HTself2: Combining p-values to Improve Classification of Differential Gene Expression in HTself

HTself is a web-based bioinformatics tool designed to deal with the classification of differential gene expression for low replication microarray studies. It is based on a statistical test that uses self-self experiments to derive intensity-dependent cutoffs. The method was previously described in Vêncio et al, (DNA Res. 12: 211- e 214, 2005). In this work we consider an extension of HTself by calculating p-values instead of using a fixed credibility level α. As before, the statistic used to compute single spots p-values is obtained from the gaussian Kernel Density Estimator method applied to self-self data. Different spots corresponding to the same biological gene (replicas) give rise to a set of independent p-values which can be combined by well known statistical methods. The combined p-value can be used to decide whether a gene can be considered differentially expressed or not. HTself2 is a new version of HTself that uses the idea of p-values combination. It was implemented as a user-friendly desktop application to help laboratories without a bioinformatics infrastructure

Uniqueness of the Fock quantization of a free scalar field on S1S^1 with time dependent mass

We analyze the quantum description of a free scalar field on the circle in the presence of an explicitly time dependent potential, also interpretable as a time dependent mass. Classically, the field satisfies a linear wave equation of the form $\ddot{\xi}-\xi"+f(t)\xi=0$. We prove that the representation of the canonical commutation relations corresponding to the particular case of a massless free field ($f=0$) provides a unitary implementation of the dynamics for sufficiently general mass terms, $f(t)$. Furthermore, this representation is uniquely specified, among the class of representations determined by $S^1$-invariant complex structures, as the only one allowing a unitary dynamics. These conclusions can be extended in fact to fields on the two-sphere possessing axial symmetry. This generalizes a uniqueness result previously obtained in the context of the quantum field description of the Gowdy cosmologies, in the case of linear polarization and for any of the possible topologies of the spatial sections.Comment: 13 pages, typos corrected, version accepted for publication in Physical Review

K-means clustering combined with principal component analysis for material profiling in automotive supply chains

At a time where available data is rapidly increasing in both volume and variety, descrip- tive Data Mining (DM) can be an important tool to support meaningful decision-making processes in dynamic Supply Chain (SC) contexts. Up until now, however, scarce attention has been given to the application of DM techniques in the field of inventory management. Here, we take advantage of descriptive DM to detect and grasp important patterns among several features that coexist in a real-world automotive electronics SC. Concretely, Principal Component Analysis (PCA) is employed to analyze and understand the interrelations between ten quantitative and dependent variables in a multi-item/multi-supplier environment. Afterwards, the principal component scores are character- ized via a K-means clustering, allowing us to classify the samples into four clusters and to derive di↵erent profiles for the multiple inventory items. This work provides evidence that descriptive DM contributes to find interesting feature-patterns, resulting in the identification of important risk profiles that may e↵ectively leverage inventory management for superior performance.This work has been supported by FCT - Fundacao para a Ciencia e Tecnologia within the R&D Units Project Scope: UIDB/00319/2020. The authors want to extend grateful thanks to the editors and reviewers, whose comments have greatly improved the quality of the paper

Selection of trees for rubbing by red and roe deer in forest plantations

Antler rubbing is a form of behaviour by which deer may damage and ultimately induce mortality of trees. Understanding factors affecting selection of trees for rubbing may contribute to mitigation of negative effects of such behaviour in plantations or woodlands. We analysed characteristics of trees rubbed by red and roe deer along transects established in plantations of Pinus pinaster (Aiton), Pseudotsuga menziesii (Mirbel) Franco, Betula alba L. and Quercus robur L. in Northeast Portugal. Transects were walked during five sampling periods covering mating seasons of red and roe deer. Red deer preferentially rubbed trees adjacent to the edge of plantations and large clearings whilst roe deer selected those inside plantations within small clearings. There was seasonal segregation in the number of trees rubbed by each deer species with red deer rubbing trees mainly between September and February and roe deer mainly between December and June. Both red and roe deer selected trees with smaller diameter than those of available trees although trees selected by red deer had larger diameters than those selected by roe deer. Roe, but not red deer, tended to avoid trees protected by shrubs. Overall, the selection of trees for rubbing was site-dependent suggesting that generalizations across sites should be made with caution. Mitigating measures, such as deer control, tree protection or provision of alternative rubbing posts should target stands of particular tree species, location of trees in relation to stand clearings and tree size classes.http://www.sciencedirect.com/science/article/B6T6X-4HGM78R-2/1/29fe58190c40581f0716e977b7847d3

Fock quantization of a scalar field with time dependent mass on the three-sphere: unitarity and uniqueness

We study the Fock description of a quantum free field on the three-sphere with a mass that depends explicitly on time, also interpretable as an explicitly time dependent quadratic potential. We show that, under quite mild restrictions on the time dependence of the mass, the specific Fock representation of the canonical commutation relations which is naturally associated with a massless free field provides a unitary dynamics even when the time varying mass is present. Moreover, we demonstrate that this Fock representation is the only acceptable one, up to unitary equivalence, if the vacuum has to be SO(4)-invariant (i.e., invariant under the symmetries of the field equation) and the dynamics is required to be unitary. In particular, the analysis and uniqueness of the quantization can be applied to the treatment of cosmological perturbations around Friedmann-Robertson-Walker spacetimes with the spatial topology of the three-sphere, like e.g. for gravitational waves (tensor perturbations). In addition, we analyze the extension of our results to free fields with a time dependent mass defined on other compact spatial manifolds. We prove the uniqueness of the Fock representation in the case of a two-sphere as well, and discuss the case of a three-torus.Comment: 30 page

Cellular and molecular remodeling of inguinal adipose tissue mitochondria by dietary methionine restriction

© 2015 Elsevier Inc. Dietary methionine restriction (MR) produces a coordinated series of biochemical and physiological responses that improve biomarkers of metabolic health, increase energy expenditure, limit fat accretion and improve overall insulin sensitivity. Inguinal white adipose tissue (IWAT) is a primary target and site of action where the diet initiates transcriptional programs linked to enhancing both synthesis and oxidation of lipid. Using a combination of ex vivo approaches to assess dietary effects on cell morphology and function, we report that dietary MR produced a fourfold increase in multilocular, UCP1-expressing cells within this depot in conjunction with significant increases in mitochondrial content, size and cristae density. Dietary MR increased expression of multiple enzymes within the citric acid cycle, as well as respiratory complexes I, II and III. The physiological significance of these responses, evaluated in isolated mitochondria by high-resolution respirometry, was a significant increase in respiratory capacity measured using multiple substrates. The morphological, transcriptional and biochemical remodeling of IWAT mitochondria enhances the synthetic and oxidative capacity of this tissue and collectively underlies its expanded role as a significant contributor to the overall increase in metabolic flexibility and uncoupled respiration produced by the diet

A multivariate approach for multi-step demand forecasting in assembly industries: Empirical evidence from an automotive supply chain

PreprintDemand forecasting works as a basis for operating, business and production planning decisions in many supply chain contexts. Yet, how to accurately predict the manufacturer's demand for components in the presence of end-customer demand uncertainty remains poorly understood. Assigning the proper order quantities of components to suppliers thus becomes a nontrivial task, with a significant impact on planning, capacity and inventory-related costs. This paper introduces a multivariate approach to predict manufacturer's demand for components throughout multiple forecast horizons using different leading indicators of demand shifts. We compare the autoregressive integrated moving average model with exogenous inputs (ARIMAX) with Machine Learning (ML) models. Using a real case study, we empirically evaluate the forecasting and supply chain performance of the multivariate regression models over the component's life-cycle. The experiments show that the proposed multivariate approach provides superior forecasting and inventory performance compared with traditional univariate benchmarks. Moreover, it reveals applicable throughout the component's life-cycle, not just to a single stage. Particularly, we found that demand signals at the beginning of the life-cycle are predicted better by the ARIMAX model, but it is outperformed by ML-based models in later life-cycle stages.INCT-EN - Instituto Nacional de Ciência e Tecnologia para Excitotoxicidade e Neuroproteção(UIDB/00319/2020

Rapid Estimation of Drifting Parameters in Continuously Measured Quantum Systems

We investigate the determination of a Hamiltonian parameter in a quantum system undergoing continuous measurement. We demonstrate a computationally rapid method to estimate an unknown and possibly timedependent parameter, where we maximize the likelihood of the observed stochastic readout. By dealing directly with the raw measurement record rather than the quantum-state trajectories, the estimation can be performed while the data are being acquired, permitting continuous tracking of the parameter during slow drifts in real time. Furthermore, we incorporate realistic nonidealities, such as decoherence processes and measurement inefficiency. As an example, we focus on estimating the value of the Rabi frequency of a continuously measured qubit and compare maximum likelihood estimation to a simpler fast Fourier transform. Using this example, we discuss how the quality of the estimation depends on both the strength and the duration of the measurement; we also discuss the trade-off between the accuracy of the estimate and the sensitivity to drift as the estimation duration is varied

Availability of timber housing construction techniques in Brazil

Se analiza la representatividad de las viviendas hechas en madera, en Brasil, indicando el porcentaje de cada técnica constructiva según la oferta de las empresas evaluadas. Los porcentajes que evidencian la frecuencia de utilización de las técnicas de construcción en madera fueron medidos por medio de dos metodologías aplicadas en las empresas: encuesta por entrevistas personales a sus propietarios y búsqueda de datos en sus sitios web. El método de encuestas por entrevistas evaluó 107 empresas brasileñas, y el de búsqueda en los sitios web alcanzó 207 empresas; se consiguió 50,95 y 98,57 %, respectivamente, de la población estimada. A pesar de esta diferencia, ambos métodos demostraron un escenario similar. Las entrevistas presentaron mayores costos de aplicación. Las técnicas contemporáneas están disponibles en más del 90 % de los productores brasileros. Las casas de tablas horizontales clavadas y las casas de tablas horizontales entre pilares fueron las que tuvieron mayores ofertas.This paper analyzes the representativeness of timber housing in Brazil, identifying the percentage of construction techniques offered by each evaluated company. Percentages that evidence the frequency of use of wooden building techniques were measured using two methods applied in the companies: survey through face-to-face interviews with owners and data search on their websites. The survey through interviews evaluated 107 Brazilian companies, while the data search included 207 companies, obtaining 50.95% and 98.57% of the estimated population, respectively. In spite of this difference, both methods showed a similar scenario. Interviews evidenced higher application costs. Contemporary techniques are available in more than 90% of Brazilian constructors. Houses with nailed horizontal boards and houses with horizontal wooden boards between columns were offered the most

Coffee Diterpene Derivatives as Anti-angiogenesis Agent

Among the several compounds present in coffee, the coffee-specific diterpenes have been identified as important chemoprotective agents which possess anti-carcinogenic properties.info:eu-repo/semantics/publishedVersio