Overview of the ImageCLEF 2017 Population Estimation (Remote) Task

Estimating population has many applications as planning disaster responses, communication infrastructure, or development activities. In 2017, ImageCLEF Lab introduced a new pilot task: the Population Estimation (or Remote) task which aims at estimating the population of an area of interest by exploring Copernicus earth observation data (i.e. free Sentinel-2 satellite images). In line with the goal of FabSpace 2.0 project, a European Unions initiative to bring Geo-Enthusiast together around the 6 European universities in collaboration with Business Incubation Centers, participated to this challenge. This paper presents the results that were obtained by the participants as well as a brief summary of some of the approaches that were used

Breast tumor segmentation and shape classification in mammograms using generative adversarial and convolutional neural network.

Mammogram inspection in search of breast tumors is a tough assignment that radiologists must carry out frequently. Therefore, image analysis methods are needed for the detection and delineation of breast tumors, which portray crucial morphological information that will support reliable diagnosis. In this paper, we proposed a conditional Generative Adversarial Network (cGAN) devised to segment a breast tumor within a region of interest (ROI) in a mammogram. The generative network learns to recognize the tumor area and to create the binary mask that outlines it. In turn, the adversarial network learns to distinguish between real (ground truth) and synthetic segmentations, thus enforcing the generative network to create binary masks as realistic as possible. The cGAN works well even when the number of training samples are limited. As a consequence, the proposed method outperforms several state-of-the-art approaches. Our working hypothesis is corroborated by diverse segmentation experiments performed on INbreast and a private in-house dataset. The proposed segmentation model, working on an image crop containing the tumor as well as a significant surrounding area of healthy tissue (loose frame ROI), provides a high Dice coefficient and Intersection over Union (IoU) of 94% and 87%, respectively. In addition, a shape descriptor based on a Convolutional Neural Network (CNN) is proposed to classify the generated masks into four tumor shapes: irregular, lobular, oval and round. The proposed shape descriptor was trained on DDSM, since it provides shape ground truth (while the other two datasets does not), yielding an overall accuracy of 80%, which outperforms the current state-of-the-art

Mesoscopic organization reveals the constraints governing C. elegans nervous system

One of the biggest challenges in biology is to understand how activity at the cellular level of neurons, as a result of their mutual interactions, leads to the observed behavior of an organism responding to a variety of environmental stimuli. Investigating the intermediate or mesoscopic level of organization in the nervous system is a vital step towards understanding how the integration of micro-level dynamics results in macro-level functioning. In this paper, we have considered the somatic nervous system of the nematode Caenorhabditis elegans, for which the entire neuronal connectivity diagram is known. We focus on the organization of the system into modules, i.e., neuronal groups having relatively higher connection density compared to that of the overall network. We show that this mesoscopic feature cannot be explained exclusively in terms of considerations, such as optimizing for resource constraints (viz., total wiring cost) and communication efficiency (i.e., network path length). Comparison with other complex networks designed for efficient transport (of signals or resources) implies that neuronal networks form a distinct class. This suggests that the principal function of the network, viz., processing of sensory information resulting in appropriate motor response, may be playing a vital role in determining the connection topology. Using modular spectral analysis, we make explicit the intimate relation between function and structure in the nervous system. This is further brought out by identifying functionally critical neurons purely on the basis of patterns of intra- and inter-modular connections. Our study reveals how the design of the nervous system reflects several constraints, including its key functional role as a processor of information.Comment: Published version, Minor modifications, 16 pages, 9 figure

The emergence of waves in random discrete systems

Essential criteria for the emergence of wave-like manifestations occurring in an entirely discrete system are identified using a simple model for the movement of particles through a network. The dynamics are entirely stochastic and memoryless involving a birth-death-migration process. The requirements are that the network should have at least three nodes, that migration should have a directional bias, and that the particle dynamics have a non-local dependence. Well defined bifurcations mark transitions between amorphous, wave-like and collapsed states with an intermittent regime between the latter two

Data Integration for Open Data on the Web

In this lecture we will discuss and introduce challenges of integrating openly available Web data and how to solve them. Firstly, while we will address this topic from the viewpoint of Semantic Web research, not all data is readily available as RDF or Linked Data, so we will give an introduction to different data formats prevalent on the Web, namely, standard formats for publishing and exchanging tabular, tree-shaped, and graph data. Secondly, not all Open Data is really completely open, so we will discuss and address issues around licences, terms of usage associated with Open Data, as well as documentation of data provenance. Thirdly, we will discuss issues connected with (meta-)data quality issues associated with Open Data on the Web and how Semantic Web techniques and vocabularies can be used to describe and remedy them. Fourth, we will address issues about searchability and integration of Open Data and discuss in how far semantic search can help to overcome these. We close with briefly summarizing further issues not covered explicitly herein, such as multi-linguality, temporal aspects (archiving, evolution, temporal querying), as well as how/whether OWL and RDFS reasoning on top of integrated open data could be help

Do aluminium-based phosphate binders continue to have a role in contemporary nephrology practice?

Background: Aluminium-containing phosphate binders have long been used for treatment of hyperphosphatemia in dialysis patients. Their safety became controversial in the early 1980's after reports of aluminium related neurological and bone disease began to appear. Available historical evidence however, suggests that neurological toxicity may have primarily been caused by excessive exposure to aluminium in dialysis fluid, rather than aluminium-containing oral phosphate binders. Limited evidence suggests that aluminium bone disease may also be on the decline in the era of aluminium removal from dialysis fluid, even with continued use of aluminium binders

Neurocranium versus Face: A Morphometric Approach with Classical Anthropometric Variables for Characterizing Patterns of Cranial Integration in Extant Hominoids and Extinct Hominins

The relative importance of the two main cranial complexes, the neurocranium and the splanchnocranium, has been examined in the five species of extant hominoids and in a huge sample of extinct hominins using six standard craniometric variables that measure the length, width and height of each cranial module. Factor analysis and two-block partial least squares were used for establishing the major patterns of developmental and evolutionary integration between both cranial modules. The results obtained show that all extant hominoids (including the anatomically modern humans) share a conserved pattern of developmental integration, a result that agrees with previous studies. The pattern of evolutionary integration between both cranial modules in australopiths runs in parallel to developmental integration. In contrast, the pattern of evolutionary and developmental integration of the species of the genus Homo is the opposite, which is probably the consequence of distinctive selective regimes for both hominin groups.JAPC, JMJA and PP received fundings from Ministerio de Ciencia e Innovación, Gobierno de España (http://www.idi.mineco.gob.es), project CGL2011-30334, and Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía, España (http://www.juntadeandalucia.es/organismo​s/economiainnovacioncienciayempleo.html), project P11-HUM-7248 and Research Groups RNM-146 and HUM-607

Genome-wide association analysis of thirty one production, health, reproduction and body conformation traits in contemporary U.S. Holstein cows

<p>Abstract</p> <p>Background</p> <p>Genome-wide association analysis is a powerful tool for annotating phenotypic effects on the genome and knowledge of genes and chromosomal regions associated with dairy phenotypes is useful for genome and gene-based selection. Here, we report results of a genome-wide analysis of predicted transmitting ability (PTA) of 31 production, health, reproduction and body conformation traits in contemporary Holstein cows.</p> <p>Results</p> <p>Genome-wide association analysis identified a number of candidate genes and chromosome regions associated with 31 dairy traits in contemporary U.S. Holstein cows. Highly significant genes and chromosome regions include: BTA13's <it>GNAS </it>region for milk, fat and protein yields; BTA7's <it>INSR </it>region and BTAX's <it>LOC520057 </it>and <it>GRIA3 </it>for daughter pregnancy rate, somatic cell score and productive life; BTA2's <it>LRP1B </it>for somatic cell score; BTA14's <it>DGAT1-NIBP </it>region for fat percentage; <it>BTA1</it>'s <it>FKBP2 </it>for protein yields and percentage, BTA26's <it>MGMT </it>and BTA6's <it>PDGFRA </it>for protein percentage; BTA18's 53.9-58.7 Mb region for service-sire and daughter calving ease and service-sire stillbirth; BTA18's <it>PGLYRP1</it>-<it>IGFL1 </it>region for a large number of traits; BTA18's <it>LOC787057 </it>for service-sire stillbirth and daughter calving ease; BTA15's <it>CD82</it>, BTA23's <it>DST </it>and the <it>MOCS1</it>-<it>LRFN2 </it>region for daughter stillbirth; and BTAX's <it>LOC520057 </it>and <it>GRIA3 </it>for daughter pregnancy rate. For body conformation traits, BTA11, BTAX, BTA10, BTA5, and BTA26 had the largest concentrations of SNP effects, and <it>PHKA2 </it>of BTAX and <it>REN </it>of BTA16 had the most significant effects for body size traits. For body shape traits, BTAX, BTA19 and BTA3 were most significant. Udder traits were affected by BTA16, BTA22, BTAX, BTA2, BTA10, BTA11, BTA20, BTA22 and BTA25, teat traits were affected by BTA6, BTA7, BTA9, BTA16, BTA11, BTA26 and BTA17, and feet/legs traits were affected by BTA11, BTA13, BTA18, BTA20, and BTA26.</p> <p>Conclusions</p> <p>Genome-wide association analysis identified a number of genes and chromosome regions associated with 31 production, health, reproduction and body conformation traits in contemporary Holstein cows. The results provide useful information for annotating phenotypic effects on the dairy genome and for building consensus of dairy QTL effects.</p