Quantifying and contextualizing the impact of bioRxiv preprints through automated social media audience segmentation.

Engagement with scientific manuscripts is frequently facilitated by Twitter and other social media platforms. As such, the demographics of a paper's social media audience provide a wealth of information about how scholarly research is transmitted, consumed, and interpreted by online communities. By paying attention to public perceptions of their publications, scientists can learn whether their research is stimulating positive scholarly and public thought. They can also become aware of potentially negative patterns of interest from groups that misinterpret their work in harmful ways, either willfully or unintentionally, and devise strategies for altering their messaging to mitigate these impacts. In this study, we collected 331,696 Twitter posts referencing 1,800 highly tweeted bioRxiv preprints and leveraged topic modeling to infer the characteristics of various communities engaging with each preprint on Twitter. We agnostically learned the characteristics of these audience sectors from keywords each user's followers provide in their Twitter biographies. We estimate that 96% of the preprints analyzed are dominated by academic audiences on Twitter, suggesting that social media attention does not always correspond to greater public exposure. We further demonstrate how our audience segmentation method can quantify the level of interest from nonspecialist audience sectors such as mental health advocates, dog lovers, video game developers, vegans, bitcoin investors, conspiracy theorists, journalists, religious groups, and political constituencies. Surprisingly, we also found that 10% of the preprints analyzed have sizable (>5%) audience sectors that are associated with right-wing white nationalist communities. Although none of these preprints appear to intentionally espouse any right-wing extremist messages, cases exist in which extremist appropriation comprises more than 50% of the tweets referencing a given preprint. These results present unique opportunities for improving and contextualizing the public discourse surrounding scientific research.

The use of an electronic health record system reduces errors in the National Hip Fracture Database.

AIM: to compare the validity of data submitted from a UK level 1 trauma centre to the National Hip Fracture Database (NHFD) before and after the introduction of an electronic health record system (EHRS). PATIENTS AND METHODS: a total of 3224 records were reviewed from July 2009 to July 2017. 2,133 were submitted between July 2009 and October 2014 and 1,091 between October 2014 and July 2017, representing data submitted before and after the introduction of the EHRS, respectively. Data submitted to the NHFD were scrutinised against locally held data. RESULTS: use of an EHRS was associated with significant reductions in NHFD errors. The operation coding error rate fell significantly from 23.2% (494/2133) to 7.6% (83/1091); P < 0.001. Prior to EHRS introduction, of the 109 deaths recorded in the NHFD, 64 (59%) were incorrect. In the EHRS dataset, all the 112 recorded deaths were correct (P < 0.001). There was no significant difference in the error rate for fracture coding. In the EHRS dataset, after controlling for sample month, entries utilising an operation note template with mandatory fields relevant to NHFD data were more likely to be error free than those not using the template (OR 2.69; 95% CI 1.92-3.78). CONCLUSION: this study highlights a potential benefit of EHR systems, which offer automated data collection for auditing purposes. However, errors in data submitted to the NHFD remain, particularly in cases where an NHFD-specific operation note template is not used. Clinician engagement with new technologies is vital to avoid human error and ensure database integrity.

The Italian autism network (ITAN): a resource for molecular genetics and biomarker investigations.

BACKGROUND: A substantial genetic component accounts for Autism Spectrum Disorders (ASD) aetiology, with some rare and common genetic risk factors recently identified. Large collections of DNAs from thoroughly characterized ASD families are an essential step to confirm genetic risk factors, identify new variants and investigate genotype-phenotype correlations. The Italian Autism Network aimed at constituting a clinical database and a biorepository of samples derived from ASD subjects and first-degree relatives extensively and consistently characterized by child psychiatry centers in Italy. METHODS: The study was approved by the ethical committee of the University of Verona, the coordinating site, and by the local ethical committees of each recruiting site. Certified staff was specifically trained at each site for the overall study conduct, for clinical protocol administration and handling of biological material. A centralized database was developed to collect clinical assessment and medical records from each recruiting site. Children were eligible for recruitment based on the following inclusion criteria: age 4-18 years, at least one parent or legal guardian giving voluntary written consent, meeting DSM-IV criteria for Autistic Disorder or Asperger's Disorder or Pervasive Developmental Disorder NOS. Affected individuals were assessed by full psychiatric, neurological and physical examination, evaluation with ADI-R and ADOS scales, cognitive assessment with Wechsler Intelligence Scale for Children or Preschool and Primary, Leiter International Performance Scale or Griffiths Mental Developmental Scale. Additional evaluations included language assessment, the Krug Asperger's Disorder Index, and instrumental examination such as EEG and structural MRI. DNA, RNA and plasma were collected from eligible individuals and relatives. A central laboratory was established to host the biorepository, perform DNA and RNA extraction and lymphocytes immortalisation. DISCUSSION: The study has led to an extensive collection of biological samples associated with standardised clinical assessments from a network of expert clinicians and psychologists. Eighteen sites have received ADI/ADOS training, thirteen of which have been actively recruiting. The clinical database currently includes information on 812 individuals from 249 families, and the biorepository has samples for 98% of the subjects. This effort has generated a highly valuable resource for conducting clinical and genetic research of ASD, amenable to further expansion.

MINDMAP: establishing an integrated database infrastructure for research in ageing, mental well-being, and the urban environment.

BACKGROUND: Urbanization and ageing have important implications for public mental health and well-being. Cities pose major challenges for older citizens, but also offer opportunities to develop, test, and implement policies, services, infrastructure, and interventions that promote mental well-being. The MINDMAP project aims to identify the opportunities and challenges posed by urban environmental characteristics for the promotion and management of mental well-being and cognitive function of older individuals. METHODS: MINDMAP aims to achieve its research objectives by bringing together longitudinal studies from 11 countries covering over 35 cities linked to databases of area-level environmental exposures and social and urban policy indicators. The infrastructure supporting integration of this data will allow multiple MINDMAP investigators to safely and remotely co-analyse individual-level and area-level data. Individual-level data is derived from baseline and follow-up measurements of ten participating cohort studies and provides information on mental well-being outcomes, sociodemographic variables, health behaviour characteristics, social factors, measures of frailty, physical function indicators, and chronic conditions, as well as blood derived clinical biochemistry-based biomarkers and genetic biomarkers. Area-level information on physical environment characteristics (e.g. green spaces, transportation), socioeconomic and sociodemographic characteristics (e.g. neighbourhood income, residential segregation, residential density), and social environment characteristics (e.g. social cohesion, criminality) and national and urban social policies is derived from publically available sources such as geoportals and administrative databases. The linkage, harmonization, and analysis of data from different sources are being carried out using piloted tools to optimize the validity of the research results and transparency of the methodology. DISCUSSION: MINDMAP is a novel research collaboration that is combining population-based cohort data with publicly available datasets not typically used for ageing and mental well-being research. Integration of various data sources and observational units into a single platform will help to explain the differences in ageing-related mental and cognitive disorders both within as well as between cities in Europe, the US, Canada, and Russia and to assess the causal pathways and interactions between the urban environment and the individual determinants of mental well-being and cognitive ageing in older adults.

Advanced Robotic Therapy Integrated Centers (ARTIC): an international collaboration facilitating the application of rehabilitation technologies.

BACKGROUND: The application of rehabilitation robots has grown during the last decade. While meta-analyses have shown beneficial effects of robotic interventions for some patient groups, the evidence is less in others. We established the Advanced Robotic Therapy Integrated Centers (ARTIC) network with the goal of advancing the science and clinical practice of rehabilitation robotics. The investigators hope to exploit variations in practice to learn about current clinical application and outcomes. The aim of this paper is to introduce the ARTIC network to the clinical and research community, present the initial data set and its characteristics and compare the outcome data collected so far with data from prior studies. METHODS: ARTIC is a pragmatic observational study of clinical care. The database includes patients with various neurological and gait deficits who used the driven gait orthosis Lokomat® as part of their treatment. Patient characteristics, diagnosis-specific information, and indicators of impairment severity are collected. Core clinical assessments include the 10-Meter Walk Test and the Goal Attainment Scaling. Data from each Lokomat® training session are automatically collected. RESULTS: At time of analysis, the database contained data collected from 595 patients (cerebral palsy: n = 208; stroke: n = 129; spinal cord injury: n = 93; traumatic brain injury: n = 39; and various other diagnoses: n = 126). At onset, average walking speeds were slow. The training intensity increased from the first to the final therapy session and most patients achieved their goals. CONCLUSIONS: The characteristics of the patients matched epidemiological data for the target populations. When patient characteristics differed from epidemiological data, this was mainly due to the selection criteria used to assess eligibility for Lokomat® training. While patients included in randomized controlled interventional trials have to fulfill many inclusion and exclusion criteria, the only selection criteria applying to patients in the ARTIC database are those required for use of the Lokomat®. We suggest that the ARTIC network offers an opportunity to investigate the clinical application and effectiveness of rehabilitation technologies for various diagnoses. Due to the standardization of assessments and the use of a common technology, this network could serve as a basis for researchers interested in specific interventional studies expanding beyond the Lokomat®.

Imbalanced target prediction with pattern discovery on clinical data repositories.

BACKGROUND: Clinical data repositories (CDR) have great potential to improve outcome prediction and risk modeling. However, most clinical studies require careful study design, dedicated data collection efforts, and sophisticated modeling techniques before a hypothesis can be tested. We aim to bridge this gap, so that clinical domain users can perform first-hand prediction on existing repository data without complicated handling, and obtain insightful patterns of imbalanced targets for a formal study before it is conducted. We specifically target for interpretability for domain users where the model can be conveniently explained and applied in clinical practice. METHODS: We propose an interpretable pattern model which is noise (missing) tolerant for practice data. To address the challenge of imbalanced targets of interest in clinical research, e.g., deaths less than a few percent, the geometric mean of sensitivity and specificity (G-mean) optimization criterion is employed, with which a simple but effective heuristic algorithm is developed. RESULTS: We compared pattern discovery to clinically interpretable methods on two retrospective clinical datasets. They contain 14.9% deaths in 1 year in the thoracic dataset and 9.1% deaths in the cardiac dataset, respectively. In spite of the imbalance challenge shown on other methods, pattern discovery consistently shows competitive cross-validated prediction performance. Compared to logistic regression, Naïve Bayes, and decision tree, pattern discovery achieves statistically significant (p-values < 0.01, Wilcoxon signed rank test) favorable averaged testing G-means and F1-scores (harmonic mean of precision and sensitivity). Without requiring sophisticated technical processing of data and tweaking, the prediction performance of pattern discovery is consistently comparable to the best achievable performance. CONCLUSIONS: Pattern discovery has demonstrated to be robust and valuable for target prediction on existing clinical data repositories with imbalance and noise. The prediction results and interpretable patterns can provide insights in an agile and inexpensive way for the potential formal studies.

Secondary Use of Clinical Data to Enable Data-Driven Translational Science with Trustworthy Access Management.

University of Missouri (MU) Health Care produces a large amount of digitized clinical data that can be used in clinical and translational research for cohort identification, retrospective data analysis, feasibility study, and hypothesis generation. In this article, the implementation of an integrated clinical research data repository is discussed. We developed trustworthy access-management protocol for providing access to both clinically relevant data and protected health information. As of September 2014, the database contains approximately 400,000 patients and 82 million observations; and is growing daily. The system will facilitate the secondary use of electronic health record (EHR) data at MU to promote data-driven clinical and translational research, in turn enabling better healthcare through research.

CORE-Hom: a powerful and exhaustive database of clinical trials in homeopathy.

The CORE-Hom database was created to answer the need for a reliable and publicly available source of information in the field of clinical research in homeopathy. As of May 2014 it held 1048 entries of clinical trials, observational studies and surveys in the field of homeopathy, including second publications and re-analyses. 352 of the trials referenced in the database were published in peer reviewed journals, 198 of which were randomised controlled trials. The most often used remedies were Arnica montana (n = 103) and Traumeel(®) (n = 40). The most studied medical conditions were respiratory tract infections (n = 126) and traumatic injuries (n = 110). The aim of this article is to introduce the database to the public, describing and explaining the interface, features and content of the CORE-Hom database.

[Development and use of an APHAB database]. / Entwicklung und Anwendung einer APHAB-Datenbank.

A specific quality assurance questionnaire concerned with the provision of hearing aids was introduced that assesses elements of patient satisfaction within Germany's statutory healthcare system. A questionnaire-based assessment is now relevant for all physicians involved in the care of statutorily insured patients in Germany. The APHAB (Abbreviated Profile of Hearing Aid Benefit) questionnaire is the most widely used. The APHAB assesses several different situations: the normal hearing situation, hearing in noise, comprehension of speech in situations of echo or reverberation and hearing in loud situations. The APHAB questionnaire-based patient evaluation of the benefit of hearing aids represents the third pillar of audiological diagnostics, alongside classical pure-tone and speech audiometry. The objective of the APHAB database is to allow evaluation of individual patient data on the basis of a larger volume of data.

Why share data? Lessons learned from the fMRIDC.

Neuroimaging and the discipline of cognitive neuroscience have grown together in lock-step with each pushing the other toward an improved ability to explore and examine brain function and form. However successful neuroimaging and the examination of cognitive processes may seem today, the culture of data sharing in these fields remains underdeveloped. In this article, we discuss our own experience in the development of the fMRI Data Center (fMRIDC) - a large-scale effort to gather, curate, and openly share the complete data sets from published research articles of brain activation studies using fMRI. We outline the fMRIDC effort's beginnings, how it operated, note some of the sociological reactions we received, and provide several examples of prominent new studies performed using data drawn from the archive. Finally, we provide comment on what considerations are needed for successful neuroimaging databasing and data sharing as existing and emerging efforts take the next steps in archiving and disseminating the field's valuable and irreplaceable data.

Studies using English administrative data (Hospital Episode Statistics) to assess health-care outcomes--systematic review and recommendations for reporting.

BACKGROUND: Studies using English administrative data from the Hospital Episode Statistics (HES) are increasingly used for the assessment of health-care quality. This study aims to catalogue the published body of studies using HES data to assess health-care outcomes, to assess their methodological qualities and to determine if reporting recommendations can be formulated. METHODS: Systematic searches of the EMBASE, Medline and Cochrane databases were performed using defined search terms. Included studies were those that described the use of HES data extracts to assess health-care outcomes. RESULTS: A total of 148 studies were included. The majority of published studies were on surgical specialties (60.8%), and the most common analytic theme was of inequalities and variations in treatment or outcome (27%). The volume of published studies has increased with time (r = 0.82, P < 0.0001), as has the length of study period (r = 0.76, P < 0.001) and the number of outcomes assessed per study (r = 0.72, P = 0.0023). Age (80%) and gender (57.4%) were the most commonly used factors in risk adjustment, and regression modelling was used most commonly (65.2%) to adjust for confounders. Generic methodologic data were better reported than those specific to HES data extraction. For the majority of parameters, there were no improvements with time. CONCLUSIONS: Studies published using HES data to report health-care outcomes have increased in volume, scope and complexity with time. However, persisting deficiencies related to both generic and context-specific reporting have been identified. Recommendations have been made to improve these aspects as it is likely that the role of these studies in assessing health care, benchmarking practice and planning service delivery will continue to increase.

Using photos to develop text messages to promote walking.

PURPOSE: Sending text messages (TMs) is a promising global intervention to help adults increase their engagement in walking as a form of physical activity (PA). But, little is known about how effective and acceptable TMs are developed. DESIGN: Our study was designed to (a) determine the acceptability, among low-income adults, of receiving TMs to increase their walking and (b) develop, using photos to prompt discussion, a participant-generated database of TMs to promote walking. METHODS: In 2011, three focus groups (low-income, sedentary adults) met at community clinics (one focus group at each of three clinics). To promote dialogue to help develop TMs, we created a discussion guide and a set of 40 photos depicting barriers to increasing PA or showing people walking. A content analysis of TMs developed was done using audiotaped transcripts, photo page notes, flip chart notes, and field notes. FINDINGS: Twelve TM themes emerged, including 172 TMs developed by the 23 study participants (age 50 ± 6.3 years). CONCLUSIONS: Using TMs to help achieve walking goals is an acceptable method of promoting PA with adults. Using culturally relevant photos to prompt discussion, focus groups can develop a database of PA-related TMs to promote walking. CLINICAL RELEVANCE: Physical inactivity is a significant contributor to adult health problems worldwide, and walking is a realistic method of increasing PA. Using focus groups and photos, individuals can generate acceptable, personalized and innovative TMs to promote walking.

The care processes for acute cholecystitis according to clinical practice guidelines based on the Japanese administrative database.

Acute cholecystitis is one of the most frequently encountered conditions in daily practice in Japan. However, there is a shortage of detailed data about treatments that have been performed according to the clinical practice guidelines (CPGs) for acute cholecystitis. We therefore examined the management of acute cholecystitis for adherence to the appropriate CPGs using the Japanese administrative database associated with the Diagnosis Procedure Combination (DPC) system. We collected data from 6,070 patients with acute cholecystitis, examining for the application of four recommended treatments (administration of antimicrobial drugs and nonsteroidal anti-inflammatory drugs (NSAIDs) and performance of early and laparoscopic cholecystectomy). The patients were classified according to the procedures documented for each case: no gallbladder drainage (n = 4,333), gallbladder drainage without supportive care (ventilation or hemodiafiltration or the use of vasopressor) (n = 1,591) and gallbladder drainage and supportive care (n = 146). Multiple logistic regression models revealed that patients with gallbladder drainage without supportive care and those with gallbladder drainage and supportive care significantly higher received administration of antimicrobial drugs and NSAIDs, while these patients underwent less early or laparoscopic cholecystectomy than did patients without gallbladder drainage, after adjusting for potential confounding effects of the clinical variables. This study demonstrated that there were various differences with regard to the performance of recommended treatments between the levels of procedures required for acute cholecystitis. In addition, this administrative database was a feasible tool for the evaluation of care processes and will provide useful information contributing to improved quality of medical care.

[Pathowiki. A free expert database for pathology]. / Pathowiki. Eine freie Wissensdatenbank für die Pathologie.

The project Pathowiki (www.pathowiki.org) is a free expert database for texts, images, virtual slides and links to all subject areas of pathology in the internet. The aim of this project is to integrate all available information and media, in particular virtual microscopy, to achieve a fast overview of a relevant subject area. Here we present the project's basic functions and applications and evaluate the project with respect to the ongoing digital developments in pathology.

[Design of the general population study NEMESIS-2: Netherlands Mental Health Survey and Incidence Study-2]. / Opzet van de bevolkingsstudie NEMESIS - 2 Netherlands Mental Health Survey and Incidence Study-2.

BACKGROUND: The longitudinal epidemiological population study NEMESIS-2 (Netherlands Mental Health Survey and Incidence Study-2) replicates the first study conducted from 1996 to 1999, and expands it by adding new subjects such as impulse-control disorders. AIM: To describe the aims and design of nemesis-2, particularly of its first round of measurements, to provide up-to-date figures on prevalence, incidence, course and consequences of mental disorders and associated factors, and to study trends in the mental health of the population aged 18-64 years and the use these people make of psychiatric services. METHOD: Face-to-face interviews were conducted (November 2007-July 2009) by means of the Composite International Diagnostic Interview 3.0. RESULTS: The response was 65.1% (n = 6646). Respondents were reasonably representative for the population, but young persons were somewhat underrepresented. Two follow-up rounds of measurements are planned with three-year intervals between the rounds. The second round of measurements began in November 2010. CONCLUSION: A qualitatively good dataset was built up. This will allow several mental health topics to be studied in the future.

From Inception to ConcePTION: Genesis of a Network to Support Better Monitoring and Communication of Medication Safety During Pregnancy and Breastfeeding.

In 2019, the Innovative Medicines Initiative (IMI) funded the ConcePTION project-Building an ecosystem for better monitoring and communicating safety of medicines use in pregnancy and breastfeeding: validated and regulatory endorsed workflows for fast, optimised evidence generation-with the vision that there is a societal obligation to rapidly reduce uncertainty about the safety of medication use in pregnancy and breastfeeding. The present paper introduces the set of concepts used to describe the European data sources involved in the ConcePTION project and illustrates the ConcePTION Common Data Model (CDM), which serves as the keystone of the federated ConcePTION network. Based on data availability and content analysis of 21 European data sources, the ConcePTION CDM has been structured with six tables designed to capture data from routine healthcare, three tables for data from public health surveillance activities, three curated tables for derived data on population (e.g., observation time and mother-child linkage), plus four metadata tables. By its first anniversary, the ConcePTION CDM has enabled 13 data sources to run common scripts to contribute to major European projects, demonstrating its capacity to facilitate effective and transparent deployment of distributed analytics, and its potential to address questions about utilization, effectiveness, and safety of medicines in special populations, including during pregnancy and breastfeeding, and, more broadly, in the general population.

Incorporation of the International Spinal Cord Injury Data Set elements into the National Institute of Neurological Disorders and Stroke Common Data Elements.

OBJECTIVES: To develop consistent variable names and a common database structure for the data elements in the International Spinal Cord Injury (SCI) Data Sets. SETTING: National Institute of Neurological Disorders and Stroke (NINDS) Common Data Elements (CDE) Project and The Executive Committee of the International SCI Standards and Data Sets committees (ECSCI). METHODS: The NINDS CDE team creates a variable name for each defined data element in the various International SCI Data Sets. Members of the ECSCI review these in an iterative process to make the variable names logical and consistent across the data sets. Following this process, the working group for the particular data set reviews the variable names, and further revisions and adjustments may be made. In addition, a database structure for each data set is developed allowing data to be stored in a uniform way in databases to promote sharing data from different studies. RESULTS: The International SCI Data Sets variable names and database specifications will be available through the web sites of the International Spinal Cord Society (http://www.iscos.org.uk), the American Spinal Injury Association (http://www.asia-spinalinjury.org) and the NINDS CDE project web site (http://www.CommonDataElements.ninds.nih.gov). CONCLUSION: This process will continue as additional International SCI Data Sets fulfill the requirements of the development and approval process and are ready for implementation.

The international spinal cord injury endocrine and metabolic function basic data set.

OBJECTIVE: To develop the International Spinal Cord Injury (SCI) Endocrine and Metabolic Function Basic Data Set within the framework of the International SCI Data Sets that would facilitate consistent collection and reporting of basic endocrine and metabolic findings in the SCI population. SETTING: International. METHODS: The International SCI Endocrine and Metabolic Function Data Set was developed by a working group. The initial data set document was revised on the basis of suggestions from members of the Executive Committee of the International SCI Standards and Data Sets, the International Spinal Cord Society (ISCoS) Executive and Scientific Committees, American Spinal Injury Association (ASIA) Board, other interested organizations and societies, and individual reviewers. In addition, the data set was posted for 2 months on ISCoS and ASIA websites for comments. RESULTS: The final International SCI Endocrine and Metabolic Function Data Set contains questions on the endocrine and metabolic conditions diagnosed before and after spinal cord lesion. If available, information collected before injury is to be obtained only once, whereas information after injury may be collected at any time. These data include information on diabetes mellitus, lipid disorders, osteoporosis, thyroid disease, adrenal disease, gonadal disease and pituitary disease. The question of gonadal status includes stage of sexual development and that for females also includes menopausal status. Data will be collected for body mass index and for the fasting serum lipid profile. The complete instructions for data collection and the data sheet itself are freely available on the websites of ISCoS (http://www.iscos.org.uk) and ASIA (http://www.asia-spinalinjury.org).