Computing (optimal) embeddings of directed bigraphs

Bigraphs and bigraphical reactive systems are a well-known meta-model successfully used for formalizing a wide range of models and situations, such as process calculi, service oriented architectures, multi-agent systems, biological systems, etc. A key problem in the theory and the implementations of bigraphs is how to compute embeddings, i.e., structure-preserving mappings of a given bigraph (the pattern or guest) inside another (the target or host). In this paper, we present an algorithm for computing embeddings for directed bigraphs, an extension of Milner's bigraphs which take into account the request directions between controls and names. This algorithm solves the embedding problem by means of a reduction to a constraint satisfaction problem. We first prove soundness and completeness of this algorithm; then we present an implementation in jLibBig, a general Java library for manipulating bigraphical reactive systems. The effectiveness of this implementation is shown by several experimental results. Finally, we show that this algorithm can be readily adapted to find the optimal embeddings in a weighted variant of the embedding problem

Typing pictures: linguistic processing cascades into finger movements

The present study investigated the effect of psycholinguistic variables on measures of response latency and mean interkeystroke interval in a typewritten picture naming task, with the aim to outline the functional organization of the stages of cognitive processing and response execution associated with typewritten word production. Onset latencies were modulated by lexical and semantic variables traditionally linked to lexical retrieval, such as word frequency, age of acquisition, and naming agreement. Orthographic variables, both at the lexical and sublexical level, appear to influence just within-word interkeystroke intervals, suggesting that orthographic information may play a relevant role in controlling actual response execution. Lexical-semantic variables also influenced speed of execution. This points towards cascaded flow of activation between stages of lexical access and response execution

Flexible control of movement in plants

Although plants are essentially sessile in nature, these organisms are very much in tune with their environment and are capable of a variety of movements. This may come as a surprise to many non-botanists, but not to Charles Darwin, who reported that plants do produce movements. Following Darwin\u2019s specific interest on climbing plants, this paper will focus on the attachment mechanisms by the tendrils. We draw attention to an unsolved problem in available literature: whether during the approach phase the tendrils of climbing plants consider the structure of the support they intend to grasp and plan the movement accordingly ahead of time. Here we report the first empirical evidence that this might be the case. The three-dimensional (3D) kinematic analysis of a climbing plant (Pisum sativum L.) demonstrates that the plant not only perceives the support, but it scales the kinematics of tendrils\u2019 aperture according to its thickness. When the same support is represented in two-dimensions (2D), and thus unclimbable, there is no evidence for such scaling. In these circumstances the tendrils\u2019 kinematics resemble those observed for the condition in which no support was offered. We discuss these data in light of the evidence suggesting that plants are equipped with sensory mechanisms able to provide the necessary information to plan and control a movement

A chlorophyll-deficient, highly reflective soybean mutant: radiative forcing and yield gaps

Sunlight absorbed at the Earth’s surface is re-emitted as longwave radiation. Increasing atmospheric concentrations of CO2 and other greenhouse gases trap an increasing fraction of such heat, leading to global climate change. Here we show that when a chlorophyll (Chl)-deficient soybean mutant is grown in the field, the fraction of solar-irradiance which is reflected, rather than absorbed, is consistently higher than in commercial varieties. But, while the effect on radiative forcing during the crop cycle at the scale of the individual experimental plot was found to be large (−4.1± 0.6 W m−2 ), global substitution of the current varieties with this genotype would cause a small increase in global surface albedo, resulting in a global shortwave radiative forcing of −0.003 W m−2 , corresponding to 4.4 Gt CO2eq. At present, this offsetting effect would come at the expense of reductions to yields, probably associated with different dynamic of photosynthetic response in the Chl-deficient mutant. The idea of reducing surface-driven radiative forcing by means of Chl-deficient crops therefore requires that novel high-yielding and high-albedo crops are made available soon.publishedVersio

Relación entre el valor del ratio elastográfico y la clasificación citológica de Bethesda en la patología tiroidea

ResumenObjetivoPresentar nuestra experiencia en la categorización de la patología tiroidea, a través de la utilización de parámetros ecográficos de malignidad y elastografía con medición del ratio de la deformación tisular, y la correlación de los hallazgos obtenidos con la clasificación citológica de Bethesda.Materiales y métodosSe llevó a cabo un estudio prospectivo y observacional, entre septiembre de 2012 y abril de 2013, que incluyó 137 nódulos tiroideos. Se excluyeron 10 casos Bethesda III-IV. Se realizó ecografía, power Doppler, visualización de micropartículas (Micropure) y elastografía con medición del ratio elastográfico, así como también punción aspirativa con aguja fina guiada por ecografía (con el citólogo presente), utilizando la clasificación Bethesda. Los estudios fueron hechos por el mismo operador con un ecógrafo Toshiba Aplio 400 y los datos estadísticos se evaluaron con el programa IBM SPSS Statistics 20.ResultadosSe estudiaron 127 nódulos en pacientes con una edad promedio de 59±16 años. El 82% de los casos ocurrió en mujeres. Ciento veinte nódulos (94%) fueron clasificados como Bethesda II. La media elastográfica para Bethesda I-II fue de 1,94±2,12 vs. 7,07±5,46 para V-VI (p: 0,048). El punto de corte elastográfico ≤ 2 (87 de 127) presentó una sensibilidad del 85,7% y una especificidad del 81,7% para predecir Bethesda asociada a patología benigna, con un valor predictivo negativo (VPN) del 99% y un valor predictivo positivo del 15%.ConclusionesEl ratio elastográfico permitió descartar la patología tiroidea maligna con valores ≤ 2 y un VPN del 99%, mejorando la selección de los pacientes a punzar. El incremento del ratio elastográfico se asoció a una mayor probabilidad de patología maligna, aunque no se pudo establecer un valor de corte debido al bajo número de casos con Bethesda V-VI.AbstractObjectivesWe present our experience in the categorization of thyroid pathology using the sonographic parameters of malignancy and elastography with measurement elastography strain ratio, to evaluate the relationship between the results found and the Bethesda classification.Materials and methodsProspective observational study, included 137 thyroid nodules studied between September 2012- April 2013. We excluded 10 cases with Bethesda categories III-IV. Ultrasonography, Doppler, Micropure, elastogrphy strain ratio between the lesion and the normal tissue, fine needle aspiration cytology (FNAC),were the diagnosis methods used. The pathologist was always present and the cytological classi fication of Bethesda was used. All study was made by the same physician used Toshiba Aplio 400 ultrasound unit. Results were analyzed with IBM SPSS Statistics 20.ResultsWe studied 127 nodules in patients 59±16 years old, 82% were female; 120 were Bethesda II (94%). The average strain ratio for nodules Bethesda I-II was 1.94±2.12 vs. 7.07±5.46 for those nodules Bethesda V-VI (p:0,048). This means that an elastography strain ratio ≤ 2 (87 of 127 nodules) has a sensibility of 85.7% and a specificity of 81.7% of predicting Bethesda associated with benign pathology with a negative predictive value (NPV) of 99% and a positive predictive value of 15%.ConclusionThe elastography strain ratio allowed to discard malignant nodules with strain ratio ≤ 2 with a NPV of 99% improves the selection of patients for FNAC. The increment in the elastography strain ratio was associated to a higher possibility of malignant thyroid pathology, being unable to determine a limit value due to the low amount of cases with nodules Bethesda V-VI

Impact of woody encroachment on soil organic carbon and nitrogen in abandoned agricultural lands along a rainfall gradient in Italy

Land use changes represent one of the most important components of global environmental change andhave a strong influence on carbon cycling. As a consequence of changes in economy during the last century, areas of marginal agriculture have been abandoned leading to secondary successions. The encroachment of woody plants into grasslands, pastures and croplands is generally thought to increase the carbon stored in these ecosystems even though there are evidences for a decrease in soil carbon stocks after land use change. In this paper, we investigate the effects of woody plant invasion on soil carbon and nitrogen stocks along a precipitation gradient (200–2,500 mm) using original data from paired experiment in Italian Alps and Sicily and data from literature (Guo and Gifford Glob Change Biol 8(4):345–360, 2002). We found a clear negative relationship (-0.05% C mm-1) between changes in soil organic carbon and precipitation explaining 70% of the variation in soil Cstocks after recolonization: dry sites gain carbon (up to? 67%) while wet sites lose carbon (up to -45%). In our data set, there seem to be two threshold values for soil carbon accumulation: the first one is 900 mm of mean annual rainfall, which separates the negative from the positive ratio values; the second one is 750 mm, which divides the positive values in two groups of sites. Most interestingly, this threshold of 750 mm corresponds exactly to a bioclimatic threshold: sites with\750 mm mean annual rainfall is classified as thermo-mediterranean sites, while the ones [750 mm are classified as mesomediterranean sites. This suggests that apart from rainfall also temperature values have an important influence on soil carbon accumulation after abandonment. Moreover, our results confirmed that the correlation between rainfall and trend in soil organic carbon may be related to nitrogen dynamics: carbon losses may occur only if there is a substantial decrease in soil nitrogen stock which occurs in wetter sites probably because of the higher leaching

Developing a methodology for three-dimensional correlation of PET–CT images and whole-mount histopathology in non-small-cell lung cancer

Background: Understanding the three-dimensional (3D) volumetric relationship between imaging and functional or histopathologic heterogeneity of tumours is a key concept in the development of image-guided radiotherapy. Our aim was to develop a methodologic framework to enable the reconstruction of resected lung specimens containing non-small-cell lung cancer (NSCLC), to register the result in 3D with diagnostic imaging, and to import the reconstruction into a radiation treatment planning system. Methods and Results: We recruited 12 patients for an investigation of radiology-pathology correlation (RPC) in NSCLC. Before resection, imaging by positron emission tomography (PET) or computed tomography (CT) was obtained. Resected specimens were formalin-fixed for 1-24 hours before sectioning at 3-mm to 10-mm intervals. To try to retain the original shape, we embedded the specimens in agar before sectioning. Consecutive sections were laid out for photography and manually adjusted to maintain shape. Following embedding, the tissue blocks underwent whole-mount sectioning (4-μm sections) and staining with hematoxylin and eosin. Large histopathology slides were used to whole-mount entire sections for digitization. The correct sequence was maintained to assist in subsequent reconstruction. Using Photoshop (Adobe Systems Incorporated, San Jose, CA, U.S.A.), contours were placed on the photographic images to represent the external borders of the section and the extent of macroscopic disease. Sections were stacked in sequence and manually oriented in Photoshop. The macroscopic tumour contours were then transferred to MATLAB (The Mathworks, Natick, MA, U.S.A.) and stacked, producing 3D surface renderings of the resected specimen and embedded gross tumour. To evaluate the microscopic extent of disease, customized "tile-based" and commercial confocal panoramic laser scanning (TISSUEscope: Biomedical Photometrics, Waterloo, ON) systems were used to generate digital images of whole-mount histopathology sections. Using the digital whole-mount images and imaging software, we contoured the gross and microscopic extent of disease. Two methods of registering pathology and imaging were used. First, selected PET and CT images were transferred into Photoshop, where they were contoured, stacked, and reconstructed. After importing the pathology and the imaging contours to MATLAB, the contours were reconstructed, manually rotated, and rigidly registered. In the second method, MATLAB tumour renderings were exported to a software platform for manual registration with the original PET and CT images in multiple planes. Data from this software platform were then exported to the Pinnacle radiation treatment planning system in DICOM (Digital Imaging and Communications in Medicine) format. Conclusions: There is no one definitive method for 3D volumetric RPC in NSCLC. An innovative approach to the 3D reconstruction of resected NSCLC specimens incorporates agar embedding of the specimen and whole-mount digital histopathology. The reconstructions can be rigidly and manually registered to imaging modalities such as CT and PET and exported to a radiation treatment planning system

Cambiamenti nel regime pluviometrico in ecosistemi mediterranei: il progetto MIND

Changes in rainfall patterns in Mediterranean ecosystems: the MIND project. Will Mediterranean terrestrial ecosystems be affected by the expected changes in precipitation regimes? If so, by how much and in which direction? These questions are at the basis of the research performed in context of the EU MIND project, whose key objectives were: i) to investigate the potential effects of increasing drought on Mediterranean terrestrial ecosystems at the process, ecosystem and regional scales and ii) to assess ecosystem vulnerability to changes in rainfall patterns. A network of experimental study sites has been created in Portugal, Spain, France and Italy, where field manipulations alter the amount of water available to the ecosystem. The most up-to-date methods of ecophysiology, micrometeorology, soil ecology and remote sensing have been used to elucidate the mechanisms that regulate the response of vegetation and soil to changes in water availability. This information is providing the basis for the implementation and validation of simulation models capable of predicting the drought response of Mediterranean terrestrial ecosystems, and their vulnerability to future climate change, on a larger scale. The out-coming results are elucidating how water availability affects plant ecophysiological processes, the dynamics of soil carbon and the overall exchange of mass and energy between the land and the atmosphere. This paper focuses on some of the important, yet preliminary, results on C and energy fluxes that have been obtained at the large scale troughfall manipulation experiment (Tolfa, Italy), in a forest dominated by Arbutus unedo L