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Abstract Objective This article describes a scalable, performant, sustainable global network of electronic health record data for biomedical and clinical research. Materials and Methods TriNetX has created a technology platform characterized by a conservative security and governance model that facilitates collaboration and cooperation between industry participants, such as pharmaceutical companies and contract research organizations, and academic and community-based healthcare organizations (HCOs). HCOs participate on the network in return for access to a suite of analytics capabilities, large networks of de-identified data, and more sponsored trial opportunities. Industry participants provide the financial resources to support, expand, and improve the technology platform in return for access to network data, which provides increased efficiencies in clinical trial design and deployment. Results TriNetX is a growing global network, expanding from 55 HCOs and 7 countries in 2017 to over 220 HCOs and 30 countries in 2022. Over 19 000 sponsored clinical trial opportunities have been initiated through the TriNetX network. There have been over 350 peer-reviewed scientific publications based on the network’s data. Conclusions The continued growth of the TriNetX network and its yield of clinical trial collaborations and published studies indicates that this academic-industry structure is a safe, proven, sustainable path for building and maintaining research-centric data networks. Lay Summary This article describes a network—a series of interconnected data repositories—where clinical data about patients is stored after being extracted from electronic health record systems. The data on this network are meant to be used by researchers working in healthcare institutions as well as the life sciences industry. This network aims to make it easier, faster, and cheaper to find patients for recruitment into clinical trials and to conduct research using the clinical data. This network is being developed and maintained by a commercial company TriNetX, LLC. It is growing rapidly, expanding from 55 healthcare organizations and 7 countries in 2017 to over 220 healthcare organizations and 30 countries in 2022. The privacy and security of patient as well as member organizations’ data are of paramount concern. TriNetX takes a very conservative stand with respect to privacy protection and data governance. The data on this network have been used extensively for research and there’s currently over 350 peer-reviewed scientific publications based on the network’s data. The continued growth of the TriNetX network demonstrates that this approach to clinical data sharing is a safe, proven, and sustainable path for supporting the data needs of healthcare and life sciences researchers.

This study aimed to obtain a comprehensive view of the risk of developing diabetes in patients with obstructive sleep apnea (OSA) and to compare this risk between patients receiving continuous positive airway pressure (CPAP) therapy versus upper airway surgery (UAS). We used local and the global-scale federated data research network TriNetX to obtain access to electronic medical records, including those for patients diagnosed with OSA, from health-care organizations (HCOs) worldwide. Using propensity score matching and the score-matched analyses of data for 5 years of follow-up, we found that patients who had undergone UAS had a lower risk of developing diabetes than those who used CPAP (risk ratio 0.415, 95% confidence interval (CI) 0.349–0.493). The risk for newly diagnosed diabetes patients showed a similar pattern (hazard ratio 0.382; 95% CI 0.317–0.459). Both therapies seem to protect against diabetes (Risk 0.081 after UAS vs. 0.195 after CPAP). Analysis of the large data sets collected from HCOs in Europe and globally lead us to conclude that, in patients with OSA, UAS can prevent the development of diabetes better than CPAP.

A recent Letter published, in the Journal of Otolaryngology—Head & Neck Surgery in response to our original article “Risk of diabetes in patients with sleep apnea: comparison of surgery versus Continous Positive Airway Pressure in a long-term follow-up study” raised some issues we would like to address here. However, we thank the authors for their effort and time in analyzing our manuscript and we want to facilitate a balanced discussion on this topic with our reply.

Background: Uterine adenomyosis is an increasingly frequent disorder. Our study aimed to demonstrate the presence of obstetric complications in the population affected by this condition to demonstrate the need for follow-up in high-risk obstetric units. Material and Methods: The data for the study were obtained from TriNetX, LLC, between 2010 and 2020. The outcomes analyzed were intrauterine growth restriction (IUGR), preterm delivery, cesarean delivery, hypertension, abruption placentae, and spontaneous abortion. Seven thousand six hundred and eight patients were included in the cohort of pregnant patients with adenomyosis, and 566,153 women in the cohort of pregnant patients without any history of endometriosis. Results: Upon calculating the total risk of presenting any of these problems during pregnancy, we obtained an OR = 1.521, implying that a pregnancy with adenomyosis was 52.1% more likely to present some complication. We found: IUGR OR = 1.257 (95% CI: 1.064–1.485) (p = 0.007); preterm delivery OR = 1.422 (95% CI: 1.264–1.600) (p = 0.0001); cesarean delivery OR = 1.099 (95% CI: 1.002–1.205) (p = 0.046); hypertensive disorders OR = 1.177 (95% CI: 1.076–1.288) (p = 0.0001); abruption placentae OR = 1.197 (95% CI: 1.008–1.422) (p = 0.040), and spontaneous abortion OR = 1.529 (95% CI: 1.360–1.718) (p = 0.0001). Conclusion: We conclude that the review carried out and the data we obtained on increased risk provide sufficient evidence to recommend that patients with adenomyosis should be managed in obstetric high-risk units.

Nanoinformatics is an emerging research field that uses informatics techniques to collect, process, store, and retrieve data, information, and knowledge on nanoparticles, nanomaterials, and nanodevices and their potential applications in health care. In this paper, we have focused on the solutions that nanoinformatics can provide to facilitate nanotoxicology research. For this, we have taken a computational approach to automatically recognize and extract nanotoxicology-related entities from the scientific literature. The desired entities belong to four different categories: nanoparticles, routes of exposure, toxic effects, and targets. The entity recognizer was trained using a corpus that we specifically created for this purpose and was validated by two nanomedicine/nanotoxicology experts. We evaluated the performance of our entity recognizer using 10-fold cross-validation. The precisions range from 87.6% (targets) to 93.0% (routes of exposure), while recall values range from 82.6% (routes of exposure) to 87.4% (toxic effects). These results prove the feasibility of using computational approaches to reliably perform different named entity recognition (NER)-dependent tasks, such as for instance augmented reading or semantic searches. This research is a “proof of concept” that can be expanded to stimulate further developments that could assist researchers in managing data, information, and knowledge at the nanolevel, thus accelerating research in nanomedicine.

Purpose This study aimed to obtain a comprehensive view of the risk of developing cancer in patients with obstructive sleep apnea (OSA) and to compare this risk between patients receiving continuous positive airway pressure (CPAP) therapy versus upper airway surgery (UAS). Methods We used both local data and a global-scale federated data research network, TriNetX, to access electronic medical records, including those of patients diagnosed with OSA from health-care organizations (HCOs) worldwide. We used propensity score matching and the score-matched analyses of data for 5 years of follow-up, Results We found that patients who had undergone UAS had a similar risk of developing cancer than those who used CPAP [hazard ratio of 0.767 (95% CI 0.559–1.053; P  = 0.100)]. Conclusion Analysis of the large data sets collected from HCOs in Europe and globally lead us to conclude that in patients with OSA, neither CPAP nor UAS were associated with the development of cancer better than in non-treated patients.

Background Over the last few decades, the ever-increasing output of scientific publications has led to new challenges to keep up to date with the literature. In the biomedical area, this growth has introduced new requirements for professionals, e.g., physicians, who have to locate the exact papers that they need for their clinical and research work amongst a huge number of publications. Against this backdrop, novel information retrieval methods are even more necessary. While web search engines are widespread in many areas, facilitating access to all kinds of information, additional tools are required to automatically link information retrieved from these engines to specific biomedical applications. In the case of clinical environments, this also means considering aspects such as patient data security and confidentiality or structured contents, e.g., electronic health records (EHRs). In this scenario, we have developed a new tool to facilitate query building to retrieve scientific literature related to EHRs. Results We have developed CDAPubMed, an open-source web browser extension to integrate EHR features in biomedical literature retrieval approaches. Clinical users can use CDAPubMed to: (i) load patient clinical documents, i.e., EHRs based on the Health Level 7-Clinical Document Architecture Standard (HL7-CDA), (ii) identify relevant terms for scientific literature search in these documents, i.e., Medical Subject Headings (MeSH), automatically driven by the CDAPubMed configuration, which advanced users can optimize to adapt to each specific situation, and (iii) generate and launch literature search queries to a major search engine, i.e., PubMed, to retrieve citations related to the EHR under examination. Conclusions CDAPubMed is a platform-independent tool designed to facilitate literature searching using keywords contained in specific EHRs. CDAPubMed is visually integrated, as an extension of a widespread web browser, within the standard PubMed interface. It has been tested on a public dataset of HL7-CDA documents, returning significantly fewer citations since queries are focused on characteristics identified within the EHR. For instance, compared with more than 200,000 citations retrieved by breast neoplasm , fewer than ten citations were retrieved when ten patient features were added using CDAPubMed. This is an open source tool that can be freely used for non-profit purposes and integrated with other existing systems.

Background Primer and probe sequences are the main components of nucleic acid-based detection systems. Biologists use primers and probes for different tasks, some related to the diagnosis and prescription of infectious diseases. The biological literature is the main information source for empirically validated primer and probe sequences. Therefore, it is becoming increasingly important for researchers to navigate this important information. In this paper, we present a four-phase method for extracting and annotating primer/probe sequences from the literature. These phases are: (1) convert each document into a tree of paper sections, (2) detect the candidate sequences using a set of finite state machine-based recognizers, (3) refine problem sequences using a rule-based expert system, and (4) annotate the extracted sequences with their related organism/gene information. Results We tested our approach using a test set composed of 297 manuscripts. The extracted sequences and their organism/gene annotations were manually evaluated by a panel of molecular biologists. The results of the evaluation show that our approach is suitable for automatically extracting DNA sequences, achieving precision/recall rates of 97.98% and 95.77%, respectively. In addition, 76.66% of the detected sequences were correctly annotated with their organism name. The system also provided correct gene-related information for 46.18% of the sequences assigned a correct organism name. Conclusions We believe that the proposed method can facilitate routine tasks for biomedical researchers using molecular methods to diagnose and prescribe different infectious diseases. In addition, the proposed method can be expanded to detect and extract other biological sequences from the literature. The extracted information can also be used to readily update available primer/probe databases or to create new databases from scratch.

Computer literacy is not negotiable for any professional in an increasingly computerised environment. Educational institutions should be equipped to provide this new basic training for modern life. Accordingly, computer labs are an essential medium for education in almost any field. Computer labs are one of the most popular IT infrastructures for technical training in primary and secondary schools, universities and other educational institutions all over the world. Unfortunately, a computer lab is expensive, in terms of both initial purchase and annual maintenance costs, and especially when we want to run the latest software. Hence, research efforts addressing computer lab efficiency, performance or cost reduction would have a worldwide repercussion. In response to this concern, this paper presents a survey on thin client technology for computer labs in educational environments. Besides setting out the advantages and drawbacks of this technology, we aim to refute false prejudices against thin clients, identifying a set of educational scenarios where thin clients are a better choice and others requiring traditional solutions.

PurposeCuenca, a World Heritage City, faces urban expansion as residents move to the outskirts, leaving the historic center abandoned and deteriorating. The challenge now is to relocate these spaces into sustainable and cohesive nodes. This research aims to identify cultural facility oversupply in the city center and understand the required usage for heritage buildings to promote a habitable, sustainable and cohesive historic center.Design/methodology/approachThe study consisted of two phases. Firstly, a georeferenced spatial analysis and monthly usage frequency of each facility is proposed. Secondly, interviews explored the criteria for designating heritage buildings as cultural facilities. Additionally, a survey assessed urban habitability in three historic center parishes, measuring aspects like coverage, satisfaction and security from residents' perspectives.FindingsThe underutilization of cultural facilities demonstrates both inefficient heritage management and a lack of resident interest in cultural activities and neighborhood decision-making. Thus, ensuring collective ownership of heritage assets becomes crucial. Additionally, the municipality's approach to heritage must be reconsidered. While implementing a cultural program may seem faster and cheaper, the long-term cost-benefit of maintaining a cohesive historical center outweighs that of a dispersed city.Originality/valueThis paper calls for a fundamental reimagining of the concept of built heritage, emphasizing the need for a more inclusive and integrated approach that goes beyond museum and tourism-driven strategies. This perspective recognizes the importance of social, cultural and environmental sustainability in revitalizing the historic center, considering the broader context of the city and its diverse inhabitants.