PubMed Medical Subject Headings Research Articles

Sunscreen Use for Photoprotection in Skin of Color: A Literature Review.

To understand the prevalence and types of publications addressing darker skin types within the existing evidence base for sunscreen use.  Evidence Review: PubMed was searched from 1988, the time point at which the first skin of color (SOC) article was identified, through December 2022 using PubMed's Medical Subject Headings terms and keyword searches in title and abstract, with and without terms for SOC and ethnicity. Identified articles were reviewed for relevance, de-duplicated, and categorized; results are summarized. Of the 5927 articles on sunscreen overall, only 314 (5.3%) articles addressed SOC, with the majority published since 2007 and representing only 4% to 7% of total publications annually except in 2022 when the proportion of SOC articles was 23.5%. Of the articles on SOC, many reported sunscreen knowledge and patient behaviors (29%), but very few reported clinical trials (5%). The 3 conditions most often discussed were melasma, post-inflammatory hyperpigmentation, and dyschromia. South Asian ethnicities (India, Pakistan, Bangladesh) had the highest representation within the literature, followed by Hispanics. Although it was assumed there would be fewer papers discussing the use of sunscreen in darker skin types, the scale of the disparity revealed by this study is stark. The increase in a number of articles in 2022 suggests an increasing focus on SOC, but further discussion of the issues presented here will help the SOC community address gaps in the evidence base and better inform discussions on sunscreen and photoprotection between clinicians and patients.J Drugs Dermatol. 2024;23(7):575-577.  doi:10.36849/JDD.8250.

Epigenetics of conotruncal congenital heart disease: Protocol for a systematic review and meta-analysis.

Conotruncal congenital heart defects (CTD) are a subset of congenital heart diseases (CHD) that involve structural anomalies of the right, left, or both cardiac outflow tracts. CHD is caused by multifactorial inheritance and changes in the genes or chromosomes. Recently, CHD was found to be due to epigenetic alterations, which are a combination of genetic and other environmental factors. Epigenetics is the study of how a gene's function changes as a result of environmental and behavioral influences. These causative factors can indirectly cause CHD by altering the DNA through epigenetic modifications. This is a protocol for a systematic review and meta-analysis that aims to explore whether the strength of association between various epigenetic changes and CTD types varies by race. Furthermore, to determine and compare the changes in gene expression of each mutation. Our protocol follows the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocol (PRISMA-P) guidelines. A comprehensive pre-search has been developed in PubMed and PubMed's Medical Subject Headings (MeSH). The final search will be performed in June 2023 in PubMed, Embase, Scopus, Web of Science, Cochrane Library, CIANHL, and PsycInfo, without restrictions on publication years. The Covidence systematic review software will be used for blinded screening and selection. Conflicts will be resolved by a third, independent reviewer. The risk of bias in selected studies will be assessed using the National Heart, Lung, and Blood Institute (NHLBI) Quality Assessment Tool for Observational Cohort and Cross-Sectional Studies. The data to be extracted will cover basic information on the included studies, study sample size, number of patients with various types of epigenetic changes, number of patients with various CTD types, measures of association and their 95% confidence interval between each epigenetic change and each CTD. The protocol has been registered with the International Prospero Register of Systematic Review (PROSPERO) [CRD42023377597]. To the best of our knowledge, this protocol outlines the first systematic review and meta-analysis of the epigenetics of CTD. There is a growing body of evidence on epigenetics and its indirect involvement in disease by altering the DNA through epigenetic modifications in the genes associated with the causative factors for CHD. We will conduct a comprehensive and systematic search for literature in the above-mentioned seven core biomedical databases. It is very important to identify population-specific risk factors for CHD, which will have significant creative, custom-made, and effective prevention programs for the future generation.

Atrial Fibrillation Patients with Immune Thrombocytopenia: A Review of Management Options and Bleeding Risks

Aim : The objective of this research is to review the bleeding risks in patients with atrial fibrillation (Afib) and immune thrombocytopenia (ITP) and explore various management strategies to formulate an optimal therapeutic approach that improves the prognosis of these patients. Methods: In this study, we devised our search approach by utilizing PubMed's Medical Subject Headings (MeSH) terms and incorporating pertinent keywords extracted from article titles and abstracts. To ensure a comprehensive scope, we integrated terms associated with immune thrombocytopenia purpura, such as “Immune Thrombocytopenia,” and similar expressions. Additionally, terms related to atrial fibrillation, including “atrial fibrillation,” were included to identify articles discussing atrial fibrillation in the context of immune thrombocytopenia. To adapt the initial search strategy for Embase, Web of Science, and Scopus databases, we employed a polyglot translator. All identified studies resulting from the search strategy were imported into EndNote, where duplicate articles were meticulously removed. The remaining studies were then transferred to Rayyan for further duplicate elimination and to initiate the screening process. The study incorporates full-text articles, submitted abstracts, and conference abstracts. Excluded from this analysis were studies falling into the following categories: (1) animal studies, (2) reviews or non-original articles, and (3) non-English articles. Results: A total of 1891 articles were retrieved from four databases, and after careful selection, 14 relevant full-text articles were analyzed. Among these, 12 studies investigated the efficacy of anticoagulants in managing cases of concurrent Afib and ITP as well as their bleeding risks. Comparing bleeding risk between groups was usually done through measuring by CHA 2DS 2 VASc or HAS BLED scoring systems and survival was also compared by using Kaplan-Meier curves A few of them also compared the efficacy and safety of warfarin against Non-Vitamin K Antagonists which has shown that Non-Vitamin K Antagonists have a lower event rate of major bleeding, lower hazard ration of systemic embolism and higher survival rate compared to warfarin The remaining two papers explored the efficacy and safety of surgical interventions, specifically left atrial appendage closure. Many studies reported that anticoagulant therapies were associated with reduced bleeding risk and have shown promising outcomes in managing patients with Afib and ITP. Additionally, percutaneous left atrial appendage closure has been reported to be a potentially safe management option for atrial fibrillation in patients with primary hemostatic disorders, including thrombocytopenia. Conclusion: In essence, this review focused on investigating the bleeding risk associated with atrial fibrillation (Afib) in patients with immune thrombocytopenia (ITP) and examining available management strategies. While the precise pathophysiological mechanisms linking atrial fibrillation and ITP remain incompletely understood, the review emphasized the intricate interplay between thromboembolic risk and bleeding complications in this specific patient group. The findings suggest that certain anticoagulation regimens and also left atrial appendage closure have shown promising safety and effectiveness in Afib patients with thrombocytopenia. Nevertheless, further research with larger sample sizes and diverse populations is needed to enhance our understanding of the Afib-ITP relationship. Such studies will yield more definitive conclusions and valuable insights into optimal anticoagulation approaches and alternative therapies for patients with both Afib and ITP.

Exploring the Role of Wearable Electronic Medical Devices in Improving Cardiovascular Risk Factors and Outcomes Among Adults: A Systematic Review.

There is a developing trend of using wearable electronic devices as health aides, spurred on by telecommunication companies as fitness devices and marketed as such. They have been shown to count steps, pulse, and record arrhythmias, doubling as communication devices and prompting healthcare providers in some instances. We sought to determine if there was a direct correlation between device use and increased physical activity as recommended by the World Health Organization, or if this physical activity increase was only marginal at best. In addition, we sought to investigate if there were additional benefits to using these devices besides increased self-awareness of health. This systematic review used Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Keywords for searching articles centered around cardiovascular disease, wearable electronic devices, and their synonyms. Most of the data were obtained from PubMed, although other contributing databases were used, including ResearchGate, Science.gov, ScienceDirect, and PubMed Medical Subject Headings database. Only full-text articles were used. We identified 62 articles that met our search criteria but narrowed them down to 19 following qualitative assessment. Increased physical activity was found to be the one parameter that stood out by way of benefit from the device. Other findings, such as reduced waist circumference, obesity, glycated hemoglobin, and lipid levels, shared mixed results. At this time, we do not have a definition of what duration of device use is deemed standard for health. We have no consensus on which devices are superior health-wise. Our study, however, indicates that these devices, used with adequate health professional supervision, have a role to play in motivation and increased physical activity, enough to cause impactful gains in cardiovascular health.

Necrotizing Enterocolitis: Clinical Features, Histopathological Characteristics, and Genetic Associations.

Necrotizing enterocolitis (NEC) is an inflammatory bowel necrosis seen in premature infants. Although the etiopathogenesis of NEC is unclear, genetic factors may alter a patient's susceptibility, clinical course, and outcomes. This review draws from existing studies focused on individual genes and others based on microarray-based high-throughput discovery techniques. We have included evidence from our own studies and from an extensive literature search in the databases PubMed, EMBASE, and Scopus. To avoid bias in the identification of studies, keywords were short-listed a priori from anecdotal experience and PubMed's Medical Subject Heading (MeSH) thesaurus.

Hotness prediction of scientific topics based on a bibliographic knowledge graph

As a part of innovation in forecasting, scientific topic hotness prediction plays an essential role in dynamic scientific topic assessment and domain knowledge transformation modeling. To improve the topic hotness prediction performance, we propose an innovative model to estimate the co-evolution of scientific topic and bibliographic entities, which leverages a novel dynamic Bibliographic Knowledge Graph (BKG). Then, one can predict the topic hotness by using various kinds of topological entity information, i.e., TopicRank, PaperRank, AuthorRank, and VenueRank, along with pre-trained node embedding, i.e., node2vec embedding, and different pooling techniques. To validate the proposed method, we constructed a new BKG by using 4.5 million PubMed Central publications plus MeSH (Medical Subject Heading) thesaurus and witnessed the essential prediction improvement with extensive experiment outcomes over 10 years observations.

Health Effects of Naphthalene Exposure: A Systematic Evidence Map and Analysis of Potential Considerations for Dose-Response Evaluation.

Background:Naphthalene is a polycyclic aromatic hydrocarbon that has been associated with health effects, including cancer. As the state of the science on naphthalene toxicity continues to evolve, updated toxicity reference value(s) may be required to support human health risk assessment.Objectives:We present a systematic evidence map of studies that could be used to derive toxicity reference value(s) for naphthalene.Methods:Human and animal health effect studies and physiologically based pharmacokinetic (PBPK) models were identified from a literature search based on populations, exposures, comparators, and outcomes (PECO) criteria. Human and animal studies meeting PECO criteria were refined to a smaller subset considered most informative for deriving chronic reference value(s), which are preferred for assessing risk to the general public. This subset was evaluated for risk of bias and sensitivity, and the suitability of each study for dose–response analysis was qualitatively assessed. Lowest observed adverse effect levels (LOAELs) were extracted and summarized. Other potentially relevant studies (e.g., mechanistic and toxicokinetic studies) were tracked as supplemental information but not evaluated further. Existing reference values for naphthalene are also summarized.Results:We identified 26 epidemiology studies and 16 animal studies that were considered most informative for further analysis. Eleven PBPK models were identified. The available epidemiology studies generally had significant risk of bias and/or sensitivity concerns and were mostly found to have low suitability for dose–response analysis due to the nature of the exposure measurements. The animal studies had fewer risk of bias and sensitivity concerns and were mostly found to be suitable for dose–response analysis.Conclusion:Although both epidemiological and animal studies of naphthalene provide weight of evidence for hazard identification, the available animal studies appear more suitable for reference value derivation. PBPK models and mechanistic and toxicokinetic data can be applied to extrapolate these animal data to humans, considering mode of action and interspecies metabolic differences. https://doi.org/10.1289/EHP7381

Rural health cancer care: A literature review.

e18500 Background: A recent review of the medical literature of rural health cancer care delivery has not been published. We conducted a preliminary review of the last twenty years of rural health cancer care delivery literature utilizing medical subject headings (MeSH) within the PubMed NCBI) database. Methods: Using PubMed MeSH Major Topic terms “rural population” and “cancer” we identified publications published from 2000 to 2020. We searched PubMed for publications that included the major topic MeSH terms “rural population” and “cancer”. We individually reviewed articles, confirmed the focus of the article, and subcategorized the articles. Results: We identified 580 publications which met the search criteria, the majority were focused on the United States (266), followed by China (56), Australia (54), and India (27). Among the publications focusing on the United States, 76 involved Appalachian States. Kentucky (18) and Georgia (10) were the states most frequently represented. Malignancies most commonly represented were: breast cancer (148), uterine/cervical (84), and colorectal cancers (68). The journals which published the most rural health cancer care delivery were The Journal of Rural Health (42), Asian Pacific Journal of Cancer Prevention (20), Cancer (14), Rural and Remote Health (13), Journal of Cancer Education (13), Australian Journal of Rural Health (12). Conclusions: The rural health cancer care literature in the last two decades focuses primarily on the United States, China, Australia, and India. Within the United States, the research focus is Appalachia. The majority of articles focus on breast cancer, uterine/cervical, and colorectal cancers. The journal which published the majority of rural health cancer care articles was the Journal of Rural Health.

Developing Literature Search Strategies and Strings to Identify Fate, Exposure and Physical-Chemical Property References

While the process for developing search strings for physical-chemical properties is relatively straight-forward due to availability of existing data presented in a controlled manner, identifying published fate and human environmental chemical exposure-related studies is difficult. Challenges also exist for identifying health-related studies, but controlled vocabularies for indexing and PubMed Medical Subject Headings (MeSH) help to identify such studies, while relatively fewer developed vocabularies exist for identifying fate and exposure studies. In addition, the scope of ‘exposure’ is broad and comprises several sub-categories. Provision of these search strings will facilitate and standardize the approach for systematic review of scientific evidence needed for transparent chemical assessment. To develop the search strings, a team of topic-specific experts and librarians was assembled and developed keyword lists. To create the physical-chemical string, librarians used the keyword list and a series of iterative exchanges with the expert to draft, and revise strings based on performance. For fate strings, librarians drafted strings utilizing the keyword list and analysis tools such as the Keyword Analysis Tool (KAT) and SWIFT-Review’s fingerprinting feature, and on-topic reference lists to determine performance; exposure strings will be developed in a similar manner. The quality of all test strings will be further evaluated by human manual screening of on- and off-topic search string generated results. This presentation overviews various approaches taken to develop the fate, chemical-physical property and exposure literature search strings, including development and testing of broad verses minimal search strings (where we identify terms that are unambiguous and/or necessary to retrieve the greatest number of on-topic references while minimizing retrieval of off-topic references); discusses the organization of keywords and search strings into main and subcategory headings; and outlines the process for incorporating keyword analysis tools. The recall and precision performance results of the broad versus minimal search strings are also presented.

Role of platelets in neonatal necrotizing enterocolitis.

Necrotizing enterocolitis (NEC) is an inflammatory bowel necrosis of premature infants, and is a leading cause of morbidity and mortality in infants born between 23–28 weeks of gestation. Fifty to 95% of all infants with NEC develop thrombocytopenia (platelet counts <150 × 109/L) within 24–72 hours of receiving this diagnosis. In many patients, thrombocytopenia is severe and is treated with one or more platelet transfusions. However, the underlying mechanism(s) and biological implications of NEC-related thrombocytopenia remain unclear. This review presents current evidence from human and animal studies on the clinical features and mechanisms of platelet depletion in NEC. Anecdotal clinical experience is combined with evidence from laboratory studies and from an extensive literature search in databases PubMed, EMBASE, Scopus, and the electronic archives of abstracts presented at the annual meetings of the Pediatric Academic Societies. To avoid bias in identification of existing studies, key words were short-listed prior to the actual search both from anecdotal experience and from PubMed’s Medical Subject Heading (MeSH) thesaurus.

Erratum to: Large expert-curated database for benchmarking document similarity detection in biomedical literature search.

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency–Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.

Time evolution of the hierarchical networks between PubMed MeSH terms.

Hierarchical organisation is a prevalent feature of many complex networks appearing in nature and society. A relating interesting, yet less studied question is how does a hierarchical network evolve over time? Here we take a data driven approach and examine the time evolution of the network between the Medical Subject Headings (MeSH) provided by the National Center for Biotechnology Information (NCBI, part of the U. S. National Library of Medicine). The network between the MeSH terms is organised into 16 different, yearly updated hierarchies such as “Anatomy”, “Diseases”, “Chemicals and Drugs”, etc. The natural representation of these hierarchies is given by directed acyclic graphs, composed of links pointing from nodes higher in the hierarchy towards nodes in lower levels. Due to the yearly updates, the structure of these networks is subject to constant evolution: new MeSH terms can appear, terms becoming obsolete can be deleted or be merged with other terms, and also already existing parts of the network may be rewired. We examine various statistical properties of the time evolution, with a special focus on the attachment and detachment mechanisms of the links, and find a few general features that are characteristic for all MeSH hierarchies. According to the results, the hierarchies investigated display an interesting interplay between non-uniform preference with respect to multiple different topological and hierarchical properties.

Large expert-curated database for benchmarking document similarity detection in biomedical literature search.

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency–Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.

Using Informatics Tools to Characterize Precision Medicine Treatments for Diffuse Large B-Cell Lymphoma (DLBCL)

▪Diffuse large B-cell lymphoma (DLBCL) is genetically and clinically heterogeneous. Despite immunohistochemical and genomic subtyping, standard firstline DLBCL treatment remains rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP). As genetic profiling becomes more accessible and pervasive, studies identifying specific drug-gene interactions in DLBCL are needed to develop future patient-specific DLBCL treatment strategies that improve the delivery of effective and cost-effective, patient-centered care. Methods: We performed a systematic literature review using PubMed Medical Subject Heading and text word terms for DLBCL/genetics and exome sequencing and recorded DLBCL mutations, associated mutation frequencies, pathways, and implications for overall survival (OS) with a focus on recent publications from Reddy et al 2017, Chapuy et al 2018, and Schmitz et al 2018 and related articles. Data for mutation frequencies and OS were extracted from Reddy et al (2017; https://dlbcl.davelab.org/). Mutations were categorized as either favorable or unfavorable. Favorable mutations were associated with 3-year OS ≥ OS for patients equivalent or better than IPI score ≤1 in this dataset (≥90.1%), whereas unfavorable mutations were associated with 3-year OS ≤ OS for patients with an IPI score ≥2 from this dataset (≤64.0%). Potential mutation-specific treatments were identified from the initial literature review, using the Drug-Gene Interaction database (DGIdb, http://www.dgidb.org/, Cotto et al, 2017) and the Open Targets Platform (OTP, https://www.targetvalidation.org/, Koscielny et al, 2017). DLBCL therapeutic groups were defined for mutations/mutation groups that affected ≥5% of DLBCL patients and were associated with targeted therapies based on DGIdb and OTP. Specific drug-gene interactions were characterized using a series of PubMed searches. Results: The analysis identified 32 articles with 55 total therapeutic clusters. 3 mutations were associated with favorable outcomes with an expected 3-year OS of 90.1% (95% CI: 81.1%-95.0%], and 7 mutations were associated with unfavorable outcomes with an expected 3-year OS of 64.0% (95% CI: 56.3%-70.7%) (Figure). The intersection of mutations associated with unfavorable outcomes and mutations associated with targeted therapies yielded 16 therapeutic clusters and revealed a predicted population of 17.6% of DLBCL with poor risk disease and potentially targetable mutations (Table). Drug-gene interaction characterizations identified 267 pertinent studies that included: in vitro studies, mouse models, or clinical trials of the interactions' roles in any cancer. Of these, 7 studies (1 clinical trial, 6 in vitro studies, and 1 mouse model) directly investigated DLBCL specific effects for fostamatinib, ibrutinib, and crizotinib. Conclusions: Linking systematic review with informatics tools identified DLBCL populations, DLBCL specific gene-drug interactions, and potential therapies for trials for patients who relapse and frontline combinations with R-CHOP that can be used in precision medicine strategies for improving outcomes in this disease. DisclosuresFlowers:Genentech/Roche (unpaid): Consultancy; Pharmacyclics/ Janssen: Consultancy; Gilead: Research Funding; Millennium/Takeda: Research Funding; TG Therapeutics: Research Funding; Janssen Pharmaceutical: Research Funding; Karyopharm: Consultancy; Denovo Biopharma: Consultancy; Abbvie: Consultancy; Genentech/Roche: Research Funding; Gilead: Consultancy; Bayer: Consultancy; Celgene: Research Funding; Abbvie: Research Funding; Acerta: Consultancy; Beigene: Consultancy; Pharmacyclics: Research Funding.

Bibliometric Analysis of Traditional Chinese Medicine Scientific Production between 1982 and 2016 Indexed in PubMed.

Background: Traditional Chinese medicine (TCM) may be understood as a system of sensations and findings designed to establish the functional vegetative state of the body. This state may be treated by several therapeutic methods such as acupuncture, Chinese pharmacotherapy, dietetics, Tuina, and Qigong. Nowadays, as a result of several evidence-based reported beneficial effects over specific pathological conditions, there is an increasing tendency to integrate some of these practices in Western medicine. The main goal of this study was to perform a bibliometric analysis of TCM scientific production between 1982 and 2016 indexed in PubMed, by analyzing several parameters including time and location distribution, publication quality, experimental design, and treatment methods. Methods: The methodology was based on the quantitative inventory of published scientific research indexed in PubMed medical subject headings (MeSH), sorted within the broad term “Traditional Chinese Medicine” and integrating the following criteria as limit filters: “Species: Humans”, “Article Type: Clinical Trial”. In addition, the articles’ triage was ruled by temporal limitations set between 1945 and 2016. Results: The overall analysis of data allowed observation of an average annual growth of approximately 33%, with a productive peak of 122 articles in 2007. The scientific production was distributed in 27 countries, led by China (76.1%), followed by the United States of America (3.0%) and South Korea (2.1%). A significant amount of references were published in Chinese journals: more than 50%; however, these journals had a low impact factor. The most cited treatments in the keywords section of the articles were phytotherapy (55%) and acupuncture (40%). Conclusion: The increasing demand for TCM seems to be due to factors such as lower side effects and greater efficacy in some patients not responding well to conventional therapy. As a result, a considerable amount of TCM science-based literature has been produced, supporting the rational integration of these practices in Western healthcare systems and research. Our results show that the quality of TCM research and inherent publications have been increasing over the last decades, with a higher incidence of studies published in well-ranked journals.

The Saliva Exposome for Monitoring of Individuals' Health Trajectories.

Background:There is increasing evidence that environmental, rather than genetic, factors are the major causes of most chronic diseases. By measuring entire classes of chemicals in archived biospecimens, exposome-wide association studies (EWAS) are being conducted to investigate associations between a myriad of exposures received during life and chronic diseases.Objectives:Because the intraindividual variability in biomarker levels, arising from changes in environmental exposures from conception onwards, leads to attenuation of exposure–disease associations, we posit that saliva can be collected repeatedly in longitudinal studies to reduce exposure–measurement errors in EWAS.Methods:From the literature and an open-source saliva–metabolome database, we obtained concentrations of 1,233 chemicals that had been detected in saliva. We connected salivary metabolites with human metabolic pathways and PubMed Medical Subject Heading (MeSH) terms, and performed pathway enrichment and pathway topology analyses.Results:One hundred ninety-six salivary metabolites were mapped into 49 metabolic pathways and connected with human metabolic diseases, central nervous system diseases, and neoplasms. We found that the saliva exposome represents at least 14 metabolic pathways, including amino acid metabolism, TCA cycle, gluconeogenesis, glutathione metabolism, pantothenate and CoA biosynthesis, and butanoate metabolism.Conclusions:Saliva contains molecular information worthy of interrogation via EWAS. The simplicity of specimen collection suggests that saliva offers a practical alternative to blood for measurements that can be used to characterize individual exposomes. https://doi.org/10.1289/EHP1011

Emergency Preparedness and Disaster Response: There's An App for That.

Smartphone applications (or apps) are becoming increasingly popular with emergency responders and health care providers, as well as the public as a whole. There are thousands of medical apps available for Smartphones and tablet computers, with more added each day. These include apps to view textbooks, guidelines, medication databases, medical calculators, and radiology images. Hypothesis/Problem With an ever expanding catalog of apps that relate to disaster medicine, it is hard for both the lay public and responders to know where to turn for effective Smartphone apps. A systematic review of these apps was conducted. A search of the Apple iTunes store (Version 12; Apple Inc.; Cupertino, California USA) was performed using the following terms obtained from the PubMed Medical Subject Headings Database: Emergency Preparedness, Emergency Responders, Disaster, Disaster Planning, Disaster Medicine, Bioterrorism, Chemical Terrorism, Hazardous Materials (HazMat), and the Federal Emergency Management Agency (FEMA). After excluding any unrelated apps, a working list of apps was formed and categorized based on topics. Apps were grouped based on applicability to responders, the lay public, or regional preparedness, and were then ranked based on iTunes user reviews, value, relevance to audience, and user interface. This search revealed 683 applications and was narrowed to 219 based on relevance to the field. After grouping the apps as described above, and subsequently ranking them, the highest quality apps were determined from each group. The Community Emergency Response Teams and FEMA had the best apps for National Disaster Medical System responders. The Centers for Disease Control and Prevention (CDC) had high-quality apps for emergency responders in a variety of fields. The National Library of Medicine's Wireless Information System for Emergency Responders (WISER) app was an excellent app for HazMat responders. The American Red Cross had the most useful apps for natural disasters. Numerous valuable apps for public use, including alert apps, educational apps, and a well-made regional app, were also identified. Smartphone applications are fast becoming essential to emergency responders and the lay public. Many high-quality apps existing in various price ranges and serving different populations were identified. This field is changing rapidly and it deserves continued analysis as more apps are developed.

SciVerse Science Direct

ScienceDirect is a full-text database offering journal articles and book chapters from more than 2,500 peer-reviewed journals and 11,000 books. Older materials (back files) are available as archives for an additional charge. Its intended audience is librarians and researchers in the health sciences, life sciences, physical sciences, and engineering. It also has a nice complement of materials in the social sciences and business subject areas. It is PC compatible with Internet Explorer 7, 8, and 9, as well as Mozilla Firefox and Google Chrome. Mac compatible browsers are Google Chrome, Safari, and Firefox. This database uses a federated search mechanism, which is a single search portal to search and retrieve results from several electronic resources at once. Meta searching or broadcast searching are other terms commonly used for this search mechanism. ScienceDirect uses natural language searching similar to a Google search. It does not have a controlled vocabulary like PubMed's Medical Subject Headings (MeSH). The advanced search feature allows searching by author, title, volume, issue, and page, similar to PubMed's Single Citation Matcher. Natural language searching using Boolean operators can be filtered by subject and dates of publication. Searching can be limited to journals, books, images, and reference works. Tips for wildcard, truncation, and proximity searching are clearly described. Tutorials are available in English, Spanish, French, German, Portuguese, and Russian. Use of the personal login account activates the full capabilities for this database. Really simple syndication (RSS) feeds and alerts are set up and accessed through the personalized account feature. The account holder can access specialized free and for-fee applications (e.g., cancer, podcast, etc.). Quick links to a user's favorite books or journals are enabled. Through the “Manage Your Settings” page, RefWorks users are able to automatically log in and export citations to RefWorks. Past searches are accessed through the personalized account. Mobile applications for iPhone, iPad, and Android devices are set up by registering through the personal account. The free mobile app is available through the iTunes store. The display is clean and easy to read. Keyword, author, and journal searching are supported in the mobile application as well as Boolean, wildcard, and truncated searching. Retrieved articles show the abstract and outline. Full text and figures display if the institution has a subscription. The registration can be used on up to three devices such as an iPhone, iPad, and iPod. Articles saved on a mobile device cannot be accessed from a user's ScienceDirect account. To get access, articles must be emailed. Retrieved articles provide links to the article's abstract, references, related articles, and supplementary material. A link to a portable document format (PDF) file is provided if the organization subscribes to the journal. Citations export to Reference Manager, ProCite, EndNote, RefWorks, and BibTex formats. Retrieved articles can be printed, emailed, or shared using Facebook, Twitter, and CiteULike social media sites. Search history is limited to 500 items. If that number is exceeded, the oldest citations are deleted. This database is owned by Elsevier, and much of its content is limited to Elsevier-published journals and books. The database is focused on articles and materials published 1995 to the present. The publisher is aggressive in adding more pre-1995 content to its back files. Athens login is no longer available with the December 2012 update.

Google Scholar Versus PubMed in Locating Primary Literature to Answer Drug-Related Questions

Google Scholar linked more visitors to biomedical journal Web sites than did PubMed after the database's initial release; however, its usefulness in locating primary literature articles is unknown. To assess in both databases the availability of primary literature target articles; total number of citations; availability of free, full-text journal articles; and number of primary literature target articles retrieved by year within the first 100 citations of the search results. Drug information question reviews published in The Annals of Pharmacotherapy Drug Information Rounds column served as targets to determine the retrieval ability of Google Scholar and PubMed searches. Reviews printed in this column from January 2006 to June 2007 were eligible for study inclusion. Articles were chosen if at least 2 key words of the printed article were included in the PubMed Medical Subject Heading (MeSH) database, and these terms were searched in both databases. Twenty-two of 33 (67%) eligible Drug Information Rounds articles met the inclusion criteria. The median number of primary literature articles used in each of these articles was 6.5 (IQR 4.8, 8.3; mean +/- SD 8 +/- 5.4). No significant differences were found for the mean number of target primary literature articles located within the first 100 citations in Google Scholar and PubMed searches (5.1 +/- 3.9 vs 5.3 +/- 3.3; p = 0.868). Google Scholar searches located more total results than PubMed (2211.6 +/- 3999.5 vs 44.2 +/- 47.4; p = 0.019). The availability of free, full-text journal articles per Drug Information Rounds article was similar between the databases (1.8 +/- 1.7 vs 2.3 +/- 1.7; p = 0.325). More primary literature articles published prior to 2000 were located with Google Scholar searches compared with PubMed (62.8% vs 34.9%; p = 0.017); however, no statistically significant differences between the databases were observed for articles published after 2000 (66.4 vs 77.1; p = 0.074). No significant differences were identified in the number of target primary literature articles located between databases. PubMed searches yielded fewer total citations than Google Scholar results; however, PubMed appears to be more specific than Google Scholar for locating relevant primary literature articles.

An automatic method to generate domain-specific investigator networks using PubMed abstracts

BackgroundCollaboration among investigators has become critical to scientific research. This includes ad hoc collaboration established through personal contacts as well as formal consortia established by funding agencies. Continued growth in online resources for scientific research and communication has promoted the development of highly networked research communities. Extending these networks globally requires identifying additional investigators in a given domain, profiling their research interests, and collecting current contact information. We present a novel strategy for building investigator networks dynamically and producing detailed investigator profiles using data available in PubMed abstracts.ResultsWe developed a novel strategy to obtain detailed investigator information by automatically parsing the affiliation string in PubMed records. We illustrated the results by using a published literature database in human genome epidemiology (HuGE Pub Lit) as a test case. Our parsing strategy extracted country information from 92.1% of the affiliation strings in a random sample of PubMed records and in 97.0% of HuGE records, with accuracies of 94.0% and 91.0%, respectively. Institution information was parsed from 91.3% of the general PubMed records (accuracy 86.8%) and from 94.2% of HuGE PubMed records (accuracy 87.0). We demonstrated the application of our approach to dynamic creation of investigator networks by creating a prototype information system containing a large database of PubMed abstracts relevant to human genome epidemiology (HuGE Pub Lit), indexed using PubMed medical subject headings converted to Unified Medical Language System concepts. Our method was able to identify 70–90% of the investigators/collaborators in three different human genetics fields; it also successfully identified 9 of 10 genetics investigators within the PREBIC network, an existing preterm birth research network.ConclusionWe successfully created a web-based prototype capable of creating domain-specific investigator networks based on an application that accurately generates detailed investigator profiles from PubMed abstracts combined with robust standard vocabularies. This approach could be used for other biomedical fields to efficiently establish domain-specific investigator networks.