Synergies between centralized and federated approaches to data quality: a report from the national COVID cohort collaborative

OBJECTIVE

In response to COVID-19, the informatics community united to aggregate as much clinical data as possible to characterize this new disease and reduce its impact through collaborative analytics. The National COVID Cohort Collaborative (N3C) is now the largest publicly available HIPAA limited dataset in US history with over 6.4 million patients and is a testament to a partnership of over 100 organizations.

MATERIALS AND METHODS

We developed a pipeline for ingesting, harmonizing, and centralizing data from 56 contributing data partners using 4 federated Common Data Models. N3C data quality (DQ) review involves both automated and manual procedures. In the process, several DQ heuristics were discovered in our centralized context, both within the pipeline and during downstream project-based analysis. Feedback to the sites led to many local and centralized DQ improvements.

RESULTS

Beyond well-recognized DQ findings, we discovered 15 heuristics relating to source Common Data Model conformance, demographics, COVID tests, conditions, encounters, measurements, observations, coding completeness, and fitness for use. Of 56 sites, 37 sites (66%) demonstrated issues through these heuristics. These 37 sites demonstrated improvement after receiving feedback.

DISCUSSION

We encountered site-to-site differences in DQ which would have been challenging to discover using federated checks alone. We have demonstrated that centralized DQ benchmarking reveals unique opportunities for DQ improvement that will support improved research analytics locally and in aggregate.

CONCLUSION

By combining rapid, continual assessment of DQ with a large volume of multisite data, it is possible to support more nuanced scientific questions with the scale and rigor that they require.

Implementation of a Maternal Child Knowledgebase

To advance the application of clinical data to address maternal health we developed and implemented a Maternal Child Knowledgebase (MCK). The MCK integrates data from every pregnancy that received care at the University of Iowa Hospitals & Clinics (UIHC) and links information from the pregnancy episode to the delivery episode and between the mother and child. This knowledgebase contains integrated information regarding diagnoses, medications, mother and child vitals, hospital admissions, depression screenings, laboratory value results, and procedure information. It also collates information from the electronic health record (EPIC), the Social Security Death Index, and the Medication Administration Record into one knowledgebase. To enhance usability, we designed a custom viewer with several pre-designed queries and reports that eliminates the need for users to be proficient in SQL coding. The recent implementation of the MCK has supported multiple projects and reduced the number of Obstetrics-related data queries to the Biomedical Informatics group.

The effect of the COVID-19 lockdown on the epidemiology of hip fractures in the elderly: a multicentre cohort study

INTRODUCTION

The COVID-19 pandemic presented extraordinary challenges to the UK healthcare system. This study aimed to assess the impact of the COVID-19 lockdown on the epidemiology, treatment pathways and 30-day mortality rates of hip fractures. Outcomes of COVID-19 positive patients were compared against those who tested negative.

METHODS

An observational, retrospective, multicentre study was conducted across six hospitals in the South East of England. Data were retrieved from the National Hip Fracture Database and electronic medical records. Data was collected for the strictest UK lockdown period (period B=23 March 2020-11 May 2020), and the corresponding period in 2019 (period A).

RESULTS

A total of 386 patients were admitted during period A, whereas 381 were admitted during period B. Despite the suspension of the 'Best Practice Tariff' during period B, time to surgery, time to orthogeriatric assessment, and 30-day mortality were similar between period A and B. The length of inpatient stay was significantly shorter during period B (11.5 days vs 17.0 days, p<0.001). Comparison of COVID-19 positive and negative patients during period B demonstrated that a positive test was associated with a significantly higher rate of 30-day mortality (53.6% vs 6.7%), surgical delay >36h (46.4% vs 30.8%, p=0.049), and increased length of inpatient stay (15.8 vs 11.7 days, p=0.015).

CONCLUSIONS

The COVID-19 lockdown did not alter the epidemiology of hip fractures. A substantially higher mortality rate was observed among patients with a COVID-19 positive test. These findings should be taken into consideration by the healthcare policymakers while formulating contingency plans for a potential 'second wave'.

Phosphorylation and Cu+ coordination-dependent DNA binding of the transcription factor Mac1p in the regulation of copper transport

Copper ions are essential at a proper level yet toxic when present in excess. To maintain a proper intracellular level, cells must be able to sense the changes in copper ion concentrations. The yeast transcription factor Mac1p plays a critical role in the transcriptional regulation of CTR1 and CTR3, both encoding high affinity copper ion transporters. Here we report that the Mac1p binding of the copper ion-responsive elements (CuREs) in the promoters of CTR1 and CTR3 is affected by copper ions. On one hand, the Mac1p DNA binding is Cu(+) coordination-dependent, and on the other hand, exogenous Cu(+) and isoelectronic Ag(+) ions disrupt the DNA binding of Mac1p. These results suggest that the Mac1p is able to sense two different levels of copper ions. These two levels are probably the physiological and toxic copper levels in yeast cells. Furthermore, we found that Mac1p undergoes posttranslational phosphorylation modification in yeast and that the phosphorylation is required for the Mac1p to become DNA-binding active. Nonphosphorylated Mac1p is unable to bind the CTR1 promoter DNA. The data support the model of intradomain interactions and indicate further that the phosphorylation probably prevents the inhibition of DNA-binding domain activity by the activation domain of Mac1p. Taken together, these findings demonstrate that Mac1p functions critically in maintaining a proper intracellular concentration of copper ions.

Thermal debonding of ceramic brackets: an in vitro study

Thermal debonding has been developed to overcome the problems of enamel damage and high forces when debonding ceramic orthodontic brackets. However, the temperature changes with thermal debonding have the potential to damage the tooth tissues. The principal aims of this study are, first, to investigate the effects of resin type, resin thickness, and debonding force on the temperature changes in human premolars during thermal debonding of ceramic brackets and, second, to record the sites of bond failure and damage to the tooth surface. Ceramic brackets were attached to each specimen by using one of four types of bonding resin in a controlled thick or thin resin layer. The ceramic debonding unit (Dentaurum, Pforzheim, Germany) was used to thermally debond the brackets with either a 40 or 80 Nmm torsional force. Higher temperature changes at the pulpal wall (> 10 degrees C in some 40 Nmm torsional force specimens) always occurred with Concise (3M Dental Products, St. Paul, Minn.) and Transbond (Unitek/3M Dental Products, Monrovia, Calif.) resins, and lower temperature changes (< 5 degrees C) with Quasar (Rocky Mountain Orthodontics, Denver, Colo.) and Ortho. B.S. (Dentaurum, Pforzheim, Germany) resins. In general, resin thickness was not significantly associated with buccal surface or pulpal wall temperature changes. However, temperature changes at the pulpal wall were significantly associated with the temperature changes at the buccal surface (r = 0.76), with the temperature of the thermal debonder blade for thin resin layer specimens (r = 0.50), and the time required to debond the bracket for both thick (r = 0.74) and thin (r = 0.63) resin layer specimens. In most specimens, the site of bond failure occurred at the bracket-resin interface. There was no evidence of enamel damage after bracket removal.

Further analysis of the cognitive effects of tetrahydroaminoacridine (THA) in Alzheimer's disease: assessment of attentional and mnemonic function using CANTAB

Results of a placebo controlled cross-over trial (N = 89) of the anticholinesterase drug THA as a treatment for dementia of the Alzheimer's type (DAT) are reported, with reference to previous trials of the drug and the cholinergic hypothesis of aging and dementia. Using computerised tests sensitive to specific aspects of memory and attention, evidence is found for improvements in attentional function rather than memory, in patients with mild to moderate DAT. Although these improvements were significant, they were small and restricted to certain tests of attentional function. Nevertheless, they add to the growing body of evidence that the cholinergic system is involved in the control of attentional processes. The results will be relevant to future investigations into the therapeutic effects of enhancement of the cholinergic system in DAT sufferers.

Relationship of bacteriocin-like inhibitor production to the pigmentation and hemolytic activity of mutans streptococci

An inhibitor production typing (P-typing) scheme originally devised for hemolytic streptococci of Lancefield groups A-G has been successfully applied to 35 mutans streptococcus isolates recovered from plaque cultures of 60 Dunedin schoolchildren. Thirteen different P-type designations were identified. Although 11 (31%) of the isolates failed to produce detectable inhibitory activity on the conventional blood agar medium used for P-typing, four of these isolates were inhibitor-positive on Trypticase Soy agar supplemented with 2% yeast extract and 0.5% calcium carbonate (TSYCa). Four mutans strains displayed strong beta-hemolysis on Columbia agar base containing human blood when incubated in a 5% CO2 in air atmosphere. Three of these also produced weak beta-hemolysis on sheep blood-supplemented medium and were further distinctive in that they were the only inhibitor P-type 767 strains to be detected in the present study. Five mutans isolates were pigment producers and this property seemed to occur independently of both the beta-hemolytic activity and the P-type designation. Upon testing an additional collection of 18 mutans strains of various serotypes, only seven (39%) were inhibitor-positive. However, three of the four serotype c strains were inhibitor producers. Two strains of serotype d and one of serotype g were more hemolytic on sheep than on human blood agar medium. In general, it seems that the most common human mutans streptococci (serotype c strains) are more likely than are other mutans strains to produce bacteriocin-like inhibitory activity and to be hemolytic for human rather than sheep erythrocytes.