Locomotor Assays in Drosophila Larvae and Adult Flies.

Brain defects often lead to motor dysfunctions in humans. Drosophila melanogaster has been one of the most useful organisms in the study of neuronal biology due to its similarities with humans and has contributed to a more detailed understanding of the effects of genetic dysfunctions in the brain on behavior. We herein present modified protocols for the crawling assay with larvae and the climbing assay with adult flies that are simple to perform as well as a series of commands for ImageJ to automatically analyze data for the crawling assay.

Novel AI-Based Algorithm for the Automated Measurement of Cervical Sagittal Balance Parameters. A Validation Study on Pre- and Postoperative Radiographs of 129 Patients.

STUDY DESIGN: Retrospective, mono-centric cohort research study. OBJECTIVES: The analysis of cervical sagittal balance parameters is essential for preoperative planning and dependent on the physician's experience. A fully automated artificial intelligence-based algorithm could contribute to an objective analysis and save time. Therefore, this algorithm should be validated in this study. METHODS: Two surgeons measured C2-C7 lordosis, C1-C7 Sagittal Vertical Axis (SVA), C2-C7-SVA, C7-slope and T1-slope in pre- and postoperative lateral cervical X-rays of 129 patients undergoing anterior cervical surgery. All parameters were measured twice by surgeons and compared to the measurements by the AI algorithm consisting of 4 deep convolutional neural networks. Agreement between raters was quantified, among other metrics, by mean errors and single measure intraclass correlation coefficients for absolute agreement. RESULTS: ICC-values for intra- (range: .92-1.0) and inter-rater (.91-1.0) reliability reflect excellent agreement between human raters. The AI-algorithm could determine all parameters with excellent ICC-values (preop:0.80-1.0; postop:0.86-.99). For a comparison between the AI algorithm and 1 surgeon, mean errors were smallest for C1-C7 SVA (preop: -.3 mm (95% CI:-.6 to -.1 mm), post: .3 mm (.0-.7 mm)) and largest for C2-C7 lordosis (preop:-2.2° (-2.9 to -1.6°), postop: 2.3°(-3.0 to -1.7°)). The automatic measurement was possible in 99% and 98% of pre- and postoperative images for all parameters except T1 slope, which had a detection rate of 48% and 51% in pre- and postoperative images. CONCLUSION: This study validates that an AI-algorithm can reliably measure cervical sagittal balance parameters automatically in patients suffering from degenerative spinal diseases. It may simplify manual measurements and autonomously analyze large-scale datasets. Further studies are required to validate the algorithm on a larger and more diverse patient cohort.

Development of a tool for monitoring the jaw-opening pace and preliminary comparison the pace between young and old ages.

OBJECTIVES: Studies have demonstrated that high-speed jaw-opening exercises are effective in improving swallowing function. However, there has been no objective tool available for monitoring jaw-opening pace. This study aimed to develop an objective tool for monitoring and validating jaw-opening pace and compare it between young and old ages from different age groups. MATERIALS AND METHODS: A load cell plug-in jaw pad connected to an automatic recording and analysis system was used to record jaw-opening motions for offline analysis. We recruited 58 healthy volunteers from different age groups (20-39 y/o; 40-59y/o; 60-79y/o). During a 2-min recording session, each participant was instructed to fully open and close their jaw as quickly as possible while wearing a sensor. Bland-Altman plot, paired t-test and Pearson's correlation test were used to compare the number of jaw-opening motions between manual counting and automatic software analysis. The number of jaw-opening motions during the 2-min recording was compared between the three age groups. RESULTS: Automated analysis of jaw-opening pace was efficient and equally comparable with the traditional manual counting method across the three age groups. A declining trend in jaw-opening pace among the old age group was found but with no statistically significant difference. CONCLUSIONS: A jaw-opening motion monitoring tool with reliable automatic pace analysis software was validated in young and old ages. The jaw-opening pace demonstrated a tendency to decline with age. CLINICAL RELEVANCE: This monitoring tool can also be used to provide visual feedback during jaw-opening motion training in pace control.

Speech changes in old age: Methodological considerations for speech-based discrimination of healthy ageing and Alzheimer's disease.

BACKGROUND: Recent evidence suggests that speech substantially changes in ageing. As a complex neurophysiological process, it can accurately reflect changes in the motor and cognitive systems underpinning human speech. Since healthy ageing is not always easily discriminable from early stages of dementia based on cognitive and behavioural hallmarks, speech is explored as a preclinical biomarker of pathological itineraries in old age. A greater and more specific impairment of neuromuscular activation, as well as  a specific cognitive and linguistic impairment in dementia, unchain discriminating changes in speech. Yet, there is no consensus on such discriminatory speech parameters, neither on how they should be elicited and assessed. AIMS: To provide a state-of-the-art on speech parameters that allow for early discrimination between healthy and pathological ageing; the aetiology of these parameters; the effect of the type of experimental stimuli on speech elicitation and the predictive power of different speech parameters; and the most promising methods for speech analysis and their clinical implications. METHODS & PROCEDURES: A scoping review methodology is used in accordance with the PRISMA model. Following a systematic search of PubMed, PsycINFO and CINAHL, 24 studies are included and analysed in the review. MAIN CONTRIBUTION: The results of this review yield three key questions for the clinical assessment of speech in ageing. First, acoustic and temporal parameters are more sensitive to changes in pathological ageing and, of these two, temporal variables are more affected by cognitive impairment. Second, different types of stimuli can trigger speech parameters with different degree of accuracy for the discrimination of clinical groups. Tasks with higher cognitive load are more precise in eliciting higher levels of accuracy. Finally, automatic speech analysis for the discrimination of healthy and pathological ageing should be improved for both research and clinical practice. CONCLUSIONS & IMPLICATIONS: Speech analysis is a promising non-invasive tool for the preclinical screening of healthy and pathological ageing. The main current challenges of speech analysis in ageing are the automatization of its clinical assessment and the consideration of the speaker's cognitive background during evaluation. WHAT THIS PAPER ADDS: What is already known on the subject Societal aging  goes hand in hand with the rising incidence of ageing-related neurodegenerations, mainly Alzheimer's disease (AD). This is particularly noteworthy in countries with longer life expectancies. Healthy ageing and early stages of AD share a set of cognitive and behavioural characteristics. Since there is no cure for dementias, developing methods for accurate discrimination of healthy ageing and early AD is currently a priority. Speech has been described as one of the most significantly impaired features in AD. Neuropathological alterations in motor and cognitive systems would underlie specific speech impairment in dementia. Since speech can be evaluated quickly, non-invasively and inexpensively, its value for the clinical assessment of ageing itineraries may be particularly high. What this paper adds to existing knowledge Theoretical and experimental advances in the assessment of speech as a marker of AD have developed rapidly over the last decade. Yet, they are not always known to clinicians. Furthermore, there is a need to provide an updated state-of-the-art on which speech features are discriminatory to AD, how they can be assessed, what kind of results they can yield, and how such results should be interpreted. This article provides an updated overview of speech profiling, methods of speech measurement and analysis, and the clinical power of speech assessment for early discrimination of AD as the most common cause of dementia. What are the potential or actual clinical implications of this work? This article provides an overview of the predictive potential of different speech parameters in relation to AD cognitive impairment. In addition, it discusses the effect that the cognitive state, the type of elicitation task and the type of assessment method may have on the results of the speech-based analysis in ageing.

Challenges of Applying Automated Polysomnography Scoring at Scale.

Automatic polysomnography analysis can be leveraged to shorten scoring times, reduce associated costs, and ultimately improve the overall diagnosis of sleep disorders. Multiple and diverse strategies have been attempted for implementation of this technology at scale in the routine workflow of sleep centers. The field, however, is complex and presents unsolved challenges in a number of areas. Recent developments in computer science and artificial intelligence are nevertheless closing the gap. Technological advances are also opening new pathways for expanding our current understanding of the domain and its analysis.

Ultrasensitive Automatic Detection of Small Molecules by Membrane Imaging of Single Molecule Assays.

Determination of trace amounts of targets or even a single molecule target has always been a challenge in the detection field. Digital measurement methods established for single molecule counting of proteins, such as single molecule arrays (Simoa) or dropcast single molecule assays (dSimoa), are not suitable for detecting small molecule, because of the limited category of small molecule antibodies and the weak signal that can be captured. To address this issue, we have developed a strategy for single molecule detection of small molecules, called small molecule detection with single molecule assays (smSimoa). In this strategy, an aptamer is used as a recognition element, and an addressable DNA Nanoflower (DNF) attached on the magnetic beads surface, which exhibit fluorescence imaging, is employed as the output signal. Accompanied by digital imaging and automated counting analysis, E2 at the attomolar level can be measured. The smSimoa breaks the barrier of small molecule detection concentration and provides a basis for high throughput detection of multiple substances with fluorescence encoded magnetic beads.

Capturing Eating Behavior from Video Analysis: A Systematic Review.

Current methods to detect eating behavior events (i.e., bites, chews, and swallows) lack objective measurements, standard procedures, and automation. The video recordings of eating episodes provide a non-invasive and scalable source for automation. Here, we reviewed the current methods to automatically detect eating behavior events from video recordings. According to PRISMA guidelines, publications from 2010-2021 in PubMed, Scopus, ScienceDirect, and Google Scholar were screened through title and abstract, leading to the identification of 277 publications. We screened the full text of 52 publications and included 13 for analysis. We classified the methods in five distinct categories based on their similarities and analyzed their accuracy. Facial landmarks can count bites, chews, and food liking automatically (accuracy: 90%, 60%, 25%). Deep neural networks can detect bites and gesture intake (accuracy: 91%, 86%). The active appearance model can detect chewing (accuracy: 93%), and optical flow can count chews (accuracy: 88%). Video fluoroscopy can track swallows but is currently not suitable beyond clinical settings. The optimal method for automated counts of bites and chews is facial landmarks, although further improvements are required. Future methods should accurately predict bites, chews, and swallows using inexpensive hardware and limited computational capacity. Automatic eating behavior analysis will allow the study of eating behavior and real-time interventions to promote healthy eating behaviors.

Automated Artificial Intelligence-Based Assessment of Lower Limb Alignment Validated on Weight-Bearing Pre- and Postoperative Full-Leg Radiographs.

The assessment of the knee alignment using standing weight-bearing full-leg radiographs (FLR) is a standardized method. Determining the load-bearing axis of the leg requires time-consuming manual measurements. The aim of this study is to develop and validate a novel algorithm based on artificial intelligence (AI) for the automated assessment of lower limb alignment. In the first stage, a customized mask-RCNN model was trained to automatically detect and segment anatomical structures and implants in FLR. In the second stage, four region-specific neural network models (adaptations of UNet) were trained to automatically place anatomical landmarks. In the final stage, this information was used to automatically determine five key lower limb alignment angles. For the validation dataset, weight-bearing, antero-posterior FLR were captured preoperatively and 3 months postoperatively. Preoperative images were measured by the operating orthopedic surgeon and an independent physician. Postoperative images were measured by the second rater only. The final validation dataset consisted of 95 preoperative and 105 postoperative FLR. The detection rate for the different angles ranged between 92.4% and 98.9%. Human vs. human inter-(ICCs: 0.85−0.99) and intra-rater (ICCs: 0.95−1.0) reliability analysis achieved significant agreement. The ICC-values of human vs. AI inter-rater reliability analysis ranged between 0.8 and 1.0 preoperatively and between 0.83 and 0.99 postoperatively (all p < 0.001). An independent and external validation of the proposed algorithm on pre- and postoperative FLR, with excellent reliability for human measurements, could be demonstrated. Hence, the algorithm might allow for the objective and time saving analysis of large datasets and support physicians in daily routine.

Airflow Analysis in the Context of Sleep Apnea.

The airflow (AF) is a physiological signal involved in the overnight polysomnography (PSG) that reflects the respiratory activity. This signal is able to show the particularities of sleep apnea and is therefore used to define apneic events. In this regard, a growing number of studies have shown the usefulness of employing the overnight airflow as the only or combined information source for diagnosing sleep apnea in both children and adults. Due to its easy acquisition and interpretation, this biosignal has been widely analyzed by means of different signal processing techniques. In this chapter, we review the main methodological approaches applied to characterize and extract relevant information from this signal. In view of the results, we can conclude that the overnight airflow successfully reflects the particularities caused by the occurrence of apneic and hypopneic events and provides useful information for obtaining relevant biomarkers that characterize this disease.

Towards label-efficient automatic diagnosis and analysis: a comprehensive survey of advanced deep learning-based weakly-supervised, semi-supervised and self-supervised techniques in histopathological image analysis.

Histopathological images contain abundant phenotypic information and pathological patterns, which are the gold standards for disease diagnosis and essential for the prediction of patient prognosis and treatment outcome. In recent years, computer-automated analysis techniques for histopathological images have been urgently required in clinical practice, and deep learning methods represented by convolutional neural networks have gradually become the mainstream in the field of digital pathology. However, obtaining large numbers of fine-grained annotated data in this field is a very expensive and difficult task, which hinders the further development of traditional supervised algorithms based on large numbers of annotated data. More recent studies have started to liberate from the traditional supervised paradigm, and the most representative ones are the studies on weakly supervised learning paradigm based on weak annotation, semi-supervised learning paradigm based on limited annotation, and self-supervised learning paradigm based on pathological image representation learning. These new methods have led a new wave of automatic pathological image diagnosis and analysis targeted at annotation efficiency. With a survey of over 130 papers, we present a comprehensive and systematic review of the latest studies on weakly supervised learning, semi-supervised learning, and self-supervised learning in the field of computational pathology from both technical and methodological perspectives. Finally, we present the key challenges and future trends for these techniques.

ABOSA - Freely available automatic blood oxygen saturation signal analysis software: Structure and validation.

BACKGROUND AND OBJECTIVE: Many sleep recording software used in clinical settings have some tools to automatically analyze the blood oxygen saturation (SpO2) signal by detecting desaturations. However, these tools are often inadequate for scientific research as they do not provide SpO2 signal-based parameters which are superior in the estimation of sleep apnea severity and related medical consequences. In addition, these software require expensive licenses and they lack batch analysis tools. Thus, we developed the first freely available automatic blood oxygen saturation analysis software (ABOSA) that provides sophisticated SpO2 signal-based parameters and enables batch analysis of large datasets. METHODS: ABOSA was programmed with MATLAB. ABOSA automatically detects desaturation and recovery events from the SpO2 signals (EDF files) and calculates numerous parameters, such as oxygen desaturation index (ODI) and desaturation severity (DesSev). The accuracy of the ABOSA software was evaluated by comparing its desaturation scorings to manual scorings in Kuopio (n = 1981) and Loewenstein (n = 930) sleep apnea patient datasets. Validation was performed in a second-by-second manner by calculating Matthew's correlation coefficients (MCC) and median differences in parameter values. Finally, the performance of the ABOSA software was compared to two commercial software, Noxturnal and Profusion, in 100 patient subpopulations. As Noxturnal or Profusion does not calculate novel desaturation parameters, these were calculated with custom-made functions. RESULTS: The agreements between ABOSA and manual scorings were great in both Kuopio (MCC = 0.801) and Loewenstein (MCC = 0.898) datasets. However, ABOSA slightly overestimated the desaturation parameter values. The median differences in ODIs were 0.8 (Kuopio) and 0.0 (Loewenstein) events/h. Similarly, the median differences in DesSevs were 0.02 (Kuopio) and 0.01 (Loewenstein) percentage points. In a second-by-second analysis, ABOSA performed very similarly to Noxturnal and Profusion software in both Kuopio (MCCABOSA = 0.807, MCCNoxturnal = 0.807, MCCProfusion = 0.811) and Loewenstein (MCCABOSA = 0.904, MCCNoxturnal = 0.911, MCCProfusion = 0.871) datasets. Based on Noxturnal and Profusion scorings, the desaturation parameter values were similarly overestimated compared to ABOSA. CONCLUSIONS: ABOSA is an accurate and freely available software that calculates both traditional clinical parameters and novel parameters, provides a detailed characterization of desaturation and recovery events, and enables batch analysis of large datasets. These are features that no other software currently provides making ABOSA uniquely suitable for scientific research use.

Towards an automatic narcolepsy detection on ambiguous sleep staging and sleep transition dynamics joint model.

Objective. Mixing/dissociation of sleep stages in narcolepsy adds to the difficulty in automatic sleep staging. Moreover, automatic analytical studies for narcolepsy and multiple sleep latency test (MSLT) have only done automatic sleep staging without leveraging the sleep stage profile for further patient identification. This study aims to establish an automatic narcolepsy detection method for MSLT.Approach.We construct a two-phase model on MSLT recordings, where ambiguous sleep staging and sleep transition dynamics make joint efforts to address this issue. In phase 1, we extract representative features from electroencephalogram (EEG) and electrooculogram (EOG) signals. Then, the features are input to an EasyEnsemble classifier for automatic sleep staging. In phase 2, we investigate sleep transition dynamics, including sleep stage transitions and sleep stages, and output likelihood of narcolepsy by virtue of principal component analysis (PCA) and a logistic regression classifier. To demonstrate the proposed framework in clinical application, we conduct experiments on 24 participants from the Children's Hospital of Fudan University, considering ten patients with narcolepsy and fourteen patients with MSLT negative.Main results.Applying the two-phase leave-one-subject-out testing scheme, the model reaches an accuracy, sensitivity, and specificity of 87.5%, 80.0%, and 92.9% for narcolepsy detection. Influenced by disease pathology, accuracy of automatic sleep staging in narcolepsy appears to decrease compared to that in the non-narcoleptic population.Significance.This method can automatically and efficiently distinguish patients with narcolepsy based on MSLT. It probes into the amalgamation of automatic sleep staging and sleep transition dynamics for narcolepsy detection, which would assist clinic and neuroelectrophysiology specialists in visual interpretation and diagnosis.

Comparison between Automatic and Semiautomatic System for the 3D Echocardiographic Multiparametric Evaluation of RV Function and Dimension.

BACKGROUND: The right ventricle (RV) plays a pivotal role in cardiovascular diseases and 3-dimensional echocardiography (3DE) has gained acceptance for the evaluation of RV volumes and function. Recently, a new artificial intelligence (AI)-based automated 3DE software for RV evaluation has been proposed and validated against cardiac magnetic resonance. The aims of this study were three-fold: (i) feasibility of the AI-based 3DE RV quantification, (ii) comparison with the semi-automatic 3DE method and (iii) assessment of 2-dimensional echocardiography (2DE) and strain measurements obtained automatically. METHODS: A total of 203 subject (122 normal and 81 patients) underwent a 2DE and both the semi-automatic and automatic 3DE methods for Doppler standard, RV volumes and ejection fraction (RVEF) measurements. RESULTS: The automatic 3DE method was highly feasible, faster than 2DE and semi-automatic 3DE and data obtained were comparable with traditional measurements. Both in normal subjects and patients, the RVEF was similar to the two 3DE methods and 2DE and strain measurements obtained by the automated system correlated very well with the standard 2DE and strain ones. CONCLUSIONS: results showed that rapid analysis and excellent reproducibility of AI-based 3DE RV analysis supported the routine adoption of this automated method in the daily clinical workflow.

Can artificial intelligence support or even replace physicians in measuring sagittal balance? A validation study on preoperative and postoperative full spine images of 170 patients.

PURPOSE: Sagittal balance (SB) plays an important role in the surgical treatment of spinal disorders. The aim of this research study is to provide a detailed evaluation of a new, fully automated algorithm based on artificial intelligence (AI) for the determination of SB parameters on a large number of patients with and without instrumentation. METHODS: Pre- and postoperative sagittal full body radiographs of 170 patients were measured by two human raters, twice by one rater and by the AI algorithm which determined: pelvic incidence, pelvic tilt, sacral slope, L1-S1 lordosis, T4-T12 thoracic kyphosis (TK) and the spino-sacral angle (SSA). To evaluate the agreement between human raters and AI, the mean error (95% confidence interval (CI)), standard deviation and an intra- and inter-rater reliability was conducted using intra-class correlation (ICC) coefficients. RESULTS: ICC values for the assessment of the intra- (range: 0.88-0.97) and inter-rater (0.86-0.97) reliability of human raters are excellent. The algorithm is able to determine all parameters in 95% of all pre- and in 91% of all postoperative images with excellent ICC values (PreOP-range: 0.83-0.91, PostOP: 0.72-0.89). Mean errors are smallest for the SSA (PreOP: -0.1° (95%-CI: -0.9°-0.6°); PostOP: -0.5° (-1.4°-0.4°)) and largest for TK (7.0° (6.1°-7.8°); 7.1° (6.1°-8.1°)). CONCLUSION: A new, fully automated algorithm that determines SB parameters has excellent reliability and agreement with human raters, particularly on preoperative full spine images. The presented solution will relieve physicians from time-consuming routine work of measuring SB parameters and allow the analysis of large databases efficiently.

Automatic 3D+t four-chamber CMR quantification of the UK biobank: integrating imaging and non-imaging data priors at scale.

Accurate 3D modelling of cardiac chambers is essential for clinical assessment of cardiac volume and function, including structural, and motion analysis. Furthermore, to study the correlation between cardiac morphology and other patient information within a large population, it is necessary to automatically generate cardiac mesh models of each subject within the population. In this study, we introduce MCSI-Net (Multi-Cue Shape Inference Network), where we embed a statistical shape model inside a convolutional neural network and leverage both phenotypic and demographic information from the cohort to infer subject-specific reconstructions of all four cardiac chambers in 3D. In this way, we leverage the ability of the network to learn the appearance of cardiac chambers in cine cardiac magnetic resonance (CMR) images, and generate plausible 3D cardiac shapes, by constraining the prediction using a shape prior, in the form of the statistical modes of shape variation learned a priori from a subset of the population. This, in turn, enables the network to generalise to samples across the entire population. To the best of our knowledge, this is the first work that uses such an approach for patient-specific cardiac shape generation. MCSI-Net is capable of producing accurate 3D shapes using just a fraction (about 23% to 46%) of the available image data, which is of significant importance to the community as it supports the acceleration of CMR scan acquisitions. Cardiac MR images from the UK Biobank were used to train and validate the proposed method. We also present the results from analysing 40,000 subjects of the UK Biobank at 50 time-frames, totalling two million image volumes. Our model can generate more globally consistent heart shape than that of manual annotations in the presence of inter-slice motion and shows strong agreement with the reference ranges for cardiac structure and function across cardiac ventricles and atria.

Automatic measurements of fetal intracranial volume from 3D ultrasound scans.

Three-dimensional fetal ultrasound is commonly used to study the volumetric development of brain structures. To date, only a limited number of automatic procedures for delineating the intracranial volume exist. Hence, intracranial volume measurements from three-dimensional ultrasound images are predominantly performed manually. Here, we present and validate an automated tool to extract the intracranial volume from three-dimensional fetal ultrasound scans. The procedure is based on the registration of a brain model to a subject brain. The intracranial volume of the subject is measured by applying the inverse of the final transformation to an intracranial mask of the brain model. The automatic measurements showed a high correlation with manual delineation of the same subjects at two gestational ages, namely, around 20 and 30 weeks (linear fitting R2(20 weeks) = 0.88, R2(30 weeks) = 0.77; Intraclass Correlation Coefficients: 20 weeks=0.94, 30 weeks = 0.84). Overall, the automatic intracranial volumes were larger than the manually delineated ones (84 ± 16 vs. 76 ± 15 cm3; and 274 ± 35 vs. 237 ± 28 cm3), probably due to differences in cerebellum delineation. Notably, the automated measurements reproduced both the non-linear pattern of fetal brain growth and the increased inter-subject variability for older fetuses. By contrast, there was some disagreement between the manual and automatic delineation concerning the size of sexual dimorphism differences. The method presented here provides a relatively efficient way to delineate volumes of fetal brain structures like the intracranial volume automatically. It can be used as a research tool to investigate these structures in large cohorts, which will ultimately aid in understanding fetal structural human brain development.

An Automatic on Top Analysis of Single Scan Tracks to Evaluate the Laser Powder Bed Fusion Building Parameters.

The production of dense samples produced by laser powder bed fusion (LPBF) is mainly determined by the choice of the best combination of construction parameters. Parameter optimization is the first step in the definition of an LPBF process for new alloys or systems. With this goal, much research uses the single scan track (SST) approach for a preliminary parameter screening. This study investigates the definition of a computer-aided method by using an automatic on top analysis for the characterization of SSTs, with the aim of finding ranges of laser power and scan speed values for massive production. An innovative algorithm was implemented to discard non-continuous scans and to measure the SSTs quality using three regularity indexes. Only open source software were used to fine tune this approach. The obtained results on Al4Cu and AlSi10Mg realized with two different commercial systems suggest that it is possible to use this method to easily narrow the process parameter window that allows the production of dense samples.

Quantitative Assessment of Ciliary Ultrastructure with the Use of Automatic Analysis: PCD Quant.

The ciliary ultrastructure can be damaged in various situations. Such changes include primary defects found in primary ciliary dyskinesia (PCD) and secondary defects developing in secondary ciliary dyskinesia (SCD). PCD is a genetic disease resulting from impaired ciliary motility causing chronic disease of the respiratory tract. SCD is an acquired condition that can be caused, for example, by respiratory infection or exposure to tobacco smoke. The diagnosis of these diseases is a complex process with many diagnostic methods, including the evaluation of ciliary ultrastructure using transmission electron microscopy (the golden standard of examination). Our goal was to create a program capable of automatic quantitative analysis of the ciliary ultrastructure, determining the ratio of primary and secondary defects, as well as analysis of the mutual orientation of cilia in the ciliary border. PCD Quant, a program developed for the automatic quantitative analysis of cilia, cannot yet be used as a stand-alone method for evaluation and provides limited assistance in classifying primary and secondary defect classes and evaluating central pair angle deviations. Nevertheless, we see great potential for the future in automatic analysis of the ciliary ultrastructure.

Automated Reverse Transcription Polymerase Chain Reaction Data Analysis for Sars-CoV-2 Detection.

BACKGROUND: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is a current public health concern. Rapid diagnosis is crucial, and reverse transcription polymerase chain reaction (RT-PCR) is presently the reference standard for SARS-CoV-2 detection. OBJECTIVE: Automated RT-PCR analysis (ARPA) is a software designed to analyze RT-PCR data for SARSCoV-2 detection. ARPA loads the RT-PCR data, classifies each sample by assessing its amplification curve behavior, evaluates the experiment's quality, and generates reports. METHODS: ARPA was implemented in the R language and deployed as a Shiny application. We evaluated the performance of ARPA in 140 samples. The samples were manually classified and automatically analyzed using ARPA. RESULTS: ARPA had a true-positive rate = 1, true-negative rate = 0.98, positive-predictive value = 0.95, and negative-predictive value = 1, with 36 samples correctly classified as positive, 100 samples correctly classified as negative, and two samples classified as positive even when labeled as negative by manual inspection. Two samples were labeled as invalid by ARPA and were not considered in the performance metrics calculation. CONCLUSIONS: ARPA is a sensitive and specific software that facilitates the analysis of RT-PCR data, and its implementation can reduce the time required in the diagnostic pipeline.

A deep learning pipeline for automatic analysis of multi-scan cardiovascular magnetic resonance.

BACKGROUND: Cardiovascular magnetic resonance (CMR) sequences are commonly used to obtain a complete description of the function and structure of the heart, provided that accurate measurements are extracted from images. New methods of extraction of information are being developed, among them, deep neural networks are powerful tools that showed the ability to perform fast and accurate segmentation. Iq1n order to reduce the time spent by reading physicians to process data and minimize intra- and inter-observer variability, we propose a fully automatic multi-scan CMR image analysis pipeline. METHODS: Sequence specific U-Net 2D models were trained to perform the segmentation of the left ventricle (LV), right ventricle (RV) and aorta in cine short-axis, late gadolinium enhancement (LGE), native T1 map, post-contrast T1, native T2 map and aortic flow sequences depending on the need. The models were trained and tested on a set of data manually segmented by experts using semi-automatic and manual tools. A set of parameters were computed from the resulting segmentations such as the left ventricular and right ventricular ejection fraction (EF), LGE scar percentage, the mean T1, T1 post, T2 values within the myocardium, and aortic flow. The Dice similarity coefficient, Hausdorff distance, mean surface distance, and Pearson correlation coefficient R were used to assess and compare the results of the U-Net based pipeline with intra-observer variability. Additionally, the pipeline was validated on two clinical studies. RESULTS: The sequence specific U-Net 2D models trained achieved fast (≤ 0.2 s/image on GPU) and precise segmentation over all the targeted region of interest with high Dice scores (= 0.91 for LV, = 0.92 for RV, = 0.93 for Aorta in average) comparable to intra-observer Dice scores (= 0.86 for LV, = 0.87 for RV, = 0.95 for aorta flow in average). The automatically and manually computed parameters were highly correlated (R = 0.91 in average) showing results superior to the intra-observer variability (R = 0.85 in average) for every sequence presented here. CONCLUSION: The proposed pipeline allows for fast and robust analysis of large CMR studies while guaranteeing reproducibility, hence potentially improving patient's diagnosis as well as clinical studies outcome.