214 results match your criteria pwm models

MOCCA: a flexible suite for modelling DNA sequence motif occurrence combinatorics.

BMC Bioinformatics 2021 May 7;22(1):234. Epub 2021 May 7.

Department of Biology, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany.

Background: Cis-regulatory elements (CREs) are DNA sequence segments that regulate gene expression. Among CREs are promoters, enhancers, Boundary Elements (BEs) and Polycomb Response Elements (PREs), all of which are enriched in specific sequence motifs that form particular occurrence landscapes. We have recently introduced a hierarchical machine learning approach (SVM-MOCCA) in which Support Vector Machines (SVMs) are applied on the level of individual motif occurrences, modelling local sequence composition, and then combined for the prediction of whole regulatory elements. Read More

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Comparing Theoretical Models for the Understanding of Health-Risk Behaviour: Towards an Integrative Model of Adolescent Alcohol Consumption.

Andrea Caputo

Eur J Psychol 2020 Aug 31;16(3):418-436. Epub 2020 Aug 31.

Department of Dynamic and Clinical Psychology, Sapienza University of Rome, Rome, Italy.

The aim of the present manuscript is to test and compare the theory of reasoned action (TRA), theory of planned behaviour (TPB) and prototype-willingness model (PWM) in predicting risky alcohol consumption among adolescents and to build an integrative model to get a more comprehensive understanding of such risky behaviour. A total sample of 518 adolescents (55% females; 13-19 aged) recruited from Italian schools (7th to 12th grade) participated in a cross-sectional research study and completed an online questionnaire. Risky alcohol use assessed through the AUDIT-C was the dependent variable; whereas, variables from the TRA, TPB, and PWM (i. Read More

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On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF.

NAR Genom Bioinform 2020 Sep 1;2(3):lqaa046. Epub 2020 Jul 1.

Structural Bioinformatics Lab (GRIB-IMIM), Department of Experimental and Health Science, University Pompeu Fabra, Barcelona, Catalonia 08005, Spain.

Cis2-His2 zinc finger (C2H2-ZF) proteins are the largest family of transcription factors in human and higher metazoans. To date, the DNA-binding preferences of many members of this family remain unknown. We have developed a computational method to predict their DNA-binding preferences. Read More

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September 2020

A modified modeling and dynamical behavior analysis method for fractional-order positive Luo converter.

PLoS One 2020 14;15(8):e0237169. Epub 2020 Aug 14.

State Key Laboratory of Electrical Insulation and Power Equipment, Xi'an Jiaotong University, Xi'an, Shannxi, China.

Compared to the integer-order modeling, the fractional-order modeling can achieve higher accuracy for designing and analyzing the DC-DC power converters. However, its applications in pulse width modulation (PWM) converters are limited due to the computational complexities. In this paper, a modified fractional-order modeling methodology for DC-DC converters is proposed, and its effectiveness is verified on the fractional-order positive Luo converters. Read More

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October 2020

iterb-PPse: Identification of transcriptional terminators in bacterial by incorporating nucleotide properties into PseKNC.

PLoS One 2020 15;15(5):e0228479. Epub 2020 May 15.

School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin, China.

Terminator is a DNA sequence that gives the RNA polymerase the transcriptional termination signal. Identifying terminators correctly can optimize the genome annotation, more importantly, it has considerable application value in disease diagnosis and therapies. However, accurate prediction methods are deficient and in urgent need. Read More

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Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study.

Genome Biol 2020 05 11;21(1):114. Epub 2020 May 11.

School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.

Background: Positional weight matrix (PWM) is a de facto standard model to describe transcription factor (TF) DNA binding specificities. PWMs inferred from in vivo or in vitro data are stored in many databases and used in a plethora of biological applications. This calls for comprehensive benchmarking of public PWM models with large experimental reference sets. Read More

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Regulatory mechanisms of major depressive disorder risk variants.

Mol Psychiatry 2020 09 25;25(9):1926-1945. Epub 2020 Mar 25.

Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.

Major depressive disorder (MDD) is one of the most prevalent psychiatric disorders and a leading cause of disability worldwide. Though recent genome-wide association studies (GWAS) have identified multiple risk variants for MDD, how these variants confer MDD risk remains largely unknown. Here we systematically characterize the regulatory mechanism of MDD risk variants using a functional genomics approach. Read More

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September 2020

Fault diagnosis for three-phase PWM rectifier based on deep feedforward network with transient synthetic features.

ISA Trans 2020 Jun 23;101:399-407. Epub 2020 Jan 23.

School of Electrical Engineering, Northeast Electric Power University, Jilin 132012, China. Electronic address:

Three-phase PWM rectifiers are adopted extensively in industry because of their excellent properties and potential advantages. However, while the IGBT has an open-circuit fault, the system does not crash suddenly, the performance will be reduced for instance voltages fluctuation and current harmonics. A fault diagnosis method based on deep feedforward network with transient synthetic features is proposed to reduce the dependence on the fault mathematical models in this paper, which mainly uses the transient phase current to train the deep feedforward network classifier. Read More

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iCrotoK-PseAAC: Identify lysine crotonylation sites by blending position relative statistical features according to the Chou's 5-step rule.

PLoS One 2019 21;14(11):e0223993. Epub 2019 Nov 21.

Department of Computer Science, School of Systems and Technology, University of Management and Technology, Lahore, Pakistan.

Among different post-translational modifications (PTMs), one of the most important one is the lysine crotonylation in proteins. Its importance cannot be undermined related to different diseases and essential biological practice. The key step for finding the hidden mechanisms of crotonylation along with their occurrence sites is to completely apprehend the mechanism behind this biological process. Read More

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Examining the ecological validity of the prototype willingness model for adolescent and young adult alcohol use.

Psychol Addict Behav 2020 Mar 21;34(2):293-302. Epub 2019 Nov 21.

Department of Psychiatry and Behavioral Sciences.

The present study is the first ecologically valid, daily level test of the prototype willingness model (PWM), a model previously tested with hypothetical scenarios to investigate the social reaction and reasoned pathways toward engaging in health-risk behavior. The purpose of the present study is to examine whether days with elevated alcohol-favorable PWM cognitions are also associated with greater intentions and willingness to drink and increased drinking behavior on that day. Participants included 15-25-year-olds ( = 124; 57. Read More

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Predicting Future Academic Willingness, Intentions, and Nonmedical Prescription Stimulant (NPS) Use with the Theory of Reasoned Action and Prototype/Willingness Model.

Subst Use Misuse 2019 30;54(14):2251-2263. Epub 2019 Jul 30.

Department of Psychology, The George Washington University, Washington, DC, USA.

Nonmedical prescription stimulant (NPS) use for academic reasons (e.g., to improve concentration) is a growing problem among college students. Read More

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Predictive models of protease specificity based on quantitative protease-activity profiling data.

Biochim Biophys Acta Proteins Proteom 2019 11 19;1867(11):140253. Epub 2019 Jul 19.

A.A.Kharkevich Institute of Information Transmission Problems, Moscow 127051, Russia; Skolkovo Institute of Science and Technology, Moscow 121205, Russia; Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow 117997, Russia. Electronic address:

Bioinformatics-based prediction of protease substrates can help to elucidate regulatory proteolytic pathways that control a broad range of biological processes such as apoptosis and blood coagulation. The majority of published predictive models are position weight matrices (PWM) reflecting specificity of proteases toward target sequence. These models are typically derived from experimental data on positions of hydrolyzed peptide bonds and show a reasonable predictive power. Read More

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November 2019

Exploring the application of the Prototype Willingness Model to weight loss dieting behaviour among UK adults.

Psychol Health Med 2019 10 27;24(9):1075-1089. Epub 2019 May 27.

a Department of Psychology, Faculty of Health and Life Sciences , Oxford Brookes University , Oxford , UK.

Frequent weight loss dieting leads to increased BMI and is associated with eating pathologies. Theoretical models can aid the development of interventions to reduce risk behaviours such as frequent dieting if they are able to adequately account for the target behaviour. The Prototype Willingness Model (PWM) may be able to account for weight loss dieting as this behaviour is often associated with social images. Read More

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October 2019

QBiC-Pred: quantitative predictions of transcription factor binding changes due to sequence variants.

Nucleic Acids Res 2019 07;47(W1):W127-W135

Department of Computer Science, Duke University, Durham, NC 27708, USA.

Non-coding genetic variants/mutations can play functional roles in the cell by disrupting regulatory interactions between transcription factors (TFs) and their genomic target sites. For most human TFs, a myriad of DNA-binding models are available and could be used to predict the effects of DNA mutations on TF binding. However, information on the quality of these models is scarce, making it hard to evaluate the statistical significance of predicted binding changes. Read More

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Analysis, modeling, control and operation of an interleaved three-port boost converter for DMPPT systems including PV and storage at module level.

Heliyon 2019 Mar 21;5(3):e01402. Epub 2019 Mar 21.

Bio Electro and Mechanical Systems (BEAMS) Department, Université Libre de Bruxelles, 50 Franklin Roosevelt Ave. (CP165/52), B-1050, Brussels, Belgium.

This paper presents the analysis, control and implementation of the interleaved three-port boost converter. The scope of this paper is the interfacing of photovoltaic systems that include storage. A new symmetrical PWM modulation strategy that prevents unwanted switching states without requiring external circuitry is presented. Read More

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Sambucus australis Modulates Inflammatory Response via Inhibition of Nuclear Factor Kappa B (NF-kB) in vitro.

An Acad Bras Cienc 2019 Mar 21;91(1):e20170831. Epub 2019 Mar 21.

Laboratório de Imunofarmacologia e Biologia Molecular, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Avenida Reitor Calmon, s/n, Vale do Canela, 41110-100 Salvador, BA, Brazil.

Medicinal plants have long been used as an alternative to traditional drugs for the treatment of inflammatory conditions due to the classical side effects and restricted access of various commercially available drugs, such as steroids (GCs) and nonsteroidal anti-inflammatory drugs (NSAIDs). Sambucus australis is a Brazilian herb that is commonly used to treat inflammatory diseases; however, few studies have examined the use of this species in the treatment of inflammatory conditions. The present study aims to evaluate the potential anti-inflammatory activity of S. Read More

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A magnetic resonance spectroscopy investigation in symptomatic former NFL players.

Brain Imaging Behav 2020 Oct;14(5):1419-1429

Center for Clinical Spectroscopy, Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, 4 Blackfan Street HIM-820, Boston, MA, 02115, USA.

The long-term neurologic consequences of exposure to repetitive head impacts (RHI) are not well understood. This study used magnetic resonance spectroscopy (MRS) to examine later-life neurochemistry and its association with RHI and clinical function in former National Football League (NFL) players. The sample included 77 symptomatic former NFL players and 23 asymptomatic individuals without a head trauma history. Read More

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October 2020

Socio-cognitive determinants of safe road-crossing behaviors: an application of the prototype willingness model.

J Inj Violence Res 2019 Jan 16;11(1):93-100. Epub 2019 Feb 16.

Research Center for Environmental Determinants of Health, Kermanshah University of Medical Sciences, Kermanshah, Iran.

Background: Pedestrians are one of the most vulnerable groups of road users that potentially are at risk for road traffic injuries and deaths. The present paper reports an application of the Prototype Willingness Model (PWM) to the prediction of road-crossing behaviors among students from Kermanshah University of Medical Sciences (KUMS) in the west of Iran.

Methods: This cross-sectional study was carried out among a sample of 315 medical students who were randomly selected from seven faculties of KUMS in 2017 according to their size, and who filled out a self-administered questionnaire containing a scenario depicting a potentially hazardous road-crossing behavior, followed by items measuring the PWM constructs. Read More

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January 2019

Functional genomics reveal gene regulatory mechanisms underlying schizophrenia risk.

Nat Commun 2019 02 8;10(1):670. Epub 2019 Feb 8.

Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.

Genome-wide association studies (GWASs) have identified over 180 independent schizophrenia risk loci. Nevertheless, how the risk variants in the reported loci confer schizophrenia susceptibility remains largely unknown. Here we systematically investigate the gene regulatory mechanisms underpinning schizophrenia risk through integrating data from functional genomics (including 30 ChIP-Seq experiments) and position weight matrix (PWM). Read More

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February 2019

Probing transcription factor combinatorics in different promoter classes and in enhancers.

BMC Genomics 2019 Feb 1;20(1):103. Epub 2019 Feb 1.

LIRMM, Univ. Montpellier, CNRS, Montpellier, France.

Background: In eukaryotic cells, transcription factors (TFs) are thought to act in a combinatorial way, by competing and collaborating to regulate common target genes. However, several questions remain regarding the conservation of these combinations among different gene classes, regulatory regions and cell types.

Results: We propose a new approach named TFcoop to infer the TF combinations involved in the binding of a target TF in a particular cell type. Read More

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February 2019

Model-based opti mization of phosphorus management strategies in Sur WWTP, Madrid.

Water Res 2019 04 19;153:39-52. Epub 2019 Jan 19.

Ceit and Tecnun (University of Navarra) Manuel de Lardizábal 15, 20018, San Sebastián, Spain. Electronic address:

Phosphorus has been considered as a pollutant to be removed from the wastewater. In the last years, however, it has been considered a valuable asset that needs to be recovered due to its shortage in nature. The study of optimum phosphorus management in wastewater treatment plants is not straightforward, due to the complexity of technologies and configurations that may be applied for phosphorus removal and recovery. Read More

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Similarity to prototypical heavy drinkers and non-drinkers predicts AUDIT-C and risky drinking in young adults: prospective study.

Emma L Davies

Psychol Health 2019 04 7;34(4):403-421. Epub 2019 Jan 7.

a Faculty of Health and Life Sciences , Oxford Brookes University , Oxford , United Kingdom.

Objective: The aim of the present study was to explore whether constructs within the Prototype Willingness Model (PWM) predicted risky drinking as measured by AUDIT-C, drinking harms and unplanned drunkenness in a sample of UK young adults. Previous studies exploring the PWM often do not use validated measures of alcohol consumption, and the outcomes of risky drinking are underexplored.

Design: An online prospective study design with 4 week follow-up was employed and 385 young adults completed the study (M age = 21. Read More

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Sodium arsenite exposure impairs B cell proliferation and enhances vascular inflammation in Plasmodium berghei mouse model.

Environ Toxicol Pharmacol 2019 Feb 16;66:7-13. Epub 2018 Dec 16.

Laboratory of Pharmacology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), Office of Higher Education Commission, Ministry of Education, Bangkok 10400, Thailand. Electronic address:

Arsenic exposure has been linked to an impaired immune response and inflammation. Our study investigated the effects of sodium arsenite on host immune response and vascular inflammation during malarial infection. Mice were divided into three groups: control (C), Plasmodium berghei infection (I) and sodium arsenite exposure with Plasmodium berghei infection (As-I). Read More

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February 2019

beRBP: binding estimation for human RNA-binding proteins.

Nucleic Acids Res 2019 03;47(5):e26

Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA.

Identifying binding targets of RNA-binding proteins (RBPs) can greatly facilitate our understanding of their functional mechanisms. Most computational methods employ machine learning to train classifiers on either RBP-specific targets or pooled RBP-RNA interactions. The former strategy is more powerful, but it only applies to a few RBPs with a large number of known targets; conversely, the latter strategy sacrifices prediction accuracy for a wider application, since specific interaction features are inevitably obscured through pooling heterogeneous datasets. Read More

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Functional regulatory mechanism of smooth muscle cell-restricted LMOD1 coronary artery disease locus.

PLoS Genet 2018 11 16;14(11):e1007755. Epub 2018 Nov 16.

Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America.

Recent genome-wide association studies (GWAS) have identified multiple new loci which appear to alter coronary artery disease (CAD) risk via arterial wall-specific mechanisms. One of the annotated genes encodes LMOD1 (Leiomodin 1), a member of the actin filament nucleator family that is highly enriched in smooth muscle-containing tissues such as the artery wall. However, it is still unknown whether LMOD1 is the causal gene at this locus and also how the associated variants alter LMOD1 expression/function and CAD risk. Read More

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November 2018

Quantifying Discretization Errors in Electrophoretically-Guided Micro Additive Manufacturing.

Micromachines (Basel) 2018 Sep 7;9(9). Epub 2018 Sep 7.

Materials Science and Engineering Department, Northwestern University, Evanston, IL 60208, USA.

This paper presents process models for a new micro additive manufacturing process termed Electrophoretically-guided Micro Additive Manufacturing (EPμAM). In EPμAM, a planar microelectrode array generates the electric potential distributions which cause colloidal particles to agglomerate and deposit in desired regions. The discrete microelectrode array nature and the used pulse width modulation (PWM) technique for microelectrode actuation create unavoidable process errors-space and time discretization errors-that distort particle trajectories. Read More

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September 2018

Anti-nerve growth factor monoclonal antibodies for the control of pain in dogs and cats.

Vet Rec 2019 Jan 27;184(1):23. Epub 2018 Oct 27.

Translational Research in Pain, Comparative Pain Research and Education Centre, Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA.

Nerve growth factor (NGF) is essential for the survival of sensory and sympathetic neurons during development. However, in the adult, NGF and its interaction with tropomyosin receptor kinase A receptor (TrkA) has been found to play a critical role in nociception and nervous system plasticity in pain conditions. Thus, various monoclonal antibody (mAb) therapies targeting this pathway have been investigated in the development of new pharmacotherapies for chronic pain. Read More

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January 2019

Perceived effectiveness of objective features of pictorial warning messages.

Tob Control 2019 08 25;28(e1):e24-e30. Epub 2018 Oct 25.

Annenberg School for Communication, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

Background: Previous research shows that pictorial warning messages (PWMs) for tobacco cigarettes increase quit attempts and smoking-related knowledge. However, few studies have investigated what specific features within PWMs are most effective. The current study sought to examine the specific features of PWMs associated with effectiveness using four outcome measures as indicators. Read More

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Phonological working memory in developmental stuttering: Potential insights from the neurobiology of language and cognition.

J Fluency Disord 2018 12 1;58:94-117. Epub 2018 Sep 1.

Idaho State University, 650 Memorial Dr. Bldg. 68, Pocatello, ID 83201, United States. Electronic address:

The current review examines how neurobiological models of language and cognition could shed light on the role of phonological working memory (PWM) in developmental stuttering (DS). Toward that aim, we review Baddeley's influential multicomponent model of PWM and evidence for load-dependent differences between children and adults who stutter and typically fluent speakers in nonword repetition and dual-task paradigms. We suggest that, while nonword repetition and dual-task findings implicate processes related to PWM, it is unclear from behavioral studies alone what mechanisms are involved. Read More

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December 2018

High effective time-dependent THz spectroscopy method for the detection and identification of substances with inhomogeneous surface.

PLoS One 2018 9;13(8):e0201297. Epub 2018 Aug 9.

Faculty of Computational Mathematics and Cybernetics, Lomonosov Moscow State University, Moscow, Russia.

We discuss an effective time-dependent THz spectroscopy method for the detection and identification of a substance with an inhomogeneous surface using a broadband THz signal reflected from the substance. We show that a successful and reliable identification can be made using the single long-duration THz signal, which contains not only the main reflected pulse, but also several sub-pulses. The method does not use averaging of the measured THz signals over the viewing angles and scanning over the surface area, which significantly increases the signal processing speed. Read More

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January 2019