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A container-based approach for sharing environmental models as web services

International Journal of Digital Earth 2021年第8期14卷 1067-1086页

作者： Xiaohui Qiao Zhiyu Li Fengyuan Zhang daniel p.ames Min Chen E.James Nelsona Rohit Khattar Civil and Environmental Engineering Brigham Young UniversityProvoUTUSA Key Laboratory of Virtual Geographic Environment(Ministry of Education of pRC) Nanjing Normal UniversityNanjingPeople’s Republic of China Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application NanjingPeople’s Republic of China State Key Laboratory Cultivation Base of Geographical Environment Evolution(Jiangsu province) NanjingPeople’s Republic of China

As researchers globally work towards a fully digital representation of the earth and its processes-i.e.a true Digital Earth-the need grows for software and systems to link disparate computer simulation models of various parts of the earth in a reliable and highly functional *** services have been demonstrated as an effective way to share and reuse models as they enable communication and interoperation among applications via the ***,even using well-designed software tools,it remains a daunting process to publish heterogeneous environmental models as web services and provide long-term maintenance in response to changing computational *** present an approach that enables environmental models to be published as long-term functional web services on the same platform regardless of execution mode,programming language,and computational environment *** approach adopts the OpenGMS Wrapper System(OGMS-WS)for service publishing and Docker containers for model isolation.A streamflow prediction service is developed using this approach and is applied to analyze historical streamflow trends in *** demonstrate that this approach can lower the barrier to deploying heterogeneous environmental models as long-term functional web services,contributing to the development of a Digital Earth.

关键词： Environmental models container OpenGMS platform web service

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A new academic impact metric for evaluating geographic simulation models

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International Journal of Digital Earth 2022年第1期15卷 1855-1880页

作者： Kai Xu Min Chen Albert J.Kettner C.Michael Barton Barry F.W.Croke Anthony J.Jakeman daniel p.ames Hsiao-Hsuan Wang Susan M.Cuddy Songshan Yue Yongning Wen Fengyuan Zhang Yixuan Zhang Guonian Lü Key Laboratory of Virtual Geographic Environment (Ministry of Education of pRC) Nanjing Normal UniversityNanjingJiangsuPeople’s Republic of China Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application NanjingJiangsuPeople’s Republic of China State Key Laboratory Cultivation Base of Geographical Environment Evolution(Jiangsu province) NanjingJiangsuPeople’s Republic of China Community Surface Dynamics Modelling System (CSDMS) Institute of Arctic and Alpine Research (INSTAAR)University of ColoradoBoulderCOUSA School of Human Evolution and Social Change Arizona State UniversityTempeAZUSA School of Complex Adaptive Systems Arizona State UniversityTempeAZUSA Institute for Water Futures Fenner School of Environment and SocietyAustralian National UniversityCanberraAustralia Mathematical Sciences Institute The Australian National UniversityCanberraAustralia Department of Civil and Construction Engineering Brigham Young UniversityProvoUTUSA Ecological Systems Laboratory Department of Ecology and Conservation BiologyTexas A&M UniversityCollege StationTXUSA CSIRO Land and Water CanberraAustralia

Geographic simulation models can be used to explore and better understand the geographical environment. Recent advances in geographic and socio-environmental research have led to a dramatic increase in the number of models used for this purpose. Some model repositories provide opportunities for users to explore and apply models,but few provide a general evaluation method for assessing the applicability and recognition of models. In this study,an academic impact evaluation method for models is proposed. Five indices are designed based on their pertinence. The analytical hierarchy process is used to calculate the index weights,and the academic impacts of models are quantified with the weighted sum method. The time range is controlled to evaluate the life-term and annual academic impacts of the models. Some models that met the evaluation criteria from different domains are then evaluated. The results show that the academic impact of a model can be quantified with the proposed method,and the major research areas that models impact are identified.

关键词： Geographic simulation model academic impact analytic hierarchy process model impact evaluation

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Considerations for Implementing OGC WMS and WFS Specifications in a Desktop GIS

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Journal of Geographic Information System 2012年第2期4卷 161-167页

作者： Christopher D. Michaelis daniel p. ames Department of Geosciences Idaho State University Idaho Falls USA

An implementation of the Open Geospatial Consortium Web Feature Service (WFS) and Web Map Service (WMS) specifications in an open source desktop GIS is presented together with a discussion of considerations for improving the use of web services data in desktop applications. In our implementation, WFS and WMS services are consumed by a plug-in to MapWindow GIS [1], allowing the end user to view WFS, WMS and ArcIMS data, including data from the ESRI Geography Network, in a transparent manner that can be configured for either data analysis and modeling, or data visualization. This implementation in an open source GIS allows for others to view and use the code, improve it, and otherwise implement the suggested considerations in other GIS platforms. Specific considerations proposed here include: pre-fetching through envelope optimization, tile display, and feature complexity reduction. These strategies improve the speed and responsiveness with which data can be viewed and analyzed. Comparisons made with other web-based data access implementations are used to evaluate whether these techniques provide performance benefits, and under which circumstances.

关键词： OGC WFS WMS Geographic Information Systems Open Source GIS

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Challenges to Coordination: Understanding Intergovernmental Friction During Disasters

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International Journal of Disaster Risk Science 2019年第3期10卷 306-316页

作者： daniel p.Aldrich Department of political Science School of Public Policy and Urban Affairs Northeastern UniversityBoston

While idealized crisis response involves smooth coordination between relevant actors, friction between levels of government and between the state and civil society in responding to catastrophe may be more *** article builds a theory of cross-level friction during and after crisis by analyzing the conditions when discord is most likely. With a medium-N dataset(N = 18) of disaster responses from, among other countries, Chile, Haiti, Japan,North America, the philippines, and Somalia, I carry out quantitative and qualitative analysis of cases with a variety of levels of friction to investigate the conditions that lead to misalignment. Tobit regression, qualitative comparative analysis, and case studies that take into account levels of economic development, government structure, nongovernmental organization density, and levels of damage demonstrate that low levels of development, lower levels of economic costs from the crisis, and poor planning and logistical infrastructure correlate with a higher likelihood of friction between disaster response *** not definitive, these findings come with theoretical and practical implications as climate change makes extreme weather events and future disasters more likely and more powerful.

关键词： Bottom up culture Case studies Disaster coordination Qualitative comparative analysis Tobit regression analysis Top down institutions

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New developments in the treatment of castration resistant prostate cancer

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Asian Journal of Andrology 2014年第4期16卷 555-560页

作者： Roxanne Wadia daniel p petrylak Department of Medicine Smilow Cancer Center Yale University School of Medicine Yale Comprehensive Cancer Center New Haven Connecticut USA

In the past 5 years, the treatment and understanding of metastatic castrate resistant prostate cancer （CRpC） have improved dramatically. Our understanding of the mechanisms of castration resistance has allowed for the development of new drugs to target prostate cancer, and our understanding of genetic mutations may give us new tools with which to more accurately diagnose and be able to predict the course of this heterogeneous disease. This article summarizes the recent advances in the understanding of the development of CRpC, as well as the new drugs and targets, which have evolved from this basic research.

关键词： castration resistant prostate cancer abiraterone enzalutamide chemotherapy docetaxel cabazitaxel pSMA antibody

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Nanomechanical hydrodynamic force sensing using suspended microfluidic channels

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Microsystems & Nanoengineering 2023年第3期9卷 95-102页

作者： Alberto Martín-pérez daniel Ramos Optomechanics Lab Instituto de Ciencia de Materiales de Madrid(ICMMCSIC)3 Sor Juana Inés de la Cruz(Madrid)E-28049 MadridSpain

Microfluidics has demonstrated high versatility in the analysis of in-flow particles and can even achieve mechanical properties measurements of biological cells by applying hydrodynamic ***,there is currently no available technique that enables the direct measurement and tracking of these hydrodynamic forces acting on a flowing *** this work,we introduce a novel method for the direct measurement of the hydrodynamic force actuating on an in-flow particle based on the analysis of the induced resonance changes of suspended microchannel resonators(SMRs).This hydrodynamic force sensitivity depends on the device used;therefore,we considered the geometry and materials to advance this dependency on the SMR resonance frequency.

关键词： hydrodynamic applying flow

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Quantitative Methods for Comparing Different polyline Stream Network Models

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Journal of Geographic Information System 2014年第2期6卷 88-98页

作者： Danny L. Anderson daniel p. ames ping Yang Department of Civil and Environmental Engineering Brigham Young University Provo USA Idaho National Laboratory Idaho Falls USA Texas Institute for Applied Environmental Research Tarleton State University Stephenville USA

Two techniques for exploring relative horizontal accuracy of complex linear spatial features are described and sample source code (pseudo code) is presented for this purpose. The first technique, relative sinuosity, is presented as a measure of the complexity or detail of a polyline network in comparison to a reference network. We term the second technique longitudinal root mean squared error (LRMSE) and present it as a means for quantitatively assessing the horizontal variance between two polyline data sets representing digitized (reference) and derived stream and river networks. Both relative sinuosity and LRMSE are shown to be suitable measures of horizontal stream network accuracy for assessing quality and variation in linear features. Both techniques have been used in two recent investigations involving extraction of hydrographic features from LiDAR elevation data. One confirmed that, with the greatly increased resolution of LiDAR data, smaller cell sizes yielded better stream network delineations, based on sinuosity and LRMSE, when using LiDAR-derived DEMs. The other demonstrated a new method of delineating stream channels directly from LiDAR point clouds, without the intermediate step of deriving a DEM, showing that the direct delineation from LiDAR point clouds yielded an excellent and much better match, as indicated by the LRMSE.

关键词： LiDAR Stream Channels Accuracy RMSE Sinuosity Terrain Analysis

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Managing water for life

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Frontiers of Environmental Science & Engineering 2012年第2期6卷 255-264页

作者： daniel p.LOUCKS Haifeng JIA Civil and Environmental Engineering Comell UniversityIthaca NY 14853USA School of Environment Tsinghua UniversityBeijing 100084China

Water is essential for life. In spite of the entire engineering infrastructure devoted to the treatment, regulation and beneficial uses of water, occasionally sufficient quantities and qualities of water become scarce. When this happens, just how do we decide how much less water to allocate to all of us and the activities we engage in to sustain and enhance our quality of life？ This paper addresses some of the complexities of answering such a question, especially as society increasingly recognizes the need to provide flow regimes that will maintain healthy aquatic and floodplain ecosystems that also impact the economic, physical and even the spiritual quality of our lives. For we depend on these ecosystems to sustain our wellbeing. We are indeed a part of our ecosystems. We depend upon on aquatic ecosystems to moderate river flow qualities and quantities, reduce the extremes of floods and droughts, reduce erosion, detoxify and decompose water- borne wastes, generate and preserve flood plain soils and renew their fertility, regulate disease carrying organisms, and to enhance recreational benefits of river systems. This question of deciding just how much water to allocate to each water user and for the maintenance of viable aquatic ecosystems, especially when there is not enough, is a complex, and largely political, issue. This issue is likely to become even more complex and political and contentious in the future as populations grow and as water quantities and their qualities become even more variable and uncertain.

关键词： water stress aquatic ecosystems sustainablewater resource allocations ecosystem water requirements

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Comparison of reduced point charge models of proteins: Molecular Dynamics simulations of Ubiquitin

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Science China Chemistry 2014年第10期57卷 1340-1354页

作者： LEHERTE Laurence VERCAUTEREN daniel p. Unité de Chimie physique Théorique et Structurale Laboratoire de Physico-Chimie Informatique Namur MEdicine & Drug Innovation Center (NAMEDIC) Department of Chemistry University of Namur Rue de Bruxelles 61 B-5000 Namur Belgium

Reduced point charge models of amino acids are used to model Ubiquitin （pDB： 1UBQ）. They are designed （i） from local ex- tremum positions in charge density （CD） distribution functions built from the poisson equation applied to smoothed molecular electrostatic potential functions, or （ii） from local maximum positions in promolecular electron density distribution （ED） func- tions. Charge values are fitted versus all-atom Amber99 molecular electrostatic potentials. The program GROMACS is used to generate molecular dynamics trajectories of the protein, under various implementation schemes, solvation, and temperature conditions. point charges that are not located on atoms are considered as virtual sites with a null mass and radius. The results illustrate that secondary structure is best preserved with the CD-based model at low temperatures and in vacuum. This indi- cates that local potential energy wells are consistent with the all-atom model. However, at room temperature, the structure is best conserved when point charges are forced to be located on atoms, due to a better description of the Coulomb l-4 energy terms. The ED-based model, generated at a lower resolution, led to the largest discrepancies versus the all-atom case. The CD-based model allows the formation of protein-water H-bonds with geometrical properties similar to the all-atom ones. Con- trarily, intra-molecular H-bonds are not well described. Structural, thermodynamical, and dynamical properties of proteins modelled with reduced point charge models are also significantly affected by the choice of the solvent force field.

关键词： molecular electrostatic potential electron density smoothing of molecular fields critical points point charge model protein Ubiquitin

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Deciphering the dual role and prognostic potential of pINK1 across cancer types

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Neural Regeneration Research 2021年第4期16卷 659-665页

作者： Katherine Dai daniel p.Radin Donna Leonardi Department of Molecular Cellularand Developmental BiologyYale UniversityNew HavenCTUSA Department of pharmacology Stony Brook University School of MedicineStony BrookNYUSA Bergen County Academies HackensackNJUSA

Metabolic rewiring and deregulation of the cell cycle are hallmarks shared by many *** mutations in key tumor suppressor genes,such as pTEN,and oncogenes predispose cancer cells for marked utilization of resources to fuel accelerated cell proliferation and chemotherapeutic *** research has demonstrated that pTEN-induced putative kinase 1(pINK1)acts as a pivotal regulator of mitochondrial homeostasis in several cancer types,a function that also extends to the regulation of tumor cell proliferative *** addition,involvement of pINK1 in modulating inflammatory responses has been highlighted by recent studies,further expounding pINK1’s multifunctional *** review discusses the oncogenic roles of pINK1 in multiple tumor cell types,with an emphasis on maintenance of mitochondrial homeostasis,while also evaluating literature suggesting a dual oncolytic mechanism based on pINK1’s modulation of the Warburg *** a clinical standpoint,its expression may also dictate the response to genotoxic stressors commonly used to treat multiple *** detailing the evidence suggesting that pINK1 possesses distinct prognostic value in the clinical setting and reviewing the duality of pINK1 function in a context-dependent manner,we present avenues for future studies of this dynamic protein.

关键词： apoptosis cancer cell cycle inflammation metabolic stress mitochondral quality control mitophagy pINK1 tumor Warburg effect

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