A data mining framework based on boundary-points for gene selection from DNA-microarrays: Pancreatic Ductal Adenocarcinoma as a case study

[EN] Gene selection (or feature selection) from DNA-microarray data can be focused on different techniques, which generally involve statistical tests, data mining and machine learning. In recent years there has been an increasing interest in using hybrid-technique sets to face the problem of meaningful gene selection; nevertheless, this issue remains a challenge. In an effort to address the situation, this paper proposes a novel hybrid framework based on data mining techniques and tuned to select gene subsets, which are meaningfully related to the target disease conducted in DNA-microarray experiments. For this purpose, the framework above deals with approaches such as statistical significance tests, cluster analysis, evolutionary computation, visual analytics and boundary points. The latter is the core technique of our proposal, allowing the framework to define two methods of gene selection. Another novelty of this work is the inclusion of the age of patients as an additional factor in our analysis, which can leading to gaining more insight into the disease. In fact, the results reached in this research have been very promising and have shown their biological validity. Hence, our proposal has resulted in a methodology that can be followed in the gene selection process from DNA-microarray data

Growth at moulth, intermoult period and moulting seasonality of the spider crab "Maja brachydactyla" : combining information from mark-recapture and experimental studies

[Abstract] An analysis of growth at moult (for both the prepubertal and terminal moults), moulting seasonality and the intermoult period in the spider crab Maja squinado in the Ría de A Coruña (NW Spain) was carried out based on a mark-recapture experiment. Crabs between 70 and 130 mm carapace length (CL) undergo a mean increase at moult of 32.4% from their pre-moult size. Generalised Linear Models (GLMs) were used to construct growth models, employing a combination of information from the mark-recapture study and other previous studies performed in both laboratory and extensive culture, to estimate the effects of the biological variables and the study method. No differences were found in the growth rate between males and females. However, the effects of the study method, the premoult CL and the interaction between them were significant. The smallest-sized crabs undergo a greater increase in size in the laboratory and culture studies, while the largest individuals undergo greater growth in the field. The mean intermoult period estimated for prepubertal moults in the field ranged from 50 to 86 days, which Corgos et al., GROWTH AT MOULT OF MAJA BRACHYDACTYLA is similar to the 84.7 days observed in the laboratory study. The prepubertal moults occurred primarily in spring and autumn in the field, while under culture conditions, the crabs moulted mainly in the spring. The intermoult period for terminal moults was estimated to be around 90 days, slightly lower than the value of 104 days obtained in the laboratory. The terminal moult took place generally in summer (June-September) both at sea as well as in culture experiments. The intermoult period of juveniles at sea was highly variable, and some of the specimens did not moult for more than 5 months.Ministerio de Ciencia y Tecnología; REN2000-0446MARXunta de Galicia; XUGA10301B9

An Ensemble Framework Coping with Instability in the Gene Selection Process

[EN] This paper proposes an ensemble framework for gene selection, which is aimed at addressing instability problems presented in the gene filtering task. The complex process of gene selection from gene expression data faces different instability problems from the informative gene subsets found by different filter methods. This makes the identification of significant genes by the experts difficult. The instability of results can come from filter methods, gene classifier methods, different datasets of the same disease and multiple valid groups of biomarkers. Even though there is a wide number of proposals, the complexity imposed by this problem remains a challenge today. This work proposes a framework involving five stages of gene filtering to discover biomarkers for diagnosis and classification tasks. This framework performs a process of stable feature selection, facing the problems above and, thus, providing a more suitable and reliable solution for clinical and research purposes. Our proposal involves a process of multistage gene filtering, in which several ensemble strategies for gene selection were added in such a way that different classifiers simultaneously assess gene subsets to face instability. Firstly, we apply an ensemble of recent gene selection methods to obtain diversity in the genes found (stability according to filter methods). Next, we apply an ensemble of known classifiers to filter genes relevant to all classifiers at a time (stability according to classification methods). The achieved results were evaluated in two different datasets of the same disease (pancreatic ductal adenocarcinoma), in search of stability according to the disease, for which promising results were achieved

An agent-based clustering approach for gene selection in gene expression microarray

Gene selection is a major research area in microarray analysis, which seeks to discover differentially expressed genes for a particular target annotation. Such genes also often called informative genes are able to differentiate tissue samples belonging to different classes of the studied disease. Despite the fact that there is a wide number of proposals, the complexity imposed by this problem remains a challenge today. This research proposes a gene selection approach by means of a clustering-based multiagent system. This proposal manages different filter methods and gene clustering through coordinated agents to discover informative gene subsets. To assess the reliability of our approach, we have used four important and public gene expression datasets, two Lung cancer datasets, Colon and Leukemia cancer dataset. The achieved results have been validated through cluster validity measures, visual analytics, a classifier and compared with other gene selection methods, proving the reliability of our proposal

Management strategies for sustainable invertebrate fisheries in coastal ecosystems of Galicia (NW Spain)

The original publication in avaliable at www. springerlink.comArtisanal coastal invertebrate fisheries in Galicia are socio-economically important and ecologically relevant. Their management, however, has been based on models of fish population dynamics appropriate for highly mobile demersal or pelagic resources and for industrial fisheries. These management systems focus on regulating fishing effort, but in coastal ecosystems activities that change or destruct key habitats may have a greater effect on population abundance than does fishing mortality. The Golfo Artabro was analysed as a representative example of a coastal ecosystem in Galicia, and the spider crab "Maja squinado" used as a model of an exploited coastal invertebrate, for which shallow coastal areas are key habitats for juvenile stages. The commercial legal gillnet fishery for the spider crab harvests adults during their reproductive migrations to deep waters and in their wintering habitats. Illegal fisheries operate in shallow waters. The annual rate of exploitation is higher to 90%, and lower to 10% of the primiparous females reproduce effectively at least once. A simple spatially-explicit cohort model was constructed to simulate the population dynamics of spider crab females. Yield- and egg-per-recruit analyses corresponding to different exploitation regimes were performed to compare management policies directed to control the fishing effort or to protect key habitats. It was found that the protection of juvenile habitats could allow increases in yield and reproductive effort higher than in the present system, with such protection based in the control of the fishing effort of the legal fishery. Additionally, there is an urgent need for alternative research and management strategies in artisanal coastal fisheries based on the implementation of a system of territorial use rights for fishers, the integration of the fishers into assessment and management processes, and the protection of key habitats (marine reserves) as a basic tool for the regulation of the fisheries.Xunta de Galicia; XUGA10301B9

Relationship of Body Composition with the Strength and Functional Capacity of People over 70 Years

Producción CientíficaBackground: Aging is a multifactorial physiological phenomenon, in which a series of changes in the body composition occur, such as a decrease in muscle mass and bone mineral density and an increase in fat mass. This study aimed to determine the relationship of muscle mass, osteoporosis, and obesity with the strength and functional capacity of non-dependent people over 70 years of age. Methods: A cross-sectional study was designed, whose study population was all people aged over 70 years, living independently and attending academic and recreational programs. Muscle strength and functional capacity of the participants were assessed by isometric exercises of lower and upper limbs and by four tests taken from the Senior Fitness Test, respectively. Bone mineral density, total mass, fat mass, total lean mass, arms lean mass, legs lean mass, and appendicular lean mass (ALM) was calculated by dual energy X-ray absorptiometry. Differences in muscle strength and functional capacity, according to the sex, muscle mass, mineral bone density and fat mass, were measured by χ2 test, independent samples Student’s t-test, analysis of covariance and a 2-factor analysis of covariance; Results: 143 subjects were included in the study group. Men and women with an adequate amount of ALM adjusted for body mass index (BMI) had a maximal dynamic biceps strength in a single repetition, a maximal isometric leg extension strength, a maximal dynamic leg extension strength in a single repetition, a maximum right hand grip strength and maximum hand grip strength (the highest). Significantly higher values were observed in the maximal isometric biceps’ strength in men with osteoporosis. Obese men had less isometric strength in the biceps and took longer to perform the chair stand test; Conclusions: Men and women with an adequate amount of ALM adjusted for BMI obtained better results in tests of muscle strength and functional capacity. However, osteoporosis and obesity are not related to these parameters

Wireless Sensor Networks in Home Care

Ambient Intelligence has acquired great importance in recent years and requires the development of new innovative solutions. This paper presents a novel architecture which integrates a service oriented approach into Wireless Sensor Networks to optimize the construction of Ambient Intelligence environments. The architecture proposes a new and easier method to develop distributed intelligent ubiquitous systems, where devices can communicate in a distributed way independent of time and location restrictions. The architecture is easily adapted to changing environments. A prototype system has been proposed to test this architecture. This system is aimed to improve health care and assistance to dependent persons in their homes. Preliminary results are presented in this paper

Similar incidence of coronavirus disease 2019 (COVID-19) in patients with rheumatic diseases with and without hydroxychloroquine therapy

Background Hydroxychloroquine is not efficacious as post-exposure prophylaxis against coronavirus disease 2019 (COVID-19). It is not known whether as pre-exposure prophylaxis it may prevent COVID-19. Objective To compare the incidence of COVID-19 in Spanish patients with autoimmune rheumatic diseases treated with and without hydroxychloroquine. Patients and methods Retrospective electronic record review, from February 27th to June 21st, 2020, of patients with autoimmune inflammatory diseases followed at two academic tertiary care hospitals in Seville, Spain. The cumulative incidence of confirmed COVID-19, by PCR or serology, was compared between patients with and without hydroxychloroquine as part of their treatment of autoimmune inflammatory diseases. Results Among 722 included patients, 290 (40%) were receiving hydroxychloroquine. During the seventeen-week study period, 10 (3.4% [95% CI: 1.7%-6.7%] cases of COVID-19 were registered among patients with hydroxychloroquine and 13 (3.0% [1.6%-5.1%]) (p = 0.565) in those without hydroxychloroquine. COVID-19 was diagnosed by PCR in four (1.4%, 95% CI 0.38%-3.5%) subject with hydroxychloroquine and six (1.4%, 95% CI 0.5%-3.0%) without hydroxychloroquine (p = 0.697). Three patients on hydroxychloroquine and four patients without hydroxychloroquine were admitted to the hospital, none of them required to be transferred to the intensive care unit and no patient died during the episode. Conclusions The incidence and severity of COVID-19 among patients with autoimmune rheumatic diseases with and without hydroxychloroquine was not significantly different.Instituto de Salud Carlos III I3SNSMinisterio de Ciencia, Innovación y Universidades CP18/0014

Polyphenolic content, in vitro antioxidant activity and chemical composition of extract from Nephelium lappaceum L. (Mexican rambutan) husk

Objective: To determinate the recovery of total polyphenolic compounds content, in vitro antioxidant activity and HPLC/ESI/MS characterization of extract from Nephelium lappaceum L. (Mexican rambutan). Methods: The rambutan husk extract was obtained by aqueous extraction and a polyphenolic fraction was recovered using Amberlite XAD-16. The total polyphenolic compounds content was determined by the Folin Ciocalteu and butanol-HCI methods. In vitro antioxidant activity was performed using ABTS and ferric reducing antioxidant power methods. Results: Mexican rambutan husk showed a total polyphenolic content of 582 mg/g and an evident antioxidant activity by ABTS and ferric reducing antioxidant power analysis. The HPLC/ESI/MS assay allowed the identification of 13 compounds, most of which belong to ellagitannins. Geraniin, corilagin and ellagic acid were present in the sample; the mineral composition was also evaluated. Conclusions: Rambutan husk cultivated in Mexico is a promising source for the recovery of added value bioactive compounds with antioxidant activity, which have potentialapplications as bioactive antioxidant agents for the treatment of diseases