Performance Of Kit Research Articles

The SARS-CoV-2 Variants and their Impacts

Since the first detection of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the virus remains a public health concern. Several public health measures have been implemented in an effort to curb the infections. However, the effectiveness of these strategies was threatened with the emergence of numerous SARS-CoV-2 variants in all parts of the globe, due to the persistent mutations as part of the viral evolution. Mutations that usually occur in its spike glycoprotein, allow SARS-CoV-2 to possess advantageous characteristics for its survivability and persistence. This has led to poor performance of diagnostic kits which have caused non-specific and insensitive detection of these variants, resulting in undetermined infection. The variants also have caused the increased severity of COVID-19, involving hospitalisation rates, ICU admissions, and deaths. Many have reported the vaccine-breakthrough infections and reduced effectiveness of vaccination, which is supposed to provide an effective degree of protection against COVID-19 infections. Due to these issues, this review summarises the impacts related to SARS-CoV-2 variants emergence towards the performance of diagnostic kits, transmissibility of the virus, severity of disease, and effectiveness of COVID-19 vaccines.

A comparative analysis of extraction protocol performance on degraded mammalian museum specimens

The extraction of nucleic acids is one of the most routine procedures used in molecular biology laboratories, yet kit performance may influence the downstream processing of samples, particularly for samples which are degraded, and in low concentrations. Here we tested several commercial kits for specific use on commonly sampled mammalian museum specimens to evaluate the yield, size distribution, and endogenous content. Samples were weighed and had approximately equal input material for each extraction. These sample types are typical of natural history repositories ranged from 53 to 130 years old. The tested protocols spanned spin-column based extractions, magnetic bead purification, phenol/chloroform isolation, and specific modifications for ancient DNA. Diverse types of mammalian specimens were tested including adherent osteological material, bone and teeth, skin, and baleen. The concentration of DNA was quantified via fluorometry, and the size distributions of extracts visualized on an Agilent TapeStation. Overall, when DNA isolation was successful, all methods had quantifiable concentrations, albeit with variation across extracts. The length distributions varied based on the extraction protocol used. Shotgun sequencing was performed to evaluate if the extraction methods influenced the amount of endogenous versus exogenous content. The DNA content was similar across extraction methods indicating no obvious biases for DNA derived from different sources. Qiagen kits and phenol/chloroform isolation outperformed the Zymo magnetic bead isolations in these types of samples. Statistical analyses revealed that extraction method only explained 5% of the observed variation, and that specimen age explained variation (29%) more effectively.

Metagenomic survey of agricultural water using long read sequencing: Considerations for a successful analysis

Leafy greens are responsible for nearly half of the produce-related Shiga toxin-producing Escherichia coli (STEC) outbreaks in the United States and recent investigations have implicated agricultural water as a potential source. Current FDA detection protocols require extensive analysis time. We aimed to use Oxford Nanopore rapid sequencing kits for an in-field determination of agricultural water microbiome and possible detection and characterization of STECs strain(s) in these samples. We tested the performance of the nanopore rapid sequencing kit (RAD004) for fast microbiome determination using the well characterized ZymoBIOMICS mock microbial community and the number of reads for each identified species was present in the expected proportion. Rapid sequencing kit (LRK001 and RAD004) library preparation of DNA extracted from agricultural water resulted in poor nanopore sequencing reactions, with low output (0.3–1.7 M reads), a high proportion of failed reads (50–60%), and highly sheared DNA before and after a magnetic bead clean up. To improve performance, we prepared a DNA library with the ligation kit (LSK109), which includes multiple cleaning steps, reducing inherent inhibitors and producing a better outcome (2.2 M reads, 15% failed reads). No definitive presence of STEC could be confirmed in any of the sites. Approximately 100 reads from each site (0.02% of total reads) were identified as Escherichia coli, but the specific strain or their virulence genes could not be detected. Sites 9, 10, and 12 were found to be positive for STEC presence by microbiological techniques after enrichment. The rapid sequencing kits can be appropriate for genus or species level microbial identification, but we recommend the use of the ligation kit for increased sequencing depth and removal of contaminants in agricultural water. However, we were not able to identify any STEC strains in these nanopore microbiome samples, due to low initial concentrations. The results from this pilot study provide preliminary evidence that MinION sequencing of agricultural water using the ligation kit has the potential to be used for rapid microbiome determination in the field with optimal results for water quality surveillance.

Developing whole cell standards for the microbiome field

BackgroundEffective standardisation of the microbiome field is essential to facilitate global translational research and increase the reproducibility of microbiome studies. In this study, we describe the development and validation of a whole cell reference reagent specific to the gut microbiome by the UK National Institute for Biological Standards and Control. We also provide and test a two-step reporting framework to allow microbiome researchers to quickly and accurately validate choices of DNA extraction, sequencing, and bioinformatic pipelines.ResultsUsing 20 strains that are commonly found in the gut, we developed a whole cell reference reagent (WC-Gut RR) for the evaluation of the DNA extraction protocols commonly used in microbiome pipelines. DNA was first analysed using the physicochemical measures of yield, integrity, and purity, which demonstrated kits widely differed in the quality of the DNA they produced. Importantly, the combination of the WC-Gut RR and the three physicochemical measures allowed us to differentiate clearly between kit performance. We next assessed the ability of WC-Gut RR to evaluate kit performance in the reconstitution of accurate taxonomic profiles. We applied a four-measure framework consisting of Sensitivity, false-positive relative abundance (FPRA), Diversity, and Similarity as previously described for DNA reagents. Using the WC-Gut RR and these four measures, we could reliably identify the DNA extraction kits’ biases when using with both 16S rRNA sequencing and shotgun sequencing. Moreover, when combining this with complementary DNA standards, we could estimate the relative bias contributions of DNA extraction kits vs bioinformatic analysis. Finally, we assessed WC-Gut RR alongside other commercially available reagents. The analysis here clearly demonstrates that reagents of lower complexity, not composed of anaerobic and hard-to-lyse strains from the gut, can artificially inflate the performance of microbiome DNA extraction kits and bioinformatic pipelines.ConclusionsWe produced a complex whole cell reagent that is specific for the gut microbiome and can be used to evaluate and benchmark DNA extractions in microbiome studies. Used alongside a DNA standard, the NIBSC DNA-Gut-Mix RR helps estimating where biases occur in microbiome pipelines. In the future, we aim to establish minimum thresholds for data quality through an interlaboratory collaborative study.BEU9jL7xnwncT84Rof_ZoXVideo

An Evaluation of a New Quantitative Point-of Care Diagnostic to Measure Glucose-6-phosphate Dehydrogenase Activity

Malaria continues to be one of the most crucial infectious burdens in endemic areas worldwide, as well as for travelers visiting malaria transmission regions. It has been reported that 8-aminoquinolines are effective against the Plasmodium species, particularly primaquine, for anti-hypnozoite therapy in P. vivax malaria. However, primaquine causes acute hemolytic anemia in individuals with glucose-6-phosphate dehydrogenase (G6PD) deficiency. Therefore, G6PD deficiency testing should precede hypnozoite elimination with 8-aminoquinoline. Several point-of-care devices have been developed to detect G6PD deficiency. The aim of the present study was to evaluate the performance of a novel, quantitative G6PD diagnostics based on a metagenomic blue fluorescent protein (mBFP). We comparatively evaluated the sensitivity and specificity of the G6PD diagnostic modality with standard methods using 120 human whole blood samples. The G6PD deficiency was spectrophotometrically confirmed. The performance of the G6PD quantitative test kit was compared with that of a licensed control medical device, the G6PD strip. The G6PD quantitative test kit had a sensitivity of 95% (95% confidence interval (CI): 89.3–100%) and a specificity of 100% (95% CI: 94.3–100%). This study shows that the novel diagnostic G6PD quantitative test kit could be a cost-effective and time-efficient, and universally mandated screening tool for G6PD deficiency.

The Comparative Analysis of Two RT-qPCR Kits for Detecting SARS-CoV-2 Reveals a Higher Risk of False-Negative Diagnosis in Samples with High Quantification Cycles for Viral and Internal Genes.

The early detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using the real-time quantitative polymerase chain reaction (RT-qPCR) as a gold-standard molecular tool has allowed to test and trace the viral spread and the isolation of COVID-19-infected patients. The detection capacity of viral and internal genes is an essential parameter to consider and analyze during the assay. In this study, we analyze the performance of the two commercial RT-qPCR kits used in Chile, TaqMan™ 2019-nCoV Control Kit v1 (Thermo Fisher) and MaxCov19 (TAAG Genetics), for the COVID-19 diagnosis from nasopharyngeal swab samples (NPSs). Our results show a lower sensitivity of the TAAG kit compared to the Thermo Fisher kit, even in the detection of SARS-CoV-2 mutations associated with its variants. This study reinforces the relevance of evaluating the performance of RT-qPCR kits before being used massively since those with lower sensitivity can generate false negatives and produce outbreaks of local infections.

Performance comparison between Elecsys Anti-SARS-CoV-2 and Anti-SARS-CoV-2 S and Atellica IM SARS-CoV-2 Total and SARS-CoV-2 IgG assays

Background: Although serological severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) tests from several manufacturers have been introduced in South Korea and some are commercially available, the performance of these test kits has not yet been sufficiently validated. Therefore, we compared the performance of Elecsys Anti-SARS-CoV-2 (ACOV2) and Anti-SARS-CoV-2 S (ACOV2S) and Atellica IM SARS-CoV-2 Total (COV2T) and SARS-CoV-2 IgG (sCOVG) serological tests in this study.Methods: A total of 186 patient samples were used. For each test, we analyzed the positive rate of serological antibody tests, precision, linearity, and agreement among the four assays.Results: The positive rates of COV2T, sCOVG, and ACOV2S were high (81.7%–89.2%) in total, with those for ACOV2S being the highest, while those of ACOV2 were as low as 44.6%. This may be related to the high completion rate of vaccination in Korea. The repeatability and within-laboratory coefficients of variation were within the claimed allowable imprecision; however, further research is needed to establish an allowable imprecision at low concentrations. COV2T showed a linear fit, whereas sCOVG and ACOV2S were appropriately modeled with a nonlinear fit. Good agreement was found among COV2T, sCOVG, and ACOV2S; however, the agreement between ACOV2 and any one of the other methods was poor.Conclusions: Considering the different antigens used in serological SARS-CoV-2 antibody assays, the performance of the tested assays is thought to show no significant difference for the qualitative detection of antibodies to SARS-CoV-2.

Comparison between MACSprep™ forensic sperm microbead kit and Erase Sperm Isolation kit for the enrichment of sperm fractions recovered from sexual assault samples

Sexual assault samples often contain mixtures of cells coming from at least two donors. Ideally, one would need to separate the cells into two cellular fractions: one consisting of the alleged aggressor’s spermatozoa (the sperm fraction) and the other containing the victim’s epithelial cells (the non-sperm fraction). This separation increases the probability of obtaining the alleged offender’s autosomal DNA profile. However, spermatozoa are often collected along with an excess of biological material originating from the victim, and with unfavorable male:female biological material ratios, the absence of separation could result in the PCR amplification of the victim’s DNA profile only. Several approaches are available to enrich/purify the spermatozoa present on sexual assault samples. In this paper, we compare a new method, the MACSprep™ Forensic Sperm MicroBead Kit (MACSprep, based on microbeads conjugated with antibodies bound to spermatozoa and their retention within a magnetic column) with the Erase Sperm Isolation Kit (Erase, a standard differential lysis separation procedure combined with a specific removal of free DNA) routinely used in our lab. The performance of both kits was tested using sets of vaginal and buccal swabs loaded with different dilutions of sperm, or azoospermic semen, representing a total of 120 independent samples. For the samples containing undiluted sperm, an average recovery of 58% was observed for the MACSprep’s sperm fractions and 43% for Erase’s. Significantly better recovery of azoospermic semen was observed in MACSprep’s non-sperm fractions (~ 85%) compared to Erase (~ 28%). Erase performed significantly better than MACSprep in terms of recovery for diluted sperm samples (1:10 to 1:800 sperm dilutions) in the presence of vaginal cells, while the purities of the achieved sperm fractions were in favor of MACSprep for the highest sperm dilutions tested. Similar trends were observed with buccal swabs loaded with 1:200 sperm dilutions. Increased sperm dilutions on vaginal swabs resulted in higher variability in the male material recovered, whatever the separation method used. Both methods were easy to perform and resulted in male DNA extracts ready to use in less than 2 h. Both kits showed their specificities in terms of recovery efficiency and purity of the sperm fractions. Ideally, additional experiments should be performed in different laboratories, using workflow and chemistries different than ours, to better define the peculiarities observed with MACSprep for high dilutions. Improving the recovery of MACSprep for diluted samples, in addition to its better purity observed in the experiments performed, could make it a method of choice for laboratory workflow, despite MACSprep’s current price per sample being about twice the price of Erase’s.

Performance of the TaqMan COVID-19 Pooling Kit for detection of SARS-CoV-2 in asymptomatic and symptomatic populations.

Clinical evidence for asymptomatic cases of coronavirus disease (COVID-19) has reinforced the significance of effective surveillance testing programs. Quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) assays are considered the ‘gold standard’ for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. However, the labor and resource requirements can be prohibitive with respect to large testing volumes associated with the pandemic. Pooled testing algorithms may serve to increase testing capacity with more efficient resource utilization. Due to the lack of carefully curated cohorts, there is limited evidence for the applicability of RT-PCR pooling in asymptomatic COVID-19 cases. In this study, we compared the analytical sensitivity of the TaqMan™ SARS-CoV-2 Pooling Assay to detect one positive sample in a pool of five anterior nares swabs in symptomatic and asymptomatic cohorts at an institute of higher education. Positive pools were deconvoluted and each individual sample was retested using the TaqPath™ COVID-19 Combo Kit. Both assays target the open reading frame (ORF) 1ab, nucleocapsid (N), and spike (S) gene of the strain that originated in Wuhan, Hubei, China. Qualitative results demonstrated absolute agreement between pooled and deconvoluted samples in both cohorts. Independent t-test performed on Ct shifts supported an insignificant difference between cohorts with p-values of 0.306 (Orf1ab), 0.147 (N), and 0.052 (S). All negative pools were correctly reported as negative. Pooled PCR testing up to five samples is a valid method for surveillance testing of students and staff in a university setting, especially when the prevalence is expected to be low.

What Is an Antibody Test? Characteristics of Antibodies against SARS-CoV-2 and Their Tests

Antibodies play a major role in immune responses against viruses, which inhibit infection by binding to target viral antigen. Antibodies are induced by viral entry to the body and vaccination that artificially induces immune responses; therefore, antibody tests are used in research for infection history and evaluation of vaccine efficacy. Currently, antibody tests against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) by immunochromatography, enzyme-linked immunosorbent assay (ELISA), and electrochemiluminescence immunoassay (ECLIA), or other kits used for automated analyzer are available. However, the test results should be carefully interpreted because requirements for the antibody test to obtain reliable results have not been established. Also, antibodies in human samples are heterogeneous, and their expression level changes over time. This review briefly explains the basic knowledge about antibodies against SARS-CoV-2 and outlines the classification and characteristics of the antibody tests with points to consider in their use. A summary of the collaborative study that evaluated the analytical performance of antibody test kits conducted by the National Institute of Health Sciences is also introduced. Then, the issues in ensuring the reliability of antibody tests results are discussed by considering the usefulness and availability of the World Health Organization international standard for anti-SARS-CoV-2 immunoglobulin.

A novel NGS kit solution for multi-cancer early detection using circulating cell free DNA based methylation analysis.

10542 Background: Cancer patient survival can be greatly improved by early detection. Cell-free DNA (cfDNA)-based cancer detection using targeted methylation sequencing (TMS) holds great promise. Here, we report the performance of the first cfDNA TMS kit for early cancer detection. Methods: We developed a comprehensive multi-cancer TMS panel, named “Omni1” (900kb) containing ̃3000 cancer specific hypermethylation markers for the detection of the 16 most prevalent solid tumor cancer types in the US. These selected biomarkers all have high signals in cancer, low signals in normal tissue and close to zero background in plasma. The TMS analysis is empowered by Point-n-Seq DNA enrichment and soft bisulfite sequencing technology. Across the different cancer types, the Point-n-Seq Methylation Index (PMI) derived from the Omni1 panel showed over 10 times the difference in the genomic DNA of tumor compared to normal tissues. 8 to 32 early-stage plasma samples from each of the 7 most prevalent cancer types were used for assay testing. cfDNA extracted from each donor was subjected to our Point-n-Seq TMS analysis with the Omni1 panel. The TMS workflow took around five hours, from cfDNA to a sequencing ready library. 6M reads were assigned to each sample resulting in ̃1400X average raw coverage across the target regions. Results: A computational model to calculate the methylation index and the thresholds were established on independent training data sets for each cancer type. For the testing, specificity was set at 89% (CI = 0.81, 0.97, n = 55 self-claimed healthy individuals). The detection rate for stage I (n = 55) and stage II (n = 56) of all 7 cancer types combined is 65% (CI = 0.53,0.78) and 75% (CI = 0.64, 0.86) respectively. Even within this small sample size, it was clear that the detection sensitivity varied among different cancer types, and it increased from stage I to II: colorectal (65%, n = 20; 75%, n = 12), lung (75% n = 8; 92%, n = 12), pancreas (80%, n = 10; 100%, n = 10), ovary (60%, n = 5; 80%, n = 5), breast (40%, n = 7; 100%, n = 3), and prostate cancer (0%, n = 2; 22% n = 9) for stage I and II respectively. A decrease in sensitivity from stage I to II in liver (100%, n = 3; 60%, n = 5) is possibly due to variability from the small sample size. For the cases of CRC, the detection rates obtained from Omni1 are comparable to the stand-alone CRC560 panel (170 kb). Conclusions: In this study we demonstrated that by leveraging an economy-size panel, a robust methylation sequencing kit, and a straightforward analysis methodology, early cancer detection for multiple cancer types can be done with just 1ml plasma. The kit strategy provides an easy-to-use and distributable solution, without the complications of developing a lab-specific test that uses a large methylation panel and a high sequencing cost.

Assessing homologous recombination deficiency (HRD) in ovarian cancer: Optimizing concordance of the regulatory-approved companion diagnostic and a next-generation sequencing (NGS) assay kit.

e17571 Background: Olaparib + bevacizumab is approved as first-line maintenance treatment of ovarian cancer that is HRD positive, defined as the presence of a deleterious/suspected deleterious BRCA mutation (BRCAm) and/or genomic instability. HRD genomic instability score (GIS) has been assessed in clinical trials using a regulatory-approved companion diagnostic, Myriad myChoice® CDx. We evaluated the performance of an in-development NGS assay kit that identifies BRCA variants based on genomic content from Illumina’s TruSight™ Oncology 500 research assay, and, with additional genomic content, measures HRD GIS in tumor tissue (Illumina test) in parallel. Analytic concordance of the Illumina test versus the Myriad myChoice® PLUS assay (Myriad test) under improved algorithms for calculating GIS scores is reported. Methods: Ovarian cancer tissue samples were analyzed with the Illumina (40 ng DNA; N = 227) and Myriad (200 ng DNA; N = 254) tests. Agreement rates for BRCA analysis, HRD GIS, and overall HRD status (includes BRCAm and HRD GIS [cutoff, 42]) were analyzed. For the overall and the non-BRCAm analysis cohorts, Pearson correlation between the continuous HRD GIS of the Illumina and Myriad tests was determined. Analytic sensitivity and specificity of the Illumina-derived HRD GIS to classify HRD GIS (cutoff, 42) were evaluated using AUROC. After initial concordance calculations, modifications were made to increase the quality of the Illumina preprocessing data (ie, reducing allele dosage noise and allele bias) upstream of the GIS calling algorithm. Reprocessing of the existing raw data led to further improvement in the point estimates of positive and negative percent agreement. Results: Prevalence using the Illumina and Myriad tests was 51.2% and 49.2% (overall HRD positive) and 27.6% and 25.5% (BRCAm), respectively. Agreement rates are reported in the Table. Correlation of the Illumina HRD GIS with Myriad HRD GIS was 0.980 (all samples) and 0.976 (non-BRCAm cohort); AUROCs were 0.995 and 0.992, respectively. Conclusions: Comparison between the Illumina and Myriad tests showed that overall HRD status, BRCA analysis, and HRD GIS detection results were > 90% concordant; HRD GIS was highly correlated (r > 0.98); and prevalence estimates were similar. These data suggest that a distributable kit solution, such as the Illumina test under development, will approach the performance of the Myriad myChoice HRD assay.[Table: see text]

Diagnostic performance of a Rapid Test Kit for white spot syndrome virus (WSSV)

White spot syndrome virus (WSSV) is a highly infectious and influential pathogen that causes mass mortality. Particularly, this virus has had the most severe impact on global shrimp culture over the past 30 years. There are currently no vaccines or treatments for WSSV, and therefore accurate diagnosis strategies are critical for the management of shrimp farms. In this study, a commercial WSSV lateral flow immunoassay (WSSV RP Rapid Test Kit, Innocreate Bioscience Co., Ltd., Taiwan) can be used to assess the level of WSSV infection in shrimp farms was tested. Sensitivity analyses indicated that 0.4 ng of a recombinant target protein could be reliably detected after 15 min. Additionally, this kit did not return false-positive reactions when testing samples infected with PirABVP-producing strain of Vibrio parahaemolyticus (the causative agent of acute hepatopancreatic necrosis disease, AHPND), haematopoietic necrosis virus (IHHNV), and Enterocytozoon hepatopenaei (EHP). Furthermore, the accuracy and sensitivity of our proposed procedure were assessed using the OIE TaqMan real-time PCR method. Upon analyzing 231 samples, our WSSV immunoassay achieved a sensitivity and specificity of 99.21% and 100%, respectively. Collectively, our findings demonstrated the convenience, stability, sensitivity, and specificity of the WSSV RP Rapid Test Kit, and therefore this kit can be widely used in aquaculture farms to assist disease management.

Portable Devices for Measurement of Vitamin A Concentrations in Edible Oil: Field Readiness of Available Options.

Vitamin A (VA) deficiency continues to be a major global health issue, despite measures to increase VA intake via consumption of staple foods such as edible oil. Portable quantitative and semiquantitative devices or test kits for internal quality control have the potential to overcome some of the limitations of traditional methods of testing, such as centralized laboratory, expensive equipment, and specially trained staff. This landscape analysis and comprehensive systematic mini-review catalogs and summarizes evidence on the analytical performance of portable quantitative and semiquantitative devices and test kits for the analysis of VA in edible oil. Studies or reports detailing the usability and validation of portable devices and/or test kits, as well as studies comparing device/test kit performance to a reference standard such as high-performance liquid chromatography (HPLC), were included. Identified devices and test kits were compared for performance versus the reference standard, usability, availability, and other characteristics. We identified four portable methods: two devices, the iCheck CHROMA and iCheck Chroma 3 from BioAnalyt; and two test kits, the QuickView from Bagco Enterprises and the Strategic Alliance for the Fortification of Vegetable Oils (SAFO) Test Kit by Badische Anilin and Soda Fabrik (BASF). Included studies reported the following: an internal validation of the portable method, a comparison of the portable method against a reference standard, a comparison of the portable method against another portable method, and several videos and company websites, which detailed device characteristics. iCheck CHROMA and QuickView quantified VA concentrations with high accuracy and precision compared to the reference standard for field-based quantification, were user-friendly, and provided results within 5 min. iCheck Chroma 3 requires more robust validation against a reference standard. We did not find data on internal validation or comparison against a reference standard for the current version of the SAFO test. Compared to QuickView and SAFO, the iCheck devices can transfer results to a hard drive or the Web, have an online order form for purchase, and meet a minimal set of criteria for point-of-need devices. iCheck, QuickView, and SAFO can quantify VA concentrations in the edible oils tested and determine whether a fortified oil meets country standards. Additional research is needed to validate these devices and test kits across additional oil types and document the ability to meet the minimal criteria for point-of-need devices suggested in this mini-review. Validation against a reference standard is required for SAFO. The limited number of portable methods available may be due to market saturation. Future market and use case analyses to inform the market size and utility of the different tests with publicly available data will allow new manufacturers, particularly those in lower-to-middle-income countries, to enter the market.

Injury Prevention Considerations for Drum Kit Performance.

For any skilled performer to deliver their optimal performance, preparation must extend beyond task-specific skill development to include psychological skills training, physical conditioning, and injury prevention. The keynote lecture upon which this article is based (delivered at the International Symposium on Performance Science 2021) explored current research that demonstrates the importance of physical conditioning and injury prevention for drummers (i.e., percussionists who play the drum kit). Early results revealed that professional drummers’ heart rates during live performances can reach similar levels to those of other professional athletes during competitions. They also established that playing-related musculoskeletal disorders (PRMDs) are very common in drummers, particularly those affecting the upper limbs such as tendinitis and carpal tunnel syndrome. Evidence from laboratory-based studies supports non-neutral postures, repetitive movements, and exposure to hand-arm vibration as risk factors for the development of these injuries in drummers. Embedding injury prevention education within drum kit curricula is a promising strategy for reducing the rates at which drummers report experiencing PRMDs, and the barriers and facilitators that drum kit educators encounter when attempting to do so are currently under investigation. When drummers include both physical conditioning and injury prevention within their overall preparation regimen, they will maximize their potential to deliver their peak performance.

Natural Language Processing of Radiology Reports to Detect Complications of Ischemic Stroke.

Abstraction of critical data from unstructured radiologic reports using natural language processing (NLP) is a powerful tool to automate the detection of important clinical features and enhance research efforts. We present a set of NLP approaches to identify critical findings in patients with acute ischemic stroke from radiology reports of computed tomography (CT) and magnetic resonance imaging (MRI). We trained machine learning classifiers to identify categorical outcomes of edema, midline shift (MLS), hemorrhagic transformation, and parenchymal hematoma, as well as rule-based systems (RBS) to identify intraventricular hemorrhage (IVH) and continuous MLS measurements within CT/MRI reports. Using a derivation cohort of 2289 reports from 550 individuals with acute middle cerebral artery territory ischemic strokes, we externally validated our models on reports from a separate institution as well as from patients with ischemic strokes in any vascular territory. In all data sets, a deep neural network with pretrained biomedical word embeddings (BioClinicalBERT) achieved the highest discrimination performance for binary prediction of edema (area under precision recall curve [AUPRC] > 0.94), MLS (AUPRC > 0.98), hemorrhagic conversion (AUPRC > 0.89), and parenchymal hematoma (AUPRC > 0.76). BioClinicalBERT outperformed lasso regression (p < 0.001) for all outcomes except parenchymal hematoma (p = 0.755). Tailored RBS for IVH and continuous MLS outperformed BioClinicalBERT (p < 0.001) and linear regression, respectively (p < 0.001). Our study demonstrates robust performance and external validity of a core NLP tool kit for identifying both categorical and continuous outcomes of ischemic stroke from unstructured radiographic text data. Medically tailored NLP methods have multiple important big data applications, including scalable electronic phenotyping, augmentation of clinical risk prediction models, and facilitation of automatic alert systems in the hospital setting.

Performance evaluation of the Asante Rapid Recency Assay for verification of HIV diagnosis and detection of recent HIV-1 infections: Implications for epidemic control.

We previously described development of a rapid test for recent infection (RTRI) that can diagnose HIV infection and detect HIV-1 recent infections in a single device. This technology was transferred to a commercial partner as Asante Rapid Recency Assay (ARRA). We evaluated performance of the ARRA kits in the laboratory using a well-characterized panel of specimens. The plasma specimen panel (N = 1500) included HIV-1 (N = 570), HIV-2 (N = 10), and HIV-negatives (N = 920) representing multiple subtypes and geographic locations. Reference diagnostic data were generated using the Bio-Rad HIV-1-2-O EIA/Western blot algorithm with further serotyping performed using the Multispot HIV-1/2 assay. The LAg-Avidity EIA was used to generate reference data on recent and long-term infection for HIV-1 positive specimens at a normalized optical density (ODn) cutoff of 2.0 corresponding to a mean duration of about 6 months. All specimens were tested with ARRA according to the manufacturer's recommendations. Test strips were also read for line intensities using a reader and results were correlated with visual interpretation. ARRA's positive verification line (PVL) correctly classified 575 of 580 HIV-positive and 910 of 920 negative specimens resulting in a sensitivity of 99.1% (95% CI: 98.0-99.6) and specificity of 98.9% (95% CI: 98.1-99.4), respectively. The reader-based classification was similar for PVL with sensitivity of 99.3% (576/580) and specificity of 98.8% (909/920). ARRA's long-term line (LTL) classified 109 of 565 HIV-1 specimens as recent and 456 as long-term compared to 98 as recent and 467 as long-term (LT) by LAg-Avidity EIA (cutoff ODn = 2.0), suggesting a mean duration of recent infection (MDRI) close to 6 months. Agreement of ARRA with LAg recent cases was 81.6% (80/98) and LT cases was 93.8% (438/467), with an overall agreement of 91.7% (kappa = 0.72). The reader (cutoff 2.9) classified 109/566 specimens as recent infections compared to 99 by the LAg-Avidity EIA for recency agreement of 81.8% (81/99), LT agreement of 9% (439/467) with overall agreement of 91.9% (kappa = 0.72). The agreement between visual interpretation and strip reader was 99.9% (95% CI: 99.6-99.9) for the PVL and 98.1% (95% CI: 96.6-98.9) for the LTL. ARRA performed well with HIV diagnostic sensitivity >99% and specificity >98%. Its ability to identify recent infections is comparable to the LA-Avidity EIA corresponding to an MDRI of about 6 months. This point-of-care assay has implications for real-time surveillance of new infections among newly diagnosed individuals for targeted prevention and interrupting ongoing transmission thus accelerating epidemic control.

HIV oral self-screening test among HIV/STD/TB clinic attendees

Globally, several countries consider HIV self-test as an important element in the toolbox to end AIDS by 2030. Against this background, the present investigation was conducted to pilot test the performance of an indigenous HIV oral self-test (HIVOST) and explore its acceptability. The overall purpose was to examine if this kit could serve as a promising tool and merit future larger clinical evaluation. A concurrent mixed-method investigation was undertaken during March-October 2019. One hundred and thirty two consecutive HIV/sexually transmitted diseases/tuberculosis clinic attendees were invited for participation; of whom, 100 were enrolled, and among them, 40 provided consent for qualitative in-depth interviews. The HIVOST kit assessed for its performance served as the 'index test', which worked on the principle of lateral flow chromatography. The results of the HIVOST were interpreted independently by the study physicians and participants at 20 min. HIVOST kit performance was assessed against the HIV confirmatory blood test result based on the national algorithm (3 rapid test or 1 ELISA and 2 rapid test) serving as the 'reference'. Sensitivity, specificity, positive predictive value, negative predictive value and inter-rater agreement were estimated. The voices and concerns of the study participants were coded followed by identification of qualitative themes and ideas. The sensitivity and specificity of the index test at the end of 20 min as interpreted by the participants were 83.3 per cent [95% confidence interval (CI): 69.8 to 92.5] and 98 per cent (95% CI: 89.4 to 99.5), respectively. Study physicians and participants independently interpreted HIVOST results with substantial inter-rater agreement (kappa value 0.88; 95% CI: 0.78-0.97). All HIVOST test strips were valid. Majority of the participants preferred saliva over blood for HIV self-test. 'Comfort', 'confidentiality' and 'convenience' were the perceived advantages of HIVOST. Some of the participants wished the package inserts contained 'how-to-do instructions in local languages', 'expiry date (if any)' and 'contact helpline number'. A few of them highlighted the need for a confirmatory HIV result following oral self-test. Concerns of the participants revolved around potential self-harm following HIVOST-positive result and safe disposal of kits. Two major highlights of the present investigation are (i) high level of concordance in HIVOST results interpreted by participants and physicians, and (ii) encouraging level of acceptance of HIVOST. These findings and encouraging HIVOST performance statistics lend support towards large-scale clinical evaluation of this index test.

Meta-analysis of the robustness of COVID-19 diagnostic kit performance during the early pandemic

BackgroundAccurate detection of SARS-CoV-2 is necessary to mitigate the COVID-19 pandemic. However, the test reagents and assay platforms are varied and may not be sufficiently robust to diagnose COVID-19.MethodsWe reviewed...

Evaluation of the Vitek Ms system for the identification of filamentous fungi.

The use of MALDI-TOF for fungal identification remains a challenge. In this study, using a commercial protein extraction kit and updated database, VITEK MS system was able to identify up to 89.0% of a diverse collection of 200 filamentous fungi representing 43 fungal species.