Cruise Report R.V. Alkor Cruise No.: AL478

Dates of Cruise: 16.05. – 28.05.2016 Areas of Research: Physical, chemical, biological and fishery oceanography Port Calls: Klaipeda, Lithuania, 21.05. – 23.05.201

Profound effect of profiling platform and normalization strategy on detection of differentially expressed microRNAs

Adequate normalization minimizes the effects of systematic technical variations and is a prerequisite for getting meaningful biological changes. However, there is inconsistency about miRNA normalization performances and recommendations. Thus, we investigated the impact of seven different normalization methods (reference gene index, global geometric mean, quantile, invariant selection, loess, loessM, and generalized procrustes analysis) on intra- and inter-platform performance of two distinct and commonly used miRNA profiling platforms. We included data from miRNA profiling analyses derived from a hybridization-based platform (Agilent Technologies) and an RT-qPCR platform (Applied Biosystems). Furthermore, we validated a subset of miRNAs by individual RT-qPCR assays. Our analyses incorporated data from the effect of differentiation and tumor necrosis factor alpha treatment on primary human skeletal muscle cells and a murine skeletal muscle cell line. Distinct normalization methods differed in their impact on (i) standard deviations, (ii) the area under the receiver operating characteristic (ROC) curve, (iii) the similarity of differential expression. Loess, loessM, and quantile analysis were most effective in minimizing standard deviations on the Agilent and TLDA platform. Moreover, loess, loessM, invariant selection and generalized procrustes analysis increased the area under the ROC curve, a measure for the statistical performance of a test. The Jaccard index revealed that inter-platform concordance of differential expression tended to be increased by loess, loessM, quantile, and GPA normalization of AGL and TLDA data as well as RGI normalization of TLDA data. We recommend the application of loess, or loessM, and GPA normalization for miRNA Agilent arrays and qPCR cards as these normalization approaches showed to (i) effectively reduce standard deviations, (ii) increase sensitivity and accuracy of differential miRNA expression detection as well as (iii) increase inter-platform concordance. Results showed the successful adoption of loessM and generalized procrustes analysis to one-color miRNA profiling experiments

Pflanzen- und ackerbauliche Maßnahmen zur Ampferbekämpfung auf Acker- und Grünlandflächen unter den Produktionsbedingungen des Ökologischen Landbaus

In Ökologisch wirtschaftenden Betrieben stellen Ampferarten, vor allen Dingen Rumex crispus und R. obtusifolius, weit verbreitete und hartnäckige Unkräuter sowohl im Acker als auch im Grünland dar. In diesem Beitrag werden Ergebnisse zur vegetativen und generativen Vermehrung von Ampfer vorgestellt, die auf der Versuchsstation für Ökologischen Landbau Kleinhohenheim der Universität Hohenheim im Jahr 2000 erhoben wurden. In Keimtests wurde die Keimbereitschaft von Ampfersamen unterschiedlichen Alters (Zeiternten in wöchentlichen Abständen von Mitte Mai bis Ende Juni) untersucht, um so einen Anhaltspunkt über den Einfluß des Schnittzeitpunkts von Grünland auf die generative Verbreitung von Ampfer zu erhalten. Die Ergebnisse zeigten, daß die Keimbereitschaft der Samen zur Heureife nur gering war. Mit zunehmender Reife der Pflanzen stieg jedoch die Keimbereitschaft auf Werte über 80 % an (Prüfung bei Dauerlicht und Wechseltemperatur). In einem zweiten Versuch wurden auf einer Ackerfläche etablierte Ampferpflanzen durch teilweises Entfernen von Sproß- und Wurzelmasse beschädigt und nach sechs Wochen Sproß- und Wurzelmasse erhoben. Hierbei zeigte sich, daß eine nachhaltige Bekämpfung um so eher möglich war, je mehr Biomasse von den Pflanzen entfernt wurde. Die Beschädigung der Pflanzen mit dem Ampferstecher erwies sich hierbei als eine besonders effektive Methode. Die Ergebnisse der beiden Versuche zeigen somit, daß es wirkungsvolle nicht chemische Kontrollmaßnahmen gibt, um die Verbreitung von Ampfer einzuschränken. In dem Beitrag wird die Frage diskutiert, warum Ampferarten im Ökologischen Landbau dennoch ein weit verbreitetes Problem darstellen. Pekrun, Carola und Jund, Dorothea und Hofrichter, Veit und Wagner, Susanne und Thumm, Ulrich und Claupein, Wilhelm (2002) Pflanzen- und ackerbauliche Maßnahmen zur Ampferbekämpfung auf Acker- und Grünlandflächen unter den Produktionsbedingungen des Ökologischen Landbaus [Indirect means of weed control against Rumex spec. on arable fields and grassland in organic farming]. Zeitschrift Pflanzenkrankheiten Pflanzenschutz, Sonderheft XVIII:533-540

Discrepancy-based Evolutionary Diversity Optimization

Diversity plays a crucial role in evolutionary computation. While diversity has been mainly used to prevent the population of an evolutionary algorithm from premature convergence, the use of evolutionary algorithms to obtain a diverse set of solutions has gained increasing attention in recent years. Diversity optimization in terms of features on the underlying problem allows to obtain a better understanding of possible solutions to the problem at hand and can be used for algorithm selection when dealing with combinatorial optimization problems such as the Traveling Salesperson Problem. We explore the use of the star-discrepancy measure to guide the diversity optimization process of an evolutionary algorithm. In our experimental investigations, we consider our discrepancy-based diversity optimization approaches for evolving diverse sets of images as well as instances of the Traveling Salesperson problem where a local search is not able to find near optimal solutions. Our experimental investigations comparing three diversity optimization approaches show that a discrepancy-based diversity optimization approach using a tie-breaking rule based on weighted differences to surrounding feature points provides the best results in terms of the star discrepancy measure

Faster Black-Box Algorithms Through Higher Arity Operators

We extend the work of Lehre and Witt (GECCO 2010) on the unbiased black-box model by considering higher arity variation operators. In particular, we show that already for binary operators the black-box complexity of \leadingones drops from $\Theta(n^2)$ for unary operators to $O(n \log n)$. For \onemax, the $\Omega(n \log n)$ unary black-box complexity drops to O(n) in the binary case. For $k$-ary operators, $k \leq n$, the \onemax-complexity further decreases to $O(n/\log k)$.Comment: To appear at FOGA 201

Planning training seminars in palliative care: a cross-sectional survey on the preferences of general practitioners and nurses in Austria

<p>Abstract</p> <p>Background</p> <p>Training in palliative care is frequently requested by health care professionals. However, little is known in detail about the subject matters and the educational preferences of physicians and staff or assistant nurses in this field.</p> <p>Methods</p> <p>All 897 registered GPs and all 933 registered home care nurses in the district of Steiermark/Austria were sent postal questionnaires.</p> <p>Results</p> <p>Results from 546 (30%) respondents revealed that GPs prefer evening courses and weekend seminars, whereas staff and assistant nurses prefer one-day courses. Multidisciplinary sessions are preferred by almost 80% of all professional groups. GPs preferred multi disciplinary groups most frequently when <it>addressing psychosocial needs </it>(88.8%) and <it>ethical questions </it>(85.8%). Staff and assistant nurses preferred multidisciplinary groups most frequently in the area of <it>pain </it>management (88%) and opted for multi disciplinary learning to a significantly higher extent than GPs (69%; p < 0.01). Those topics were ranked first which are not only deepening, but supplementing the professional training. On average, GPs were willing to spend a maximum amount of € 400 per year for training seminars in palliative care, whereas nurses would spend approximately € 190 for such classes.</p> <p>The results provide a detailed analysis of the preferences of GPs and nurses and offer guidance for the organisation of training seminars in palliative care.</p> <p>Conclusions</p> <p>Medical and nursing education programs often pursue separate paths. Yet our findings indicate that in palliative care multidisciplinary training seminars are favoured by both, doctors and nurses. Also, both groups prefer topics that are not only deepening, but supplementing their professional knowledge.</p