.00 (-59.8 to -8.25) m, and the differences from the Control group were statistically significant. The patients who underwent the Multidisciplinary treatment had improved functional status, physical activity level, and exercise regularity. The functional improvements were maintained 1 year after treatment completion.

Deletion of the transcriptional coactivator PGC1α in skeletal muscles is associated with reduced expression of genes related to oxidative muscle function.

PubMed

Hatazawa, Yukino; Minami, Kimiko; Yoshimura, Ryoji; Onishi, Takumi; Manio, Mark Christian; Inoue, Kazuo; Sawada, Naoki; Suzuki, Osamu; Miura, Shinji; Kamei, Yasutomi

2016-12-09

The expression of the transcriptional coactivator PGC1α is increased in skeletal muscles during exercise. Previously, we showed that increased PGC1α leads to prolonged exercise performance (the duration for which running can be continued) and, at the same time, increases the expression of branched-chain amino acid (BCAA) metabolism-related enzymes and genes that are involved in supplying substrates for the TCA cycle. We recently created mice with PGC1α knockout specifically in the skeletal muscles (PGC1α KO mice), which show decreased mitochondrial content. In this study, global gene expression (microarray) analysis was performed in the skeletal muscles of PGC1α KO mice compared with that of wild-type control mice. As a result, decreased expression of genes involved in the TCA cycle, oxidative phosphorylation, and BCAA metabolism were observed. Compared with previously obtained microarray data on PGC1α-overexpressing transgenic mice, each gene showed the completely opposite direction of expression change. Bioinformatic analysis of the promoter region of genes with decreased expression in PGC1α KO mice predicted the involvement of several transcription factors, including a nuclear receptor, ERR, in their regulation. As PGC1α KO microarray data in this study show opposing findings to the PGC1α transgenic data, a loss-of-function experiment, as well as a gain-of-function experiment, revealed PGC1α's function in the oxidative energy metabolism of skeletal muscles. Copyright © 2016 Elsevier Inc. All rights reserved.

Insulin growth factor-I promotes functional recovery after a focal lesion in the dentate gyrus.

PubMed

Liquitaya-Montiel, Adhemar; Aguilar-Arredondo, Andrea; Arias, Clorinda; Zepeda, Angélica

2012-11-01

The adult brain is plastic and able to reorganize structurally and functionally after damage. Growth factors are key molecules underlying the recovery process and among trophic molecules, Insulin-Like Growth Factor-I (IGF-I) is of particular interest given that it modulates neuronal and glial responses in the hippocampus including neurogenesis, which has been proposed as a mechanism of neurorepair. In this study we analyzed the effect of intracerebroventricular chronic infusion of IGF-I on functional recovery and morphological restoration after the induction of an excitotoxic lesion in the dentate gyrus (DG) of young-adult rats. Our results show that the lesion impairs contextual fear memory which is a DG dependent task, but not cued fear memory or performance in the open field motor task, which are independent of the DG integrity. Chronic administration of IGF-I, but not vehicle, promotes functional recovery to control levels in injured subjects. Analysis in NeuN immunoprocessed tissue revealed that the lesion volume was not different between groups and that the DG was not evidently restructured in the IGF-I treated group. Glial fibrillary acidic protein (GFAP) analysis revealed an increased astrocytic response in the injured region in both groups and Doublecortin (DCX) analysis showed a similar increase in number of newly born neurons in both groups. However, a remarkable increase in young neurons dendritic arborization was observed in the IGF-I treated group. These results provide evidence for IGF-I as a molecule mediating functional and cellular plasticity during a reorganization process after damage to a neurogenic niche.

A network of automatic atmospherics analyzer

NASA Technical Reports Server (NTRS)

Schaefer, J.; Volland, H.; Ingmann, P.; Eriksson, A. J.; Heydt, G.

1980-01-01

The design and function of an atmospheric analyzer which uses a computer are discussed. Mathematical models which show the method of measurement are presented. The data analysis and recording procedures of the analyzer are discussed.

freeQuant: A Mass Spectrometry Label-Free Quantification Software Tool for Complex Proteome Analysis.

PubMed

Deng, Ning; Li, Zhenye; Pan, Chao; Duan, Huilong

2015-01-01

Study of complex proteome brings forward higher request for the quantification method using mass spectrometry technology. In this paper, we present a mass spectrometry label-free quantification tool for complex proteomes, called freeQuant, which integrated quantification with functional analysis effectively. freeQuant consists of two well-integrated modules: label-free quantification and functional analysis with biomedical knowledge. freeQuant supports label-free quantitative analysis which makes full use of tandem mass spectrometry (MS/MS) spectral count, protein sequence length, shared peptides, and ion intensity. It adopts spectral count for quantitative analysis and builds a new method for shared peptides to accurately evaluate abundance of isoforms. For proteins with low abundance, MS/MS total ion count coupled with spectral count is included to ensure accurate protein quantification. Furthermore, freeQuant supports the large-scale functional annotations for complex proteomes. Mitochondrial proteomes from the mouse heart, the mouse liver, and the human heart were used to evaluate the usability and performance of freeQuant. The evaluation showed that the quantitative algorithms implemented in freeQuant can improve accuracy of quantification with better dynamic range.

Forecast Vienna Mapping Functions 1 for real-time analysis of space geodetic observations

NASA Astrophysics Data System (ADS)

Boehm, J.; Kouba, J.; Schuh, H.

2009-05-01

The Vienna Mapping Functions 1 (VMF1) as provided by the Institute of Geodesy and Geophysics (IGG) at the Vienna University of Technology are the most accurate mapping functions for the troposphere delays that are available globally and for the entire history of space geodetic observations. So far, the VMF1 coefficients have been released with a time delay of almost two days; however, many scientific applications require their availability in near real-time, e.g. the Ultra Rapid solutions of the International GNSS Service (IGS) or the analysis of the Intensive sessions of the International VLBI Service (IVS). Here we present coefficients of the VMF1 as well as the hydrostatic and wet zenith delays that have been determined from forecasting data of the European Centre for Medium-Range Weather Forecasts (ECMWF) and provided on global grids. The comparison with parameters derived from ECMWF analysis data shows that the agreement is at the 1 mm level in terms of station height, and that the differences are larger for the wet mapping functions than for the hydrostatic mapping functions and the hydrostatic zenith delays. These new products (VMF1-FC and hydrostatic zenith delays from forecast data) can be used in real-time analysis of geodetic data without significant loss of accuracy.

LARG at chromosome 11q23 has functional characteristics of a tumor suppressor in human breast cancer

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

Ong, Danny C.T.; Rudduck, Christina; Chin, Koei

2008-05-06

Deletion of 11q23-q24 is frequent in a diverse variety of malignancies, including breast and colorectal carcinoma, implicating the presence of a tumor suppressor gene at that chromosomal region. We show here that LARG, from 11q23, has functional characteristics of a tumor suppressor. We examined a 6-Mb region on 11q23 by high-resolution deletion mapping, utilizing both loss of heterozygosity (LOH) analysis and microarray comparative genomic hybridization (CGH). LARG (also called ARHGEF12), identified from the analyzed region, was underexpressed in 34% of primary breast carcinomas and 80% of breast cancer cell lines including the MCF-7 line. Multiplex ligation-dependent probe amplification on 30more » primary breast cancers and six breast cancer cell lines showed that LARG had the highest frequency of deletion compared to the BCSC-1 and TSLC1 genes, two known candidate tumor suppressor genes from 11q. In vitro analysis of breast cancer cell lines that underexpress LARG showed that LARG could be reactivated by trichostatin A, a histone deacetylase inhibitor, but not by 5-Aza-2{prime}-deoxycytidine, a demethylating agent. Bisulfite sequencing and quantitative high-throughput analysis of DNA methylation confirmed the lack of CpG island methylation in LARG in breast cancer. Restoration of LARG expression in MCF-7 cells by stable transfection resulted in reduced proliferation and colony formation, suggesting that LARG has functional characteristics of a tumor suppressor gene.« less

Extracting functional components of neural dynamics with Independent Component Analysis and inverse Current Source Density.

PubMed

Lęski, Szymon; Kublik, Ewa; Swiejkowski, Daniel A; Wróbel, Andrzej; Wójcik, Daniel K

2010-12-01

Local field potentials have good temporal resolution but are blurred due to the slow spatial decay of the electric field. For simultaneous recordings on regular grids one can reconstruct efficiently the current sources (CSD) using the inverse Current Source Density method (iCSD). It is possible to decompose the resultant spatiotemporal information about the current dynamics into functional components using Independent Component Analysis (ICA). We show on test data modeling recordings of evoked potentials on a grid of 4 × 5 × 7 points that meaningful results are obtained with spatial ICA decomposition of reconstructed CSD. The components obtained through decomposition of CSD are better defined and allow easier physiological interpretation than the results of similar analysis of corresponding evoked potentials in the thalamus. We show that spatiotemporal ICA decompositions can perform better for certain types of sources but it does not seem to be the case for the experimental data studied. Having found the appropriate approach to decomposing neural dynamics into functional components we use the technique to study the somatosensory evoked potentials recorded on a grid spanning a large part of the forebrain. We discuss two example components associated with the first waves of activation of the somatosensory thalamus. We show that the proposed method brings up new, more detailed information on the time and spatial location of specific activity conveyed through various parts of the somatosensory thalamus in the rat.

Identifying arsenic trioxide (ATO) functions in leukemia cells by using time series gene expression profiles.

PubMed

Yang, Hong; Lin, Shan; Cui, Jingru

2014-02-10

Arsenic trioxide (ATO) is presently the most active single agent in the treatment of acute promyelocytic leukemia (APL). In order to explore the molecular mechanism of ATO in leukemia cells with time series, we adopted bioinformatics strategy to analyze expression changing patterns and changes in transcription regulation modules of time series genes filtered from Gene Expression Omnibus database (GSE24946). We totally screened out 1847 time series genes for subsequent analysis. The KEGG (Kyoto encyclopedia of genes and genomes) pathways enrichment analysis of these genes showed that oxidative phosphorylation and ribosome were the top 2 significantly enriched pathways. STEM software was employed to compare changing patterns of gene expression with assigned 50 expression patterns. We screened out 7 significantly enriched patterns and 4 tendency charts of time series genes. The result of Gene Ontology showed that functions of times series genes mainly distributed in profiles 41, 40, 39 and 38. Seven genes with positive regulation of cell adhesion function were enriched in profile 40, and presented the same first increased model then decreased model as profile 40. The transcription module analysis showed that they mainly involved in oxidative phosphorylation pathway and ribosome pathway. Overall, our data summarized the gene expression changes in ATO treated K562-r cell lines with time and suggested that time series genes mainly regulated cell adhesive. Furthermore, our result may provide theoretical basis of molecular biology in treating acute promyelocytic leukemia. Copyright © 2013 Elsevier B.V. All rights reserved.

Subthreshold Depressive Symptoms have a Negative Impact on Cognitive Functioning in Middle-Aged and Older Males.

PubMed

Brevik, Erlend J; Eikeland, Rune A; Lundervold, Astri J

2013-01-01

Cognitive aging is associated with a decline on measures of fluid intelligence (gF), whereas crystallized intelligence (gC) tends to remain stable. In the present study we asked if depressive symptoms might contribute to explain the decline on gF in a sample of healthy middle-aged and older adults. The Norwegian sample included 83 females and 42 males (M = 60, SD = 7.9 years). gF was calculated from factor-analysis, including tests of matrix reasoning (WASI), memory function (CVLT-II), processing speed and executive function (CDT; CWIT). gC was derived from a Vocabulary subtest (WASI). Depressive symptoms were assessed by self-reports on Beck's Depression Index (BDI) and ranged from 0 to 21 (M = 6, SD = 4.5). Increased age was correlated with a decline on gF (r = -0.436, p  < 0.001), but not gC (r=-0.103, p = ns.). The BDI score in the whole sample was correlated with gF (r = -0.313, p < 0.001). A more detailed analysis showed that the BDI score correlated with measures of both gF and gC in males. The correlations were non-significant for females on all measures, with the exception of a measure of processing speed/executive function. A regression analysis including age and sex in the first step, showed that symptoms of depression significantly contributed to explain decline on gF, F(3, 124) = 16.653, p < 0.001, R? = 0.292, ΔR? = 0.054. The results showed that symptoms of depression were negatively correlated with cognitive functioning in males even when the symptom-level was below clinical threshold. This indicates that minimal symptoms of depression in older men are clinically relevant to address.

A comparative analysis of the avirulence and translational transactivator functions of gene VI of Cauliflower mosaic virus.

PubMed

Palanichelvam, Karuppaiah; Schoelz, James E

2002-02-15

The primary function associated at present with the gene VI product of Cauliflower mosaic virus (CaMV) is that of a translational transactivator (TAV). In this capacity, it alters the host translational machinery to allow reinitiation of translation of other CaMV genes on the polycistronic 35S RNA of CaMV. In addition, the gene VI protein can elicit a specific type of plant defense response called the hypersensitive response (HR) in Nicotiana edwardsonii. In this study, we have adapted the agroinfiltration technique to compare the sequences of CaMV gene VI required for TAV function and elicitation of HR. To measure the activity of the TAV, we coagroinfiltrated gene VI of CaMV strain W260 with a bicistronic GUS reporter plasmid. TAV function could be assayed 4 days postinfiltration, before the onset of HR in N. edwardsonii. Through the use of the TAV and HR assays, we could show that the TAV functions of gene VI of CaMV strains W260 and D4 were equivalent, but only W260 gene VI elicited HR. A mutational analysis of W260 gene VI showed that the structural requirements for elicitation of HR were much more stringent than those for TAV function. Small deletions from either the 5' or 3' end of W260 gene VI abolished its ability to elicit HR, although the TAV function was retained in the mutant. The TAV function could also tolerate a small insertion within gene VI; this insertion abolished the elicitor function. This study provides direct evidence that the TAV function of gene VI is separate from its role as an elicitor of HR.

Differential expression pattern of UBX family genes in Caenorhabditis elegans

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

Yamauchi, Seiji; Sasagawa, Yohei; Ogura, Teru

2007-06-29

UBX (ubiquitin regulatory X)-containing proteins belong to an evolutionary conserved protein family and determine the specificity of p97/VCP/Cdc48p function by binding as its adaptors. Caenorhabditis elegans was found to possess six UBX-containing proteins, named UBXN-1 to -6. However, no general or specific function of them has been revealed. During the course of understanding not only their function but also specified function of p97, we investigated spatial and temporal expression patterns of six ubxn genes in this study. Transcript analyses showed that the expression pattern of each ubxn gene was different throughout worm's development and may show potential developmental dynamics inmore » their function, especially ubxn-5 was expressed specifically in the spermatogenic germline, suggesting a crucial role in spermatogenesis. In addition, as ubxn-4 expression was induced by ER stress, it would function as an ERAD factor in C. elegans. In vivo expression analysis by using GFP translational fusion constructs revealed that six ubxn genes show distinct expression patterns. These results altogether demonstrate that the expression of all six ubxn genes of C. elegans is differently regulated.« less

Comparative study of nonlinear properties of EEG signals of normal persons and epileptic patients

PubMed Central

2009-01-01

Background Investigation of the functioning of the brain in living systems has been a major effort amongst scientists and medical practitioners. Amongst the various disorder of the brain, epilepsy has drawn the most attention because this disorder can affect the quality of life of a person. In this paper we have reinvestigated the EEGs for normal and epileptic patients using surrogate analysis, probability distribution function and Hurst exponent. Results Using random shuffled surrogate analysis, we have obtained some of the nonlinear features that was obtained by Andrzejak et al. [Phys Rev E 2001, 64:061907], for the epileptic patients during seizure. Probability distribution function shows that the activity of an epileptic brain is nongaussian in nature. Hurst exponent has been shown to be useful to characterize a normal and an epileptic brain and it shows that the epileptic brain is long term anticorrelated whereas, the normal brain is more or less stochastic. Among all the techniques, used here, Hurst exponent is found very useful for characterization different cases. Conclusion In this article, differences in characteristics for normal subjects with eyes open and closed, epileptic subjects during seizure and seizure free intervals have been shown mainly using Hurst exponent. The H shows that the brain activity of a normal man is uncorrelated in nature whereas, epileptic brain activity shows long range anticorrelation. PMID:19619290

Peroxisomal monodehydroascorbate reductase. Genomic clone characterization and functional analysis under environmental stress conditions.

PubMed

Leterrier, Marina; Corpas, Francisco J; Barroso, Juan B; Sandalio, Luisa M; del Río, Luis A

2005-08-01

In plant cells, ascorbate is a major antioxidant that is involved in the ascorbate-glutathione cycle. Monodehydroascorbate reductase (MDAR) is the enzymatic component of this cycle involved in the regeneration of reduced ascorbate. The identification of the intron-exon organization and the promoter region of the pea (Pisum sativum) MDAR 1 gene was achieved in pea leaves using the method of walking polymerase chain reaction on genomic DNA. The nuclear gene of MDAR 1 comprises nine exons and eight introns, giving a total length of 3,770 bp. The sequence of 544 bp upstream of the initiation codon, which contains the promoter and 5' untranslated region, and 190 bp downstream of the stop codon were also determined. The presence of different regulatory motifs in the promoter region of the gene might indicate distinct responses to various conditions. The expression analysis in different plant organs by northern blots showed that fruits had the highest level of MDAR. Confocal laser scanning microscopy analysis of pea leaves transformed with Agrobacterium tumefaciens having the binary vectors pGD, which contain the autofluorescent proteins enhanced green fluorescent protein and enhanced yellow fluorescent protein with the full-length cDNA for MDAR 1 and catalase, indicated that the MDAR 1 encoded the peroxisomal isoform. The functional analysis of MDAR by activity and protein expression was studied in pea plants grown under eight stress conditions, including continuous light, high light intensity, continuous dark, mechanical wounding, low and high temperature, cadmium, and the herbicide 2,4-dichlorophenoxyacetic acid. This functional analysis is representative of all the MDAR isoforms present in the different cell compartments. Results obtained showed a significant induction by high light intensity and cadmium. On the other hand, expression studies, performed by semiquantitative reverse transcription-polymerase chain reaction demonstrated differential expression patterns of peroxisomal MDAR 1 transcripts in pea plants grown under the mentioned stress conditions. These findings show that the peroxisomal MDAR 1 has a differential regulation that could be indicative of its specific function in peroxisomes. All these biochemical and molecular data represent a significant step to understand the specific physiological role of each MDAR isoenzyme and its participation in the antioxidant mechanisms of plant cells.

Long-term effects of musical training and functional plasticity in salience system.

PubMed

Luo, Cheng; Tu, Shipeng; Peng, Yueheng; Gao, Shan; Li, Jianfu; Dong, Li; Li, Gujing; Lai, Yongxiu; Li, Hong; Yao, Dezhong

2014-01-01

Musicians undergoing long-term musical training show improved emotional and cognitive function, which suggests the presence of neuroplasticity. The structural and functional impacts of the human brain have been observed in musicians. In this study, we used data-driven functional connectivity analysis to map local and distant functional connectivity in resting-state functional magnetic resonance imaging data from 28 professional musicians and 28 nonmusicians. Compared with nonmusicians, musicians exhibited significantly greater local functional connectivity density in 10 regions, including the bilateral dorsal anterior cingulate cortex, anterior insula, and anterior temporoparietal junction. A distant functional connectivity analysis demonstrated that most of these regions were included in salience system, which is associated with high-level cognitive control and fundamental attentional process. Additionally, musicians had significantly greater functional integration in this system, especially for connections to the left insula. Increased functional connectivity between the left insula and right temporoparietal junction may be a response to long-term musical training. Our findings indicate that the improvement of salience network is involved in musical training. The salience system may represent a new avenue for exploration regarding the underlying foundations of enhanced higher-level cognitive processes in musicians.

Functional and structural neural alterations in Internet gaming disorder: A systematic review and meta-analysis.

PubMed

Yao, Yuan-Wei; Liu, Lu; Ma, Shan-Shan; Shi, Xin-Hui; Zhou, Nan; Zhang, Jin-Tao; Potenza, Marc N

2017-12-01

This meta-analytic study aimed to identify the common and specific neural alterations in Internet gaming disorder (IGD) across different domains and modalities. Two separate meta-analyses for functional neural activation and gray-matter volume were conducted. Sub-meta-analyses for the domains of reward, cold-executive, and hot-executive functions were also performed, respectively. IGD subjects, compared with healthy controls, showed: (1) hyperactivation in the anterior and posterior cingulate cortices, caudate, posterior inferior frontal gyrus (IFG), which were mainly associated with studies measuring reward and cold-executive functions; and, (2) hypoactivation in the anterior IFG in relation to hot-executive function, the posterior insula, somatomotor and somatosensory cortices in relation to reward function. Furthermore, IGD subjects showed reduced gray-matter volume in the anterior cingulate, orbitofrontal, dorsolateral prefrontal, and premotor cortices. These findings suggest that IGD is associated with both functional and structural neural alterations in fronto-striatal and fronto-cingulate regions. Moreover, multi-domain assessments capture different aspects of neural alterations in IGD, which may be helpful for developing effective interventions targeting specific functions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Association of presence/absence and on/off patterns of Helicobacter pylori oipA gene with peptic ulcer disease and gastric cancer risks: a meta-analysis.

PubMed

Liu, Jingwei; He, Caiyun; Chen, Moye; Wang, Zhenning; Xing, Chengzhong; Yuan, Yuan

2013-11-20

There are increasing studies examining the relationship between the status of H. pylori oipA gene and peptic ulcer disease (PUD) and gastric cancer (GC) but the results turn out to be controversial. We attempted to clarify whether oipA gene status is linked with PUD and/or GC risks. A systematically literature search was performed through four electronic databases. According to the specific inclusion and exclusion criteria, seven articles were ultimately available for the meta-analysis of oipA presence/absence with PUD and GC, and eleven articles were included for the meta-analysis of oipA on/off status with PUD and GC. For the on/off functional status analysis of oipA gene, the "on" status showed significant associations with increased risks of PUD (OR = 3.97, 95% CI: 2.89, 5.45; P < 0.001) and GC (OR = 2.43, 95% CI: 1.45, 4.07; P = 0.001) compared with gastritis and functional dyspepsia controls. Results of the homogeneity test indicated different effects of oipA "on" status on PUD risk between children and adult subgroups and on GC risk between PCR-sequencing and immunoblot subgroups. For the presence/absence analysis of oipA gene, we found null association of the presence of oipA gene with the risks of PUD (OR = 1.93, 95% CI: 0.60, 6.25; P = 0.278) and GC (OR = 2.09, 95% CI: 0.51, 8.66; P = 0.308) compared with gastritis and functional dyspepsia controls. To be concluded, when oipA exists, the functional "on" status of this gene showed association with increased risks for PUD and GC compared with gastritis and FD controls. However, merely investigating the presence/absence of oipA would overlook the importance of its functional on/off status and would not be reliable to predict risks of PUD and GC. Further large-scale and well-designed studies concerning on/off status of oipA are required to confirm our meta-analysis results.

Spatio-temporal coordination among functional residues in protein

NASA Astrophysics Data System (ADS)

Dutta, Sutapa; Ghosh, Mahua; Chakrabarti, J.

2017-01-01

The microscopic basis of communication among the functional sites in bio-macromolecules is a fundamental challenge in uncovering their functions. We study the communication through temporal cross-correlation among the binding sites. We illustrate via Molecular Dynamics simulations the properties of the temporal cross-correlation between the dihedrals of a small protein, ubiquitin which participates in protein degradation in eukaryotes. We show that the dihedral angles of the residues possess non-trivial temporal cross-correlations with asymmetry with respect to exchange of the dihedrals, having peaks at low frequencies with time scales in nano-seconds and an algebraic tail with a universal exponent for large frequencies. We show the existence of path for temporally correlated degrees of freedom among the functional residues. We explain the qualitative features of the cross-correlations through a general mathematical model. The generality of our analysis suggests that temporal cross-correlation functions may provide convenient theoretical framework to understand bio-molecular functions on microscopic basis.

For Function or Transformation? A Critical Discourse Analysis of Education under the Sustainable Development Goals

ERIC Educational Resources Information Center

Brissett, Nigel; Mitter, Radhika

2017-01-01

We conduct a critical discourse analysis of the extent to which Sustainable Development Goal 4, "to ensure inclusive and equitable quality education for all and promote lifelong learning," promotes a utilitarian and/or transformative approach to education. Our findings show that despite transformative language used throughout the Agenda,…

Altered functional MR imaging language activation in elderly individuals with cerebral leukoaraiosis.

PubMed

Welker, Kirk M; De Jesus, Reordan O; Watson, Robert E; Machulda, Mary M; Jack, Clifford R

2012-10-01

To test the hypothesis that leukoaraiosis alters functional activation during a semantic decision language task. With institutional review board approval and written informed consent, 18 right-handed, cognitively healthy elderly participants with an aggregate leukoaraiosis lesion volume of more than 25 cm(3) and 18 age-matched control participants with less than 5 cm(3) of leukoaraiosis underwent functional MR imaging to allow comparison of activation during semantic decisions with that during visual perceptual decisions. Brain statistical maps were derived from the general linear model. Spatially normalized group t maps were created from individual contrast images. A cluster extent threshold of 215 voxels was used to correct for multiple comparisons. Intergroup random effects analysis was performed. Language laterality indexes were calculated for each participant. In control participants, semantic decisions activated the bilateral visual cortex, left posteroinferior temporal lobe, left posterior cingulate gyrus, left frontal lobe expressive language regions, and left basal ganglia. Visual perceptual decisions activated the right parietal and posterior temporal lobes. Participants with leukoaraiosis showed reduced activation in all regions associated with semantic decisions; however, activation associated with visual perceptual decisions increased in extent. Intergroup analysis showed significant activation decreases in the left anterior occipital lobe (P=.016), right posterior temporal lobe (P=.048), and right basal ganglia (P=.009) in particpants with leukoariosis. Individual participant laterality indexes showed a strong trend (P=.059) toward greater left lateralization in the leukoaraiosis group. Moderate leukoaraiosis is associated with atypical functional activation during semantic decision tasks. Consequently, leukoaraiosis is an important confounding variable in functional MR imaging studies of elderly individuals. © RSNA, 2012.

Conformational diversity analysis reveals three functional mechanisms in proteins

PubMed Central

Fornasari, María Silvina

2017-01-01

Protein motions are a key feature to understand biological function. Recently, a large-scale analysis of protein conformational diversity showed a positively skewed distribution with a peak at 0.5 Å C-alpha root-mean-square-deviation (RMSD). To understand this distribution in terms of structure-function relationships, we studied a well curated and large dataset of ~5,000 proteins with experimentally determined conformational diversity. We searched for global behaviour patterns studying how structure-based features change among the available conformer population for each protein. This procedure allowed us to describe the RMSD distribution in terms of three main protein classes sharing given properties. The largest of these protein subsets (~60%), which we call “rigid” (average RMSD = 0.83 Å), has no disordered regions, shows low conformational diversity, the largest tunnels and smaller and buried cavities. The two additional subsets contain disordered regions, but with differential sequence composition and behaviour. Partially disordered proteins have on average 67% of their conformers with disordered regions, average RMSD = 1.1 Å, the highest number of hinges and the longest disordered regions. In contrast, malleable proteins have on average only 25% of disordered conformers and average RMSD = 1.3 Å, flexible cavities affected in size by the presence of disordered regions and show the highest diversity of cognate ligands. Proteins in each set are mostly non-homologous to each other, share no given fold class, nor functional similarity but do share features derived from their conformer population. These shared features could represent conformational mechanisms related with biological functions. PMID:28192432

Electrophysiologic and functional evaluations of regenerated facial nerve defects with a tube containing dental pulp cells in rats.

PubMed

Sasaki, Ryo; Matsumine, Hajime; Watanabe, Yorikatsu; Takeuchi, Yuichi; Yamato, Masayuki; Okano, Teruo; Miyata, Mariko; Ando, Tomohiro

2014-11-01

Dental pulp tissue contains Schwann and neural progenitor cells. Tissue-engineered nerve conduits with dental pulp cells promote facial nerve regeneration in rats. However, no nerve functional or electrophysiologic evaluations were performed. This study investigated the compound muscle action potential recordings and facial functional analysis of dental pulp cell regenerated nerve in rats. A silicone tube containing rat dental pulp cells in type I collagen gel was transplanted into a 7-mm gap of the buccal branch of the facial nerve in Lewis rats; the same defect was created in the marginal mandibular branch, which was ligatured. Compound muscle action potential recordings of vibrissal muscles and facial functional analysis with facial palsy score of the nerve were performed. Tubulation with dental pulp cells showed significantly lower facial palsy scores than the autograft group between 3 and 10 weeks postoperatively. However, the dental pulp cell facial palsy scores showed no significant difference from those of autograft after 11 weeks. Amplitude and duration of compound muscle action potentials in the dental pulp cell group showed no significant difference from those of the intact and autograft groups, and there was no significant difference in the latency of compound muscle action potentials between the groups at 13 weeks postoperatively. However, the latency in the dental pulp cell group was prolonged more than that of the intact group. Tubulation with dental pulp cells could recover facial nerve defects functionally and electrophysiologically, and the recovery became comparable to that of nerve autografting in rats.

Resting-State Brain Activity in Adult Males Who Stutter

PubMed Central

Zhu, Chaozhe; Wang, Liang; Yan, Qian; Lin, Chunlan; Yu, Chunshui

2012-01-01

Although developmental stuttering has been extensively studied with structural and task-based functional magnetic resonance imaging (fMRI), few studies have focused on resting-state brain activity in this disorder. We investigated resting-state brain activity of stuttering subjects by analyzing the amplitude of low-frequency fluctuation (ALFF), region of interest (ROI)-based functional connectivity (FC) and independent component analysis (ICA)-based FC. Forty-four adult males with developmental stuttering and 46 age-matched fluent male controls were scanned using resting-state fMRI. ALFF, ROI-based FCs and ICA-based FCs were compared between male stuttering subjects and fluent controls in a voxel-wise manner. Compared with fluent controls, stuttering subjects showed increased ALFF in left brain areas related to speech motor and auditory functions and bilateral prefrontal cortices related to cognitive control. However, stuttering subjects showed decreased ALFF in the left posterior language reception area and bilateral non-speech motor areas. ROI-based FC analysis revealed decreased FC between the posterior language area involved in the perception and decoding of sensory information and anterior brain area involved in the initiation of speech motor function, as well as increased FC within anterior or posterior speech- and language-associated areas and between the prefrontal areas and default-mode network (DMN) in stuttering subjects. ICA showed that stuttering subjects had decreased FC in the DMN and increased FC in the sensorimotor network. Our findings support the concept that stuttering subjects have deficits in multiple functional systems (motor, language, auditory and DMN) and in the connections between them. PMID:22276215

Functional overestimation due to spatial smoothing of fMRI data.

PubMed

Liu, Peng; Calhoun, Vince; Chen, Zikuan

2017-11-01

Pearson correlation (simply correlation) is a basic technique for neuroimage function analysis. It has been observed that the spatial smoothing may cause functional overestimation, which however remains a lack of complete understanding. Herein, we present a theoretical explanation from the perspective of correlation scale invariance. For a task-evoked spatiotemporal functional dataset, we can extract the functional spatial map by calculating the temporal correlations (tcorr) of voxel timecourses against the task timecourse. From the relationship between image noise level (changed through spatial smoothing) and the tcorr map calculation, we show that the spatial smoothing causes a noise reduction, which in turn smooths the tcorr map and leads to a spatial expansion on neuroactivity blob estimation. Through numerical simulations and subject experiments, we show that the spatial smoothing of fMRI data may overestimate activation spots in the correlation functional map. Our results suggest a small spatial smoothing (with a smoothing kernel with a full width at half maximum (FWHM) of no more than two voxels) on fMRI data processing for correlation-based functional mapping COMPARISON WITH EXISTING METHODS: In extreme noiselessness, the correlation of scale-invariance property defines a meaningless binary tcorr map. In reality, a functional activity blob in a tcorr map is shaped due to the spoilage of image noise on correlative responses. We may reduce data noise level by smoothing processing, which poses a smoothing effect on correlation. This logic allows us to understand the noise dependence and the smoothing effect of correlation-based fMRI data analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

Quantitative investigation of red blood cell three-dimensional geometric and chemical changes in the storage lesion using digital holographic microscopy.

PubMed

Jaferzadeh, Keyvan; Moon, Inkyu

2015-11-01

Quantitative phase information obtained by digital holographic microscopy (DHM) can provide new insight into the functions and morphology of single red blood cells (RBCs). Since the functionality of a RBC is related to its three-dimensional (3-D) shape, quantitative 3-D geometric changes induced by storage time can help hematologists realize its optimal functionality period. We quantitatively investigate RBC 3-D geometric changes in the storage lesion using DHM. Our experimental results show that the substantial geometric transformation of the biconcave-shaped RBCs to the spherocyte occurs due to RBC storage lesion. This transformation leads to progressive loss of cell surface area, surface-to-volume ratio, and functionality of RBCs. Furthermore, our quantitative analysis shows that there are significant correlations between chemical and morphological properties of RBCs.

Rare event computation in deterministic chaotic systems using genealogical particle analysis

NASA Astrophysics Data System (ADS)

Wouters, J.; Bouchet, F.

2016-09-01

In this paper we address the use of rare event computation techniques to estimate small over-threshold probabilities of observables in deterministic dynamical systems. We demonstrate that genealogical particle analysis algorithms can be successfully applied to a toy model of atmospheric dynamics, the Lorenz ’96 model. We furthermore use the Ornstein-Uhlenbeck system to illustrate a number of implementation issues. We also show how a time-dependent objective function based on the fluctuation path to a high threshold can greatly improve the performance of the estimator compared to a fixed-in-time objective function.

Factoring the brain signatures of anesthesia concentration and level of arousal across individuals.

PubMed

Barttfeld, Pablo; Bekinschtein, Tristan A; Salles, Alejo; Stamatakis, Emmanuel A; Adapa, Ram; Menon, David K; Sigman, Mariano

2015-01-01

Combining resting-state functional magnetic resonance imaging (fMRI) connectivity and behavioral analysis during sedation, we factored out general effects of the anesthetic drug propofol and a specific index of conscious report, participants' level of responsiveness. The factorial analysis shows that increasing concentration of propofol in blood specifically decreases the connectivity strength of fronto-parietal cortical loops. In contrast, loss of responsiveness is indexed by a functional disconnection between the thalamus and the frontal cortex, balanced by an increase in connectivity strength of the thalamus to the occipital and temporal regions of the cortex.

Factoring the brain signatures of anesthesia concentration and level of arousal across individuals

PubMed Central

Barttfeld, Pablo; Bekinschtein, Tristan A.; Salles, Alejo; Stamatakis, Emmanuel A.; Adapa, Ram; Menon, David K.; Sigman, Mariano

2015-01-01

Combining resting-state functional magnetic resonance imaging (fMRI) connectivity and behavioral analysis during sedation, we factored out general effects of the anesthetic drug propofol and a specific index of conscious report, participants’ level of responsiveness. The factorial analysis shows that increasing concentration of propofol in blood specifically decreases the connectivity strength of fronto-parietal cortical loops. In contrast, loss of responsiveness is indexed by a functional disconnection between the thalamus and the frontal cortex, balanced by an increase in connectivity strength of the thalamus to the occipital and temporal regions of the cortex. PMID:26509121

A Decision Analysis Perspective on Multiple Response Robust Optimization

DTIC Science & Technology

2012-03-01

the utility function in question is monotonically increasing and is twice differentiable . If γ(y) = 0, the utility function is describing risk neutral...twice differentiable , the risk aversion function with respect to a single attribute, yi, i = 1, . . . , n, is given in Equation 2.9, γUyi = − U ′′yi U...UV (V (y1, y2)) and fol- lowing the chain rule of differentiation , Matheson and Abbas [31] show that the risk aversion with respect to a single

A Paradoxical Effect of Presession Attention on Stereotypy: Antecedent Attention as an Establishing, Not an Abolishing, Operation

PubMed Central

Roantree, Christina F; Kennedy, Craig H

2006-01-01

Previous studies have shown that presession attention for problem behavior can serve as an abolishing operation when attention functions as a positive reinforcer. In the current study, we show that the stereotypy of a child with severe disabilities was undifferentiated during standard analogue functional analysis conditions. However, when noncontingent presession attention was provided, stereotypy occurred for social attention as a positive reinforcer, suggesting that the antecedent manipulation functioned as an establishing operation. PMID:17020219

A paradoxical effect of presession attention on stereotypy: antecedent attention as an establishing, not an abolishing, operation.

PubMed

Roantree, Christina F; Kennedy, Craig H

2006-01-01

Previous studies have shown that presession attention for problem behavior can serve as an abolishing operation when attention functions as a positive reinforcer. In the current study, we show that the stereotypy of a child with severe disabilities was undifferentiated during standard analogue functional analysis conditions. However, when noncontingent presession attention was provided, stereotypy occurred for social attention as a positive reinforcer, suggesting that the antecedent manipulation functioned as an establishing operation.

Micro-RNA Binding Site Polymorphisms in the WFS1 Gene Are Risk Factors of Diabetes Mellitus

PubMed Central

Elek, Zsuzsanna; Németh, Nóra; Nagy, Géza; Németh, Helga; Somogyi, Anikó; Hosszufalusi, Nóra; Sasvári-Székely, Mária; Rónai, Zsolt

2015-01-01

The absolute or relative lack of insulin is the key factor in the pathogenesis of diabetes mellitus. Although the connection between loss of function mutations of the WFS1 gene and DIDMOAD-syndrome including diabetes mellitus underpins the significance of wolframin in the pathogenesis, exact role of WFS1 polymorphic variants in the development of type 1 and type 2 diabetes has not been discovered yet. In this analysis, 787 patients with diabetes and 900 healthy people participated. Genotyping of the 7 WFS1 SNPs was carried out by TaqMan assays. Association study was performed by χ 2-test in combination with correction for multiple testing. For functional analysis, the entire 3’ UTR of the WFS1 gene was subcloned in a pMIR-Report plasmid and relative luciferase activities were determined. Linkage disequilibrium analysis showed a generally high LD within the investigated region, however the rs1046322 locus was not in LD with the other SNPs. The two miR-SNPs, rs1046322 and rs9457 showed significant association with T1DM and T2DM, respectively. Haplotype analysis also confirmed the association between the 3’ UTR loci and both disease types. In vitro experiments showed that miR-185 reduces the amount of the resulting protein, and rs9457 miRSNP significantly influences the rate of reduction in a luciferase reporter assay. Genetic variants of the WFS1 gene might contribute to the genetic risk of T1DM and T2DM. Furthermore demonstrating the effect of rs9457 in binding of miR-185, we suggest that the optimal level of wolframin protein, potentially influenced by miR-regulation, is crucial in normal beta cell function. PMID:26426397

Micro-RNA Binding Site Polymorphisms in the WFS1 Gene Are Risk Factors of Diabetes Mellitus.

PubMed

Elek, Zsuzsanna; Németh, Nóra; Nagy, Géza; Németh, Helga; Somogyi, Anikó; Hosszufalusi, Nóra; Sasvári-Székely, Mária; Rónai, Zsolt

2015-01-01

The absolute or relative lack of insulin is the key factor in the pathogenesis of diabetes mellitus. Although the connection between loss of function mutations of the WFS1 gene and DIDMOAD-syndrome including diabetes mellitus underpins the significance of wolframin in the pathogenesis, exact role of WFS1 polymorphic variants in the development of type 1 and type 2 diabetes has not been discovered yet. In this analysis, 787 patients with diabetes and 900 healthy people participated. Genotyping of the 7 WFS1 SNPs was carried out by TaqMan assays. Association study was performed by χ2-test in combination with correction for multiple testing. For functional analysis, the entire 3' UTR of the WFS1 gene was subcloned in a pMIR-Report plasmid and relative luciferase activities were determined. Linkage disequilibrium analysis showed a generally high LD within the investigated region, however the rs1046322 locus was not in LD with the other SNPs. The two miR-SNPs, rs1046322 and rs9457 showed significant association with T1DM and T2DM, respectively. Haplotype analysis also confirmed the association between the 3' UTR loci and both disease types. In vitro experiments showed that miR-185 reduces the amount of the resulting protein, and rs9457 miRSNP significantly influences the rate of reduction in a luciferase reporter assay. Genetic variants of the WFS1 gene might contribute to the genetic risk of T1DM and T2DM. Furthermore demonstrating the effect of rs9457 in binding of miR-185, we suggest that the optimal level of wolframin protein, potentially influenced by miR-regulation, is crucial in normal beta cell function.

Functional changes of neural circuits in stroke patients with dysphagia: A meta-analysis.

PubMed

Liu, Lu; Xiao, Yuan; Zhang, Wenjing; Yao, Li; Gao, Xin; Chandan, Shah; Lui, Su

2017-08-01

Dysphagia is a common problem in stroke patients with unclear pathogenesis. Several recent functional magnetic resonance imaging (fMRI) studies had been carried out to explore the cerebral functional changes in dysphagic stroke patients. The aim of this study was to analysis these imaging findings using a meta-analysis. We used seed-based d mapping (SDM) to conduct a meta-analysis for dysphagic stroke patients prior to any kind of special treatment for dysphagia. A systematic search was conducted for the relevant studies. SDM meta-analysis method was used to examine regions of increased and decreased functional activation between dysphagic stroke patients and healthy controls. Finally, six studies including 81 stroke patients with dysphagia and 78 healthy controls met the inclusion standards. When compared with healthy controls, stroke patients with dysphagia showed hyperactivation in left cingulate gyrus, left precentral gyrus and right posterior cingulate gyrus, and hypoactivation in right cuneus and left middle frontal gyrus. The hyperactivity of precentral gyrus is crucial in stroke patients with dysphagia and may be associated with the severity of stroke. Besides the motor areas, the default-mode network regions (DMN) and affective network regions (AN) circuits are also involved in dysphagia after stroke. © 2017 Chinese Cochrane Center, West China Hospital of Sichuan University and John Wiley & Sons Australia, Ltd.

Volunteering as a means to an equal end? The impact of a social justice function on intention to volunteer.

PubMed

Jiranek, Patrick; Kals, Elisabeth; Humm, Julia Sophia; Strubel, Isabel Theresia; Wehner, Theo

2013-01-01

In the present study, we combined components of the theory of planned behavior and the functional approach to predict the social sector volunteering intention of nonvolunteers (N = 513). Moreover, we added a new other-oriented "social justice function" to the Volunteer Functions Inventory of Clary and colleagues (1998), which contains mainly self-oriented functions. We distinguished the social justice function from the other five measured volunteer functions in confirmatory factor analysis, and showed its incremental validity in predicting intention to volunteer beyond established constructs such as self-efficacy, subjective norm, and the five volunteer functions. This study suggests that emphasizing potential social justice improvements by means of volunteering may attract new volunteers.

Intrinsic Resting-State Functional Connectivity in the Human Spinal Cord at 3.0 T.

PubMed

San Emeterio Nateras, Oscar; Yu, Fang; Muir, Eric R; Bazan, Carlos; Franklin, Crystal G; Li, Wei; Li, Jinqi; Lancaster, Jack L; Duong, Timothy Q

2016-04-01

To apply resting-state functional magnetic resonance (MR) imaging to map functional connectivity of the human spinal cord. Studies were performed in nine self-declared healthy volunteers with informed consent and institutional review board approval. Resting-state functional MR imaging was performed to map functional connectivity of the human cervical spinal cord from C1 to C4 at 1 × 1 × 3-mm resolution with a 3.0-T clinical MR imaging unit. Independent component analysis (ICA) was performed to derive resting-state functional MR imaging z-score maps rendered on two-dimensional and three-dimensional images. Seed-based analysis was performed for cross validation with ICA networks by using Pearson correlation. Reproducibility analysis of resting-state functional MR imaging maps from four repeated trials in a single participant yielded a mean z score of 6 ± 1 (P < .0001). The centroid coordinates across the four trials deviated by 2 in-plane voxels ± 2 mm (standard deviation) and up to one adjacent image section ± 3 mm. ICA of group resting-state functional MR imaging data revealed prominent functional connectivity patterns within the spinal cord gray matter. There were statistically significant (z score > 3, P < .001) bilateral, unilateral, and intersegmental correlations in the ventral horns, dorsal horns, and central spinal cord gray matter. Three-dimensional surface rendering provided visualization of these components along the length of the spinal cord. Seed-based analysis showed that many ICA components exhibited strong and significant (P < .05) correlations, corroborating the ICA results. Resting-state functional MR imaging connectivity networks are qualitatively consistent with known neuroanatomic and functional structures in the spinal cord. Resting-state functional MR imaging of the human cervical spinal cord with a 3.0-T clinical MR imaging unit and standard MR imaging protocols and hardware reveals prominent functional connectivity patterns within the spinal cord gray matter, consistent with known functional and anatomic layouts of the spinal cord.

Comparing rainfall patterns between regions in Peninsular Malaysia via a functional data analysis technique

NASA Astrophysics Data System (ADS)

Suhaila, Jamaludin; Jemain, Abdul Aziz; Hamdan, Muhammad Fauzee; Wan Zin, Wan Zawiah

2011-12-01

SummaryNormally, rainfall data is collected on a daily, monthly or annual basis in the form of discrete observations. The aim of this study is to convert these rainfall values into a smooth curve or function which could be used to represent the continuous rainfall process at each region via a technique known as functional data analysis. Since rainfall data shows a periodic pattern in each region, the Fourier basis is introduced to capture these variations. Eleven basis functions with five harmonics are used to describe the unimodal rainfall pattern for stations in the East while five basis functions which represent two harmonics are needed to describe the rainfall pattern in the West. Based on the fitted smooth curve, the wet and dry periods as well as the maximum and minimum rainfall values could be determined. Different rainfall patterns are observed among the studied regions based on the smooth curve. Using the functional analysis of variance, the test results indicated that there exist significant differences in the functional means between each region. The largest differences in the functional means are found between the East and Northwest regions and these differences may probably be due to the effect of topography and, geographical location and are mostly influenced by the monsoons. Therefore, the same inputs or approaches might not be useful in modeling the hydrological process for different regions.

Structural and functional changes in the somatosensory cortex in euthymic females with bipolar disorder.

PubMed

Minuzzi, Luciano; Syan, Sabrina K; Smith, Mara; Hall, Alexander; Hall, Geoffrey Bc; Frey, Benicio N

2017-12-01

Current evidence from neuroimaging data suggests possible dysfunction of the fronto-striatal-limbic circuits in individuals with bipolar disorder. Somatosensory cortical function has been implicated in emotional recognition, risk-taking and affective responses through sensory modalities. This study investigates anatomy and function of the somatosensory cortex in euthymic bipolar women. In total, 68 right-handed euthymic women (bipolar disorder = 32 and healthy controls = 36) between 16 and 45 years of age underwent high-resolution anatomical and functional magnetic resonance imaging during the mid-follicular menstrual phase. The somatosensory cortex was used as a seed region for resting-state functional connectivity analysis. Voxel-based morphometry was used to evaluate somatosensory cortical gray matter volume between groups. We found increased resting-state functional connectivity between the somatosensory cortex and insular cortex, inferior prefrontal gyrus and frontal orbital cortex in euthymic bipolar disorder subjects compared to healthy controls. Voxel-based morphometry analysis showed decreased gray matter in the left somatosensory cortex in the bipolar disorder group. Whole-brain voxel-based morphometry analysis controlled by age did not reveal any additional significant difference between groups. This study is the first to date to evaluate anatomy and function of the somatosensory cortex in a well-characterized sample of euthymic bipolar disorder females. Anatomical and functional changes in the somatosensory cortex in this population might contribute to the pathophysiology of bipolar disorder.

Shedding light into the function of the earliest vertebrate skeleton

NASA Astrophysics Data System (ADS)

Martinez-Perez, Carlos; Purnell, Mark; Rayfield, Emily; Donoghue, Philip

2016-04-01

Conodonts are an extinct group of jawless vertebrates, the first in our evolutionary lineage to develop a biomineralized skeleton. As such, the conodont skeleton is of great significance because of the insights it provides concerning the biology and function of the primitive vertebrate skeleton. Conodont function has been debated for a century and a half on the basis of its paleocological importance in the Palaezoic ecosystems. However, due to the lack of extanct close representatives and the small size of the conodont element (under a milimiter in length) strongly limited their functional analysis, traditional restricted to analogy. More recently, qualitative approaches have been developed, facilitating tests of element function based on occlusal performance and analysis of microwear and microstructure. In this work we extend these approaches using novel quantitative experimental methods including Synchrotron Radiation X-ray Tomographic Microscopy or Finite Element Analysis to test hypotheses of conodont function. The development of high resolution virtual models of conodont elements, together with biomechanical approaches using Finite Element analysis, informed by occlusal and microwear analyses, provided conclusive support to test hypothesis of structural adaptation within the crown tissue microstructure, showing a close topological co-variation patterns of compressive and tensile stress distribution with different crystallite orientation. In addition, our computational analyses strongly support a tooth-like function for many conodont species. Above all, our study establishes a framework (experimental approach) in which the functional ecology of conodonts can be read from their rich taxonomy and phylogeny, representing an important attempt to understand the role of this abundant and diverse clade in the Phanerozoic marine ecosystems.

Comparative bioinformatics analyses and profiling of lysosome-related organelle proteomes

NASA Astrophysics Data System (ADS)

Hu, Zhang-Zhi; Valencia, Julio C.; Huang, Hongzhan; Chi, An; Shabanowitz, Jeffrey; Hearing, Vincent J.; Appella, Ettore; Wu, Cathy

2007-01-01

Complete and accurate profiling of cellular organelle proteomes, while challenging, is important for the understanding of detailed cellular processes at the organelle level. Mass spectrometry technologies coupled with bioinformatics analysis provide an effective approach for protein identification and functional interpretation of organelle proteomes. In this study, we have compiled human organelle reference datasets from large-scale proteomic studies and protein databases for seven lysosome-related organelles (LROs), as well as the endoplasmic reticulum and mitochondria, for comparative organelle proteome analysis. Heterogeneous sources of human organelle proteins and rodent homologs are mapped to human UniProtKB protein entries based on ID and/or peptide mappings, followed by functional annotation and categorization using the iProXpress proteomic expression analysis system. Cataloging organelle proteomes allows close examination of both shared and unique proteins among various LROs and reveals their functional relevance. The proteomic comparisons show that LROs are a closely related family of organelles. The shared proteins indicate the dynamic and hybrid nature of LROs, while the unique transmembrane proteins may represent additional candidate marker proteins for LROs. This comparative analysis, therefore, provides a basis for hypothesis formulation and experimental validation of organelle proteins and their functional roles.

Gradient descent for robust kernel-based regression

NASA Astrophysics Data System (ADS)

Guo, Zheng-Chu; Hu, Ting; Shi, Lei

2018-06-01

In this paper, we study the gradient descent algorithm generated by a robust loss function over a reproducing kernel Hilbert space (RKHS). The loss function is defined by a windowing function G and a scale parameter σ, which can include a wide range of commonly used robust losses for regression. There is still a gap between theoretical analysis and optimization process of empirical risk minimization based on loss: the estimator needs to be global optimal in the theoretical analysis while the optimization method can not ensure the global optimality of its solutions. In this paper, we aim to fill this gap by developing a novel theoretical analysis on the performance of estimators generated by the gradient descent algorithm. We demonstrate that with an appropriately chosen scale parameter σ, the gradient update with early stopping rules can approximate the regression function. Our elegant error analysis can lead to convergence in the standard L 2 norm and the strong RKHS norm, both of which are optimal in the mini-max sense. We show that the scale parameter σ plays an important role in providing robustness as well as fast convergence. The numerical experiments implemented on synthetic examples and real data set also support our theoretical results.

Finite element analysis of functionally graded bone plate at femur bone fracture site

NASA Astrophysics Data System (ADS)

Satapathy, Pravat Kumar; Sahoo, Bamadev; Panda, L. N.; Das, S.

2018-03-01

This paper focuses on the analysis of fractured Femur bone with functionally graded bone plate. The Femur bone is modeled by using the data from the CT (Computerized Tomography) scan and the material properties are assigned using Mimics software. The fracture fixation plate used here is composed of Functionally Graded Material (FGM). The functionally graded bone plate is considered to be composed of different layers of homogeneous materials. Finite element method approach is adopted for analysis. The volume fraction of the material is calculated by considering its variation along the thickness direction (z) according to a power law and the effective properties of the homogeneous layers are estimated. The model developed is validated by comparing numerical results available in the literature. Static analysis has been performed for the bone plate system by considering both axial compressive load and torsional load. The investigation shows that by introducing FG bone plate instead of titanium, the stress at the fracture site increases by 63 percentage and the deformation decreases by 15 percentage, especially when torsional load is taken into consideration. The present model yields better results in comparison with the commercially available bone plates.

Poor sleep quality predicts decreased cognitive function independently of chronic mountain sickness score in young soldiers with polycythemia stationed in Tibet.

PubMed

Kong, Fan-Yi; Li, Qiang; Liu, Shi-Xiang

2011-01-01

Little is known about the association between poor sleep and cognitive function in people with polycythemia at high altitude. The aim of this study was to survey the sleep quality of individuals with polycythemia at high altitude and determine its association with cognitive abilities. We surveyed 230 soldiers stationed in Tibet (all men; mean age 21-52±4.30 yr) at altitudes ranging from 3658 to 3996 m. All participants were given a blood tests for hemoglobin level and a questionnaire survey of cognitive function. Polycythemia was defined as excessive erythrocytosis (Hb≥21 g/dL in men or ≥19 g/dL in women). Poor sleepers were defined as having a global Pittsburgh Sleep Quality Index score (PSQI)>5. Cognitive abilities were determined by the Chinese revision of the Wechsler Adult Intelligence Scale and the Benton Visual Retention Test. Multiple linear regression analysis was used to determine the association between the PSQI and cognitive function. Logistic regression analysis was performed to determine the independent effect of sleep quality on cognitive function. The global PSQI score of enrolled participants was 8.14±3.79. Seventy-five (32.6%) soldiers were diagnosed with polycythemia. The proportion of poor sleepers was 1.45 times greater in those with polycythemia compared with those without polycythemia [95% (confidence interval) CI 1.82-2.56], and they had a statistically significant lower score for cognitive function. Multiple linear regression analysis showed that the global PSQI score was negatively associated with IQ (β=0.11, 95% CI -0.16 to -0.05) and digit symbol scores (β=0.66, 95% CI -0.86 to -0.44). Poor sleep quality was determined to be an independent predictor of impaired IQ [odds ratio (OR) 1.59, 95% CI 1.30-1.95] and digit symbol score (OR 1.18, 95% CI 1.07-1.31) in logistic regression analysis. The present study showed that for young soldiers with polycythemia at high altitude impaired subjective sleep quality was an independent predictor of decreased cognitive function, especially IQ and verbal short-term memory.

Adolescent Maturation of Dopamine D1 and D2 Receptor Function and Interactions in Rodents

PubMed Central

Dwyer, Jennifer B.; Leslie, Frances M.

2016-01-01

Adolescence is a developmental period characterized by heightened vulnerability to illicit drug use and the onset of neuropsychiatric disorders. These clinical phenomena likely share common neurobiological substrates, as mesocorticolimbic dopamine systems actively mature during this period. Whereas prior studies have examined age-dependent changes in dopamine receptor binding, there have been fewer functional analyses. The aim of the present study was therefore to determine whether the functional consequences of D1 and D2-like activation are age-dependent. Adolescent and adult rats were given direct D1 and D2 agonists, alone and in combination. Locomotor and stereotypic behaviors were measured, and brains were collected for analysis of mRNA expression for the immediate early genes (IEGs), cfos and arc. Adolescents showed enhanced D2-like receptor control of locomotor and repetitive behaviors, which transitioned to dominant D1-like mechanisms in adulthood. When low doses of agonists were co-administered, adults showed supra-additive behavioral responses to D1/D2 combinations, whereas adolescents did not, which may suggest age differences in D1/D2 synergy. D1/D2-stimulated IEG expression was particularly prominent in the bed nucleus of the stria terminalis (BNST). Given the BNST’s function as an integrator of corticostriatal, hippocampal, and stress-related circuitry, and the importance of neural network dynamics in producing behavior, an exploratory functional network analysis of regional IEG expression was performed. This data-driven analysis demonstrated similar developmental trajectories as those described in humans and suggested that dopaminergic drugs alter forebrain coordinated gene expression age dependently. D1/D2 recruitment of stress nuclei into functional networks was associated with low behavioral output in adolescents. Network analysis presents a novel tool to assess pharmacological action, and highlights critical developmental changes in functional neural circuitry. Immature D1/D2 interactions in adolescents may underlie their unique responses to drugs of abuse and vulnerability to psychopathology. These data highlight the need for age-specific pharmacotherapy design and clinical application in adolescence. PMID:26784516

Sex estimation standards for medieval and contemporary Croats

PubMed Central

Bašić, Željana; Kružić, Ivana; Jerković, Ivan; Anđelinović, Deny; Anđelinović, Šimun

2017-01-01

Aim To develop discriminant functions for sex estimation on medieval Croatian population and test their application on contemporary Croatian population. Methods From a total of 519 skeletons, we chose 84 adult excellently preserved skeletons free of antemortem and postmortem changes and took all standard measurements. Sex was estimated/determined using standard anthropological procedures and ancient DNA (amelogenin analysis) where pelvis was insufficiently preserved or where sex morphological indicators were not consistent. We explored which measurements showed sexual dimorphism and used them for developing univariate and multivariate discriminant functions for sex estimation. We included only those functions that reached accuracy rate ≥80%. We tested the applicability of developed functions on modern Croatian sample (n = 37). Results From 69 standard skeletal measurements used in this study, 56 of them showed statistically significant sexual dimorphism (74.7%). We developed five univariate discriminant functions with classification rate 80.6%-85.2% and seven multivariate discriminant functions with an accuracy rate of 81.8%-93.0%. When tested on the modern population functions showed classification rates 74.1%-100%, and ten of them reached aimed accuracy rate. Females showed higher classification rates in the medieval populations, whereas males were better classified in the modern populations. Conclusion Developed discriminant functions are sufficiently accurate for reliable sex estimation in both medieval Croatian population and modern Croatian samples and may be used in forensic settings. The methodological issues that emerged regarding the importance of considering external factors in development and application of discriminant functions for sex estimation should be further explored. PMID:28613039

Functional connectivity in the resting-state motor networks influences the kinematic processes during motor sequence learning

PubMed Central

Bonzano, Laura; Palmaro, Eleonora; Teodorescu, Roxana; Fleysher, Lazar; Inglese, Matilde; Bove, Marco

2014-01-01

Neuroimaging studies support the involvement of the cerebello-cortical and striato-cortical motor loops in motor sequence learning. Here, we investigated whether the gain of motor sequence learning could depend on a priori resting-state functional connectivity (rsFC) between motor areas and structures belonging to these circuits. Fourteen healthy subjects underwent a resting-state fMRI session. Afterward, they were asked to reproduce a verbally-learned sequence of finger opposition movements as fast and accurate as possible. All subjects increased their movement rate with practice, by reducing touch duration and/or inter tapping interval. The rsFC analysis showed that at rest left and right M1 and left and right supplementary motor cortex (SMA) were mainly connected with other motor areas. The covariate analysis taking into account the different kinematic parameters indicated that the subjects achieving greater movement rate increase were those showing stronger rsFC of the left M1 and SMA with the right lobule VIII of the cerebellum. Notably, the subjects with greater inter tapping interval reduction showed stronger rsFC of the left M1 and SMA with the association nuclei of the thalamus. Conversely, the regression analysis with the right M1 and SMA seeds showed only few significant clusters for the different covariates not located in the cerebellum and thalamus. No common clusters were found between right M1 and SMA. All these findings indicate important functional connections at rest of those neural circuits responsible of motor learning improvement, involving the motor areas related to the hemisphere directly controlling the finger movements, the thalamus and the cerebellum. PMID:25328043

Comparative gene expression analysis between coronary arteries and internal mammary arteries identifies a role for the TES gene in endothelial cell functions relevant to coronary artery disease.

PubMed

Archacki, Stephen R; Angheloiu, George; Moravec, Christine S; Liu, Hui; Topol, Eric J; Wang, Qing Kenneth

2012-03-15

Coronary artery disease (CAD) is the leading cause of death worldwide. It has been established that internal mammary arteries (IMA) are resistant to the development of atherosclerosis, whereas left anterior descending (LAD) coronary arteries are athero-prone. The contrasting properties of these two arteries provide an innovative strategy to identify the genes that play important roles in the development of atherosclerosis. We carried out microarray analysis to identify genes differentially expressed between IMA and LAD. Twenty-nine genes showed significant differences in their expression levels between IMA and LAD, which included the TES gene encoding Testin. The role of TES in the cardiovascular system is unknown. Here we show that TES is involved in endothelial cell (EC) functions relevant to atherosclerosis. Western blot analysis showed higher TES expression in IMA than in LAD. Reverse transcription polymerase chain reaction and western blot analyses showed that TES was consistently and markedly down-regulated by more than 6-fold at both mRNA and protein levels in patients with CAD compared with controls without CAD (P= 0.000049). The data suggest that reduced TES expression is associated with the development of CAD. Knockdown of TES expression by small-interfering RNA promoted oxidized-LDL-mediated monocyte adhesion to ECs, EC migration and the transendothelial migration of monocytes, while the over-expression of TES in ECs blunted these processes. These results demonstrate association between reduced TES expression and CAD, establish a novel role for TES in EC functions and raise the possibility that reduced TES expression increases susceptibility to the development of CAD.

Going outdoors and cognitive function among community-dwelling older adults: Moderating role of physical function.

PubMed

Harada, Kazuhiro; Lee, Sangyoon; Park, Hyuntae; Shimada, Hiroyuki; Makizako, Hyuma; Doi, Takehiko; Yoshida, Daisuke; Tsutsumimoto, Kota; Anan, Yuya; Uemura, Kazuki; Suzuki, Takao

2016-01-01

Identifying the risk factors of cognitive impairment is essential for implementing effective prevention strategies for dementia. Previous studies have shown that the frequency of going outdoors is inversely associated with cognitive decline. Little research has examined whether the relationship between going outdoors and cognitive decline varies with physical functioning in older adults. The aim of the present study was to examine the relationship between going outdoors and cognitive function in older adults with and without physical function limitations. The present study analyzed the data of 4450 individuals (aged 65 years or older) who participated in the Obu Study of Health Promotion for the Elderly. The measures were the Mini-Mental State Examination (MMSE), going outdoors (at least once a week or not), self-reported physical function limitations (with or without), and demographic and health-related factors as potential confounders. Analysis of covariance and post-hoc comparisons showed that although going outdoors at least once a week was associated with higher MMSE scores among older adults with limited physical function, it was not significantly associated with the MMSE scores among older adults without limited physical function. Similarly, logistic regression analyses, stratified by physical function, showed a significant association between going outdoors and MMSE (<24 points or not) among older adults with limited physical function. The results show that going outdoors less than once a week is associated with decreased cognitive function among older adults with limited physical function, but it is not associated with cognitive function among older adults without limited physical function. © 2015 Japan Geriatrics Society.

'Executive' functions and normal aging: selective impairment in conditional exclusion compared to abstraction and inhibition.

PubMed

Silver, Henry; Goodman, Craig; Gur, Ruben C; Gur, Raquel E; Bilker, Warren B

2011-01-01

Some executive functions may be selectively impaired in normal aging over and above the general cognitive decline. We examined the performance of healthy high functioning young (n = 77) and older (n = 57) individuals on three 'executive' tests: conditional exclusion, abstraction, and inhibition of prepotent responses. We compared their relationships to each other and to other cognitive functions including attention, psychomotor speed and working memory. Conditional exclusion was significantly more impaired than abstraction or inhibition in the elderly compared to the younger group and unlike them, showed a nonlinear relationship with age. These findings were independent of other cognitive functions. Analysis of PCET performance characteristics showed that older individuals were particularly impaired in attaining the last of the three achievable categories, were slower, and had fewer error monitoring resources compared to the younger group. Conditional exclusion shows an age-related pattern of impairment distinct from inhibition and abstraction. We propose that in healthy well-functioning individuals, it taps processes integrating task set establishment and shifting in context of accumulating information. It may thus be useful as a specific marker of complex cognitive functions in studies of normal cognitive aging and in early detection of cognitive dysfunction. Copyright © 2010 S. Karger AG, Basel.

A personality classification system for eating disorders: a longitudinal study.

PubMed

Thompson-Brenner, Heather; Eddy, Kamryn T; Franko, Debra L; Dorer, David J; Vashchenko, Maryna; Kass, Andrea E; Herzog, David B

2008-01-01

Studies of eating disorders (EDs) suggest that empirically derived personality subtypes may explain heterogeneity in ED samples that is not captured by the current diagnostic system. Longitudinal outcomes for personality subtypes have not been examined. In this study, personality pathology was assessed by clinical interview in 213 individuals with anorexia nervosa and bulimia nervosa at baseline. Interview data on EDs, comorbid diagnoses, global functioning, and treatment utilization were collected at baseline and at 6-month follow-up intervals over a median of 9 years. Q-factor analysis of the participants based on personality items produced a 5-prototype system, including high-functioning, behaviorally dysregulated, emotionally dysregulated, avoidant-insecure, and obsessional-sensitive types. Dimensional prototype scores were associated with baseline functioning and longitudinal outcome. Avoidant-Insecure scores showed consistent associations with poor functioning and outcome, including failure to show ED improvement, poor global functioning after 5 years, and high treatment utilization after 5 years. Behavioral dysregulation was associated with poor baseline functioning but did not show strong associations with ED or global outcome when histories of major depression and substance use disorder were covaried. Emotional dysregulation and obsessional-sensitivity were not associated with negative outcomes. High-functioning prototype scores were consistently associated with positive outcomes. Longitudinal results support the importance of personality subtypes to ED classification.

Treatment-Induced Autophagy Associated with Tumor Dormancy and Relapse

DTIC Science & Technology

2017-07-01

disease function by Ingenuity Pathway Analysis (IPA). The 239 genes involved in dormancy showed a z-score increase in disease states related to acute ...genes shared by both week 6 groups, one relapsing and the other dormant, showed predicted activation of both chronic and acute disease states. In...genes among 239 shared probe sets involved in maintenance of dormancy shows predicted activation of disease states related to acute inflammation, 682

Analysis of noise in quorum sensing.

PubMed

Cox, Chris D; Peterson, Gregory D; Allen, Michael S; Lancaster, Joseph M; McCollum, James M; Austin, Derek; Yan, Ling; Sayler, Gary S; Simpson, Michael L

2003-01-01

Noise may play a pivotal role in gene circuit functionality, as demonstrated for the genetic switch in the bacterial phage lambda. Like the lambda switch, bacterial quorum sensing (QS) systems operate within a population and contain a bistable switching element, making it likely that noise plays a functional role in QS circuit operation. Therefore, a detailed analysis of the noise behavior of QS systems is needed. We have developed a set of tools generally applicable to the analysis of gene circuits, with an emphasis on investigations in the frequency domain (FD), that we apply here to the QS system in the marine bacterium Vibrio fischeri. We demonstrate that a tight coupling between exact stochastic simulation and FD analysis provides insights into the structure/function relationships in the QS circuit. Furthermore, we argue that a noise analysis is incomplete without consideration of the power spectral densities (PSDs) of the important molecular output signals. As an example we consider reversible reactions in the QS circuit, and show through analysis and exact stochastic simulation that these circuits make significant and dynamic modifications to the noise spectra. In particular, we demonstrate a "whitening" effect, which occurs as the noise is processed through these reversible reactions.

Creativity and the default network: A functional connectivity analysis of the creative brain at rest☆

PubMed Central

Beaty, Roger E.; Benedek, Mathias; Wilkins, Robin W.; Jauk, Emanuel; Fink, Andreas; Silvia, Paul J.; Hodges, Donald A.; Koschutnig, Karl; Neubauer, Aljoscha C.

2014-01-01

The present research used resting-state functional magnetic resonance imaging (fMRI) to examine whether the ability to generate creative ideas corresponds to differences in the intrinsic organization of functional networks in the brain. We examined the functional connectivity between regions commonly implicated in neuroimaging studies of divergent thinking, including the inferior prefrontal cortex and the core hubs of the default network. Participants were prescreened on a battery of divergent thinking tests and assigned to high- and low-creative groups based on task performance. Seed-based functional connectivity analysis revealed greater connectivity between the left inferior frontal gyrus (IFG) and the entire default mode network in the high-creative group. The right IFG also showed greater functional connectivity with bilateral inferior parietal cortex and the left dorsolateral prefrontal cortex in the high-creative group. The results suggest that the ability to generate creative ideas is characterized by increased functional connectivity between the inferior prefrontal cortex and the default network, pointing to a greater cooperation between brain regions associated with cognitive control and low-level imaginative processes. PMID:25245940

Graphene-induced band gap renormalization in polythiophene: a many-body perturbation study

NASA Astrophysics Data System (ADS)

Marsusi, F.; Fedorov, I. A.; Gerivani, S.

2018-01-01

Density functional theory and many-body perturbation theory at the G0W0 level are employed to study the electronic properties of polythiophene (PT) adsorbed on the graphene surface. Analysis of the charge density difference shows that substrate-adsorbate interaction leads to a strong physisorption and interfacial electric dipole moment formation. The electrostatic potential displays a  -0.19 eV shift in the graphene work function from its initial value of 4.53 eV, as the result of the interaction. The LDA band gap of the polymer does not show any change. However, the band structure exhibits weak orbital hybridizations resulting from slight overlapping between the polymer and graphene states wave functions. The interfacial polarization effects on the band gap and levels alignment are investigated at the G0W0 level and show a notable reduction of PT band gap compared to that of the isolated chain.

Nppa and Nppb act redundantly during zebrafish cardiac development to confine AVC marker expression and reduce cardiac jelly volume.

PubMed

Grassini, Daniela R; Lagendijk, Anne K; De Angelis, Jessica E; Da Silva, Jason; Jeanes, Angela; Zettler, Nicole; Bower, Neil I; Hogan, Benjamin M; Smith, Kelly A

2018-05-11

Atrial natriuretic peptide ( nppa/anf ) and brain natriuretic peptide ( nppb/bnp ) form a gene cluster with expression in the chambers of the developing heart. Despite restricted expression, a function in cardiac development has not been demonstrated by mutant analysis. This is attributed to functional redundancy however their genomic location in cis has impeded formal analysis. Using genome-editing, we generated mutants for nppa and nppb and found single mutants indistinguishable from wildtype whereas nppa / nppb double mutants display heart morphogenesis defects and pericardial oedema. Analysis of atrioventricular canal (AVC) markers show expansion of bmp4 , tbx2b, has2 and versican expression into the atrium of double mutants. This expanded expression correlates with increased extracellular matrix in the atrium. Using a biosensor for Hyaluronic acid to measure the cardiac jelly (cardiac extracellular matrix), we confirm cardiac jelly expansion in nppa / nppb double mutants. Finally, bmp4 knockdown rescues the expansion of has2 expression and cardiac jelly in double mutants. This definitively shows that nppa and nppb function redundantly during cardiac development to restrict gene expression to the AVC, preventing excessive cardiac jelly synthesis in the atrial chamber. © 2018. Published by The Company of Biologists Ltd.

Normal Mode Analysis of Polytheonamide B

NASA Astrophysics Data System (ADS)

Mori, Takaharu; Kokubo, Hironori; Shimizu, Hirofumi; Iwamoto, Masayuki; Oiki, Shigetoshi; Okamoto, Yuko

2007-09-01

Polytheonamide B is a linear 48-residue peptide which forms a single β-helix structure with alternating d- and l-amino acids and contains methylated and hydroxy variants of proteinogenic amino acids. To investigate the dynamical properties of polytheonamide B we perform the normal mode analysis. Root-mean-square displacements of all backbone atoms, root-mean-square fluctuations of the backbone dihedral angles (φ,\\psi), and correlation factors for the Cα atom fluctuations and for the dihedral angle fluctuations are calculated. The normal mode analysis reveals that polytheonamide B shows the elastic rod behavior in the very low-frequency regions and that librational motions of backbone amide planes have the modes with relatively low frequencies, which is relevant to the function of polytheonamide B. In addition, these librational motions occur almost independently and weakly anticorrelate with those of the hydrogen-bonded neighboring amide planes. Calculations of the backbone fluctuations show that the flexibility of polytheonamide B is roughly uniform over the entire helix. We compare our results with those of gramicidin A, the analogue of polytheonamide B, to discuss the structures and functions, and obtain some common features in the flexibilities and dynamics of the backbone atoms. These results present important clues for clarifying the function of polytheonamide B at the atomic level.

Extraction and characterization of beta-D-glucan from oat for industrial utilization.

PubMed

Ahmad, Asif; Anjum, Faqir Muhammad; Zahoor, Tahir; Nawaz, Haq; Ahmed, Zaheer

2010-04-01

Oat beta-D-glucan is a valuable functional ingredient having numerous industrial, nutritional and health benefits. Its extraction needs careful attention as extraction process may affect the physiochemical and functional properties of extracted beta-D-glucan. The present study aimed at analyzing the effect of extraction of beta-D-glucan gum pellets from oat cultivar followed by detailed chemical and functional analysis. Enzymatic extraction process resulted in highest yield and recovery. Chemical analysis revealed protein as a dominating impurity. The water binding capacity of the beta-D-glucan ranged between 3.14 and 4.52 g g(-1) of sample. beta-D-Glucan exhibited ideal foaming stability when appropriate extraction technique was used. The viscosity of beta-D-glucan gum ranged between 35.6 and 56.16 cp. The color analysis showed L* value of beta-D-glucan gum pellet ranged between 72.18 and 83.54. Phosphorus, potassium and calcium appeared as major minerals in beta-D-glucan gum whereas iron, manganese and copper appeared as minor minerals. FTIR spectroscopy also confirms the presence of beta-D-glucan, protein and other components in extracted beta-D-glucan gum pellets. Overall, extracted beta-D-glucan showed a good potential for industrial usage. Copyright 2010 Elsevier B.V. All rights reserved.

[Study on the classification of dominant pathogens related to febrile respiratory syndrome, based on the method of Bayes discriminant analysis].

PubMed

Li, X C; Li, J S; Meng, L; Bai, Y N; Yu, D S; Liu, X N; Liu, X F; Jiang, X J; Ren, X W; Yang, X T; Shen, X P; Zhang, J W

2017-08-10

Objective: To understand the dominant pathogens of febrile respiratory syndrome (FRS) patients in Gansu province and to establish the Bayes discriminant function in order to identify the patients infected with the dominant pathogens. Methods: FRS patients were collected in various sentinel hospitals of Gansu province from 2009 to 2015 and the dominant pathogens were determined by describing the composition of pathogenic profile. Significant clinical variables were selected by stepwise discriminant analysis to establish the Bayes discriminant function. Results: In the detection of pathogens for FRS, both influenza virus and rhinovirus showed higher positive rates than those caused by other viruses (13.79%, 8.63%), that accounting for 54.38%, 13.73% of total viral positive patients. Most frequently detected bacteria would include Streptococcus pneumoniae , and haemophilus influenza (44.41%, 18.07%) that accounting for 66.21% and 24.55% among the bacterial positive patients. The original-validated rate of discriminant function, established by 11 clinical variables, was 73.1%, with the cross-validated rate as 70.6%. Conclusion: Influenza virus, Rhinovirus, Streptococcus pneumoniae and Haemophilus influenzae were the dominant pathogens of FRS in Gansu province. Results from the Bayes discriminant analysis showed both higher accuracy in the classification of dominant pathogens, and applicative value for FRS.

Demise of the essay question.

PubMed Central

Tombleson, P.

1990-01-01

Psychometric studies of the essay paper in 1988 showed this instrument to have unacceptably low levels of reliability and generalizability. Furthermore, factor analysis showed that the paper's perceived functions could not be supported statistically. It was decided to discontinue the paper and introduce a replacement which would reflect the line of development envisaged by the College in the 1990s. PMID:1670202

Bidirectional reflectance distribution function measurements and analysis of retroreflective materials.

PubMed

Belcour, Laurent; Pacanowski, Romain; Delahaie, Marion; Laville-Geay, Aude; Eupherte, Laure

2014-12-01

We compare the performance of various analytical retroreflecting bidirectional reflectance distribution function (BRDF) models to assess how they reproduce accurately measured data of retroreflecting materials. We introduce a new parametrization, the back vector parametrization, to analyze retroreflecting data, and we show that this parametrization better preserves the isotropy of data. Furthermore, we update existing BRDF models to improve the representation of retroreflective data.

Profiling Hyporheic Microbial Community Nitrogen Cycle and Carbohydrate Active Enzyme Gene Abundances across Seasons

NASA Astrophysics Data System (ADS)

Nelson, W. C.; Graham, E.; Stegen, J.

2016-12-01

The hyporheic zone (HZ) is the permanently inundated sediment layer between a surface channel and adjacent groundwater-saturated sediments. It has been hypothesized to play a major role in macronutrient (C, N, P) cycling in rivers. The correlation between community taxonomic composition dynamics and functional gene representation is poorly understood for hyporheic communities. To explore how microbial communities respond to temporal changes in environmental conditions, metagenomes were derived from communities captured in sterile sandpacks deployed within the HZ of the Columbia River. HMM databases were used to enumerate protein families present. Functional classification of reads allowed a general assessment of community function over time, while targeted assembly of specific genes enabled investigation of the diversity of organisms encoding these functions. Preliminary analysis of nitrogen cycle pathways shows most gene families examined to have quite steady representation across seasons, with most observed changes being less than an order of magnitude. Analysis of ammonia oxidation genes showed bacterial ammonia oxidizers (AOB) to be stably present across the year, while the archaeal amoA gene increased in late summer, peaking sharply in November, mirroring results from 16S rRNA amplicon analysis which showed an increase in Thaumarcheal OTUs during that same period. Most glycosyl hydrolase GH families had low representation. Highly abundant classes of GH included the GH94 (beta-glucosidase), GH95 (1-2-alpha-L-fucosidase) and GH103 (lytic transglycosylase) families, suggesting activity on plant, fungus and insect polysaccharides and peptidoglycans. Further work is investigating the taxonomy of the sequences identified, to determine how changes in the community composition contribute to the stable gene family profiles observed. These results are intended to work towards a greater understanding of the role of species diversity and functional redundancy in the dynamics of community composition in response to changes in environmental conditions and stochastic processes. In addition, it will serve as a foundation enabling modeling of generalized microbial function in the hyporheic zone, improving our ability to predict fluxes of carbon and nitrogen through riverine systems.

Effect of Increased Intensity of Physiotherapy on Patient Outcomes After Stroke: An Evidence-Based Analysis

PubMed Central

Sehatzadeh, S

2015-01-01

Background After stroke, impairment of the upper and lower limb can limit patients’ motor function and ability to perform activities of daily living (ADL). Physiotherapy (PT) is an established clinical practice for stroke patients, playing an important role in improving limb function. Recently, several randomized trials have evaluated the effect of higher-intensity physiotherapy (increased duration and/or frequency) on patients’ functional ability. Objectives Our objective is to investigate whether an increased intensity of PT after stroke results in better outcomes for patients. Data Sources A literature search was performed on June 7, 2013, for English-language randomized controlled trials published from January 1, 2003, to June 7, 2013. Ovid MEDLINE, Ovid MEDLINE In-Process and Other Non-Indexed Citations, Ovid Embase, EBSCO Cumulative Index to Nursing & Allied Health Literature (CINAHL), and EBM Reviews were searched. Review Methods We reviewed the full text of articles that compared 2 or more levels of PT intensity. Outcomes of interest included motor function, ADL, and quality of life (QOL). Results High-quality evidence showed that higher-intensity upper-limb PT and higher-intensity lower-limb PT both resulted in significantly greater improvements in motor function. Moderate-quality evidence showed that higher-intensity general PT did not. Moderate-quality evidence showed a significant improvement in ADL performance with higher-intensity upper-limb PT, but no improvement with higher-intensity general PT; no studies reported on ADL outcomes on lower-limb PT specifically. According to moderate-quality evidence, patient QOL did not change significantly after increased intensity of upper-limb, lower-limb, or general PT. When considering the results, one difference should be noted: Compared with the studies examining upper- and lower-limb PT, the studies examining general PT looked at a smaller increase—2 hours or less of additional therapy per week. Limitations This analysis is limited to the earlier post-stroke phase and is not equipped to comment on expected outcomes of later-stage PT. Conclusions Overall, this analysis found support for the use of more intensive PT to improve motor function and ability to perform ADL after stroke. PMID:26356355

Role of Escherichia coli dnaG function in coliphage M13 DNA synthesis

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

Dasgupta, S.; Mitra, S.

Examination of the role of Escherichia coli dnaG function in different stages of M13 phage DNA synthesis by ultracentrifugal analysis of intracellular phage DNA in a thermosensitive dnaG mutant shows that: (a) the formation of parental double-strand replicative-form DNA (rfDNA) from the infecting virus is independent of dnaG function; (b) the synthesis of progeny rfDNA requires dnaG product; (c) after a pool of rfDNA is made up, dnaG function is not required for the progeny single-strand DNA (ssDNA) synthesis. The ssDNAs produced under nonpermissive condition are mostly circular and biologically functional.

Analog computation of auto and cross-correlation functions

NASA Technical Reports Server (NTRS)

1974-01-01

For analysis of the data obtained from the cross beam systems it was deemed desirable to compute the auto- and cross-correlation functions by both digital and analog methods to provide a cross-check of the analysis methods and an indication as to which of the two methods would be most suitable for routine use in the analysis of such data. It is the purpose of this appendix to provide a concise description of the equipment and procedures used for the electronic analog analysis of the cross beam data. A block diagram showing the signal processing and computation set-up used for most of the analog data analysis is provided. The data obtained at the field test sites were recorded on magnetic tape using wide-band FM recording techniques. The data as recorded were band-pass filtered by electronic signal processing in the data acquisition systems.

Multiscale analysis of neural spike trains.

PubMed

Ramezan, Reza; Marriott, Paul; Chenouri, Shojaeddin

2014-01-30

This paper studies the multiscale analysis of neural spike trains, through both graphical and Poisson process approaches. We introduce the interspike interval plot, which simultaneously visualizes characteristics of neural spiking activity at different time scales. Using an inhomogeneous Poisson process framework, we discuss multiscale estimates of the intensity functions of spike trains. We also introduce the windowing effect for two multiscale methods. Using quasi-likelihood, we develop bootstrap confidence intervals for the multiscale intensity function. We provide a cross-validation scheme, to choose the tuning parameters, and study its unbiasedness. Studying the relationship between the spike rate and the stimulus signal, we observe that adjusting for the first spike latency is important in cross-validation. We show, through examples, that the correlation between spike trains and spike count variability can be multiscale phenomena. Furthermore, we address the modeling of the periodicity of the spike trains caused by a stimulus signal or by brain rhythms. Within the multiscale framework, we introduce intensity functions for spike trains with multiplicative and additive periodic components. Analyzing a dataset from the retinogeniculate synapse, we compare the fit of these models with the Bayesian adaptive regression splines method and discuss the limitations of the methodology. Computational efficiency, which is usually a challenge in the analysis of spike trains, is one of the highlights of these new models. In an example, we show that the reconstruction quality of a complex intensity function demonstrates the ability of the multiscale methodology to crack the neural code. Copyright © 2013 John Wiley & Sons, Ltd.

[Results from the German shoulder- and elbow arthroplasty register (SEPR) : Anatomic or reverse shoulder arthroplasty in B2-glenoids?

PubMed

Magosch, P; Habermeyer, P; Lichtenberg, S; Tauber, M; Gohlke, F; Mauch, F; Boehm, D; Loew, M; Zeifang, F; Pötzl, W

2017-12-01

Anatomic shoulder arthroplasty in osteoarthritis with biconcave glenoid wear results in decreased functional results and a higher rate of early glenoid loosening. The aim of the data analysis of the German shoulder arthroplasty register was to clarify whether reverse shoulder arthroplasty can provide better functional results and a lower complication rate than anatomic arthroplasty in osteoarthritis with biconcave glenoid wear. The analysis included 1052 completely documented primary implanted arthroplasties with a minimum follow-up of 2 years. In 119 cases, a B2-type glenoid was present. Out of these cases, 86 were treated with an anatomic shoulder arthroplasty, and in 33 cases a reverse shoulder arthroplasty was implanted. The mean follow-up was 47.6 months. The Constant score with its subcategories, as well as the active range of movement improved significantly after anatomic and after reverse shoulder arthroplasty. We observed no difference in functional results between both types of arthroplasty; however, reverse arthroplasty showed a significant higher revision rate (21.2%) (3% glenoid loosening, 6% prosthetic instability) than anatomic shoulder arthroplasty (12.8%) (11.6% glenoid loosening, 1.2% prosthetic instability), whereas anatomic shoulder arthroplasty showed a higher rate of glenoid loosening. Functional and radiographic results of both types of arthroplasty are comparable with the results reported in the literature, although our analysis represents results from an implant registry (data pertaining to medical care quality).

Craniometric relationships among medieval Central European populations: implications for Croat migration and expansion.

PubMed

Slaus, Mario; Tomicić, Zeljko; Uglesić, Ante; Jurić, Radomir

2004-08-01

To determine the ethnic composition of the early medieval Croats, the location from which they migrated to the east coast of the Adriatic, and to separate early medieval Croats from Bijelo brdo culture members, using principal components analysis and discriminant function analysis of craniometric data from Central and South-East European medieval archaeological sites. Mean male values for 8 cranial measurements from 39 European and 5 Iranian sites were analyzed by principal components analysis. Raw data for 17 cranial measurements for 103 female and 112 male skulls were used to develop discriminant functions. The scatter-plot of the analyzed sites on the first 2 principal components showed a pattern of intergroup relationships consistent with geographical and archaeological information not included in the data set. The first 2 principal components separated the sites into 4 distinct clusters: Avaroslav sites west of the Danube, Avaroslav sites east of the Danube, Bijelo brdo sites, and Polish sites. All early medieval Croat sites were located in the cluster of Polish sites. Two discriminant functions successfully differentiated between early medieval Croats and Bijelo brdo members. Overall accuracies were high -- 89.3% for males, and 97.1% for females. Early medieval Croats seem to be of Slavic ancestry, and at one time shared a common homeland with medieval Poles. Application of unstandardized discriminant function coefficients to unclassified crania from 18 sites showed an expansion of early medieval Croats into continental Croatia during the 10th to 13th century.

Assessing the validity of discourse analysis: transdisciplinary convergence

NASA Astrophysics Data System (ADS)

Jaipal-Jamani, Kamini

2014-12-01

Research studies using discourse analysis approaches make claims about phenomena or issues based on interpretation of written or spoken text, which includes images and gestures. How are findings/interpretations from discourse analysis validated? This paper proposes transdisciplinary convergence as a way to validate discourse analysis approaches to research. The argument is made that discourse analysis explicitly grounded in semiotics, systemic functional linguistics, and critical theory, offers a credible research methodology. The underlying assumptions, constructs, and techniques of analysis of these three theoretical disciplines can be drawn on to show convergence of data at multiple levels, validating interpretations from text analysis.

A Comparison of Voice Activity and Participation Profiles Among Etiological Groups.

PubMed

Lee, Seung Jin; Choi, Hong-Shik; Kim, HyangHee

2018-05-11

The purpose of this study was to determine whether patients with functional voice disorders show voice activity and participation profiles different from those of the organic and neurogenic groups. The Korean Version of the Voice Activity and Participation Profile (K-VAPP) was administered to 200 participants (150 patients with functional, organic, and neurogenic voice disorders, 50 for each etiological group, 50 controls without vocal complaint). The K-VAPP subscale scores of the etiological groups were compared, controlling for age, professional use of voice, and severity of voice disorder measured by overall severity of the Consensus Auditory-Perceptual Evaluation of Voice (CAPE-V). Results of a one-way analysis of variance indicated significant differences in the overall severity across groups (neurogenic > functional = organic > control). Among four groups, the organic group showed higher mean Z-scores of the K-VAPP than the control group, and the functional group showed higher mean Z-scores of the K-VAPP than the organic group. Compared with the neurogenic group, the functional group showed lower mean Z-scores for total score, Activity Limitation Score, SUB3, and SUB5. A comparison among three etiological groups showed that the functional group did not show higher scores than the organic group. On the contrary, the functional group showed a lower total score, Participation Restriction Score, and score for subsection 3 (effect on daily communication) than the neurogenic group. Psychometric assessment of voice disorders using the K-VAPP could provide clinicians with baseline information that is applicable to various voice disorders. Further studies pertaining to the follow-up of voice disorders with various etiologies are needed to extend its clinical usefulness. Copyright © 2018 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

Four Theorems on the Psychometric Function

PubMed Central

May, Keith A.; Solomon, Joshua A.

2013-01-01

In a 2-alternative forced-choice (2AFC) discrimination task, observers choose which of two stimuli has the higher value. The psychometric function for this task gives the probability of a correct response for a given stimulus difference, . This paper proves four theorems about the psychometric function. Assuming the observer applies a transducer and adds noise, Theorem 1 derives a convenient general expression for the psychometric function. Discrimination data are often fitted with a Weibull function. Theorem 2 proves that the Weibull “slope” parameter, , can be approximated by , where is the of the Weibull function that fits best to the cumulative noise distribution, and depends on the transducer. We derive general expressions for and , from which we derive expressions for specific cases. One case that follows naturally from our general analysis is Pelli's finding that, when , . We also consider two limiting cases. Theorem 3 proves that, as sensitivity improves, 2AFC performance will usually approach that for a linear transducer, whatever the actual transducer; we show that this does not apply at signal levels where the transducer gradient is zero, which explains why it does not apply to contrast detection. Theorem 4 proves that, when the exponent of a power-function transducer approaches zero, 2AFC performance approaches that of a logarithmic transducer. We show that the power-function exponents of 0.4–0.5 fitted to suprathreshold contrast discrimination data are close enough to zero for the fitted psychometric function to be practically indistinguishable from that of a log transducer. Finally, Weibull reflects the shape of the noise distribution, and we used our results to assess the recent claim that internal noise has higher kurtosis than a Gaussian. Our analysis of for contrast discrimination suggests that, if internal noise is stimulus-independent, it has lower kurtosis than a Gaussian. PMID:24124456

The use of dwell time cross-correlation functions to study single-ion channel gating kinetics.

PubMed Central

Ball, F G; Kerry, C J; Ramsey, R L; Sansom, M S; Usherwood, P N

1988-01-01

The derivation of cross-correlation functions from single-channel dwell (open and closed) times is described. Simulation of single-channel data for simple gating models, alongside theoretical treatment, is used to demonstrate the relationship of cross-correlation functions to underlying gating mechanisms. It is shown that time irreversibility of gating kinetics may be revealed in cross-correlation functions. Application of cross-correlation function analysis to data derived from the locust muscle glutamate receptor-channel provides evidence for multiple gateway states and time reversibility of gating. A model for the gating of this channel is used to show the effect of omission of brief channel events on cross-correlation functions. PMID:2462924

Transcortical Sensory Aphasia after Left Frontal Lobe Infarction: Loss of Functional Connectivity.

PubMed

Kwon, Miseon; Shim, Woo Hyun; Kim, Sang-Joon; Kim, Jong S

2017-01-01

The underlying mechanism of transcortical sensory aphasia (TSA) caused by lesions occurring in the left frontal lobe remains unclear. We attempted to investigate the mechanism with the use of functional MRI (fMRI). We studied 2 patients with TSA after a left frontal infarction identified by diffusion-weighted MRI. As control subjects, a patient with transcortical motor aphasia and a healthy normal adult were chosen. The Korean version of Western Aphasia Battery was performed initially and at 3 months post stroke. We performed fMRI using verb generation and sentence completion tasks. Resting-state fMRI (rs-fMRI) was also obtained for network-level analysis initially and at 3 months post stroke. The results of diffusion- and perfusion-weighted MRI revealed no diffusion-perfusion mismatch. Initial fMRI in patients with TSA showed no reversed inter-/intrahemispheric activation patterns. rs-fMRI showed significantly decreased resting-state functional connectivity in the language network in patients with TSA compared with the control subjects. Follow-up rs-fMRI studies showed improvement in functional connectivity along with the recovery of patients' language function. Our data showed that the auditory comprehension deficits in patients with frontal lobe infarcts is attributed to difficulty accessing the posterior language area due to functional disconnection between language centers in the acute stage of stroke. © 2017 S. Karger AG, Basel.

Scaling Analysis of Ocean Surface Turbulent Heterogeneities from Satellite Remote Sensing: Use of 2D Structure Functions.

PubMed

Renosh, P R; Schmitt, Francois G; Loisel, Hubert

2015-01-01

Satellite remote sensing observations allow the ocean surface to be sampled synoptically over large spatio-temporal scales. The images provided from visible and thermal infrared satellite observations are widely used in physical, biological, and ecological oceanography. The present work proposes a method to understand the multi-scaling properties of satellite products such as the Chlorophyll-a (Chl-a), and the Sea Surface Temperature (SST), rarely studied. The specific objectives of this study are to show how the small scale heterogeneities of satellite images can be characterised using tools borrowed from the fields of turbulence. For that purpose, we show how the structure function, which is classically used in the frame of scaling time series analysis, can be used also in 2D. The main advantage of this method is that it can be applied to process images which have missing data. Based on both simulated and real images, we demonstrate that coarse-graining (CG) of a gradient modulus transform of the original image does not provide correct scaling exponents. We show, using a fractional Brownian simulation in 2D, that the structure function (SF) can be used with randomly sampled couple of points, and verify that 1 million of couple of points provides enough statistics.

Computational analysis of molt-inhibiting hormone from selected crustaceans.

PubMed

C, Kumaraswamy Naidu; Y, Suneetha; P, Sreenivasula Reddy

2013-12-01

Molt-inhibiting hormone (MIH) is a principal endocrine hormone regulating the growth in crustaceans. In total, nine MIH peptide sequences representing members of the family Penaeidae (Penaeus monodon, Litopenaeus vannamei, Marsupenaeus japonicus), Portunidae (Portunus trituberculatus, Charybdis japonica, Charybdis feriata), Cambaridae (Procambarus bouvieri), Parastacidae (Cherax quadricarinatus) and Varunidae (Eriocheir sinensis) were selected for our study. In order to develop a structure based phylogeny, predict functionally important regions and to define stability changes upon single site mutations, the 3D structure of MIH for the crustaceans were built by using homology modeling based on the known structure of MIH from M. japonicus (1J0T). Structure based phylogeny showed a close relationship between P. bouvieri and C. japonica. ConSurf server analysis showed that the residues Cys(8), Arg(15), Cys(25), Asp(27), Cys(28), Asn(30), Arg(33), Cys(41), Cys(45), Phe(51), and Cys(54) may be functionally significant among the MIH of crustaceans. Single amino acid substitutions 'Y' and 'G' at the positions 71 and 72 of the MIH C-terminal region showed an alteration in the stability indicating that a change in this region may alter the function of MIH. In conclusion, we proposed a computational approach to analyze the structure, phylogeny and stability of MIH from crustaceans. © 2013.

Chemical-genetic profile analysis in yeast suggests that a previously uncharacterized open reading frame, YBR261C, affects protein synthesis

PubMed Central

Alamgir, Md; Eroukova, Veronika; Jessulat, Matthew; Xu, Jianhua; Golshani, Ashkan

2008-01-01

Background Functional genomics has received considerable attention in the post-genomic era, as it aims to identify function(s) for different genes. One way to study gene function is to investigate the alterations in the responses of deletion mutants to different stimuli. Here we investigate the genetic profile of yeast non-essential gene deletion array (yGDA, ~4700 strains) for increased sensitivity to paromomycin, which targets the process of protein synthesis. Results As expected, our analysis indicated that the majority of deletion strains (134) with increased sensitivity to paromomycin, are involved in protein biosynthesis. The remaining strains can be divided into smaller functional categories: metabolism (45), cellular component biogenesis and organization (28), DNA maintenance (21), transport (20), others (38) and unknown (39). These may represent minor cellular target sites (side-effects) for paromomycin. They may also represent novel links to protein synthesis. One of these strains carries a deletion for a previously uncharacterized ORF, YBR261C, that we term TAE1 for Translation Associated Element 1. Our focused follow-up experiments indicated that deletion of TAE1 alters the ribosomal profile of the mutant cells. Also, gene deletion strain for TAE1 has defects in both translation efficiency and fidelity. Miniaturized synthetic genetic array analysis further indicates that TAE1 genetically interacts with 16 ribosomal protein genes. Phenotypic suppression analysis using TAE1 overexpression also links TAE1 to protein synthesis. Conclusion We show that a previously uncharacterized ORF, YBR261C, affects the process of protein synthesis and reaffirm that large-scale genetic profile analysis can be a useful tool to study novel gene function(s). PMID:19055778

Chemical-genetic profile analysis in yeast suggests that a previously uncharacterized open reading frame, YBR261C, affects protein synthesis.

PubMed

Alamgir, Md; Eroukova, Veronika; Jessulat, Matthew; Xu, Jianhua; Golshani, Ashkan

2008-12-03

Functional genomics has received considerable attention in the post-genomic era, as it aims to identify function(s) for different genes. One way to study gene function is to investigate the alterations in the responses of deletion mutants to different stimuli. Here we investigate the genetic profile of yeast non-essential gene deletion array (yGDA, approximately 4700 strains) for increased sensitivity to paromomycin, which targets the process of protein synthesis. As expected, our analysis indicated that the majority of deletion strains (134) with increased sensitivity to paromomycin, are involved in protein biosynthesis. The remaining strains can be divided into smaller functional categories: metabolism (45), cellular component biogenesis and organization (28), DNA maintenance (21), transport (20), others (38) and unknown (39). These may represent minor cellular target sites (side-effects) for paromomycin. They may also represent novel links to protein synthesis. One of these strains carries a deletion for a previously uncharacterized ORF, YBR261C, that we term TAE1 for Translation Associated Element 1. Our focused follow-up experiments indicated that deletion of TAE1 alters the ribosomal profile of the mutant cells. Also, gene deletion strain for TAE1 has defects in both translation efficiency and fidelity. Miniaturized synthetic genetic array analysis further indicates that TAE1 genetically interacts with 16 ribosomal protein genes. Phenotypic suppression analysis using TAE1 overexpression also links TAE1 to protein synthesis. We show that a previously uncharacterized ORF, YBR261C, affects the process of protein synthesis and reaffirm that large-scale genetic profile analysis can be a useful tool to study novel gene function(s).

Sparse dictionary learning for resting-state fMRI analysis

NASA Astrophysics Data System (ADS)

Lee, Kangjoo; Han, Paul Kyu; Ye, Jong Chul

2011-09-01

Recently, there has been increased interest in the usage of neuroimaging techniques to investigate what happens in the brain at rest. Functional imaging studies have revealed that the default-mode network activity is disrupted in Alzheimer's disease (AD). However, there is no consensus, as yet, on the choice of analysis method for the application of resting-state analysis for disease classification. This paper proposes a novel compressed sensing based resting-state fMRI analysis tool called Sparse-SPM. As the brain's functional systems has shown to have features of complex networks according to graph theoretical analysis, we apply a graph model to represent a sparse combination of information flows in complex network perspectives. In particular, a new concept of spatially adaptive design matrix has been proposed by implementing sparse dictionary learning based on sparsity. The proposed approach shows better performance compared to other conventional methods, such as independent component analysis (ICA) and seed-based approach, in classifying the AD patients from normal using resting-state analysis.

[Soil microbial functional diversity of different altitude Pinus koraiensis forests].

PubMed

Han, Dong-xue; Wang, Ning; Wang, Nan-nan; Sun, Xue; Feng, Fu-juan

2015-12-01

In order to comprehensively understand the soil microbial carbon utilization characteristics of Pinus koraiensis forests, we took the topsoil (0-5 cm and 5-10 cm) along the 700-1100 m altitude in Changbai Mountains and analyzed the vertical distributed characteristics and variation of microbial functional diversity along the elevation gradient by Biolog microplate method. The results showed that there were significant differences in functional diversity of microbial communities at different elevations. AWCD increased with the extension of incubation time and AWCD at the same soil depth gradually decreased along with increasing altitude; Shannon, Simpson and McIntosh diversity index also showed the same trend with AWCD and three different diversity indices were significantly different along the elevation gradient; Species diversity and functional diversity showed the same variation. The utilization intensities of six categories carbon sources had differences while amino acids were constantly the most dominant carbon source. Principal component analysis (PCA) identified that soil microbial carbon utilization at different altitudes had obvious spatial differentiation, as reflected in the use of carbohydrates, amino acids and carboxylic acids. In addition, the cluster of the microbial diversity indexes and AWCD values of different altitudes showed that the composition of vegetation had a significant impact on soil microbial composition and functional activity.

Guided Wave Delamination Detection and Quantification With Wavefield Data Analysis

NASA Technical Reports Server (NTRS)

Tian, Zhenhua; Campbell Leckey, Cara A.; Seebo, Jeffrey P.; Yu, Lingyu

2014-01-01

Unexpected damage can occur in aerospace composites due to impact events or material stress during off-nominal loading events. In particular, laminated composites are susceptible to delamination damage due to weak transverse tensile and inter-laminar shear strengths. Developments of reliable and quantitative techniques to detect delamination damage in laminated composites are imperative for safe and functional optimally-designed next-generation composite structures. In this paper, we investigate guided wave interactions with delamination damage and develop quantification algorithms by using wavefield data analysis. The trapped guided waves in the delamination region are observed from the wavefield data and further quantitatively interpreted by using different wavenumber analysis methods. The frequency-wavenumber representation of the wavefield shows that new wavenumbers are present and correlate to trapped waves in the damage region. These new wavenumbers are used to detect and quantify the delamination damage through the wavenumber analysis, which can show how the wavenumber changes as a function of wave propagation distance. The location and spatial duration of the new wavenumbers can be identified, providing a useful means not only for detecting the presence of delamination damage but also allowing for estimation of the delamination size. Our method has been applied to detect and quantify real delamination damage with complex geometry (grown using a quasi-static indentation technique). The detection and quantification results show the location, size, and shape of the delamination damage.

Functional expression of a cattle MHC class II DR-like antigen on mouse L cells

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

Fraser, D.C.; Craigmile, S.; Campbell, J.D.M.

1996-09-01

Cattle DRA and DRB genes, cloned by reverse-transcription polymerase chain reaction, were transfected into mouse L cells. The cattle DR-expressing L-cell transfectant generated was analyzed serologically, biochemically, and functionally. Sequence analysis of the transfected DRB gene clearly showed showed that it was DRB3 allele DRB3*0101, which corresponds to the 1D-IEF-determined allele DRBF3. 1D-IEF analysis of the tranfectant confirmed that the expressed DR product was DRBF3. Functional integrity of the transfected gene products was demonstrated by the ability of the transfectant cell line to present two antigens (the foot-and-mouth disease virus-derived peptide FMDV15, and ovalbumin) to antigen-specific CD4{sup +} T cellsmore » from both the original animal used to obtain the genes, and also from an unrelated DRBF3{sup +} heterozygous animal. Such transfectants will be invaluable tools, allowing us to dissect the precise contributions each locus product makes to the overall immune response in heterozygous animals, information essential for rational vaccine design. 45 refs., 5 figs., 1 tab.« less

Depth resolved grazing incidence neutron scattering experiments from semi-infinite interfaces: a statistical analysis of the scattering contributions

NASA Astrophysics Data System (ADS)

Adlmann, Franz A.; Herbel, Jörg; Korolkovas, Airidas; Bliersbach, Andreas; Toperverg, Boris; Van Herck, Walter; Pálsson, Gunnar K.; Kitchen, Brian; Wolff, Max

2018-04-01

Grazing incidence neutron scattering experiments offer surface sensitivity by reflecting from an interface at momentum transfers close to total external reflection. Under these conditions the penetration depth is strongly non-linear and may change by many orders of magnitude. This fact imposes severe challenges for depth resolved experiments, since the brilliance of neutron beams is relatively low in comparison to e.g. synchrotron radiation. In this article we use probability density functions to calculate the contribution of scattering at different distances from an interface to the intensities registered on the detector. Our method has the particular advantage that the depth sensitivity is directly extracted from the scattering pattern itself. Hence for perfectly known samples exact resolution functions can be calculated and visa versa. We show that any tails in the resolution function, e.g. Gaussian shaped, hinders depth resolved experiments. More importantly we provide means for a descriptive statistical analysis of detector images with respect to the scattering contributions and show that even for perfect resolution near surface scattering is hardly accessible.

Parametric Model Based On Imputations Techniques for Partly Interval Censored Data

NASA Astrophysics Data System (ADS)

Zyoud, Abdallah; Elfaki, F. A. M.; Hrairi, Meftah

2017-12-01

The term ‘survival analysis’ has been used in a broad sense to describe collection of statistical procedures for data analysis. In this case, outcome variable of interest is time until an event occurs where the time to failure of a specific experimental unit might be censored which can be right, left, interval, and Partly Interval Censored data (PIC). In this paper, analysis of this model was conducted based on parametric Cox model via PIC data. Moreover, several imputation techniques were used, which are: midpoint, left & right point, random, mean, and median. Maximum likelihood estimate was considered to obtain the estimated survival function. These estimations were then compared with the existing model, such as: Turnbull and Cox model based on clinical trial data (breast cancer data), for which it showed the validity of the proposed model. Result of data set indicated that the parametric of Cox model proved to be more superior in terms of estimation of survival functions, likelihood ratio tests, and their P-values. Moreover, based on imputation techniques; the midpoint, random, mean, and median showed better results with respect to the estimation of survival function.

In vivo optical microscopy of peripheral nerve myelination with polarization sensitive-optical coherence tomography

PubMed Central

Henry, Francis P.; Wang, Yan; Rodriguez, Carissa L. R.; Randolph, Mark A.; Rust, Esther A. Z.; Winograd, Jonathan M.; de Boer, Johannes F.; Park, B. Hyle

2015-01-01

Abstract. Assessing nerve integrity and myelination after injury is necessary to provide insight for treatment strategies aimed at restoring neuromuscular function. Currently, this is largely done with electrical analysis, which lacks direct quantitative information. In vivo optical imaging with sufficient imaging depth and resolution could be used to assess the nerve microarchitecture. In this study, we examine the use of polarization sensitive-optical coherence tomography (PS-OCT) to quantitatively assess the sciatic nerve microenvironment through measurements of birefringence after applying a nerve crush injury in a rat model. Initial loss of function and subsequent recovery were demonstrated by calculating the sciatic function index (SFI). We found that the PS-OCT phase retardation slope, which is proportional to birefringence, increased monotonically with the SFI. Additionally, histomorphometric analysis of the myelin thickness and g-ratio shows that the PS-OCT slope is a good indicator of myelin health and recovery after injury. These results demonstrate that PS-OCT is capable of providing nondestructive and quantitative assessment of nerve health after injury and shows promise for continued use both clinically and experimentally in neuroscience. PMID:25858593

In vivo optical microscopy of peripheral nerve myelination with polarization sensitive-optical coherence tomography.

PubMed

Henry, Francis P; Wang, Yan; Rodriguez, Carissa L R; Randolph, Mark A; Rust, Esther A Z; Winograd, Jonathan M; de Boer, Johannes F; Park, B Hyle

2015-04-01

Assessing nerve integrity and myelination after injury is necessary to provide insight for treatment strategies aimed at restoring neuromuscular function. Currently, this is largely done with electrical analysis, which lacks direct quantitative information. In vivo optical imaging with sufficient imaging depth and resolution could be used to assess the nerve microarchitecture. In this study, we examine the use of polarization sensitive-optical coherence tomography (PS-OCT) to quantitatively assess the sciatic nerve microenvironment through measurements of birefringence after applying a nerve crush injury in a rat model. Initial loss of function and subsequent recovery were demonstrated by calculating the sciatic function index (SFI). We found that the PS-OCT phase retardation slope, which is proportional to birefringence, increased monotonically with the SFI. Additionally, histomorphometric analysis of the myelin thickness and g-ratio shows that the PS-OCT slope is a good indicator of myelin health and recovery after injury. These results demonstrate that PS-OCT is capable of providing nondestructive and quantitative assessment of nerve health after injury and shows promise for continued use both clinically and experimentally in neuroscience.

The function of prehistoric lithic tools: a combined study of use-wear analysis and FTIR microspectroscopy.

PubMed

Nunziante Cesaro, Stella; Lemorini, Cristina

2012-02-01

The application of combined use-wear analysis and FTIR micro spectroscopy for the investigation of the flint and obsidian tools from the archaeological sites of Masseria Candelaro (Foggia, Italy) and Sant'Anna di Oria (Brindisi, Italy) aiming to clarify their functional use is described. The tools excavated in the former site showed in a very high percentage spectroscopically detectable residues on their working edges. The identification of micro deposits is based on comparison with a great number of replicas studied in the same experimental conditions. FTIR data confirmed in almost all cases the use-wear analysis suggestions and added details about the material processed and about the working procedures. Copyright © 2011 Elsevier B.V. All rights reserved.

Separate enrichment analysis of pathways for up- and downregulated genes.

PubMed

Hong, Guini; Zhang, Wenjing; Li, Hongdong; Shen, Xiaopei; Guo, Zheng

2014-03-06

Two strategies are often adopted for enrichment analysis of pathways: the analysis of all differentially expressed (DE) genes together or the analysis of up- and downregulated genes separately. However, few studies have examined the rationales of these enrichment analysis strategies. Using both microarray and RNA-seq data, we show that gene pairs with functional links in pathways tended to have positively correlated expression levels, which could result in an imbalance between the up- and downregulated genes in particular pathways. We then show that the imbalance could greatly reduce the statistical power for finding disease-associated pathways through the analysis of all-DE genes. Further, using gene expression profiles from five types of tumours, we illustrate that the separate analysis of up- and downregulated genes could identify more pathways that are really pertinent to phenotypic difference. In conclusion, analysing up- and downregulated genes separately is more powerful than analysing all of the DE genes together.

Percolation analysis for cosmic web with discrete points

NASA Astrophysics Data System (ADS)

Zhang, Jiajun; Cheng, Dalong; Chu, Ming-Chung

2016-03-01

Percolation analysis has long been used to quantify the connectivity of the cosmic web. Unlike most of the previous works using density field on grids, we have studied percolation analysis based on discrete points. Using a Friends-of-Friends (FoF) algorithm, we generate the S-bb relation, between the fractional mass of the largest connected group (S) and the FoF linking length (bb). We propose a new model, the Probability Cloud Cluster Expansion Theory (PCCET) to relate the S-bb relation with correlation functions. We show that the S-bb relation reflects a combination of all orders of correlation functions. We have studied the S-bb relation with simulation and find that the S-bb relation is robust against redshift distortion and incompleteness in observation. From the Bolshoi simulation, with Halo Abundance Matching (HAM), we have generated a mock galaxy catalogue. Good matching of the projected two-point correlation function with observation is confirmed. However, comparing the mock catalogue with the latest galaxy catalogue from SDSS DR12, we have found significant differences in their S-bb relations. This indicates that the mock catalogue cannot accurately recover higher order correlation functions than the two-point correlation function, which reveals the limit of HAM method.

Scalable analysis of nonlinear systems using convex optimization

NASA Astrophysics Data System (ADS)

Papachristodoulou, Antonis

In this thesis, we investigate how convex optimization can be used to analyze different classes of nonlinear systems at various scales algorithmically. The methodology is based on the construction of appropriate Lyapunov-type certificates using sum of squares techniques. After a brief introduction on the mathematical tools that we will be using, we turn our attention to robust stability and performance analysis of systems described by Ordinary Differential Equations. A general framework for constrained systems analysis is developed, under which stability of systems with polynomial, non-polynomial vector fields and switching systems, as well estimating the region of attraction and the L2 gain can be treated in a unified manner. We apply our results to examples from biology and aerospace. We then consider systems described by Functional Differential Equations (FDEs), i.e., time-delay systems. Their main characteristic is that they are infinite dimensional, which complicates their analysis. We first show how the complete Lyapunov-Krasovskii functional can be constructed algorithmically for linear time-delay systems. Then, we concentrate on delay-independent and delay-dependent stability analysis of nonlinear FDEs using sum of squares techniques. An example from ecology is given. The scalable stability analysis of congestion control algorithms for the Internet is investigated next. The models we use result in an arbitrary interconnection of FDE subsystems, for which we require that stability holds for arbitrary delays, network topologies and link capacities. Through a constructive proof, we develop a Lyapunov functional for FAST---a recently developed network congestion control scheme---so that the Lyapunov stability properties scale with the system size. We also show how other network congestion control schemes can be analyzed in the same way. Finally, we concentrate on systems described by Partial Differential Equations. We show that axially constant perturbations of the Navier-Stokes equations for Hagen-Poiseuille flow are globally stable, even though the background noise is amplified as R3 where R is the Reynolds number, giving a 'robust yet fragile' interpretation. We also propose a sum of squares methodology for the analysis of systems described by parabolic PDEs. We conclude this work with an account for future research.

Comparison of Two Multifractal Analysis Methods: Generalized Structure Function and Multifractal Spectrum

NASA Astrophysics Data System (ADS)

Morato, M. Carmen; Castellanos, M. Teresa; Bird, Nigel; Tarquis, Ana M.

2016-04-01

Soil variability has often been a constant expected factor to take in account in soil studies. This variability could be considered to be composed of "functional" variations plus random fluctuations or noise. Multifractal formalism, first proposed by Mandelbrot (1982), is suitable for variables with self-similar distribution on a spatial domain. Multifractal analysis can provide insight into spatial variability of crop or soil parameters. In soil science, it has been quite popular to characterize the scaling property of a variable measured along a transect as a mass distribution of a statistical measure on a length domain of the studied transect. To do this, it divides it into a number of self similar segments and estimate the partition function and mass function. Based on this, the multifractal spectra (MFS) is calculated. However, another technique can be applied focus its attention in the variations of a measure analyzing the moments of the absolute differences at different scales, the Generalized Structure Function (GSF), and extracting the Generalized Hurst exponents. The aim of this study is to compare both techniques in a transect data. A common 1024 m transect across arable fields at Silsoe in Bedfordshire, east-central England were analyzed with these two multifractal methods. Properties studied were total porosity (Porosity), gravimetric water content (GWC) and nitrogen oxide flux (NO2 flux). The results showed in both methods that NO2 flux presents a clear multifractal character and a weak one in the GWC and Porosity cases. Several parameters were calculated from both methods and are discussed. On the other hand, using the partition function all the scale ranges were used, meanwhile in the GSF a shorter range of scales showed linear behavior in the bilog plots used to estimate the parameters. GWC exhibits a linear pattern from increments of 4 till 256 meters, Porosity showed this behavior from 4 till 64 meters. In case of NO2 flux only from 32 to 256 meters showed it. However, the relation between the mass exponent function and the GSF, found in the literature, was positively verified in the three variables.

Genome-Wide Distribution, Organisation and Functional Characterization of Disease Resistance and Defence Response Genes across Rice Species

PubMed Central

Singh, Sangeeta; Chand, Suresh; Singh, N. K.; Sharma, Tilak Raj

2015-01-01

The resistance (R) genes and defense response (DR) genes have become very important resources for the development of disease resistant cultivars. In the present investigation, genome-wide identification, expression, phylogenetic and synteny analysis was done for R and DR-genes across three species of rice viz: Oryza sativa ssp indica cv 93-11, Oryza sativa ssp japonica and wild rice species, Oryza brachyantha. We used the in silico approach to identify and map 786 R -genes and 167 DR-genes, 672 R-genes and 142 DR-genes, 251 R-genes and 86 DR-genes in the japonica, indica and O. brachyanth a genomes, respectively. Our analysis showed that 60.5% and 55.6% of the R-genes are tandemly repeated within clusters and distributed over all the rice chromosomes in indica and japonica genomes, respectively. The phylogenetic analysis along with motif distribution shows high degree of conservation of R- and DR-genes in clusters. In silico expression analysis of R-genes and DR-genes showed more than 85% were expressed genes showing corresponding EST matches in the databases. This study gave special emphasis on mechanisms of gene evolution and duplication for R and DR genes across species. Analysis of paralogs across rice species indicated 17% and 4.38% R-genes, 29% and 11.63% DR-genes duplication in indica and Oryza brachyantha, as compared to 20% and 26% duplication of R-genes and DR-genes in japonica respectively. We found that during the course of duplication only 9.5% of R- and DR-genes changed their function and rest of the genes have maintained their identity. Syntenic relationship across three genomes inferred that more orthology is shared between indica and japonica genomes as compared to brachyantha genome. Genome wide identification of R-genes and DR-genes in the rice genome will help in allele mining and functional validation of these genes, and to understand molecular mechanism of disease resistance and their evolution in rice and related species. PMID:25902056

A Prototype System for Retrieval of Gene Functional Information

PubMed Central

Folk, Lillian C.; Patrick, Timothy B.; Pattison, James S.; Wolfinger, Russell D.; Mitchell, Joyce A.

2003-01-01

Microarrays allow researchers to gather data about the expression patterns of thousands of genes simultaneously. Statistical analysis can reveal which genes show statistically significant results. Making biological sense of those results requires the retrieval of functional information about the genes thus identified, typically a manual gene-by-gene retrieval of information from various on-line databases. For experiments generating thousands of genes of interest, retrieval of functional information can become a significant bottleneck. To address this issue, we are currently developing a prototype system to automate the process of retrieval of functional information from multiple on-line sources. PMID:14728346

An arc tangent function demodulation method of fiber-optic Fabry-Perot high-temperature pressure sensor

NASA Astrophysics Data System (ADS)

Ren, Qianyu; Li, Junhong; Hong, Yingping; Jia, Pinggang; Xiong, Jijun

2017-09-01

A new demodulation algorithm of the fiber-optic Fabry-Perot cavity length based on the phase generated carrier (PGC) is proposed in this paper, which can be applied in the high-temperature pressure sensor. This new algorithm based on arc tangent function outputs two orthogonal signals by utilizing an optical system, which is designed based on the field-programmable gate array (FPGA) to overcome the range limit of the original PGC arc tangent function demodulation algorithm. The simulation and analysis are also carried on. According to the analysis of demodulation speed and precision, the simulation of different numbers of sampling points, and measurement results of the pressure sensor, the arc tangent function demodulation method has good demodulation results: 1 MHz processing speed of single data and less than 1% error showing practical feasibility in the fiber-optic Fabry-Perot cavity length demodulation of the Fabry-Perot high-temperature pressure sensor.

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

Wang, Weizhou, E-mail: wzw@lynu.edu.cn, E-mail: ybw@gzu.edu.cn; Zhang, Yu; Sun, Tao

High-level coupled cluster singles, doubles, and perturbative triples [CCSD(T)] computations with up to the aug-cc-pVQZ basis set (1924 basis functions) and various extrapolations toward the complete basis set (CBS) limit are presented for the sandwich, T-shaped, and parallel-displaced benzene⋯naphthalene complex. Using the CCSD(T)/CBS interaction energies as a benchmark, the performance of some newly developed wave function and density functional theory methods has been evaluated. The best performing methods were found to be the dispersion-corrected PBE0 functional (PBE0-D3) and spin-component scaled zeroth-order symmetry-adapted perturbation theory (SCS-SAPT0). The success of SCS-SAPT0 is very encouraging because it provides one method for energy componentmore » analysis of π-stacked complexes with 200 atoms or more. Most newly developed methods do, however, overestimate the interaction energies. The results of energy component analysis show that interaction energies are overestimated mainly due to the overestimation of dispersion energy.« less

On the Tracy-Widomβ Distribution for β=6

NASA Astrophysics Data System (ADS)

Grava, Tamara; Its, Alexander; Kapaev, Andrei; Mezzadri, Francesco

2016-11-01

We study the Tracy-Widom distribution function for Dyson's β-ensemble with β = 6. The starting point of our analysis is the recent work of I. Rumanov where he produces a Lax-pair representation for the Bloemendal-Virág equation. The latter is a linear PDE which describes the Tracy-Widom functions corresponding to general values of β. Using his Lax pair, Rumanov derives an explicit formula for the Tracy-Widom β=6 function in terms of the second Painlevé transcendent and the solution of an auxiliary ODE. Rumanov also shows that this formula allows him to derive formally the asymptotic expansion of the Tracy-Widom function. Our goal is to make Rumanov's approach and hence the asymptotic analysis it provides rigorous. In this paper, the first one in a sequel, we show that Rumanov's Lax-pair can be interpreted as a certain gauge transformation of the standard Lax pair for the second Painlevé equation. This gauge transformation though contains functional parameters which are defined via some auxiliary nonlinear ODE which is equivalent to the auxiliary ODE of Rumanov's formula. The gauge-interpretation of Rumanov's Lax-pair allows us to highlight the steps of the original Rumanov's method which needs rigorous justifications in order to make the method complete. We provide a rigorous justification of one of these steps. Namely, we prove that the Painlevé function involved in Rumanov's formula is indeed, as it has been suggested by Rumanov, the Hastings-McLeod solution of the second Painlevé equation. The key issue which we also discuss and which is still open is the question of integrability of the auxiliary ODE in Rumanov's formula. We note that this question is crucial for the rigorous asymptotic analysis of the Tracy-Widom function. We also notice that our work is a partial answer to one of the problems related to the β-ensembles formulated by Percy Deift during the June 2015 Montreal Conference on integrable systems.

Molecular Phylogenetic and Expression Analysis of the Complete WRKY Transcription Factor Family in Maize

PubMed Central

Wei, Kai-Fa; Chen, Juan; Chen, Yan-Feng; Wu, Ling-Juan; Xie, Dao-Xin

2012-01-01

The WRKY transcription factors function in plant growth and development, and response to the biotic and abiotic stresses. Although many studies have focused on the functional identification of the WRKY transcription factors, much less is known about molecular phylogenetic and global expression analysis of the complete WRKY family in maize. In this study, we identified 136 WRKY proteins coded by 119 genes in the B73 inbred line from the complete genome and named them in an orderly manner. Then, a comprehensive phylogenetic analysis of five species was performed to explore the origin and evolutionary patterns of these WRKY genes, and the result showed that gene duplication is the major driving force for the origin of new groups and subgroups and functional divergence during evolution. Chromosomal location analysis of maize WRKY genes indicated that 20 gene clusters are distributed unevenly in the genome. Microarray-based expression analysis has revealed that 131 WRKY transcripts encoded by 116 genes may participate in the regulation of maize growth and development. Among them, 102 transcripts are stably expressed with a coefficient of variation (CV) value of <15%. The remaining 29 transcripts produced by 25 WRKY genes with the CV value of >15% are further analysed to discover new organ- or tissue-specific genes. In addition, microarray analyses of transcriptional responses to drought stress and fungal infection showed that maize WRKY proteins are involved in stress responses. All these results contribute to a deep probing into the roles of WRKY transcription factors in maize growth and development and stress tolerance. PMID:22279089

Molecular phylogenetic and expression analysis of the complete WRKY transcription factor family in maize.

PubMed

Wei, Kai-Fa; Chen, Juan; Chen, Yan-Feng; Wu, Ling-Juan; Xie, Dao-Xin

2012-04-01

The WRKY transcription factors function in plant growth and development, and response to the biotic and abiotic stresses. Although many studies have focused on the functional identification of the WRKY transcription factors, much less is known about molecular phylogenetic and global expression analysis of the complete WRKY family in maize. In this study, we identified 136 WRKY proteins coded by 119 genes in the B73 inbred line from the complete genome and named them in an orderly manner. Then, a comprehensive phylogenetic analysis of five species was performed to explore the origin and evolutionary patterns of these WRKY genes, and the result showed that gene duplication is the major driving force for the origin of new groups and subgroups and functional divergence during evolution. Chromosomal location analysis of maize WRKY genes indicated that 20 gene clusters are distributed unevenly in the genome. Microarray-based expression analysis has revealed that 131 WRKY transcripts encoded by 116 genes may participate in the regulation of maize growth and development. Among them, 102 transcripts are stably expressed with a coefficient of variation (CV) value of <15%. The remaining 29 transcripts produced by 25 WRKY genes with the CV value of >15% are further analysed to discover new organ- or tissue-specific genes. In addition, microarray analyses of transcriptional responses to drought stress and fungal infection showed that maize WRKY proteins are involved in stress responses. All these results contribute to a deep probing into the roles of WRKY transcription factors in maize growth and development and stress tolerance.

Diagnostic Power of Macular Retinal Thickness Analysis and Structure-Function Relationship in Glaucoma Diagnosis Using SPECTRALIS OCT.

PubMed

Rolle, Teresa; Manerba, Linda; Lanzafame, Pietro; Grignolo, Federico M

2016-05-01

To evaluate the diagnostic power of the Posterior Pole Asymmetry Analysis (PPAA) from the SPECTRALIS OCT in glaucoma diagnosis and to define the correlation between the visual field sensitivity (VFS) and macular retinal thickness (MRT). 90 consecutive open-angle glaucoma patients and 23 healthy subjects were enrolled. All subjects underwent Visual Field test (Humphrey Field Analyzer, central 24-2 SITA-Standard) and SD-OCT volume scans (SPECTRALIS, Posterior Pole Asymmetry Analysis). The areas under the Receiving Operating Characteristic curve (AROC) were calculated to assess discriminating power for glaucoma, at first considering total MRT values and hemisphere MRT value and then quadrant MRT values from 16 square cells in a 8 x 8 posterior pole retinal thickness map that were averaged for a mean retinal thickness value. Structure function correlation was performed for total values, hemisphere values and for each quadrant compared to the matching central test points of the VF. The AROCs ranged from 0.70 to 0.82 (p < 0.0001), with no significant differences between each other. The highest AROC observed was in inferior nasal quadrant. The VFS showed a strong correlation only with the corresponding MRT value s for quadrant analysis: Superior Temporal (r = 0.33, p = 0.0013), Superior Nasal (r = 0.43, p < 0.0001), Inferior Temporal (r = 0.57, p < 0.0001) and Inferior Nasal (r = 0.55, p < 0.0001). the quadrant analysis showed statistically significant structure-function correlations and may provide additional data for the diagnostic performance of SPECTRALIS OCT.

Light scattering Q-space analysis of irregularly shaped particles

NASA Astrophysics Data System (ADS)

Heinson, Yuli W.; Maughan, Justin B.; Heinson, William R.; Chakrabarti, Amitabha; Sorensen, Christopher M.

2016-01-01

We report Q-space analysis of light scattering phase function data for irregularly shaped dust particles and of theoretical model output to describe them. This analysis involves plotting the scattered intensity versus the magnitude of the scattering wave vector q = (4π/λ)sin(θ/2), where λ is the optical wavelength and θ is the scattering angle, on a double-logarithmic plot. In q-space all the particle shapes studied display a scattering pattern which includes a q-independent forward scattering regime; a crossover, Guinier regime when q is near the inverse size; a power law regime; and an enhanced backscattering regime. Power law exponents show a quasi-universal functionality with the internal coupling parameter ρ'. The absolute value of the exponents start from 4 when ρ' < 1, the diffraction limit, and decreases as ρ' increases until a constant 1.75 ± 0.25 when ρ' ≳ 10. The diffraction limit exponent implies that despite their irregular structures, all the particles studied have mass and surface scaling dimensions of Dm = 3 and Ds = 2, respectively. This is different from fractal aggregates that have a power law equal to the fractal dimension Df because Df = Dm = Ds < 3. Spheres have Dm = 3 and Ds = 2 but do not show a single power law nor the same functionality with ρ'. The results presented here imply that Q-space analysis can differentiate between spheres and these two types of irregularly shaped particles. Furthermore, they are applicable to analysis of the contribution of aerosol radiative forcing to climate change and of aerosol remote sensing data.

Laminin α5 substrates promote survival, network formation and functional development of human pluripotent stem cell-derived neurons in vitro.

PubMed

Hyysalo, Anu; Ristola, Mervi; Mäkinen, Meeri E-L; Häyrynen, Sergei; Nykter, Matti; Narkilahti, Susanna

2017-10-01

Laminins are one of the major protein groups in the extracellular matrix (ECM) and specific laminin isoforms are crucial for neuronal functions in the central nervous system in vivo. In the present study, we compared recombinant human laminin isoforms (LN211, LN332, LN411, LN511, and LN521) and laminin isoform fragment (LN511-E8) in in vitro cultures of human pluripotent stem cell (hPSC)-derived neurons. We showed that laminin substrates containing the α5-chain are important for neuronal attachment, viability and network formation, as detected by phase contrast imaging, viability staining, and immunocytochemistry. Gene expression analysis showed that the molecular mechanisms involved in the preference of hPSC-derived neurons for specific laminin isoforms could be related to ECM remodeling and cell adhesion. Importantly, the microelectrode array analysis revealed the widest distribution of electrophysiologically active neurons on laminin α5 substrates, indicating most efficient development of neuronal network functionality. This study shows that specific laminin α5 substrates provide a controlled in vitro culture environment for hPSC-derived neurons. These substrates can be utilized not only to enhance the production of functional hPSC-derived neurons for in vitro applications like disease modeling, toxicological studies, and drug discovery, but also for the production of clinical grade hPSC-derived cells for regenerative medicine applications. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Comprehensive Genomic Analysis and Expression Profiling of the NOX Gene Families under Abiotic Stresses and Hormones in Plants.

PubMed

Chang, Yan-Li; Li, Wen-Yan; Miao, Hai; Yang, Shuai-Qi; Li, Ri; Wang, Xiang; Li, Wen-Qiang; Chen, Kun-Ming

2016-02-23

Plasma membrane NADPH oxidases (NOXs) are key producers of reactive oxygen species under both normal and stress conditions in plants and they form functional subfamilies. Studies of these subfamilies indicated that they show considerable evolutionary selection. We performed a comparative genomic analysis that identified 50 ferric reduction oxidases (FRO) and 77 NOX gene homologs from 20 species representing the eight major plant lineages within the supergroup Plantae: glaucophytes, rhodophytes, chlorophytes, bryophytes, lycophytes, gymnosperms, monocots, and eudicots. Phylogenetic and structural analysis classified these FRO and NOX genes into four well-conserved groups represented as NOX, FRO I, FRO II, and FRO III. Further analysis of NOXs of phylogenetic and exon/intron structures showed that single intron loss and gain had occurred, yielding the diversified gene structures during the evolution of NOXs family genes and which were classified into four conserved subfamilies which are represented as Sub.I, Sub.II, Sub.III, and Sub.IV. Additionally, both available global microarray data analysis and quantitative real-time PCR experiments revealed that the NOX genes in Arabidopsis and rice (Oryza sativa) have different expression patterns in different developmental stages, various abiotic stresses and hormone treatments. Finally, coexpression network analysis of NOX genes in Arabidopsis and rice revealed that NOXs have significantly correlated expression profiles with genes which are involved in plants metabolic and resistance progresses. All these results suggest that NOX family underscores the functional diversity and divergence in plants. This finding will facilitate further studies of the NOX family and provide valuable information for functional validation of this family in plants. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

The Efficacy of Liposomal Bupivacaine Using Periarticular Injection in Total Knee Arthroplasty: A Systematic Review and Meta-Analysis.

PubMed

Kuang, Ming-Jie; Du, Yuren; Ma, Jian-Xiong; He, Weiwei; Fu, Lin; Ma, Xin-Long

2017-04-01

Total knee arthroplasty (TKA) is gradually emerging as the treatment of choice for end-stage osteoarthritis. In the past, the method of liposomal bupivacaine by periarticular injection (PAI) showed better effects on pain reduction and opioid consumption after surgery. However, some recent studies have reported that liposomal bupivacaine by PAI did not improve pain control and functional recovery in patients undergoing TKA. Therefore, this meta-analysis was conducted to determine whether liposomal bupivacaine provides better pain relief and functional recovery after TKA. Web of Science, PubMed, Embase, and the Cochrane Library were comprehensively searched. Randomized controlled trials, controlled clinical trials, and cohort studies were included in our meta-analysis. Eleven studies that compared liposomal bupivacaine using the PAI technique with the conventional PAI method were included in our meta-analysis. The preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines and Cochrane Handbook were applied to assess the quality of the results published in all included studies to ensure that the results of our meta-analysis were reliable and veritable. Our pooled data analysis demonstrated that liposomal bupivacaine was as effective as the control group in terms of visual analog scale score at 24 hours (P = .46), 48 hours (P = .43), 72 hours (P = .21), total amount of opioid consumption (P = .25), range of motion (P = .28), length of hospital stay (P = .53), postoperative nausea (P = .34), and ambulation distance (P = .07). Compared with the conventional PAI method, liposomal bupivacaine shows similar pain control and functional recovery after TKA. Considering the cost for pain control, liposomal bupivacaine is not worthy of being recommended as a long-acting alternative analgesic agent using the PAI method. Copyright © 2016 Elsevier Inc. All rights reserved.

Effectiveness of Functional Electrical Stimulation in Improving Clinical Outcomes in the Upper Arm following Stroke: A Systematic Review and Meta-Analysis

PubMed Central

Vafadar, Amir K.; Côté, Julie N.; Archambault, Philippe S.

2015-01-01

Background. Different therapeutic methods are being used to prevent or decrease long-term impairments of the upper arm in stroke patients. Functional electrical stimulation (FES) is one of these methods, which aims to stimulate the nerves of the weakened muscles so that the resulting muscle contractions resemble those of a functional task. Objectives. The objective of this study was to review the evidence for the effect of FES on (1) shoulder subluxation, (2) pain, and (3) upper arm motor function in stroke patients, when added to conventional therapy. Methods. From the 727 retrieved articles, 10 (9 RCTs, 1 quasi-RCT) were selected for final analysis and were rated based on the PEDro (Physiotherapy Evidence Database) scores and the Sackett's levels of evidence. A meta-analysis was performed for all three considered outcomes. Results. The results of the meta-analyses showed a significant difference in shoulder subluxation in experimental groups compared to control groups, only if FES was applied early after stroke. No effects were found on pain or motor function outcomes. Conclusion. FES can be used to prevent or reduce shoulder subluxation early after stroke. However, it should not be used to reduce pain or improve upper arm motor function after stroke. PMID:25685805

Factors affecting cognitive function according to gender in community-dwelling elderly individuals.

PubMed

Kim, Miwon; Park, Jeong-Mo

2017-01-01

This study aimed to identify the factors affecting the cognitive function of elderly people in a community by gender. We obtained 4,878 secondary data of people aged ≥65 years in 2016 at a dementia prevention center in Gyeyang-gu, Incheon. Data were obtained through Mini-Mental Status Examination optimized for screening dementia and a questionnaire. The data were statistically analyzed using analysis of variance, analysis of covariance, and hierarchical regression. There were significant differences in cognitive function according to gender, and the differences were significant even when age was controlled, but gender differences disappeared when education was controlled. Age, education, social activities, number of comorbid diseases, and alcohol drinking affected cognitive function through interaction with gender, but interaction with gender disappeared when education was controlled. Regression analysis showed that depression, cohabitant, social activities etc., had a significant impact on both men and women under controlled education and age. In men, the effect of social activities was greater than that of women, and hyperlipidemia had the effect only in women. The differences in gender-related cognitive functions were due to differences in gender education period. The period of education is considered to have a great influence on cognitive function in relation to the economic level, occupation, and social activity.

Factors affecting cognitive function according to gender in community-dwelling elderly individuals

PubMed Central

2017-01-01

OBJECTIVES This study aimed to identify the factors affecting the cognitive function of elderly people in a community by gender. METHODS We obtained 4,878 secondary data of people aged ≥65 years in 2016 at a dementia prevention center in Gyeyang-gu, Incheon. Data were obtained through Mini-Mental Status Examination optimized for screening dementia and a questionnaire. The data were statistically analyzed using analysis of variance, analysis of covariance, and hierarchical regression. RESULTS There were significant differences in cognitive function according to gender, and the differences were significant even when age was controlled, but gender differences disappeared when education was controlled. Age, education, social activities, number of comorbid diseases, and alcohol drinking affected cognitive function through interaction with gender, but interaction with gender disappeared when education was controlled. Regression analysis showed that depression, cohabitant, social activities etc., had a significant impact on both men and women under controlled education and age. In men, the effect of social activities was greater than that of women, and hyperlipidemia had the effect only in women. CONCLUSIONS The differences in gender-related cognitive functions were due to differences in gender education period. The period of education is considered to have a great influence on cognitive function in relation to the economic level, occupation, and social activity. PMID:29141399

Genome-Wide Detection and Analysis of Multifunctional Genes

PubMed Central

Pritykin, Yuri; Ghersi, Dario; Singh, Mona

2015-01-01

Many genes can play a role in multiple biological processes or molecular functions. Identifying multifunctional genes at the genome-wide level and studying their properties can shed light upon the complexity of molecular events that underpin cellular functioning, thereby leading to a better understanding of the functional landscape of the cell. However, to date, genome-wide analysis of multifunctional genes (and the proteins they encode) has been limited. Here we introduce a computational approach that uses known functional annotations to extract genes playing a role in at least two distinct biological processes. We leverage functional genomics data sets for three organisms—H. sapiens, D. melanogaster, and S. cerevisiae—and show that, as compared to other annotated genes, genes involved in multiple biological processes possess distinct physicochemical properties, are more broadly expressed, tend to be more central in protein interaction networks, tend to be more evolutionarily conserved, and are more likely to be essential. We also find that multifunctional genes are significantly more likely to be involved in human disorders. These same features also hold when multifunctionality is defined with respect to molecular functions instead of biological processes. Our analysis uncovers key features about multifunctional genes, and is a step towards a better genome-wide understanding of gene multifunctionality. PMID:26436655

The effect of subtalar inversion/eversion on the dynamic function of the tibialis anterior, soleus, and gastrocnemius during the stance phase of gait.

PubMed

Wang, Ruoli; Gutierrez-Farewik, Elena M

2011-05-01

The purpose of this study was to determine how gait deviation in one plane (i.e. excessive subtalar inversion/eversion) can affect the dynamic function of the tibialis anterior, gastrocnemius, and soleus to accelerate the subtalar, ankle, knee and hip joints, as well as the body center of mass. Induced acceleration analysis was performed based on a subject-specific three-dimensional linkage model configured by stance phase gait data and driven by one unit of muscle force. Eight healthy adult subjects were examined in gait analysis. The subtalar inversion/eversion was modeled by offsetting up to 20° from the normal subtalar angle while other configurations remained unaltered. This study showed that the gastrocnemius, soleus and tibialis anterior generally functioned as their anatomical definition in normal gait, but counterintuitive function was occasionally found in the bi-articular gastrocnemius. The plantarflexors play important roles in the body support and forward progression. Excessive subtalar eversion was found to enlarge the plantarflexors and tibialis anterior's function. Induced acceleration analysis demonstrated its ability to isolate the contributions of individual muscle to a given factor, and as a means of studying effect of pathological gait on the dynamic muscle functions. Copyright © 2011 Elsevier B.V. All rights reserved.

Some dissociating factors in the analysis of structural and functional progressive damage in open-angle glaucoma.

PubMed

Hudson, C J W; Kim, L S; Hancock, S A; Cunliffe, I A; Wild, J M

2007-05-01

To identify the presence, and origin, of any "dissociating factors" inherent to the techniques for evaluating progression that mask the relationship between structural and functional progression in open-angle glaucoma (OAG). 23 patients (14 with OAG and 9 with ocular hypertension (OHT)) who had received serial Heidelberg Retina Tomograph (HRT II) and Humphrey Field Analyser (HFA) examinations for >or=5 years (mean 78.4 months (SD 9.5), range 60-101 months) were identified. Evidence of progressive disease was retrospectively evaluated in one eye of each patient using the Topographic Change Analysis (TCA) and Glaucoma Progression Analysis (GPA) for the HRT II and HFA, respectively. Six patients were stable by both techniques; four exhibited both structural and functional progression; seven exhibited structural progression, only, and six showed functional progression, only. Three types of dissociating factors were identified. TCA failed to identify progressive structural damage in the presence of advanced optic nerve head damage. GPA failed to identify progressive functional damage at stimulus locations, with sensitivities exhibiting test-retest variability beyond the maximum stimulus luminance of the perimeter, and where a perimetric learning effect was apparent. The three dissociating factors accounted for nine of the 13 patients who exhibited a lack of concordance between structural and functional progressive damage.

[Brain function recovery after prolonged posttraumatic coma].

PubMed

Klimash, A V; Zhanaidarov, Z S

2016-01-01

To explore the characteristics of brain function recovery in patients after prolonged posttraumatic coma and with long-unconscious states. Eighty-seven patients after prolonged posttraumatic coma were followed-up for two years. An analysis of a clinical/neurological picture after a prolonged episode of coma was based on the dynamics of vital functions, neurological status and patient's reactions to external stimuli. Based on the dynamics of the clinical/neurological picture that shows the recovery of functions of the certain brain areas, three stages of brain function recovery after a prolonged episode of coma were singled out: brain stem areas, diencephalic areas and telencephalic areas. These functional/anatomic areas of brain function recovery after prolonged coma were compared to the present classifications.

Biocompatible polyurethane/thiacalix[4]arenes functionalized Fe3O4 magnetic nanocomposites: Synthesis and properties.

PubMed

Mohammadi, Abbas; Barikani, Mehdi; Lakouraj, Moslem Mansour

2016-09-01

In this study, a series of magnetic polyurethane/Fe3O4 elastomer nanocomposites were prepared by covalently embedding novel thiacalix[4]arenes (TC4As) functionalized Fe3O4 nanoparticles (TC4As-Fe3O4) which contain macrocycles with reactive hydroxyl groups. Surface functionalization of Fe3O4 nanoparticles with TC4As macrocycles as unique reactive surface modifier not only gives specific characteristics to Fe3O4 nanoparticles but also improves the interphase interaction between nanoparticles and the polyurethane matrices through covalent attachment of polymer chains to nanoparticle surfaces. The novel synthesized TC4As-Fe3O4 nanoparticles were characterized by FTIR, XRD, TGA, VSM and SEM analysis. Furthermore, the effect of functionalization of Fe3O4 nanoparticles on the various properties of resulting nanocomposites was studied by XRD, TGA, DMTA, SEM, and a universal tensile tester. It was found that the functionalization of nanoparticles with TC4As affords better mechanical and thermal properties to polyurethane nanocomposites in comparison with unmodified nanoparticles. The SEM analysis showed finer dispersion of TC4As-Fe3O4 nanoparticles than unmodified Fe3O4 nanoparticles within the polyurethane matrices, which arising from formation of covalent bonding between TC4As functionalized Fe3O4 nanoparticles and polyurethane matrices. Moreover, the investigation of in vitro biocompatibility of novel nanocomposites showed that these samples are excellent candidate for biomedical use. Copyright © 2016 Elsevier B.V. All rights reserved.

Functional magnetic resonance imaging phase synchronization as a measure of dynamic functional connectivity.

PubMed

Glerean, Enrico; Salmi, Juha; Lahnakoski, Juha M; Jääskeläinen, Iiro P; Sams, Mikko

2012-01-01

Functional brain activity and connectivity have been studied by calculating intersubject and seed-based correlations of hemodynamic data acquired with functional magnetic resonance imaging (fMRI). To inspect temporal dynamics, these correlation measures have been calculated over sliding time windows with necessary restrictions on the length of the temporal window that compromises the temporal resolution. Here, we show that it is possible to increase temporal resolution by using instantaneous phase synchronization (PS) as a measure of dynamic (time-varying) functional connectivity. We applied PS on an fMRI dataset obtained while 12 healthy volunteers watched a feature film. Narrow frequency band (0.04-0.07 Hz) was used in the PS analysis to avoid artifactual results. We defined three metrics for computing time-varying functional connectivity and time-varying intersubject reliability based on estimation of instantaneous PS across the subjects: (1) seed-based PS, (2) intersubject PS, and (3) intersubject seed-based PS. Our findings show that these PS-based metrics yield results consistent with both seed-based correlation and intersubject correlation methods when inspected over the whole time series, but provide an important advantage of maximal single-TR temporal resolution. These metrics can be applied both in studies with complex naturalistic stimuli (e.g., watching a movie or listening to music in the MRI scanner) and more controlled (e.g., event-related or blocked design) paradigms. A MATLAB toolbox FUNPSY ( http://becs.aalto.fi/bml/software.html ) is openly available for using these metrics in fMRI data analysis.

The relationship between executive functions and IQ in Korean children and the comparison with Chinese children.

PubMed

Song, Hyunjoo; Jinyu, An

2017-01-01

This study aimed to investigate the relationship between perceived/performance-based executive function and IQ. Additionally, the relationship between perceived executive function and intelligence was investigated cross-culturally between South Korea and China. Korean children (60; M = 34, F = 26, Mean age = 10.35) were included in study 1, and Korean children (43, M = 23, F = 20, Mean age = 10.05) and Chinese children (56; M = 29, F = 27, Mean age = 10.40) were included in study 2. The Korean-Wechsler Intelligence Scale for Children-IV, the Stroop test, the CTT-2, and the executive function questionnaire were used for Korean subjects, and the Raven's matrix test and the executive function questionnaire were used for Korean and Chinese subjects. Multiple regression showed that CTT-2(RT), emotional control difficulty, and Color Word within a 45' Stroop test trial were significant predictors of total IQ. The cross-cultural analysis showed a statistically significant difference between the two countries in the emotional control aspect of perceived executive function. There were no interactions between country and intelligence. In conclusion, intelligence was related to overall executive function. Korean children and Chinese children showed cultural differences in processing emotion. These results are expected to contribute to developing therapeutic strategies for executive function in children and to exchanging these strategies between Korea and China.

Protein domains of unknown function are essential in bacteria.

PubMed

Goodacre, Norman F; Gerloff, Dietlind L; Uetz, Peter

2013-12-31

More than 20% of all protein domains are currently annotated as "domains of unknown function" (DUFs). About 2,700 DUFs are found in bacteria compared with just over 1,500 in eukaryotes. Over 800 DUFs are shared between bacteria and eukaryotes, and about 300 of these are also present in archaea. A total of 2,786 bacterial Pfam domains even occur in animals, including 320 DUFs. Evolutionary conservation suggests that many of these DUFs are important. Here we show that 355 essential proteins in 16 model bacterial species contain 238 DUFs, most of which represent single-domain proteins, clearly establishing the biological essentiality of DUFs. We suggest that experimental research should focus on conserved and essential DUFs (eDUFs) for functional analysis given their important function and wide taxonomic distribution, including bacterial pathogens. The functional units of proteins are domains. Typically, each domain has a distinct structure and function. Genomes encode thousands of domains, and many of the domains have no known function (domains of unknown function [DUFs]). They are often ignored as of little relevance, given that many of them are found in only a few genomes. Here we show that many DUFs are essential DUFs (eDUFs) based on their presence in essential proteins. We also show that eDUFs are often essential even if they are found in relatively few genomes. However, in general, more common DUFs are more often essential than rare DUFs.

The joint return period analysis of natural disasters based on monitoring and statistical modeling of multidimensional hazard factors.

PubMed

Liu, Xueqin; Li, Ning; Yuan, Shuai; Xu, Ning; Shi, Wenqin; Chen, Weibin

2015-12-15

As a random event, a natural disaster has the complex occurrence mechanism. The comprehensive analysis of multiple hazard factors is important in disaster risk assessment. In order to improve the accuracy of risk analysis and forecasting, the formation mechanism of a disaster should be considered in the analysis and calculation of multi-factors. Based on the consideration of the importance and deficiencies of multivariate analysis of dust storm disasters, 91 severe dust storm disasters in Inner Mongolia from 1990 to 2013 were selected as study cases in the paper. Main hazard factors from 500-hPa atmospheric circulation system, near-surface meteorological system, and underlying surface conditions were selected to simulate and calculate the multidimensional joint return periods. After comparing the simulation results with actual dust storm events in 54years, we found that the two-dimensional Frank Copula function showed the better fitting results at the lower tail of hazard factors and that three-dimensional Frank Copula function displayed the better fitting results at the middle and upper tails of hazard factors. However, for dust storm disasters with the short return period, three-dimensional joint return period simulation shows no obvious advantage. If the return period is longer than 10years, it shows significant advantages in extreme value fitting. Therefore, we suggest the multivariate analysis method may be adopted in forecasting and risk analysis of serious disasters with the longer return period, such as earthquake and tsunami. Furthermore, the exploration of this method laid the foundation for the prediction and warning of other nature disasters. Copyright © 2015 Elsevier B.V. All rights reserved.

The analysis of thin walled composite laminated helicopter rotor with hierarchical warping functions and finite element method

NASA Astrophysics Data System (ADS)

Zhu, Dechao; Deng, Zhongmin; Wang, Xingwei

2001-08-01

In the present paper, a series of hierarchical warping functions is developed to analyze the static and dynamic problems of thin walled composite laminated helicopter rotors composed of several layers with single closed cell. This method is the development and extension of the traditional constrained warping theory of thin walled metallic beams, which had been proved very successful since 1940s. The warping distribution along the perimeter of each layer is expanded into a series of successively corrective warping functions with the traditional warping function caused by free torsion or free bending as the first term, and is assumed to be piecewise linear along the thickness direction of layers. The governing equations are derived based upon the variational principle of minimum potential energy for static analysis and Rayleigh Quotient for free vibration analysis. Then the hierarchical finite element method is introduced to form a numerical algorithm. Both static and natural vibration problems of sample box beams are analyzed with the present method to show the main mechanical behavior of the thin walled composite laminated helicopter rotor.

Prediction of functional profiles of gut microbiota from 16S rRNA metagenomic data provides a more robust evaluation of gut dysbiosis occurring in Japanese type 2 diabetic patients.

PubMed

Inoue, Ryo; Ohue-Kitano, Ryuji; Tsukahara, Takamitsu; Tanaka, Masashi; Masuda, Shinya; Inoue, Takayuki; Yamakage, Hajime; Kusakabe, Toru; Hasegawa, Koji; Shimatsu, Akira; Satoh-Asahara, Noriko

2017-11-01

We assessed whether gut microbial functional profiles predicted from 16S rRNA metagenomics differed in Japanese type 2 diabetic patients. A total of 22 Japanese subjects were recruited from our outpatient clinic in an observational study. Fecal samples were obtained from 12 control and 10 type 2 diabetic subjects. 16S rRNA metagenomic data were generated and functional profiles predicted using "Phylogenetic Investigation of Communities by Reconstruction of Unobserved States" software. We measured the parameters of glucose metabolism, gut bacterial taxonomy and functional profile, and examined the associations in a cross-sectional manner. Eleven of 288 "Kyoto Encyclopedia of Genes and Genomes" pathways were significantly enriched in diabetic patients compared with control subjects ( p <0.05, q<0.1). The relative abundance of almost all pathways, including the Insulin signaling pathway and Glycolysis/Gluconeogenesis , showed strong, positive correlations with hemoglobin A 1c (HbA 1c ) and fasting plasma glucose (FPG) levels. Bacterial taxonomic analysis showed that genus Blautia significantly differed between groups and had negative correlations with HbA 1c and FPG levels. Our findings suggest a novel pathophysiological relationship between gut microbial communities and diabetes, further highlighting the significance and utility of combining prediction of functional profiles with ordinal bacterial taxonomic analysis (UMIN Clinical Trails Registry number: UMIN000026592).

Numerical evaluation of longitudinal motions of Wigley hulls advancing in waves by using Bessho form translating-pulsating source Green'S function

NASA Astrophysics Data System (ADS)

Xiao, Wenbin; Dong, Wencai

2016-06-01

In the framework of 3D potential flow theory, Bessho form translating-pulsating source Green's function in frequency domain is chosen as the integral kernel in this study and hybrid source-and-dipole distribution model of the boundary element method is applied to directly solve the velocity potential for advancing ship in regular waves. Numerical characteristics of the Green function show that the contribution of local-flow components to velocity potential is concentrated at the nearby source point area and the wave component dominates the magnitude of velocity potential in the far field. Two kinds of mathematical models, with or without local-flow components taken into account, are adopted to numerically calculate the longitudinal motions of Wigley hulls, which demonstrates the applicability of translating-pulsating source Green's function method for various ship forms. In addition, the mesh analysis of discrete surface is carried out from the perspective of ship-form characteristics. The study shows that the longitudinal motion results by the simplified model are somewhat greater than the experimental data in the resonant zone, and the model can be used as an effective tool to predict ship seakeeping properties. However, translating-pulsating source Green function method is only appropriate for the qualitative analysis of motion response in waves if the ship geometrical shape fails to satisfy the slender-body assumption.

Structure-based Markov random field model for representing evolutionary constraints on functional sites.

PubMed

Jeong, Chan-Seok; Kim, Dongsup

2016-02-24

Elucidating the cooperative mechanism of interconnected residues is an important component toward understanding the biological function of a protein. Coevolution analysis has been developed to model the coevolutionary information reflecting structural and functional constraints. Recently, several methods have been developed based on a probabilistic graphical model called the Markov random field (MRF), which have led to significant improvements for coevolution analysis; however, thus far, the performance of these models has mainly been assessed by focusing on the aspect of protein structure. In this study, we built an MRF model whose graphical topology is determined by the residue proximity in the protein structure, and derived a novel positional coevolution estimate utilizing the node weight of the MRF model. This structure-based MRF method was evaluated for three data sets, each of which annotates catalytic site, allosteric site, and comprehensively determined functional site information. We demonstrate that the structure-based MRF architecture can encode the evolutionary information associated with biological function. Furthermore, we show that the node weight can more accurately represent positional coevolution information compared to the edge weight. Lastly, we demonstrate that the structure-based MRF model can be reliably built with only a few aligned sequences in linear time. The results show that adoption of a structure-based architecture could be an acceptable approximation for coevolution modeling with efficient computation complexity.

GeoChip 3.0 as a high-thoughput tool for analyzing microbial community composition, structure, and functional activity

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

He, Z.; Deng, Y.; Van Nostrand, J.D.

A new generation of functional gene arrays (FGAs; GeoChip 3.0) has been developed, with {approx}28,000 probes covering approximately 57,000 gene variants from 292 functional gene families involved in carbon, nitrogen, phosphorus and sulfur cycles, energy metabolism, antibiotic resistance, metal resistance and organic contaminant degradation. GeoChip 3.0 also has several other distinct features, such as a common oligo reference standard (CORS) for data normalization and comparison, a software package for data management and future updating and the gyrB gene for phylogenetic analysis. Computational evaluation of probe specificity indicated that all designed probes would have a high specificity to their corresponding targets.more » Experimental analysis with synthesized oligonucleotides and genomic DNAs showed that only 0.0036-0.025% false-positive rates were observed, suggesting that the designed probes are highly specific under the experimental conditions examined. In addition, GeoChip 3.0 was applied to analyze soil microbial communities in a multifactor grassland ecosystem in Minnesota, USA, which showed that the structure, composition and potential activity of soil microbial communities significantly changed with the plant species diversity. As expected, GeoChip 3.0 is a high-throughput powerful tool for studying microbial community functional structure, and linking microbial communities to ecosystem processes and functioning.« less

MDAS: an integrated system for metabonomic data analysis.

PubMed

Liu, Juan; Li, Bo; Xiong, Jiang-Hui

2009-03-01

Metabonomics, the latest 'omics' research field, shows great promise as a tool in biomarker discovery, drug efficacy and toxicity analysis, disease diagnosis and prognosis. One of the major challenges now facing researchers is how to process this data to yield useful information about a biological system, e.g., the mechanism of diseases. Traditional methods employed in metabonomic data analysis use multivariate analysis methods developed independently in chemometrics research. Additionally, with the development of machine learning approaches, some methods such as SVMs also show promise for use in metabonomic data analysis. Aside from the application of general multivariate analysis and machine learning methods to this problem, there is also a need for an integrated tool customized for metabonomic data analysis which can be easily used by biologists to reveal interesting patterns in metabonomic data.In this paper, we present a novel software tool MDAS (Metabonomic Data Analysis System) for metabonomic data analysis which integrates traditional chemometrics methods and newly introduced machine learning approaches. MDAS contains a suite of functional models for metabonomic data analysis and optimizes the flow of data analysis. Several file formats can be accepted as input. The input data can be optionally preprocessed and can then be processed with operations such as feature analysis and dimensionality reduction. The data with reduced dimensionalities can be used for training or testing through machine learning models. The system supplies proper visualization for data preprocessing, feature analysis, and classification which can be a powerful function for users to extract knowledge from the data. MDAS is an integrated platform for metabonomic data analysis, which transforms a complex analysis procedure into a more formalized and simplified one. The software package can be obtained from the authors.

Genetic deletion of the EGFR ligand epigen does not affect mouse embryonic development and tissue homeostasis.

PubMed

Dahlhoff, Maik; Schäfer, Matthias; Wolf, Eckhard; Schneider, Marlon R

2013-02-15

The epidermal growth factor receptor (EGFR) is a tyrosine kinase receptor with manifold functions during development, tissue homeostasis and disease. EGFR activation, the formation of homodimers or heterodimers (with the related ERBB2-4 receptors) and downstream signaling is initiated by the binding of a family of structurally related growth factors, the EGFR ligands. Genetic deletion experiments clarified the biological function of all family members except for the last characterized ligand, epigen. We employed gene targeting in mouse embryonic stem cells to generate mice lacking epigen expression. Loss of epigen did not affect mouse development, fertility, or organ physiology. Quantitative RT-PCR analysis revealed increased expression of betacellulin and EGF in a few organs of epigen-deficient mice, suggesting a functional compensation by these ligands. In conclusion, we completed the genetic analysis of EGFR ligands and show that epigen has non-essential functions or functions that can be compensated by other EGFR ligands during growth and tissue homeostasis. Copyright © 2012 Elsevier Inc. All rights reserved.

Influence of the fiber from agro-industrial co-products as functional food ingredient on the acceptance, neophobia and sensory characteristics of cooked sausages.

PubMed

Díaz-Vela, Juan; Totosaus, Alfonso; Escalona-Buendía, Héctor B; Pérez-Chabela, M Lourdes

2017-02-01

The sensory analysis of new products is essential for subsequent acceptance by consumers, moreover in the functional food market. The acceptance and food neophobia of cooked sausages formulated with cactus pear fiber or pineapple pear fiber, as functional ingredient, was complemented with a sensory characterization by R-index and qualitative descriptive analysis (QDA). Female consumers aged between 40 and 50 years showed greater interest in the consumption of healthy foods, with a higher level of food neophobia towards pineapple fiber sausages. R-index for taste was higher in pineapple fiber samples. Cactus pear fiber samples presented higher R-index score for texture. In QDA, color, sweet, astringent and bitter flavors, pork meat smell and a firm and plastic texture were significant, with a good relationship (38%) between the evaluated attributes. Sensory attributes are important on the acceptance and neophobia of functional foods like cooked sausages with fruit peel fiber as functional ingredient.

Analysis of the Underlying Cognitive Activity in the Resolution of a Task on Derivability of the Absolute-Value Function: Two Theoretical Perspectives

ERIC Educational Resources Information Center

Pino-Fan, Luis R.; Guzmán, Ismenia; Font, Vicenç; Duval, Raymond

2017-01-01

This paper presents a study of networking of theories between the theory of registers of semiotic representation (TRSR) and the onto-semiotic approach of mathematical cognition and instruction (OSA). The results obtained show complementarities between these two theoretical perspectives, which might allow more detailed analysis of the students'…

Girls' Doll Play in Educational, Virtual, Ideological and Market Contexts: A Case Analysis of Controversy

ERIC Educational Resources Information Center

Reifel, Stuart

2009-01-01

The purpose of this study was to explore an example of girls' doll play in contemporary US culture, including its virtual, political, marketing, and other contextual meanings. The narrative that provoked the analysis was a brief news report about a controversial school function--a school fund-raiser fashion show featuring American Girl doll…