Kaos en la Red 2.0

La página Web de Kaosenlared es un medio de comunicación libre y alternativo. Se quiere dar un paso adelante y profundizar en lo que se llama Web 2.0. La aplicación Web deberá permitir a usuarios registrarse, iniciar sesión, hacerse un perfil, consultar, editar y eliminar sus noticias y comentarios, hacerse su “Kaos” personalizando la página principal y tener un blog. Es un proyecto que va dirigido principalmente a más de 25.000 usuarios de IP’s diferentes que se conectan a la página Web para informarse de noticias de interés.

MSight: an image analysis software for liquid chromatography-mass spectrometry.

Images obtained from high-throughput mass spectrometry (MS) contain information that remains hidden when looking at a single spectrum at a time. Image processing of liquid chromatography-MS datasets can be extremely useful for quality control, experimental monitoring and knowledge extraction. The importance of imaging in differential analysis of proteomic experiments has already been established through two-dimensional gels and can now be foreseen with MS images. We present MSight, a new software designed to construct and manipulate MS images, as well as to facilitate their analysis and comparison.

The multipoint Morisita index for the analysis of spatial patterns

In many fields, the spatial clustering of sampled data points has many consequences. Therefore, several indices have been proposed to assess the level of clustering affecting datasets (e.g. the Morisita index, Ripley's Kfunction and Rényi's generalized entropy). The classical Morisita index measures how many times it is more likely to select two measurement points from the same quadrats (the data set is covered by a regular grid of changing size) than it would be in the case of a random distribution generated from a Poisson process. The multipoint version (k-Morisita) takes into account k points with k >= 2. The present research deals with a new development of the k-Morisita index for (1) monitoring network characterization and for (2) detection of patterns in monitored phenomena. From a theoretical perspective, a connection between the k-Morisita index and multifractality has also been found and highlighted on a mathematical multifractal set.

Stability analysis of the 2007 Chehalis lake landslide based on long-range terrestrial photogrammetry and airborne LIDAR data

On December 4th 2007, a 3-Mm3 landslide occurred along the northwestern shore of Chehalis Lake. The initiation zone is located at the intersection of the main valley slope and the northern sidewall of a prominent gully. The slope failure caused a displacement wave that ran up to 38 m on the opposite shore of the lake. The landslide is temporally associated with a rain-on-snow meteorological event which is thought to have triggered it. This paper describes the Chehalis Lake landslide and presents a comparison of discontinuity orientation datasets obtained using three techniques: field measurements, terrestrial photogrammetric 3D models and an airborne LiDAR digital elevation model to describe the orientation and characteristics of the five discontinuity sets present. The discontinuity orientation data are used to perform kinematic, surface wedge limit equilibrium and three-dimensional distinct element analyses. The kinematic and surface wedge analyses suggest that the location of the slope failure (intersection of the valley slope and a gully wall) has facilitated the development of the unstable rock mass which initiated as a planar sliding failure. Results from the three-dimensional distinct element analyses suggest that the presence, orientation and high persistence of a discontinuity set dipping obliquely to the slope were critical to the development of the landslide and led to a failure mechanism dominated by planar sliding. The three-dimensional distinct element modelling also suggests that the presence of a steeply dipping discontinuity set striking perpendicular to the slope and associated with a fault exerted a significant control on the volume and extent of the failed rock mass but not on the overall stability of the slope.

Big data and other challenges in the quest for orthologs.

Given the rapid increase of species with a sequenced genome, the need to identify orthologous genes between them has emerged as a central bioinformatics task. Many different methods exist for orthology detection, which makes it difficult to decide which one to choose for a particular application. Here, we review the latest developments and issues in the orthology field, and summarize the most recent results reported at the third 'Quest for Orthologs' meeting. We focus on community efforts such as the adoption of reference proteomes, standard file formats and benchmarking. Progress in these areas is good, and they are already beneficial to both orthology consumers and providers. However, a major current issue is that the massive increase in complete proteomes poses computational challenges to many of the ortholog database providers, as most orthology inference algorithms scale at least quadratically with the number of proteomes. The Quest for Orthologs consortium is an open community with a number of working groups that join efforts to enhance various aspects of orthology analysis, such as defining standard formats and datasets, documenting community resources and benchmarking. AVAILABILITY AND IMPLEMENTATION: All such materials are available at http://questfororthologs.org. CONTACT: erik.sonnhammer@scilifelab.se or c.dessimoz@ucl.ac.uk.

Can the trabecular bone score be considered as a major clinical risk factor of osteoporotic fractures? A meta-like analysis.

To have an added value over BMD, a CRF of osteoporotic fracture must be predictable of the fracture, independent of BMD, reversible and quantifiable. Many major recognized CRF exist. Out of these factors many of them are indirect factor of bone quality. TBS predicts fracture independently of BMD as demonstrated from previous studies. The aim of the study is to verify if TBS can be considered as a major CRF of osteoporotic fracture. Existing validated datasets of Caucasian women were analyzed. These datasets stem from different studies performed by the authors of this report or provided to our group. However, the level of evidence of these studies will vary. Thus, the different datasets were weighted differently according to their design. This meta-like analysis involves more than 32000 women (≥50years) with 2000 osteoporotic fractures from two prospective studies (OFELY&MANITOBA) and 7 cross-sectional studies. Weighted relative risk (RR) for TBS was expressed for each decrease of one standard deviation as well as per tertile difference (TBS=1.300 and 1.200) and compared with those obtained for the major CRF included in FRAX®. Overall TBS RR obtained (adjusted for age) was 1.79 [95%CI-1.37-2.37]. For all women combined, RR for fracture for the lowest compared with the middle TBS tertile was 1.55[1.46-1.68] and for the lowest compared with the highest TBS tertile was 2.8[2.70-3.00]. TBS is comparable to most of the major CRF and thus could be used as one of them. Further studies have to be conducted to confirm these first findings.

Banc electrònic d'objectes i recursos d'aprenentatge dels estudis de comunicació audiovisual

OdACAV és un banc electrònic d’objectes d’aprenentatge (OdA) que te com a finalitat principal servir als docents de les assignatures troncals dels Estudis de Comunicació Audiovisual (CAV) de la UB (obert també a altres universitats catalanes) implicats o que es vulguin implicar en la innovació docent i pretén facilitar i potenciar la documentació per a la investigació i la recerca a l’entorn del paper innovador dels OdA digitals; així com la patrimonialització dels mateixos. Què és i que no és un OdA de CAV? És tot allò que serveix en un procés d'ensinistrament, d'aprenentatge, de formació - que en els cas que ens ocupa, es tradueix en una col·lecció d'imatges fixes, en un hipertext, en una hipermèdia, un vídeo, etc.-, i la missió dels quals és suscitar l’interès i l'aprofitament en el transvasament dels continguts de les assignatures dels estudis actuals (de la Llicenciatura) i futurs (del Grau) de Comunicació Audiovisual. El projecte sorgeix com a necessitat orgànica de la mateixa naturalesa de l'ensenyament de Comunicació Audiovisual, on en el pla dels continguts els exemples, els referents, els models no són encara prou desenvolupats i costa molt disposar d'OdAs suficientment competents. Les fonts documentals del cinema, de la televisió i dels mitjans en general són la base sobre la que s’han bastit els OdA de la base de dades del web http://www.lmi.ub.es/repositori/ amb l’esperança que resultin adequats a la innovació en els Estudis de Comunicació Audiovisual. És, doncs, un repositori de condició cooperativa, dinàmic i flexible; amb esperit blog/wiki, els objectius del qual són: la creació d'un sistema de dipositació dels OdA; l'establiment d'un sistema de recuperació dels mateixos; la implantació de fluxos d'entrada i sortida; la consolidació d'un observatori d'investigació i de recerca sobre la innovació dels OdA en els entorns i els sistemes educatius actuals; l’articulació de possibles accions patrimonials al voltant de la creació i preservació d’aquests.

Quality assurance in the EORTC 22033-26033/CE5 phase III randomized trial for low grade glioma: the digital individual case review.

INTRODUCTION: The phase III EORTC 22033-26033/NCIC CE5 intergroup trial compares 50.4 Gy radiotherapy with up-front temozolomide in previously untreated low-grade glioma. We describe the digital EORTC individual case review (ICR) performed to evaluate protocol radiotherapy (RT) compliance. METHODS: Fifty-eight institutions were asked to submit 1-2 randomly selected cases. Digital ICR datasets were uploaded to the EORTC server and accessed by three central reviewers. Twenty-seven parameters were analysed including volume delineation, treatment planning, organ at risk (OAR) dosimetry and verification. Consensus reviews were collated and summary statistics calculated. RESULTS: Fifty-seven of seventy-two requested datasets from forty-eight institutions were technically usable. 31/57 received a major deviation for at least one section. Relocation accuracy was according to protocol in 45. Just over 30% had acceptable target volumes. OAR contours were missing in an average of 25% of cases. Up to one-third of those present were incorrectly drawn while dosimetry was largely protocol compliant. Beam energy was acceptable in 97% and 48 patients had per protocol beam arrangements. CONCLUSIONS: Digital RT plan submission and review within the EORTC 22033-26033 ICR provide a solid foundation for future quality assurance procedures. Strict evaluation resulted in overall grades of minor and major deviation for 37% and 32%, respectively.

Genome-wide association study of recurrent major depressive disorder in two European case-control cohorts.

Major depressive disorder (MDD) is a highly prevalent disorder with substantial heritability. Heritability has been shown to be substantial and higher in the variant of MDD characterized by recurrent episodes of depression. Genetic studies have thus far failed to identify clear and consistent evidence of genetic risk factors for MDD. We conducted a genome-wide association study (GWAS) in two independent datasets. The first GWAS was performed on 1022 recurrent MDD patients and 1000 controls genotyped on the Illumina 550 platform. The second was conducted on 492 recurrent MDD patients and 1052 controls selected from a population-based collection, genotyped on the Affymetrix 5.0 platform. Neither GWAS identified any SNP that achieved GWAS significance. We obtained imputed genotypes at the Illumina loci for the individuals genotyped on the Affymetrix platform, and performed a meta-analysis of the two GWASs for this common set of approximately half a million SNPs. The meta-analysis did not yield genome-wide significant results either. The results from our study suggest that SNPs with substantial odds ratio are unlikely to exist for MDD, at least in our datasets and among the relatively common SNPs genotyped or tagged by the half-million-loci arrays. Meta-analysis of larger datasets is warranted to identify SNPs with smaller effects or with rarer allele frequencies that contribute to the risk of MDD.

All-Ireland Health Data Inventory. Part 1: Metadata for key data sources, version 1.0

The All-Ireland Health Data Inventory. Part 1 is a catalogue of key sources of health data in the Republic and Northern Ireland. It includes relevant datasets from the major information reviews, conducted in the North and South, in the past few years. Information is essential for informed decision making and service provision. This inventory draws together information sources to facilitate such decision making. The inventory is intended as a resource for health professionals, researchers and the general public, providing the first phase of a ‘one-stop’ catalogue of health data. The datasets have been catalogued using an expanding numbering system which will allow for the inclusion of future resources. The Institute of Public Health in Ireland is in the process of expanding the Inventory to include further data sources.

Analisi espacial del canvi climàtic al continent europeu. Incerteses i exposicions principals

El canvi climàtic del segle XXI és una realitat, hi ha moltes evidències científiques que indiquen que l’escalfament del sistema climàtic és inequívoc. Malgrat això, també hi ha moltes incerteses respecte els impactes que pot comportar aquest canvi climàtic global. L’objectiu d’aquest projecte és estudiar la possible evolució futura de tres variables climàtiques, que són el rang de la temperatura diürna a prop de la superfície (DTR), la temperatura mitjana a prop de la superfície (MT) i la precipitació mensual (PL_mes) i valorar l’exposició que poden experimentar diferents cobertes del sòl i diferents regions biogeogràfiques del continent europeu davant d’aquests possibles patrons de canvi. Per això s’han utilitzat Models Climàtics Globals que fan projeccions de variables climàtiques que permeten preveure el possible clima futur. Mitjançant l’aplicatiu informàtic Tetyn s’han extret els paràmetres climàtics dels conjunts de dades del Tyndall Centre for Climate Change Research, del futur (TYN SC) i del passat (CRU TS). Les variables obtingudes s’han processat amb eines de sistemes d’informació geogràfica (SIG) per obtenir els patrons de canvi de les variables a cada coberta del sòl. Els resultats obtinguts mostren que hi ha una gran variabilitat, que augmenta amb el temps, entre els diferents models climàtics i escenaris considerats, que posa de manifest la incertesa associada a la modelització climàtica, a la generació d’escenaris d’emissions i a la naturalesa dinàmica i no determinista del sistema climàtic. Però en general, mostren que les glaceres seran una de les cobertes més exposades al canvi climàtic, i la mediterrània, una de les regions més vulnerables

Evaluating the ability of habitat suitability models to predict species presences.

Models predicting species spatial distribution are increasingly applied to wildlife management issues, emphasising the need for reliable methods to evaluate the accuracy of their predictions. As many available datasets (e.g. museums, herbariums, atlas) do not provide reliable information about species absences, several presence-only based analyses have been developed. However, methods to evaluate the accuracy of their predictions are few and have never been validated. The aim of this paper is to compare existing and new presenceonly evaluators to usual presence/absence measures. We use a reliable, diverse, presence/absence dataset of 114 plant species to test how common presence/absence indices (Kappa, MaxKappa, AUC, adjusted D-2) compare to presenceonly measures (AVI, CVI, Boyce index) for evaluating generalised linear models (GLM). Moreover we propose a new, threshold-independent evaluator, which we call "continuous Boyce index". All indices were implemented in the B10MAPPER software. We show that the presence-only evaluators are fairly correlated (p > 0.7) to the presence/absence ones. The Boyce indices are closer to AUC than to MaxKappa and are fairly insensitive to species prevalence. In addition, the Boyce indices provide predicted-toexpected ratio curves that offer further insights into the model quality: robustness, habitat suitability resolution and deviation from randomness. This information helps reclassifying predicted maps into meaningful habitat suitability classes. The continuous Boyce index is thus both a complement to usual evaluation of presence/absence models and a reliable measure of presence-only based predictions.

Hierarchical conditional random fields for parts based models matching

A parts based model is a parametrization of an object class using a collection of landmarks following the object structure. The matching of parts based models is one of the problems where pairwise Conditional Random Fields have been successfully applied. The main reason of their effectiveness is tractable inference and learning due to the simplicity of involved graphs, usually trees. However, these models do not consider possible patterns of statistics among sets of landmarks, and thus they sufffer from using too myopic information. To overcome this limitation, we propoese a novel structure based on a hierarchical Conditional Random Fields, which we explain in the first part of this memory. We build a hierarchy of combinations of landmarks, where matching is performed taking into account the whole hierarchy. To preserve tractable inference we effectively sample the label set. We test our method on facial feature selection and human pose estimation on two challenging datasets: Buffy and MultiPIE. In the second part of this memory, we present a novel approach to multiple kernel combination that relies on stacked classification. This method can be used to evaluate the landmarks of the parts-based model approach. Our method is based on combining responses of a set of independent classifiers for each individual kernel. Unlike earlier approaches that linearly combine kernel responses, our approach uses them as inputs to another set of classifiers. We will show that we outperform state-of-the-art methods on most of the standard benchmark datasets.

Perfusion ct based thrombolysis in acute ischaemic stroke

Background Despite use in clinical practice and trials of thrombolysis, a non-contrast CT is not sensitive for identifying penumbral tissue in acute stroke. This study evaluated how it compares with physiological imaging using CT perfusion.Methods 40 imaging datasets with non-contrast CT (NCCT) and perfusion CT (CTP) were retrospectively identified. 2 sets of observers (n¼6) and a neuroradiologist made a blind evaluation of the images. Inter-observer agreement was calculated for identifying ischaemic change on NCCT, and abnormalities on cerebral blood flow, time to peak and cerebral blood volume maps. A prospective cohort of 73 patients with anterior circulation cortical strokes were thrombolysed based on qualitative assessment of penumbral tissue on CTP within 3 h of stroke onset. Functional outcome was assessed at 3 months.Results Inter-rater agreement was moderate (k¼0.54) for early ischaemic change on NCCT. Perfusion maps improved this to substantial for deficit in cerebral blood volume (k¼0.67) and almost perfect for time to peak and cerebral blood flow (both k¼0.87). In the prospective arm, 58.9% of patients with cortical strokes were thrombolysed. There was no significant difference in attainment of complete recovery (p¼0.184) between the thrombolysed and nonthrombolysed group.Conclusions We demonstrate how perfusion CT aids clinical decision- making in acute stroke. Good functional outcomes from thrombolysis can be safely achieved using this physiologically informed approach.