ALBERT

Description: The Mezquital Valley (MV) hosts the largest unmanaged aquifer recharge scheme in the world. The metropolitan area of Mexico City discharges ~60 m3/s of raw wastewater into the valley, a substantial share of which infiltrates into the regional aquifer. In this work, we aim to develop a comprehensive approach, adapted from oil and gas reservoir modeling frameworks, to assess water supply sources located downgradient from unmanaged aquifer recharge zones. The methodology is demonstrated through its application to the Mezquital Valley region. Geological, geoelectrical, petrophysical and hydraulic information is combined into a 3D subsurface model and used to evaluate downgradient supply sources. Although hydrogeochemical variables are yet to be assessed, outcomes suggest that the newly-found groundwater sources may provide a long-term solution for water supply. Piezometric analyses based on 25-year records suggest that the MV is close to steady-state conditions. Thus, unmanaged recharge seems to have been regulating the groundwater balance for the last decades. The transition from unmanaged to managed recharge is expected to provide benefits to the MV inhabitants. It will also be likely to generate new uncertainties in relation to aquifer dynamics and downgradient systems.

Description: Background: Analysis of single cells in their native environment is a powerful method to address key questions in developmental systems biology. Confocal microscopy imaging of intact tissues, followed by automatic image segmentation, provides a means to conduct cytometric studies while at the same time preserving crucial information about the spatial organization of the tissue and morphological features of the cells. This technique is rapidly evolving but is still not in widespread use among research groups that do not specialize in technique development, perhaps in part for lack of tools that automate repetitive tasks while allowing experts to make the best use of their time in injecting their domain-specific knowledge. Results: Here we focus on a well-established stem cell model system, the C. elegans gonad, as well as on two other model systems widely used to study cell fate specification and morphogenesis: the pre-implantation mouse embryo and the developing mouse olfactory epithelium. We report a pipeline that integrates machine-learning-based cell detection, fast human-in-the-loop curation of these detections, and running of active contours seeded from detections to segment cells. The procedure can be bootstrapped by a small number of manual detections, and outperforms alternative pieces of software we benchmarked on C. elegans gonad datasets. Using cell segmentations to quantify fluorescence contents, we report previously-uncharacterized cell behaviors in the model systems we used. We further show how cell morphological features can be used to identify cell cycle phase; this provides a basis for future tools that will streamline cell cycle experiments by minimizing the need for exogenous cell cycle phase labels. Conclusions: High-throughput 3D segmentation makes it possible to extract rich information from images that are routinely acquired by biologists, and provides insights — in particular with respect to the cell cycle — that would be difficult to derive otherwise.

Description: Cardiac complications constitute a rare clinical manifestation of cytomegalovirus (CMV) infection. This virus is usually asymptomatic in immunocompetent individuals. We report a case of myocarditis and cardiac...

Description: Functional Diversity is considered an important driver of community assembly in environmental and successional gradients. To understand tree assembly processes in a semideciduous tropical forest, we analyzed the variation of Functional Richness (FRic), Functional Divergence (FDiv), and Functional Evenness (FEve) of small vs. large trees in relation to fallow age after slash-and-burn agriculture and topographical position (flat sites vs. hills). FRic of small trees was lower than null model predicted values across the successional gradient, and decreased unexpectedly in older successional ages. FRic of large trees was higher than null model predictions early in succession and lower in late-successional stands on hills. Dominant species were more similar (low FDiv) in early and intermediate successional stands for small trees, and on hills for large trees, suggesting that species that are best adapted to harsh conditions share similar traits. We also found evidence of competitive exclusion among similar species (high FEve) for small trees in early successional stands. Overall, our results indicate that community assembly of small trees is strongly affected by the changing biotic and abiotic conditions along the successional and topographical gradient. For large trees, hills may represent the most stressful conditions in this landscape.

Description: Background: The exponential growth of protein structural and sequence databases is enabling multifaceted approaches to understanding the long sought sequence-structure-function relationship. Advances in computation now make it possible to apply well-established data mining and pattern recognition techniques to these data to learn models that effectively relate structure and function. However, extracting meaningful numerical descriptors of protein sequence and structure is a key issue that requires an efficient and widely available solution. Results: We here introduce ProtDCal, a new computational software suite capable of generating tens of thousands of features considering both sequence-based and 3D-structural descriptors. We demonstrate, by means of principle component analysis and Shannon entropy tests, how ProtDCal’s sequence-based descriptors provide new and more relevant information not encoded by currently available servers for sequence-based protein feature generation. The wide diversity of the 3D-structure-based features generated by ProtDCal is shown to provide additional complementary information and effectively completes its general protein encoding capability. As demonstration of the utility of ProtDCal’s features, prediction models of N-linked glycosylation sites are trained and evaluated. Classification performance compares favourably with that of contemporary predictors of N-linked glycosylation sites, in spite of not using domain-specific features as input information. Conclusions: ProtDCal provides a friendly and cross-platform graphical user interface, developed in the Java programming language and is freely available at: http://bioinf.sce.carleton.ca/ProtDCal/. ProtDCal introduces local and group-based encoding which enhances the diversity of the information captured by the computed features. Furthermore, we have shown that adding structure-based descriptors contributes non-redundant additional information to the features-based characterization of polypeptide systems. This software is intended to provide a useful tool for general-purpose encoding of protein sequences and structures for applications is protein classification, similarity analyses and function prediction.

Description: Although most insect species are specialized on one or few groups of plants, there are phytophagous insects that seem to use virtually any kind of plant as food. Understanding the nature of this ability to fee...

Description: Grapevine flowering and fruit set greatly determine crop yield. This paper presents a new smartphone application for automatically counting, non-invasively and directly in the vineyard, the flower number in grapevine inflorescence photos by implementing artificial vision techniques. The application, called vitisFlower®, firstly guides the user to appropriately take an inflorescence photo using the smartphone’s camera. Then, by means of image analysis, the flowers in the image are detected and counted. vitisFlower® has been developed for Android devices and uses the OpenCV libraries to maximize computational efficiency. The application was tested on 140 inflorescence images of 11 grapevine varieties taken with two different devices. On average, more than 84% of flowers in the captures were found, with a precision exceeding 94%. Additionally, the application’s efficiency on four different devices covering a wide range of the market’s spectrum was also studied. The results of this benchmarking study showed significant differences among devices, although indicating that the application is efficiently usable even with low-range devices. vitisFlower is one of the first applications for viticulture that is currently freely available on Google Play.

Description: Background: Stem cells are thought to play a critical role in minimizing the accumulation of mutations, but it is not clear which strategies they follow to fulfill that performance objective. Slow cycling of stem cells provides a simple strategy that can minimize cell pedigree depth and thereby minimize the accumulation of replication-dependent mutations. Although the power of this strategy was recognized early on, a quantitative assessment of whether and how it is employed by biological systems is missing. Results: Here we address this problem using a simple self-renewing organ — the C. elegans gonad — whose overall organization is shared with many self-renewing organs. Computational simulations of mutation accumulation characterize a tradeoff between fast development and low mutation accumulation, and show that slow-cycling stem cells allow for an advantageous compromise to be reached. This compromise is such that worm germline stem cells should cycle more slowly than their differentiating counterparts, but only by a modest amount. Experimental measurements of cell cycle lengths derived using a new, quantitative technique are consistent with these predictions. Conclusions: Our findings shed light both on design principles that underlie the role of stem cells in delaying aging, and on evolutionary forces that shape stem cell gene regulatory networks.

Description: In plant-feeding insects, the evolutionary retention of polyphagy remains puzzling. A better understanding of the relationship between these organisms and changes in the metabolome of their host plants is like...

Description: This paper addresses the problem of developing user interfaces for Ubiquitous Computing (UC) and Ambient Intelligence (AmI) systems. These kind of systems are expected to provide a natural user experience, considering interaction modalities adapted to the user abilities and preferences and using whatever interaction devices are present in the environment. These interaction devices are not necessarily known at design time. The task is quite complicated due to the variety of devices and technologies, and the diversity of scenarios, and it usually burdens the developer with the need to create many different UIs in order to consider the foreseeable user-environment combinations. Here, we propose an UI abstraction framework for UC and AmI systems that effectively improves the portability of those systems between different environments and for different users. It allows developers to design and implement a single UI capable of being deployed with different devices and modalities regardless the physical location.