How to add academic journal articles to PubMed: An overview for publishers

“If you work with journals in the biomedical or life sciences, getting the articles you publish added to PubMed to make them more discoverable is likely one of your top goals. But, you may be wondering how to go about it.

We caught up with PubMed Central (PMC) Program Manager Kathryn Funk to get answers to some of the most common questions that we hear from journal publishers about PubMed and the related literature databases at the National Library of Medicine (NLM), MEDLINE and PMC. Read on to learn more about how the PubMed database works and how to apply to have a journal included in MEDLINE or PMC in order to make its articles searchable via PubMed….”

E.P.A. to Limit Science Used to Write Public Health Rules – The New York Times

“The Trump administration is preparing to significantly limit the scientific and medical research that the government can use to determine public health regulations, overriding protests from scientists and physicians who say the new rule would undermine the scientific underpinnings of government policymaking….”

Potential risks and solutions for sharing genome summary data from African populations | BMC Medical Genomics | Full Text

Abstract:  Genome data from African population can substantially assist the global effort to identify aetiological genetic variants, but open access to aggregated genomic data from these populations poses some significant risks of community- and population- level harms. A recent amendment to National Institutes of Health policy, following various engagements with predominantly North American scientists, requires that genomic summary results must be made available openly on the internet without access oversight or controls.

The policy does recognise that some sensitive, identifiable population groups might be harmed by such exposure of their data, and allows for exemption in these cases. African populations have a very wide and complex genomic landscape, and because of this diversity, individual African populations may be uniquely re-identified by their genomic profiles and genome summary data. Given this identifiability, combined with additional vulnerabilities such as poor access to health care, socioeconomic challenges and the risk of ethnic discrimination, it would be prudent for the National Institutes of Health to recognise the potential of their current policy for community harms to Africans; and to exempt all African populations as sensitive or vulnerable populations with regard to the unregulated exposure of their genome summary data online.

Three risk-mitigating mechanisms for sharing genome summary results from African populations to inform global genomic health research are proposed here; namely use of the Beacon Protocol developed by the Global Alliance for Genomics and Health, user access control through the planned African Genome Variation Database, and regional aggregation of population data to protect individual African populations from re-identification and associated harms.

Who Owns H.I.V.-Prevention Drugs? The Taxpayers, U.S. Says – The New York Times

“After years of prodding by patient advocates, federal officials on Wednesday sued the drug maker Gilead Sciences, charging that it had infringed government patents on the idea of preventing H.I.V. with a daily pill.

The suit, by the Department of Health and Human Services, came as a pleasant shock to many critics of the company, including Democratic members of Congress who had pressed the administration to act.

It is very rare for the government to take on a drug maker over patents. But the medications made by Gilead are necessary to end the AIDS epidemic by 2030, which the Trump administration has set as a goal. That cannot be accomplished if the drugs are not made more affordable….”

Open Systems Pharmacology community – an open access, open source, open science approach to modeling and simulation in pharmaceutical sciences. – PubMed – NCBI

Abstract:  Systems Pharmacology integrates structural biological and pharmacological knowledge and experimental data enabling dissection of organism and drug properties and providing excellent predictivity. The development of systems pharmacology models is a significant task requiring massive amounts of background information beyond individual trial data. Qualification of models needs repetitive demonstration of successful predictions. Open Systems Pharmacology is a community that develops, qualifies and shares professional open source software tools and models in a collaborative open science way.

3D printing revives skeletal study program at Countway – Harvard Gazette

“Now, staff members at the Medical School’s Countway Library are reviving the initiative with a 21st-century twist. They’re planning to assemble new boxes of replica human bones and skulls rendered through 3D printing in a program they’re calling Beyond the Bone Box….

The library houses an anatomical museum, which is expected to preserve rare anatomical specimens in perpetuity, but as part of the library system, it also has an educational mission. Creating 3D models of rare specimens allows the museum to safeguard the originals while still allowing Countway’s special collections to be used as teaching tools….

“A bone box is mostly about access,” Hall said. “With a collection that has human remains in it … education is critical to your existence. Otherwise this is just a strange horde that you never share, and ethically that’s irresponsible.” …”

The Personal Genome Project-UK, an open access resource of human multi-omics data | Scientific Data

“Integrative analysis of multi-omics data is a powerful approach for gaining functional insights into biological and medical processes. Conducting these multifaceted analyses on human samples is often complicated by the fact that the raw sequencing output is rarely available under open access. The Personal Genome Project UK (PGP-UK) is one of few resources that recruits its participants under open consent and makes the resulting multi-omics data freely and openly available. As part of this resource, we describe the PGP-UK multi-omics reference panel consisting of ten genomic, methylomic and transcriptomic data. Specifically, we outline the data processing, quality control and validation procedures which were implemented to ensure data integrity and exclude sample mix-ups. In addition, we provide a REST API to facilitate the download of the entire PGP-UK dataset. The data are also available from two cloud-based environments, providing platforms for free integrated analysis. In conclusion, the genotype-validated PGP-UK multi-omics human reference panel described here provides a valuable new open access resource for integrated analyses in support of personal and medical genomics….”

Animal Research, Accountability, Openness and Public Engagement: Report from an International Expert Forum

Abstract:  In November 2013, a group of international experts in animal research policy (n = 11) gathered in Vancouver, Canada, to discuss openness and accountability in animal research. The primary objective was to bring together participants from various jurisdictions (United States, Sweden, Australia, New Zealand, Germany, Canada and the United Kingdom) to share practices regarding the governance of animals used in research, testing and education, with emphasis on the governance process followed, the methods of community engagement, and the balance of openness versus confidentiality. During the forum, participants came to a broad consensus on the need for: (a) evidence-based metrics to allow a “virtuous feedback” system for evaluation and quality assurance of animal research, (b) the need for increased public access to information, together with opportunities for stakeholder dialogue about animal research, (c) a greater diversity of views to be represented on decision-making committees to allow for greater balance and (d) a standardized and robust ethical decision-making process that incorporates some sort of societal input. These recommendations encourage aspirations beyond merely imparting information and towards a genuine dialogue that represents a shared agenda surrounding laboratory animal use.

Animal Research, Accountability, Openness and Public Engagement: Report from an International Expert Forum

Abstract:  In November 2013, a group of international experts in animal research policy (n = 11) gathered in Vancouver, Canada, to discuss openness and accountability in animal research. The primary objective was to bring together participants from various jurisdictions (United States, Sweden, Australia, New Zealand, Germany, Canada and the United Kingdom) to share practices regarding the governance of animals used in research, testing and education, with emphasis on the governance process followed, the methods of community engagement, and the balance of openness versus confidentiality. During the forum, participants came to a broad consensus on the need for: (a) evidence-based metrics to allow a “virtuous feedback” system for evaluation and quality assurance of animal research, (b) the need for increased public access to information, together with opportunities for stakeholder dialogue about animal research, (c) a greater diversity of views to be represented on decision-making committees to allow for greater balance and (d) a standardized and robust ethical decision-making process that incorporates some sort of societal input. These recommendations encourage aspirations beyond merely imparting information and towards a genuine dialogue that represents a shared agenda surrounding laboratory animal use.