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  • High-Throughput Screening of Metal-Organic Frameworks for Kinetic Separation of Propane and Propene

    Pramudya, Yohanes; Bonakala, Satyanarayana; Antypov, Dmytro; Bhatt, Prashant; Shkurenko, Aleksander; Eddaoudi, Mohamed; Rosseinsky, Matthew J.; Dyer, Matthew S (Physical Chemistry Chemical Physics, Royal Society of Chemistry (RSC), 2020-10-06) [Article]
    We apply molecular simulations to screen a database of reported metal-organic framework structures from the Computation-Ready, Experimental (CoRE) MOF database to identify materials potentially capable of separating propane and propene...
  • Programmable constant phase element realization with crossbar arrays

    Fouda, M. E.; AbdelAty, A. M.; Elwakil, A. S.; Radwan, A. G.; Eltawil, Ahmed (Journal of Advanced Research, Elsevier BV, 2020-08-26) [Article]
    In this paper, we propose a new programmable Constant Phase Element (CPE) realization using resistive crossbar arrays. The programmability of the resistive devices is used to program the CPE. Due to the structure of the crossbar, a new approximation of the CPE element is investigated. The approximation consists of parallel branches where each one can be seen as a weighted sum of low and high pass filters having the same cut-off frequency (i.e., Lapicque model). The closed-form approximation expression is derived, and then the Flower Pollination Algorithm (FPA) is used to find the optimal values of the network components. Different design examples are given over the frequency range of 106-109 rad/s to prove the ability of this realization to achieve any fractional order with less than 5% relative error in both phase and pseudo-capacitance and to demonstrate its programmability. Monte-Carlo simulations are performed to evaluate the sensitivity of the proposed realization against device variability. In addition, the proposed realization is compared with two other state-of-art realizations showing comparable results as standalone realization and within fractional-order relaxation oscillator application.
  • Initial data release and announcement of the 10,000 Fish Genomes Project (Fish10K)

    Fan, Guangyi; Song, Yue; Yang, Liandong; Huang, Xiaoyun; Zhang, Suyu; Zhang, Mengqi; Yang, Xianwei; Chang, Yue; Zhang, He; Li, Yongxin; Liu, Shanshan; Yu, Lili; Chu, Jeffery; Seim, Inge; Feng, Chenguang; Near, Thomas J; Wing, Rod Anthony; Wang, Wen; Wang, Kun; Wang, Jing; Xu, Xun; Yang, Huanming; Liu, Xin; Chen, Nansheng; He, Shunping (GigaScience, Oxford University Press (OUP), 2020-08-18) [Article]
    Background With more than 30,000 species, fish—including bony, jawless, and cartilaginous fish—are the largest vertebrate group, and include some of the earliest vertebrates. Despite their critical roles in many ecosystems and human society, fish genomics lags behind work on birds and mammals. This severely limits our understanding of evolution and hinders progress on the conservation and sustainable utilization of fish. Results Here, we announce the Fish10K project, a portion of the Earth BioGenome Project aiming to sequence 10,000 representative fish genomes in a systematic fashion within 10 years, and we officially welcome collaborators to join this effort. As a step towards this goal, we herein describe a feasible workflow for the procurement and storage of biospecimens, as well as sequencing and assembly strategies. Conclusions To illustrate, we present the genomes of 10 fish species from a cohort of 93 species chosen for technology development.
  • Metastatic State of Colorectal Cancer can be Accurately Predicted with Methylome

    Albaradei, Somayah; Thafar, Maha; Van Neste, Christophe; Essack, Magbubah; Bajic, Vladimir B. (ACM, 2020-05-04) [Conference Paper]
    Colorectal cancer (CRC) appears to be the third most common cancer as well as the fourth most common cause of cancer deaths in the world. Its most lethal states are when it becomes metastatic. It is of interest to find tests that can quickly and accurately determine if the patient has already developed metastasis. Changes in methylation profiles have been found to be characteristic of cancers at different stages and can therefore be used to develop diagnostic panels. We developed a deep learning (DL) model (Deep2Met) using methylation profiles of patients with CRC to predict if the cancer is in its metastatic state. Results suggest that our method achieves an AUPR and an average F-score of 96.99% and 94.71%, respectively, making Deep2Met potentially useful for diagnostic purposes. The DL model Deep2Met we developed, shows promise in the diagnosis of CRC based on methylation profiles of individual patients.
  • Open access panel discussion on preprints: introduction

    Vijayakumar, J.K.; Grenz, Daryl M.; Baessa, Mohamed A. (2019-11-19) [Presentation]
    This introductory talk provides back ground of preprint servers, its recent growth, usage of preprint servers by KAUST researchers, KAUST library's support on open access and open infrastrucutre initiatives world wide.
  • Library Strategic Plan 2019-2024

    University Library, KAUST (University Library, KAUST, 2019-08) [Other]
  • Data mining of Citations in Theses: a workflow for automated analysis of Open Access and library holdings coverage

    Martin, Jose; Han, Lee Yen (2019-06-19) [Poster]
    A systems specialist and a liaison librarian worked together in this project to analyze resource usage, Open Access coverage, library holdings coverage and citation patterns from a collection of doctoral theses in a graduate research university. The extracted citations and some basic metadata about the theses and their authors were processed using a workflow created with KNIME, an open source data-mining software. The workflow uses Summon and Crossref APIs for library holdings coverage, CORE and Unpaywall APIs for Open Access coverage and an SQLite database to store the output and enable detailed analysis. This tool provides an insight into the resources that have been effectively used to produce doctoral theses. It would be useful for academic libraries interested in evaluating the impact of Open Access resources and how they contribute to their scholarly output, and to evaluate the coverage provided by their holdings to the research activity in their institutions beyond the usual usage reports provided by publishers or third parties.
  • Introductory Remarks

    Vijayakumar, J.K. (2019-04-18)
  • The liaison librarian’s role in the acquisition process

    Han, Lee Yen (2019-04-18) [Presentation]
    As a born-digital user-centric library, KAUST University Library adopts a patron-driven acquisition model which allows patrons to recommend monographs and other resources to be added to the library collection. This presentation focuses on the role of the liaison librarian in this acquisition model and the process which takes place when a recommendation is first initiated by the patron (faculty, researcher, or student), to resource identification, review of license agreements, before the recommendation is handled over to the Acquisitions Team.
  • An overview of e-resources acquisitions in KAUST

    Kabli, Ola A. (2019-04-18)
    Within a changing and flexible environment and in a digitally born library, this presentation will cover the library electronic resources acquisition lifecycle from receiving the request from the subject specialists until the access is provided going through acquiring quotations, invoices, getting the LA signed, and get it paid by finance in addition to the role we play to serve other university departments. It will address the best practices as well as the challenges throughout the process and how to keep a smooth workflow and highlight on the value of communication between library staff internally and with other departments to meet the patrons needs accurately and promptly. A glance on the number of e- resources, types and number of publishers we’re dealing with will be covered too. With a ‘dealing directly with publishers’ policy we of course are working collaboratively with them to maintain the productive professional relationship. It will also focus on the systems we use and the record keeping for all renewal information including license agreements and make it accessible to stakeholders. The effort of improving and enhancing e- resources acquisition is continuing. With a good future plan and a strategy, future can always be better.
  • Print Resources Acquisition Process

    Al Qahtani, Ali (2019-04-18)
  • Variation on a Theme: Scoping our Institutional Repository Service Bundle

    Grenz, Daryl M. (2019-04-11) [Presentation]
    Repository services at KAUST encompass a variety of activities ranging from maintaining a digital repository platform, implementing an open access policy, supporting use of scholarly persistent identifiers, managing metadata and content files, and developing system integrations in support of the above. This presentation will discuss all of this within the broader visions prevalent in the global repository landscape so as to illustrate the choices that we have made to pursue and devote resources to certain service opportunities over others. I will also look at how we measure the success of various services in achieving their stated aims. The overall goal is for audience members to have an improved framework for thinking about the scope and focus of similar services in their own institutions.
  • Institutional ORCID Integration: The KAUST Experience

    Grenz, Daryl M. (2019-04-10) [Presentation]
  • ePosters Replace Print Posters: KAUST Library Initiative to Better Prepare Students and Preserve Scholarly Resources

    Vijayakumar, J.K.; Hall, Garry; Afandi, Eman (2019-04-05) [Presentation]
    Scientific posters are popular in conferences run by professional organizations in the UK, Europe, and North America, with the majority focused on medicine and health care disciplines. Individual events may include hundreds (and even thousands) of posters with cumulative numbers from all events (including academia) estimated in the millions annually (1). Generally, posters are not retained, in spite of their value as scholarly resources; many are the first reporting of new research and contain information months in advance of peer-reviewed articles. Printed posters have been around for many years and, with recent digital advances can be transformed into dynamic displays through multimedia inclusion and zoom functionality, whilst being made available via the web to large, geographically distributed audiences. Electronic posters (ePosters) are environmentally friendly, they eliminate printing and transport problems, and they scale well for large conferences (e.g. American Society of Anesthesiologists has used ePosters since 2013, recently with over 3000 posters at multiple sites). Most importantly, they lend themselves to being easily captured and retained as scientific resources. Following successful pilot projects (for which data on student and faculty support and cost-effectiveness will be presented), KAUST University Library has introduced a campus-wide ePoster service for the University beginning in January 2019. This service replaces printed posters and better prepares students for ePoster presentation scenarios commonplace within professional organizations and provides open access via the KAUST Research Repository. Training overheads for both students and organizers are low and uptake has been high, with weekly events scheduled for the first four months of 2019. Academia is notably behind this practitioner-driven trend. KAUST Library believes that, by rolling out an ePoster system to the University, it is the first campus in the world to offer such a campus-wide solution, reflecting a digital smart campus vision of KAUST.
  • CCDC 1838597: Experimental Crystal Structure Determination

    Zinser, Caroline M.; Nahra, Fady; Falivene, Laura; Brill, Marcel; Cordes, David B.; Slawin, Alexandra M. Z.; Cavallo, Luigi; Cazin, Catherine S. J.; Nolan, Steven P. (Cambridge Crystallographic Data Centre, 2019) [Dataset]
  • Supplementary material from "Beyond the visual: using metabarcoding to characterize the hidden reef cryptobiome"

    Carvalho, Susana; Aylagas, Eva; Villalobos, Rodrigo; Kattan, Yasser; Berumen, Michael L.; Pearman, John K. (figshare, 2019) [Dataset]
    In an era of coral reef degradation, our knowledge of ecological patterns in reefs is biased towards large conspicuous organisms. The majority of biodiversity, however, inhabits small cryptic spaces within the framework of the reef. To assess this biodiverse community, which we term the ‘reef cryptobiome’, we deployed 87 autonomous reef monitoring structures (ARMS), on 22 reefs across 16 degrees latitude of the Red Sea. Combining ARMS with metabarcoding of the mitochondrial cytochrome oxidase I gene, we reveal a rich community, including the identification of 14 metazoan phyla within 10 416 operational taxonomic units (OTUs). While mobile and sessile subsets were similarly structured along the basin, the main environmental driver was different (particulate organic matter and sea surface temperature, respectively). Distribution patterns of OTUs showed that only 1.5% were present in all reefs, while over half were present in a single reef. On both local and regional scales, the majority of OTUs were rare. The high heterogeneity in community patterns of the reef cryptobiome has implications for reef conservation. Understanding the biodiversity patterns of this critical component of reef functioning will enable a sound knowledge of how coral reefs will respond to future anthropogenic impacts.
  • Data mining of Citations in Doctoral Dissertations: Tool for Collection Development and Instructional Services

    Han, Lee Yen; Martin, Jose (2018-12) [Poster]
    Usage statistics, such as access and download data, are a widely used tool in a collection development librarian’s toolkit to assess the relevance and usefulness of a library’s collection to its patrons. The use of citation analysis of students’ theses and dissertations adds another dimension to this evidence-based user-centered approach to assessing collection development activities of the library. In this project, a liaison librarian and a systems specialist teamed up to make use of a systems approach to analyze the citations of doctoral dissertations from the Biological and Environmental Science and Engineering (BESE) Division in a graduate research institution. Making use of KNIME, an open source data-mining software, we created a workflow to examine citation data to discover citation patterns of student dissertations across the different programs within the BESE division and resource usage. This is matched against the current library holdings as well as compared with usage statistics obtained from JUSP. Results suggest that as an academic division, the BESE Division is not a homogenous division and citation patterns are different across the different programs. What and how references are cited are also valuable information to inform, direct and focus our collection development and information literacy program. The use of an open source data-mining software helps to automate the citation analysis process and provides an efficient and replicable framework to analyze citation data to supplement usage statistics. This would be useful for academic libraries planning to conduct similar studies to assess the usefulness of their collection with respect to the research activities of graduate students.
  • Using ePosters to promote scientific outcomes through Open Access

    Hall, Garry; Vijayakumar, J.K. (2018-10-10) [Presentation]
    King Abdullah University of Science and Technology (KAUST), established in 2009 as an international research University in Saudi Arabia, has adopted the first Open Access mandate for scientific publications in the region and leads with a well-established research repository managed and promoted by the University Library. Having several scientific poster events annually at the campus, with hosting supported by the Library, printed posters have remained static, highly localized and short-lived. These characteristics are at odds with what is often the first formal communication of scientific research and, as such would be of great interest to other researchers. Addressing these limitations was a major motivator behind the trialing of an ePoster alternative at KAUST. This project was conceived, piloted and will be implemented and managed by the University Library, in collaboration with IT Services. In addition to digitally capturing research content for display and preservation, ePoster functionality changes the engagement dynamics whilst helping to bridge the gap between academia and professional practice. ePosters have been extensively embraced by international professional organizations, however, academic institutions remain bound to printed posters. This project identified a short-list of possible companies that responded to criteria identified by KAUST as requirements for its campus wide ePoster management system. The evaluation process included student and researcher participation, as well as webinars and demonstrations and culminated with site visits to the company headquarters of the two finalists. The preferred supplier was then involved with several pilot conferences at KAUST to demonstrate their system’s capabilities and, as importantly, to expose academic staff to ePosters in operational settings. Surveys were conducted of conference participants, academic staff, students and conference organizers to obtain feedback and reaction to this approach. Advantages were both obvious and embraced by respondents; they appreciated the functionality which included ongoing editing and/or updating of content by authors, the ability of organizers to monitor progress of submissions and control content display and statistics being available via a dashboard. ePoster presentations engage the audience better; they are more interactive, dynamic and informative as a result of incorporating high resolution images and videos (with associated zoom capabilities) and audio. In addition, the elimination of print and poster mounting aligns with KAUST commitment to environmental stewardship and open access to scientific output through a direct upload of content to the Research Repository. Interest in ePosters is expanding; this has seen the Library involved in associated skills training and outreach. Academia is notably behind this practitioner-driven trend. KAUST Library believes that, by rolling out an ePoster system to the University, it is the first campus in the world to offer this as a campus-wide solution, truly reflecting a digital smart campus vision of KAUST.
  • University Library Annual Report 2017/2018

    University Library, KAUST (University Library, KAUST, 2018-09-30) [Report]
    2017/2018 Annual Report

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