Exploiting Conceptual Modeling for Searching Genomic Metadata: A Quantitative and Qualitative Empirical Study

Providing a common data model for the metadata of several heterogenous genomic data sources is hard, as they do not share any standard or agreed practice for metadata description. Two years ago we managed to discover a subset of common metadata present in most sources and to organize it as a smart genomic conceptual model (GCM); the model has been instrumental to our efforts in the development of a major software pipeline for data integration. More recently, we developed a user-friendly search interface, based on a simplified version of GCM. In this paper, we report our evaluation of the effectiveness of this new user interface. Specifically, we present the results of a compendious empirical study to answer the research question: How much is such a simple interface well-understood by a standard user? The target of this study is a mixed population, composed by biologists, bioinformaticians and computer scientists. The result of our empirical study shows that the users were successful in producing search queries starting from their natural language description, as they did it with good accuracy and small error rate. The study also shows that most users were generally satisfied; it provides indications on how to improve our search system and how to continue our effort in integration of genomic sources. We are consequently adapting the user interface, that will be soon opened to public use

Observations of gas flows inside a protoplanetary gap

Gaseous giant planet formation is thought to occur in the first few million years following stellar birth. Models predict that giant planet formation carves a deep gap in the dust component (shallower in the gas). Infrared observations of the disk around the young star HD142527, at ~140pc, found an inner disk ~10AU in radius, surrounded by a particularly large gap, with a disrupted outer disk beyond 140AU, indicative of a perturbing planetary-mass body at ~90 AU. From radio observations, the bulk mass is molecular and lies in the outer disk, whose continuum emission has a horseshoe morphology. The vigorous stellar accretion rate would deplete the inner disk in less than a year, so in order to sustain the observed accretion, matter must flow from the outer-disk into the cavity and cross the gap. In dynamical models, the putative protoplanets channel outer-disk material into gap-crossing bridges that feed stellar accretion through the inner disk. Here we report observations with the Atacama Large Millimetre Array (ALMA) that reveal diffuse CO gas inside the gap, with denser HCO+ gas along gap-crossing filaments, and that confirm the horseshoe morphology of the outer disk. The estimated flow rate of the gas is in the range 7E-9 to 2E-7 Msun/yr, which is sufficient to maintain accretion onto the star at the present rate

From a Conceptual Model to a Knowledge Graph for Genomic Datasets

Data access at genomic repositories is problematic, as data is described by heterogeneous and hardly comparable metadata. We previously introduced a unified conceptual schema, collected metadata in a single repository and provided classical search methods upon them. We here propose a new paradigm to support semantic search of integrated genomic metadata, based on the Genomic Knowledge Graph, a semantic graph of genomic terms and concepts, which combines the original information provided by each source with curated terminological content from specialized ontologies. Commercial knowledge-assisted search is designed for transparently supporting keyword-based search without explaining inferences; in biology, inference understanding is instead critical. For this reason, we propose a graph-based visual search for data exploration; some expert users can navigate the semantic graph along the conceptual schema, enriched with simple forms of homonyms and term hierarchies, thus understanding the semantic reasoning behind query results

STAT6 variants associate with relapse of fosinophilic esophagitis in patients receiving long-term proton pump inhibitor therapy

Background & Aims: Based on histologic features, variants in STAT6 are associated with a poor initial response to proton pump inhibitor (PPI) therapy in pediatric patients with eosinophilic esophagitis (EoE). We investigated whether these genetic variants are associated with a poor long-term response in children with EoE who initially responded to PPI therapy. Methods: We performed a prospective longitudinal cohort study of children ages 2 to 16 years who met the diagnostic criteria for EoE (≥15 eosinophils/high-power field [eos/hpf]), responded to 8 weeks of treatment with 2 mg/kg/d PPI (<15 eos/hpf), and whose dose then was reduced to 1 mg/kg/d PPI (maintenance therapy) for 1 year, at which point biopsy specimens were collected by endoscopy. Genomic DNA was isolated from formalin-fixed paraffin-embedded biopsy tissue and was genotyped for variants of STAT6. Remission of inflammation was assessed at eos/hpf thresholds of <15 and ≤5. Results: Among 73 patients who received 1 mg/kg/d PPI maintenance therapy for 1 year, 13 patients (18%) had 6 to 14 eos/hpf, 36 patients (49%) had 5 or fewer eos/hpf, and 24 patients (33%) relapsed to EoE (≥15 eos/hpf). Carriage of any of 3 STAT6 variants in linkage disequilibrium (r2 ≥0.8; rs324011, rs167769, or rs12368672) was associated with a 2.3- to 2.8-fold increase in the odds of EoE relapse, and with a 2.8- to 4.1-fold increase in the odds of having 6 to 14 eos/hpf. For rs324011, the odds ratio [95% CI] for relapse was 2.77 [1.11, 6.92]; P = .029, and the odds ratio [95% CI] for having 6 to 14 eos/hpf was 3.06 [1.27, 7.36]; P = .012. Conclusions: Pediatric EoE patients who initially respond to PPI therapy and carry STAT6 variants rs324011, rs167769, or rs12368672 are at increased risk of relapse after 1 year of PPI maintenance therapy

Dependence of the microporosity of activated carbons on the lignocellulosic composition of the precursors

Se preparó una serie de carbones activados mediante gasificación física con vapor de vapor en condiciones experimentales idénticas para comparar el desarrollo de poros de los caracteres de poda de almendros y los carbonos activados de cáscara de nuez. Los resultados obtenidos mostraron que la gasificación por vapor produce carbones microporosos en ambos casos, y el aumento de la temperatura provoca un aumento de los volúmenes de poros de los carbones activados, hasta un cierto grado de combustión. Este efecto fue más marcado para la cáscara de nuez, que dio lugar a carbones activados con valores de superficie aparentes de hasta 1434 m2. g-1. Además, se encontró un ligero ensanchamiento de la porosidad en bajos grados de combustión. Esta ampliación de poros fue más marcada en el caso de los carbones activados de la poda de almendros, que también tienen un alto volumen de macroporos. Se encontró que las propiedades lignocelulósicas y de porosidad de las materias primas pueden causar este comportamiento diferente hacia los procesos de activación.A series of activated carbons were prepared by physical steam gasification under identical experimental conditions to compare the pore development from almond tree pruning chars and walnut shell activated carbons. The results obtained showed that steam gasification yields microporous carbons in both cases, and the rise in temperature causes an increase of the pore volumes of the activated carbons, up to a certain degree of burn-off. This effect was more marked for walnut shell, which gave rise to activated carbons with apparent surface values of up to 1434 m2.g-1. Also, a slight widening of porosity was found at low burn-off degrees. This pore widening was more marked in the case of activated carbons from almond tree pruning, which also have a high macropore volume. It was found that the lignocellulosic and porosity properties of the raw materials can cause this different behavior towards activation processes.• Ministerio de Economía y Competitividad. Proyecto CTM2016-75937-R • Gobierno de Extremadura . Ayuda GR15034 • Universidad de Extremadura. AyudapeerReviewe

Brucella abortus S19 GFP-tagged vaccine allows the serological identification of vaccinated cattle

Bovine brucellosis induces abortion in cows, produces important economic losses, and causes a widely distributed zoonosis. Its eradication was achieved in several countries after sustained vaccination with the live attenuated Brucella abortus S19 vaccine, in combination with the slaughtering of serologically positive animals. S19 induces antibodies against the smooth lipopolysaccharide (S-LPS), making difficult the differentiation of infected from vaccinated bovines. We developed an S19 strain constitutively expressing the green fluorescent protein (S19-GFP) coded in chromosome II. The S19-GFP displays similar biological characteristics and immunogenic and protective efficacies in mice to the parental S19 strain. S19-GFP can be distinguished from S19 and B. abortus field strains by fluorescence and multiplex PCR. Twenty-five heifers were vaccinated withS19-GFP (5×109 CFU) by the subcutaneous or conjunctival routes and some boosted with GFP seven weeks thereafter. Immunized animals were followed up for over three years and tested for anti-S-LPS antibodies by both the Rose Bengal test and a competitive ELISA. Anti-GFP antibodies were detected by an indirect ELISA and Western blotting. In most cases, anti-S-LPS antibodies preceded for several weeks those against GFP. The anti-GFP antibody response was higher in the GFP boosted than in the non-boosted animals. In all cases, the anti-GFP antibodies persisted longer, or at least as long, as those against S-LPS. The drawbacks and potential advantages of using the S19-GFP vaccine for identifying vaccinated animals in infected environments are discussed.Publishe

Is there a role for melatonin in fibromyalgia?

Fibromyalgia, characterised by persistent pain, fatigue, sleep disturbance and cognitive dysfunction, is a central sensitivity syndrome that also involves abnormality in peripheral generators and in the hypothalamic pituitary adrenal axis. Heterogeneity of clinical expression of fibromyalgia with a multifactorial aetiology has made the development of effective therapeutic strategies challenging. Physiological properties of the neurohormone melatonin appear related to the symptom profile exhibited by patients with fibromyalgia and thus disturbance of it’s production would be compatible with the pathophysiology. Altered levels of melatonin have been observed in patients with fibromyalgia which are associated with lower secretion during dark hours and higher secretion during daytime. However, inconsistencies of available clinical evidence limit conclusion of a relationship between levels of melatonin and symptom profiles in patients with fibromyalgia. Administration of melatonin to patients with fibromyalgia has demonstrated suppression of many symptoms and an improved quality of life consistent with benefit as a therapy for the management of this condition. Further studies with larger samples, however, are required to explore the potential role of melatonin in the pathophysiology of fibromyalgia and determine the optimal dosing regimen of melatonin for the management of fibromyalgia

Improvement of mead fermentation by honey-must supplementation

Through honey's fermentation, diverse beverages can be obtained, among which is mead, an alcoholic drink with 8 to 18% of ethanol (v/v). Since honey is a matrix with a low nutrient concentration and other unfavourable growth conditions, several problems are usually encountered, namely delayed or arrested fermentations, unsatisfactory quality parameters and lack of uniformity of the final product, as well as unpleasant sensory properties. In this context, the aim of this work was to optimize mead production through honey-must supplementation with (a) salts, (b) vitamins or (c) salts+vitamins. The effects of the honey-must formulation on the fermentation kinetics, growth profile and physicochemical characteristics of final meads were evaluated. The results showed minor differences in the fermentation profile and time between fermentations with the different formulations. The growth profile was influenced more by the yeast strain than by the supplements added to the honey-must. In general, the honey-must composition did not influence meads' final characteristics, except regarding the SO 2 concentration of the meads produced using the strain QA23. In summary, the addition of salts and/or vitamins to honey-must had no positive effects on the fermentation, growth profile or characteristics of the final products.The research presented in this paper was partially funded by the Fundação para a Ciência e Tecnologia (FCT) and by PTDC projects (contracts PTDC/AGR-ALI/68284/2006). A. P. Pereira is a recipient of a PhD grant from the FCT (SFRH/BD/45820/2008).info:eu-repo/semantics/publishedVersio

Updating known distribution models for forecasting climate change impact on endangered species

To plan endangered species conservation and to design adequate management programmes, it is necessary to predict their distributional response to climate change, especially under the current situation of rapid change. However, these predictions are customarily done by relating de novo the distribution of the species with climatic conditions with no regard of previously available knowledge about the factors affecting the species distribution. We propose to take advantage of known species distribution models, but proceeding to update them with the variables yielded by climatic models before projecting them to the future. To exemplify our proposal, the availability of suitable habitat across Spain for the endangered Bonelli’s Eagle (Aquila fasciata) was modelled by updating a pre-existing model based on current climate and topography to a combination of different general circulation models and Special Report on Emissions Scenarios. Our results suggested that the main threat for this endangered species would not be climate change, since all forecasting models show that its distribution will be maintained and increased in mainland Spain for all the XXI century. We remark on the importance of linking conservation biology with distribution modelling by updating existing models, frequently available for endangered species, considering all the known factors conditioning the species’ distribution, instead of building new models that are based on climate change variables only.Ministerio de Ciencia e Innovación and FEDER (project CGL2009-11316/BOS

Ambient-aware continuous care through semantic context dissemination

Background: The ultimate ambient-intelligent care room contains numerous sensors and devices to monitor the patient, sense and adjust the environment and support the staff. This sensor-based approach results in a large amount of data, which can be processed by current and future applications, e. g., task management and alerting systems. Today, nurses are responsible for coordinating all these applications and supplied information, which reduces the added value and slows down the adoption rate. The aim of the presented research is the design of a pervasive and scalable framework that is able to optimize continuous care processes by intelligently reasoning on the large amount of heterogeneous care data. Methods: The developed Ontology-based Care Platform (OCarePlatform) consists of modular components that perform a specific reasoning task. Consequently, they can easily be replicated and distributed. Complex reasoning is achieved by combining the results of different components. To ensure that the components only receive information, which is of interest to them at that time, they are able to dynamically generate and register filter rules with a Semantic Communication Bus (SCB). This SCB semantically filters all the heterogeneous care data according to the registered rules by using a continuous care ontology. The SCB can be distributed and a cache can be employed to ensure scalability. Results: A prototype implementation is presented consisting of a new-generation nurse call system supported by a localization and a home automation component. The amount of data that is filtered and the performance of the SCB are evaluated by testing the prototype in a living lab. The delay introduced by processing the filter rules is negligible when 10 or fewer rules are registered. Conclusions: The OCarePlatform allows disseminating relevant care data for the different applications and additionally supports composing complex applications from a set of smaller independent components. This way, the platform significantly reduces the amount of information that needs to be processed by the nurses. The delay resulting from processing the filter rules is linear in the amount of rules. Distributed deployment of the SCB and using a cache allows further improvement of these performance results