Daniel Pérez

Risk factors of treatment failure in community acquired pneumonia: implications for disease outcome

Background: An inadequate response to initial empirical treatment of community acquired pneumonia (CAP) represents a challenge for clinicians and requires early identification and intervention. A study was undertaken to quantify the incidence of failure of empirical treatment in CAP, to identify risk factors for treatment failure, and to determine the implications of treatment failure on the outcome. Methods: A prospective multicentre cohort study was performed in 1424 hospitalised patients from 15 hospitals. Early treatment failure (<72 hours), late treatment failure, and in-hospital mortality were recorded. Results: Treatment failure occurred in 215 patients (15.1%): 134 early failure (62.3%) and 81 late failure (37.7%). The causes were infectious in 86 patients (40%), non-infectious in 34 (15.8%), and undetermined in 95. The independent risk factors associated with treatment failure in a stepwise logistic regression analysis were liver disease, pneumonia risk class, leucopenia, multilobar CAP, pleural effusion, and radiological signs of cavitation. Independent factors associated with a lower risk of treatment failure were influenza vaccination, initial treatment with fluoroquinolones, and chronic obstructive pulmonary disease (COPD). Mortality was significantly higher in patients with treatment failure (25% v 2%). Failure of empirical treatment increased the mortality of CAP 11-fold after adjustment for risk class. Conclusions: Although these findings need to be confirmed by randomised studies, they suggest possible interventions to decrease mortality due to CAP.

Transcriptome sequencing for SNP discovery across Cucumis melo

BackgroundMelon (Cucumis melo L.) is a highly diverse species that is cultivated worldwide. Recent advances in massively parallel sequencing have begun to allow the study of nucleotide diversity in this species. The Sanger method combined with medium-throughput 454 technology were used in a previous study to analyze the genetic diversity of germplasm representing 3 botanical varieties, yielding a collection of about 40,000 SNPs distributed in 14,000 unigenes. However, the usefulness of this resource is limited as the sequenced genotypes do not represent the whole diversity of the species, which is divided into two subspecies with many botanical varieties variable in plant, flowering, and fruit traits, as well as in stress response. As a first step to extensively document levels and patterns of nucleotide variability across the species, we used the high-throughput SOLiD™ system to resequence the transcriptomes of a set of 67 genotypes that had previously been selected from a core collection representing the extant variation of the entire species.ResultsThe deep transcriptome resequencing of all of the genotypes, grouped into 8 pools (wild African agrestis, Asian agrestis and acidulus, exotic Far Eastern conomon, Indian momordica and Asian dudaim and flexuosus, commercial cantalupensis, subsp. melo Asian and European landraces, Spanish inodorus landraces, and Piel de Sapo breeding lines) yielded about 300 M reads. Short reads were mapped to the recently generated draft genome assembly of the DHL line Piel de Sapo (inodorus) x Songwhan Charmi (conomon) and to a new version of melon transcriptome. Regions with at least 6X coverage were used in SNV calling, generating a melon collection with 303,883 variants. These SNVs were dispersed across the entire C. melo genome, and distributed in 15,064 annotated genes. The number and variability of in silico SNVs differed considerably between pools. Our finding of higher genomic diversity in wild and exotic agrestis melons from India and Africa as compared to commercial cultivars, cultigens and landraces from Eastern Europe, Western Asia and the Mediterranean basin is consistent with the evolutionary history proposed for the species. Group-specific SNVs that will be useful in introgression programs were also detected. In a sample of 143 selected putative SNPs, we verified 93% of the polymorphisms in a panel of 78 genotypes.ConclusionsThis study provides the first comprehensive resequencing data for wild, exotic, and cultivated (landraces and commercial) melon transcriptomes, yielding the largest melon SNP collection available to date and representing a notable sample of the species diversity. This data provides a valuable resource for creating a catalog of allelic variants of melon genes and it will aid in future in-depth studies of population genetics, marker-assisted breeding, and gene identification aimed at developing improved varieties.

A high-brightness source of polarization-entangled photons optimized for applications in free space.

We present a simple but highly efficient source of polarization entangled photons based on SPDC in bulk PPKTP. Utilizing the highest available nonlinear coefficient in a type 0 collinear configuration, as well as an optimized geometry of the setup, we expect to exceed the brightness achieved in current schemes by at least an order of magnitude.

The GERMANA Database

A new handwritten text database, GERMANA, is presented to facilitate empirical comparison of different approaches to text line extraction and off-line handwriting recognition. GERMANA is the result of digitising and annotating a 764-page Spanish manuscript from 1891, in which most pages only contain nearly calligraphed text written on ruled sheets of well-separated lines. To our knowledge, it is the first publicly available database for handwriting research, mostly written in Spanish and comparable in size to standard databases. Due to its sequential book structure, it is also well-suited for realistic assessment of interactive handwriting recognition systems. To provide baseline results for reference in future studies, empirical results are also reported, using standard techniques and tools for preprocessing, feature extraction, HMM-based image modelling, and language modelling.

Software-defined reconfigurable microwave photonics processor

We propose, for the first time to our knowledge, a software-defined reconfigurable microwave photonics signal processor architecture that can be integrated on a chip and is capable of performing all the main functionalities by suitable programming of its control signals. The basic configuration is presented and a thorough end-to-end design model derived that accounts for the performance of the overall processor taking into consideration the impact and interdependencies of both its photonic and RF parts. We demonstrate the model versatility by applying it to several relevant application examples.

Multipurpose silicon photonics signal processor core

Integrated photonics changes the scaling laws of information and communication systems offering architectural choices that combine photonics with electronics to optimize performance, power, footprint, and cost. Application-specific photonic integrated circuits, where particular circuits/chips are designed to optimally perform particular functionalities, require a considerable number of design and fabrication iterations leading to long development times. A different approach inspired by electronic Field Programmable Gate Arrays is the programmable photonic processor, where a common hardware implemented by a two-dimensional photonic waveguide mesh realizes different functionalities through programming. Here, we report the demonstration of such reconfigurable waveguide mesh in silicon. We demonstrate over 20 different functionalities with a simple seven hexagonal cell structure, which can be applied to different fields including communications, chemical and biomedical sensing, signal processing, multiprocessor networks, and quantum information systems. Our work is an important step toward this paradigm.Integrated optical circuits today are typically designed for a few special functionalities and require complex design and development procedures. Here, the authors demonstrate a reconfigurable but simple silicon waveguide mesh with different functionalities.

Reconfigurable lattice mesh designs for programmable photonic processors.

We propose and analyse two novel mesh design geometries, the hexagonal and the triangular lattice, for the implementation of tunable optical cores in programmable photonic processors and universal couplers. They are compared to a previously proposed square mesh topology in terms of a series of figures of merit that account for metrics that are relevant to on-chip integration of the mesh finding that hexagonal mesh is the most suitable option. We then exemplify the use of this mesh topology in the implementation of a universal coupler device.

Adaptation from partially supervised handwritten text transcriptions

An effective approach to transcribe handwritten text documents is to follow an interactive-predictive paradigm in which both, the system is guided by the user, and the user is assisted by the system to complete the transcription task as efficiently as possible. This approach has been recently implemented in a system prototype called GIDOC, in which standard speech technology is adapted to handwritten text (line) images: HMM-based text image modelling, n-gram language modelling, and also confidence measures on recognized words. Confidence measures are used to assist the user in locating possible transcription errors, and thus validate system output after only supervising those (few) words for which the system is not highly confident. Here, we study the effect of using these partially supervised transcriptions on the adaptation of image and language models to the task.

Confidence Measures for Error Correction in Interactive Transcription Handwritten Text

An effective approach to transcribe old text documents is to follow an interactive-predictive paradigm in which both, the system is guided by the human supervisor, and the supervisor is assisted by the system to complete the transcription task as efficiently as possible. In this paper, we focus on a particular system prototype called GIDOC, which can be seen as a first attempt to provide user-friendly, integrated support for interactive-predictive page layout analysis, text line detection and handwritten text transcription. More specifically, we focus on the handwriting recognition part of GIDOC, for which we propose the use of confidence measures to guide the human supervisor in locating possible system errors and deciding how to proceed. Empirical results are reported on two datasets showing that a word error rate not larger than a 10% can be achieved by only checking the 32% of words that are recognised with less confidence.

Figures of merit for self-beating filtered microwave photonic systems.

We present a model to compute the figures of merit of self-beating Microwave Photonic systems, a novel class of systems that work on a self-homodyne fashion by sharing the same laser source for information bearing and local oscillator tasks. General and simplified expressions are given and, as an example, we have considered their application to the design of a tunable RF MWP BS/UE front end for band selection, based on a Chebyshev Type-II optical filter. The applicability and usefulness of the model are also discussed.