Marky: a tool supporting annotation consistency in multi-user and iterative document annotation projects

Background and Objectives Document annotation is a key task in the development of Text Mining methods and applications. High quality annotated corpora are invaluable, but their preparation requires a considerable amount of resources and time. Although the existing annotation tools offer good user interaction interfaces to domain experts, project management and quality control abilities are still limited. Therefore, the current work introduces Marky, a new Web-based document annotation tool equipped to manage multi-user and iterative projects, and to evaluate annotation quality throughout the project life cycle. Methods At the core, Marky is a Web application based on the open source CakePHP framework. User interface relies on HTML5 and CSS3 technologies. Rangy library assists in browser-independent implementation of common DOM range and selection tasks, and Ajax and JQuery technologies are used to enhance user-system interaction. Results Marky grants solid management of inter- and intra-annotator work. Most notably, its annotation tracking system supports systematic and on-demand agreement analysis and annotation amendment. Each annotator may work over documents as usual, but all the annotations made are saved by the tracking system and may be further compared. So, the project administrator is able to evaluate annotation consistency among annotators and across rounds of annotation, while annotators are able to reject or amend subsets of annotations made in previous rounds. As a side effect, the tracking system minimises resource and time consumption. Conclusions Marky is a novel environment for managing multi-user and iterative document annotation projects. Compared to other tools, Marky offers a similar visually intuitive annotation experience while providing unique means to minimise annotation effort and enforce annotation quality, and therefore corpus consistency. Marky is freely available for non-commercial use at http://sing.ei.uvigo.es/markyThe authors thank the project PTDC/SAU-ESA/646091/2006/FCOMP-01-0124-FEDER-007480FCT, the Strategic Project PEst-OE/EQB/LA0023/2013, the Project "Bio-Health - Biotechnology and Bioengineering approaches to improve health quality", Ref. NORTE-07-0124-FEDER-000027, co-funded by the Programa Operacional Regional do Norte (ON.2 - O Novo Norte), QREN, FEDER, the project "RECI/BBB-EBI/0179/2012 - Consolidating Research Expertise and Resources on Cellular and Molecular Biotechnology at CEB/IBB", Ref. FCOMP-01-0124-FEDER-027462, FEDER, and the Agrupamento INBIOMED from DXPCTSUG-FEDER unha maneira de facer Europa (2012/273). The research leading to these results has received funding from the European Union's Seventh Framework Programme FP7/REGPOT-2012-2013.1 under grant agreement no. 316265 (BIOCAPS) and the [14VI05] Contract-Programme from the University of Vigo. This document reflects only the author's views and the European Union is not liable for any use that may be made of the information contained herein

Agent-based spatiotemporal simulation of biomolecular systems within the open source MASON framework

Agent-based modelling is being used to represent biological systems with increasing frequency and success. This paper presents the implementation of a new tool for biomolecular reaction modelling in the open source Multiagent Simulator of Neighborhoods framework. The rationale behind this new tool is the necessity to describe interactions at the molecular level to be able to grasp emergent and meaningful biological behaviour. We are particularly interested in characterising and quantifying the various effects that facilitate biocatalysis. Enzymes may display high specificity for their substrates and this information is crucial to the engineering and optimisation of bioprocesses. Simulation results demonstrate that molecule distributions, reaction rate parameters, and structural parameters can be adjusted separately in the simulation allowing a comprehensive study of individual effects in the context of realistic cell environments. While higher percentage of collisions with occurrence of reaction increases the affinity of the enzyme to the substrate, a faster reaction (i.e., turnover number) leads to a smaller number of time steps. Slower diffusion rates and molecular crowding (physical hurdles) decrease the collision rate of reactants, hence reducing the reaction rate, as expected. Also, the random distribution of molecules affects the results significantly.The authors thank the Agrupamento INBIOMED from DXPCTSUG-FEDER unha maneira de facer Europa (2012/273). The research leading to these results has received funding from the European Union's Seventh Framework Programme FP7/REGPOT-2012-2013.1 under Grant Agreement no. 316265 (BIOCAPS) and the [14VI05] Contract-Programme from the University of Vigo. This document reflects only the authors' views and the European Union is not liable for any use that may be made of the information contained herein

Biquaternionic Reformulation of a Fractional Monochromatic Maxwell System

In this work we propose a biquaternionic reformulation of a fractional monochromatic Maxwell system. Additionally, some examples are given to illustrate how the quaternionic fractional approach emerges in linear hydrodynamic and elasticity

Geología de la cueva

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La Cueva de Castañar y su centro de interpretación

Comunicación presentada en Cuevatur 2016: VI Congreso Español sobre Cuevas Turísticas, Nerja (Málaga), 2016.[ES] La Cueva de Castañar constituye una cavidad única tanto por la variedad de minerales y formas de sus espeleotemas, como por el tono rojizo de sus paredes. Estas dos características responden a las características de los materiales sobre los que se desarrolla la cueva. Son materiales correspondientes al Ediácarico (635-541 M.a.), que incluyen una amplia variedad de rocas (dolomías, magnesitas, pizarras y areniscas). Estos materiales, muy ricos en magnesio y sílice, son los que se disuelven y alteran para dar lugar a la formación de la cavidad y de sus espeleotemas. La alteración de las pizarras y areniscas, la disolución de las dolomías y magnesitas y la infiltración de arcillas desde el suelo dan lugar a la formación de un fino tapiz de color rojo intenso que se deposita sobre las paredes de la cueva, sobre el que muchas veces nuclean los espeleotemas. La disolución de las dolomías y magnesitas aporta mucho magnesio a las aguas que circulan por la cueva, lo cual favorece la formación no sólo de calcita (que es lo habitual), sino también de aragonito. Pero además la composición de las aguas no se ha mantenido constante, lo que ha favorecido que se produjeran muchas transformaciones entre los minerales ya formados. En definitiva, el amplio espectro mineralógico y las variadas transformaciones mineralógicas que se observan en la cueva, hacen de esta un laboratorio natural y por tanto una cavidad única, que se debe conocer, para así poderla conservar en las mejores condiciones posibles. Estas condiciones son las que hacen que el número de visitantes sea muy limitado, por ello el Centro de Interpretación inaugurado en 2010, cumple sobradamente la labor de dar a conocer los valores únicos de la Cueva de Castañar.[EN] Castañar Cave is a unique cavity due to the variety and morphology of the speleothems it contains, as well as to the red colour of their walls. These characteristics are due to the hostrocks in which it developed, Ediacaric (635-541 M.a) dolostones, magnesites and siliciclastic rocks. These materials very rich in Mg and silica, weather and dissolve to give place to the formation of the cavity and their speleothems. The weathering of the siliciclastic rocks, the dissolution of dolostones and magnesites and the infiltration of the clays from the overlying soil, allows the formation of a thin red (clays and Fe-oxides) layer that coats the cavity, and constitute the nucleation site for many speleothems. The dissolution of dolostones and magnesites supplies Mg to the cave waters enabling the formation not only of calcite, but also aragonite and dolomite (which are rarer in caves). In addition water cave composition has changed over time, allowing many transformations between the previously formed minerals. When relatively more dilute waters prevail aragonite transforms into calcite or even both can dissolve, forming the large pores visible in some speleothems. On the contrary Mg-rich minerals (huntite, dolomite and Mg-rich clays) form in more concentrated waters. In short, the wide mineralogical spectra and their transformations make this cave a unique cavity and a natural lab, whose detailed study will help to preserve it under the best possible conditions. This is why the number of visitors is very limited; however the renewed Centro de Interpretación shows in great detail the characteristics of the Castañar Cave.Este trabajo se incluye en los proyectos: “Estudio ambiental y geológico del Monumento Natural Cueva de Castañar”, financiado por fondos FEADER (contrato Gobierno de Extremadura y CSIC) y CGL2014-54818P del MINECO.Peer reviewe

La Comarca de Las Villuercas

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Open Source Robot Localization for Non-Planar Environments

The operational environments in which a mobile robot executes its missions often exhibit non-flat terrain characteristics, encompassing outdoor and indoor settings featuring ramps and slopes. In such scenarios, the conventional methodologies employed for localization encounter novel challenges and limitations. This study delineates a localization framework incorporating ground elevation and inclination considerations, deviating from traditional 2D localization paradigms that may falter in such contexts. In our proposed approach, the map encompasses elevation and spatial occupancy information, employing Gridmaps and Octomaps. At the same time, the perception model is designed to accommodate the robot's inclined orientation and the potential presence of ground as an obstacle, besides usual structural and dynamic obstacles. We have developed and rigorously validated our approach within Nav2, and esteemed open-source framework renowned for robot navigation. Our findings demonstrate that our methodology represents a viable and effective alternative for mobile robots operating in challenging outdoor environments or intrincate terrains

Sexual differences in hippocampal microglia of adult mice subjected to maternal separation stress.

Introduction: It is well known that early life adversities could a"ect brain development and increase the vulnerability to stress-related disorders later in adulthood. Nevertheless, the neurobiological mechanisms underlying this susceptibility have been poorly characterized and sex could be an important variable. Recently, microglia, which is involved in many neurodevelopmental processes such as neurogenesis and synaptic plasticity, has been proposed as a mediator of this stress response and early life stress could “prime” microglia to be over- responsive in future challenges. Objective: The analysis of hippocampal microglia morphology and distribution in the dentate gyrus (DG) of mice subjected to early stress. Methods: Female and male C57BL/6J mice were subjected to 3h daily maternal separation (MS) for 21 days. In postnatal day 60, adult mice undertook a single 2h restriction stress (RS). Accordingly, the experimental groups were as follows: CTRL, RS, MS, MS+RS. The DG was analyzed using immunohistochemistry techniques against Iba1 (microglia) following image analysis (ImageJ) to obtain morphological and distribution data of microglial somas and DG surface area. Results: Smaller DG surface area was observed in MS male mice compared with the CTRL group, but not in female. Furthermore, microglial soma area changed in a sex-dependent manner, having female mice from MS group an increased soma area than those of MS male mice. This was also observed to be region-specific, with a larger microglia soma in DG subgranular zone (SGZ) of MS female compared to MS male. Since microglia in this DG zone is involved in neurogenesis, this might suggest a possible change in the formation of new born neurons. Conclusion: These results revealed a di"erent microglial response to stress depending on the animal sex and open the door to a better understanding of neurobiological basis in pathologies like depression. .University of Málaga, the project PID2020-117464RB-I00 from Ministerio de Ciencia e Innovación (MCIN/AEI) Spain, awarded to Pedraza, C. and Pérez-Martín, M. ; the project P20_00460 from Consejería de Conocimiento, Investigación y Universidades, Junta de Andalucía awarded to Pedraza, C. and predoctoral fellowship FPU21/01318 awarded to Munoz- Martin, J. funded by MCIN/AEI, Spain. Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Estado nutricional en las personas con insuficiencia cardíaca crónica y/o enfermedad pulmonar obstructiva crónica. Impacto en la calidad de vida y en las exacerbaciones

Targets: To know the nutritional status in patients with heart failure (HF) and with chronic obstructive pulmonary disease (COPD), cared in a Barcelona’s primary health center and to describe the clinical and socio-demographic characteristics which may be related with the nutritional status.Method: A transversal descriptive study was performed during de year 2014. In nursing visits the following variables were collected: in HF patients, levels of functionality based in NYHA scale, in COPD patients, dyspnea grade based in BMRC scale. In both cases the body mass index (BMI) was determined; MNA scale is used, and also the physical activity and quality of life is evaluated by the EQ-5D scale.Results: Of the 192 participants, 59, 4% were men and had a mean age of 77, 64 years (ds10, 12. Of the studied diseases, 40, 1% were HF, 45, 8% COPD and 14, 1% both diseases). The risk of malnutrition was 11, 4% in COPD patients, 16, and 9% in people with HF and 33, 3% in both HF and COPD patients. (P 0,028)With the logistic regression with the other variables, the only associated factor was gender, having men an OR 3 (1,008-8, 95)Conclusions: The nutritional status gets worse in people with both pathologies in concomitantly way.Gender plays a crucial role in malnutrition or risk of the disease.Objetivo: Conocer el estado nutricional de los pacientes con Insuficiencia cardiaca (IC) y/o Enfermedad pulmonar obstructiva crónica (EPOC) atendidos en un centro de atención primaria de la ciudad de Barcelona y describir las características clínicas y sociodemográficas que puedan tener relación con el estado nutricional.Método: Estudio descriptivo transversal, durante los meses del 2014. En las visitas realizadas por enfermería, se recogieron las siguientes variables: en el caso de la IC grado de funcionalidad mediante la escala NYHA, en el caso de la EPOC, Grado de disnea mediante la escala BMRC. En ambos se determina el IMC, se administra la escala MNA, se valora el nivel de actividad física y la calidad de vida a través de la escala EQ-5D.Resultado: De los 192 participantes, el 59,4% eran Hombres y la media de edad de 77,64 años(ds10,12). De las enfermedades estudiadas el 40,1% eran IC, el 45,8% EPOC y ambas enfermedades el 14,1%. El riesgo de malnutrición fue del 11,4% de las personas con EPOC, el 16,9% de las personas con IC y el 33,3% de las personas con ambas patologías.(P 0,028)Al hacer la regresión logística con el resto de variables, el único factor asociado es el sexo, obteniendo los Hombres un OR 3 (1,008-8,95).Conclusiones El estado nutricional empeora cuando se padecen las dos patologías de manera concomitante.En la malnutrición o en el riesgo de padecerla, el sexo juega un papel muy importante.. &nbsp

Mild juvenile stress increases resilience to the development of anxious behaviors and prevents neurogenic reduction after stress exposure in adulthood.

Stress, especially during sensitive periods of development, can induce neuroplastic changes in brain regions such as the hippocampus, which increases vulnerability to the negative effects of a second stressor during adulthood, precipitating the development of depressive symptoms. For this reason, C57BL/6J mice were subjected to two stress protocols, the first in the juvenile period and the second in adulthood. Neurogenic and behavioral changes (saccharin preference test and social behavior test) were analyzed. The results revealed that juvenile stress increased basal saccharin preference in adulthood. However, animals subjected to stress in both juvenile and adulthood showed anhedonic behavior. In addition, stress in adulthood resulted in increased anxious behavior without affecting interest in social relationships. Stress in adulthood reduced neurogenesis. In contrast, juvenile stress prevented the development of anxious behavior and the reduction of hippocampal neurogenesis induced by stress in adulthood. In conclusion, juvenile stress increases the risk of developing anhedonia after exposure to a second stress, but, in contrast to our expectations, mild stress during the juvenile period increases resilience to the development of anxious behaviors and prevents neurogenic reduction after stress exposure in adulthoodUniversidad de Málaga. Campus de Excelencia Internacional Andalucía Tech