Search

IntroductionThe National Library of Medicine (NLM) launched a pilot in June 2020 to 1) explore the feasibility and utility of adding preprints to PubMed Central (PMC) and making them discoverable in PubMed and 2) to support accelerated discoverability of NIH-supported research without compromising user trust in NLM’s widely used literature services.MethodsThe first phase of the Pilot focused on archiving preprints reporting NIH-supported SARS-CoV-2 virus and COVID-19 research. To launch Phase 1, NLM identified eligible preprint servers and developed processes for identifying NIH-supported preprints within scope in these servers. Processes were also developed for the ingest and conversion of preprints in PMC and to send corresponding records to PubMed. User interfaces were modified for display of preprint records. NLM collected data on the preprints ingested and discovery of preprint records in PMC and PubMed and engaged users through focus groups and a survey to obtain direct feedback on the Pilot and perceptions of preprints.ResultsBetween June 2020 and June 2022, NLM added more than 3,300 preprint records to PMC and PubMed, which were viewed 4 million times and 3 million times, respectively. Nearly a quarter of preprints in the Pilot were not associated with a peer-reviewed published journal article. User feedback revealed that the inclusion of preprints did not have a notable impact on trust in PMC or PubMed.DiscussionNIH-supported preprints can be identified and added to PMC and PubMed without disrupting existing operations processes. Additionally, inclusion of preprints in PMC and PubMed accelerates discovery of NIH research without reducing trust in NLM literature services. Phase 1 of the Pilot provided a useful testbed for studying NIH investigator preprint posting practices, as well as knowledge gaps among user groups, during the COVID-19 public health emergency, an unusual time with heightened interest in immediate access to research results.

Tag sets change over time. Tag set designers manage a complex system where everything is connected to everything else and new user requirements continue to surface. Tag set users manage complex systems to create, manage, and archive documents. Users strongly resist backward-incompatible change, so as JATS has grown we have made compromises in the design to meet new requirements while maintaining backward-compatability. We think it is time to consolidate redundant models, remove deprecated items, and generally reduce confusion. Can we guide users towards a new, backwards incompatible version in a way that they'll find palatable? We have a plan. We're going to extend the JATS 1.x schema so that it contains the new, 2.0 models in addition to the old models. Then we'll make an "Onramp" subset of 1.x that has the deprecated items removed. Documents valid against the onramp subset of 1.x will also be valid against 2.0.

The Crossref Preprint Advisory Group (AG) was formed in June 2021 to discuss metadata issues related to preprints. It has the following aims...

We present closed-form expressions for low-order-aberration-removed, aperture-averaged anisoplanatic error across horizontal paths. These solutions are not only computationally inexpensive but easily invertible to numerically calculate extended isoplanatic angles in a given propagation scenario.

Handedness has low heritability and epigenetic mechanisms have been proposed as an etiological mechanism. To examine this hypothesis, we performed an epigenome-wide association study (EWAS) of left-handedness. In a meta-analysis of 3,914 adults of whole-blood DNA methylation, we observed that CpG sites located in proximity of handedness-associated genetic variants were more strongly associated with left-handedness than other CpG sites (P = 0.04), but did not identify any differentially methylated positions. We identified differentially methylated regions at 20q11.23 (P = 0.00004) and 2p25.1 (P = 0.03), which were less methylated in left-handed adults. In longitudinal analyses of DNA methylation in peripheral blood and buccal cells from children (N = 1,737), we observed moderately stable associations across age (correlation range [0.355–0.578]) but inconsistent across tissues (correlation range [-0.384-0.318]). We conclude that DNA methylation in peripheral tissues captures little of the variance in handedness. Future investigations should consider other more targeted sources of tissue, such as the brain.

On January 20 and 21, 2020, ASAPbio, in collaboration with EMBL-EBI and Ithaka S+R, convened over 30 representatives from academia, preprint servers, publishers, funders, and standards, indexing and metadata infrastructure organisations at EMBL-EBI (Hinxton, UK) to develop a series of recommendations for best practices for posting and linking of preprints in the life sciences and ideally the broader research community. We hope that these recommendations offer guidance for new preprint platforms and projects looking to enact best practices and ultimately serve to improve the experience of using preprints for all.

Maximal flexibility of rules, or ease of reuse — choose one. The tighter the rules, the more consistent documents will be and the easier it will be to reuse them, but only if the rules are reasonable enough to be adopted. (If all the data creators ignore the rules, reuse doesn’t get easier.) JATS4R (JATS for Reuse) is a NISO working group devoted to optimizing the reusability of scholarly content by developing best-practice recommendations for tagging content in JATS XML. The group has devoted particular attention to the flexibility/reuse tradeoff for rules on attribute use and controlled values, and we eventually decided that we needed some rules for ourselves, on how to write rules for attributes in our recommendations. In the process of developing our guidance document for writing rules for attribute values in our recommendations, we learned (or at least articulated) some things along the way.

Markup makes it easier to share. We share documents with our peers, our partners, and even our competitors. Communities of interest form, they define document structures, test them in practice, and affirm them by adoption. Joining a community has obvious advantages: reduced development costs, ease of interchange, tried and tested tools, and an available pool of authors, editors, and developers already familiar with the vocabulary. Over time, the pace of vocabulary evolution slows naturally. The major structures are developed, applied, tested, and accepted. New structures are added more slowly, and more reluctantly. The community has transitioned into maintenance mode where large scale refactorings and backwards-incompatible changes are known to have burdonsome costs and “best practices” are known to make sharing easier. What can the “Markup Community in General” do to support these stricter best practices communities?

PubMed Central (PMC) is a free full-text XML-based archive of biomedical and life sciences journal literature at the U.S. National Library of Medicine. Publishers submit XML, images, and supplemental files for their articles, the text converts to a common JATS XML, and they load to the database cleanly. The power of XML compels it! But that is not the whole story (or even a true story). Policies, miscommunications, and technical misunderstandings conspire against our Utopian XML workflow. We will share the details of how we get 30,000 new articles into the archive each month.

Model verification has traditionally relied upon in situ observations, which typically exist on a sparse network, making nonsurface model forecast verification difficult. Given increasing model resolution, supplemental observational datasets are needed. Multiple-Doppler wind retrievals using a national network of radars provide an opportunity to assess the accuracy of wind forecasts at multiple levels, as well as verification within a three-dimensional domain. Wind speed and direction verification results are presented for a 9-day period of forecasts from the French Application of Research to Operations at Mesoscale-Western Mediterranean (AROME-WMED) model using multiple-Doppler retrievals from the French Application Radar à la Météorologie Infrasynoptique (ARAMIS) network. For the analyzed period, relationships were found that suggest that errors are not only linked to forecasted evolution of meteorological phenomena, but are sensitive to terrain height below the analyzed level as well as mesoscale processes. The spatial distribution of errors at initialization and forecast times shows that biases are generally independent of location and terrain height at initialization, but that the impact of terrain below the analysis level affects the forecasted wind magnitude and direction over time. These comparisons illustrate that multiple-Doppler wind retrieval measurements accurately identify model error and can serve as an invaluable dataset for model verification.

The effect of wet radome attenuation is estimated on a French operational X-band weather radar deployed in the Maritime Alps of southeastern France. As the radar is deployed in a remote location, the reflectivity factor in the immediate vicinity of the radar is used as a proxy for rain rate at the radar and by extension, to the radome wetting. By means of intercomparison with a neighboring radar that lacks a radome, a wet radome correction is deduced. The correction is reasonably consistent with theoretical expectations and with other evaluations done, for example, via disdrometer. The improvement is evaluated by comparison to a Micro Rain Radar located under the point of comparison, and the impact on quantitative precipitation estimation (QPE) retrievals is positive. The intercomparison of such observations permits a routine means of monitoring radome attenuation.

Tag Sets, or XML Vocabularies, are often created from other Tag Sets or Vocabularies. Users expect significant efficiencies from using derived or “based on” vocabularies, including the ability to intermingle the documents in databases, to use tools created for the original Tag Set with minimal additional work, and to adopt rendering/formatting applications and change only those aspects specific to the new vocabulary. Some model changes create compatible documents, which can interoperate with documents tagged to the source specification gracefully. Some model changes are disruptive. We discuss what types of changes can be integrated into existing XML environments and which may be disruptive.

The article considers the concept of pinstripe patronage put forth in Pinstripe Patronage: Political Favoritism from the Clubhouse to the White House and Beyond, by Martin and Susan J. Tolchin (Boulder, Colorado: Paradigm Publishers, 2011) as it applies to the realm of health policy and politics.

Alcohol use and abuse on American college campuses has raised significant concerns among university officials, scholars, and social critics. One of the principal concerns is that heavy drinking is associated with risky sexual behavior and sexual victimization among college samples. The current study seeks to enhance our understanding regarding the relationship between alcohol intoxication and sex by investigating the ways in which college students use alcohol as a tool to facilitate, explain, and justify sexual encounters and casual coupling (e.g., kissing, “making out,” petting, touching). Guided by theoretical perspectives designed to explain the role of rhetoric in explaining and justifying deviant behavior, we analyze 469 qualitative “drinking stories” and 32 interviews collected at three university sites. Our findings suggest that college drinkers view alcohol as a disinhibiting force that elevates the potential for sexuality and that alcohol intoxication is also used as a resource to justify casual ...

The Book Interchagnge Tag Suite (BITS) is a book model based on the JATS article model. There are many things that can be structured the same way in both a Journal Article and a Book (or a part of a book), and some things that are very different. We'll review the things you 'get for free' if you are already familiar with the article model, and what parts of the book model you will need to pay a little more attention to.

On 29 May 2001, Doppler on Wheels radars collected data on a supercell near Kress, Texas. The supercellular storm, cyclic in nature, produced multiple mesocyclones throughout its lifetime. Dual-Doppler syntheses were conducted using a grid spacing of 100 m, resulting in the highest-resolution observational analysis of a cyclic supercell to date. In addition, collection of data from ground-based radar allowed for the analysis of near-ground features irresolvable with airborne radar, providing another advantage over previous studies. The syntheses revealed a number of evolving low-level mesocyclones over the observation period of 900 s. While nontornadic during the synthesis period, the supercell exhibited evidence of strong (vertical vorticity greater than 10−2 s−1) low-level circulation with classic cyclic structure and multiple tornadoes beginning 3600 s later. A comparison between the current results, conceptual models, and previous lower-resolution analyses is presented. A striking similarity exists between the cyclic evolution of the Kress storm during the synthesis time period and other previous cyclic conceptual models. However, differences did exist between the Kress storm and previously studied tornadic storms. Analysis showed that the rear-flank downdraft provided the only surface boundary associated with low-level mesocyclogenesis. Other characteristics, including forward-flank gust front structure and the orientation of low-level horizontal vorticity, also differed. In addition, there was a general lack of surface convergence associated with the forward-flank reflectivity gradient, yet convergence associated with the forward-flank gust front increased with height. Finally, a large component of crosswise horizontal vorticity was found to exist throughout the supercell environment, within both the inflow and outflow. Incorporating these differences, an attempt was made to identify possible mechanisms responsible for the lack of tornadogenesis during the synthesis time period.

The existing French Application Radar à la Météorologie Infrasynoptique (ARAMIS) operational radar network covers a vast majority of the country of France, yet like many national networks, gaps in coverage are present in regions of mountainous and high terrain. Many of these areas are prone to extreme, orography-induced precipitation events, and therefore expansion of national radar networks into these regions is very important. The addition of small X-band radars, strategically placed to supplement the ARAMIS network, is discussed with emphasis on the ability to expand three-dimensional wind and reflectivity field retrieval. This expanded coverage is particularly important for terrain-related precipitation in the southern Alps. Successful dual- and multiple-Doppler syntheses were conducted using the existing ARAMIS network and two new radars located in mountainous terrain, installed within the context of the Risques Hydrométéorologiques en Territoires de Montagnes et Mediterranéens (RHYTMME) program. To illustrate the coverage and advantage that gap-filling radars can add to an existing national radar network, two case studies are presented, with multiple-Doppler syntheses revealing that terrain relief and low-level atmospheric stability influence the resulting wind field. In addition to the added coverage, the RHYTMME gap-filling radars improve wind-flow retrieval and the accuracy of reflectivity measurements over extreme southeast France and into the Mediterranean Sea.

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank(®) nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. Additional NCBI resources focus on literature (Bookshelf, PubMed Central (PMC) and PubReader); medical genetics (ClinVar, dbMHC, the Genetic Testing Registry, HIV-1/Human Protein Interaction Database and MedGen); genes and genomics (BioProject, BioSample, dbSNP, dbVar, Epigenomics, Gene, Gene Expression Omnibus (GEO), Genome, HomoloGene, the Map Viewer, Nucleotide, PopSet, Probe, RefSeq, Sequence Read Archive, the Taxonomy Browser, Trace Archive and UniGene); and proteins and chemicals (Biosystems, COBALT, the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB), Protein Clusters, Protein and the PubChem suite of small molecule databases). The Entrez system provides search and retrieval operations for many of these databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov.

Creating and using XML documents in a closes system gives a false sense of “All’s Well”. A Closed XML system is one where a single party creates and uses the XML documents. Certainly this happens all of the time. We all create little XML documents with one-off throw-away models for one task or another that only we use. These documents will not be the focus here. When documents are created in a closed XML workflow and sent to another entity - such as an archive - for reuse, publishers can quickly learn that the content they have been accumulating is not useful for anything outside of their system and may not be useful if their own systems are upgraded or changed. The checks and procedures that must be put in place to support XML interchange between entities should be applied within closed XML systems to keep the content usable and useful.

Guidance, navigation, and control (GNC the knowledge of the system's current location, orientation, or state; and the application of forces

Discharged psychiatric patients at a large community residence were noted to be experiencing increased agitation, anger and anxiety in connection with repeated vandalism and unauthorized visits by members of the surrounding community. An intervention based on behavioral concepts and technology was formulated utilizing many parts of the social matrix of the residence, including clinical staff, direct care staff and the residents. Resident behavior was successfully changed as a result of the intervention. It appears that behaviorally based, clinical-administrative solutions to “real world” problems can be effective in teaching passive, chronic mental patients safety conscious behavior and helping them to assume responsibility for their community-based living space.

Among the many issues regarding the care of chronic mental patients, none is more pressing than the need for administrative and clinical models designed to organize and systematize the efforts of diverse community service providers. This paper describes the functioning of the Community Residential Treatment Service of the South Beach Psychiatric Center, a large-scale project of a state facility created to respond to this tissue. By blending sophisticated clinical and administrative technology, programs operated by the state, voluntary, and proprietary health care sectors have been integrated to form a balanced service delivery system. This system provides a broad continuum of inpatient and outpatient residential settings developed in accordance with social learning principles. The components of the system, with the Community Residential Treatment Service as the major integrative force, are linked together by detailed contracts as well as common behavioral clinical and behavioral administrative language. The treatment successes f this system have been significant enough to suggest that a positive synergistic effect is generated by this programming combination.