scholarly journals A New Comprehensive Catalog of the Human Virome Reveals Hidden Associations with Chronic Diseases

2020 ◽  
Author(s):  
Michael J. Tisza ◽  
Christopher B. Buck
Keyword(s):  
Virus Disease ◽  
High Sensitivity ◽  
High Specificity ◽  
Metagenomic Data ◽  
Case Control Studies ◽  
Operational Taxonomic Units ◽  
Bioinformatic Tool ◽  
Disease Associations ◽  
Microbiome Research ◽  
Viral Sequences

AbstractWhile there have been remarkable strides in microbiome research, the viral component of the microbiome has generally presented a more challenging target than the bacteriome. This is despite the fact that many thousands of shotgun sequencing runs from human metagenomic samples exist in public databases and all of them encompass large amounts of viral sequences. The lack of a comprehensive database for human-associated viruses, along with inadequate methods for high-throughput identification of highly divergent viruses in metagenomic data, has historically stymied efforts to characterize virus sequences in a comprehensive way. In this study, a new high-specificity and high-sensitivity bioinformatic tool, Cenote-Taker 2, was applied to thousands of human metagenome datasets, uncovering over 50,000 unique virus operational taxonomic units. Publicly available case-control studies were re-analyzed, and over 1,700 strong virus-disease associations were found.

scholarly journals A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases

2021 ◽  
Vol 118 (23) ◽  
pp. e2023202118
Author(s):  
Michael J. Tisza ◽  
Christopher B. Buck
Keyword(s):  
Human Health ◽  
Chronic Diseases ◽  
Sequence Data ◽  
Virus Disease ◽  
Case Control ◽  
Viral Sequence ◽  
Case Control Studies ◽  
Disease Associations ◽  
Microbiome Research ◽  
The Impact

Despite remarkable strides in microbiome research, the viral component of the microbiome has generally presented a more challenging target than the bacteriome. This gap persists, even though many thousands of shotgun sequencing runs from human metagenomic samples exist in public databases, and all of them encompass large amounts of viral sequence data. The lack of a comprehensive database for human-associated viruses has historically stymied efforts to interrogate the impact of the virome on human health. This study probes thousands of datasets to uncover sequences from over 45,000 unique virus taxa, with historically high per-genome completeness. Large publicly available case-control studies are reanalyzed, and over 2,200 strong virus–disease associations are found.

scholarly journals The effect of misclassification error on risk estimation in case-control studies

2015 ◽  
Vol 18 (2) ◽  
pp. 341-356 ◽  
Author(s):  
Armando Baena ◽  
Isabel Cristina Garcés-Palacio ◽  
Hugo Grisales
Keyword(s):  
Linear Models ◽  
Risk Estimation ◽  
High Sensitivity ◽  
High Specificity ◽  
Epidemiological Studies ◽  
Case Control ◽  
Misclassification Error ◽  
Case Control Studies ◽  
Differential Misclassification ◽  
Study Bias

INTRODUCTION: In epidemiological studies, misclassification error, especially differential misclassification, has serious implications. OBJECTIVE: To illustrate how differential misclassification error (DME) and non-differential misclassification error (NDME) occur in a case-control design and to describe the trends in DME and NDME. METHODS: Different sensitivity levels, specificity levels, prevalence rates and odds ratios were simulated. Interaction graphics were constructed to study bias in the different settings, and the effect of the different factors on bias was described using linear models. RESULTS: One hundred per cent of the biases caused by NDME were negative. DME biased the association positively more often than it did negatively (70 versus 30%), increasing or decreasing the OR estimate towards the null hypothesis. CONCLUSIONS: The effect of the sensitivity and specificity in classifying exposure, the prevalence of exposure in controls and true OR differed between positive and negative biases. The use of valid exposure classification instruments with high sensitivity and high specificity is recommended to mitigate this type of bias.

scholarly journals Radiochemistry, Production Processes, Labeling Methods, and ImmunoPET Imaging Pharmaceuticals of Iodine-124

Molecules ◽  
2021 ◽  
Vol 26 (2) ◽  
pp. 414
Author(s):  
Krishan Kumar ◽  
Arijit Ghosh
Keyword(s):  
Physical Properties ◽  
Imaging Modality ◽  
Target Selection ◽  
Positron Emission Tomography Imaging ◽  
High Sensitivity ◽  
High Specificity ◽  
Production Processes ◽  
Positron Emission ◽  
Significant Research ◽  
Clinical Environments

Target-specific biomolecules, monoclonal antibodies (mAb), proteins, and protein fragments are known to have high specificity and affinity for receptors associated with tumors and other pathological conditions. However, the large biomolecules have relatively intermediate to long circulation half-lives (>day) and tumor localization times. Combining superior target specificity of mAbs and high sensitivity and resolution of the PET (Positron Emission Tomography) imaging technique has created a paradigm-shifting imaging modality, ImmunoPET. In addition to metallic PET radionuclides, 124I is an attractive radionuclide for radiolabeling of mAbs as potential immunoPET imaging pharmaceuticals due to its physical properties (decay characteristics and half-life), easy and routine production by cyclotrons, and well-established methodologies for radioiodination. The objective of this report is to provide a comprehensive review of the physical properties of iodine and iodine radionuclides, production processes of 124I, various 124I-labeling methodologies for large biomolecules, mAbs, and the development of 124I-labeled immunoPET imaging pharmaceuticals for various cancer targets in preclinical and clinical environments. A summary of several production processes, including 123Te(d,n)124I, 124Te(d,2n)124I, 121Sb(α,n)124I, 123Sb(α,3n)124I, 123Sb(3He,2n)124I, natSb(α, xn)124I, natSb(3He,n)124I reactions, a detailed overview of the 124Te(p,n)124I reaction (including target selection, preparation, processing, and recovery of 124I), and a fully automated process that can be scaled up for GMP (Good Manufacturing Practices) production of large quantities of 124I is provided. Direct, using inorganic and organic oxidizing agents and enzyme catalysis, and indirect, using prosthetic groups, 124I-labeling techniques have been discussed. Significant research has been conducted, in more than the last two decades, in the development of 124I-labeled immunoPET imaging pharmaceuticals for target-specific cancer detection. Details of preclinical and clinical evaluations of the potential 124I-labeled immunoPET imaging pharmaceuticals are described here.

scholarly journals Highly Sensitive Fluorescent Detection of Acetylcholine Based on the Enhanced Peroxidase-Like Activity of Histidine Coated Magnetic Nanoparticles

Nanomaterials ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1207
Author(s):  
Hong Jae Cheon ◽  
Quynh Huong Nguyen ◽  
Moon Il Kim
Keyword(s):  
Magnetic Nanoparticles ◽  
High Sensitivity ◽  
High Specificity ◽  
Choline Oxidase ◽  
Fluorescent Detection ◽  
One Pot ◽  
Site Structure ◽  
Specificity And Sensitivity ◽  
Highly Sensitive ◽  
Peroxidase Mimics

Inspired by the active site structure of natural horseradish peroxidase having iron as a pivotal element with coordinated histidine residues, we have developed histidine coated magnetic nanoparticles (His@MNPs) with relatively uniform and small sizes (less than 10 nm) through one-pot heat treatment. In comparison to pristine MNPs and other amino acid coated MNPs, His@MNPs exhibited a considerably enhanced peroxidase-imitating activity, approaching 10-fold higher in catalytic reactions. With the high activity, His@MNPs then were exploited to detect the important neurotransmitter acetylcholine. By coupling choline oxidase and acetylcholine esterase with His@MNPs as peroxidase mimics, target choline and acetylcholine were successfully detected via fluorescent mode with high specificity and sensitivity with the limits of detection down to 200 and 100 nM, respectively. The diagnostic capability of the method is demonstrated by analyzing acetylcholine in human blood serum. This study thus demonstrates the potential of utilizing His@MNPs as peroxidase-mimicking nanozymes for detecting important biological and clinical targets with high sensitivity and reliability.

Cds nanocrystal enhanced TiO2photoelectrochemical aptasensor for sensitive detection of cytochrome c

2021 ◽  
Vol 11 (11) ◽  
pp. 1774-1780
Author(s):  
Shanji Fan ◽  
Hong Huang ◽  
Hong Chen ◽  
Jiachi Xu ◽  
Zecheng Hu ◽  
...  
Keyword(s):  
Cytochrome C ◽  
Limit Of Detection ◽  
Specific Binding ◽  
High Sensitivity ◽  
High Specificity ◽  
Linear Range ◽  
Current Intensity ◽  
Sensitive Detection ◽  
Layer Adsorption ◽  
Ionic Layer

A CdS nanocrystal enhanced TiO2 nanotubes (CdS@TiO2 NATs) photoelectrode was prepared via successive ionic layer adsorption and reaction (SILAR) of CdS on the surface of TiO2 NATs. A HS-aptamer owing a specific binding toward cytochrome c was modified onto the CdS@TiO2 NATs, which resulting a decrease in the photoelectrical current intensity. Cytochrome c is therefore quantified based on the decrease in photoelectrical current. High specificity and high sensitivity were obtained with a linear range from 3 pM to 80 nM, and a limit of detection of 2.53 pM.

scholarly journals A 16S rDNA-based nested PCR protocol to detect Campylobacter gracilis in oral infections

2003 ◽  
Vol 17 (2) ◽  
pp. 142-146 ◽  
Author(s):  
José Freitas Siqueira Júnior ◽  
Isabela das Neves Rôças
Keyword(s):  
16S Rdna ◽  
High Sensitivity ◽  
High Specificity ◽  
Cross Reactivity ◽  
Nested Polymerase Chain Reaction ◽  
Oral Infections ◽  
Root Canals ◽  
Infected Root ◽  
Pcr Products ◽  
Species Specific

The aim of this study was to describe a 16S rDNA-based nested polymerase chain reaction (nPCR) assay to investigate the occurrence of Campylobacter gracilis in oral infections. Samples were collected from ten infected root canals, ten cases of acute periradicular abscesses and eight cases of adult marginal periodontitis. DNA extracted from the samples was initially amplified using universal 16S rDNA primers. A second round of amplification used the first PCR products to detect C. gracilis using oligonucleotide primers designed from species-specific 16S rDNA signature sequences. The nPCR assay used in this study showed a detection limit of 10 C. gracilis cells and no cross-reactivity was observed with nontarget bacteria. C. gracilis was detected in the three types of oral infections investigated - 4/10 infected root canals; 2/10 acute periradicular abscesses; and 1/8 subgingival specimens from adult periodontitis. The method proposed in this study showed both high sensitivity and high specificity to directly detect C. gracilis in samples from root canal infections, abscesses, and subgingival plaque. Our findings confirmed that C. gracilis may be a member of the microbiota associated with distinct oral infections, and its specific role in such diseases requires further clarification.

scholarly journals Comparison between near miss criteria in a maternal intensive care unit

2018 ◽  
Vol 52 (0) ◽  
Author(s):  
Alana Santos Monte ◽  
Liana Mara Rocha Teles ◽  
Mônica Oliveira Batista Oriá ◽  
Francisco Herlânio Costa Carvalho ◽  
Helen Brown ◽  
...  
Keyword(s):  
Intensive Care Unit ◽  
Intensive Care ◽  
Maternal Death ◽  
High Sensitivity ◽  
High Specificity ◽  
Near Miss ◽  
World Health ◽  
Maternal Near Miss ◽  
Chi Square ◽  
Cross Sectional

ABSTRACT Objective: The aim of this study was to compare the incidence of different criteria of maternal near miss in women admitted to an obstetric intensive care unit and their sensitivity and specificity in identifying cases that have evolved to morbidity. Method: A cross-sectional analytical epidemiological study was conducted with women admitted to the intensive care unit of the Maternity School Assis Chateaubriand in Ceará, Brazil. The Chi-square test and odds ratio were used. Results: 560 records were analyzed. The incidence of maternal near miss ranged from 20.7 in the Waterstone criteria to 12.4 in the Geller criteria. The maternal near-miss mortality ratio varied from 4.6:1 to 7.1:1, showing better index in the Waterstone criteria, which encompasses a greater spectrum of severity. The Geller and Mantel criteria, however, presented high sensitivity and low specificity. Except for the Waterstone criteria, there was an association between the three other criteria and maternal death. Conclusion: The high specificity of Geller and Mantel criteria in identifying maternal near miss considering the World Health Organization criteria as a gold standard and a lack of association between the criteria of Waterstone with maternal death.

scholarly journals Electroanalytical Biosensors for Circulating Tumor DNA Detection—A Brief Review

2021 ◽  
Author(s):  
Zhijia Peng ◽  
Xiaogang Lin ◽  
Weiqi Nian ◽  
Xiaodong Zheng ◽  
Jayne Wu
Keyword(s):  
Real Time ◽  
Point Of Care ◽  
Low Cost ◽  
High Sensitivity ◽  
High Specificity ◽  
Circulating Tumor Dna ◽  
Minimal Invasive ◽  
Diagnosis And Treatment ◽  
Detection Technology ◽  
Tumor Dna

Early diagnosis and treatment have always been highly desired in the fight against cancer, and detection of circulating tumor DNA (ctDNA) has recently been touted as highly promising for early cancer screening. Consequently, the detection of ctDNA in liquid biopsy gains much attention in the field of tumor diagnosis and treatment, which has also attracted research interest from the industry. However, traditional gene detection technology is difficult to achieve low cost, real-time and portable measurement of ctDNA. Electroanalytical biosensors have many unique advantages such as high sensitivity, high specificity, low cost and good portability. Therefore, this review aims to discuss the latest development of biosensors for minimal-invasive, rapid, and real-time ctDNA detection. Various ctDNA sensors are reviewed with respect to their choices of receptor probes, detection strategies and figures of merit. Aiming at the portable, real-time and non-destructive characteristics of biosensors, we analyze their development in the Internet of Things, point-of-care testing, big data and big health.

scholarly journals SARS-CoV-2 Direct Detection Without RNA Isolation With Loop-Mediated Isothermal Amplification (LAMP) and CRISPR-Cas12

2021 ◽  
Vol 8 ◽  
Author(s):  
Alfredo Garcia-Venzor ◽  
Bertha Rueda-Zarazua ◽  
Eduardo Marquez-Garcia ◽  
Vilma Maldonado ◽  
Angelica Moncada-Morales ◽  
...  
Keyword(s):  
Limit Of Detection ◽  
Direct Detection ◽  
Direct Method ◽  
Rna Extraction ◽  
Rna Isolation ◽  
High Sensitivity ◽  
High Specificity ◽  
Isothermal Amplification ◽  
Clinical Samples ◽  
Loop Mediated Isothermal Amplification

As to date, more than 49 million confirmed cases of Coronavirus Disease 19 (COVID-19) have been reported worldwide. Current diagnostic protocols use qRT-PCR for viral RNA detection, which is expensive and requires sophisticated equipment, trained personnel and previous RNA extraction. For this reason, we need a faster, direct and more versatile detection method for better epidemiological management of the COVID-19 outbreak. In this work, we propose a direct method without RNA extraction, based on the Loop-mediated isothermal amplification (LAMP) and Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR associated protein (CRISPR-Cas12) technique that allows the fast detection of SARS-CoV-2 from patient samples with high sensitivity and specificity. We obtained a limit of detection of 16 copies/μL with high specificity and at an affordable cost. The diagnostic test readout can be done with a real-time PCR thermocycler or with the naked eye in a blue-light transilluminator. Our method has been evaluated on a small set of clinical samples with promising results.

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