bluuebunny/crossref_metadata_2025_split huggingface dataset:
Having Medicaid insurance negatively impacts outcomes in patients with head and neck malignancies
Authors: Naghavi Arash O. , Echevarria Michelle I. , Grass G. Daniel , Strom Tobin J. , Abuodeh Yazan A. , Ahmed Kamran A. , Kim Youngchul , Trotti Andy M. , Harrison Louis B. , Yamoah Kosj , Caudell Jimmy J. 
Published: August 2016

BACKGROUNDPatients covered by Medicaid insurance appear to have poorer cancer outcomes. Herein, the authors sought to test whether Medicaid was associated with worse outcomes among patients with head and neck cancer (HNC).METHODSThe records of 1698 patients with squamous cell HNC without distant metastatic disease were retrospectively reviewed from an institutional database between 1998 and 2011. At the time of diagnosis, insurance status was categorized as Medicaid, Medicare/other government insurance, or private insurance. Outcomes including locoregional control (LRC) and overall survival (OS) were estimated using the Kaplan‐Meier method and Cox regression multivariate analysis (MVA).RESULTSThe median follow‐up for all patients was 35 months. Medicaid patients comprised 11% of the population; the remaining patients were privately insured (56%) or had Medicare/government insurance (34%). On MVA, Medicaid patients were younger, were current smokers, had higher tumor T and N classifications, and experienced a longer time from diagnosis to treatment initiation (all P<.005). Medicaid insurance status was associated with a deficit of 13% in LRC (69% vs 82%) and 26% in OS (46% vs 72%) at 3 years (all with P<.001). A time from diagnosis to treatment initiation of >45 days was found to be associated with worse 3‐year LRC (77% vs 83%; P = .009) and OS (68% vs 71%; P = .008). On MVA, Medicaid remained associated with a deficit in LRC (P = .002) and OS (P<.001).CONCLUSIONSPatients with Medicaid insurance more often present with locally advanced HNC and experience a higher rate of treatment delays compared with non‐Medicaid patients. Medicaid insurance status appears to be independently associated with deficits in LRC and OS. Improvements in the health care system, such as expediting treatment initiation, may improve the outcomes of patients with HNC. Cancer 2016;122:3529–3537. © 2016 American Cancer Society
Proposing prognostic thresholds for lymph node yield in clinically lymph node‐negative and lymph node‐positive cancers of the oral cavity
Authors: Kuo Phoebe , Mehra Saral , Sosa Julie A. , Roman Sanziana A. , Husain Zain A. , Burtness Barbara A. , Tate Janet P. , Yarbrough Wendell G. , Judson Benjamin L. 
Published: August 2016

BACKGROUNDPrognostic lymph node yield thresholds have been identified and incorporated into treatment guidelines for multiple cancer sites, but not for oral cancer. The objective of this study was to identify optimal thresholds in elective and therapeutic neck dissection for oral cavity cancers.METHODSPatients with oral cavity cancers in the National Cancer Database (NCDB) were stratified into clinically lymph node‐negative (cN0) and clinically lymph node‐positive (cN+) cohorts to reflect the differing surgical management for these diseases. Univariate and multivariate analyses were performed to assess the relation between lymph node yield and overall survival, adjusting for other prognostic factors. Thresholds derived from the NCDB were validated in the Surveillance, Epidemiology, and End Results database.RESULTSIn patients with cN0 cancers of the oral cavity from the NCDB, those who had <16 lymph nodes had significantly decreased survival. The proportion of positive lymph nodes was higher for patients who had ≥16 lymph nodes (27.2% vs 16.3% for < 16 lymph nodes; P < .001). This threshold was validated in 2715 lymph node‐negative cancers from SEER, with a mortality hazard ratio of 0.825 for ≥ 16 lymph nodes (95% confidence interval, 0.764‐0.950; P = .004). In patients with cN + oral cavity cancers from the NCDB, groups with <26 lymph nodes had significantly decreased survival. This threshold was validated in 1903 lymph node‐positive cancers from SEER, with a mortality hazard ratio of 0.791 (95% confidence interval, 0.692‐0.903; P = .001). Academic centers, higher volume centers, and geographic location predicted higher lymph node yields.CONCLUSIONSMore extensive neck dissection (≥16 lymph nodes in cN0, ≥ 26 lymph nodes in cN+) was associated with better survival. Further evaluation of practice patterns in lymph node yield may represent an opportunity for improved quality of care. Cancer 2016;122:3624‐31. © 2016 American Cancer Society.
Grid‐based high performance ensemble classification for evolving data stream
Authors: Qian Quan , Xie Mengbo , Xiao Chaojie , Zhang Rui 
Published: August 2016

SummaryEnsemble learning is one of the main topics of focus in machine learning research. This paper proposes a novel multi‐thread grid‐based multi‐chunk multi‐level ensemble (GMCE) for data stream classification. In order to improve the learning efficiency, GMCE maps different raw data to multiple grids, represents the feature of the grid by the grid first‐order geometric center, and then classifies data based on the grid. Because this grid mapping method compresses the data size significantly, GMCE can increase both the classification accuracy and the computation efficiency. This method has been tested using public KDDCUP99 intrusion detection competition data and five popular P2P applications data. The results show that the GMCE is better than the original multi‐chunk multi‐level ensemble (MCE) in terms of classification accuracy and operation efficiency. For KDDCUP99 data, GMCE has shown more than 98% classification accuracy and 10 times speedup. And for P2P traffic data, GMCE has improved the classification accuracy by 3–4% and achieved greater than four times speedup. Copyright © 2016 John Wiley & Sons, Ltd.
A new closed frequent itemset mining algorithm based on GPU and improved vertical structure
Authors: Li Yun , Xu Jie , Yuan Yun‐Hao , Chen Ling 
Published: August 2016

SummaryVertical data structure is very important for closed frequent itemset mining. All closed frequent itemsets can be found by simply using the operations of AND/OR. However, it consumes a large amount of storage space, especially in the case of large‐size dataset. This paper proposes an algorithm for mining closed frequent itemsets based on a new vertical data structure. The proposed data structure is helpful to save storage space by using a multi‐layer index. At the same time, numerous CPU and graphics processing unit can be employed in parallel to achieve high‐efficiency computing. Especially when dealing with large datasets, the proposed algorithm can obtain a high‐speed computing with the help of graphics processing unit. The improved vertical structure reduces the storage space of the data. The experimental results show that our proposed algorithm requires much less computation time than other related methods. Copyright © 2016 John Wiley & Sons, Ltd.
Semi‐supervised incremental feature extraction algorithm for large‐scale data stream
Authors: Tan Chao , Ji Genlin 
Published: August 2016

SummaryIn big data era, how to process large‐scale data stream is one of the existing challenges. Feature extraction method has attracted much attention because of its effectiveness to data classification. Traditional classification algorithms may take less advantage of labeled samples information. Online learning and out‐of‐sample problems are also hot topics recently. To solve these problems, a novel algorithm named semi‐supervised incremental feature extraction algorithm is proposed in this paper. First, we extract feature incrementally in unsupervised way. Then we propose a semi‐supervised subspace learning algorithm by taking advantage of class information to adjust k‐nearest neighbor weights. Third, we combine the unsupervised and semi‐supervised feature extraction approaches to obtain objective function, in order to solve the out‐of‐sample learning problem. Experiments have been carried out on Machine learning datasets of University of California Irvine (UCI) datasets and real‐world face image datasets (Olivetti faces (ORL), Yale, YaleB, and Rendered face). To demonstrate the proposed algorithm's expandability to process the large‐scale data stream, classification experiments using Spark skill in parallel computation environment are performed, with comparisons with some related semi‐supervised feature extraction methods. The experiment results and computational complex comparison demonstrate that the proposed algorithm can obtain good performance. Copyright © 2016 John Wiley & Sons, Ltd.
Discovering abnormal behaviors via HTTP header fields measurement
Authors: Gou Gaopeng , Bai Quan , Xiong Gang , Li Zhenzhen 
Published: August 2016

SummaryIn recent years, more and more intrusion detection systems and firewalls have been used to detect and block malicious applications or unknown protocols in order to enhance the security of systems. Therefore, some malicious applications begin to shape themselves as common ones to escape malicious protocol detection. Being an important protocol for many Internet services, hypertext transfer protocol (HTTP) is responsible for nearly 10% of the traffic volume on the Internet. Therefore, many malicious applications pretend their traffic to be HTTP protocol to go into hiding their malicious behaviors. In the paper, we study the problem of discovering these abnormal behaviors in HTTP protocol traffic. We find that the characteristics of many abnormal behaviors are performed in the header fields of their shaping HTTP such as Tor and malicious web crawlers, and the information of HTTP header fields of HTTP traffic generated by normal application is also discussed. And then, a method based on the measurement of HTTP header fields proposed three patterns that make them specific to detect abnormal behaviors of shaping HTTP protocol. The experimental results indicate that the proposed method is effective for abnormal behaviors by shaping to be HTTP on large‐scale traffic of one Internet service provider. The experimental results also show that the proposed method could be extended to large‐scale and high‐speed network environment for detecting abnormal behaviors of shaping HTTP protocol. Copyright © 2016 John Wiley & Sons, Ltd.
Assessment of Inflammasome Formation by Flow Cytometry
Authors: Sester David P. , Zamoshnikova Alina , Thygesen Sara J. , Vajjhala Parimala R. , Cridland Simon O. , Schroder Kate , Stacey Katryn J. 
Published: August 2016

AbstractInflammasomes are large protein complexes formed in response to cellular stresses that are platforms for recruitment and activation of caspase 1. Central to most inflammasome functions is the adapter molecule ASC (apoptosis‐associated speck‐like protein containing a caspase‐recruitment domain) that links the inflammasome initiator protein to the recruited caspases. ASC is normally diffuse within the cell but within minutes of inflammasome activation relocates to a dense speck in the cytosol. The dramatic redistribution of ASC can be monitored by flow cytometry using parameters of fluorescence peak height and width when immunostained or tagged with a fluorescent protein. This can be used to define cells with active inflammasomes within populations of primary macrophages and monocytes, allowing quantification of responses and flow‐sorting of responding cells. Protein structural requirements for ASC speck formation and recruitment of caspases to ASC specks can be assessed by expressing components in HEK293 cells. This provides rapid quantification of responding cell number and correlation with the expression level of inflammasome components within single cells. © 2016 by John Wiley & Sons, Inc.
Correlative Förster Resonance Electron Transfer‐Proximity Ligation Assay (FRET‐PLA) Technique for Studying Interactions Involving Membrane Proteins
Authors: Ivanusic Daniel , Denner Joachim , Bannert Norbert 
Published: August 2016

AbstractThis unit provides a guide and detailed protocol for studying membrane protein‐protein interactions (PPI) using the acceptor‐sensitized Förster resonance electron transfer (FRET) method in combination with the proximity ligation assay (PLA). The protocol in this unit is focused on the preparation of FRET‐PLA samples and the detection of correlative FRET/PLA signals as well as on the analysis of FRET‐PLA data and interpretation of correlative results when using cyan fluorescent protein (CFP) as a FRET donor and yellow fluorescent protein (YFP) as a FRET acceptor. The correlative application of FRET and PLA combines two powerful tools for monitoring PPI, yielding results that are more reliable than with either technique alone. © 2016 by John Wiley & Sons, Inc.
Separation of Peptides on HALO 2‐Micron Particles
Authors: Mant Colin T. , Hodges Robert S. 
Published: August 2016

AbstractReversed‐phase high‐performance liquid chromatography (RP‐HPLC) is of fundamental importance to the isolation and separation of peptides, proteins, and other biomolecules. Hence, there is a continuing high demand for the development of RP‐HPLC stationary‐phase materials with enhanced separation efficiency. HALO packing materials began the revolution in “core‐shell” technology with the advantages of faster separations, higher resolution and peak capacity, high temperature stability, and rugged reliable performance compared to traditional HPLC and UHPLC. These materials are characterized by a solid core surrounded by a thin layer of porous material, and represent a technology for the future with continuing refinements. Such refinements are aided via the use of designed synthetic peptide standards during stationary‐phase development. Concomitantly, such standards also enable the researcher to monitor RP‐HPLC column performance and develop optimized separation protocols for peptides from a wide array of sources. © 2016 by John Wiley & Sons, Inc.
Introduction to Atomic Force Microscopy (AFM) in Biology
Authors: Kreplak Laurent 
Published: August 2016

AbstractThe atomic force microscope (AFM) has the unique capability of imaging biological samples with molecular resolution in buffer solution over a wide range of time scales from milliseconds to hours. In addition to providing topographical images of surfaces with nanometer‐ to angstrom‐scale resolution, forces between single molecules and mechanical properties of biological samples can be investigated from the nano‐scale to the micro‐scale. Importantly, the measurements are made in buffer solutions, allowing biological samples to “stay alive” within a physiological‐like environment while temporal changes in structure are measured—e.g., before and after addition of chemical reagents. These qualities distinguish AFM from conventional imaging techniques of comparable resolution, e.g., electron microscopy (EM). This unit provides an introduction to AFM on biological systems and describes specific examples of AFM on proteins, cells, and tissues. The physical principles of the technique and methodological aspects of its practical use and applications are also described. © 2016 by John Wiley & Sons, Inc.
Numerical characterization of nonlinear oscillatory waves in a composite right‐ and left‐handed traveling‐wave field‐effect transistor
Authors: Narahara Koichi 
Published: August 2016

SummaryA specialized type of traveling‐wave field‐effect transistor, the gate and drain lines of which have composite right‐ and left‐handed structures, is considered as the platform to support nonlinear oscillatory waves. The cubic–quintic complex Ginzburg–Landau equation is obtained by application of the reductive perturbation method, by which we quantify the homogeneous oscillations including the property of the Andronov–Hopf bifurcation point, oscillation frequency, and amplitude. Several numerical calculations follow to validate the Ginzburg–Landau equation‐based analysis. Finally, the dynamics of numerically obtained stationary flat‐top pulses are discussed. Copyright © 2016 John Wiley & Sons, Ltd.
Numerical analysis of stochastic resonance in a bistable circuit
Authors: Djurhuus Torsten , Krozer Viktor 
Published: August 2016

SummaryThe paper documents the construction of a novel nonlinear model of a noise‐driven, multi‐dimensional, bistable circuit employing stochastic resonance. Simulations are performed in order to characterize the various relevant device performance measures and their sensitivity to parameter values. The numerical results are considered in the context of nonlinear energy harvesting, and it is explained how the developed simulation tools could prove useful for the development of such devices. The topic of reduced‐order modelling is discussed, and it is shown that this approach leads to incorrect results. Copyright © 2016 John Wiley & Sons, Ltd.
Cytomorphology and flow cytometry of brain biopsy rinse fluid enables faster and multidisciplinary diagnosis of large B‐cell lymphoma of the central nervous system
Authors: Debliquis Agathe , Voirin Jimmy , Harzallah Inès , Maurer Maxime , Lerintiu Felix , Drénou Bernard , Ahle Guido 
Published: August 2016

BackgroundCentral nervous system lymphomas are aggressive tumors requiring a prompt diagnosis for successful treatment. Stereotactic biopsy remains the standard procedure, but the time needed for histopathology is usually over 2 days. We evaluated the contribution of cytomorphology and flow cytometry to histopathology of the brain biopsy in particular on the rinse fluid usually removed.MethodsEighteen patients with suspected localized brain lymphoma underwent stereotactic brain biopsy. Brain biopsy tissue sample and/or brain biopsy rinse fluid were analyzed by cytomorphology combined with flow cytometry. Histopathology was used as a reference.ResultsHistopathology characterized ten diffuse large B‐cell lymphomas and eight other diseases. Cytomorphology and flow cytometry showed lymphoma cells in nine out of the ten lymphomas. Three cytomorphology or flow cytometry negative results were reported for lymphomas in tissue samples due to low cellularity and biopsy sample conditioning. No lymphomatous cells were found by cytomorphology or flow cytometry in the eight other diseases. Rinse fluid results were consistent with histology in all cases studied (sensitivity and specificity, 100%). The median time to result was 4.5 days (range, 2–10 days) for histopathology, while 5 h (range, 3–20 h) were required for both cytomorphology and flow cytometry.ConclusionsBrain biopsy rinse fluid alleviates problems of tissue sample distribution compared to tissue sample. Its analysis performs the diagnosis of B‐cell lymphoma in a few hours and, associated with histopathology, allows a multidisciplinary diagnosis. This study shows that cytomorphology combined with flow cytometry on brain biopsy rinse fluid is a new, fast, and useful strategy. © 2016 International Clinical Cytometry Society
Protocol for a systematic review of effect sizes and statistical power in the rodent fear conditioning literature
Authors: Moulin T.C. , Carneiro C.F.D. , Macleod M.R. , Amaral O.B. 
Published: August 2016

AbstractThe concepts of effect size and statistical power are often disregarded in basic neuroscience, and most articles in the field draw their conclusions solely based on the arbitrary significance thresholds of statistical inference tests. Moreover, studies are often underpowered, making conclusions from significance tests less reliable. With this in mind, we present the protocol of a systematic review to study the distribution of effect sizes and statistical power in the rodent fear conditioning literature, and to analyse how these factors influence the description and publication of results. To do this, we will conduct a search in PubMed for “fear conditioning” AND “mouse” OR “mice” OR “rat” OR “rats” and obtain all articles published online in 2013. Experiments will be included if they: (1) describe the effect(s) of a single intervention on fear conditioning acquisition or consolidation; (2) have a control group to which the experimental group is compared; (3) use freezing as a measure of conditioned fear and (4) have available data on mean freezing, standard deviation and sample size of each group and on the statistical significance of the comparison. We will use the extracted data to calculate the distribution of effect sizes in these experiments as well as the distribution of statistical power curves for detecting a range of differences at a threshold of α = 0.05. We will assess correlations between these variables and (1) the chances of a result being statistically significant, (2) the way the result is described in the article text, (3) measures to reduce risk of bias in the article and (4) the impact factor of the journal and the number of citations of the article. We will also perform analyses to see whether effect sizes vary systematically across species, gender, conditioning protocols or intervention types.
The effect of demographic correlations on the stochastic population dynamics of perennial plants
Authors: Compagnoni Aldo , Bibian Andrew J. , Ochocki Brad M. , Rogers Haldre S. , Schultz Emily L. , Sneck Michelle E. , Elderd Bret D. , Iler Amy M. , Inouye David W. , Jacquemyn Hans , Miller Tom E. X. 
Published: August 2016

AbstractUnderstanding the influence of environmental variability on population dynamics is a fundamental goal of ecology. Theory suggests that, for populations in variable environments, temporal correlations between demographic vital rates (e.g., growth, survival, reproduction) can increase (if positive) or decrease (if negative) the variability of year‐to‐year population growth. Because this variability generally decreases long‐term population viability, vital rate correlations may importantly affect population dynamics in stochastic environments. Despite long‐standing theoretical interest, it is unclear whether vital rate correlations are common in nature, whether their directions are predominantly negative or positive, and whether they are of sufficient magnitude to warrant broad consideration in studies of stochastic population dynamics. We used long‐term demographic data for three perennial plant species, hierarchical Bayesian parameterization of population projection models, and stochastic simulations to address the following questions: (1) What are the sign, magnitude, and uncertainty of temporal correlations between vital rates? (2) How do specific pairwise correlations affect the year‐to‐year variability of population growth? (3) Does the net effect of all vital rate correlations increase or decrease year‐to‐year variability? (4) What is the net effect of vital rate correlations on the long‐term stochastic population growth rate (λs)? We found only four moderate to strong correlations, both positive and negative in sign, across all species and vital rate pairs; otherwise, correlations were generally weak in magnitude and variable in sign. The net effect of vital rate correlations ranged from a slight decrease to an increase in the year‐to‐year variability of population growth, with average changes in variance ranging from −1% to +22%. However, vital rate correlations caused virtually no change in the estimates of λs(mean effects ranging from −0.01% to +0.17%). Therefore, the proportional changes in the variance of population growth caused by demographic correlations were too small on an absolute scale to importantly affect population growth and viability. We conclude that, in our three focal populations and perhaps more generally, vital rate correlations have little effect on stochastic population dynamics. This may be good news for population ecologists, because estimating vital rate correlations and incorporating them into population models can be data intensive and technically challenging.