cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
The Impact of a Sorghum-Based Ethanol Plant on Local Sorghum Basis and Cotton Acreage: A Spatial Approach
Creators: name: Liu, Bing
name: Hudson, Darren
name: Pavlik, Jamie Bologna
name: Farmer, Michael
name: Liu, Bing
name: Hudson, Darren
name: Pavlik, Jamie Bologna
name: Farmer, Michael
Publisher: name: Unknown
Year: 2018
Subjects: Agribusiness
Crop Production/Industries

description: This study examines the impacts of a sorghum-based ethanol plant established in a major cotton-producing area on local sorghum basis and cotton acreage distribution using county-level panel data from 2002 to 2014. Spatial econometric models are employed to account for any spatial dependence. Our results support the conclusion that sorghum basis and cotton acreage within a county depends on characteristics of its neighbors. Specifically, the findings indicate that the sorghum basis increased by 1.5 cents per bushel in the short run resulting from hosting a 40-million-gallon ethanol plant, and a short-run increase by 0.2% in cotton acres over all counties.
How Determinants of Thoroughbred Stud Fees Change Over Time: A Hedonic Price Approach
Creators: name: Hansen, Charlotte R.
name: Stowe, C. Jill
name: Saghaian, Sayed
name: Hansen, Charlotte R.
name: Stowe, C. Jill
name: Saghaian, Sayed
Publisher: name: Unknown
Year: 2018
Subjects: Agribusiness

description: By the time a Thoroughbred stallion produces four crops of foals, the success of his entire breeding career is largely determined. One hundred and sixty-three Thoroughbred sires beginning their breeding careers between 2002 and 2005 are tracked for five consecutive years. Adopting a hedonic pricing method, we observe how determinants of stud fees change as new information about the sire’s quality becomes available. Results show that initially, a sire’s own racetrack performance is influential in predicting stud fees; eventually, this information becomes irrelevant as information about progeny performance (both on the racetrack and in the auction ring) is learned.
Demo: Co-Scheduling HPC and BigData jobs using Apache Mesos
Creators: name: Yodage, Shameera
name: Marru, Suresh
name: Pierce, Marlon
Publisher: name: figshare
Year: 2017
Subjects: subject: Distributed Computing
subject: FOS: Computer and information sciences
subject: 80501 Distributed and Grid Systems
subject: Applied Computer Science
subject: Computer Software
subject: 80505 Web Technologies (excl. Web Search)

description: Scientific computing, by many measures, is becoming more complicated and heterogeneous. At the application level, cloud-native and data-intensive computing based on MapReduce and its descendants require computing resources that go beyond the traditional batch queuing model. Computing resources themselves have become more heterogeneous as hybrid architectures with graphical processing units (GPUs) and coprocessors (Xeon PHI) are providing alternatives to CPU based parallelizing techniques for traditional High-Performance Computing (HPC). Science gateways have traditionally provided simplifying interfaces for end users that hide the complications of using complicated resources. Thus the core reason for science gateways to exist is becoming more important, while the challenges for building science gateway middleware increases. In this demonstration, we showcase developments in the Apache Airavata science gateway framework that address these challenges by leveraging the Apache Mesos ecosystem to schedule both HPC and BigData jobs; we use XSEDE’s next generation JetStream, Comet, Bridges and Wrangler clusters. Each of these clusters provide unique capabilities; this demonstration will highlight how gateways can take advantage of these capabilities through a unified approach to middleware.
Creating a Gateway for Collaborative Learning
Creators: name: Corwin, Bev
name: Ewen, Christie
name: Auriti, Sean
name: Ulmer, John
name: Medina, Janine
name: Whysel, Noreen
Publisher: name: figshare
Year: 2016
Subjects: subject: Distributed Computing
subject: FOS: Computer and information sciences
subject: 80501 Distributed and Grid Systems
subject: Applied Computer Science
subject: Computer Software
subject: 80505 Web Technologies (excl. Web Search)

description: The OWASP Learning Gateway Project proposes developing a platform that is adaptable to the learning needs and user requirements of a global community of technology learners. The gateway will offer learning pathways that connect learners with mentors and the knowledge needed to be successful. Our ultimate goal is to be a successful Science Gateways Incubation Project.
The CIPRES Science Gateway at Year 6: Lessons learned and best practices
Creators: name: Miller, Mark
name: Schwartz, Terri
name: Pfeiffer, Wayne
Publisher: name: figshare
Year: 2017
Subjects: subject: Distributed Computing
subject: FOS: Computer and information sciences
subject: 80501 Distributed and Grid Systems
subject: Applied Computer Science
subject: Computer Software
subject: 80505 Web Technologies (excl. Web Search)

description: The CIPRES Science Gateway was created in 2009 to provide the international phylogenetic community with easy access to parallel versions of community codes run on High Performance Computing resources available through the XSEDE project. After six years of operation, job submissions continue to increase each month, and more than 19,000 individual users have been provided with access. Here we describe the lessons learned and best practices acquired over the lifetime of the CIPRES Science Gateway.
Editorial
Creators: name: Cardoso, Diogo N.
name: Monteiro, Hugo
name: Silva, Patrícia V.
name: Coelho, Sónia D.
Publisher: name: Revista Captar: Ciência e Ambiente para Todos
Year: 2016

description: Revista Captar: Ciência e Ambiente para Todos, vol. 6 n.º 1 (2016)
Carnet nº 21, commencé à Canton (p. 92)
Creators: name: Péraire, Lucien
name: CNRS
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2023

description: created: 6-8-1931
Expenditures on Wine in General and Local Wine in Particular: Marketing and Econometric Analysis
Creators: name: Deng, Xueting
name: Butler, J.S.
name: Deng, Xueting
name: Butler, J.S.
Publisher: name: Unknown
Year: 2018
Subjects: subject: Agribusiness
subject: Marketing
subject: FOS: Economics and business

description: This article explores factors explaining wine spending patterns for consumers in Kentucky, Ohio, Pennsylvania, and Tennessee. We apply and compare five market segmentation measurements: wine purchase frequency, wine prices, local involvement levels, wine knowledge, and past local wine experiences. Data shows expenditures on wine. The econometric estimation employs interval estimation to interpret wine expenditures as reported in intervals and selection bias corrections to separate factors associated with decisions to purchase wine from factors associated with the amount expended. Results show that market segmentation measurements have stronger effects on local wine purchasing probability and purchasing quantity, compared with demographics.
Reactive, Interactive, and High Throughput Computation in the Agave Platform
Creators: name: Rion Dooley
name: Stubbs, Joe
Publisher: name: figshare
Year: 2016
Subjects: subject: Distributed Computing
subject: FOS: Computer and information sciences
subject: 80501 Distributed and Grid Systems
subject: Applied Computer Science
subject: Computer Software
subject: 80505 Web Technologies (excl. Web Search)

description: The Agave Platform is an open Science-as-a-Service platform that empowers users to run code, manage data, collaborate meaningfully, and integrate easily with the world around them. In this extended abstract, we examine how new use cases have helped evolve the ways in which Agave supports code execution. We start out by identifying three new code execution paradigms identified in the past 2 years: Interactive, Reactive, and High Throughput computing. We then briefly describe the primary use cases driving each paradigm and how the platform evolved in response to them. Finally, we highlight areas of future work in the platform related to code execution.
Coupons and Manufacturer Market Shares: A Brand-Level Analysis of the Ready-to-Eat Breakfast Cereal Market
Creators: name: Bakhtavoryan, Rafael
name: Meloyan, Artak
name: Hovhannisyan, Vardges
name: Bakhtavoryan, Rafael
name: Meloyan, Artak
name: Hovhannisyan, Vardges
Publisher: name: Unknown
Year: 2018
Subjects: subject: Agribusiness
subject: Marketing
subject: FOS: Economics and business

description: This study builds on a theory-consistent demand system, namely the Almost Ideal Demand System, utilizing the Nielsen Homescan Panel data on household purchases, and models potential effects of coupons on market shares of related ready-to-eat breakfast cereal brands. The results emerging from this brand-level analysis reveal an important link between coupons and brand market shares. Specifically, based on the coupon elasticities of market shares derived in this study, coupons are found to have contributed to expanding national brand market shares, while not affecting those for private labels.
The DesignSafe-CI Architecture
Creators: name: Mock, Stephen
name: Hanlon, Matthew
name: Stanzione, Dan
name: Rathje, Ellen
Publisher: name: figshare
Year: 2016
Subjects: subject: Distributed Computing
subject: FOS: Computer and information sciences
subject: 80501 Distributed and Grid Systems
subject: Applied Computer Science
subject: Computer Software
subject: 80505 Web Technologies (excl. Web Search)

description: Natural hazards threaten life and property across the United States and the world. The DesignSafe cyberinfrastructure (CI) supports multi-hazard engineering by addressing the big challenges associated with multi-hazard research. The DesignSafe CI was recently deployed and is under active development. This paper outlines the existing and planned architecture of the DesignSafe CI.
Estimation and Decomposition of Economic Inefficiency of Maize Producers in Benin: A Directional Distance Function Framework
Creators: name: Adeguelou, Raoul
name: Adegbola, Patrice Y.
name: Singbo, Alphonse
name: Savadogo, Kimseyinga
name: Adeguelou, Raoul
name: Adegbola, Patrice Y.
name: Singbo, Alphonse
name: Savadogo, Kimseyinga
Publisher: name: Unknown
Year: 2018
Subjects: Agribusiness
Crop Production/Industries

description: A directional distance function is used to decompose short-run profit inefficiency into technical, allocative, scale inefficiency and contributions of output and input of maize producers in Benin. The sample consists of 151 maize producers including 42 for improved varieties (IV) and 109 for traditional varieties (TV). Results show that only 33% and 16% of IV and TV producers, respectively, are economically efficient, indicating that most producers present substantial overall inefficiency sources, notably pure technical and allocative inefficiency. Also, decreasing returns to scale characterized maize production. Agricultural extension services need to facilitate the use of IV with high yielding potential by producers.
The Role of Foreign Direct Investment in the Elasticity of Substitution between Exports and Imports
Creators: name: Peña-Lévano, Luis M.
name: Peña-Lévano, Luis M.
Publisher: name: Unknown
Year: 2018
Subjects: Agribusiness
Demand and Price Analysis

description: The Armington elasticity of substitution captures the trade-off interaction between imports and domestic sales. Recently, foreign direct investment (FDI) has become a significant source of international investment. This study incorporates the effect of horizontal FDI in this elasticity. Including FDI affects the modeling and value of the trade elasticity, providing new insights on the behavior of U.S. firms vis-a-vis the tradeoff between horizontal FDI and exports. This new Armington elasticity of substitution estimates provide a lower value than predecessors. This means that the impacts of a trade policy (such as tariffs) are expected to be lower due to FDI substitution.
The “Liability of Newness” in the Food/Agribusiness Sector
Creators: name: Johnson, Aaron J.
name: Dibrell, Clay
name: Inman, Ruth
name: Holcomb, Rodney B.
name: Johnson, Aaron J.
name: Dibrell, Clay
name: Inman, Ruth
name: Holcomb, Rodney B.
Publisher: name: Unknown
Year: 2018
Subjects: Agribusiness

description: “Liability of Newness” reflects the reality that only half of new businesses survive the first five years and less than one-third survive beyond 10 years. This study is designed to help new businesses—and assist organizations (e.g. universities, nonprofits) —address this liability of newness and achieve “legitimacy” by exploring the connection between organizational legitimacy and firm performance. A survey of food businesses in the Western United States was performed to examine legitimacy strategies and legitimacy forms. This study offers a first-ever quantified look at legitimacy and its impact and, as such, offers some answers and questions for future consideration.
Capturing the “Whole Tale” of Computational Research: Reproducibility in Computing Environments
Creators: name: Ludascher, Bertram
name: Chard, Kyle
name: Gaffney, Niall
name: Jones, Matthew
name: Jaroslaw Nabrzyski
name: Turk, Matthew
name: Stodden, Victoria
Publisher: name: figshare
Year: 2017
Subjects: subject: Distributed Computing
subject: FOS: Computer and information sciences
subject: 80501 Distributed and Grid Systems
subject: Applied Computer Science
subject: Computer Software
subject: 80505 Web Technologies (excl. Web Search)

description: We present an overview of the recently funded “Merging Science and Cyberinfrastructure Pathways: The Whole Tale” project (NSF award #1541450). Our approach has two nested goals: 1) deliver an environment that enables researchers to create a complete narrative of the research process including exposure of the data-to-publication lifecycle, and 2) systematically and persistently link research publications to their associated digital scholarly objects such as the data, code, and workflows. To enable this, Whole Tale will create an environment where researchers can collaborate on data, workspaces, and workflows and then publish them for future adoption or modification. Published data and applications will be consumed either directly by users using the Whole Tale or can be integrated into existing or future domain Science Gateways. Our approach is analogous to a general science gateway as it aims to deliver a collection of services and integration software that simplifies the use of scientific services and cyberinfrastructure.
Estimating Agricultural Losses from a Hurricane
Creators: name: Dorfman, Jeffrey H.
name: Liu, Yangxuan
name: Rabinowitz, Adam N.
name: Dorfman, Jeffrey H.
name: Liu, Yangxuan
name: Rabinowitz, Adam N.
Publisher: name: Unknown
Year: 2018
Subjects: Agribusiness
Community/Rural/Urban Development

description: Natural disasters such as hurricanes, floods, and droughts often cause significant economic damages for agricultural producers and agribusinesses. Agricultural economics departments and colleges of agriculture are often asked to help compute economic losses resulting from such events. The resulting loss estimates are used to lobby for various forms of disaster relief and to show that regions, states, or commodities are eligible for existing government programs. This paper documents how agricultural economists and their colleagues at The University of Georgia went about estimating losses suffered in Georgia from Hurricane Michael in October 2018.
Organizational Attributes of Successful Science Gateways and Cyberinfrastructure Projects
Creators: name: Kerk Kee
Publisher: name: figshare
Year: 2017
Subjects: subject: Distributed Computing
subject: FOS: Computer and information sciences
subject: 80501 Distributed and Grid Systems
subject: Applied Computer Science
subject: Computer Software
subject: 80505 Web Technologies (excl. Web Search)

description: While much of the adoption and diffusion of science gateways and/or computational tools for e-science is driven by the attributes of the tools [see 1], the organizations behind the tools play a critical role in determining the ultimate diffusion. This paper reports 10 organizational attributes of successful gateways and cyberinfrastructure projects. Based on a systematic analysis of 135 interviews, the organizational attributes include having leaders with credibility, multidisciplinary expertise, collaborative environment, shared goals, a common language, strategic structure, productive routines, organizational capacity, sustainable funding, and personnel continuity.
Demo: Co-Scheduling HPC and BigData jobs using Apache Mesos
Creators: name: Yodage, Shameera
name: Marru, Suresh
name: Pierce, Marlon
Publisher: name: figshare
Year: 2016
Subjects: subject: Distributed Computing
subject: FOS: Computer and information sciences
subject: 80501 Distributed and Grid Systems
subject: Applied Computer Science
subject: Computer Software
subject: 80505 Web Technologies (excl. Web Search)

description: Scientific computing, by many measures, is becoming more complicated and heterogeneous. At the application level, cloud-native and data-intensive computing based on MapReduce and its descendants require computing resources that go beyond the traditional batch queuing model. Computing resources themselves have become more heterogeneous as hybrid architectures with graphical processing units (GPUs) and coprocessors (Xeon PHI) are providing alternatives to CPU based parallelizing techniques for traditional High-Performance Computing (HPC). Science gateways have traditionally provided simplifying interfaces for end users that hide the complications of using complicated resources. Thus the core reason for science gateways to exist is becoming more important, while the challenges for building science gateway middleware increases. In this demonstration, we showcase developments in the Apache Airavata science gateway framework that address these challenges by leveraging the Apache Mesos ecosystem to schedule both HPC and BigData jobs; we use XSEDE’s next generation JetStream, Comet, Bridges and Wrangler clusters. Each of these clusters provide unique capabilities; this demonstration will highlight how gateways can take advantage of these capabilities through a unified approach to middleware.
Mikroplastik in landwirtschaftlichen Böden - eine versteckte Gefahr?
Creators: name: Leifheit, Eva F.
name: Rillig, Matthias C.
Publisher: name: Berichte über Landwirtschaft - Zeitschrift für Agrarpolitik und Landwirtschaft
Year: 2020

description: Mikroplastik vermischt sich relativ schnell mit dem Boden und ist dann für das bloße Auge nicht mehr sichtbar. Stellt es vielleicht eine versteckte Gefahr für Bodenorganismen, Pflanzen oder den Menschen dar? Bisherige Ergebnisse haben gezeigt, dass die Form der Mikroplastikpartikel eine wichtige Rolle spielt: Insbesondere Fasern scheinen negative Auswirkungen auf Bodenprozesse wie die Bodenaggregation zu haben, also das Zusammenhalten von Bodenpartikeln in Aggregaten und deren Stabilität. Möglicherweise stören die Mikroplastikpartikel den Zusammenhalt der Aggregate durch das Einfügen von Sollbruchstellen. Fragmente wie Folienstücke oder Kügelchen hatten bisher unterschiedlich starke Effekte auf Bodenprozesse. In mehreren Versuchen wurde experimentell gezeigt, dass Regenwürmer in Mitleidenschaft gezogen wurden und die Aktivität der mikrobiellen Bodenlebensgemeinschaft verändert wird. Die Keimung von Samen kann negativ beeinflusst werden; das Wachstum von Pflanzen wurde in Laborversuchen sowohl positiv als auch negativ beeinflusst. Die unterschiedlichen Versuchsergebnisse sind in erster Linie vermutlich auf die immens große Zahl an unterschiedlichen Plastikarten, deren Zusatzstoffen und Versuchsbedingungen zurückzuführen. Die Frage aus unserem Titel kann daher momentan nicht abschließend beantwortet werden. Die Forschung auf diesem Gebiet steht noch am Anfang, wird aktuell jedoch massiv ausgebaut. Hier ist momentan eine genaue Dokumentation der Forschungsergebnisse gefordert, die darauf hinführen sollte, Effekte zukünftig zusammenfassen zu können.
description: Berichte über Landwirtschaft - Zeitschrift für Agrarpolitik und Landwirtschaft, Aktuelle Beiträge
The CIPRES Science Gateway at Year 6: Lessons learned and best practices
Creators: name: Miller, Mark
name: Schwartz, Terri
name: Pfeiffer, Wayne
Publisher: name: figshare
Year: 2016
Subjects: subject: Distributed Computing
subject: FOS: Computer and information sciences
subject: 80501 Distributed and Grid Systems
subject: Applied Computer Science
subject: Computer Software
subject: 80505 Web Technologies (excl. Web Search)

description: The CIPRES Science Gateway was created in 2009 to provide the international phylogenetic community with easy access to parallel versions of community codes run on High Performance Computing resources available through the XSEDE project. After six years of operation, job submissions continue to increase each month, and more than 19,000 individual users have been provided with access. Here we describe the lessons learned and best practices acquired over the lifetime of the CIPRES Science Gateway.
MyGene2 automated match report: SCNN1A
Creators: name: Team, The MyGene2
Publisher: name: figshare
Year: 2017
Subjects: subject: 110311 Medical Genetics (excl. Cancer Genetics)
subject: FOS: Basic medicine

description: MyGene2.org is free, public, searchable & browsable website. Families with rare genetic conditions, clinicians, and researchers families who are interested in sharing health and genetic information can create MyGene2 profiles and use these to connect with other families, clinicians, and researchers who may have or be studying the same condition. If multiple MyGene2 profiles potentially match on a shared gene of interest, MyGene2 automatically generates a match report summarizing the information in these profiles. This automated match report is shared publicly to help facilitate further research and/or connections between the submitters of the MyGene2 profiles and other interested parties. This is an automated match report for SCNN1A.
Capturing the “Whole Tale” of Computational Research: Reproducibility in Computing Environments
Creators: name: Ludascher, Bertram
name: Chard, Kyle
name: Gaffney, Niall
name: Jones, Matthew
name: Jaroslaw Nabrzyski
name: Turk, Matthew
name: Stodden, Victoria
Publisher: name: figshare
Year: 2016
Subjects: subject: Distributed Computing
subject: FOS: Computer and information sciences
subject: 80501 Distributed and Grid Systems
subject: Applied Computer Science
subject: Computer Software
subject: 80505 Web Technologies (excl. Web Search)

description: We present an overview of the recently funded “Merging Science and Cyberinfrastructure Pathways: The Whole Tale” project (NSF award #1541450). Our approach has two nested goals: 1) deliver an environment that enables researchers to create a complete narrative of the research process including exposure of the data-to-publication lifecycle, and 2) systematically and persistently link research publications to their associated digital scholarly objects such as the data, code, and workflows. To enable this, Whole Tale will create an environment where researchers can collaborate on data, workspaces, and workflows and then publish them for future adoption or modification. Published data and applications will be consumed either directly by users using the Whole Tale or can be integrated into existing or future domain Science Gateways. Our approach is analogous to a general science gateway as it aims to deliver a collection of services and integration software that simplifies the use of scientific services and cyberinfrastructure.
Organizational Attributes of Successful Science Gateways and Cyberinfrastructure Projects
Creators: name: Kerk Kee
Publisher: name: figshare
Year: 2016
Subjects: subject: Distributed Computing
subject: FOS: Computer and information sciences
subject: 80501 Distributed and Grid Systems
subject: Applied Computer Science
subject: Computer Software
subject: 80505 Web Technologies (excl. Web Search)

description: While much of the adoption and diffusion of science gateways and/or computational tools for e-science is driven by the attributes of the tools [see 1], the organizations behind the tools play a critical role in determining the ultimate diffusion. This paper reports 10 organizational attributes of successful gateways and cyberinfrastructure projects. Based on a systematic analysis of 135 interviews, the organizational attributes include having leaders with credibility, multidisciplinary expertise, collaborative environment, shared goals, a common language, strategic structure, productive routines, organizational capacity, sustainable funding, and personnel continuity.
Exploring Women’s Resistance to Legal Remedies Against Domestic Violence in Pakistan
Creators: name: Ashiq, Misbah
Publisher: name: Manara - Qatar Research Repository
Year: 2024
Subjects: classificationCode: 44
subject: Human society

description: In this research I will explore the variables behind the women‘s resistance to seek legal remedies against domestic violence in Pakistan. I focus on the experiences of three domestic violence victims and also interviewed a lawyer to trace and understand women‘s experiences as part of a broader system and structures. I utilize the theory of continuum of violence (Cockburn, 2004) to understand the intertwining of different forms of violence that impact victims and limit their choices and behaviours. Using a qualitative methodology including in-depth semi-structured interviews and a close critical reading of the Punjab Protection of Women against Violence Act of 2016, I argue that the domestic violence victims in Pakistan face physical violence, in addition the justice system and law also perpetuate structural violence that hinders women‘s way to access justice. These, largely invisible social, legal and cultural pressures, combined with the fear of shame and blame from society and family, lead many victims to suffer in silence. My data analysis and literature research reveals the existence of a continuum of violence that operates on multiple levels from the hidden to the physical (visible) structures of state and family.
Identification and characterization of adult mouse meniscus stem/progenitor cells
Creators: name: Gamer, Laura W.
name: Shi, Rui Rui
name: Ashira Gendelman
name: Mathewson, Dylan
name: Gamer, Jackson
name: Rosen, Vicki
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology

description: Meniscal damage is a common problem that accelerates the onset of knee osteoarthritis. Stem cell-based tissue engineering treatment approaches have shown promise in preserving meniscal tissue and restoring meniscal function. The purpose of our study was to identify meniscus-derived stem/progenitor cells (MSPCs) from mouse, a model system that allows for in vivo analysis of the mechanisms underlying meniscal injury and healing. MSPCs were isolated from murine menisci grown in explant culture and characterized for stem cell properties. Flow cytometry was used to detect the presence of surface antigens related to stem cells, and qRT-PCR was used to examine the gene expression profile of MSPCs. Major proteins associated with MSPCs were localized in the adult mouse knee using immunohistochemistry. Our data show that MSPCs have universal stem cell-like properties including clonogenicity and multi-potentiality. MSPCs expressed the mesenchymal stem cell markers CD44, Sca-1, CD90, and CD73 and when cultured had elevated levels of biglycan and collagen type I, important extracellular matrix components of adult meniscus. MSPC also expressed significant levels of Lox and Igf-1, genes associated with the embryonic meniscus. Localization studies showed staining for these same proteins in the superficial and outer zones of the adult mouse meniscus, regions thought to harbor endogenous repair cells. MSPCs represent a novel resident stem cell population in the murine meniscus. Analysis of MSPCs in mice will allow for a greater understanding of the cell biology of the meniscus, essential information for enhancing therapeutic strategies for treating knee joint injury and disease.
Identification and Characterization of Adult Mouse Meniscus Stem/Progenitor Cells
Creators: name: Gamer, Laura W.
name: Shi, Rui Rui
name: Ashira Gendelman
name: Mathewson, Dylan
name: Gamer, Jackson
name: Rosen, Vicki
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology

description: Meniscal damage is a common problem that accelerates the onset of knee osteoarthritis. Stem cell based tissue engineering treatment approaches have shown promise in preserving meniscal tissue and restoring meniscal function. The purpose of our study was to identify meniscus-derived stem/progenitor cells (MSPCs) from mouse, a model system that allows for in vivo analysis of the mechanisms underlying meniscal injury and healing. MSPCs were isolated from murine menisci grown in explant culture and characterized for stem cell properties. Flow cytometry was used to detect the presence of surface antigens related to stem cells, and qRT-PCR was used to examine the gene expression profile of MSPCs. Major proteins associated with MSPCs were localized in the adult mouse knee using immunohistochemistry. Our data show that MSPCs have universal stem cell like properties including clonogenicity and multi-potentiality. MSPCs expressed the mesenchymal stem cell markers CD44, Sca-1, CD90 and CD73, and when cultured had elevated levels of biglycan and collagen type I, important extracellular matrix components of adult meniscus. MSPC also expressed significant levels of Lox and Igf-1, genes associated with the embryonic meniscus. Localization studies showed staining for these same proteins in the superficial and outer zones of the adult mouse meniscus, regions thought to harbor endogenous repair cells. MSPCs represent a novel resident stem cell population in the murine meniscus. Analysis of MSPCs in mice will allow for a greater understanding of the cell biology of the meniscus, essential information for enhancing therapeutic strategies for treating knee joint injury and disease.
MultiCloud Resource Management using Apache Mesos with Apache Airavata
Creators: name: Saha, Pankaj
name: Madhusudhan Govindaraju
name: Marru, Suresh
name: Pierce, Marlon
Publisher: name: figshare
Year: 2017
Subjects: subject: Distributed Computing
subject: FOS: Computer and information sciences
subject: 80501 Distributed and Grid Systems
subject: Applied Computer Science
subject: Computer Software
subject: 80505 Web Technologies (excl. Web Search)

description: We discuss initial results and our planned approach for incorporating Apache Mesos based resource management that will enable design and development of scheduling strategies for Apache Airavata jobs so that they can be launched on multiple clouds, wherein several VMs do not have Public IP addresses. We present initial work and next steps on the design of a meta-scheduler for Apache Airavata, which uses Apache Mesos to present a unified view of resources available across several clouds and clusters. This meta-scheduler can potentially examine and identify the cases where multiple small jobs have been submitted by the same scientists and then redirect job from the same community account or user to different clusters. Our approach uses a NAT firewall to make cloud VMs, without a Public IP, visible to Mesos for the unified view.
The Renaissance Simulations Laboratory
Creators: name: Kowalik, Kacper
name: Norman, Michael
name: Smith, Britton
name: Turk, Matthew
Publisher: name: figshare
Year: 2017
Subjects: subject: Distributed Computing
subject: FOS: Computer and information sciences
subject: 80501 Distributed and Grid Systems
subject: Applied Computer Science
subject: Computer Software
subject: 80505 Web Technologies (excl. Web Search)

description: The Renaissance Simulations are a set of astrophysical calculations run on the Blue Waters supercomputer, designed to study the way that the Universe was reionized. The simulations are cutting edge, featuring radiation transport, chemical processes, hydrodynamics, gravity and star formation prescriptions; they have been run on the Blue Waters supercomputer using the ENZO simulation platform. We present the Renaissance Simulations Laboratory (RSL), a web-based mechanism of accessing, analyzing, visualizing, and then studying the outputs from the Renaissance Simulations, taking a hybrid approach of utilizing both general-purpose systems such as the Jupyter Notebook and bespoke, and constructed widgets such as SQL queries around halo catalogs.
Interactive Leaderboard for Requesting and Tracking Expensive Calculations of Optional Properties across a Database of Materials
Creators: name: Winston, Donald
name: Montoya, Joseph H.
name: Persson, Kristin A.
Publisher: name: figshare
Year: 2017
Subjects: subject: Distributed Computing
subject: FOS: Computer and information sciences
subject: 80501 Distributed and Grid Systems
subject: Applied Computer Science
subject: Computer Software
subject: 80505 Web Technologies (excl. Web Search)

description: Databases of crystalline compounds typically have core properties such as relaxed structure, energy of formation, etc. pre-computed and available to users. However, additional material properties such as full elastic tensor, band structure, etc. may be both not of interest to all users of the database and computationally expensive to determine. Furthermore, researchers interested in such properties may only be interested in their values for specific compounds or chemistries. To crowdsource prioritization of optional-property calculations, we built an interactive leaderboard that serves as a gateway to our cyberinfrastructure (CI) for queuing jobs and dynamically reassigning job priorities. Users browse an ordered list of queued jobs, filter by chemistry for materials that are missing the property of interest, vote on existing or new jobs, and receive email notification when voted-on material properties are online. Here we will detail the use case of full elastic tensor calculations for the Materials Project, though the leaderboard interface can be run as a standalone web service and customized for contexts other than computational materials science.
MultiCloud Resource Management using Apache Mesos with Apache Airavata
Creators: name: Saha, Pankaj
name: Madhusudhan Govindaraju
name: Marru, Suresh
name: Pierce, Marlon
Publisher: name: figshare
Year: 2016
Subjects: subject: Distributed Computing
subject: FOS: Computer and information sciences
subject: 80501 Distributed and Grid Systems
subject: Applied Computer Science
subject: Computer Software
subject: 80505 Web Technologies (excl. Web Search)

description: We discuss initial results and our planned approach for incorporating Apache Mesos based resource management that will enable design and development of scheduling strategies for Apache Airavata jobs so that they can be launched on multiple clouds, wherein several VMs do not have Public IP addresses. We present initial work and next steps on the design of a meta-scheduler for Apache Airavata, which uses Apache Mesos to present a unified view of resources available across several clouds and clusters. This meta-scheduler can potentially examine and identify the cases where multiple small jobs have been submitted by the same scientists and then redirect job from the same community account or user to different clusters. Our approach uses a NAT firewall to make cloud VMs, without a Public IP, visible to Mesos for the unified view.
The Renaissance Simulations Laboratory
Creators: name: Kowalik, Kacper
name: Norman, Michael
name: Smith, Britton
name: Turk, Matthew
Publisher: name: figshare
Year: 2016
Subjects: subject: Distributed Computing
subject: FOS: Computer and information sciences
subject: 80501 Distributed and Grid Systems
subject: Applied Computer Science
subject: Computer Software
subject: 80505 Web Technologies (excl. Web Search)

description: The Renaissance Simulations are a set of astrophysical calculations run on the Blue Waters supercomputer, designed to study the way that the Universe was reionized. The simulations are cutting edge, featuring radiation transport, chemical processes, hydrodynamics, gravity and star formation prescriptions; they have been run on the Blue Waters supercomputer using the ENZO simulation platform. We present the Renaissance Simulations Laboratory (RSL), a web-based mechanism of accessing, analyzing, visualizing, and then studying the outputs from the Renaissance Simulations, taking a hybrid approach of utilizing both general-purpose systems such as the Jupyter Notebook and bespoke, and constructed widgets such as SQL queries around halo catalogs.
Organ burden and pulmonary toxicity of nano-sized copper (II) oxide particles after short-term inhalation exposure
Creators: name: Gosens, Ilse
name: Cassee, Flemming R.
name: Zanella, Michela
name: Manodori, Laura
name: Brunelli, Andrea
name: Costa, Anna Luisa
name: Bokkers, Bas G. H.
name: Jong, Wim H. De
name: Brown, David
name: Hristozov, Danail
name: Stone, Vicki
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Introduction: Increased use of nanomaterials has raised concerns about the potential for undesirable human health and environmental effects. Releases into the air may occur and, therefore, the inhalation route is of specific interest. Here we tested copper oxide nanoparticles (CuO NPs) after repeated inhalation as hazard data for this material and exposure route is currently lacking for risk assessment. Methods: Rats were exposed nose-only to a single exposure concentration and by varying the exposure time, different dose levels were obtained (C × T protocol). The dose is expressed as 6 h-concentration equivalents of 0, 0.6, 2.4, 3.3, 6.3, and 13.2 mg/m3 CuO NPs, with a primary particle size of 10 9.2–14 nm and an MMAD of 1.5 μm. Results: Twenty-four hours after a 5-d exposure, dose-dependent lung inflammation and cytotoxicity were observed. Histopathological examinations indicated alveolitis, bronchiolitis, vacuolation of the respiratory epithelium, and emphysema in the lung starting at 2.4 mg/m3. After a recovery period of 22 d, limited inflammation was still observed, but only at the highest dose of 13.2 mg/m3. The olfactory epithelium in the nose degenerated 24 h after exposure to 6.3 and 13.2 mg/m3, but this was restored after 22 d. No histopathological changes were detected in the brain, olfactory bulb, spleen, kidney and liver. Conclusion: A 5-d, 6-h/day exposure equivalent to an aerosol of agglomerated CuO NPs resulted in a dose-dependent toxicity in rats, which almost completely resolved during a 3-week post-exposure period.
Generalist Eimeria species in rodents
Creators: name: Jarquín-Díaz, Víctor Hugo
name: Balard, Alice
name: Mácová, Anna
name: Jost, Jenny
name: Roth Von Szepesbéla, Tabea
name: Berktold, Karin
name: Tank, Steffen
name: Kvičerová, Jana
name: Heitlinger, Emanuel
Publisher: name: Humboldt-Universität zu Berlin
Year: 2020
Subjects: subject: 18S
subject: COI
subject: Eimeria
subject: multilocus sequence typing
subject: phylogenetics
subject: rodents
subject: 570 Biowissenschaften; Biologie

description: Intracellular parasites of the genus Eimeria are described as tissue/host-specific. Phylogenetic classification of rodent Eimeria suggested that some species have a broader host range than previously assumed. We explore whether Eimeria spp. infecting house mice are misclassified by the most widely used molecular markers due to a lack of resolution, or whether, instead, these parasite species are indeed infecting multiple host species. With the commonly used markers (18S/COI), we recovered monophyletic clades of E. falciformis and E. vermiformis from Mus that included E. apionodes identified in other rodent host species (Apodemus spp., Myodes glareolus, and Microtus arvalis). A lack of internal resolution in these clades could suggest the existence of a species complex with a wide host range infecting murid and cricetid rodents. We question, however, the power of COI and 18S markers to provide adequate resolution for assessing host specificity. In addition to the rarely used marker ORF470 from the apicoplast genome, we present multilocus genotyping as an alternative approach. Phylogenetic analysis of 35 nuclear markers differentiated E. falciformis from house mice from isolates from Apodemus hosts. Isolates of E. vermiformis from Mus are still found in clusters interspersed with non-Mus isolates, even with this high-resolution data. In conclusion, we show that species-level resolution should not be assumed for COI and 18S markers in coccidia. Host–parasite cospeciation at shallow phylogenetic nodes, as well as contemporary coccidian host ranges more generally, is still open questions that need to be addressed using novel genetic markers with higher resolution.
Effective and interactive dissemination of diffusion data using MPContribs, plus a demo of UW/SI2 and MPContribs
Creators: name: Huck, Patrick
name: Persson, Kristin
name: Gunter, Dan
name: Morgan, Dane
name: Morgan, Dane
name: Mayeshiba, Tam
name: Boyer, Everett
Publisher: name: figshare
Year: 2017
Subjects: subject: Distributed Computing
subject: FOS: Computer and information sciences
subject: 80501 Distributed and Grid Systems
subject: Applied Computer Science
subject: Computer Software
subject: 80505 Web Technologies (excl. Web Search)

description: We will describe in this talk how the general approach taken by MPContribs solves the very specific challenges faced by the UW researchers in effectively disseminating their data to the public. The presented solution developed in the collaborative effort between UW and LBNL is the first to demonstrate how MPContribs can empower research groups through the rapid development and deployment of customized but MP-compatible web applications either using on-site or MP resources. It will also be shown how these efforts directly translate into solutions for the ongoing collaboration with researchers at the Advanced Light Source at LBNL [1] in which we aim to develop a processing pipeline for experimental XAS data from the beamline computer to integrated analysis web apps on MP.In our demo portion, we show the integration of the UW/SI2 workflow with MPContribs and JupyterHub. See [2] for a quick impression of the general functionality for the UW/SI2 use case. The video and the demo illustrate how MPContribs can be used to contribute, explore and feed data to the generic contribution details pages as well as a project-specific web application.[1] MPContribs, arXiv:1510.05024, arXiv:1510.05727, MRS Spring 2016[2] https://www.youtube.com/watch?v=wbWde5StHnU (3:43min)
O papel da epigenética na compreensão das respostas dos organismos dulçaquícolas às flutuações ambientais: teria Lamarck razão?
Creators: name: Barbosa, João
name: Jeremias, Guilherme
name: Marques, Sérgio
name: JM Gonçalves, Fernando
name: L Pereira, Joana
Publisher: name: Revista Captar: Ciência e Ambiente para Todos
Year: 2019

description: A epigenética tem sido apontada como uma evidência de que a ideia defendida por Lamarck, acerca da aquisição de caracteres pelo uso e desuso, poderá ter algum sentido na explicação de determinados processos evolutivos. De facto, a epigenética caracteriza-se pelo estudo da herdabilidade, tanto meiótica como mitótica, de variações na expressão ou atividade dos genes, sem que se observe qualquer alteração na sequência de ADN. As alterações epigenéticas podem surgir como resposta a fatores ambientais naturais, como a variação da temperatura, ou a fatores ambientais exógenos, como a exposição a metais ou a poluentes orgânicos. Tendo efeito na expressão dos genes, estas marcas epigenéticas podem provocar alterações fenotípicas nos organismos. Sabe-se ainda que estas alterações podem ser transmitidas ao longo das gerações, permanecendo mesmo naquelas que já não se encontram expostas a qualquer agente de stress, configurando, portanto, um efeito transgeracional. Apesar dos estudos iniciais de epigenética terem sido em mamíferos, o género Daphnia é visto como um modelo de investigação nesta área, uma vez que, para além das suas características morfofisiológicas, reúne ainda um conjunto de condições favoráveis a este tipo de estudos: vasta base bibliográfica relativa à sua morfo- e eco-fisiologia; especificidade de resposta a diversos tipos de flutuações ambientais; ciclo de vida curto, passível de ser mantido em partenogénese a longo-prazo, o que permite eliminar a variabilidade genética do conjunto de fatores experimentais; fácil manutenção e manuseamento em laboratório em ciclos muito produtivos que proporcionam trabalhos com elevado número de organismos. Apesar de já existirem alguns estudos epigenéticos com recurso a Daphnia, é essencial que a investigação seja incrementada de modo a possibilitar a melhor compreensão de alguns mecanismos epigenéticos e das implicações que estes podem ter, quer a nível fenotípico do indivíduo, quer ao nível da dinâmica das populações nos ecossistemas, atualmente sob constante pressão ambiental.
description: Revista Captar: Ciência e Ambiente para Todos, vol. 7 n.º 1 (2018)
Quantification of nanoparticle pesticide adsorption: computational approaches based on experimental data
Creators: name: Chen, Ran
name: Yuntao Zhang
name: Monteiro-Riviere, Nancy A.
name: Riviere, Jim E.
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Space Science
subject: Medicine
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Inorganic Chemistry
subject: Plant Biology

description: Quantitative analysis of the interactions between nanomaterials and environmental contamINANts, such as pesticides, in natural water systems and food residuals is crucial for the application of nanomaterials-based tools for the detection of the presence of toxic substances, monitoring pollution levels and environmental remediation. Previously, the Biological Surface Adsorption Index (BSAI) has demonstrated promising capabilities of interaction characterization and prediction based on experimental data from small organic molecules. In this article, the first attempt of the application of such quantitative measures toward environmental endpoints by analyzing the interactions of a selected group of nanomaterials with a variety of pesticides was made. Statistical modeling was conducted on the experimental obtained adsorption data based on polynomial BSAI models, as well as models with the incorporation of artificial neural network methodologies. Finally, clustering analyzes were performed for the categorization of nanomaterials based on surface physicochemical properties using both polynomial indices and physical adsorption modeling parameters. These quantitative computational approaches support the application of BSAI modeling in the area of environmental contamINANt detection and remediation.