The Pole Behaviour of the Phase Derivative of the Short-Time Fourier Transform

The short-time Fourier transform (STFT) is a time-frequency representation widely used in applications, for example in audio signal processing. Recently it has been shown that not only the amplitude, but also the phase of this representation can be successfully exploited for improved analysis and processing. In this paper we describe a rather peculiar pole phenomenon in the phase derivative, a recurring pattern that appears in a characteristic way in the neighborhood around any of the zeros of the STFT, a negative peak followed by a positive one. We describe this phenomenon numerically and provide a complete analytical explanation.Comment: 15 pages, 4 figures; Applied and Computational Harmonic Analysis (in press), available online 22 October 201

Continuous integral kernels for unbounded Schroedinger semigroups and their spectral projections

By suitably extending a Feynman-Kac formula of Simon [Canadian Math. Soc. Conf. Proc, 28 (2000), 317-321], we study one-parameter semigroups generated by (the negative of) rather general Schroedinger operators, which may be unbounded from below and include a magnetic vector potential. In particular, a common domain of essential self-adjointness for such a semigroup is specified. Moreover, each member of the semigroup is proven to be a maximal Carleman operator with a continuous integral kernel given by a Brownian-bridge expectation. The results are used to show that the spectral projections of the generating Schroedinger operator also act as Carleman operators with continuous integral kernels. Applications to Schroedinger operators with rather general random scalar potentials include a rigorous justification of an integral-kernel representation of their integrated density of states - a relation frequently used in the physics literature on disordered solids.Comment: 41 pages. Final version. Dedicated to Volker Enss on the occasion of his 60th birthda

Experimental and theoretical characterization of the Zn - Zn bond in [Zn2(η5-C5Me5)2]

The existence and characterization of a bond between the Zn atoms in the recently synthesized complex [Zn2(5-C5Me5)2], as well as between Zn and ligand C atoms is firmly based on neutron diffraction and low-temperature X-ray synchrotron diffraction experiments. The multipolar analysis of the experimental electron density and its topological analysis by means of the Atoms in Molecules (AIM) approach reveals details of the Zn - Zn bond, such as its open-shell intermediate character (the results are consistent with a typical metal-metal single bond), as well as many other topological properties of the compound. Experimental results are also compared with theoretical ab initio calculations of the DFT (density functional theory) and MP2 (Mller-Plesset perturbation theory) electron densities, giving a coherent view of the bonding in the complex. For instance, charges calculated from the AIM approach applied to the atomic basin of each Zn atom are, on average, +0.72 e from both the experimental and the theoretical electron density, showing a moderate charge transfer from the metal, confirmed by the calculated topological indexes.Ministerio de Educación y Ciencia MAT2006-0199

Haiti: coffee and mango production in a changing climate

Coffee and mango contribute significantly to Haiti’s agricultural gross domestic product and export revenues. Generating income valued at US$11 million in 2011, mango has become one of the country’s most important export commodities. In contrast, coffee exports steadily declined from$7 million to $1 million between 2000 and 2010, even though demand for high-quality Haitian coffee has actually increased on the global market. A recent study conducted by the International Center for Tropical Agriculture (CIAT) and Catholic Relief Services (CRS) revealed that future changes in temperature and rainfall patterns will have significant effects on the suitability of coffee and mango for production in Haiti. While mango will continue to be highly viable, coffee will become considerably less suitable for production at lower elevations. Changing climatic conditions could also lower quality and yields in current coffee-producing regions, such as Plaisance and Dondon in the North and Beaumont in the Southwest. To cope with the challenges that coffee and mango growers are likely to face, it will be important to promote the diversification of agricultural systems, introduce improved coffee varieties, offer financial incentives to adopt sustainable land use practices, build capacity among smallholders, and foster the sharing of expertise

Development of an Automatic Pipeline for Participation in the CELPP Challenge

The prediction of how a ligand binds to its target is an essential step for Structure-Based Drug Design (SBDD) methods. Molecular docking is a standard tool to predict the binding mode of a ligand to its macromolecular receptor and to quantify their mutual complementarity, with multiple applications in drug design. However, docking programs do not always find correct solutions, either because they are not sampled or due to inaccuracies in the scoring functions. Quantifying the docking performance in real scenarios is essential to understanding their limitations, managing expectations and guiding future developments. Here, we present a fully automated pipeline for pose prediction validated by participating in the Continuous Evaluation of Ligand Pose Prediction (CELPP) Challenge. Acknowledging the intrinsic limitations of the docking method, we devised a strategy to automatically mine and exploit pre-existing data, defining-whenever possible-empirical restraints to guide the docking process. We prove that the pipeline is able to generate predictions for most of the proposed targets as well as obtain poses with low RMSD values when compared to the crystal structure. All things considered, our pipeline highlights some major challenges in the automatic prediction of protein-ligand complexes, which will be addressed in future versions of the pipeline. Keywords: D3R; automated pipeline; binding mode prediction; docking; pocket detection

Evolutionary dynamics of rhomboid proteases in Streptomycetes

Background Proteolytic enzymes are ubiquitous and active in a myriad of biochemical pathways. One type, the rhomboids are intramembrane serine proteases that release their products extracellularly. These proteases are present in all forms of life and their function is not fully understood, although some evidence suggests they participate in cell signaling. Streptomycetes are prolific soil bacteria with diverse physiological and metabolic properties that respond to signals from other cells and from the environment. In the present study, we investigate the evolutionary dynamics of rhomboids in Streptomycetes, as this can shed light into the possible involvement of rhomboids in the complex lifestyles of these bacteria. Results Analysis of Streptomyces genomes revealed that they harbor up to five divergent putative rhomboid genes (arbitrarily labeled families A–E), two of which are orthologous to rhomboids previously described in Mycobacteria. Characterization of each of these rhomboid families reveals that each group is distinctive, and has its own evolutionary history. Two of the Streptomyces rhomboid families are highly conserved across all analyzed genomes suggesting they are essential. At least one family has been horizontally transferred, while others have been lost in several genomes. Additionally, the transcription of the four rhomboid genes identified in Streptomyces coelicolor, the model organism of this genus, was verified by reverse transcription. Conclusions Using phylogenetic and genomic analysis, this study demonstrates the existence of five distinct families of rhomboid genes in Streptomycetes. Families A and D are present in all nine species analyzed indicating a potentially important role for these genes. The four rhomboids present in S. coelicolor are transcribed suggesting they could participate in cellular metabolism. Future studies are needed to provide insight into the involvement of rhomboids in Streptomyces physiology. We are currently constructing knock out (KO) mutants for each of the rhomboid genes from S. coelicolor and will compare the phenotypes of the KOs to the wild type strain

Single molecule spectroscopy of polyfluorene chains reveals β-phase content and phase reversibility in organic solvents

Conjugated polymers are an important class of organic semiconductors that can be deposited from solution to make optoelectronic devices. Among them, poly(9,9′-dioctylfluorene) (PFO) has distinctive optical properties arising from its ability to adopt an ordered planar conformation (β phase) from a disordered glassy phase (α phase). The β phase has attractive optical properties, but the precise mechanism of its formation in solution remains unknown. Here, we have combined specifically tailored polymer synthesis and surface-passivation strategies to provide the first spectroscopic characterization of single PFO chains in solution at room temperature. By anchoring PFO molecules at one end on an anti-adherent surface, we show that isolated chains can adopt the β-phase conformation in a solvent-dependent manner. Furthermore, we find that individual PFO chains can reversibly switch multiple times between phases in response to solvent-exchange events. The methodology presented here for polymer synthesis and immobilization is widely applicable to investigate other luminescent polymers.PostprintPostprintPeer reviewe

Super-extended noncommutative Landau problem and conformal symmetry

A supersymmetric spin-1/2 particle in the noncommutative plane, subject to an arbitrary magnetic field, is considered, with particular attention paid to the homogeneous case. The system has three different phases, depending on the magnetic field. Due to supersymmetry, the boundary critical phase which separates the sub- and super-critical cases can be viewed as a reduction to the zero-energy eigensubspace. In the sub-critical phase the system is described by the superextension of exotic Newton-Hooke symmetry, combined with the conformal so(2,1) ~ su(1,1) symmetry; the latter is changed into so(3) ~ su(2) in the super-critical phase. In the critical phase the spin degrees of freedom are frozen and supersymmetry disappears.Comment: 12 pages, references added, published versio