bluuebunny/crossref_metadata_2025_split huggingface dataset:
Failure analysis and prediction for the CIPRES science gateway
Authors: Singh Kritika , Smallen Shava , Tilak Sameer , Saul Lawrence 
Published: November 2015

SummaryScience gateways promote collaboration among researchers by providing them with access to community‐developed tools and data collections. The Cyberinfrastructure for Phylogenetic Research (CIPRES) science gateway is one of the most popular gateways, with approximately 3000 active users since 2012, and the user base is growing each year. While increasing the number of compute resources available to CIPRES would address their growth needs, it also introduces additional complexity as the likelihood of failure increases. In this paper, we analyze historical job data from CIPRES and combine it with historical software and services monitoring data to create a machine learning model to predict where a user's job will complete successfully on resources. At one operating point of our classifier, we are able to detect 50% of jobs that will fail with a false detection rate less than 5%. In 2014, accurately predicting 50% of CIPRES job failures and redirecting them to other resources would have resulted in 900K compute core hours saved, furthering phylogenetic research. These statistical models will also be used as a base to build a more generic automated monitoring analysis service for science gateways. Copyright © 2015 John Wiley & Sons, Ltd.
Parallelizing and optimizing large‐scale 3D multi‐phase flow simulations on the Tianhe‐2 supercomputer
Authors: Li Dali , Xu Chuanfu , Wang Yongxian , Song Zhifang , Xiong Min , Gao Xiang , Deng Xiaogang 
Published: November 2015

SummaryThe lattice Boltzmann method (LBM) is a widely used computational fluid dynamics method for flow problems with complex geometries and various boundary conditions. Large‐scale LBM simulations with increasing resolution and extending temporal range require massive high‐performance computing (HPC) resources, thus motivating us to port it onto modern many‐core heterogeneous supercomputers like Tianhe‐2. Although many‐core accelerators such as graphics processing unit and Intel MIC have a dramatic advantage of floating‐point performance and power efficiency over CPUs, they also pose a tough challenge to parallelize and optimize computational fluid dynamics codes on large‐scale heterogeneous system.In this paper, we parallelize and optimize the open source 3D multi‐phase LBM code openlbmflow on the Intel Xeon Phi (MIC) accelerated Tianhe‐2 supercomputer using a hybrid and heterogeneous MPI+OpenMP+Offload+single instruction, mulitple data (SIMD) programming model. With cache blocking and SIMD‐friendly data structure transformation, we dramatically improve the SIMD and cache efficiency for the single‐thread performance on both CPU and Phi, achieving a speedup of 7.9X and 8.8X, respectively, compared with the baseline code. To collaborate CPUs and Phi processors efficiently, we propose a load‐balance scheme to distribute workloads among intra‐node two CPUs and three Phi processors and use an asynchronous model to overlap the collaborative computation and communication as far as possible. The collaborative approach with two CPUs and three Phi processors improves the performance by around 3.2X compared with the CPU‐only approach. Scalability tests show that openlbmflow can achieve a parallel efficiency of about 60% on 2048 nodes, with about 400K cores in total. To the best of our knowledge, this is the largest scale CPU‐MIC collaborative LBM simulation for 3D multi‐phase flow problems. Copyright © 2015 John Wiley & Sons, Ltd.
Thermal biology of flight in a butterfly: genotype, flight metabolism, and environmental conditions
Authors: Mattila Anniina L. K. 
Published: November 2015

AbstractKnowledge of the effects of thermal conditions on animal movement and dispersal is necessary for a mechanistic understanding of the consequences of climate change and habitat fragmentation. In particular, the flight of ectothermic insects such as small butterflies is greatly influenced by ambient temperature. Here, variation in body temperature during flight is investigated in an ecological model species, the Glanville fritillary butterfly (Melitaea cinxia). Attention is paid on the effects of flight metabolism, genotypes at candidate loci, and environmental conditions. Measurements were made under a natural range of conditions using infrared thermal imaging. Heating of flight muscles by flight metabolism has been presumed to be negligible in small butterflies. However, the results demonstrate that Glanville fritillary males with high flight metabolic rate maintain elevated body temperature better during flight than males with a low rate of flight metabolism. This effect is likely to have a significant influence on the dispersal performance and fitness of butterflies and demonstrates the possible importance of intraspecific physiological variation on dispersal in other similar ectothermic insects. The results also suggest that individuals having an advantage in low ambient temperatures can be susceptible to overheating at high temperatures. Further, tolerance of high temperatures may be important for flight performance, as indicated by an association ofheat‐shock protein(Hsp70) genotype with flight metabolic rate and body temperature at takeoff. The dynamics of body temperature at flight and factors affecting it also differed significantly between female and male butterflies, indicating that thermal dynamics are governed by different mechanisms in the two sexes. This study contributes to knowledge about factors affecting intraspecific variation in dispersal‐related thermal performance in butterflies and other insects. Such information is needed for predictive models of the evolution of dispersal in the face of habitat fragmentation and climate change.
Persistence of distinctive morphotypes in the native range of the CITES‐listed Aldabra giant tortoise
Authors: Turnbull Lindsay A. , Ozgul Arpat , Accouche Wilna , Baxter Rich , ChongSeng Lindsay , Currie Jock C. , Doak Naomi , Hansen Dennis M. , Pistorius Pierre , Richards Heather , van de Crommenacker Janske , von Brandis Rainer , Fleischer‐Dogley Frauke , Bunbury Nancy 
Published: November 2015

AbstractUnderstanding the extent of morphological variation in the wild population of Aldabra giant tortoises is important for conservation, as morphological variation in captive populations has been interpreted as evidence for lingering genes from extinct tortoise lineages. If true, this could impact reintroduction programmes in the region. The population of giant tortoises on Aldabra Atoll is subdivided and distributed around several islands. Although pronounced morphological variation was recorded in the late 1960s, it was thought to be a temporary phenomenon. Early researchers also raised concerns over the future of the population, which was perceived to have exceeded its carrying capacity. We analyzed monthly monitoring data from 12 transects spanning a recent 15‐year period (1998–2012) during which animals from four subpopulations were counted, measured, and sexed. In addition, we analyzed survival data from individuals first tagged during the early 1970s. The population is stable with no sign of significant decline. Subpopulations differ in density, but these differences are mostly due to differences in the prevailing vegetation type. However, subpopulations differ greatly in both the size of animals and the degree of sexual dimorphism. Comparisons with historical data reveal that phenotypic differences among the subpopulations of tortoises on Aldabra have been apparent for the last 50 years with no sign of diminishing. We conclude that the giant tortoise population on Aldabra is subject to varying ecological selection pressures, giving rise to stable morphotypes in discrete subpopulations. We suggest therefore that (1) the presence of morphological differences among captive Aldabra tortoises does not alone provide convincing evidence of genes from other extinct species; and (2) Aldabra serves as an important example of how conservation and management in situ can add to the scientific value of populations and perhaps enable them to better adapt to future ecological pressures.
Effect of winter cold duration on spring phenology of the orange tip butterfly, Anthocharis cardamines
Authors: Stålhandske Sandra , Lehmann Philipp , Pruisscher Peter , Leimar Olof 
Published: November 2015

AbstractThe effect of spring temperature on spring phenology is well understood in a wide range of taxa. However, studies on how winter conditions may affect spring phenology are underrepresented. Previous work on Anthocharis cardamines (orange tip butterfly) has shown population‐specific reaction norms of spring development in relation to spring temperature and a speeding up of post‐winter development with longer winter durations. In this experiment, we examined the effects of a greater and ecologically relevant range of winter durations on post‐winter pupal development of A. cardamines of two populations from the United Kingdom and two from Sweden. By analyzing pupal weight loss and metabolic rate, we were able to separate the overall post‐winter pupal development into diapause duration and post‐diapause development. We found differences in the duration of cold needed to break diapause among populations, with the southern UK population requiring a shorter duration than the other populations. We also found that the overall post‐winter pupal development time, following removal from winter cold, was negatively related to cold duration, through a combined effect of cold duration on diapause duration and on post‐diapause development time. Longer cold durations also lead to higher population synchrony in hatching. For current winter durations in the field, the A. cardamines population of southern UK could have a reduced development rate and lower synchrony in emergence because of short winters. With future climate change, this might become an issue also for other populations. Differences in winter conditions in the field among these four populations are large enough to have driven local adaptation of characteristics controlling spring phenology in response to winter duration. The observed phenology of these populations depends on a combination of winter and spring temperatures; thus, both must be taken into account for accurate predictions of phenology.
Quantifying and understanding reproductive allocation schedules in plants
Authors: Wenk Elizabeth Hedi , Falster Daniel S. 
Published: November 2015

AbstractA plant's reproductive allocation (RA) schedule describes the fraction of surplus energy allocated to reproduction as it increases in size. While theorists useRAschedules as the connection between life history and energy allocation, little is known aboutRAschedules in real vegetation. Here we review what is known aboutRAschedules for perennial plants using studies either directly quantifyingRAor that collected data from which the shape of anRAschedule can be inferred. We also briefly review theoretical models describing factors by which variation inRAmay arise. We identified 34 studies from which aspects of anRAschedule could be inferred. Within those,RAschedules varied considerably across species: some species abruptly shift all resources from growth to reproduction; most others gradually shift resources into reproduction, but under a variety of graded schedules. Available data indicate the maximum fraction of energy allocated to production ranges from 0.1 to 1 and that shorter lived species tend to have higher initialRAand increase theirRAmore quickly than do longer‐lived species. Overall, our findings indicate, little data exist aboutRAschedules in perennial plants. Available data suggest a wide range of schedules across species. Collection of more data onRAschedules would enable a tighter integration between observation and a variety of models predicting optimal energy allocation, plant growth rates, and biogeochemical cycles.
Nitrogen‐Based Alternative Fuels: Progress and Future Prospects
Authors: Grinberg Dana Alon , Shter Gennady E. , Grader Gideon S. 
Published: November 2015

AbstractWe describe and review recent research of a low‐carbon nitrogen‐based alternative fuel consisting of an aqueous solution of urea and ammonium nitrate (UAN). This fuel possesses a volumetric energy density of 4.44 MJ L−1. Conceptually, it is intriguing to think of ample atmospheric nitrogen as a future storage hub for sustainable and economic hydrogen derived from water rather than fossil fuels. First, we discuss and compare the nitrogen‐ and carbon‐based routes for chemical hydrogen storage. Second, we review recent research developments of this fuel: continuous combustion with lower NOx emissions than US regulation, computerized combustion simulations, ambient and high pressure thermal analyses, safety and stability considerations, catalytic effect on the effluent, and metal corrosion resistance at reaction and storage conditions. Aqueous UAN is found to yield about 99.9 % N2 when combusted at 25 MPa without a catalyst. Finally, future prospects and research needs are discussed.
Pyrolysis of polyurethane foam: optimized search for kinetic properties via simultaneous K–K method, genetic algorithm and elemental analysis
Authors: Li Kaiyuan , Pau Dennis Suwee , Zhang Heping 
Published: November 2015

SummaryThis study focuses on the determination of kinetic properties for non‐fire retardant (NFR) and fire retardant (FR) polyurethane foams. Based on the experimental thermogravimetric (TG) curves, this paper describes the application of an in‐depth mathematical analysis and genetic algorithm (GA) to produce the kinetic properties. A recent developed technique, K–K method, is used for calculating kinetic properties and determining the search regions of these properties for GA. Elemental analysis is also used to study the pyrolysis mechanism. Three decomposition models were investigated for comparison, and the results show that the decomposition model with three sub‐reactions achieves the closest representation with experimental results. In the model, two sub‐reactions capture the foam and melt decompositions, and another sub‐reaction with relatively lower activation energy captures the early onset of foam decomposition. The kinetic properties of melt decomposition are found similar because of the similarity of melt chemical formulas and decomposition of NFR and FR foams. The kinetic properties of foam decomposition between NFR and FR foams are different because of the mechanism of FR additives. Validation of the successive and parallel reaction schemes shows no noticeable difference between the two schemes in the modelling decomposition. Copyright © 2015 John Wiley & Sons, Ltd.
Reducing suicidal ideation in home health care: results from the CAREPATH depression care management trial
Authors: Lohman Matthew C. , Raue Patrick J. , Greenberg Rebecca L. , Bruce Martha L. 
Published: November 2015

ObjectivesThe study evaluated the effectiveness of a depression care management intervention in reducing suicidal ideation (SI) among home health patients.MethodsData come from the cluster‐randomized effectiveness trial of the Depression Care for Patients at Home (Depression CAREPATH), an intervention that integrates depression care management into the routine nursing visits of Medicare home health patients screening positive for depression. Patients were interviewed at baseline, 3, 6, and 12‐month follow‐up. SI was measured using the Hamilton Rating Scale for Depression item. We compared likelihood of any level of SI between intervention and usual care patients using longitudinal logistic mixed‐effects models.ResultsA total of 306 eligible patients enrolled in the trial. Among them, 70 patients (22.9%) reported SI at baseline. Among patients with SI, patients under the care of nurses randomized to CAREPATH were less likely to report SI over the study period (odds ratio = 0.51, 95% CI; 0.24–1.07), with 63.6% of usual care versus 31.3% of CAREPATH participants continuing to report SI after one year. Baseline major depression, greater perceived burdensomeness, and greater functional disability were associated with greater likelihood of SI.ConclusionSI is reported in more than 10% of Medicare home health patients. The Depression CAREPATH intervention was associated with a reduction in patients reporting SI at one year, compared to enhanced usual care. Given relative low burden on nursing staff, depression care management may be an important component of routine home health practices producing long‐term reduction in SI among high‐risk patients. Copyright © 2015 John Wiley & Sons, Ltd.
Heterogeneity in the three‐year course of major depression among older adults
Authors: Hybels Celia F. , Pieper Carl F. , Blazer Dan G. , Steffens David C. 
Published: November 2015

ObjectiveThe objective of this research was to identify distinct trajectories of recovery in older depressed patients in order to identify optimal samples and points for interventions. Methods: The sample was 368 patients ages 60 years and older diagnosed with major depression and enrolled in a naturalistic treatment study and followed for up to 3 years. Results: A model with four trajectory classes fit the data best: a quick recovery class (43%), a persistent moderate symptom class (27%), a persistent high symptom class (15%), and a slow recovery class (15%). Compared with patients in the quick recovery class, patients in the persistent moderate symptom class had more instrumental activities of daily living/mobility limitations and lower levels of subjective social support. Patients in the persistent high symptom class had higher levels of perceived stress and lower levels of social support compared with those with a quick recovery. Patients in the slow recovery class had a younger age of onset compared with those in the quick recovery group. In multinomial logistic regression, levels of perceived stress and social support at baseline significantly differed across classes controlling for demographic and health variables. Conclusions: Older patients diagnosed with major depression can have varying patterns of response to treatment. Interventions targeting those patients with higher levels of perceived stress and lower levels of subjective social support at the time of the index episode may lead to more favorable long‐term trajectories. Copyright © 2015 John Wiley & Sons, Ltd.
Transmission in near‐infrared optical windows for deep brain imaging
Authors: Shi Lingyan , Sordillo Laura A. , Rodríguez‐Contreras Adrián , Alfano Robert 
Published: November 2015

Near‐infrared (NIR) radiation has been employed using one‐ and two‐photon excitation of fluorescence imaging at wavelengths 650–950 nm (optical window I) for deep brain imaging; however, longer wavelengths in NIR have been overlooked due to a lack of suitable NIR‐low band gap semiconductor imaging detectors and/or femtosecond laser sources. This research introduces three new optical windows in NIR and demonstrates their potential for deep brain tissue imaging. The transmittances are measured in rat brain tissue in the second (II, 1,100–1,350 nm), third (III, 1,600–1,870 nm), and fourth (IV, centered at 2,200 nm) NIR optical tissue windows. The relationship between transmission and tissue thickness is measured and compared with the theory. Due to a reduction in scattering and minimal absorption, window III is shown to be the best for deep brain imaging, and windows II and IV show similar but better potential for deep imaging than window I.
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Randomized Placebo-Controlled and Controlled Non-Inferiority Phase III Trials Comparing Trafermin, a Recombinant Human Fibroblast Growth Factor 2, and Enamel Matrix Derivative in Periodontal Regeneration in Intrabony Defects
Authors: Kitamura Masahiro , Akamatsu Motoki , Kawanami Masamitsu , Furuichi Yasushi , Fujii Takeo , Mori Mari , Kunimatsu Kazushi , Shimauchi Hidetoshi , Ogata Yorimasa , Yamamoto Matsuo , Nakagawa Taneaki , Sato Shuichi , Ito Koichi , Ogasawara Takefumi , Izumi Yuichi , Gomi Kazuhiro , Yamazaki Kazuhisa , Yoshie Hiromasa , Fukuda Mitsuo , Noguchi Toshihide , Takashiba Shogo , Kurihara Hidemi , Nagata Toshihiko , Hamachi Takafumi , Maeda Katsumasa , Yokota Makoto , Sakagami Ryuji , Hara Yoshitaka , Noguchi Kazuyuki , Furuuchi Toshi , Sasano Takashi , Imai Enyu , Ohmae Masatoshi , Koizumi Hayuru , Watanuki Mitsuru , Murakami Shinya 
Published: November 2015

ABSTRACT

We investigated the efficacy, safety, and clinical significance of trafermin, a recombinant human fibroblast growth factor (rhFGF)-2, for periodontal regeneration in intrabony defects in Phase III trials. Study A, a multicenter, randomized, double-blind, placebo-controlled study, was conducted at 24 centers. Patients with periodontitis with 4-mm and 3-mm or deeper probing pocket depth and intrabony defects, respectively, were included. A total of 328 patients were randomly assigned (2:1) to receive 0.3% rhFGF-2 or placebo, and 323 patients received the assigned investigational drug during flap surgery. One of the co-primary endpoints, the percentage of bone fill at 36 weeks after drug administration, was significantly greater in the rhFGF-2 group at 37.131% (95% confidence interval [CI], 32.7502 to 41.5123; n = 208) than it was in the placebo group at 21.579% (95% CI, 16.3571 to 26.8011; n = 100; p &lt; 0.001). The other endpoint, the clinical attachment level regained at 36 weeks, was not significantly different between groups. Study B, a multicenter, randomized, blinded (patients and evaluators of radiographs), and active-controlled study was conducted at 15 centers to clarify the clinical significance of rhFGF-2. Patients with 6-mm and 4-mm or deeper probing pocket depth and intrabony defects, respectively, were included. A total of 274 patients were randomly assigned (5:5:2) to receive rhFGF-2, enamel matrix derivative (EMD), or flap surgery alone. A total of 267 patients received the assigned treatment during flap surgery. The primary endpoint, the linear alveolar bone growth at 36 weeks, was 1.927 mm (95% CI, 1.6615 to 2.1920; n = 108) in the rhFGF-2 group and 1.359 mm (95% CI, 1.0683 to 1.6495; n = 109) in the EMD group, showing non-inferiority (a prespecified margin of 0.3 mm) and superiority of rhFGF-2 to EMD. Safety problems were not identified in either study. Therefore, trafermin is an effective and safe treatment for periodontal regeneration in intrabony defect, and its efficacy was superior in rhFGF-2 compared to EMD treatments. © 2015 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals, Inc. on behalf of American Society for Bone and Mineral Research (ASBMR).