GFINDer: Genome Function INtegrated Discoverer through dynamic annotation, statistical analysis, and mining

Statisticalandclustering analyses ofgeneexpression results from high-density microarray experiments produce lists of hundreds of genes regulated differentially, or with particular expression profiles, in the conditions under study. Independent of the microarray platforms and analysis methods used, these lists must be biologically interpreted to gain a better knowledge of the patho-physiological phenomena involved. To this end, numerous biological annotations are available within heterogeneous and widely distributed databases. Although several tools have been developed for annotating lists of genes, most of them do not give methods for evaluating the relevance of the annotations provided, or for estimating the functional bias introduced by the gene set on the array used to identify the gene list considered. We developed Genome Functional INtegrated Discoverer (GFINDer ), a web server able to automatically provide large-scale lists of user-classified genes with functional profiles biologically characterizing the different gene classes in the list. GFINDer automatically retrieves annotations of several functional categories from different sources, identifies the categories enriched in each class of a user-classified gene list and calculates statistical significance values for each category. Moreover, GFINDer enables the functional classification of genes according to mined functional categories and the statistical analysis is of the classifications obtained, aiding better interpretationof microarray experiment results. GFINDer is available online at http://www.medinfopoli.polimi.it/GFINDer/

Exponential distribution of long heart beat intervals during atrial fibrillation and their relevance for white noise behaviour in power spectrum

The statistical properties of heart beat intervals of 130 long-term surface electrocardiogram recordings during atrial fibrillation (AF) are investigated. We find that the distribution of interbeat intervals exhibits a characteristic exponential tail, which is absent during sinus rhythm, as tested in a corresponding control study with 72 healthy persons. The rate of the exponential decay lies in the range 3-12 Hz and shows diurnal variations. It equals, up to statistical uncertainties, the level of the previously uncovered white noise part in the power spectrum, which is also characteristic for AF. The overall statistical features can be described by decomposing the intervals into two statistically independent times, where the first one is associated with a correlated process with 1/f noise characteristics, while the second one belongs to an uncorrelated process and is responsible for the exponential tail. It is suggested to use the rate of the exponential decay as a further parameter for a better classification of AF and for the medical diagnosis. The relevance of the findings with respect to a general understanding of AF is pointed out

Arándanos: modificaciones en la calidad de frutos refrigerados previa fertilización foliar con calcio y potasio

El arándano presenta un comportamiento climatérico, caracterizado por un alza en la actividad respiratoria y producción de etileno durante la madurez. Es importante considerar que el comportamiento en postcosecha puede ser distinto entre variedades, ya que éstas pueden presentar un metabolismo diferente en relación a la respiración y producción de etileno, susceptibilidad a pudriciones, firmeza a la cosecha y postcosecha, relación azúcar/ácidos, etc. Sin embargo, existe un punto común para todas ellas, y es que se caracterizan por ser muy perecibles después de cosecha. Entre las principales causas de deterioro en arándano están: pudriciones, deshidratación, pérdida de firmeza, pérdida de apariencia, desarrollo de desórdenes y calidad sensorial. El estudio se realizó durante la temporada 2021 en una plantación de 13 años de edad, de la variedad O´Neil, ubicado en la Estación Experimental “Julio Hirschhorn”, perteneciente a la Facultad de Ciencias Agrarias y Forestales de la Universidad Nacional de la Plata.Facultad de Ciencias Agrarias y Forestale

Coherent movement of error-prone individuals through mechanical coupling

We investigate how reliable movement can emerge in aggregates of highly error-prone individuals. The individuals - robotic modules - move stochastically using vibration motors. By coupling them via elastic links, soft-bodied aggregates can be created. We present distributed algorithms that enable the aggregates to move and deform reliably. The concept and algorithms are validated through formal analysis of the elastic couplings and experiments with aggregates comprising up to 49 physical modules - among the biggest soft-bodied aggregates to date made of autonomous modules. The experiments show that aggregates with elastic couplings can shrink and stretch their bodies, move with a precision that increases with the number of modules, and outperform aggregates with no, or rigid, couplings. Our findings demonstrate that mechanical couplings can play a vital role in reaching coherent motion among individuals with exceedingly limited and error-prone abilities, and may pave the way for low-power, stretchable robots for high-resolution monitoring and manipulation

An improved algorithm for respiration signal extraction from electrocardiogram measured by conductive textile electrodes using instantaneous frequency estimation

In this paper, an improved algorithm for the extraction of respiration signal from the electrocardiogram (ECG) in home healthcare is proposed. The whole system consists of two-lead electrocardiogram acquisition using conductive textile electrodes located in bed, baseline fluctuation elimination, R-wave detection, adjustment of sudden change in R-wave area using moving average, and optimal lead selection. In order to solve the problems of previous algorithms for the ECG-derived respiration (EDR) signal acquisition, we are proposing a method for the optimal lead selection. An optimal EDR signal among the three EDR signals derived from each lead (and arctangent of their ratio) is selected by estimating the instantaneous frequency using the Hilbert transform, and then choosing the signal with minimum variation of the instantaneous frequency. The proposed algorithm was tested on 15 male subjects, and we obtained satisfactory respiration signals that showed high correlation (r2 > 0.8) with the signal acquired from the chest-belt respiration sensor

A Fisher-Rao metric for paracatadioptric images of lines

In a central paracatadioptric imaging system a perspective camera takes an image of a scene reflected in a paraboloidal mirror. A 360° field of view is obtained, but the image is severely distorted. In particular, straight lines in the scene project to circles in the image. These distortions make it diffcult to detect projected lines using standard image processing algorithms. The distortions are removed using a Fisher-Rao metric which is defined on the space of projected lines in the paracatadioptric image. The space of projected lines is divided into subsets such that on each subset the Fisher-Rao metric is closely approximated by the Euclidean metric. Each subset is sampled at the vertices of a square grid and values are assigned to the sampled points using an adaptation of the trace transform. The result is a set of digital images to which standard image processing algorithms can be applied. The effectiveness of this approach to line detection is illustrated using two algorithms, both of which are based on the Sobel edge operator. The task of line detection is reduced to the task of finding isolated peaks in a Sobel image. An experimental comparison is made between these two algorithms and third algorithm taken from the literature and based on the Hough transform

Statement of Foliar Fertilization Impact on Yield, Composition, and Oxidative Biomarkers in Rice

In rice crops, fertilization is a naturalized practice, although inefficient, that could be improved by applying foliar fertilization. Phytoprostanes (PhytoPs) and phytofurans (PhytoFs) are products of α-linolenic acid peroxidation, useful as biomarkers of oxidative degradation in higher plants. The objective was to determine the effect of the foliar fertilization on the concentration of PhytoPs and PhytoFs and its relationships with modifications of yield and quality of rice productions. It was described that the concentration of biomarkers of stress decreased with the application of foliar fertilization, being the response significantly different depending the genotypes and compound monitored. Moreover, fertilization did not modify significantly the parameters of yield (961.2 g m−2), 1000 whole-grain (21.2 g), and protein content (10.7% dry matter). Therefore, this is the first work that describes the effect of fertilization on PhytoPs and PhytoFs in rice genotypes and reinforces the capacity of these compounds as biomarkers to monitor specific abiotic stress, in this case, represented by nutritional stress.Facultad de Ciencias Agrarias y Forestale

Quality-sensitive foraging by a robot swarm through virtual pheromone trails

Large swarms of simple autonomous robots can be employed to find objects clustered at random locations, and transport them to a central depot. This solution offers system parallelisation through concurrent environment exploration and object collection by several robots, but it also introduces the challenge of robot coordination. Inspired by ants’ foraging behaviour, we successfully tackle robot swarm coordination through indirect stigmergic communication in the form of virtual pheromone trails. We design and implement a robot swarm composed of up to 100 Kilobots using the recent technology Augmented Reality for Kilobots (ARK). Using pheromone trails, our memoryless robots rediscover object sources that have been located previously. The emerging collective dynamics show a throughput inversely proportional to the source distance. We assume environments with multiple sources, each providing objects of different qualities, and we investigate how the robot swarm balances the quality-distance trade-off by using quality-sensitive pheromone trails. To our knowledge this work represents the largest robotic experiment in stigmergic foraging, and is the first complete demonstration of ARK, showcasing the set of unique functionalities it provides

Rapidly detecting disorder in rhythmic biological signals: A spectral entropy measure to identify cardiac arrhythmias

We consider the use of a running measure of power spectrum disorder to distinguish between the normal sinus rhythm of the heart and two forms of cardiac arrhythmia: atrial fibrillation and atrial flutter. This spectral entropy measure is motivated by characteristic differences in the spectra of beat timings during the three rhythms. We plot patient data derived from ten-beat windows on a "disorder map" and identify rhythm-defining ranges in the level and variance of spectral entropy values. Employing the spectral entropy within an automatic arrhythmia detection algorithm enables the classification of periods of atrial fibrillation from the time series of patients' beats. When the algorithm is set to identify abnormal rhythms within 6 s it agrees with 85.7% of the annotations of professional rhythm assessors; for a response time of 30 s this becomes 89.5%, and with 60 s it is 90.3%. The algorithm provides a rapid way to detect atrial fibrillation, demonstrating usable response times as low as 6 s. Measures of disorder in the frequency domain have practical significance in a range of biological signals: the techniques described in this paper have potential application for the rapid identification of disorder in other rhythmic signals.Comment: 11 page

Methodological Guidelines for Engineering Self-organization and Emergence

The ASCENS project deals with the design and development of complex self-adaptive systems, where self-organization is one of the possible means by which to achieve self-adaptation. However, to support the development of self-organising systems, one has to extensively re-situate their engineering from a software architectures and requirements point of view. In particular, in this chapter, we highlight the importance of the decomposition in components to go from the problem to the engineered solution. This leads us to explain and rationalise the following architectural strategy: designing by following the problem organisation. We discuss architectural advantages for development and documentation, and its coherence with existing methodological approaches to self-organisation, and we illustrate the approach with an example on the area of swarm robotics