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1

Şah, Melike, and Wendy Hall. "Dynamic Linking and Personalization on the Web using Linked Open Data." International Journal on Semantic Web and Information Systems 9, no. 2 (April 2013): 31–61. http://dx.doi.org/10.4018/jswis.2013040102.

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This paper presents a novel Semantic Web browser, called SemWeB. SemWeB supports Web browsing using Linked Open Data and personalization. This is the first time a Semantic Web browser combines the advances in Adaptive Hypermedia (i.e. personalization) and Linked Open Data. In particular, users are provided with a personalized and semantically rich Web browsing experience. For example, SemWeB supplies goal-based adaptive information retrieval from the LOD, adaptive link recommendation using a novel semantic relatedness measure and adaptive content creation. A user based study was used to assess the value of LOD-based hyperlinks and personally relevant content compared with a standard Web browser (Firefox). Results showed that users were able to browse and view more relevant information, as well as, value significance of LOD-based hyperlinks and personalized content in comparison to a standard Web browser.
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Corno, Fulvio, and Faisal Razzak. "Publishing LO(D)D: Linked Open (Dynamic) Data for Smart Sensing and Measuring Environments." Procedia Computer Science 10 (2012): 381–88. http://dx.doi.org/10.1016/j.procs.2012.06.050.

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Triperina, Evangelia, Cleo Sgouropoulou, Ioannis Xydas, Olivier Terraz, and Georgios Miaoulis. "Creating the Context for Exploiting Linked Open Data in Multidimensional Academic Ranking." International Journal of Recent Contributions from Engineering, Science & IT (iJES) 3, no. 3 (October 19, 2015): 33. http://dx.doi.org/10.3991/ijes.v3i3.5023.

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Academia is a complex socio-technical system with multiple aspects and constituents that involve various stakeholders. In order to address stakeholders’ needs and to assist the institutional accountability, this complexity should be considered during the development of academic services. We have designed a dynamic multidimensional ranking approach, easily modifiable to address user requirements, so as to assess and compare the university performance with a clear view to the support of effective institutional strategic planning and policy making. Our approach comprises the following components: the AcademIS ontology to model the academic domain and its multiple dimensions, the AcademIS Information System to manage and display the academic information, published in Linked Open Data format and the visual-aided Multiple Criteria Decision Making component, to evaluate and rank the performance of the academic units. The data are aggregated from several sources, in different formats, LODified by our system, and presented to the user by the interface to ultimately assist the decision making process.
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Zhu, Yueqin, Wenwen Zhou, Yang Xu, Ji Liu, and Yongjie Tan. "Intelligent Learning for Knowledge Graph towards Geological Data." Scientific Programming 2017 (2017): 1–13. http://dx.doi.org/10.1155/2017/5072427.

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Knowledge graph (KG) as a popular semantic network has been widely used. It provides an effective way to describe semantic entities and their relationships by extending ontology in the entity level. This article focuses on the application of KG in the traditional geological field and proposes a novel method to construct KG. On the basis of natural language processing (NLP) and data mining (DM) algorithms, we analyze those key technologies for designing a KG towards geological data, including geological knowledge extraction and semantic association. Through this typical geological ontology extracting on a large number of geological documents and open linked data, the semantic interconnection is achieved, KG framework for geological data is designed, application system of KG towards geological data is constructed, and dynamic updating of the geological information is completed accordingly. Specifically, unsupervised intelligent learning method using linked open data is incorporated into the geological document preprocessing, which generates a geological domain vocabulary ultimately. Furthermore, some application cases in the KG system are provided to show the effectiveness and efficiency of our proposed intelligent learning approach for KG.
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Thomas, Stacy, Tara Lichtenberg, Kristen Dang, Michael Fitzsimons, Robert L. Grossman, Ritika Kundra, Jessica A. Lavery, et al. "Linked Entity Attribute Pair (LEAP): A Harmonization Framework for Data Pooling." JCO Clinical Cancer Informatics, no. 4 (September 2020): 691–99. http://dx.doi.org/10.1200/cci.20.00037.

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PURPOSE As data-sharing projects become increasingly frequent, so does the need to map data elements between multiple classification systems. A generic, robust, shareable architecture will result in increased efficiency and transparency of the mapping process, while upholding the integrity of the data. MATERIALS AND METHODS The American Association for Cancer Research’s Genomics Evidence Neoplasia Information Exchange (GENIE) collects clinical and genomic data for precision cancer medicine. As part of its commitment to open science, GENIE has partnered with the National Cancer Institute’s Genomic Data Commons (GDC) as a secondary repository. After initial efforts to submit data from GENIE to GDC failed, we realized the need for a solution to allow for the iterative mapping of data elements between dynamic classification systems. We developed the Linked Entity Attribute Pair (LEAP) database framework to store and manage the term mappings used to submit data from GENIE to GDC. RESULTS After creating and populating the LEAP framework, we identified 195 mappings from GENIE to GDC requiring remediation and observed a 28% reduction in effort to resolve these issues, as well as a reduction in inadvertent errors. These results led to a decrease in the time to map between OncoTree, the cancer type ontology used by GENIE, and International Classification of Disease for Oncology, 3rd Edition, used by GDC, from several months to less than 1 week. CONCLUSION The LEAP framework provides a streamlined mapping process among various classification systems and allows for reusability so that efforts to create or adjust mappings are straightforward. The ability of the framework to track changes over time streamlines the process to map data elements across various dynamic classification systems.
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Hong, Sung Min, Kyoung Nam Ha, and Joon-Young Kim. "Dynamics Modeling and Motion Simulation of USV/UUV with Linked Underwater Cable." Journal of Marine Science and Engineering 8, no. 5 (April 30, 2020): 318. http://dx.doi.org/10.3390/jmse8050318.

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This paper describes a study on the dynamic modeling and the motion simulation of an unmanned ocean platform to overcome the limitations of existing unmanned ocean platforms for ocean exploration. The proposed unmanned ocean vehicle combines an unmanned surface vehicle and unmanned underwater vehicle with an underwater cable. This platform is connected by underwater cable, and the forces generated in each platform can influence each other’s dynamic motion. Therefore, before developing and operating an unmanned ocean platform, it is necessary to derive a dynamic equation and analyze dynamic behavior using it. In this paper, Newton’s second law and lumped-mass method are used to derive the equations of motion of unmanned surface vehicle, unmanned underwater vehicle, and underwater cable. As the underwater cable among the components of the unmanned ocean platform is expected to affect the motion of unmanned surface vehicle and unmanned underwater vehicle, the similarity of modeling is described by comparing with the cable modeling results and the experimental data. Finally, we constructed a dynamic simulator using Matlab and Simulink, and analyzed the dynamic behavior of the unmanned ocean platform through open-loop simulation.
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Sateli, Bahar, and René Witte. "Semantic representation of scientific literature: bringing claims, contributions and named entities onto the Linked Open Data cloud." PeerJ Computer Science 1 (December 9, 2015): e37. http://dx.doi.org/10.7717/peerj-cs.37.

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Motivation.Finding relevant scientific literature is one of the essential tasks researchers are facing on a daily basis. Digital libraries and web information retrieval techniques provide rapid access to a vast amount of scientific literature. However, no further automated support is available that would enable fine-grained access to the knowledge ‘stored’ in these documents. The emerging domain ofSemantic Publishingaims at making scientific knowledge accessible to both humans and machines, by adding semantic annotations to content, such as a publication’s contributions, methods, or application domains. However, despite the promises of better knowledge access, the manual annotation of existing research literature is prohibitively expensive for wide-spread adoption. We argue that a novel combination of three distinct methods can significantly advance this vision in a fully-automated way: (i) Natural Language Processing (NLP) forRhetorical Entity(RE) detection; (ii)Named Entity(NE) recognition based on the Linked Open Data (LOD) cloud; and (iii) automatic knowledge base construction for both NEs and REs using semantic web ontologies that interconnect entities in documents with the machine-readable LOD cloud.Results.We present a complete workflow to transform scientific literature into a semantic knowledge base, based on the W3C standards RDF and RDFS. A text mining pipeline, implemented based on the GATE framework, automatically extracts rhetorical entities of typeClaimsandContributionsfrom full-text scientific literature. These REs are further enriched with named entities, represented as URIs to the linked open data cloud, by integrating the DBpedia Spotlight tool into our workflow. Text mining results are stored in a knowledge base through a flexible export process that provides for a dynamic mapping of semantic annotations to LOD vocabularies through rules stored in the knowledge base. We created a gold standard corpus from computer science conference proceedings and journal articles, whereClaimandContributionsentences are manually annotated with their respective types using LOD URIs. The performance of the RE detection phase is evaluated against this corpus, where it achieves an averageF-measure of 0.73. We further demonstrate a number of semantic queries that show how the generated knowledge base can provide support for numerous use cases in managing scientific literature.Availability.All software presented in this paper is available under open source licenses athttp://www.semanticsoftware.info/semantic-scientific-literature-peerj-2015-supplements. Development releases of individual components are additionally available on our GitHub page athttps://github.com/SemanticSoftwareLab.
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Hiranyakorn, Methanee, Saeko Yanaka, Tadashi Satoh, Thunchanok Wilasri, Benchawan Jityuti, Maho Yagi-Utsumi, and Koichi Kato. "NMR Characterization of Conformational Interconversions of Lys48-Linked Ubiquitin Chains." International Journal of Molecular Sciences 21, no. 15 (July 28, 2020): 5351. http://dx.doi.org/10.3390/ijms21155351.

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Ubiquitin (Ub) molecules can be enzymatically connected through a specific isopeptide linkage, thereby mediating various cellular processes by binding to Ub-interacting proteins through their hydrophobic surfaces. The Lys48-linked Ub chains, which serve as tags for proteasomal degradation, undergo conformational interconversions between open and closed states, in which the hydrophobic surfaces are exposed and shielded, respectively. Here, we provide a quantitative view of such dynamic processes of Lys48-linked triUb and tetraUb in solution. The native and cyclic forms of Ub chains are prepared with isotope labeling by in vitro enzymatic reactions. Our comparative NMR analyses using monomeric Ub and cyclic diUb as reference molecules enabled the quantification of populations of the open and closed states for each Ub unit of the native Ub chains. The data indicate that the most distal Ub unit in the Ub chains is the most apt to expose its hydrophobic surface, suggesting its preferential involvement in interactions with the Ub-recognizing proteins. We also demonstrate that a mutational modification of the distal end of the Ub chain can remotely affect the solvent exposure of the hydrophobic surfaces of the other Ub units, suggesting that Ub chains could be unique design frameworks for the creation of allosterically controllable multidomain proteins.
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Voith von Voithenberg, Lena, Carolina Sánchez-Rico, Hyun-Seo Kang, Tobias Madl, Katia Zanier, Anders Barth, Lisa R. Warner, Michael Sattler, and Don C. Lamb. "Recognition of the 3′ splice site RNA by the U2AF heterodimer involves a dynamic population shift." Proceedings of the National Academy of Sciences 113, no. 46 (October 31, 2016): E7169—E7175. http://dx.doi.org/10.1073/pnas.1605873113.

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An essential early step in the assembly of human spliceosomes onto pre-mRNA involves the recognition of regulatory RNA cis elements in the 3′ splice site by the U2 auxiliary factor (U2AF). The large (U2AF65) and small (U2AF35) subunits of the U2AF heterodimer contact the polypyrimidine tract (Py-tract) and the AG-dinucleotide, respectively. The tandem RNA recognition motif domains (RRM1,2) of U2AF65 adopt closed/inactive and open/active conformations in the free form and when bound to bona fide Py-tract RNA ligands. To investigate the molecular mechanism and dynamics of 3′ splice site recognition by U2AF65 and the role of U2AF35 in the U2AF heterodimer, we have combined single-pair FRET and NMR experiments. In the absence of RNA, the RRM1,2 domain arrangement is highly dynamic on a submillisecond time scale, switching between closed and open conformations. The addition of Py-tract RNA ligands with increasing binding affinity (strength) gradually shifts the equilibrium toward an open conformation. Notably, the protein–RNA complex is rigid in the presence of a strong Py-tract but exhibits internal motion with weak Py-tracts. Surprisingly, the presence of U2AF35, whose UHM domain interacts with U2AF65 RRM1, increases the population of the open arrangement of U2AF65 RRM1,2 in the absence and presence of a weak Py-tract. These data indicate that the U2AF heterodimer promotes spliceosome assembly by a dynamic population shift toward the open conformation of U2AF65 to facilitate the recognition of weak Py-tracts at the 3′ splice site. The structure and RNA binding of the heterodimer was unaffected by cancer-linked myelodysplastic syndrome mutants.
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Eren, A. Murat, Özcan C. Esen, Christopher Quince, Joseph H. Vineis, Hilary G. Morrison, Mitchell L. Sogin, and Tom O. Delmont. "Anvi’o: an advanced analysis and visualization platform for ‘omics data." PeerJ 3 (October 8, 2015): e1319. http://dx.doi.org/10.7717/peerj.1319.

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Advances in high-throughput sequencing and ‘omics technologies are revolutionizing studies of naturally occurring microbial communities. Comprehensive investigations of microbial lifestyles require the ability to interactively organize and visualize genetic information and to incorporate subtle differences that enable greater resolution of complex data. Here we introduce anvi’o, an advanced analysis and visualization platform that offers automated and human-guided characterization of microbial genomes in metagenomic assemblies, with interactive interfaces that can link ‘omics data from multiple sources into a single, intuitive display. Its extensible visualization approach distills multiple dimensions of information about each contig, offering a dynamic and unified work environment for data exploration, manipulation, and reporting. Using anvi’o, we re-analyzed publicly available datasets and explored temporal genomic changes within naturally occurring microbial populations throughde novocharacterization of single nucleotide variations, and linked cultivar and single-cell genomes with metagenomic and metatranscriptomic data. Anvi’o is an open-source platform that empowers researchers without extensive bioinformatics skills to perform and communicate in-depth analyses on large ‘omics datasets.
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Nogales, Alberto, Miguel Angel Sicilia-Urban, and Elena García-Barriocanal. "Measuring vocabulary use in the Linked Data Cloud." Online Information Review 41, no. 2 (April 10, 2017): 252–71. http://dx.doi.org/10.1108/oir-06-2015-0183.

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Purpose This paper reports on a quantitative study of data gathered from the Linked Open Vocabularies (LOV) catalogue, including the use of network analysis and metrics. The purpose of this paper is to gain insights into the structure of LOV and the use of vocabularies in the Web of Data. It is important to note that not all the vocabularies in it are registered in LOV. Given the de-centralised and collaborative nature of the use and adoption of these vocabularies, the results of the study can be used to identify emergent important vocabularies that are shaping the Web of Data. Design/methodology/approach The methodology is based on an analytical approach to a data set that captures a complete snapshot of the LOV catalogue dated April 2014. An initial analysis of the data is presented in order to obtain insights into the characteristics of the vocabularies found in LOV. This is followed by an analysis of the use of Vocabulary of a Friend properties that describe relations among vocabularies. Finally, the study is complemented with an analysis of the usage of the different vocabularies, and concludes by proposing a number of metrics. Findings The most relevant insight is that unsurprisingly the vocabularies with more presence are those used to model Semantic Web data, such as Resource Description Framework, RDF Schema and OWL, as well as broadly used standards as Simple Knowledge Organization System, DCTERMS and DCE. It was also discovered that the most used language is English and the vocabularies are not considered to be highly specialised in a field. Also, there is not a dominant scope of the vocabularies. Regarding the structural analysis, it is concluded that LOV is a heterogeneous network. Originality/value The paper provides an empirical analysis of the structure of LOV and the relations between its vocabularies, together with some metrics that may be of help to determine the important vocabularies from a practical perspective. The results are of interest for a better understanding of the evolution and dynamics of the Web of Data, and for applications that attempt to retrieve data in the Linked Data Cloud. These applications can benefit from the insights into the important vocabularies to be supported and the value added when mapping between and using the vocabularies.
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Gnoffo, Salvatore. "A dynamic performance management approach to frame corruption in public procurement: a case study." Journal of Public Procurement 21, no. 1 (March 24, 2021): 75–96. http://dx.doi.org/10.1108/jopp-08-2020-0063.

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Purpose The purpose of this paper is to frame the causal relationships between corruption in public procurement and performance of local governments. Design/methodology/approach An outcome-based dynamic performance management approach is adopted to explore a representative case study of a small Italian municipality. The model is based on three sources: qualitative primary data generated by face-to-face convergent interviews; secondary data retrieved from documents describing legal cases linked to procurement and open-access repositories; and an extensive literature review. Findings Emphasizing the role of community civic morality systemically may help to understand some counterintuitive results in the past research and support decision-makers and policymakers in setting effective strategies to curb the associated negative implications. Social implications A dynamic approach of performance management aimed at framing corruption in public procurement may guide policymakers and decision-makers in keeping their “cognitive radar” constantly active, in a way to detect emerging corruptive phenomena that could be otherwise ignored by normal diagnostical approaches. It may also help to promote organizational ethical learning and improve community outcomes. Originality/value This research provides a causal and systemic framework of relationships involving local government performance and wrongdoings in public procurement, by including performance risk indicators linked to structural and individualistic causes of corruption.
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Dultz, Elisa, Roberta Mancini, Guido Polles, Pascal Vallotton, Frank Alber, and Karsten Weis. "Quantitative imaging of chromatin decompaction in living cells." Molecular Biology of the Cell 29, no. 14 (July 15, 2018): 1763–77. http://dx.doi.org/10.1091/mbc.e17-11-0648.

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Chromatin organization is highly dynamic and regulates transcription. Upon transcriptional activation, chromatin is remodeled and referred to as “open,” but quantitative and dynamic data of this decompaction process are lacking. Here, we have developed a quantitative high resolution–microscopy assay in living yeast cells to visualize and quantify chromatin dynamics using the GAL7-10-1 locus as a model system. Upon transcriptional activation of these three clustered genes, we detect an increase of the mean distance across this locus by >100 nm. This decompaction is linked to active transcription but is not sensitive to the histone deacetylase inhibitor trichostatin A or to deletion of the histone acetyl transferase Gcn5. In contrast, the deletion of SNF2 (encoding the ATPase of the SWI/SNF chromatin remodeling complex) or the deactivation of the histone chaperone complex FACT lead to a strongly reduced decompaction without significant effects on transcriptional induction in FACT mutants. Our findings are consistent with nucleosome remodeling and eviction activities being major contributors to chromatin reorganization during transcription but also suggest that transcription can occur in the absence of detectable decompaction.
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Shi, Wenbo, Jie Li, Zhao Yang, and Heng Zhang. "CFD Analysis of Contrarotating Open Rotor Aerodynamic Interactions." International Journal of Aerospace Engineering 2018 (October 11, 2018): 1–13. http://dx.doi.org/10.1155/2018/9538787.

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High efficiency and low fuel consumption make the contrarotating open rotor (CROR) system a viable economic and environmentally friendly powerplant for future aircraft. While the potential benefits are well accepted, concerns still exist with respect to the vibrations and noise caused by the aerodynamic interactions of CROR systems. In this paper, emphasis is placed on the detailed analysis of the aerodynamic interactions between the front and aft propellers of a puller CROR configuration. For the first step, unsteady Reynolds-averaged Navier-Stokes (URANS) simulations coupled with dynamic patched grid technology are implemented on the isolated single-rotating propeller (SRP) configuration in various operating conditions in order to test the accuracy and feasibility of the numerical approach. The numerical results are verified by a wind tunnel test, showing good agreements with the experimental data. Subsequently, the URANS approach is applied to the CROR configuration. The numerical results obtained through the URANS approach help to improve the understanding of the complex flow field generated by the CROR configuration, and the comparison of SRP flow field and CROR flow field allows for a detailed analysis of the aerodynamic interactions of the front propeller blade wakes and tip vortices with the aft propeller. The main reason of the aerodynamic interactions is the mutual effects of the blade tip vortices, and the aft propeller reduces the strength of the blade tip vortices of the front propeller. Aerodynamic interactions will lead to the periodic oscillations of the aerodynamic forces, and the frequency of the oscillations is linked to the blade numbers. In addition, a CROR has a larger thrust and power coefficient than that of the SRP configuration in the same operating conditions. The URANS approach coupled with a dynamic patched grid method is tested to be an efficient and accurate tool in the analysis of propeller aerodynamic interactions.
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Thompson, Caroline A., and Ming-Hsiang Tsou. "Abstract IA08: Improving researcher accessibility to publicly available data through creative integration, geospatial visualization, and open data portals." Cancer Epidemiology, Biomarkers & Prevention 29, no. 9_Supplement (September 1, 2020): IA08. http://dx.doi.org/10.1158/1538-7755.modpop19-ia08.

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Abstract The increased accessibility of population-level data made available by the government and public health and consumer agencies provides a unique opportunity for integrative data analysis, spatial visualization with much higher resolution to identify clusters of disease, and their correlation with geospatial, socioeconomic, and demographic predictors. However, interactive mapping and spatial analysis tools are underutilized by health researchers and decision-makers as a result of scarce training materials, few examples demonstrating their successful use, and poor mechanisms for sharing results generated by geovisualization. Further, in the wake of massive amounts of new data and analytical tool availability, consumers of cancer population health data, such as academic researchers and public health practitioners, are facing an ongoing transformation of practice resulting in the need for effective collaboration and sharing of resources within and across disciplinary and geographic boundaries. In this talk we will summarize three of our ongoing projects that leverage web-based technologies with the aim to reduce barriers to data sharing, promote simultaneous analysis of multiple datasets, and enable geovisualization of cancer outcomes and their interrelationships with social and spatial factors. The Disentangling Disparities Data Warehouse, or D3W, is a population-based data resource that includes geotagged California Cancer Registry data linked to census, American Community Survey, and other curated sources of neighborhood-level contextual and environmental data. The D3W allows ecologic and/or multilevel statistical analysis and supports sophisticated analysis of the spatial dynamics of cancer in California. The HealthWebMapper is a highly interactive data visualization tool with a simple two-tier web geographic information systems (GIS) framework. This dynamic web GIS/mapping tool was created with open-source JavaScript library, Leaflet, and free web authoring tools (bootstrap, jquery, and Google Chart) to provide user-friendly maps and data-mining functions, including multiple classification methods, correlation analysis, data export, and side-by-side displays. HealthWebMapper is an open source application and available via a public Github repository, and it can be easily installed on any website without specialized GIS servers or databases. Finally, to promote ease of access to the D3W and HealthWebMapper as well as other research data resources, we are developing the Health Data Open Analytic Portal, with support from the newly established NIH-funded HealthLINK Center for Population Health and Health Disparities Research at San Diego State University. The key functions of the open data portal are to archive, manage, download, and integrate disease, environmental, socioeconomic, and health behavior data. The data portal will enable the sharing, archiving, and learning of research procedures and health data resources. The searchable and downloadable data portal will also provide comprehensive research investigator profiles and online training materials to facilitate transdisciplinary research collaborations in cancer population health and beyond. Citation Format: Caroline A. Thompson, Ming-Hsiang Tsou. Improving researcher accessibility to publicly available data through creative integration, geospatial visualization, and open data portals [abstract]. In: Proceedings of the AACR Special Conference on Modernizing Population Sciences in the Digital Age; 2019 Feb 19-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(9 Suppl):Abstract nr IA08.
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Shyam, Gopal, and Shankar Ramamoorthy. "Performance Management in Cloud Computing." ECS Transactions 107, no. 1 (April 24, 2022): 1245–53. http://dx.doi.org/10.1149/10701.1245ecst.

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Cloud service providers encounter a challenge in managing remote resources due to the dynamic nature of the cloud environment. The complexity of the process is increased by the requirement of maintaining service quality in line with customer expectations, as well as the extremely dynamic nature of cloud-hosted applications. As a result of developments in big data learning methodologies, traditional systems have given way to intricate systems. In the existing studies, it is shown that the resource adjustment decision-making process is intimately linked to the system's behavior, including resource utilization and application components. The most essential requirements and restrictions in cloud resource management, as well as workload and anomaly analysis approaches in the context of cloud performance management, are discussed in this paper. The related works are provided, with major methodologies in current studies ranging from data analysis to performance techniques. Finally, a list of open challenges is compiled, taking into account the identified gaps in the overall direction of the tasks under consideration.
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Gariazzo, Claudio, Armando Pelliccioni, and Maria Paola Bogliolo. "Spatiotemporal Analysis of Urban Mobility Using Aggregate Mobile Phone Derived Presence and Demographic Data: A Case Study in the City of Rome, Italy." Data 4, no. 1 (January 8, 2019): 8. http://dx.doi.org/10.3390/data4010008.

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Urban mobility is known to have a relevant impact on work related car accidents especially during commuting. It is characterized by highly dynamic spatial–temporal variability. There are open questions about the size of this phenomenon; its spatial, temporal, and demographic characteristics; and driving mechanisms. A case study is here presented for the city of Rome, Italy. High-resolution population presence and demographic data, derived from mobile phone traffic, were used. Hourly profiles of a defined mobility factor (NPM) were calculated for a gridded domain during working days and cluster analyzed to obtain mean diurnal NPM mobility patterns. Age distributions of the population were calculated from demographic data to get insight in the type of population involved in mobility, and spatially linked with the mobility patterns. Census data about production units and their employees were related with the classified NPM mobility patterns. Seven different NPM mobility patterns were identified and mapped over the study area. The mobility slightly deviates from the census-based demography (0.15 on average, in a range of 0 to 1). The number of employees per 100 inhabitants was found to be the main driving mechanism of mobility. Finally, contributions of people employed in different economic macrocategories were assigned to each mobility time-pattern. Results provide a deeper knowledge of urban dynamics and their driving mechanisms in Rome.
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Aljamel, Abduladem, Taha Osman, and Dhavalkumar Thakker. "A Semantic Knowledge-Based Framework for Information Extraction and Exploration." International Journal of Decision Support System Technology 13, no. 2 (April 2021): 85–109. http://dx.doi.org/10.4018/ijdsst.2021040105.

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The availability of online documents that describe domain-specific information provides an opportunity in employing a knowledge-based approach in extracting information from web data. This research proposes a novel comprehensive semantic knowledge-based framework that helps to transform unstructured data to be easily exploited by data scientists. The resultant sematic knowledgebase is reasoned to infer new facts and classify events that might be of importance to end users. The target use case for the framework implementation was the financial domain, which represents an important class of dynamic applications that require the modelling of non-binary relations. Such complex relations are becoming increasingly common in the era of linked open data. This research in modelling and reasoning upon such relations is a further contribution of the proposed semantic framework, where non-binary relations are semantically modelled by adapting the semantic reasoning axioms to fit the intermediate resources in the N-ary relations requirements.
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Córdova-Lepe, Fernando, and Katia Vogt-Geisse. "Adding a reaction-restoration type transmission rate dynamic-law to the basic SEIR COVID-19 model." PLOS ONE 17, no. 6 (June 16, 2022): e0269843. http://dx.doi.org/10.1371/journal.pone.0269843.

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The classical SEIR model, being an autonomous system of differential equations, has important limitations when representing a pandemic situation. Particularly, the geometric unimodal shape of the epidemic curve is not what is generally observed. This work introduces the βSEIR model, which adds to the classical SEIR model a differential law to model the variation in the transmission rate. It considers two opposite thrives generally found in a population: first, reaction to disease presence that may be linked to mitigation strategies, which tends to decrease transmission, and second, the urge to return to normal conditions that pulls to restore the initial value of the transmission rate. Our results open a wide spectrum of dynamic variabilities in the curve of new infected, which are justified by reaction and restoration thrives that affect disease transmission over time. Some of these dynamics have been observed in the existing COVID-19 disease data. In particular and to further exemplify the potential of the model proposed in this article, we show its capability of capturing the evolution of the number of new confirmed cases of Chile and Italy for several months after epidemic onset, while incorporating a reaction to disease presence with decreasing adherence to mitigation strategies, as well as a seasonal effect on the restoration of the initial transmissibility conditions.
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Darsan, Junior. "Beach Morphological Dynamics at Cocos Bay (Manzanilla), Trinidad." Atlantic Geology 49 (November 15, 2013): 151. http://dx.doi.org/10.4138/atlgeol.2013.008.

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The Manzanillabeach in Cocos Bay, Trinidad is a barrier beach that protects the freshwaterNariva Swamp from the marine environment of the Atlantic. The Manzanilla beachis a very dynamic system owing to the open bay morphology, and its exposure tothe Atlantic Ocean. This study evaluated thespatial and temporal morphological and sedimentological characteristics,alongside hydrodynamic conditions operating on the beach. This studyinvestigates the beach’s response to tidal cycles diurnally, from spring toneap tide, and seasonally. Data from nine sites during the period December 2005to September 2007 are analyzed. Coastal parameters such as beach profiles,littoral data and sediment samples were obtained using standardgeomorphological techniques. The beach volumetric changes that occurred overthe tidal cycles are also quantified. Results indicate that wave height andwave energy were good predictors of beach change. The study showed that erosionwas linked to rising tide and accretion to falling tide diurnally. Erosionoccurred during spring tide conditions and accretion dominated during neaptides. Seasonally more erosion occurred in the winter period (dry season) andbeach changes in the summer period (wet season) were controlled by theformation and migration of bars.
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Zimmermann, Tycho, Norbert Hort, Yuqiuhan Zhang, Wolf-Dieter Müller, and Andreas Schwitalla. "The Video Microscopy-Linked Electrochemical Cell: An Innovative Method to Improve Electrochemical Investigations of Biodegradable Metals." Materials 14, no. 7 (March 25, 2021): 1601. http://dx.doi.org/10.3390/ma14071601.

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An innovative, miniature video-optical-electrochemical cell was developed and tested that allows for the conducting of electrochemical corrosion measurements and simultaneous microscopic observations over a small, well-defined surface area of corroding or degrading samples. The setup consisted of a miniature electrochemical cell that was clamped onto the metal sample and fixed under a video microscope before being filled with electrolyte. The miniature cell was comprised of afferent/efferent electrolyte ducts as well as a connection to the Mini Cell System (MCS) for electrochemical measurements. Consequently, all measured and induced currents and voltages referred to the same small area corroding completely within the field of view of the microscope, thus allowing for real-time observation and linking of surface phenomena such as hydrogen evolution and oxide deposition to electrochemical data. The experimental setup was tested on commercial purity (cp) and extra-high purity (XHP) magnesium (Mg) samples using open circuit potential and cyclic voltammetry methods under static and flowing conditions. The corrosion potential was shifted more anodically for cp Mg in comparison to XHP Mg under dynamic conditions. The corrosion current assessed from the cyclic voltametric curves were higher for the cp Mg in comparison to XHP Mg. However, there were no differences between static and flow conditions in the case of XHP Mg in contrast to cp Mg, where the current density was two times higher at dynamic conditions. The measurements and observations with this new method pave the way for a more detailed understanding of magnesium corrosion mechanisms, thus improving predictive power of electrochemical corrosion measurements on newly developed magnesium or other biodegradable alloys applied for medical devices. Different electrochemical tests can be run under various conditions, while being easy to set up and reproduce as well as being minimally destructive to the sample.
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22

Pattuelli, M. Cristina, and Matthew Miller. "Semantic network edges: a human-machine approach to represent typed relations in social networks." Journal of Knowledge Management 19, no. 1 (February 9, 2015): 71–81. http://dx.doi.org/10.1108/jkm-11-2014-0453.

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Purpose – The purpose of this paper is to describe a novel approach to the development and semantic enhancement of a social network to support the analysis and interpretation of digital oral history data from jazz archives and special collections. Design/methodology/approach – A multi-method approach was applied including automated named entity recognition and extraction to create a social network, and crowdsourcing techniques to semantically enhance the data through the classification of relations and the integration of contextual information. Linked open data standards provided the knowledge representation technique for the data set underlying the network. Findings – The study described here identifies the challenges and opportunities of a combination of a machine and a human-driven approach to the development of social networks from textual documents. The creation, visualization and enrichment of a social network are presented within a real-world scenario. The data set from which the network is based is accessible via an application programming interface and, thus, shareable with the knowledge management community for reuse and mash-ups. Originality/value – This paper presents original methods to address the issue of detecting and representing semantic relationships from text. Another element of novelty is in that it applies semantic web technologies to the construction and enhancement of the network and underlying data set, making the data readable across platforms and linkable with external data sets. This approach has the potential to make social networks dynamic and open to integration with external data sources.
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23

Smiraglia, Richard P., Joshua Henry, Elizabeth Milonas, Chris Marchese, and Sergey Zherebchevsky. "A Formal Taxonomy of Knowledge Organization: Meta-Analysis and Facet Analysis." KNOWLEDGE ORGANIZATION 47, no. 7 (2020): 558–73. http://dx.doi.org/10.5771/0943-7444-2020-7-558.

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Nearly fifty years after the incorporation of the International Society for Knowledge Organization and the introduction of its formal scientific journal Knowledge Organization, a comprehensive encyclopedia of the domain appeared. The practice of domain analysis for knowledge organization, twenty years after its introduction as a core methodology, has created the largest corpus of theoretical knowledge in the domain analysis of knowledge organization itself. A substantial body of research data, therefore, is available in the corpus of articles and conference papers reporting on the epistemological and ontological pillars of the science of knowledge organization. This paper is a report on the evolution of a formal taxonomy of knowledge organization, which is a product of an exhaustive meta-analysis of the KO domain. Our team compiled the corpus of twenty-nine formal published analyses together with key formative historical documents. We then analyzed the corpus thematically, bibliographically, and using co-word analysis to extract key concepts and the underlying faceted conceptual infrastructure. The taxonomy itself is faceted and is linked where possible to published definitions in the KO literature and as well as to the online ISKO Encyclopedia of Knowledge Organization. A dynamic project, the taxonomy will be maintained as linked open data and will grow as emergent research contributes new concepts or generates new facets.
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24

Espinasse, Boris, Brian P. V. Hunt, Yago Doson Coll, and Evgeny A. Pakhomov. "Investigating high seas foraging conditions for salmon in the North Pacific: insights from a 100-year scale archive for Rivers Inlet sockeye salmon." Canadian Journal of Fisheries and Aquatic Sciences 76, no. 6 (June 2019): 918–27. http://dx.doi.org/10.1139/cjfas-2018-0010.

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The high seas phase of Pacific salmon life history remains particularly data-limited, and the potential implications of climate impacts on ocean productivity for salmon condition and reproductive success is poorly understood. We used carbon and nitrogen stable isotopes (SI) from salmon scales to reconstruct aspects of the marine environment experienced by Rivers Inlet sockeye salmon (Oncorhynchus nerka) over the last century (1915–2016). Time series of SI compositions of salmon scales showed a greater variability after 1950, probably linked to more dynamic high seas environmental conditions. However, climate indices (e.g., Pacific Decadal Oscillation, El Niño Southern Oscillation) did not explain the SI variability. We assessed the time series with respect to changes in food web dynamics, including shifting trophic baselines, changes in prey–salmon diet, and changes in salmon foraging location. A significant correlation (r = 0.53) between sea surface temperature and δ13C enabled us to define the area of potential salmon distribution in the open ocean for approximately 9 months prior to sampling. This method shows high potential for stock-specific high seas distribution mapping that could be combined with prey isotope values to inform stock-specific foraging experience.
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Giusepponi, Simone, and Massimo Celino. "Numerical Simulation of Hydrogen Dynamics at a Mg-MgH2 Interface." Advances in Science and Technology 72 (October 2010): 205–12. http://dx.doi.org/10.4028/www.scientific.net/ast.72.205.

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Hydrogen desorption from hydride matrix is still an open field of research. Extensive abinitio molecular dynamics simulations are performed to characterize the desorption process at the interface MgH2-Mg. The numerical model succesfully repoduces the experimental desorption temperature for the hydride with and without Fe catalyst. Formation energies and work of adhesion are computed and linked to the desorption mechanism. Moreover a detailed analysis of the structural data reveals the role played by the catalysts in the lowering the desorption temperature.
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Nguyen, Phuc, Sylvia Chien, Jin Dai, Raymond J. Monnat, Pamela S. Becker, and Hao Yuan Kueh. "Unsupervised discovery of dynamic cell phenotypic states from transmitted light movies." PLOS Computational Biology 17, no. 12 (December 30, 2021): e1009626. http://dx.doi.org/10.1371/journal.pcbi.1009626.

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Identification of cell phenotypic states within heterogeneous populations, along with elucidation of their switching dynamics, is a central challenge in modern biology. Conventional single-cell analysis methods typically provide only indirect, static phenotypic readouts. Transmitted light images, on the other hand, provide direct morphological readouts and can be acquired over time to provide a rich data source for dynamic cell phenotypic state identification. Here, we describe an end-to-end deep learning platform, UPSIDE (Unsupervised Phenotypic State IDEntification), for discovering cell states and their dynamics from transmitted light movies. UPSIDE uses the variational auto-encoder architecture to learn latent cell representations, which are then clustered for state identification, decoded for feature interpretation, and linked across movie frames for transition rate inference. Using UPSIDE, we identified distinct blood cell types in a heterogeneous dataset. We then analyzed movies of patient-derived acute myeloid leukemia cells, from which we identified stem-cell associated morphological states as well as the transition rates to and from these states. UPSIDE opens up the use of transmitted light movies for systematic exploration of cell state heterogeneity and dynamics in biology and medicine.
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Guo, Dongliang, Li Feng, Taoxiang Zhang, Yaoyao Guo, Yanfen Wang, and Ximing Xu. "PNMAVis: Visual Analysis Tool of Protein Normal Mode for Understanding Cavity Dynamics." Applied Sciences 12, no. 15 (August 7, 2022): 7919. http://dx.doi.org/10.3390/app12157919.

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Molecular cavities play a critical role in our understanding of molecular phenomena. Recently, a number of works on the visual analysis of protein cavity dynamics have been developed to allow experts and users to interactively research dynamic cavity data. However, previous explorations are limited to studying cavity-lining amino acids and they lack a consideration of the impact of the key amino acids, which are far away from the cavity but have an important impact on the cavity. When studying protein amino acids, biochemists use normal mode decomposition to analyze protein changes on a time scale. However, the high-dimensional parameter space generated via decomposition is too large to be analyzed in detail. We present a novel approach that combines cavity characterization and normal mode analysis (NMA) for cavity dynamics analysis to reduce and explore this vast space through interactive visualization. PNMAVis can analyze whether direct factors (cavity-lining amino acids) or indirect factors (key amino acids) affect cavity changes, through multiple linked 2D and 3D views. The visual analysis method we proposed is based on close cooperation with domain experts, aiming to meet their needs to explore the relationship between cavity stability and cavity-lining amino acids fluctuations and key amino acids fluctuations as much as possible, and also to help domain experts identify potential allosteric residues. The effectiveness of our new method is demonstrated by the case study conducted by cooperative protein experts on a biological field case and an open normal mode data set.
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Naumova, Vera Viktorovna. "V International Conference «Information Technologies in Earth Sciences and Applications for Geology, Mining And Economy. Ites&Mp-2019»." Russian Digital Libraries Journal 23, no. 6 (July 8, 2020): 1279–300. http://dx.doi.org/10.26907/1562-5419-2020-23-6-1279-1300.

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The materials presented at the Conference describe the results of recent years in the following areas: Open access to scientific data and knowledge in Earth Sciences; Data peculiarities in Earth Sciences: new concepts and methods, tools for their collection, integration and processing in different information systems, including systems with intensive use of data; Data mining and mathematical simulation of natural processes in Earth Sciences. Evolution of classical GIS-applications in Earth Sciences; Application to Critical Raw Materials (CRM); social aspects of mining (e.g., the Social Licence to Operate [SLO]); predictive mapping and applications to exploration, landuse and search for extensions of known deposits; Intelligent data analysis, elicitation of facts and knowledge from scientific publications. Thesauruses, ontologies and conceptual modeling. Semantic WEB, linked data. Services. Content semantic structuring. Applications for geosciences, e.g., Ontology-based Dynamic Decision Graphs for Expert systems and decision-aid tools; Application of methods and technologies of the remote sensing in Earth Sciences: from satellites to unmanned aerial vehicles; Information technologies for demonstration and popularization of scientific achievements in Earth Sciences; Applications: environmental risks including mining wastes, natural hazards, water resource management, etc.
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Paladini de Mendoza, Francesco, Katrin Schroeder, Leonardo Langone, Jacopo Chiggiato, Mireno Borghini, Patrizia Giordano, Giulio Verazzo, and Stefano Miserocchi. "Deep-water hydrodynamic observations of two moorings sites on the continental slope of the southern Adriatic Sea (Mediterranean Sea)." Earth System Science Data 14, no. 12 (December 20, 2022): 5617–35. http://dx.doi.org/10.5194/essd-14-5617-2022.

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Abstract. This work presents an 8-years-long dataset of monitoring activities conducted on the western margin of the southern Adriatic Sea where two moorings have been placed since 2012 in sites that are representative of different morpho-dynamic conditions of the continental slope (open slope vs. submarine canyon). The dataset includes measurements conducted with both current meters and conductivity, temperature and depth (CTD) probes, and it provides information about the hydrodynamics and thermohaline properties of the last 100 m of the water column. The hydrodynamics in both sites are dominated by weak currents (< 0.1 m s−1) which undergo yearly to episodic pulsation able to exceed intensity greater than 0.5 m s−1, which are linked to the passage of dense waters. The 8-years records presented here represent a starting point for the continuous observation activity set up on occasion of the “Operation Dense Water” in 2012 focussed on the southern Adriatic deep-water dynamics. Since then, the observatory has been ongoing since 2012 and the database is regularly updated. All the data described here are made publicly available from https://doi.org/10.5281/zenodo.6770201 (Paladini de Mendoza et al., 2022) and are compliant with the FAIR principles (findable, accessible, interoperable and reusable).
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Naceri, Sarah, Daniel Marc, Anne-Claude Camproux, and Delphine Flatters. "Influenza A Virus NS1 Protein Structural Flexibility Analysis According to Its Structural Polymorphism Using Computational Approaches." International Journal of Molecular Sciences 23, no. 3 (February 4, 2022): 1805. http://dx.doi.org/10.3390/ijms23031805.

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Influenza A viruses are highly contagious RNA viruses that cause respiratory tract infections in humans and animals. Their non-structural protein NS1, a homodimer of two 230-residue chains, is the main viral factor in counteracting the antiviral defenses of the host cell. Its RNA-binding domain is an obligate dimer that is connected to each of the two effector domains by a highly flexible unstructured linker region of ten amino acids. The flexibility of NS1 is a key property that allows its effector domains and its RNA binding domain to interact with several protein partners or RNAs. The three-dimensional structures of full-length NS1 dimers revealed that the effector domains could adopt three distinct conformations as regards their mutual interactions and their orientation relative to the RNA binding domain (closed, semi-open and open). The origin of this structural polymorphism is currently being investigated and several hypotheses are proposed, among which one posits that it is a strain-specific property. In the present study, we explored through computational molecular modeling the dynamic and flexibility properties of NS1 from three important influenza virus A strains belonging to three distinct subtypes (H1N1, H6N6, H5N1), for which at least one conformation is available in the Protein Data Bank. In order to verify whether NS1 is stable in three forms for the three strains, we constructed homology models if the corresponding forms were not available in the Protein Data Bank. Molecular dynamics simulations were performed in order to predict the stability over time of the three distinct sequence variants of NS1, in each of their three distinct conformations. Our results favor the co-existence of three stable structural forms, regardless of the strain, but also suggest that the length of the linker, along with the presence of specific amino acids, modulate the dynamic properties and the flexibility of NS1.
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31

Hakanson, L. "Models to predict net and gross sedimentation in lakes." Marine and Freshwater Research 46, no. 1 (1995): 305. http://dx.doi.org/10.1071/mf9950305.

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This study models net and gross sedimentation in lakes. The fluxes of material play an important role in most lake contexts. They influence transport, bio-uptake and ecological effects of most toxins and nutrients. The aim is to present a new type of 'mixed' dynamic/statistical model and to discuss advantages and disadvantages with this approach. Empirical data to validate the model emanate from sediment traps from 25 lakes. Rates of gross sedimentation in traps were compared to catchment and morphometric parameters determined from maps in an attempt to identify the processes that influence sedimentation. The most important variables are relative depth (linked to resuspension), forest and open land cover (of the near area of the catchment), relief of catchment, coverage of mires and lakes, and the lake water retention time. This study shows that it is easy to lose predictive power in dynamic models relative to empirical models, in which each parameter constant and x-parameter automatically accounts for the complexities in natural ecosystems. In dynamic models empirical knowledge is replaced by logical constructions, which may not be accurate. The mixed model would need to be extended with new large submodels to predict, for example mean distribution coefficient of total-P in tributaries, tributary suspended load, rate of sedimentation and resuspension rate. This would result in a huge 'prescriptive' model with wide uncertainty limits for the predicted mean values for net and gross sedimentation.
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32

Cioncolini, Andrea, and Mirco Magnini. "Shapes and Rise Velocities of Single Bubbles in a Confined Annular Channel: Experiments and Numerical Simulations." Fluids 6, no. 12 (December 2, 2021): 437. http://dx.doi.org/10.3390/fluids6120437.

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Shapes and rise velocities of single air bubbles rising through stagnant water confined inside an annular channel were investigated by means of experiments and numerical simulations. Fast video imaging and image processing were used for the experiments, whilst the numerical simulations were carried out using the volume of fluid method and the open-source package OpenFOAM. The confinement of the annular channel did not affect the qualitative behavior of the bubbles, which exhibited a wobbling rise dynamic similar to that observed in bubbles rising through unconfined liquids. The effect of the confinement on the shape and rise velocity was evident; the bubbles were less deformed and rose slower in comparison with bubbles rising through unconfined liquids. The present data and numerical simulations, as well as the data collected from the literature for use here, indicate that the size, shape, and rise velocity of single bubbles are closely linked together, and prediction methods that fail to recognize this perform poorly. This study and the limited evidence documented in the literature indicate that the confinement effects observed in non-circular channels of complex shape are more complicated than those observed with circular tubes, and much less well understood.
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33

Abankwa, Daniel, and Alemayehu A. Gorfe. "Mechanisms of Ras Membrane Organization and Signaling: Ras Rocks Again." Biomolecules 10, no. 11 (November 6, 2020): 1522. http://dx.doi.org/10.3390/biom10111522.

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Ras is the most frequently mutated oncogene and recent drug development efforts have spurred significant new research interest. Here we review progress toward understanding how Ras functions in nanoscale, proteo-lipid signaling complexes on the plasma membrane, called nanoclusters. We discuss how G-domain reorientation is plausibly linked to Ras-nanoclustering and -dimerization. We then look at how these mechanistic features could cooperate in the engagement and activation of RAF by Ras. Moreover, we show how this structural information can be integrated with microscopy data that provide nanoscale resolution in cell biological experiments. Synthesizing the available data, we propose to distinguish between two types of Ras nanoclusters, an active, immobile RAF-dependent type and an inactive/neutral membrane anchor-dependent. We conclude that it is possible that Ras reorientation enables dynamic Ras dimerization while the whole Ras/RAF complex transits into an active state. These transient di/oligomer interfaces of Ras may be amenable to pharmacological intervention. We close by highlighting a number of open questions including whether all effectors form active nanoclusters and whether there is an isoform specific composition of Ras nanocluster.
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34

Wicaksono, Banyu, and Maria Goretti Adiyanti. "Understanding the dynamics of friendship formation among high school adolescent: Indigenous psychology approach." Psychological Research and Intervention 2, no. 1 (November 26, 2019): 28–35. http://dx.doi.org/10.21831/pri.v2i1.28048.

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How friendship between adolescent peers was formed is yet to be understood clearly. Whereas number of studies has clearly linked quality of friendship to various adaptive ability, school performance, and academic achievements. This study attempted to understand the dynamics of friendship formation in sample Javanese adolescents using indigenous psychology as its’ paradigm. Data was obtained from 120 respondents, (82 Girls, and 38 Boys) using open-ended questionnaire, which asks about how friendship between the respondent and their best friend(s) was formed. Data was analyzed using thematic analysis to identify themes and subthemes that indicates how friendship was formed. The result showed that there are two major theme that emerges in the beginning of friendship formation followed by other qualities related to it. This study reveals one more important aspect to be considered in understanding friendship formation between adolescents and their close friends
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35

SCHMITT, FRANÇOIS G., MARIE DE ROSA, GILLES DURRIEU, MOHAMEDOU SOW, PIERRE CIRET, DAMIEN TRAN, and JEAN-CHARLES MASSABUAU. "STATISTICAL STUDY OF BIVALVE HIGH FREQUENCY MICROCLOSING BEHAVIOR: SCALING PROPERTIES AND SHOT NOISE ANALYSIS." International Journal of Bifurcation and Chaos 21, no. 12 (December 2011): 3565–76. http://dx.doi.org/10.1142/s0218127411030738.

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We consider bivalve (oyster) behavior using high frequency valvometry data. These data are obtained in the field in the Arcachon bay, with light-weight electrodes of millimeters size, attached to the molluscs, and linked by flexible wires to an electronic control unit which measures valve activity. The latter are able to move freely and open their valve with an amplitude which is linked to environmental and physiological conditions, in order to filter surrounding waters. We consider here daily data recorded every 0.1 sec for 16 different animals, corresponding to a total of 1 728 000 data points. Valvometry data show important intermittent activity at high frequency, with frequent and sudden "microclosing" events (meaning partial closures), at apparently random times and with random amplitudes. The overall frequency spectrum of valve opening time series show power-law behavior with a slope β = 1.6 ± 0.1. The random succession of closing events with random amplitudes suggests to consider a shot-noise analysis, with two independent stochastic processes representing respectively the times of these discrete shot noise events and their amplitudes. This shows that methods and approaches devoted to extreme values, chaotic dynamics, recurrence time statistics in geosciences and climate studies can also be used to study living organisms and their interactions with complex environments such as their local ecosystem.
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36

Vichi, M., P. Ruardij, and J. W. Baretta. "Link or sink: a modelling interpretation of the open Baltic biogeochemistry." Biogeosciences 1, no. 1 (November 4, 2004): 79–100. http://dx.doi.org/10.5194/bg-1-79-2004.

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Abstract. A 1-D model system, consisting of the 1-D version of the Princeton Ocean Model (POM) coupled with the European Regional Seas Ecosystem Model (ERSEM) has been applied to a sub-basin of the Baltic Proper, the Bornholm basin. The model has been forced with 3h meteorological data for the period 1979-1990, producing a 12-year hindcast validated with datasets from the Baltic Environmental Database for the same period. The model results demonstrate the model to hindcast the time-evolution of the physical structure very well, confirming the view of the open Baltic water column as a three layer system of surface, intermediate and bottom waters. Comparative analyses of modelled hydrochemical components with respect to the independent data have shown that the long-term system behaviour of the model is within the observed ranges. Also primary production processes, deduced from oxygen (over)saturation are hindcast correctly over the entire period and the annual net primary production is within the observed range. The largest mismatch with observations is found in simulating the biogeochemistry of the Baltic intermediate waters. Modifications in the structure of the model (addition of fast-sinking detritus and polysaccharide dynamics) have shown that the nutrient dynamics are linked to the quality and dimensions of the organic matter produced in the euphotic zone, highlighting the importance of the residence time of the organic matter within the microbial foodweb in the intermediate waters. Experiments with different scenarios of riverine nutrient loads, assessed in the limits of a 1-D setup, have shown that the external input of organic matter makes the open Baltic model more heterotrophic. The characteristics of the inputs also drive the dynamics of nitrogen in the bottom layers leading either to nitrate accumulation (when the external sources are inorganic), or to coupled nitrification-denitrification (under strong organic inputs). The model indicates the permanent stratification to be the main feature of the system as regulator of carbon and nutrient budgets. The model predicts that most of the carbon produced in the euphotic zone is also consumed in the water column and this enhances the importance of heterotrophic benthic processes as final closure of carbon and nutrient cycles in the open Baltic.
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37

Vichi, M., P. Ruardij, and J. W. Baretta. "Link or sink: a modelling interpretation of the open Baltic biogeochemistry." Biogeosciences Discussions 1, no. 1 (August 5, 2004): 219–74. http://dx.doi.org/10.5194/bgd-1-219-2004.

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Abstract. A 1-D model system, consisting of the 1-D version of the Princeton Ocean Model (POM) coupled with the European Regional Seas Ecosystem Model (ERSEM) has been applied to a sub-basin of the Baltic Proper, the Bornholm basin. The model has been forced with 3h meteorological data for the period 1979-1990, producing a 12-year hindcast validated with datasets from the Baltic Environmental Database for the same period. The model results demonstrate the model to hindcast the time-evolution of the physical structure very well, confirming the view of the open Baltic water column as a three layer system of surface, intermediate and bottom waters. Comparative analyses of modelled hydrochemical components with respect to the independent data have shown that the long-term system behaviour of the model is within the observed ranges. Also primary production processes, deduced from oxygen (over)saturation are hindcast correctly over the entire period and the annual net primary production is within the observed range. The largest mismatch with observations is found in simulating the biogeochemistry of the Baltic intermediate waters. Modifications in the structure of the model (addition of fast-sinking detritus and polysaccharide dynamics) have shown that the nutrient dynamics is linked to the quality and dimensions of the organic matter produced in the euphotic zone, highlighting the importance of the residence time of the organic matter within the microbial foodweb in the intermediate waters. Experiments with different scenarios of riverine nutrient loads, assessed in the limits of a 1-D setup, have shown that the external input of organic matter makes the open Baltic model more heterotrophic. The characteristics of the inputs also drive the dynamics of nitrogen in the bottom layers leading either to nitrate accumulation (when the external sources are inorganic), or to coupled nitrification-denitrification (under strong organic inputs). The model indicates the permanent stratification to be the main feature of the system as regulator of carbon and nutrient budgets. The model predicts that most of the carbon produced in the euphotic zone is also consumed in the water column and this enhances the importance of heterotrophic benthic processes as final closures of carbon and nutrient cycles in the open Baltic.
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38

Labuce, Astra, Anda Ikauniece, Iveta Jurgensone, and Juris Aigars. "Environmental Impacts on Zooplankton Functional Diversity in Brackish Semi-Enclosed Gulf." Water 13, no. 14 (July 7, 2021): 1881. http://dx.doi.org/10.3390/w13141881.

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Zooplankton as an essential component in the pelagic food web are directly linked to pelagic ecosystem functioning. Therefore, comprehension of zooplankton functional diversity (FD) and its responses to environmental changes is crucial for ecosystem-based view. To identify FD responses to environmental drivers, we analysed 25 years of summer data on the brackish mesozooplankton community (including rotifers, cladocerans, copepods, and meroplankton) from the eutrophied, shallow Gulf of Riga (Baltic Sea). We established that within the Gulf of Riga, open waters are notably different from coastal regions based on the dynamics of hydrological conditions (temperature, salinity), cyanobacterial dominance, abundance of mesozooplankton functional groups, and mesozooplankton FD indices. Competition over resources in combination with hydrodynamic features and predation by adult herring were seemingly the central structuring mechanism behind the dynamics of FD metrics (richness, evenness, divergence, and dispersion) within coastal mesozooplankton communities. Whereas predation by young herring was an important driver only for the mesozooplankton communities in the open waters. Cyanobacterial dominance, used as a proxy for food quality and availability, had no effect on summer mesozooplankton FD metrics.
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39

Zhuravlev, A. G. "The issues of optimization parameters of quarry transport systems." Mining informational and analytical bulletin, no. 3-1 (March 20, 2020): 583–601. http://dx.doi.org/10.25018/0236-1493-2020-31-0-583-601.

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The cost of technological transport in open-pit mining for medium-depth quarries reaches 50 % of the total cost of production of commercial ore, and for deep-exceed this figure. Therefore, optimization of quarry transport systems is an important element in improving the efficiency of mining. The most important element of optimization is through her character the use of optimization to all linked processes on the basis of objective criteria of efficiency, unity and objectivity of the source data, using multilevel data from sensors mounted on the mining and transport machines to total economic values for processing. A promising direction for the implementation of tools for optimizing the processes of open pit mining and in particular transport systems of quarries, as one of the most important subsystems, is the end-to-end digitalization of mining production. The article presents the results of research and methodological approach to the creation of methods of optimization of complex transport systems on the basis of complex computer modeling, both simulation and economic and mathematical. The concept of TSC optimization methods in the absence of expressed maxima or minima of the parameters reflecting the optimization parameters is proposed. The possibilities of optimization of transport systems due to controlled transients are shown, it is established that the rational organization of the transition process provides cost savings of up to 2 times or more. The concept of a dynamic model of the quarry transport system development, reflecting the transition processes in its formation, is presented.
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40

Nikitiuk, A. S., E. A. Korznikova, S. V. Dmitriev, and O. B. Naimark. "DNA Breathers and Cell Dynamics." Mathematical Biology and Bioinformatics 14, no. 1 (April 11, 2019): 137–49. http://dx.doi.org/10.17537/2019.14.137.

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Molecular-morphological signs of oncogenesis can be linked to multiscale collective effects in molecular and cell ensembles. It was shown that nonlinear behavior of biological systems can be associated with the generation of characteristic collective modes representing the open states in molecular and cell organization as the mechanism of the coherent expression dynamics. The mechanical DNA model is developed to study the nonlinear dynamics of the helicoidal geometry DNA molecule. To construct the model of DNA the Peyrard–Bishop–Barbi approach has been applied. The analytical small localized solutions as the discrete breather and the antikink have been obtained by multiple scale expansion method for multicomponent lattices. The set of collective open states (breathers) in the molecular ensembles provides the collective expression dynamics to attract cells toward a few preferred global states. This result allows the formulation of the experimental strategy to analyze the qualitative changes in cell dynamics induced by mentioned collective modes. The biomechanical changes have been shown experimentally using the original data of Coherent Phase Microscopy analyzing the time series of phase thickness fluctuations. Study of the mechanical aspects of the behavior of single cells is a prerequisite for the understanding of cell functions in the case of qualitative changes in diseases affecting the properties of cells and tissues morphology to develop diagnostic and treatment design methodology.
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41

Parada, Maria Jose, and Alexandra Dawson. "Building family business identity through transgenerational narratives." Journal of Organizational Change Management 30, no. 3 (May 8, 2017): 344–56. http://dx.doi.org/10.1108/jocm-10-2016-0200.

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Purpose The purpose of this paper is to understand how family businesses (FBs) build their collective identity through transgenerational narratives. The authors examine the processes through which organizational meanings are socially constructed through narratives about individuals who are closely linked to the organizations (and their family). Design/methodology/approach Based on qualitative research, the authors study a 180-year old Spanish Pharmaceutical FB. Using longitudinal data, the authors analyze the narratives of six family members and two non-family executives. The authors use open-ended questions to allow interviewees to elaborate their own stories, following previous studies using extended narratives that leave the stage to the narrator. Findings Findings based on the stories of the eight interviewees (voice) suggest that the FB identity was initiated by the founder’s way to grow the business (fictionality). In turn the family shaped the identity of the FB, being reshaped by the stories arising from next generations’ entry into the business (reflexivity). While the FB identity reflects that of the owners, this identity is enduring but dynamic (temporality), not only shaped by the business family behind, but also conditioned by the environment. Originality/value The authors contribute to the growing literature adopting a narrative method to study phenomena in FBs. Thanks to the richness of the empirical material, a narrative method is particularly suited – and novel – for understanding collective identity, a crucial organizational resource that is closely linked to leadership in the FB.
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42

Songsirisak, Prommin, Jutharat Jitpranee, Albert Lisec, Prasobkan Boonjanawiroj, Bhudtree Wetpichetkosol, and Kannikar Kantamas. "CHINESE STUDENTS’ METAPHORICAL DESCRIPTIONS OF THAI TEACHERS AT A THAI UNIVERSITY." Malaysian Journal of Learning and Instruction 19, no. 1 (January 31, 2022): 213–41. http://dx.doi.org/10.32890/mjli2022.19.1.8.

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Purpose – This paper discusses Chinese students’ negative and positive written feedback about Thai teachers using metaphorical descriptions and the links between it and their classroom experiences. Methodology – An open-response questionnaire was employed to collect the data from 21 Chinese female students. The questionnaire provided both positive and negative “people” or “thing” metaphors of Thai teachers for students’ selection. In addition, students were allowed to use their own metaphors to describe their teachers. Data was analyzed by using open and axial coding techniques. Findings – The results revealed that Chinese students were able to compare Thai teachers with either a “person” or “thing” metaphor and could write a metaphorical description that reflected different aspects of their instructors’ teaching, both positively and negatively. The quality of their descriptions was rich enough to link with their classroom learning experiences. Both positive and negative “people” and “thing” metaphorical descriptions were associated with three different viewpoints: academic, power dynamics, and emotion. The positive “people” metaphorical descriptions were linked to four classroom issues: knowledge and experience, teaching style, motivation, and guardian/protector. In contrast, the positive “thing” and negative “people” and “thing” metaphorical descriptions were linked to three classroom issues: knowledge and experience, teaching style, and emotion. Significance – These findings help to strengthen Thai-Sino understanding of the relationship between Chinese students and Thai teachers. Findings also suggested that Chinese students’ metaphorical feedback should be used with the non-metaphorical assessment form to evaluate and improve Thai teachers’ instructional practices in the Thai-Chinese student exchange curriculum.
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Prentoe, Jannick, Rodrigo Velázquez-Moctezuma, Elias H. Augestad, Andrea Galli, Richard Wang, Mansun Law, Harvey Alter, and Jens Bukh. "Hypervariable region 1 and N-linked glycans of hepatitis C regulate virion neutralization by modulating envelope conformations." Proceedings of the National Academy of Sciences 116, no. 20 (April 30, 2019): 10039–47. http://dx.doi.org/10.1073/pnas.1822002116.

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About two million new cases of hepatitis C virus (HCV) infections annually underscore the urgent need for a vaccine. However, this effort has proven challenging because HCV evades neutralizing antibodies (NAbs) through molecular features of viral envelope glycoprotein E2, including hypervariable region 1 (HVR1) and N-linked glycans. Here, we observe large variation in the effects of removing individual E2 glycans across HCV strains H77(genotype 1a), J6(2a), and S52(3a) in Huh7.5 cell infections. Also, glycan-mediated effects on neutralization sensitivity were completely HVR1-dependent, and neutralization data were consistent with indirect protection of epitopes, as opposed to direct steric shielding. Indeed, the effect of removing each glycan was similar both in type (protective or sensitizing) and relative strength across four nonoverlapping neutralization epitopes. Temperature-dependent neutralization (e.g., virus breathing) assays indicated that both HVR1 and protective glycans stabilized a closed, difficult to neutralize, envelope conformation. This stabilizing effect was hierarchical as removal of HVR1 fully destabilized closed conformations, irrespective of glycan status, consistent with increased instability at acidic pH and high temperatures. Finally, we observed a strong correlation between neutralization sensitivity and scavenger receptor BI dependency during viral entry. In conclusion, our study indicates that HVR1 and glycans regulate HCV neutralization by shifting the equilibrium between open and closed envelope conformations. This regulation appears tightly linked with scavenger receptor BI dependency, suggesting a role of this receptor in transitions from closed to open conformations during entry. This importance of structural dynamics of HCV envelope glycoproteins has critical implications for vaccine development and suggests that similar phenomena could contribute to immune evasion of other viruses.
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Henninger, Maureen. "From mud to the museum: Metadata challenges in archaeology." Journal of Information Science 44, no. 5 (November 17, 2017): 658–70. http://dx.doi.org/10.1177/0165551517741790.

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An archaeological site is a palimpsest in which the evidence of the depositional episodes is destroyed through the excavation processes; all that remains are the artefacts and their documentary evidence manifested in registers, datasets, dig diaries and reports. While the reports may represent the end product of a specific excavation, the archaeological record tells a story; it is interpretative and dynamic, with later excavations adding new knowledge and narratives. Museums preserve the artefacts but unless the documentary evidence is preserved in standard formats, it cannot be easily re-used by the archaeology community to create that knowledge; nor can museums provide the narratives for the general public whose cultural heritage it is. This article presents a case study from the Ness of Brodgar excavations that examines possibilities for reconciling one part of the data of an archaeological dig, the small finds register (SFR) and its sparse amount of descriptive metadata, with the potentiality of data re-use and with the requirements of a museum that may have custody of the artefacts. It maps and enriches messy domain-specific ontologies to standard archaeological and cultural heritage ontologies and taxonomies using simple natural language processing, linked open data and the museum CIDOC conceptual reference model (CRM). This research, in examining the application of ontology mapping tools, explores common practices and processes that are useful in any discipline within the cultural heritage domain.
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45

Contreras, Alejandro, Tracy K. Hale, David L. Stenoien, Jeffrey M. Rosen, Michael A. Mancini, and Rafael E. Herrera. "The Dynamic Mobility of Histone H1 Is Regulated by Cyclin/CDK Phosphorylation." Molecular and Cellular Biology 23, no. 23 (December 1, 2003): 8626–36. http://dx.doi.org/10.1128/mcb.23.23.8626-8636.2003.

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ABSTRACT The linker histone H1 is involved in maintaining higher-order chromatin structures and displays dynamic nuclear mobility, which may be regulated by posttranslational modifications. To analyze the effect of H1 tail phosphorylation on the modulation of the histone's nuclear dynamics, we generated a mutant histone H1, referred to as M1-5, in which the five cyclin-dependent kinase phosphorylation consensus sites were mutated from serine or threonine residues into alanines. Cyclin E/CDK2 or cyclin A/CDK2 cannot phosphorylate the mutant in vitro. Using the technique of fluorescence recovery after photobleaching, we observed that the mobility of a green fluorescent protein (GFP)-M1-5 fusion protein is decreased compared to that of a GFP-wild-type H1 fusion protein. In addition, recovery of H1 correlated with CDK2 activity, as GFP-H1 mobility was decreased in cells with low CDK2 activity. Blocking the activity of CDK2 by p21 expression decreased the mobility of GFP-H1 but not that of GFP-M1-5. Finally, the level and rate of recovery of cyan fluorescent protein (CFP)-M1-5 were lower than those of CFP-H1 specifically in heterochromatic regions. These data suggest that CDK2 phosphorylates histone H1 in vivo, resulting in a more open chromatin structure by destabilizing H1-chromatin interactions.
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46

Tolotti, R., C. Salvi, G. Salvi, and M. C. Bonci. "Late Quaternary climate variability as recorded by micropalaeontological diatom data and geochemical data in the western Ross Sea, Antarctica." Antarctic Science 25, no. 6 (March 28, 2013): 804–20. http://dx.doi.org/10.1017/s0954102013000199.

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AbstractCores acquired from the Ross Sea continental shelf and continental slope during the XXX Italian Programma Nazionale di Ricerche in Antartide (PNRA) were analysed and yielded interesting micropalaeontological, biostratigraphic diatom results and palaeoceanographic implications. These multi-proxy analyses enabled us to reconstruct the glacial/deglacial history of this sector of the Ross embayment over the last 40 000 years, advancing our understanding of the Last Glacial Maximum (LGM) environmental and sedimentological processes linked to the Ross Sea ice sheet/ice shelf fluctuations in a basin and continental-slope environment, and allowed us to measure some of the palaeoceanographic dynamics. The central sector of the Ross Sea and part of its coast (south of the Drygalski Ice Tongue) enjoyed open marine conditions in the pre-LGM era (27 500–24 000 years bp). The retreat of the ice sheet could have been influenced by a southward shift of a branch of the Ross gyre, which triggered early deglaciation at c. 18 600 cal bp with a significant Modified Circumpolar Deep Water inflow over the continental slope at c. 14 380 cal BP. We assume that a lack of depositional material in each core, although at different times, represents a hiatus. Other than problems in core collection, this could be due to the onset of modern oceanographic conditions, with strong gravity currents and strong High Salinity Shelf Water exportation. Moreover, we presume that improvements in biostratigraphy, study of reworked diatom taxa, and lithological and geochemical analyses will provide important constraints for the reconstruction of the LGM grounding line, ice-flow lines and ice-flow paths and an interesting tool for reconstructing palaeo-sub-bottom currents in this sector of the Ross embayment.
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Dowling, Daniel, Jonathan F. Schmitz, and Erich Bornberg-Bauer. "Stochastic Gain and Loss of Novel Transcribed Open Reading Frames in the Human Lineage." Genome Biology and Evolution 12, no. 11 (September 16, 2020): 2183–95. http://dx.doi.org/10.1093/gbe/evaa194.

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Abstract In addition to known genes, much of the human genome is transcribed into RNA. Chance formation of novel open reading frames (ORFs) can lead to the translation of myriad new proteins. Some of these ORFs may yield advantageous adaptive de novo proteins. However, widespread translation of noncoding DNA can also produce hazardous protein molecules, which can misfold and/or form toxic aggregates. The dynamics of how de novo proteins emerge from potentially toxic raw materials and what influences their long-term survival are unknown. Here, using transcriptomic data from human and five other primates, we generate a set of transcribed human ORFs at six conservation levels to investigate which properties influence the early emergence and long-term retention of these expressed ORFs. As these taxa diverged from each other relatively recently, we present a fine scale view of the evolution of novel sequences over recent evolutionary time. We find that novel human-restricted ORFs are preferentially located on GC-rich gene-dense chromosomes, suggesting their retention is linked to pre-existing genes. Sequence properties such as intrinsic structural disorder and aggregation propensity—which have been proposed to play a role in survival of de novo genes—remain unchanged over time. Even very young sequences code for proteins with low aggregation propensities, suggesting that genomic regions with many novel transcribed ORFs are concomitantly less likely to produce ORFs which code for harmful toxic proteins. Our data indicate that the survival of these novel ORFs is largely stochastic rather than shaped by selection.
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Fernandez-Cortes, A., R. Perez-Lopez, S. Cuezva, J. M. Calaforra, J. C. Cañaveras, and S. Sanchez-Moral. "Geochemical Fingerprinting of Rising Deep Endogenous Gases in an Active Hypogenic Karst System." Geofluids 2018 (December 6, 2018): 1–19. http://dx.doi.org/10.1155/2018/4934520.

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The hydrothermal caves linked to active faulting can potentially harbour subterranean atmospheres with a distinctive gaseous composition with deep endogenous gases, such as carbon dioxide (CO2) and methane (CH4). In this study, we provide insight into the sourcing, mixing, and biogeochemical processes involved in the dynamic of deep endogenous gas formation in an exceptionally dynamic hypogenic karst system (Vapour Cave, southern Spain) associated with active faulting. The cave environment is characterized by a prevailing combination of rising warm air with large CO2 outgassing (>1%) and highly diluted CH4 with an endogenous origin. The δ13CCO2 data, which ranges from −4.5 to −7.5‰, point to a mantle-rooted CO2 that is likely generated by the thermal decarbonation of underlying marine carbonates, combined with degassing from CO2-rich groundwater. A pooled analysis of δ13CCO2 data from exterior, cave, and soil indicates that the upwelling of geogenic CO2 has a clear influence on soil air, which further suggests a potential for the release of CO2 along fractured carbonates. CH4 molar fractions and their δD and δ13C values (ranging from −77 to −48‰ and from −52 to −30‰, respectively) suggest that the methane reaching Vapour Cave is the remnant of a larger source of CH4, which was likely generated by microbial reduction of carbonates. This CH4 has been affected by a postgenetic microbial oxidation, such that the gas samples have changed in both molecular and isotopic composition after formation and during migration through the cave environment. Yet, in the deepest cave locations (i.e., 30 m below the surface), measured concentration values of deep endogenous CH4 are higher than in atmospheric with lighter δ13C values with respect to those found in the local atmosphere, which indicates that Vapour Cave may occasionally act as a net source of CH4 to the open atmosphere.
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Baratin, L., A. Cattaneo, F. Gasparetto, E. Moretti, and S. Lonati. "DOCUMENTING THE CONSERVATIVE EVOLUTION OF THE CITY WALLS THANKS TO THE INTEGRATION OF DIGITAL SYSTEMS OF VARIOUS TYPOLOGIES. THE CASE STUDY OF VALBONA GATE." ISPRS - International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences XLII-2/W11 (May 4, 2019): 167–72. http://dx.doi.org/10.5194/isprs-archives-xlii-2-w11-167-2019.

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<p><strong>Abstract.</strong> The presented study describes how to document in a dynamic way a complex and full of historical information architecture with a flexible system. Thanks to the collaboration between various professional figures and the integration of various digital systems, it has been possible to create an open documentary model able to satisfy the need to manage complex information.</p></p>Our case study is the Valbona gate, the main entrance of the city of Urbino. The project presents two different phases: a first study is characterised by the setting up of a Datawarehouse concerning state of conservation and restoration managed with a GIS system; the second part is focused on a new type of documentation, developed with an online software, CDR - Conservation Digital Report.</p><p>Thanks to the capacity of organising all data into a single Geodatabase system, the information relating to the conservation status and to deterioration, restoration interventions carried out.</p><p>The result is a geodatabase linked with conservative sheets expressly scheduled. In this way the documentation is completed by a system which allows a simple updating of information and its implementation, if necessary.</p>
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Schäfer, Benjamin, Leonardo Rydin Gorjão, G. Cigdem Yalcin, Ellen Förstner, Richard Jumar, Heiko Maass, Uwe Kühnapfel, and Veit Hagenmeyer. "Microscopic Fluctuations in Power-Grid Frequency Recordings at the Subsecond Scale." Complexity 2023 (March 6, 2023): 1–13. http://dx.doi.org/10.1155/2023/2657039.

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Complex systems, such as the power grid, are essential for our daily lives. Many complex systems display multifractal behavior, correlated fluctuations and power laws. Whether the power-grid frequency, an indicator of the balance of supply and demand in the electricity grid, also displays such complexity remains a mostly open question. Within the present article, we utilize highly resolved measurements to quantify the properties of the power-grid frequency, making three key contributions: First, we demonstrate the existence of power laws in power-grid frequency measurements. Second, we show that below one second, the dynamics may fundamentally change, including a suddenly increasing power spectral density, emergence of multifractality and a change of correlation behavior. Third, we provide a simplified stochastic model involving positively correlated noise to reproduce the observed dynamics, possibly linked to frequency-dependent loads. Finally, we stress the need for high-quality measurements and discuss how we obtained the data analyzed here.
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