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Time series analysis

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https://www.readbyqxmd.com/read/28098915/somatic-mutational-spectrum-analysis-in-a-prospective-series-of-104-gastrointestinal-stromal-tumors
#1
David Guenat, Olivier Deroo, Sandrine Magnin, Loïc Chaigneau, Franck Monnien, Christophe Borg, Christiane Mougin, Jean-François Emile, Jean-Luc Prétet
Gastrointestinal stromal tumors (GISTs) are mesenchymal tumors distinguished by driver mutations in proto-oncogenes KIT or PDGFRA in 85-90% of cases. These mutations have been linked to the response to imatinib, a multikinase inhibitor, and have independent prognostic impact. Here, we describe the prospective study of the molecular characteristics of 104 GISTs from French adult patients analyzed routinely through the National Hospital Program of Molecular Cancer Diagnosis. All patients with GISTs diagnosed at the University Hospital of Besançon between August 2005 and October 2014 were prospectively included in the present study...
January 17, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28098255/annual-time-series-analysis-of-aqueous-edna-reveals-ecologically-relevant-dynamics-of-lake-ecosystem-biodiversity
#2
Iliana Bista, Gary R Carvalho, Kerry Walsh, Mathew Seymour, Mehrdad Hajibabaei, Delphine Lallias, Martin Christmas, Simon Creer
The use of environmental DNA (eDNA) in biodiversity assessments offers a step-change in sensitivity, throughput and simultaneous measures of ecosystem diversity and function. There remains, however, a need to examine eDNA persistence in the wild through simultaneous temporal measures of eDNA and biota. Here, we use metabarcoding of two markers of different lengths, derived from an annual time series of aqueous lake eDNA to examine temporal shifts in ecosystem biodiversity and in an ecologically important group of macroinvertebrates (Diptera: Chironomidae)...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28097328/diabetes-outpatient-care-and-acute-complications-before-and-after-high-deductible-insurance-enrollment-a-natural-experiment-for-translation-in-diabetes-next-d-study
#3
J Frank Wharam, Fang Zhang, Emma M Eggleston, Christine Y Lu, Stephen Soumerai, Dennis Ross-Degnan
Importance: High-deductible health plans (HDHPs) have expanded under the Affordable Care Act and are expected to play a major role in the future of US health policy. The effects of modern HDHPs on chronically ill patients and adverse outcomes are unknown. Objective: To determine the association of HDHP with high-priority diabetes outpatient care and preventable acute complications. Design, Setting, and Participants: Controlled interrupted-time-series study using a large national health insurer database from January 1, 2003, to December 31, 2012...
January 9, 2017: JAMA Internal Medicine
https://www.readbyqxmd.com/read/28096084/timesvector-a-vectorized-clustering-approach-to-the-analysis-of-time-series-transcriptome-data-from-multiple-phenotypes
#4
Inuk Jung, Kyuri Jo, Hyejin Kang, Hongryul Ahn, Youngjae Yu, Sun Kim
MOTIVATION: Identifying biologically meaningful gene expression patterns from time series gene expression data is important to understand the underlying biological mechanisms. To identify significantly perturbed gene sets between different phenotypes, analysis of time series transcriptome data requires consideration of time and sample dimensions. Thus, the analysis of such time series data seeks to search gene sets that exhibit similar or different expression patterns between two or more sample conditions, constituting the three-dimensional data, i...
January 17, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28095114/flowering-time-regulation-by-the-constans-like-gene-oscol10
#5
Junjie Tan, Fuqing Wu, Jianmin Wan
Plant flowering at the appropriate time is critical for reproductive success and influenced by a series of environmental factors such as photoperiod and temperature. A number of genes involved in photoperiodic flowering of have been cloned and their roles in modulating expression of the flowering genes have been characterized to a certain extent. However, much less is known about the pathway in transmitting the day length response signal(s) to induce transition to reproductive growth. Recently, we characterized a constitutive flowering repressor OsCOL10 encoding for a member of the CONSTANS-like (COL) family...
January 17, 2017: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/28094043/incidence-and-clinical-course-of-immune-reactions-after-descemet-membrane-endothelial-keratoplasty-retrospective-analysis-of-1000-consecutive-eyes
#6
Deniz Hos, Onur Tuac, Friederike Schaub, Tisha P Stanzel, Silvia Schrittenlocher, Martin Hellmich, Björn O Bachmann, Claus Cursiefen
PURPOSE: To analyze the incidence and clinical course of graft rejection episodes after Descemet membrane endothelial keratoplasty (DMEK). DESIGN: Retrospective analysis of a consecutive, interventional case series. PARTICIPANTS: One thousand eyes that underwent DMEK from July 2011 through August 2015 at the Department of Ophthalmology, University of Cologne. METHODS: All cases with follow-up of at least 1 month were included (mean follow-up, 18...
January 13, 2017: Ophthalmology
https://www.readbyqxmd.com/read/28092985/plague-and-war-political-breakdown-and-the-spread-of-hiv
#7
Nathan A Paxton
This exploratory data analysis finds a negative relationship between some types of war and HIV prevalence (i.e. as the former increases in intensity, the latter decreases). The study uses a longer time-frame and broader range of countries than similar studies, with explicit differentiation between sub-Saharan African and other developing countries. The study uses a variety of methods for analyzing time-series-cross-section data. These methods serve as both a robustness check for the results as well as a real-world demonstration of common suggestions for TSCS data...
January 16, 2017: Medicine, Conflict, and Survival
https://www.readbyqxmd.com/read/28092562/line-graph-or-scatter-plot-automatic-selection-of-methods-for-visualizing-trends-in-time-series
#8
Yunhai Wang, Fubo Han, Lifeng Zhu, Oliver Deussen, Baoquan Chen
Line graphs are usually considered to be the best choice for visualizing time series data, whereas sometimes also scatter plots are used for showing main trends. So far there are no guidelines that indicate which of these visualization methods better display trends in time series for a given canvas. Assuming that the main information in a time series is its overall trend, we propose an algorithm that automatically picks the visualization method that reveals this trend best. This is achieved by measuring the visual consistency between the trend curve represented by a LOESS fit and the trend described by a scatter plot or a line graph...
January 16, 2017: IEEE Transactions on Visualization and Computer Graphics
https://www.readbyqxmd.com/read/28089812/clinical-manifestations-and-outcomes-in-surgically-managed-gartner-duct-cysts-1
#9
Adela G Cope, Shannon Laughlin-Tommaso, Abimbola Famuyide, John B Gebhart, Matthew R Hopkins, Daniel M Breitkopf
STUDY OBJECTIVE: Gartner duct cysts (GDC) are rare embryological remnants of the mesonephric duct with the majority of cases discovered incidentally in asymptomatic patients. The largest prior published series evaluating surgical management of GDC included 4 patients. The present study aims to determine the manifestations and outcomes of surgically managed patients with GDC with important implications for surveillance, monitoring, and management of patients. DESIGN: Retrospective chart review DESIGN: Classification: Canadian Task Force Classification III SETTING: Tertiary care center PATIENTS: All women diagnosed with GDC from 1/1994-4/2014 at our institution were identified...
January 12, 2017: Journal of Minimally Invasive Gynecology
https://www.readbyqxmd.com/read/28089301/time-since-discharge-of-9mm-cartridges-by-headspace-analysis-part-2-ageing-study-and-estimation-of-the-time-since-discharge-using-multivariate-regression
#10
M Gallidabino, F S Romolo, C Weyermann
Estimating the time since discharge of spent cartridges can be a valuable tool in the forensic investigation of firearm-related crimes. To reach this aim, it was previously proposed that the decrease of volatile organic compounds released during discharge is monitored over time using non-destructive headspace extraction techniques. While promising results were obtained for large-calibre cartridges (e.g., shotgun shells), handgun calibres yielded unsatisfying results. In addition to the natural complexity of the specimen itself, these can also be attributed to some selective choices in the methods development...
December 27, 2016: Forensic Science International
https://www.readbyqxmd.com/read/28089297/time-since-discharge-of-9mm-cartridges-by-headspace-analysis-part-1-comprehensive-optimisation-and-validation-of-a-headspace-sorptive-extraction-hsse-method
#11
M Gallidabino, F S Romolo, C Weyermann
Estimating the time since discharge of spent cartridges can be a valuable tool in the forensic investigation of firearm-related crimes. To reach this aim, it was previously proposed that the decrease of volatile organic compounds released during discharge is monitored over time using non-destructive headspace extraction techniques. While promising results were obtained for large-calibre cartridges (e.g., shotgun shells), handgun calibres yielded unsatisfying results. In addition to the natural complexity of the specimen itself, these can also be attributed to some selective choices in the methods development...
December 24, 2016: Forensic Science International
https://www.readbyqxmd.com/read/28088214/determinants-and-materno-fetal-outcomes-related-to-cesarean-section-delivery-in-private-and-public-hospitals-in-low-and-middle-income-countries-a-systematic-review-and-meta-analysis-protocol
#12
Idrissa Beogo, Bomar Mendez Rojas, Marie-Pierre Gagnon
BACKGROUND: Despite the well-established morbidity, mortality, long-term effects, and unnecessary extra-cost burden associated with cesarean section delivery (CSD) worldwide, its rate has grown exponentially. This has become a great topical challenge for the international healthcare community and individual countries. Estimated at three times the acceptable rate as defined by the World Health Organization in 1985, the continued upward trend has been fuelled by higher income countries...
January 14, 2017: Systematic Reviews
https://www.readbyqxmd.com/read/28088176/ttca-an-r-package-for-the-identification-of-differentially-expressed-genes-in-time-course-microarray-data
#13
Marco Albrecht, Damian Stichel, Benedikt Müller, Ruth Merkle, Carsten Sticht, Norbert Gretz, Ursula Klingmüller, Kai Breuhahn, Franziska Matthäus
BACKGROUND: The analysis of microarray time series promises a deeper insight into the dynamics of the cellular response following stimulation. A common observation in this type of data is that some genes respond with quick, transient dynamics, while other genes change their expression slowly over time. The existing methods for detecting significant expression dynamics often fail when the expression dynamics show a large heterogeneity. Moreover, these methods often cannot cope with irregular and sparse measurements...
January 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28088034/an-evaluation-of-nova-scotia-s-alcohol-ignition-interlock-program
#14
Ward G M Vanlaar, Marisela Mainegra Hing, Robyn D Robertson
Alcohol ignition interlock programs for offenders aim to reduce recidivism among convicted drink drivers. This study presents an evaluation of Nova Scotia's interlock program implemented in 2008 in order to assess its effectiveness to reduce impaired driving and to help identify areas for improvement. Data used include conviction and crash records of individual participants; provincial monthly counts of alcohol-related charges, convictions and fatal and serious crashes; and interlock logged events. Methods used include descriptive statistics, survival analysis, time series and logistic regression analysis...
January 11, 2017: Accident; Analysis and Prevention
https://www.readbyqxmd.com/read/28086902/exploiting-temporal-and-nonstationary-features-in-breathing-sound-analysis-for-multiple-obstructive-sleep-apnea-severity-classification
#15
Jaepil Kim, Taehoon Kim, Donmoon Lee, Jeong-Whun Kim, Kyogu Lee
BACKGROUND: Polysomnography (PSG) is the gold standard test for obstructive sleep apnea (OSA), but it incurs high costs, requires inconvenient measurements, and is limited by a one-night test. Thus, a repetitive OSA screening test using affordable data would be effective both for patients interested in their own OSA risk and in-hospital PSG. The purpose of this research was to develop a four-OSA severity classification model using a patient's breathing sounds. METHODS: Breathing sounds were recorded from 83 subjects during a PSG test...
January 7, 2017: Biomedical Engineering Online
https://www.readbyqxmd.com/read/28086822/assessment-of-quality-of-care-among-in-patients-with-postpartum-haemorrhage-and-severe-pre-eclampsia-at-st-francis-hospital-nsambya-a-criteria-based-audit
#16
Alfred Lumala, Peter Sekweyama, Andrew Abaasa, Humphrey Lwanga, Romano Byaruhanga
BACKGROUND: The maternal mortality ratio of Uganda is still high and the leading causes of maternal mortality are postpartum haemorrhage (PPH), severe pre-eclampsia and eclampsia. Criteria-based audit (CBA) is a way of improving quality of care that has not been commonly used in low income countries. This study aimed at finding out the quality of care provided to patients with these conditions and to find out if the implementation of recommendations from the audit cycle resulted in improvement in quality of care...
January 13, 2017: BMC Pregnancy and Childbirth
https://www.readbyqxmd.com/read/28081141/could-a-neuroscientist-understand-a-microprocessor
#17
Eric Jonas, Konrad Paul Kording
There is a popular belief in neuroscience that we are primarily data limited, and that producing large, multimodal, and complex datasets will, with the help of advanced data analysis algorithms, lead to fundamental insights into the way the brain processes information. These datasets do not yet exist, and if they did we would have no way of evaluating whether or not the algorithmically-generated insights were sufficient or even correct. To address this, here we take a classical microprocessor as a model organism, and use our ability to perform arbitrary experiments on it to see if popular data analysis methods from neuroscience can elucidate the way it processes information...
January 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28079286/design-synthesis-biological-evaluation-and-3d-qsar-analysis-of-podophyllotoxin-dioxazole-combination-as-tubulin-targeting-anticancer-agents
#18
Zi-Zhen Wang, Wen-Xue Sun, Xue Wang, Ya-Han Zhang, Han-Yue Qiu, Jin-Liang Qi, Yan-Jun Pang, Gui-Hua Lu, Xiao-Ming Wang, Fu-Gen Yu, Yong-Hua Yang
The advancement of cancer fighting drugs has never been a simple linear process. Those drugs design professionals begin to find inspiration from the nature after failing to find the ideal products by creative drugs design and high-throughput screening. To obtain new molecules for inhibiting tubulin, podophyllotoxin was adopted as the leading compound and 1,3,4-oxadiazole was brought in to the C-4 site of podophyllotoxin in this research. A series of seventeen podophyllotoxin derived esters have been achieved and then evaluated their antitumor activities against four different cancer cell lines: A549, MCF-7, HepG2 and HeLa...
January 12, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28077303/analysis-and-correction-of-field-fluctuations-in-fmri-data-using-field-monitoring
#19
Saskia Bollmann, Lars Kasper, S Johanna Vannesjo, Andreea O Diaconescu, Benjamin E Dietrich, Simon Gross, Klaas E Stephan, Klaas P Pruessmann
This work investigates the role of magnetic field fluctuations as a confound in fMRI. In standard fMRI experiments with single-shot EPI acquisition the uniform and gradient components of the magnetic field were recorded with NMR field sensors. By principal component analysis it is found that differences of field evolution between the EPI readouts are explainable by few components relating to slow and within-shot field dynamics of hardware and physiological origin. The impact of fluctuating field components is studied by selective data correction and assessment of its influence on image fluctuation and SFNR...
January 8, 2017: NeuroImage
https://www.readbyqxmd.com/read/28076801/msmbuilder-statistical-models-for-biomolecular-dynamics
#20
Matthew P Harrigan, Mohammad M Sultan, Carlos X Hernández, Brooke E Husic, Peter Eastman, Christian R Schwantes, Kyle A Beauchamp, Robert T McGibbon, Vijay S Pande
MSMBuilder is a software package for building statistical models of high-dimensional time-series data. It is designed with a particular focus on the analysis of atomistic simulations of biomolecular dynamics such as protein folding and conformational change. MSMBuilder is named for its ability to construct Markov state models (MSMs), a class of models that has gained favor among computational biophysicists. In addition to both well-established and newer MSM methods, the package includes complementary algorithms for understanding time-series data such as hidden Markov models and time-structure based independent component analysis...
January 10, 2017: Biophysical Journal
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