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Causal inference

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https://www.readbyqxmd.com/read/28319694/sexual-trauma-is-more-strongly-associated-with-tonic-immobility-than-other-types-of-trauma-a-population-based-study
#1
Juliana Kalaf, Evandro Silva Freire Coutinho, Liliane Maria Pereira Vilete, Mariana Pires Luz, William Berger, Mauro Mendlowicz, Eliane Volchan, Sergio Baxter Andreoli, Maria Inês Quintana, Jair de Jesus Mari, Ivan Figueira
BACKGROUND: Tonic immobility is an involuntary motor and vocal inhibition reaction, considered the last-ditch response of the defensive cascade model. It is elicited in context of inescapable threat and perception of entrapment. Our aim was to investigate the association between different traumatic events and peritraumatic tonic immobility (PTI) in a representative sample of the general population. METHODS: This is a cross-sectional study of general population from Rio de Janeiro and São Paulo with 3231 victims of traumatic events aged 15-75 years who completed the Tonic Immobility Scale (TIS)...
March 7, 2017: Journal of Affective Disorders
https://www.readbyqxmd.com/read/28317296/how-to-make-more-out-of-community-data-a-conceptual-framework-and-its-implementation-as-models-and-software
#2
Otso Ovaskainen, Gleb Tikhonov, Anna Norberg, F Guillaume Blanchet, Leo Duan, David Dunson, Tomas Roslin, Nerea Abrego
Community ecology aims to understand what factors determine the assembly and dynamics of species assemblages at different spatiotemporal scales. To facilitate the integration between conceptual and statistical approaches in community ecology, we propose Hierarchical Modelling of Species Communities (HMSC) as a general, flexible framework for modern analysis of community data. While non-manipulative data allow for only correlative and not causal inference, this framework facilitates the formulation of data-driven hypotheses regarding the processes that structure communities...
March 20, 2017: Ecology Letters
https://www.readbyqxmd.com/read/28301504/identification-of-marginal-causal-relationships-in-gene-networks-from-observational-and-interventional-expression-data
#3
Gilles Monneret, Florence Jaffrézic, Andrea Rau, Tatiana Zerjal, Grégory Nuel
Causal network inference is an important methodological challenge in biology as well as other areas of application. Although several causal network inference methods have been proposed in recent years, they are typically applicable for only a small number of genes, due to the large number of parameters to be estimated and the limited number of biological replicates available. In this work, we consider the specific case of transcriptomic studies made up of both observational and interventional data in which a single gene of biological interest is knocked out...
2017: PloS One
https://www.readbyqxmd.com/read/28291617/blood-pressure-before-initiation-of-maintenance-dialysis-and-subsequent-mortality
#4
Keiichi Sumida, Miklos Z Molnar, Praveen K Potukuchi, Fridtjof Thomas, Jun Ling Lu, Vanessa A Ravel, Melissa Soohoo, Connie M Rhee, Elani Streja, John J Sim, Kunihiro Yamagata, Kamyar Kalantar-Zadeh, Csaba P Kovesdy
BACKGROUND: Mortality is extremely high immediately after the transition to dialysis therapy, but the association of blood pressure (BP) before dialysis therapy initiation with mortality after dialysis therapy initiation remains unknown. STUDY DESIGN: Observational study. SETTING & PARTICIPANTS: 17,729 US veterans transitioning to dialysis therapy in October 2007 to September 2011, with a median follow-up of 2.0 years. PREDICTOR: Systolic (SBP) and diastolic BP (DBP) averaged over the last 1-year predialysis transition period as 6 (<120 to ≥160mmHg in 10-mmHg increments) and 5 (<60 to ≥90mmHg in 10-mmHg increments) categories, respectively, and as continuous measures...
March 10, 2017: American Journal of Kidney Diseases: the Official Journal of the National Kidney Foundation
https://www.readbyqxmd.com/read/28288803/the-relationship-of-approach-avoidance-motivation-and-asymmetric-frontal-cortical-activity-a-review-of-studies-manipulating-frontal-asymmetry
#5
Nicholas J Kelley, Ruud Hortensius, Dennis J L G Schutter, Eddie Harmon-Jones
The balance between activity in the left and right frontal cortex, commonly referred to as asymmetric frontal cortical activity, has served as a proxy for an organism's motivational direction (i.e., approach vs. avoidance). Many studies have examined the influence of the manipulation of motivational direction on asymmetrical frontal cortical activity and found results consistent with the idea that greater relative left (right) frontal cortical activity is associated with approach (avoidance) motivation. We critically review literature employing physical (versus psychological) manipulations of frontal asymmetry using a variety of methodologies including neurofeedback training, muscular contractions, and non-invasive brain stimulation...
March 10, 2017: International Journal of Psychophysiology
https://www.readbyqxmd.com/read/28285768/dynamic-role-of-trans-regulation-of-gene-expression-in-relation-to-complex-traits
#6
Chen Yao, Roby Joehanes, Andrew D Johnson, Tianxiao Huan, Chunyu Liu, Jane E Freedman, Peter J Munson, David E Hill, Marc Vidal, Daniel Levy
Identifying causal genetic variants and understanding their mechanisms of effect on traits remains a challenge in genome-wide association studies (GWASs). In particular, how genetic variants (i.e., trans-eQTLs) affect expression of remote genes (i.e., trans-eGenes) remains unknown. We hypothesized that some trans-eQTLs regulate expression of distant genes by altering the expression of nearby genes (cis-eGenes). Using published GWAS datasets with 39,165 single-nucleotide polymorphisms (SNPs) associated with 1,960 traits, we explored whole blood gene expression associations of trait-associated SNPs in 5,257 individuals from the Framingham Heart Study...
March 8, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28282955/parental-supply-of-alcohol-in-childhood-and-risky-drinking-in-adolescence-systematic-review-and-meta-analysis
#7
REVIEW
Sonia Sharmin, Kypros Kypri, Masuma Khanam, Monika Wadolowski, Raimondo Bruno, Richard P Mattick
Whether parental supply of alcohol affects the likelihood of later adolescent risky drinking remains unclear. We conducted a systematic review and meta-analysis to synthesize findings from longitudinal studies investigating this association. We searched eight electronic databases up to 10 September 2016 for relevant terms and included only original English language peer-reviewed journal articles with a prospective design. Two reviewers independently screened articles, extracted data and assessed risk of bias...
March 9, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28279349/navigating-the-neural-space-in-search-of-the-neural-code
#8
REVIEW
Mehrdad Jazayeri, Arash Afraz
The advent of powerful perturbation tools, such as optogenetics, has created new frontiers for probing causal dependencies in neural and behavioral states. These approaches have significantly enhanced the ability to characterize the contribution of different cells and circuits to neural function in health and disease. They have shifted the emphasis of research toward causal interrogations and increased the demand for more precise and powerful tools to control and manipulate neural activity. Here, we clarify the conditions under which measurements and perturbations support causal inferences...
March 8, 2017: Neuron
https://www.readbyqxmd.com/read/28273693/outcome-adaptive-lasso-variable-selection-for-causal-inference
#9
Susan M Shortreed, Ashkan Ertefaie
Methodological advancements, including propensity score methods, have resulted in improved unbiased estimation of treatment effects from observational data. Traditionally, a "throw in the kitchen sink" approach has been used to select covariates for inclusion into the propensity score, but recent work shows including unnecessary covariates can impact both the bias and statistical efficiency of propensity score estimators. In particular, the inclusion of covariates that impact exposure but not the outcome, can inflate standard errors without improving bias, while the inclusion of covariates associated with the outcome but unrelated to exposure can improve precision...
March 8, 2017: Biometrics
https://www.readbyqxmd.com/read/28269454/prediction-of-oral-cancer-recurrence-using-dynamic-bayesian-networks
#10
Konstantina Kourou, George Rigas, Konstantinos P Exarchos, Costas Papaloukas, Dimitrios I Fotiadis
We propose a methodology for predicting oral cancer recurrence using Dynamic Bayesian Networks. The methodology takes into consideration time series gene expression data collected at the follow-up study of patients that had or had not suffered a disease relapse. Based on that knowledge, our aim is to infer the corresponding dynamic Bayesian networks and subsequently conjecture about the causal relationships among genes within the same time-slice and between consecutive time-slices. Moreover, the proposed methodology aims to (i) assess the prognosis of patients regarding oral cancer recurrence and at the same time, (ii) provide important information about the underlying biological processes of the disease...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28265119/evidence-for-neuroplastic-compensation-in-the-cerebral-cortex-of-persons-with-depressive-illness
#11
R Bansal, D J Hellerstein, B S Peterson
We yoked anatomical brain magnetic resonance imaging to a randomized, double-blind, placebo-controlled trial (RCT) of antidepressant medication for 10-week's duration in patients with dysthymia. The RCT study design mitigated ascertainment bias by randomizing patients to receive either duloxetine or placebo, and it supported true causal inferences about treatment effects on the brain by controlling treatment assignment experimentally. We acquired 121 anatomical scans: at baseline and end point in 41 patients and once in 39 healthy controls...
March 7, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28263941/assessing-hospital-performance-after-percutaneous-coronary-intervention-using-big-data
#12
Jacob V Spertus, Sharon-Lise T Normand, Robert Wolf, Matt Cioffi, Ann Lovett, Sherri Rose
BACKGROUND: Although risk adjustment remains a cornerstone for comparing outcomes across hospitals, optimal strategies continue to evolve in the presence of many confounders. We compared conventional regression-based model to approaches particularly suited to leveraging big data. METHODS AND RESULTS: We assessed hospital all-cause 30-day excess mortality risk among 8952 adults undergoing percutaneous coronary intervention between October 1, 2011, and September 30, 2012, in 24 Massachusetts hospitals using clinical registry data linked with billing data...
November 2016: Circulation. Cardiovascular Quality and Outcomes
https://www.readbyqxmd.com/read/28259780/regression-dcm-for-fmri
#13
Stefan Frässle, Ekaterina I Lomakina, Adeel Razi, Karl J Friston, Joachim M Buhmann, Klaas E Stephan
The development of large-scale network models that infer the effective (directed) connectivity among neuronal populations from neuroimaging data represents a key challenge for computational neuroscience. Dynamic causal models (DCMs) of neuroimaging and electrophysiological data are frequently used for inferring effective connectivity but are presently restricted to small graphs (typically up to 10 regions) in order to keep model inversion computationally feasible. Here, we present a novel variant of DCM for functional magnetic resonance imaging (fMRI) data that is suited to assess effective connectivity in large (whole-brain) networks...
March 1, 2017: NeuroImage
https://www.readbyqxmd.com/read/28255761/a-causal-and-mediation-analysis-of-the-comorbidity-between-attention-deficit-hyperactivity-disorder-adhd-and-autism-spectrum-disorder-asd
#14
Elena Sokolova, Anoek M Oerlemans, Nanda N Rommelse, Perry Groot, Catharina A Hartman, Jeffrey C Glennon, Tom Claassen, Tom Heskes, Jan K Buitelaar
Autism spectrum disorder (ASD) and Attention-deficit/hyperactivity disorder (ADHD) are often comorbid. The purpose of this study is to explore the relationships between ASD and ADHD symptoms by applying causal modeling. We used a large phenotypic data set of 417 children with ASD and/or ADHD, 562 affected and unaffected siblings, and 414 controls, to infer a structural equation model using a causal discovery algorithm. Three distinct pathways between ASD and ADHD were identified: (1) from impulsivity to difficulties with understanding social information, (2) from hyperactivity to stereotypic, repetitive behavior, (3) a pairwise pathway between inattention, difficulties with understanding social information, and verbal IQ...
March 2, 2017: Journal of Autism and Developmental Disorders
https://www.readbyqxmd.com/read/28255294/multilevel-pharmacokinetics-driven-modeling-of-metabolomics-data
#15
Emilia Daghir-Wojtkowiak, Paweł Wiczling, Małgorzata Waszczuk-Jankowska, Roman Kaliszan, Michał Jan Markuszewski
INTRODUCTION: Multilevel modeling is a quantitative statistical method to investigate variability and relationships between variables of interest, taking into account population structure and dependencies. It can be used for prediction, data reduction and causal inference from experiments and observational studies allowing for more efficient elucidation of knowledge. OBJECTIVES: In this study we introduced the concept of multilevel pharmacokinetics (PK)-driven modelling for large-sample, unbalanced and unadjusted metabolomics data comprising nucleoside and creatinine concentration measurements in urine of healthy and cancer patients...
2017: Metabolomics: Official Journal of the Metabolomic Society
https://www.readbyqxmd.com/read/28251646/introduction-to-the-special-section-advances-in-psychological-prevention-and-treatment-interventions-to-promote-children-s-mental-health
#16
Abigail H Gewirtz, Adriana Youssef
This paper introduces the Special Section on Advances in Psychological Prevention and Treatment Interventions to Promote Children's Mental Health. The three articles in the Special Section provide perspectives on the adaptation, evaluation, and implementation of evidence-based psychological interventions for children in countries in Northern and Eastern Europe, and Latin America. The articles highlight disparate methodologies for the examination of intervention data, including addressing causal inference in the absence of availability of true experiment data (i...
April 2017: International Journal of Psychology: Journal International de Psychologie
https://www.readbyqxmd.com/read/28251576/-cognitive-impairments-accompanying-the-burnout-syndrome-a-review
#17
REVIEW
Karin Riedrich, Elisabeth M Weiss, Nina Dalkner, Eva Reininghaus, Ilona Papousek, Andreas Schwerdtfeger, Helmut K Lackner, Bernd Reininghaus
BACKGROUND: The rising prevalence of the burnout syndrome has increasingly moved it into the focus of scientific interest. In addition to emotional exhaustion and depersonalization, particularly reduced personal accomplishment has strong societal and economic effects. In recent years reduced personal accomplishment has increasingly been linked to cognitive impairment. However, up to now only a few studies have objectively assessed cognitive deficits in burnout patients. This article gives an overview of 16 studies which examined cognitive abilities in burnout patients...
March 2017: Neuropsychiatrie: Klinik, Diagnostik, Therapie und Rehabilitation
https://www.readbyqxmd.com/read/28249733/moving-research-beyond-the-spanking-debate
#18
Harriet L MacMillan, Christopher R Mikton
Despite numerous studies identifying a broad range of harms associated with the use of spanking and other types of physical punishment, debate continues about its use as a form of discipline. In this commentary, we recommend four strategies to move the field forward and beyond the spanking debate including: 1) use of methodological approaches that allow for stronger causal inference; 2) consideration of human rights issues; 3) a focus on understanding the causes of spanking and reasons for its decline in certain countries; and 4) more emphasis on evidence-based approaches to changing social norms to reject spanking as a form of discipline...
February 26, 2017: Child Abuse & Neglect
https://www.readbyqxmd.com/read/28245736/digital-flexor-musculotendinous-contracture-in-two-devon-rex-cats
#19
Leonie K Thom, Roy R Pool, Richard Malik
Clinical summary: A 13-year-old, spayed Devon Rex with unilateral digital flexor musculotendinous contracture of the forelimb was treated by surgical tenotomy. The condition improved transiently, but recurred rapidly and became bilateral. Histopathologic analysis of necropsy tissues resulted in a morphologic diagnosis of fibromyositis of the antebrachial muscles causing contracture and flexural deformity of the carpi and phalanges of both thoracic limbs. A search for similar cases yielded the clinical notes of a second cat, a 10-year-old, spayed Devon Rex, also with bilateral disease...
March 2017: Journal of Feline Medicine and Surgery
https://www.readbyqxmd.com/read/28243742/integrative-multi-omics-analysis-revealed-snp-lncrna-mrna-slm-networks-in-human-peripheral-blood-mononuclear-cells
#20
Wei Xia, Xiao-Wei Zhu, Xin-Bo Mo, Long-Fei Wu, Jian Wu, Yu-Fan Guo, Ke-Qin Zeng, Ming-Jun Wang, Xiang Lin, Ying-Hua Qiu, Lan Wang, Pei He, Fang-Fei Xie, Peng-Fei Bing, Xin Lu, Yao-Zhong Liu, Neng-Jun Yi, Fei-Yan Deng, Shu-Feng Lei
Long non-coding RNAs (lncRNAs) serve as important controller of cellular functions via regulating RNA transcription, degradation and translation. However, what are the regulation patterns of lncRNAs on downstream mRNA and how the upstream genetic variants regulate lncRNAs are largely unknown. We first performed a comprehensive expression quantitative trait locus (eQTL) analysis (MatrixeQTL package, R) using genome-wide lncRNA expression and SNP genotype data from human peripheral blood mononuclear cells (PBMCs) of 43 unrelated individuals...
April 2017: Human Genetics
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