Natural language processing for mimicking clinical trial recruitment in critical care: a semi-automated simulation based on the LeoPARDS trial

Clinical trials often fail to recruit an adequate number of appropriate patients. Identifying eligible trial participants is resource-intensive when relying on manual review of clinical notes, particularly in critical care settings where the time window is short. Automated review of electronic health records (EHR) may help, but much of the information is in free text rather than a computable form. We applied natural language processing (NLP) to free text EHR data using the CogStack platform to simulate recruitment into the LeoPARDS study, a clinical trial aiming to reduce organ dysfunction in septic shock. We applied an algorithm to identify eligible patients using a moving 1-hour time window, and compared patients identified by our approach with those actually screened and recruited for the trial, for the time period that data were available. We manually reviewed records of a random sample of patients identified by the algorithm but not screened in the original trial. Our method identified 376 patients, including 34 patients with EHR data available who were actually recruited to LeoPARDS in our centre. The sensitivity of CogStack for identifying patients screened was 90% (95% CI 85%, 93%). Of the 203 patients identified by both manual screening and CogStack, the index date matched in 95 (47%) and CogStack was earlier in 94 (47%). In conclusion, analysis of EHR data using NLP could effectively replicate recruitment in a critical care trial, and identify some eligible patients at an earlier stage, potentially improving trial recruitment if implemented in real time

ACE-inhibitors and Angiotensin-2 Receptor Blockers are not associated with severe SARS-COVID19 infection in a multi-site UK acute Hospital Trust

Aims: The SARS‐CoV‐2 virus binds to the angiotensin‐converting enzyme 2 (ACE2) receptor for cell entry. It has been suggested that angiotensin‐converting enzyme inhibitors (ACEi) and angiotensin II receptor blockers (ARB), which are commonly used in patients with hypertension or diabetes and may raise tissue ACE2 levels, could increase the risk of severe COVID‐19 infection. Methods and results: We evaluated this hypothesis in a consecutive cohort of 1200 acute inpatients with COVID‐19 at two hospitals with a multi‐ethnic catchment population in London (UK). The mean age was 68 ± 17 years (57% male) and 74% of patients had at least one comorbidity. Overall, 415 patients (34.6%) reached the primary endpoint of death or transfer to a critical care unit for organ support within 21 days of symptom onset. A total of 399 patients (33.3%) were taking ACEi or ARB. Patients on ACEi/ARB were significantly older and had more comorbidities. The odds ratio for the primary endpoint in patients on ACEi and ARB, after adjustment for age, sex and co‐morbidities, was 0.63 (95% confidence interval 0.47–0.84, P < 0.01). Conclusions: There was no evidence for increased severity of COVID‐19 in hospitalised patients on chronic treatment with ACEi or ARB. A trend towards a beneficial effect of ACEi/ARB requires further evaluation in larger meta‐analyses and randomised clinical trials

Multi-domain clinical natural language processing with MedCAT: The Medical Concept Annotation Toolkit

Electronic health records (EHR) contain large volumes of unstructured text, requiring the application of information extraction (IE) technologies to enable clinical analysis. We present the open source Medical Concept Annotation Toolkit (MedCAT) that provides: (a) a novel self-supervised machine learning algorithm for extracting concepts using any concept vocabulary including UMLS/SNOMED-CT; (b) a feature-rich annotation interface for customizing and training IE models; and (c) integrations to the broader CogStack ecosystem for vendor-agnostic health system deployment. We show improved performance in extracting UMLS concepts from open datasets (F1:0.448-0.738 vs 0.429-0.650). Further real-world validation demonstrates SNOMED-CT extraction at 3 large London hospitals with self-supervised training over ∼8.8B words from ∼17M clinical records and further fine-tuning with ∼6K clinician annotated examples. We show strong transferability (F1 > 0.94) between hospitals, datasets and concept types indicating cross-domain EHR-agnostic utility for accelerated clinical and research use cases

Investigating light sensitivity in bipolar disorder (HELIOS-BD)

Many people with bipolar disorder have disrupted circadian rhythms. This means that the timing of sleep and wake activities becomes out-of-sync with the standard 24-hour cycle. Circadian rhythms are strongly influenced by light levels and previous research suggests that people with bipolar disorder might have a heightened sensitivity to light, causing more circadian rhythm disruption, increasing the potential for triggering a mood switch into mania or depression. Lithium has been in clinical use for over 70 years and is acknowledged to be the most effective long-term treatment for bipolar disorder. Lithium has many reported actions in the body but the precise mechanism of action in bipolar disorder remains an active area of research. Central to this project is recent evidence that lithium may work by stabilising circadian rhythms of mood, cognition and rest/activity. Our primary hypothesis is that people with bipolar disorder have some pathophysiological change at the level of the retina which makes them hypersensitive to the visual and non-visual effects of light, and therefore more susceptible to circadian rhythm dysfunction. We additionally hypothesise that the mood-stabilising medication lithium is effective in bipolar disorder because it reduces this hypersensitivity, making individuals less vulnerable to light-induced circadian disruption. We will recruit 180 participants into the HELIOS-BD study. Over an 18-month period, we will assess visual and non-visual responses to light, as well as retinal microstructure, in people with bipolar disorder compared to healthy controls. Further, we will assess whether individuals with bipolar disorder who are being treated with lithium have less pronounced light responses and attenuated retinal changes compared to individuals with bipolar disorder not being treated with lithium. This study represents a comprehensive investigation of visual and non-visual light responses in a large bipolar disorder population, with great translational potential for patient stratification and treatment innovation.</p

Within-Compound Versus Public Latrine Access and Child Feces Disposal Practices in Low-Income Neighborhoods of Accra, Ghana.

In crowded urban settlements in low-income countries, many households rely on shared sanitation facilities. Shared facilities are not currently considered "improved sanitation" because of concerns about whether hygiene conditions sufficiently protect users from the feces of others. Prevention of fecal exposure at a latrine is only one aspect of sanitary safety. Ensuring consistent use of latrines for feces disposal, especially child feces, is required to reduce fecal contamination in households and communities. Household crowding and shared latrine access are correlated in these settings, rendering latrine use by neighbors sharing communal living areas as critically important for protecting one's own household. This study in Accra, Ghana, found that household access to a within-compound basic latrine was associated with higher latrine use by children of ages 5-12 years and for disposal of feces of children < 5 years, compared with households using public latrines. However, within-compound access was not associated with improved child feces disposal by other caregivers in the compound. Feces was rarely observed in household compounds but was observed more often in compounds with latrines versus compounds relying on public latrines. Escherichia coli and human adenovirus were detected frequently on household surfaces, but concentrations did not differ when compared by latrine access or usage practices. The differences in latrine use for households sharing within-compound versus public latrines in Accra suggest that disaggregated shared sanitation categories may be useful in monitoring global progress in sanitation coverage. However, compound access did not completely ensure that households were protected from feces and microbial contamination

Evapotranspiration and yielding of 2-cut meadow on peat-moorsh soil in the Noteć river valley

W pracy przedstawiono wyniki trzyletnich (1999-2001) badań ewapotranspiracji i plonowania łąki dwukośnej w dolinie Noteci. Celem badań, prowadzonych w lizymetrach, było określenie przebiegu i zmienności ewapotranspiracji oraz plonowania nienawadnianej łąki dwukośnej, nawożonej w małych ilościach, w naturalnych warunkach położenia wody gruntowej i uwilgotnienia gleby. Stosując małą ilość nawozów mineralnych (160 kg NPK&#183ha-&#185), w warunkach braku nawodnień lub z krótkotrwałym nawodnieniem podsiąkowym w okresie szczególnie suchym na glebie torfowo-murszowej średnio zmurszałej, można uzyskać plon siana z łąki dwukośnej około 9 t&#183ha-&#185. Zużycie wody na ewapotransprację wynosi wówczas około 400 mm. Na podstawie uzyskanych wyników pomiarów ewapotranspiracji oraz pomiarów meteorologicznych określono współczynniki roślinno-glebowe do wzoru Penmana w okresach dekadowych. Wykazano ponadto przydatność modelu ewapotranspiracji opartego na metodzie współczynnika roślinno-glebowego do obliczania ewapotranspiracji łąki dwukośnej.Results of the 3-year (1999-2001) study on evapotranspiration and yielding of a 2-cut meadow in the upper Noteć river valley are presented in the paper. The study was aimed to determine in lysimetric experiments the course and variability of evapotranspiration and yielding of a non-irrigated and low-fertilised 2-cut meadow in natural conditions of ground water level and soil moisture. Using low rates of fertilisation (160 kg NPK&#183ha-&#185) without irrigation or with a short-term capillary rising one may obtain a hay yield of 9 t&#183ha-&#185 from moderately mineralised peat-moorsh soil in particularly dry period. Water consumption for evapotranspiration equals then 400 mm. Basing on meteorological and evapotranspiration measurements, the crop-soil coefficients were calculated for the Penman's formula in ten-days time intervals. Evapotranspiration model based on the method of crop-soil coefficients was shown to be useful in calculating water consumption by a two-cut meadow

Daily variability of air temperature and humidity at a height of 2.0 m and 0.5 m in the wet site of the Noteć river valley and the dry site in Bydgoszcz

W pracy przestawiono analizę dobowej zmienności temperatury i wilgotności powietrza w okresie wegetacyjnym w dwóch siedliskach w rejonie Bydgoszczy. Wykazano duże zróżnicowanie wartości, przebiegu w ciągu doby i rozkładu pionowego w przyziemnej warstwie atmosfery: temperatury, wilgotności względnej, ciśnienia pary wodnej i niedosytu wilgotności powietrza. Przyczyną tego zróżnicowania jest uwilgotnienie siedliska glebowo-wodnego oraz pokrywa roślinna. Zmienność temperatury i wilgotności powietrza w ciągu doby i ich pionowy rozkład powodują, że zależności parowania wody od średniego dobowego niedosytu wilgotności powietrza są różne w badanych siedliskach.The paper presents analyses of the variability of air temperature and humidity in the growing season at two sites in the Bydgoszcz region. The values, daily course and vertical distribution of air temperature, relative humidity, vapour pressure and vapour pressure deficit were different in the near ground layer of atmosphere. The moisture of soil-water site and plant cover are the reasons of this variability. Daily variability of air temperature and humidity and their vertical distribution are responsible for different relationships between evapotranspiration and vapour pressure deficit in the studied sites