Showing papers by "Rovira i Virgili University published in 2012"

Innovation: Metabolomics: the apogee of the omics trilogy

Abstract: Metabolites, the chemical entities that are transformed during metabolism, provide a functional readout of cellular biochemistry. With emerging technologies in mass spectrometry, thousands of metabolites can now be quantitatively measured from minimal amounts of biological material, which has thereby enabled systems-level analyses. By performing global metabolite profiling, also known as untargeted metabolomics, new discoveries linking cellular pathways to biological mechanism are being revealed and are shaping our understanding of cell biology, physiology and medicine.

Evolution of Cooperation in Multiplex Networks

Abstract: We study evolutionary game dynamics on structured populations in which individuals take part in several layers of networks of interactions simultaneously. This multiplex of interdependent networks accounts for the different kind of social ties each individual has. By coupling the evolutionary dynamics of a Prisoner's Dilemma game in each of the networks, we show that the resilience of cooperative behaviors for extremely large values of the temptation to defect is enhanced by the multiplex structure. Furthermore, this resilience is intrinsically related to a non-trivial organization of cooperation across the network layers, thus providing a new way out for cooperation to survive in structured populations.

Ontology-based semantic similarity: A new feature-based approach

Abstract: Estimation of the semantic likeness between words is of great importance in many applications dealing with textual data such as natural language processing, knowledge acquisition and information retrieval. Semantic similarity measures exploit knowledge sources as the base to perform the estimations. In recent years, ontologies have grown in interest thanks to global initiatives such as the Semantic Web, offering an structured knowledge representation. Thanks to the possibilities that ontologies enable regarding semantic interpretation of terms many ontology-based similarity measures have been developed. According to the principle in which those measures base the similarity assessment and the way in which ontologies are exploited or complemented with other sources several families of measures can be identified. In this paper, we survey and classify most of the ontology-based approaches developed in order to evaluate their advantages and limitations and compare their expected performance both from theoretical and practical points of view. We also present a new ontology-based measure relying on the exploitation of taxonomical features. The evaluation and comparison of our approach's results against those reported by related works under a common framework suggest that our measure provides a high accuracy without some of the limitations observed in other works.

Structure, properties and reactivity of polyoxometalates: a theoretical perspective

Abstract: In the thematic review dedicated to polyoxometalate (POM) chemistry published in Chemical Reviews in 1998, no contribution was devoted to theory This is not surprising because computational modelling of molecular metal-oxide clusters was in its infancy at that time Nowadays, the situation has completely changed and modern computational methods have been successfully applied to study the structure, electronic properties, spectroscopy and reactivity of POM clusters Indeed, the progress achieved during the past decade has been spectacular and herein we critically review the most important papers to provide the reader with an almost complete perspective of the field

Benchmarking homogenization algorithms for monthly data

Abstract: The COST (European Cooperation in Science and Technology) Action ES0601: advances in homogenization methods of climate series: an integrated approach (HOME) has executed a blind intercomparison and validation study for monthly homogenization algorithms. Time series of monthly temperature and precipitation were evaluated because of their importance for climate studies and because they represent two important types of statistics (additive and multiplicative). The algorithms were validated against a realistic benchmark dataset. The benchmark contains real inhomogeneous data as well as simulated data with inserted inhomogeneities. Random independent break-type inhomogeneities with nor- mally distributed breakpoint sizes were added to the simu- lated datasets. To approximate real world conditions, breaks were introduced that occur simultaneously in multiple station series within a simulated network of station data. The sim- ulated time series also contained outliers, missing data peri- ods and local station trends. Further, a stochastic nonlinear global (network-wide) trend was added.

Inhibition of Angiotensin-Converting Enzyme Activity by Flavonoids: Structure-Activity Relationship Studies

Abstract: Previous studies have demonstrated that certain flavonoids can have an inhibitory effect on angiotensin-converting enzyme (ACE) activity, which plays a key role in the regulation of arterial blood pressure. In the present study, 17 flavonoids belonging to five structural subtypes were evaluated in vitro for their ability to inhibit ACE in order to establish the structural basis of their bioactivity. The ACE inhibitory (ACEI) activity of these 17 flavonoids was determined by fluorimetric method at two concentrations (500 µM and 100 µM). Their inhibitory potencies ranged from 17 to 95% at 500 µM and from 0 to 57% at 100 µM. In both cases, the highest ACEI activity was obtained for luteolin. Following the determination of ACEI activity, the flavonoids with higher ACEI activity (i.e., ACEI >60% at 500 µM) were selected for further IC50 determination. The IC50 values for luteolin, quercetin, rutin, kaempferol, rhoifolin and apigenin K were 23, 43, 64, 178, 183 and 196 µM, respectively. Our results suggest that flavonoids are an excellent source of functional antihypertensive products. Furthermore, our structure-activity relationship studies show that the combination of sub-structures on the flavonoid skeleton that increase ACEI activity is made up of the following elements: (a) the catechol group in the B-ring, (b) the double bond between C2 and C3 at the C-ring, and (c) the cetone group in C4 at the C-ring. Protein-ligand docking studies are used to understand the molecular basis for these results.

A Guideline to Univariate Statistical Analysis for LC/MS-Based Untargeted Metabolomics-Derived Data

Abstract: Several metabolomic software programs provide methods for peak picking, retention time alignment and quantification of metabolite features in LC/MS-based metabolomics. Statistical analysis, however, is needed in order to discover those features significantly altered between samples. By comparing the retention time and MS/MS data of a model compound to that from the altered feature of interest in the research sample, metabolites can be then unequivocally identified. This paper reports on a comprehensive overview of a workflow for statistical analysis to rank relevant metabolite features that will be selected for further MS/MS experiments. We focus on univariate data analysis applied in parallel on all detected features. Characteristics and challenges of this analysis are discussed and illustrated using four different real LC/MS untargeted metabolomic datasets. We demonstrate the influence of considering or violating mathematical assumptions on which univariate statistical test rely, using high-dimensional LC/MS datasets. Issues in data analysis such as determination of sample size, analytical variation, assumption of normality and homocedasticity, or correction for multiple testing are discussed and illustrated in the context of our four untargeted LC/MS working examples.

The Possible Role of Resource Requirements and Academic Career-Choice Risk on Gender Differences in Publication Rate and Impact

Abstract: Many studies demonstrate that there is still a significant gender bias, especially at higher career levels, in many areas including science, technology, engineering, and mathematics (STEM). We investigated field-dependent, gender-specific effects of the selective pressures individuals experience as they pursue a career in academia within seven STEM disciplines. We built a unique database that comprises 437,787 publications authored by 4,292 faculty members at top United States research universities. Our analyses reveal that gender differences in publication rate and impact are discipline-specific. Our results also support two hypotheses. First, the widely-reported lower publication rates of female faculty are correlated with the amount of research resources typically needed in the discipline considered, and thus may be explained by the lower level of institutional support historically received by females. Second, in disciplines where pursuing an academic position incurs greater career risk, female faculty tend to have a greater fraction of higher impact publications than males. Our findings have significant, field-specific, policy implications for achieving diversity at the faculty level within the STEM disciplines.

Birds of a Feather: Neanderthal Exploitation of Raptors and Corvids

Abstract: The hypothesis that Neanderthals exploited birds for the use of their feathers or claws as personal ornaments in symbolic behaviour is revolutionary as it assigns unprecedented cognitive abilities to these hominins. This inference, however, is based on modest faunal samples and thus may not represent a regular or systematic behaviour. Here we address this issue by looking for evidence of such behaviour across a large temporal and geographical framework. Our analyses try to answer four main questions: 1) does a Neanderthal to raptor-corvid connection exist at a large scale, thus avoiding associations that might be regarded as local in space or time?; 2) did Middle (associated with Neanderthals) and Upper Palaeolithic (associated with modern humans) sites contain a greater range of these species than Late Pleistocene paleontological sites?; 3) is there a taphonomic association between Neanderthals and corvids-raptors at Middle Palaeolithic sites on Gibraltar, specifically Gorham's, Vanguard and Ibex Caves? and; 4) was the extraction of wing feathers a local phenomenon exclusive to the Neanderthals at these sites or was it a geographically wider phenomenon?. We compiled a database of 1699 Pleistocene Palearctic sites based on fossil bird sites. We also compiled a taphonomical database from the Middle Palaeolithic assemblages of Gibraltar. We establish a clear, previously unknown and widespread, association between Neanderthals, raptors and corvids. We show that the association involved the direct intervention of Neanderthals on the bones of these birds, which we interpret as evidence of extraction of large flight feathers. The large number of bones, the variety of species processed and the different temporal periods when the behaviour is observed, indicate that this was a systematic, geographically and temporally broad, activity that the Neanderthals undertook. Our results, providing clear evidence that Neanderthal cognitive capacities were comparable to those of Modern Humans, constitute a major advance in the study of human evolution.

Metabolomics implicates altered sphingolipids in chronic pain of neuropathic origin

Abstract: Neuropathic pain is a debilitating condition for which the development of effective treatments has been limited by an incomplete understanding of its chemical basis. We show by using untargeted metabolomics that sphingomyelin-ceramide metabolism is altered in the dorsal horn of rats with neuropathic pain and that the upregulated, endogenous metabolite N,N-dimethylsphingosine induces mechanical hypersensitivity in vivo. These results demonstrate the utility of metabolomics to implicate unexplored biochemical pathways in disease.

Passive Wireless Temperature Sensor Based on Time-Coded UWB Chipless RFID Tags

Abstract: In this paper, an RF identification sensor system is developed. It comprises passive sensors and an ultra-wideband (UWB) reader. The sensors are based on time-coded chipless tags. They consist of an UWB antenna connected to a delay line that is, in turn, loaded with a resistive temperature sensor. This sensor modulates the amplitude of the backscattered signals as a function of the temperature. The sensor tags are identified by changing the length of the delay line. In this paper, the operation principle and design of time-coded tags is presented and the integration of sensors in these tags is addressed. In addition, two measurement techniques are compared to implement the UWB reader. The first one is based on frequency sweeping and uses a vector network analyzer. The second one is based on a low-cost UWB radar. A full characterization of the sensor system is provided.

Customer loyalty to service providers: examining the role of service quality, customer satisfaction and trust

Abstract: In recent years, the concept of customer loyalty has become increasingly popular. Both academics and practitioners regard customer loyalty as being fundamental to a company's success. Developing customer loyalty is also a strategy that is well suited to the service industry precisely because services offer more opportunities for such development to take place. Yet despite the obvious importance of customer loyalty to all businesses, and in particular to services, there is still much to be learnt. The purpose of this study is to analyse the impact of service quality, satisfaction and trust on customer loyalty to the service provider by means of structural equation modelling. The results of the empirical research on travel agencies reveal how loyalty depends on the customer's degree of satisfaction and trust. In turn, satisfaction is influenced by service quality. Most previous studies have focused on quality and satisfaction but in this study, we extend the list of factors which predict loyalty by emphasis...

Anti-inflammatory effects of low-dose radiotherapy. Indications, dose, and radiobiological mechanisms involved.

Abstract: Low-dose radiotherapy (LD-RT) has been used for several benign diseases, including arthrodegenerative and inflammatory pathologies. Despite its effectiveness in clinical practice, little is known about the mechanisms through which LD-RT modulates the various phases of the inflammatory response and about the optimal dose fractionation. The objective of this review is to deepen knowledge about the most effective LD-RT treatment schedule and radiobiological mechanisms underlying the anti-inflammatory effects of LD-RT in various in vitro experiments, in vivo studies, and clinical studies.

Design and planning of infrastructures for bioethanol and sugar production under demand uncertainty

Abstract: In this paper, we address the strategic planning of integrated bioethanol–sugar supply chains (SC) under uncertainty in the demand. The design task is formulated as a multi-scenario mixed-integer linear programming (MILP) problem that decides on the capacity expansions of the production and storage facilities of the network over time along with the associated planning decisions (i.e., production rates, sales, etc.). The MILP model seeks to optimize the expected performance of the SC under several financial risk mitigation options. This consideration gives a rise to a multi-objective formulation, whose solution is given by a set of network designs that respond in different ways to the actual realization of the demand (the uncertain parameter). The capabilities of our approach are demonstrated through a case study based on the Argentinean sugarcane industry. Results include the investment strategy for the optimal SC configuration along with an analysis of the effect of demand uncertainty on the economic performance of several biofuels SC structures.

Nanoporous Anodic Alumina Barcodes: Toward Smart Optical Biosensors

Abstract: Toward a smart optical biosensor based on nanoporous anodic alumina (NAA): by modifying the pore geometry in nanoporous anodic alumina we are able to change the effective medium at will and tune the photoluminescence of NAA. The oscillations in the PL spectrum are converted into exclusive barcodes, which are useful for developing optical biomedical sensors in the UV-Visible region.

Sc2S@C(s)(10528)-C72: a dimetallic sulfide endohedral fullerene with a non isolated pentagon rule cage.

Abstract: A non isolated pentagon rule metallic sulfide clusterfullerene, Sc2S@Cs(10528)-C72, has been isolated from a raw mixture of Sc2S@C2n (n = 35–50) obtained by arc-discharging graphite rods packed with Sc2O3 and graphite powder under an atmosphere of SO2 and helium. Multistage HPLC methods were utilized to isolate and purify the Sc2S@C72. The purified Sc2S@Cs(10528)-C72 was characterized by mass spectrometry, UV–vis–NIR absorption spectroscopy, cyclic voltammetry, and single-crystal X-ray diffraction. The crystallographic analysis unambiguously elucidated that the C72 fullerene cage violates the isolated pentagon rule, and the cage symmetry was assigned to Cs(10528)-C72. The electrochemical behavior of Sc2S@Cs(10528)-C72 shows a major difference from those of Sc2S@Cs(6)-C82 and Sc2S@C3v(8)-C82 as well as the other metallic clusterfullerenes. Computational studies show that the Sc2S cluster transfers four electrons to the C72 cage and Cs(10528)-C72 is the most stable cage isomer for both empty C724– and Sc2S@...

Procyanidins and inflammation: molecular targets and health implications.

Abstract: The inflammatory response has been implicated in the pathogenesis of many chronic diseases. Thus, the modulation of the inflammatory response by the consumption of bioactive food compounds, such as procyanidins, is a powerful tool to promote health. Procyanidin-mediated anti-inflammatory molecular mechanisms include, among others, the modulation of the arachidonic acid pathway, the inhibition of the gene transcription, protein expression and enzymatic activity of eicosanoid generating enzymes, the production and secretion of inflammatory mediators (such as cytokines and nitric oxide), the inhibition of mitogen-activated protein kinase (MAPK) pathway activation, and the modulation of the nuclear factor-κB (NF-κB) pathway. The NF-κB pathway can be regulated by procyanidins at several levels. During early events in NF-κB signaling, procyanidins modulate Iκκ activity, and the cytoplasmic retention of p65:p50 NF-κB by the inhibition of IκB phosphorylation and proteasomal degradation, while at late stages, they affect the nuclear translocation of pro/anti-inflammatory NF-κB homo/hetero dimers and their subsequent binding to the promoter regions of target genes. To identify and understand the value of procyanidins in the modulation of the inflammatory response, the molecular mechanisms underlying the anti-inflammatory activities and prohomeostatic effects of procyanidins need to be investigated further.

Human Exposure to Perfluorinated Compounds in Catalonia, Spain: Contribution of Drinking Water and Fish and Shellfish

Abstract: In this study, the concentrations of 15 perfluorinated compounds (PFCs) were analyzed in 30 water samples collected in Catalonia (Spain) at three stages of the drinking water treatment process in several water purification plants. In addition, the concentrations of 13 PFCs were determined in samples of fish and shellfish collected from coastal areas of Catalonia. The intake of PFCs through both pathways, drinking water intake and fish and shellfish consumption, was also estimated. In water samples, the highest mean concentrations corresponded to perfluorooctane sulfonate (PFOS) and perfluorooctanoate (PFOA) (1.81 and 2.40 ng/L, respectively), whereas perfluorodecanosulfonate (PFDS) and perfluorotetradecanoic acid (PFTDA) were under their respective limits of detection in all analyzed samples. The results show that although the current treatment processes caused slight reductions in PFC concentrations, these processes did not mean significant changes in the amounts of PFCs already contained in the raw water. Among the analyzed PFCs in fish and shellfish, only seven compounds could be detected in at least one composite sample. PFOS showed the highest mean concentration (2.70 ng/g fw), being detected in all species with the exception of mussels. With regard to PFOA (mean, 0.074 ng/g fw), the highest concentrations were detected in prawn and hake (0.098 and 0.091 ng/g fw, respectively). The current exposure to PFCs through consumption of fish and shellfish indicates that it should not be of concern for the consumers. The amounts ingested are well below the recommended tolerable daily intakes, at least for those PFCs for which information is available.

Evaluation of the safety and efficacy of hydroxycitric acid or Garcinia cambogia extracts in humans.

Abstract: Several studies have shown that Garcinia cambogia plays an important role in the regulation of endogenous lipid biosynthesis. This effect is specially attributed to (-)-hydroxycitric acid (HCA) inhibiting the enzyme ATP-dependent citrate lyase, which catalyzes the cleavage of citrate to oxaloacetate and acetyl-CoA. Although several studies have found that the administration of G. cambogia extracts is associated with body weight and fat loss in both experimental animals and humans, we should be cautious when interpreting the results as other randomized, placebo-controlled clinical trials have not reported the same outcomes. Furthermore, most studies in humans have been conducted on small samples and mainly in the short term. None of them have shown whether these effects persist beyond 12 weeks of intervention. Therefore, there is still little evidence to support the potential effectiveness and long-term benefits of G. cambogia extracts. With regard to toxicity and safety, it is important to note that except in rare cases, studies conducted in experimental animals have not reported increased mortality or significant toxicity. Furthermore, at the doses usually administered, no differences have been reported in terms of side effects or adverse events (those studied) in humans between individuals treated with G. cambogia and controls.