Validation of scientific topic models using graph analysis and corpus metadata

Probabilistic topic modeling algorithms like Latent Dirichlet Allocation (LDA) have become powerful tools for the analysis of large collections of documents (such as papers, projects, or funding applications) in science, technology an innovation (STI) policy design and monitoring. However, selecting an appropriate and stable topic model for a specific application (by adjusting the hyperparameters of the algorithm) is not a trivial problem. Common validation metrics like coherence or perplexity, which are focused on the quality of topics, are not a good fit in applications where the quality of the document similarity relations inferred from the topic model is especially relevant. Relying on graph analysis techniques, the aim of our work is to state a new methodology for the selection of hyperparameters which is specifically oriented to optimize the similarity metrics emanating from the topic model. In order to do this, we propose two graph metrics: the first measures the variability of the similarity graphs that result from different runs of the algorithm for a fixed value of the hyperparameters, while the second metric measures the alignment between the graph derived from the LDA model and another obtained using metadata available for the corresponding corpus. Through experiments on various corpora related to STI, it is shown that the proposed metrics provide relevant indicators to select the number of topics and build persistent topic models that are consistent with the metadata. Their use, which can be extended to other topic models beyond LDA, could facilitate the systematic adoption of this kind of techniques in STI policy analysis and design.

     

Influence of the dispersion of Nanoclays on the cellular structure of foams based on polystyrene

In the present work blends of polystyrene (PS) with sepiolites have been produced using a melt extrusion process. The dispersion degree of the sepiolites in the PS has been analyzed by dynamic shear rheology and X-ray micro-computed tomography. Sepiolites treated with quaternary ammonium salts (O-QASEP) are better dispersed in the PS matrix than natural sepiolites (N-SEP) or sepiolites organo-modified with silane groups (O-SGSEP). A percolated network is obtained when using 6.0 wt% of O-QASEP, 8.0 wt% of N-SEP and 10.0 wt% of O-SGSEP. It has been shown that multiple extrusion processes have a negative effect on the polymer architecture. They produce a reduction in the length of the polymeric chains, and they do not lead to a better dispersion of the particles in the polymer matrix. Foams have been produced using a gas dissolution foaming process, where a strong effect of the dispersion degree on the cellular structure of the different foams was found. The effects on the cellular structure obtained by using different types of sepiolites, different contents of sepiolites and different extrusion conditions have been analyzed. The foams produced with the formulations containing O-QASEP present the lowest cell size and the most homogeneous cellular structures.     

Structural Cues for Understanding eEF1A2 Moonlighting

Spontaneous mutations in the EEF1A2 gene cause epilepsy and severe neurological disabilities in children. The crystal structure of eEF1A2 protein purified from rabbit skeletal muscle reveals a post-translationally modified dimer that provides information about the sites of interaction with numerous binding partners, including itself, and maps these mutations onto the dimer and tetramer interfaces. The spatial locations of the side chain carboxylates of Glu301 and Glu374, to which phosphatidylethanolamine is uniquely attached via an amide bond, define the anchoring points of eEF1A2 to cellular membranes and interorganellar membrane contact sites. Additional bioinformatic and molecular modeling results provide novel structural insight into the demonstrated binding of eEF1A2 to SH3 domains, the common MAPK docking groove, filamentous actin, and phosphatidylinositol-4 kinase IIIβ. In this new light, the role of eEF1A2 as an ancient, multifaceted, and articulated G protein at the crossroads of autophagy, oncogenesis and viral replication appears very distant from the “canonical” one of delivering aminoacyl-tRNAs to the ribosome that has dominated the scene and much of the thinking for many decades.     

Microtubule Destabilizing Sulfonamides as an Alternative to Taxane-Based Chemotherapy

Pan-Gyn cancers entail 1 in 5 cancer cases worldwide, breast cancer being the most commonly diagnosed and responsible for most cancer deaths in women. The high incidence and mortality of these malignancies, together with the handicaps of taxanes—first-line treatments—turn the development of alternative therapeutics into an urgency. Taxanes exhibit low water solubility that require formulations that involve side effects. These drugs are often associated with dose-limiting toxicities and with the appearance of multi-drug resistance (MDR). Here, we propose targeting tubulin with compounds directed to the colchicine site, as their smaller size offer pharmacokinetic advantages and make them less prone to MDR efflux. We have prepared 52 new Microtubule Destabilizing Sulfonamides (MDS) that mostly avoid MDR-mediated resistance and with improved aqueous solubility. The most potent compounds, N-methyl-N-(3,4,5-trimethoxyphenyl-4-methylaminobenzenesulfonamide 38, N-methyl-N-(3,4,5-trimethoxyphenyl-4-methoxy-3-aminobenzenesulfonamide 42, and N-benzyl-N-(3,4,5-trimethoxyphenyl-4-methoxy-3-aminobenzenesulfonamide 45 show nanomolar antiproliferative potencies against ovarian, breast, and cervix carcinoma cells, similar or even better than paclitaxel. Compounds behave as tubulin-binding agents, causing an evident disruption of the microtubule network, in vitro Tubulin Polymerization Inhibition (TPI), and mitotic catastrophe followed by apoptosis. Our results suggest that these novel MDS may be promising alternatives to taxane-based chemotherapy in chemoresistant Pan-Gyn cancers.     

Software assurance practices for mobile applications

Mobile software applications have to cope with a particular environment that involves small size, limited resources, high autonomy requirements, competitive business models and many other challenges. To provide development guidelines that respond to these needs, several practices have been introduced; however, it is not clear how these guidelines may contribute to solve the issues present in the mobile domain. Furthermore, the rapid evolution of the mobile ecosystem challenges many of the premises upon which the proposed practices were designed. In this paper, we present a survey of the literature on software assurance practices for mobile applications, with the objective of describing them and assessing their contribution and success. We identified, organized and reviewed a body of research that spans in three levels: software development processes, software product assurance practices, and software implementation practices. By carrying out this literature survey, we reviewed the different approaches that researchers on Software Engineering have provided to address the needs that raise in the mobile software development arena. Moreover, we review the evolution of these practices, identifying how the constant changes and modernization of the mobile execution environment has impacted the methods proposed in the literature. Finally, we introduced discussion on the application of these practices in a real productive setting, opening an area for further research that may determine if practitioners have followed the proposed assurance paradigms.     

ProVoc: An app to train vocabulary depth in order to foster children's reading comprehension

Many studies have demonstrated the crucial role of vocabulary in predicting reading performance in general. More recent work has indicated that one particular facet of vocabulary (its depth) is more closely related to language comprehension, especially inferential comprehension. On this basis, we developed a training application to specifically improve vocabulary depth. The objective of this study was to test the effectiveness of a mobile application designed to improve vocabulary depth. The effectiveness of this training was examined on 3rd and 4th grade children's vocabulary (breadth and depth), decoding and comprehension performances. A randomized waiting-list control paradigm was used in which an experimental group first received the intervention during the first 4 weeks (between pretest and post-test1), thereafter, a waiting control group received the training for the next 4 weeks (between postest1 and posttest2). Results showed that the developed application led to significant improvements in terms of vocabulary depth performance, as well as a significant transfer effect to reading comprehension. However, we did not observe such a beneficial effect on either vocabulary breadth or written word identification. These results are discussed in terms of the links between vocabulary depth and comprehension, and the opportunities the app presents for remedying language comprehension deficits in children.     

A local and global tour on MOMoT

Software and Systems Modeling - Many model transformation scenarios require flexible execution strategies as they should produce models with the highest possible quality. At the same time,...     

One-Pot Methods for the Protection and Assembly of Sugars

In recent years, there has been rapid expansion of glycan synthesis, fueled by the recognition that the structural complexity of sugars translates to a myriad of biological functions. Such chemical syntheses involve many challenges, mostly due to the regio- and stereochemical aspects of glycosidic bond formation. One-pot strategies were developed to assist in attaining faster and more economical access to the glycan constructs. In this front, achievements in protecting group manipulation, glycosylation, and combinations of these have been reported. Protecting group manipulations in one pot take advantage of the reaction compatibility of commonly used transformations, many of which occur in high regioselectivity. Sequential glycosylations, on the other hand, rely on leaving group orthogonalities and reactivity tuning, as well as the preactivation technique. Altogether, these approaches offer attractive means to the much needed glycan structures and, consequently, help usher in advances in glycoscience.     

Microwave heating controlled reactive melt infiltration for graphite-Si-SiC ceramics manufacturing

In this work, we investigated a procedure which exploits microwave ovens to produce SiC- based components by reactive melt infiltration of silicon into graphite preforms. The employed oven is designed to grant optical access to the sample surface, which allows to measure its temperature evolution though a noncontact pyrometer. This signal was used as a feedback to control the power provided to the preform and as an experimental output whose analysis provides insight into the reaction mechanism. Specifically, it is found that complete infiltration is achieved much before the end of the reaction. The latter is not fully self-sustained as the global reaction rate continuously decreases with time until it is no more able to keep the temperature above the silicon solidification value. At that point, the reaction stops. The analysis of the processed samples proved that this procedure allows producing fully infiltrated samples without material failure by adjusting the heat provided during the infiltration stage rather than by tuning the preform structure and composition, which is the usual approach. The proposed method is less time and energy consuming than the standard one.