Studying hypertension in ocular fundus images using Hausdorff dispersion ordering.
Retinal arterial and vein diameters are altered in individuals at risk of cardiovascular events mainly due to high blood pressure. The measurement of retinal vessel diameters has been proved to reflect individuals' vascular health. Dispersion of such measures which are obtained by means of ocular fundus images is a major factor not usually considered in clinical research. In this paper, a method to evaluate if different levels of clinically relevant covariables induce greater dispersion in retinal arterial and vein diameters is proposed. A multivariate dispersion ordering, the Hausdorff dispersion order, is used to compare the level of dispersion in such diameters for different groups of pa…
Fuzzy temporal random sets with an application to cell biology
Total Internal Reflection Fluorescence Microscopy (TIRFM) greatly facilitates to imaging the first steps of endocytosis, a process whereby cells traffic cargo from the cell surface to endosomes. Using TIRFM, fluorescent-tagged endocytic proteins are observed as overlapped areas forming random clumps of different sizes, shapes and durations. A common procedure to segment these objects consists of thresholding the original gray-level images to produce binary sequences in which a pixel is covered or not by a given fluorescent-tagged protein. This binary logic is not appropriate because it leaves a free tuning parameter to be set by the user which can influence on the conclusions of the statist…
Functional statistics based method for the evaluation of the registration of sequences of 3D perfusion MR images
Accurate registration of medical images is a necessary task for several important diagnosis techniques. Nevertheless, it is a difficult challenge due to movement of the patient, deformations, noise in the signal, etc. Besides, evaluation of the quality of the performed registration is also troublesome, specially when no golden pattern (true result) is available and/or when the signal values may have changed between successive images/volumes to be registered.
Clustering of spatial point patterns
Spatial point patterns arise as the natural sampling information in many problems. An ophthalmologic problem gave rise to the problem of detecting clusters of point patterns. A set of human corneal endothelium images is given. Each image is described by using a point pattern, the cell centroids. The main problem is to find groups of images corresponding with groups of spatial point patterns. This is interesting from a descriptive point of view and for clinical purposes. A new image can be compared with prototypes of each group and finally evaluated by the physician. Usual descriptors of spatial point patterns such as the empty-space function, the nearest distribution function or Ripley's K-…
Towards a mean body for apparel design
This paper focuses on shape average with applications to the apparel industry. Apparel industry uses a consensus sizing system; its major concern is to fit most of the population into it. Since anthropometric measures do not grow linearly, it is important to find prototypes to accurately represent each size. This is done using random compact mean sets, obtained from a cloud of 3D points given by a scanner and applying to the sample a previous definition of mean set. Additionally, two approaches to define confidence sets are introduced. The methodology is applied to data obtained from a real anthropometric survey. This paper has been partially supported by the following grants: TIN2009-14392…
Sparse Sampling and Maximum Likelihood Estimation for Boolean Models
A condition for practical independence of contact distribution functions in Boolean models is obtained. This result allows the authors to use maximum likelihcod methods, via sparse sampling, for estimating unknown parameters of an isotropic Boolean model. The second part of this paper is devoted to a simulation study of the proposed method. AMS classification: 60D05
Different averages of a fuzzy set with an application to vessel segmentation
Image segmentation is a major problem in image processing, particularly in medical image analysis. A great number of segmentation procedures produce intermediate gray-scale images that can be understood as fuzzy sets. Additionally, some segmentation procedures tend to leave free tuning parameters (very influential in the final binary image) for the user. These different binary images can be easily aggregated (into a fuzzy set) by making use of fuzzy set theory. In any case, a single binary image is required so our interest is to associate a crisp set to a given fuzzy set in an intelligent and unsupervised manner. The main idea of this paper is to define the averages of a given fuzzy set by …
The relative importance of transcription rate, cryptic transcription and mRNA stability on shaping stress responses in yeast
It has been recently stated that stress-responding genes in yeast are enriched in cryptic transcripts and that this is the cause of the differences observed between mRNA amount and RNA polymerase occupancy profiles. Other studies have shown that such differences are mainly due to modulation of mRNA stabilities. Here we analyze the relationship between the presence of cryptic transcripts in genes and their stress response profiles. Despite some of the stress-responding gene groups being indeed enriched in specific classes of cryptic transcripts, we found no statistically significant evidence that cryptic transcription is responsible for the differences observed between mRNA and transcription…
In silico RNA-seq and experimental analyses reveal the differential expression and splicing of EPDR1 and ZNF518B genes in relation to KRAS mutations in colorectal cancer cells.
Several drugs used for the treatment of colorectal cancer (CRC) are targeted at the epidermal growth factor receptor, but mutations in genes of the RAS family cause resistance to these drugs. Thus, extensive research is being carried out to counterbalance this resistance. The G13D mutation of KRAS is common in humans, and we previously reported that this mutation results in the epigenetic modification of hnRNP proteins, involved in RNA splicing. As aberrant splicing often results in oncogenicity, the present study aimed to identify the genes which show altered splicing patterns in connection with the G13D KRAS mutation. To accomplish this, we first carried out an in silico analysis of RNA-s…
Fuzzy Logic for Medical Engineering: An Application to Vessel Segmentation
Functional Data Analysis for ECG Recordings of Paroxysmal Atrial Fibrillation Patients Before and After Pulmonary Vein Isolation
Pulmonary vein isolation is the cornestone of current ablation techniques for patients with paroxysmal atrial fibrillation in order avoid recurrences of the arrhythmia and maintain sinus rhythm. This study aimed to analyse the existence of significant variations in surface ECG after pulmonary vein isolation by means of functional data analysis. 12 consecutive unselected patients suffering from paroxysmal atrial fibrillation who underwent catheter ablation were included in the study. Each patient was monitored in sinus rhythm before and after catheter ablation. P-waves of bipolar lead II were delineated. Functional data were fitted from these segments and the first and second derivatives eva…
Working with (too) Few Samples
This paper is concerned with gene set differential expression analysis. We compare the transcriptomic behaviour of each gene set between different experimental conditions.The gene set is previously defined. It has been used a gene set collection downloaded from Gene Ontology.A randomization test is proposed and compared with other previous procedures using a RNA-seq experiment of colorectal cancer (CRC).
Loss of endocytic clathrin-coated pits upon acute depletion of phosphatidylinositol 4,5-bisphosphate.
Phosphatidylinositol 4,5-bisphosphate [PI(4,5) P 2 ], a phosphoinositide concentrated predominantly in the plasma membrane, binds endocytic clathrin adaptors, many of their accessory factors, and a variety of actin-regulatory proteins. Here we have used fluorescent fusion proteins and total internal reflection fluorescence microscopy to investigate the effect of acute PI(4,5) P 2 breakdown on the dynamics of endocytic clathrin-coated pit components and of the actin regulatory complex, Arp2/3. PI(4,5) P 2 breakdown was achieved by the inducible recruitment to the plasma membrane of an inositol 5-phosphatase module through the rapamycin/FRB/FKBP system or by treatment with ionomycin. PI(4,5)…
Applying logistic regression to relevance feedback in image retrieval systems
This paper deals with the problem of image retrieval from large image databases. A particularly interesting problem is the retrieval of all images which are similar to one in the user's mind, taking into account his/her feedback which is expressed as positive or negative preferences for the images that the system progressively shows during the search. Here we present a novel algorithm for the incorporation of user preferences in an image retrieval system based exclusively on the visual content of the image, which is stored as a vector of low-level features. The algorithm considers the probability of an image belonging to the set of those sought by the user, and models the logit of this prob…
Measuring Spatiotemporal Dependencies in Bivariate Temporal Random Sets with Applications to Cell Biology
Analyzing spatiotemporal dependencies between different types of events is highly relevant to many biological phenomena (e.g., signaling and trafficking), especially as advances in probes and microscopy have facilitated the imaging of dynamic processes in living cells. For many types of events, the segmented areas can overlap spatially and temporally, forming random clumps. In this paper, we model the binary image sequences of two different event types as a realization of a bivariate temporal random set and propose a nonparametric approach to quantify spatial and spatiotemporal interrelations using the pair correlation, cross-covariance, and the Ripley K functions. Based on these summary st…
Using mathematical morphology for unsupervised classification of functional data
This paper is concerned with the unsupervised classification of functional data by using mathematical morphology. Different morphological operators are used to extract relevant structures of the functions (considered as sets through their subgraph representations). These operators can be considered as preprocessing tools whose outputs are also functional data. We explore some dissimilarity measures and clustering methods for the classification of the transformed data. Our approach is illustrated through a detailed analysis of two data sets. These techniques, which have mainly been used in image processing, provide a flexible and robust toolbox for improving the results in unsupervised funct…
OMICfpp: a fuzzy approach for paired RNA-Seq counts
© The Author(s) 2019.
Measuring the Spatial Homogeneity in Corneal Endotheliums by Means of a Randomization Test
Quantification of regularity of cell sizes and the spatial arrangement of cells in corneal endotheliums becomes of a great importance associated to stress situations such as cataract surgery, corneal transplantation or implantation of intra-ocular lenses. A new index of regularity of the spatial distribution of cell sizes in corneal endotheliums is proposed. The corneal endothelium is described by means of a spatial marked point pattern (the cell centroids marked with the cell areas). The hypothesis of no dependency between mark and locations is tested by a Monte Carlo test. The new index is the p-value of the test validating the hypothesis. Pairs of endotheliums from different eyes of the …
Looking for representative fit models for apparel sizing
This paper is concerned with the generation of optimal fit models for use in apparel design. Representative fit models or prototypes are important for defining a meaningful sizing system. However, there is no agreement among apparel manufacturers and each one has their own prototypes and size charts i.e. there is a lack of standard sizes in garments from different apparel manufacturers. We propose two algorithms based on a new hierarchical partitioning around medoids clustering method originally developed for gene expression data. We are concerned with a different application; therefore, the dissimilarity between the objects has to be different and must be designed to deal with anthropometr…
Accurate detection and characterization of corner points using circular statistics and fuzzy clustering
Accurate detection and characterization of corner points in grey level images is considered as a pattern recognition problem. The method considers circular statistic tests to detect 2D features. A fuzzy clustering algorithm is applied to the edge orientations near the prospective corners to detect and classify them. The method is based on formulating hypotheses about the distribution of these orientations around an edge, corner or other 2-D feature. The method may provide accurate estimates of the direction of the edges that converge in a corner, along with their confidence intervals. Experimental results show the method to be robust enough against noise and contrast changes. Fuzzy membersh…
Studying endocytosis in space and time by means of temporal Boolean models
Endocytosis is a process by which cells carry traffic from the extracellular space into various intracellular compartments. Visualization of fluorescently tagged clathrin proteins (mediators of endocytosis) allows us to image endocytosis in real time. When imaging the plasma membrane, areas of fluorescence generated by different endocytic processes overlap spatially and temporally, forming random clumps. Here, a sequence of segmented clathrin spots is considered a realization of a non-isotropic 3D Boolean model. Estimates of the intensity, the mean perimeter and the density function of the durations of endocytic events are obtained.
R Code for Hausdorff and Simplex Dispersion Orderings in the 2D Case
This paper proposes a software implementation using R of the Hausdorff and simplex dispersion orderings. A copy can be downloaded from http://www.uv.es/~ayala/software/fun-disp.R . The paper provides some examples using the functions exactHausdorff for the Hausdorff dispersion ordering and the function simplex for the simplex dispersion orderings. Some auxiliary functions are commented too.
Analyzing Protein-Protein Spatial-Temporal Dependencies from Image Sequences Using Fuzzy Temporal Random Sets
Total Internal Reflection Fluorescence Microscopy (TIRFM) allows us to image fluorescenttagged proteins near the plasma membrane of living cells with high spatial-temporal resolution. Using TIRFM imaging of GFP-tagged clathrin endocytic proteins, areas of fluorescence are observed as overlapping spots of different sizes and durations. Standard procedures to measure protein-protein colocalization of dual labeled samples threshold the original graylevel images to segment areas covered by different proteins. This binary logic is not appropriate as it leaves a free tuning parameter which can influence the conclusions. Moreover, these procedures rely on simple statistical analysis based on corre…
Analysis of Spatially and Temporally Overlapping Events with Application to Image Sequences
Counting spatially and temporally overlapping events in image sequences and estimating their shape-size and duration features are important issues in some applications. We propose a stochastic model, a particular case of the nonisotropic 3D Boolean model, for performing this analysis: the temporal Boolean model. Some probabilistic properties are derived and a methodology for parameter estimation from time-lapse image sequences is proposed using an explicit treatment of the temporal dimension. We estimate the mean number of germs per unit area and time, the mean grain size and the duration distribution. A wide simulation study in order to assess the proposed estimators showed promising resul…
A granulometric analysis of specular microscopy images of human corneal endothelia
The inner layer of the human cornea, called the corneal endothelium, plays an important role in the maintenance of corneal transparency. Specular microscopy is the most widely used technique to study the corneal endothelium in vivo. Improvements in technology have allowed us to obtain good quality specular images, but the detection and quantification of small size-shape cell changes is not obvious, specially when the physician wants to evaluate endothelial cell changes after some surgical procedures. This paper proposes a methodology to analyze specular microscopy images. Every corneal endothelium is described by means of different cumulative distribution functions or some moments (mean, st…
The simplex dispersion ordering and its application to the evaluation of human corneal endothelia
A multivariate dispersion ordering based on random simplices is proposed in this paper. Given a R^d-valued random vector, we consider two random simplices determined by the convex hulls of two independent random samples of sizes d+1 of the vector. By means of the stochastic comparison of the Hausdorff distances between such simplices, a multivariate dispersion ordering is introduced. Main properties of the new ordering are studied. Relationships with other dispersion orderings are considered, placing emphasis on the univariate version. Some statistical tests for the new order are proposed. An application of such ordering to the clinical evaluation of human corneal endothelia is provided. Di…
Macular edema computer-aided evaluation in ocular vein occlusions.
This paper is concerned with the use of digital fundus imaging to detect, quantify, and follow up macular angiographic leakage due to retinal vein occlusions. Images were matched automatically. We detected those pixels with a high increment in gray level within the closest area to the foveal center. Binary images displaying leakage were obtained. The procedure was checked against two observers' agreement. Twenty-one angiographic studies were collected. Two images of each sequence were selected for digitalization. Numerical descriptors of the leakage were proposed and quantification plots were designed for each pair of images. Interobserver concordance ranged between 82 and 98% when manually…
Set Descriptors for Visual Evaluation of Human Corneal Endothelia
Images of corneal endothelium obtained from specular microscopy are of great importance in the evaluation of the corneal endothelium status. Several commercial tools provide some numerical descriptors to characterize these images in terms of cell density, hexagonality, and some descriptive statistics of the cell areas. However, it is a too simple analysis that only detects severe abnormal endothelia with many irregular and large cells. Detection of subtle abnormalities needs a more refined analysis. This paper proposes a shape-size descriptor based on some modified versions of the geometric covariogram. This descriptor is presented as a valid alternative to the classical analysis that provi…
Image retrieval system for citizen services using penalized logistic regression models
This paper describes a procedure to deal with large image collections obtained by smart city services based on interaction with citizens providing pictures. The semantic gap between the low-level image features and represented concepts and situations has been addressed using image retrieval techniques. A relevance feedback procedure is proposed for Content-Based Image Retrieval (CBIR) based on the modelling of user responses. One of the novelties of the proposal is that the feedback learning procedure can use the information that citizens themselves can provide when using these services.The proposed algorithm considers the probability of an image belonging to the set of those sought by the …
Evaluation of the registration of temporal series of contrast-enhanced perfusion magnetic resonance 3D images of the liver.
The registration of 2D and 3D images is one of the key tasks in medical image processing and analysis. Accurate registration is a crucial preprocessing step for many tasks; consequently, the evaluation of its accuracy becomes necessary. Unfortunately, this is a difficult task, especially when no golden pattern (true result) is available and when the signal values may have changed between successive images to be registered. This is the case this paper deals with: we have a series of 3D images, magnetic resonance images (MRI) of the liver and adjacent areas that have to be registered. They have been taken while a contrast is diffused through the liver tissue, so intensity of each observed poi…
Automatic detection of large dense-core vesicles in secretory cells and statistical analysis of their intracellular distribution.
Analyzing the morphological appearance and the spatial distribution of large dense-core vesicles (granules) in the cell cytoplasm is central to the understanding of regulated exocytosis. This paper is concerned with the automatic detection of granules and the statistical analysis of their spatial locations in different cell groups. We model the locations of granules of a given cell as a realization of a finite spatial point process and the point patterns associated with the cell groups as replicated point patterns of different spatial point processes. First, an algorithm to segment the granules using electron microscopy images is proposed. Second, the relative locations of the granules with…
A novel Bayesian framework for relevance feedback in image content-based retrieval systems
This paper presents a new algorithm for image retrieval in content-based image retrieval systems. The objective of these systems is to get the images which are as similar as possible to a user query from those contained in the global image database without using textual annotations attached to the images. The main problem in obtaining a robust and effective retrieval is the gap between the low level descriptors that can be automatically extracted from the images and the user intention. The algorithm proposed here to address this problem is based on the modeling of user preferences as a probability distribution on the image space. Following a Bayesian methodology, this distribution is the pr…
Spatio-Temporal Analysis of Constitutive Exocytosis in Epithelial Cells
Exocytosis is an essential cellular trafficking process integral to the proper distribution and function of a plethora of molecules, including transporters, receptors, and enzymes. Moreover, incorrect protein targeting can lead to pathological conditions. Recently, the application of evanescent wave microscopy has allowed us to image the final steps of exocytosis. However, spatio-temporal analysis of fusion of constitutive vesicular traffic with the plasma membrane has not been systematically performed. Also, the spatial sites and times of vesicle fusion have not yet been analyzed together. In addition, more formal tests are required in testing biological hypotheses, rather than visual insp…
Resuming Shapes with Applications
Many image processing tasks need some kind of average of different shapes. Frequently, different shapes obtained from several images have to be summarized. If these shapes can be considered as different realizations of a given random compact set, then the natural summaries are the different mean sets proposed in the literature. In this paper, new mean sets are defined by using the basic transformations of Mathematical Morphology (dilation, erosion, opening and closing). These new definitions can be considered, under some additional assumptions, as particular cases of the distance average of Baddeley and Molchanov. The use of the former and new mean sets as summary descriptors of shapes is i…
Immunological Diagnosis of Human Cystic Echinococcosis: Utility of Discriminant Analysis Applied to the Enzyme-Linked Immunoelectrotransfer Blot
ABSTRACT An enzyme-linked immunoelectrotransfer blot for the diagnosis of human hydatid disease was performed, and the different antibody responses were analyzed by a discriminant analysis. This multivariate technique gave us, first, a selection of the most important responses against Echinococcus granulosus infection and, second, a procedure for the classification of patients into two groups: patients with hydatid disease and patients without a history of hydatid disease. This method was applied to 67 patients, 25 with active hydatid cysts (24 hepatic and 1 pulmonary) and 42 without a history of hydatid disease and was compared with the results obtained by conventional serology: indirect h…
A novel dynamic multi-model relevance feedback procedure for content-based image retrieval
This paper deals with the problem of image retrieval in large databases with a big semantic gap by a relevance feedback procedure. We present a novel algorithm for modelling the users's preferences in the content-based image retrieval system.The proposed algorithm considers the probability of an image belonging to the set of those sought by the user, and estimates the parameters of several local logistic regression models whose inputs are the low-level image features. A Principal Component Analysis method is applied to the original vector to reduce its high dimensionality. The relevance probabilities predicted by these local models are combined by means of a weighted average. These weights …
Bayesian estimation of edge orientations in junctions
Abstract Junctions, defined as those points of an image where two or more edges meet, play a significant role in many computer vision applications. Junction detection is a widely treated problem, and some detectors can provide even the directions of the edges that meet in a junction. The main objective of this paper is the precise estimation of such directions. It is supposed that the junction point has been previously found by some detector. Also, it is assumed that samples, possibly noisy, of orientations of the edges found in a circular window surrounding the point are available. A mixture of von Mises distributions is assumed for these data, and then a Bayesian methodology is applied to…
Granulometric moments and corneal endothelium status
Abstract Specular microscopy is a common practice in Ophthalmology. The corneal endothelium status is usually evaluated by means of the density, the hexagonality, the mean, the standard deviation and the coefficient of variation of cell areas. We propose to replace the cell area moments by the corresponding moments of a different probability distribution, the granulometric size distribution associated to a disc. All cells touching the frame are ignored by the area moments but used by the granulometric moments. Twenty images have been analyzed. When the size of the focused region is reduced, the area moments show a greater variation than the corresponding granulometric moments.
The cellular growth rate controls overall mRNA turnover, and modulates either transcription or degradation rates of particular gene regulons
We analyzed 80 different genomic experiments, and found a positive correlation between both RNA polymerase II transcription and mRNA degradation with growth rates in yeast. Thus, in spite of the marked variation in mRNA turnover, the total mRNA concentration remained approximately constant. Some genes, however, regulated their mRNA concentration by uncoupling mRNA stability from the transcription rate. Ribosome-related genes modulated their transcription rates to increase mRNA levels under fast growth. In contrast, mitochondria-related and stress-induced genes lowered mRNA levels by reducing mRNA stability or the transcription rate, respectively. We also detected these regulations within th…
Normalizing temporal patterns to analyze sit-to-stand movements by using registration of functional data
Functional data analysis techniques provide an alternative way of representing movement and movement variability as a function of time. In particular, the registration of functional data provides a local normalization of time functions. This normalization transforms a set of curves, records of repeated trials, yielding a new set of curves that only vary in terms of amplitude. Therefore, main events occur at the "same time" for all transformed curves and interesting features of individual recordings remain after averaging processes. This paper presents an application of the registration process to the analysis of the vertical forces exerted on the ground by both feet during the sit-to-stand …
Stochastic labelling of biological images
Many hypotheses made by experimental researchers can be formulated as a stochastic labelling of a given image. Some stochastic labelling methods for random closed sets are proposed in this paper. Molchanov (I. Molchanov, 1984, Theor. Probability and Math. Statist.29, 113–119) provided the probabilistic background for this problem. However, there is a lack of specific labelling models. Ayala and Simo (G. Ayala and A. Simo, 1995, Advances in Applied Probability27, 293–305) proposed a method in which, given the whole set of connected components, every component is classified in a certain phase or category in a completely random way. Alternative methods are necessary in case the random labellin…
Preoperative factors influencing success in pterygium surgery
Abstract Background To identify preoperative, perioperative and postoperative risk factors that influence the success of pterygium surgery. Methods This is a prospective study of thirty-six patients with primary or recurrent pterygia. A detailed anamnesis and an ophthalmological examination were performed looking for the following factors: age, race, latitude and altitude of the main place of residence, hours of exposure to the sun, use of protective measures against UV-radiation, classification of pterygium, width of the pterygium at limbus, surgical technique (conjunctival autograft plus suturing versus tissue glue), graft alterations (misapposition, granuloma, haemorrhage, oedema, retrac…
Suction catheter guided insertion of the ProSeal™ laryngeal mask airway is superior to the digital technique
We tested the hypothesis that digital insertion of the ProSeal laryngeal mask airway (ProSeal LMA) is more successful when using a suction catheter (SC) as a guide.Two hundred and forty-three patients (ASA physical status I-III; aged 18-84 yr) were randomly allocated for the digital or SC-guided technique. The digital technique was performed according to the manufacturer's instructions. The SC technique involved priming the drain tube with the SC so that it protruded by 15 cm, blindly inserting the SC into the pharynx to a depth of 15 cm, followed by the digital technique. Failed insertion was defined by any of the following criteria: 1) failed passage into the pharynx; 2) malposition; and …
IOWA Operators and Its Application to Image Retrieval
This paper presents a relevance feedback procedure based on logistic regression analysis. Since, the dimension of the feature vector associated to each image is typically larger than the number of evaluated images by the user, different logistic regression models have to be fitted separately. Each fitted model provides us with a relevance probability and a confidence interval for that probability. In order to aggregate these set of probabilities and confidence intervals we use an IOWA operator. The results will show the success of our algorithm and that OWA operators are an efficient and natural way of dealing with this kind of fusion problems.
Modeling of female human body shapes for apparel design based on cross mean sets
This paper is concerned with a method to build prototypes of human bodies that can be used for apparel design. One of the most important issues in the apparel development process is to define a sizing system to provide a good fitting for the majority of the population. Since anthropometric measures do not present the same linear growth with size in each dimension, it is very important to find a prototype that represents as accurately as possible each class in the sizing system. In this paper we propose a method based on the concept of random compact mean set to define prototypes in apparel design. From a cloud of 3D points obtained with a 3D scanner a solid that represents the human body is…
EPDR1 up-regulation in human colorectal cancer is related to staging and favours cell proliferation and invasiveness
The finding of novel molecular markers for prediction or prognosis of invasiveness in colorectal cancer (CRC) constitutes an appealing challenge. Here we show the up-regulation of EPDR1 in a prospective cohort of 101 CRC patients, in a cDNA array of 43 patients and in in silico analyses. EPDR1 encodes a protein related to ependymins, a family of glycoproteins involved in intercellular contacts. A thorough statistical model allowed us to conclude that the gene is significantly up-regulated in tumour tissues when compared with normal mucosa. These results agree with those obtained by the analysis of three publicly available databases. EPDR1 up-regulation correlates with the TNM staging parame…
Quantifying Mean Shape and Variability of Footprints Using Mean Sets
This paper1 presents an application of several definitions of a mean set for use in footwear design. For a given size, footprint pressure images corresponding to different individuals constitute our raw data. Appropriate footwear design needs to have knowledge of some kind of typical footprint. Former methods based on contour relevant points are highly sensitive to contour noise; moreover, they lack repeatability because of the need for the intervention of human designers. The method proposed in this paper is based on using mean sets on the thresholded images of the pressure footprints. Three definitions are used, two of them from Vorob’ev and Baddeley-Molchanov and one morphological mean p…
MORPHOMETRIC ANALYSIS OF HUMAN CORNEAL ENDOTHELIUM BY MEANS OF SPATIAL POINT PATTERNS
This paper presents a method for detecting abnormalities in spatial arrangements of cells within any tissue that can be described by different sets of relevant points. The method has been applied to the detection of subtle abnormalities in corneal endothelia. Images of this type of tissue can be characterized by two types of points: cell centroids and triple points associated with the apical intersections as it was proposed by Díaz.7 Both types of points jointly considered are modeled using a bivariate spatial point process; then a statistical analysis based on certain distributional descriptors proposed by Doguwa4,9 is carried out to discriminate severe and subtle abnormalities from contr…
Apparel sizing using trimmed PAM and OWA operators
This paper is concerned with apparel sizing system design. One of the most important issues in the apparel development process is to define a sizing system that provides a good fit to the majority of the population. A sizing system classifies a specific population into homogeneous subgroups based on some key body dimensions. Standard sizing systems range linearly from very small to very large. However, anthropometric measures do not grow linearly with size, so they can not accommodate all body types. It is important to determine each class in the sizing system based on a real prototype that is as representative as possible of each class. In this paper we propose a methodology to develop an …
Motherhood‐induced gene expression in the mouse medial amygdala: Changes induced by pregnancy and lactation but not by pup stimuli
During lactation, adult female mice display aggressive responses toward male intrud-ers, triggered by male- derived chemosensory signals. This aggressive behavior is not shown by pup- sensitized virgin females sharing pup care with dams. The genetic mechanisms underlying the switch from attraction to aggression are unknown. In this work, we investigate the differential gene expression in lactating females ex-pressing maternal aggression compared to pup- sensitized virgin females in the me-dial amygdala (Me), a key neural structure integrating chemosensory and hormonal information. The results showed 197 genes upregulated in dams, including genes encoding hormones such as prolactin, growth h…
Modeling user preferences in content-based image retrieval: A novel attempt to bridge the semantic gap
This paper is concerned with content-based image retrieval from a stochastic point of view. The semantic gap problem is addressed in two ways. First, a dimensional reduction is applied using the (pre-calculated) distances among images. The dimension of the reduced vector is the number of preferences that we allow the user to choose from, in this case, three levels. Second, the conditional probability distribution of the random user preference, given this reduced feature vector, is modeled using a proportional odds model. A new model is fitted at each iteration. The score used to rank the image database is based on the estimated probability function of the random preference. Additionally, so…
Biofilm development by potentially pathogenic non-pigmented rapidly growing mycobacteria
Abstract Background A study to evaluate the biofilm-development ability in three different media (Middlebrook 7H9, sterile tap water and PBS-5% glucose) was performed with 19 collection strains from 15 different species on non-pigmented rapidly growing mycobacteria (NPRGM). A microtiter plate assay was developed to evaluate the percentage of covered surface of the microtiter plate wells in different days from day 1 to day 69. Results All strains were able to develop biofilm in all the tested media. Middlebrook 7H9 showed the fastest growth, followed by sterile tap water and PBS-5% glucose. A sigmoid growth curve was detected in all the strains both in Middlebrook 7H9 and in sterile tap wate…
A gray-level 2D feature detector using circular statistics
Abstract This paper presents a new method for corner and circular feature detection in gray-level images. It is based on the application of standard statistical techniques to the distribution of gradient orientations in a circular neighborhood of the prospective feature point. An evaluation using standard procedures and a comparison with other approaches is presented. Results show the robustness of this method as compared to the other corner detectors analyzed. The main novelties are the possibility of detecting points that are centers of circular symmetries, and discriminating between junctions, which are classified into corners (two-edge junctions) and multiple edge junctions.
Immunological diagnosis of human hydatid cyst relapse: utility of the enzyme-linked immunoelectrotransfer blot and discriminant analysis.
ABSTRACT A discriminant technique was applied to the different serological patterns obtained by enzyme-linked immunoelectrotransfer blotting (EITB) and by conventional immunological tests, in order to differentiate the residual antibody patterns present in healed hydatidosis from the ones present in patients with active hydatidosis. For this purpose, specific antibodies against Echinococcus granulosus were detected by indirect hemagglutination, agglutination of latex particles, basophil degranulation, and EITB for 23 patients with active hydatidosis and 45 patients with surgically cured hydatidosis. Discriminant analysis of the different serological patterns obtained by EITB and conventiona…
Boolean Models: Maximum Likelihood Estimation from Circular Clumps
This paper deals with the problem of making inferences on the maximum radius and the intensity of the Poisson point process associated to a Boolean Model of circular primary grains with uniformly distributed random radii. The only sample information used is observed radii of circular clumps (DUPAC, 1980). The behaviour of maximum likelihood estimation has been evaluated by means of Monte Carlo methods.
Semi-automated evaluation tool for retinal vasculopathy.
The ocular fundus is the only area of human body where vascular system is visible using relatively simple instrumentation. Furthermore, there is medical suggestive evidence of a direct relationship between certain measures of vascular characteristics in the ocular fundus (arteriolar and venular calibers and focal arteriolar narrowing) and cardiovascular diseases. In order to establish such relationship on sound statistical basis a method must be provided to measure the needed values in an easy, yet precise and repeatable way. This paper presents a system to assist physicians in signaling and storing the data associated to signs of vascular deterioration and vascular calibers in non-mydriati…
Biofilm development by clinical strains of non-pigmented rapidly growing mycobacteria
AbstractThe relationship between clinical significance of non-pigmented, rapidly growing mycobacteria (NPRGM), in vitro biofilm development and sliding motility was evaluated in this study. One hundred and sixty-eight clinical strains of NPRGM were included. Forty-one of these were clinically significant isolates. Biofilm was formed by 123 strains. Seventy-six biofilm-positive and 25 biofilm-negative strains showed sliding motility. There was a relationship between clinical significance and biofilm development (p <0.000 001), sliding motility (p 0.0037) and species (p <0.000 001). No relationship was found between motility and biofilm development. The ability to develop biofilm is a charact…
Probabilistic liver atlas construction
Background Anatomical atlases are 3D volumes or shapes representing an organ or structure of the human body. They contain either the prototypical shape of the object of interest together with other shapes representing its statistical variations (statistical atlas) or a probability map of belonging to the object (probabilistic atlas). Probabilistic atlases are mostly built with simple estimations only involving the data at each spatial location. Results A new method for probabilistic atlas construction that uses a generalized linear model is proposed. This method aims to improve the estimation of the probability to be covered by the liver. Furthermore, all methods to build an atlas involve p…
Testing abnormality in the spatial arrangement of cells in the corneal endothelium using spatial point processes
The study of central corneal endothelium morphology is important in Ophthalmology. Some of the pathologies that could compromise endothelial cell morphology are trauma, cataract, surgery, use of contact lenses, corneal dystrophies or degenerations. The quantitative analysis of cell shape and cellular pattern is more sensitive in detecting subtle changes in endothelial morphology than cell density measurement or cell area analysis. In this paper, the morphology of the central cornea, the most important area from the point of view of vision, is studied through an associated bivariate spatial point pattern: the centroids of the cells and the triple points, that is, the points where three diffe…
Classifying human endothelial cells based on individual granulometric size distributions
Abstract This paper presents an application to a medical problem of methods of shape analysis based on mathematical morphology. The medical problem consists on the detection of abnormalities in the corneal endothelium, a tissue composed by quasi-planar cells of ideally regular hexagonal shape. Images of this tissue are taken by a specular microscope and used to evaluate the corneal endothelium status. Up to now, cell density, hexagonality and an analysis of cell areas are the usual descriptors of a corneal endothelium. These parameters are not sensitive enough to detect subtle lesions. What this paper proposes is an analysis based on granulometries, which are size-shape descriptors widely u…
Means of 2D and 3D Shapes and Their Application in Anatomical Atlas Building
This works deals with the concept of mean when applied to 2D or 3D shapes and with its applicability to the construction of digital atlases to be used in digital anatomy. Unlike numerical data, there are several possible definitions of the mean of a shape distribution and procedures for its estimation from a sample of shapes. Most popular definitions are based in the distance function or in the coverage function, each with its strengths and limitations. Closely related to the concept of mean shape is the concept of atlas, here understood as a probability or membership map that tells how likely is that a point belongs to a shape drawn from the shape distribution at hand. We devise a procedur…
Statistical tools and control of internal lubricant content of inhalation grade HPMC capsules during manufacture
The internal lubricant content (ILC) of inhalation grade HPMC capsules is a key factor to ensure good powder release when the patient inhales a medicine from a dry powder inhaler (DPI). Powder release from capsules has been shown to be influenced by the ILC. The characteristics used to measure this are the emitted dose, fine particle fraction and mass median aerodynamic diameter. In addition the ILC level is critical for capsule shell manufacture because it is an essential part of the process that cannot work without it. An experiment has been applied to the manufacture of inhalation capsules with the required ILC. A full factorial model was used to identify the controlling factors and from…
Granulometric analysis of corneal endothelium specular images by using a germ–grain model
Specular microscopy is widely used to study the human corneal endothelium status in vivo. In this paper, the corneal endothelium is represented as a binary image composed of the cell inscribed circles. The granulometric distribution function of the complement of this image is used as a functional descriptor, which provides information about the shape, size and spatial arrangement of cells. Experimental evaluation using bootstrap techniques shows its ability to discriminate between controls and pathological cases. It represents a reliable and graphical alternative to the classical indices (cell density, hexagonality and coefficient of variation of cell areas), which behave poorly when detect…
Irregular motion recovery in fluorescein angiograms
Abstract Fluorescein angiography is a common procedure in ophthalmic practice, mainly to evaluate vascular retinopathies and choroidopathies from sequences of ocular fundus images. In order to compare the images, a reliable overlying is essential. This paper proposes some methods for the recovery of irregular motion in fluorescein angiograms (FA). The overlying is done by a three step procedure: detection of relevant points, matching points from different images and estimation of the assumed linear geometric transformation. A stochastic model (closely related to the general linear model) allows to fuse the second and third steps. Two different estimators of the geometric transformation are …
Measuring Dissimilarity Between Curves by Means of Their Granulometric Size Distributions
The choice of a dissimilarity measure between curves is a key point for clustering functional data. Functions are usually pointwise compared and, in many situations, this approach is not appropriate. Mathematical Morphology provides us with a toolbox to overcome this problem. We propose some dissimilarity measures based on morphological granulometries and their performance is evaluated on some functional datasets.
Additional file 1 of OMICfpp: a fuzzy approach for paired RNA-Seq counts
All procedures and data needed to reproduce the whole study have been included in the file SupplementaryMaterial.tar.gz. Once decompressed the file SupplementaryMaterialMethods.pdf contains a detailed description of the methods used and the results obtained. The whole paper can be reproduced reading this file. Other data files generated during the analysis are included in the folder Methods. The detailed html reports with the results can be found in the folder Results. (GZ 118,244 kb)