Access to biomedical terminologies is hampered by the high degree of variability inherent in natural language terms and in the terminologies themselves. The lexicon, lexical programs, databases, and indexes included with the 1994 release of the UMLS Knowledge Sources are designed to help users manage this variability. We describe these resources and illustrate their flexibility and usefulness in providing enhanced access to data in the UMLS Metathesaurus.
This report reviews some of the extensive literature in health literacy, much of it focused on the intersection of low literacy and the understanding of basic health care information. Several articles describe methods for assessing health literacy as well as methods for assessing the readability of texts, although generally these latter have not been developed with health materials in mind. Other studies have looked more closely at the mismatch between patients' literacy levels and the readability of materials intended for use by those patients. A number of studies have investigated the phenomenon of literacy from the perspective of patients' interactions in the health care setting, the disenfranchisement of some patients because of their low literacy skills, the difficulty some patients have in navigating the health care system, the quality of the communication between doctors and their patients including the cultural overlay of such exchanges, and ultimately the effect of low literacy on health outcomes. Finally, the impact of new information technologies has been studied by a number of investigators. There remain many opportunities for conducting further research to gain a better understanding of the complex interactions between general literacy, health literacy, information technologies, and the existing health care infrastructure.
Abstract Background Short tandem repeats (STRs) are widely distributed across the human genome and are associated with numerous neurological disorders. However, the extent that STRs contribute to disease is likely under-estimated because of the challenges calling these variants in short read next generation sequencing data. Several computational tools have been developed for STR variant calling, but none fully address all of the complexities associated with this variant class. Results Here we introduce LUSTR which is designed to address some of the challenges associated with STR variant calling by enabling more flexibility in defining STR loci, allowing for customizable modules to tailor analyses, and expanding the capability to call somatic and multiallelic STR variants. LUSTR is a user-friendly and easily customizable tool for targeted or unbiased genome-wide STR variant screening that can use either predefined or novel genome builds. Using both simulated and real data sets, we demonstrated that LUSTR accurately infers germline and somatic STR expansions in individuals with and without diseases. Conclusions LUSTR offers a powerful and user-friendly approach that allows for the identification of STR variants and can facilitate more comprehensive studies evaluating the role of pathogenic STR variants across human diseases.
The Large Scale Vocabulary Test, sponsored by the National Library of Medicine (NLM) and the Agency for Health Care Policy and Research (AHCPR), was conducted to determine the extent to which a combination of existing health-related terminologies cover vocabulary needed in health care information systems. The test was conducted over the Internet using a sophisticated World Wide Web interface with over 60 participants and over 40,000 terms submitted. This paper discusses the issues encountered in the design and execution of the experiment, including the design of the interface and the issues of recruitment, training, and guidance of remote participants over the Internet. Test data are currently undergoing expert review. Upon completion of the expert review, the results of the test will be fully reported.
Digital information in any form is at risk. Software and hardware become obsolete, and versions and file formats change, making data inaccessible. Data stored in even the simplest form are in danger due to computer media degradation and obsolescence. On-line information such as e-journals and databases are susceptible. They may become partially or entirely unreadable, and may not be recoverable by the time the problem is detected. Preservation strategies such as emulation (keeping alive the software and hardware needed to access a digital object), migration (converting the digital object to new versions and formats), and other long-term archival methods have been proposed [1-7]. Models such as the Open Archival Information System (OAIS) provide an architecture for conducting digital preservation research and experimentation [8-10]. The importance of preservation metadata has been recognized by a number of groups and efforts to develop and deploy metadata standards are underway [11-14].As more and more digital information is created, attention must be paid to what information should be preserved and how it can be preserved most economically and effectively. It is clear that for preservation to be successful, we need to pay attention not only to the format of digital objects, but also to the commitment we make to providing long-term access to the information. Thus, decisions about digital preservation will involve technical issues as well as economic, legal, social, and organizational ones. Is it possible or feasible to preserve all digital data automatically and in a cost effective way? How much functionality can or must be preserved? What type of metadata will be needed to ensure both access and preservation? What metrics do we use to evaluate whether our methods will be successful.Panelists will make short presentations about work in which they have been involved and which reflect a variety of aspects of digital preservation. Reagan Moore will discuss the levels of abstraction that are needed to create infrastructure independent representations for data, information, and knowledge, and he will discuss a prototype persistent digital archive. The persistent archive infrastructure has been developed for use by the National Archives and Records Administration and other Federal agencies. William Underwood will report on lessons learned in preserving digital records created on personal computers. The records being examined are the digital records created on personal computers during the administration of President George Bush (1988-1992). Vicky Reich will present work on the LOCKSS (Lots of Copies Keep Stuff Safe) project, which is a permanent web publishing and access system. LOCKSS software allows libraries to retain local collection control of materials delivered through the web while preserving the functionality of the original web based content. Robin Dale will report on activities of the preservation program of the Research Libraries Group (RLG). She will focus on the joint work of RLG and OCLC (Online Computer Library Center) on preservation metadata. Following the presentations by the four panelists, Alexa McCray will provide brief comments and then open the discussion for audience participation.
The Unified Medical Language System (UMLS) is an extensive source of biomedical knowledge developed and maintained by the U.S. National Library of Medicine (NLM). The UMLS began to include biomedical terms in other languages a few years ago. However, providing foreign terms for existing concepts is only the first step for the UMLS to become international. The current limits of the use of the UMLS in French are analyzed (partial translation, unique source of the translated concepts, improper character set, and absence of lexical resources for lexical matching tools). Some suggestions are given for French to be better integrated into the UMLS, especially for adapting the lexical resources to French. Once completed, our present work is expected to give the UMLS the capability to be effectively queried in French.
Diphthamide is a post-translationally modified histidine essential for messenger RNA translation and ribosomal protein synthesis. We present evidence for DPH5 as a novel cause of embryonic lethality and profound neurodevelopmental delays (NDDs).Molecular testing was performed using exome or genome sequencing. A targeted Dph5 knockin mouse (C57BL/6Ncrl-Dph5em1Mbp/Mmucd) was created for a DPH5 p.His260Arg homozygous variant identified in 1 family. Adenosine diphosphate-ribosylation assays in DPH5-knockout human and yeast cells and in silico modeling were performed for the identified DPH5 potential pathogenic variants.DPH5 variants p.His260Arg (homozygous), p.Asn110Ser and p.Arg207Ter (heterozygous), and p.Asn174LysfsTer10 (homozygous) were identified in 3 unrelated families with distinct overlapping craniofacial features, profound NDDs, multisystem abnormalities, and miscarriages. Dph5 p.His260Arg homozygous knockin was embryonically lethal with only 1 subviable mouse exhibiting impaired growth, craniofacial dysmorphology, and multisystem dysfunction recapitulating the human phenotype. Adenosine diphosphate-ribosylation assays showed absent to decreased function in DPH5-knockout human and yeast cells. In silico modeling of the variants showed altered DPH5 structure and disruption of its interaction with eEF2.We provide strong clinical, biochemical, and functional evidence for DPH5 as a novel cause of embryonic lethality or profound NDDs with multisystem involvement and expand diphthamide-deficiency syndromes and ribosomopathies.
There is great value in understanding the patient perspective in rare disease diagnosis and research, and in partnering actively with patients and their families throughout the process. Meaningful and respectful interaction between patients and researchers leads to learning on both sides, and ultimately, to better research outcomes. Researchers can help patients understand how research is conducted and what the latest advances and perceived gaps in research are, and patients, who have direct experience living with their health conditions, can impart to researchers what is most important to them. We describe our engagement with patients in the Undiagnosed Diseases Network (UDN) program, as well as the lessons we have learned to date. In the UDN, patients have been instrumental in bringing meaning to the work of clinicians and researchers, building patient communities, making the network aware of unmet patient needs, advocating for additional research funding, and disseminating UDN research findings. Although patient engagement in the UDN has already had a significant positive impact on our work, we continue to strive to involve patients earlier in the process, in the research design itself, and in addressing power dynamics that may arise between clinicians, researchers, and patients.
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