bluuebunny/crossref_metadata_2025_split huggingface dataset:
Real-Time Dynamics Simulation of Unmanned Sea Surface Vehicle for Virtual Environments
Authors: Thakur Atul , Gupta Satyandra K. 
Published: August 2011

Abstract
The role of virtual environments (VEs) is crucial in efficient design and operation of unmanned vehicles. VEs are extensively used in operator training for tele-operation, planning using programming by demonstration, and hardware and software designs. VE for unmanned sea surface vehicles (USSV) requires a 6 degree of freedom dynamics simulation in the time domain. In order to be interactive, the VE requires real-time performance of the underlying dynamics simulator. In general, the dynamics simulation of USSVs involves the following four main operations: (1) computation of dynamic pressure head due to fluid flow around the hull under the ocean wave, (2) computation of wet surface, (3) computing the surface integral of the dynamic pressure head over the wet surface, and (4) solving the rigid body dynamics equation. The first three operations depend upon the boat geometry complexity and need to be performed at each time step, making the simulation run very slow. In this paper, we address the problem of physics preserving model simplification for real-time potential flow based simulator for a USSV in the time domain, with an arbitrary hull geometry. This paper reports model simplification algorithms based on clustering, temporal coherence, and hardware acceleration using parallel computing on multiple cores to obtain real time simulation performance for the developed VE.
Nonlytic Exocytosis of Cryptococcus neoformans from Macrophages OccursIn Vivoand Is Influenced by Phagosomal pH
Authors: Nicola André Moraes , Robertson Emma J. , Albuquerque Patrícia , Derengowski Lorena da Silveira , Casadevall Arturo 
Published: August 2011

ABSTRACTA unique aspect of the interaction of the fungusCryptococcus neoformanswith macrophages is the phenomenon of nonlytic exocytosis, also referred to as “vomocytosis” or phagosome extrusion/expulsion, which involves the escape of fungal cells from the phagocyte with the survival of both cell types. This phenomenon has been observed onlyin vitrousing subjective and time-consuming microscopic techniques. In spite of recent advances in our knowledge about its mechanisms, a major question still remaining is whether this phenomenon also occursin vivo. In this study, we describe a novel flow cytometric method that resulted in a substantial gain in throughput for studying phagocytosis and nonlytic exocytosisin vitroand used it to explore the occurrence of this phenomenon in a mouse model of infection. Furthermore, we tested the hypothesis that host cell phagosomal pH affected nonlytic exocytosis. The addition of the weak bases ammonium chloride and chloroquine resulted in a significant increase of nonlytic exocytosis events, whereas the vacuolar ATPase inhibitor bafilomycin A1 had the opposite effect. Although all three agents are known to neutralize phagosomal acidity, their disparate effects suggest that phagosomal pH is an important and complex variable in this process. Our experiments established that nonlytic exocytosis occurredin vivowith a frequency that is possibly much higher than that observedin vitro. These results in turn suggest that nonlytic exocytosis has a potential role in the pathogenesis of cryptococcosis.IMPORTANCECryptococcus neoformanscauses disease in people with immune deficiencies such as AIDS. Upon infection,C. neoformanscells are ingested by macrophage immune cells, which provide a niche for survival and replication. After ingestion, macrophages can expel the fungi without causing harm to either cell type, a process named nonlytic exocytosis. To dissect this phenomenon, we evaluated its dependence on the pH inside the macrophage and addressed its occurrence during infection of mice. We developed new techniques using flow cytometry to measureC. neoformansinternalization by and nonlytic exocytosis from macrophages. Neutralizing the phagosome acidity changed the rate of nonlytic exocytosis: activity increased with the weak bases chloroquine and ammonium chloride, whereas the vacuolar ATPase inhibitor bafilomycin A1 caused it to decrease. Experiments in mice suggested that nonlytic exocytosis occurred during infection withC. neoformans. These results shed new light on the interaction betweenC. neoformansand host macrophages.
Pharmacokinetic research in children: an analysis of registered records of clinical trials
Authors: Viergever Roderik F , Rademaker Carin M A , Ghersi Davina 
Published: August 2011

BackgroundReported off-label/unlicensed prescribing rates in children range from 11% to 80%. Research into pharmacokinetic profiles of children's medicines is essential in the creation of more knowledge on the safety and efficacy of medicines in children. This study investigated how often pharmacokinetic data are collected in clinical trials of medicines in children by analysing registered records of clinical trials.MethodsThe registered records of all clinical trials in children that were recruiting on 22 May 2009 were identified on the International Clinical Trials Registry Platform using a Clinical Trials in Children search filter. The records of trials in children below 12 years of age, in which the intervention was one or more medicines, were assessed for evidence that pharmacokinetic data would be collected.ResultsOf 1081 eligible trial records, 257 (24%) declared that pharmacokinetic data would be collected. Of these trials, 199 (77%) recruited in Northern America; recruitment in all other regions was below 20%. Trials recruited most often in children over 2 years of age (74%), and least often in newborn infants (32%). Most trials researched medicines in the field of cancer (29%). Trials investigated one-third of the medicines that were indicated as a priority for pharmacokinetic research by the European Medicines Agency.ConclusionsThere is a need for increased knowledge of the pharmacokinetic profiles of children's medicines. The amount of currently ongoing pharmacokinetic research does not seem to address adequately the lack of knowledge in this area. This study sets a baseline for monitoring of future progress on the amount of ongoing pharmacokinetic research in children.
Exploring health professionals' views regarding the optimum physical environment for palliative and end of life care in the acute hospital setting: a qualitative study: Table 1
Authors: Gardiner Clare , Brereton Louise , Gott Merryn , Ingleton Christine , Barnes Sarah 
Published: August 2011

BackgroundLimited evidence exists relating to key elements of the optimum physical hospital environment for patients receiving palliative and end of life care in acute hospitals. The aim of this study was to explore the perspectives of health professionals regarding the optimum physical environment for palliative and end of life care in the acute hospital setting.MethodsQualitative focus group study with 24 health professionals from an acute hospital, a community hospital and a hospice.Findings Participants agreed that provision of appropriate privacy options was key to achieving an optimum physical environment. However, there was little consensus as to whether single room accommodation or multi-bed accommodation was the most appropriate. A comfortable and homely environment is important, but difficult to achieve in a clinically focused environment. The hospital environment may also be suboptimal for staff provision of care. The environmental needs of families should be considered alongside the needs of patients.ConclusionMany deficiencies exist in physical hospital environments for patients at the end of life. However, changes to the hospital environment are limited by resource restrictions, increasing rules and regulations, and a focus on clinical aspects of care. Further research is needed to establish patient and family views about the optimum physical hospital environment, to explore ways in which an appropriate environment can be most effectively achieved and to ensure engagement with planners, designers and stakeholders when commissioning new hospitals or renovating existing facilities.
The reciprocal relationships between changes in adolescent perceived prevalence of smoking in movies and progression of smoking status
Authors: Choi Kelvin , Forster Jean , Erickson Darin , Lazovich DeAnn , Southwell Brian G 
Published: August 2011

BackgroundSmoking in movies is associated with adolescent smoking worldwide. To date, studies of the association mostly are restricted to the exposure to smoking images viewed by 9–15-year-olds. The association among older adolescents is rarely examined. In addition, the reciprocal effect of smoking behaviour on subsequent reported exposure to smoking in movies has not been reported.MethodsData were from the Minnesota Adolescent Community Cohort Study collected every 6 months from 2000 to 2007 when participants were between the ages of 12 and 18 (n=4745). We estimated the prospective effect of the perceived prevalence of smoking in movies (four levels, from never to most of the time) on smoking stage (SS) measured 6 months later (six stages, from never-smoker to established smoker) and the reciprocal prospective association between the two factors. Estimates were adjusted for demographic factors.ResultsThe perceived prevalence of smoking in movies measured between ages 13½ and 15½ consistently predicted subsequent SS. The association was inconsistent after the age of 15½. SS did not consistently predict subsequent perception of the prevalence of smoking in movies.ConclusionsPerceived exposure to movie smoking primarily influenced teenagers' smoking behaviour at younger ages. If future studies confirm this finding, developing and evaluating interventions to improve young teenagers' resistance to these images may complement policies to reduce smoking in movies to reduce prevalence of adolescent smoking.
β-Glucosidases from a new Aspergillus species can substitute commercial β-glucosidases for saccharification of lignocellulosic biomass
Authors: Sørensen Annette , Lübeck Peter Stephensen , Lübeck Mette , Teller Philip Johan , Ahring Birgitte Kiær 
Published: August 2011

β-Glucosidase activity plays an essential role for efficient and complete hydrolysis of lignocellulosic biomass. Direct use of fungal fermentation broths can be cost saving relative to using commercial enzymes for production of biofuels and bioproducts. Through a fungal screening program for β-glucosidase activity, strain AP (CBS 127449, Aspergillus saccharolyticus ) showed 10 times greater β-glucosidase activity than the average of all other fungi screened, with Aspergillus niger showing second greatest activity. The potential of a fermentation broth of strain AP was compared with the commercial β-glucosidase-containing enzyme preparations Novozym 188 and Cellic CTec. The fermentation broth was found to be a valid substitute for Novozym 188 in cellobiose hydrolysis. The Michaelis–Menten kinetics affinity constant as well as performance in cellobiose hydrolysis with regard to product inhibition were found to be the same for Novozym 188 and the broth of strain AP. Compared with Novozym 188, the fermentation broth had higher specific activity (11.3 U/mg total protein compared with 7.5 U/mg total protein) and also increased thermostability, identified by the thermal activity number of 66.8 vs. 63.4 °C for Novozym 188. The significant thermostability of strain AP β-glucosidases was further confirmed when compared with Cellic CTec. The β-glucosidases of strain AP were able to degrade cellodextrins with an exo-acting approach and could hydrolyse pretreated bagasse to monomeric sugars when combined with Celluclast 1.5L. The fungus therefore showed great potential as an onsite producer for β-glucosidase activity.
A few useful considerations in the development of intra-day trading software
Authors: Sharma Arun , Gupta Samarth 
Published: August 2011

Trading has evolved from being merely an "open outcry" to becoming tech-savvy and computer intensive. With the stock exchanges computerizing the trading procedures and the traders following suit there was a need felt to upgrade the trading systems in sync with the innovational changes in technology like ECN (Electronic Communication Network) and SOES (Short Order Execution System). In their quest for maximizing gains while reducing risk and brokerage, trading companies fell over the idea of using computers for latency based arbitrage in an intra-day trading setup. It became quite empirical that better machinery meant more profits.
The present paper realizes that for a vendor to develop the most efficient intra-day trading systems, it is necessary to incorporate various software standards that are otherwise of very little concern in other domains. This paper focuses on how the Indian software industry can put their clients at an advantage by adopting certain strategies which are a general feature of their western counterparts. Hence it is attempted to compare how the Indian trading software lag behind the internationally accepted software and how these shortcomings can be overcome.
Mobile computing
Authors: Satyanarayanan Mahadev 
Published: August 2011

In the inaugural issue of MC2R in April 1997 [24], I highlighted the seminal influence of mobility in computing. At that time, the goal of "information at your fingertips anywhere, anytime" was only a dream. Today, through relentless pursuit of innovations in wireless technology, energy-efficient portable hardware and adaptive software, we have largely attained this goal. Ubiquitous email and Web access is a reality that is experienced by millions of users worldwide through their Blackberries, iPhones, iPads, Windows Phone devices, and Android-based devices. Mobile Web-based services and location-aware advertising opportunities have emerged, triggering large commercial investments. Mobile computing has arrived as a lucrative business proposition.
Looking ahead, what are the dreams that will inspire our future efforts in mobile computing? We begin this paper by considering some imaginary mobile computing scenarios from the future. We then extract the deep assumptions implicit in these scenarios, and use them to speculate on the future trajectory of mobile computing.
Long Noncoding RNA, Polycomb, and the Ghosts Haunting INK4b-ARF-INK4a Expression
Authors: Aguilo Francesca , Zhou Ming-Ming , Walsh Martin J. 
Published: August 2011

Abstract
Polycomb group proteins (PcG) function as transcriptional repressors of gene expression. The important role of PcG in mediating repression of the INK4b-ARF-INK4a locus, by directly binding to the long noncoding RNA (lncRNA) transcript antisense noncoding RNA in the INK4 locus (ANRIL), was recently shown. INK4b-ARF-INK4a encodes 3 tumor-suppressor proteins, p15INK4b, p14ARF, and p16INK4a, and its transcription is a key requirement for replicative or oncogene-induced senescence and constitutes an important barrier for tumor growth. ANRIL gene is transcribed in the antisense orientation of the INK4b-ARF-INK4a gene cluster, and different single-nucleotide polymorphisms are associated with increased susceptibility to several diseases. Although lncRNA-mediated regulation of INK4b-ARF-INK4a gene is not restricted to ANRIL, both polycomb repressive complex-1 (PRC1) and -2 (PRC2) interact with ANRIL to form heterochromatin surrounding the INK4b-ARF-INK4a locus, leading to its repression. This mechanism would provide an increased advantage for bypassing senescence, sustaining the requirements for the proliferation of stem and/or progenitor cell populations or inappropriately leading to oncogenesis through the aberrant saturation of the INK4b-ARF-INK4a locus by PcG complexes. In this review, we summarize recent findings on the underlying epigenetic mechanisms that link PcG function with ANRIL, which impose gene silencing to control cellular homeostasis as well as cancer development. Cancer Res; 71(16); 5365–9. ©2011 AACR.
B-Myb, Cancer, Senescence, and MicroRNAs
Authors: Martinez Ivan , DiMaio Daniel 
Published: August 2011

Abstract
The transcription factor B-Myb plays a critical role in regulating gene expression and is implicated in controlling carcinogenesis and cellular senescence. Transcription of the B-Myb gene is regulated by retinoblastoma proteins acting directly on the B-Myb promoter. Recently, we found that microRNAs also control the abundance of B-Myb mRNA during senescence, adding another level of complexity to B-Myb regulation. This review focuses on the importance of B-Myb in cancer and senescence, with an emphasis on the regulation of B-Myb expression and activity. Cancer Res; 71(16); 5370–3. ©2011 AACR.
Prognostic Model for Survival in Patients with Metastatic Renal Cell Carcinoma: Results from the International Kidney Cancer Working Group
Authors: Manola Judith , Royston Patrick , Elson Paul , McCormack Jennifer Bacik , Mazumdar Madhu , Négrier Sylvie , Escudier Bernard , Eisen Tim , Dutcher Janice , Atkins Michael , Heng Daniel Y.C. , Choueiri Toni K. , Motzer Robert , Bukowski Ronald 
Published: August 2011

Abstract
Purpose: To develop a single validated model for survival in metastatic renal cell carcinoma (mRCC) using a comprehensive international database.
Experimental Design: A comprehensive database of 3,748 patients including previously reported clinical prognostic factors was established by pooling patient-level data from clinical trials. Following quality control and standardization, descriptive statistics were generated. Univariate analyses were conducted using proportional hazards models. Multivariable analysis using a log–logistic model stratified by center and multivariable fractional polynomials was conducted to identify independent predictors of survival. Missing data were handled using multiple imputation methods. Three risk groups were formed using the 25th and 75th percentiles of the resulting prognostic index. The model was validated using an independent data set of 645 patients treated with tyrosine kinase inhibitor (TKI) therapy.
Results: Median survival in the favorable, intermediate and poor risk groups was 26.9 months, 11.5 months, and 4.2 months, respectively. Factors contributing to the prognostic index included treatment, performance status, number of metastatic sites, time from diagnosis to treatment, and pretreatment hemoglobin, white blood count, lactate dehydrogenase, alkaline phosphatase, and serum calcium. The model showed good concordance when tested among patients treated with TKI therapy (C statistic = 0.741, 95% CI: 0.714–0.768).
Conclusions: Nine clinical factors can be used to model survival in mRCC and form distinct prognostic groups. The model shows utility among patients treated in the TKI era. Clin Cancer Res; 17(16); 5443–50. ©2011 AACR.
Stimulating Cardiac Muscle by Light
Authors: Jia Zhiheng , Valiunas Virginijus , Lu Zongju , Bien Harold , Liu Huilin , Wang Hong-Zhang , Rosati Barbara , Brink Peter R. , Cohen Ira S. , Entcheva Emilia 
Published: August 2011

Background—
After the recent cloning of light-sensitive ion channels and their expression in mammalian cells, a new field, optogenetics, emerged in neuroscience, allowing for precise perturbations of neural circuits by light. However, functionality of optogenetic tools has not been fully explored outside neuroscience, and a nonviral, nonembryogenesis-based strategy for optogenetics has not been shown before.

Methods and Results—
We demonstrate the utility of optogenetics to cardiac muscle by a tandem cell unit (TCU) strategy, in which nonexcitable cells carry exogenous light-sensitive ion channels, and, when electrically coupled to cardiomyocytes, produce optically excitable heart tissue. A stable channelrhodopsin2 (ChR2)-expressing cell line was developed, characterized, and used as a cell delivery system. The TCU strategy was validated in vitro in cell pairs with adult canine myocytes (for a wide range of coupling strengths) and in cardiac syncytium with neonatal rat cardiomyocytes. For the first time, we combined optical excitation and optical imaging to capture light-triggered muscle contractions and high-resolution propagation maps of light-triggered electric waves, found to be quantitatively indistinguishable from electrically triggered waves.

Conclusions—
Our results demonstrate feasibility to control excitation and contraction in cardiac muscle by light, using the TCU approach. Optical pacing in this case uses less energy, offers superior spatiotemporal control and remote access and can serve not only as an elegant tool in arrhythmia research but may form the basis for a new generation of light-driven cardiac pacemakers and muscle actuators. The TCU strategy is extendable to (nonviral) stem cell therapy and is directly relevant to in vivo applications.
Reciprocal Transcriptional Regulation of Metabolic and Signaling Pathways Correlates With Disease Severity in Heart Failure
Authors: Barth Andreas S. , Kumordzie Ami , Frangakis Constantine , Margulies Kenneth B. , Cappola Thomas P. , Tomaselli Gordon F. 
Published: August 2011

Background—
Systolic heart failure (HF) is a complex systemic syndrome that can result from a wide variety of clinical conditions and gene mutations. Despite phenotypic similarities, characterized by ventricular dilatation and reduced contractility, the extent of common and divergent gene expression between different forms of HF remains a matter of intense debate.

Methods and Results—
Using a meta-analysis of 28 experimental (mouse, rat, dog) and human HF microarray studies, we demonstrate that gene expression changes are characterized by a coordinated and reciprocal regulation of major metabolic and signaling pathways. In response to a wide variety of stressors in animal models of HF, including ischemia, pressure overload, tachypacing, chronic isoproterenol infusion, Chagas disease, and transgenic mouse models, major metabolic pathways are invariably downregulated, whereas cell signaling pathways are upregulated. In contrast to this uniform transcriptional pattern that recapitulates a fetal gene expression program in experimental animal models of HF, human HF microarray studies displayed a greater heterogeneity, with some studies even showing upregulation of metabolic and downregulation of signaling pathways in end-stage human hearts. These discrepant results between animal and human studies are due to a number of factors, prominently cardiac disease and variable exposure to cold cardioplegic solution in nonfailing human samples, which can downregulate transcripts involved in oxidative phosphorylation (OXPHOS), thus mimicking gene expression patterns observed in failing samples. Additionally, β-blockers and ACE inhibitor use in end-stage human HF was associated with higher levels of myocardial OXPHOS transcripts, thus partially reversing the fetal gene expression pattern. In human failing samples, downregulation of metabolism was associated with hemodynamic markers of disease severity.

Conclusions—
Irrespective of the etiology, gene expression in failing myocardium is characterized by downregulation of metabolic transcripts and concomitant upregulation of cell signaling pathways. Gene expression changes along this metabolic-signaling axis in mammalian myocardium are a consistent feature in the heterogeneous transcriptional response observed in phenotypically similar models of HF.