CORRELATION OF TRANSCRIPTOME-WIDE PROTEIN BINDING TO INFORM RNA REGULATION

Dysregulated control of RNA can cause abnormal development and disease. RNA is targeted and regulated via the interaction of RNA structure, modifications, and RNA-binding proteins. Information about the interactions of transcriptomic features can therefore provide biologically relevant insight into RNA control. We develop a new algorithm, nearBynding, to calculate spatial correlations between transcriptomic data types and demonstrate its ability to recapitulate known biological relationships. We apply nearBynding to formulate new hypotheses about proteins that bind in regions of the transcriptome that are prone to G-quadruplex formation. We use nearBynding to observe the colocalization of G3BP1 and UPF1 within 3'UTRs for structure-mediated RNA decay (SRD) and to identify additional candidate factors involved in SRD. We provide evidence that there is a discrepancy in SRD activity between breast cancer samples derived from African American and European American patients. Finally, we investigate the role of the RNA-binding protein PARP13 in the innate immune response via integration of genomics data types. Evidence from genomic data, nearBynding analysis, and molecular biology experiments provides insight into the geometry of PARP13's interface with its cofactor TRIM25 and implicates PARP13 in creating and maintaining a cellular environment poised for an antiviral response

CAOS spectroscopy of Am stars Kepler targets

The {\it Kepler} space mission and its {\it K2} extension provide photometric time series data with unprecedented accuracy. These data challenge our current understanding of the metallic-lined A stars (Am stars) for what concerns the onset of pulsations in their atmospheres. It turns out that the predictions of current diffusion models do not agree with observations. To understand this discrepancy, it is of crucial importance to obtain ground-based spectroscopic observations of Am stars in the {\it Kepler} and {\it K2} fields in order to determine the best estimates of the stellar parameters. In this paper, we present a detailed analysis of high-resolution spectroscopic data for seven stars previously classified as Am stars. We determine the effective temperatures, surface gravities, projected rotational velocities, microturbulent velocities and chemical abundances of these stars using spectral synthesis. These spectra were obtained with {\it CAOS}, a new instrument recently installed at the observing station of the Catania Astrophysical Observatory on Mt. Etna. Three stars have already been observed during quarters Q0-Q17, namely: HD\,180347, HD\,181206, and HD\,185658, while HD\,43509 was already observed during {\it K2} C0 campaign. We confirm that HD\,43509 and HD\,180347 are Am stars, while HD 52403, HD\,50766, HD\,58246, HD\,181206 and HD\,185658 are marginal Am stars. By means of non-LTE analysis, we derived oxygen abundances from O{\sc I}$\lambda$7771--5{\AA} triplet and we also discussed the results obtained with both non-LTE and LTE approaches.Comment: accepted in MNRAS main journal 13 pages, 11 figures, 3 tables. arXiv admin note: text overlap with arXiv:1404.095

Handbook on the effective use of virtual learning platform and ICT tools for online courses

One of the major aims of IN2RURAL Erasmus+ Strategic Partnerships project is to develop online learning courses with high-level interactive online and offline educational material particularly for higher education students who intend to obtain specific information on renewable energy resources. There will be two different types of online course developed during the project. One of the courses is called “Technical English for renewable energy” (IO8) course, providing a base for the online course of “Renewable energy for local development” (IO9) with professional and academic content consisting of four modules: renewable energy and rural development module, photovoltaic module, biomass module and wind energy module. The compiled materials will include information about delivering online learning materials to students by means of assessments and tracking, collaboration and communication tools by delivering them with a high degree of practical information. The elaboration of each section within the “Renewable energy for local development” course has been divided between the participating project partners. The Spanish lead partner is responsible for the elaboration of the renewable energy and rural development module along with the photovoltaic module, while the Hungarian partners have created the biomass module and the wind energy section has been developed by the participating Romanian organisations. Both online courses and all four modules within “Renewable energy for local development” course follow a homogeneous structure. One of the main purposes of the handbook is to provide useful information for teachers on how to plan and prepare online educational material by defining the common elements that the course material of each module should include, providing a short documentation on how the sample files have to be prepared and then uploaded to the online learning platform. It also provides instructions with orientation purposes and samples to teachers on how to prepare the suitable framework for a learning material. Besides the e-learning material, the online courses also involve self-introductions of students and topic discussion forums, a glossary for each renewable energy resource module and additional extra materials, such as photos, presentations and extra bibliography. The “Technical English for Renewable Energy” course will contain a glossary providing students with the specific words and expressions, allowing them to follow the modules of the “Renewable energy for local development” online course. The online course provides opportunities both for individual and/or group discussion work, and the present handbook will guide the user how to become acquainted with the effective uses of virtual learning platform and ICTs along with some teaching methods to convey learning information. One of the main reasons for providing e-learning material through an electronic website is to promote interactivity among future students. These days, both teachers and students must rely on interactive learning materials besides the traditional printed texts during their professional work. ICT-based education has undoubtedly affected and is affecting the learning process of students and it is important to underline that a good ICT-based education has the potential to increase students’ motivation towards acquiring the required knowledge. Furthermore, it can be declared that ICT-based education undoubtedly helps to promote in connecting school experiences with work practices. In sum, the principal aims of the present “Handbook on the effective use of virtual learning platform and ICT tools for online courses” is to provide practical guidelines for teachers on how to provide learning material in ~.doc and ~.xls sample files that will be later transformed as an output into interactive and enjoyable electronic learning material, specifications for each parts of the learning platform, so that all the teachers working in different modules have a clear idea of the material they have to prepare for the course, a standardized evaluation for the modules

Multiboost: a multi-purpose boosting package

http://jmlr.csail.mit.edu/papers/v13/benbouzid12a.htmlThe MultiBoost package provides a fast C++ implementation of multi-class/multi-label/multi-task boosting algorithms. It is based on AdaBoost.MH but it also implements popular cascade classifiers and FilterBoost. The package contains common multi-class base learners (stumps, trees, products, Haar filters). Further base learners and strong learners following the boosting paradigm can be easily implemented in a flexible framework

Interfacing and Verifying ALHAT Safe Precision Landing Systems with the Morpheus Vehicle

The NASA Autonomous precision Landing and Hazard Avoidance Technology (ALHAT) project developed a suite of prototype sensors to enable autonomous and safe precision landing of robotic or crewed vehicles under any terrain lighting conditions. Development of the ALHAT sensor suite was a cross-NASA effort, culminating in integration and testing on-board a variety of terrestrial vehicles toward infusion into future spaceflight applications. Terrestrial tests were conducted on specialized test gantries, moving trucks, helicopter flights, and a flight test onboard the NASA Morpheus free-flying, rocket-propulsive flight-test vehicle. To accomplish these tests, a tedious integration process was developed and followed, which included both command and telemetry interfacing, as well as sensor alignment and calibration verification to ensure valid test data to analyze ALHAT and Guidance, Navigation and Control (GNC) performance. This was especially true for the flight test campaign of ALHAT onboard Morpheus. For interfacing of ALHAT sensors to the Morpheus flight system, an adaptable command and telemetry architecture was developed to allow for the evolution of per-sensor Interface Control Design/Documents (ICDs). Additionally, individual-sensor and on-vehicle verification testing was developed to ensure functional operation of the ALHAT sensors onboard the vehicle, as well as precision-measurement validity for each ALHAT sensor when integrated within the Morpheus GNC system. This paper provides some insight into the interface development and the integrated-systems verification that were a part of the build-up toward success of the ALHAT and Morpheus flight test campaigns in 2014. These campaigns provided valuable performance data that is refining the path toward spaceflight infusion of the ALHAT sensor suite

Mutation update for the GPC3 gene involved in Simpson-Golabi-Behmel syndrome and review of the literature

Simpson-Golabi-Behmel syndrome (SGBS) is an X-linked multiple congenital anomalies and overgrowth syndrome caused by a defect in the glypican-3 gene (GPC3). Until now, GPC3 mutations have been reported in isolated cases or small series and the global genotypic spectrum of these mutations has never been delineated. In this study, we review the 57 previously described GPC3 mutations and significantly expand this mutational spectrum with the description of 29 novel mutations. Compiling our data and those of the literature, we provide an overview of 86 distinct GPC3 mutations identified in 120 unrelated families, ranging from single nucleotide variations to complex genomic rearrangements and dispersed throughout the entire coding region of GPC3. The vast majority of them are deletions or truncating mutations (frameshift, nonsense mutations) predicted to result in a loss-of-function. Missense mutations are rare and the two which were functionally characterized, impaired GPC3 function by preventing GPC3 cleavage and cell surface addressing respectively. This report by describing for the first time the wide mutational spectrum of GPC3 could help clinicians and geneticists in interpreting GPC3 variants identified incidentally by high-throughput sequencing technologies and also reinforces the need for functional validation of non-truncating mutations (missense, in frame mutations, duplications)

Financial crises and the attainment of the SDGs: an adjusted multidimensional poverty approach

This paper analyses the impact of financial crises on the Sustainable Development Goal of eradicating poverty. To do so, we develop an adjusted Multidimensional Poverty Framework (MPF) that includes 15 indicators that span across key poverty aspects related to income, basic needs, health, education and the environment. We then use an econometric model that allows us to examine the impact of financial crises on these indicators in 150 countries over the period 1980–2015. Our analysis produces new estimates on the impact of financial crises on poverty’s multiple social, economic and environmental aspects and equally important captures dynamic linkages between these aspects. Thus, we offer a better understanding of the potential impact of current debt dynamics on Multidimensional Poverty and demonstrate the need to move beyond the boundaries of SDG1, if we are to meet the target of eradicating poverty. Our results indicate that the current financial distress experienced by many low-income countries may reverse the progress that has been made hitherto in reducing poverty. We find that financial crises are associated with an approximately 10% increase of extreme poor in low-income countries. The impact is even stronger in some other poverty aspects. For instance, crises are associated with an average decrease of government spending in education by 17.72% in low-income countries. The dynamic linkages between most of the Multidimensional Poverty indicators, warn of a negative domino effect on a number of SDGs related to poverty, if there is a financial crisis shock. To pre-empt such a domino effect, the specific SDG target 17.4 on attaining long-term debt sustainability through coordinated policies plays a key role and requires urgent attention by the international community

A Multi-Wavelength Perspective of Flares on HR 1099: Four Years of Coordinated Campaigns

We report on four years of multiple wavelength observations of the RS CVn system V711 Tau (HR 1099) from 1993, 1994, 1996, and 1998. This combination of radio, ultraviolet, extreme ultraviolet, and X-ray observations allows us to view, in the most comprehensive manner currently possible, the coronal and upper atmospheric variability of this active binary system. We report on the changing activity state of the system as recorded in the EUV and radio across the four years of the observations, and study the high energy variability using an assemblage of X-ray telescopes. (Longer abstract in paper).Comment: manuscript is 110 pages in length; 36 figures tota