Trainable COSFIRE filters for vessel delineation with application to retinal images

Retinal imaging provides a non-invasive opportunity for the diagnosis of several medical pathologies. The automatic segmentation of the vessel tree is an important pre-processing step which facilitates subsequent automatic processes that contribute to such diagnosis. We introduce a novel method for the automatic segmentation of vessel trees in retinal fundus images. We propose a filter that selectively responds to vessels and that we call B-COSFIRE with B standing for bar which is an abstraction for a vessel. It is based on the existing COSFIRE (Combination Of Shifted Filter Responses) approach. A B-COSFIRE filter achieves orientation selectivity by computing the weighted geometric mean of the output of a pool of Difference-of-Gaussians filters, whose supports are aligned in a collinear manner. It achieves rotation invariance efficiently by simple shifting operations. The proposed filter is versatile as its selectivity is determined from any given vessel-like prototype pattern in an automatic configuration process. We configure two B-COSFIRE filters, namely symmetric and asymmetric, that are selective for bars and bar-endings, respectively. We achieve vessel segmentation by summing up the responses of the two rotation-invariant B-COSFIRE filters followed by thresholding. The results that we achieve on three publicly available data sets (DRIVE: Se = 0.7655, Sp = 0.9704; STARE: Se = 0.7716, Sp = 0.9701; CHASE_DB1: Se = 0.7585, Sp = 0.9587) are higher than many of the state-of-the-art methods. The proposed segmentation approach is also very efficient with a time complexity that is significantly lower than existing methods.peer-reviewe

A Novel Real-Time Non-invasive Hemoglobin Level Detection Using Video Images from Smartphone Camera

Hemoglobin level detection is necessary for evaluating health condition in the human. In the laboratory setting, it is detected by shining light through a small volume of blood and using a colorimetric electronic particle counting algorithm. This invasive process requires time, blood specimens, laboratory equipment, and facilities. There are also many studies on non-invasive hemoglobin level detection. Existing solutions are expensive and require buying additional devices. In this paper, we present a smartphone-based non-invasive hemoglobin detection method. It uses the video images collected from the fingertip of a person. We hypothesized that there is a significant relation between the fingertip mini-video images and the hemoglobin level by laboratory gold standard. We also discussed other non-invasive methods and compared with our model. Finally, we described our findings and discussed future works

A computational pipeline for the diagnosis of CVID patients

Common variable immunodeficiency (CVID) is one of the most frequently diagnosed primary antibody deficiencies (PADs), a group of disorders characterized by a decrease in one or more immunoglobulin (sub) classes and/or impaired antibody responses caused by inborn defects in B cells in the absence of other major immune defects. CVID patients suffer from recurrent infections and disease-related, non-infectious, complications such as autoimmune manifestations, lymphoproliferation, and malignancies. A timely diagnosis is essential for optimal follow-up and treatment. However, CVID is by definition a diagnosis of exclusion, thereby covering a heterogeneous patient population and making it difficult to establish a definite diagnosis. To aid the diagnosis of CVID patients, and distinguish them from other PADs, we developed an automated machine learning pipeline which performs automated diagnosis based on flow cytometric immunophenotyping. Using this pipeline, we analyzed the immunophenotypic profile in a pediatric and adult cohort of 28 patients with CVID, 23 patients with idiopathic primary hypogammaglobulinemia, 21 patients with IgG subclass deficiency, six patients with isolated IgA deficiency, one patient with isolated IgM deficiency, and 100 unrelated healthy controls. Flow cytometry analysis is traditionally done by manual identification of the cell populations of interest. Yet, this approach has severe limitations including subjectivity of the manual gating and bias toward known populations. To overcome these limitations, we here propose an automated computational flow cytometry pipeline that successfully distinguishes CVID phenotypes from other PADs and healthy controls. Compared to the traditional, manual analysis, our pipeline is fully automated, performing automated quality control and data pre-processing, automated population identification (gating) and deriving features from these populations to build a machine learning classifier to distinguish CVID from other PADs and healthy controls. This results in a more reproducible flow cytometry analysis, and improves the diagnosis compared to manual analysis: our pipelines achieve on average a balanced accuracy score of 0.93 (+/- 0.07), whereas using the manually extracted populations, an averaged balanced accuracy score of 0.72 (+/- 0.23) is achieved

Chronic helminth infection burden differentially affects haematopoietic cell development while ageing selectively impairs adaptive responses to infection

Throughout the lifespan of an individual, the immune system undergoes complex changes while facing novel and chronic infections. Helminths, which infect over one billion people and impose heavy livestock productivity losses, typically cause chronic infections by avoiding and suppressing host immunity. Yet, how age affects immune responses to lifelong parasitic infection is poorly understood. To disentangle the processes involved, we employed supervised statistical learning techniques to identify which factors among haematopoietic stem and progenitor cells (HSPC), and both innate and adaptive responses regulate parasite burdens and how they are affected by host age. Older mice harboured greater numbers of the parasites’ offspring than younger mice. Protective immune responses that did not vary with age were dominated by HSPC, while ageing specifically eroded adaptive immunity, with reduced numbers of naïve T cells, poor T cell responsiveness to parasites, and impaired antibody production. We identified immune factors consistent with previously-reported immune responses to helminths, and also revealed novel interactions between helminths and HSPC maturation. Our approach thus allowed disentangling the concurrent effects of ageing and infection across the full maturation cycle of the immune response and highlights the potential of such approaches to improve understanding of the immune system within the whole organism

Affinity proteomics reveals elevated muscle proteins in plasma of children with cerebral malaria

Systemic inflammation and sequestration of parasitized erythrocytes are central processes in the pathophysiology of severe Plasmodium falciparum childhood malaria. However, it is still not understood why some children are more at risks to develop malaria complications than others. To identify human proteins in plasma related to childhood malaria syndromes, multiplex antibody suspension bead arrays were employed. Out of the 1,015 proteins analyzed in plasma from more than 700 children, 41 differed between malaria infected children and community controls, whereas 13 discriminated uncomplicated malaria from severe malaria syndromes. Markers of oxidative stress were found related to severe malaria anemia while markers of endothelial activation, platelet adhesion and muscular damage were identified in relation to children with cerebral malaria. These findings suggest the presence of generalized vascular inflammation, vascular wall modulations, activation of endothelium and unbalanced glucose metabolism in severe malaria. The increased levels of specific muscle proteins in plasma implicate potential muscle damage and microvasculature lesions during the course of cerebral malaria

A urinary Common Rejection Module (uCRM) score for non-invasive kidney transplant monitoring.

A Common Rejection Module (CRM) consisting of 11 genes expressed in allograft biopsies was previously reported to serve as a biomarker for acute rejection (AR), correlate with the extent of graft injury, and predict future allograft damage. We investigated the use of this gene panel on the urine cell pellet of kidney transplant patients. Urinary cell sediments collected from patients with biopsy-confirmed acute rejection, borderline AR (bAR), BK virus nephropathy (BKVN), and stable kidney grafts with normal protocol biopsies (STA) were analyzed for expression of these 11 genes using quantitative polymerase chain reaction (qPCR). We assessed these 11 CRM genes for their abundance, autocorrelation, and individual expression levels. Expression of 10/11 genes were elevated in AR when compared to STA. Psmb9 and Cxcl10could classify AR versus STA as accurately as the 11-gene model (sensitivity = 93.6%, specificity = 97.6%). A uCRM score, based on the geometric mean of the expression levels, could distinguish AR from STA with high accuracy (AUC = 0.9886) and correlated specifically with histologic measures of tubulitis and interstitial inflammation rather than tubular atrophy, glomerulosclerosis, intimal proliferation, tubular vacuolization or acute glomerulitis. This urine gene expression-based score may enable the non-invasive and quantitative monitoring of AR

Beta Thalassemia Carriers detection empowered federated Learning

Thalassemia is a group of inherited blood disorders that happen when hemoglobin, the protein in red blood cells that carries oxygen, is not made enough. It is found all over the body and is needed for survival. If both parents have thalassemia, a child's chance of getting it increases. Genetic counselling and early diagnosis are essential for treating thalassemia and stopping it from being passed on to future generations. It may be hard for healthcare professionals to differentiate between people with thalassemia carriers and those without. The current blood tests for beta thalassemia carriers are too expensive, take too long, and require too much screening equipment. The World Health Organization says there is a high death rate for people with thalassemia. Therefore, it is essential to find thalassemia carriers to act quickly. High-performance liquid chromatography (HPLC), the standard test method, has problems such as cost, time, and equipment needs. So, there must be a quick and cheap way to find people carrying the thalassemia gene. Using federated learning (FL) techniques, this study shows a new way to find people with the beta-thalassemia gene. FL allows data to be collected and processed on-site while following privacy rules, making it an excellent choice for sensitive health data. Researchers used FL to train a model for beta-thalassemia carriers by looking at the complete blood count results and red blood cell indices. The model was 92.38 % accurate at telling the difference between beta-thalassemia carriers and people who did not have the disease. The proposed FL model is better than other published methods in terms of how well it works, how reliable it is, and how private it is. This research shows a promising, quick, accurate, and low-cost way to find thalassemia carriers and opens the door for screening them on a large scale.Comment: pages 17, figures

Artificial Immune Systems - Models, algorithms and applications

Copyright © 2010 Academic Research Publishing Agency.This article has been made available through the Brunel Open Access Publishing Fund.Artificial Immune Systems (AIS) are computational paradigms that belong to the computational intelligence family and are inspired by the biological immune system. During the past decade, they have attracted a lot of interest from researchers aiming to develop immune-based models and techniques to solve complex computational or engineering problems. This work presents a survey of existing AIS models and algorithms with a focus on the last five years.This article is available through the Brunel Open Access Publishing Fun