bluuebunny/crossref_metadata_2025 huggingface dataset:
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

The 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.
Three steps multiobjective decision process for software release planning
Authors: Del Águila Isabel M. , Del Sagrado José
Published: November 2015

This paper deals with how to determine which features should be included in the software to be developed. Metaheuristic techniques have been applied to this problem and can help software developers when they face contradictory goals. We show how the knowledge and experience of human experts can be enriched by these techniques, with the idea of obtaining a better requirements selection than that produced by expert judgment alone. This objective is achieved by embedding metaheuristics techniques into a requirements management tool that takes advantage of them during the execution of the development stages of any software development project. © 2015 Wiley Periodicals, Inc. Complexity 21: 250–262, 2016
Thermal biology of flight in a butterfly: genotype, flight metabolism, and environmental conditions
Authors: Mattila Anniina L. K.
Published: November 2015

Knowledge 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

Understanding 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

The 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

A 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

We 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

This 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

Objectives

The study evaluated the effectiveness of a depression care management intervention in reducing suicidal ideation (SI) among home health patients.

Methods

Data 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.

Results

A 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.

Conclusion

SI 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

Objective

The 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.
Safety and efficacy of ledipasvir‐sofosbuvir in black patients with hepatitis C virus infection: A retrospective analysis of phase 3 data
Authors: Wilder Julius M. , Jeffers Lennox J. , Ravendhran Natarajan , Shiffman Mitchell L. , Poulos John , Sulkowski Mark S. , Gitlin Norman , Workowski Kimberly , Zhu Yanni , Yang Jenny C. , Pang Phillip S. , McHutchison John G. , Muir Andrew J. , Howell Charles , Kowdley Kris , Afdhal Nezam , Reddy K. Rajender
Published: November 2015

Black patients chronically infected with genotype 1 hepatitis C virus (HCV) have historically had lower rates of response to interferon‐based treatment than patients of other races. In the phase 3 ION program, the single‐tablet regimen of the NS5A inhibitor ledipasvir and NS5B nucleotide polymerase inhibitor sofosbuvir was shown to be safe and highly effective in the general population. The aim of this study was to evaluate the safety and efficacy of ledipasvir/sofosbuvir in black patients using data from the three open‐label ION clinical trials, which evaluated the safety and efficacy of 8, 12, and 24 weeks of ledipasvir/sofosbuvir with or without ribavirin for the treatment of treatment‐naïve and treatment‐experienced patients with genotype 1 HCV, including those with compensated cirrhosis. The primary endpoint was sustained virologic response at 12 weeks after the end of therapy (SVR12). For our analysis, rates of SVR12, treatment‐emergent adverse events, and graded laboratory abnormalities were analyzed in black versus non‐black patients. Of the 1949 patients evaluated, 308 (16%) were black. On average, black patients were older, had higher body mass index, were more likely to be IL28B non‐CC, and had a lower serum alanine aminotransferase at baseline than non‐black patients. Overall, 95% of black and 97% of non‐black patients achieved SVR12. The rate of relapse was 3% in black patients as compared with 2% in non‐black patients. The most common adverse events included fatigue, headache, nausea, and insomnia. The majority of adverse events occurred more frequently in the ribavirin‐containing arms of the studies. No differences were observed in overall safety by race. Conclusion: A once‐daily dosage of ledipasvir/sofosbuvir was similarly effective in black and non‐black patients with genotype 1 HCV infection. The addition of ribavirin did not appear to increase SVR12 but was associated with higher rates of adverse events. (Hepatology 2016;63:437–444)
High hemoglobin A1c levels within the non‐diabetic range are associated with the risk of all cancers
Authors: Goto Atsushi , Noda Mitsuhiko , Sawada Norie , Kato Masayuki , Hidaka Akihisa , Mizoue Tetsuya , Shimazu Taichi , Yamaji Taiki , Iwasaki Motoki , Sasazuki Shizuka , Inoue Manami , Kadowaki Takashi , Tsugane Shoichiro ,   for the JPHC Study Group
Published: November 2015

Previous studies have reported associations between diabetes and cancer risk. However, specific association of hemoglobin A1c (HbA1c) levels with cancer risk remains inconclusive. We followed 29,629 individuals (11,336 men; 18,293 women) aged 46–80 years who participated in the Japan Public Health Center‐based prospective study who had HbA1c measurements available and were cancer‐free at baseline. Cancer incidence was assessed by systemic surveys. We estimated hazard ratios (HRs) for cancer risk with adjustment for age sex, geographic area, body mass index, smoking status, physical activity, alcohol, coffee, vegetable and total energy consumption, and history of cardiovascular disease. After a median follow‐up of 8.5 years, 1,955 individuals had developed cancer. Higher HbA1c levels within both the non‐diabetic and diabetic ranges in individuals without known diabetes were associated with overall cancer risk. Compared with individuals without known diabetes and HbA1c levels of 5.0–5.4%, the HRs for all cancers were 1.27 (95% confidence interval, 1.07–1.52); 1.01 (0.90–1.14); 1.28 (1.09–1.49); and 1.43 (1.14–1.80) for individuals without known diabetes and HbA1c levels <5.0%, 5.5–5.9%, 6.0–6.4%, and ≥6.5%, respectively, and 1.23 (1.02–1.47) for individuals with known diabetes. The lowest HbA1c group had the highest risk of liver cancer, and HbA1c levels were linearly associated with the risk of all cancers after excluding liver cancer (P for linear trend, 0.004). In conclusion, our findings corroborate the notion that glycemic control in individuals with high HbA1c levels may be important not only to prevent diabetes but also to prevent cancer.
Key signaling pathways in the muscle‐invasive bladder carcinoma: Clinical markers for disease modeling and optimized treatment
Authors: Kiselyov Alex , Bunimovich‐Mendrazitsky Svetlana , Startsev Vladimir
Published: November 2015

In this review, we evaluate key molecular pathways and markers of muscle‐invasive bladder cancer (MIBC). Overexpression and activation of EGFR, p63, and EMT genes are suggestive of basal MIBC subtype generally responsive to chemotherapy. Alterations in PPARγ, ERBB2/3, and FGFR3 gene products and their signaling along with deregulated p53, cytokeratins KRT5/6/14 in combination with the cellular proliferation (Ki‐67), and cell cycle markers (p16) indicate the need for more radical treatment protocols. Similarly, the “bell‐shape” dynamics of Shh expression levels may suggest aggressive MIBC. A panel of diverse biological markers may be suitable for simulation studies of MIBC and development of an optimized treatment protocol. We conducted a critical evaluation of PubMed/Medline and SciFinder databases related to MIBC covering the period 2009–2015. The free‐text search was extended by adding the following keywords and phrases: bladder cancer, metastatic, muscle‐invasive, basal, luminal, epithelial‐to‐mesenchymal transition, cancer stem cell, mutations, immune response, signaling, biological markers, molecular markers, mathematical models, simulation, epigenetics, transmembrane, transcription factor, kinase, predictor, prognosis. The resulting selection of ca 500 abstracts was further analyzed in order to select the latest publications relevant to MIBC molecular markers of immediate clinical significance.
Folylpolyglutamate synthetase splicing alterations in acute lymphoblastic leukemia are provoked by methotrexate and other chemotherapeutics and mediate chemoresistance
Authors: Wojtuszkiewicz Anna , Raz Shachar , Stark Michal , Assaraf Yehuda G. , Jansen Gerrit , Peters Godefridus J. , Sonneveld Edwin , Kaspers Gertjan J. L. , Cloos Jacqueline
Published: November 2015

Methotrexate (MTX), a folate antagonist which blocks de novo nucleotide biosynthesis and DNA replication, is an anchor drug in acute lymphoblastic leukemia (ALL) treatment. However, drug resistance is a primary hindrance to curative chemotherapy in leukemia and its molecular mechanisms remain poorly understood. We have recently shown that impaired folylpolyglutamate synthetase (FPGS) splicing possibly contributes to the loss of FPGS activity in MTX‐resistant leukemia cell line models and adult leukemia patients. However, no information is available on the possible splicing alterations in FPGS in pediatric ALL. Here, using a comprehensive PCR‐based screen we discovered and characterized a spectrum of FPGS splicing alterations including exon skipping and intron retention, all of which proved to frequently emerge in both pediatric and adult leukemia patient specimens. Furthermore, an FPGS activity assay revealed that these splicing alterations resulted in loss of FPGS function. Strikingly, pulse‐exposure of leukemia cells to antifolates and other chemotherapeutics markedly enhanced the prevalence of several FPGS splicing alterations in antifolate‐resistant cells, but not in their parental antifolate‐sensitive counterparts. These novel findings suggest that an assortment of deleterious FPGS splicing alterations may constitute a mechanism of antifolate resistance in childhood ALL. Our findings have important implications for the rational overcoming of drug resistance in individual leukemia patients.
Integrative analysis of copy number and gene expression data suggests novel pathogenetic mechanisms in primary myelofibrosis
Authors: Salati Simona , Zini Roberta , Nuzzo Simona , Guglielmelli Paola , Pennucci Valentina , Prudente Zelia , Ruberti Samantha , Rontauroli Sebastiano , Norfo Ruggiero , Bianchi Elisa , Bogani Costanza , Rotunno Giada , Fanelli Tiziana , Mannarelli Carmela , Rosti Vittorio , Salmoiraghi Silvia , Pietra Daniela , Ferrari Sergio , Barosi Giovanni , Rambaldi Alessandro , Cazzola Mario , Bicciato Silvio , Tagliafico Enrico , Vannucchi Alessandro M. , Manfredini Rossella ,   on behalf of the AGIMM (AIRC Gruppo Italiano Malattie Mieloproliferative) investigators
Published: November 2015

Primary myelofibrosis (PMF) is a Myeloproliferative Neoplasm (MPN) characterized by megakaryocyte hyperplasia, progressive bone marrow fibrosis, extramedullary hematopoiesis and transformation to Acute Myeloid Leukemia (AML). A number of phenotypic driver (JAK2, CALR, MPL) and additional subclonal mutations have been described in PMF, pointing to a complex genomic landscape. To discover novel genomic lesions that can contribute to disease phenotype and/or development, gene expression and copy number signals were integrated and several genomic abnormalities leading to a concordant alteration in gene expression levels were identified. In particular, copy number gain in the polyamine oxidase (PAOX) gene locus was accompanied by a coordinated transcriptional up‐regulation in PMF patients. PAOX inhibition resulted in rapid cell death of PMF progenitor cells, while sparing normal cells, suggesting that PAOX inhibition could represent a therapeutic strategy to selectively target PMF cells without affecting normal hematopoietic cells' survival. Moreover, copy number loss in the chromatin modifier HMGXB4 gene correlates with a concomitant transcriptional down‐regulation in PMF patients. Interestingly, silencing of HMGXB4 induces megakaryocyte differentiation, while inhibiting erythroid development, in human hematopoietic stem/progenitor cells. These results highlight a previously un‐reported, yet potentially interesting role of HMGXB4 in the hematopoietic system and suggest that genomic and transcriptional imbalances of HMGXB4 could contribute to the aberrant expansion of the megakaryocytic lineage that characterizes PMF patients.
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

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 < 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).
Frailty Change and Major Osteoporotic Fracture in the Elderly: Data from the Global Longitudinal Study of Osteoporosis in Women 3-Year Hamilton Cohort
Authors: Li Guowei , Papaioannou Alexandra , Thabane Lehana , Cheng Ji , Adachi Jonathan D
Published: November 2015

Investigating the cumulative rate of deficits and the change of a frailty index (FI) chronologically is helpful in clinical and research settings in the elderly. However, limited evidence for the change of frailty before and after some nonfatal adverse health event such as a major osteoporotic fracture (MOF) is available. Data from the Global Longitudinal Study of Osteoporosis in Women 3-Year Hamilton cohort were used in this study. The changes of FI before and after onset of MOF were compared between the women with and without incident MOF. We also evaluated the relationship between risk of MOF, falls, and death and the change of FI and the absolute FI measures. There were 3985 women included in this study (mean age 69.4 years). The change of FI was significantly larger in the women with MOF than those without MOF at year 1 (0.085 versus 0.067, p = 0.036) and year 2 (0.080 versus 0.052, p = 0.042) post-baseline. The FI change was not significantly related with risk of MOF independently of age. However, the absolute FI measures were significantly associated with increased risk of MOF, falls, and death independently of age. In summary, the increase of the FI is significantly larger in the elderly women experiencing a MOF than their peer controls, indicating their worsening frailty and greater deficit accumulation after a MOF. Measures of the FI change may aid in the understanding of cumulative aging nature in the elderly and serve as an instrument for intervention planning and assessment. © 2015 American Society for Bone and Mineral Research.
Prediction of conformationally dependent atomic multipole moments in carbohydrates
Authors: Cardamone Salvatore , Popelier Paul L. A.
Published: November 2015

The conformational flexibility of carbohydrates is challenging within the field of computational chemistry. This flexibility causes the electron density to change, which leads to fluctuating atomic multipole moments. Quantum Chemical Topology (QCT) allows for the partitioning of an “atom in a molecule,” thus localizing electron density to finite atomic domains, which permits the unambiguous evaluation of atomic multipole moments. By selecting an ensemble of physically realistic conformers of a chemical system, one evaluates the various multipole moments at defined points in configuration space. The subsequent implementation of the machine learning method kriging delivers the evaluation of an analytical function, which smoothly interpolates between these points. This allows for the prediction of atomic multipole moments at new points in conformational space, not trained for but within prediction range.

In this work, we demonstrate that the carbohydrates erythrose and threose are amenable to the above methodology. We investigate how kriging models respond when the training ensemble incorporating multiple energy minima and their environment in conformational space. Additionally, we evaluate the gains in predictive capacity of our models as the size of the training ensemble increases. We believe this approach to be entirely novel within the field of carbohydrates. For a modest training set size of 600, more than 90% of the external test configurations have an error in the total (predicted) electrostatic energy (relative toab initio) of maximum 1 kJ mol−1for open chains and just over 90% an error of maximum 4 kJ mol−1for rings. © 2015 Wiley Periodicals, Inc.
Mitochondrial phenotype of marsupial torpor: Fuel metabolic switch in the Chilean mouse–opossum Thylamys elegans
Authors: Cortés Pablo Andres , Bacigalupe Leonardo Daniel , Mondaca Fredy , Desrosiers Véronique , Blier Pierre U.
Published: November 2015

Torpor is a phenotype characterized by a controlled decline of metabolic rate and body temperature. During arousal from torpor, organs undergo rapid metabolic reactivation and rewarming to near normal levels. As torpor progress, animals show a preference for fatty acids over glucose as primary source of energy. Here, we analyzed for first time the changes in the maximal activity of key enzymes related to fatty acid (Carnitine palmitoyltransferase and β‐Hydroxyacyl CoA dehydrogenase) and carbohydrate (Pyruvate kinase, Phosphofructokinase and Lactate dehydrogenase) catabolism, as well as mitochondrial oxidative capacity (Citrate synthase), in six organs of torpid, arousing and euthermic Chilean mouse‐opossums (Thylamys elegans). Our results showed that activity of enzymes related to fatty acid and carbohydrate catabolism were different among torpor phases and the pattern of variation differs among tissues. In terms of lipid utilization, maximal enzymatic activities differ in tissues with high oxidative capacity such as heart, kidney, and liver. In terms of carbohydrate use, lower enzymatic activities were observed during torpor in brain and liver. Interestingly, citrate synthase activity did not differ thought torpor‐arousal cycle in any tissues analyzed, suggesting no modulation of mitochondrial content in T. elegans. Overall results provide an indication that modulation of enzymes associated with carbohydrate and fatty‐acid pathways is mainly oriented to limit energy expensive processes and sustain energy metabolism during transition from torpor to euthermy. Future studies are required to elucidate if physiological events observed for T. elegans are unique from other marsupials, or represents a general response in marsupials. J. Exp. Zool. 325A:41–51, 2016. © 2015 Wiley Periodicals, Inc.
Aid, Political Business Cycles and Growth in Africa
Authors: Chiripanhura Blessing , Niño‐Zarazúa Miguel
Published: November 2015

This study develops a model of opportunistic behaviour in which an incumbent government resorts to expansionary fiscal and/or monetary stimuli to foster economic growth and thus, maximize the probability of re‐election. Using a panel dataset of 31 African countries covering the period 1980 to 2009, we test whether donor aid facilitates such political business cycles and investigate their effect on growth. We find evidence that donors, through guaranteeing support to incumbent governments, may unwittingly instigate political business cycles. With forbearance, and sometimes complicity by donors, aid seems to allow incumbent governments to instigate macroeconomic stimuli that ensure electoral victory with no fear of losing aid support. © 2015 UNU‐WIDER. Journal of International Development published by John Wiley & Sons, Ltd.
How to Assess the Effectiveness of Development Aid Projects: Evaluation Ratings versus Project Indicators
Authors: Metzger Laura , Guenther Isabel
Published: November 2015

Most studies on project‐based aid effectiveness rely on subjective evaluation ratings to measure projects' performance. Using the example of drinking water projects, this study compares evaluation ratings to objective, quantitative project indicators based on water supply to better understand the drivers of evaluation ratings. We find that evaluation ratings are only weakly correlated with improvements in water supply. Whereas the water supply‐based project indicators are best explained by project design variables, evaluation ratings put more weight on project management and implementation. © 2015 UNU‐WIDER. Journal of International Development published by John Wiley & Sons, Ltd.
A comparison between porcine, ovine, and bovine intervertebral disc anatomy and single lamella annulus fibrosus tensile properties
Authors: Monaco Lauren A. , DeWitte‐Orr Stephanie J. , Gregory Diane E.
Published: November 2015

This project aimed to compare gross anatomical measures and biomechanical properties of single lamellae from the annulus fibrosus of ovine and porcine lumbar vertebrae, and bovine tail vertebrae. The morphology of the vertebrae of these species differ significantly both from each other and from human, yet how these differences alter biomechanical properties is unknown. Geometric parameters measured in this study included: 1) absolute and relative intervertebral (IVD) and vertebral body height and 2) absolute and relative intervertebral disc (IVD) anterior‐posterior (AP) and medial‐lateral (ML) widths. Single lamella tensile properties included toe‐region stress and stretch ratio, stiffness, and tensile strength. As expected, the bovine tail IVD revealed a more circular shape compared with both the ovine and porcine lumbar IVD. The bovine tail also had the largest IVD to vertebral body height ratio (due to having the highest absolute IVD height). Bovine tail lamellae were also found to be strongest and stiffest (in tension) while ovine lumbar lamellae were weakest and most compliant. Histological analysis revealed the greatest proportion of collagen in the bovine corroborating findings of increased strength and stiffness. The observed differences in anatomical shape, connective tissue composition, and tensile properties need to be considered when choosing an appropriate model for IVD research. J. Morphol. 277:244–251, 2016. © 2015 Wiley Periodicals, Inc.
Molecular epidemiology of genogroup II norovirus infection among hospitalized children with acute gastroenteritis in Suzhou (Jiangsu, China) from 2010 to 2013
Authors: Fu Jian‐Guang , Ai Jing , Zhang Jun , Wu Qing‐Bin , Qi Xian , Ji Hong , Jin Miao , Liu Cheng , Wang Shen‐Jiao , Shan Jun , Bao Chang‐Jun , Tang Fen‐Yang , Zhu Ye‐Fei
Published: November 2015

Noroviruses (NoVs) are the most common cause of acute gastroenteritis in both sporadic and outbreak cases. Genotyping and recombination analyses were performed in order to help getting more knowledge of the distribution and genetic diversity of NoVs in Suzhou, located in Jiangsu province of China. All stool samples were collected from hospitalized children younger than 5 years old with acute gastroenteritis. For genotyping, the open reading frame (ORF) 1 and ORF2 were partially amplified and sequenced. 26.9% of stool samples were positive for genogroup II NoVs. The most common genotype was GII.4 and its variants included Den Haag‐2006b, New Orleans‐2009, and Sydney‐2012. The Den Haag‐2006b variants predominated during 2010–2012. In 2013, it was replaced by the Sydney‐2012 variant. The second most common genotype was GII.12/GII.3. NoVs could be detected throughout the year, with GII.4 and GII.12/GII.3 coexisting during the cold months, and GII.4 was the main genotype during the warm months. The highest prevalence of NoV was detected in young children aged <24 months. Patients infected with GII.4 had a higher chance of getting moderate fever than other NoV‐positive patients, while those infected with GII.12/GII.3 tended to have a mild degree of fever. NoV is an important pathogen responsible for viral gastroenteritis among children in Suzhou. Analyses of NoV circulating between 2010 and 2013 revealed a change of predominant variant of NoV GII.4 in each epidemic season and intergenotype recombinant strains represented an important part. J. Med. Virol. 88:954–960, 2016. © 2015 Wiley Periodicals, Inc.
Prolapse repair with and without apical resuspension—Practice patterns among certifying American urologists
Authors: Liu Joceline S. , Nettey Oluwarotimi , Vo Amanda X. , Hofer Matthias D. , Flury Sarah C. , Kielb Stephanie J.
Published: November 2015

Aims

To examine surgeon characteristics in certifying urologists performing prolapse surgeries. Anterior compartment prolapse is often associated with apical prolapse, with high rates of recurrence when anterior repair is performed without apical resuspension.

Methods

Six‐month case log data of certifying urologists between 2003 and 2013 was obtained from the American Board of Urology (ABU). Cases with a CPT code for common prolapse repairs in females ≥18 years were analyzed.

Results

Among 2,588 urologists logging at least one prolapse surgery and a total of 30,983 surgeries, 320 (1.0% of all cases) uterosacral ligament suspension, 3,673 (11.9%) sacrospinous ligament suspension, and 2,618 (8.4%) abdominal sacrocolpopexy were identified. The remaining 14,585 cases were logged as anterior repair. 54.7% of anterior repairs did not include apical suspension. The proportion of anterior repairs without apical suspension has decreased from 77.7% in 2004 to 41.4% in 2012 (P < 0.001). Female subspecialists before 2011 performed anterior repair without apical suspension in 58.5%, versus 70.3% by all others. Since 2011 there has been a decrease in number of anterior repairs without apical suspension, notably in those applying for Female Pelvic Medicine and Reconstructive Surgery (FPMRS) certification (17.1% vs. 30.7% by all other urologists, P < 0.001); nonacademically affiliated urologists are 2.1 times more likely to report anterior repair without apical suspension than academically affiliated colleagues (P < 0.001).

Conclusions

The proportion of prolapse repairs reported as anterior repairs without apical suspension is decreasing, although it remains a substantial portion. Recent log year, FPMRS, and academic affiliation were associated with prolapse repairs addressing apical support. Neurourol. Urodynam. 36:344–348, 2017. © 2015 Wiley Periodicals, Inc.
A simple integration algorithm for a non‐associated anisotropic plasticity model for sheet metal forming
Authors: Wali M. , Autay R. , Mars J. , Dammak F.
Published: November 2015

In this paper, an anisotropic material model based on a non‐associated flow rule and nonlinear mixed isotropic‐kinematic hardening is developed. The quadratic Hill48 yield criterion is considered in the non‐associated model for both yield function and plastic potential to account for anisotropic behavior. The developed model is integrated based on fully implicit backward Euler's method. The resulting problem is reduced to only two simple scalar equations. The consistent local tangent modulus is obtained by exact linearization of the algorithm. All numerical development was implemented into user‐defined material subroutine for the commercial finite element code ABAQUS/Standard. The performance of the present algorithm is demonstrated by numerical examples. Copyright © 2015 John Wiley & Sons, Ltd.
A new Leapfrog scheme for rotational motion in 3D
Authors: Mariotti C.
Published: November 2015

Discrete element codes use complex geometric solid particles, so it is necessary to integrate three‐dimensional rigid‐body rotation correctly with external torque. This article presents an interpretation of the Leapfrog scheme. We begin with some rotation formulae before presenting an efficient and high‐order recurrent Taylor series method for rotation. Integrating this method with Leapfrog interpretation provides a complete scheme for rotational motion with external torque. This new Leapfrog scheme has been integrated into the CeaMka3D Discrete Element code, and we present some verifications and simulations to illustrate the capabilities of this scheme. Copyright © 2016 John Wiley & Sons, Ltd.