Modeling the economic impacts of mobility scores in dairy cows under Irish spring pasture-based management

Moderate to severe forms of suboptimal mobility on dairy cows are associated with yield losses, whereas mild forms of suboptimal mobility are associated with elevated somatic cell count and an increased risk to be culled. Although the economic consequences of severe forms of suboptimal mobility (also referred as clinical lameness) have been studied extensively, the mild forms are generally ignored. Therefore, the aim of the current study was to determine the economic consequences associated with varying prevalence and forms of suboptimal mobility within spring calving, pasture-based dairy herds. A new submodel predicting mobility scores was developed and integrated within an existing pastured-based herd dynamic model. Using a daily timestep, this model simulates claw disorders, and the consequent mobility score of individual cows. The impact of a cow having varying forms of suboptimal mobility on production and reproduction was simulated. The economic impact was simulated including treatment costs, as well as the production and reproductive impacts of varying levels of suboptimal mobility. Furthermore, different genetic predispositions for mobility issues and their interaction with herd-level management associated with each level of suboptimal mobility were simulated. Overall, 13 scenarios were simulated, representing a typical spring calving, pasture-based dairy herd with 100 cows. The first scenario represents a perfect herd wherein 100% of the cows had mobility score 0 (optimal mobility) throughout the lactation. The remaining 12 scenarios represent a combination of (1) 3 different herd-management levels, and (2) 4 different levels of a genetic predisposition for suboptimal mobility. The analysis showed that a 17% decrease in farm net profit was achieved in the worst outcome (wherein just 5% of the herd had optimal mobility) compared with the perfect herd. This was due to reduced milk yield, increased culling, and increased treatment costs for mobility issues compared the ideal scenario.

A Topological Loss Function for Deep-Learning Based Image Segmentation Using Persistent Homology

We introduce a method for training neural networks to perform image or volume segmentation in which prior knowledge about the topology of the segmented object can be explicitly provided and then incorporated into the training process. By using the differentiable properties of persistent homology, a concept used in topological data analysis, we can specify the desired topology of segmented objects in terms of their Betti numbers and then drive the proposed segmentations to contain the specified topological features. Importantly this process does not require any ground-truth labels, just prior knowledge of the topology of the structure being segmented. We demonstrate our approach in four experiments: one on MNIST image denoising and digit recognition, one on left ventricular myocardium segmentation from magnetic resonance imaging data from the UK Biobank, one on the ACDC public challenge dataset and one on placenta segmentation from 3-D ultrasound. We find that embedding explicit prior knowledge in neural network segmentation tasks is most beneficial when the segmentation task is especially challenging and that it can be used in either a semi-supervised or post-processing context to extract a useful training gradient from images without pixelwise labels.

Cow and herd-level risk factors associated with mobility scores in pasture-based dairy cows

Lameness in dairy cows is an area of concern from an economic, environmental and animal welfare point of view. While the potential risk factors associated with suboptimal mobility in non-pasture-based systems are evident throughout the literature, the same information is less abundant for pasture-based systems specifically those coupled with seasonal calving, like those in Ireland. Therefore, the objective of this study was to determine the potential risk factors associated with specific mobility scores (0 = good, 1 = imperfect, 2 = impaired, and 3 = severely impaired mobility) for pasture-based dairy cows. Various cow and herd-level potential risk factors from Irish pasture-based systems were collected and analyzed for their association with suboptimal mobility, whereby a mobility score of 0 refers to cows with optimal mobility and a mobility score ≥ 1 refers to a cow with some form of suboptimal mobility. Combined cow and herd-level statistical models were used to determine the increased or decreased risk for mobility score 1, 2, and 3 (any form of suboptimal mobility) compared to the risk for mobility score 0 (optimal mobility), as the outcome variable and the various potential risk factors at both the cow and herd-level were included as predictor type variables. Cow-level variables included body condition score, milk yield, genetic predicted transmitting ability for 'lameness', somatic cell score, calving month and cow breed. Herd-level variables included various environmental and management practices on farm. These analyses have identified several cow-level potential risk factors (including low body condition score, high milk yield, elevated somatic cell count, stage of lactation, calving month, and certain breed types), as well as various herd-level potential risk factors (including the amount of time taken to complete the milking process, claw trimmer training, farm layout factors and foot bathing practices) which are associated with suboptimal mobility. The results of this study should be considered by farm advisors when advising and implementing a cow/herd health program for dairy cows in pasture-based systems.

An Update on Health-Related Quality of Life and Patient-Reported Outcomes in Hidradenitis Suppurativa

Hidradenitis suppurativa is a common inflammatory skin condition which causes recurrent abscesses, sinuses and scarring in the axillae, groin and inframammary areas. As well as causing significant physical distress due to pain and discharge, the condition impacts psychological well-being with markedly impaired quality of life. Patients suffer pain, embarrassment and psychological distress with impairment of their work and intimate relationships marking it as one of the most distressing dermatological conditions. Numerous studies have documented markers of psychological distress encompassing the physical effects such as pain and itch, affects on mood and impaired function.

Improved co-registration of ex-vivo and in-vivo cardiovascular magnetic resonance images using heart-specific flexible 3D printed acrylic scaffold combined with non-rigid registration

BACKGROUND

Ex-vivo cardiovascular magnetic resonance (CMR) imaging has played an important role in the validation of in-vivo CMR characterization of pathological processes. However, comparison between in-vivo and ex-vivo imaging remains challenging due to shape changes occurring between the two states, which may be non-uniform across the diseased heart. A novel two-step process to facilitate registration between ex-vivo and in-vivo CMR was developed and evaluated in a porcine model of chronic myocardial infarction (MI).

METHODS

Seven weeks after ischemia-reperfusion MI, 12 swine underwent in-vivo CMR imaging with late gadolinium enhancement followed by ex-vivo CMR 1 week later. Five animals comprised the control group, in which ex-vivo imaging was undertaken without any support in the LV cavity, 7 animals comprised the experimental group, in which a two-step registration optimization process was undertaken. The first step involved a heart specific flexible 3D printed scaffold generated from in-vivo CMR, which was used to maintain left ventricular (LV) shape during ex-vivo imaging. In the second step, a non-rigid co-registration algorithm was applied to align in-vivo and ex-vivo data. Tissue dimension changes between in-vivo and ex-vivo imaging were compared between the experimental and control group. In the experimental group, tissue compartment volumes and thickness were compared between in-vivo and ex-vivo data before and after non-rigid registration. The effectiveness of the alignment was assessed quantitatively using the DICE similarity coefficient.

RESULTS

LV cavity volume changed more in the control group (ratio of cavity volume between ex-vivo and in-vivo imaging in control and experimental group 0.14 vs 0.56, p < 0.0001) and there was a significantly greater change in the short axis dimensions in the control group (ratio of short axis dimensions in control and experimental group 0.38 vs 0.79, p < 0.001). In the experimental group, prior to non-rigid co-registration the LV cavity contracted isotropically in the ex-vivo condition by less than 20% in each dimension. There was a significant proportional change in tissue thickness in the healthy myocardium (change = 29 ± 21%), but not in dense scar (change = - 2 ± 2%, p = 0.034). Following the non-rigid co-registration step of the process, the DICE similarity coefficients for the myocardium, LV cavity and scar were 0.93 (±0.02), 0.89 (±0.01) and 0.77 (±0.07) respectively and the myocardial tissue and LV cavity volumes had a ratio of 1.03 and 1.00 respectively.

CONCLUSIONS

The pattern of the morphological changes seen between the in-vivo and the ex-vivo LV differs between scar and healthy myocardium. A 3D printed flexible scaffold based on the in-vivo shape of the LV cavity is an effective strategy to minimize morphological changes in the ex-vivo LV. The subsequent non-rigid registration step further improved the co-registration and local comparison between in-vivo and ex-vivo data.

Associating cow characteristics with mobility scores in pasture-based dairy cows

The quality of dairy cow mobility can have significant welfare, economic, and environmental consequences that have yet to be extensively quantified for pasture-based systems. The objective of this study was to characterize mobility quality by examining associations between specific mobility scores, claw disorders (both the type and severity), body condition score (BCS), and cow parity. Data were collected for 6,927 cows from 52 pasture-based dairy herds, including mobility score (0 = optimal mobility; 1, 2, or 3 = increasing severities of suboptimal mobility), claw disorder type and severity, BCS, and cow parity. Multinomial logistic regression was used for analysis. The outcome variable was mobility score, and the predictor variables were BCS, type and severity of claw disorders, and cow parity. Three models were run, each with 1 reference category (mobility score 0, 1, or 2). Each model also included claw disorders (overgrown claw, sole hemorrhage, white line disease, sole ulcer, and digital dermatitis), BCS, and cow parity as predictor variables. The presence of most types of claw disorders had odds ratios >1, indicating an increased likelihood of a cow having suboptimal mobility. Low BCS (BCS <3.00) was associated with an increased risk of a cow having suboptimal mobility, and relatively higher parity was also associated with an increased risk of suboptimal mobility. These results confirm an association between claw disorders, BCS, cow parity, and dairy cow mobility score. Therefore, mobility score should be routinely practiced to identify cows with slight deviations from the optimal mobility pattern and to take preventive measures to keep the problem from worsening.

Creating three dimensional models of the right ventricular outflow tract: influence of contrast, sequence, operator, and threshold

The use of 3D printed models of the right ventricular outflow tract (RVOT) for surgical and interventional planning is growing and often requires image segmentation of cardiac magnetic resonance (CMR) images. Segmentation results may vary based on contrast, image sequence, signal threshold chosen by the operator, and manual post-processing. The purpose of this study was to determine potential biases and post-processing errors in image segmentation to enable informed decisions. Models of the RVOT and pulmonary arteries from twelve patients who had contrast enhanced CMR angiography with gadopentetate dimeglumine (GPD), gadofosveset trisodium (GFT), and a post-GFT inversion-recovery (IR) whole heart sequence were segmented, trimmed, and aligned by three operators. Geometric agreement and minimal RVOT diameters were compared between sequences and operators. To determine the contribution of threshold, interoperator variability was compared between models created by the same two operators using the same versus different thresholds. Geometric agreement by Dice between objects was high (intraoperator: 0.89-0.95; interoperator: 0.95-0.97), without differences between sequences. Minimal RVOT diameters differed on average by - 1.9 to - 1.3 mm (intraoperator) and by 0.4 to 1.4 mm (interoperator). The contribution of threshold to interoperator geometric agreement was not significant (same threshold: 0.96 ± 0.06, different threshold: 0.93 ± 0.05; p = 0.181), but minimal RVOT diameters were more variable with different versus constant thresholds (- 9.12% vs. 2.42%; p < 0.05). Thresholding does not significantly change interoperator variability for geometric agreement, but does for minimal RVOT diameter. Minimal RVOT diameters showed clinically relevant variation within and between operators.

Three-dimensional printed models for surgical planning of complex congenital heart defects: an international multicentre study

OBJECTIVES

To evaluate the impact of 3D printed models (3D models) on surgical planning in complex congenital heart disease (CHD).

METHODS

A prospective case-crossover study involving 10 international centres and 40 patients with complex CHD (median age 3 years, range 1 month-34 years) was conducted. Magnetic resonance imaging and computed tomography were used to acquire and segment the 3D cardiovascular anatomy. Models were fabricated by fused deposition modelling of polyurethane filament, and dimensions were compared with medical images. Decisions after the evaluation of routine clinical images were compared with those after inspection of the 3D model and intraoperative findings. Subjective satisfaction questionnaire was provided.

RESULTS

3D models accurately replicate anatomy with a mean bias of -0.27 ± 0.73 mm. Ninety-six percent of the surgeons agree or strongly agree that 3D models provided better understanding of CHD morphology and improved surgical planning. 3D models changed the surgical decision in 19 of the 40 cases. Consideration of a 3D model refined the planned biventricular repair, achieving an improved surgical correction in 8 cases. In 4 cases initially considered for conservative management or univentricular palliation, inspection of the 3D model enabled successful biventricular repair.

CONCLUSIONS

3D models are accurate replicas of the cardiovascular anatomy and improve the understanding of complex CHD. 3D models did not change the surgical decision in most of the cases (21 of 40 cases, 52.5% cases). However, in 19 of the 40 selected complex cases, 3D model helped redefining the surgical approach.

Evaluation of a modified Cheatham-Platinum stent for the treatment of aortic coarctation by finite element modelling

Objectives

Stent implantation for the treatment of aortic coarctation has become a standard approach for the management of older children and adults. Criteria for optimal stent design and construction remain undefined. This study used computational modelling to compare the performance of two generations of the Cheatham-Platinum stent (NuMED, Hopkinton, NY, USA) deployed in aortic coarctation using finite element analysis.

Design

Three-dimensional models of both stents, reverse engineered from microCT scans, were implanted in the aortic model of one representative patient. They were virtually expanded in the vessel with a 16 mm balloon and a pressure of 2 atm.

Results

The conventional stent foreshortened to 96.5% of its initial length, whereas the new stent to 99.2% of its initial length. Diameters in 15 slices across the conventional stent were 11.6–15 mm (median 14.2 mm) and slightly higher across the new stent: 10.7–15.3 mm (median 14.5 mm) (p= 0.021). Apposition to the vessel wall was similar: conventional stent 31.1% and new stent 28.6% of total stent area.

Conclusions

The new design Cheatham-Platinum stent showed similar deployment results compared to the conventional design. The new stent design showed slightly higher expansion, using the same delivery balloon. Patient-specific computational models can be used for virtual implantation of new aortic stents and promise to inform subsequent in vivo trials.

Genetic variability in the humoral immune response to bovine herpesvirus-1 infection in dairy cattle and genetic correlations with performance traits

Bovine herpesvirus-1 (BoHV-1) is a viral pathogen of global significance that is known to instigate several diseases in cattle, the most notable of which include infectious bovine rhinotracheitis and bovine respiratory disease. The genetic variability in the humoral immune response to BoHV-1 has, to our knowledge, not ever been quantified. Therefore, the objectives of the present study were to estimate the genetic parameters for the humoral immune response to BoHV-1 in Irish female dairy cattle, as well as to investigate the genetic relationship between the humoral immune response to BoHV-1 with milk production performance, fertility performance, and animal mortality. Information on antibody response to BoHV-1 was available to the present study from 2 BoHV-1 sero-prevalence research studies conducted between the years 2010 to 2015, inclusive; after edits, BoHV-1 antibody test results were available on a total of 7,501 female cattle from 58 dairy herds. National records of milk production (i.e., 305-d milk yield, fat yield, protein yield, and somatic cell score; n = 1,211,905 milk-recorded cows), fertility performance (i.e., calving performance, pregnancy diagnosis, and insemination data; n = 2,365,657 cows) together with animal mortality data (i.e., birth, farm movement, death, slaughter, and export events; n = 12,853,257 animals) were also available. Animal linear mixed models were used to quantify variance components for BoHV-1 as well as to estimate genetic correlations among traits. The estimated genetic parameters for the humoral immune response to BoHV-1 in the present study (i.e., heritability range: 0.09 to 0.16) were similar to estimates previously reported for clinical signs of bovine respiratory disease in dairy and beef cattle (i.e., heritability range: 0.05 to 0.11). Results from the present study suggest that breeding for resistance to BoHV-1 infection could reduce the incidence of respiratory disease in cattle while having little or no effect on genetic selection for milk yield or milk constituents (i.e., genetic correlations ranged from -0.13 to 0.17). Moreover, even though standard errors were large, results also suggest that breeding for resistance to BoHV-1 infection may indirectly improve fertility performance while also reducing the incidence of mortality in older animals (i.e., animals >182 d of age). Results can be used to inform breeding programs of potential genetic gains achievable for resistance to BoHV-1 infection in cattle.

Improved passive catheter tracking with positive contrast for CMR-guided cardiac catheterization using partial saturation (pSAT)

BACKGROUND

Cardiac catheterization is a common procedure in patients with congenital heart disease (CHD). Although cardiovascular magnetic resonance imaging (CMR) represents a promising alternative approach to fluoroscopy guidance, simultaneous high contrast visualization of catheter, soft tissue and the blood pool remains challenging. In this study, a novel passive tracking technique is proposed for enhanced positive contrast visualization of gadolinium-filled balloon catheters using partial saturation (pSAT) magnetization preparation.

METHODS

The proposed pSAT sequence uses a single shot acquisition with balanced steady-state free precession (bSSFP) readout preceded by a partial saturation pre-pulse. This technique was initially evaluated in five healthy subjects. The pSAT sequence was compared to conventional bSSFP images acquired with (SAT) and without (Non-SAT) saturation pre-pulse. Signal-to-noise ratio (SNR) of the catheter balloon, blood and myocardium and the corresponding contrast-to-noise ratio (CNR) are reported. Subjective assessment of image suitability for CMR-guidance and ideal pSAT angle was performed by three cardiologists. The feasibility of the pSAT sequence is demonstrated in two adult patients undergoing CMR-guided cardiac catheterization.

RESULTS

The proposed pSAT approach provided better catheter balloon/blood contrast and catheter balloon/myocardium contrast than conventional Non-SAT sequences. It also resulted in better blood and myocardium SNR than SAT sequences. When averaged over all volunteers, images acquired with a pSAT angle of 20° to 40° enabled simultaneous visualization of the catheter balloon and the cardiovascular anatomy (blood and myocardium) and were found suitable for CMR-guidance in >93% of cases. The pSAT sequence was successfully used in two patients undergoing CMR-guided diagnostic cardiac catheterization.

CONCLUSIONS

The proposed pSAT sequence offers real-time, simultaneous, enhanced contrast visualization of the catheter balloon, soft tissues and blood. This technique provides improved passive tracking capabilities during CMR-guided catheterization in patients.

Genetic parameters for both a liver damage phenotype caused by and antibody response to phenotype in dairy and beef cattle

is a helminth parasite of economic importance to the global cattle industry, with documented high international herd prevalence. The objective of the present study was to generate the first published genetic parameter estimates for liver damage caused by as well as antibody response to in cattle. Abattoir data on the presence of live , or -damaged livers, were available between the years 2012 and 2015, inclusive. A second data set was available on cows from 68 selected dairy herds with a blood ELISA test for antibody response to in autumn 2015. Animals were identified as exposed by using herd mate phenotype, and only exposed animals were retained for analysis. The abattoir data set consisted of 20,481 dairy cows and 75,041 young dairy and beef animals, whereas the study herd data set consisted of 6,912 dairy cows. (Co)variance components for phenotypes in both data sets were estimated using animal linear mixed models. Fixed effects included in the model for both data sets were contemporary group, heterosis coefficient, recombination loss coefficient, parity, age relative to parity/age group, and stage of lactation. An additional fixed effect of abattoir by date of slaughter was included in the model for the analysis of the abattoir data. Direct additive genetic effects and a residual effect were included as random effects for all analyses. After data edits, the prevalence of liver damage caused by in cows and young cattle was 47% and 20%, respectively. The prevalence of a positive antibody response to in cows from the study herd data was 36% after data edits. The heritability of as a binary trait for dairy cows in abattoir data and study herd data was 0.03 ± 0.01 and 0.09 ± 0.02, respectively; heritability in young cattle was 0.01 ± 0.005. The additive genetic SD of as a binary trait was 0.069 and 0.050 for cows and young cattle from the abattoir data, respectively, and 0.112 from the study herd cows. The genetic correlation between liver damage caused by in young cattle and cows from the abattoir data was 0.94 ± 0.312 and the genetic correlation between liver damage caused by in cows and positive antibody response to in cows in the study herd data was 0.37 ± 0.283.

Shiitake Flagellate Dermatitis: the First Case Reported in Ireland

Shiitake (Lentinula edodes) is the second most commonly consumed mushroom worldwide. The first case of shiitake mushroom flagellate dermatitis was described in Japan in 1977 and it is now being reported in the western world. We describe the first reported case in Ireland.

Lighten the Load: Scaffolding Visual Literacy in Biochemistry and Molecular Biology

The development of scientific visual literacy has been identified as critical to the training of tomorrow's scientists and citizens alike. Within the context of the molecular life sciences in particular, visual representations frequently incorporate various components, such as discipline-specific graphical and diagrammatic features, varied levels of abstraction, and spatial arrangements of visual elements to convey information. Visual literacy is achieved when an individual understands the various ways in which a discipline uses these components to represent a particular way of knowing. Owing to the complex nature of visual representations, the activities through which visual literacy is developed have high cognitive load. Cognitive load can be reduced by first helping students to become fluent with the discrete components of visual representations before asking them to simultaneously integrate these components to extract the intended meaning of a representation. We present a taxonomy for characterizing one component of visual representations-the level of abstraction-as a first step in understanding the opportunities afforded students to develop fluency. Further, we demonstrate how our taxonomy can be used to analyze course assessments and spur discussions regarding the extent to which the development of visual literacy skills is supported by instruction within an undergraduate biochemistry curriculum.

Six-year longitudinal study of Fasciola hepatica bulk milk antibody ELISA in the dairy dense region of the Republic Ireland

Completion of the F. hepatica lifecycle is dependent on suitable climatic conditions for development of immature stages of the parasite, and its snail intermediate host. Few investigations have been conducted regarding temporal variations in F. hepatica status in Irish dairy herds. The current study aimed to conduct a longitudinal study examining annual and seasonal trends in bulk milk seropositivity over six years, while also investigating associations with soil temperature, rainfall and flukicide treatment. Monthly bulk milk samples (BTM) were submitted by 28 herds between March 2009 and December 2014. In all, 1337 samples were analysed using a Cathepsin L1 ELISA. Soil temperature, rainfall and management data were obtained for general estimating equation and regression analyses. A general decrease in milk seropositivity was observed over the six year study period and was associated with an increased likelihood of treating for liver fluke (OR range=2.73-6.96). Annual and seasonal analyses of rainfall and F. hepatica BTM status yielded conflicting results. Higher annual rainfall (>1150mm) yielded a lower likelihood of being BTM positive than annual rainfall of <1000mm (OR=0.47; P=0.036). This was most likely due to farmers being more proactive in treating for F. hepatica in wetter years, although a 'wash effect' by high rainfall of the free living stages and snails cannot be ruled out. Higher seasonal rainfall (>120mm), however, was associated with increased ELISA S/P% values (Coefficient=9.63S/P%; P=0.001). Soil temperature was not found to influence F. hepatica to the same extent as rainfall and may reflect the lack of severe temperature fluctuations in Ireland. Flukicides active against both immature and mature F. hepatica were approximately half as likely to record a positive F. hepatica herd BTM status than a flukicide active against only the mature stage of the parasite (OR≅0.45; P<0.01). This study highlights the importance of examining both annual and seasonal F. hepatica data, which can vary significantly. Additionally, it highlights the progress that can be achieved in fluke control by application of a continuous BTM monitoring program.

Neurosensory deficit following mandibular sagittal split osteotomy: A comparative study between positional screws and miniplates fixation

This retrospective study compared the incidence of long-term inferior alveolar nerve injury for positional screws and miniplate fixation of bilateral sagittal split osteotomies carried out in 2 hospitals in Scotland. The study involved a mixture of mandibular setback and advancement surgery. The outcome of neurosensory deficit (NSD) was solely based on subjective assessment by the surgeons and patients' reported alteration in sensation. Numbness, tingling and any alterations in sensation beyond 6 months were considered long-term inferior alveolar nerve injury. This study was conducted on 28 sagittal split osteotomies (group 1) which were fixed with three upper border fixation screws and 36 sagittal split osteotomies (group 2) which were fixed with upper border sliding plate. The reported and documented neurosensory deficits were analysed. The difference in the number of cases of long-term inferior alveolar nerve injury between the 2 methods was 10.3%; the 95% confidence interval for the difference was [-2.94 to 23.5], p = 0.1612. Upper border plate was associated with more long-term NSD but there is insufficient evidence to prove that one method was more superior to the other. The need for a prospective randomized trial was highlighted.

Use of a semi-automated cardiac segmentation tool improves reproducibility and speed of segmentation of contaminated right heart magnetic resonance angiography

Three-dimensional printing has an increasing number of clinical applications in pediatric cardiology. Time required for dataset segmentation and conversion to stereolithography (STL) format remains a significant limitation. We investigated the impact of semi-automated cardiovascular-specific segmentation software on time and reproducibility of segmentation. Magnetic resonance angiograms (MRAs) of 19 patients undergoing intervention for right ventricular outflow lesions were segmented to demonstrate the right heart. STLs were created by two independent clinicians using semi-automated cardiovascular segmentation (SAS) and traditional manual segmentation (MS). Time was recorded and geometric STL disagreement was determined (0 % = no disagreement, 100 % = complete disagreement). MRA datasets were categorized as clean when only right heart structures were present in the MRA, or contaminated when left heart structures were also present and required removal. Eighteen (seven clean and 11 contaminated) cases were successfully segmented with both methods. Time to STL for clean datasets was faster with MS than SAS [median 209 s (IQR 192-252) vs. 296 s (272-317), p = 0.018] while contaminated datasets were faster with SAS [455 s (384-561) vs. 866 s (310-1429), p = 0.033]. Interobserver STL geometric disagreement was significantly lower using SAS than MS overall (0.70 ± 1.15 % vs. 1.31 ± 1.52 %, p = 0.030), and for the contaminated subset (0.81 ± 1.08 % vs. 1.75 ± 1.57 %, p = 0.036). Most geometric disagreement occurred at areas where left heart contamination was removed. Semi-automated segmentation was faster and more reproducible for contaminated datasets, while MS was faster but equally reproducible for clean datasets. Semi-automated segmentation methods are preferable for contaminated datasets and continued refinement of these tools should be supported.

A systematic review of image segmentation methodology, used in the additive manufacture of patient-specific 3D printed models of the cardiovascular system

Background

Shortcomings in existing methods of image segmentation preclude the widespread adoption of patient-specific 3D printing as a routine decision-making tool in the care of those with congenital heart disease. We sought to determine the range of cardiovascular segmentation methods and how long each of these methods takes.

Methods

A systematic review of literature was undertaken. Medical imaging modality, segmentation methods, segmentation time, segmentation descriptive quality (SDQ) and segmentation software were recorded.

Results

Totally 136 studies met the inclusion criteria (1 clinical trial; 80 journal articles; 55 conference, technical and case reports). The most frequently used image segmentation methods were brightness thresholding, region growing and manual editing, as supported by the most popular piece of proprietary software: Mimics (Materialise NV, Leuven, Belgium, 1992–2015). The use of bespoke software developed by individual authors was not uncommon. SDQ indicated that reporting of image segmentation methods was generally poor with only one in three accounts providing sufficient detail for their procedure to be reproduced.

Conclusions and implication of key findings

Predominantly anecdotal and case reporting precluded rigorous assessment of risk of bias and strength of evidence. This review finds a reliance on manual and semi-automated segmentation methods which demand a high level of expertise and a significant time commitment on the part of the operator. In light of the findings, we have made recommendations regarding reporting of 3D printing studies. We anticipate that these findings will encourage the development of advanced image segmentation methods.

Analysis of Johne's disease ELISA status and associated performance parameters in Irish dairy cows

BACKGROUND

Infection with Mycobacterium avium subspecies paratuberculosis (MAP) has been associated with reductions in milk production in dairy cows and sub optimal fertility. The aim of this study was to highlight the production losses associated with testing MAP ELISA positive in Irish dairy cows. Secondary objectives included investigation of risk factors associated with testing MAP ELISA positive. A survey of management practices on study farms was also conducted, with examination of associations between management practices and herd MAP status. Blood samples were collected from 4188 breeding animals on 22 farms. Samples were ELISA tested using the ID Screen Paratuberculosis Indirect Screening Test. Production parameters examined included milk yield, milk fat, milk protein, somatic cell count, and calving interval. The association between MAP ELISA status and production data was investigated using multi-level mixed models. Logistic regression was used to identify risk factors for testing JD blood ELISA positive at individual cow level and to identify associations between farm management practices and herd MAP status.

RESULTS

Data were available for 3528 cows. The apparent prevalence recorded was 7.4%. Mixed model analysis revealed no statistically significant association between testing MAP ELISA positive and dairy cow production parameters. Risk factors associated with testing positive included larger sized herds being over twice more likely to test positive than smaller herds (OR 2.4 P = <0.001). Friesians were less likely to test positive relative to other breeds. A number of study farmers were engaged in management practices that have previously been identified as high risk for MAP transmission e.g., 73.1% pooled colostrum and 84.6% of study farmers used the calving area to house sick animals throughout the year. No significant associations however, were identified between farm management practices and herd MAP status.

CONCLUSION

No production losses were identified; however an apparent prevalence of 7.4% was recorded. With the abolition of EU milk quotas herd size in Ireland is expanding, as herds included in this study were larger than the national average, results may be indicative of future JD levels if no JD control programmes are implemented to minimise transmission.

Utilising ionic liquids for the in situ swelling of Avicel towards enhanced enzymatic saccharification

In this study, choline carboxylate ionic liquids were explored as solvents to enhance the hydrolysis of cellulose by enzymes.

Study of the viral interference between infectious pancreatic necrosis virus (IPNV) and infectious haematopoietic necrosis virus (IHNV) in rainbow trout (Oncorhynchus mykiss)

The resistance of rainbow trout (Oncorhynchus mykiss) to an infectious haematopoietic necrosis virus (IHNV) challenge following a preceding non-lethal infection with infectious pancreatic necrosis virus (IPNV) was investigated through experimental dual infections. Trout initially infected with IPNV were inoculated 14 days later with IHNV. Single infections of trout with 1 of the 2 viruses or with cell culture supernatant were also carried out and constituted control groups. No mortality was noted in fish after a single infection with IPNV. This virus had no influence on the head kidney leucocyte phagocytic activity and plasma haemolytic complement activity. IHNV induced a high mortality (72%) and reduced the macrophage phagocytic activity and complement haemolytic activity. It also induced a late production of anti-IHNV antibodies which occurred after clearance of the virus in the fish. In trout co-infected with both viruses, a mortality rate of 2% occurred and the immune parameters were similar to those observed in the fish infected with IPNV only, demonstrating that in co-infected trout IPNV inhibits the effects of IHNV. The studied parameters did not allow us to define the mechanism of interference occurring between these 2 viruses, but some hypothesis are put forward to explain the interference between the 2 viruses.