7,043 Works

Incorporating FAIR data principles in Agricultural Research Management Information System (ARMIS) database (Bangladesh)

Hamidur Rahman
An online database named Agricultural Research Management Information System (ARMIS) (http://armis.barcapps.gov.bd) is developed which incorporates agricultural research data in Bangladesh. The agricultural research organizations specifically, National Agricultural Research System (NARS) institutes and universities have long been engaged in agricultural research in Bangladesh and the research information was mostly scattered/poorly organized. The centralized online ARMIS database is developed by Computer and GIS Unit of Bangladesh Agricultural Research Council (BARC) to provide real time information for conducting,...

Privacy preserving synthetic health data

Andrew Yale, Saloni Dash, Ritik Dutta, Isabelle Guyon, Adrien Pavao & Kristin P. Bennett
We examine the feasibility of using synthetic medical data generated by GANs in the classroom, to teach data science in health informatics. Teaching data analysis with actual medical data such as electronic healthcare records is greatly restrained by laws protecting patient's privacy, such as HIPAA in the United States. While beneficial, these laws severely limit access to medical data thus stagnating innovation and limiting educational opportunities. The process of obfuscation of medical data is costly...

Object substitution masking, stimulus noise and perceptual fidelity

Michael Pilling, Duncan Guest & Mark Andrews
The poster looks at how Object substitution masking (OSM, or four-dot masking as it is sometimes known) affects the perceptibility of the target. This is done using an adjustment task (rather than a conventional forced choice decision task) in which observers have to set the gap position of a test stimulus to match that of the target. The effect on target perceptibility is compared between OSM and simultaneous noise mask. It is found that both...

Agricultural innovation in Sub-Saharan Africa and South Asia

Rachel Percy, Josephine Tsui & Andrew Sutherland
Agricultural innovation in Sub-Saharan Africa and South Asia

Changes in free amino acids, reducing sugars, fat oxidation and browning during drying of milkfish (Chanos chanos)

M.Sc. Norqueen Taruc-Dumadaug
Drying of fish in Zamboanga Philippines is one of the oldest but very much applicable technology in the local community. Knowing the factors that contributes to the spoilage of the dried product is important knowledge to enhance the shelf-life and acceptability of the product.

24 hr noise exposure aboard US navy aircraft carriers

Nicholas Schaal, Raushan Salaam, Michael Stevens & Alex Stubner
Background: Personnel assigned to aircraft carriers are exposed to a variety of noise sources from equipment and flight deck operations for durations >12 h. Personnel work and live in environments where hazardous noise areas and hearing recovery spaces such as sleeping and relaxation areas are in proximity to one another which provides little recovery time from hazardous noise. This investigation describes noise levels measured over a 24-h period on a US Navy aircraft carrier during...

FAIRsharing.org – mapping the landscape of databases, standards and policies (describing, linking and assessing their FAIRness)

Peter McQuilton
This short set of slides was presented at the 12th International Society of Biocuration conference in Cambridge April 2019. In these slides, we discuss the FAIRsharing project and our quest to map the landscape of repositories, knowledgebases, data standards (ontologies, reporting guidelines, models/formats, identifier schema and metrics), and data policies from funders and journal publishers. We also touch on how FAIRsharing can help Biocurators identify which standards to use in their work and to understand...

Analysis of small non-coding RNAs of poorly annotated species in Galaxy with the help of ortholog information of well annotated species

Jochen Bick, Susanne E. Ulbrich & Stefan Bauersachs
The analysis of RNA-seq data with a basic analysis pipeline including quality control, filtering, trimming, and adapter clipping followed by mapping to a reference genome or transcriptome is a straightforward task using Galaxy. For processing of smallRNA-Seq data it is necessary to modify this analysis pipeline because the resulting reads correspond, at least in theory directly to a small RNA. This leads to a different mapping strategy using BLASTn for short sequences. An additional common...

TeSS: the ELIXIR training portal

Patricia M. Palagi, Peter McQuilton & Niall Beard
The TeSS ELIXIR Training Portal was developed to harvest training information from ELIXIR Nodes and 3rd-party content providers, to facilitate discovery of life-science training events and materials, and offer visual navigation tools (‘workflows’) to link ELIXIR core resources to training opportunities, and signpost their relevance to users (in terms of their target audience, duration, location, etc.).

MoCA : Tool for Motif Conservation Analysis

Saket Choudhary & Anton Valouev
MoCA makes use of GERP and PhastCons scores to assess the conservation profile of TFBS and compares it with the neighboring sequence. Input to MoCA is a bed file indicating ChIP-seq peak summits. The summits are then slopped to obtain flanking sequences. MoCA makes use of MEME to perform \emph{de-novo} motif discovery. The motif logos are then plotted against their conservation scores. Other diagnostic plots include a regression plot indicating the correlation between the most...

FAIRsharing: Mapping the landscape of biocuration – what standards should you use, what kind of data is in each database, which resources are FAIR?

Peter McQuilton, Milo Thurston, Massimiliano Izzo, Ramon Granell, Dominique Batista, Allyson L. Lister, Delphine Dauga, Melanie Adekale, Alejandra Gonzalez-Beltran, Philippe Rocca-Serra & Susanna-Assunta Sansone
FAIRsharing (https://www.fairsharing.org) is a cross-discipline, manually curated registry that monitors the development and evolution of standards across all scientific disciplines and the humanities, and cross-links them to the knowledgebases and repositories that use them and the journal and funder data policies that endorse their use. In this poster we describe the FAIRsharing model, the use of our Subject (SRAO) and Domain (DRAO) ontologies and show an example record, including all the metadata captured therein. In...

Artificial intelligence for reuse of free-text radiology reports

Michoel Snow, Glen Ferguson, Boudewijn Aasman, G Anthony Reina & Parsa Mirhaji
As in any large healthcare system, the Montefiore Medical Center produces thousands of radiological exams and associated reports each day. These exams depend on expensive infrastructure and require radiologists with years of experience to interpret them, but are only reviewed a few times, and very rarely in the context of other patients. This treasure trove of untapped data is ripe for reuse for research, clinical decision support, operational efficiency, and care coordination. However, there is...

Evolution of internal colouration of Neotropical anurans

Diogo Borges Provete, Lilian Franco-Belussi & Classius De Oliveira
In this talk, given at a symposium in the Argentinian Congress of Herpetology, we showed the results of two recent papers we publish demonstrating the role of climatic factors and phylogeny on the degree of internal pigmentation in anurans.

AI for biological discovery: data integration and self-driving instruments

Robert Murphy
AI for Biological Discovery: Data Integration and Self-Driving Instruments

Robert F. Murphy
Computational Biology Department, Carnegie Mellon University

Self-driving cars are changing transportation and setting a precedent for automated decision-making in the physical world. Following that precedent, self-driving instruments will revolutionize the way in which experimental science is done. A major task in biomedical research is creating empiricalmodels that can predict, for example, how a person with a particular genetic makeup will respond to a particular...

Nematode filarial Worms in cerebrospinal fluid of a Multiple Sclerosis patient at autopsy

Alan MacDonald
First case report in the world's literature linking Multiple Sclerosis with Cerebrospinal Nematodiasis

New evidence models: clinical trials in the age of AI and precision medicine

Glen De Vries
The "gold standard" by which physicians, scientists, and regulators have evaluated safety and efficacy in clinical research, the randomized controlled trial, has been consistent for over two hundred years. Today, digital transformation and AI are making new evidence models possible. These evidence models address both practical and ethical issues in human research. We will examine those issues, how precision medicine make them more acute, how digital and AI are allowing for new comparators and unprecedented...

The case for machine-actionable data management plans in ELIXIR

João Cardoso & José Borbinha
A Data Management Plan (DMP) is a document detailing how the data from a research project is to be managed throughout its lifecycle. This implies describing the techniques, methods and policies on how data is to be created, documented, accessed, preserved and disseminated.
Nowadays several funding agents require funding applications to be accompanied by a DMP, but than it rarely is required for anything else. Consequently, the DMP is frequently a text document holding a static...

Identification of causal genetic network for Alzheimer’s disease

Biwei Huang, Yandong Wen & Zhipeng Yang
Alzheimer’s Disease (AD) is a chronic neural degenerative disease characterized by progressive cognitive impairment. Commonly as it occurs, the underlying mechanism of AD is poorly understood. It is generally agreed that AD is a heterogeneous disease with a combination of genetic and environmental risks. Identifying new AD-related loci in human genome would provide valuable information for the underlying mechanism of the disease and potential new therapeutic targets for treatment. Single nucleotide polymorphisms (SNPs) refer to...

Promoting open data by empowering stakeholders: what data should authors share?

Tim Vines & Kristen Ratan
Compliance with data sharing policies is easier when you know how and where to share your data. DataSeer bridges the implementation gap between general policy and the actions required for a particular article. It uses Natural Language Processing to identify data collection sentences, then works out what type of data have been collected. Authors are given detailed guidance on how and where to share those data, and funders/journals receive a report on what was shared...

Layer-fMRI methods for applications in human neuroscience: beyond block designs and beyond primary brain areas

Laurentius Huber, Emily Finn, Rainer Goebel, Peter Bandettini & Benedikt Poser
Methodological advancements of functional Magnetic Resonance Imaging (fMRI) in recent years allow researchers to approach the mesoscopic spatial regime of cortical layers and cortical columns. This revolutionizes the ability to tackle cortical information processing within brain systems. However, until now, most layer fMRI studies are confined to primary cortices in combination with basic fMRI task block-designs. Thus, to become an established method for user-friendly applicability in neuroscience practice, layer fMRI acquisition and analysis methods need...

Pushing the resolution of 7T fMRI: Layer-fMRI with CBV

Laurentius Huber
This is an invited presentation for the Symposium Advances in High Field Brain Imaging.
On May 17th, 2019 in Montreal (Mc Gill, The Neuro)

iDSI Health Technology Assessment Toolkit

Mairi Jeffrey, Y-Ling Chi & Madeleine Stewart
An accessible resource for technical staff working in health policy keen to build Health Technology Assessment (HTA) processes in their own countries, developed in consultation with end users.

The Toolkit document is broken down into ‘building blocks’, enabling readers to develop their understanding of: setting the scene for HTA; compiling the best HTA evidence; HTA as an inclusive process; building capacity to support HTA; ensuring political commitment; and setting up a transparent and consistent process.


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