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https://www.readbyqxmd.com/read/28636276/covariate-selection-with-group-lasso-and-doubly-robust-estimation-of-causal-effects
#1
Brandon Koch, David M Vock, Julian Wolfson
The efficiency of doubly robust estimators of the average causal effect (ACE) of a treatment can be improved by including in the treatment and outcome models only those covariates which are related to both treatment and outcome (i.e., confounders) or related only to the outcome. However, it is often challenging to identify such covariates among the large number that may be measured in a given study. In this article, we propose GLiDeR (Group Lasso and Doubly Robust Estimation), a novel variable selection technique for identifying confounders and predictors of outcome using an adaptive group lasso approach that simultaneously performs coefficient selection, regularization, and estimation across the treatment and outcome models...
June 21, 2017: Biometrics
https://www.readbyqxmd.com/read/28634742/outcomes-of-coronoid-first-repair-in-terrible-triad-injuries-of-the-elbow
#2
Junren Zhang, Mark Tan, Ernest Beng Kee Kwek
BACKGROUND: Clinical outcomes of terrible triad injuries (TTIs) of the elbow are historically poor. To date, it is still debatable whether the coronoid needs to be fixed and if so, how and in which sequence. METHODOLOGY: Between 2010 and 2013, 13 patients were treated surgically for acute TTIs of the elbow at a Tertiary Level 1 Trauma Centre by a single surgeon, using a standardized protocol, which included coronoid-brachialis complex fixation via pull-through trans-osseous sutures, radial head fixation or prosthetic replacement and a repair of the lateral ulnar collateral ligament...
June 20, 2017: Archives of Orthopaedic and Trauma Surgery
https://www.readbyqxmd.com/read/28629325/quasi-linear-score-for-capturing-heterogeneous-structure-in-biomarkers
#3
Katsuhiro Omae, Osamu Komori, Shinto Eguchi
BACKGROUND: Linear scores are widely used to predict dichotomous outcomes in biomedical studies because of their learnability and understandability. Such approaches, however, cannot be used to elucidate biodiversity when there is heterogeneous structure in target population. RESULTS: Our study was focused on describing intrinsic heterogeneity in predictions. Because heterogeneity can be captured by a clustering method, integrating different information from different clusters should yield better predictions...
June 19, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28627406/multi-omics-facilitated-variable-selection-in-cox-regression-model-for-cancer-prognosis-prediction
#4
Cong Liu, Xujun Wang, Georgi Z Genchev, Hui Lu
Motivation New developments in high-throughput genomic technologies have enabled the measurement of diverse types of omics biomarkers in a cost-efficient and clinically-feasible manner. Developing computational methods and tools for analysis and translation of such genomic data into clinically-relevant information is an ongoing and active area of investigation. For example, several studies have utilized an unsupervised learning framework to cluster patients by integrating omics data. Despite such recent advances, predicting cancer prognosis using integrated omics biomarkers remains a challenge...
June 13, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28624800/identifying-drug-pathway-association-pairs-based-on-l1l2-1-integrative-penalized-matrix-decomposition
#5
Dong-Qin Wang, Ying-Lian Gao, Jin-Xing Liu, Chun-Hou Zheng, Xiang-Zhen Kong
The traditional methods of drug discovery follow the "one drug-one target" approach, which ignores the cellular and physiological environment of the action mechanism of drugs. However, pathway-based drug discovery methods can overcome this limitation. This kind of method, such as the Integrative Penalized Matrix Decomposition (iPaD) method, identifies the drug-pathway associations by taking the lasso-type penalty on the regularization term. Moreover, instead of imposing the L1-norm regularization, the L2,1-Integrative Penalized Matrix Decomposition (L2,1-iPaD) method imposes the L2,1-norm penalty on the regularization term...
May 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28623948/one-carbon-metabolism-cognitive-impairment-and-csf-measures-of-alzheimer-pathology-homocysteine-and-beyond
#6
Loïc Dayon, Seu Ping Guiraud, John Corthésy, Laeticia Da Silva, Eugenia Migliavacca, Domilė Tautvydaitė, Aikaterini Oikonomidi, Barbara Moullet, Hugues Henry, Sylviane Métairon, Julien Marquis, Patrick Descombes, Sebastiano Collino, François-Pierre J Martin, Ivan Montoliu, Martin Kussmann, Jérôme Wojcik, Gene L Bowman, Julius Popp
BACKGROUND: Hyperhomocysteinemia is a risk factor for cognitive decline and dementia, including Alzheimer disease (AD). Homocysteine (Hcy) is a sulfur-containing amino acid and metabolite of the methionine pathway. The interrelated methionine, purine, and thymidylate cycles constitute the one-carbon metabolism that plays a critical role in the synthesis of DNA, neurotransmitters, phospholipids, and myelin. In this study, we tested the hypothesis that one-carbon metabolites beyond Hcy are relevant to cognitive function and cerebrospinal fluid (CSF) measures of AD pathology in older adults...
June 17, 2017: Alzheimer's Research & Therapy
https://www.readbyqxmd.com/read/28622469/free-energy-calculations-of-microcin-j25-variants-binding-to-the-fhua-receptor
#7
Pin-Kuang Lai, Yiannis N Kaznessis
Computer simulations are performed to study the antimicrobial peptide microcin J25 (MJ25), a 21-mer peptide with an unusual lasso structure and high activity against Gram-negative bacteria. MJ25 has intracellular targets. The initial step for MJ25 acquisition in bacterial cells is binding to the outer membrane receptor FhuA. Molecular dynamics simulation is implemented to study the binding mechanism of MJ25 to FhuA and to search for important binding residues. The absolute binding free energy calculated from combined free energy perturbation (FEP) and thermodynamic integration (TI) methods agrees well with experimental data...
June 16, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28618771/logistic-lasso-regression-for-the-diagnosis-of-breast-cancer-using-clinical-demographic-data-and-the-bi-rads-lexicon-for-ultrasonography
#8
Sun Mi Kim, Yongdai Kim, Kuhwan Jeong, Heeyeong Jeong, Jiyoung Kim
Purpose: The aim of this study was to compare the performance of image analysis for predicting breast cancer using two distinct regression models and to evaluate the usefulness of incorporating clinical and demographic data (CDD) into the image analysis in order to improve the diagnosis of breast cancer. Methods: This study included 139 solid masses from 139 patients who underwent a ultrasonography-guided core biopsy and had available CDD between June 2009 and April 2010...
April 14, 2017: Ultrasonography
https://www.readbyqxmd.com/read/28612601/classification-of-bladder-cancer-patients-via-penalized-linear-discriminant-analysis
#9
Hadi Raeisi Shahraki, Peyman Bemani, Maryam Jalali
Objectives: In order to identify genes with the greatest contribution to bladder cancer, we proposed a sparse model making the best discrimination from other patients. Methods: In a cross-sectional study, 22 genes with a key role in most cancers were considered in 21 bladder cancer patients and 14 participants of the same age (± 3 years) without bladder cancer in Shiraz city, Southern Iran. Real time-PCR was carried out using SYBR Green and for each of the 22 target genes 2-Δct as a quantitative index of gene expression was reported...
May 1, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/28609157/prediction-of-short-distance-aerial-transport-of-phakopsora-pachyrhizi-urediniospores-using-machine-learning
#10
Liwei Wen, Charles Bowen, Glen Hartman
Dispersal of urediniospores by wind is the primary means of spread for Phakopsora pachyrhizi, the cause of soybean rust. Our research focused on the short distance transport of urediniospores from movement within and out of the canopy up to 61 m from a source. Environmental variables were used to develop and compare lasso regression, random forest, and neural network models to describe deposition of urediniospores collected in passive and active traps. A random sample consisting of 80% of the data was used for training (referred to as a training dataset) and validating (validation dataset) the models from both types of traps...
June 13, 2017: Phytopathology
https://www.readbyqxmd.com/read/28607614/pulmonary-vein-potential-mapping-in-atrial-fibrillation-with-high-density-and-standard-spiral-lasso-catheters-a-comparative-study
#11
Axel Meissner, Petra Maagh, Arnd Christoph, Ahmet Oernek, Gunnar Plehn
BACKGROUND: The dominant single-shot procedure for Pulmonary Vein Isolation (PVI) is the Cryoballoon Ablation (CBA) technique using a spiral catheter (Achieve™, AC) for mapping and monitoring purposes. We hypothesized that Basket Catheters, such as the High Density Mesh Mapper (HDMM), with its high-density mapping properties, could detect Pulmonary Vein Potentials (PVPs) that the octapolar AC would not be able to identify. METHODS: Twenty-four patients (average age 61...
June 2017: Journal of Arrhythmia
https://www.readbyqxmd.com/read/28604790/sparse-eeg-meg-source-estimation-via-a-group-lasso
#12
Michael Lim, Justin M Ales, Benoit R Cottereau, Trevor Hastie, Anthony M Norcia
Non-invasive recordings of human brain activity through electroencephalography (EEG) or magnetoencelphalography (MEG) are of value for both basic science and clinical applications in sensory, cognitive, and affective neuroscience. Here we introduce a new approach to estimating the intra-cranial sources of EEG/MEG activity measured from extra-cranial sensors. The approach is based on the group lasso, a sparse-prior inverse that has been adapted to take advantage of functionally-defined regions of interest for the definition of physiologically meaningful groups within a functionally-based common space...
2017: PloS One
https://www.readbyqxmd.com/read/28601399/erratum-to-lasso-plate%C3%A2-%C3%A2-an-original-implant-for-fixation-of-type-i-and-ii-regan-morrey-coronoid-fractures-orthop-traumatol-surg-res-103-2017-447-51
#13
P Wang, Y Zhuang, Z Li, W Wei, Y Fu, X Wei, K Zhang
No abstract text is available yet for this article.
June 7, 2017: Orthopaedics & Traumatology, Surgery & Research: OTSR
https://www.readbyqxmd.com/read/28600986/neonatal-exposure-to-environmental-pollutants-and-placental-mitochondrial-dna-content-a-multi-pollutant-approach
#14
Annette Vriens, Tim S Nawrot, Willy Baeyens, Elly Den Hond, Liesbeth Bruckers, Adrian Covaci, Kim Croes, Sam De Craemer, Eva Govarts, Nathalie Lambrechts, Ilse Loots, Vera Nelen, Martien Peusens, Stefaan De Henauw, Greet Schoeters, Michelle Plusquin
BACKGROUND: Placental mitochondrial DNA (mtDNA) content can be indicative of oxidative damage to the placenta during fetal development and is responsive to external stressors. In utero exposure to environmental pollutants that may influence placental mtDNA needs further exploration. OBJECTIVES: We evaluated if placental mtDNA content is altered by environmental pollution in newborns and identified pollutants independently associated to alterations in placental mtDNA content...
June 7, 2017: Environment International
https://www.readbyqxmd.com/read/28600253/robust-granger-analysis-in-lp-norm-space-for-directed-eeg-network-analysis
#15
PeiYang Li, Xiaoye Huang, Fali Li, Xurui Wang, Weiwei Zhou, Huan Liu, Teng Ma, Tao Zhang, Daqing Guo, Dezhong Yao, Peng Xu
Granger analysis (GA) is widely used to construct directed brain networks based on various physiological recordings, such as functional magnetic resonance imaging (fMRI), electroencephalogram (EEG), etc. However, in real applications, EEGs are inevitably contaminated by unexpected artifacts that may distort the networks because of the L2 norm structure utilized in GAs when estimating directed links. Compared with the L2 norm, the Lp (p ≤ 1) norm can compress outlier effects. In this study, an extended GA is constructed by applying the Lp (p ≤ 1) norm strategy to estimate robust causalities under outlier conditions, and a feasible iteration procedure is utilized to solve the new GA model...
June 5, 2017: IEEE Transactions on Neural Systems and Rehabilitation Engineering
https://www.readbyqxmd.com/read/28598971/expression-of-inhibitory-receptors-and-polyfunctional-responses-of-t-cells-are-linked-to-the-risk-of-congenital-transmission-of-t-cruzi
#16
Adriana Egui, Paola Lasso, María Carmen Thomas, Bartolomé Carrilero, John Mario González, Adriana Cuéllar, Manuel Segovia, Concepción Judith Puerta, Manuel Carlos López
Congenital T. cruzi infections involve multiple factors in which complex interactions between the parasite and the immune system of pregnant women play important roles. In this study, we used an experimental murine model of chronic infection with T. cruzi to evaluate the changes in the expression of inhibitory receptors and the polyfunctionality of T cells during gestation and their association with congenital transmission rate of T. cruzi infection. The results showed that pregnant naïve mice had a higher percentage of CD4+ and CD8+ T cells that expressed inhibitory receptors than cells from non-pregnant naïve mice...
June 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28598845/discovery-and-confirmation-of-diagnostic-serum-lipid-biomarkers-for-alzheimer-s-disease-using-direct-infusion-mass-spectrometry
#17
Swati Anand, Justin M Barnes, Sydney A Young, Diana M Garcia, H Dennis Tolley, John S K Kauwe, Steven W Graves
Alzheimer's disease (AD) is a neurodegenerative disorder lacking early biochemical diagnosis and treatment. Lipids have been implicated in neurodegenerative disorders including AD. A shotgun lipidomic approach was undertaken to determine if lipid biomarkers exist that can discriminate AD cases from controls. The discovery study involved sera from 29 different stage AD cases and 32 controls. Lipid extraction was performed using organic solvent and the samples were directly infused into a time-of-flight mass spectrometer...
June 9, 2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28597316/substrate-translocation-involves-specific-lysine-residues-of-the-central-channel-of-the-conjugative-coupling-protein-trwb
#18
Delfina Larrea, Héctor D de Paz, Inmaculada Matilla, Dolores L Guzmán-Herrador, Gorka Lasso, Fernando de la Cruz, Elena Cabezón, Matxalen Llosa
Conjugative transfer of plasmid R388 requires the coupling protein TrwB for protein and DNA transport, but their molecular role in transport has not been deciphered. We investigated the role of residues protruding into the central channel of the TrwB hexamer by a mutational analysis. Mutations affecting lysine residues K275, K398, and K421, and residue S441, all facing the internal channel, affected transport of both DNA and the relaxase protein in vivo. The ATPase activity of the purified soluble variants was affected significantly in the presence of accessory protein TrwA or DNA, correlating with their behaviour in vivo...
June 8, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28594935/a-nested-case-control-study-of-277-prediagnostic-serum-cytokines-and-glioma
#19
Judith Schwartzbaum, Min Wang, Elisabeth Root, Maciej Pietrzak, Grzegorz A Rempala, Ruo-Pan Huang, Tom Borge Johannesen, Tom K Grimsrud
Recent research shows bidirectional communication between the normal brain and the peripheral immune system. Glioma is a primary brain tumor characterized by systemic immunosuppression. To better understand gliomagenesis, we evaluated associations between 277 prediagnostic serum cytokines and glioma. We used glioma (n = 487) and matched control (n = 487) specimens from the Janus Serum Bank Cohort in Oslo, Norway. Conditional logistic regression allowed us to identify those cytokines that were individually associated with glioma...
2017: PloS One
https://www.readbyqxmd.com/read/28594839/exploratory-graph-analysis-a-new-approach-for-estimating-the-number-of-dimensions-in-psychological-research
#20
Hudson F Golino, Sacha Epskamp
The estimation of the correct number of dimensions is a long-standing problem in psychometrics. Several methods have been proposed, such as parallel analysis (PA), Kaiser-Guttman's eigenvalue-greater-than-one rule, multiple average partial procedure (MAP), the maximum-likelihood approaches that use fit indexes as BIC and EBIC and the less used and studied approach called very simple structure (VSS). In the present paper a new approach to estimate the number of dimensions will be introduced and compared via simulation to the traditional techniques pointed above...
2017: PloS One
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