bluuebunny/crossref_metadata_2025_split huggingface dataset:
EPIC: A framework to exploit parallelism in irregular codes
Authors: Neves Diogo Telmo 
Published: May 2016

SummaryTo harness the performance potential of current multicore processors, a multitude of algorithms, frameworks and libraries have been developed. Nevertheless, it is still extremely difficult to take advantage of the full potential of multicore processors. Moreover, when using third‐party tools and/or in the presence of asymmetric sets of tasks, this problem would only aggravate. The EPIC framework was developed to ease the exploitation of task parallelism in irregular applications that use third‐party tools and/or generate asymmetric sets of tasks. It is based on a software design and implements two algorithms that, together, allow, in a seamlessly way, the efficient exploitation of coarse‐grained parallelism, fine‐grained parallelism, and the combination of both of these types. Thus, it becomes possible to make a better and transparent usage of the performance potential of current multicore processors on shared‐memory systems. In this paper, we present two refinements to the EPIC framework: one that refines the software design of the EPIC framework and another that refines the scheduling algorithm of the EPIC framework. Together, these refinements allow to cope with a special class of sets of tasks: sets of tasks where asymmetry is insignificant or can be neglected. Thus, these refinements broaden the applicability of the EPIC framework to a large class of irregular applications where task parallelism can be exploited. To assess the feasibility and the benefit of using this new version of the EPIC framework to exploit task parallelism, we used four real‐world irregular applications—three from phylogenetics and another from astrophysics—and several input data sets with different characteristics. Our studies show groundbreaking results in terms of the achieved speedups and that scalability is not impaired, even when using third‐party tools and/or in the presence of (a)symmetric sets of tasks. Copyright © 2016 John Wiley & Sons, Ltd.
WISP: A pattern‐based approach to the interchange of scientific workflow specifications
Authors: Bastos Bruno F. , Braga Regina Maria M. , Gomes Antonio Tadeu A. 
Published: May 2016

SummaryScientific workflows are used for dealing with complex problems in different e‐science domains. These workflows are modeled and executed using Scientific Workflow Management Systems (SWfMSs). Generally, SWfMSs provide their own Workflow Specification Language, and this is a challenge considering the possibility of interchanging workflow specifications between different SWfMSs. In this paper, we propose the use of workflow patterns combined with software architecture concepts to capture the key semantics expressed in scientific workflows specified in different Workflow Specification Languages. These concepts are materialized in a novel specification interchange language (and associated tooling) called Workflow Interchange in Science with Patterns (WISP), which is the main contribution of our work. We have evaluated WISP based on real world specifications; in this paper, we present the results of such evaluation (including an assessment of the quality of the research material available), which has eventually led us to reformulate our initial proposal with more stringent assumptions on the input and output specifications. Copyright © 2016 John Wiley & Sons, Ltd.
A social content delivery network for e‐Science
Authors: Chard Kyle , Caton Simon , Kugler Kai , Rana Omer , Katz Daniel S. 
Published: May 2016

SummaryWe are in the midst of a scientific data explosion in which the rate of data growth is rapidly increasing. While large‐scale research projects have developed sophisticated data distribution networks to share their data with researchers globally, there is no such support for the many millions of research projects generating data of interest to much smaller audiences (as exemplified by the long tail scientist). In data‐oriented research, every aspect of the research process is influenced by data access. However, sharing and accessing data efficiently as well as lowering access barriers are difficult. In the absence of dedicated large‐scale storage, many have noted that there is an enormous storage capacity available via connected peers, none more so than the storage resources of many research groups. With widespread usage of the content delivery network model for disseminating web content, we believe a similar model can be applied to distributing, sharing, and accessing long tail research data in an e‐Science context. We describe the vision and architecture of a social content delivery network – a model that leverages the social networks of researchers to automatically share and replicate data on peers' resources based upon shared interests and trust. Using this model, we describe a simulator and investigate how aspects such as user activity, geographic distribution, trust, and replica selection algorithms affect data access and storage performance. From these results, we show that socially informed replication strategies are comparable with more general strategies in terms of availability and outperform them in terms of spatial efficiency. Copyright © 2016 John Wiley & Sons, Ltd.
A dedicated private‐shared cache design for scalable multiprocessors
Authors: Cebrián Juan M. , Fernández‐Pascual Ricardo , Jimborean Alexandra , Acacio Manuel E. , Ros Alberto 
Published: May 2016

SummaryMost modern architectures are based on a shared‐memory design. Correctness of these architectures is ensured by means of coherence protocols and consistency models. However, performance and scalability of shared‐memory systems is usually constrained by the amount and size of the messages used to keep the memory subsystem coherent. This is not only important in high performance computing, but also in low power embedded systems, specially if coherence is required between different components of the system‐on‐chip. We argue that using the same mechanism to keep coherence for all memory accesses can be counterproductive, because it incurs unnecessary overhead for data addresses that would remain coherent after the access (i.e., private data and read‐only shared data). This paper proposes the use of dedicated caches for two different kinds of data (i) data that can be accessed without contacting other nodes and (ii) modifiable shared data. The private cache (L1P) will be independent for each core and will store private data and read‐only shared data. On the other hand, the shared cache (L1S), will be logically shared but physically distributed for all cores. With this design, we can significantly simplify the coherence protocol, reduce the on‐chip area requirements and reduce invalidation time. However, this dedicated cache design requires a classification mechanism to detect the nature of the data that is being accessed. Results show two drawbacks to this approach: first, the accuracy of the classification mechanism has a huge impact on performance. Second, a traditional interconnection network is not optimal for accessing the L1S, increasing register‐to‐cache latency when accessing shared data. Copyright © 2016 John Wiley & Sons, Ltd.
Production of 3‐D Airway Organoids From Primary Human Airway Basal Cells and Their Use in High‐Throughput Screening
Authors: Hild Marc , Jaffe Aron B. 
Published: May 2016

AbstractThe ability of human airway basal cells to serve as progenitor cells in the conducting airway makes them an attractive target in a number of respiratory diseases associated with epithelial remodeling. This unit describes a protocol for the culture of ‘bronchospheres’, three‐dimensional (3‐D) organoids that are derived from primary human airway basal cells. Mature bronchospheres are composed of functional multi‐ciliated cells, mucin‐producing goblet cells, and airway basal cells. In contrast to existing methods used for the culture of well‐differentiated human airway epithelial cells, bronchospheres do not require growth on a permeable support and can be cultured in 384‐well assay plates. The system provides a mechanism for investigating the regulation of basal cell fate during airway epithelial morphogenesis, as well as a basis for studying the function of the human airway epithelium in high‐throughput assays. © 2016 by John Wiley & Sons, Inc.
European canine lymphoma network consensus recommendations for reporting flow cytometry in canine hematopoietic neoplasms
Authors: Comazzi S. , Avery P. R. , Garden O. A. , Riondato F. , Rütgen B. , Vernau W. ,   on behalf of the European Canine Lymphoma Network
Published: May 2016

BackgroundFlow cytometry (FC) is assuming increasing importance in diagnosis in veterinary oncology. The European Canine Lymphoma Network (ECLN) is an international cooperation of different institutions working on canine lymphoma diagnosis and therapy. The ECLN panel of experts on FC has defined the issue of reporting FC on canine lymphoma and leukemia as their first hot topic, since a standardized report that includes all the important information is still lacking in veterinary medicine.MethodsThe flow cytometry panel of the ECLN started a consensus initiative using the Delphi approach. Clinicians were considered the main target of FC reports. A panel of experts in FC was interrogated about the important information needed from a report.ResultsUsing the feedback from clinicians and subsequent discussion, a list of information to be included in the report was made, with four different levels of recommendation. The final report should include both a quantitative part and a qualitative or descriptive part with interpretation of the salient results. Other items discussed included the necessity of reporting data regarding the quality of samples, use of absolute numbers of positive cells, cutoff values, the intensity of fluorescence, and possible aberrant patterns of antigen expression useful from a clinical point of view.ConclusionThe consensus initiative is a first step toward standardization of diagnostic approach to canine hematopoietic neoplasms among different institutions and countries. This harmonization will improve communication and patient care and also facilitate the multicenter studies necessary to further our knowledge of canine hematopoietic neoplasms. © 2016 International Clinical Cytometry Society
Isobolographic Analysis of the Interaction Between Tapentadol and Ketorolac in a Mouse Model of Visceral Pain
Authors: Zapata‐Morales Juan R. , Aragon‐Martinez Othoniel H. , Adriana Soto‐Castro Tely , Alonso‐Castro Ángel J. , Castañeda‐Santana Demian I. , Isiordia‐Espinoza Mario A. 
Published: May 2016

Abstract

Preclinical Research

The aim of this experimental assay was to assess the antinociceptive interaction between tapentadol and ketorolac in the acetic acid‐induced writhing model in mice. Tapentadol (5.62–31.6 mg/kg ip) or ketorolac (5.62–31.6 mg/kg ip) were administered 15 min before the acetic acid administration. The ED50 values of the individual drugs were determined and different proportions (tapentadol–ketorolac in 1:1, 3:1, and 1:3) were assayed in combination in the writhing test. Isobolographic analysis and the interaction index demonstrated an antinociceptive synergistic interaction between tapentadol and ketorolac in all combination. Thus, the experimental ED50 values were lower when compared with their theoretical ED50 values. These data suggest that the tapentadol–ketorolac combination produces an antinociceptive synergistic interaction in the mouse acetic acid‐induced writhing model. Drug Dev Res 77 : 187–191, 2016.   © 2016 Wiley Periodicals, Inc.
Dynamic Lightpath Establishment Considering Four‐Wave Mixing for Achieving Low‐Power All‐Optical Networks
Authors: HIRATA KOUJI , MURAGUCHI MASAHIRO 
Published: May 2016

SUMMARYThis paper proposes a method for dynamically establishing a lightpath that takes into consideration power consumption and four‐wave mixing (FWM) in an all‐optical network. In an all‐optical network, an optical fiber amplifier is used to amplify a group of optical signals of different wavelengths in a fiber without O/E/O conversion. Even if only one optical signal passes through an optical fiber amplifier in a fiber, the optical fiber amplifier operates. Thus, to efficiently use the power of an optical fiber amplifier, multiple optical signals in the fiber should be simultaneously amplified. FWM is one of the most important physical impediments to be resolved an in all‐optical network because FWM degrades the performance of such networks. The FWM power in a fiber increases with the number of wavelengths used in the fiber. Therefore, in order to reduce the FWM power, it is preferable to have optical signals be transmitted on different fibers. The proposed method provides an ingenious path, wavelength, and fiber selection strategy that takes the trade‐off between power consumption and FWM power into account. Furthermore, the proposed method avoids blocking of lightpath establishment due to depletion of wavelength resources. Through simulation experiments, we show that the proposed method can efficiently reduce the blocking probability, power consumption, and FWM power when the number of fibers is fixed.
Estimation of Number of Comparators Required in N‐Bit Stochastic Flash AD Converters
Authors: SUGIMOTO TOSHIKI , TANIMOTO HIROSHI , YOSHIZAWA SHINGO 
Published: May 2016

SUMMARYThe peak SQNR is theoretically calculated for stochastic flash AD converters (SFADC) composed of n comparators with uniformly distributed threshold voltages. A systematic estimation method is presented to obtain the minimum required number of comparators for realizing specified SFADC resolution by using comparators with uniformly distributed threshold voltages. The proposed method has been supported by numerical simulations.
Preparation of Phosphorescent Polymer Patterns by Spin‐Coating Photoreactive Small Molecules
Authors: MIYAGAWA DAICHI , MUROYAMA MASAKAZU , TANAKA KUNIAKI , USUI HIROAKI 
Published: May 2016

SUMMARYPatterned polymer thin films were prepared by spin‐coating a solution consisting of an acryl monomer of 2‐(9H‐carbazol‐9‐yl)ethylmethacrylate, a photoinitiator of 4‐(dimethylamino)benzophenone, and a phosphorescent dopant of iridium(III) bis(2‐phenylpyridinate(4‐vinylphenylpyridine)). The film was exposed to ultraviolet (UV) light through a photomask and rinsed with an organic solvent to develop a patterned polymer thin film. A mixture of tetrahydrofuran and 1,4‐dioxane was used as the spin‐coating solvent, and ethanol was used as the developing solution. The effects of solvent, exposure time, UV intensity, and the phosphorescent dopant were examined to optimize the patterning condition. The patterned film was utilized as an emissive layer to construct an organic light‐emitting diode.
Initiating sacubitril/valsartan (LCZ696) in heart failure: results of TITRATION, a double‐blind, randomized comparison of two uptitration regimens
Authors: Senni Michele , McMurray John J.V. , Wachter Rolf , McIntyre Hugh F. , Reyes Antonio , Majercak Ivan , Andreka Peter , Shehova‐Yankova Nina , Anand Inder , Yilmaz Mehmet B. , Gogia Harinder , Martinez‐Selles Manuel , Fischer Steffen , Zilahi Zsolt , Cosmi Franco , Gelev Valeri , Galve Enrique , Gómez‐Doblas Juanjo J. , Nociar Jan , Radomska Maria , Sokolova Beata , Volterrani Maurizio , Sarkar Arnab , Reimund Bernard , Chen Fabian , Charney Alan 
Published: May 2016

AbstractAimsTo assess the tolerability of initiating/uptitrating sacubitril/valsartan (LCZ696) from 50 to 200 mg twice daily (target dose) over 3 and 6 weeks in heart failure (HF) patients (ejection fraction ≤35%).Methods and resultsA 5‐day open‐label run‐in (sacubitril/valsartan 50 mg twice daily) preceded an 11‐week, double‐blind, randomization period [100 mg twice daily for 2 weeks followed by 200 mg twice daily (‘condensed’ regimen) vs. 50 mg twice daily for 2 weeks, 100 mg twice daily for 3 weeks, followed by 200 mg twice daily (‘conservative’ regimen)]. Patients were stratified by pre‐study dose of angiotensin‐converting enzyme inhibitor/angiotensin‐receptor blocker (ACEI/ARB; low‐dose stratum included ACEI/ARB‐naïve patients). Of 540 patients entering run‐in, 498 (92%) were randomized and 429 (86.1% of randomized) completed the study. Pre‐defined tolerability criteria were hypotension, renal dysfunction and hyperkalaemia; and adjudicated angioedema, which occurred in (‘condensed’ vs. ‘conservative’) 9.7% vs. 8.4% (P = 0.570), 7.3% vs. 7.6% (P = 0.990), 7.7% vs. 4.4% (P = 0.114), and 0.0% vs. 0.8% of patients, respectively. Corresponding proportions for pre‐defined systolic blood pressure <95 mmHg, serum potassium >5.5 mmol/L, and serum creatinine >3.0 mg/dL were 8.9% vs. 5.2% (P = 0.102), 7.3% vs. 4.0% (P = 0.097), and 0.4% vs. 0%, respectively. In total, 378 (76%) patients achieved and maintained sacubitril/valsartan 200 mg twice daily without dose interruption/down‐titration over 12 weeks (77.8% vs. 84.3% for ‘condensed’ vs. ‘conservative’; P = 0.078). Rates by ACEI/ARB pre‐study dose stratification were 82.6% vs. 83.8% (P = 0.783) for high‐dose/‘condensed’ vs. high‐dose/‘conservative’ and 84.9% vs. 73.6% (P = 0.030) for low‐dose/‘conservative’ vs. low‐dose/‘condensed’.ConclusionsInitiation/uptitration of sacubitril/valsartan from 50 to 200 mg twice daily over 3 or 6 weeks had a tolerability profile in line with other HF treatments. More gradual initiation/uptitration maximized attainment of target dose in the low‐dose ACEI/ARB group.
PESERA‐PEAT: a fluvial erosion model for blanket peatlands
Authors: Li Pengfei , Holden Joseph , Irvine Brian , Grayson Richard 
Published: May 2016

AbstractIn peatlands, fluvial erosion can lead to a dramatic decline in hydrological function, major changes in the net carbon balance and loss of biodiversity. Climate and land management change are thought to be important influences on rates of peat erosion. However, sediment production in peatlands is different to that of other soils and no models of erosion specifically for peatlands currently exist. Hence, forecasting the influence of future climate or spatially‐distributed management interventions on peat erosion is difficult. The PESERA‐GRID model was substantially modified in this study to include dominant blanket peat erosion processes. In the resulting fluvial erosion model, PESERA‐PEAT, freeze–thaw and desiccation processes were accounted for by a novel sediment supply index as key features of erosion. Land management practices were parameterized for their influence on vegetation cover, biomass and soil moisture condition. PESERA‐PEAT was numerically evaluated using available field data from four blanket peat‐covered catchments with different erosion conditions and management intensity. PESERA‐PEAT was found to be robust in modelling fluvial erosion in blanket peat. A sensitivity analysis of PESERA‐PEAT showed that modelled sediment yield was more sensitive to vegetation cover than other tested factors such as precipitation, temperature, drainage density and ditch/gully depth. Two versions of PESERA‐PEAT, equilibrium and time‐series, produced similar results under the same environmental conditions, facilitating the use of the model at different scales. The equilibrium model is suitable for assessing the high‐resolution spatial variability of average monthly peat erosion over the study period across large areas (national or global assessments), while the time‐series model is appropriate for investigating continuous monthly peat erosion throughout study periods across smaller areas or large regions using a coarser‐spatial resolution. PESERA‐PEAT will therefore support future investigations into the impact of climate change and management options on blanket peat erosion at various spatial and temporal scales. Copyright © 2016 John Wiley & Sons, Ltd.
Water flow and solute transport model of potentially toxic elements through unsaturated zone at regional wellfield Kosnica
Authors: Ružičić Stanko , Mileusnić Marta , Posavec Kristijan , Nakić Zoran , Durn Goran , Filipović Vilim 
Published: May 2016

AbstractThe objective of this work was to build a prognostic water flow model and potentially toxic elements (lead, cadmium, zinc) transport model in the unsaturated zone. Research was conducted in the catchment area of Kosnica regional wellfield, where the unsaturated zone is characterised by Fluvisol. Lower sorption capacities were determined in the first horizons for all three potentially toxic elements. Correlation coefficient of the measured and simulated values of tracer concentration is 0.58 for the AC horizon and 0.84 for the 2C/C1 horizon. Based on calibrated water flow and transport parameters, a prognostic water flow model and potentially toxic elements (lead, cadmium, zinc) transport model in the unsaturated zone was built. In case of an accidental spill of potentially toxic elements with concentrations of 1000 mg/l, the risk of contamination of the aquifer is present. Copyright © 2016 John Wiley & Sons, Ltd.
Sensitivity of physical lake processes to climate change within a large Precambrian Shield catchment
Authors: Crossman J. , Eimers M. C. , Kerr J. G. , Yao H. 
Published: May 2016

AbstractPotential future changes in lake physical processes (e.g. stratification and freezing) can be assessed through exploring their sensitivity to climate change, and assessing the current vulnerability of different lake types to plausible changes in meteorological drivers. This study quantifies the impacts of climate change and sensitivity of lake physical processes within a large (5100 km2) Precambrian Shield catchment in south‐central Ontario. Historic regional relationships are established between climate drivers, lake morphology, and lake physical changes through generalized linear modelling (GLM), and are used to quantify likely changes in timing of ice phenology and lake stratification across 72 lakes under a range of future climate models and scenarios.In response to projections of increased temperature (ensemble mean of +3.3 °C), both earlier ice‐off and onset of summer stratification were projected, with later ice‐on and fall turnover compared to the baseline. Process sensitivity to climate change varied by lake type; shallower lakes with a smaller volume (less than 15 m deep and less than 0.05 km3) were more sensitive to processes associated with lake heating (stratification onset and ice‐off), and deeper lakes with a larger surface area (greater than 30 m deep and greater than 1000 ha) were more sensitive to processes associated with lake cooling (fall turnover and ice‐on). These results indicate that whereas small lakes are vulnerable to climate warming because of changes that occur in spring and summer, larger lakes are particularly sensitive during the fall. The findings suggest that lake morphology and associated sensitivity should be considered in the development of sustainable lake management strategies. Copyright © 2016 John Wiley & Sons, Ltd.