EHRSQL: A Practical Text-to-SQL Benchmark for Electronic Health Records

We present a new text-to-SQL dataset for electronic health records (EHRs). The utterances were collected from 222 hospital staff, including physicians, nurses, insurance review and health records teams, and more. To construct the QA dataset on structured EHR data, we conducted a poll at a university hospital and templatized the responses to create seed questions. Then, we manually linked them to two open-source EHR databases, MIMIC-III and eICU, and included them with various time expressions and held-out unanswerable questions in the dataset, which were all collected from the poll. Our dataset poses a unique set of challenges: the model needs to 1) generate SQL queries that reflect a wide range of needs in the hospital, including simple retrieval and complex operations such as calculating survival rate, 2) understand various time expressions to answer time-sensitive questions in healthcare, and 3) distinguish whether a given question is answerable or unanswerable based on the prediction confidence. We believe our dataset, EHRSQL, could serve as a practical benchmark to develop and assess QA models on structured EHR data and take one step further towards bridging the gap between text-to-SQL research and its real-life deployment in healthcare. EHRSQL is available at https://github.com/glee4810/EHRSQL.Comment: Published as a conference paper at NeurIPS 2022 (Track on Datasets and Benchmarks)

Sequencing and characterization of Varicella-Zoster virus vaccine strain SuduVax

<p>Abstract</p> <p>Background</p> <p>Varicella-zoster virus (VZV) causes chickenpox in children and shingles in older people. Currently, live attenuated vaccines based on the Oka strain are available worldwide. In Korea, an attenuated VZV vaccine has been developed from a Korean isolate and has been commercially available since 1994. Despite this long history of use, the mechanism for the attenuation of the vaccine strain is still elusive. We attempted to understand the molecular basis of attenuation mechanism by full genome sequencing and comparative genomic analyses of the Korean vaccine strain SuduVax.</p> <p>Results</p> <p>SuduVax was found to contain a genome that was 124,759 bp and possessed 74 open reading frames (ORFs). SuduVax was genetically most close to Oka strains and these Korean-Japanese strains formed a strong clade in phylogenetic trees. SuduVax, similar to the Oka vaccine strains, underwent T- > C substitution at the stop codon of ORF0, resulting in a read-through mutation to code for an extended form of ORF0 protein. SuduVax also shared certain deletion and insertion mutations in ORFs 17, 29, 56 and 60 with Oka vaccine strains and some clinical strains.</p> <p>Conclusions</p> <p>The Korean VZV vaccine strain SuduVax is genetically similar to the Oka vaccine strains. Further comparative genomic and bioinformatics analyses will help to elucidate the molecular basis of the attenuation of the VZV vaccine strains.</p

KNOW-KT (KoreaN cohort study for outcome in patients with kidney transplantation: a 9-year longitudinal cohort study): study rationale and methodology

BACKGROUND: Asian patients undergoing kidney transplantation (KT) generally have better renal allograft survival and a lower burden of cardiovascular disease than those of other racial groups. The KNOW-KT aims to explore allograft survival rate, cardiovascular events, and metabolic profiles and to elucidate the risk factors in Korean KT patients. METHODS: KNOW-KT is a multicenter, observational cohort study encompassing 8 transplant centers in the Republic of Korea. KNOW-KT will enroll 1,000 KT recipients between 2012 and 2015 and follow them up to 9 years. At the time of KT and at pre-specified intervals, clinical information, laboratory test results, and functional and imaging studies on cardiovascular disease and metabolic complications will be recorded. Comorbid status will be assessed by the age-adjusted Charlson co-morbidity index. Medication adherence and information on quality of life (QoL) will be monitored periodically. The QoL will be assessed by the Kidney Disease Quality of Life Short Form. Donors will include both living donors and deceased donors whose status will be assessed by the Kidney Donor Risk Index. Primary endpoints include graft loss and patient mortality. Secondary endpoints include renal functional deterioration (a decrease in eGFR to <30 mL/min/1.73 m(2)), acute rejection, cardiovascular event, albuminuria, new-onset diabetes after transplant, and QoL. Data on other adverse outcomes including episodes of infection, malignancy, recurrence of original renal disease, fracture, and hospitalization will also be collected. A bio-bank has been established for the acquisition of DNA, RNA, and protein from serum and urine samples of recipients at regular intervals. Bio-samples from donors will also be collected at the time of KT. KNOW-KT was registered in an international clinical trial registry (NCT02042963 at http://www.clinicaltrials.gov) on January 20(th), 2014. CONCLUSION: The KNOW-KT, the first large-scale cohort study in Asian KT patients, is expected to represent the Asian KT population and provide information on their natural course, complications, and risk factors for complications

Sudden Sensorineural Hearing Loss May Increase the Risk of Retinal Vein Occlusion: A Nationwide Cohort Study

Sudden sensorineural hearing loss (SSNHL) is thought to be a vascular disease. Retinal vein occlusion (RVO) is an also common ophthalmic vascular disease. Thus, we investigated the potential relationship between these using a retrospective nationwide cohort dataset. We compared 49,584 subjects in the SSNHL and the comparison (non-SSNHL) groups using patients randomly selected via propensity-score matching. We calculated the incidence, survival rate, and hazards ratio (HR) using log-rank test, and Cox proportional hazards regression models. This study examined a total of 375,490.4 person-years in the SSNHL group and 373,698.2 person-years in the comparison group. We found that 673 patients in the SSNHL group (1.8 cases per 1000 person-years) and 592 in the comparison group (1.6 cases per 1000 person-years) developed RVO during the 8-year follow-up period. The adjusted HR of RVO was 1.13 (95% confidence interval [CI] 1.01&ndash;1.26). The adjusted HR of developing RVO in SSNHL was the greatest in elderly patients (adjusted HR, 1.21; 95% CI, 1.01&ndash;1.46) and male patients (adjusted HR, 1.18; 95% CI, 1.03&ndash;1.34). Our findings suggest that clinicians should remain vigilant of the possibility of RVO development in SSNHL patients, specifically elderly male patients

Association of adenotonsillectomy with asthma and upper respiratory infection: A nationwide cohort study.

Adenotonsillectomy is a common paediatric surgery for treating obstructed breathing or recurrent inflammation; however, the long-term health consequences on the developing immune system are unknown. This study investigated the potential association between adenotonsillectomy and the development of asthma and upper respiratory infections (URI). This propensity score-matched retrospective cohort study utilized data from the National Sample Cohort 2002-2013. In the asthma cohort, we used a Cox-proportional hazards model to analyze the hazard ratio (HR) of adenotonsillectomy for asthma events. In the URI cohort, equivalence testing of postoperative visits for URI was performed. The margin of equivalence of the difference was set at -0.5-0.5. Asthma incidence was 66.97/1000 person-years in children who underwent adenotonsillectomy and 30.43/1000 person-years in those who did not. Adjusted asthma HRs were 2.25 (95% confidence interval, 1.96-2.57) in the adenotonsillectomy vs. non-adenotonsillectomy groups. In a subgroup analysis, children aged 5-9 years living in metropolitan areas showed a higher incidence of subsequent asthma than those of other ages and areas. However, any significant difference between the groups in terms of URI events in the 1-11-year postoperative period was not identified. Adenotonsillectomy in children is associated with an increased incidence of asthma, with no significant impact on postoperative visits for URI

Oral Nutritional Supplements Reduce Body Weight Loss after Gastrectomy in Patients with Gastric Cancer: A Systematic Review and Meta-Analysis of Randomized Controlled Trials

This systematic review and meta-analysis aimed to summarize the effects of oral nutritional supplements (ONSs) on body weight loss (BWL) after gastrectomy. A systematic search was conducted across the PubMed, Cochrane, and Embase databases through May 2023. The study inclusion criteria were as follows: (1) studies on interventions including ONSs after gastrectomy in patients with gastric cancer; (2) studies in which comparisons were specified according to standard, regular, or usual postoperative diets; and (3) randomized controlled trial studies including outcomes measured as mean differences in BWL. The data were pooled using the random-effects model and expressed as mean differences with 95% confidence intervals (CI). Based on data from seven studies including 1743 patients (891 for ONSs and 852 for the control), the overall pooled mean difference was 0.848 (95% CI: 0.466 to 1.230) and the Higgins I2 value was 86.0%. This systematic review and meta-analysis is the first study to show that ONSs are significantly associated with reducing BWL, compared with standard diets, after gastrectomy in patients with gastric cancer. Furthermore, we found that ONSs were more effective in patients with lower nutritional kilocalorie intake after gastrectomy

Dependence of local atomic structure on piezoelectric properties of PbZr1−xTixO3 materials

Lead zirconate titanate (PZT, [Formula: see text]) is a piezoelectric ceramic which can be used for several applications such as actuators, sensors, and microelectronic devices. Depending on its composition, PZT can exhibit rhombohedral, orthorhombic (tetragonal) phases, with the piezoelectric charge constant ([Formula: see text]) key to evaluating its piezoelectric properties. In this study, ([Formula: see text]) was calculated using density functional perturbation theory (DFPT) based on first-principles methods. First, we reveal that the rhombohedral structure is stable for Zr-rich compositions. Second, extending the study to [Formula: see text] and [Formula: see text] (PSZT), we evaluated the values of [Formula: see text] both theoretically and experimentally to investigate how they are affected by doping. The microscopic movements of individual atoms within the optimized crystal were analyzed to investigate the correlations between the structural characteristics and [Formula: see text]. The results show that the relative positions of Ti and Zr (B-site) atoms and the quadratic elongation in the PZT octahedron depend strongly on the piezoelectric charge constant [Formula: see text], which itself depends on the Ti content. The local atomic structural parameters described in this study can be used as a descriptor for the high-throughput screening of PZT materials

The 2011–2020 Trends of Data-Driven Approaches in Medical Informatics for Active Pharmacovigilance

Pharmacovigilance, the scientific discipline pertaining to drug safety, has been studied extensively and is progressing continuously. In this field, medical informatics techniques and interpretation play important roles, and appropriate approaches are required. In this study, we investigated and analyzed the trends of pharmacovigilance systems, especially the data collection, detection, assessment, and monitoring processes. We used PubMed to collect papers on pharmacovigilance published over the past 10 years, and analyzed a total of 40 significant papers to determine the characteristics of the databases and data analysis methods used to identify drug safety indicators. Through systematic reviews, we identified the difficulty of standardizing data and terminology and establishing an adverse drug reactions (ADR) evaluation system in pharmacovigilance, and their corresponding implications. We found that appropriate methods and guidelines for active pharmacovigilance using medical big data are still required and should continue to be developed

A Data-Driven Reference Standard for Adverse Drug Reaction (RS-ADR) Signal Assessment: Development and Validation

BackgroundPharmacovigilance using real-world data (RWD), such as multicenter electronic health records (EHRs), yields massively parallel adverse drug reaction (ADR) signals. However, proper validation of computationally detected ADR signals is not possible due to the lack of a reference standard for positive and negative associations. ObjectiveThis study aimed to develop a reference standard for ADR (RS-ADR) to streamline the systematic detection, assessment, and understanding of almost all drug-ADR associations suggested by RWD analyses. MethodsWe integrated well-known reference sets for drug-ADR pairs, including Side Effect Resource, Observational Medical Outcomes Partnership, and EU-ADR. We created a pharmacovigilance dictionary using controlled vocabularies and systematically annotated EHR data. Drug-ADR associations computed from MetaLAB and MetaNurse analyses of multicenter EHRs and extracted from the Food and Drug Administration Adverse Event Reporting System were integrated as “empirically determined” positive and negative reference sets by means of cross-validation between institutions. ResultsThe RS-ADR consisted of 1344 drugs, 4485 ADRs, and 6,027,840 drug-ADR pairs with positive and negative consensus votes as pharmacovigilance reference sets. After the curation of the initial version of RS-ADR, novel ADR signals such as “famotidine–hepatic function abnormal” were detected and reasonably validated by RS-ADR. Although the validation of the entire reference standard is challenging, especially with this initial version, the reference standard will improve as more RWD participate in the consensus voting with advanced pharmacovigilance dictionaries and analytic algorithms. One can check if a drug-ADR pair has been reported by our web-based search interface for RS-ADRs. ConclusionsRS-ADRs enriched with the pharmacovigilance dictionary, ADR knowledge, and real-world evidence from EHRs may streamline the systematic detection, evaluation, and causality assessment of computationally detected ADR signals