Biometeorology in austria: past,present and future

Biometeorology in Austria has been shaped by concepts, personalities, and technology. In early times, the branches of biometeorology that are usual today were already evident: agricultural and forest meteorology, phenology, medical biometeorology and balneology, aerial biometeorology, urban housing and stabling meteorology all started to emerge several centuries ago. From the 1920 up to 1936, Wilhelm Schmidt at the Agricultural University of Austria laid the foundations of modern biometeorology. He was followed by Franz Sauberer, who headed a Department of Biometeorology at the National Weather Service and devoted his active life totally to biometeorology. Several years after his untimely death, the Department was dissolved. Not until 1981 was biometeorology taken up again at the Agricultural University, where the tradition of Schmidt and Sauberer now lives on in several courses within the area of applied biometeorology: Micro-and Topoclimatology, Agricultural and Forest Meteorology and Atmospheric Radiation. Biometeorology, being an experimental science, has also been influenced by new technological developments. The early period was exclusively observational. During the late nineteenth and early twentieth centuries mechanical and simple electric instruments were used with strip-chart recorders. These time consuming methods have now been replaced by electronic devices, including data loggers and portable computers along with many new electronic sensors, which provide additional insight into biometeorological problems. Since computers also make it possible to solve some of the complicated equations of biometeorology, the future of this science seems to be bright, not only in Austria but throughout the world.     

A comparison of parametric versus permutation methods with applications to general and temporal microarray gene expression data

MOTIVATION: In analyses of microarray data with a design of different biological conditions, ranking genes by their differential 'importance' is often desired so that biologists can focus research on a small subset of genes that are most likely related to the experiment conditions. Permutation methods are often recommended and used, in place of their parametric counterparts, due to the small sample sizes of microarray experiments and possible non-normality of the data. The recommendations, however, are based on classical knowledge in the hypothesis test setting. RESULTS: We explore the relationship between hypothesis testing and gene ranking. We indicate that the permutation method does not provide a metric for the distance between two underlying distributions. In our simulation studies permutation methods tend to be equally or less accurate than parametric methods in ranking genes. This is partially due to the discreteness of the permutation distributions, as well as the non-metric property. In data analysis the variability in ranking genes can be assessed by bootstrap. It turns out that the variability is much lower for permutation than parametric methods, which agrees with the known robustness of permutation methods to individual outliers in the data.     

Entomological biometeorology

Summary I would appear to have given a rather pessimistic picture of the problems in entomological biometeorology as a result of emphasizing the areas of research that are most vitally concerned with a full understanding of the insect's relation to its environment. An important part of continuing scientific study is capacity to define problems for future investigation from past experience. In spite of the fact that many research results in border fields between meteorology and biology have accumulated without any serious organization toward unifying concepts, it is encouraging that we have achieved enough insight to define some of the basic problems. Future research is in a position in many ways to contribute to the organized approach that is required to make biometeorology a science.It should also be observed that the major limiting problem of handling large volumes of data in complicated ecological studies has been solved in principle to a large extent by the digital and the analogue electronic computers. Digital computer programming has already been incorporated in some population studies for insects. Eventual extension of analogue computer methods to behaviour problems may well facilitate an understanding of more complicated systems,especially those basic to the dispersal and migration of insects.     

Optimal use of conservation and accessibility filters in microRNA target prediction

It is generally accepted that filtering microRNA (miRNA) target predictions by conservation or by accessibility can reduce the false discovery rate. However, these two strategies are usually not exploited in a combined and flexible manner. Here, we introduce PACCMIT, a flexible method that filters miRNA binding sites by their conservation, accessibility, or both. The improvement in performance obtained with each of these three filters is demonstrated on the prediction of targets for both i) highly and ii) weakly conserved miRNAs, i.e., in two scenarios in which the miRNA-target interactions are subjected to different evolutionary pressures. We show that in the first scenario conservation is a better filter than accessibility (as both sensitivity and precision are higher among the top predictions) and that the combined filter improves performance of PACCMIT even further. In the second scenario, on the other hand, the accessibility filter performs better than both the conservation and combined filters, suggesting that the site conservation is not equally effective in rejecting false positive predictions for all miRNAs. Regarding the quality of the ranking criterion proposed by Robins and Press and used in PACCMIT, it is shown that top ranking interactions correspond to more downregulated proteins than do the lower ranking interactions. Comparison with several other target prediction algorithms shows that the ranking of predictions provided by PACCMIT is at least as good as the ranking generated by other conservation-based methods and considerably better than the energy-based ranking used in other accessibility-based methods.     

The importance of air quality in human biometeorology

Often we encounter a misunderstanding based on the assertion that the criterion of air quality is excluded from studies into meteorology and climatology. In contrast to this, it must be stressed that the admixtures and pollutants pertaining to air quality criteria belong to the atmosphere and therefore, of course, to the field of meteorology, and due to their possible effects also to human biometeorology. A normal weather forecast should include data concerning the concentrations of ozone, nitrogen dioxide, and other substances. Biometeorological weather classifications should also include mention of air quality rather more than previously. For instance, the classification after Bucher used in Germany is referred to and supplemented with respect to air quality. Analogous relationships hold true for the global classification of climates. As an example, the well-known classification after Koeppen is supplemented according to air quality.     

Classifying aquatic macrophytes as indicators of eutrophication in European lakes

Aquatic macrophytes are one of the biological quality elements in the Water Framework Directive (WFD) for which status assessments must be defined. We tested two methods to classify macrophyte species and their response to eutrophication pressure: one based on percentiles of occurrence along a phosphorous gradient and another based on trophic ranking of species using Canonical Correspondence Analyses in the ranking procedure. The methods were tested at Europe-wide, regional and national scale as well as by alkalinity category, using 1,147 lakes from 12 European states. The grouping of species as sensitive, tolerant or indifferent to eutrophication was evaluated for some taxa, such as the sensitive Chara spp. and the large isoetids, by analysing the (non-linear) response curve along a phosphorous gradient. These thresholds revealed in these response curves can be used to set boundaries among different ecological status classes. In total 48 taxa out of 114 taxa were classified identically regardless of dataset or classification method. These taxa can be considered the most consistent and reliable indicators of sensitivity or tolerance to eutrophication at European scale. Although the general response of well known indicator species seems to hold, there are many species that were evaluated differently according to the database selection and classification methods. This hampers a Europe-wide comparison of classified species lists as used for the status assessment within the WFD implementation process.     

Deciphering human prehistory through the geoarcheological study of cave sediments

Throughout human history, caves and rockshelters have been favored habitation places. These unique environments preserve sediments derived from an assortment of geological and human processes that are typically absent or masked at open‐air sites. Cave sediments are parts of larger stratigraphic frameworks that can reflect environmental changes, shifting microenvironments, and the nature of human activity within these confined and sheltered spaces. Stone tools and faunal material compose the artifact assemblages from caves that are typically studied. Cave sediments, on the other hand, which encase the archeological finds and which have both geological and human origins, have been understudied relative to traditional artifacts, in spite of their ubiquity and importance. Thus, anthropogenic sediments, the most striking of which are organic‐rich deposits, and combustion features merit the same attention as any other artifacts that result from human activities and behaviors. The purpose of this paper is to highlight some of the most salient aspects of prehistoric cave sediments and the processes revealed by recent studies of these accumulations. We review methods and techniques that are used to analyze cave sediments and illustrate how their careful study can be used to reconstruct local and regional cave environments, as well as the nature of the human activities that produced them. Finally, we show how such study can place important constraints on our archeological interpretations, ultimately having a profound effect on how we decipher human prehistory.     

Application of a simple likelihood ratio approximant to protein sequence classification

MOTIVATION: Likelihood ratio approximants (LRA) have been widely used for model comparison in statistics. The present study was undertaken in order to explore their utility as a scoring (ranking) function in the classification of protein sequences. RESULTS: We used a simple LRA-based on the maximal similarity (or minimal distance) scores of the two top ranking sequence classes. The scoring methods (Smith-Waterman, BLAST, local alignment kernel and compression based distances) were compared on datasets designed to test sequence similarities between proteins distantly related in terms of structure or evolution. It was found that LRA-based scoring can significantly outperform simple scoring methods.     

Behavioral processes and costs of co-existence in female spotted hyenas: a life history perspective

We assessed the importance of three behavioral processes on the fitness of individual females as mediated via maternal care in matrilineally organized social groups of spotted hyenas Crocuta crocuta. These were maternal choice of foraging tactic, the maintenance of individual dominance rank (social status) within the adult female hierarchy, and the behavioral support provided by mothers to their daughters when daughters acquired their position in the adult female hierarchy. The effects of all behavioral processes were closely linked. Maternal care was dependent on maternal social status because high ranking females had priority of access to food, and individual maternal choice of foraging tactic was frequency – and social status-dependent when medium prey abundance provided an opportunity for such a choice. At medium prey abundance, low ranking females went on costly long distance commuting trips to forage on migratory herds outside the group territory, whereas high ranking females fed on kills within the group territory. As a consequence, offspring of high ranking females grew faster, had a higher chance of survival to adulthood, and thus high ranking females had a higher lifetime reproductive success. Daughters of high ranking females usually acquired a social status immediately below that of their mother provided they enjoyed the effective support from their mothers as coalition partners, and they gave birth to their first litter at an earlier age than daughters of low ranking mothers. Spotted hyenas are therefore an example of the silver-spoon effect. This study shows that the frequency-dependent outcome of behavioral processes can be a key determinant of maternal reproductive success in social carnivores and have a profound influence on the reproductive career prospects of offspring.     

A Ranking Approach to Genomic Selection

Background

Genomic selection (GS) is a recent selective breeding method which uses predictive models based on whole-genome molecular markers. Until now, existing studies formulated GS as the problem of modeling an individual’s breeding value for a particular trait of interest, i.e., as a regression problem. To assess predictive accuracy of the model, the Pearson correlation between observed and predicted trait values was used.

Contributions

In this paper, we propose to formulate GS as the problem of ranking individuals according to their breeding value. Our proposed framework allows us to employ machine learning methods for ranking which had previously not been considered in the GS literature. To assess ranking accuracy of a model, we introduce a new measure originating from the information retrieval literature called normalized discounted cumulative gain (NDCG). NDCG rewards more strongly models which assign a high rank to individuals with high breeding value. Therefore, NDCG reflects a prerequisite objective in selective breeding: accurate selection of individuals with high breeding value.

Results

We conducted a comparison of 10 existing regression methods and 3 new ranking methods on 6 datasets, consisting of 4 plant species and 25 traits. Our experimental results suggest that tree-based ensemble methods including McRank, Random Forests and Gradient Boosting Regression Trees achieve excellent ranking accuracy. RKHS regression and RankSVM also achieve good accuracy when used with an RBF kernel. Traditional regression methods such as Bayesian lasso, wBSR and BayesC were found less suitable for ranking. Pearson correlation was found to correlate poorly with NDCG. Our study suggests two important messages. First, ranking methods are a promising research direction in GS. Second, NDCG can be a useful evaluation measure for GS.     

Species selection by interactive ranking

Ranking methods represent a means of giving weight to species according to their measured or perceived importance. Stepwise methods, such as Orlóci's (1973) yield a small list of species which can effectively describe groups and gradients in the data. These lists often include species which are difficult to use and the method does not allow incorporation of internal information in the analysis. The present method overcomes these problems. It uses Orlóci's (1973) ranking as a basis, but allows the user to reject species if undesired on ecological or practical grounds. The method is illustrated on a set of 34 relevés from peat bogs, and interactive ranking proves only slightly less efficient than un iased ranking.Nomenclature follows Hess et al. (1967–1972) for vascular plants.Acknowledgement. The author expresses his thanks to Dr L. Orlóci for advice and comments.     

The signifiance of meteorology in animal production

The production of meat, milk and eggs is highest and occurs at a maximal efficiency if the meteorological elements are within a certain range (zone of indifference). Outside this range the animal has to combat meteorological stress. This requires extra energy, so that less energy is available for productive processes. It is therefore important to find out at which levels the various meteorological elements become stressful to the animal organism. This study has to take into consideration the diversity of domestic animals, both with regard to structural features and functional traits. Responses of various categories of domestic animals to the following potentially stress producing meteorological conditions are briefly reviewed: cold, heat, solar radiation, high altitude and indoor environment. Knowledge so derived can be applied either by adapting the animal to the environment by breeding and selection, or by adapting the environment to the animal by technical and managerial means. Some suggestions are made for future considerations in the field of biometeorology of domestic animals.     

A Review and Evaluation of Plant Protection Product Ranking Tools Used in Agriculture

Pesticides used in the agricultural sector could potentially negatively impact the ecosystem, and consequently human and animal health. At the European level, legislation such as European Directive 67/548EEC stipulates that prior to the use of plant protection products, a risk assessment has to be performed. Due to the large number of chemicals used worldwide, it is practically impossible to implement a full quantitative risk assessment for all chemicals. Therefore, chemical ranking systems can be used as an initial screening of pesticides with the view to identifying those requiring further analysis. Nineteen commonly used pesticide ranking tools were evaluated according to: scale of intervention; environmental compartments; human and ecosystem effects; and stage of development and functionality. The tools were assigned a numerical score (maximum of 15) based on their fulfilment of these criteria. This facilitated identification of tools that could be used for a given set of input data and user requirements. The results showed great diversity with total scores between 6 and 13.5. The advantages and disadvantages of each individual model are described. Care needs to be taken in selecting a pesticide ranking tool that fulfills the required criteria in terms of scale, effects, functionality, and environmental compartments analyzed.     

The incompatibility of the United Nations' goals and conventionalist ethical relativism

The Universal Draft Declaration on Bioethics and Human Rights seeks to provide moral direction to nations and their citizens on a series of bioethical concerns. In articulating principles, it ranks respect for human rights, human dignity and fundamental freedoms ahead of respect for cultural diversity and pluralism. This ranking is controversial because it entails the rejection of the popular theory, conventionalist ethical relativism. If consistently defended, this theory also undercuts other United Nations activities that assume member states and people around the world can reach trans-cultural judgments having moral authority about health, pollution, aggression, rights, slavery, and so on. To illustrate problems with conventionalist ethical relativism and the importance of rejecting it for reasons of health, human rights, human dignity and fundamental freedoms, the widespread practice of female genital circumcision or cutting is discussed. These surgeries are virtually a test case for conventionalist ethical relativism since they are widely supported within these cultures as religious and health practices and widely condemned outside them, including by the United Nations.     

Efficient cloud service ranking based on uncertain user requirements

In a cloud computing environment, there are many providers offering various services of different quality attributes. Selecting a cloud service that meets user requirements from such a large number of cloud services is a complex and time-consuming process. At the same time, user requirements are sometimes described as uncertain (sets or intervals), something which should be taken into account while selecting cloud services. This paper proposes an efficient method for ranking cloud services while accounting for uncertain user requirements. For this purpose, a requirement interval is defined to fulfill uncertain user requirements. Since there are a large number of cloud services, the services falling outside the requirement interval are filtered out. Finally, the analytic hierarchy process is employed for ranking. The results evaluate the proposed method in terms of optimality of ranking, scalability, and sensitivity analyses. According to the test results, the proposed method outperforms the previous methods.

     

The value of cell cultures in leukemias, aplastic anemias and bone marrow transplantations

In a survey different methods of culture are represented for the purpose of identifying and quantifying haemopoietic stem cells (CFU-GEMM, CFU-GM, CFU-E/BFU-E) in human bone-marrow or peripheral blood respectively. On the basis of findings from international medical literature their validity is explained in the diagnostics and prognosis of some haematological diseases, such as acute and chronic myeloic leukemia, aplastic anemia, preleukemia. Special attention is given to their significance within bone-marrow transplantation. Their importance in evaluating transplantations after their preceding in-vitro manipulation as to the separation of rest tumour and T-cells is particularly referred to.     

Ranking Reputation and Quality in Online Rating Systems

How to design an accurate and robust ranking algorithm is a fundamental problem with wide applications in many real systems. It is especially significant in online rating systems due to the existence of some spammers. In the literature, many well-performed iterative ranking methods have been proposed. These methods can effectively recognize the unreliable users and reduce their weight in judging the quality of objects, and finally lead to a more accurate evaluation of the online products. In this paper, we design an iterative ranking method with high performance in both accuracy and robustness. More specifically, a reputation redistribution process is introduced to enhance the influence of highly reputed users and two penalty factors enable the algorithm resistance to malicious behaviors. Validation of our method is performed in both artificial and real user-object bipartite networks.     

Reconstructed human epidermis for skin absorption testing: results of the German prevalidation study

Exposure to chemicals absorbed by the skin can threaten human health. In order to standardise the predictive testing of percutaneous absorption for regulatory purposes, the OECD adopted guideline 428, which describes methods for assessing absorption by using human and animal skin. In this study, a protocol based on the OECD principles was developed and prevalidated by using reconstructed human epidermis (RHE). The permeation of the OECD standard compounds, caffeine and testosterone, through commercially available RHE models was compared to that of human epidermis and animal skin. In comparison to human epidermis, the permeation of the chemicals was overestimated when using RHE. The following ranking of the permeation coefficients for testosterone was obtained: SkinEthic > EpiDerm, EPISKIN > human epidermis, bovine udder skin, pig skin. The ranking for caffeine was: SkinEthic, EPISKIN > bovine udder skin, EpiDerm, pig skin, human epidermis. The inter-laboratory and intra-laboratory reproducibility was good. Long and variable lag times, which are a matter of concern when using human and pig skin, did not occur with RHE. Due to the successful transfer of the protocol, it is now in the validation process.