Automated indexing using NLM's Medical Text Indexer (MTI) compared to human indexing in Medline: a pilot study.

Objective: In 2002, the National Library of Medicine (NLM) introduced semi-automated indexing of Medline using the Medical Text Indexer (MTI). In 2021, NLM announced that it would fully automate its indexing in Medline with an improved MTI by mid-2022. This pilot study examines indexing using a sample of records in Medline from 2000, and how an early, public version of MTI's outputs compares to records created by human indexers. Methods: This pilot study examines twenty Medline records from 2000, a year before the MTI was introduced as a MeSH term recommender. We identified twenty higher- and lower-impact biomedical journals based on Journal Impact Factor (JIF) and examined the indexing of papers by feeding their PubMed records into the Interactive MTI tool. Results: In the sample, we found key differences between automated and human-indexed Medline records: MTI assigned more terms and used them more accurately for citations in the higher JIF group, and MTI tended to rank the Male check tag more highly than the Female check tag and to omit Aged check tags. Sometimes MTI chose more specific terms than human indexers but was inconsistent in applying specificity principles. Conclusion: NLM's transition to fully automated indexing of the biomedical literature could introduce or perpetuate inconsistencies and biases in Medline. Librarians and searchers should assess changes to index terms, and their impact on PubMed's mapping features for a range of topics. Future research should evaluate automated indexing as it pertains to finding clinical information effectively, and in performing systematic searches.

Pindex: Private multi-linked index for encrypted document retrieval.

Cryptographic cloud storage is used to make optimal use of the cloud storage infrastructure to outsource sensitive and mission-critical data. The continuous growth of encrypted data outsourced to cloud storage requires continuous updating. Attacks like file-injection are reported to compromise confidentiality of the user as a consequence of information leakage during update. It is required that dynamic schemes provide forward privacy guarantees. Updates should not leak information to the untrusted server regarding the previously issued queries. Therefore, the challenge is to design an efficient searchable encryption scheme with dynamic updates and forward privacy guarantees. In this paper, a novel private multi-linked dynamic index for encrypted document retrieval namely Pindex is proposed. The multi-linked dynamic index is constructed using probabilistic homomorphic encryption mechanism and secret orthogonal vectors. Full security proofs for correctness and forward privacy in the random oracle model is provided. Experiments on real world Enron dataset demonstrates that our construction is practical and efficient. The security and performance analysis of Pindex shows that the dynamic multi-linked index guarantees forward privacy without significant loss of efficiency.

Guias de prática clínica: orientações para indexação de acordo com a Metodologia LILACS / Clinical practice guides: guidelines for indexing according to the LILACS Methodology

Objetivo: Orientar a análise e leitura técnica dos documentos para identificar Guias de Prática Clínica, seja como tipo de publicação ou descritor de assunto. Público-alvo: Profissionais da informação que atuam na indexação de documentos usando a Metodologia LILACS ou na elaboração de estratégias de busca na LILACS e nas Bibliotecas Virtuais em Saúde (BVS).

A review of pragmatic trials found a high degree of diversity in design and scope, deficiencies in reporting and trial registry data, and poor indexing.

OBJECTIVE: We established a large database of trials to serve as a resource for future methodological and ethical analyses. Here, we use meta-data to describe the broad landscape of pragmatic trials including research areas, identification as pragmatic, quality of trial registry data and enrolment. STUDY DESIGN AND SETTING: Trials were identified by a validated search filter and included if a primary report of a health-related randomized trial published January 2014-April 2019. Data were collated from MEDLINE, Web of Science, ClinicalTrials.gov, and full text. RESULTS: 4337 eligible trials were identified from 13,065 records, of which 1988 were registered in ClinicalTrials.gov. Research areas were diverse, with the most common being general and internal medicine; public, environmental and occupational health; and health care sciences and services. The term "pragmatic" was seldom used in titles or abstracts. Several domains in ClinicalTrials.gov had questionable data quality. We estimated that one-fifth of trials under-accrued by at least 15%. CONCLUSION: There is a need to improve reporting of pragmatic trials and quality of trial registry data. Under accrual remains a challenge in pragmatic RCTs despite calls for more streamlined recruitment approaches. The diversity of pragmatic trials should be reflected in future ethical analyses.

Natural language processing was effective in assisting rapid title and abstract screening when updating systematic reviews.

BACKGROUND AND OBJECTIVE: To examine whether the use of natural language processing (NLP) technology is effective in assisting rapid title and abstract screening when updating a systematic review. STUDY DESIGN: Using the searched literature from a published systematic review, we trained and tested an NLP model that enables rapid title and abstract screening when updating a systematic review. The model was a light gradient boosting machine (LightGBM), an ensemble learning classifier which integrates four pretrained Bidirectional Encoder Representations from Transformers (BERT) models. We divided the searched citations into two sets (ie, training and test sets). The model was trained using the training set and assessed for screening performance using the test set. The searched citations, whose eligibility was determined by two independent reviewers, were treated as the reference standard. RESULTS: The test set included 947 citations; our model included 340 citations, excluded 607 citations, and achieved 96% sensitivity, and 78% specificity. If the classifier assessment in the case study was accepted, reviewers would lose 8 of 180 eligible citations (4%), none of which were ultimately included in the systematic review after full-text consideration, while decreasing the workload by 64.1%. CONCLUSION: NLP technology using the ensemble learning method may effectively assist in rapid literature screening when updating systematic reviews.

Gene-Centric Database Reveals Environmental and Lifestyle Relationships for Potential Risk Modification and Prevention.

The database at Nutrigenetics.net has been under development since 2007 to facilitate the identification and classification of PubMed articles relevant to human genetics. A controlled vocabulary (i.e., standardized terminology) is used to index these records, with links back to PubMed for every article title. This enables the display of indexes (alphabetical subtopic listings) for any given topic, or for any given combination of topics, including for genes and specific genetic variants. Stepwise use of such indexes (first for one topic, then for combinations of topics) can reveal relationships that are otherwise easily overlooked. These relationships include environmental and lifestyle variables with potential relevance to risk modification (both beneficial and detrimental), and to prevention, or at least to the potential delay of symptom onset for health conditions like Alzheimer disease among many others. Thirty-four specific genetic variants have each been mentioned in at least ≥1,000 PubMed titles/abstracts, and these numbers are steadily increasing. The benefits of indexing with standardized terminology are illustrated for genetic variants like MTHFR 677C-T and its various synonyms (e.g., rs1801133 or Ala222Val). Such use of a controlled vocabulary is also helpful for numerous health conditions, and for potential risk modifiers (i.e., potential risk/effect modifiers).

A randomized trial of an editorial intervention to reduce spin in the abstract's conclusion of manuscripts showed no significant effect.

OBJECTIVE: To estimate the effect of an intervention compared to the usual peer-review process on reducing spin in the abstract's conclusion of biomedical study reports. STUDY DESIGN AND SETTING: We conducted a two-arm, parallel-group RCT in a sample of primary research manuscripts submitted to BMJ Open. The authors received short instructions alongside the peer reviewers' comments in the intervention group. We assessed the presence of spin (primary outcome), types of spin, and wording change in the revised abstract's conclusion. Outcome assessors were blinded to the intervention assignment. RESULTS: Of the 184 manuscripts randomized, 108 (54 intervention, 54 control) were selected for revision and could be evaluated for the presence of spin. The proportion of manuscripts with spin was 6% lower (95% CI: 24% lower to 13% higher) in the intervention group (57%, 31/54) than in the control group (63%, 34/54). The wording of the revised abstract's conclusion was changed in 34/54 (63%) manuscripts in the intervention group and 26/54 (48%) in the control group. The four prespecified types of spin involved (i) selective reporting (12 in the intervention group vs. 8 in the control group), (ii) including information not supported by evidence (9 vs. 9), and (iii) interpretation not consistent with the study results (14 vs. 18), and (iv) unjustified recommendations for practice (5 vs. 11). CONCLUSION: These short instructions to authors did not have a statistically significant effect on reducing spin in revised abstract conclusions, and based on the confidence interval, the existence of a large effect can be excluded. Other interventions to reduce spin in reports of original research should be evaluated. STUDY REGISTRATION: osf.io/xnuyt.

Trends in prenatal diagnosis: An analysis of 40 years of Medical Subject Heading (MeSH) terms in publications.

OBJECTIVE: To understand the evolution of the field of prenatal diagnosis over the past four decades. METHOD: We analyzed the publications in the journal Prenatal Diagnosis from its inception in 1980 to 2019 using Medical Subject Headings (MeSH) to examine the major research topics and trends. The results were analyzed by 10-year intervals. RESULTS: Publications on prenatal cytogenetics, congenital anomalies and fetal imaging predominated during the first three decades, with a steady increase in molecular genetics over time. Publications on NIPT did not appear until the most recent decade and are likely under-counted because there was no MeSH term for NIPT until 2020. CONCLUSION: The topics covered in Prenatal Diagnosis articles have evolved considerably over the past four decades and reflect a response to advances in technology and widespread incorporation of prenatal screening and diagnosis into standard obstetric care. The strengths of this analysis are its objective nature, its use of the standard MeSH terms used for coding, and application of a novel cluster analysis to visualize trends. The analysis also pointed out the fact that MeSH terms in this sub-specialty area are often inconsistent due to manually coding based on individual subject matter expertise.

Cómo leer y generar publicaciones científicas: la importancia del título y el resumen de un artículo científico / Scientific communication: the importance of the title and abstract of a scientific paper

The abstract of a scientific research paper must be well written and reviewed. Sometimes is the only section of a paper that is read, therefore must have the problem, research question, objective, hypothesis, method, results and conclusions, with the limitation of the study. Editors through the abstract deduce what a paper is about and its scientific relevance. The title condenses the paper's content in a few words, must capture the reader's attention and includes patients and methods. Both, the research summary and title of the paper are used for references databases. The paper gives some tips to write a good research abstract and title.

El resumen de un artículo científico debe ser prolíjamente redactado y revisado ya que muchas veces es lo único que se lee. Debe ser específico y representativo del texto, describiendo el problema, el objetivo, la hipótesis, cómo se hizo la investigación y que resultados se obtuvieron con sus conclusiones, mostrando las limitaciones del estudio. El título debe llamar la atención del lector y describir los pacientes y el método en forma breve. Es en base al resumen que editores evaluan la validez y relevancia del artículo científico. El título y resumen es lo que se incorpora en las bases de datos bibliográficas. En este artículo se describen los pasos para la redacción de un resumen de un buen artículo científico.

All of gene expression (AOE): An integrated index for public gene expression databases.

Gene expression data have been archived as microarray and RNA-seq datasets in two public databases, Gene Expression Omnibus (GEO) and ArrayExpress (AE). In 2018, the DNA DataBank of Japan started a similar repository called the Genomic Expression Archive (GEA). These databases are useful resources for the functional interpretation of genes, but have been separately maintained and may lack RNA-seq data, while the original sequence data are available in the Sequence Read Archive (SRA). We constructed an index for those gene expression data repositories, called All Of gene Expression (AOE), to integrate publicly available gene expression data. The web interface of AOE can graphically query data in addition to the application programming interface. By collecting gene expression data from RNA-seq in the SRA, AOE also includes data not included in GEO and AE. AOE is accessible as a search tool from the GEA website and is freely available at https://aoe.dbcls.jp/.

Single-reviewer abstract screening missed 13 percent of relevant studies: a crowd-based, randomized controlled trial.

OBJECTIVES: To determine the accuracy of single-reviewer screening in correctly classifying abstracts as relevant or irrelevant for literature reviews. STUDY DESIGN AND SETTING: We conducted a crowd-based, parallel-group randomized controlled trial. Using the Cochrane Crowd platform, we randomly assigned eligible participants to 100 abstracts each of a pharmacological or a public health topic. After completing a training exercise, participants screened abstracts online based on predefined inclusion and exclusion criteria. We calculated sensitivities and specificities of single- and dual-reviewer screening using two published systematic reviews as reference standards. RESULTS: Two hundred and eighty participants made 24,942 screening decisions on 2,000 randomly selected abstracts from the reference standard reviews. On average, each abstract was screened 12 times. Overall, single-reviewer abstract screening missed 13% of relevant studies (sensitivity: 86.6%; 95% confidence interval [CI], 80.6%-91.2%). By comparison, dual-reviewer abstract screening missed 3% of relevant studies (sensitivity: 97.5%; 95% CI, 95.1%-98.8%). The corresponding specificities were 79.2% (95% CI, 77.4%-80.9%) and 68.7% (95% CI, 66.4%-71.0%), respectively. CONCLUSIONS: Single-reviewer abstract screening does not appear to fulfill the high methodological standards that decisionmakers expect from systematic reviews. It may be a viable option for rapid reviews, which deliberately lower methodological standards to provide decision makers with accelerated evidence synthesis products.

Frequency of Alterations in Apheresis-Related Abstracts Prior to Publications as Peer-Reviewed Articles.

High-quality evidence supporting clinical practice is lacking in apheresis. A potential source of evidence is provided by abstracts submitted to the Annual Meetings of the American Association of Blood Banks (AABB) and the American Society for Apheresis (ASFA). However, there is potential for study conclusions to be altered significantly following abstract presentations prior to publications in peer-reviewed journals. Therefore, we evaluated the discordance rate between apheresis-related meeting abstracts and their corresponding published articles. Abstracts accepted to either AABB or ASFA Annual Meetings from 2005 to 2012 and corresponding PubMed-indexed peer-reviewed articles' abstracts published prior to 9/2014 were reviewed for altered methods, results, and conclusions. When present, changes were evaluated for clinical significance. During the 8-year period, 198 out of 1152 abstracts were published as peer-reviewed articles. Of these, 36 (18.2%) presented discordant results, six of which (16.7%) were potentially clinically significant. An alteration in results (58.3%) was the leading reason for discordance. The discordance rate for ASFA abstracts was significantly higher (HR = 4.69, P = 0.0028) than the AABB ones. However, clinically significant alterations occurred more frequently among AABB abstracts (P = 0.025). Approximately 18% of meeting abstracts demonstrated alterations prior to publication in peer-reviewed journals. Given that approximately one in six changes represented clinically significant alterations, potentially affecting clinical practice, we recommend caution when modifying one's clinical practice based on abstract presentations at Annual Meetings. Future studies involving abstracts from both the International Society for Apheresis and the World Apheresis Association should also be performed.

Overviews of reviews incompletely report methods for handling overlapping, discordant, and problematic data.

OBJECTIVES: The aim of the study was to assess the completeness of reporting of methods in overviews. STUDY DESIGN AND SETTING: Assessment of the adequacy of reporting of methods in a random sample of 50 overviews was based on a published framework of methods for conducting overviews. Descriptive summary statistics were presented. RESULTS: We screened 848 randomly selected abstracts to obtain the required 50 overviews. Overviews included a median of 13 (interquartile range 7-32) systematic reviews (SRs), 22% reported working from a protocol, 36% reported using reporting standards (e.g., Preferred Reporting Items for Systematic Reviews and Meta-Analyses), and 34% reported using methodological guidance (e.g., Cochrane Handbook). Methods common to both overviews and SRs of primary studies were reported in majority of overviews (e.g., 56% framed the overview question by Population, Intervention(s), Comparison(s), Outcome(s) [PICO] elements; 44% reported eligibility criteria based on PICO, and 76% reported assessing the risk of bias of SRs), except for methods for summarizing evidence (20%) or statistical synthesis (26%). A minority reported methods for handling unique aspects of overviews (e.g., overlap in the primary studies [30%], discrepant or missing data [14%], and discordant results/conclusions across reviews [20%]). CONCLUSION: Reporting of methods unique to overviews requires improvement. Our findings provide a benchmark of the completeness of reporting and may inform guidance on the conduct and reporting of overviews.

Conference abstracts describing systematic reviews on pain were selectively published, not reliable, and poorly reported.

OBJECTIVE: The objective of the study was to determine the reporting quality of systematic review (SR) abstracts presented at World Congresses on Pain (WCPs) and to quantify agreement in results presented in those abstracts with their corresponding full-length publications. STUDY DESIGN AND SETTING: We screened abstracts of five WCPs held from 2008 to 2016 to find abstracts describing SRs. Two authors searched for corresponding full publications using PubMed and Google Scholar in April 2018. Methods and outcomes extracted from abstracts were compared with their corresponding full publications. The reporting quality of abstracts was evaluated against the PRISMA for Abstracts (PRISMA-A) checklist. RESULTS: We identified 143 conference abstracts describing SRs. Of these, 90 (63%) were published as full-length articles in peer-reviewed journals by April 2018, with a median time from conference presentation to publication of 5 months (interquartile range: -0.25 to 14 months). Among 79 abstract-publication pairs evaluable for discordance, there was some form of discordance in 40% of pairs. Qualitative discordance (different direction of the effect) was found in 13 analyzed pairs (16%). The median adherence by abstracts to each PRISMA-A checklist item was 33% (interquartile range: 29% to 42%). CONCLUSION: Conference abstracts of pain SRs are selectively published, not reliable, and poorly reported.

Assessment of the abstract reporting of systematic reviews of dose-response meta-analysis: a literature survey.

BACKGROUND: There is an increasing number of published systematic reviews (SR) of dose-response meta-analyses (DRMAs) over the past decades. However, the quality of abstract reporting of these SR-DRMAs remains to be understood. We conducted a literature survey to investigate the abstract reporting of SR-DRMAs. METHODS: Medline, Embase, and Wiley online Library were searched for eligible SR-DRMAs. The reporting quality of SR-DRMAs was assessed by the modified PRISMA-for-Abstract checklist (14 items). We summarized the adherence rate of each item and categorized them as well complied (adhered by 80% or above), moderately complied (50 to 79%), and poorly complied (less than 50%). We used total score to reflect the abstract quality and regression analysis was employed to explore the potential influence factors for it. RESULTS: We included 529 SR-DRMAs. Eight of 14 items were moderately (3 items) or poorly complied (5 items) while only 6 were well complied by these SR-DRMAs. Most of the SR-DRMAs failed to describe the methods for risk of bias assessment (30.2, 95% CI: 26.4, 34.4%) and the results of bias assessment (48.8, 95% CI: 44.4, 53.1%). Few SR-DRMAs reported the funding (2.3, 95% CI: 1.2, 3.9%) and registration (0.6, 95% CI: 0.1, 1.6%) information in the abstract. Multivariable regression analysis suggested word number of abstracts [> 250 vs. ≤ 250 (estimated ß = 0.31; 95% CI: 0.02, 0.61; P = 0.039)] was positively associated with the abstract reporting quality. CONCLUSION: The abstract reporting of SR-DRMAs is suboptimal, substantial effort is needed to improve the reporting. More word number may benefit for the abstract reporting. Given that reporting of abstract largely depends on the reporting and conduct of the SR-DRMA, review authors should also focus on the completeness of SR-DRMA itself.

Single screening versus conventional double screening for study selection in systematic reviews: a methodological systematic review.

BACKGROUND: Stringent requirements exist regarding the transparency of the study selection process and the reliability of results. A 2-step selection process is generally recommended; this is conducted by 2 reviewers independently of each other (conventional double-screening). However, the approach is resource intensive, which can be a problem, as systematic reviews generally need to be completed within a defined period with a limited budget. The aim of the following methodological systematic review was to analyse the evidence available on whether single screening is equivalent to double screening in the screening process conducted in systematic reviews. METHODS: We searched Medline, PubMed and the Cochrane Methodology Register (last search 10/2018). We also used supplementary search techniques and sources ("similar articles" function in PubMed, conference abstracts and reference lists). We included all evaluations comparing single with double screening. Data were summarized in a structured, narrative way. RESULTS: The 4 evaluations included investigated a total of 23 single screenings (12 sets for screening involving 9 reviewers). The median proportion of missed studies was 5% (range 0 to 58%). The median proportion of missed studies was 3% for the 6 experienced reviewers (range: 0 to 21%) and 13% for the 3 reviewers with less experience (range: 0 to 58%). The impact of missing studies on the findings of meta-analyses had been reported in 2 evaluations for 7 single screenings including a total of 18,148 references. In 3 of these 7 single screenings - all conducted by the same reviewer (with less experience) - the findings would have changed substantially. The remaining 4 of these 7 screenings were conducted by experienced reviewers and the missing studies had no impact or a negligible on the findings of the meta-analyses. CONCLUSIONS: Single screening of the titles and abstracts of studies retrieved in bibliographic searches is not equivalent to double screening, as substantially more studies are missed. However, in our opinion such an approach could still represent an appropriate methodological shortcut in rapid reviews, as long as it is conducted by an experienced reviewer. Further research on single screening is required, for instance, regarding factors influencing the number of studies missed.