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Data Availability Statement: All relevant data are available from the Zenodo database, under the DOI: http://dx.doi.org/10.5281/zenodo.15685. ; Respiratory gating helps to overcome the problem of breathing motion in cardiothoracic small-animal imaging by acquiring multiple images for each projection angle and then assigning projections to different phases. When this approach is used with a dose similar to that of a static acquisition, a low number of noisy projections are available for the reconstruction of each respiratory phase, thus leading to streak artifacts in the reconstructed images. This problem can be alleviated using a prior image constrained compressed sensing (PICCS) algorithm, which enables accurate reconstruction of highly undersampled data when a prior image is available. We compared variants of the PICCS algorithm with different transforms in the prior penalty function: gradient, unitary, and wavelet transform. In all cases the problem was solved using the Split Bregman approach, which is efficient for convex constrained optimization. The algorithms were evaluated using simulations generated from data previously acquired on a micro-CT scanner following a high-dose protocol (four times the dose of a standard static protocol). The resulting data were used to simulate scenarios with different dose levels and numbers of projections. All compressed sensing methods performed very similarly in terms of noise, spatiotemporal resolution, and streak reduction, and filtered back-projection was greatly improved. Nevertheless, the wavelet domain was found to be less prone to patchy cartoon-like artifacts than the commonly used gradient domain. ; This work was partially funded by the RICRETIC network (RD12/0042/0057) from the Ministerio de Economía y Competitividad (www.mineco.gob.es/) and projects TEC2010-21619-C04-01 and PI11/00616 from Ministerio de Ciencia e Innovación (www.micinn.es/). The research leading to these results was supported by funding from the Innovative Medicines Initiative (www.imi.europa.eu) Joint Undertaking under grant agreement n°115337, the resources of which comprise financial contributions from the European Union's Seventh Framework Programme (FP7/2007-2013) and EFPIA companies ("in kind contribution"). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

In the past two decades, 7 coronaviruses have infected the human population, with two major outbreaks caused by SARS-CoV and MERS-CoV in the year 2002 and 2012, respectively. Currently, the entire world is facing a pandemic of another coronavirus, SARS-CoV-2, with a high fatality rate. The spike glycoprotein of SARS-CoV-2 mediates entry of virus into the host cell and is one of the most important antigenic determinants, making it a potential candidate for a vaccine. In this study, we have computationally designed a multi-epitope vaccine using spike glycoprotein of SARS-CoV-2. The overall quality of the candidate vaccine was validated in silico and Molecular Dynamics Simulation confirmed the stability of the designed vaccine. Docking studies revealed stable interactions of the vaccine with Toll-Like Receptors and MHC Receptors. The in silico cloning and codon optimization supported the proficient expression of the designed vaccine in E. coli expression system. The efficiency of the candidate vaccine to trigger an effective immune response was assessed by an in silico immune simulation. The computational analyses suggest that the designed multi-epitope vaccine is structurally stable which can induce specific immune responses and thus, can be a potential vaccine candidate against SARS-CoV-2. ; The authors thank Dr. Joseph V.G., Chancellor Garden City University for his constant support to carry out this research work. FC acknowledges partial support from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No. 853989 (Project ERA4TB). This Joint Undertaking receives support from the European Union's Horizon 2020 research and innovation program and EFPIA and Global Alliance for TBDrug Development non profit organization Bill & D.M.Melinda Gates Foundation and University of Dundee. D.M.M was supported by a grant from NIH, R35 GM131731.

Hollow organs such as the lungs pose a considerable challenge for post-mortem imaging in preclinical research owing to their extremely low contrast and high structural complexity. The aim of our study was to enhance the contrast of tuberculosis lesions for their stratification by 3D x-ray&-based virtual slicing. Organ samples were taken from five control and five tuberculosis-infected mice. Micro-Computed Tomography (CT) scans of the subjects were acquired in vivo (without contrast agent) and post-mortem (with contrast agent). The proposed contrast-enhancing technique consists of x-ray contrast agent uptake (silver nitrate and iodine) by immersion. To create the histology ground-truth, the CT scan of the paraffin block guided the sectioning towards specific planes of interest. The digitalized histological slides reveal the presence, extent, and appearance of the contrast agents in lung structures and organized aggregates of immune cells. These findings correlate with the contrast-enhanced micro-CT slice. The abnormal densities in the lungs due to tuberculosis disease are concentrated in the right tail of the lung intensity histograms. The increase in the width of the right tail (~376%) indicates a contrast enhancement of the details of the abnormal densities. Postmortem contrast agents enhance the x-ray attenuation in tuberculosis lesions to allow 3D visualization by polychromatic x-ray CT, providing an advantageous tool for virtual slicing of whole lungs. The proposed contrast-enhancing technique combined with computational methods and the diverse micro-CT modalities will open the doors to the stratification of lesion types associated with infectious diseases. ; The research leading to these results received funding from the Innovative Medicines Initiative (www.imi.europa.eu) Joint Undertaking under grant agreement no. 115337, whose resources comprise funding from the European Union Seventh Framework Programme (FP7/2007–2013) and EFPIA companies in kind contribution. This work was partially funded by projects RTC-2015-3772-1, TEC2015-73064-EXP and TEC2016-78052-R from the Spanish Ministry of Economy, TOPUS S2013/MIT-3024 project from the regional government of Madrid and by the Department of Health, UK. This study (was supported by the Instituto de Salud Carlos III (Plan Estatal de I + D + i 2013–2016) and co-financed by the European Social Fund (ESF) "ESF investing in your future". The authors thank Dr.Guembe from CIMA-Universidad de Navarra for preparing and staining the tissue sections, and to Dr. Guerrero-Aspizua and Prof. Conti of the Department of Bioengineering, Universidad Carlos III de Madrid for the pathology evaluation.

Proceeding of: 2010 IEEE Nuclear Science Symposium, Medical Imaging Conference and 17th Room Temperature Semiconductor Detector Workshop (IEEE), Knoxville, Tennessee, USA, October 30 - November 6, 2010 ; Positron range depends on the materials in which positron propagates and on positron emitter isotope. As positron range limits the spatial resolution of PET images, good quantitative estimates of it should be included in any realistic simulation of PET acquisitions. In this work we compare positron range estimates obtained with PeneloPET to previous available simulations and experimental data. PeneloPET was used to simulate the positron range of 18F, 11C, 13N, 15O, 68Ga and 82Rb in the following tissues: cortical bone, soft bone, skin, muscle, brain, water, adipose tissue and lung. The 3D and 1D annihilation Point Spread Functions (aPSF) were calculated for each isotope-material combination. We have studied with more detail the 3D aPSF (radial distributions) and the cumulative fraction of annihilation events. These aPSF distributions were also studied for non-uniform media. Results obtained were consistent with other results previously reported in the literature as well as with experimentally measured data. ; This work has been supported by MEC (FPA2007-62216), UCM (Grupos UCM, 910059), CPAN (Consolider- Ingenio 2010) CSPD-2007-00042, European Regional Development and ENTEPRASE grant, PSE-300000-2009-5, and the CENIT program project AMIT, Ministerio de Ciencia e Innovación, Spanish Government. Part of the calculations of this work were performed in the "Clúster de Cálculo de Alta Capacidad para Técnicas Físicas" funded in part by UCM and in part by UE under FEDER programme". ; Publicado

Proceeding of: 2010 IEEE Nuclear Science Symposium, Medical Imaging Conference, Knoxville, Tennessee, USA, October 30 - November 6, 2010 ; The scatter fraction (SF) in PET data represents the fraction of coincidence events in which at least one of the two emitted photons have been scattered before being detected. It is usually estimated as the ratio of scattered events to total number of coincidences, when the number of random counts is negligible (less than 1% of true rates). SF provides a measurement of the relative sensitivity of the scanner to scattered radiation. It depends on object size, density and location inside the field of view, as well as on detector size, type of detector crystal and energy window. The performance evaluation guideline for smallanimal PET NEMA (National Electrical Manufacturers Association) NU4-2008 proposes the estimation of the SF for three test phantoms made in proportion to the most widely used small animals in the laboratory: mouse, rat and monkey. The method estimates the different coincidence types in sinogram profiles from an off-centered line source inserted in these phantoms. We benchmark the procedure proposed by NEMA to estimate SF with 18F and also with 68Ga, a radionuclide with lager positron range. Real data acquired with the ARGUS smallanimal PET scanner (SEDECAL, Madrid, Spain) as well as simulations of the same scanner with peneloPET are used. The results show that, though SF should be practically the same with both 18F and 68Ga isotopes (and indeed our simulations indicate this) NEMA SF estimations with 68Ga acquisitions are higher. This is due to the fact that 68Ga positron range affects on the width of the line source profiles. Suggestions to modify the protocol to obtain similar SF estimations when using isotopes with larger positron range than 18F are made. ; This work has been supported by MEC (FPA2007-62216), UCM (Grupos UCM, 910059), CPAN (Consolider-Ingenio 2010) CSPD-2007-00042, European Regional Funds. AMIT Project funded by CDTI (CENIT Programme), ARTEMIS S2009/DPI-1802, European Regional Development and ENTEPRASE grant, PSE-300000-2009-5, Ministerio de Ciencia e Innovación. Spanish Government. ; Publicado

We describe a PET detector module that provides three levels of depth-of-interaction (DOI) information. The detector is a 9 x 9 array of 2 mm x 2 mm x 12 mm deep phoswich crystal elements, each consisting of 4 mm long LSO (entrance layer), GSO (middle layer) and BGO (exit layer) crystals joined optically together end-to-end. The BGO exit layer is directly coupled to a miniature position-sensitive photomultiplier tube (PSPMT). Delayed charge integration, a method that exploits differences in the light decay times of these scintillators, is used to determine the layer-of-interaction. DO1 accuracy, measured by scanning a slit source of 5 1 1 keV radiation along the length of the module was 86% for the LSO layer, 80% for the GSO layer and 84% for the BGO layer. Energy resolution at 511 keV was 19% for LSO, 21% for GSO and 40% for BGO. Apparent gain differed between layers in the ratios 2.7: 1.9: 1 .O (LS0:GSO:BGO). Crystal separation was good between crystals in the LSO layer, acceptable between crystals in the GSO layer and poor between crystals in the BGO layer due, primarily, to the pronounced spatial non-linearity of the PSPMT. The delayed charge integration method, however, does appear suitable for obtaining multi-level depth information when DO1 effects are particularly significant, e.g. in very small ring diameter PET scanners for small animal imaging. ; Was supported, in part, by a grant from CICYT (Spanish Government). S. S. was supported by a grant from the National Research Council. ; Publicado

Tesis doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Medicina, Departamento de Bioquímica. Fecha de lectura: 13-12-2018 ; Dendritic cells (DCs) are the most specialized antigen presenting cells (APCs), being a key link between innate and acquired immunity. A previous study in our group identified a cell subset that expresses CD8α and major histocompatibility complex II (MHC II) on the cell membrane in rainbow trout skin (Oncorhynchus mykiss) (CD8+ DCs). These CD8+ cells shown phenotypical and functional characteristics of cross-presenting DCs such us expression of CD8, CD103, CD141, Batf3, and others. In this work, we report the identification of homologue populations in rainbow trout gills and intestine. Consequently, we have carried out a broad phenotypic and functional characterization of these new populations that includes the confirmation of novel capacities for DCs in teleost. Interestingly, phenotypic and functional differences were found between the three populations suggesting that the location of DCs strongly shape their mature stage and their immune capacities. Despite the differences found among these populations, some common characteristics were identified in all subset such as the expression of cross presenting markers and regulatory B cell cytokines belonging to the tumor necrosis factor (TNF) superfamily of ligands such us B cell activating factor (BAFF) a proliferation-inducing ligand (APRIL) and BAFF and APRIL like molecule (BALM). These members of the TNF superfamily are produced mainly by innate cells like DCs and play and important role in activation and differentiation of B cells. For this reason, we have studied how these cytokines and their potential receptors are regulated throughout an inflammation model. To carry this out, we have studied the response of the peritoneal cavity to an intraperitoneal injection (i.p) with viral hemorrhagic septicemia virus (VHSV), given that previous studies had described that this inflammatory process is mainly mediated by IgM+ B cells. We first performed a transcriptional analysis in total leukocytes from peritoneum, observing an up regulation of the BAFF and BAFF receptor (BAFF-R) mRNA levels after the (i.p) of VHSV. On the other hand, when we analyzed the regulation of these genes in sorted IgM+ B cells, we observed increases in the levels of transcription of BAFF, APRIL, BALM and their receptors. These results reveal that these cytokines as well as their receptors play a key role in peritoneal inflammation processes mediated by IgM+ B cells. Finally, having demonstrated that fish DCs also produce APRIL, we studied the functionality of this cytokine on IgM+ B cells, using in this case splenic B cells. We have compared the effects produced by APRIL on IgM+ B cells to those previously reported for BAFF, to increase our knowledge on the relation between these phylogenetically close cytokines. In the current work, we have demonstrated that APRIL induces an exclusive proliferation of IgM+ B cells, increases the number of IgM secreting cells and also increases the levels on MHC II on the surface of these cells as well as their antigen processing capacity. The results of this study increase our knowledge concerning the crosstalk between innate and adaptive immune responses and on how B cells are regulated by innate cells such as DCs. This knowledge will be essential for the rational design of vaccines, one of the most important goals of aquaculture at the moment ; The work presented in this thesis has been founded by the following projects: AGL2014-53061-R and AGL2014-54556-JIN from the Spanish Ministry of Economy and Competitiveness (MINECO); by the European Commission under the Seventh Framework Programme for Research and Technological Development (FP7) of the European Union (Grant Agreement 311993 TARGETFISH); and by the European Research Council (ERC) Starting Grant 2011 (TEBLYM 280469) and ERC Consolidator Grant 2016 (TEMUBLYM 725061). Irene Soleto has been founded by a BES-2015-072193 scholarship from MINECO

Horizontal gene transfer drives the rapid evolution of bacterial populations. Classical processes that promote the lateral flow of genetic information are conserved throughout the prokaryotic world. However, some species have nonconserved transfer mechanisms that are not well known. This is the case for the ancient extreme thermophile Thermus thermophilus. In this work, we show that T. thermophilus strains are capable of exchanging large DNA fragments by a novel mechanism that requires cell-tocell contacts and employs components of the natural transformation machinery. This process facilitates the bidirectional transfer of virtually any DNA locus but favors by 10-fold loci found in the megaplasmid over those in the chromosome. In contrast to naked DNA acquisition by transformation, the system does not activate the recently described DNA-DNA interference mechanism mediated by the prokaryotic Argonaute protein, thus allowing the organism to distinguish between DNA transferred from a mate and exogenous DNA acquired from unknown hosts. This Argonaute-mediated discrimination may be tentatively viewed as a strategy for safe sharing of potentially "useful" traits by the components of a given population of Thermus spp. without increasing the genome sizes of its individuals ; This work has been supported by grant BIO2013-44963-R from the Spanish Ministry of Economy and Competence and FP7-PEOPLE-2012-IAPP grant 324439 from the European Union to J. Berenguer and by grant AV9/6-1 from the Deutsche Forschungsgemeinschaft to B. Averhoff. An institutional grant from the Fundación Ramón Areces to CBMSO and financial support to the Spanish National Network for Extremophilic Microorganisms (BIO2011-12879-E) are also acknowledged. An FPI fellowship for A. Blesa from the Ministry of Education is acknowledged. C. E. César thanks the Ministry of Science and Innovation for a Juan de la Cierva contract

Viking missions reported adverse conditions for life in Mars surface. High hydrogen signal obtained by Mars orbiters has increased the interest in subsurface prospection as putative protected Mars environment with life potential. Permafrost has attracted considerable interest from an astrobiological point of view due to the recently reported results from the Mars exploration rovers. Considerable studies have been developed on extreme ecosystems and permafrost in particular, to evaluate the possibility of life on Mars and to test specific automated life detection instruments for space missions. The biodiversity of permafrost located on the Bering Land Bridge National Preserve has been studied as an example of subsurface protected niche of astrobiological interest. Different conventional (enrichment and isolation) and molecular ecology techniques (cloning, fluorescence "in situ" probe hybridization, FISH) have been used for isolation and bacterial identification ; The expedition to Imuruk Lake was supported by Centro de Astrobiología-INTA (Spain). The laboratory experimental procedures were supported by Grant AYA 2010–20213 "Desarrollo de Tecnología para la identificación de vida de forma automática" from the Spanish Government

This is an electronic version of an article published in Nucleic Acids Research. Rodríguez Mateos, M., García Gómez, J. J., Francisco Velilla, R., Remacha, M., Cruz, J. de la and J. P. G. Ballesta. Role and dynamics of the ribosomal protein P0 and its related trans-acting factor Mrt4 during ribosome assembly in Saccharomyces cerevisiae. Nucleic Acids Research 37.22 (2009): 7519–7532 ; Spanish Ministry of Science and Innovation (MICINN) and FEDER (BFU2007-60151 to J.d.l.C., BFU2007- 64280 to M.R. and BFU2006-00365 to J.P.G.B.), the Andalusian Government (CVI-271, P07-CVI-02623 and P08-CVI-03508 to J.d.l.C.) and Ramon Areces Foundation (Institutional Grant to C.B.M.S.O.). Funding for open access charge: Ministerio de Ciencia e Innovacion, Spain

Mycolicibacterium hassiacum is the most thermophilic of all the mycobacteria. A partial sequence based on Illumina technology of around 5 Mbp was published in 2012. Here, we report the 5,269,097-bp complete genome sequence assembled into a single circular chromosome ; This work was supported by grants RTC2014-14391-1 and BIO2016-77031-R from the Spanish Ministry of Economy and Competitiveness and grant 685474 from the H2020 research and innovation program of the European Union. An institutional grant from Fundación Ramón Areces to the Centro de Biología Molecular Severo Ochoa (CBMSO) is acknowledged

The Dallol geothermal area in the northern part of the Danakil Depression (up to 124–155 meter below sea level) is deemed one of the most extreme environments on Earth. The area is notable for being part of the Afar Depression, an incipient seafloor-spreading center located at the triple junction, between Nubian, Somali and Arabian plates, and for hosting environments at the very edge of natural physical-chemical extremities. The northern part of the Danakil Depression is dominated by the Assale salt plain (an accumulation of marine evaporite deposits) and hosts the Dallol volcano. Here, the interaction between the evaporitic deposit and the volcanisms have created the unique Dallol hot springs, which are highly acidic (pH ~ 0) and saline (saturation) with maximum temperatures ranging between 90 and 109 °C. Here we report for the first time evidence of life existing with these hot springs using a combination of morphological and molecular analyses. Ultra-small structures are shown to be entombed within mineral deposits, which are identified as members of the Order Nanohaloarchaea. The results from this study suggest the microorganisms can survive, and potential live, within this extreme environment, which has implications for understanding the limits of habitability on Earth and on (early) Mars ; Europlanet 2020 RI received funding from the European Union's Horizon 2020 research and innovation program under Grant Agreement No 654208

Tesis doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología Molecular. Fecha de lectura: 29-10-2014 ; The need for updating the existing processes, or finding new methods to meet environmental and legislation requirements, is an imminent task for all Chemical Industries. The path towards sustainability encourages the interest to find alternatives to traditional methods; this way, biocatalysis appears as a potential alternative to cope with the basis of a 'greener' chemistry. The use of enzymes as catalysts includes important advantages: mild operational conditions (temperature, pressure and pH), the possibility of shortening the steps of synthesis using high efficient, and selective transformations, as well as, obtaining safer and purer chiral products. Nevertheless, to call the attention of industrial transformations, enzymes must gather a set of improvements before their application. In this concern, in the last decades, a wide research in different enzimatical, biological and engineering fields, has been developed and definitely, contributed to the emergence of the first biotransformations in the Industry. Immobilization is a powerful tool that when carefully designed, could deal with some of the drawbacks of enzymes as biocatalists for industrial applications, and improve interesting properties; this tool is the simplest way for to reduce the cost of the enzymatic biocatalists, making them reusable; but it also may stabilize the enzyme or change its specificity. In this thesis, a group of lipases were immobilized in different hydrophobic supports. This is an easy-­‐to-­‐perform method that gathers immobilization and purification. The pool of immobilized lipases prepared, and other commercial available biocatalists, were studied and compared in terms of stability against several inactivating media and activity using different substrates. Two important biotransformations were also studied using these biocatalysts; esterifications, employed for the ...

Abstracts of the XVIII Congreso de Biometría CEBMADRID held from 25 to 27 May in Madrid ; Interactive modelling and prediction of patient evolution via multistate models / Leire Garmendia Bergés, Jordi Cortés Martínez and Guadalupe Gómez Melis : This research was funded by the Ministerio de Ciencia e Innovación (Spain) [PID2019104830RBI00]; and the Generalitat de Catalunya (Spain) [2017SGR622 and 2020PANDE00148]. ; Operating characteristics of a model-based approach to incorporate non-concurrent controls in platform trials / Pavla Krotka, Martin Posch, Marta Bofill Roig : EU-PEARL (EU Patient-cEntric clinicAl tRial pLatforms) project has received funding from the Innovative Medicines Initiative (IMI) 2 Joint Undertaking (JU) under grant agreement No 853966. This Joint Undertaking receives support from the European Union's Horizon 2020 research and innovation programme and EFPIA and Children's Tumor Foundation, Global Alliance for TB Drug Development non-profit organisation, Spring works Therapeutics Inc. ; Modeling COPD hospitalizations using variable domain functional regression / Pavel Hernández Amaro, María Durbán Reguera, María del Carmen Aguilera Morillo, Cristobal Esteban Gonzalez, Inma Arostegui : This work is supported by the grant ID2019-104901RB-I00 from the Spanish Ministry of Science, Innovation and Universities MCIN/AEI/10.13039/501100011033. ; Spatio-temporal quantile autoregression for detecting changes in daily temperature in northeastern Spain / Jorge Castillo-Mateo, Alan E. Gelfand, Jesús Asín, Ana C. Cebrián / Spatio-temporal quantile autoregression for detecting changes in daily temperature in northeastern Spain : This work was partially supported by the Ministerio de Ciencia e Innovación under Grant PID2020-116873GB-I00; Gobierno de Aragón under Research Group E46_20R: Modelos Estocásticos; and JC-M was supported by Gobierno de Aragón under Doctoral Scholarship ORDEN CUS/581/2020. ; Estimation of the area under the ROC curve with complex survey data / Amaia Iparragirre, Irantzu Barrio, ...

Tesis Doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología. Fecha de lectura: 30-06-2017 ; Esta tesis tiene embargado el acceso al texto completo hasta el 30-12-2018 ; The thesis was supported by the Spanish Government (Projects MICIN CGL2010-15675 and MINECO CTM2013-45775-C2-2-R) and the Dirección General de Universidades e Investigación de la Comunidad de Madrid, Research Network (Comunidad de Madrid S-2009/AMB/1511)