scholarly journals Identification of consistent functional genetic modules

2016 ◽  
Vol 15 (1) ◽  
pp. 1-18 ◽  
Author(s):  
Jeffrey C. Miecznikowski ◽  
Daniel P. Gaile ◽  
Xiwei Chen ◽  
David L. Tritchler
Keyword(s):  
Functional Module ◽  
Biological Response ◽  
Superior Performance ◽  
Outcome Variable ◽  
Functional Networks ◽  
Transcription Regulatory Network ◽  
Pathway Discovery ◽  
Discovery Method ◽  
Network Consistency ◽  
Expression Module

AbstractIt is often of scientific interest to find a set of genes that may represent an independent functional module or network, such as a functional gene expression module causing a biological response, a transcription regulatory network, or a constellation of mutations jointly causing a disease. In this paper we are specifically interested in identifying modules that control a particular outcome variable such as a disease biomarker. We discuss the statistical properties that functional networks should possess and introduce the concept of network consistency which should be satisfied by real functional networks of cooperating genes, and directly use the concept in the pathway discovery method we present. Our method gives superior performance for all but the simplest functional networks.

scholarly journals Preparation of phospholipid-based polycarbonate urethanes for potential applications of blood-contacting implants

2020 ◽  
Vol 7 (5) ◽  
pp. 491-504
Author(s):  
Peichuang Li ◽  
Wanhao Cai ◽  
Xin Li ◽  
Kebing Wang ◽  
Lei Zhou ◽  
...  
Keyword(s):  
Microphase Separation ◽  
Blood Compatibility ◽  
Ex Vivo ◽  
Raw Materials ◽  
Direct Synthesis ◽  
Animal Experiments ◽  
Biological Response ◽  
Superior Performance ◽  
Scanning Calorimetry

Abstract Polyurethanes are widely used in interventional devices due to the excellent physicochemical property. However, non-specific adhesion and severe inflammatory response of ordinary polyurethanes may lead to severe complications of intravenous devices. Herein, a novel phospholipid-based polycarbonate urethanes (PCUs) were developed via two-step solution polymerization by direct synthesis based on functional raw materials. Furthermore, PCUs were coated on biomedical metal sheets to construct biomimetic anti-fouling surface. The results of stress–strain curves exhibited excellent tensile properties of PCUs films. Differential scanning calorimetry results indicated that the microphase separation of such PCUs polymers could be well regulated by adjusting the formulation of chain extender, leading to different biological response. In vitro blood compatibility tests including bovine serum albumin adsorption, fibrinogen adsorption and denaturation, platelet adhesion and whole-blood experiment showed superior performance in inhibition non-specific adhesion of PCUs samples. Endothelial cells and smooth muscle cells culture tests further revealed a good anti-cell adhesion ability. Finally, animal experiments including ex vivo blood circulation and subcutaneous inflammation animal experiments indicated a strong ability in anti-thrombosis and histocompatibility. These results high light the strong anti-adhesion property of phospholipid-based PCUs films, which may be applied to the blood-contacting implants such as intravenous catheter or antithrombotic surface in the future.

scholarly journals Balanced Functional Module Detection in Genomic Data

2020 ◽  
Author(s):  
David Tritchler ◽  
Lorin M Towle-Miller ◽  
Jeffrey C Miecznikowski
Keyword(s):  
Graphical Models ◽  
Functional Module ◽  
Genomic Data ◽  
The Cancer Genome Atlas ◽  
Internal Conflict ◽  
Detection Methods ◽  
Outcome Variable ◽  
Functional Modules ◽  
Module Detection ◽  
Multiple Variables

AbstractHigh dimensional genomic data can be analyzed to understand the effects of multiple variables on a target variable such as a clinical outcome, risk factor or diagnosis. Of special interest are functional modules, cooperating sets of variables affecting the target. Graphical models of various types are often useful for characterizing such networks of variables. In other applications such as social networks, the concept of balance in undirected signed graphs characterizes the consistency of associations within the network. To extend this concept to applications where a set of predictor variables influences an outcome variable, we define balance for functional modules. This property specifies that the module variables have a joint effect on the target outcome with no internal conflict, an efficiency that evolution may use for selection in biological networks. We show that for this class of graphs, observed correlations directly reflect paths in the underlying graph. Consequences of the balance property are exploited to implement a new module discovery algorithm, bFMD, which selects a subset of variables from highdimensional data that compose a balanced functional module. Our bFMD algorithm performed favorably in simulations as compared to other module detection methods that do not consider balance properties. Additionally, bFMD detected interpretable results in a real application for RNA-seq data obtained from The Cancer Genome Atlas (TCGA) for Uterine Corpus Endometrial Carcinoma using the percentage of tumor invasion as the target outcome of interest. bFMD detects sparse sets of variables within highdimensional datasets such that interpretability may be favorable as compared to other similar methods by leveraging balance properties used in other graphical applications.

scholarly journals SPABBATS: A pathway-discovery method based on Boolean satisfiability that facilitates the characterization of suppressor mutants

2011 ◽  
Vol 5 (1) ◽  
pp. 5 ◽  
Author(s):  
Lope A Flórez ◽  
Katrin Gunka ◽  
Rafael Polanía ◽  
Stefan Tholen ◽  
Jörg Stülke
Keyword(s):  
Boolean Satisfiability ◽  
Suppressor Mutants ◽  
Pathway Discovery ◽  
Discovery Method

In situ TEM Studies of agglomeration of sub-nanometer Ru layers in Ru/C multilayers

1992 ◽  
Vol 50 (1) ◽  
pp. 256-257
Author(s):  
Tai D. Nguyen ◽  
Ronald Gronsky ◽  
Jeffrey B. Kortright
Keyword(s):  
Layered Structure ◽  
Driving Force ◽  
High Energy ◽  
Superior Performance ◽  
In Situ Tem ◽  
Rayleigh Instability ◽  
Practical Applications ◽  
Transmission Electron ◽  
Diffraction Patterns

Nanometer period Ru/C multilayers are one of the prime candidates for normal incident reflecting mirrors at wavelengths < 10 nm. Superior performance, which requires uniform layers and smooth interfaces, and high stability of the layered structure under thermal loadings are some of the demands in practical applications. Previous studies however show that the Ru layers in the 2 nm period Ru/C multilayer agglomerate upon moderate annealing, and the layered structure is no longer retained. This agglomeration and crystallization of the Ru layers upon annealing to form almost spherical crystallites is a result of the reduction of surface or interfacial energy from die amorphous high energy non-equilibrium state of the as-prepared sample dirough diffusive arrangements of the atoms. Proposed models for mechanism of thin film agglomeration include one analogous to Rayleigh instability, and grain boundary grooving in polycrystalline films. These models however are not necessarily appropriate to explain for the agglomeration in the sub-nanometer amorphous Ru layers in Ru/C multilayers. The Ru-C phase diagram shows a wide miscible gap, which indicates the preference of phase separation between these two materials and provides an additional driving force for agglomeration. In this paper, we study the evolution of the microstructures and layered structure via in-situ Transmission Electron Microscopy (TEM), and attempt to determine the order of occurence of agglomeration and crystallization in the Ru layers by observing the diffraction patterns.

Reliability of the Minimum Masking Level as Outcome Variable in Tinnitus Clinical Research

2020 ◽  
Vol 29 (3) ◽  
pp. 429-435
Author(s):  
Patricia C. Mancini ◽  
Richard S. Tyler ◽  
Hyung Jin Jun ◽  
Tang-Chuan Wang ◽  
Helena Ji ◽  
...  
Keyword(s):  
Standard Deviation ◽  
High Frequency ◽  
Pearson Correlation ◽  
Correlation Coefficients ◽  
Outcome Variable ◽  
Reliable Estimate ◽  
Moderate Correlation ◽  
Trained Subjects ◽  
The Relationship ◽  
Minimum Intensity

Purpose The minimum masking level (MML) is the minimum intensity of a stimulus required to just totally mask the tinnitus. Treatments aimed at reducing the tinnitus itself should attempt to measure the magnitude of the tinnitus. The objective of this study was to evaluate the reliability of the MML. Method Sample consisted of 59 tinnitus patients who reported stable tinnitus. We obtained MML measures on two visits, separated by about 2–3 weeks. We used two noise types: speech-shaped noise and high-frequency emphasis noise. We also investigated the relationship between the MML and tinnitus loudness estimates and the Tinnitus Handicap Questionnaire (THQ). Results There were differences across the different noise types. The within-session standard deviation averaged across subjects varied between 1.3 and 1.8 dB. Across the two sessions, the Pearson correlation coefficients, range was r = .84. There was a weak relationship between the dB SL MML and loudness, and between the MML and the THQ. A moderate correlation ( r = .44) was found between the THQ and loudness estimates. Conclusions We conclude that the dB SL MML can be a reliable estimate of tinnitus magnitude, with expected standard deviations in trained subjects of about 1.5 dB. It appears that the dB SL MML and loudness estimates are not closely related.

Functional Anatomy of Intensity Aspects of Attention

2003 ◽  
Vol 14 (3) ◽  
pp. 181-190 ◽  
Author(s):  
Walter Sturm
Keyword(s):  
Right Hemisphere ◽  
Functional Anatomy ◽  
Fmri Data ◽  
Functional Networks ◽  
Top Down ◽  
Stimulus Modality ◽  
Spatial Orienting ◽  
Phasic Alertness ◽  
Co Activation ◽  
Attention System

Abstract: Behavioral and PET/fMRI-data are presented to delineate the functional networks subserving alertness, sustained attention, and vigilance as different aspects of attention intensity. The data suggest that a mostly right-hemisphere frontal, parietal, thalamic, and brainstem network plays an important role in the regulation of attention intensity, irrespective of stimulus modality. Under conditions of phasic alertness there is less right frontal activation reflecting a diminished need for top-down regulation with phasic extrinsic stimulation. Furthermore, a high overlap between the functional networks for alerting and spatial orienting of attention is demonstrated. These findings support the hypothesis of a co-activation of the posterior attention system involved in spatial orienting by the anterior alerting network. Possible implications of these findings for the therapy of neglect are proposed.

Bidirectional Associations Between Self-Perceptions of Aging and Processing Speed Across 3 Years

GeroPsych ◽  
2017 ◽  
Vol 30 (2) ◽  
pp. 49-59 ◽  
Author(s):  
Anna L. Seidler ◽  
Julia K. Wolff
Keyword(s):  
Processing Speed ◽  
Personal Growth ◽  
Significant Loss ◽  
Path Model ◽  
Outcome Variable ◽  
Beneficial Effects ◽  
Self Perceptions ◽  
Chi Squared ◽  
Perceptions Of Aging ◽  
Bidirectional Associations

Abstract. Background: Previous studies point to a potential relationship between self-perceptions of aging (SPA) and cognitive performance. However, most of these studies are limited by their experimental design. Previous longitudinal studies looked solely at memory as an outcome variable without examining the directionality of effects. The present study examines the direction of effects between two domains of SPA (personal growth and physical losses) and processing speed (PS). Methods: The sample consists of 8,198 participants of the German Ageing Survey (DEAS), aged between 40 and 93 years. A cross-lagged path model was estimated to examine directions of relationships across 3 years via chi-squared difference tests for each domain of SPA. Results: In the unconstrained models, the effect of SPA domain personal growth in 2008 on PS in 2011 and vice versa were marginally significant. For SPA domain physical losses, the effect of SPA on PS was significant, whereas the other direction of the effect did not reach significance. However, the cross-lagged paths of both domains of SPA on PS and vice versa could be set equal without a significant loss of model fit. The resulting associations indicate a significant bidirectional relationship between both domains of SPA and PS. Discussion and conclusion: This study provides initial evidence that SPA can influence trajectories of cognitive decline and vice versa. The results emphasize the detrimental and beneficial effects that stereotypes can have on individuals and add further evidence to the theory of stereotype embodiment.

Cognitive Health Counseling 40+

2013 ◽  
Vol 21 (1) ◽  
pp. 24-33 ◽  
Author(s):  
Anne Eschen ◽  
Franzisca Zehnder ◽  
Mike Martin
Keyword(s):  
Outcome Variable ◽  
Pilot Phase ◽  
Subjective Memory ◽  
Cognitive Health ◽  
Health Counseling ◽  
Agents Of Change ◽  
Main Outcome Variable ◽  
Further Development

This article introduces Cognitive Health Counseling 40+ (CH.CO40+), an individualized intervention that is conceptually based on the orchestration model of quality-of-life management ( Martin & Kliegel, 2010 ) and aims at improving satisfaction with cognitive health in adults aged 40 years and older. We describe the theoretically deduced characteristics of CH.CO40+, its target group, its multifactorial nature, its individualization, the application of subjective and objective measures, the role of participants as agents of change, and the rationale for choosing participants’ satisfaction with their cognitive health as main outcome variable. A pilot phase with 15 middle-aged and six older adults suggests that CH.CO40+ attracts, and may be particularly suitable for, subjective memory complainers. Implications of the pilot data for the further development of the intervention are discussed.

Risk Factors and Mediators of Suicidal Ideation Among Korean Adolescents

Crisis ◽  
2018 ◽  
Vol 39 (1) ◽  
pp. 4-12 ◽  
Author(s):  
Yi Jin Kim ◽  
Sung Seek Moon ◽  
Jang Hyun Lee ◽  
Joon Kyung Kim
Keyword(s):  
High School Students ◽  
Suicidal Ideation ◽  
Structural Equation ◽  
Equation Modeling ◽  
Outcome Variable ◽  
Suicidal Behaviors ◽  
Thwarted Belongingness ◽  
Perceived Burdensomeness ◽  
Korean Adolescents ◽  
Related Stress

Abstract. Background: A significant number of Korean adolescents have suicidal ideations and it is more prevalent among adolescents than any other age group in Korea. Aims: This study was conducted to attain a better understanding of the contributing factors to suicidal ideation among Korean adolescents. Method: We recruited 569 high school students in Grades 10 and 11 in Pyeongtaek, Korea. The Beck Scale for Suicidal Ideation was used to measure suicidal ideation as the outcome variable. The Interpersonal Needs Questionnaire, the Beck Hopelessness Scale, the School Related Stress Scale, the Olweus Bully/Victim Questionnaire, and the Youth Risk Behavior Surveillance questions were used to measure thwarted belongingness and perceived burdensomeness, hopelessness, school-related stress, bullying, and previous suicidal behaviors, respectively. Data analyses included descriptive statistics and structural equation modeling. Results: The findings suggest that perceived burdensomeness, hopelessness, school-related stress, and previous suicidal behaviors have significant direct effects on suicidal ideation. Hopelessness fully mediated the relation between thwarted belongingness and suicidal ideation, and partially mediated between perceived burdensomeness, school-related stress, and suicidal ideation. Conclusion: These findings provide more specific directions for a multidimensional suicide prevention program in order to be successful in reducing suicide rates among Korean adolescents.

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