Visualization of automatically combined disease maps and pathway diagrams for rare diseases.

Introduction: Investigation of molecular mechanisms of human disorders, especially rare diseases, require exploration of various knowledge repositories for building precise hypotheses and complex data interpretation. Recently, increasingly more resources offer diagrammatic representation of such mechanisms, including disease-dedicated schematics in pathway databases and disease maps. However, collection of knowledge across them is challenging, especially for research projects with limited manpower. Methods: In this article we present an automated workflow for construction of maps of molecular mechanisms for rare diseases. The workflow requires a standardized definition of a disease using Orphanet or HPO identifiers to collect relevant genes and variants, and to assemble a functional, visual repository of related mechanisms, including data overlays. The diagrams composing the final map are unified to a common systems biology format from CellDesigner SBML, GPML and SBML+layout+render. The constructed resource contains disease-relevant genes and variants as data overlays for immediate visual exploration, including embedded genetic variant browser and protein structure viewer. Results: We demonstrate the functionality of our workflow on two examples of rare diseases: Kawasaki disease and retinitis pigmentosa. Two maps are constructed based on their corresponding identifiers. Moreover, for the retinitis pigmentosa use-case, we include a list of differentially expressed genes to demonstrate how to tailor the workflow using omics datasets. Discussion: In summary, our work allows for an ad-hoc construction of molecular diagrams combined from different sources, preserving their layout and graphical style, but integrating them into a single resource. This allows to reduce time consuming tasks of prototyping of a molecular disease map, enabling visual exploration, hypothesis building, data visualization and further refinement. The code of the workflow is open and accessible at https://gitlab.lcsb.uni.lu/minerva/automap/.

Clinical presentation and outcome across age categories among patients with COVID-19 admitted to a Spanish Emergency Department.

PURPOSE: To determine the differences by age-dependent categories in the clinical profile, presentation, management, and short-term outcomes of patients with laboratory-confirmed COVID-19 admitted to a Spanish Emergency Department (ED). METHODS: Secondary analysis of COVID-19_URG-HCSC registry. We included all consecutive patients with laboratory-confirmed COVID-19 admitted to the ED of the University Hospital Clinico San Carlos (Madrid, Spain). The population was divided into six age groups. Demographic, baseline and acute clinical data, and in-hospital and 30-day outcomes were collected. RESULTS: 1379 confirmed COVID-19 cases (mean age 62 (SD 18) years old; 53.5% male) were included (18.1% < 45 years; 17.8% 45-54 years; 17.9% 55-64 years; 17.2% 65-74 years; 17.0% 75-84 years; and 11.9% ≥ 85 years). A statistically significant association was found between demographic, comorbidity, clinical, radiographic, analytical, and therapeutic variables and short-term results according to age-dependent categories. There were less COVID-specific symptoms and more atypical symptoms among older people. Age was a prognostic factor for hospital admission (aOR = 1.04; 95% CI 1.02-1.05) and in-hospital (aOR = 1.08; 95% CI 1.05-1.10) and 30-day mortality (aOR = 1.07; 95% CI 1.04-1.09), and was associated with not being admitted to intensive care (aOR = 0.95; 95% CI 0.93-0.98). CONCLUSIONS: Older age is associated with less COVID-specific symptoms and more atypical symptoms, and poor short-term outcomes. Age has independent prognostic value and may help in shared decision-making in patients with confirmed COVID-19 infection.

Observational study comparing the accuracy/variability between the ERSPC and the PCPT risk calculators for the prediction of significant prostate cancer in patients with PSA <10 ng/mL.

INTRODUCTION: Risk calculators (RCs) are easy-to-use tools considering available clinical variables that could help to select those patients with risk of prostate cancer (PCa) who should undergo a prostate biopsy. OBJECTIVE: To perform a comparison for the prediction of significant PCa (SigPCa) between the European Randomised Study of Screening for PCa (ERSPC) and the PCa Prevention Trial (PCPT) RCs in patients with prostate-specific antigen (PSA) between 3 and 10 ng/mL through an evaluation of the accuracy/variability between two consecutive PSA values. SETTING: An observational study in a major university hospital in the south of Spain. METHODS AND PARTICIPANTS: An observational study was performed in patients who underwent a prostate biopsy. SigPCa probabilities were calculated with the two PSA measures using ERSPC3/4+digital rectal examination and PCPT v2+free PSA RCs. The prediction of SigPCa was determined by the area under the receiver operating characteristic curve (AUC). Calibration, discrimination and decision curve analysis were studied. The variability between both RCs' agreement was compared using Cohen's kappa coefficient. RESULTS: 510 patients were analysed (87 diagnosed with SigPCa). The median PSA values were 5.3 and 5 ng/mL for PSA1 and PSA2, respectively. Both RCs overestimated the risk in the case of high-risk probabilities. Discriminative ability for SigPCa was similar between models with an AUC=0.73 (0.68-0.79) for ERSPC-RC versus 0.73 (0.67-0.79) for PCPT-RC. ERSPC-RC showed less variability than PCPT-RC, with a constant agreement (k=0.7-0.8) for usual range of clinical decision-making. Remarkably, a higher number of biopsies would be avoided using the ERSPC-RC, but more SigPCa would be missed along all the risk probabilities. CONCLUSIONS: Both RCs performed similar in the prediction of SigPCa. However, ERSPC-RC seems to be more stable for intraindividual PSA variations.

Evolution of international collaborative research efforts to develop non-Cochrane systematic reviews.

This research-on-research study describes efforts to develop non-Cochrane systematic reviews (SRs) by analyzing demographical and time-course collaborations between international institutions using protocols registered in the International Prospective Register of Systematic Reviews (PROSPERO) or published in scientific journals. We have published an a priori protocol to develop this study. Protocols published in scientific journals were searched using the MEDLINE and Embase databases; the query terms "Systematic review" [Title] AND "protocol" [Title] were searched from February 2011 to December 2017. Protocols registered at PROSPERO during the same period were obtained by web scraping all non-Cochrane records with a Python script. After excluding protocols that had a fulfillment or duplication rate of less than 90%, they were classified as published "only in PROSPERO", "only in journals", or in "journals and PROSPERO". Results of data and metadata extraction using text mining processes were curated by two reviewers. These Datasets and R scripts are freely available to facilitate reproducibility. We obtained 20,814 protocols of non-Cochrane SRs. While "unique protocols" by reviewers' institutions from 60 countries were the most frequent, a median of 6 (2-150) institutions from 130 different countries were involved in the preparation of "collaborative protocols". The highest Ranked countries involved in overall protocol production were the UK, the U.S., Australia, Brazil, China, Canada, the Netherlands, Germany, and Italy. Most protocols were registered only in PROSPERO. However, the number of protocols published in scientific journals (924) or in both PROSPERO and journals (807) has increased over the last three years. Syst Rev and BMJ Open published more than half of the total protocols. While the more productive countries were involved in "unique" and "collaborative protocols", less productive countries only participated in "collaborative protocols" that were mainly published in PROSPERO. Our results suggest that, although most countries were involved in solitary production of protocols for non-Cochrane SRs during the study period, it would be useful to develop new strategies to promote international collaborations, especially with less productive countries.

Evaluating characteristics of PROSPERO records as predictors of eventual publication of non-Cochrane systematic reviews: a meta-epidemiological study protocol.

BACKGROUND: Epidemiology and the reporting characteristics of systematic reviews (SRs) and meta-analyses (MAs) are well known. However, no study has analyzed the influence of protocol features on the probability that a study's results will be finally reported, thereby indirectly assessing the reporting bias of International Prospective Register of Systematic Reviews (PROSPERO) registration records. OBJECTIVE: The objective of this study is to explore which factors are associated with a higher probability that results derived from a non-Cochrane PROSPERO registration record for a systematic review will be finally reported as an original article in a scientific journal. METHODS/DESIGN: The PROSPERO repository will be web scraped to automatically and iteratively obtain all completed non-Cochrane registration records stored from February 2011 to December 2017. Downloaded records will be screened, and those with less than 90% fulfilled or are duplicated (i.e., those sharing titles and reviewers) will be excluded. Manual and human-supervised automatic methods will be used for data extraction, depending on the data source (fields of PROSPERO registration records, bibliometric databases, etc.). Records will be classified into published, discontinued, and abandoned review subgroups. All articles derived from published reviews will be obtained through multiple parallel searches using the full protocol "title" and/or "list reviewers" in MEDLINE/PubMed databases and Google Scholar. Reviewer, author, article, and journal metadata will be obtained using different sources. R and Python programming and analysis languages will be used to describe the datasets; perform text mining, machine learning, and deep learning analyses; and visualize the data. We will report the study according to the recommendations for meta-epidemiological studies adapted from the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement for SRs and MAs. DISCUSSION: This meta-epidemiological study will explore, for the first time, characteristics of PROSPERO records that may be associated with the publication of a completed systematic review. The evidence may help to improve review workflow performance in terms of research topic selection, decision-making regarding team selection, planning relationships with funding sources, implementing literature search strategies, and efficient data extraction and analysis. We expect to make our results, datasets, and R and Python code scripts publicly available during the third quarter of 2018.

European Randomized Study of Screening for Prostate Cancer Risk Calculator: External Validation, Variability, and Clinical Significance.

OBJECTIVE: To externally validate the European Randomized Study of Screening for Prostate Cancer (ERSPC) risk calculator (RC) and to evaluate its variability between 2 consecutive prostate-specific antigen (PSA) values. MATERIALS AND METHODS: We prospectively catalogued 1021 consecutive patients before prostate biopsy for suspicion of prostate cancer (PCa). The risk of PCa and significant PCa (Gleason score ≥7) from 749 patients was calculated according to ERSPC-RC (digital rectal examination-based version 3 of 4) for 2 consecutive PSA tests per patient. The calculators' predictions were analyzed using calibration plots and the area under the receiver operating characteristic curve (area under the curve). Cohen kappa coefficient was used to compare the ability and variability. RESULTS: Of 749 patients, PCa was detected in 251 (33.5%) and significant PCa was detected in 133 (17.8%). Calibration plots showed an acceptable parallelism and similar discrimination ability for both PSA levels with an area under the curve of 0.69 for PCa and 0.74 for significant PCa. The ERSPC showed 226 (30.2%) unnecessary biopsies with the loss of 10 significant PCa. The variability of the RC was 16% for PCa and 20% for significant PCa, and a higher variability was associated with a reduced risk of significant PCa. CONCLUSION: We can conclude that the performance of the ERSPC-RC in the present cohort shows a high similitude between the 2 PSA levels; however, the RC variability value is associated with a decreased risk of significant PCa. The use of the ERSPC in our cohort detects a high number of unnecessary biopsies. Thus, the incorporation of ERSPC-RC could help the clinical decision to carry out a prostate biopsy.

Influencia de las condiciones climáticas en el empeoramiento de los síntomas de artritis reumatoide: el posible efecto de la temperatura / Weather conditions may worsen symptoms in rheumatoid arthritis patients: the possible effect of temperature

Objetivo. Los pacientes con artritis reumatoide (AR) se quejan de que las condiciones meteorológicas empeoran sus síntomas. Este estudio trata de ver los efectos a corto plazo de las condiciones climáticas en empeoramiento sintomático en pacientes con AR y determinar posibles fluctuaciones estacionales. Métodos. Se realizó un estudio de casos cruzados en Madrid, España. Los casos diarios de empeoramiento de la AR se obtuvieron de la sala de urgencias de un hospital terciario entre 2004 y 2007. Resultados. 245 pacientes con AR con 306 visitas a urgencias con AR como diagnostico principal se incluyeron en el estudio. Los pacientes de 50 a 65 años tuvieron un 16% más de probabilidades de presentar empeoramiento sintomático de la AR con una menor temperatura media. Conclusiones. Nuestros resultados apoyan la creencia de que el clima influye en el dolor reumático de los pacientes con mediana edad (AU)

Objective: Patients with rheumatoid arthritis (RA) complain that weather conditions aggravate their symptoms. We investigated the short-term effects of weather conditions on worsening of RA and determined possible seasonal fluctuations. Methods: We conducted a case-crossover study in Madrid, Spain. Daily cases of RA flares were collected from the emergency room of a tertiary level hospital between 2004 and 2007. Results: 245 RA patients who visited the emergency room 306 times due to RA related complaints as the main diagnostic reason were included in the study. Patients from 50 to 65 years old were 16% more likely to present a flare with lower mean temperatures. Conclusions: Our results support the belief that weather influences rheumatic pain in middle aged patients (AU)

Weather conditions may worsen symptoms in rheumatoid arthritis patients: the possible effect of temperature.

OBJECTIVE: Patients with rheumatoid arthritis (RA) complain that weather conditions aggravate their symptoms. We investigated the short-term effects of weather conditions on worsening of RA and determined possible seasonal fluctuations. METHODS: We conducted a case-crossover study in Madrid, Spain. Daily cases of RA flares were collected from the emergency room of a tertiary level hospital between 2004 and 2007. RESULTS: 245 RA patients who visited the emergency room 306 times due to RA related complaints as the main diagnostic reason were included in the study. Patients from 50 to 65 years old were 16% more likely to present a flare with lower mean temperatures. CONCLUSIONS: Our results support the belief that weather influences rheumatic pain in middle aged patients.