GNCnn: A QuPath extension for glomerulosclerosis and glomerulonephritis characterization based on deep learning.

The digitalization of traditional glass slide microscopy into whole slide images has opened up new opportunities for pathology, such as the application of artificial intelligence techniques. Specialized software is necessary to visualize and analyze these images. One of these applications is QuPath, a popular bioimage analysis tool.

Comparison of deep learning models for digital H&E staining from unpaired label-free multispectral microscopy images.

Background And Objective: This paper presents the quantitative comparison of three generative models of digital staining, also known as virtual staining, in H&E modality (i.e., Hematoxylin and Eosin) that are applied to 5 types of breast tissue.

A Dynamic Interplay of Circulating Extracellular Vesicles and Galectin-1 Reprograms Viral Latency during HIV-1 Infection.

Combined Antiretroviral therapy (cART) suppresses HIV replication but fails to eradicate the virus, which persists in a small pool of long-lived latently infected cells. Immune activation and residual inflammation during cART are considered to contribute to viral persistence. Galectins, a family of β-galactoside-binding proteins, play central roles in host-pathogen interactions and inflammatory responses.

A review on low-cost microscopes for Open Science.

This article presents a review after an exhaustive search that yielded 23 works carried out in the last decade for the availability of optical microscopes with open hardware as a low-cost alternative to commercial systems. These works were developed with the aim of covering needs within several areas such as: Bio Sciences research in institutions with limited resources, diagnosis of diseases and health screenings in large populations in developing countries, and training in educational contexts with a need for high availability of equipment and low replacement cost. The analysis of the selected works allows us to classify the analyzed solutions into two main categories, for which their essential characteristics are enumerated: portable field microscopes and multipurpose automated microscopes.

Pre-cART Immune Parameters in People Living With HIV Might Help Predict CD8+ T-Cell Characteristics, Inflammation Levels, and Reservoir Composition After Effective cART.

Background: Combined antiretroviral treatment (cART) for HIV infection is highly effective in controlling viral replication. However, it cannot achieve a sterilizing cure. Several strategies have been proposed to achieve a functional cure, some of them based on immune-mediated clearing of persistently infected cells.

MicroHikari3D: an automated DIY digital microscopy platform with deep learning capabilities.

A microscope is an essential tool in biosciences and production quality laboratories for unveiling the secrets of microworlds. This paper describes the development of MicroHikari3D, an affordable DIY optical microscopy platform with automated sample positioning, autofocus and several illumination modalities to provide a high-quality flexible microscopy tool for labs with a short budget. This proposed optical microscope design aims to achieve high customization capabilities to allow whole 2D slide imaging and observation of 3D live specimens.

Influence of fulfilment patient expectations in outcomes after total knee arthroplasty.

Background And Objective: Compliance with preoperative expectations of patients undergoing total knee arthroplasty (TKA) is related to the degree of satisfaction, but its effect on other outcomes has not been studied. The aim of this study is to determine whether meeting expectations influences clinical, functional and quality of life outcomes at one year after surgery.

Material And Methods: The expectations of 183 patients were evaluated through the Hospital for Special Surgery Knee Replacement Expectations Survey.

Impact of HIV-ART on the restoration of Th17 and Treg cells in blood and female genital mucosa.

The aim of this study was to evaluate the effectiveness of antiretroviral treatment (ART) on the proportion and functions of Th17 and Treg cells in peripheral blood and female genital tract (FGT) respectively. To this aim, samples from 41 HIV-neg, 33 HIV+ ART-naïve and 32 HIV+ ART+ subjects were obtained. In peripheral blood, altered Th17 and Th17/Treg proportions were normalized in HIV+ ART+, but certain abnormal Treg and activated T-cell proportions were still observed.

Phenotype, Polyfunctionality, and Antiviral Activity of Stimulated CD8 T-Cells From HIV Subjects Who Initiated cART at Different Time-Points After Acute Infection.

Since anti-HIV treatment cannot cure the infection, many strategies have been proposed to eradicate the viral reservoir, which still remains as a major challenge. The success of some of these strategies will rely on the ability of HIV-specific CD8 T-cells (CD8TC) to clear reactivated infected cells. Here, we aimed to investigate the phenotype and function of expanded CD8TC obtained from HIV subjects on combination antiretroviral therapy (cART), either initiated earlier (median = 3 months postinfection, ET: Early treatment) or later (median = 20 months postinfection, DT: Delayed treatment) after infection.

PD-1 Expression in HIV-Specific CD8+ T cells Before Antiretroviral Therapy Is Associated With HIV Persistence.

Background: The persistence of latently infected T cells remains the principal barrier to HIV cure. Understanding how the early immune responses shape persistence of HIV on antiretroviral therapy (ART) will be fundamental for potential eradication. Here, we aimed to determine the relationship between CD8 T-cell function and phenotype before therapy and HIV persistence on ART.

Induction of HIF-1α by HIV-1 Infection in CD4 T Cells Promotes Viral Replication and Drives Extracellular Vesicle-Mediated Inflammation.

Chronic immune activation and inflammation are hallmarks of HIV-1 infection and a major cause of serious non-AIDS events in HIV-1-infected individuals on antiretroviral treatment (ART). Herein, we show that cytosolic double-stranded DNA (dsDNA) generated in infected CD4 T cells during the HIV-1 replication cycle promotes the mitochondrial reactive oxygen species (ROS)-dependent stabilization of the transcription factor hypoxia-inducible factor 1α (HIF-1α), which in turn, enhances viral replication. Furthermore, we show that induction of HIF-1α promotes the release of extracellular vesicles (EVs).

Interaction Between Macrophage Migration Inhibitory Factor and CD74 in Human Immunodeficiency Virus Type I Infected Primary Monocyte-Derived Macrophages Triggers the Production of Proinflammatory Mediators and Enhances Infection of Unactivated CD4 T Cells.

Understanding the mechanisms of human immunodeficiency virus type I (HIV-1) pathogenesis would facilitate the identification of new therapeutic targets to control the infection in face of current antiretroviral therapy limitations. CD74 membrane expression is upregulated in HIV-1-infected cells and the magnitude of its modulation correlates with immune hyperactivation in HIV-infected individuals. In addition, plasma level of the CD74 activating ligand macrophage migration inhibitory factor (MIF) is increased in infected subjects.

Biomarkers of Progression after HIV Acute/Early Infection: Nothing Compares to CD4⁺ T-cell Count?

Progression of HIV infection is variable among individuals, and definition disease progression biomarkers is still needed. Here, we aimed to categorize the predictive potential of several variables using feature selection methods and decision trees. A total of seventy-five treatment-naïve subjects were enrolled during acute/early HIV infection.

Modification of the HIV-specific CD8+ T-cell response in an HIV elite controller after chikungunya virus infection.

Objective: To evaluate the impact of chikungunya virus (CHIKV) infection on the quality of the HIV-specific CD8 T-cell (CTL) response in an HIV elite controller.

Design: Three blood samples were obtained from an elite controller at 27 days (EC-CHIKV, Sample 1, S1), 41 days (S2) and 1 year (S3) after CHIKV infection. Additionally, samples from another nine elite controllers and nine viremic chronics were obtained.

Low Proviral Load is Associated with Indeterminate Western Blot Patterns in Human T-Cell Lymphotropic Virus Type 1 Infected Individuals: Could Punctual Mutations be Related?

Background: indeterminate Western blot (WB) patterns are a major concern for diagnosis of human T-cell lymphotropic virus type 1 (HTLV-1) infection, even in non-endemic areas.

Objectives: (a) to define the prevalence of indeterminate WB among different populations from Argentina; (b) to evaluate if low proviral load (PVL) is associated with indeterminate WB profiles; and (c) to describe mutations in LTR and tax sequence of these cases.

Results: Among 2031 samples, 294 were reactive by screening.

Influence of Texture and Colour in Breast TMA Classification.

Breast cancer diagnosis is still done by observation of biopsies under the microscope. The development of automated methods for breast TMA classification would reduce diagnostic time. This paper is a step towards the solution for this problem and shows a complete study of breast TMA classification based on colour models and texture descriptors.

A CAD System for the Acquisition and Classification of Breast TMA in Pathology.

Breast cancer is the most common type of cancer and the fifth leading cause of death in women over 40. Therefore, prompt diagnostic and treatment is essential. In this work a TMA Computer Aided Diagnosis (CAD) system has been implemented to provide support to pathologists in their daily work.

Frequential versus spatial colour textons for breast TMA classification.

Advances in digital pathology are generating huge volumes of whole slide (WSI) and tissue microarray images (TMA) which are providing new insights into the causes of cancer. The challenge is to extract and process effectively all the information in order to characterize all the heterogeneous tissue-derived data. This study aims to identify an optimal set of features that best separates different classes in breast TMA.

[Does pre-surgical cognitive impairment affect knee replacement results?].

Objective: To determine the influence of the pre-operative cognitive impairment on results of the total knee arthroplasty according to a doctor and patient perspective.

Material And Method: A prospective study was conducted on patient from the surgical waiting list who had undergone a primary total knee arthroplasty. The sample initially included 265 patients, but 50 were subsequently excluded.

An automated system for whole microscopic image acquisition and analysis.

The field of anatomic pathology has experienced major changes over the last decade. Virtual microscopy (VM) systems have allowed experts in pathology and other biomedical areas to work in a safer and more collaborative way. VMs are automated systems capable of digitizing microscopic samples that were traditionally examined one by one.

TMA vessel segmentation based on color and morphological features: application to angiogenesis research.

Given that angiogenesis and lymphangiogenesis are strongly related to prognosis in neoplastic and other pathologies and that many methods exist that provide different results, we aim to construct a morphometric tool allowing us to measure different aspects of the shape and size of vascular vessels in a complete and accurate way. The developed tool presented is based on vessel closing which is an essential property to properly characterize the size and the shape of vascular and lymphatic vessels. The method is fast and accurate improving existing tools for angiogenesis analysis.

Automatic handling of tissue microarray cores in high-dimensional microscopy images.

This paper describes a specific tool for automatically segmenting and archiving of tissue microarray (TMA) cores in microscopy images at different magnifications. TMA enables researchers to extract the small cylinders of a single tissue (core sections) from histological sections and arrange them in an array on a paraffin block such that hundreds can be analyzed simultaneously. A crucial step to improve the speed and quality of this process is the correct localization of each tissue core in the array.

Emerging trends: grid technology in pathology.

Grid technology has enabled clustering and access to, and interaction among, a wide variety of geographically distributed resources such as supercomputers, storage systems, data sources, instruments as well as special devices and services, realizing network-centric operations. Their main applications include large scale computational and data intensive problems in science and engineering. Grids are likely to have a deep impact on health related applications.