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https://www.readbyqxmd.com/read/29228134/genotype-specific-measles-transmissibility-a-branching-process-analysis
#1
S F Ackley, J K Hacker, W T A Enanoria, L Worden, S Blumberg, T C Porco, J Zipprich
Background: Substantial heterogeneity in measles outbreak sizes may be due to genotype- specific transmissibility. Using a branching process analysis, we characterize differences in measles transmission by estimating the association between genotype and the reproduction num- ber R among post-elimination California measles cases from 2000-2015 (400 cases, 165 outbreaks). Methods: Assuming a negative binomial secondary case distribution, we fit a branching process model to the distribution of outbreak sizes using maximum likelihood and estimated the effective reproduction number R for a multi-genotype model...
November 6, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/29223012/support-vector-machine-with-dirichlet-feature-mapping
#2
Ali Nedaie, Amir Abbas Najafi
The Support Vector Machine (SVM) is a supervised learning algorithm to analyze data and recognize patterns. The standard SVM suffers from some limitations in nonlinear classification problems. To tackle these limitations, the nonlinear form of the SVM poses a modified machine based on the kernel functions or other nonlinear feature mappings obviating the mentioned imperfection. However, choosing an efficient kernel or feature mapping function is strongly dependent on data structure. Thus, a flexible feature mapping can be confidently applied in different types of data structures without challenging a kernel selection and its tuning...
November 16, 2017: Neural Networks: the Official Journal of the International Neural Network Society
https://www.readbyqxmd.com/read/29220828/prediction-of-radiation-esophagitis-in-non-small-cell-lung-cancer-using-clinical-factors-dosimetric-parameters-and-pretreatment-cytokine-levels
#3
Peter G Hawkins, Philip S Boonstra, Stephen T Hobson, James A Hayman, Randall K Ten Haken, Martha M Matuszak, Paul Stanton, Gregory P Kalemkerian, Theodore S Lawrence, Matthew J Schipper, Feng-Ming Spring Kong, Shruti Jolly
Radiation esophagitis (RE) is a common adverse event associated with radiotherapy for non-small cell lung cancer (NSCLC). While plasma cytokine levels have been correlated with other forms of radiation-induced toxicity, their association with RE has been less well studied. We analyzed data from 126 patients treated on 4 prospective clinical trials. Logistic regression models based on combinations of dosimetric factors [maximum dose to 2 cubic cm (D2cc) and generalized equivalent uniform dose (gEUD)], clinical variables, and pretreatment plasma levels of 30 cytokines were developed...
December 5, 2017: Translational Oncology
https://www.readbyqxmd.com/read/29220511/unbiased-estimate-of-synonymous-and-non-synonymous-substitution-rates-with-non-stationary-base-composition
#4
Laurent Guéeguen, Laurent Duret
The measurement of synonymous and non-synonymous substitution rates (dS and dN) is useful for assessing selection operating on protein sequences or for investigating mutational processes affecting genomes. In particular, the ratio dNdS is expected to be a good proxy for ω, the ratio of fixation robabilities of non-synonymous mutations relative to that of neutral mutations. Standard methods for estimating dN, dS or ω rely on the assumption that the base composition of sequences is at the equilibrium of the evolutionary process...
December 6, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29219558/analog-quantum-error-correction-with-encoding-a-qubit-into-an-oscillator
#5
Kosuke Fukui, Akihisa Tomita, Atsushi Okamoto
To implement fault-tolerant quantum computation with continuous variables, Gottesman-Kitaev-Preskill (GKP) qubits have been recognized as an important technological element. However, the analog outcome of GKP qubits, which includes beneficial information to improve the error tolerance, has been wasted, because the GKP qubits have been treated as only discrete variables. In this Letter, we propose a hybrid quantum error correction approach that combines digital information with the analog information of the GKP qubits using a maximum-likelihood method...
November 3, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/29216219/wrapped-an-r-package-for-circular-data
#6
Saralees Nadarajah, Yuanyuan Zhang
The Wrapped package computes the probability density function, cumulative distribution function, quantile function and also generates random samples for many univariate wrapped distributions. It also computes maximum likelihood estimates, standard errors, confidence intervals and measures of goodness of fit for nearly fifty univariate wrapped distributions. Numerical illustrations of the package are given.
2017: PloS One
https://www.readbyqxmd.com/read/29214550/the-wally-plot-approach-to-assess-the-calibration-of-clinical-prediction-models
#7
Paul Blanche, Thomas A Gerds, Claus T Ekstrøm
A prediction model is calibrated if, roughly, for any percentage x we can expect that x subjects out of 100 experience the event among all subjects that have a predicted risk of x%. Typically, the calibration assumption is assessed graphically but in practice it is often challenging to judge whether a "disappointing" calibration plot is the consequence of a departure from the calibration assumption, or alternatively just "bad luck" due to sampling variability. We propose a graphical approach which enables the visualization of how much a calibration plot agrees with the calibration assumption to address this issue...
December 6, 2017: Lifetime Data Analysis
https://www.readbyqxmd.com/read/29211707/obesity-and-obesogenic-growth-are-both-highly-heritable-and-modified-by-diet-in-a-nonhuman-primate-model-the-african-green-monkey-chlorocebus-aethiops-sabaeus
#8
C A Schmitt, S K Service, A J Jasinska, T D Dyer, M J Jorgensen, R M Cantor, G M Weinstock, J Blangero, J R Kaplan, N B Freimer
OBJECTIVE: In humans, the ontogeny of obesity throughout the life course and the genetics underlying it has been historically difficult to study. We compared, in a non-human primate model, the lifelong growth trajectories of obese and non-obese adults, to assess the heritability of and map potential genomic regions implicated in growth and obesity. STUDY POPULATION: A total of 905 African green monkeys, or vervets (Chlorocebus aethiops sabaeus) (472 females, 433 males) from a pedigreed captive colony...
December 6, 2017: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/29211107/trypanosoma-janseni-n-sp-trypanosomatida-trypanosomatidae-isolated-from-didelphis-aurita-mammalia-didelphidae-in-the-atlantic-rainforest-of-rio-de-janeiro-brazil-integrative-taxonomy-and-phylogeography-within-the-trypanosoma-cruzi-clade
#9
Camila Madeira Tavares Lopes, Rubem Figueiredo Sadok Menna-Barreto, Márcio Galvão Pavan, Mirian Cláudia De Souza Pereira, André Luiz R Roque
BACKGROUND: Didelphis spp. are a South American marsupial species that are among the most ancient hosts for the Trypanosoma spp. OBJECTIVES: We characterise a new species (Trypanosoma janseni n. sp.) isolated from the spleen and liver tissues of Didelphis aurita in the Atlantic Rainforest of Rio de Janeiro, Brazil. METHODS: The parasites were isolated and a growth curve was performed in NNN and Schneider's media containing 10% foetal bovine serum...
January 2018: Memórias do Instituto Oswaldo Cruz
https://www.readbyqxmd.com/read/29207961/when-and-how-should-multiple-imputation-be-used-for-handling-missing-data-in-randomised-clinical-trials-a-practical-guide-with-flowcharts
#10
Janus Christian Jakobsen, Christian Gluud, Jørn Wetterslev, Per Winkel
BACKGROUND: Missing data may seriously compromise inferences from randomised clinical trials, especially if missing data are not handled appropriately. The potential bias due to missing data depends on the mechanism causing the data to be missing, and the analytical methods applied to amend the missingness. Therefore, the analysis of trial data with missing values requires careful planning and attention. METHODS: The authors had several meetings and discussions considering optimal ways of handling missing data to minimise the bias potential...
December 6, 2017: BMC Medical Research Methodology
https://www.readbyqxmd.com/read/29206922/pie-a-prior-knowledge-guided-integrated-likelihood-estimation-method-for-bias-reduction-in-association-studies-using-electronic-health-records-data
#11
Jing Huang, Rui Duan, Rebecca A Hubbard, Yonghui Wu, Jason H Moore, Hua Xu, Yong Chen
Objectives: This study proposes a novel Prior knowledge guided Integrated likelihood Estimation (PIE) method to correct bias in estimations of associations due to misclassification of electronic health record (EHR)-derived binary phenotypes, and evaluates the performance of the proposed method by comparing it to 2 methods in common practice. Methods: We conducted simulation studies and data analysis of real EHR-derived data on diabetes from Kaiser Permanente Washington to compare the estimation bias of associations using the proposed method, the method ignoring phenotyping errors, the maximum likelihood method with misspecified sensitivity and specificity, and the maximum likelihood method with correctly specified sensitivity and specificity (gold standard)...
December 1, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29206765/the-new-york-sepsis-severity-score-development-of-a-risk-adjusted-severity-model-for-sepsis
#12
Gary S Phillips, Tiffany M Osborn, Kathleen M Terry, Foster Gesten, Mitchell M Levy, Stanley Lemeshow
OBJECTIVES: In accordance with Rory's Regulations, hospitals across New York State developed and implemented protocols for sepsis recognition and treatment to reduce variations in evidence informed care and preventable mortality. The New York Department of Health sought to develop a risk assessment model for accurate and standardized hospital mortality comparisons of adult septic patients across institutions using case-mix adjustment. DESIGN: Retrospective evaluation of prospectively collected data...
December 4, 2017: Critical Care Medicine
https://www.readbyqxmd.com/read/29206593/glioma-grade-discrimination-with-mr-diffusion-kurtosis-imaging-a-meta-analysis-of-diagnostic-accuracy
#13
Anna Falk Delgado, Markus Nilsson, Danielle van Westen, Alberto Falk Delgado
Purpose To assess the diagnostic test accuracy and sources of heterogeneity for the discriminative potential of diffusion kurtosis imaging (DKI) to differentiate low-grade glioma (LGG) (World Health Organization [WHO] grade II) from high-grade glioma (HGG) (WHO grade III or IV). Materials and Methods The Cochrane Library, Embase, Medline, and the Web of Science Core Collection were systematically searched by two librarians. Retrieved hits were screened for inclusion and were evaluated with the revised tool for quality assessment for diagnostic accuracy studies (commonly known as QUADAS-2) by two researchers...
December 4, 2017: Radiology
https://www.readbyqxmd.com/read/29206062/discrimination-between-primary-low-grade-and-high-grade-glioma-with-11c-methionine-pet-a-bivariate-diagnostic-test-accuracy-meta-analysis
#14
Anna F Delgado, Alberto F Delgado
OBJECTIVE: To perform a meta-analysis evaluating the diagnostic accuracy of 11C-methionine (MET) positron emission tomography (PET) to discriminate between primary low-grade glioma (LGG) and high-grade glioma (HGG). METHODS: A systematic database search was performed by a librarian in relevant databases with the latest search in November 7th, 2016. Hits were assessed for inclusion independently by two authors. Individual patient data (IPD) on relative MET uptake was extracted on patients examined preoperatively with MET PET and subsequent neuropathological diagnosis of astrocytoma or oligodendroglioma...
December 5, 2017: British Journal of Radiology
https://www.readbyqxmd.com/read/29205454/joint-mixed-effects-models-for-causal-inference-with-longitudinal-data
#15
Michelle Shardell, Luigi Ferrucci
Causal inference with observational longitudinal data and time-varying exposures is complicated due to the potential for time-dependent confounding and unmeasured confounding. Most causal inference methods that handle time-dependent confounding rely on either the assumption of no unmeasured confounders or the availability of an unconfounded variable that is associated with the exposure (eg, an instrumental variable). Furthermore, when data are incomplete, validity of many methods often depends on the assumption of missing at random...
December 4, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/29205366/diagnostic-staging-laparoscopy-in-gastric-cancer-treatment-a-cost-effectiveness-analysis
#16
Kevin Li, John G D Cannon, Sam Y Jiang, Tanmaya D Sambare, Douglas K Owens, Eran Bendavid, George A Poultsides
BACKGROUND AND OBJECTIVES: Accurate preoperative staging helps avert morbidity, mortality, and cost associated with non-therapeutic laparotomy in gastric cancer (GC) patients. Diagnostic staging laparoscopy (DSL) can detect metastases with high sensitivity, but its cost-effectiveness has not been previously studied. We developed a decision analysis model to assess the cost-effectiveness of preoperative DSL in GC workup. METHODS: Analysis was based on a hypothetical cohort of GC patients in the U...
December 4, 2017: Journal of Surgical Oncology
https://www.readbyqxmd.com/read/29205297/meta-analysis-of-the-procedural-risks-of-carotid-endarterectomy-and-carotid-artery-stenting-over-time
#17
REVIEW
K Lokuge, D D de Waard, A Halliday, A Gray, R Bulbulia, B Mihaylova
BACKGROUND: Stroke/death rates within 30 days of carotid endarterectomy (CEA) and carotid artery stenting (CAS) in RCTs inform current clinical guidelines. However, the risks may have changed in recent years with wider use of effective stroke prevention therapies, especially statins, improved patient selection and growing operator expertise. The aim of this study was to investigate whether the procedural stroke/death risks from CEA and CAS have changed over time. METHODS: MEDLINE and Embase were searched systematically from inception to May 2016 for observational cohort studies of CEA and CAS...
December 4, 2017: British Journal of Surgery
https://www.readbyqxmd.com/read/29203875/the-individual-environment-not-the-family-is-the-most-important-influence-on-preferences-for-common-non-alcoholic-beverages-in-adolescence
#18
Andrea D Smith, Alison Fildes, Suzanna Forwood, Lucy Cooke, Clare Llewellyn
Beverage preferences are an important driver of consumption, and strong liking for beverages high in energy (e.g. sugar-sweetened beverages [SSBs]) and dislike for beverages low in energy (e.g. non-nutritive sweetened beverages [NNSBs]) are potentially modifiable risk factors contributing to variation in intake. Twin studies have established that both genes and environment play important roles in shaping food preferences; but the aetiology of variation in non-alcoholic beverage preferences is unknown. 2865 adolescent twins (18-19-years old) from the Twins Early Development Study were used to quantify genetic and environmental influence on variation in liking for seven non-alcoholic beverages: SSBs; NNSBs; fruit cordials, orange juice, milk, coffee, and tea...
December 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29203807/mitochondrial-genomic-variation-and-phylogenetic-relationships-of-three-groups-in-the-genus-scaphoideus-hemiptera-cicadellidae-deltocephalinae
#19
Yimin Du, Wu Dai, Christopher H Dietrich
The widespread leafhopper genus Scaphoideus Uhler is the most diverse genus in Scaphoideini and includes some species that are serious pests and vectors of plant pathogens. Here the first Scaphoideus mitogenome sequences are provided for three species, S. maai, S. nigrivalveus and S. varius, representing three main species groups in the Oriental region based on color pattern. The lengths of these three mitogenomes were 15,188, 15,235 and 15,207 bp, respectively. Gene order of three mitogenomes is highly conserved and identical to that of the putative ancestral insect...
December 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29197202/factor-structure-and-cut-off-scores-of-the-hospital-anxiety-and-depression-scale-hads-in-a-croatian-sample-of-adult-patients-suffering-from-advanced-cancer
#20
Maja Miljanović, Joško Sindik, Vibor Milunović, Vesna Kralj Škoc, Marijana Braš, Veljko Đorđević
BACKGROUND: Patients with cancer should be systematically screened for psychological problems at key points in their pathway. Usage of self-report scales for measuring anxiety and depression (such as Hospital Anxiety and Depression scale (HADS)) is a very practical methodfor detecting anxiety and depression. The aim of this research was to determine latent structure, reliability and cut-off scores of HADSin a Croatian sample of adult patients suffering from advanced metastatic cancer...
December 2017: Psychiatria Danubina
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