On the Challenges of Collaborative Data Processing

The last 30 years have seen the creation of a variety of electronic collaboration tools for science and business. Some of the best-known collaboration tools support text editing (e.g., wikis). Wikipedia's success shows that large-scale collaboration can produce highly valuable content. Meanwhile much structured data is being collected and made publicly available. We have never had access to more powerful databases and statistical packages. Is large-scale collaborative data analysis now possible? Using a quantitative analysis of Web 2.0 data visualization sites, we find evidence that at least moderate open collaboration occurs. We then explore some of the limiting factors of collaboration over data.Comment: to appear as a chapter in an upcoming book (Collaborative Information Behavior

TICAL - a web-tool for multivariate image clustering and data topology preserving visualization

In life science research bioimaging is often used to study two kinds of features in a sample simultaneously: morphology and co-location of molecular components. While bioimaging technology is rapidly proposing and improving new multidimensional imaging platforms, bioimage informatics has to keep pace in order to develop algorithmic approaches to support biology experts in the complex task of data analysis. One particular problem is the availability and applicability of sophisticated image analysis algorithms via the web so different users can apply the same algorithms to their data (sometimes even to the same data to get the same results) and independently from her/his whereabouts and from the technical features of her/his computer. In this paper we describe TICAL, a visual data mining approach to multivariate microscopy analysis which can be applied fully through the web.We describe the algorithmic approach, the software concept and present results obtained for different example images

Qualitative analysis of Request For Information to identify design flaws in steel construction projects

Request for information (RFI) is a formal process used in the Architecture, Engineering and Construction industry to address design flaws that affect communication between designers and contractors. A large number of RFIs are a sign of a lack of precision or coordination in the design documents. However, RFIs produce rich, precise, and structured information. Analyzing their content can help to identify recurring problems between designers and construction teams and better tailor future projects to the working context of the contractors. This article presents a method for identifying recurring issues during the design phase of steel construction projects through the analysis of the contents of RFIs. It is original in using a qualitative content analysis tool that can analyze large quantities of RFIs rapidly. Identifying the recurrent problems of contractors will allow the establishment of rules to be taken into consideration during the design phase of future steel construction projects. A case study of 26 steel construction projects demonstrates the feasibility of this method. This case study shows that, given the same designers and construction teams, recurring problems shown in RFIs do not differ according to the scale of the projects. In this case, the main issue between designers and contractors is the lack and inadequate presentation of information related to the connection of steel components. Identifying these problems can pave the way for initiatives to improve the design phase and can be an essential step in making contractors’ knowledge available to designers early in the projects

The centrosomal deubiquitylase USP21 regulates Gli1 transcriptional activity and stability

USP21 is a centrosome-associated deubiquitylase (DUB) that has been implicated in the formation of primary cilia - crucial organelles for the regulation of the Hedgehog (Hh) signaling pathway in vertebrates. Here, we identify KCTD6 - a cullin-3 E3-ligase substrate adapter that has been previously linked to Hh signaling - as well as Gli1, the key transcription factor responsible for Hh signal amplification, as new interacting partners of USP21. We identify a cryptic structured protein interaction domain in KCTD6, which is predicted to have a similar fold to Smr domains. Importantly, we show that both depletion and overexpression of catalytically active USP21 suppress Gli1-dependent transcription. Gli proteins are negatively regulated through protein kinase A (PKA)-dependent phosphorylation. We provide evidence that USP21 recruits and stabilises Gli1 at the centrosome where it promotes its phosphorylation by PKA. By revealing an intriguing functional pairing between a spatially restricted deubiquitylase and a kinase, our study highlights the centrosome as an important hub for signal coordination

Alterations in prefrontal-limbic functional activation and connectivity in chronic stress-induced visceral hyperalgesia.

Repeated water avoidance stress (WAS) induces sustained visceral hyperalgesia (VH) in rats measured as enhanced visceromotor response to colorectal distension (CRD). This model incorporates two characteristic features of human irritable bowel syndrome (IBS), VH and a prominent role of stress in the onset and exacerbation of IBS symptoms. Little is known regarding central mechanisms underlying the stress-induced VH. Here, we applied an autoradiographic perfusion method to map regional and network-level neural correlates of VH. Adult male rats were exposed to WAS or sham treatment for 1 hour/day for 10 days. The visceromotor response was measured before and after the treatment. Cerebral blood flow (CBF) mapping was performed by intravenous injection of radiotracer ([(14)C]-iodoantipyrine) while the rat was receiving a 60-mmHg CRD or no distension. Regional CBF-related tissue radioactivity was quantified in autoradiographic images of brain slices and analyzed in 3-dimensionally reconstructed brains with statistical parametric mapping. Compared to sham rats, stressed rats showed VH in association with greater CRD-evoked activation in the insular cortex, amygdala, and hypothalamus, but reduced activation in the prelimbic area (PrL) of prefrontal cortex. We constrained results of seed correlation analysis by known structural connectivity of the PrL to generate structurally linked functional connectivity (SLFC) of the PrL. Dramatic differences in the SLFC of PrL were noted between stressed and sham rats under distension. In particular, sham rats showed negative correlation between the PrL and amygdala, which was absent in stressed rats. The altered pattern of functional brain activation is in general agreement with that observed in IBS patients in human brain imaging studies, providing further support for the face and construct validity of the WAS model for IBS. The absence of prefrontal cortex-amygdala anticorrelation in stressed rats is consistent with the notion that impaired corticolimbic modulation acts as a central mechanism underlying stress-induced VH

Emergent simplicity in microbial community assembly

Published in final edited form as: Science. 2018 August 03; 361(6401): 469–474. doi:10.1126/science.aat1168.A major unresolved question in microbiome research is whether the complex taxonomic architectures observed in surveys of natural communities can be explained and predicted by fundamental, quantitative principles. Bridging theory and experiment is hampered by the multiplicity of ecological processes that simultaneously affect community assembly in natural ecosystems. We addressed this challenge by monitoring the assembly of hundreds of soil- and plant-derived microbiomes in well-controlled minimal synthetic media. Both the community-level function and the coarse-grained taxonomy of the resulting communities are highly predictable and governed by nutrient availability, despite substantial species variability. By generalizing classical ecological models to include widespread nonspecific cross-feeding, we show that these features are all emergent properties of the assembly of large microbial communities, explaining their ubiquity in natural microbiomes.The funding for this work partly results from a Scialog Program sponsored jointly by the Research Corporation, for Science Advancement and. the Gordon and Betty Moore Foundation through grants to Yale University and Boston University by the Research Corporation and by the Simons Foundation. This work was also supported by a young; investigator award from the Human Frontier Science Program to A.S. (RGY0077/2016) and by NIH NIGMS grant 1R35GM119461 and a Simons Investigator as in the Mathematical Modeling of Living Systems (MMLS) to P.M.; D.S. and J.E.G. additionally acknowledge funding from the Defense Advanced Research Projects Agency (purchase request no. HR0011515303, contract no.. HR0011-15-0-0091), the U.S. Department of Energy (DE-SC0012627), the NIH (T32GM100842, 5R01DE024468, R01GM121950, and Sub_P30DK036836_P&F), the National Science Foundation (1457695), the Human Frontier Science Program (RGP0020/2016) and the Boston University Interdisciplinary Biomedical Research Office. (Research Corporation, for Science Advancement; Gordon and Betty Moore Foundation; Boston University by the Research Corporation; Simons Foundation.; RGY0077/2016 - uman Frontier Science Program; 1R35GM119461 - NIH NIGMS grant; Simons Investigator as in the Mathematical Modeling of Living Systems (MMLS); HR0011515303 - Defense Advanced Research Projects Agency; HR0011-15-0-0091 - Defense Advanced Research Projects Agency; T32GM100842 - NIH; 5R01DE024468 - NIH; R01GM121950 - NIH; ub_P30DK036836 - NIH; 1457695 - National Science Foundation; RGP0020/2016 - Human Frontier Science Program; Boston University Interdisciplinary Biomedical Research Office)Accepted manuscrip

Limited energy consumption in positioning control of an electropneumatic actuator

International audienceThis paper shows the possibility of using two three-way servo-distributors in place of one five-way for position control of an electropneumatic actuator. Two nonlinear control laws are developed and compared. The aim is to prove the advantage of a multi-input control law in terms of stability and energy consumption due to the flatness property