Development of polymorphic markers in the immune gene complex loci of cattle

The addition of cattle health and immunity traits to genomic selection indices holds promise to increase individual animal longevity and productivity, and decrease economic losses from disease. However, highly variable genomic loci that contain multiple immune-related genes were poorly assembled in the first iterations of the cattle reference genome assembly and underrepresented during the development of most commercial genotyping platforms. As a consequence, there is a paucity of genetic markers within these loci that may track haplotypes related to disease susceptibility. By using hierarchical assembly of bacterial artificial chromosome inserts spanning 3 of these immune-related gene regions, we were able to assemble multiple full-length haplotypes of the major histocompatibility complex, the leukocyte receptor complex, and the natural killer cell complex. Using these new assemblies and the recently released ARS-UCD1.2 reference, we aligned whole-genome shotgun reads from 125 sequenced Holstein bulls to discover candidate variants for genetic marker development. We selected 124 SNPs, using heuristic and statistical models to develop a custom genotyping panel. In a proof-of-principle study, we used this custom panel to genotype 1,797 Holstein cows exposed to bovine tuberculosis (bTB) that were the subject of a previous GWAS study using the Illumina BovineHD array. Although we did not identify any significant association of bTB phenotypes with these new genetic markers, 2 markers exhibited substantial effects on bTB phenotypic prediction. The models and parameters trained in this study serve as a guide for future marker discovery surveys particularly in previously unassembled regions of the cattle genome.

94 An Observational Cohort Study to Evaluate Volume and Severity of Emergency General Surgery Admissions During The COVID-19 Pandemic: Is There A “Lockdown” Effect?

Introduction

The COVID-19 pandemic has led to changes in NHS surgical service provision. This, combined with the government-imposed lockdown, may have impacted on patient attendance, severity of surgical disease, and outcomes. This study aimed to investigate a possible ‘lockdown’ effect on the volume and severity of surgical admissions and outcomes.

Method

Two cohorts of adult emergency general surgery admissions 30 days immediately before (16/2/2020 to 15/3/2020), and after UK government advice (16/3/2020 to 15/4/2020). Data were collected relating to patient characteristics, disease severity, clinical outcomes, and compared between these groups.

Results

Following lockdown, a significant reduction in median daily admissions from 7 to 3 (p < 0.001) was observed. Post-lockdown patients were significantly older, frailer with higher inflammatory indices and rates of AKI, and more likely to present with gastrointestinal cancer, obstruction, and perforation. Patients had significantly higher rates of Clavien-Dindo Grade ≥3 complications (p = 0.001), all-cause 30-day mortality (8.5% vs. 2.9%, p = 0.028), but no significant difference was observed in operative 30-day mortality.

Conclusions

There appears to be a “lockdown” effect on general surgical admissions with fewer admissions, more acutely unwell patients, and an increase in all-cause 30-day mortality. Patients should be advised to present promptly, and this should be reinforced for future lockdowns during the pandemic.

Assessment of various continual reassessment method models for dose-escalation phase 1 oncology clinical trials: using real clinical data and simulation studies

Background

The continual reassessment method (CRM) identifies the maximum tolerated dose (MTD) more efficiently and identifies the true MTD more frequently compared to standard methods such as the 3 + 3 method. An initial estimate of the dose-toxicity relationship (prior skeleton) is required, and there is limited guidance on how to select this. Previously, we compared the CRM with six different skeletons to the 3 + 3 method by conducting post-hoc analysis on a phase 1 oncology study (AZD3514), each CRM model reduced the number of patients allocated to suboptimal and toxic doses. This manuscript extends this work by assessing the ability of the 3 + 3 method and the CRM with different skeletons in determining the true MTD of various “true” dose-toxicity relationships.

Methods

One thousand studies were simulated for each “true” dose toxicity relationship considered, four were based on clinical trial data (AZD3514, AZD1208, AZD1480, AZD4877), and four were theoretical. The 3 + 3 method and 2-stage extended CRM with six skeletons were applied to identify the MTD, where the true MTD was considered as the largest dose where the probability of experiencing a dose limiting toxicity (DLT) is ≤33%.

Results

For every true dose-toxicity relationship, the CRM selected the MTD that matched the true MTD in a higher proportion of studies compared to the 3 + 3 method. The CRM overestimated the MTD in a higher proportion of simulations compared to the 3 + 3 method.

The proportion of studies where the correct MTD was selected varied considerably between skeletons. For some true dose-toxicity relationships, some skeletons identified the true MTD in a higher proportion of scenarios compared to the skeleton that matched the true dose-toxicity relationship.

Conclusion

Through simulation, the CRM generally outperformed the 3 + 3 method for the clinical and theoretical true dose-toxicity relationships. It was observed that accurate estimates of the true skeleton do not always outperform a generic skeleton, therefore the application of wide confidence intervals may enable a generic skeleton to be used. Further work is needed to determine the optimum skeleton.

Combined neurosurgical and orbital intervention for spheno-orbital meningiomas - the Manchester experience

PURPOSE

Surgical resection of spheno-orbital meningioma (SOM) is challenging, requiring a multidisciplinary surgical approach. We present our experience of the surgical management of patients with SOM.

METHODS

A retrospective analysis of patients with SOM who underwent joint neurosurgical and orbital surgical procedures between January 2000 and June 2017. Pre-operative clinical signs, indication for surgery, surgical complications and post-operative outcomes were recorded.

RESULTS

Twenty-four operations were performed. Mean age was 49.5 years. Ninety-two percent of patients were female. Pre-operatively mean Snellen acuity vision was 6/12; 13 (54%) had an RAPD; 12 (50%) had reduced colour vision; 16 (67%) had a visual field defect. The majority (21 patients, 88%) had proptosis (average 4.5 mm ± 2.8 mm). The indication for surgery was evidence of visual dysfunction in 17 (71%), the remaining 7 (29%) had high risk of visual loss clinically or radiologically. Three-months post operatively, vision was stable in 13 (58%), improved in 6 (21%) and worse in 5 (17%). Average long-term follow-up was 82 months (1-220). Fourteen (58%) maintain improved or stable visual function. Four (17%) had reduced vision due to regrowth of the tumour at an average of 24 months.

CONCLUSION

SOMs are very challenging to treat surgically. In this cohort the patients were predominantly young females with aggressive disease. Visual function was improved or stabilised in 79% of the patients.

Persistent cortisol response to desmopressin predicts recurrence of Cushing's disease in patients with post-operative corticotropic insufficiency

OBJECTIVE

Cushing's disease (CD) may recur despite corticotropic insufficiency (COI) following pituitary surgery. The predictive value of the desmopressin test (DT) for recurrence in this setting remains controversial. We have evaluated whether the disappearance of the response to DT predicts a low probability recurrence in a large cohort of patients with post-operative COI.

DESIGN

Multicentre retrospective study.

METHODS

Ninety-five patients with CD (women 82%, age 41 ± 14 years), responding preoperatively to DT and with early post-operative COI (08 00 am cortisol: <138 nmol/L), underwent a DT within 3 months post-surgery. Association between DT findings and the prediction of recurrence was tested using regression and ROC analyses.

RESULTS

Recurrence occurred in 17/95 patients within 29 to 91 months. The cortisol peak (327, 95% CI (237-417) vs 121 (79-164) nmol/L, P = 0.0001) and absolute increment during DT (208 (136-280) vs 56 (22-90) nmol/L, P = 0.005) were greater in the recurrence vs remission group. Cortisol peak (AUC: 0.786 (0.670-0.902)) and increment (0.793 (0.672-0.914)) yielded a higher prognostic performance for recurrence than did the early post-operative 08 00 am cortisol (0.655 (0.505-0.804)). In the context of COI, cortisol peak >100 nmol/L and increment >30 nmol/L had a high negative predictive value (94, 95% CI (88-100) and 94, (88-100), respectively). Patients with a cortisol peak ≤100 nmol/L (vs >100) or an increment ≤30 nmol/L (vs >30) were less likely to have CD recurrence (odds ratios: 0.12, 95% CI (0.03-0.41) and 0.11 (0.02-0.36), respectively).

CONCLUSION

The disappearance of the response to the post-operative DT was independently associated with a lower odds of CD recurrence and offers an incremental prognostic value, which may help to stratify patients with COI and refine their follow-up according to the risk of recurrence.

Evaluation of Beef Cattle Temperament Attributes Using Infrared Thermography Technology

ObjectivesThe objective of this study was to evaluate beef cattle temperament scores using infrared thermography technology.Materials and MethodsAngus and Angus × Hereford calves (total n = 650) were brought through a handling chute system over two weaning sessions (October 2016 and 2017). Beef cattle temperament was subjectively quantified by (1) temperament score (TS), the disposition of the animal observed by an individual evaluator on a scale of 1 (calm) to 5 (excitable); (2) docility score (DS), the level of observed calmness of the animal displayed (1 = calm to 6 = excitable); and (3) qualitative behavior assessment (QBA), scored on twelve different attributes, (i.e., active, relaxed, etc.). There were two traits measured on a four-platform standing scale: (1) the standard deviation of total weight over time (SSD); and (2) the SSD’s coefficient of variation (CVSSD). Thermal images of the animal’s head were acquired by industrial fixed focus infrared camera (TiS40, Fluke Corporation, Everett, WA). The maximum, minimum, average, and standard deviation of temperature of the eye region were extracted from the thermal images. Stepwise and linear regression analyses to estimate subjective temperament traits from thermal imaging data and scale data were conducted using the reg procedure in SAS (v. 9.4, SAS Institute, Inc., Cary, NC). Correlations were estimated using the corr procedure in SAS.ResultsThe results showed low correlations between thermal imaging and subjective temperament traits. The correlations that were significant were around an absolute value of 0.1. However, all four thermal imaging traits were significantly correlated when the animal exhibited distress observed by QBA. When fitting only thermal imaging data into the regression analyses, R2 values were all under 0.03. When including SSD and CVSSD, there were a few traits with an R2 > 0.1 and none having an R2 > 0.15. The QBA traits that had an R2 between 0.1 and 0.15 were active, fearful, calm, apathetic, happy, and distressed for both linear and stepwise regressions.ConclusionAdditional validation research on this thermal imaging technology needs to be conducted with temperamental cattle as this current data was collected using observed calmer cattle, to give a more realistic application to beef cattle production. Overall this result shows potential to achieve beef cattle temperament evaluation with thermal imaging.Figure 1.

Predicting Early Stages of Beef Respiratory Disease Using Thermal Imaging Technology

ObjectivesThe objective of this research was to utilize thermal imaging technology to estimate body temperature, so that an early stage of BRD can be detected.Materials and MethodsNinety-two steers were restrained in a squeeze chute that is housed in an indoor handling facility on 6 separate occasions. At least one image was taken of each side of the head using a thermal infrared camera (FLIR E8 WiFi, FLIR, Wilsonville, OR). The distance at which the images were taken was approximately 1 m from the steer. The rectal temperature was used as the control method to compare thermal imaging data. After thermal image acquisition, images were analyzed using the FLIR ResearchIR Max software (v. 4.40.8.28, FLIR, Wilsonville, OR), with the regions of interest being the eye and nasal cavity.ResultsThe analysis focused on minimum (MIN), maximum (MAX), mean, standard deviation (SD), and range of temperatures in the regions of interest. The REG procedure in SAS (v. 9.4, SAS Institute, Inc., Cary, NC) was used to perform stepwise regression to predict rectal temperature from the outdoor temperature (OTEMP) and all imaging features. When OTEMP was greater than –17.8°C, the regression model contained OTEMP, left nasal MAX, left nasal SD, and left eye MAX temperature and right eye temperature range, with an R2 of 0.24. When OTEMP was above freezing (0°C), the regression model contained left nasal temperature range, right eye temperature range, and average nasal mean temperature, with an R2 increase to 0.50. When using all data, the regression model fit left nasal MAX, right nasal MIN, average nasal mean, and left eye MAX temperatures and right eye temperature range, with an R2 of 0.08. These results show that thermal imaging technology has higher prediction accuracy in warmer temperature ranges than extreme cold conditions.ConclusionMore validation research on this thermal imaging technology needs to be conducted at warmer temperatures since all the current data was collected on cold winter days and a large portion of U.S. cattle are reared in more temperate and warmer areas than North Dakota such as Nebraska, Kansas, Texas, Oklahoma, and Florida. Overall, these results show promise for using thermal imaging technology to help detect BRD in an earlier stage by detecting fever before other clinical signs of BRD are present.

Correlation of Computer Vision System Data with Traditional Methods of Evaluating Pork Color and Marbling on the Ventral Side on the Whole Loin and on Individual Loin Chops

ObjectivesPork quality is a combination of many different attributes, including color, intramuscular fat percentage (IMF), pH, drip loss, and tenderness. Currently, in the pork industry, color and marbling of the whole loins are commonly assessed subjectively by a trained evaluator according to the National Pork Board’s color and marbling standard cards. However, subjective color (SCS) and marbling (SMS) scores can be influenced by lighting and evaluator fatigue. Colorimeters are a common technology that are utilized for measurement of color in the meat industry but have their limitations as they only measure a small portion of the surface and cannot separate lean and fat tissue. Ether extract is commonly used for crude fat determination, but it requires a longer time for analysis and a sample that will be consumed by the process. Computer vision system (CVS) is a technology that has been applied in the food industry and is a non-invasive, efficient, and consistent method. Therefore, the objectives of this study were to compare pork color and marbling measured from the whole loin versus its individual chops and to compare the results from different pork quality measurement methods on the same sample.Materials and MethodsWhole pork loins (n = 1400) were obtained from 6 major pork processing plants, with SCS, SMS, Hunter L, a, and b, and CVS images being collected on the ventral side of the loin in the plant. Samples were vacuum packed, shipped, and stored at 4°C for 14 d. Then whole loins were sliced into chops and the third (A) and 10th (B) rib chops were evaluated for SCS and SMS after a 10 min bloom. After SCS and SMS evaluation, Hunter L, a, and b, and CVS images were collected. The A and B chops were vacuum packaged, shipped, trimmed, freeze dried, and then evaluated for crude fat percentage (CF%) using ether extract method. The CF% of the whole loin was estimated as the average of the A and B chops. From the CVS images, lean and fat pixels were segmented to estimate L*, a*, and b* of the lean tissue and CVS IMF.ResultsA lower L* was found for both CVS and colorimeter when evaluating the whole loin (63.06 & 53.63, respectively) compared to the average of A and B chops (68.65 & 58.10, respectively). However, for SCS, individual chops, on average, were darker than the whole loin (2.88 vs. 2.67, respectively). Of all color measurements, Hunter L had the highest correlation when comparing the whole loin to A and B chops (r = 0.72 and 0.72, respectively). When comparing marbling results of the whole loin to the A and B chops, a moderate correlation was found using both SMS (r = 0.67 and 0.60, respectively) and CVS IMF (r = 0.52 and 0.54, respectively). When comparing methods, CVS L* had a stronger correlation with Hunter L than SCS for the whole loin and A and B chops. (r = 0.40 vs. 0.34, 0.82 vs. 0.47, and 0.84 vs. 0.40, respectively). For IMF, SMS had a stronger correlation with CF% than CVS IMF (r = 0.48 vs. 0.34, 0.62 vs. 0.39, and 0.54 vs. 0.38, respectively).ConclusionThese results show great potential for CVS to be used in evaluating pork quality, specifically color and marbling. Additionally, it is possible to predict individual chop color and marbling based on the ventral side of the loin. Further research should be conducted to look at more technologies that can predict pork quality attributes.

Parenting, Effortful Control, and Adolescents' Externalizing Problem Behavior: Moderation by Dopaminergic Genes

Research shows that genetics and effortful control play an important role in the link between parenting and problem behavior. However, little is known about how these factors act simultaneously. This article used a moderated mediation model to examine whether effortful control mediated the link between parenting and externalizing problem behavior, and whether dopaminergic genes (i.e., polygenic index score including DAT1, DRD2, DRD4, COMT) moderated this link. Two three-wave studies were conducted on community samples (adolescents: Study 1: N = 457; M_age = 15.74; Study 2: N = 221; M_age = 12.84). There was no mediation by effortful control, but a moderation by dopaminergic reactivity was observed. Despite inconsistent evidence, this article indicates that the development of externalizing problem behavior is subject to genetic characteristics and parenting.

P2674Rapid rule-out of myocardial infarction with a novel high precision point-of-care troponin assay appears safe and effective

Background

High sensitivity troponin assays were developed to improve analytical sensitivity and precision at the decision cut-points for the diagnosis and rule out of acute myocardial infarction (AMI). Central laboratory assays have achieved this but point of care assays, which have the ability to accelerate decision making due to much shorter turnaround times, have remained lacking.

Purpose

To ascertain the threshold for decision making and subsequent clinical utility for ruling out AMI on presentation in patients attending the emergency department acutely with chest pain, using a high precision point of care troponin assay (TnI Nx), (i-STAT, Abbott).

Methods

We measured arrival TnI-Nx concentrations in stored plasma samples in adults presenting acutely to the emergency department with chest pain. The primary outcome was an AMI or cardiac death on index admission or within 30 days. We used 2000 bootstrapped data sets to derive and validate a suitable threshold for TnI-Nx before calculating diagnostic test performance. We pre-specified this threshold must have a <1% false negative rate for the primary outcome. We compared this with a core laboratory high sensitivity troponin I (hs-TnI) (Abbott Architect) using the early rule-out cut-point (European Society of Cardiology) at the limit of detection (2 ng/L).

Results

We recruited 1320 patients of whom 192 (14.1%) had the primary outcome. The TnI-Nx threshold was determined to be 8 ng/L with subsequent sensitivity of 99.0% (95% confidence interval: 97.3% to 100%), negative predictive value of 99.7% (99.2% to 100%) and specificity of 59.0% (56.0% to 62.0%). The hs-TnI had a sensitivity of 99.5% (98.2% to 100%), negative predictive value of 99.7% (99.0% to 100%), and specificity of 28.4% (25.8% to 31.2%) at 2ng/L.

Conclusion

A high precision point of care assay, TnI-Nx, with a decision threshold of 8ng/L, has comparable rule out performance compared with a core laboratory high sensitivity assay and therefore could potentially be used for early decision making in the assessment of acute chest pain.

Acknowledgement/Funding

Research grant from Abbott Point of Care. Senior Research Fellowship from ECF, CMRF and CDHB. Clinical Research Fellowship from NZ HRC

Filament identification in wide-angle high speed imaging of the mega amp spherical tokamak

A new tomographic inversion technique is presented for the identification of plasma filaments in wide-angle visible camera data. The technique works on the assumption that background subtracted images of filaments can be represented as a superposition of uniformly emitting magnetic equilibrium field lines. A large collection of equilibrium magnetic field lines is traced and projected onto the camera field of view and combined to form a geometry matrix describing the coordinate transformation from magnetic field aligned coordinates to image pixel coordinates. Inverting this matrix enables the reprojection of the emission in the camera images onto a field aligned basis, from which filaments are readily identifiable. The inversion is a poorly conditioned problem which is overcome using a least-squares approach with Laplacian regularization. Blobs are identified using the "watershed" algorithm and 2D Gaussians are fitted to get the positions, widths, and amplitudes of the filaments. A synthetic camera diagnostic generating images containing experimentally representative filaments is utilized to rigorously benchmark the accuracy and reliability of the technique. 74% of synthetic filaments above the detection amplitude threshold are successfully detected, with 98.8% of detected filaments being true positives. The accuracy with which filament properties and their probability density functions are recovered is discussed, along with sources of error and methods to minimize them.

Generalisability of randomised trials of the programmed intermittent epidural bolus technique for maintenance of labour analgesia: a prospective single centre cohort study

BACKGROUND

Several randomised controlled trials show that maintenance of labour epidural analgesia with programmed intermittent epidural bolus reduces the maternal motor block compared with maintenance with a continuous infusion. However, these trials were usually restricted to healthy nulliparous parturients. To assess the generalisability of these randomised controlled trials to 'real-world' conditions, we compared maternal motor function (modified Bromage score) over time between healthy nulliparous and parous women using routinely collected quality-control data.

METHODS

After ethical approval, all parturients receiving programmed intermittent epidural bolus labour analgesia between June 2013 and October 2014 were included in this prospective cohort study. Bupivacaine 0.1% with fentanyl 2 μg ml^-1 was used allowing for patient-controlled bolus every 20 min. The maternal motor function (primary outcome) was regularly assessed from insertion of the epidural catheter until delivery.

RESULTS

Of the 839 parturients included, 553 (66%) were nulliparous and 286 (34%) were parous. The parous women had a shorter median duration of epidural analgesia (3 h 59 min vs 5 h 45 min) and a higher incidence of spontaneous delivery (66% vs 37%). The probability of being in a certain Bromage category at birth was similar in nulliparous and parous women in a general additive model adjusting for duration of epidural analgesia, number of rescue top-ups, and number of catheter manipulations (cumulative odds ratio: 1.18; 95% confidence interval: 0.98-1.41). Parous women required a higher time-weighted number and volume of rescue top-ups.

CONCLUSIONS

The results of the randomised controlled trials on a reduced motor block with programmed intermittent epidural bolus seem generalisable to parturients typically not included in these trials.

Prevalence and predictors of airflow obstruction in an HIV tertiary care clinic in Montreal, Canada: a cross-sectional study

Objectives

The reported prevalence of chronic obstructive pulmonary disease (COPD) in people living with HIV (PLWHIV) varies widely. Our objective was to estimate the prevalence of airflow obstruction and COPD in unselected PLWHIV and identify characteristics that increase the risk of nonreversible airflow obstruction in order to guide case finding strategies for COPD.

Methods

All adults attending the Chronic Viral Illness Service were invited to participate in the study, regardless of smoking status or history of known COPD/asthma. Individuals underwent spirometric testing both before and after use of a salbutamol bronchodilator. Airflow obstruction was defined as forced expiratory volume in 1 s (FEV₁)/forced vital capacity (FVC) < 0.7 post‐bronchodilation, whereas COPD was defined as FEV₁/FVC < 0.7 post‐bronchodilation and Medical Research Council (MRC) score > 2. Multivariate logistic regression was used to evaluate risk factors associated with airflow obstruction, reported as adjusted odds ratios (aORs).

Results

Five hundred and three participants successfully completed spirometry testing. The median (Q1; Q3) age was 52 (44; 58) years. The median (Q1; Q3) CD4 count was 598 (438; 784) cells/μL and the median (Q1; Q3) nadir CD4 count was 224 (121; 351) cells/μL. There were 119 (24%) current smokers and 145 (29%) former smokers. Among those screened, 54 (11%) had airflow obstruction whereas three (1%) of the participants had COPD. Factors that were associated with airflow obstruction included a history of smoking [aOR 2.2; 95% confidence interval (CI) 1.1; 4.7], older age (aOR 1.6; 95% CI 1.2; 2.2), and lower CD4 count (aOR 0.8; 95% CI 0.7; 1.0).

Conclusions

Airflow obstruction was relatively uncommon. Our findings suggest that PLWHIV who are ≥50 years old, smokers and those with nadir CD4 counts ≤ 200 cells/μL could be targeted to undergo spirometry to diagnose chronic airflow obstruction.