University of Coimbra

About: University of Coimbra is a(n) education organization based out in Coimbra, Portugal. It is known for research contribution in the topic(s): Population & Mitochondrion. The organization has 14318 authors who have published 43067 publication(s) receiving 994733 citation(s). The organization is also known as: UC & Universidade dos Estudos Gerais.

Atoms, molecules, solids, and surfaces: Applications of the generalized gradient approximation for exchange and correlation.

Abstract: Generalized gradient approximations (GGA's) seek to improve upon the accuracy of the local-spin-density (LSD) approximation in electronic-structure calculations. Perdew and Wang have developed a GGA based on real-space cutoff of the spurious long-range components of the second-order gradient expansion for the exchange-correlation hole. We have found that this density functional performs well in numerical tests for a variety of systems: (1) Total energies of 30 atoms are highly accurate. (2) Ionization energies and electron affinities are improved in a statistical sense, although significant interconfigurational and interterm errors remain. (3) Accurate atomization energies are found for seven hydrocarbon molecules, with a rms error per bond of 0.1 eV, compared with 0.7 eV for the LSD approximation and 2.4 eV for the Hartree-Fock approximation. (4) For atoms and molecules, there is a cancellation of error between density functionals for exchange and correlation, which is most striking whenever the Hartree-Fock result is furthest from experiment. (5) The surprising LSD underestimation of the lattice constants of Li and Na by 3--4 % is corrected, and the magnetic ground state of solid Fe is restored. (6) The work function, surface energy (neglecting the long-range contribution), and curvature energy of a metallic surface are all slightly reduced in comparison with LSD. Taking account of the positive long-range contribution, we find surface and curvature energies in good agreement with experimental or exact values. Finally, a way is found to visualize and understand the nonlocality of exchange and correlation, its origins, and its physical effects.

Observation of a new particle in the search for the Standard Model Higgs boson with the ATLAS detector at the LHC

Abstract: A search for the Standard Model Higgs boson in proton–proton collisions with the ATLAS detector at the LHC is presented. The datasets used correspond to integrated luminosities of approximately 4.8 fb−1 collected at View the MathML source in 2011 and 5.8 fb−1 at View the MathML source in 2012. Individual searches in the channels H→ZZ(⁎)→4l, H→γγ and H→WW(⁎)→eνμν in the 8 TeV data are combined with previously published results of searches for H→ZZ(⁎), WW(⁎), View the MathML source and τ+τ− in the 7 TeV data and results from improved analyses of the H→ZZ(⁎)→4l and H→γγ channels in the 7 TeV data. Clear evidence for the production of a neutral boson with a measured mass of View the MathML source is presented. This observation, which has a significance of 5.9 standard deviations, corresponding to a background fluctuation probability of 1.7×10−9, is compatible with the production and decay of the Standard Model Higgs boson.

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.

Common polygenic variation contributes to risk of schizophrenia and bipolar disorder

Abstract: Schizophrenia is a severe mental disorder with a lifetime risk of about 1%, characterized by hallucinations, delusions and cognitive deficits, with heritability estimated at up to 80%(1,2). We performed a genome-wide association study of 3,322 European individuals with schizophrenia and 3,587 controls. Here we show, using two analytic approaches, the extent to which common genetic variation underlies the risk of schizophrenia. First, we implicate the major histocompatibility complex. Second, we provide molecular genetic evidence for a substantial polygenic component to the risk of schizophrenia involving thousands of common alleles of very small effect. We show that this component also contributes to the risk of bipolar disorder, but not to several non-psychiatric diseases.

High-Speed Tracking with Kernelized Correlation Filters

Abstract: The core component of most modern trackers is a discriminative classifier, tasked with distinguishing between the target and the surrounding environment. To cope with natural image changes, this classifier is typically trained with translated and scaled sample patches. Such sets of samples are riddled with redundancies—any overlapping pixels are constrained to be the same. Based on this simple observation, we propose an analytic model for datasets of thousands of translated patches. By showing that the resulting data matrix is circulant, we can diagonalize it with the discrete Fourier transform, reducing both storage and computation by several orders of magnitude. Interestingly, for linear regression our formulation is equivalent to a correlation filter, used by some of the fastest competitive trackers. For kernel regression, however, we derive a new kernelized correlation filter (KCF), that unlike other kernel algorithms has the exact same complexity as its linear counterpart. Building on it, we also propose a fast multi-channel extension of linear correlation filters, via a linear kernel, which we call dual correlation filter (DCF). Both KCF and DCF outperform top-ranking trackers such as Struck or TLD on a 50 videos benchmark, despite running at hundreds of frames-per-second, and being implemented in a few lines of code (Algorithm 1). To encourage further developments, our tracking framework was made open-source.