Biologists meet statisticians: A workshop for young scientists to foster interdisciplinary team work

Life science and statistics have necessarily become essential partners. The need to plan complex, structured experiments, involving elaborated designs, and the need to analyse datasets in the era of systems biology and high throughput technologies has to build upon professional statistical expertise. On the other hand, conducting such analyses and also developing improved or new methods, also for novel kinds of data, has to build upon solid biological understanding and practise. However, the meeting of scientists of both fields is often hampered by a variety of communicative hurdles - which are based on field-specific working languages and cultural differences. As a step towards a better mutual understanding, we developed a workshop concept bringing together young experimental biologists and statisticians, to work as pairs and learn to value each others competences and practise interdisciplinary communication in a casual atmosphere. The first implementation of our concept was a cooperation of the German Region of the International Biometrical Society and the Leibnitz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (short: DSMZ), Braunschweig, Germany. We collected feedback in form of three questionnaires, oral comments, and gathered experiences for the improvement of this concept. The long-term challenge for both disciplines is the establishment of systematic schedules and strategic partnerships which use the proposed workshop concept to foster mutual understanding, to seed the necessary interdisciplinary cooperation network, and to start training the indispensable communication skills at the earliest possible phase of education

Root Zone Sensors for Irrigation Management in Intensive Agriculture

Crop irrigation uses more than 70% of the world’s water, and thus, improving irrigation efficiency is decisive to sustain the food demand from a fast-growing world population. This objective may be accomplished by cultivating more water-efficient crop species and/or through the application of efficient irrigation systems, which includes the implementation of a suitable method for precise scheduling. At the farm level, irrigation is generally scheduled based on the grower’s experience or on the determination of soil water balance (weather-based method). An alternative approach entails the measurement of soil water status. Expensive and sophisticated root zone sensors (RZS), such as neutron probes, are available for the use of soil and plant scientists, while cheap and practical devices are needed for irrigation management in commercial crops. The paper illustrates the main features of RZS’ (for both soil moisture and salinity) marketed for the irrigation industry and discusses how such sensors may be integrated in a wireless network for computer-controlled irrigation and used for innovative irrigation strategies, such as deficit or dual-water irrigation. The paper also consider the main results of recent or current research works conducted by the authors in Tuscany (Italy) on the irrigation management of container-grown ornamental plants, which is an important agricultural sector in Italy

Helminth parasites of sheep and goats in Eastern Ethiopia

A two-year epidemiology study of helminths of small ruminants involved the collection of viscera from 655 sheep and 632 goats from 4 abattoirs in eastern Ethiopia. A further more detailed epidemiology study of gastro-intestinal nematode infections used the Haramaya University (HU) flock of 60 Black Head Ogaden sheep. The parasitological data included numbers of nematode eggs per gram of faeces (EPG), faecal culture L3 larvae, packed red cell volume (PCV), adult worm and early L4 counts, and FAMACHA eye-colour score estimates, along with animal performance (body weight change). There were 13 species of nematodes and 4 species of flukes present in the sheep and goats, with Haemonchus contortus being the most prevalent (65–80%), followed by Trichostrongylus spp. The nematode infection levels of both sheep and goats followed the bi-modal annual rainfall pattern, with the highest worm burdens occurring during the two rain seasons (peaks in May and September). There were significant differences in worm burdens between the 4 geographic locations for both sheep and goats. Similar seasonal but not geographical variations occurred in the prevalence of flukes. There were significant correlations between EPG and PCV, EPG and FAMACHA scores, and PCV and FAMACHA scores. Moreover, H. contortus showed an increased propensity for arrested development during the dry seasons. Faecal egg count reduction tests (FECRT) conducted on the HU flocks, and flocks in surrounding small-holder communities, evaluated the efficacy of commonly used anthelmintics, including albendazole (ABZ), tetramisole (TET), a combination (ABZ + TET) and ivermectin (IVM). Initially, high levels of resistance to all of the anthelmintics were found in the HU goat flock but not in the sheep. In an attempt to restore the anthelmintic efficacy a new management system was applied to the HU goat flock, including: eliminating the existing parasite infections in the goats, exclusion from the traditional goat pastures, and initiation of communal grazing of the goats with the HU sheep and animals of the local small-holder farmers. Subsequent FECRTs revealed high levels of efficacy of all three drugs in the goat and sheep flocks, demonstrating that anthelmintic efficacy can be restored by exploiting refugia. Individual FECRTs were also conducted on 8 sheep and goat flocks owned by neighbouring small-holder farmers, who received breeding stock from the HU. In each FECRT, 50 local breed sheep and goats, 6–9 months old, were divided into 5 treatment groups: ABZ, TET, ABZ + TET, IVM and untreated control. There was no evidence of anthelmintic resistance in the nematodes, indicating that dilution of resistant parasites, which are likely to be imported with introduced breeding goats, and the low selection pressure imposed by the small-holder farmers, had prevented anthelmintic resistance from emerging

myTea: Connecting the Web to Digital Science on the Desktop

Bioinformaticians regularly access the hundreds of databases and tools that are available to them on the Web. None of these tools communicate with each other, causing the scientist to copy results manually from a Web site into a spreadsheet or word processor. myGrids' Taverna has made it possible to create templates (workflows) that automatically run searches using these databases and tools, cutting down what previously took days of work into hours, and enabling the automated capture of experimental details. What is still missing in the capture process, however, is the details of work done on that material once it moves from the Web to the desktop: if a scientist runs a process on some data, there is nothing to record why that action was taken; it is likewise not easy to publish a record of this process back to the community on the Web. In this paper, we present a novel interaction framework, built on Semantic Web technologies, and grounded in usability design practice, in particular the Making Tea method. Through this work, we introduce a new model of practice designed specifically to (1) support the scientists' interactions with data from the Web to the desktop, (2) provide automatic annotation of process to capture what has previously been lost and (3) associate provenance services automatically with that data in order to enable meaningful interrogation of the process and controlled sharing of the results

Development and Characterisation of a Gas System and its Associated Slow-Control System for an ATLAS Small-Strip Thin Gap Chamber Testing Facility

A quality assurance and performance qualification laboratory was built at McGill University for the Canadian-made small-strip Thin Gap Chamber (sTGC) muon detectors produced for the 2019-2020 ATLAS experiment muon spectrometer upgrade. The facility uses cosmic rays as a muon source to ionise the quenching gas mixture of pentane and carbon dioxide flowing through the sTGC detector. A gas system was developed and characterised for this purpose, with a simple and efficient gas condenser design utilizing a Peltier thermoelectric cooler (TEC). The gas system was tested to provide the desired 45 vol% pentane concentration. For continuous operations, a state-machine system was implemented with alerting and remote monitoring features to run all cosmic-ray data-acquisition associated slow-control systems, such as high/low voltage, gas system and environmental monitoring, in a safe and continuous mode, even in the absence of an operator.Comment: 23 pages, LaTeX, 14 figures, 4 tables, proof corrections for Journal of Instrumentation (JINST), including corrected Fig. 8b

Distributed environmental monitoring

With increasingly ubiquitous use of web-based technologies in society today, autonomous sensor networks represent the future in large-scale information acquisition for applications ranging from environmental monitoring to in vivo sensing. This chapter presents a range of on-going projects with an emphasis on environmental sensing; relevant literature pertaining to sensor networks is reviewed, validated sensing applications are described and the contribution of high-resolution temporal data to better decision-making is discussed