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

Novel MicroRNA Regulators of Atrial Natriuretic Peptide Production

Atrial natriuretic peptide (ANP) has a central role in regulating blood pressure in humans. Recently, microRNA 425 (miR-425) was found to regulate ANP production by binding to the mRNA of NPPA, the gene encoding ANP. mRNAs typically contain multiple predicted microRNA (miRNA)-binding sites, and binding of different miRNAs may independently or coordinately regulate the expression of any given mRNA. We used a multifaceted screening strategy that integrates bioinformatics, next-generation sequencing data, human genetic association data, and cellular models to identify additional functional NPPA-targeting miRNAs. Two novel miRNAs, miR-155 and miR-105, were found to modulate ANP production in human cardiomyocytes and target genetic variants whose minor alleles are associated with higher human plasma ANP levels. Both miR-15 and miR-105 repressed NPPA mRNA in an allele-specific manner, with the minor allele of each respective variant conferrin resistance to the miRNA either by disruption of miRNA base pairing or by creation of wobble base pairing. Moreover, miR-15 enhanced the repressive effects of miR-425 on ANP production in human cardiomyocytes. Our study combines computational genomic, and cellular tools to identify novel miRNA regulators of ANP production that could be targeted to raise ANP levels which may have applications for the treatment of hypertension or heart failure

Advanced maturation of human cardiac tissue grown from pluripotent stem cells

Cardiac tissues generated from human induced pluripotent stem cells (iPSCs) can serve as platforms for patient-specific studies of physiology and disease1-6. However, the predictive power of these models is presently limited by the immature state of the cells1, 2, 5, 6. Here we show that this fundamental limitation can be overcome if cardiac tissues are formed from early-stage iPSC-derived cardiomyocytes soon after the initiation of spontaneous contractions and are subjected to physical conditioning with increasing intensity over time. After only four weeks of culture, for all iPSC lines studied, such tissues displayed adult-like gene expression profiles, remarkably organized ultrastructure, physiological sarcomere length (2.2 µm) and density of mitochondria (30%), the presence of transverse tubules, oxidative metabolism, a positive force-frequency relationship and functional calcium handling. Electromechanical properties developed more slowly and did not achieve the stage of maturity seen in adult human myocardium. Tissue maturity was necessary for achieving physiological responses to isoproterenol and recapitulating pathological hypertrophy, supporting the utility of this tissue model for studies of cardiac development and disease.The authors acknowledge funding support from the National Institutes of Health of the USA (NIBIB and NCATS grant EB17103 (G.V.-N.); NIBIB, NCATS, NIAMS, NIDCR and NIEHS grant EB025765 (G.V.-N.); NHLBI grants HL076485 (G.V.-N.) and HL138486 (M.Y.); Columbia University MD/PhD program (S.P.M., T.C.); University of Minho MD/PhD program (D.T.); Japan Society for the Promotion of Science fellowship (K.M.); and Columbia University Stem Cell Initiative (D.S., L.S., M.Y.). We thank S. Duncan and B. Conklin for providing human iPSCs, M.B. Bouchard for assistance with image and video analysis, and L. Cohen-Gould for transmission electron microscopy services.info:eu-repo/semantics/publishedVersio

Model-Based Deconvolution of Cell Cycle Time-Series Data Reveals Gene Expression Details at High Resolution

In both prokaryotic and eukaryotic cells, gene expression is regulated across the cell cycle to ensure “just-in-time” assembly of select cellular structures and molecular machines. However, present in all time-series gene expression measurements is variability that arises from both systematic error in the cell synchrony process and variance in the timing of cell division at the level of the single cell. Thus, gene or protein expression data collected from a population of synchronized cells is an inaccurate measure of what occurs in the average single-cell across a cell cycle. Here, we present a general computational method to extract “single-cell”-like information from population-level time-series expression data. This method removes the effects of 1) variance in growth rate and 2) variance in the physiological and developmental state of the cell. Moreover, this method represents an advance in the deconvolution of molecular expression data in its flexibility, minimal assumptions, and the use of a cross-validation analysis to determine the appropriate level of regularization. Applying our deconvolution algorithm to cell cycle gene expression data from the dimorphic bacterium Caulobacter crescentus, we recovered critical features of cell cycle regulation in essential genes, including ctrA and ftsZ, that were obscured in population-based measurements. In doing so, we highlight the problem with using population data alone to decipher cellular regulatory mechanisms and demonstrate how our deconvolution algorithm can be applied to produce a more realistic picture of temporal regulation in a cell

Abstracts from the 8th International Conference on cGMP Generators, Effectors and Therapeutic Implications

This work was supported by a restricted research grant of Bayer AG

Wstępne badania grzybów w Biebrzańskim Parku Narodowym. II. Grzyby wielkoowocnikowe

This paper presents the second part of the results of the first short-term inventory of fungi species occurring in the Biebrza National Park and is focused on a survey of macrofungi. The total number of macrofungi found during the survey in late August 2012 was 289 taxa: 17 ascomycetes and 272 basidiomycetes, inhabiting diverse ecological niches. The identified fungi belonged to ectomycorrhizal symbionts and saprobionts decomposing wood, plant litter and animal remnants. The identity of 25 mycorrhizal fungi species has been confirmed using molecular techniques. Five species are newly reported for Poland (Amanita olivaceogrisea, Lepiota lepida, Stropharia alcis, Xerocomus fennicus, X. cisalpinus) and 225 taxa (79 %) were not known in the Biebrza National Park. Fifty nine species are endangered in Poland, of which nine species are protected by law. Data on species richness and the taxonomic diversity of the identified fungi are briefly commented in terms of their significance for nature conservation and future research.Prezentowane dane są wynikiem badań prowadzonych w dniach od 28 sierpnia do 1 września 2012 w ramach sesji terenowej Polskiego Towarzystwa Mykologicznego. Celem była wstępna inwentaryzacja grzybów wielkoowocnikowych występujących na terenie Biebrzańskiego Parku Narodowego (BbPN), terenu niemal zupełnie nie poznanego pod względem mykobioty. W artykule zamieszczono wykaz zidentyfikowanych 289 taksonów (gatunków, odmian i form) grzybów workowych i podstawkowych. Wśród znalezionych gatunków są grzyby bardzo rzadkie, znane z zaledwie jednego lub kilku stanowisk w Polsce (16 gatunków), a także wykazane w literaturze z Polski po raz pierwszy (5) oraz zagrożone i objęte ochroną (59), w tym Phellodon confluens – uznawany za wymarły. Jak wskazano w części pierwszej artykułu (Ruszkiewicz-Michalska et al. 2012), badania przeprowadzone w BbPN są pierwszymi z planowanego przez Polskie Towarzystwo Mykologiczne cyklu inwentaryzacji w obiektach objętych różnymi formami ochrony. W wielu takich obiektach (parkach narodowych, rezerwatach, parkach krajobrazowych oraz obszarach Natura 2000) brak jest danych mykologicznych lub są fragmentaryczne albo wymagające aktualizacji. Podstawową przesłanką do prowadzenia badań inwentaryzacyjnych jest potrzeba uwzględniania grzybów w polityce ochrony przyrody, zarówno na obszarze parków narodowych, jak i w szerszej skali