RepViz: A replicate-driven R tool for visualizing genomic regions

Objective: Visualization of sequencing data is an integral part of genomic data analysis. Although there are several tools to visualize sequencing data on genomic regions, they do not ofer user-friendly ways to view simultaneously diferent groups of replicates. To address this need, we developed a tool that allows efcient viewing of both intraand intergroup variation of sequencing counts on a genomic region, as well as their comparison to the output of user selected analysis methods, such as peak calling. Results: We present an R package RepViz for replicate-driven visualization of genomic regions. With ChIP-seq and ATAC-seq data we demonstrate its potential to aid visual inspection involved in the evaluation of normalization, outlier behavior, detected features from diferential peak calling analysis, and combined analysis of multiple data types. RepViz is readily available on Bioconductor (https://www.bioconductor.org/packages/devel/bioc/html/RepViz.html) and on Github (https://github.com/elolab/RepViz).</p

From critters to cancers: bridging comparative and clinical research on oxygen sensing, HIF signaling, and adaptations towards hypoxia

The objective of this symposium at the First International Congress of Respiratory Biology (ICRB) was to enhance communication between comparative biologists and cancer researchers working on O2 sensing via the HIF pathway. Representatives from both camps came together on August 13-16, 2006, in Bonn, Germany, to discuss molecular adaptations that occur after cells have been challenged by a reduced (hypoxia) or completely absent (anoxia) supply of oxygen. This brief "critters-to-cancer” survey discusses current projects and new directions aimed at improving understanding of hypoxic signaling and developing therapeutic intervention

Ionic and electronic structure of sodium clusters up to N=59

We determined the ionic and electronic structure of sodium clusters with even electron numbers and 2 to 59 atoms in axially averaged and three-dimensional density functional calculations. A local, phenomenological pseudopotential that reproduces important bulk and atomic properties and facilitates structure calculations has been developed. Photoabsorption spectra have been calculated for $\mathrm{Na}_2$, $\mathrm{Na}_8$, and $\mathrm{Na}_9^+$ to $\mathrm{Na}_{59}^+$. The consistent inclusion of ionic structure considerably improves agreement with experiment. An icosahedral growth pattern is observed for $\mathrm{Na}_{19}^+$ to $\mathrm{Na}_{59}^+$. This finding is supported by photoabsorption data.Comment: To appear in Phys. Rev. B 62. Version with figures in better quality can be requested from the author

A relational database to identify differentially expressed genes in the endometrium and endometriosis lesions

Endometriosis is a common inflammatory estrogen-dependent gynecological disorder, associated with pelvic pain and reduced fertility in women. Several aspects of this disorder and its cellular and molecular etiology remain unresolved. We have analyzed the global gene expression patterns in the endometrium, peritoneum and in endometriosis lesions of endometriosis patients and in the endometrium and peritoneum of healthy women. In this report, we present the EndometDB, an interactive web-based user interface for browsing the gene expression database of collected samples without the need for computational skills. The EndometDB incorporates the expression data from 115 patients and 53 controls, with over 24000 genes and clinical features, such as their age, disease stages, hormonal medication, menstrual cycle phase, and the different endometriosis lesion types. Using the web-tool, the end-user can easily generate various plot outputs and projections, including boxplots, and heatmaps and the generated outputs can be downloaded in pdf-format.Availability and implementationThe web-based user interface is implemented using HTML5, JavaScript, CSS, Plotly and R. It is freely available from https://endometdb.utu.fi/

Thermodynamics of Na_8 and Na_{20} clusters studied with ab-initio electronic structure methods

We study the thermodynamics of Na_8 and Na_{20} clusters using multiple-histogram methods and an ab initio treatment of the valence electrons within density functional theory. We consider the influence of various electron kinetic-energy functionals and pseudopotentials on the canonical ionic specific heats. The results for all models we consider show qualitative similarities, but also significant temperature shifts from model to model of peaks and other features in the specific-heat curves. The use of phenomenological pseudopotentials shifts the melting peak substantially (~ 50--100 K) when compared to ab-initio results. It is argued that the choice of a good pseudopotential and use of better electronic kinetic-energy functionals has the potential for performing large time scale and large sized thermodynamical simulations on clusters.Comment: LaTeX file and EPS figures. 24 pages, 13 figures. Submitted to Phys. Rev.

An orbital-free molecular dynamics study of melting in K_20, K_55, K_92, K_142, Rb_55 and Cs_55 clusters

The melting-like transition in potasium clusters K_N, with N=20, 55, 92 and 142, is studied by using an orbital-free density-functional constant-energy molecular dynamics simulation method, and compared to previous theoretical results on the melting-like transition in sodium clusters of the same sizes. Melting in potasium and sodium clusters proceeds in a similar way: a surface melting stage develops upon heating before the homogeneous melting temperature is reached. Premelting effects are nevertheless more important and more easily established in potasium clusters, and the transition regions spread over temperature intervals which are wider than in the case of sodium. For all the sizes considered, the percentage melting temperature reduction when passing from Na to K clusters is substantially larger than in the bulk. Once those two materials have been compared for a number of different cluster sizes, we study the melting-like transition in Rb_55 and Cs_55 clusters and make a comparison with the melting behavior of Na_55 and K_55. As the atomic number increases, the height of the specific heat peaks decreases, their width increases, and the melting temperature decreases as in bulk melting, but in a more pronounced way.Comment: LaTeX file. 6 pages with 17 pictures. Final version with minor change

Threat-sensitive anti-predator defence in precocial wader, the northern lapwing Vanellus vanellus

Birds exhibit various forms of anti-predator behaviours to avoid reproductive failure, with mobbing—observation, approach and usually harassment of a predator—being one of the most commonly observed. Here, we investigate patterns of temporal variation in the mobbing response exhibited by a precocial species, the northern lapwing (Vanellus vanellus). We test whether brood age and self-reliance, or the perceived risk posed by various predators, affect mobbing response of lapwings. We quantified aggressive interactions between lapwings and their natural avian predators and used generalized additive models to test how timing and predator species identity are related to the mobbing response of lapwings. Lapwings diversified mobbing response within the breeding season and depending on predator species. Raven Corvus corax, hooded crow Corvus cornix and harriers evoked the strongest response, while common buzzard Buteo buteo, white stork Ciconia ciconia, black-headed gull Chroicocephalus ridibundus and rook Corvus frugilegus were less frequently attacked. Lapwings increased their mobbing response against raven, common buzzard, white stork and rook throughout the breeding season, while defence against hooded crow, harriers and black-headed gull did not exhibit clear temporal patterns. Mobbing behaviour of lapwings apparently constitutes a flexible anti-predator strategy. The anti-predator response depends on predator species, which may suggest that lapwings distinguish between predator types and match mobbing response to the perceived hazard at different stages of the breeding cycle. We conclude that a single species may exhibit various patterns of temporal variation in anti-predator defence, which may correspond with various hypotheses derived from parental investment theory

Performance of the electromagnetic and hadronic prototype segments of the ALICE Forward Calorimeter

We present the performance of a full-length prototype of the ALICE Forward Calorimeter (FoCal). The detector is composed of a silicon-tungsten electromagnetic sampling calorimeter with longitudinal and transverse segmentation (FoCal-E) of about 20$X_0$ and a hadronic copper-scintillating-fiber calorimeter (FoCal-H) of about 5$\lambda_{\rm int}$. The data were taken between 2021 and 2023 at the CERN PS and SPS beam lines with hadron (electron) beams up to energies of 350 (300) GeV. Regarding FoCal-E, we report a comprehensive analysis of its response to minimum ionizing particles across all pad layers. The longitudinal shower profile of electromagnetic showers is measured with a layer-wise segmentation of 1$X_0$. As a projection to the performance of the final detector in electromagnetic showers, we demonstrate linearity in the full energy range, and show that the energy resolution fulfills the requirements for the physics needs. Additionally, the performance to separate two-showers events was studied by quantifying the transverse shower width. Regarding FoCal-H, we report a detailed analysis of the response to hadron beams between 60 and 350 GeV. The results are compared to simulations obtained with a Geant4 model of the test beam setup, which in particular for FoCal-E are in good agreement with the data. The energy resolution of FoCal-E was found to be lower than 3% at energies larger than 100 GeV. The response of FoCal-H to hadron beams was found to be linear, albeit with a significant intercept that is about factor 2 larger than in simulations. Its resolution, which is non-Gaussian and generally larger than in simulations, was quantified using the FWHM, and decreases from about 16% at 100 GeV to about 11% at 350 GeV. The discrepancy to simulations, which is particularly evident at low hadron energies, needs to be further investigated.Comment: 55 pages (without acronyms), 45 captioned figure

Impacts of climate change on plant diseases – opinions and trends

There has been a remarkable scientific output on the topic of how climate change is likely to affect plant diseases in the coming decades. This review addresses the need for review of this burgeoning literature by summarizing opinions of previous reviews and trends in recent studies on the impacts of climate change on plant health. Sudden Oak Death is used as an introductory case study: Californian forests could become even more susceptible to this emerging plant disease, if spring precipitations will be accompanied by warmer temperatures, although climate shifts may also affect the current synchronicity between host cambium activity and pathogen colonization rate. A summary of observed and predicted climate changes, as well as of direct effects of climate change on pathosystems, is provided. Prediction and management of climate change effects on plant health are complicated by indirect effects and the interactions with global change drivers. Uncertainty in models of plant disease development under climate change calls for a diversity of management strategies, from more participatory approaches to interdisciplinary science. Involvement of stakeholders and scientists from outside plant pathology shows the importance of trade-offs, for example in the land-sharing vs. sparing debate. Further research is needed on climate change and plant health in mountain, boreal, Mediterranean and tropical regions, with multiple climate change factors and scenarios (including our responses to it, e.g. the assisted migration of plants), in relation to endophytes, viruses and mycorrhiza, using long-term and large-scale datasets and considering various plant disease control methods

Particulate air pollution and chronic ischemic heart disease in the eastern United States: a county level ecological study using satellite aerosol data

<p>Abstract</p> <p>Background</p> <p>There are several known factors that cause ischemic heart disease. However, the part played by air pollution still remains something of a mystery. Recent attention has focused on the chronic effect of particulate matter on heart disease. Satellite-derived aerosol optical depth (AOD) was found to be correlated with <it>PM</it>_2.5in the eastern US. The objective of this study was to examine if there is an association between aerosol air pollution as indicated by AOD and chronic ischemic heart disease (CIHD) in the eastern US.</p> <p>Methods</p> <p>An ecological geographic study method was employed. Race and age standardized mortality rate (SMR) of CIHD was computed for each of the 2306 counties for the time period 2003–2004. A mean AOD raster grid for the same period was derived from Moderate Resolution Imaging Spectrometer (MODIS) aerosol data and the average AOD was calculated for each county. A bivariate Moran's I scatter plot, a map of local indicator of spatial association (LISA) clusters, and three regression models (ordinary least square, spatial lag, and spatial error) were used to analyze the relationship between AOD and CIHD SMR.</p> <p>Results</p> <p>The global Moran's I value is 0.2673 (<it>p </it>= 0.001), indicating an overall positive spatial correlation of CIHD SMR and AOD. The entire study area is dominated by spatial clusters of AOD against SMR (high AOD and high SMR in the east, and low AOD and low SMR in the west) (permutations = 999, <it>p </it>= 0.05). Of the three regression models, the spatial error model achieved the best fit (R²= 0.28). The effect of AOD is positive and significant (beta = 0.7774, p = 0.01).</p> <p>Conclusion</p> <p>Aerosol particle pollution has adverse effect on CIHD mortality risk in the eastern US. High risk of CIHD mortality was found in areas with elevated levels of outdoor aerosol air pollution as indicated by satellite derived AOD. The evidence of the association would support targeting of policy interventions on such areas to reduce air pollution levels. Remote sensing AOD data could be used as an alternative health-related indictor of air quality.</p