Political economy and the ghosts of the past: revisiting the Spanish and Romanian transitions to democracy

Juan Linz and Alfred Stepan’s opus on democratic transition and consolidation put Spain and Romania at the extreme ends of these processes and paid little attention to the domestic and external economic constraints on the transition process. This paper interrogates these claims. It shows that in retrospect Spain looks a lot less exemplary and Romania a lot less hopeless than this iconic contribution suggested at the time. Moreover, while external economic shocks and local attempts to buffer them through social compensation shaped both transitions, Romanian governments faced balance of payments crises and international policy conditionality constraints, while their Spanish counterparts did not. This difference invites a greater appreciation of the role of political economy analyses when comparing the policy options of political elites ruling in times of democratic transition and consolidation

The frontier between cell and organelle: genome analysis of Candidatus Carsonella ruddii

<p>Abstract</p> <p>Background</p> <p>Bacterial symbioses are widespread among insects. The early establishment of such symbiotic associations has probably been one of the key factors for the evolutionary success of insects, since it may have allowed access to novel ecological niches and to new imbalanced food resources, such as plant sap or blood. Several genomes of bacterial endosymbionts of different insect species have been recently sequenced, and their biology has been extensively studied. Recently, the complete genome sequence of <it>Candidatus </it>Carsonella ruddii, considered the primary endosymbiont of the psyllid <it>Pachpsylla venusta</it>, has been published. This genome consists of a circular chromosome of 159,662 bp and has been proposed as the smallest bacterial endosymbiont genome known to date.</p> <p>Results</p> <p>The detailed analysis of the gene content of <it>C. ruddii </it>shows that the extensive degradation of the genome is not compatible with its consideration as a mutualistic endosymbiont and, even more, as a living organism. The ability to perform most essential functions for a cell to be considered alive is heavily impaired by the lack of genes involved in DNA replication, transcription and translation. Furthermore, the shortening of genes causes, in some cases, the loss of essential domains and functional residues needed to fulfill such vital functions. In addition, at least half of the pathways towards the biosynthesis of essential amino acids, its proposed symbiotic function, are completely or partially lost.</p> <p>Conclusion</p> <p>We propose that this strain of <it>C. ruddii </it>can be viewed as a further step towards the degeneration of the former primary endosymbiont and its transformation in a subcellular new entity between living cells and organelles. Although the transition of genes from <it>C. ruddii </it>to the host nucleus has been proposed, the amount of genes that should have been transferred to the germinal line of the insect would be so big that it would be more plausible to consider the implication of the mitochondrial machinery encoded in the insect nucleus. Furthermore, since most genes for the biosynthesis of essential amino acids have also been lost, it is likely that the host depends on another yet unidentified symbiont to complement its deficient diet.</p

Neuromelanin-MRI using 2D GRE and deep learning: considerations for improving the visualization of substantia nigra and locus coeruleus

An optimized clinically feasible neuromelanin-MRI imaging protocol for visualising the SN and LC simultaneously using deep learning reconstruction is presented. We optimize flip-angle for optimal combined SN and LC depiction. We also experimented with combinations of anisotropic and isotropic in-plane resolution, partial vs full echoes and the number of averages. Phantom and in-vivo experiments on three healthy volunteers illustrate that high-resolution imaging combined with deep-learning denoising shows good depiction of the SN and LC with a clinically feasible sequence of around 7 minutes.Comment: An article based on ECR and ISMRM abstracts, with more text & figure

Metagenomics reveals our incomplete knowledge of global diversity

Financial support was provided by projects BFU2006-06003 from the Spanish Ministry of Education and Science (MEC) and GV/2007/050 from the Generalitat Valenciana, Spain. J.T. is a recipient of a contract in the FIS Program from ISCIII, Spanish Ministry of Health.Pignatelli, M.; Aparicio Pla, G.; Blanquer Espert, I.; Hernández García, V.; Moya, A.; Tamames, J. (2008). Metagenomics reveals our incomplete knowledge of global diversity. Bioinformatics. 24(18):2124-2125. https://doi.org/10.1093/bioinformatics/btn355S212421252418Koski, L. B., & Golding, G. B. (2001). The Closest BLAST Hit Is Often Not the Nearest Neighbor. Journal of Molecular Evolution, 52(6), 540-542. doi:10.1007/s002390010184Krause, L., Diaz, N. N., Goesmann, A., Kelley, S., Nattkemper, T. W., Rohwer, F., … Stoye, J. (2008). Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Research, 36(7), 2230-2239. doi:10.1093/nar/gkn038Mavromatis, K., Ivanova, N., Barry, K., Shapiro, H., Goltsman, E., McHardy, A. C., … Kyrpides, N. C. (2007). Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nature Methods, 4(6), 495-500. doi:10.1038/nmeth1043Tamames, J., & Moya, A. (2008). Estimating the extent of horizontal gene transfer in metagenomic sequences. BMC Genomics, 9(1), 136. doi:10.1186/1471-2164-9-136Tringe, S. G. (2005). Comparative Metagenomics of Microbial Communities. Science, 308(5721), 554-557. doi:10.1126/science.1107851Tringe, S. G., Zhang, T., Liu, X., Yu, Y., Lee, W. H., Yap, J., … Ruan, Y. (2008). The Airborne Metagenome in an Indoor Urban Environment. PLoS ONE, 3(4), e1862. doi:10.1371/journal.pone.0001862COLE, F. N. (1900). AMERICAN MATHEMATICAL SOCIETY. Science, 11(263), 66-67. doi:10.1126/science.11.263.6

Bismuth coordination networks containing deferiprone: synthesis, characterisation, stability and antibacterial activity

A series of bismuth–dicarboxylate–deferiprone coordination networks have been prepared and structurally characterised. The new compounds have been demonstrated to release the iron overload drug deferiprone on treatment with PBS and have also been shown to have antibacterial activity against H. pylori

Accuracy and repeatability of joint sparsity multi-component estimation in MR Fingerprinting

MR fingerprinting (MRF) is a promising method for quantitative characterization of tissues. Often, voxel-wise measurements are made, assuming a single tissue-type per voxel. Alternatively, the Sparsity Promoting Iterative Joint Non-negative least squares Multi-Component MRF method (SPIJN-MRF) facilitates tissue parameter estima-tion for identified components as well as partial volume segmentations. The aim of this paper was to evaluate the accuracy and repeatability of the SPIJN-MRF parameter estimations and partial volume segmentations. This was done (1) through numerical simulations based on the BrainWeb phantoms and (2) using in vivo acquired MRF data from 5 subjects that were scanned on the same week-day for 8 consecutive weeks. The partial volume segmen-tations of the SPIJN-MRF method were compared to those obtained by two conventional methods: SPM12 and FSL. SPIJN-MRF showed higher accuracy in simulations in comparison to FSL-and SPM12-based segmentations: Fuzzy Tanimoto Coefficients (FTC) comparing these segmentations and Brainweb references were higher than 0.95 for SPIJN-MRF in all the tissues and between 0.6 and 0.7 for SPM12 and FSL in white and gray matter and between 0.5 and 0.6 in CSF. For the in vivo MRF data, the estimated relaxation times were in line with literature and minimal variation was observed. Furthermore, the coefficient of variation (CoV) for estimated tissue volumes with SPIJN-MRF were 10.5% for the myelin water, 6.0% for the white matter, 5.6% for the gray matter, 4.6% for the CSF and 1.1% for the total brain volume. CoVs for CSF and total brain volume measured on the scanned data for SPIJN-MRF were in line with those obtained with SPM12 and FSL. The CoVs for white and gray mat-ter volumes were distinctively higher for SPIJN-MRF than those measured with SPM12 and FSL. In conclusion, the use of SPIJN-MRF provides accurate and precise tissue relaxation parameter estimations taking into account intrinsic partial volume effects. It facilitates obtaining tissue fraction maps of prevalent tissues including myelin water which can be relevant for evaluating diseases affecting the white matter.Radiolog

The GNAT library for local and remote gene mention normalization

Summary: Identifying mentions of named entities, such as genes or diseases, and normalizing them to database identifiers have become an important step in many text and data mining pipelines. Despite this need, very few entity normalization systems are publicly available as source code or web services for biomedical text mining. Here we present the Gnat Java library for text retrieval, named entity recognition, and normalization of gene and protein mentions in biomedical text. The library can be used as a component to be integrated with other text-mining systems, as a framework to add user-specific extensions, and as an efficient stand-alone application for the identification of gene and protein names for data analysis. On the BioCreative III test data, the current version of Gnat achieves a Tap-20 score of 0.1987

Fast pseudo-CT synthesis from MRI T1-weighted images using a patch-based approach

MRI-based bone segmentation is a challenging task because bone tissue and air both present low signal intensity on MR images, making it difficult to accurately delimit the bone boundaries. However, estimating bone from MRI images may allow decreasing patient ionization by removing the need of patient-specific CT acquisition in several applications. In this work, we propose a fast GPU-based pseudo-CT generation from a patient-specific MRI T1-weighted image using a group-wise patch-based approach and a limited MRI and CT atlas dictionary. For every voxel in the input MR image, we compute the similarity of the patch containing that voxel with the patches of all MR images in the database, which lie in a certain anatomical neighborhood. The pseudo-CT is obtained as a local weighted linear combination of the CT values of the corresponding patches. The algorithm was implemented in a GPU. The use of patch-based techniques allows a fast and accurate estimation of the pseudo-CT from MR T1-weighted images, with a similar accuracy as the patient-specific CT. The experimental normalized cross correlation reaches 0.9324±0.0048 for an atlas with 10 datasets. The high NCC values indicate how our method can accurately approximate the patient-specific CT. The GPU implementation led to a substantial decrease in computational time making the approach suitable for real applications

EnvMine: A text-mining system for the automatic extraction of contextual information

<p>Abstract</p> <p>Background</p> <p>For ecological studies, it is crucial to count on adequate descriptions of the environments and samples being studied. Such a description must be done in terms of their physicochemical characteristics, allowing a direct comparison between different environments that would be difficult to do otherwise. Also the characterization must include the precise geographical location, to make possible the study of geographical distributions and biogeographical patterns. Currently, there is no schema for annotating these environmental features, and these data have to be extracted from textual sources (published articles). So far, this had to be performed by manual inspection of the corresponding documents. To facilitate this task, we have developed EnvMine, a set of text-mining tools devoted to retrieve contextual information (physicochemical variables and geographical locations) from textual sources of any kind.</p> <p>Results</p> <p>EnvMine is capable of retrieving the physicochemical variables cited in the text, by means of the accurate identification of their associated units of measurement. In this task, the system achieves a recall (percentage of items retrieved) of 92% with less than 1% error. Also a Bayesian classifier was tested for distinguishing parts of the text describing environmental characteristics from others dealing with, for instance, experimental settings.</p> <p>Regarding the identification of geographical locations, the system takes advantage of existing databases such as GeoNames to achieve 86% recall with 92% precision. The identification of a location includes also the determination of its exact coordinates (latitude and longitude), thus allowing the calculation of distance between the individual locations.</p> <p>Conclusion</p> <p>EnvMine is a very efficient method for extracting contextual information from different text sources, like published articles or web pages. This tool can help in determining the precise location and physicochemical variables of sampling sites, thus facilitating the performance of ecological analyses. EnvMine can also help in the development of standards for the annotation of environmental features.</p