Statistical region based active contour using a fractional entropy descriptor: Application to nuclei cell segmentation in confocal microscopy images

We propose an unsupervised statistical region based active contour approach integrating an original fractional entropy measure for image segmentation with a particular application to single channel actin tagged fluorescence confocal microscopy image segmentation. Following description of statistical based active contour segmentation and the mathematical definition of the proposed fractional entropy descriptor, we demonstrate comparative segmentation results between the proposed approach and standard Shannon’s entropy on synthetic and natural images. We also show that the proposed unsupervised statistical based approach, integrating the fractional entropy measure, leads to very satisfactory segmentation of the cell nuclei from which shape characterization can be calculated

Targeting intraplaque angiogenesis : imaging and therapeutic interventions

Despite the available treatment options and sophisticated imaging technologies for monitoring lesion development, the morbidity and mortality from acute cardiovascular events remain unacceptably high.While cholesterol-lowering, anti-inflammatory and anti-platelet therapies benefits can increase survival as a primary or secondary prevention, they are not sufficient for plaque rupture prevention. Moreover, the most advance imaging technologies to detect high-risk atherosclerotic patients fail to visualize and explore cellular events in small preclinical models. Therefore, there is a clear need for the development of new therapies and the application of high-resolution imaging modalities.In the current thesis, we evaluated new possibilities to inhibit and image intraplaque angiogenesis.LUMC / Geneeskund

It’s what’s inside that counts: an assessment method to measure the residual strength of anobiids infested timber using micro-computed tomography

The safety assessment of old timber structures is an important issue due to the long-term behavior of wood and the structural complexity found in some older constructions. If the structure is de-graded due to the action of wood-boring insects, the complexity of the analysis increases. The objective of the work reported in this paper is to provide an assessment method to measure the residual strength of pine structural elements degraded by anobiids. Samples of degraded tim-ber were submitted to micro-computed tomography (μ-XCT) to quantify density loss being this parameter of fundamental importance for the assessment of timber structures as it is highly corre-lated with timber mechanical properties. During the μ-XCT study an empirical correlation be-tween lost material percentage (consumed by beetles) and timber apparent densities (original – before degradation and residual – after degradation) was established. The results showed an experimental high correlation (r2=0.66) between original apparent density and lost material percentage and an even higher correlation (r2=0.87) between residual apparent density and lost material percentage which confirms that μ-XCT can be validly used contributing to the 3D visualization and quantification of timber degraded elements. After the μ-XCT study, screw withdrawal and shear parallel to grain tests have been made in mar-itime pine degraded timber. Screw withdrawal force and shear strength values were related with density loss (r2=0.64 for screw withdrawal; r2=0.65 for shear strength parallel to grain). A novel assessment method for evaluating the impact of anobiid damage on timber degraded structural elements based in four major steps is proposed enabling a more quantitative assessment of the timber elements residual strength and, therefore, contributing to reduce unnecessary replacement and to provide foundations required to perform experimental modelling tests.authorsversionpublishe

In the trail of “Maçã de Alcobaça” protected geographical indication (PGI): Multielement chemometrics as a security and anti-fraud tool to depict clones, cultivars and geographical origins and nutritional value

Food fraud associated with the intentional mislabelling of non-Protected Geographical Indication (PGI) is a concern for consumers. “Maçã de Alcobaça” (Alcobaça apple) is one of the oldest Portuguese PGI products, characteristic of the main apple-growing regions in the country, being of utmost importance to develop traceability and authenticity tools to depict the PGI certification status of these products. Pulp multielement signatures were able to discriminate with moderate accuracy (65.7 %) different Royal Gala clones, grown within the same cultivation area. Moreover, Variable Importance in Projection Partial Least-Squares Discriminant Analysis (VIP-PLS-DA) allowed the discrimination of the Royal Gala samples from different PGI producers with 70.0 % accuracy. Apple PGI cultivars were also discriminated accurately (82.0 %). Expanding the approach to non-PGI production areas, several cultivars could be distinguished, according to their provenance with high accuracy, namely Starking (100.0 % accuracy), Granny Smith (100.0 % accuracy), Fuji (100.0 % accuracy), Royal Gala (86.7 % accuracy) and Reineta (90.3 % accuracy). The PGI fruit's microelement nutritional traits highlighted their higher nutritional value, an important trait for food fraud reduction, informing the consumer of the product authenticity, and providing insights on the nutritional value of these high-value market products.info:eu-repo/semantics/publishedVersio

Neural correlates of phonological, orthographic and semantic reading processing in dyslexia

Available online 10 August 2018Developmental dyslexia is one of the most prevalent learning disabilities, thought to be associated with dysfunction in the neural systems underlying typical reading acquisition. Neuroimaging research has shown that readers with dyslexia exhibit regional hypoactivation in left hemisphere reading nodes, relative to control counterparts. This evidence, however, comes from studies that have focused only on isolated aspects of reading. The present study aims to characterize left hemisphere regional hypoactivation in readers with dyslexia for the main processes involved in successful reading: phonological, orthographic and semantic. Forty-one participants performed a demanding reading task during MRI scanning. Results showed that readers with dyslexia exhibited hypoactivation associated with phonological processing in parietal regions; with orthographic processing in parietal regions, Broca's area, ventral occipitotemporal cortex and thalamus; and with semantic processing in angular gyrus and hippocampus. Stronger functional connectivity was observed for readers with dyslexia than for control readers 1) between the thalamus and the inferior parietal cortex/ventral occipitotemporal cortex during pseudoword reading; and, 2) between the hippocampus and the pars opercularis during word reading. These findings constitute the strongest evidence to date for the interplay between regional hypoactivation and functional connectivity in the main processes supporting reading in dyslexia.Supported by grants (RYC-2014-15440, PSI2015-65696) from the Spanish Ministry of Economy and Competitiveness (MINECO), a grant (PI2016-12) from the Basque Government and a grant (Exp. 65/15) from the Programa Red guipuzcoana de Ciencia, Tecnología e Innovación from the Diputación Foral de Gipuzkoa (P.M.P-A.); a predoctoral grant from the Department of Education, Universities and Research from the Basque Government (M.O.); grant (PSI2015-64174P) from the MINECO (F.C.); grants (PSI2015-67353-R) from the MINECO and (ERC-2011-ADG-295362) from the European Research Council (M.C.). BCBL acknowledges funding from Ayuda Centro de Excelencia Severo OchoaSEV-2015-0490 from the MINECO

Synthesis, biological evaluation, and molecular modeling of nitrile-containing compounds : exploring multiple activities as anti-Alzheimer agents

Funding: EC COST Actions D34 and CM1103 for Short-term Scientific Mission funding (EM, DS, MM); the School of Biology at the University of St. Andrews (EJS, RRR); the Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa (AN, ACJ, TR, MCC); FCT, the Portuguese Foundation for Science and Technology (Project PTDC/SAU-NEU/64151/2006 (MCC), and project grant (DS) Vega 2/0127/18 and the contract No. APVV-15-0455 of Slovak Research and Development Agency (MM).Based on the monoamine oxidase (MAO) inhibition properties of aminoheterocycles with a carbonitrile group we have carried out a systematic exploration to discover new classes of carbonitriles endowed with dual MAO and AChE inhibitory activities, and Aβ anti‐aggregating properties. Eighty‐three nitrile‐containing compounds, 13 of which are new, were synthesized and evaluated. in vitro screening revealed that 31 , a new compound, presented the best lead for trifunctional inhibition against MAO A (0.34 μM), MAO B (0.26 μM), and AChE (52 μM), while 32 exhibited a lead for selective MAO A (0.12 μM) inhibition coupled to AChE (48 μM) inhibition. Computational analysis revealed that the malononitrile group can find an advantageous position with the aromatic cleft and FAD of MAO A or MAO B. However, the total binding energy can be handicapped by an internal penalty caused by twisting of the ligand molecule and subsequent disruption of the conjugation ( 32 in MAO B compared to the conjugated 31 ). Conjugation is also important for AChE as well as the hydrophilic character of malononitrile that allows this group to be in close contact with the aqueous environment as seen for 83 . Although the effect of 31 and 32 against Aβ1–42, was very weak, the effect of 63 and 65 , and of the new compound 75 , indicated that these compounds were able to disaggregate Aβ1–42 fibrils. The most effective was 63 , a (phenylhydrazinylidene)propanedinitrile derivative that also inhibited MAO A (1.65 μM), making it a potential lead for Alzheimer's disease application.PostprintPeer reviewe

Ascites induces modulation of α6β1 integrin and urokinase plasminogen activator receptor expression and associated functions in ovarian carcinoma

Interactions between cancer cells and the surrounding medium are not fully understood. In this study, we demonstrate that ascites induces selective changes in the expression of integrins and urokinase plasminogen activator/urokinase plasminogen activator receptor (uPA/uPAR) in ovarian cancer cells. We hypothesise that this change of integrin and uPA/uPAR expression triggers signalling pathways responsible for modulating phenotype-dependent functional changes in ovarian cancer cells. Human ovarian surface epithelial (HOSE) cell lines and epithelial ovarian cancer cell lines were treated with ascites for 48 h. Ascites induced upregulation of α6 integrin, without any change in the expression of αv, β1 and β4 integrin subunits. Out of the four ovarian cancer cell lines studied, ascites induced enhancement in the expression of uPA/uPAR in the more invasive OVCA 433 and HEY cell lines without any change in the noninvasive OVHS1 and moderately invasive PEO.36 cell lines. On the other hand, no change in the expression of α6 integrin or uPAR, in response to ascites, was observed in HOSE cells. In response to ascites, enhancement in proliferation and in adhesion was observed in all four ovarian cancer cell lines studied. In contrast, no significant increase in proliferation or adhesion by ascites was observed in HOSE cells. Ascites-induced expression of uPA/uPAR correlated with the increased invasiveness of HEY and OVCA 433 cell lines but was not seen in OVHS1, PEO.36 and HOSE cell lines. Upregulation of α6 integrin and uPA/uPAR correlated with the activation of Ras and downstream Erk pathways. Ascites-induced activation of Ras and downstream Erk can be inhibited by using inhibitory antibodies against α6 and β1 integrin and uPAR, consistent with the inhibition of proliferation, adhesion and invasive functions of ovarian cancer cell lines. Based on these findings, we conclude that ascites can induce selective upregulation of integrin and uPA/uPAR in ovarian cancer cells and these changes may modulate the functions of ovarian carcinomas

Spatial and temporal dimensions of landscape fragmentation across the Brazilian Amazon

The Brazilian Amazon in the past decades has been suffering severe landscape alteration, mainly due to anthropogenic activities, such as road building and land clearing for agriculture. Using a high-resolution time series of land cover maps (classified as mature forest, non-forest, secondary forest) spanning from 1984 through 2011, and four uncorrelated fragmentation metrics (edge density, clumpiness index, area-weighted mean patch size and shape index), we examined the temporal and spatial dynamics of forest fragmentation in three study areas across the Brazilian Amazon (Manaus, Santarém and Machadinho d’Oeste), inside and outside conservation units. Moreover, we compared the impacts on the landscape of: (1) different land uses (e.g. cattle ranching, crop production), (2) occupation processes (spontaneous vs. planned settlements) and (3) implementation of conservation units. By 2010/2011, municipalities located along the Arc of Deforestation had more than 55% of the remaining mature forest strictly confined to conservation units. Further, the planned settlement showed a higher rate of forest loss, a more persistent increase in deforested areas and a higher relative incidence of deforestation inside conservation units. Distinct agricultural activities did not lead to significantly different landscape structures; the accessibility of the municipality showed greater influence in the degree of degradation of the landscapes. Even with a high proportion of the landscapes covered by conservation units, which showed a strong inhibitory effect on forest fragmentation, we show that dynamic agriculturally driven economic activities, in municipalities with extensive road development, led to more regularly shaped, heavily fragmented landscapes, with higher densities of forest edge

Smart Phone, Smart Science: How the Use of Smartphones Can Revolutionize Research in Cognitive Science

Investigating human cognitive faculties such as language, attention, and memory most often relies on testing small and homogeneous groups of volunteers coming to research facilities where they are asked to participate in behavioral experiments. We show that this limitation and sampling bias can be overcome by using smartphone technology to collect data in cognitive science experiments from thousands of subjects from all over the world. This mass coordinated use of smartphones creates a novel and powerful scientific “instrument” that yields the data necessary to test universal theories of cognition. This increase in power represents a potential revolution in cognitive science