An automated and high-throughput data processing workflow for PFAS identification in biota by direct infusion ultra-high resolution mass spectrometry.

The increasing recognition of the health impacts from human exposure to per- and polyfluorinated alkyl substances (PFAS) has surged the need for sophisticated analytical techniques and advanced data analyses, especially for assessing exposure by food of animal origin. Despite the existence of nearly 15,000 PFAS listed in the CompTox chemicals dashboard by the US Environmental Protection Agency, conventional monitoring and suspect screening methods often fall short, covering only a fraction of these substances. This study introduces an innovative automated data processing workflow, named PFlow, for identifying PFAS in environmental samples using direct infusion Fourier transform ion cyclotron resonance mass spectrometry (DI-FT-ICR MS). PFlow's validation on a bream liver sample, representative of low-concentration biota, involves data pre-processing, annotation of PFAS based on their precursor masses, and verification through isotopologues. Notably, PFlow annotated 17 PFAS absent in the comprehensive targeted approach and tentatively identified an additional 53 compounds, thereby demonstrating its efficiency in enhancing PFAS detection coverage. From an initial dataset of 30,332 distinct m/z values, PFlow thoroughly narrowed down the candidates to 84 potential PFAS compounds, utilizing precise mass measurements and chemical logic criteria, underscoring its potential in advancing our understanding of PFAS prevalence and of human exposure.

Fully automated OCT-based tissue screening system.

This study introduces an innovative optical coherence tomography (OCT) imaging system dedicated to high-throughput screening applications using ex vivo tissue culture. Leveraging OCT's non-invasive, high-resolution capabilities, the system is equipped with a custom-designed motorized platform and tissue detection ability for automated, successive imaging across samples. Transformer-based deep-learning segmentation algorithms further ensure robust, consistent, and efficient readouts meeting the standards for screening assays. Validated using retinal explant cultures from a mouse model of retinal degeneration, the system provides robust, rapid, reliable, unbiased, and comprehensive readouts of tissue response to treatments. This fully automated OCT-based system marks a significant advancement in tissue screening, promising to transform drug discovery, as well as other relevant research fields.

[Development of ECG Common Mode Rejection Ratio Automatic Test System].

To comprehensively meet the test requirements for the common mode rejection ratio (CMRR) across different ECG-particular standards, this paper presents the design of an ECG CMRR automatic test system. The hardware component primarily consists of a test signal generation module, an automatic control network (which includes a resistance-capacitance network control module and a polarization voltage control module), and a noise level switching module. The software portion enables automatic control and user interaction. Experimental results indicate that the system is stable, reliable, and highly automated, capable of satisfying the test requirements of various ECG-particular standards, thus demonstrating a promising application prospect.

Automation in Flow Cytometry.

Automation in clinical flow cytometry has the potential to revolutionize the field by improving processes and enhancing efficiency and accuracy. Integrating advanced robotics and artificial intelligence, these technologies can streamline sample preparation, data acquisition, and analysis. Automated sample handling reduces human error and increases throughput, allowing laboratories to handle larger volumes with consistent precision. Intelligent algorithms contribute to rapid data interpretation, aiding in the identification of cellular markers for disease diagnosis and monitoring. This automation not only accelerates turnaround times but also ensures reproducibility, making clinical flow cytometry a reliable tool in the realm of personalized medicine and diagnostics.

Automation of duplicate record detection for systematic reviews: Deduplicator.

BACKGROUND: To describe the algorithm and investigate the efficacy of a novel systematic review automation tool "the Deduplicator" to remove duplicate records from a multi-database systematic review search. METHODS: We constructed and tested the efficacy of the Deduplicator tool by using 10 previous Cochrane systematic review search results to compare the Deduplicator's 'balanced' algorithm to a semi-manual EndNote method. Two researchers each performed deduplication on the 10 libraries of search results. For five of those libraries, one researcher used the Deduplicator, while the other performed semi-manual deduplication with EndNote. They then switched methods for the remaining five libraries. In addition to this analysis, comparison between the three different Deduplicator algorithms ('balanced', 'focused' and 'relaxed') was performed on two datasets of previously deduplicated search results. RESULTS: Before deduplication, the mean library size for the 10 systematic reviews was 1962 records. When using the Deduplicator, the mean time to deduplicate was 5 min per 1000 records compared to 15 min with EndNote. The mean error rate with Deduplicator was 1.8 errors per 1000 records in comparison to 3.1 with EndNote. Evaluation of the different Deduplicator algorithms found that the 'balanced' algorithm had the highest mean F1 score of 0.9647. The 'focused' algorithm had the highest mean accuracy of 0.9798 and the highest recall of 0.9757. The 'relaxed' algorithm had the highest mean precision of 0.9896. CONCLUSIONS: This demonstrates that using the Deduplicator for duplicate record detection reduces the time taken to deduplicate, while maintaining or improving accuracy compared to using a semi-manual EndNote method. However, further research should be performed comparing more deduplication methods to establish relative performance of the Deduplicator against other deduplication methods.

A graph-learning based model for automatic diagnosis of Sjögren's syndrome on digital pathological images: a multicentre cohort study.

BACKGROUND: Sjögren's Syndrome (SS) is a rare chronic autoimmune disorder primarily affecting adult females, characterized by chronic inflammation and salivary and lacrimal gland dysfunction. It is often associated with systemic lupus erythematosus, rheumatoid arthritis and kidney disease, which can lead to increased mortality. Early diagnosis is critical, but traditional methods for diagnosing SS, mainly through histopathological evaluation of salivary gland tissue, have limitations. METHODS: The study used 100 labial gland biopsy, creating whole-slide images (WSIs) for analysis. The proposed model, named Cell-tissue-graph-based pathological image analysis model (CTG-PAM) and based on graph theory, characterizes single-cell feature, cell-cell feature, and cell-tissue feature. Building upon these features, CTG-PAM achieves cellular-level classification, enabling lymphocyte recognition. Furthermore, it leverages connected component analysis techniques in the cell graph structure to perform SS diagnosis based on lymphocyte counts. FINDINGS: CTG-PAM outperforms traditional deep learning methods in diagnosing SS. Its area under the receiver operating characteristic curve (AUC) is 1.0 for the internal validation dataset and 0.8035 for the external test dataset. This indicates high accuracy. The sensitivity of CTG-PAM for the external dataset is 98.21%, while the accuracy is 93.75%. In comparison, the sensitivity and accuracy for traditional deep learning methods (ResNet-50) are lower. The study also shows that CTG-PAM's diagnostic accuracy is closer to skilled pathologists compared to beginners. INTERPRETATION: Our findings indicate that CTG-PAM is a reliable method for diagnosing SS. Additionally, CTG-PAM shows promise in enhancing the prognosis of SS patients and holds significant potential for the differential diagnosis of both non-neoplastic and neoplastic diseases. The AI model potentially extends its application to diagnosing immune cells in tumor microenvironments.

Safety improvement requires data: the case for automation and artificial intelligence during incident reporting.

The reporting of incidents has a long association with safety in healthcare and anaesthesia, yet many incident reporting systems substantially under-report critical events. Better understanding the underlying reasons for low levels of critical incident reporting can allow such factors to be addressed systematically to arrive at a better reporting culture. However, new forms of automation in anaesthesia also provide powerful new approaches to be adopted in the future.

Flexible/Regenerative Nanosensor with Automatic Sweat Collection for Cytokine Storm Biomarker Detection.

The real-time monitoring of low-concentration cytokines such as TNF-α in sweat can aid clinical physicians in assessing the severity of inflammation. The challenges associated with the collection and the presence of impurities can significantly impede the detection of proteins in sweat. This issue is addressed by incorporating a nanosphere array designed for automatic sweat transportation, coupled with a reusable sensor that employs a Nafion/aptamer-modified MoS2 field-effect transistor. The nanosphere array with stepwise wettability enables automatic collection of sweat and blocks impurities from contaminating the detection zone. This device enables direct detection of TNF-α proteins in undiluted sweat, within a detection range of 10 fM to 1 nM. The use of an ultrathin, ultraflexible substrate ensures stable electrical performance, even after up to 30 extreme deformations. The findings indicate that in clinical scenarios, this device could potentially provide real-time evaluation and management of patients' immune status via sweat testing.

MRMQuant: Automated MRM Data Quantitation for Large-Scale Targeted Metabolomics Analysis.

Multiple reaction monitoring (MRM) is a powerful and popular technique used for metabolite quantification in targeted metabolomics. Accurate and consistent quantitation of metabolites from the MRM data is essential for subsequent analyses. Here, we developed an automated tool, MRMQuant, for targeted metabolomic quantitation using high-throughput liquid chromatography-tandem mass spectrometry MRM data to provide users with an easy-to-use tool for accurate MRM data quantitation with minimal human intervention. This tool has many user-friendly functions and features to inspect and correct the quantitation results as required. MRMQuant possesses the following features to ensure accurate quantitation: (1) dynamic signal smoothing, (2) automatic deconvolution of coeluted peaks, (3) absolute quantitation via standard curves and/or internal standards, (4) visualized inspection and correction, (5) corrections applicable to multiple samples, and (6) batch-effect correction.

Assessing Patient Trust in Automation in Health Care Systems: Within-Subjects Experimental Study.

BACKGROUND: Health care technology has the ability to change patient outcomes for the betterment when designed appropriately. Automation is becoming smarter and is increasingly being integrated into health care work systems. OBJECTIVE: This study focuses on investigating trust between patients and an automated cardiac risk assessment tool (CRAT) in a simulated emergency department setting. METHODS: A within-subjects experimental study was performed to investigate differences in automation modes for the CRAT: (1) no automation, (2) automation only, and (3) semiautomation. Participants were asked to enter their simulated symptoms for each scenario into the CRAT as instructed by the experimenter, and they would automatically be classified as high, medium, or low risk depending on the symptoms entered. Participants were asked to provide their trust ratings for each combination of risk classification and automation mode on a scale of 1 to 10 (1=absolutely no trust and 10=complete trust). RESULTS: Results from this study indicate that the participants significantly trusted the semiautomation condition more compared to the automation-only condition (P=.002), and they trusted the no automation condition significantly more than the automation-only condition (P=.03). Additionally, participants significantly trusted the CRAT more in the high-severity scenario compared to the medium-severity scenario (P=.004). CONCLUSIONS: The findings from this study emphasize the importance of the human component of automation when designing automated technology in health care systems. Automation and artificially intelligent systems are becoming more prevalent in health care systems, and this work emphasizes the need to consider the human element when designing automation into care delivery.

Application of Microfluidic Devices for Automated Two-Step Radiolabeling of Antibodies.

Radioimmunoconjugates (RICs) composed of tumor-targeting monoclonal antibodies and radionuclides have been developed for diagnostic and therapeutic application. A new radiolabeling method using microfluidic devices is expected to facilitate simpler and more rapid synthesis of RICs. In the microfluidic method, microfluidic chips can promote the reaction between reactants by mixing them efficiently, and pumping systems enable automated synthesis. In this study, we synthesized RICs by the pre-labeling method, in which the radiometal is coordinated to the chelator and then the radiolabeled chelator is incorporated into the antibodies, using microfluidic devices for the first time. As a result of examining the reaction parameters including the material of mixing units, reaction temperature, and flow rate, RICs with radiochemical purity (RCP) exceeding 90% were obtained. These high-purity RICs were successfully synthesized without any purification simply by pumping three solutions of a chelating agent, radiometal, and antibody into microfluidic devices. Under the same conditions, the RCP of RICs labeled by conventional methods was below 50%. These findings indicate the utility of microfluidic devices for automatic and rapid synthesis of high-quality RICs.

An automated faecal egg count system for detection of Ascaridia galli ova in chickens.

Chicken production has increased over the past decade, resulting in a concomitant rise in the demand for more humane options for poultry products including cage-free, free-range, and organic meat and eggs. These husbandry changes, however, have come hand-in-hand with increased prevalence of Ascaridia galli infection, which can cause clinical disease in chickens as well as the occasional appearance of worms in eggs. Additionally, development of anthelmintic resistance in closely related helminths of turkeys highlights the need for closely monitored anthelmintic treatment programs. Manual faecal egg counts (FECs) can be time-consuming and require specialist training. As such, this study sought to validate an automated FEC system for use in detection and quantification of A. galli eggs in chicken faeces. Automated counts using the Parasight System (PS) were compared to traditional manual McMaster counting for both precision and correlation between methods. Overall, ten repeated counts were performed on twenty individual samples for a total of 200 counts performed for each method. A strong, statistically significant correlation was found between methods (R2 = 0.7879, P < 0.0001), and PS counted more eggs and performed with statistically significant higher precision (P = 0.0391) than manual McMaster counting. This study suggests that PS is a good alternative method for performing A. galli FECs and provides a new tool for use in helminth treatment and control programs in chicken operations.

Construction of a Calibration Curve for Lycopene on a Liquid-Handling Platform─Wider Lessons for the Development of Automated Dilution Protocols.

Liquid-handling is a fundamental operation in synthetic biology─all protocols involve one or more liquid-handling operations. It is, therefore, crucial that this step be carefully automated in order to unlock the benefits of automation (e.g., higher throughput, higher replicability). In the paper, we present a study, conducted at the London Biofoundry at SynbiCITE, that approaches liquid-handling and its reliable automation from the standpoint of the construction of the calibration curve for lycopene in dimethyl sulfoxide (DMSO). The study has important practical industrial applications (e.g., lycopene is a carotenoid of industrial interest, DMSO is a popular extractant). The study was also an effective testbed for the automation of liquid-handling. It necessitated the development of flexible liquid-handling methods, which can be generalizable to other automated applications. In addition, because lycopene/DMSO is a difficult mix, it was capable of revealing issues with automated liquid-handling protocols and stress-testing them. An important component of the study is the constraint that, due to the omnipresence of liquid-handling steps, errors should be controlled to a high standard. It is important to avoid such errors propagating to other parts of the protocol. To achieve this, a practical framework based on regression was developed and utilized throughout the study to identify, assess, and monitor transfer errors. The paper concludes with recommendations regarding automation of liquid-handling, which are applicable to a large set of applications (not just to complex liquids such as lycopene in DMSO or calibration curves).

Using machine learning to automatically measure kyphotic and lordotic angle measurements on radiographs for children with adolescent idiopathic scoliosis.

Measuring the kyphotic angle (KA) and lordotic angle (LA) on lateral radiographs is important to truly diagnose children with adolescent idiopathic scoliosis. However, it is a time-consuming process to measure the KA because the endplate of the upper thoracic vertebra is normally difficult to identify. To save time and improve measurement accuracy, a machine learning algorithm was developed to automatically extract the KA and LA. The accuracy and reliability of the T1-T12 KA, T5-T12 KA, and L1-L5 LA were reported. A convolutional neural network was trained using 100 radiographs with data augmentation to segment the T1-L5 vertebrae. Sixty radiographs were used to test the method. Accuracy and reliability were reported using the percentage of measurements within clinical acceptance (≤9°), standard error of measurement (SEM), and inter-method intraclass correlation coefficient (ICC2,1). The automatic method detected 95 % (57/60), 100 %, and 100 % for T1-T12 KA, T5-T12 KA, and L1-L5 LA, respectively. The clinical acceptance rate, SEM, and ICC2,1 for T1-T12 KA, T5-T12 KA, and L1-L5 LA were (98 %, 0.80°, 0.91), (75 %, 4.08°, 0.60), and (97 %, 1.38°, 0.88), respectively. The automatic method measured quickly with an average of 4 ± 2 s per radiograph and illustrated how measurements were made on the image, allowing verifications by clinicians.

Automatic diagnosis of epileptic seizures using entropy-based features and multimodel deep learning approaches.

Epilepsy is one of the most common brain diseases, characterised by repeated seizures that occur on a regular basis. During a seizure, a patient's muscles flex uncontrollably, causing a loss of mobility and balance, which can be harmful or even fatal. Developing an automatic approach for warning patients of oncoming seizures necessitates substantial research. Analyzing the electroencephalogram (EEG) output from the human brain's scalp region can help predict seizures. EEG data were analyzed to extract time domain features such as Hurst exponent (Hur), Tsallis entropy (TsEn), enhanced permutation entropy (impe), and amplitude-aware permutation entropy (AAPE). In order to automatically diagnose epileptic seizure in children from normal children, this study conducted two sessions. In the first session, the extracted features from the EEG dataset were classified using three machine learning (ML)-based models, including support vector machine (SVM), K nearest neighbor (KNN), or decision tree (DT), and in the second session, the dataset was classified using three deep learning (DL)-based recurrent neural network (RNN) classifiers in The EEG dataset was obtained from the Neurology Clinic of the Ibn Rushd Training Hospital. In this regard, extensive explanations and research from the time domain and entropy characteristics demonstrate that employing GRU, LSTM, and BiLSTM RNN deep learning classifiers on the All-time-entropy fusion feature improves the final classification results.

Automated explainable wavelet-based sleep scoring system for a population suspected with insomnia, apnea and periodic leg movement.

Sleep is an integral and vital component of human life, contributing significantly to overall health and well-being, but a considerable number of people worldwide experience sleep disorders. Sleep disorder diagnosis heavily depends on accurately classifying sleep stages. Traditionally, this classification has been performed manually by trained sleep technologists that visually inspect polysomnography records. However, in order to mitigate the labor-intensive nature of this process, automated approaches have been developed. These automated methods aim to streamline and facilitate sleep stage classification. This study aims to classify sleep stages in a dataset comprising subjects with insomnia, PLM, and sleep apnea. The dataset consists of PSG recordings from the multi-ethnic study of atherosclerosis (MESA) cohort of the national sleep research resource (NSRR), including 2056 subjects. Among these subjects, 130 have insomnia, 39 suffer from PLM, 156 have sleep apnea, and the remaining 1731 are classified as good sleepers. This study proposes an automated computerized technique to classify sleep stages, developing a machine-learning model with explainable artificial intelligence (XAI) capabilities using wavelet-based Hjorth parameters. An optimal biorthogonal wavelet filter bank (BOWFB) has been employed to extract subbands (SBs) from 30 seconds of electroencephalogram (EEG) epochs. Three EEG channels, namely: Fz_Cz, Cz_Oz, and C4_M1, are employed to yield an optimum outcome. The Hjorth parameters extracted from SBs were then fed to different machine learning algorithms. To gain an understanding of the model, in this study, we used SHAP (Shapley Additive explanations) method. For subjects suffering from the aforementioned diseases, the model utilized features derived from all channels and employed an ensembled bagged trees (EnBT) classifier. The highest accuracy of 86.8%, 87.3%, 85.0%, 84.5%, and 83.8% is obtained for the insomniac, PLM, apniac, good sleepers and complete datasets, respectively. Using these techniques and datasets, the study aims to enhance sleep stage classification accuracy and improve understanding of sleep disorders such as insomnia, PLM, and sleep apnea.