Showing papers by "Polytechnic University of Valencia published in 2016"

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagy-related protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.

A survey of best practices for RNA-seq data analysis

Abstract: RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data analysis, including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping. We highlight the challenges associated with each step. We discuss the analysis of small RNAs and the integration of RNA-seq with other functional genomics techniques. Finally, we discuss the outlook for novel technologies that are changing the state of the art in transcriptomics.

Letter of intent for KM3NeT 2.0

Abstract: The main objectives of the KM3NeT Collaboration are (i) the discovery and subsequent observation of high-energy neutrino sources in the Universe and (ii) the determination of the mass hierarchy of neutrinos. These objectives are strongly motivated by two recent important discoveries, namely: (1) the high-energy astrophysical neutrino signal reported by IceCube and (2) the sizable contribution of electron neutrinos to the third neutrino mass eigenstate as reported by Daya Bay, Reno and others. To meet these objectives, the KM3NeT Collaboration plans to build a new Research Infrastructure consisting of a network of deep-sea neutrino telescopes in the Mediterranean Sea. A phased and distributed implementation is pursued which maximises the access to regional funds, the availability of human resources and the synergistic opportunities for the Earth and sea sciences community. Three suitable deep-sea sites are selected, namely off-shore Toulon (France), Capo Passero (Sicily, Italy) and Pylos (Peloponnese, Greece). The infrastructure will consist of three so-called building blocks. A building block comprises 115 strings, each string comprises 18 optical modules and each optical module comprises 31 photo-multiplier tubes. Each building block thus constitutes a three-dimensional array of photo sensors that can be used to detect the Cherenkov light produced by relativistic particles emerging from neutrino interactions. Two building blocks will be sparsely configured to fully explore the IceCube signal with similar instrumented volume, different methodology, improved resolution and complementary field of view, including the galactic plane. One building block will be densely configured to precisely measure atmospheric neutrino oscillations.

Essential oils as additives in biodegradable films and coatings for active food packaging

Abstract: The authors acknowledge the financial support from the Spanish Ministerio de Educacion y Ciencia through Project AGL2010-20694, from Universidad Politecnica de Valencia through Project PAID-06-11-2013 and from Conselleria de Empresa, Universidad y Ciencia (Project GV/2013/152).

An open access database for the evaluation of heart sound algorithms.

Abstract: In the past few decades, analysis of heart sound signals (i.e. the phonocardiogram or PCG), especially for automated heart sound segmentation and classification, has been widely studied and has been reported to have the potential value to detect pathology accurately in clinical applications. However, comparative analyses of algorithms in the literature have been hindered by the lack of high-quality, rigorously validated, and standardized open databases of heart sound recordings. This paper describes a public heart sound database, assembled for an international competition, the PhysioNet/Computing in Cardiology (CinC) Challenge 2016. The archive comprises nine different heart sound databases sourced from multiple research groups around the world. It includes 2435 heart sound recordings in total collected from 1297 healthy subjects and patients with a variety of conditions, including heart valve disease and coronary artery disease. The recordings were collected from a variety of clinical or nonclinical (such as in-home visits) environments and equipment. The length of recording varied from several seconds to several minutes. This article reports detailed information about the subjects/patients including demographics (number, age, gender), recordings (number, location, state and time length), associated synchronously recorded signals, sampling frequency and sensor type used. We also provide a brief summary of the commonly used heart sound segmentation and classification methods, including open source code provided concurrently for the Challenge. A description of the PhysioNet/CinC Challenge 2016, including the main aims, the training and test sets, the hand corrected annotations for different heart sound states, the scoring mechanism, and associated open source code are provided. In addition, several potential benefits from the public heart sound database are discussed.

Dark Matter Search Results from the PICO-2L C3F8 Bubble Chamber.

Abstract: New results are reported from the operation of the PICO-60 dark matter detector, a bubble chamber filled with 52 kg of C_{3}F_{8} located in the SNOLAB underground laboratory. As in previous PICO bubble chambers, PICO-60 C_{3}F_{8} exhibits excellent electron recoil and alpha decay rejection, and the observed multiple-scattering neutron rate indicates a single-scatter neutron background of less than one event per month. A blind analysis of an efficiency-corrected 1167-kg day exposure at a 3.3-keV thermodynamic threshold reveals no single-scattering nuclear recoil candidates, consistent with the predicted background. These results set the most stringent direct-detection constraint to date on the weakly interacting massive particle (WIMP)-proton spin-dependent cross section at 3.4×10^{-41} cm^{2} for a 30-GeV c^{-2} WIMP, more than 1 order of magnitude improvement from previous PICO results.

Gated Materials for On-Command Release of Guest Molecules

Abstract: Multidisciplinary research at the forefront of the field of hybrid materials has paved the way to the development of endless examples of smart devices. One appealing concept in this fertile field is related to the design of gated materials. These are constructed for finely tuning the delivery of chemical or biochemical species from voids of porous supports to a solution in response to predefined stimuli. Such gated materials are composed mainly of two subunits: (i) a porous inorganic support in which a cargo is loaded and (ii) certain molecular or supramolecular entities, generally grafted onto the external surface, which can control mass transport from pores. On the basis of this concept, a large number of imaginative examples have been developed. This review intends to be a comprehensive analysis of papers published until 2014 on hybrid mesoporous gated materials. The molecules used as gates, the opening mechanisms, and controlled release behavior are detailed. We hope this review will not only help res...

volBrain: An Online MRI Brain Volumetry System

Abstract: The amount of medical image data produced in clinical and research settings is rapidly growing resulting in vast amount of data to analyze. Automatic and reliable quantitative analysis tools, including segmentation, allow to analyze brain development and to understand specific patterns of many neurological diseases. This field has recently experienced many advances with successful techniques based on non-linear warping and label fusion. In this work we present a novel and fully automatic pipeline for volumetric brain analysis based on multi-atlas label fusion technology that is able to provide accurate volumetric information at different levels of detail in a short time. This method is available through the volBrain online web interface (http://volbrain.upv.es), which is publically and freely accessible to the scientific community. Our new framework has been compared with current state-of-the-art methods showing very competitive results.

Effect of Infill Parameters on Tensile Mechanical Behavior in Desktop 3D Printing

Abstract: The recent creation and growth of desktop three-dimensional (3D) printing has led to a new way of building objects. In the manufacture of pieces using Open-Source 3D printing it is very common to use a range of infill patterns and densities with the aim of reducing printing time and material consumption. However, it is not well understood how these factors influence the characteristics of the pieces obtained. Due to the differences with FDM technology, it is necessary to evaluate the strength of the pieces manufactured with this technology. In this work, the influence of two controllable variables, such as pattern and density of the infill has been evaluated. A series of test pieces with different density characteristics and infill patterns were produced using an open-source 3D printer. The results obtained show that the influence of the different printing patterns causes a variation of less than 5% in maximum tensile strength, although the behavior is similar. The change in infill density determ...

Enhanced superconductivity in atomically thin TaS2.

Abstract: The ability to exfoliate layered materials down to the single layer limit has presented the opportunity to understand how a gradual reduction in dimensionality affects the properties of bulk materials. Here we use this top-down approach to address the problem of superconductivity in the two-dimensional limit. The transport properties of electronic devices based on 2H tantalum disulfide flakes of different thicknesses are presented. We observe that superconductivity persists down to the thinnest layer investigated (3.5 nm), and interestingly, we find a pronounced enhancement in the critical temperature from 0.5 to 2.2 K as the layers are thinned down. In addition, we propose a tight-binding model, which allows us to attribute this phenomenon to an enhancement of the effective electron-phonon coupling constant. This work provides evidence that reducing the dimensionality can strengthen superconductivity as opposed to the weakening effect that has been reported in other 2D materials so far.

Direct conversion of methane to aromatics in a catalytic co-ionic membrane reactor

Abstract: Nonoxidative methane dehydroaromatization (MDA: 6CH4 ↔ C6H6 + 9H2) using shape-selective Mo/zeolite catalysts is a key technology for exploitation of stranded natural gas reserves by direct conversion into transportable liquids. However, this reaction faces two major issues: The one-pass conversion is limited by thermodynamics, and the catalyst deactivates quickly through kinetically favored formation of coke. We show that integration of an electrochemical BaZrO3-based membrane exhibiting both proton and oxide ion conductivity into an MDA reactor gives rise to high aromatic yields and improved catalyst stability. These effects originate from the simultaneous extraction of hydrogen and distributed injection of oxide ions along the reactor length. Further, we demonstrate that the electrochemical co-ionic membrane reactor enables high carbon efficiencies (up to 80%) that improve the technoeconomic process viability.

Reversible Transformation of Pt Nanoparticles into Single Atoms inside High-Silica Chabazite Zeolite

Abstract: We report the encapsulation of platinum species in highly siliceous chabazite (CHA) crystallized in the presence of N,N,N-trimethyl-1-adamantammonium and a thiol-stabilized Pt complex. When compared to Pt/SiO2 or Pt-containing Al-rich zeolites, the materials in this work show enhanced stability toward metal sintering in a variety of industrial conditions, including H2, O2, and H2O. Remarkably, temperatures in the range 650–750 °C can be reached without significant sintering of the noble metal. Detailed structural determinations by X-ray absorption spectroscopy and aberration-corrected high-angle annular dark-field scanning transmission electron microscopy demonstrate subtle control of the supported metal structures from ∼1 nm nanoparticles to site-isolated single Pt atoms via reversible interconversion of one species into another in reducing and oxidizing atmospheres. The combined used of microscopy and spectroscopy is critical to understand these surface-mediated transformations. When tested in hydrogena...

Energy efficiency and thermal comfort in historic buildings: A review

Abstract: In recent years, energy efficiency and thermal comfort in historic buildings have become high-interest topics among scholars. Research has demonstrated that retrofitting buildings to current energy efficiency and thermal comfort standards is essential for improving sustainability and energy performance and for maintaining built heritage of historic structures. This study is an extensive overview of the literature surrounding this topic. This paper summarizes the different methods and techniques that have been used around the world to achieve performance refurbishments. Articles are organized based on the different building types used as case studies (residential, religious, academic and palace, museums, libraries and theaters, urban areas, and others). The results reveal that residential, religious and museum building types, especially from the last two centuries, have been most often used as case studies. Moreover, Europe, particularly Italy, is leading the research. The aim of this note is to demonstrate the feasibility of maintaining built heritage values of historic buildings while achieving significant improvements in their energy efficiency and thermal comfort.

Environmental conflict analysis using an integrated grey clustering and entropy-weight method

Abstract: Environmental conflict analysis (henceforth ECA) has become a key factor for the viability of projects and welfare of affected populations. In this study, we propose an approach for ECA using an integrated grey clustering and entropy-weight method (The IGCEW method). The case study considered a mining project in northern Peru. Three stakeholder groups and seven criteria were identified. The data were gathered by conducting field interviews. The results revealed that for the groups urban population, rural population and specialists, the project would have a positive, negative and normal social impact, respectively. We also noted that the criteria most likely to generate environmental conflicts in order of importance were: access to drinking water, poverty, GDP per capita and employment. These results could help regional and central governments to seek appropriate measures to prevent environmental conflicts. The proposed method showed practical results and a potential for application to other types of projects. A new integrated method for environmental conflict analysis.The grey clustering method applied to quantify qualitative information.The entropy-weight method applied to identify divergent criteria.A case study of a mining project in northern Peru.

Accelerated crystallization of zeolites via hydroxyl free radicals

Abstract: In the hydrothermal crystallization of zeolites from basic media, hydroxide ions (OH(-)) catalyze the depolymerization of the aluminosilicate gel by breaking the Si,Al-O-Si,Al bonds and catalyze the polymerization of the aluminosilicate anions around the hydrated cation species by remaking the Si,Al-O-Si,Al bonds. We report that hydroxyl free radicals (•OH) are involved in the zeolite crystallization under hydrothermal conditions. The crystallization processes of zeolites-such as Na-A, Na-X, NaZ-21, and silicalite-1-can be accelerated with hydroxyl free radicals generated by ultraviolet irradiation or Fenton's reagent.

Widespread Phytophthora infestations in European nurseries put forest, semi-natural and horticultural ecosystems at high risk of Phytophthora diseases

Abstract: An analysis of incidence of Phytophthora spp. in 732 European nurseries producing forest transplants, larger specimen trees, landscape plants and ornamentals, plus 2525 areas in which trees and shrubs were planted, is presented based on work conducted by 37 research groups in 23 European countries between 1972 and 2013. Forty-nine Phytophthora taxa were recorded in 670 nurseries (91.5%); within these nurseries, 1614 of 1992 nursery stands (81.0%) were infested, although most affected plants appeared healthy. In forest and landscape plantings, 56 Phytophthora taxa were recovered from 1667 of 2525 tested sites (66.0%). Affected plants frequently showed symptoms such as crown thinning, chlorosis and dieback caused by extensive fine root losses and/or collar rot. Many well-known highly damaging host-Phytophthora combinations were frequently detected but 297 and 407 new Phytophthora-host associations were also observed in nurseries and plantings, respectively. On average, 1.3 Phytophthora species/taxa per infested nursery stand and planting site were isolated. At least 47 of the 68 Phytophthora species/taxa detected in nurseries and plantings were exotic species several of which are considered well established in both nurseries and plantings in Europe. Seven known Phytophthora species/taxa were found for the first time in Europe, while 10 taxa had not been previously recorded from nurseries or plantings; in addition, 5 taxa were first detections on woody plant species. Seven Phytophthora taxa were previously unknown to science. The reasons for these failures of plant biosecurity in Europe, implications for forest and semi-natural ecosystems and possible ways to improve biosecurity are discussed.

An Overview of the ATSC 3.0 Physical Layer Specification

Abstract: This paper provides an overview of the physical layer specification of Advanced Television Systems Committee (ATSC) 3.0, the next-generation digital terrestrial broadcasting standard. ATSC 3.0 does not have any backwards-compatibility constraint with existing ATSC standards, and it uses orthogonal frequency division multiplexing-based waveforms along with powerful low-density parity check (LDPC) forward error correction codes similar to existing state-of-the-art. However, it introduces many new technological features such as 2-D non-uniform constellations, improved and ultra-robust LDPC codes, power-based layered division multiplexing to efficiently provide mobile and fixed services in the same radio frequency (RF) channel, as well as a novel frequency pre-distortion multiple-input single-output antenna scheme. ATSC 3.0 also allows bonding of two RF channels to increase the service peak data rate and to exploit inter-RF channel frequency diversity, and to employ dual-polarized multiple-input multiple-output antenna system. Furthermore, ATSC 3.0 provides great flexibility in terms of configuration parameters (e.g., 12 coding rates, 6 modulation orders, 16 pilot patterns, 12 guard intervals, and 2 time interleavers), and also a very flexible data multiplexing scheme using time, frequency, and power dimensions. As a consequence, ATSC 3.0 not only improves the spectral efficiency and robustness well beyond the first generation ATSC broadcast television standard, but also it is positioned to become the reference terrestrial broadcasting technology worldwide due to its unprecedented performance and flexibility. Another key aspect of ATSC 3.0 is its extensible signaling, which will allow including new technologies in the future without disrupting ATSC 3.0 services. This paper provides an overview of the physical layer technologies of ATSC 3.0, covering the ATSC A/321 standard that describes the so-called bootstrap, which is the universal entry point to an ATSC 3.0 signal, and the ATSC A/322 standard that describes the physical layer downlink signals after the bootstrap. A summary comparison between ATSC 3.0 and DVB-T2 is also provided.

A Comparative Study of Multiple-Criteria Decision-Making Methods under Stochastic Inputs

Abstract: This paper presents an application and extension of multiple-criteria decision-making (MCDM) methods to account for stochastic input variables. More in particular, a comparative study is carried out among well-known and widely-applied methods in MCDM, when applied to the reference problem of the selection of wind turbine support structures for a given deployment location. Along with data from industrial experts, six deterministic MCDM methods are studied, so as to determine the best alternative among the available options, assessed against selected criteria with a view toward assigning confidence levels to each option. Following an overview of the literature around MCDM problems, the best practice implementation of each method is presented aiming to assist stakeholders and decision-makers to support decisions in real-world applications, where many and often conflicting criteria are present within uncertain environments. The outcomes of this research highlight that more sophisticated methods, such as technique for the order of preference by similarity to the ideal solution (TOPSIS) and Preference Ranking Organization method for enrichment evaluation (PROMETHEE), better predict the optimum design alternative.

An Integrated IoT Architecture for Smart Metering

Abstract: Advanced meter infrastructures (AMIs) are systems that measure, collect, and analyze utilities distribution and consumption, and communicate with metering devices either on a schedule or on request. AMIs are becoming a vital part of utilities distribution network and allow the development of Smart Cities. In this article we propose an integrated Internet of Things architecture for smart meter networks to be deployed in smart cities. We discuss the communication protocol, the data format, the data gathering procedure, and the decision system based on big data treatment. The architecture includes electricity, water, and gas smart meters. Real measurements show the benefits of the proposed IoT architecture for both the customers and the utilities.

Use of barley straw residues to avoid high erosion and runoff rates on persimmon plantations in Eastern Spain under low frequency–high magnitude simulated rainfall events

Abstract: Soil and water losses due to agricultural mismanagement are high and non-sustainable in many orchards. An experiment was set up with rainfall simulation at 78 mm h–1 over 1 hour on 20 paired plots of 2 m2 (bare and straw covered) in new persimmon plantations in Eastern Spain. Effects of straw cover on the control of soil and water losses were assessed. An addition of 60% straw cover (75 g m–2) resulted in delayed ponding and runoff generation and consequently reduced water losses from 60% to 13% of total rainfall. The straw cover reduced raindrop impact and thus sediment detachment from 1014 to 47 g plot–1 h–1. The erosion rate was reduced from 5.1 to 0.2 Mg ha–1 h–1. The straw mulch was found to be extremely efficient in reducing soil erosion rates.

Underwater Acoustic Modems

Abstract: Due to the growing interest using underwater acoustic networks, there are more and more research papers about underwater communications. These papers are mainly focused on deployments and studies about the constraints of the underwater medium. The underwater acoustic channel is highly variable and the signal transmission can change according to environmental factors, such as the temperature, pressure, or salinity of the water. For this reason, it is important to know how these devices are developed and the maximum distance and data transfer rates they can achieve. To this end, this paper presents an exhaustive study of existing underwater acoustic modems where their main features are highlighted. We also review the main features of their hardware. All presented proposals in the research literature are compared with commercial underwater acoustic modems. Finally, we analyze different programs and improvements of existing network simulators that are often used to simulate and estimate the behavior of underwater networks.

Electronic noses and tongues to assess food authenticity and adulteration

Abstract: Background There is a growing concern for the problem of food authenticity assessment (and hence the detection of food adulteration), since it cheats the consumer and can pose serious risk to health in some instances. Unfortunately, food safety/integrity incidents occur with worrying regularity, and therefore there is clearly a need for the development of new analytical techniques. Scope and approach In this review, after briefly commenting the principles behind the design of electronic noses and electronic tongues, the most relevant contributions of these sensor systems in food adulteration control and authenticity assessment over the past ten years are discussed. It is also remarked that future developments in the utilization of advanced sensors arrays will lead to superior electronic senses with more capabilities, thus making the authenticity and falsification assessment of food products a faster and more reliable process. Key findings and conclusions The use of both types of e-devices in this field has been steadily increasing along the present century, mainly due to the fact that their efficiency has been significantly improved as important developments are taking place in the area of data handling and multivariate data analysis methods.

Tomato as a Source of Carotenoids and Polyphenols Targeted to Cancer Prevention

Abstract: A diet rich in vegetables has been associated with a reduced risk of many diseases related to aging and modern lifestyle. Over the past several decades, many researches have pointed out the direct relation between the intake of bioactive compounds present in tomato and a reduced risk of suffering different types of cancer. These bioactive constituents comprise phytochemicals such as carotenoids and polyphenols. The direct intake of these chemoprotective molecules seems to show higher efficiencies when they are ingested in its natural biological matrix than when they are ingested isolated or in dietary supplements. Consequently, there is a growing trend for improvement of the contents of these bioactive compounds in foods. The control of growing environment and processing conditions can ensure the maximum potential accumulation or moderate the loss of bioactive compounds, but the best results are obtained developing new varieties via plant breeding. The modification of single steps of metabolic pathways or their regulation via conventional breeding or genetic engineering has offered excellent results in crops such as tomato. In this review, we analyse the potential of tomato as source of the bioactive constituents with cancer-preventive properties and the result of modern breeding programs as a strategy to increase the levels of these compounds in the diet.