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gekkoFS—A Temporary Burst Buffer File System for HPC Applications

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Journal of Computer Science & Technology 2020年第1期35卷 72-91页

作者： Marc-AndréVef Nafiseh Moti Tim Süβ Markus Tacke Tommaso Tocci Ramon Nou Alberto miranda Toni Cortes AndréBrinkmann Zentrum für Datenverarbeitung Johannes Gutenberg University MainzMainz 55128Germany Barcelona Supercomputing Center Barcelona 08034Spain Computer Architecture Department Universitat Politècnica de CatalunyaBarcelona 08034Spain

Many scientific fields increasingly use high-performance computing(HPC)to process and analyze massive amounts of experimental data while storage systems in today's HPC environments have to cope with new access *** patterns include many metadata operations,small I/O requests,or randomized file I/O,while general-purpose parallel file systems have been optimized for sequential shared access to large *** buffer file systems create a separate file system that applications can use to store temporary *** aggregate node-local storage available within the compute nodes or use dedicated SSD clusters and offer a peak bandwidth higher than that of the backend parallel file system without interfering with ***,burst buffer file systems typically offer many features that a scientific application,running in isolation for a limited amount of time,does not *** present gekkoFS,a temporary,highly-scalable file system which has been specifically optimized for the aforementioned use *** provides relaxed POSIX semantics which only offers features which are actually required by most(not all)*** is,therefore,able to provide scalable I/O performance and reaches millions of metadata operations already for a small number of nodes,significantly outperforming the capabilities of common parallel file systems.

关键词： distributed file system high-performance computing(HPC) burst buffer POSIX(portable operating system interface)

Injury severity analysis： comparison of multilevel logistic regression models and effects of collision data aggregation

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Journal of Modern Transportation 2016年第1期24卷 73-87页

作者： Taimur Usman Liping Fu Luis F.miranda-Moreno Department of Civil & Environmental Engineering University of Waterloo Waterloo ON N2L 3GI Canada School of Transportation and Logistics Southwest Jiaotong University Chengdu 610031 China Department of Civil Engineering & Applied Mechanics McGill University Montreal QC H3A 2K6 Canada

This paper describes an empirical study aiming at identifying the main differences between different logistic regression models and collision data aggregation methods that are commonly applied in road safety literature for modeling collision severity. In particular, the research compares three popular multilevel logistic models （i.e., sequential binary logit models, ordered logit models, and multinomial logit models） as well as three data aggregation methods （i.e., occupant based, vehicle based, and collision based）. Six years of collision data （2001-2006） from 31 highway routes from across the province of Ontario, Canada were used for this analysis. It was found that a multilevel multinomial logit model has the best fit to the data than the other two models while the results obtained from occupant-based data are more reliable than those from vehicle- and collision-based data. More importantly, while generally consistent in terms of factors that were found to be significant between different models and data aggregation methods, the effect size of each factor differ sub- stantially, which could have significant implications forevaluating the effects of different safety-related policies and countermeasures.

关键词： Injury severity - Multilevel logistic regressionmodels Collision data aggregation

Tamoxifen and Src kinase inhibitors as neuroprotective/neuroregenerative drugs after spinal cord injury

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Neural Regeneration Research 2015年第3期10卷 385-390页

作者： Iris K.Salgado Aranza I.Torrado Jose M.Santiago Jorge D.miranda Department of Physiology School of MedicineUniversity of Puerto Rico Medical Sciences Campus University of Puerto Rico Carolina Campus Department of Natural Sciences

Spinal cord injury （SCI） is a devastating condition that produces significant changes in the life- style of patients. Many molecular and cellular events are triggered after the initial physical impact to the cord. Two major phases have been described in the field of SCI： an acute phase and late phase. Most of the therapeutic strategies are focused on the late phase because this provides an opportunity to target cellular events like apoptosis, demyelination, scar formation and axonal outgrowth. In this mini-review, we will focus on two agents （tamoxifen and a Src kinase family inhibitor known as PP2） that have been shown in our laboratory to produce neuroprotective （increase cell survival） and/or regenerative （axonal outgrowth） actions. The animal model used in our laboratory is adult female rat （N250 g） with a moderate contusion （12.5 mm） to the spinal cord at the T10 level, using the MASCIS impactor device. Tamoxifen or PP2 was administered by implantation of a 15 mg pellet （Innovative Research of America, Sarasota, FL, USA） or by intraperitoneal injections （1.5 mg/kg, every 3 days）, respectively, to produce a long-term effect （28 days）. Tamoxifen and the Src kinase inhibitor, PP2, are drugs that in rats with a moderate spinal cord injury promote functional locomotor recovery, increase spared white matter tissue, and stimulate axonal outgrowth. Moreover, tamoxifen reduces the formation of reactive oxygen species. Therefore, these drugs are possible therapeutic agents that have a neuroprotective/regen- erative activity in vertebrates with SCI.

关键词： tamoxifen Src kinase PP2 trauma regeneration neuroprotection

Extrapolating plot-scale CO_(2) and ozone enrichment experimental results to novel conditions and scales using mechanistic modeling

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Ecological Processes 2018年第1期7卷 348-367页

作者： Eric J.gustafson Mark E.Kubiske Brian R.miranda Yasutomo Hoshika Elena Paoletti Institute for Applied Ecosystem Studies Northern Research StationUSDA Forest Service5985 Highway KRhinelanderWIUSA Institute of Sustainable Plant Protection National Council of ResearchVia Madonna del Piano 1050019 Sesto FiorentinoItaly

Introduction:The Aspen-FACE experiment was an 11-year study of the effect of elevated CO_(2) and ozone(alone and in combination)on the growth of model aspen communities(pure aspen,aspen-birch,and aspen-maple)in the field in northern Wisconsin,*** remains about how these short-term plotlevel responses might play out over broader temporal and spatial scales where climate change,competition,succession,and disturbances interact with tree-level *** this study,we used a new physiologybased approach(PnET-Succession v3.1)within the forest landscape model LANDIS-II to extrapolate the FACE results to broader temporal scales(and ultimately to landscape scale)by mechanistically accounting for the globally changing drivers of temperature,precipitation,CO_(2),and *** added novel algorithms to the model to mechanistically simulate the effects of ozone on photosynthesis through ozone-induced impairment of stomatal control(i.e.,stomatal sluggishness)and damage of photosynthetic capacity at the chloroplast ***:We calibrated the model to empirical observations of competitive interactions on the elevated CO_(2) and O_(3) plots of the Aspen-FACE experiment and successfully validated it on the combined factor *** used the validated model to extend the Aspen-FACE experiment for 80 *** only aspen clones competed,we found that clone 271 always dominated,although the ozone-tolerant clone was co-dominant when ozone was *** all treatments,when aspen clone 216 and birch competed,birch was always dominant or co-dominant,and when clone 216 and maple competed,clone 216 was dominant,although maple was able to grow steadily because of its shade *** also predicted long-term competitive outcomes for novel assemblages of taxa under each treatment and discovered that future composition and dominant taxa depend on treatment,and that short-term trends do not always persist in the long ***:We identified the strengths and weakne

关键词： Scaling global change Elevated CO_(2) Ozone pollution Aspen-FACE Forest composition Carbon dynamics Forest landscape modeling LANDIS-II PnET-succession

geomechanical characterization of volcanic rocks using empirical systems and data mining techniques

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Journal of Rock Mechanics and geotechnical Engineering 2018年第1期10卷 138-150页

作者： T.miranda L.R.Sousa A.T.gomes J.Tinoco C.Ferreira University of Minho GuimarasPortugal State Key Laboratory of geomechanics and Deep Underground Engineering China University of Mining and TechnologyBeijingChina University of Porto PortoPortugal

This paper tries to characterize volcanic rocks through the development and application of an empirical geomechanical system. geotechnical information was collected from the samples from several Atlantic Ocean islands including Madeira, Azores and Canarias archipelagos. An empirical rock classification system termed as the volcanic rock system(VRS) is developed and presented in detail. Results using the VRS are compared with those obtained using the traditional rock mass rating(RMR) system. Data mining(DM) techniques are applied to a database of volcanic rock geomechanical information from the *** algorithms were developed and consequently approaches were followed for predicting rock mass classes using the VRS and RMR classification systems. Finally, some conclusions are drawn with emphasis on the fact that a better performance was achieved using attributes from VRS.

关键词： Volcanic rocks geomechanical characterization Volcanic rock system(VRS) Data mining(DM)

Development of a Ready-to-Use PSMA-11 Kit Formulation and Biological Evaluation of Binding Affinity

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Advances in Molecular Imaging 2024年第2期13卷 7-22页

作者： Maria Renata Valente Brandão Freire Natália Marchesan Bexiga Marco Antonio Stephano João Ezequiel Oliveira Carlos Roberto Jorge Soares Ana Cláudia Camargo miranda Anna Carolina de Alcântara Barbosa Marycel Figols de Barboza Laura Fernanda garcia Luiz Felipe S. Teixeira Maria Helena Marumo Bellini Natanael gomes da Silva Luiza Mascarenhas Balieiro Joel Mendes Elaine Bortoleti de Araújo Centro de Radiofarmcia Instituto de Pesquisas Energticas e Nucleares (IPEN) Cidade Universitria So Paulo Brasil Departamento de Tecnologia Farmacutica Faculdade de Cincias Farmacuticas (USP) Cidade Universitria So Paulo Brasil Centro de Biotecnologia Instituto de Pesquisas Energticas e Nucleares (IPEN) Cidade Universitria So Paulo Brasil Departamento de Medicina Nuclear do Hospital Israelita Albert Einstein So Paulo/SP Brasil

Introduction: 68ga-PSMA-11 is considered the gold standard in detection of micro and oligometastases in advanced prostate cancer, being used for therapeutic planning, as well as, potentially, for evaluating response to treatment. The development of ready-to-use lyophilized kit of PSMA-11 adds quality and safety to the routine use of this radiopharmaceutical and represents a pharmacotechnical challenge as it must preserve the integrity and specificity of the ligand. Methods: PSMA-11 kit formulation was proposed, considering radiolabeling parameters and the preservation of the peptide during the lyophilization process, using mannitol as an excipient. Critical temperature characterization studies were carried out using DSC equipment and the freeze-drying process was developed. The direct radiolabeling conditions were evaluated and standardized using 68ge/68ga generator eluate from two different manufacturers (ITg and Eckert & Ziegler). The radiochemical purity was evaluated by TLC and HPLC. Biological evaluation was carried out with lyophilized PSMA-11 to demonstrate the integrity of the peptide and preservation of biological activity after the lyophilization process. Results: Based on critical temperature characterization studies, the freeze-drying cycle was designed to reach a freezing temperature of around −40˚C and primary drying at 2˚C. Using 20 mg of mannitol, an intact and elegant lyophilized cake was obtained. PSMA-11 lyophilized kit was directly labeled with 68ga eluate from 68ge/68ga gMP generators (ITg and Eckert & Ziegler) resulting in % RP > 95% at pH 4.0 to 4.5. The results obtained from in vitro and in vivo biological competition studies confirmed the preservation of PSMA-11 affinity for the receptor after lyophilization. Conclusion: A lyophilized formulation (Kit) of PSMA-11 was successfully obtained, which preserved the integrity and biological activity of the peptide and guaranteed radiolabeling efficiency.

关键词： 68ga-PSMA-11 Prostate-Specific Membrane Antigen (PSMA) Ready-to-Use Kit gMP-grade generators Metastatic Prostate Cancer PET Imaging

Effectiveness of Acupuncture on Pain, Physical Function and Health-Related Quality of Life in Patients with Rheumatoid Arthritis: A Systematic Review of Quantitative Evidence

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Chinese Journal of Integrative Medicine 2019年第9期25卷 704-709页

作者： Susana Seca Diana miranda Daniela Cardoso Bernice Nogueira Henry J.greten Antonio Cabrita Manuel Alves Rodrigues Faculty of Medicine University of CoimbraInstitute of Science Biomedicine Abel Salazar University of Porto Porto PortugalHeidelberg School of Chinese Medicine Heidelberg Germany Institute of Science Biomedicine Abel Salazar University of Porto Porto Portugal Health Sciences Research Unit:Nursing (UICISA: E) Nursing School of Coimbra (ESEnfC) Portugal Centre for Evidenee Based Practice: A Joanna Briggs Institute Centre of Excellence Coimbra Portugal School of Health Sciences Macao Polytechnic Institute Macao SAR China Institute of Science Biomedicine Abel Salazar University of PortoHeidelberg School of Chinese Medicine Heidelberg Germany Faculty of Medicine University of Coimbra Portugal Health Sciences Research Unit: Nursing (UICISA:E) Nursing School of Coimbra (ESEnfC)Portugal Centre for Evidence Based Practice: A Joanna Briggs Institute Centre of Excellence Portugal

Objective: To identify and synthesize the most recent available evidence of effectiveness of acupuncture on pain, physical function and health-related quality of life(HRQoL) in patients with rheumatoid arthritis(RA). Methods: A comprehensive search of 12 Western and Chinese databases was undertaken from their inception up to end of 2016. Randomized controlled trials(RCTs), concerning patients with RA treated with needle acupuncture, written in English, Portuguese, german or Chinese were included. Primary outcomes included pain, physical function and HRQoL. Secondary outcomes included morning stiffness, functional impairment, number of tender and swollen joints and serum concentrations of inflamatory markers. Methodological quality was assessed by three independent reviewers using the standardized critical appraisal instrument from the Joanna Briggs Institute Meta-Analysis of Statistics Assessment and Review Instrument. Results: Twenty-two studies met the inclusion criteria. Of those, 9 studies were excluded after assessment of their methodological quality. The remaining 13 original RCTs included 974 patients. Ten of these studies published in China, showed favorable statistical significant effects of acupuncture in relieving symptoms of RA compared with controls. Conclusions: Evidence suggests that acupuncture interventions may have a positive effect in pain relief, physical function and HRQo L in RA patients. However, due to the heterogeneity and methodologic limitations of the studies included in this systematic review, evidence is not strong enough to produce a best practice guideline.

关键词： acupuncture rheumatoid arthritis quality of life pain physical function randomized clinical trial

Modelling potential distribution of a pine bark beetle in Mexican temperate forests using forecast data and spatial analysis tools

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Journal of Forestry Research 2020年第2期31卷 649-659页

作者： Antonio gonzalez-Hernandez Rene Morales-Villafana Martin Enrique Romero-Sanchez Brenda Islas-Trejo Ramiro Perez-miranda Conservation and Enhancement of Forest Ecosystems National Institute of ForestryAgriculture and Livestock ResearchProgreso 504010 Coyoacan Mexico CityMexico geography Department The National Autonomous University of MexicoUniversidad 300004010 Coyoacan Mexico CityMexico

Accurate and reliable predictions of pest species distributions in forest ecosystems are urgently needed by forest managers to develop management plans and monitor new areas of potential ***-only species distribution models are commonly used in these *** maximum entropy algorithm(MaxEnt)has gained popularity for modelling species ***,MaxEnt was used to model the spatial distribution of the Mexican pine bark beetle(Dendroctonus mexicanus)in a daily fashion by using forecast data from the Weather Research and Forecasting *** study aimed to exploit freely available geographic and environmental data and software and thus provide a pathway to overcome the lack of costly data and technical guidance that are a challenge to implementing national monitoring and management strategies in developing *** results showed overall agreement values between 60 and 87%.The results of this research can be used for *** monitoring and management and may aid as a model to monitor similar species.

关键词： Spatial analysis Dendroctonus mexicanus geodatabases MaxEnt Forest modelling

Nanoparticles with high payloads of pipemidic acid, a poorly soluble crystalline drug: drug-initiated polymerization and self-assembly approach

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Acta Pharmaceutica Sinica B 2018年第3期8卷 420-431页

作者： Elisabetta Pancani Mario Menendez-miranda Alexandra Pastor Francois Brisset Marie-Francoise Bernet-Camard Didier Desmaele Ruxandra gref Institut de Sciences Moléculaires d'Orsay(ISMO) Univ.of Paris-SudUniversitéParis-Saclay Institut galien UMR8612 Univ.of Paris-SudUniversitéParis-Saclay Institut de Chimie Moléculaire et des Matériaux d'Orsay(ICMMO) Univ.of Paris-SudUniversitéParis-Saclay EA4043" UnitéBactéries Pathogènes et Santé"(UBaPS) Univ.of Paris-SudUniversitéParis-Saclay

Nowadays, biodegradable polymers such as poly(lactic acid)(PLA), poly(D,L-lactic-coglycolic acid)(PLgA) and poly(ε-caprolactone)(PCL) remain the most common biomaterials to produce drug-loaded nanoparticles(NPs). Pipemidic acid(PIP) is a poorly soluble antibiotic with a strong tendency to crystallize. PIP incorporation in PLA/PLgA NPs was challenging because of PIP crystals formation and burst release. As PIP had a poor affinity for the NPs, an alternative approach to encapsulation was used, consisting in coupling PIP to PCL. Thus, a PCL–PIP conjugate was successfully synthesized by an original drug-initiated polymerization in a single step without the need of ***–PIP was characterized by NMR, IR, SEC and mass spectrometry. PCL–PIP was used to prepare selfassembled NPs with PIP contents as high as 27%(w/w). The NPs were characterized by microscopy,DLS, NTA and TRPS. This study paves the way towards the production of NPs with high antibiotic payloads by drug-initiated polymerization. Further studies will deal with the synthesis of novel polymer–PIP conjugates with ester bonds between the drug and PCL. PIP can be considered as a model drug and the strategy developed here could be extended to other challenging antibiotics or anticancer drugs and employed to efficiently incorporate them in NPs.

关键词： Pipemidic acid Nanoparticle Antibiotic Nanoprecipitation Crystalline drug Drug-initiated polymerization