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Causal inference

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https://www.readbyqxmd.com/read/28090665/can-patel-s-%C3%AF-accurately-estimate-directionality-of-connections-in-brain-networks-from-fmri
#1
Yunzhi Wang, Olivier David, Xiaoping Hu, Gopikrishna Deshpande
PURPOSE: Investigating directional interactions between brain regions plays a critical role in fully understanding brain function. Consequently, multiple methods have been developed for noninvasively inferring directional connectivity in human brain networks using functional MRI (fMRI). Recent simulations by Smith et al showed that Patel's τ, a method based on higher-order statistics, was the best approach for inferring directional interactions from fMRI. Because simulations make restrictive assumptions about reality, we set out to verify this finding using experimental fMRI data obtained from a three-region network in a rat model with electrophysiological validation...
January 16, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28089956/robust-causal-inference-using-directed-acyclic-graphs-the-r-package-dagitty
#2
Johannes Textor, Benito van der Zander, Mark S Gilthorpe, Maciej Liśkiewicz, George T H Ellison
Directed acyclic graphs (DAGs), which offer systematic representations of causal relationships, have become an established framework for the analysis of causal inference in epidemiology, often being used to determine covariate adjustment sets for minimizing confounding bias. DAGitty is a popular web application for drawing and analysing DAGs. Here we introduce the R package 'dagitty', which provides access to all of the capabilities of the DAGitty web application within the R platform for statistical computing, and also offers several new functions...
January 15, 2017: International Journal of Epidemiology
https://www.readbyqxmd.com/read/28088170/application-of-a-bayesian-dominance-model-improves-power-in-quantitative-trait-genome-wide-association-analysis
#3
Jörn Bennewitz, Christian Edel, Ruedi Fries, Theo H E Meuwissen, Robin Wellmann
BACKGROUND: Multi-marker methods, which fit all markers simultaneously, were originally tailored for genomic selection purposes, but have proven to be useful also in association analyses, especially the so-called BayesC Bayesian methods. In a recent study, BayesD extended BayesC towards accounting for dominance effects and improved prediction accuracy and persistence in genomic selection. The current study investigated the power and precision of BayesC and BayesD in genome-wide association studies by means of stochastic simulations and applied these methods to a dairy cattle dataset...
January 14, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28087598/bayesian-network-inference-modeling-identifies-trib1-as-a-novel-regulator-of-cell-cycle-progression-and-survival-in-cancer-cells
#4
Rina Gendelman, Heming Xing, Olga K Mirzoeva, Preeti Sarde, Christina Curtis, Heidi Feiler, Paul McDonagh, Joe W Gray, Iya Khalil, W Michael Korn
Molecular networks governing cellular responses to targeted therapies are complex dynamic systems with non-intuitive behaviors. Here we applied a novel computational strategy to infer probabilistic causal relationships between network components based on gene expression. We constructed a model comprised of an ensemble of networks using multidimensional data from cell line models of cell cycle arrest caused by inhibition of MEK1/2. Through simulation of reverse-engineered Bayesian network modeling, we generated predictions of G1-S transition...
January 13, 2017: Cancer Research
https://www.readbyqxmd.com/read/28081134/pain-a-statistical-account
#5
REVIEW
Abby Tabor, Michael A Thacker, G Lorimer Moseley, Konrad P Körding
Perception is seen as a process that utilises partial and noisy information to construct a coherent understanding of the world. Here we argue that the experience of pain is no different; it is based on incomplete, multimodal information, which is used to estimate potential bodily threat. We outline a Bayesian inference model, incorporating the key components of cue combination, causal inference, and temporal integration, which highlights the statistical problems in everyday perception. It is from this platform that we are able to review the pain literature, providing evidence from experimental, acute, and persistent phenomena to demonstrate the advantages of adopting a statistical account in pain...
January 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28079875/early-postnatal-illness-severity-scores-predict-neurodevelopmental-impairments-at-10-years-of-age-in-children-born-extremely-preterm
#6
J W Logan, O Dammann, E N Allred, C Dammann, K Beam, R M Joseph, T M O'Shea, A Leviton, K C K Kuban
OBJECTIVE: A neonatal illness severity score, The Score for Neonatal Acute Physiology-II (SNAP-II), predicts neurodevelopmental impairments at two years of age among children born extremely preterm. We sought to evaluate to what extent SNAP-II is predictive of cognitive and other neurodevelopmental impairments at 10 years of age. STUDY DESIGN: In a cohort of 874 children born before 28 weeks of gestation, we prospectively collected clinical, physiologic and laboratory data to calculate SNAP-II for each infant...
January 12, 2017: Journal of Perinatology: Official Journal of the California Perinatal Association
https://www.readbyqxmd.com/read/28077403/gene-co-expression-analysis-for-functional-classification-and-gene-disease-predictions
#7
Sipko van Dam, Urmo Võsa, Adriaan van der Graaf, Lude Franke, João Pedro de Magalhães
Gene co-expression networks can be used to associate genes of unknown function with biological processes, to prioritize candidate disease genes or to discern transcriptional regulatory programmes. With recent advances in transcriptomics and next-generation sequencing, co-expression networks constructed from RNA sequencing data also enable the inference of functions and disease associations for non-coding genes and splice variants. Although gene co-expression networks typically do not provide information about causality, emerging methods for differential co-expression analysis are enabling the identification of regulatory genes underlying various phenotypes...
January 10, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28077398/mild-traumatic-brain-injury-is-associated-with-reduced-cortical-thickness-in-those-at-risk-for-alzheimer-s-disease
#8
Jasmeet P Hayes, Mark W Logue, Naomi Sadeh, Jeffrey M Spielberg, Mieke Verfaellie, Scott M Hayes, Andrew Reagan, David H Salat, Erika J Wolf, Regina E McGlinchey, William P Milberg, Annjanette Stone, Steven A Schichman, Mark W Miller
Moderate-to-severe traumatic brain injury is one of the strongest environmental risk factors for the development of neurodegenerative diseases such as late-onset Alzheimer's disease, although it is unclear whether mild traumatic brain injury, or concussion, also confers risk. This study examined mild traumatic brain injury and genetic risk as predictors of reduced cortical thickness in brain regions previously associated with early Alzheimer's disease, and their relationship with episodic memory. Participants were 160 Iraq and Afghanistan War veterans between the ages of 19 and 58, many of whom carried mild traumatic brain injury and post-traumatic stress disorder diagnoses...
January 11, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/28076398/identification-of-a-novel-mutation-in-brd4-that-causes-autosomal-dominant-syndromic-congenital-cataracts-associated-with-other-neuro-skeletal-anomalies
#9
Hyun-Seok Jin, Jeonhyun Kim, Woori Kwak, Hyeonsoo Jeong, Gyu-Bin Lim, Cha Gon Lee
Congenital cataracts can occur as a non-syndromic isolated ocular disease or as a part of genetic syndromes accompanied by a multi-systemic disease. Approximately 50% of all congenital cataract cases have a heterogeneous genetic basis. Here, we describe three generations of a family with an autosomal dominant inheritance pattern and common complex phenotypes, including bilateral congenital cataracts, short stature, macrocephaly, and minor skeletal anomalies. We did not find any chromosomal aberrations or gene copy number abnormalities using conventional genetic tests; accordingly, we conducted whole-exome sequencing (WES) to identify disease-causing genetic alterations in this family...
2017: PloS One
https://www.readbyqxmd.com/read/28074569/screening-brief-intervention-and-referral-to-treatment-implications-of-samhsa-s-sbirt-initiative-for-substance-abuse-policy-and-practice
#10
Thomas F Babor, Frances Del Boca, Jeremy W Bray
AIMS: This paper describes the major findings and public health implications of a cross-site evaluation of a national Screening, Brief Intervention and Referral to Treatment (SBIRT) demonstration program funded by the US Substance Abuse and Mental Health Services Administration (SAMHSA). METHODS: Eleven multi-site programs in two cohorts of SAMHSA grant recipients were each funded for 5 years to promote the adoption and sustained implementation of SBIRT. The SBIRT cross-site evaluation used a multi-method evaluation design to provide comprehensive information on the processes, outcomes and costs of SBIRT as implemented in a variety of medical and community settings...
February 2017: Addiction
https://www.readbyqxmd.com/read/28072816/systematic-analysis-of-transcriptional-and-post-transcriptional-regulation-of-metabolism-in-yeast
#11
Emanuel Gonçalves, Zrinka Raguz Nakic, Mattia Zampieri, Omar Wagih, David Ochoa, Uwe Sauer, Pedro Beltrao, Julio Saez-Rodriguez
Cells react to extracellular perturbations with complex and intertwined responses. Systematic identification of the regulatory mechanisms that control these responses is still a challenge and requires tailored analyses integrating different types of molecular data. Here we acquired time-resolved metabolomics measurements in yeast under salt and pheromone stimulation and developed a machine learning approach to explore regulatory associations between metabolism and signal transduction. Existing phosphoproteomics measurements under the same conditions and kinase-substrate regulatory interactions were used to in silico estimate the enzymatic activity of signalling kinases...
January 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28064466/instrumental-variable-with-competing-risk-model
#12
Cheng Zheng, Ran Dai, Parameswaran N Hari, Mei-Jie Zhang
In this paper, we discuss causal inference on the efficacy of a treatment or medication on a time-to-event outcome with competing risks. Although the treatment group can be randomized, there can be confoundings between the compliance and the outcome. Unmeasured confoundings may exist even after adjustment for measured covariates. Instrumental variable methods are commonly used to yield consistent estimations of causal parameters in the presence of unmeasured confoundings. On the basis of a semiparametric additive hazard model for the subdistribution hazard, we propose an instrumental variable estimator to yield consistent estimation of efficacy in the presence of unmeasured confoundings for competing risk settings...
January 8, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/28062134/vascular-expansion-during-worsening-of-heart-failure-effects-on-clinical-features-and-its-determinants
#13
Hajime Kataoka
BACKGROUND: This study investigated the relation of the changes in serum solutes/albumin to the level of vascular expansion and clinical features during worsening HF. METHODS: Data from 47 patients with acute on chronic HF worsening were analyzed. Blood tests included hemoglobin, hematocrit, albumin, solutes (Na/K/Cl/BUN/Cr), and b-type natriuretic peptide (BNP). The relative change in the vascular expansion from stable to worsening HF was estimated based on changes in the plasma volume (%PV)...
December 27, 2016: International Journal of Cardiology
https://www.readbyqxmd.com/read/28060957/causal-inference-in-multisensory-heading-estimation
#14
Ksander N de Winkel, Mikhail Katliar, Heinrich H Bülthoff
A large body of research shows that the Central Nervous System (CNS) integrates multisensory information. However, this strategy should only apply to multisensory signals that have a common cause; independent signals should be segregated. Causal Inference (CI) models account for this notion. Surprisingly, previous findings suggested that visual and inertial cues on heading of self-motion are integrated regardless of discrepancy. We hypothesized that CI does occur, but that characteristics of the motion profiles affect multisensory processing...
2017: PloS One
https://www.readbyqxmd.com/read/28057833/cognitive-skills-and-the-evolution-of-social-systems
#15
REVIEW
Russell D Fernald
How do animal social skills influence evolution? Complex animal social behaviors require many cognitive skills including individual recognition and observational learning. For social systems to evolve, these abilities need to be transmitted genetically or culturally and supported by the evolution of underlying neural systems. Because animal skill sets are so varied, it seems best to describe animal cognitive behaviors as being a social calculus that can change with experience, which has evolved to match and facilitate the complexity of the social system where it arose...
January 1, 2017: Journal of Experimental Biology
https://www.readbyqxmd.com/read/28057396/inverse-reasoning-processes-in-obsessive-compulsive-disorder
#16
Shiu F Wong, Jessica R Grisham
The inference-based approach (IBA) is one cognitive model that aims to explain the aetiology and maintenance of obsessive-compulsive disorder (OCD). The model proposes that certain reasoning processes lead an individual with OCD to confuse an imagined possibility with an actual probability, a state termed inferential confusion. One such reasoning process is inverse reasoning, in which hypothetical causes form the basis of conclusions about reality. Although previous research has found associations between a self-report measure of inferential confusion and OCD symptoms, evidence of a specific association between inverse reasoning and OCD symptoms is lacking...
December 28, 2016: Journal of Anxiety Disorders
https://www.readbyqxmd.com/read/28042740/the-association-between-shift-work-and-treatment-seeking-migraine-in-denmark
#17
Gitte Sofie Jakobsen, Anne Matilde Timm, Åse Marie Hansen, Anne Helene Garde, Kirsten Nabe-Nielsen
In Europe, the one-year prevalence of migraine is 14.9% and migraine is on the top-ten list of leading causes of years lost to disability. Sleep disturbances and irregular daily routines are considered triggers of migraine and these factors are well-known consequences of shift work. We studied the association between treatment-seeking migraine and shift work, categorised as fixed evening work, fixed night work and variable working hours with and without night work in a Danish working population of 5,872 participants...
January 2, 2017: Ergonomics
https://www.readbyqxmd.com/read/28030639/limits-to-causal-inference-with-state-space-reconstruction-for-infectious-disease
#18
Sarah Cobey, Edward B Baskerville
Infectious diseases are notorious for their complex dynamics, which make it difficult to fit models to test hypotheses. Methods based on state-space reconstruction have been proposed to infer causal interactions in noisy, nonlinear dynamical systems. These "model-free" methods are collectively known as convergent cross-mapping (CCM). Although CCM has theoretical support, natural systems routinely violate its assumptions. To identify the practical limits of causal inference under CCM, we simulated the dynamics of two pathogen strains with varying interaction strengths...
2016: PloS One
https://www.readbyqxmd.com/read/28030583/discounting-and-augmentation-in-causal-conditional-reasoning-causal-models-or-shallow-encoding
#19
Simon Hall, Nilufa Ali, Nick Chater, Mike Oaksford
Recent research comparing mental models theory and causal Bayes nets for their ability to account for discounting and augmentation inferences in causal conditional reasoning had some limitations. One of the experiments used an ordinal scale and multiple items and analysed the data by subjects and items. This procedure can create a variety of problems that can be resolved by using an appropriate cumulative link function mixed models approach in which items are treated as random effects. Experiment 1 replicated this earlier experiment and analysed the results using appropriate data analytic techniques...
2016: PloS One
https://www.readbyqxmd.com/read/28029429/high-cognitive-reserve-in-bipolar-disorders-as-a-moderator-of-neurocognitive-impairment
#20
I Grande, J Sanchez-Moreno, B Sole, E Jimenez, C Torrent, C M Bonnin, C Varo, R Tabares-Seisdedos, V Balanzá-Martínez, E Valls, I Morilla, A F Carvalho, J L Ayuso-Mateos, E Vieta, A Martinez-Aran
BACKGROUND: Cognitive reserve (CR) reflects the capacity of the brain to endure neuropathology, minimize clinical manifestations and successfully complete cognitive tasks. The present study aims to determine whether high CR may constitute a moderator of cognitive functioning in bipolar disorder (BD). METHODS: 102 patients with BD and 32 healthy controls were enrolled. All patients met DSM-IV criteria for I or II BD and were euthymic (YMRS≤6 and HDRS≤8) during a 6-month period...
October 18, 2016: Journal of Affective Disorders
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