80 research outputs found
Diversity and distribution of freshwater amphipod species in Switzerland (Crustacea: Amphipoda).
Amphipods are key organisms in many freshwater systems and contribute substantially to the diversity and functioning of macroinvertebrate communities. Furthermore, they are commonly used as bioindicators and for ecotoxicological tests. For many areas, however, diversity and distribution of amphipods is inadequately known, which limits their use in ecological and ecotoxicological studies and handicaps conservation initiatives. We studied the diversity and distribution of amphipods in Switzerland (Central Europe), covering four major drainage basins, an altitudinal gradient of>2,500 m, and various habitats (rivers, streams, lakes and groundwater). We provide the first provisional checklist and detailed information on the distribution and diversity of all amphipod species from Switzerland. In total, we found 29 amphipod species. This includes 16 native and 13 non-native species, one of the latter (Orchestia cavimana) reported here for the first time for Switzerland. The diversity is compared to neighboring countries. We specifically discuss species of the genus Niphargus, which are often receiving less attention. We also found evidence of an even higher level of hidden diversity, and the potential occurrence of further cryptic species. This diversity reflects the biogeographic past of Switzerland, and suggests that amphipods are ideally suited to address questions on endemism and adaptive radiations, post-glaciation re-colonization and invasion dynamics as well as biodiversity-ecosystem functioning relationships in aquatic systems
Comparison of scores for bimodality of gene expression distributions and genome-wide evaluation of the prognostic relevance of high-scoring genes
<p>Abstract</p> <p>Background</p> <p>A major goal of the analysis of high-dimensional RNA expression data from tumor tissue is to identify prognostic signatures for discriminating patient subgroups. For this purpose genome-wide identification of bimodally expressed genes from gene array data is relevant because distinguishability of high and low expression groups is easier compared to genes with unimodal expression distributions.</p> <p>Recently, several methods for the identification of genes with bimodal distributions have been introduced. A straightforward approach is to cluster the expression values and score the distance between the two distributions. Other scores directly measure properties of the distribution. The kurtosis, e.g., measures divergence from a normal distribution. An alternative is the outlier-sum statistic that identifies genes with extremely high or low expression values in a subset of the samples.</p> <p>Results</p> <p>We compare and discuss scores for bimodality for expression data. For the genome-wide identification of bimodal genes we apply all scores to expression data from 194 patients with node-negative breast cancer. Further, we present the first comprehensive genome-wide evaluation of the prognostic relevance of bimodal genes. We first rank genes according to bimodality scores and define two patient subgroups based on expression values. Then we assess the prognostic significance of the top ranking bimodal genes by comparing the survival functions of the two patient subgroups. We also evaluate the global association between the bimodal shape of expression distributions and survival times with an enrichment type analysis.</p> <p>Various cluster-based methods lead to a significant overrepresentation of prognostic genes. A striking result is obtained with the outlier-sum statistic (<it>p </it>< 10<sup>-12</sup>). Many genes with heavy tails generate subgroups of patients with different prognosis.</p> <p>Conclusions</p> <p>Genes with high bimodality scores are promising candidates for defining prognostic patient subgroups from expression data. We discuss advantages and disadvantages of the different scores for prognostic purposes. The outlier-sum statistic may be particularly valuable for the identification of genes to be included in prognostic signatures. Among the genes identified as bimodal in the breast cancer data set several have not yet previously been recognized to be prognostic and bimodally expressed in breast cancer.</p
Imaging neutral hydrogen on large-scales during the Epoch of Reionization with LOFAR
The first generation of redshifted 21 cm detection experiments, carried out
with arrays like LOFAR, MWA and GMRT, will have a very low signal-to-noise
ratio per resolution element (\sim 0.2). In addition, whereas the variance of
the cosmological signal decreases on scales larger than the typical size of
ionization bubbles, the variance of the formidable galactic foregrounds
increases, making it hard to disentangle the two on such large scales. The poor
sensitivity on small scales on the one hand, and the foregrounds effect on
large scales on the other hand, make direct imaging of the Epoch of
Reionization of the Universe very difficult, and detection of the signal
therefore is expected to be statistical.Despite these hurdles, in this paper we
argue that for many reionization scenarios low resolution images could be
obtained from the expected data. This is because at the later stages of the
process one still finds very large pockets of neutral regions in the IGM,
reflecting the clustering of the large-scale structure, which stays strong up
to scales of \sim 120 comoving Mpc/h (\sim 1 degree). The coherence of the
emission on those scales allows us to reach sufficient S/N (\sim 3) so as to
obtain reionization 21 cm images. Such images will be extremely valuable for
answering many cosmological questions but above all they will be a very
powerful tool to test our control of the systematics in the data. The existence
of this typical scale (\sim 120 comoving Mpc/h) also argues for designing
future EoR experiments, e.g., with SKA, with a field of view of at least 4
degree.Comment: Replaced with final version (minor changes), 9 figures, 11 pages,
accepted for publication in MNRA
Hydroecology of Amazonian lacustrine Arcellinida (testate amoebae): A case study from Lake Quistococha, Peru
Organic rich sediments were obtained from seven core tops taken in Lake Quistococha, near the city of Iquitos in the Peruvian Amazon. Subsamples from 0 to 4 cm depth in each core were analyzed under dissecting light microscopy to carry out the first investigation of Arcellinida (testate lobose amoebae) from a lacustrine environment in this ecologically important region. The fauna was characterized by a low diversity, low abundance community dominated by centropyxids. This fauna is similar to ‘stressed’ assemblages reported from temperate latitudes, except that test concentrations were two orders of magnitude lower than typical in temperate lakes. Principle arcellinidan stressors in Lake Quistococha likely include the low pH 4 conditions in the lake, and a general lack of suitable minerogenic material to construct tests in the organic rich lake substrate. The low pH conditions are the result of runoff and seepage of water high in dissolved organic carbon from the adjacent similarly low pH 4 terrestrial peatland. The dearth of minerogenic material is the result of the lake being isolated from riverine input for the past ∼2000 years, even during flooding events. Other limiting factors contributing to depressed arcellinidan populations may include nutrient supply, predation pressure, competition, and post-mortem taphonomic factors
Biodiversity increases and decreases ecosystem stability
International audienc
MedShapeNet -- A Large-Scale Dataset of 3D Medical Shapes for Computer Vision
Prior to the deep learning era, shape was commonly used to describe the
objects. Nowadays, state-of-the-art (SOTA) algorithms in medical imaging are
predominantly diverging from computer vision, where voxel grids, meshes, point
clouds, and implicit surface models are used. This is seen from numerous
shape-related publications in premier vision conferences as well as the growing
popularity of ShapeNet (about 51,300 models) and Princeton ModelNet (127,915
models). For the medical domain, we present a large collection of anatomical
shapes (e.g., bones, organs, vessels) and 3D models of surgical instrument,
called MedShapeNet, created to facilitate the translation of data-driven vision
algorithms to medical applications and to adapt SOTA vision algorithms to
medical problems. As a unique feature, we directly model the majority of shapes
on the imaging data of real patients. As of today, MedShapeNet includes 23
dataset with more than 100,000 shapes that are paired with annotations (ground
truth). Our data is freely accessible via a web interface and a Python
application programming interface (API) and can be used for discriminative,
reconstructive, and variational benchmarks as well as various applications in
virtual, augmented, or mixed reality, and 3D printing. Exemplary, we present
use cases in the fields of classification of brain tumors, facial and skull
reconstructions, multi-class anatomy completion, education, and 3D printing. In
future, we will extend the data and improve the interfaces. The project pages
are: https://medshapenet.ikim.nrw/ and
https://github.com/Jianningli/medshapenet-feedbackComment: 16 page
Optimising sampling and analysis protocols in environmental DNA studies
Ecological surveys risk incurring false negative and false positive detections of the target species. With indirect survey methods, such as environmental DNA, such error can occur at two stages: sample collection and laboratory analysis. Here we analyse a large qPCR based eDNA data set using two occupancy models, one of which accounts for false positive error by Griffin et al. (2020), and a second that assumes no false positive error by Stratton et al. (2020). Additionally, we apply the Griffin et al. (2020) model to simulated data to determine optimal levels of replication at both sampling stages. The Stratton et al. (2020) model, which assumes no false positive results, consistently overestimated both overall and individual site occupancy compared to both the Griffin et al. (2020) model and to previous estimates of pond occupancy for the target species. The inclusion of replication at both stages of eDNA analysis (sample collection and in the laboratory) reduces both bias and credible interval width in estimates of both occupancy and detectability. Even the collection of >1 sample from a site can improve parameter estimates more than having a high number of replicates only within the laboratory analysis
Malariaprophylaxe und Selbsttherapie 1990 - Probleme und aktuelle Lösungen
For successful malaria prophylaxis, future travelers need to be informed about the risks of infection and about systematic measures to be taken against mosquito bites. For visits in areas of high transmission, continuous chemoprophylaxis is recommended, whereas in regions with low transmission a stand-by medication for self-therapy is sufficient. Each of these four measures has some problems which are discussed here in addition to the recently published recommendations by the Swiss Working Group for Medical Advice to Travelers
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