Standardised quantitative assays for anti-SARS-CoV-2 immune response used in vaccine clinical trials by the CEPI Centralized Laboratory Network: a qualification analysis.

Background: Accurate quantitation of immune markers is crucial for ensuring reliable assessment of vaccine efficacy against infectious diseases. This study was designed to confirm standardised performance of SARS-CoV-2 assays used to evaluate COVID-19 vaccine candidates at the initial seven laboratories (in North America, Europe, and Asia) of the Coalition for Epidemic Preparedness Innovations (CEPI) Centralized Laboratory Network (CLN).

Methods: Three ELISAs (pre-spike protein, receptor binding domain, and nucleocapsid), a microneutralisation assay (MNA), a pseudotyped virus-based neutralisation assay (PNA), and an IFN-γ T-cell ELISpot assay were developed, validated or qualified, and transferred to participating laboratories.

Use of laboratory-developed assays in global HIV-1 treatment-monitoring and research.

There has been a surge in the emergence of HIV-1 drug resistance in Low and Middle-Income Countries (LMICs) due to poor drug-adherence and limited access to viral load testing, the current standard for treatment-monitoring. It is estimated that only 75% of people living with HIV (PLWH) worldwide have access to viral load testing. In LMICs, this figure is below 50%.

Desmoplastic Ameloblastoma of anterior maxilla - A case report.

The recently recognized desmoplastic ameloblastoma is considered a rare variant of central ameloblastoma. It has been included in the World Health Organization's histopathological typing of odontogenic tumors, similar to benign, locally invasive tumors with low recurrence rate and peculiar histological features, characterized by epithelial changes due to the pressure of stroma on epithelial tissue. The aim of this paper is to report a unique case of desmoplastic ameloblastoma in the mandible of a 21-year-old male with a painless swelling in the anterior region of the maxilla.

Development of a sensitive, quantitative assay with broad subtype specificity for detection of total HIV-1 nucleic acids in plasma and PBMC.

An LTR-based quantitative PCR (qPCR) assay was modified and optimized for the quantification of total HIV-1 nucleic acids in plasma and PBMC. TaqMan qPCR primers and probes were designed against the NCBI/LANL HIV-1 compendium database by analyzing sequences used in assays for sensitive cross-clade detection of HIV-1 as reported in the literature and elucidating regions of improved cross-subtype specificity. Inosine and mixed nucleotide bases were included at polymorphic sites.

i-MANN: A Web-Based System for Data Management of Mental Health Research in India.

Background: National Mental Health Program (NMHP) was launched by the government with an aim to improve mental health of the society through precise and focused interventions and policies. In order to provide reliable data and evidence for NMHP, there is a strong requirement of a comprehensive system for integrative collection, storage, and analysis of data generated by this program.

Methods: Data collection tools, questionnaires, instruments, and scales provided by the National Coordinating Unit were digitized using the District Health Information Software 2 (DHIS2) framework (version 2.

Performance evaluation of a laboratory developed PCR test for quantitation of HIV-2 viral RNA.

Management of Human Immunodeficiency Virus Type 2 (HIV-2) infections present unique challenges due to low viral titers, slow disease progression, and poor response to standard antiviral therapies. The need for a nucleic acid assay to detect and quantify HIV-2 virus has led to the development of a number of molecular-based assays for detection and/or quantification of HIV-2 viral RNA in plasma in order to provide laboratory evidence of HIV-2 infection and viral loads for use in treatment decisions. As HIV-2 is less pathogenic and transmissible than HIV-1 and has resistance to several of the antiretroviral drugs, delay of treatment is common.

Predictive compression of molecular dynamics trajectories.

Molecular dynamics simulations help to understand the complex behavior of molecules. The output of such a simulation describes the trajectories of individual atoms as snapshots of atom positions in time. Many compression schemes were developed to reduce the amount of data needed for storing long trajectories.

Application of Artificial Intelligence/Machine Vision & Learning for the Development of a Live Single-cell Phenotypic Biomarker Test to Predict Prostate Cancer Tumor Aggressiveness.

To the usefulness and applications of machine vision (MV) and machine learning (ML) techniques that have been used to develop a single cell-based phenotypic (live and fixed biomarkers) platform that correlates with tumor biological aggressiveness and risk stratification, 100 fresh prostate samples were acquired, and areas of prostate cancer were determined by post-surgery pathology reports logged by an independent pathologist. The prostate samples were dissociated into single-cell suspensions in the presence of an extracellular matrix formulation. These samples were analyzed via live-cell microscopy.

Decreased Seroreactivity in Individuals Initiating Antiretroviral Therapy during Acute HIV Infection.

Antiretroviral therapy (ART) during acute HIV infection (AHI) interrupts viral dynamics and may delay the emergence of serological markers targeted by current HIV screening and confirmatory assays, thus creating challenges for correctly classifying HIV infection status. The performance of three HIV antigen/antibody combination (HIV Ag/Ab Combo) assays (the Bio-Rad GS, Abbott Architect, and Bio-Rad BioPlex 2200 assays) was evaluated with samples collected from RV254/South East Asia Research Collaboration in HIV 010 (RV254/SEARCH010) study (Bangkok, Thailand) participants at weeks 12 and 24 following the initiation of ART at Fiebig stage I (FI) ( = 23), FII ( = 39), or FIII/IV ( = 22). Supplemental, confirmatory testing was performed by the Geenius HIV 1/2 and HIV-1 Western blot assays (Bio-Rad).

Voronoi-based detection of pockets in proteins defined by large and small probes.

The function of enzymatic proteins is given by their ability to bind specific small molecules into their active sites. These sites can often be found in pockets on a hypothetical boundary between the protein and its environment. Detection, analysis, and visualization of pockets find its use in protein engineering and drug discovery.

Live-cell phenotypic-biomarker microfluidic assay for the risk stratification of cancer patients via machine learning.

The risk stratification of prostate cancer and breast cancer tumours from patients relies on histopathology, selective genomic testing, or on other methods employing fixed formalin tissue samples. However, static biomarker measurements from bulk fixed-tissue samples provide limited accuracy and actionability. Here, we report the development of a live-primary-cell phenotypic-biomarker assay with single-cell resolution, and its validation with prostate cancer and breast cancer tissue samples for the prediction of post-surgical adverse pathology.

Impact of Early Antiretroviral Therapy on Detection of Cell-Associated HIV-1 Nucleic Acid in Blood by the Roche Cobas TaqMan Test.

The Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 test, v2.0 (the CAP/CTM assay), was used to quantify cell-associated HIV-1 (CAH) nucleic acid in peripheral blood mononuclear cells (PBMC) from well-characterized clinical specimens from HIV-1-infected individuals on antiretroviral therapy (ART). Chronically infected individuals on ART with no detectable plasma HIV-1 RNA demonstrated average CAH burdens of 3.

Clinical Proof-of-concept of a Novel Platform Utilizing Biopsy-derived Live Single Cells, Phenotypic Biomarkers, and Machine Learning Toward a Precision Risk Stratification Test for Prostate Cancer Grade Groups 1 and 2 (Gleason 3 + 3 and 3 + 4).

Objective: To examine the ability of a novel live primary-cell phenotypic (LPCP) test to predict postsurgical adverse pathology (P-SAP) features and risk stratify patients based on SAP features in a blinded study utilizing radical prostatectomy (RP) surgical specimens.

Methods: Two hundred fifty-one men undergoing RP were enrolled in a prospective, multicenter (10), and proof-of-concept study in the United States. Fresh prostate samples were taken from known areas of cancer in the operating room immediately after RP.

Comparison of Detection Limits of Fourth- and Fifth-Generation Combination HIV Antigen-Antibody, p24 Antigen, and Viral Load Assays on Diverse HIV Isolates.

Detection of acute HIV infection is critical for HIV public health and diagnostics. Clinical fourth-generation antigen (Ag)/antibody (Ab) combination (combo) and p24 Ag immunoassays have enhanced detection of acute infection compared to Ab-alone assays but require ongoing evaluation with currently circulating diverse subtypes. Genetically and geographically diverse HIV clinical isolates were used to assess clinical HIV diagnostic, blood screening, and next-generation assays.

CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories.

Motivation: Studying the transport paths of ligands, solvents, or ions in transmembrane proteins and proteins with buried binding sites is fundamental to the understanding of their biological function. A detailed analysis of the structural features influencing the transport paths is also important for engineering proteins for biomedical and biotechnological applications.

Results: CAVER Analyst 2.

Rural Palliative Care in North India: Rapid Evaluation of a Program Using a Realist Mixed Method Approach.

Context: Palliative care has not developed widely in rural North India. Since 2010, the Emmanuel Hospitals Association (EHA) has been developing a model of palliative care appropriate for this setting, based on teams undertaking home visits with the backup of outpatient and inpatient services. A project to further develop the model operated from 2012 to 2015 supported by funding from the UK.

Hybrid Voronoi diagrams, their computation and reduction for applications in computational biochemistry.

Geometric models of molecular structures are often described as a set of balls, where balls represent individual atoms. The ability to describe and explore the empty space among these balls is important, e.g.

Identification of Acute HIV-1 Infection by Hologic Aptima HIV-1 RNA Qualitative Assay.

The Hologic Aptima HIV-1 Qualitative RNA assay was used in a rigorous screening approach designed to identify individuals at the earliest stage of HIV-1 infection for enrollment into subsequent studies of cellular and viral events in early infection (RV 217/Early Capture HIV Cohort [ECHO] study). Volunteers at high risk for HIV-1 infection were recruited from study sites in Thailand, Tanzania, Uganda, and Kenya with high HIV-1 prevalence rates among the populations examined. Small-volume blood samples were collected by finger stick at twice-weekly intervals and tested with the Aptima assay.

Rapid and Short-term Extracellular Matrix-mediated In Vitro Culturing of Tumor and Nontumor Human Primary Prostate Cells From Fresh Radical Prostatectomy Tissue.

Objective: To culture prostate cells from fresh biopsy core samples from radical prostatectomy (RP) tissue. Further, given the genetic heterogeneity of prostate cells, the ability to culture single cells from primary prostate tissue may be of importance toward enabling single-cell characterization of primary prostate tissue via molecular and cellular phenotypic biomarkers.

Methods: A total of 260 consecutive tissue samples from RPs were collected between October 2014 and January 2016, transported at 4°C in serum-free media to an off-site central laboratory, dissociated, and cultured.

Poverty Reduction in India through Palliative Care: A Pilot Project.

Introduction: EMMS International and Emmanuel Hospital Association (EHA) implemented a pilot project, poverty reduction in India through palliative care (PRIPCare). A total of 129 interviews with patients and family enrolled in palliative care at three EHA hospitals (in Fatehpur, Lalitpur and Utraula) and staff discussions established that 66% of palliative care patients had lost livelihoods due to illness, 26% of patients' families had members who had lost livelihoods due to the illness, 98% of enrolled households had debts, 59% had loans for which they had sold assets, 69% of households took out debt after their family member fell ill, many patients do not know about government benefits and lack necessary documents, many village headmen require bribes to give people access to benefits, and many bereaved women and children lose everything. Palliative care enabled 85% of patients and families to spend less on medicines, 31% of patients received free medicines, all patients reduced use of out-patient departments (OPDs), 20% reduced use of inpatient departments (IPDs), and therefore spent less on travel, 8% of patients had started earning again due to improved health, members of 10% of families started earning again, and one hospital educated 171 village headmen and increased by 5% the number of patients and their families receiving government benefits.