A presentation to the DBMI department at the University of Pittsburgh about data sharing and reuse: what this means, why it is important, some of what we’ve learned, and what we still don’t know.
Recomendations for infrastructure and incentives for open science, presented to the Research Data Alliance 6th Plenary. Presenter: William Gunn, Director of Scholarly Communications for Mendeley.
Research in the time of Covid: Surveying impacts on Early Career ResearchersRebecca Grant
Based on a survey of over 4,500 researchers published in the white paper The State of Open Data 2020, this session will explore the impacts of the pandemic on early career reearchers (ECRs), their research practice, and how they interact with open data. We will discuss the specific challenges reported by ECRs, as well as the gaps in training and support that they have identified that would encourage their sharing and reuse of research data.
Presentation at the E-ARMA conference 2021.
Do Open data badges influence author behaviour? A case study at Springer NatureRebecca Grant
Digital badges have previously been shown to incentivise journal authors to share their data openly. In this paper we introduce an Open data badging project at the Springer Nature journal BMC Microbiology. The development of the Open data badge is described, as well as the challenges of developing standard badging criteria and ensuring authors’ awareness of the badges. Next steps for the badging project are outlined, which are based on the experiences of the team assessing the badges, the number of badges awarded at the journal to date, and the results of an author survey.
Increasing transparency in Medical Education through Open Data Rebecca Grant
Slides presented at the AMEE Virtual Conference 2021, introducing the MedEdPublish platform and data policies. Approaches to sharing sensitive human data, and particulary qualitative data, are discussed.
Recomendations for infrastructure and incentives for open science, presented to the Research Data Alliance 6th Plenary. Presenter: William Gunn, Director of Scholarly Communications for Mendeley.
Research in the time of Covid: Surveying impacts on Early Career ResearchersRebecca Grant
Based on a survey of over 4,500 researchers published in the white paper The State of Open Data 2020, this session will explore the impacts of the pandemic on early career reearchers (ECRs), their research practice, and how they interact with open data. We will discuss the specific challenges reported by ECRs, as well as the gaps in training and support that they have identified that would encourage their sharing and reuse of research data.
Presentation at the E-ARMA conference 2021.
Do Open data badges influence author behaviour? A case study at Springer NatureRebecca Grant
Digital badges have previously been shown to incentivise journal authors to share their data openly. In this paper we introduce an Open data badging project at the Springer Nature journal BMC Microbiology. The development of the Open data badge is described, as well as the challenges of developing standard badging criteria and ensuring authors’ awareness of the badges. Next steps for the badging project are outlined, which are based on the experiences of the team assessing the badges, the number of badges awarded at the journal to date, and the results of an author survey.
Increasing transparency in Medical Education through Open Data Rebecca Grant
Slides presented at the AMEE Virtual Conference 2021, introducing the MedEdPublish platform and data policies. Approaches to sharing sensitive human data, and particulary qualitative data, are discussed.
Keynote presented to KE workshop held in conjunction with the release of the report "A Surfboard for Riding the Wave
Towards a four country action programme on research data": http://www.knowledge-exchange.info/Default.aspx?ID=469
Genome sharing projects around the world nijmegen oct 29 - 2015Fiona Nielsen
Genome sharing projects across the world
Did you ever wonder what happened to the exponential increase in genome sequencing data? It is out there around the world and a lot of it is consented for research use. This means that if you just know where to find the data, you can potentially analyse gigabytes of data to power your research.
In this talk Fiona will present community genome initiatives, the genome sharing projects across the world, how you can benefit from this wealth of data in your work, and how you can boost your academic career by sharing and collaboration.
by Fiona Nielsen, Founder and CEO of DNAdigest and Repositive
With a background in software development Fiona pursued her career in bioinformatics research at Radboud University Nijmegen. Now a scientist-turned-entrepreneur Fiona founded DNAdigest and its social enterprise spin-out Repositive Ltd. Both the charity and company focus on efficient and ethical sharing of genetics data for research to accelerate diagnostics and cures for genetic diseases.
BIOLINK 2008: Linking database submissions to primary citations with PubMe...Heather Piwowar
Abstract: Background: Dataset submissions are growing exponentially. Links between dataset submissions and primary literature that describe the data collection are useful for many reasons: rich documentation, proper attribution, improved information retrieval, and enhanced text/data integration for analysis. Unfortunately, many database submissions do not include primary citation links, as database submissions are often made prior to publication. We suggest that automated tools can be developed to help identify links between dataset submissions and the primary literature. These tools require full text to differentiate cases of data sharing from data reuse and other contexts. In this study, we explore the possibility that deep analysis of full text may not be necessary, thereby enabling the querying of all reports in PubMed Central. Methods: We trained machine learning tree and rule-based classifiers on full-text open-access article unigram vectors, with the existence of a primary citation link from NCBI’s Gene Expression Omnibus (GEO) database submission records as the binary output class. We manually combined and simplified the classifier trees and rules to create a query compatible with the interface for PubMed Central. Results: The query identified 40% of non-OA articles with dataset submission links from GEO (recall), and 65% of the returned articles without dataset submission links were manually judged to include statements of dataset deposit despite having no link from the database (applicable precision). Conclusion: We hope this work inspires future enhancements, and highlights the opportunities for simple full-text queries in PubMed Central given the mandated influx of NIH-funded research reports.
The State of Open Data Report by @figshare.
A selection of analyses and articles about open data, curated by Figshare
Foreword by Professor Sir Nigel Shadbolt
OCTOBER 2016
Dr. Dennis Wang discusses possible ways to enable ML methods to be more powerful for discovery and to reduce ambiguity within translational medicine, allowing data-informed decision-making to deliver the next generation of diagnostics and therapeutics to patients quicker, at lowered costs, and at scale.
The talk by Dr. Dennis Wang was followed by a panel discussion with Mr. Albert Wang, M. Eng., Head, IT Business Partner, Translational Research & Technologies, Bristol-Myers Squibb.
With the explosion of interest in both enhanced knowledge management and open science, the past few years have seen considerable discussion about making scientific data “FAIR” — findable, accessible, interoperable, and reusable. The problem is that most scientific datasets are not FAIR. When left to their own devices, scientists do an absolutely terrible job creating the metadata that describe the experimental datasets that make their way in online repositories. The lack of standardization makes it extremely difficult for other investigators to locate relevant datasets, to re-analyse them, and to integrate those datasets with other data. The Center for Expanded Data Annotation and Retrieval (CEDAR) has the goal of enhancing the authoring of experimental metadata to make online datasets more useful to the scientific community. The CEDAR work bench for metadata management will be presented in this webinar. CEDAR illustrates the importance of semantic technology to driving open science. It also demonstrates a means for simplifying access to scientific data sets and enhancing the reuse of the data to drive new discoveries.
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?
ISMB/ECCB 2013 Keynote Goble Results may vary: what is reproducible? why do o...Carole Goble
Keynote given by Carole Goble on 23rd July 2013 at ISMB/ECCB 2013
http://www.iscb.org/ismbeccb2013
How could we evaluate research and researchers? Reproducibility underpins the scientific method: at least in principle if not practice. The willing exchange of results and the transparent conduct of research can only be expected up to a point in a competitive environment. Contributions to science are acknowledged, but not if the credit is for data curation or software. From a bioinformatics view point, how far could our results be reproducible before the pain is just too high? Is open science a dangerous, utopian vision or a legitimate, feasible expectation? How do we move bioinformatics from one where results are post-hoc "made reproducible", to pre-hoc "born reproducible"? And why, in our computational information age, do we communicate results through fragmented, fixed documents rather than cohesive, versioned releases? I will explore these questions drawing on 20 years of experience in both the development of technical infrastructure for Life Science and the social infrastructure in which Life Science operates.
Laurie Goodman at #aibsdata: Beyond Data Release Mandates - Helping Authors M...GigaScience, BGI Hong Kong
Laurie Goodman at the AIBS Changing Practices in Data Pub workshop: Beyond Data Release Mandates - Helping Authors Make Data Available. 3rd December 2014
Managing Ireland's Research Data - 3 Research MethodsRebecca Grant
Slides providing an overview of the research methods used in the author's thesis, "Managing Ireland's Research Data: Recognising Roles for Recordkeepers". The methods discussed are online surveys, comparative case studies, and autoethnography.
Licensed as CC-BY.
With its focus on investigating the basis for the sustained existence
of living systems, modern biology has always been a fertile, if not
challenging, domain for formal knowledge representation and automated
reasoning. With thousands of databases and hundreds of ontologies now
available, there is a salient opportunity to integrate these for
discovery. In this talk, I will discuss our efforts to build a rich
foundational network of ontology-annotated linked data, develop
methods to intelligently retrieve content of interest, uncover
significant biological associations, and pursue new avenues for drug
discovery. As the portfolio of Semantic Web technologies continue to
mature in terms of functionality, scalability, and an understanding of
how to maximize their value, researchers will be strategically poised
to pursue increasingly sophisticated KR projects aimed at improving
our overall understanding of human health and disease.
bio: Dr. Michel Dumontier is an Associate Professor of Medicine
(Biomedical Informatics) at Stanford University. His research aims to
find new treatments for rare and complex diseases. His research
interest lie in the publication, integration, and discovery of
scientific knowledge. Dr. Dumontier serves as a co-chair for the World
Wide Web Consortium Semantic Web in Health Care and Life Sciences
Interest Group (W3C HCLSIG) and is the Scientific Director for
Bio2RDF, a widely used open-source project to create and provide
linked data for life sciences.
Making it Easier, Possibly Even Pleasant, to Author Rich Experimental MetadataMichel Dumontier
Biomedical researchers will remain stymied in their ability to take full advantage of the Big Data revolution if they can never find the datasets that they need to analyze, if there is lack of clarity about what particular datasets contain, and if data are insufficiently described.
CEDAR, an NIH BD2K Center of Excellence, aims to develop methods and tools to vastly ease the burden of authoring good experimental metadata, and to maximally use this information to zero in on datasets of interest.
Thesis Proposal, as presented for dissertation proposal defenseHeather Piwowar
The slides I presented for my PhD proposal defense for my project, "Foundational studies for measuring the impact, prevalence, and patterns of publicly sharing biomedical research data." Dept of Biomedical Informatics, University of Pittsburgh.
Keynote presented to KE workshop held in conjunction with the release of the report "A Surfboard for Riding the Wave
Towards a four country action programme on research data": http://www.knowledge-exchange.info/Default.aspx?ID=469
Genome sharing projects around the world nijmegen oct 29 - 2015Fiona Nielsen
Genome sharing projects across the world
Did you ever wonder what happened to the exponential increase in genome sequencing data? It is out there around the world and a lot of it is consented for research use. This means that if you just know where to find the data, you can potentially analyse gigabytes of data to power your research.
In this talk Fiona will present community genome initiatives, the genome sharing projects across the world, how you can benefit from this wealth of data in your work, and how you can boost your academic career by sharing and collaboration.
by Fiona Nielsen, Founder and CEO of DNAdigest and Repositive
With a background in software development Fiona pursued her career in bioinformatics research at Radboud University Nijmegen. Now a scientist-turned-entrepreneur Fiona founded DNAdigest and its social enterprise spin-out Repositive Ltd. Both the charity and company focus on efficient and ethical sharing of genetics data for research to accelerate diagnostics and cures for genetic diseases.
BIOLINK 2008: Linking database submissions to primary citations with PubMe...Heather Piwowar
Abstract: Background: Dataset submissions are growing exponentially. Links between dataset submissions and primary literature that describe the data collection are useful for many reasons: rich documentation, proper attribution, improved information retrieval, and enhanced text/data integration for analysis. Unfortunately, many database submissions do not include primary citation links, as database submissions are often made prior to publication. We suggest that automated tools can be developed to help identify links between dataset submissions and the primary literature. These tools require full text to differentiate cases of data sharing from data reuse and other contexts. In this study, we explore the possibility that deep analysis of full text may not be necessary, thereby enabling the querying of all reports in PubMed Central. Methods: We trained machine learning tree and rule-based classifiers on full-text open-access article unigram vectors, with the existence of a primary citation link from NCBI’s Gene Expression Omnibus (GEO) database submission records as the binary output class. We manually combined and simplified the classifier trees and rules to create a query compatible with the interface for PubMed Central. Results: The query identified 40% of non-OA articles with dataset submission links from GEO (recall), and 65% of the returned articles without dataset submission links were manually judged to include statements of dataset deposit despite having no link from the database (applicable precision). Conclusion: We hope this work inspires future enhancements, and highlights the opportunities for simple full-text queries in PubMed Central given the mandated influx of NIH-funded research reports.
The State of Open Data Report by @figshare.
A selection of analyses and articles about open data, curated by Figshare
Foreword by Professor Sir Nigel Shadbolt
OCTOBER 2016
Dr. Dennis Wang discusses possible ways to enable ML methods to be more powerful for discovery and to reduce ambiguity within translational medicine, allowing data-informed decision-making to deliver the next generation of diagnostics and therapeutics to patients quicker, at lowered costs, and at scale.
The talk by Dr. Dennis Wang was followed by a panel discussion with Mr. Albert Wang, M. Eng., Head, IT Business Partner, Translational Research & Technologies, Bristol-Myers Squibb.
With the explosion of interest in both enhanced knowledge management and open science, the past few years have seen considerable discussion about making scientific data “FAIR” — findable, accessible, interoperable, and reusable. The problem is that most scientific datasets are not FAIR. When left to their own devices, scientists do an absolutely terrible job creating the metadata that describe the experimental datasets that make their way in online repositories. The lack of standardization makes it extremely difficult for other investigators to locate relevant datasets, to re-analyse them, and to integrate those datasets with other data. The Center for Expanded Data Annotation and Retrieval (CEDAR) has the goal of enhancing the authoring of experimental metadata to make online datasets more useful to the scientific community. The CEDAR work bench for metadata management will be presented in this webinar. CEDAR illustrates the importance of semantic technology to driving open science. It also demonstrates a means for simplifying access to scientific data sets and enhancing the reuse of the data to drive new discoveries.
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?
ISMB/ECCB 2013 Keynote Goble Results may vary: what is reproducible? why do o...Carole Goble
Keynote given by Carole Goble on 23rd July 2013 at ISMB/ECCB 2013
http://www.iscb.org/ismbeccb2013
How could we evaluate research and researchers? Reproducibility underpins the scientific method: at least in principle if not practice. The willing exchange of results and the transparent conduct of research can only be expected up to a point in a competitive environment. Contributions to science are acknowledged, but not if the credit is for data curation or software. From a bioinformatics view point, how far could our results be reproducible before the pain is just too high? Is open science a dangerous, utopian vision or a legitimate, feasible expectation? How do we move bioinformatics from one where results are post-hoc "made reproducible", to pre-hoc "born reproducible"? And why, in our computational information age, do we communicate results through fragmented, fixed documents rather than cohesive, versioned releases? I will explore these questions drawing on 20 years of experience in both the development of technical infrastructure for Life Science and the social infrastructure in which Life Science operates.
Laurie Goodman at #aibsdata: Beyond Data Release Mandates - Helping Authors M...GigaScience, BGI Hong Kong
Laurie Goodman at the AIBS Changing Practices in Data Pub workshop: Beyond Data Release Mandates - Helping Authors Make Data Available. 3rd December 2014
Managing Ireland's Research Data - 3 Research MethodsRebecca Grant
Slides providing an overview of the research methods used in the author's thesis, "Managing Ireland's Research Data: Recognising Roles for Recordkeepers". The methods discussed are online surveys, comparative case studies, and autoethnography.
Licensed as CC-BY.
With its focus on investigating the basis for the sustained existence
of living systems, modern biology has always been a fertile, if not
challenging, domain for formal knowledge representation and automated
reasoning. With thousands of databases and hundreds of ontologies now
available, there is a salient opportunity to integrate these for
discovery. In this talk, I will discuss our efforts to build a rich
foundational network of ontology-annotated linked data, develop
methods to intelligently retrieve content of interest, uncover
significant biological associations, and pursue new avenues for drug
discovery. As the portfolio of Semantic Web technologies continue to
mature in terms of functionality, scalability, and an understanding of
how to maximize their value, researchers will be strategically poised
to pursue increasingly sophisticated KR projects aimed at improving
our overall understanding of human health and disease.
bio: Dr. Michel Dumontier is an Associate Professor of Medicine
(Biomedical Informatics) at Stanford University. His research aims to
find new treatments for rare and complex diseases. His research
interest lie in the publication, integration, and discovery of
scientific knowledge. Dr. Dumontier serves as a co-chair for the World
Wide Web Consortium Semantic Web in Health Care and Life Sciences
Interest Group (W3C HCLSIG) and is the Scientific Director for
Bio2RDF, a widely used open-source project to create and provide
linked data for life sciences.
Making it Easier, Possibly Even Pleasant, to Author Rich Experimental MetadataMichel Dumontier
Biomedical researchers will remain stymied in their ability to take full advantage of the Big Data revolution if they can never find the datasets that they need to analyze, if there is lack of clarity about what particular datasets contain, and if data are insufficiently described.
CEDAR, an NIH BD2K Center of Excellence, aims to develop methods and tools to vastly ease the burden of authoring good experimental metadata, and to maximally use this information to zero in on datasets of interest.
Thesis Proposal, as presented for dissertation proposal defenseHeather Piwowar
The slides I presented for my PhD proposal defense for my project, "Foundational studies for measuring the impact, prevalence, and patterns of publicly sharing biomedical research data." Dept of Biomedical Informatics, University of Pittsburgh.
Big Data: Big Opportunities or Big Trouble?Shea Swauger
Big data is changing how research is being conducted and allowing new kinds of questions to be asked. Meanwhile, data management has enabled a rapid increase in the dissemination and preservation of research products and many funding agencies like the National Science Foundation and National Institute of Health now require data management plans in their grant applications. The combination of big data applications and data management processes has created new opportunities and pitfalls for researchers. In the past year, prominent scientists including the Director of the NIH have suggested that inappropriate methodology for data acquisition, analysis and storage has led to a gap in the translation of basic research findings to clinical cures. In this session we will track data through all research stages, describe best practices and university resources available to faculty grappling with these important issues.
Presented at ASIS&T 2009 in the student awards section. The presentation contains an overview of my dissertation proposal, as 2009 winner of the Thomson Reuters Information Science Doctoral Dissertation Proposal Scholarship, administered by the ASIS&T Information Science Education Committee
Thinking about Open Science practices, data sharing and lifetime, and communication from Climate Scientists. Slides based on a presentation given at the Lunchtime talk sessions from the MetOS Section, Department of Geosciences, University of Oslo, November 12th 2015.
"Leaders and Laggards in the preservation of raw biomedical research data" presented at NEDCC 2010, The Tectonics of Digital Curation
A Symposium on the Shifting Preservation and Access Landscape
This presentation summarizes Jennifer Tucker's dissertation study, entitled “Motivating Subjects: Data Sharing in Cancer Research.” The research focused on the motivational factors that influence a researcher’s decision to share data.
Data Management and Broader Impacts: a holistic approachMegan O'Donnell
[please download to view at full resolution]
The National Science Foundation’s (NSF) Broader Impacts Criterion asks scientists to frame their research beyond “science for science’s sake.” Examining data and data management through a Broader Impacts lens highlights the benefits of good data management, data management plans (DMPs), and strengthens the argument for better Data Information Literacy (DIL) in the sciences.
Thesis defense, Heather Piwowar, Sharing biomedical research dataHeather Piwowar
Presentation by Heather Piwowar as PhD dissertation defense on March 24, 2010 at the Dept of Biomedical Informatics, U of Pittsburgh. "Foundational studies for
measuring the impact, prevalence, and patterns of publicly sharing biomedical research data." I passed :)
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.
Scott Edmunds slides for class 8 from the HKU Data Curation (module MLIM7350 from the Faculty of Education) course covering science data, medical data and ethics, and the FAIR data principles.
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.
Similar to Why study Data Sharing? (+ why share your data) (20)
Calculating how much your University spends on Open Access--and what to do ab...Heather Piwowar
#NASIG2020 presentation
Librarians are working hard to understand how much money their university is spending on open access article processing fees (APCs), and how much of what they subscribe to is available as OA. This information is useful when making subscription decisions, considering Read and Publish agreements, rethinking library open access budgets, and designing Institution-wide OA policies.
This session will talk concretely about how to calculate the impact of Open Access on *your* university. It will provide an overview on how to estimate the amount of money spent across a university on Open Access fees: we will discuss underlying concepts behind calculating OA article-processing fee (APC) spend and give an overview of useful data sources, including Unsub.
Follow at @unsub_org
How to Calculate OA APC Spend for Your UniversityHeather Piwowar
Universities are hungry to know how much they spend on Open Access fees. This data is important to planning transformative and read and publish agreements, forming library strategy, and understanding scholarly communication on your campus. Unfortunately, it hasn’t been easy to calculate how much your university is spending on Open Access.
Learn how recent developments in data sources and tools have made this easier during this webinar. We will discuss the underlying concepts behind calculating OA article-processing fee (APC) spend, and provide you with paths to calculate the Open Access fees paid by your institution. ALCTS webinar.
Intro to Managing Serials with Net Cost per Paid UseHeather Piwowar
This webinar will introduce a new metric for evaluating the cost effectiveness of Serials: Net Cost Per Paid Use (NCPPU). NCPPU goes beyond the standard Cost Per Use calculation to exclude free content (OA and back catalog), incorporate ILL costs, and value citation and authorship. ALCTS webinar.
submission summary for #WSSSPE Policy session on Credit, Citation, and ImpactHeather Piwowar
submission summary for #WSSSPE Policy session on Credit, Citation, and Impact
presentation by Heather Piwowar
November 2013
agenda: http://wssspe.researchcomputing.org.uk/
New Directions in Targeted Therapeutic Approaches for Older Adults With Mantl...i3 Health
i3 Health is pleased to make the speaker slides from this activity available for use as a non-accredited self-study or teaching resource.
This slide deck presented by Dr. Kami Maddocks, Professor-Clinical in the Division of Hematology and
Associate Division Director for Ambulatory Operations
The Ohio State University Comprehensive Cancer Center, will provide insight into new directions in targeted therapeutic approaches for older adults with mantle cell lymphoma.
STATEMENT OF NEED
Mantle cell lymphoma (MCL) is a rare, aggressive B-cell non-Hodgkin lymphoma (NHL) accounting for 5% to 7% of all lymphomas. Its prognosis ranges from indolent disease that does not require treatment for years to very aggressive disease, which is associated with poor survival (Silkenstedt et al, 2021). Typically, MCL is diagnosed at advanced stage and in older patients who cannot tolerate intensive therapy (NCCN, 2022). Although recent advances have slightly increased remission rates, recurrence and relapse remain very common, leading to a median overall survival between 3 and 6 years (LLS, 2021). Though there are several effective options, progress is still needed towards establishing an accepted frontline approach for MCL (Castellino et al, 2022). Treatment selection and management of MCL are complicated by the heterogeneity of prognosis, advanced age and comorbidities of patients, and lack of an established standard approach for treatment, making it vital that clinicians be familiar with the latest research and advances in this area. In this activity chaired by Michael Wang, MD, Professor in the Department of Lymphoma & Myeloma at MD Anderson Cancer Center, expert faculty will discuss prognostic factors informing treatment, the promising results of recent trials in new therapeutic approaches, and the implications of treatment resistance in therapeutic selection for MCL.
Target Audience
Hematology/oncology fellows, attending faculty, and other health care professionals involved in the treatment of patients with mantle cell lymphoma (MCL).
Learning Objectives
1.) Identify clinical and biological prognostic factors that can guide treatment decision making for older adults with MCL
2.) Evaluate emerging data on targeted therapeutic approaches for treatment-naive and relapsed/refractory MCL and their applicability to older adults
3.) Assess mechanisms of resistance to targeted therapies for MCL and their implications for treatment selection
The prostate is an exocrine gland of the male mammalian reproductive system
It is a walnut-sized gland that forms part of the male reproductive system and is located in front of the rectum and just below the urinary bladder
Function is to store and secrete a clear, slightly alkaline fluid that constitutes 10-30% of the volume of the seminal fluid that along with the spermatozoa, constitutes semen
A healthy human prostate measures (4cm-vertical, by 3cm-horizontal, 2cm ant-post ).
It surrounds the urethra just below the urinary bladder. It has anterior, median, posterior and two lateral lobes
It’s work is regulated by androgens which are responsible for male sex characteristics
Generalised disease of the prostate due to hormonal derangement which leads to non malignant enlargement of the gland (increase in the number of epithelial cells and stromal tissue)to cause compression of the urethra leading to symptoms (LUTS
Prix Galien International 2024 Forum ProgramLevi Shapiro
June 20, 2024, Prix Galien International and Jerusalem Ethics Forum in ROME. Detailed agenda including panels:
- ADVANCES IN CARDIOLOGY: A NEW PARADIGM IS COMING
- WOMEN’S HEALTH: FERTILITY PRESERVATION
- WHAT’S NEW IN THE TREATMENT OF INFECTIOUS,
ONCOLOGICAL AND INFLAMMATORY SKIN DISEASES?
- ARTIFICIAL INTELLIGENCE AND ETHICS
- GENE THERAPY
- BEYOND BORDERS: GLOBAL INITIATIVES FOR DEMOCRATIZING LIFE SCIENCE TECHNOLOGIES AND PROMOTING ACCESS TO HEALTHCARE
- ETHICAL CHALLENGES IN LIFE SCIENCES
- Prix Galien International Awards Ceremony
Acute scrotum is a general term referring to an emergency condition affecting the contents or the wall of the scrotum.
There are a number of conditions that present acutely, predominantly with pain and/or swelling
A careful and detailed history and examination, and in some cases, investigations allow differentiation between these diagnoses. A prompt diagnosis is essential as the patient may require urgent surgical intervention
Testicular torsion refers to twisting of the spermatic cord, causing ischaemia of the testicle.
Testicular torsion results from inadequate fixation of the testis to the tunica vaginalis producing ischemia from reduced arterial inflow and venous outflow obstruction.
The prevalence of testicular torsion in adult patients hospitalized with acute scrotal pain is approximately 25 to 50 percent
Title: Sense of Taste
Presenter: Dr. Faiza, Assistant Professor of Physiology
Qualifications:
MBBS (Best Graduate, AIMC Lahore)
FCPS Physiology
ICMT, CHPE, DHPE (STMU)
MPH (GC University, Faisalabad)
MBA (Virtual University of Pakistan)
Learning Objectives:
Describe the structure and function of taste buds.
Describe the relationship between the taste threshold and taste index of common substances.
Explain the chemical basis and signal transduction of taste perception for each type of primary taste sensation.
Recognize different abnormalities of taste perception and their causes.
Key Topics:
Significance of Taste Sensation:
Differentiation between pleasant and harmful food
Influence on behavior
Selection of food based on metabolic needs
Receptors of Taste:
Taste buds on the tongue
Influence of sense of smell, texture of food, and pain stimulation (e.g., by pepper)
Primary and Secondary Taste Sensations:
Primary taste sensations: Sweet, Sour, Salty, Bitter, Umami
Chemical basis and signal transduction mechanisms for each taste
Taste Threshold and Index:
Taste threshold values for Sweet (sucrose), Salty (NaCl), Sour (HCl), and Bitter (Quinine)
Taste index relationship: Inversely proportional to taste threshold
Taste Blindness:
Inability to taste certain substances, particularly thiourea compounds
Example: Phenylthiocarbamide
Structure and Function of Taste Buds:
Composition: Epithelial cells, Sustentacular/Supporting cells, Taste cells, Basal cells
Features: Taste pores, Taste hairs/microvilli, and Taste nerve fibers
Location of Taste Buds:
Found in papillae of the tongue (Fungiform, Circumvallate, Foliate)
Also present on the palate, tonsillar pillars, epiglottis, and proximal esophagus
Mechanism of Taste Stimulation:
Interaction of taste substances with receptors on microvilli
Signal transduction pathways for Umami, Sweet, Bitter, Sour, and Salty tastes
Taste Sensitivity and Adaptation:
Decrease in sensitivity with age
Rapid adaptation of taste sensation
Role of Saliva in Taste:
Dissolution of tastants to reach receptors
Washing away the stimulus
Taste Preferences and Aversions:
Mechanisms behind taste preference and aversion
Influence of receptors and neural pathways
Impact of Sensory Nerve Damage:
Degeneration of taste buds if the sensory nerve fiber is cut
Abnormalities of Taste Detection:
Conditions: Ageusia, Hypogeusia, Dysgeusia (parageusia)
Causes: Nerve damage, neurological disorders, infections, poor oral hygiene, adverse drug effects, deficiencies, aging, tobacco use, altered neurotransmitter levels
Neurotransmitters and Taste Threshold:
Effects of serotonin (5-HT) and norepinephrine (NE) on taste sensitivity
Supertasters:
25% of the population with heightened sensitivity to taste, especially bitterness
Increased number of fungiform papillae
Title: Sense of Smell
Presenter: Dr. Faiza, Assistant Professor of Physiology
Qualifications:
MBBS (Best Graduate, AIMC Lahore)
FCPS Physiology
ICMT, CHPE, DHPE (STMU)
MPH (GC University, Faisalabad)
MBA (Virtual University of Pakistan)
Learning Objectives:
Describe the primary categories of smells and the concept of odor blindness.
Explain the structure and location of the olfactory membrane and mucosa, including the types and roles of cells involved in olfaction.
Describe the pathway and mechanisms of olfactory signal transmission from the olfactory receptors to the brain.
Illustrate the biochemical cascade triggered by odorant binding to olfactory receptors, including the role of G-proteins and second messengers in generating an action potential.
Identify different types of olfactory disorders such as anosmia, hyposmia, hyperosmia, and dysosmia, including their potential causes.
Key Topics:
Olfactory Genes:
3% of the human genome accounts for olfactory genes.
400 genes for odorant receptors.
Olfactory Membrane:
Located in the superior part of the nasal cavity.
Medially: Folds downward along the superior septum.
Laterally: Folds over the superior turbinate and upper surface of the middle turbinate.
Total surface area: 5-10 square centimeters.
Olfactory Mucosa:
Olfactory Cells: Bipolar nerve cells derived from the CNS (100 million), with 4-25 olfactory cilia per cell.
Sustentacular Cells: Produce mucus and maintain ionic and molecular environment.
Basal Cells: Replace worn-out olfactory cells with an average lifespan of 1-2 months.
Bowman’s Gland: Secretes mucus.
Stimulation of Olfactory Cells:
Odorant dissolves in mucus and attaches to receptors on olfactory cilia.
Involves a cascade effect through G-proteins and second messengers, leading to depolarization and action potential generation in the olfactory nerve.
Quality of a Good Odorant:
Small (3-20 Carbon atoms), volatile, water-soluble, and lipid-soluble.
Facilitated by odorant-binding proteins in mucus.
Membrane Potential and Action Potential:
Resting membrane potential: -55mV.
Action potential frequency in the olfactory nerve increases with odorant strength.
Adaptation Towards the Sense of Smell:
Rapid adaptation within the first second, with further slow adaptation.
Psychological adaptation greater than receptor adaptation, involving feedback inhibition from the central nervous system.
Primary Sensations of Smell:
Camphoraceous, Musky, Floral, Pepperminty, Ethereal, Pungent, Putrid.
Odor Detection Threshold:
Examples: Hydrogen sulfide (0.0005 ppm), Methyl-mercaptan (0.002 ppm).
Some toxic substances are odorless at lethal concentrations.
Characteristics of Smell:
Odor blindness for single substances due to lack of appropriate receptor protein.
Behavioral and emotional influences of smell.
Transmission of Olfactory Signals:
From olfactory cells to glomeruli in the olfactory bulb, involving lateral inhibition.
Primitive, less old, and new olfactory systems with different path
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NVBDCP.pptx Nation vector borne disease control programSapna Thakur
NVBDCP was launched in 2003-2004 . Vector-Borne Disease: Disease that results from an infection transmitted to humans and other animals by blood-feeding arthropods, such as mosquitoes, ticks, and fleas. Examples of vector-borne diseases include Dengue fever, West Nile Virus, Lyme disease, and malaria.
Ethanol (CH3CH2OH), or beverage alcohol, is a two-carbon alcohol
that is rapidly distributed in the body and brain. Ethanol alters many
neurochemical systems and has rewarding and addictive properties. It
is the oldest recreational drug and likely contributes to more morbidity,
mortality, and public health costs than all illicit drugs combined. The
5th edition of the Diagnostic and Statistical Manual of Mental Disorders
(DSM-5) integrates alcohol abuse and alcohol dependence into a single
disorder called alcohol use disorder (AUD), with mild, moderate,
and severe subclassifications (American Psychiatric Association, 2013).
In the DSM-5, all types of substance abuse and dependence have been
combined into a single substance use disorder (SUD) on a continuum
from mild to severe. A diagnosis of AUD requires that at least two of
the 11 DSM-5 behaviors be present within a 12-month period (mild
AUD: 2–3 criteria; moderate AUD: 4–5 criteria; severe AUD: 6–11 criteria).
The four main behavioral effects of AUD are impaired control over
drinking, negative social consequences, risky use, and altered physiological
effects (tolerance, withdrawal). This chapter presents an overview
of the prevalence and harmful consequences of AUD in the U.S.,
the systemic nature of the disease, neurocircuitry and stages of AUD,
comorbidities, fetal alcohol spectrum disorders, genetic risk factors, and
pharmacotherapies for AUD.
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Hemodialysis: Chapter 3, Dialysis Water Unit - Dr.Gawad
Why study Data Sharing? (+ why share your data)
1. Why study Data Sharing? (+ why share your data) Heather Piwowar DBMI Colloquium, March 28 2008 University of Pittsburgh except clipart
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16. Why share data? Foster et al. Share and share alike: deciding how to distribute the scientific and social benefits of genomic data. Nature Reviews Genetics 8, 633-639
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18. Why share: journal requirements Piwowar, Chapman. A review of journal policies for sharing research data. Accepted to ELPUB2008 Percent journal studies with links from microarray databases, by strength of journal data-sharing policy Note: Studies are about microarray data but they may not have all generated microarray data. Calculated percentages may be <100% even when universal sharing.
19. Why share: investigator benefit Piwowar, Day, and Fridsma DB (2007). PLoS ONE 2(3): e308. Number of citations received by clinical trial publications, by whether or not they publicly shared their microarray data Note the logarithmic scale
My name is Heather, and as many of you know my area of research is the evaluation of biomedical Data Sharing and Reuse. Today I’m going to be talking about what this means, why it is important, some of what we’ve learned, and what we still don’t know.