laboratory automation

As the volume of sequence data from variable pathogens increases, means of analyzing, annotating and extracting specific taxa for study becomes more difficult. To meet these challenges for datasets with hundreds to thousands of taxa, 'Phylobook' was developed. Starting with a sequence alignment file, Phylobook generates and displays phylogenetic trees adjacent to highlighter plots showing the position of mutations, and allows the user to identify lineages and recombinants, annotate and export selected subsets of sequences for downstream analysis...

AIMS: Coronary computed tomography angiography provides noninvasive assessment of coronary stenosis severity and flow impairment. Automated artificial intelligence analysis may assist in precise quantification and characterization of coronary atherosclerosis, enabling patient-specific risk determination and management strategies. This multicenter international study compared an automated deep-learning-based method for segmenting coronary atherosclerosis in coronary computed tomography angiography (CCTA) against the reference standard of intravascular ultrasound (IVUS)...

INTRODUCTION: The proactive identification of diseases through screening tests has long been endorsed as a means to preempt symptomatic onset. However, such screening endeavors are fraught with complications, such as diagnostic inaccuracies, procedural risks, and patient unease during examinations. These challenges are amplified when screenings for multiple diseases are administered concurrently. Selected Reaction Monitoring (SRM) offers a unique advantage, allowing for the high-throughput quantification of hundreds of analytes with minimal interferences...

Thyroid-stimulating hormone receptor autoantibodies (TRAbs) play a crucial role as pathogenic antibodies in both the diagnosis and management of Graves' disease (GD). GD, an autoimmune disease resulting from a combination of genetic and environmental factors, is the most common cause of hyperthyroidism. With advancements in technology for TRAb detection and the availability of automated commercial kits, TRAb has become an essential clinical laboratory marker for the diagnosis of GD, as well as extra-thyroidal manifestations like Graves' ophthalmopathy (GO)...

BACKGROUND: Current molecular diagnostics are limited in the number and type of detectable pathogens. Metagenomic next generation sequencing (mNGS) is an emerging, and increasingly feasible, pathogen-agnostic diagnostic approach. Translational barriers prohibit the widespread adoption of this technology in clinical laboratories. We validate an end-to-end mNGS assay for detection of respiratory viruses. Our assay is optimized to reduce turnaround time, lower cost-per-sample, increase throughput, and deploy secure and actionable bioinformatic results...

This research presents a novel method for objectively evaluating college badminton players' physical function levels. It examines current evaluation methods before proposing a novel model that combines Particle Swarm Optimization (PSO) with Backpropagation (BP) neural networks and data mining. The model establishes an evaluation index system that considers physical form, function, quality, and neural mechanisms. The study uses PSO-BP neural networks to adjust indicator weights for more accurate ratings. This recurrent improvement reduces errors while increasing prediction ability, resulting in accurate assessments of athletes' physical talents and neurological insights...

Although reduced representation bisulfite sequencing (RRBS) measures DNA methylation (DNAme) across CpG-rich genomic regions with high sensitivity, the assay can be time-consuming and prone to batch effects. Here, we present a high-throughput, automated RRBS protocol starting with DNA extraction from frozen rat tissues. We describe steps for RRBS library preparation, library quality control, and sequencing. We also detail an optimized pipeline for sequencing data processing. This protocol has been applied successfully to DNAme profiling across multiple rat tissues...

Dilution is a standard fluid operation widely employed in the sample preparation process of many bio(chemical) assays. It serves multiple essential functions such as sample mixing with certain reagents at specific dilution ratios, reducing sample matrix effects, bringing target analytes within the linear assay detection range, among many others. Traditionally, sample processing is performed in laboratory settings through manual or automated pipetting. When working in resource-limited settings, however, neither trained personnel nor proper laboratory equipment are available limiting the accessibility to high-quality diagnostic tests...

BACKGROUND/AIM: Automated measurement of immunostained samples can enable more convenient and objective prediction of treatment outcome from radiotherapy. We aimed to validate the performance of the QuPath image analysis software in immune cell markers detection by comparing QuPath cell counting results with those of physician manual cell counting. PATIENTS AND METHODS: CD8- and FoxP3-stained cervical, CD8-stained oropharyngeal, and Ku70-stained prostate cancer tumor sections were analyzed in 104 cervical, 92 oropharyngeal, and 58 prostate cancer patients undergoing radiotherapy at our Institution...

Syndromic testing, the simultaneous testing for multiple pathogens causing similar symptoms, has recently gained ground in clinical diagnostics. This approach can significantly shorten time to diagnosis and speed up decision-making, leading to an improved outcome for the patient. Here, we compared three automated multiplex PCR platforms for syndromic testing of respiratory samples in a retrospective study, and assessed their relative sensitivities. The PPA between BioFire and QIAstat compared to ePlex was 98...

BACKGROUND: Historically, it was assumed by some that high leg lift with windup pitching generated more ball velocity whereas pitching from the stretch was quicker to reduce the risk of base stealing but also more stressful on the arm. However, many now believe that velocity and stress do not differ between windup and stretch and always pitching from the stretch is simpler than mastering 2 techniques. PURPOSE/HYPOTHESIS: The purpose of this study was to compare windup and stretch fastball pitching biomechanics...

High throughput process development (HTPD) is established for time- and resource- efficient chromatographic process development. However, integration with non-chromatographic operations within a monoclonal antibody (mAb) purification train is less developed. An area of importance is the development of low pH viral inactivation (VI) that follows protein A chromatography. However, the lack of pH measurement devices at the micro-scale represents a barrier to implementation, which prevents integration with the surrounding unit operations, limiting overall process knowledge...

Streptococcus agalactiae [group B Streptococcus (GBS)] poses a major threat as the primary cause of early-onset neonatal invasive disease, particularly when mothers are colonized rectovaginally. Although culture remains the gold standard for antepartum GBS screening, quantitative polymerase chain reaction (qPCR) offers advantages in terms of sensitivity and turnaround time. The aim of this study was to validate the clinical utility of an automated qPCR laboratory-developed test (LDT) for antepartum GBS screening using the Panther Fusion Open Access system (Hologic, California, USA)...

Borderline oxacillin-resistant Staphylococcus aureus (BORSA) are mecA-negative strains with oxacillin minimum inhibitor concentration (MIC) close to the resistance breakpoint of ≥ 4μg/mL. Instead of producing penicillin-binding protein with low affinity to methicillin (oxacillin) mediated by mecA gene as in methicillin-resistant S. aureus (MRSA), BORSA strains are characterised by the hyperproduction of β-lactamase enzymes, thus able to break down methicillin. Common laboratory methods to detect MRSA such as cefoxitin disk diffusion alone may fail to detect methicillin resistance due to BORSA...

INTRODUCTION: Sepsis alerts based on laboratory and vital sign criteria were found insufficient to improve patient outcomes. While most early sepsis alerts were implemented into smaller scale operating systems, a centralized new approach may provide more benefits, overcoming alert fatigue, improving deployment of staff and resources, and optimizing the overall management of sepsis. The objective of the study was to assess mortality and length of stay (LOS) trends in emergency department (ED) patients, following the implementation of a centralized and automated sepsis alert system...

Immunohistochemistry (IHC) is used to guide treatment decisions in multiple cancer types. For treatment with checkpoint inhibitors, PD-L1 IHC is used as a companion diagnostic. However, the scoring of PD-L1 is complicated by its expression in cancer and immune cells. Separation of cancer and non-cancer regions is needed to calculate tumor proportion scores (TPS) of PD-L1, which is based on the percentage of PD-L1 positive cancer cells. Evaluation of PD-L1 expression requires highly experienced pathologists and is often challenging and time consuming...

Personal human identification is a crucial aspect of modern society with applications spanning from law enforcement to healthcare and digital security. This bibliometric paper presents a comprehensive analysis of recent advances in personal human identification methodologies focusing on biomedical traits. The paper examines a diverse range of research articles, reviews, and patents published over the last decade to provide insights into the evolving landscape of biometric identification techniques. The study categorizes the identified literature into distinct biomedical trait categories, including but not limited to, fingerprint and palmprint recognition, iris and retinal scanning, facial recognition, voice and speech analysis, gait recognition, and DNA-based identification...

Pseudomonas aeruginosa is an opportunistic pathogen that causes increased morbidity and mortality in risky patient groups. Nowadays, carbapenem resistance has become a threat and resistance genes are spreading among species through mobile genetic elements. The dissemination of carbapenemases among P.aeruginosa is a serious public health concern due to its limited options for the treatment of bacterial infections. In this study, it was aimed to investigate the molecular epidemiology of 47 carbapenem resistant P...

Bisphenol A (BPA) has been classified as an endocrine-disrupting substance that may cause adverse effects on human health and the environment. The development of simple and sensitive electrochemical biosensors is crucial for the rapid and effective quantitative determination of BPA. This work presents a study on electrochemical sensors utilizing gold nanoparticle-modified multi-walled carbon nanotubes (CNT/AuNPs). Glassy carbon electrodes (GCEs) and screen-printed electrodes (SPEs) were conveniently modified and used for BPA detection...

The measurement of blood glial fibrillary acidic protein (GFAP) and ubiquitin carboxy-terminal hydrolase L1 (UCH-L1) may assist in the management of mild traumatic brain injury (mTBI). This study aims to compare GFAP and UCH-L1 values measured using a handheld device with those measured using a core laboratory platform. We enrolled 230 mTBI patients at intermediate risk of complications. Following French guidelines, a negative S100B value permits the patient to be discharged without a computed tomography scan...