bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of trapped electron on the dust ion acoustic waves in dusty plasma using time fractional modified Korteweg-de Vries equation
Authors: Nazari-Golshan A. , Nourazar S. S. 
Published: October 2013

The time fractional modified Korteweg-de Vries (TFMKdV) equation is solved to study the nonlinear propagation of small but finite amplitude dust ion-acoustic (DIA) solitary waves in un-magnetized dusty plasma with trapped electrons. The plasma is composed of a cold ion fluid, stationary dust grains, and hot electrons obeying a trapped electron distribution. The TFMKdV equation is derived by using the semi-inverse and Agrawal's methods and then solved by the Laplace Adomian decomposition method. Our results show that the amplitude of the DIA solitary waves increases with the increase of time fractional order β, the wave velocity v0, and the population of the background free electrons λ. However, it is vice-versa for the deviation from isothermality parameter b, which is in agreement with the result obtained previously.
Spatial regulation dominates gene function in the ganglia chain
Authors: Hibsh Dror , Schori Hadas , Efroni Sol , Shefi Orit 
Published: October 2013

Abstract
Motivation: To understand the molecular mechanisms of neurons, it is imperative to identify genomic dissimilarities within the heterogeneity of the neural system. This is especially true for neuronal disorders in which spatial considerations are of critical nature. For this purpose, Hirudo medicinalis provides here an ideal system in which we are able to follow gene expression along the central nervous system, to affiliate location with gene behavior.
Results: In all, 221.1 million high-quality short reads were sequenced on the Illumina Hiseq2000 platform at the single ganglion level. Thereafter, a de novo assembly was performed using two state-of-the-art assemblers, Trinity and Trans-ABySS, to reconstruct a comprehensive de novo transcriptome. Classification of Trinity and Trans-ABySS transcripts produced a non-redundant set of 76 845 and 268 355 transcripts (&gt;200 bp), respectively. Remarkably, using Trinity, 82% of the published medicinal leech messenger RNAs was identified. For the innexin family, all of the 21 recently reported genes were identified. Spatial regulation analysis across three ganglia throughout the entire central nervous system revealed distinct patterns of gene expression. These transcriptome data were combined with expression distribution to produce a spatio-transcripto map along the ganglia chain. This study provides a resource for gene discovery and gene regulation in future studies.
Contact: orit.shefi@biu.ac.il or sol.efroni@biu.ac.il
Supplementary information: Supplementary data are available at Bioinformatics online.
A critical role for suppressor of cytokine signalling 3 in promoting M1 macrophage activation and function in vitro and in vivo
Authors: Arnold Christina E. , Whyte Claire S. , Gordon Peter , Barker Robert N. , Rees Andrew J. , Wilson Heather M. 
Published: October 2013

SummaryMacrophages respond to their microenvironment and develop polarized functions critical for orchestrating appropriate inflammatory responses. Classical (M1) activation eliminates pathogens while alternative (M2) activation promotes regulation and repair. M1 macrophage activation is strongly associated with suppressor of cytokine signalling 3 (SOCS3) expression in vitro, but the functional consequences of this are unclear and the role of SOCS3 in M1‐macrophage polarization in vivo remains controversial. To address these questions, we defined the characteristics and function of SOCS3‐expressing macrophages in vivo and identified potential mechanisms of SOCS3 action. Macrophages infiltrating inflamed glomeruli in a model of acute nephritis show significant up‐regulation of SOCS3 that co‐localizes with the M1‐activation marker, inducible nitric oxide synthase. Numbers of SOCS3hi‐expressing, but not SOCS1hi‐expressing, macrophages correlate strongly with the severity of renal injury, supporting their inflammatory role in vivo. Adoptive transfer of SOCS3‐short interfering RNA‐silenced macrophages into a peritonitis model demonstrated the importance of SOCS3 in driving production of pro‐inflammatory IL‐6 and nitric oxide, while curtailing expression of anti‐inflammatory IL‐10 and SOCS1. SOCS3‐induced pro‐inflammatory effects were due, at least in part, to its role in controlling activation and nuclear accumulation of nuclear factor‐κB and activity of phosphatidylinositol 3‐kinase. We show for the first time that SOCS3 also directs the functions of human monocyte‐derived macrophages, including efficient M1‐induced cytokine production (IL‐1β, IL‐6, IL‐23, IL‐12), attenuated signal transducer and activator of transcription 3 activity and ability of antigen‐loaded macrophages to drive T‐cell responses. Hence, M1‐associated SOCS3 was a positive regulator of pro‐inflammatory responses in our rodent models and up‐regulated SOCS3 is essential for effective M1‐macrophage activation and function in human macrophages.
Confidence Distribution, the Frequentist Distribution Estimator of a Parameter: A Review
Authors: Xie Min‐ge , Singh Kesar 
Published: October 2013

RésuméIl est courant, en inférence fréquentielle, d'utiliser un point unique (une estimation ponctuelle) ou un intervalle (intervalle de confiance) dans le but d'estimer un paramètre d'intér^t. Une question très simple se pose: peut‐on également utiliser, dans le même but, et dans la même optique fréquentielle, à la façon dont les Bayésiens utilisent une loi a posteriori, une distribution de probabilité? La réponse est affirmative, et les distributions de confiance apparaissent comme un choix naturel dans ce contexte. Le concept de distribution de confiance a une longue histoire, longtemps associée, à tort, aux théories d'inférence fiducielle, ce qui a compromis son développement dans l'optique fréquentielle. Les distributions de confiance ont récemment attiré un regain d'intérêt, et plusieurs résultats ont mis en évidence leur potentiel considérable en tant qu'outil inférentiel. Cet article présente une définition moderne du concept, et examine les ses évolutions récentes. Il aborde les méthodes d'inférence, les problèmes d'optimalité, et les applications. A la lumière de ces nouveaux développements, le concept de distribution de confiance englobe et unifie un large éventail de cas particuliers, depuis les exemples paramétriques réguliers (distributions fiducielles), les lois de rééchantillonnage, lesp‐valeurs et les fonctions de vraisemblance normalisées jusqu'aux a priori et posteriori bayésiens. La discussion est entièrement menée d'un point de vue fréquentiel, et met l'accent sur les applications dans lesquelles les solutions fréquentielles sont inexistantes ou d'une application difficile. Bien que nous attirions également l'attention sur les similitudes et les différences que présentent les approches fréquentielle, fiducielle, et Bayésienne, notre intention n'est pas de rouvrir un débat philosophique qui dure depuis près de deux cents ans. Nous espérons bien au contraire contribuer à combler le fossé qui existe entre les différents points de vue.
Modelling Strategies for Repeated Multiple Response Data
Authors: Suesse Thomas , Liu Ivy 
Published: October 2013

RésuméCet article examine les stratégies de modélisation pour des mesures répétées de variables á réponses multiples. Ces donnes surviennent dans le contexte de variables catégoriques oú l'on peut sélectionner une ou plusieurs catégories de réponse. Nous considérons chacune des réponses multiples comme un résultat binaire et nous utilisons une approche de modélisation marginal (ou population‐moyenne) pour analyser ses esprances. Des équations d'estimation généralisées sont utilisées pour tenir compte des différentes structures de corrélation, á la fois dans le temps et entre les éléments. Nous examinons également une approche alternative en utilisant un modéle linéaire généralisé mixte avec des interprétations conditionnelles. Nous appliquons les diffrentes méthodes et comparons les résultats en utilisant des données provenant dun groupe détudes réalisé en Australie appelé “the Household, Income and Labour Dynamics Survey” (Enquéte dynamique sur les foyers, les revenus et le travail).
What Happened to Discrete Chaos, the Quenouille Process, and the Sharp Markov Property? Some History of Stochastic Point Processes
Authors: Guttorp Peter , Thorarinsdottir Thordis L. 
Published: October 2013

SummaryThe use of properties of a Poisson process to study the randomness of stars is traced back to a 1767 paper. The process was used and rediscovered many times, and we mention some of the early scientific areas. The name Poisson process was first used in print in 1940, and we believe the term was coined in the corridors of Stockholm University some time between 1936 and 1939. We follow the early developments of doubly stochastic processes and cluster processes, and describe different efforts to apply the Markov property to point processes.
Assessing the Performance of Classification Methods
Authors: Hand David J. 
Published: October 2013

SummaryA large number of measures have been developed for evaluating the performance of classification rules. Some of these have been developed to meet the practical requirements of specific applications, but many others—which here we call “classification accuracy” criteria—represent different ways of balancing the different kinds of misclassification which may be made. This paper reviews classification accuracy criteria. However, the literature is now so large and diverse that a comprehensive list, covering all the measures and their variants, would probably be impossible. Instead, this paper embeds such measures in general framework, spanning the possibilities, and draws attention to relationships between them. Important points to note are, firstly, that different performance measures, by definition, measure different aspects of performance; secondly, that one should therefore carefully choose a measure to match the objectives of one's study; and, thirdly, that empirical comparisons between instruments measuring different aspects are of limited value.
Interval Estimation of Treatment Effects In Randomized Trials: When do Confidence Intervals Have Nominal Coverage?
Authors: Scosyrev Emil 
Published: October 2013

SummaryIn the classical theory of randomized trials (RTs), the treatment effect is defined as a mean difference of potential outcomes. To achieve nominal coverage probability for confidence intervals (CIs) on treatment effects in RTs, certain assumptions are necessary. Specifically, one must either make assumptions about the joint distribution of potential outcomes or enroll subjects in the trial by random sampling of the target population on which the treatment effect is defined. In practice, no such sampling usually takes place and assumptions about the joint distribution of potential outcomes cannot be verified based on observed data. Furthermore, the most common of these assumptions, such as treatment‐unit additivity (TUA) or independence are biologically implausible in most RTs involving human subjects. Hence, it is not usually possible to construct CIs on treatment effects with nominal coverage probability. However, for any joint distribution of potential outcomes, the standard estimator of the variance of the difference of two independent sample means produces CIs with asymptotic coverage at least at the nominal level. This interpretation of CIs as conservative bounds may not always hold in conventional regression models applied to RT data.
Multi‐state Stochastic Processes: A Statistical Flowgraph Perspective
Authors: Collins David H. , Huzurbazar Aparna V. 
Published: October 2013

SummaryTwo‐state models (working/failed or alive/dead) are widely used in reliability and survival analysis. In contrast, multi‐state stochastic processes provide a richer framework for modeling and analyzing the progression of a process from an initial to a terminal state, allowing incorporation of more details of the process mechanism. We review multi‐state models, focusing on time‐homogeneous semi‐Markov processes (SMPs), and then describe the statistical flowgraph framework, which comprises analysis methods and algorithms for computing quantities of interest such as the distribution of first passage times to a terminal state. These algorithms algebraically combine integral transforms of the waiting time distributions in each state and invert them to get the required results. The estimated transforms may be based on parametric distributions or on empirical distributions of sample transition data, which may be censored. The methods are illustrated with several applications.
Origin of the Eocene planktonic foraminifer Hantkenina by gradual evolution
Authors: Pearson Paul N. , Coxall Helen K. 
Published: October 2013

AbstractHantkenina is a distinctive planktonic foraminiferal genus characterized by the presence of tubulospines (robust hollow projections) on each adult chamber, from Middle and Upper Eocene marine sediments worldwide. Here we illustrate its evolutionary origin using c. 150 specimens from 30 stratigraphic intervals in two sediment cores from Tanzania. The specimens, which span an estimated time interval of 300 ka, show four intermediate steps in the evolution of the tubulospines that amount to a complete intergradation from Clavigerinella caucasica, which does not possess them, to Hantkenina mexicana, which does. Stable isotope analyses indicate that the transitional forms evolved in a deep planktonic habitat not occupied at that time by other species of planktonic foraminifera. We discuss the morphogenetic constraints involved in the evolutionary transition and propose an ecological/adaptive model for the selective pressures that resulted in the evolution of tubulospines. We compare our record with similar, recently described assemblages from Austria and Italy, and we update the biostratigraphy and systematic taxonomy of the key morphospecies involved in the transition.
Quantification of organ motion based on an adaptive image‐based scale invariant feature method
Authors: Paganelli Chiara , Peroni Marta , Baroni Guido , Riboldi Marco 
Published: October 2013

Purpose:The availability of corresponding landmarks in IGRT image series allows quantifying the inter and intrafractional motion of internal organs. In this study, an approach for the automatic localization of anatomical landmarks is presented, with the aim of describing the nonrigid motion of anatomo‐pathological structures in radiotherapy treatments according to local image contrast.Methods:An adaptive scale invariant feature transform (SIFT) was developed from the integration of a standard 3D SIFT approach with a local image‐based contrast definition. The robustness and invariance of the proposed method to shape‐preserving and deformable transforms were analyzed in a CT phantom study. The application of contrast transforms to the phantom images was also tested, in order to verify the variation of the local adaptive measure in relation to the modification of image contrast. The method was also applied to a lung 4D CT dataset, relying on manual feature identification by an expert user as ground truth. The 3D residual distance between matches obtained in adaptive‐SIFT was then computed to verify the internal motion quantification with respect to the expert user. Extracted corresponding features in the lungs were used as regularization landmarks in a multistage deformable image registration (DIR) mapping the inhale vs exhale phase. The residual distances between the warped manual landmarks and their reference position in the inhale phase were evaluated, in order to provide a quantitative indication of the registration performed with the three different point sets.Results:The phantom study confirmed the method invariance and robustness properties to shape‐preserving and deformable transforms, showing residual matching errors below the voxel dimension. The adapted SIFT algorithm on the 4D CT dataset provided automated and accurate motion detection of peak to peak breathing motion. The proposed method resulted in reduced residual errors with respect to standard SIFT, providing a motion description comparable to expert manual identification, as confirmed by DIR.Conclusions:The application of the method to a 4D lung CT patient dataset demonstrated adaptive‐SIFT potential as an automatic tool to detect landmarks for DIR regularization and internal motion quantification. Future works should include the optimization of the computational cost and the application of the method to other anatomical sites and image modalities.
Staphylococcus aureus Protein A Promotes Immune Suppression
Authors: Kobayashi Scott D. , DeLeo Frank R. 
Published: October 2013

ABSTRACTStaphylococcus aureusis a prominent cause of human infections worldwide and is notorious for its ability to acquire resistance to antibiotics. Methicillin-resistantS. aureus(MRSA), in particular, is endemic in hospitals and is the most frequent cause of community-associated bacterial infections in the United States. Inasmuch as treatment options for severe MRSA infections are limited, there is need for a vaccine that protects against such infections. However, recent efforts to generate a staphylococcal vaccine have met with little success in human clinical trials. These failures are somewhat puzzling, since the vaccine antigens tested promote opsonophagocytosisin vitroand confer protection in animal infection models. One possibility is that the pathogen inhibits (and/or fails to elicit) the development of protective immunity in humans. Indeed,S. aureusproduces numerous molecules that can potentially promote immune evasion, including protein A (SpA), an immunoglobulin (Ig)-binding protein present on the bacterial surface and freely secreted into the extracellular environment. SpA binds the Fc region of antibody and the Fab regions of the B-cell receptor, processes that are known to block opsonophagocytosis and cause B-cell deathin vitro. In a recent study, Falugi et al. [F. Falugi, H. K. Kim, D. M. Missiakas, and O. Schneewind, mBio 4(5):e00575-13, 2013] showed that vaccination withspamutantS. aureusstrains lacking antibody Fc- and/or Fab-binding capacity protects against subsequent challenge with the USA300 epidemic strain. The findings provide strong support for the idea that SpA promotesS. aureusimmune evasionin vivoand form the foundation for a new approach in our efforts to develop a vaccine that prevents severeS. aureusinfections.
Site-Specific Determinants of Cutaneous Melanoma: A Case–Case Comparison of Patients with Tumors Arising on the Head or Trunk
Authors: Kvaskoff Marina , Pandeya Nirmala , Green Adèle C. , Perry Susan , Baxter Catherine , Davis Marcia B. , Mortimore Rohan , Westacott Lorraine , Wood Dominic , Triscott Joe , Williamson Richard , Whiteman David C. 
Published: October 2013

Abstract
Background: Cutaneous melanomas have been hypothesized to arise through different pathways according to phenotype, body site, and sun exposure. To further test this hypothesis, we explored associations between phenotype and melanoma at different sites using a case–case comparative approach.
Methods: Melanoma patients (n = 762) aged 18 to 79 years and diagnosed from 2007 to 2010 were ascertained from pathology laboratories in Brisbane, Australia. Patients reported phenotypic information and a dermatologist counted melanocytic nevi and solar keratoses. We compared data for patients with trunk melanoma (n = 541, the reference group), head/neck melanoma (n = 122), or lentigo maligna melanoma (LMM) of the head/neck (n = 69). ORs and 95% confidence intervals were calculated using classical or polytomous logistic regression models.
Results: Compared with trunk melanoma patients, those with head/neck melanoma were significantly less likely to have high nevus counts (≥135: OR = 0.27; Ptrend = 0.0004). Associations between category of nevus count and LMM head/neck were weaker and significantly different (≥135: OR = 1.09; Ptrend = 0.69; Phomogeneity = 0.02). Patients with head/neck melanoma were more likely than those with truncal melanoma to have high solar keratosis counts (≥7: OR = 1.78, Ptrend = 0.04). Again, associations with LMM head/neck were weaker, albeit not significantly different (≥7: OR = 1.61; Ptrend = 0.42; Phomogeneity = 0.86).
Conclusion: Trunk melanomas are more strongly associated with nevus counts than head/neck melanomas, but are less strongly associated with number of solar keratoses, a marker of chronic sun exposure.
Impact: These findings underscore the notion that melanomas on the trunk typically arise through a causal pathway associated with nevus propensity, whereas melanomas on the head/neck arise through a pathway associated with cumulative sun exposure. Cancer Epidemiol Biomarkers Prev; 22(12); 2222–31. ©2013 AACR.
Weekly nab-Rapamycin in Patients with Advanced Nonhematologic Malignancies: Final Results of a Phase I Trial
Authors: Gonzalez-Angulo Ana M. , Meric-Bernstam Funda , Chawla Sant , Falchook Gerald , Hong David , Akcakanat Argun , Chen Huiqin , Naing Aung , Fu Siqing , Wheler Jennifer , Moulder Stacy , Helgason Thorunn , Li Shaoyi , Elias Ileana , Desai Neil , Kurzrock Razelle 
Published: October 2013

Abstract
Purpose: This dose-finding phase I study investigated the maximum-tolerated dose (MTD) and safety of weekly nanoparticle albumin-bound rapamycin (nab-rapamycin) in patients with untreatable advanced nonhematologic malignancies.
Experimental Design: nab-Rapamycin was administered weekly for 3 weeks followed by 1 week of rest, with a starting dose of 45 mg/m2. Additional doses were 56.25, 100, 150, and 125 mg/m2.
Results: Of 27 enrolled patients, 26 were treated. Two dose-limiting toxicities (DLT) occurred at 150 mg/m2 [grade 3 aspartate aminotransferase (AST) elevation and grade 4 thrombocytopenia], and two DLTs occurred at 125 mg/m2 (grade 3 suicidal ideation and grade 3 hypophosphatemia). Thus, the MTD was declared at 100 mg/m2. Most treatment-related adverse events (TRAE) were grade 1/2, including thrombocytopenia (58%), hypokalemia (23%), mucositis (38%), fatigue (27%), rash (23%), diarrhea (23%), nausea (19%), anemia (19%), hypophosphatemia (19%), neutropenia (15%), and hypertriglyceridemia (15%). Only one grade 3 nonhematologic TRAE (dyspnea) and one grade 3 hematologic event (anemia) occurred at the MTD. One patient with kidney cancer had a partial response and 2 patients remained on study for 365 days (patient with mesothelioma) and 238 days (patient with neuroendocrine tumor). The peak concentration (Cmax) and area under the concentration–time curve (AUC) of rapamycin increased with dose between 45 and 150 mg/m2, except for a relatively low AUC at 125 mg/m2. nab-Rapamycin significantly inhibited mTOR targets S6K and 4EBP1.
Conclusions: The clinical dose of single-agent nab-rapamycin was established at 100 mg/m2 weekly (3 of 4 weeks) given intravenously, which was well tolerated with preliminary evidence of response and stable disease, and produced a fairly dose-proportional pharmacokinetic profile in patients with unresectable advanced nonhematologic malignancies. Clin Cancer Res; 19(19); 5474–84. ©2013 AACR.