4DXpress: a database for cross-species expression pattern comparisons

In the major animal model species like mouse, fish or fly, detailed spatial information on gene expression over time can be acquired through whole mount in situ hybridization experiments. In these species, expression patterns of many genes have been studied and data has been integrated into dedicated model organism databases like ZFIN for zebrafish, MEPD for medaka, BDGP for Drosophila or GXD for mouse. However, a central repository that allows users to query and compare gene expression patterns across different species has not yet been established. Therefore, we have integrated expression patterns for zebrafish, Drosophila, medaka and mouse into a central public repository called 4DXpress (expression database in four dimensions). Users can query anatomy ontology-based expression annotations across species and quickly jump from one gene to the orthologues in other species. Genes are linked to public microarray data in ArrayExpress. We have mapped developmental stages between the species to be able to compare developmental time phases. We store the largest collection of gene expression patterns available to date in an individual resource, reflecting 16 505 annotated genes. 4DXpress will be an invaluable tool for developmental as well as for computational biologists interested in gene regulation and evolution. 4DXpress is available at http://ani.embl.de/4DXpress

Comparing open-source DEM frameworks for simulations of common bulk processes

Multiple software frameworks based on the Discrete Element Method (DEM) are available for simulating granular materials. All of them employ the same principles of explicit time integration, with each time step consisting of three main steps: contact detection, calculation of interactions, and integration of the equations of motion. However, there exist significant algorithmic differences, such as the choice of contact models, particle and wall shapes, and data analysis methods. Further differences can be observed in the practical implementation, including data structures, architecture, parallelization and domain decomposition techniques, user interaction, and the documentation of resources. This study compares, verifies, and benchmarks nine widely-used software frameworks. Only open-source packages were considered, as these are freely available and their underlying algorithms can be reviewed, edited, and tested. The benchmark consists of three common bulk processes: silo emptying, drum mixing, and particle impact. To keep it simple and comparable, only standard features were used, such as spherical particles and the Hertz-Mindlin model for dry contacts. Scripts for running the benchmarks in each software are provided as a dataset.</p

Comparing open-source DEM frameworks for simulations of common bulk processes

Multiple software frameworks based on the Discrete Element Method (DEM) are available for simulating granular materials. All of them employ the same principles of explicit time integration, with each time step consisting of three main steps: contact detection, calculation of interactions, and integration of the equations of motion. However, there exist significant algorithmic differences, such as the choice of contact models, particle and wall shapes, and data analysis methods. Further differences can be observed in the practical implementation, including data structures, architecture, parallelization and domain decomposition techniques, user interaction, and the documentation of resources.This study compares, verifies, and benchmarks nine widely-used software frameworks. Only open-source packages were considered, as these are freely available and their underlying algorithms can be reviewed, edited, and tested. The benchmark consists of three common bulk processes: silo emptying, drum mixing, and particle impact. To keep it simple and comparable, only standard features were used, such as spherical particles and the Hertz-Mindlin model for dry contacts. Scripts for running the benchmarks in each software are provided as a dataset

A FABRY-PEROT CAVITY FOR COMPTON POLARIMETRY

A new kind of Compton polarimeter using a resonant Fabry—Pe« rot cavity as a power buildup for the photon beam is proposed. A prototype of such a cavity is described, along with the results obtained in terms of source to be used in a Compton scattering polarimeter. ( 1998 Elsevier Science B.V. All rights reserved

Ozone and PM(2.5) Exposure and Acute Pulmonary Health Effects: A Study of Hikers in the Great Smoky Mountains National Park

To address the lack of research on the pulmonary health effects of ozone and fine particulate matter (≤ 2.5 μm in aerodynamic diameter; PM(2.5)) on individuals who recreate in the Great Smoky Mountains National Park (USA) and to replicate a study performed at Mt. Washington, New Hampshire (USA), we conducted an observational study of adult (18–82 years of age) day hikers of the Charlies Bunion trail during 71 days of fall 2002 and summer 2003. Volunteer hikers performed pre- and posthike pulmonary function tests (spirometry), and we continuously monitored ambient O(3), PM(2.5), temperature, and relative humidity at the trailhead. Of the 817 hikers who participated, 354 (43%) met inclusion criteria (nonsmokers and no use of bronchodilators within 48 hr) and gave acceptable and reproducible spirometry. For these 354 hikers, we calculated the posthike percentage change in forced vital capacity (FVC), forced expiratory volume in 1 sec (FEV(1)), FVC/FEV(1), peak expiratory flow, and mean flow rate between 25 and 75% of the FVC and regressed each separately against pollutant (O(3) or PM(2.5)) concentration, adjusting for age, sex, hours hiked, smoking status (former vs. never), history of asthma or wheeze symptoms, hike load, reaching the summit, and mean daily temperature. O(3) and PM(2.5) concentrations measured during the study were below the current federal standards, and we found no significant associations of acute changes in pulmonary function with either pollutant. These findings are contrasted with those in the Mt. Washington study to examine the hypothesis that pulmonary health effects are associated with exposure to O(3) and PM(2.5) in healthy adults engaged in moderate exercise

Agouti Revisited: Transcript Quantification of the ASIP Gene in Bovine Tissues Related to Protein Expression and Localization

Beside its role in melanogenesis, the agouti signaling protein (ASIP) has been related to obesity. The potentially crucial role in adipocyte development makes it a tempting candidate for economic relevant, fat related traits in farm animals. The objective of our study was to characterize the mRNA expression of different ASIP transcripts and of putative targets in different bovine tissues, as well as to study consequences on protein abundance and localization. ASIP mRNA abundance was determined by RT-qPCR in adipose and further tissues of cattle representing different breeds and crosses. ASIP mRNA was up-regulated more than 9-fold in intramuscular fat of Japanese Black cattle compared to Holstein (p<0.001). Further analyses revealed that a transposon-derived transcript was solely responsible for the increased ASIP mRNA abundance. This transcript was observed in single individuals of different breeds indicating a wide spread occurrence of this insertion at the ASIP locus in cattle. The protein was detected in different adipose tissues, skin, lung and liver, but not in skeletal muscle by Western blot with a bovine-specific ASIP antibody. However, the protein abundance was not related to the observed ASIP mRNA over-expression. Immuno-histochemical analyses revealed a putative nuclear localization of ASIP additionally to the expected cytosolic signal in different cell types. The expression of melanocortin receptors (MCR) 1 to 5 as potential targets for ASIP was analyzed by RT-PCR in subcutaneous fat. Only MC1R and MC4R were detected indicating a similar receptor expression like in human adipose tissue. Our results provide evidence for a widespread expression of ASIP in bovine tissues at mRNA and, for the first time, at protein level. ASIP protein is detectable in adipocytes as well as in further cells of adipose tissue. We generated a basis for a more detailed investigation of ASIP function in peripheral tissues of various mammalian species

The Picture Pile Tool for Rapid Image Assessment: A Demonstration using Hurricane Matthew

In 2016, Hurricane Matthew devastated many parts of the Caribbean, in particular the country of Haiti. More than 500 people died and the damage was estimated at 1.9billionUSD. At the time, the Humanitarian OpenStreetMap Team (HOT) activated their network of volunteers to create base maps of areas affected by the hurricane, in particular coastal communities in the path of the storm. To help improve HOT’s information workflow for disaster response, one strand of the Crowd4Sat project, which was funded by the European Space Agency, focussed on examining where the Picture Pile Tool, an application for rapid image interpretation and classification, could potentially contribute. Satellite images obtained from the time that Hurricane Matthew occurred were used to simulate a situation post-event, where the aim was to demonstrate how Picture Pile could be used to create a map of building damage. The aim of this paper is to present the Picture Pile tool and show the results from this simulation, which produced a crowdsourced map of damaged buildings for a selected area of Haiti in 1 week (but with increased confidence in the results over a 3 week period). A quality assessment of the results showed that the volunteers agreed with experts and the majority of individual classifications around 92% of the time, indicating that the crowd performed well in this task. The next stage will involve optimizing the workflow for the use of Picture Pile in future natural disaster situations

Signaling of angiotensin II-induced vascular protein synthesis in conduit and resistance arteries in vivo

BACKGROUND: From in vitro studies, it has become clear that several signaling cascades are involved in angiotensin II-induced cellular hypertrophy. The aim of the present study was to determine some of the signaling pathways mediating angiotensin II (Ang II)-induced protein synthesis in vivo in large and small arteries. METHODS: Newly synthesized proteins were labeled during 4 hours with tritiated leucine in conscious control animals, or animals infused for 24 hours with angiotensin II (400 ng/kg/min). Hemodynamic parameters were measure simultaneously. Pharmacological agents affecting signaling cascades were injected 5 hours before the end of Ang II infusion. RESULTS: Angiotensin II nearly doubled the protein synthesis rate in the aorta and small mesenteric arteries, without affecting arterial pressure. The AT(1 )receptor antagonist Irbesartan antagonized the actions of Ang II. The Ang II-induced protein synthesis was associated with increased extracellular signal-regulated kinases (ERK)1/2 phosphorylation in aortic, but not in mesenteric vessels. Systemic administration of PD98059, an inhibitor of the ERK-1/2 pathway, produced a significant reduction of protein synthesis rate in the aorta, and only a modest decrease in mesenteric arteries. Rapamycin, which influences protein synthesis by alternative signaling, had a significant effect in both vessel types. Rapamycin and PD98059 did not alter basal protein synthesis and had minimal effects on arterial pressure. CONCLUSION: ERK1/2 and rapamycin-sensitive pathways are involved in pressure-independent angiotensin II-induced vascular protein synthesis in vivo. However, their relative contribution may vary depending on the nature of the artery under investigation