Trends and Correlates of Breakthrough Infections With SARS-CoV-2

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) delta variant has been hypothesized to decrease the efficacy of COVID-19 vaccines. Factors associated with infections with SARS-CoV-2 after vaccination are unknown. In this observational cohort study, we examined two groups in Harris County, Texas: (1) individuals with positive Nucleic Acid Amplification test between 12/14/2020 and 9/30/2021 and (2) the subset of individuals fully vaccinated in the same time period. Infected individuals were classified as a breakthrough if their infection occurred 14 days after their vaccination had been completed. Among fully vaccinated individuals, demographic and vaccine factors associated with breakthrough infections were assessed. Of 146,731 positive SARS-CoV-2 tests, 7.5% were breakthrough infections. Correlates of breakthrough infection included young adult age, female, White race, and receiving the Janssen vaccine, after adjustments including the amount of community spread at the time of infection. Vaccines remained effective in decreasing the probability of testing positive for SARS-CoV-2. The data indicate that increased vaccine booster uptake would help decrease new infections.

Identifying Sensitive Windows of Exposure to NO2 and Fetal Growth Trajectories in a Spanish Birth Cohort

BACKGROUND

We previously identified associations between trimester-specific NO2 exposures and reduced fetal growth in the Spanish INfancia y Medio Ambiente (INMA) project. Here, we use temporally refined exposure estimates to explore the impact of narrow (weekly) windows of exposure on fetal growth.

METHODS

We included 1,685 women from INMA with serial ultrasounds at 12, 20, and 34 gestational weeks. We measured biparietal diameter (BPD), femur length, and abdominal circumference (AC) and from them calculated estimated fetal weight (EFW). We calculated z-scores describing trajectories of each parameter during early (0-12 weeks), mid (12-20 weeks), and late (20-34 weeks) pregnancy, based on longitudinal growth curves from mixed-effects models. We estimated weekly NO2 exposures at each woman's residence using land-use regression models. We applied distributed lag nonlinear models to identify sensitive windows of exposure. We present effect estimates as the percentage change in fetal growth per 10 μg/m3 increase in NO2 exposure, and we calculated cumulative effect estimates by aggregating estimates across adjacent lags.

RESULTS

We identified weeks 5-12 as a sensitive window for NO2 exposure on late EFW (cumulative β = -3.0%; 95% CI = -4.1%, -1.9%). We identified weeks 6-19 as a sensitive window for late growth in BPD (cumulative β = -2.0%; 95% CI = -2.7%, -1.4%) and weeks 8-13 for AC (cumulative β = -0.68%; 95% CI = -0.97%, -0.40%). We found suggestive evidence that third trimester NO2 exposure is associated with increased AC, BPD, and EFW growth in late pregnancy.

CONCLUSIONS

Our findings are consistent with the hypothesis that NO2 exposure is associated with alterations in growth of EFW, BPD, and AC dependent on the specific timing of exposure during gestation.

Examining Social Vulnerability and the Association With COVID-19 Incidence in Harris County, Texas

Studies have investigated the association between social vulnerability and SARS-CoV-2 incidence. However, few studies have examined small geographic units such as census tracts, examined geographic regions with large numbers of Hispanic and Black populations, controlled for testing rates, and incorporated stay-at-home measures into their analyses. Understanding the relationship between social vulnerability and SARS-CoV-2 incidence is critical to understanding the interplay between social determinants and implementing risk mitigation guidelines to curtail the spread of infectious diseases. The objective of this study was to examine the relationship between CDC's Social Vulnerability Index (SVI) and SARS-CoV-2 incidence while controlling for testing rates and the proportion of those who stayed completely at home among 783 Harris County, Texas census tracts. SARS-CoV-2 incidence data were collected between May 15 and October 1, 2020. The SVI and its themes were the primary exposures. Median percent time at home was used as a covariate to measure the effect of staying at home on the association between social vulnerability and SARS-CoV-2 incidence. Data were analyzed using Kruskal Wallis and negative binomial regressions (NBR) controlling for testing rates and staying at home. Results showed that a unit increase in the SVI score and the SVI themes were associated with significant increases in SARS-CoV-2 incidence. The incidence risk ratio (IRR) was 1.090 (95% CI, 1.082, 1.098) for the overall SVI; 1.107 (95% CI, 1.098, 1.115) for minority status/language; 1.090 (95% CI, 1.083, 1.098) for socioeconomic; 1.060 (95% CI, 1.050, 1.071) for household composition/disability, and 1.057 (95% CI, 1.047, 1.066) for housing type/transportation. When controlling for stay-at-home, the association between SVI themes and SARS-CoV-2 incidence remained significant. In the NBR model that included all four SVI themes, only the socioeconomic and minority status/language themes remained significantly associated with SARS-CoV-2 incidence. Community-level infections were not explained by a communities' inability to stay at home. These findings suggest that community-level social vulnerability, such as socioeconomic status, language barriers, use of public transportation, and housing density may play a role in the risk of SARS-CoV-2 infection regardless of the ability of some communities to stay at home because of the need to work or other reasons.

Is the Application of SNOMED CT Concept Model sufficiently Quality Assured?

The terminological content of SNOMED CT, the world's largest clinical terminology is linked to description logics expressions, which give support to consider SNOMED CT a formal ontology. The Terminology Quality Assurance (TQA) of such a terminology resource is hampered by errors in modeling, which act as a barrier for the successful use of electronic health records to ensure semantic interoperability. One application case is the new version of ICD, now in its pre-final form, the content of which is based on a subset of SNOMED CT. The ongoing alignment exercise has highlighted significant modeling issues in more than one third of cases that contrasted SNOMED CT concept model instances with the intuitive meaning given by their Fully Specified Names or synonyms lexically mapped to ICD-11 class names. We recommend prioritizing SNOMED CT TQA on the subset of the core SNOMED CT content to constitute the always true common ontology between SNOMED CT and ICD-11.

Security and Confidentiality Approach for the Clinical E-Science Framework (CLEF)

Objectives: CLEF is an MRC sponsored project in the E-Science programme that aims to establish methodologies and a technical infrastructure for the next generation of integrated clinical and bioscience research.

Methods: The heart of the CLEF approach to this challenge is to design and develop a pseudonymised repository of histories of cancer patients that can be accessed by researchers. Robust mechanisms and policies have been developed to ensure that patient privacy and confidentiality are preserved while delivering a repository of such medically rich information for the purposes of scientific research.

Results: This paper summarises the overall approach adopted by CLEF to meet data protection requirements, including the data flows, pseudonymisation measures and additional monitoring policies that are currently being developed.

Conclusion: Once evaluated, it is hoped that the CLEF approach can serve as a model for other distributed electronic health record repositories to be accessed for research.

Testing headings for communicating the personal health record: comparison from the recipients’ perspective

In the spring of 1998, 16 general practitioners and 16 community psychiatric nurses participated in a study to test a draft set of headings for communicating clinical summaries. Eight anonymized psychiatric discharge summaries were used to assess the impact of the presentational format on the time taken by professionals to read the summaries and to answer a series of standard questions about each of them. Respondents also completed a questionnaire on their opinions of the headings. There was considerable variation between individuals in the times taken to read the summaries and answer the questions, but no evidence that any of the formats was associated with decreased reading time or with improvement in retrieving information. Most respondents preferred information structured using the headings rather than the original semi-structured discharge summaries, and information on paper rather than on computer screen.

Respondents were guardedly supportive of the particular draft headings presented. A weak preference was expressed for locally defined headings, with some recognition of advantages in widely agreed headings. There was a view that there were too many headings, and there was overlap between specific heading pairs (for example, ‘aim’ and ‘goal’). Concerns were expressed about specific headings, particularly the ‘softer’ headings, such as ‘informing’ and ‘communicating’.

Security and confidentiality approach for the Clinical E-Science Framework (CLEF)

OBJECTIVES

CLEF is an MRC sponsored project in the E-Science programme that aims to establish methodologies and a technical infrastructure for the next generation of integrated clinical and bioscience research.

METHODS

The heart of the CLEF approach to this challenge is to design and develop a pseudonymised repository of histories of cancer patients that can be accessed by researchers. Robust mechanisms and policies have been developed to ensure that patient privacy and confidentiality are preserved while delivering a repository of such medically rich information for the purposes of scientific research.

RESULTS

This paper summarises the overall approach adopted by CLEF to meet data protection requirements, including the data flows, pseudonymisation measures and additional monitoring policies that are currently being developed.

CONCLUSION

Once evaluated, it is hoped that the CLEF approach can serve as a model for other distributed electronic health record repositories to be accessed for research.

Defaults, context, and knowledge: alternatives for OWL-indexed knowledge bases

The new Web Ontology Language (OWL) and its Description Logic compatible sublanguage (OWL-DL) explicitly exclude defaults and exceptions, as do all logic based formalisms for ontologies. However, many biomedical applications appear to require default reasoning, at least if they are to be engineered in a maintainable way. Default reasoning has always been one of the great strengths of Frame systems such as Protégé. Resolving this conflict requires analysis of the different uses for defaults and exceptions. In some cases, alternatives can be provided within the OWL framework; in others, it appears that hybrid reasoning about a knowledge base of contingent facts built around the core ontology is necessary. Trade-offs include both human factors and the scaling of computational performance. The analysis presented here is based on the OpenGALEN experience with large scale ontologies using a formalism, GRAIL, which explicitly incorporates constructs for hybrid reasoning, numerous experiments with OWL, and initial work on combining OWL and Protégé.

Interleukin-1 receptor antagonist VNTR-polymorphism in inflammatory bowel disease

Both genetic and environmental factors have been implicated in the etiology of inflammatory bowel diseases (IBD) i.e., Crohn's disease (CD) and ulcerative colitis (UC). Polymorphisms in cytokine genes are likely to influence an individual's predisposition to IBD. In intron 2 of the interleukin-1 receptor antagonist (IL-1ra) gene, a variable number of an 86-bp tandem repeat (VNTR) polymorphism leads to the existence of five different alleles. In order to analyze the association between certain IL-1ra VNTR-alleles and IBD, we investigated the IL-1ra genotype and allele frequencies in 342 unrelated IBD patients and in 401 healthy control individuals. CD patients were also genotyped for the three main associated variants in the NOD2/CARD15 gene. In the IBD group, a significant decrease in the frequency of IL-1ra allele 1 (P=0.048) compared to controls was observed. The frequency of IL-1ra genotype 1/1 was significantly lower in the IBD population vs the control group (P=0.018). Analysis of the CD population without NOD2 homozygotes and compound heterozygotes revealed a more significant decrease in IL-1ra genotype 1/1 compared to controls (P=0.038). These results support the hypothesis that the IL-1ra VNTR-polymorphism could be among the genetic factors that are of importance in IBD susceptibility.

GALEN ten years on: tasks and supporting tools

The GALEN technology has matured over more than a decade of use. We describe a set of software tools and associated methodologies that together are supporting ontological engineering in a production, rather than a research setting.

Mannan-binding lectin (MBL) gene polymorphisms in ulcerative colitis and Crohn's disease

The inflammatory bowel diseases (IBD), Crohn's disease (CD), and ulcerative colitis (UC), are complex multifactorial traits involving both environmental and genetic factors. Mannan-binding lectin (MBL) plays an important role in non-specific immunity and complement activation. Point mutations in codons 52, 54 and 57 of exon 1 of the MBL gene are associated with decreased MBL plasma concentrations and increased susceptibility to various infectious diseases. If these MBL mutations could lead to susceptibility to putative IBD-etiological microbial agents, or could temper the complement-mediated mucosal damage in IBD, MBL could function as the link between certain microbial, immunological and genetic factors in IBD. In this study, we investigated the presence of the codon 52, 54 and 57 mutations of the MBL gene in 431 unrelated IBD patients, 112 affected and 141 unaffected first-degree relatives, and 308 healthy control individuals. In the group of sporadic IBD patients (n = 340), the frequency of the investigated MBL variants was significantly lower in UC patients when compared with CD patients (P = 0.01) and with controls (P = 0.02). These results suggest that MBL mutations which decrease the formation of functional MBL could protect against the clinical development of sporadic UC, but not of CD. This could be explained by the differential T-helper response in both diseases.

AIM: a personal view of where I have been and where we might be going

My own career in medical informatics and AI in medicine has oscillated between concerns with medical records and concerns with knowledge representation with decision support as a pivotal integrating issue. It has focused on using AI to organise information and reduce 'muddle' and improve the user interfaces to produce 'useful and usable systems' to help doctors with a 'humanly impossible task'. Increasingly knowledge representation and ontologies have become the fulcrum for orchestrating re-use of information and integration of systems. Encouragingly, the dilemma between computational tractability and expressiveness is lessening, and ontologies and description logics are joining the mainstream both in AI in Medicine and in Intelligent Information Management generally. It has been shown possible to scale up ontologies to meet medical needs, and increasingly ontologies are playing a key role in meeting the requirements to scale up the complexity of clinical systems to meet the ever increasing demands brought about by new emphasis on reduction of errors, clinical accountability, and the explosion of knowledge on the Web.

Analysis of the CC chemokine receptor 5 (CCR5) delta-32 polymorphism in inflammatory bowel disease

The inflammatory bowel diseases (IBD) Crohn's disease (CD) and ulcerative colitis (UC) are complex multifactorial traits involving both environmental and genetic factors. Recent studies have shown the important role of pro-inflammatory cytokines and chemokines, including RANTES, in IBD. RANTES is the natural ligand for the CC-chemokine receptor 5 (CCR5). The chromosomal location of the CCR5 gene on 3p21 coincides with an IBD-susceptibility locus identified by genome-wide scanning. A 32-bp deletion (A32) in the CCR5 gene results in a nonfunctional receptor and is found with high frequency in Caucasians. In this study, we investigated the presence of the CCR5delta32 allele in a large cohort of IBD patients and in a healthy control population. Blood samples were obtained from 538 unselected IBD cases (433 unrelated IBD patients: 289 CD, 142 UC, 2 indeterminate colitis; 105 affected first-degree relatives) and 135 unaffected first-degree family members. Of the IBD patients, 36% had familial IBD with at least two members being affected. There were no significant differences in the CCR5delta32 mutation frequency between IBD patients and healthy controls, nor between CD and UC patients. There was no correlation between the CCR5delta32 genotype and the age at IBD-diagnosis, the frequency of surgical intervention, or disease localization. Only the association between CCR5delta32 homozygosity and the presence of anal lesions in CD patients was statistically significant (P=0.007). Analysis by the transmission/disequilibrium test showed no significant transmission distortion to the probands or their clinically silent siblings. Based on these results, it is unlikely that the CCR5delta32 allele is an important marker for predisposition to IBD.

GALEN's model of parts and wholes: experience and comparisons

Part-whole relations play a critical role in the OpenGALEN Common Reference Model. We describe how particular characteristics of the underlying formalism have influenced GALEN's view on partonomy, and in more detail discuss how specific modelling issues have driven development of an extended set of partitive semantic links.

Practical development of re-usable terminologies: GALEN-IN-USE and the GALEN Organisation

Medical terminology is now playing a key role in medical software. This requires new techniques with which many clinical users, classification experts and applications developers are unfamiliar. There is a conflict in that the more re-usable techniques for terminology needed to support sharing of information among many different applications are more difficult to use for any one application. A layered approach to re-use is described which combines techniques from first generation systems and relatively easily understood second generation systems with the formal rigour of third generation systems to resolve this conflict. The methodology also provides a potentially rigorous approach to defining the relationship between terminology and structure in the electronic healthcare record architecture. It provides a natural migration pathway from existing systems to powerful re-usable multilingual terminologies.

A comparison of bone mineral densities among female athletes in impact loading and active loading sports

The purpose of this study was to compare bone mineral densities (BMD) of collegiate female athletes who compete in impact loading sports; volleyball players (N = 8) and gymnasts (N = 13), to a group of athletes who participate in an active loading sport; swimmers (N = 7), and a group of controls (N = 17). All of the volleyball, swimming, and control subjects were eumenorrheic (10-12 cycles/year), whereas two of the gymnasts were amenorrheic (0-3 cycles/year), eight were oligomenorrheic (4-8 cycles/year), and three were eumenorrheic (10-12 cycles/year). Lumbar spine, proximal femur, and total body BMD were measured with dual-energy X-ray absorptiometry. The groups were compared with respect to the following regions: lumbar spine (L1-4); femoral neck; Ward's triangle; right and left arms; right and left legs; pelvis; and torso. When controlling for differences in height and weight the impact loading group (volleyball and gymnastic) had significantly greater BMD at the lumbar spine, femoral neck, Ward's Triangle, and total body when compared to the active loading (swimming) and control groups. The regional analysis from the total body scan revealed that the gymnasts had significantly (p < 0.05) greater BMD than all other groups at the right and left arm sites. The impact loading groups (gymnastic and volleyball) had a greater BMD in the legs and pelvis than the active loading (swimming) and control groups. Furthermore, the impact loading group had a greater torso BMD than the control group. There were no differences at any site between the active loading group (swimming) and control groups.(ABSTRACT TRUNCATED AT 250 WORDS)

Analysis of medical texts based on a sound medical model

Automatic understanding of natural language is a complex task due to the presence of ambiguities. In particular, semantic ambiguities which are often immediately and unconsciously solved by human beings, are raised when analyzing natural language sentences by computer. The latter has to know the implicit and contextual information in order to resolve these difficulties. Nowadays in medicine, a considerable effort is deployed to model semantic contents of the medical domain. Such a task is usually performed separately from linguistic considerations. The goal of this paper is to highlight the key issues of basing a medical language processing system on a sound semantic model. To illustrate the requirements and advantages of such a conceptual approach to the analysis process, the experiment conducted to adjust the RECIT analyzer to the GALEN model is shown.

Modelling for natural language understanding

Natural Language Understanding (NLU) is a rapidly growing field in medical informatics. Its potential for tomorrow's applications is important. However, it is limited by its ability to ground its components on a solid model of the domain. This opens the way for the emergence of the discipline of medical domain modelling, as part of the vast field of Knowledge Base (KB) engineering. This article aims at describing the current development of a multilingual natural language system, strongly oriented towards the semantics of the domain. Special emphasis is presently given to the task of building a domain model, and to establish direct links with the language platform. The result is a model-driven NLU system. Numerous benefits are expected in the long term.

PEN&PAD (Geriatrics): a Collaborative Patient Record System for the shared care of the elderly

The PEN&PAD (Geriatrics) project seeks to develop a Collaborative Patient Record System for the hospital based shared care of the elderly. The goal of the project is to produce a single, integrated information system which is both useful and usable by the different practitioner groups involved in geriatric care. A User Centred Design methodology is proposed which makes users and human issues central to the design and development process. Preliminary results indicate that the specification of a Minimum Basic Data Set as the basis of a shared record system is infeasible and undesirable. An architecture is presented which illustrates how the diversity between the different disciplines may be preserved in a Collaborative Patient Record System.