From Deadly E. coli to Endangered Polar Bear: GigaScience Provides First Cita...GigaScience, BGI Hong Kong
Slides from GigaScience press-conference at BGI's Bio-IT APAC meeting on the GigaScience website launch and release of first unpublished animal genomes released from database. Genomes include polar bear, penguin, pigeon and macaque. 6th July 2011
OBJECTIVES: Translational research focuses on the bench-to-bedside information transfer process — getting the information from researchers into the hands of clinical decision makers. At the same time, researchers who manage international research collaborations could benefit from increased knowledge and awareness of online collaboration tools to support these projects. Our goal was to support both needs through building awareness and skills with online and social media.
METHODS: The Library developed a curricula targeted specifically to academic researchers focusing on collaboration technologies and online tools to support the research process. The curricula will provide instruction at three levels: gateway, bridge, and mastery tools. The goal of Level One is to persuade researchers of the utility of online social tools. To develop the program, input was solicited from researchers identified as leaders in this area as well as focus groups of students to discover which tools are already being used.
RESULTS: Training is being provided on those tools identified as most likely to engage researchers (Google Docs, Skype, online scheduling, Adobe Connect, citation sharing tools). The curricula is being delivered as workshops duplicated as podcasts and in other online media.
CONCLUSIONS: Online and social media are practical tools for supporting distance collaborations relatively inexpensively while offering the added benefit of placing selected information in online spaces that facilitate discovery and discussion with clinical care providers, thus supporting the fundamental research processes at the same time as promoting bench-to-bedside information transfer.
Focus on the Evidence: a knowledge graph approach to profiling drug targetsNolan Nichols
Presented at D4 2020
The presentation focuses on the application of knowledge graph approach in profiling drug targets. The speaker, Nolan Nichols, highlights the potential of genetic modifiers in developing transformative therapies for patients suffering from diseases such as spinal muscular atrophy (SMA). The company, Maze Therapeutics, is utilizing advanced data science and collaboration with AWS healthcare and life sciences to access and analyze meaningful human genetics data, and build a cloud-based data architecture. The presentation also covers the use of semantic technologies in drug discovery, target discovery, and target validation, and the integration of proprietary and shared data through the knowledge graph. The presentation concludes with a summary of the company's launch in 2019 with a $190 million investment and its focus on translating genetic modifying insights into new therapeutics.
Participant-centered research design and “equal access” data sharing practice...Jason Bobe
Topics include:
What is "equal access" to data?
How have the roles of human subjects expanded over time?
Where has equal access to data been a success?
What are the barriers to equal access in research?
To tweet or not to tweet: Exploring the role of social media in public health...Kevin Clauson
This is Part II (wikis & virtual worlds) of a two-part presentation on social media and public health given at the Pan American Health Organization (PAHO) in Washington, DC in November 2009
Westminster Higher Education Forum policy conference Open research data in the UK: https://www.westminsterforumprojects.co.uk/conference/open-research-data-20
Overview of the role of FAIRsharing and a dedicated Collection of data resources (platforms and registries that collect, harmonize, and share participant-level clinical-epidemiological, OMICs, and/or imaging data) for the COVID-19 Clinical Research Coalition and The Tropical Disease Research initiatives: https://coronavirus.tghn.org/research-resources/data-sharing-covid-19
160929 teamscope presentation molecule to businessSMBBV
Teamscope; mHealth, a paradigm shift in clinical reseach. Presentation by Diego Mechaca during 'From Molecule to Business' event by SMB Life Sciences and Health Valley at NovioTechCampus, Nijmegen, The Netherlands on September 29, 2016.
A 30 minute presentation given as a webinar as part of the ELIXIR series (https://www.elixir-europe.org/events/webinars/previous). This presentation covers the history of BioSharing, what it covers (data standards, databases and data policies), and our community collaborations and data sharing.
Ginny Pannabecker, Life Science & Scholarly Communications Librarian at Virginia Tech, is an ACRL Science and Technology Section (STS) liaison to the American Institute of Biological Sciences (AIBS). This presentation shares key points for librarians and researchers from an AIBS workshop on "Changing Practices in Data Publications," which took place in December 2014 and involved representatives from federal funding agencies; publishers and librarians; scientific societies and journals; and data services / providers.
This presentation was provided by Violeta Ilik of Northwestern University during the NISO Virtual Conference held on Feb 15, 2017, entitled Institutional Repositories: Ensuring Yours is Populated, Useful and Thriving. The DOI for this presentation is http://dx.doi.org/10.18131/G3VP6R
From Deadly E. coli to Endangered Polar Bear: GigaScience Provides First Cita...GigaScience, BGI Hong Kong
Slides from GigaScience press-conference at BGI's Bio-IT APAC meeting on the GigaScience website launch and release of first unpublished animal genomes released from database. Genomes include polar bear, penguin, pigeon and macaque. 6th July 2011
OBJECTIVES: Translational research focuses on the bench-to-bedside information transfer process — getting the information from researchers into the hands of clinical decision makers. At the same time, researchers who manage international research collaborations could benefit from increased knowledge and awareness of online collaboration tools to support these projects. Our goal was to support both needs through building awareness and skills with online and social media.
METHODS: The Library developed a curricula targeted specifically to academic researchers focusing on collaboration technologies and online tools to support the research process. The curricula will provide instruction at three levels: gateway, bridge, and mastery tools. The goal of Level One is to persuade researchers of the utility of online social tools. To develop the program, input was solicited from researchers identified as leaders in this area as well as focus groups of students to discover which tools are already being used.
RESULTS: Training is being provided on those tools identified as most likely to engage researchers (Google Docs, Skype, online scheduling, Adobe Connect, citation sharing tools). The curricula is being delivered as workshops duplicated as podcasts and in other online media.
CONCLUSIONS: Online and social media are practical tools for supporting distance collaborations relatively inexpensively while offering the added benefit of placing selected information in online spaces that facilitate discovery and discussion with clinical care providers, thus supporting the fundamental research processes at the same time as promoting bench-to-bedside information transfer.
Focus on the Evidence: a knowledge graph approach to profiling drug targetsNolan Nichols
Presented at D4 2020
The presentation focuses on the application of knowledge graph approach in profiling drug targets. The speaker, Nolan Nichols, highlights the potential of genetic modifiers in developing transformative therapies for patients suffering from diseases such as spinal muscular atrophy (SMA). The company, Maze Therapeutics, is utilizing advanced data science and collaboration with AWS healthcare and life sciences to access and analyze meaningful human genetics data, and build a cloud-based data architecture. The presentation also covers the use of semantic technologies in drug discovery, target discovery, and target validation, and the integration of proprietary and shared data through the knowledge graph. The presentation concludes with a summary of the company's launch in 2019 with a $190 million investment and its focus on translating genetic modifying insights into new therapeutics.
Participant-centered research design and “equal access” data sharing practice...Jason Bobe
Topics include:
What is "equal access" to data?
How have the roles of human subjects expanded over time?
Where has equal access to data been a success?
What are the barriers to equal access in research?
To tweet or not to tweet: Exploring the role of social media in public health...Kevin Clauson
This is Part II (wikis & virtual worlds) of a two-part presentation on social media and public health given at the Pan American Health Organization (PAHO) in Washington, DC in November 2009
Westminster Higher Education Forum policy conference Open research data in the UK: https://www.westminsterforumprojects.co.uk/conference/open-research-data-20
Overview of the role of FAIRsharing and a dedicated Collection of data resources (platforms and registries that collect, harmonize, and share participant-level clinical-epidemiological, OMICs, and/or imaging data) for the COVID-19 Clinical Research Coalition and The Tropical Disease Research initiatives: https://coronavirus.tghn.org/research-resources/data-sharing-covid-19
160929 teamscope presentation molecule to businessSMBBV
Teamscope; mHealth, a paradigm shift in clinical reseach. Presentation by Diego Mechaca during 'From Molecule to Business' event by SMB Life Sciences and Health Valley at NovioTechCampus, Nijmegen, The Netherlands on September 29, 2016.
A 30 minute presentation given as a webinar as part of the ELIXIR series (https://www.elixir-europe.org/events/webinars/previous). This presentation covers the history of BioSharing, what it covers (data standards, databases and data policies), and our community collaborations and data sharing.
Ginny Pannabecker, Life Science & Scholarly Communications Librarian at Virginia Tech, is an ACRL Science and Technology Section (STS) liaison to the American Institute of Biological Sciences (AIBS). This presentation shares key points for librarians and researchers from an AIBS workshop on "Changing Practices in Data Publications," which took place in December 2014 and involved representatives from federal funding agencies; publishers and librarians; scientific societies and journals; and data services / providers.
This presentation was provided by Violeta Ilik of Northwestern University during the NISO Virtual Conference held on Feb 15, 2017, entitled Institutional Repositories: Ensuring Yours is Populated, Useful and Thriving. The DOI for this presentation is http://dx.doi.org/10.18131/G3VP6R
Data ecosystems: turning data into public valueSlim Turki, Dr.
Africa Information Highway Live Exchange #Session 7
8 October 2021
The AIH Live Exchange between the Africa Information Highway Team, partners and countries is a free monthly webinar hosted by the African Development Bank to discuss topics related to government data and statistics. This webinar series is the main platform for countries to share their experiences and best practices around open data including using their Open Data Platform of the AIH.
This session is co-organized with the Luxembourg Institute of Science and Technology (LIST) which is a mission-driven Research and Technology Organization (RTO) that develops advanced technologies and delivers innovative products and services to industry and society. These innovations can also be used to solve several societal challenges, particularly in the areas of the environment, security, education and culture, sustainable development, as well as the efficient use of resources.
Official statistical data are recognized as high-value datasets for the society and economy, to enrich research, inform decision making or develop new products and services. The use of these authoritative data sources contributes to building a society with more empowered people, better policies, more effective and accountable decision-making, greater participation and stronger democratic mechanisms.
Official statistics are produced to be used and re-used to make an impact on society through a higher degree of openness and transparency while ensuring confidentiality and, at the same time, providing equal access to information to citizens.
The value of data lies in its use and re-use. In this interactive webinar, you will learn new techniques to improve the use and re-use of your statistical data, going beyond the provision logic and adopting the ecosystem mindset. You will:
● Sharpen your capacity at identifying and engaging users and re-users and stakeholders (data ecosystem mapping)?
● Effectively tackle technical and organizational barriers to stimulate data use and re-use?
● Smartly orchestrate a self-sustainable data ecosystem to increase the impact of statistical data.
This session is an opportunity for Regional members countries to '' Sharpen their skills in making data used and re-used by developing an ecosystem mindset to effectively build sustainable community of users around their Open Data Platform thus promoting transparency and better decision-making”
Transforming Research in Collaboration with Funding AgenciesAmazon Web Services
Funding agencies constitute one of the essential pillars for research and have been the backbone for innovation. Data-driven collaborative research is an integral part of many domains. In this session, leaders from the world's largest biomedical and science research agencies, the National Institutes of Health (NIH) and the National Science Foundation (NSF) discuss their programs, including NIH Data Commons and Harnessing the Data Revolution (HDR). The goal of the NIH Data Commons is to accelerate new biomedical discoveries by providing a cloud-based platform where investigators can store, share, access, and compute on digital objects generated from biomedical research. HDR is one of the 10 "Big Ideas" for future investment from the NSF for fundamental data science research. These collaborative initiatives will enable researchers to accelerate science and engineering through improved access to data, tooling, analytic resources in the cloud. These programs will revolutionize the way scientific data and resources are utilized by the research communities.
Why the food sector needs a research infrastructure on Food and Health Consum...e-ROSA
Bent Egberg Mikkelsen and Karin Zimmermann's presentation at the eROSA Workshop “Towards Open Science in Agriculture & Food”, a side event to High Level conference on FOOD 2030, Plovdiv, Bulgaria (13/6/2018)
Lesson 2 in a set of 10 created by DataONE on Best Practices fo Data Management. The full module can be downloaded from the DataONE.org website at: http://www.dataone.org/educaiton-modules. Released under a CC0 license, attribution and citation requested.
The increased availability of biomedical data, particularly in the public domain, offers the opportunity to better understand human health and to develop effective therapeutics for a wide range of unmet medical needs. However, data scientists remain stymied by the fact that data remain hard to find and to productively reuse because data and their metadata i) are wholly inaccessible, ii) are in non-standard or incompatible representations, iii) do not conform to community standards, and iv) have unclear or highly restricted terms and conditions that preclude legitimate reuse. These limitations require a rethink on data can be made machine and AI-ready - the key motivation behind the FAIR Guiding Principles. Concurrently, while recent efforts have explored the use of deep learning to fuse disparate data into predictive models for a wide range of biomedical applications, these models often fail even when the correct answer is already known, and fail to explain individual predictions in terms that data scientists can appreciate. These limitations suggest that new methods to produce practical artificial intelligence are still needed.
In this talk, I will discuss our work in (1) building an integrative knowledge infrastructure to prepare FAIR and "AI-ready" data and services along with (2) neurosymbolic AI methods to improve the quality of predictions and to generate plausible explanations. Attention is given to standards, platforms, and methods to wrangle knowledge into simple, but effective semantic and latent representations, and to make these available into standards-compliant and discoverable interfaces that can be used in model building, validation, and explanation. Our work, and those of others in the field, creates a baseline for building trustworthy and easy to deploy AI models in biomedicine.
Bio
Dr. Michel Dumontier is the Distinguished Professor of Data Science at Maastricht University, founder and executive director of the Institute of Data Science, and co-founder of the FAIR (Findable, Accessible, Interoperable and Reusable) data principles. His research explores socio-technological approaches for responsible discovery science, which includes collaborative multi-modal knowledge graphs, privacy-preserving distributed data mining, and AI methods for drug discovery and personalized medicine. His work is supported through the Dutch National Research Agenda, the Netherlands Organisation for Scientific Research, Horizon Europe, the European Open Science Cloud, the US National Institutes of Health, and a Marie-Curie Innovative Training Network. He is the editor-in-chief for the journal Data Science and is internationally recognized for his contributions in bioinformatics, biomedical informatics, and semantic technologies including ontologies and linked data.
This pdf is about the Schizophrenia.
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
Thanks...!
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...
research participation as a social contract
1. brian m. bot | @BrianMBot | principal scientist | community manager |
2016 sep 14
sage bionetworks
international data forum
research participation
as a social contract
2. sage bionetworks
promote open systems, incentives, and norms
to redefine how complex biological data is
gathered, shared, and used
our approach
3. sage bionetworks
engage diverse communities of researchers
around biological and analytical problems
too complex for a single institution
our focus
empower citizens to track their own health
and contribute deep phenotypic data to
research topics important to them
7. mPower
‘qualified researcher’ first pass
register for a synapse account
get a validated user profile
become a certified synapse user
submit an intended data use statement
agree to the conditions for use
download the data
8. mPower
‘qualified researcher’ first pass
register for a synapse account
get a validated user profile
become a certified synapse user
submit an intended data use statement
agree to the conditions for use
download the data
9,520 unique participants
8,320 completed at least one task
198,639 total activities and surveys completed
1,087 self reported parkinson diagnosis
9. mPower
‘qualified researcher’ first pass
register for a synapse account
get a validated user profile
become a certified synapse user
submit an intended data use statement
agree to the conditions for use
download the data
seeding a community in PD research
released before any primary publication
60+ independent ‘qualified researchers’
10. 2016 sep 14
international data forumresearch participation
as a social contract
brian m. bot
————————
principal scientist
community manager
sage bionetworks
github: @brian-bot
twitter: @BrianMBot
thank you