Risk factors and implications associated with ultrasound-diagnosed nephrocalcinosis in cats with chronic kidney disease.

BACKGROUND: Microscopic nephrocalcinosis is a common pathological feature of chronic kidney disease (CKD) in cats. Detection of macroscopic nephrocalcinosis using ultrasonography and its implications remain unexplored. OBJECTIVES: Identify risk factors associated with ultrasound-diagnosed nephrocalcinosis and evaluate the influence of nephrocalcinosis on CKD progression. ANIMALS: Thirty-six euthyroid client-owned cats with CKD. METHODS: Prospective cohort study. Cats with CKD with and without ionized hypercalcemia were enrolled for renal ultrasonography. Cats were categorized according to the presence or absence of ultrasound-diagnosed nephrocalcinosis. Binary logistic regression was performed to identify nephrocalcinosis risk factors. The influence of nephrocalcinosis on CKD progression was assessed using linear mixed models. RESULTS: Ultrasound-diagnosed nephrocalcinosis was evident in 61% of CKD cats overall, with increased prevalence (81%) in those with hypercalcemia. At enrollment, higher blood ionized calcium concentration (odds ratio [OR], 1.27 per 0.1 mg/dL; P = .01), plasma phosphate concentration (OR, 1.16 per 0.1 mg/dL; P = .05), plasma creatinine concentration (OR, 1.29 per 0.1 mg/dL; P = .02) and alanine aminotransferase activity (OR, 2.08 per 10 U/L; P = .04) were independent nephrocalcinosis risk factors. The rate of change in log-transformed fibroblast growth factor-23 differed significantly between groups (P = .04). Cats with CKD and nephrocalcinosis had increasing plasma creatinine concentrations (.03 ± .01 mg/dL/month; P = .04) and phosphate concentrations (.06 ± .02 mg/dL/month; P < .001) and decreasing body weight (.02 ± .01 kg/month; P < .001) over time. CONCLUSIONS AND CLINICAL IMPORTANCE: Nephrocalcinosis is prevalent in cats with CKD, especially in those with hypercalcemia. This pathological feature appears to be associated with CKD progression in cats.

Target Trial Emulation: Does surgical versus non-surgical management of cranial cruciate ligament rupture in dogs cause different outcomes?

Target trial emulation applies design principles from randomised controlled trials to the analysis of observational data for causal inference and is increasingly used within human epidemiology. Using anonymised veterinary clinical data from the VetCompass Programme, this study applied the target trial emulation framework to determine whether surgical (compared to non-surgical) management for cranial cruciate ligament (CCL) rupture in dogs causes improved short- and long-term lameness and analgesia outcomes. The emulated target trial included dogs diagnosed with CCL rupture between January 1, 2019 and December 31, 2019 within the VetCompass database. Inclusion in the emulated trial required dogs aged ≥ 1.5 and < 12 years, first diagnosed with unilateral CCL rupture during 2019 and with no prior history of contralateral ligament rupture or stifle surgery. Dogs were retrospectively observed to have surgical or non-surgical management. Informed from a directed acyclic graph derived from expert opinion, data on the following variables were collected: age, breed, bodyweight, neuter status, insurance status, non-orthopaedic comorbidities, orthopaedic comorbidities and veterinary group. Inverse probability of treatment weighting (IPTW) was used to adjust for confounding, with weights calculated based on a binary logistic regression exposure model. Censored dogs were accounted for in the IPTW analysis using inverse probability of censoring weighting (IPCW). The IPCWs were combined with IPTWs and used to weight each dog's contribution to binary logistic regression outcome models. Standardized mean differences (SMD) examined the balance of covariate distribution between treatment groups. The emulated trial included 615 surgical CCL rupture cases and 200 non-surgical cases. The risk difference for short-term lameness in surgically managed cases (compared with non-surgically managed cases) was -25.7% (95% confidence interval (CI) -36.7% to -15.9%) and the risk difference for long-term lameness -31.7% (95% CI -37.9% to -18.1%). The study demonstrated the application of the target trial framework to veterinary observational data. The findings show that surgical management causes a reduction in short- and long-term lameness compared with non-surgical management in dogs.

Rh proteins and H+ transporters involved in ammonia excretion in Amur Ide (Leuciscus waleckii) under high alkali exposure.

High alkaline environment can lead to respiratory alkalosis and ammonia toxification to freshwater fish. However, the Amur ide (Leuciscus waleckii), which inhabits an extremely alkaline lake in China with titratable alkalinity up to 53.57 mM (pH 9.6) has developed special physiological and molecular mechanisms to adapt to such an environment. Nevertheless, how the Amur ide can maintain acid-base balance and perform ammonia detoxification effectively remains unclear. Therefore, this study was designed to study the ammonia excretion rate (Tamm), total nitrogen accumulation in blood and tissues, including identification, expression, and localization of ammonia-related transporters in gills of both the alkali and freshwater forms of the Amur ide. The results showed that the freshwater form Amur ide does not have a perfect ammonia excretion mechanism exposed to high-alkaline condition. Nevertheless, the alkali form of Amur ide was able to excrete ammonia better than freshwater from Amur ide, which was facilitated by the ionocytes transporters (Rhbg, Rhcg1, Na+/H+ exchanger 2 (NHE2), and V-type H+ ATPase (VHA)) in the gills. Converting ammonia into urea served as an ammonia detoxication strategy to reduced endogenous ammonia accumulation under high-alkaline environment.

Female tilapia, Oreochromis sp. mobilised energy differently for growth and reproduction according to living environment.

This study was conducted to investigate the energy mobilisation preference and ionoregulation pattern of female tilapia, Oreochromis sp. living in different environments. Three different treatments of tilapia as physiology compromising model were compared; tilapia cultured in recirculating aquaculture system (RAS as Treatment I-RAS), tilapia cultured in open water cage (Treatment II-Cage) and tilapia transferred from cage and cultured in RAS (Treatment III-Compensation). Results revealed that tilapia from Treatment I and III mobilised lipid to support gonadogenesis, whilst Treatment II tilapia mobilised glycogen as primary energy for daily exercise activity and reserved protein for growth. The gills and kidney Na+/K+ ATPase (NKA) activities remained relatively stable to maintain homeostasis with a stable Na+ and K+ levels. As a remark, this study revealed that tilapia strategized their energy mobilisation preference in accessing glycogen as an easy energy to support exercise metabolism and protein somatogenesis in cage culture condition, while tilapia cultured in RAS mobilised lipid for gonadagenesis purposes.

Detection of nephrocalcinosis using ultrasonography, micro-computed tomography, and histopathology in cats.

BACKGROUND: Identification of nephrocalcinosis in cats with chronic kidney disease (CKD) is of clinical interest but the ability of ultrasonography to detect nephrocalcinosis is uncertain. OBJECTIVES: To compare ultrasonography, micro-computed tomography (µCT) and histopathology for identification of nephrocalcinosis. ANIMALS: Twelve kidneys from 7 euthyroid client-owned cats with CKD. METHODS: Descriptive study. Renal ultrasonography was performed ante-mortem for nephrocalcinosis detection. Kidneys were grouped based on nephrocalcinosis: present, suspected, or absent. When cats died, necropsy was performed. Renal tissue was evaluated using µCT for macroscopic nephrocalcinosis, and nephrocalcinosis volume-to-kidney tissue ratio (macro-VN:KT) and sagittal nephrocalcinosis area-to-kidney tissue ratio (macro-AN:KT) were calculated. Each kidney subsequently was bisected longitudinally, formalin-fixed, and paraffin-embedded for microscopic nephrocalcinosis assessment using von Kossa and Alizarin red staining with AN:KT (VK-micro-AN:KT and AR-micro-AN:KT) quantified using ImageJ. Data are presented as median (range). Relationships between macroscopic and microscopic AN:KT were assessed using Spearman's correlation. RESULTS: Nephrocalcinosis by ultrasonography was considered to be absent in 3, suspected in 3, and present in 5 kidneys; 1 kidney had nephrolithiasis with nephrocalcinosis. The macro-VN:KT was 0.001%, 0.001%, and 0.019%, and the macro-AN:KT was 0.08%, 0.30%, and 1.47%, respectively. Histologically, VK-micro-AN:KT was 0.21%, 2.85%, and 4.56%, and AR-micro-AN:KT was 1.73%, 5.82%, and 8.90% for kidneys where ultrasonographic macro-nephrocalcinosis was absent, suspected, or present, respectively. A strong correlation was identified between macroscopic (macro-AN:KT) and microscopic (VK-micro-AN:KT) nephrocalcinosis (rs = 0.76; P = .01). CONCLUSIONS AND CLINICAL IMPORTANCE: Ultrasonographically diagnosed nephrocalcinosis correlates well with macroscopic and microscopic nephrocalcinosis at necropsy despite their separation in time.

Hoven's carp Leptobarbus hoevenii strategized metabolism needs to cope with changing environment.

Current water warming and freshwater acidification undoubtedly affect the life of aquatic animals especially ammonotelic teleost by altering their physiological responses. The effect of temperature (28 °C vs 32 °C) and pH (7 vs. 5) on the metabolic compromising strategies of Hoven's carp (Leptobarbus hoevenii) was investigated in this study. Fishes were conditioned to (i) 28 °C + pH 7 (N28°C); (ii) 32 °C + pH 7 (N32°C); (iii) 28 °C + pH 5 (L28°C) and (iv) 32 °C + pH 5 (L32°C) for 20 days followed by osmorespiration assay. Results showed that feeding performance of Hoven's carp was significantly depressed when exposed to low pH conditions (L28°C and L32°C). However, by exposed Hoven's carp to L32°C induced high metabolic oxygen intake and ammonia excretion to about 2x-folds higher compared to the control group. As for energy mobilization, Hoven's carp mobilized liver and muscle protein under L28°C condition. Whereas under high temperature in both pH, Hoven's carp had the tendency to reserve energy in both of liver and muscle. The findings of this study revealed that Hoven's carp is sensitive to lower water pH and high temperature, thereby they remodeled their physiological needs to cope with the environmental changes condition.

Bayesian phase II adaptive randomization by jointly modeling efficacy and toxicity as time-to-event outcomes.

The main goals of Phase II trials are to identify the therapeutic efficacy of new treatments and continue monitoring all the possible adverse effects. In Phase II trials, it is important to develop an adaptive randomization (AR) procedure that takes into account both the efficacy and toxicity. In most existing articles, toxicity is modeled as a binary endpoint through an unobservable random effect (frailty) to link the efficacy and toxicity. However, this approach does not capture toxicity profiles that evolve over time. In this article, we propose a new Bayesian adaptive randomization (BAR) procedure using the covariate-adjusted efficacy-toxicity ratio (ETR) index, where efficacy and toxicity are jointly modelled as time-to-event (TTE) outcomes. Furthermore, we also propose early stopping rules for toxicity and futility such that inferior treatments can be dropped at earlier time of trial. Simulation results show that compared to the BAR procedures based solely on the efficacy and that based on TTE efficacy and binary toxicity outcomes, the proposed BAR procedure can better identify the difference in treatment toxicity such that it can assign more patients to the superior treatment arm under some scenarios.

Factors associated with insulin responses to oral sugars in a mixed-breed cohort of ponies.

BACKGROUND: Serum insulin concentration at 60 min (InsulinT60) during an oral sugar test (OST) indicates future laminitis risk and insulin dysregulation (ID). Associations between InsulinT60 and physical and owner-reported variables may help clinicians select individuals for ID testing. Associations between InsulinT60 and other metabolic markers may help elucidate ID pathophysiology. OBJECTIVES: To describe associations between (A) season, physically-apparent and owner-reported factors and binary InsulinT60 interpretation (initial models) and (B) variables included in the initial models, other metabolic markers and continuous InsulinT60 (full models). STUDY DESIGN: Prospective longitudinal. METHODS: Non-laminitic ponies were examined and OSTs (0.3 mL/kg Karo syrup) performed every 6 months (autumn and spring) for ≤4 years. Factors associated with InsulinT60 were determined using mixed-effects models with physical, owner-reported, season and serum/plasma markers as fixed effects and pony and premises identifiers as random effects. Autumn and spring data were analysed separately for full models. RESULTS: One thousand seven hundred and sixty-three OSTs from 367 ponies were included. High-risk InsulinT60 (>153 µIU/mL) was independently associated with (odds ratio, 95% confidence interval [CI]): age (1.36, 1.16-1.60), body condition score (BCS) (2.38, 1.21-4.69), and bulging supraorbital fatpads (7.25, 2.1-24.98). However, the initial models provided little explanatory power (Nakagawa R2 = 0.1-0.27). LoginsulinT60 was independently associated with (effect estimate, 95% CI): age (0.02, 0.01-0.04), Welsh/Welsh X breed (0.22, 0.05, 0.39), sex (gelding = -0.2, -0.34 to 0.06), BCS (0.16, 0.08-0.23), plasma adiponectin (-0.02, -0.02 to 0.01) and basal insulin (0.01, 0.01-0.01) in spring, and: age (0.03, 0.02-0.04), BCS (0.17, 0.08-0.26), bulging supraorbital fatpads (0.37, 0.2-0.54), turnout score (0.05, 0.02-0.09), plasma adiponectin (-0.01, -0.02 to 0.01), ACTH (per 10 pg/mL) (0.01, 0.00-0.01), triglycerides (0.28, 0.07-0.49) and InsulinT0 (0.01, 0.01-0.01) in autumn. MAIN LIMITATIONS: Only non-laminitic ponies in one region were included. CONCLUSIONS: Owner-reported and physically-apparent data were limited InsulinT60 predictors. InsulinT60 is a complex trait, independently associated with numerous variables, some with seasonal interactions.

Intervention with impact: Reduced isolation of methicillin-resistant Staphylococcus pseudintermedius from dogs following the introduction of antimicrobial prescribing legislation in Germany.

BACKGROUND: Legislation was introduced in Germany in 2018, requiring bacterial culture and antimicrobial susceptibility testing before the prescription of fluoroquinolones and third-generation cephalosporins to dogs. We hypothesised that, following this intervention, the number of clinical samples testing positive for methicillin-resistant Staphylococcus pseudintermedius (MRSP) would reduce. METHODS: Reports of S. pseudintermedius isolated from canine clinical samples by three German veterinary diagnostic microbiology laboratories during the 38 months before the introduction of the legislation and the 46 months after were compared. Bacterial identification was performed by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry, and antimicrobial susceptibility testing followed recognised recommendations but with changes during the study period. RESULTS: Among a total of 120,571 S. pseudintermedius isolates, MRSP accounted for 7.1% overall. Following the legislative intervention, monthly submissions yielding S. pseudintermedius increased at all three laboratories. The MRSP percentage was lower in the period after the intervention in two of the three laboratories (p < 0.001); in the third laboratory, there was no change between periods, but a year-on-year reduction in MRSP percentages occurred after the intervention (p = 0.0004). LIMITATIONS: Changing susceptibility testing methods limited the direct comparison of resistance patterns among laboratories. CONCLUSION: The reduction in MRSP in canine clinical samples following the introduction of this legislation suggests a positive impact of compulsory laboratory testing on reducing antimicrobial resistance.

A direct healthcare cost analysis of recombinant LH versus hMG supplementation on FSH during controlled ovarian hyperstimulation in the GnRH-antagonist protocol.

PURPOSE: We have previously published a retrospective matched-case control study comparing the effect of recombinant LH (r-hLH) versus highly purified human menopausal gonadotropin (hMG) supplementation on the follicle-stimulating hormone (FSH) during controlled ovarian hyperstimulation (COH) in the GnRH-antagonist protocol. The result from that study showed that the cumulative live birth rate (CLBR) was significantly higher in the r-hLH group (53% vs. 64%, p = 0.02). In this study, we aim to do a cost analysis between these two groups based on our previous study. METHODS: The analysis consisted of 425 IVF and ICSI cycles in our previous study. There were 259 cycles in the r-hFSH + hMG group and 166 cycles in the r-hFSH + r-hLH group. The total cost related to the treatment of each patient was recorded. Probabilistic sensitivity analysis (PSA) and a cost-effectiveness acceptability curve (CEAC) were performed and created. RESULTS: The total treatment cost per patient was significantly higher in the r-hFSH + r-hLH group than in the r-hFSH + hMG group ($4550 ± 798.86 vs. $4290 ± 734.6, p = 0.003). However, the mean cost per live birth in the r-hFSH + hMG group was higher at $8052, vs. $7059 in the r-hFSH + r-hLH group. The CEAC showed that treatment with hFSH + r-hLH proved to be more cost-effective than treatment with r-hFSH + hMG. Willingness-to-pay was evident when considering a hypothetical threshold of $18,513, with the r-hFSH + r-hLH group exhibiting a 99% probability of being considered cost-effective. CONCLUSION: The cost analysis showed that recombinant LH is more cost-effective than hMG supplementation on r-hFSH during COH in the GnRH-antagonist protocol.

Comparison of ultrasonographic and computed tomographic imaging of equine thoracolumbar articular process joints.

BACKGROUND: Osteoarthritis of the equine thoracolumbar articular process joints (APJs) has been linked to back pain. Changes are commonly diagnosed through nuclear scintigraphy, radiography and ultrasonography (US). OBJECTIVES: (1) To assess the agreement of APJ grades between US and computed tomography (CT) images; (2) to assess the effect of location on the agreement of APJ grades between US and CT images. It was hypothesised that: (1) Periarticular modelling and modification of the joint space would have the highest and lowest agreement between US and CT images, respectively; (2) Caudal thoracolumbar APJ grades would have higher agreement between US and CT images than mid thoracic APJs. STUDY DESIGN: Comparative diagnostic imaging study using cadaveric specimens. METHODS: Disarticulated thoracolumbar spines of six equids euthanised for reasons unrelated to back pain, underwent US and CT examination of the APJs. Images were assessed for periarticular modelling, modification of the joint space and enlargement of the APJ. Intra-observer, inter-modality and inter-observer agreement using multilevel weighted kappa statistics to evaluate the effects of location, US/CT characteristic and their interaction. RESULTS: Intra-observer agreement of US and CT grades ranged from moderate to perfect. Between T15 and L1, inter-modality agreement (CT vs. US) for periarticular modelling was moderate, and fair for enlargement and modification of the joint space. Inter-observer agreement (US vs. US) of periarticular modelling was substantial between T15 and L1, moderate between L1 and L5 and fair between T10 and T15. Wide confidence intervals (CIs) seen for most grades apart from inter-observer grades of periarticular modelling at T15-L5, introducing a degree of uncertainty into the results. MAIN LIMITATIONS: Large prevalence index influenced kappa values, small sample size. CONCLUSIONS: Good inter-observer (US vs. US) and inter-modality (CT vs. US) agreement of caudal thoracolumbar APJ periarticular modelling. This US characteristic provides a measure of bone change, therefore supporting the use of diagnostic ultrasound. Inter-modality CIs were wide, highlighting the study and imaging modality limitations.

Target trial emulation: Do antimicrobials or gastrointestinal nutraceuticals prescribed at first presentation for acute diarrhoea cause a better clinical outcome in dogs under primary veterinary care in the UK?

Target trial emulation applies design principles from randomised controlled trials to the analysis of observational data for causal inference and is increasingly used within human epidemiology. Veterinary electronic clinical records represent a potentially valuable source of information to estimate real-world causal effects for companion animal species. This study employed the target trial framework to evaluate the usefulness on veterinary observational data. Acute diarrhoea in dogs was used as a clinical exemplar. Inclusion required dogs aged ≥ 3 months and < 10 years, presenting for veterinary primary care with acute diarrhoea during 2019. Treatment strategies were: 1. antimicrobial prescription compared to no antimicrobial prescription and 2. gastrointestinal nutraceutical prescription compared to no gastrointestinal nutraceutical prescription. The primary outcome was clinical resolution (defined as no revisit with ongoing diarrhoea within 30 days from the date of first presentation). Informed from a directed acyclic graph, data on the following covariates were collected: age, breed, bodyweight, insurance status, comorbidities, vomiting, reduced appetite, haematochezia, pyrexia, duration, additional treatment prescription and veterinary group. Inverse probability of treatment weighting was used to balance covariates between the treatment groups for each of the two target trials. The risk difference (RD) of 0.4% (95% CI -4.5% to 5.3%) was non-significant for clinical resolution in dogs treated with antimicrobials compared with dogs not treated with antimicrobials. The risk difference (RD) of 0.3% (95% CI -4.5% to 5.0%) was non-significant for clinical resolution in dogs treated with gastrointestinal nutraceuticals compared with dogs not treated with gastrointestinal nutraceuticals. This study successfully applied the target trial framework to veterinary observational data. The findings show that antimicrobial or gastrointestinal prescription at first presentation of acute diarrhoea in dogs causes no difference in clinical resolution. The findings support the recommendation for veterinary professionals to limit antimicrobial use for acute diarrhoea in dogs.

Assessing the potential impact of applying a higher sensitivity test to selected cattle populations for the control of bovine tuberculosis in England.

Bovine tuberculosis (bTB) continues to be the costliest, most complex animal health problem in England. The effectiveness of the test-and-slaughter policy is hampered by the imperfect sensitivity of the surveillance tests. Up to half of recurrent incidents within 24 months of a previous one could have been due to undetected infected cattle not being removed. Improving diagnostic testing with more sensitive tests, like the interferon (IFN)-gamma test, is one of the government's top priorities. However, blanket deployment of such tests could result in more false positive results (due to imperfect specificity), together with logistical and cost-efficiency challenges. A targeted application of such tests in higher prevalence scenarios, such as a subpopulation of high-risk herds, could mitigate against these challenges. We developed classification machine learning algorithms (using 80% of 2012-2019 bTB surveillance data as the training set) to evaluate the deployment of IFN-gamma testing in high-risk herds (i.e. those at risk of an incident in England) in two testing data sets: i) the remaining 20% of 2012-19 data, and ii) 2020 bTB surveillance data. The resulting model, classification tree analysis, with an area under a receiver operating characteristic (ROC) curve (AUC) > 95, showed a 73% sensitivity and a 97% specificity in the 2012-2019 test dataset. Used on 2020 data, it predicted eight percent (3 510 of 41 493) of eligible active herds as at-risk of a bTB incident, the majority of them (66% or 2 328 herds) experiencing at least one. Whilst all predicted at-risk herds could have preventive measures applied, the additional application of IFN-gamma test in parallel interpretation to the statutory skin test, if the risk materialises, would have resulted in 8 585 additional IFN-gamma reactors detected (a 217% increase over the 2 710 IFN-gamma reactors already detected by tests carried out). Only 18% (330 of 1 819) of incidents in predicted high-risk herds had the IFN-gamma test applied in 2020. We therefore conclude that this methodology provides a better way of directing the application of the IFN-gamma test towards the high-risk subgroup of herds. Classification tree analysis ensured the systematic identification of high-risk herds to consistently apply additional measures in a targeted way. This could increase the detection of infected cattle more efficiently, preventing recurrence and accelerating efforts to achieve eradication by 2038. This methodology has wider application, like targeting improved biosecurity measures in avian influenza at-risk farms to limit damage to the industry in future outbreaks.

Effect of a specially formulated diet on progression of heart enlargement in dogs with subclinical degenerative mitral valve disease.

BACKGROUND: Previous studies in dogs with degenerative mitral valve disease (DMVD) have identified altered myocardial energy metabolism and oxidation, which might contribute to cardiac hypertrophy. Diets rich in medium chain fatty acids and antioxidants are a potential means of treatment. A previous clinical study found significantly smaller left atrial diameter (LAD) and left atrium-to-aorta diameter ratio (LA : Ao) in dogs with subclinical DMVD fed a specially formulated diet vs control diet for 6 months. HYPOTHESIS/OBJECTIVES: A specially formulated diet will slow or arrest left heart enlargement in dogs with subclinical DMVD over 365 days. ANIMALS: One hundred twenty-seven dogs with unmedicated subclinical DMVD; 101 dogs in the per protocol cohort. METHODS: Randomized double-blinded controlled multicenter clinical trial. RESULTS: The study's primary composite outcome measure was the sum of percentage change in LAD and left ventricular internal dimension at end-diastole (LVIDd) at day 365. In the per protocol cohort, the outcome measure increased by 8.0% (95% confidence interval [CI], 2.9%-13.1%) in dogs receiving the test diet vs 8.8% (95% CI, 5.1%-12.5%) in dogs receiving control diet (P = .79). Neither component of the primary outcome measure was significantly different between groups (LAD, P = .65; LVIDd, P = .92). No difference was found in mitral valve E wave velocity (P = .36) or the proportion of dogs withdrawn from the study because of worsening DMVD and heart enlargement (P = .41). CONCLUSIONS AND CLINICAL IMPORTANCE: Feeding a specially formulated diet for 365 days was not associated with a significantly different rate of change of left heart size in dogs with subclinical DMVD as compared to control.

Feature weighted models to address lineage dependency in drug-resistance prediction from Mycobacterium tuberculosis genome sequences.

MOTIVATION: Tuberculosis (TB) is caused by members of the Mycobacterium tuberculosis complex (MTBC), which has a strain- or lineage-based clonal population structure. The evolution of drug-resistance in the MTBC poses a threat to successful treatment and eradication of TB. Machine learning approaches are being increasingly adopted to predict drug-resistance and characterize underlying mutations from whole genome sequences. However, such approaches may not generalize well in clinical practice due to confounding from the population structure of the MTBC. RESULTS: To investigate how population structure affects machine learning prediction, we compared three different approaches to reduce lineage dependency in random forest (RF) models, including stratification, feature selection, and feature weighted models. All RF models achieved moderate-high performance (area under the ROC curve range: 0.60-0.98). First-line drugs had higher performance than second-line drugs, but it varied depending on the lineages in the training dataset. Lineage-specific models generally had higher sensitivity than global models which may be underpinned by strain-specific drug-resistance mutations or sampling effects. The application of feature weights and feature selection approaches reduced lineage dependency in the model and had comparable performance to unweighted RF models. AVAILABILITY AND IMPLEMENTATION: https://github.com/NinaMercedes/RF_lineages.

Individual Monitoring of Activity and Lameness in Conventional and Slower-Growing Breeds of Broiler Chickens Using Accelerometers.

Accelerometers are increasingly being investigated to detect animal behavior as a method for monitoring individual welfare that overcomes manual challenges associated with time, resource, and discrete sampling. We investigated the effects of broiler chicken hybrid (hereafter breed) and weight on accelerometer activity (activityA; calculated as percentage of time spent active (%)) and its association with lameness as a major broiler welfare concern. Accelerometers were attached to birds of different breeds on between 2 and 4 occasions from 26 to 30 days old (conventional breed CNV) and 26 to 49 days old (two slower-growing breeds SGH; SGN). At 2.2 kg, lameness was scored using a 6-point gait scoring system (0: unaffected to 5: severely lame). Linear mixed effects models and breed-stratified generalized linear models together with a random-effect meta-analysis were used for data analyses. ActivityA was lower in faster-growing, heavier birds compared to slower-growing, lighter birds, showing overall consistency with previous behavioral research, but did not vary linearly with gait score. Accelerometers offer the potential for simple broad-scale continuous monitoring of broiler chicken activity behavior that requires limited data processing. Exploration of the ability of accelerometers to capture more subtle and specific changes in behavioral patterning, such as non-linear acceleration with gait score that could indicate early development of lameness, warrants further investigation.

Characterization of intestinal fibrosis in cats with chronic inflammatory enteropathy.

BACKGROUND: Intestinal fibrosis (IF) is commonly identified on histopathology of intestinal biopsy specimens (IBSp) from cats with chronic inflammatory enteropathy (CIE) however, its clinical relevance is unknown. OBJECTIVES: Characterize and determine the clinical relevance of IF in cats with CIE. ANIMALS: Sixty-five client-owned cats diagnosed with CIE after gastrointestinal histopathology from a single referral hospital in the United Kingdom. METHODS: Medical records were retrospectively searched for cases of CIE on the basis of histopathology of IBSp. The IBSp from eligible cats were re-reviewed by a single board-certified veterinary pathologist for inclusion. Masson's trichrome (MT) stain and immunohistochemical labeling using antivimentin and anticollagen I antibodies to identify IF. For each case, various variables at the time of diagnostic investigation were recorded and referring veterinarians were contacted for follow-up information. RESULTS: Mucosal fibrosis was identified in 51% of duodenal and 76% of colonic hematoxylin and eosin (HE)-stained IBSp. Vimentin labeling and MT staining identified additional cases of IF in 65% and 58% of the duodenal biopsy specimens, respectively. Vimentin labeling detected IF in 79% of the colonic biopsy specimens. Positive vimentin labeling and MT staining of the colonic mucosa were associated with decreased likelihood of attaining clinical remission and increased risk of death because of CIE (P < .05). CONCLUSIONS AND CLINICAL IMPORTANCE: Additional stains at initial histopathologic examination of IBSp allow for better identification of IF compared to routine HE staining. Identification of IF in colonic biopsy specimens by vimentin immunolabeling and MT staining may provide prognostic information in cats with CIE.

Regional modular responses in different bone compartments to the anabolic effect of PTH (1-34) and axial loading in mice.

Beneficial effects of intermittent parathyroid hormone (PTH) on bone mass and architecture are described to either simply add to, or to synergise with those of mechanical loading. We evaluate whether interaction with in vivo loading is reinforced by PTH dosing regimen and exhibits compartment-specific sensitivities. Female 12-week-old C57Bl6 mice received daily (7/7) or interrupted 5 day/week (5/7) PTH for 3 weeks (two vehicle groups). All mice had six loading episodes (12N) applied to right tibia (left, non-loaded) for the last 2 weeks. Micro-CT scans were used to evaluate mass and architecture in almost the entire cortical and proximal trabecular regions. Epiphyseal cortical, trabecular and marrow space volumes, and bony growth-plate bridge incidence were evaluated. Statistical analyses employed a linear mixed-effects model at each percentile and 2-way ANOVA with post-hoc test for epiphyses and bridging. We found that daily PTH enhances cortical mass and modifies shape along almost the entire tibia and that these effects are partly mitigated by brief interruption in treatment. Mechanical loading alone augments cortical mass and modifies shape but only in a region proximal to the tibiofibular junction. The effect of combining load and daily PTH dosing is solely additive for cortical bone mass with no significant load: PTH interaction, but exhibits clear synergy with interrupted PTH treatment. Daily, not interrupted PTH stimulates trabecular bone gains, yet load:PTH interaction is present at limited regions with both daily and interrupted treatment. PTH treatment, but not loading, modifies epiphyseal bone but, in contrast, only loading modifies bridge number and areal density. Our findings demonstrate impressive local effects on tibial mass and shape of combined loading and PTH that are sensitive to dosing regimen and exert their effects modularly. These findings emphasise a need to clarify PTH dosing regimens and that advantages could be accrued by aligning treatment accordingly to patient requirements and life-style.

Predictors of laminitis development in a cohort of nonlaminitic ponies.

BACKGROUND: Quantifying risk factors for laminitis development requires improvement. OBJECTIVES: To identify the most useful physical examination, metabolic and management factors to predict laminitis development in client-owned, nonlaminitic ponies. STUDY DESIGN: Prospective cohort study. METHODS: Physical examination, metabolic and management data were collected from a pony cohort 6 monthly for up to 4 years. Ponies were monitored for the development of laminitis. Metabolic data included basal plasma concentrations of ACTH ([ACTH]), adiponectin ([adiponectin]), triglycerides and glucose. Serum insulin concentrations ([insulin]) were measured in the unfasted basal state ([insulin]T0) and 60 minutes ([insulin]T60) after administration of corn syrup (0.3ml/kg). Separate multivariable Cox proportional-hazards models were developed for physical, management/signalment and metabolic data and later combined into two final models. Low-, medium- and high-laminitis risk categories were defined based on basal or T60 [insulin]. RESULTS: Overall, 374 ponies (age 5-32 years) and 891 pony-years were included in the main analysis. Laminitis incidence (95% confidence interval (CI)) was 4.8 (3.5-6.5) cases/100 pony-years. Laminitis development was associated with numerous univariable factors. Significant (P < .05) factors retained in the final multivariable models included [insulin]T0, [insulin]T60, [adiponectin] and divergent hoof growth. [ACTH] was not independently associated with laminitis. Based on [Insulin]T0, low- (<21.6 µIU/ml), medium- (21.6-45.2 µIU/ml) and high-risk (>45.2 µIU/ml) categories encompassed 70, 20 and 10% of the population and had estimated 4-year laminitis incidences (95%CI) of 6 (2-9)%, 22 (10-33)% and 69 (48-82)% respectively. Based on [Insulin]T60 the low- (<53.4 µIU/ml), medium- (53.4-153 µIU/ml) and high-risk (≥153 µIU/ml) categories comprised 60, 30 and 10% of the population and had estimated 4-year laminitis incidences (95%CI) of 3 (0-6)%, 20 (10-29)% and 73 (52-84)% respectively. MAIN LIMITATIONS: Results may not apply to different insulin assays, geographical regions, breeds or management types. CONCLUSIONS: [Insulin]T0 or [insulin]T60 best quantify the risk of future laminitis development in nonlaminitic ponies.

Impact of face mask microplastics pollution on the aquatic environment and aquaculture organisms.

Microplastic pollution in our environment, especially water bodies is an emerging threat to food security and human health. Inevitably, the outbreak of Covid-19 has necessitated the constant use of face masks made from polymers such as polypropylene, polyurethane, polyacrylonitrile, polystyrene, polycarbonate, polyethylene, or polyester which eventually will disintegrate into microplastic particles. They can be broken down into microplastics by the weathering action of UV radiation from the sun, heat, or ocean wave-current and precipitate in natural environments. The global adoption of face masks as a preventive measure to curb the spread of Covid-19 has made the safe management of wastes from it cumbersome. Microplastics gain access into aquaculture facilities through water sources and food including planktons. The negative impacts of microplastics on aquaculture cannot be overemphasized. The impacts includes low growth rates of animals, hindered reproductive functions, neurotoxicity, low feeding habit, oxidative stress, reduced metabolic rate, and increased mortality rate among aquatic organisms. With these, there is every tendency of microplastic pollution to negatively impact fish production through aquaculture if the menace is not curbed. It is therefore recommended that biodegradable materials rather than plastics to be considered in the production of face mask while recycle of already produced ones should be encouraged to reduce waste.