A Semantic-Based Approach to Attain Reproducibility of Computational Environments in Scientic Work ows: A Case Study

Reproducible research in scientic work ows is often addressed by tracking the provenance of the produced results. While this approach allows inspecting intermediate and nal results, improves understanding, and permits replaying a work ow execution, it does not ensure that the computational environment is available for subsequent executions to reproduce the experiment. In this work, we propose describing the resources involved in the execution of an experiment using a set of semantic vocabularies, so as to conserve the computational environment. We dene a process for documenting the work ow application, management system, and their dependencies based on 4 domain ontologies. We then conduct an experimental evaluation sing a real work ow application on an academic and a public Cloud platform. Results show that our approach can reproduce an equivalent execution environment of a predened virtual machine image on both computing platforms

A synaptically connected hypothalamic magnocellular vasopressin-locus coeruleus neuronal circuit and its plasticity in response to emotional and physiological stress

The locus coeruleus (LC)-norepinephrine (NE) system modulates a range of salient brain functions, including memory and response to stress. The LC-NE system is regulated by neurochemically diverse inputs, including a range of neuropeptides such as arginine-vasopressin (AVP). Whilst the origins of many of these LC inputs, their synaptic connectivity with LC neurons, and their contribution to LC-mediated brain functions, have been well characterized, this is not the case for the AVP-LC system. Therefore, our aims were to define the types of synapses formed by AVP+ fibers with LC neurons using immunohistochemistry together with confocal and transmission electron microscopy (TEM), the origins of such inputs, using retrograde tracers, and the plasticity of the LC AVP system in response to stress and spatial learning, using the maternal separation (MS) and Morris water maze (MWM) paradigms, respectively, in rat. Confocal microscopy revealed that AVP+ fibers contacting tyrosine hydroxylase (TH)+ LC neurons were also immunopositive for vesicular glutamate transporter 2, a marker of presynaptic glutamatergic axons. TEM confirmed that AVP+ axons formed Gray type I (asymmetric) synapses with TH+ dendrites thus confirming excitatory synaptic connections between these systems. Retrograde tracing revealed that these LC AVP+ fibers originate from hypothalamic vasopressinergic magnocellular neurosecretory neurons (AVPMNNs). MS induced a significant increase in the density of LC AVP+ fibers. Finally, AVPMNN circuit upregulation by water-deprivation improved MWM performance while increased Fos expression was found in LC and efferent regions such as hippocampus and prefrontal cortex, suggesting that AVPMMN projections to LC could integrate homeostatic responses modifying neuroplasticity

Discovery of circulating miRNAs as biomarkers of chronic Chagas heart disease via a small RNA-Seq approach

Chagas disease affects approximately 7 million people worldwide in Latin America and is a neglected tropical disease. Twenty to thirty percent of chronically infected patients develop chronic Chagas cardiomyopathy decades after acute infection. Identifying biomarkers of Chagas disease progression is necessary to develop better therapeutic and preventive strategies. Circulating microRNAs are increasingly reliable biomarkers of disease and therapeutic targets. To identify new circulating microRNAs for Chagas disease, we performed exploratory small RNA sequencing from the plasma of patients and performed de novo miRNA prediction, identifying potential new microRNAs. The levels of the new microRNAs temporarily named miR-Contig-1519 and miR-Contig-3244 and microRNAs that are biomarkers for nonchagasic cardiomyopathies, such as miR-148a-3p and miR-224-5p, were validated by quantitative reverse transcription. We found a specific circulating microRNA signature defined by low miR-Contig-3244, miR-Contig-1519, and miR-148a-3 levels but high miR-224-5p levels for patients with chronic Chagas disease. Finally, we predicted in silico that these altered circulating microRNAs could affect the expression of target genes involved in different cellular pathways and biological processes, which we will explore in the future.The funding was supported by Agencia Nacional e Promoción Científica y Tecnológica, PICT 2013-1892, Secretaría de Ciencia y Tecnología, Universidad Nacional de Rosario, 1MED410, Ministerio de Economía y competitividad and Fondo Europeo de Desarrollo Regional, SAF2016-75988-R (MINECO/FEDER), SAF2015-63868-R (MINECO/FEDER), Red de Investigación de Centros de Enfermedades Tropicales, RICET RD12/0018/0004, Consejería de Sanidad, Comunidad de Madrid, S-2010/BMD-2332, Ministerio de Ciencia, Innovación y Universidades-Agencia Estatal de Investigación and Fondo Europeo de Desarrollo Regional, PGC2018-096132-B-I00, and PID2021-123389OB-I00

Frecuencia y factores de riesgo asociados a sobrepeso y obesidad en universitarios de colima, méxico

Objetivo Determinar la frecuencia y factores de riesgo para sobrepeso y obesidad en jóvenes universitarios. Métodos Se realizó un estudio transversal analítico en 821 alumnos inscritos de la Universidad de Colima. Entre las variables analizadas se encuentran: edad, género, alcoholismo, tabaquismo y utilización de medicamentos o sustancias para control de peso. Resultados Se estudiaron 821 alumnos (380 hombres y 441 mujeres) con una edad promedio de 20,9±2,5 años. Las frecuencias de sobrepeso y obesidad en hombres fueron de 27,8 %  y  14,7 % y en mujeres de 17 % y 5,2 %. En hombres el tabaquismo (OR 2,1, IC 95% 1,4-3,8;p=0,01) y etilismo (OR 2,1, IC 95% 1,2-3,6;p=0,003), estuvieron asociados a sobrepeso y obesidad. Fueron factores protectores en ambos géneros el uso de sustancias para control de peso (OR 0,4, IC 95% 0,2-0,8;p=0,01); mientras que el control dietético fue un factor protector sólo en las mujeres (OR 2,2, IC 95% 1,1-3,4;p=0,01). Conclusiones En estudiantes universitarios, el 31,6 % presentó sobrepeso y obesidad. En hombres, el tabaquismo y etilismo se asociaron a sobrepeso y obesidad. El uso de sustancias para bajar de peso y control dietético fueron factores protectores

Respiratory viruses detected in Mexican children younger than 5 years old with community-acquired pneumonia: a national multicenter study

Background: Acute respiratory infections are the leading cause of mortality in children worldwide, especially in developing countries. Pneumonia accounts for 16% of all deaths of children under 5 years of age and was the cause of death of 935 000 children in 2015. Despite its frequency and severity, information regarding its etiology is limited. The aim of this study was to identify respiratory viruses associated with community-acquired pneumonia (CAP) in children younger than 5 years old. Methods: One thousand four hundred and four children younger than 5 years of age with a clinical and/or radiological diagnosis of CAP in 11 hospitals in Mexico were included. Nasal washes were collected, placed in viral medium, and frozen at �70 C until processing. The first 832 samples were processed using the multiplex Bio-Plex/Luminex system and the remaining 572 samples using the Anyplex multiplex RT-PCR. Clinical data regarding diagnosis, clinical signs and symptoms, radiographic pattern, and risk factors were obtained and recorded. Results: Of the samples tested, 81.6% were positive for viruses. Respiratory syncytial virus (types A and B) was found in 23.7%, human enterovirus/rhinovirus in 16.6%, metapneumovirus in 5.7%, parainfluenza virus (types 1–4) in 5.5%, influenza virus (types A and B) in 3.6%, adenovirus in 2.2%, coronavirus (NL63, OC43, 229E, and HKU1) in 2.2%, and bocavirus in 0.4%. Co-infection with two or more viruses was present in 22.1%; 18.4% of the samples were negative. Using biomass for cooking, daycare attendance, absence of breastfeeding, and co-infections were found to be statistically significant risk factors for the presence of severe pneumonia. Conclusions: Respiratory syncytial virus (types A and B), human enterovirus/rhinovirus, and metapneumovirus were the respiratory viruses identified most frequently in children younger than 5 years old with CAP. Co-infection was present in an important proportion of the children

Analyzing multitarget activity landscapes using protein-ligand interaction fingerprints: interaction cliffs.

This is the original submitted version, before peer review. The final peer-reviewed version is available from ACS at http://pubs.acs.org/doi/abs/10.1021/ci500721x.Activity landscape modeling is mostly a descriptive technique that allows rationalizing continuous and discontinuous SARs. Nevertheless, the interpretation of some landscape features, especially of activity cliffs, is not straightforward. As the nature of activity cliffs depends on the ligand and the target, information regarding both should be included in the analysis. A specific way to include this information is using protein-ligand interaction fingerprints (IFPs). In this paper we report the activity landscape modeling of 507 ligand-kinase complexes (from the KLIFS database) including IFP, which facilitates the analysis and interpretation of activity cliffs. Here we introduce the structure-activity-interaction similarity (SAIS) maps that incorporate information on ligand-target contact similarity. We also introduce the concept of interaction cliffs defined as ligand-target complexes with high structural and interaction similarity but have a large potency difference of the ligands. Moreover, the information retrieved regarding the specific interaction allowed the identification of activity cliff hot spots, which help to rationalize activity cliffs from the target point of view. In general, the information provided by IFPs provides a structure-based understanding of some activity landscape features. This paper shows examples of analyses that can be carried out when IFPs are added to the activity landscape model.M-L is very grateful to CONACyT (No. 217442/312933) and the Cambridge Overseas Trust for funding. AB thanks Unilever for funding and the European Research Council for a Starting Grant (ERC-2013- StG-336159 MIXTURE). J.L.M-F. is grateful to the School of Chemistry, Department of Pharmacy of the National Autonomous University of Mexico (UNAM) for support. This work was supported by a scholarship from the Secretariat of Public Education and the Mexican government

Epidemiologic Features and Control Measures during Monkeypox Outbreak, Spain, June 2022

During June 2022, Spain was one of the countries most affected worldwide by a multicountry monkeypox outbreak with chains of transmission without identified links to disease-endemic countries. We provide epidemiologic features of cases reported in Spain and the coordinated measures taken to respond to this outbreak.S

Aves del Parque Nacional Natural Chingaza y zona de amortiguación, Cordillera Oriental de Colombia

We describe the bird species composition in the Chingaza National Park and its buffer zone, based on a revision of 10 published studies, recent fieldwork between 2008-2017, and the Colombia Bio expedition on 2018. We report 531 species for the Chingaza National Park and its buffer zone, grouped in 339 genera and 57 families. Six species are endemic to Colombia, 14 are near-endemic, 1 is critically endangered, 6 are endangered, 4 are vulnerable, 3 are near-threatened and 37 are migratory. This list includes 149 species more than those comprised in previous information from published datasets and ornithological collections. Additionally, we generated genetic barcodes, based sequences of the mtDNA gene COI, for 74 species, and present the first genetic record from Colombia in Barcode of Life Datasystems (BOLD) for Dysithamnus leucostictus, Chamaeza turdina, Rupicola peruvianus, Atlapetes semirufus, Euphonia mesochrysa and Chlorospingus flavopectus olsoni. This list is a tool to promote the study and conservation of birds in this area of the Colombian Eastern Cordillera.Describimos la composición de especies de aves del Parque Nacional Natural (PNN) Chingaza y su zona de amortiguación, a partir de la revisión de 10 estudios ornitológicos, trabajo de campo entre 2008–2017 y la expedición Colombia Bio en 2018. Reportamos para el PNN Chingaza y su zona de amortiguación un total de 531 especies, agrupadas en 339 géneros y 57 familias. Seis especies presentes en el parque son endémicas de Colombia, 14 casi endémicas, 1 en peligro crítico, 6 en peligro, 4 vulnerables, 3 casi amenazadas y 37 migratorias. Esta lista incluye 149 especies adicionales a la información previamente conocida por datos publicados y colecciones ornitológicas. Adicionalmente, generamos códigos de barras genéticos, con base en secuencias del gen mitocondrial COI, para 74 especies y presentamos los primeros registros genéticos de Colombia en la plataforma para códigos de barra genéticos Barcode of Life Datasystems (BOLD) para Dysithamnus leucostictus, Chamaeza turdina, Rupicola peruvianus, Atlapetes semirufus, Euphonia mesochrysa y Chlorospingus flavopectus olsoni.  El presente listado es una herramienta para incentivar el estudio y conservación de las aves en este sector de la Cordillera Oriental colombiana

Structural and vibrational properties of CdAl2S4 under high pressure: Experimental and theoretical approach

"This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Physical Chemistry C, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/jp5037926.”The behavior of defect chalcopyrite CdAl2S4 at high pressures and ambient temperature has been investigated in a joint experimental and theoretical study. High-pressure X-ray diffraction and Raman scattering measurements were complemented with theoretical ab initio calculations. The equation of state and pressure dependences of the structural parameters of CdAl2S4 were determined and compared to those of other AB(2)X(4) ordered-vacancy compounds. The pressure dependence of the Raman-active mode frequencies is reported, as well as the theoretical phonon dispersion curves and phonon density of states at 1 atm. Our measurements suggest that defect chalcopyrite CdAl2S4 undergoes a phase transition above 15 GPa to a disordered-rocksalt structure, whose equation of state was also obtained up to 25 GPa. In a downstroke from 25 GPa to 1 atm, our measurements indicate that CdAl2S4 does not return to the defect chalcopyrite phase; it partially retains the disordered-rocksalt phase and partially transforms into the spinel structure. The nature of the spinel structure was confirmed by the good agreement of our experimental results with our theoretical calculations. All in all, our experimental and theoretical results provide evidence that the spinel and defect chalcopyrite phases of CdAl2S4 are competitive at 1 atm. This result opens the way to the synthesis of spinel-type CdAl2S4 at near-ambient conditions.Financial support from the Spanish Consolider Ingenio 2010 Program (Project CSD2007-00045) is acknowledged. This work was also supported by Spanish MICCIN under Project MAT2010-21270-C04-03/04 and by Vicerrectorado de Investigacion de la Universitat Politecnica de Valencia under Projects UPV2011-0914 PAID-05-11 and UPV2011-0966 PAID-06-11. Supercomputer time was provided by the Red Espanola de Supercomputacion (RES) and the MALTA cluster. J.A.S. acknowledges the Juan de la Cierva fellowship program for financial support. AM. and P.R.-H. acknowledge S. Munoz Rodriguez for providing a data-parsing application.Sans Tresserras, JÁ.; Santamaría Pérez, D.; Popescu, C.; Gomis, O.; Manjón Herrera, FJ.; Vilaplana Cerda, RI.; Muñoz, A.... (2014). Structural and vibrational properties of CdAl2S4 under high pressure: Experimental and theoretical approach. Journal of Physical Chemistry C. 118(28):15363-15374. https://doi.org/10.1021/jp5037926S15363153741182

ATP5H/KCTD2 locus is associated with Alzheimer's disease risk

To identify loci associated with Alzheimer disease, we conducted a three-stage analysis using existing genome-wide association studies (GWAS) and genotyping in a new sample. In Stage I, all suggestive single-nucleotide polymorphisms (at P<0.001) in a previously reported GWAS of seven independent studies (8082 Alzheimer's disease (AD) cases; 12 040 controls) were selected, and in Stage II these were examined in an in silico analysis within the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium GWAS (1367 cases and 12904 controls). Six novel signals reaching P<5 × 10-6 were genotyped in an independent Stage III sample (the Fundació ACE data set) of 2200 sporadic AD patients and 2301 controls. We identified a novel association with AD in the adenosine triphosphate (ATP) synthase, H+ transporting, mitochondrial F0 (ATP5H)/Potassium channel tetramerization domain-containing protein 2 (KCTD2) locus, which reached genome-wide significance in the combined discovery and genotyping sample (rs11870474, odds ratio (OR)=1.58, P=2.6 × 10 -7 in discovery and OR=1.43, P=0.004 in Fundació ACE data set; combined OR=1.53, P=4.7 × 10 -9). This ATP5H/KCTD2 locus has an important function in mitochondrial energy production and neuronal hyperpolarization during cellular stress conditions, such as hypoxia or glucose deprivation