Calves with their dams in dairy cow systems

Conclusions and future perspectives: Interviews and on-farm studies across The Netherlands, France, Norway and Denmark showed that dam-rearing is practiced in a wealth of different systems, and four main angles should be considered when organizing a dam-calf contact system to fit the context and work well: calf, cow, farmers and farming system. Dam-calf contact systems can be seen as contributing significantly to the physiology and natural behavior of calves as well as of mother cows. Three important qualities in dam-calf contact systems were described from animals’ perspective: 1) nutrition, 2) care, and 3) learning. The priorities and perceptions of the importance of these three qualities influenced very much the farmers’ choices and priorities of systems. A focus on nutrition could for example motivate the choice of part time systems and strongly restricted systems (e.g. two times two hours daily access to each other), whereas a focus on care and learning would motivate a more full-time access system. Some perceived the calves to be equipped with capacities and skills through learning from the dam and others in the system, adding to their life opportunities, and they would favor a system where mother cow and calf were together with as little restriction as possible, although such systems require major efforts to organize and keep the overview. Farmers, who were introduced to dam-calf contact systems, but without having prior experience of these systems, pointed to the need for developing systems, which were much more ‘friendly’ to both cows and calves than what they saw. That is, develop dairy systems, which allowed cows and calves to be together, and the calves to learn about life in a dairy herd (e.g. indoor and outdoor life, and eating solid feed and grass), and with minimum risk. Among some interviewed actors, the needs of the calf seemed to be more in focus and of higher priority than the natural needs and the motivation of the mother cow. This is clear when talking about foster cow systems (where the mother cow is separated early after calving from her calf), but also when talking about dam-calf contact systems, many seemed to focus most on the benefits of the calf, although many noticed that the mother cow often reacted strongly to the separation and showed much distress. Seen from the farmers’ points of view, it was remarkable that most farmers, who had dam-calf contact systems, were mainly driven by the pleasure of seeing it work, and seeing the interaction between calves and cows. They articulated how they were touched and impressed e.g. by the mother cow’s consistent ‘watching over’ her calf, and the pain of separation. A number of the farmers had never been motivated by premium price or consumer demands, but just did it because they found it right, or ‘easier’ in combination that it brought them other qualities being farmers. Farmers, who were confronted with dam rearing systems for the first time in their lives, pointed to the necessity of finding a balance between ‘trusting the animals’ (because they could clearly see that the calves found their way), and ‘being in control’, because they used to know exactly how much milk the calves were drinking on daily basis. This points to the need for the humans in the system to redirect efforts and focus when observing animals, and when spending their time with cows and calves. There was a repeated questioning of ‘naturalness’ in relation to dam-rearing. Whilst acknowledging that mother cows and calves were strongly motivated and it was ‘natural’ for them to be together, some farmers also pointed to factors which partly made it ‘unnatural’ for them. This was especially the very high milk yields of dairy cows, which could lead to overdrinking for the calf, or deep udders, which made it difficult to drink for the calf, or the fact that daily life in a large dairy herd might not give a newborn calf sufficient peace to rest. Some issues remained unsolved at the current moment, and they need future solutions. One is the difference in many herds between ‘calves to stay in the herd’ versus ‘calves to leave the herds’ and not least their mothers, which had to go through early and abrupt separation. Another aspect is whether it is best to aim at farming systems in which the calf can find its mother, or the mother find her calf, or how they both have more or less unrestricted access to each other, but then with no opportunity to seek peace in a calf hide

EXPObench:Benchmarking Surrogate-based Optimisation Algorithms on Expensive Black-box Functions

Surrogate algorithms such as Bayesian optimisation are especially designed for black-box optimisation problems with expensive objectives, such as hyperparameter tuning or simulation-based optimisation. In the literature, these algorithms are usually evaluated with synthetic benchmarks which are well established but have no expensive objective, and only on one or two real-life applications which vary wildly between papers. There is a clear lack of standardisation when it comes to benchmarking surrogate algorithms on real-life, expensive, black-box objective functions. This makes it very difficult to draw conclusions on the effect of algorithmic contributions. A new benchmark library, EXPObench, provides first steps towards such a standardisation. The library is used to provide an extensive comparison of six different surrogate algorithms on four expensive optimisation problems from different real-life applications. This has led to new insights regarding the relative importance of exploration, the evaluation time of the objective, and the used model. A further contribution is that we make the algorithms and benchmark problem instances publicly available, contributing to more uniform analysis of surrogate algorithms. Most importantly, we include the performance of the six algorithms on all evaluated problem instances. This results in a unique new dataset that lowers the bar for researching new methods as the number of expensive evaluations required for comparison is significantly reduced

Patient condition modeling in remote patient management : hospitalization prediction

In order to maintain and improve the quality of care without exploding costs, healthcare systems are undergoing a paradigm shift from patient care in the hospital to patient care at home. Remote patient management (RPM) systems offer a great potential in reducing hospitalization costs and worsening of symptoms for patients with chronic diseases, e.g., heart failure and diabetes. Different types of data collected by RPM systems provide an opportunity for personalizing information services, and alerting medical personnel about the changing conditions of the patient. In this work we focus on a particular problem of patient modeling that is the hospitalization prediction. We consider the problem definition, our approach to this problem, highlight the results of the experimental study and reflect on their use in decision making

Quantitative implications of the updated EARL 2019 PET-CT performance standards

Purpose Recently, updated EARL specifications (EARL2) have been developed and announced. This study aims at investigating the impact of the EARL2 specifications on the quantitative reads of clinical PET-CT studies and testing a method to enable the use of the EARL2 standards whilst still generating quantitative reads compliant with current EARL standards (EARL1). Methods Thirteen non-small cell lung cancer (NSCLC) and seventeen lymphoma PET-CT studies were used to derive four image datasets-the first dataset complying with EARL1 specifications and the second reconstructed using parameters as described in EARL2. For the third (EARL2F6) and fourth (EARL2F7) dataset in EARL2, respectively, 6 mm and 7 mm Gaussian post-filtering was applied. We compared the results of quantitative metrics (MATV, SUVmax, SUVpeak, SUVmean, TLG, and tumor-to-liver and tumor-to-blood pool ratios) obtained with these 4 datasets in 55 suspected malignant lesions using three commonly used segmentation/volume of interest (VOI) methods (MAX41, A50P, SUV4). Results We found that with EARL2 MAX41 VOI method, MATV decreases by 22%, TLG remains unchanged and SUV values increase by 23-30% depending on the specific metric used. The EARL2F7 dataset produced quantitative metrics best aligning with EARL1, with no significant differences between most of the datasets (p>0.05). Different VOI methods performed similarly with regard to SUV metrics but differences in MATV as well as TLG were observed. No significant difference between NSCLC and lymphoma cancer types was observed. Conclusions Application of EARL2 standards can result in higher SUVs, reduced MATV and slightly changed TLG values relative to EARL1. Applying a Gaussian filter to PET images reconstructed using EARL2 parameters successfully yielded EARL1 compliant data

Quantitative implications of the updated EARL 2019 PET-CT performance standards

Purpose Recently, updated EARL specifications (EARL2) have been developed and announced. This study aims at investigating the impact of the EARL2 specifications on the quantitative reads of clinical PET-CT studies and testing a method to enable the use of the EARL2 standards whilst still generating quantitative reads compliant with current EARL standards (EARL1). Methods Thirteen non-small cell lung cancer (NSCLC) and seventeen lymphoma PET-CT studies were used to derive four image datasets-the first dataset complying with EARL1 specifications and the second reconstructed using parameters as described in EARL2. For the third (EARL2F6) and fourth (EARL2F7) dataset in EARL2, respectively, 6 mm and 7 mm Gaussian post-filtering was applied. We compared the results of quantitative metrics (MATV, SUVmax, SUVpeak, SUVmean, TLG, and tumor-to-liver and tumor-to-blood pool ratios) obtained with these 4 datasets in 55 suspected malignant lesions using three commonly used segmentation/volume of interest (VOI) methods (MAX41, A50P, SUV4). Results We found that with EARL2 MAX41 VOI method, MATV decreases by 22%, TLG remains unchanged and SUV values increase by 23-30% depending on the specific metric used. The EARL2F7 dataset produced quantitative metrics best aligning with EARL1, with no significant differences between most of the datasets (p>0.05). Different VOI methods performed similarly with regard to SUV metrics but differences in MATV as well as TLG were observed. No significant difference between NSCLC and lymphoma cancer types was observed. Conclusions Application of EARL2 standards can result in higher SUVs, reduced MATV and slightly changed TLG values relative to EARL1. Applying a Gaussian filter to PET images reconstructed using EARL2 parameters successfully yielded EARL1 compliant data

Crystal structure prediction of organic pigments: quinacridone as an example

The structures of the α, β and γ polymorphs of quinacridone were predicted using Polymorph Predictor software in combination with X-ray powder diffraction patterns of limited quality. The present work demonstrates a method to obtain crystal structures of industrially important pigments when only a low-quality powder pattern is available

Batch solution of small PDEs with the OPS DSL

In this paper we discuss the challenges and optimisations opportunities when solving a large number of small, equally sized discretised PDEs on regular grids. We present an extension of the OPS (Oxford Parallel library for Structured meshes) embedded Domain Specific Language, and show how support can be added for solving multiple systems, and how OPS makes it easy to deploy a variety of transformations and optimisations. The new capabilities in OPS allow to automatically apply data structure transformations, as well as execution schedule transformations to deliver high performance on a variety of hardware platforms. We evaluate our work on an industrially representative finance simulation on Intel CPUs, as well as NVIDIA GPUs