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Data Analysis and Causal Loops

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https://www.readbyqxmd.com/read/29119508/endogenous-molecular-cellular-network-cancer-theory-a-systems-biology-approach
#1
Gaowei Wang, Ruoshi Yuan, Xiaomei Zhu, Ping Ao
In light of ever apparent limitation of the current dominant cancer mutation theory, a quantitative hypothesis for cancer genesis and progression, endogenous molecular-cellular network hypothesis has been proposed from the systems biology perspective, now for more than 10 years. It was intended to include both the genetic and epigenetic causes to understand cancer. Its development enters the stage of meaningful interaction with experimental and clinical data and the limitation of the traditional cancer mutation theory becomes more evident...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29049594/the-perceptual-dimensions-of-natural-dynamic-flow
#2
Yaniv Morgenstern, Daniel J Kersten
We measured perceptual judgments of category, material attributes, affordances, and similarity to investigate the perceptual dimensions underlying the visual representation of a broad class of natural dynamic flows (sea waves, smoke, and windblown foliage). The dynamic flows were looped 3-s movies windowed with circular apertures of two sizes to manipulate the level of spatial context. In low levels of spatial context (smaller apertures), human observers' judgments of material attributes and affordances were inaccurate, with estimates biased toward assumptions that the flows resulted from objects that were rigid, "pick-up-able," and not penetrable...
October 1, 2017: Journal of Vision
https://www.readbyqxmd.com/read/29017541/cardiovascular-flukes-trematoda-spirorchiidae-in-caretta-caretta-linnaeus-1758-from-the-mediterranean-sea
#3
Erica Marchiori, Enrico Negrisolo, Rudi Cassini, Luisa Garofalo, Lisa Poppi, Cinzia Tessarin, Federica Marcer
BACKGROUND: The northern Adriatic Sea represents one of the most important neritic foraging grounds for the loggerhead sea turtle Caretta caretta L. in the Mediterranean Sea. Four genera of blood flukes with variable prevalence and pathogenic impact have been reported worldwide in this species. Hapalotrema Looss, 1899 and Amphiorchis Price, 1934 are the only two genera reported in Mediterranean waters; however, updated data describing spirorchiidiasis in the central and eastern Mediterranean and infection prevalence are still lacking...
October 10, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28198522/cardiovascular-drug-utilization-post-implant-is-related-to-clinical-outcome-in-heart-failure-patients-receiving-cardiac-resynchronization-therapy
#4
Zoltan Bakos, Christian Reitan, Anna Werther-Evaldsson, Anders Roijer, Pyotr PLatonov, Rasmus Borgquist
BACKGROUND: In select patients with heart failure, cardiac resynchronization therapy (CRT) is the most common complementary treatment besides medical treatment. We aimed to assess the association between post CRT-implant changes in cardiovascular medication and cardiovascular mortality and heart failure hospitalization. METHODS: 211 patients on optimal medical therapy eligible for CRT were retrospectively included in this study (72 ± 7 years, 80% male, 66% left bundle branch block [LBBB], 48% dilated cardiomyopathy [DCMP]) and investigated at baseline and after 6 months ...
February 15, 2017: Cardiology Journal
https://www.readbyqxmd.com/read/27881959/effective-connectivity-within-the-mesocorticolimbic-system-during-resting-state-in-cocaine-users
#5
Suchismita Ray, Xin Di, Bharat B Biswal
Objective: Although effective connectivity between brain regions has been examined in cocaine users during tasks, no effective connectivity study has been conducted on cocaine users during resting-state. In the present functional magnetic resonance imaging study, we examined effective connectivity in resting-brain, between the brain regions within the mesocorticolimbic dopamine system, implicated in reward and motivated behavior, while the chronic cocaine users and controls took part in a resting-state scan by using a spectral Dynamic causal modeling (spDCM) approach...
2016: Frontiers in Human Neuroscience
https://www.readbyqxmd.com/read/27177618/understanding-the-dynamics-of-the-seguro-popular-de-salud-policy-implementation-in-mexico-from-a-complex-adaptive-systems-perspective
#6
Gustavo Nigenda, Luz María González-Robledo, Clara Juárez-Ramírez, Taghreed Adam
BACKGROUND: In 2003, Mexico's Seguro Popular de Salud (SPS), was launched as an innovative financial mechanism implemented to channel new funds to provide health insurance to 50 million Mexicans and to reduce systemic financial inequities. The objective of this article is to understand the complexity and dynamics that contributed to the adaptation of the policy in the implementation stage, how these changes occurred, and why, from a complex and adaptive systems perspective. METHODS: A complex adaptive systems (CAS) framework was used to carry out a secondary analysis of data obtained from four SPS's implementation evaluations...
May 13, 2016: Implementation Science: IS
https://www.readbyqxmd.com/read/26898941/refined-mapping-of-autoimmune-disease-associated-genetic-variants-with-gene-expression-suggests-an-important-role-for-non-coding-rnas
#7
Isis Ricaño-Ponce, Daria V Zhernakova, Patrick Deelen, Oscar Luo, Xingwang Li, Aaron Isaacs, Juha Karjalainen, Jennifer Di Tommaso, Zuzanna Agnieszka Borek, Maria M Zorro, Javier Gutierrez-Achury, Andre G Uitterlinden, Albert Hofman, Joyce van Meurs, Mihai G Netea, Iris H Jonkers, Sebo Withoff, Cornelia M van Duijn, Yang Li, Yijun Ruan, Lude Franke, Cisca Wijmenga, Vinod Kumar
Genome-wide association and fine-mapping studies in 14 autoimmune diseases (AID) have implicated more than 250 loci in one or more of these diseases. As more than 90% of AID-associated SNPs are intergenic or intronic, pinpointing the causal genes is challenging. We performed a systematic analysis to link 460 SNPs that are associated with 14 AID to causal genes using transcriptomic data from 629 blood samples. We were able to link 71 (39%) of the AID-SNPs to two or more nearby genes, providing evidence that for part of the AID loci multiple causal genes exist...
April 2016: Journal of Autoimmunity
https://www.readbyqxmd.com/read/26526319/bidirectional-relationship-between-sleep-and-optimism-with-depressive-mood-as-a-mediator-a-longitudinal-study-of-chinese-working-adults
#8
Esther Yuet Ying Lau, C Harry Hui, Shu-Fai Cheung, Jasmine Lam
OBJECTIVE: Sleep and optimism are important psycho-biological and personality constructs, respectively. However, very little work has examined the causal relationship between them, and none has examined the potential mechanisms operating in the relationship. This study aimed to understand whether sleep quality was a cause or an effect of optimism, and whether depressive mood could explain the relationship. METHOD: Internet survey data were collected from 987 Chinese working adults (63...
November 2015: Journal of Psychosomatic Research
https://www.readbyqxmd.com/read/26216142/studying-common-pool-resources-over-time-a-longitudinal-case-study-of-the-buen-hombre-fishery-in-the-dominican-republic
#9
Margaret Wilson, Tyler Pavlowich, Michael Cox
Like many small-scale fishing communities around the world, the community of Buen Hombre in the Dominican Republic is dealing with a set of challenges to reconcile its fishing activities with the ecology on which it depends. Also like many such communities, this case has been examined at a particular period in time by a group of social scientists, but not over substantial lengths of time in order to examine the longitudinal validity of the conclusions made during this period. In this paper we combine data from previous anthropological work with our own primary social and ecological data to conduct a longitudinal case study of the Buen Hombre fishery...
March 2016: Ambio
https://www.readbyqxmd.com/read/25947190/-model-for-unplanned-self-extubation-of-icu-patients-using-system-dynamics-approach
#10
Yu Gil Song, Eun Kyoung Yun
PURPOSE: In this study a system dynamics methodology was used to identify correlation and nonlinear feedback structure among factors affecting unplanned extubation (UE) of ICU patients and to construct and verify a simulation model. METHODS: Factors affecting UE were identified through a theoretical background established by reviewing literature and preceding studies and referencing various statistical data. Related variables were decided through verification of content validity by an expert group...
April 2015: Journal of Korean Academy of Nursing
https://www.readbyqxmd.com/read/25644253/id-helix-loop-helix-proteins-as-determinants-of-cell-survival-in-b-cell-chronic-lymphocytic-leukemia-cells-in-vitro
#11
Sarah Weiler, Jolaolu A Ademokun, John D Norton
BACKGROUND: Members of the inhibitor of DNA-binding (ID) family of helix-loop-helix proteins have been causally implicated in the pathogenesis of several types of B-cell lineage malignancy, either on the basis of mutation or by altered expression. B-cell chronic lymphocytic leukemia encompasses a heterogeneous group of disorders and is the commonest leukaemia type in the Western world. In this study, we have investigated the pathobiological functions of the ID2 and ID3 proteins in this disease with an emphasis on their role in regulating leukemic cell death/survival...
2015: Molecular Cancer
https://www.readbyqxmd.com/read/25523122/-path-causal-analysis-of-a-model-of-a-functional-organization-between-defense-mechanisms-and-coping-strategies
#12
B Gouvernet, J Mouchard, S Combaluzier
BACKGROUND: In the psychological literature, two concepts are often used to approach psychological and social adaptation: defense mechanisms and coping strategies. Many empirical studies deal with these strategies independently of each other. However, the nature of their relationship is still debated, making empirical studies necessary jointly evaluating these two types of strategies to better reflect the adaptive process. OBJECTIVE: To test Chabrol and Callahan's theoretical model of the relationship between defence mechanisms and coping strategies...
October 2015: L'Encéphale
https://www.readbyqxmd.com/read/25495206/gene-network-inference-using-continuous-time-bayesian-networks-a-comparative-study-and-application-to-th17-cell-differentiation
#13
Enzo Acerbi, Teresa Zelante, Vipin Narang, Fabio Stella
BACKGROUND: Dynamic aspects of gene regulatory networks are typically investigated by measuring system variables at multiple time points. Current state-of-the-art computational approaches for reconstructing gene networks directly build on such data, making a strong assumption that the system evolves in a synchronous fashion at fixed points in time. However, nowadays omics data are being generated with increasing time course granularity. Thus, modellers now have the possibility to represent the system as evolving in continuous time and to improve the models' expressiveness...
2014: BMC Bioinformatics
https://www.readbyqxmd.com/read/25298419/transethnic-replication-of-association-of-ctg18-1-repeat-expansion-of-tcf4-gene-with-fuchs-corneal-dystrophy-in-chinese-implies-common-causal-variant
#14
MULTICENTER STUDY
Chao Xing, Xin Gong, Imran Hussain, Chiea-Chuen Khor, Donald T H Tan, Tin Aung, Jodhbir S Mehta, Eranga N Vithana, V Vinod Mootha
PURPOSE: To test the association between the CTG18.1 trinucleotide repeat expansion of TCF4 gene and Fuchs' endothelial corneal dystrophy (FECD) in a Chinese population. METHODS: The trinucleotide repeat polymorphism CTG18.1 was genotyped using short tandem repeat and triplet repeat primed polymerase chain reaction assays in 57 Chinese subjects with FECD and 121 controls. Statistical association of the expanded CTG18.1 allele and 18 single nucleotide polymorphisms (SNPs) across TCF4 with FECD was evaluated...
November 2014: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/25104047/advancing-the-application-of-systems-thinking-in-health-understanding-the-dynamics-of-neonatal-mortality-in-uganda
#15
Agnes Semwanga Rwashana, Sarah Nakubulwa, Margaret Nakakeeto-Kijjambu, Taghreed Adam
BACKGROUND: Of the three million newborns that die each year, Uganda ranks fifth highest in neonatal mortality rates, with 43,000 neonatal deaths each year. Despite child survival and safe motherhood programmes towards reducing child mortality, insufficient attention has been given to this critical first month of life. There is urgent need to innovatively employ alternative solutions that take into account the intricate complexities of neonatal health and the health systems. In this paper, we set out to empirically contribute to understanding the causes of the stagnating neonatal mortality by applying a systems thinking approach to explore the dynamics arising from the neonatal health complexity and non-linearity and its interplay with health systems factors, using Uganda as a case study...
August 8, 2014: Health Research Policy and Systems
https://www.readbyqxmd.com/read/25096303/advancing-the-application-of-systems-thinking-in-health-provider-payment-and-service-supply-behaviour-and-incentives-in-the-ghana-national-health-insurance-scheme-a-systems-approach
#16
Irene A Agyepong, Geneieve C Aryeetey, Justice Nonvignon, Francis Asenso-Boadi, Helen Dzikunu, Edward Antwi, Daniel Ankrah, Charles Adjei-Acquah, Reuben Esena, Moses Aikins, Daniel K Arhinful
BACKGROUND: Assuring equitable universal access to essential health services without exposure to undue financial hardship requires adequate resource mobilization, efficient use of resources, and attention to quality and responsiveness of services. The way providers are paid is a critical part of this process because it can create incentives and patterns of behaviour related to supply. The objective of this work was to describe provider behaviour related to supply of health services to insured clients in Ghana and the influence of provider payment methods on incentives and behaviour...
2014: Health Research Policy and Systems
https://www.readbyqxmd.com/read/25083013/a-novel-bhlhe41-variant-is-associated-with-short-sleep-and-resistance-to-sleep-deprivation-in-humans
#17
Renata Pellegrino, Ibrahim Halil Kavakli, Namni Goel, Christopher J Cardinale, David F Dinges, Samuel T Kuna, Greg Maislin, Hans P A Van Dongen, Sergio Tufik, John B Hogenesch, Hakon Hakonarson, Allan I Pack
STUDY OBJECTIVES: Earlier work described a mutation in DEC2 also known as BHLHE41 (basic helix-loophelix family member e41) as causal in a family of short sleepers, who needed just 6 h sleep per night. We evaluated whether there were other variants of this gene in two well-phenotyped cohorts. DESIGN: Sequencing of the BHLHE41 gene, electroencephalographic data, and delta power analysis and functional studies using cell-based luciferase. RESULTS: We identified new variants of the BHLHE41 gene in two cohorts who had either acute sleep deprivation (n = 200) or chronic partial sleep deprivation (n = 217)...
2014: Sleep
https://www.readbyqxmd.com/read/24935521/advancing-the-application-of-systems-thinking-in-health-realist-evaluation-of-the-leadership-development-programme-for-district-manager-decision-making-in-ghana
#18
Aku Kwamie, Han van Dijk, Irene Akua Agyepong
BACKGROUND: Although there is widespread agreement that strong district manager decision-making improves health systems, understanding about how the design and implementation of capacity-strengthening interventions work is limited. The Ghana Health Service has adopted the Leadership Development Programme (LDP) as one intervention to support the development of management and leadership within district teams. This paper seeks to address how and why the LDP 'works' when it is introduced into a district health system in Ghana, and whether or not it supports systems thinking in district teams...
2014: Health Research Policy and Systems
https://www.readbyqxmd.com/read/24675868/rare-variants-detection-with-kernel-machine-learning-based-on-likelihood-ratio-test
#19
Ping Zeng, Yang Zhao, Liwei Zhang, Shuiping Huang, Feng Chen
This paper mainly utilizes likelihood-based tests to detect rare variants associated with a continuous phenotype under the framework of kernel machine learning. Both the likelihood ratio test (LRT) and the restricted likelihood ratio test (ReLRT) are investigated. The relationship between the kernel machine learning and the mixed effects model is discussed. By using the eigenvalue representation of LRT and ReLRT, their exact finite sample distributions are obtained in a simulation manner. Numerical studies are performed to evaluate the performance of the proposed approaches under the contexts of standard mixed effects model and kernel machine learning...
2014: PloS One
https://www.readbyqxmd.com/read/24566670/resting-state-functional-mri-in-parkinson-s-disease-the-impact-of-deep-brain-stimulation-on-effective-connectivity
#20
Joshua Kahan, Maren Urner, Rosalyn Moran, Guillaume Flandin, Andre Marreiros, Laura Mancini, Mark White, John Thornton, Tarek Yousry, Ludvic Zrinzo, Marwan Hariz, Patricia Limousin, Karl Friston, Tom Foltynie
Depleted of dopamine, the dynamics of the parkinsonian brain impact on both 'action' and 'resting' motor behaviour. Deep brain stimulation has become an established means of managing these symptoms, although its mechanisms of action remain unclear. Non-invasive characterizations of induced brain responses, and the effective connectivity underlying them, generally appeals to dynamic causal modelling of neuroimaging data. When the brain is at rest, however, this sort of characterization has been limited to correlations (functional connectivity)...
April 2014: Brain: a Journal of Neurology
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