Text mining for disease surveillance in veterinary clinical data: part one, the language of veterinary clinical records and searching for words.

The development of natural language processing techniques for deriving useful information from unstructured clinical narratives is a fast-paced and rapidly evolving area of machine learning research. Large volumes of veterinary clinical narratives now exist curated by projects such as the Small Animal Veterinary Surveillance Network (SAVSNET) and VetCompass, and the application of such techniques to these datasets is already (and will continue to) improve our understanding of disease and disease patterns within veterinary medicine. In part one of this two part article series, we discuss the importance of understanding the lexical structure of clinical records and discuss the use of basic tools for filtering records based on key words and more complex rule based pattern matching approaches. We discuss the strengths and weaknesses of these approaches highlighting the on-going potential value in using these "traditional" approaches but ultimately recognizing that these approaches constrain how effectively information retrieval can be automated. This sets the scene for the introduction of machine-learning methodologies and the plethora of opportunities for automation of information extraction these present which is discussed in part two of the series.

Evaluating ChatGPT text mining of clinical records for companion animal obesity monitoring.

BACKGROUND: Veterinary clinical narratives remain a largely untapped resource for addressing complex diseases. Here we compare the ability of a large language model (ChatGPT) and a previously developed regular expression (RegexT) to identify overweight body condition scores (BCS) in veterinary narratives pertaining to companion animals. METHODS: BCS values were extracted from 4415 anonymised clinical narratives using either RegexT or by appending the narrative to a prompt sent to ChatGPT, prompting the model to return the BCS information. Data were manually reviewed for comparison. RESULTS: The precision of RegexT was higher (100%, 95% confidence interval [CI] 94.81%-100%) than that of ChatGPT (89.3%, 95% CI 82.75%-93.64%). However, the recall of ChatGPT (100%, 95% CI 96.18%-100%) was considerably higher than that of RegexT (72.6%, 95% CI 63.92%-79.94%). LIMITATIONS: Prior anonymisation and subtle prompt engineering are needed to improve ChatGPT output. CONCLUSIONS: Large language models create diverse opportunities and, while complex, present an intuitive interface to information. However, they require careful implementation to avoid unpredictable errors.

'The Mind' promotes brain synchronization: an ecological evaluation of brain synchronization in co-operative tasks.

This paper presents an ecologically valid approach for using EEG hyperscanning methods to assess levels of interbrain synchrony (IBS) in teams during co-operative tasks. We employ a card-based task in an out-of-the-lab setting to evaluate levels of neural synchrony between team members completing a co-operative task. We also examine the interplay between the recorded synchronization levels and the collective performance of the team.Clinical Relevance- This study provides a simplistic and ecologically valid setup with potential to bring a better understanding of brain synchronization in clinical settings where co-operation would improve outcomes, such as home care facilities and memory clinics.

PetBERT: automated ICD-11 syndromic disease coding for outbreak detection in first opinion veterinary electronic health records.

Effective public health surveillance requires consistent monitoring of disease signals such that researchers and decision-makers can react dynamically to changes in disease occurrence. However, whilst surveillance initiatives exist in production animal veterinary medicine, comparable frameworks for companion animals are lacking. First-opinion veterinary electronic health records (EHRs) have the potential to reveal disease signals and often represent the initial reporting of clinical syndromes in animals presenting for medical attention, highlighting their possible significance in early disease detection. Yet despite their availability, there are limitations surrounding their free text-based nature, inhibiting the ability for national-level mortality and morbidity statistics to occur. This paper presents PetBERT, a large language model trained on over 500 million words from 5.1 million EHRs across the UK. PetBERT-ICD is the additional training of PetBERT as a multi-label classifier for the automated coding of veterinary clinical EHRs with the International Classification of Disease 11 framework, achieving F1 scores exceeding 83% across 20 disease codings with minimal annotations. PetBERT-ICD effectively identifies disease outbreaks, outperforming current clinician-assigned point-of-care labelling strategies up to 3 weeks earlier. The potential for PetBERT-ICD to enhance disease surveillance in veterinary medicine represents a promising avenue for advancing animal health and improving public health outcomes.

CoIR: Compressive Implicit Radar.

Using millimeter wave (mmWave) signals for imaging has an important advantage in that they can penetrate through poor environmental conditions such as fog, dust, and smoke that severely degrade optical-based imaging systems. However, mmWave radars, contrary to cameras and LiDARs, suffer from low angular resolution because of small physical apertures and conventional signal processing techniques. Sparse radar imaging, on the other hand, can increase the aperture size while minimizing the power consumption and read out bandwidth. This paper presents CoIR, an analysis by synthesis method that leverages the implicit neural network bias in convolutional decoders and compressed sensing to perform high accuracy sparse radar imaging. The proposed system is data set-agnostic and does not require any auxiliary sensors for training or testing. We introduce a sparse array design that allows for a 5.5× reduction in the number of antenna elements needed compared to conventional MIMO array designs. We demonstrate our system's improved imaging performance over standard mmWave radars and other competitive untrained methods on both simulated and experimental mmWave radar data.

Seasonality and other risk factors for fleas infestations in domestic dogs and cats.

Fleas in the genus Ctenocephalides are the most clinically important parasitic arthropods of dogs and cats worldwide yet risk factors that might increase the risk of infestation in small animals remains unclear. Here we developed a supervised text mining approach analysing key aspects of flea epidemiology using electronic health records from domestic cats and dogs seen at a sentinel network of 191 voluntary veterinary practices across Great Britain between March 2014 and July 2020. Our methods identified fleas as likely to have been present during 22,276 of 1,902,016 cat consultations (1.17%) and 12,168 of 4,844,850 dog consultations (0.25%). Multivariable logistic regression modelling found that animals originating from areas of least deprivation were associated with 50% reductions in odds of veterinary-recorded flea infestation compared to the most deprived regions in England. Age of the animal was significantly associated with flea presentation in both cats and dogs, with cases peaking before animals reached 12 months. Cases were recorded through each study years, peaking between July and October, with fluctuations between each year. Our findings can be used towards healthcare messaging for veterinary practitioners and owners.

SARS-CoV-2 neutralising antibodies in dogs and cats in the United Kingdom.

Companion animals are susceptible to SARS-CoV-2 infection and sporadic cases of pet infections have occurred in the United Kingdom. Here we present the first large-scale serological survey of SARS-CoV-2 neutralising antibodies in dogs and cats in the UK. Results are reported for 688 sera (454 canine, 234 feline) collected by a large veterinary diagnostic laboratory for routine haematology during three time periods; pre-COVID-19 (January 2020), during the first wave of UK human infections (April-May 2020) and during the second wave of UK human infections (September 2020-February 2021). Both pre-COVID-19 sera and those from the first wave tested negative. However, in sera collected during the second wave, 1.4% (n â€‹= â€‹4) of dogs and 2.2% (n â€‹= â€‹2) of cats tested positive for neutralising antibodies. The low numbers of animals testing positive suggests pet animals are unlikely to be a major reservoir for human infection in the UK. However, continued surveillance of in-contact susceptible animals should be performed as part of ongoing population health surveillance initiatives.

SARS-CoV-2 neutralising antibodies in Dogs and Cats in the United Kingdom.

Companion animals are susceptible to SARS-CoV-2 infection and sporadic cases of pet infections have occurred in the United Kingdom. Here we present the first large-scale serological survey of SARS-CoV-2 neutralising antibodies in dogs and cats in the UK. Results are reported for 688 sera (454 canine, 234 feline) collected by a large veterinary diagnostic laboratory for routine haematology during three time periods; pre-COVID-19 (January 2020), during the first wave of UK human infections (April-May 2020) and during the second wave of UK human infections (September 2020-February 2021). Both pre-COVID-19 sera and those from the first wave tested negative. However, in sera collected during the second wave, 1.4% (n=4) of dogs and 2.2% (n=2) cats tested positive for neutralising antibodies. The low numbers of animals testing positive suggests pet animals are unlikely to be a major reservoir for human infection in the UK. However, continued surveillance of in-contact susceptible animals should be performed as part of ongoing population health surveillance initiatives.

Common concerns, barriers to care, and the lived experience of individuals with hepatitis B: a qualitative study.

BACKGROUND: An estimated between 257 and 292 million people live with chronic HBV globally. While much is known about the causes, and epidemiology of HBV, little is understood about the quality of life and impact of HBV on those living with the infection. METHODS: A random sample of HBV-related email queries sent to the Hepatitis B Foundation, a U.S.-based non-profit organization, over a 12-month period in 2018-2019 were retrieved, tabulated, and analyzed qualitatively to highlight information needs and explore the experiences of people living with HBV and their families and loved ones. Codebook development was informed by the literature and through line-by-line reading of a sub-sample of queries. Data analysis was facilitated by NVivo12 software. Data were coded independently by two members of the research team and intercoder reliability was assessed to assure coding accuracy throughout the coding phase. RESULTS: A total of 338 queries from people around the globe were identified and analyzed. The analysis revealed three thematic groups: 1) health-specific challenges associated with diagnosis and treatment, 2) emotional needs related to experiences with HBV stigma, discrimination, fear, social isolation, and distress and 3) informational needs related to HBV prevention and transmission, and interpretation of laboratory tests. CONCLUSIONS: People living with HBV are in need of information to manage their disease and prevent its spread. Analysis of queries uncovered significant misconceptions about HBV transmission and treatment. Additionally, the emotional and psychological impact of an HBV diagnosis on those living with the infection is significant. There is a clear need for patient and community education to expand knowledge and awareness of HBV globally to achieve 2030 WHO HBV elimination goals.

Needs of Individuals Living With Hepatitis Delta Virus and Their Caregivers, 2016-2019.

INTRODUCTION: Hepatitis delta virus (HDV) is a serious coinfection of the hepatitis B virus (HBV) that is estimated to affect between 48 to 72 million people worldwide. Data are limited on the informational needs of people living with HDV. The Hepatitis B Foundation, a US-based nonprofit organization that provides support to people living with HBV and HDV, receives emails (queries) as part of a helpline, a service to provide information, resources, and support to people affected by HBV and HDV. METHODS: Query content was analyzed to assess the impact of HDV at the individual level. A total of 65 HDV-related queries from 17 countries were received from October 2016 to January 2019, and all were analyzed for this study. RESULTS: Thematic analysis of queries indicated 4 dominant themes. Three were related to a need for information about 1) the disease and prevention of it, 2) disease symptoms and outcomes, and 3) treatment options. The fourth theme was related to barriers and quality of life. Individuals requested information on treatment options, medication access, diagnostic test interpretation, and clinical trials. CONCLUSION: Our study highlights the needs and lived experience of patients with HDV and summarizes critical information gaps. Findings can inform health care providers, public health professionals, and the pharmaceutical and biotechnology industries about the informational needs and lived experiences of individuals living with HDV and help create future HDV-related educational resources, care, and clinical trials.

Seasonality and risk factors for myxomatosis in pet rabbits in Great Britain.

Myxomatosis is a highly contagious, frequently fatal viral disease affecting both wild and domesticated European rabbits across many areas of the world. Here we used electronic health records (EHRs) collected from pet rabbits attending a sentinel voluntary network of 191 veterinary practices across Great Britain (GB) between March 2014 and June 2019 to identify new features of this disease's epidemiology. From a total of 89,408 rabbit consultations, text mining verified by domain experts identified 207 (0.23 %) cases where myxomatosis was the only differential diagnosis recorded by the attending practitioner. Cases occurred in all months but February and were distributed across the country. Consistent with studies in wild rabbits, the majority of cases occurred between August and November. However, there was also evidence for considerable variation between years. A nested case control study identified important risk factors for myxomatosis within this pet animal population including season, sex, age, vaccination status and distance to likely wild rabbit habitats. Female entire rabbits were twice as likely to be a case (odds ratio (OR) 1.98, 95 % confidence interval (CI) 1.26-3.13, p = 0.003), suggesting a novel role for behaviour in driving transmission from wild to domesticated rabbits. Vaccination had the largest protective effect with vaccinated rabbits being 8.3 times less likely to be a case than unvaccinated rabbits (OR = 0.12, 95 % CI 0.06-0.21, p = <0.001).

Towards prompt electrocardiogram acquisition in triage: Preliminary testing of a symptom-based clinical prediction rule for the Android tablet.

BACKGROUND: For patients with suspected acute coronary syndrome, international guidelines indicate that an Electrocardiogram (ECG) should be performed within 10 min of first medical contact, however success at achieving these guidelines is limited. AIMS: The purpose of this study was to develop and perform initial testing of a clinical prediction rule embedded in a tablet application, and to expedite the identification of patients who require an electrocardiogram within 10 min. METHODS: This derivation of the Acute Coronary Syndrome Application (AcSAP) comprised of three local studies, an unpublished audit and literature critique. The AcSAP was prospectively tested over four months in patients presenting to the Emergency Department (ED) of a Dublin teaching hospital. An audit form retrieved data pertaining to times of: registration to the emergency department, triage, first electrocardiogram and diagnosis. The AcSAP was subsequently evaluated by experienced triage nurses ( n=18) who had utilised it. RESULTS: The AcSAP was activated 379 times. Patients with ST Elevation Myocardial Infarction (STEMI) and non-ST Elevation Myocardial Infarction (NSTEMI) were significantly more likely to return a categorisation of 'immediate ECG' or 'ECG within 10 min' ( p<0.001). There was a significant difference in 'triage to ECG' times across categories, the 'immediate ECG' categorisation resulting in the shortest time ( p=0.002). Evaluations suggest that staff found the tool quick and easy to use and results seemed accurate. CONCLUSION: Testing of the AcSAP suggests that it accurately identifies patients who require an ECG within 10 min. As such, it has the potential to support the meeting of clinical guidelines for ECG acquisition.

The Effect of Sacrificing the Posterior Cruciate Ligament in Total Knee Arthroplasties That Use a Highly Congruent Polyethylene Component.

BACKGROUND: There is continued debate regarding retention versus sacrificing of the posterior cruciate ligament (PCL) in total knee arthroplasty (TKA). We sought to determine if there was a difference in range of motion (ROM) after TKA between patients with PCL sacrifice versus PCL retention when using a highly congruent polyethylene insert. METHODS: We conducted an Institutional Review Board approved retrospective study of consecutive patients receiving TKA using the same implant with a highly congruent polyethylene component implanted by one surgeon from November 2013 to January 2016. Patients were placed in 2 groups based on whether the PCL was intact or released at the time of surgery. Patient charts were reviewed for age, body mass index, PCL status at surgery (incompetent, kept intact, or released), and preoperative/postoperative knee ROM. RESULTS: Both groups were similar in average age (60.5 vs 60.6, respectively) and body mass index (33.3 vs 32.6, respectively). Postoperative tibial slope (5.5° PCL release, 6.6° PCL retained, P = .028) was the only alignment variable reaching significance; all other alignment and motion variables were similar. CONCLUSION: Results indicate that the PCL can be successfully retained with the use of a congruent bearing design, with no evident limitation in postoperative ROM or loss of stability due to the bearing in comparison to patients who undergo PCL release.

Genetic susceptibility to cerebrovascular disease: A systematic review.

Investigation of genetic susceptibility to cerebrovascular disease has been of growing interest. A systematic review of human studies assessing neurogenomic aspects of cerebrovascular disease was performed according to the preferred reporting items for systematic reviews and meta-analyses (PRISMA) statement. Any association study exploring genetic variants located in the exome associated with one of the major cerebrovascular diseases with at least 500 subjects was eligible for inclusion. Of 6874 manuscripts identified, 35 studies met the inclusion criteria. Most studies of interest focused on ischemic stroke and cerebrovascular occlusive disease. Large cohort genetic association studies on hemorrhagic cerebrovascular disease were less common. In addition to rare, well-established monogenic conditions with significant risk for cerebrovascular disease, a number of genetic variants are also relevant to cerebrovascular pathogenesis as part of a multifactorial process. The 45 polymorphisms identified were located in genes involved in processes related to endothelial and vascular health (15 (33.4%) variants), plasma lipid metabolism (10 (22.2%) variants), inflammation (9 (20%) variants), coagulation (3 (6.7%) variants), and blood pressure modulation (2 (4.4%) variants), and other (6 (13.3%) variants). This work represents a comprehensive overview of genetic variants in the exome relevant to ischemic and hemorrhagic stroke pathophysiology.

Adjuvanted influenza-H1N1 vaccination reveals lymphoid signatures of age-dependent early responses and of clinical adverse events.

Adjuvanted vaccines afford invaluable protection against disease, and the molecular and cellular changes they induce offer direct insight into human immunobiology. Here we show that within 24 h of receiving adjuvanted swine flu vaccine, healthy individuals made expansive, complex molecular and cellular responses that included overt lymphoid as well as myeloid contributions. Unexpectedly, this early response was subtly but significantly different in people older than ∼35 years. Wide-ranging adverse clinical events can seriously confound vaccine adoption, but whether there are immunological correlates of these is unknown. Here we identify a molecular signature of adverse events that was commonly associated with an existing B cell phenotype. Thus immunophenotypic variation among healthy humans may be manifest in complex pathophysiological responses.

Risk of thromboembolic disease in men with prostate cancer undergoing androgen deprivation therapy.

OBJECTIVES: To investigate the risk of thromboembolic disease (TED) in men with prostate cancer (PCa) on androgen deprivation therapy (ADT), while accounting for known TED risk factors. MATERIALS AND METHODS: We assessed TED risk for 42 263 men with PCa who were receiving ADT compared with a matched cohort of 190 930 without PCa. The associations between ADT and deep vein thrombosis (DVT) or pulmonary embolism (PE) were analysed using multivariate Cox proportional hazard regression models, while accounting for previous PCa-related surgeries and the following proxies for disease progression: transurethral resection of the prostate, palliative radiotherapy and nephrostomy. RESULTS: Between 1997 and 2013, 11 242 men with PCa received anti-androgen monotherapy, 26 959 men received gonadotropin-releasing hormone (GnRH) agonists, 1 091 men received combined androgen blockade and 3 789 men underwent orchiectomy. When accounting for previous surgeries and proxies of disease progression, GnRH agonist users and surgically castrated men had a higher risk of TED than the comparison cohort: hazard ratios (HRs) 1.67 (95% confidence interval [CI] 1.40-1.98) and 1.61 (95% CI 1.15-2.28), respectively. Men on anti-androgen monotherapy had a lower risk: HR for DVT 0.49 (95% CI 0.33-0.74). TED risk was highest among those who switched from anti-androgen to GnRH agonists: HR for PE 2.55 (95% CI 1.76-3.70). This increased from 2.52 (95% CI 1.54-4.12) in year 1, to 4.05 (95% CI 2.51-6.55) in year 2. CONCLUSION: The incidence of TED among men on ADT increased with the duration of therapy and the risk was highest for those who switched regimen, suggesting that disease progression as well as ADT contribute to the propagation of TED risk. Nonetheless, these findings support the hypothesis that only men with a relevant indication should receive systemic ADT.

Risk and timing of cardiovascular disease after androgen-deprivation therapy in men with prostate cancer.

PURPOSE: Findings on the association between risk of cardiovascular disease (CVD) and the duration and type of androgen-deprivation therapy (ADT) in men with prostate cancer (PCa) are inconsistent. METHODS: By using data on filled drug prescriptions in Swedish national health care registers, we investigated the risk of CVD in a cohort of 41,362 men with PCa on ADT compared with an age-matched, PCa-free comparison cohort (n = 187,785) by use of multivariable Cox proportional hazards regression models. RESULTS: From 2006 to 2012, 10,656 men were on antiandrogens (AA), 26,959 were on gonadotropin-releasing hormone (GnRH) agonists, and 3,747 underwent surgical orchiectomy. CVD risk was increased in men on GnRH agonists compared with the comparison cohort (hazard ratio [HR] of incident CVD, 1.21; 95% CI, 1.18 to 1.25; and orchiectomy: HR, 1.16; 95% CI, 1.08 to 1.25). Men with PCa on AA were at decreased risk (HR of incident CVD, 0.87; 95% CI, 0.82 to 0.91). CVD risk was highest during the first 6 months of ADT in men who experienced two or more cardiovascular events before therapy, with an HR of CVD during the first 6 months of GnRH agonist therapy of 1.91 (95% CI, 1.66 to 2.20), an HR of CVD with AA of 1.60 (95% CI, 1.24 to 2.06), and an HR of CVD with orchiectomy of 1.79 (95% CI, 1.16 to 2.76) versus the comparison cohort. CONCLUSION: Our results support that there should be a solid indication for ADT in men with PCa so that benefit outweighs potential harm; this is of particular importance among men with a recent history of CVD.