An improved workflow for the development of MS-compatible liquid chromatography assay purity and purification methods by using automated LC Screening instrumentation and in silico modeling

The development of liquid chromatography UV and mass spectrometry (LC-UV-MS) assays in pharmaceutical analysis is pivotal to improve quality control by providing critical information about drug purity, stability, and presence and identity of byproducts and impurities. Analytical method development of these assays is time-consuming, which often causes it to become a bottle neck in drug development and poses a challenge for process chemists to quickly improve the chemistry. In this study, a systematic and efficient workflow was designed to develop purity assay and purification methods for a wide range of compounds including peptides, proteins, and small molecules with MS-compatible mobile phases (MP) by using automated LC screening instrumentation and in silico modeling tools. Initial LC MPs and chromatography column screening experiments enabled quick identification of conditions which provided the best resolution in the vicinity of the target compounds, which is further optimized using computer-assisted modeling (LC Simulator from ACD/Labs). The experimental retention times were in good agreement with the predicted retention times from LC Simulator (ΔtR < 7%). This workflow presents a practical workflow to significantly expedite the time needed to develop optimized LC-UV-MS methods, allowing for a facile, automatic method optimization and reducing the amount of manual work involved in developing new methods during drug development.

Preliminary results regarding automated identification of patients with a limited six-month survival prognosis using nursing assessment in uro-oncology patients

INTRODUCTION

Contrary to current recommendations, palliative co-management of tumor patients often occurs late in daily clinical practice. Palliative care specialist (PCS) co-management should be considered at the latest after a 6-month prognosis has been presumed. Therefore, identifying patients with a limited prognosis is a reasonable measure.

METHODS

Patients were identified using a screening tool for limited prognosis, which combined their tumor stage and data from the nursing anamnesis. In this retrospective study, a monocentric cohort of patients with urological malignancies-UICC (Union for International Cancer Control) stages III and IV - were enrolled from March to December 2019, with a 6-month follow-up period ending in May 2020.

RESULTS

Most patients were male and suffered from prostate cancer. Patients with uro-oncological tumors dying within 6 months correlated significantly with the presence of repeated hospitalizations within three months, pain on admission, malnutrition, impaired breathing and reduced mobility (P < 0.001). The test was fair in quality (AUC 0.727) at a cut-point of five; a sensitivity of 97% and a specificity of 25% were obtained. The PPV was 0.64 and NPV was 0.82.

DISCUSSION/CONCLUSION

We specifically identified the predictors of limited prognosis in urological cancer patients across several entities using an automated scoring system based on tumor stage and data from the nursing anamnesis. Therefore, we recognized hospitalization as an important transition point and determined nurses to be valuable partners in identifying unmet palliative care needs without additional technical, personnel or financial effort.

Patient-level performance evaluation of a smartphone-based malaria diagnostic application

BACKGROUND

Microscopic examination is commonly used for malaria diagnosis in the field. However, the lack of well-trained microscopists in malaria-endemic areas impacted the most by the disease is a severe problem. Besides, the examination process is time-consuming and prone to human error. Automated diagnostic systems based on machine learning offer great potential to overcome these problems. This study aims to evaluate Malaria Screener, a smartphone-based application for malaria diagnosis.

METHODS

A total of 190 patients were recruited at two sites in rural areas near Khartoum, Sudan. The Malaria Screener mobile application was deployed to screen Giemsa-stained blood smears. Both expert microscopy and nested PCR were performed to use as reference standards. First, Malaria Screener was evaluated using the two reference standards. Then, during post-study experiments, the evaluation was repeated for a newly developed algorithm, PlasmodiumVF-Net.

RESULTS

Malaria Screener reached 74.1% (95% CI 63.5-83.0) accuracy in detecting Plasmodium falciparum malaria using expert microscopy as the reference after a threshold calibration. It reached 71.8% (95% CI 61.0-81.0) accuracy when compared with PCR. The achieved accuracies meet the WHO Level 3 requirement for parasite detection. The processing time for each smear varies from 5 to 15 min, depending on the concentration of white blood cells (WBCs). In the post-study experiment, Malaria Screener reached 91.8% (95% CI 83.8-96.6) accuracy when patient-level results were calculated with a different method. This accuracy meets the WHO Level 1 requirement for parasite detection. In addition, PlasmodiumVF-Net, a newly developed algorithm, reached 83.1% (95% CI 77.0-88.1) accuracy when compared with expert microscopy and 81.0% (95% CI 74.6-86.3) accuracy when compared with PCR, reaching the WHO Level 2 requirement for detecting both Plasmodium falciparum and Plasmodium vivax malaria, without using the testing sites data for training or calibration. Results reported for both Malaria Screener and PlasmodiumVF-Net used thick smears for diagnosis. In this paper, both systems were not assessed in species identification and parasite counting, which are still under development.

CONCLUSION

Malaria Screener showed the potential to be deployed in resource-limited areas to facilitate routine malaria screening. It is the first smartphone-based system for malaria diagnosis evaluated on the patient-level in a natural field environment. Thus, the results in the field reported here can serve as a reference for future studies.

Is the future of peer review automated?

The rising rate of preprints and publications, combined with persistent inadequate reporting practices and problems with study design and execution, have strained the traditional peer review system. Automated screening tools could potentially enhance peer review by helping authors, journal editors, and reviewers to identify beneficial practices and common problems in preprints or submitted manuscripts. Tools can screen many papers quickly, and may be particularly helpful in assessing compliance with journal policies and with straightforward items in reporting guidelines. However, existing tools cannot understand or interpret the paper in the context of the scientific literature. Tools cannot yet determine whether the methods used are suitable to answer the research question, or whether the data support the authors' conclusions. Editors and peer reviewers are essential for assessing journal fit and the overall quality of a paper, including the experimental design, the soundness of the study's conclusions, potential impact and innovation. Automated screening tools cannot replace peer review, but may aid authors, reviewers, and editors in improving scientific papers. Strategies for responsible use of automated tools in peer review may include setting performance criteria for tools, transparently reporting tool performance and use, and training users to interpret reports.

Automatic stenosis recognition from coronary angiography using convolutional neural networks

BACKGROUND AND OBJECTIVE

Coronary artery disease, which is mostly caused by atherosclerotic narrowing of the coronary artery lumen, is a leading cause of death. Coronary angiography is the standard method to estimate the severity of coronary artery stenosis, but is frequently limited by intra- and inter-observer variations. We propose a deep-learning algorithm that automatically recognizes stenosis in coronary angiographic images.

METHODS

The proposed method consists of key frame detection, deep learning model training for classification of stenosis on each key frame, and visualization of the possible location of the stenosis. Firstly, we propose an algorithm that automatically extracts key frames essential for diagnosis from 452 right coronary artery angiography movie clips. Our deep learning model is then trained with image-level annotations to classify the areas narrowed by over 50 %. To make the model focus on the salient features, we apply a self-attention mechanism. The stenotic locations are visualized using the activated area of feature maps with gradient-weighted class activation mapping.

RESULTS

The automatically detected key frame was very close to the manually selected key frame (average distance (1.70 ± 0.12) frame per clip). The model was trained with key frames on internal datasets, and validated with internal and external datasets. Our training method achieved high frame-wise area-under-the-curve of 0.971, frame-wise accuracy of 0.934, and clip-wise accuracy of 0.965 in the average values of cross-validation evaluations. The external validation results showed high performances with the mean frame-wise area-under-the-curve of (0.925 and 0.956) in the single and ensemble model, respectively. Heat map visualization shows the location for different types of stenosis in both internal and external data sets. With the self-attention mechanism, the stenosis could be precisely localized, which helps to accurately classify the stenosis by type.

CONCLUSIONS

Our automated classification algorithm could recognize and localize coronary artery stenosis highly accurately. Our approach might provide the basis for a screening and assistant tool for the interpretation of coronary angiography.

Use in clinical practice of an automated screening method of diabetic retinopathy that can be derived using a diagnostic artificial intelligence system

BACKGROUND AND OBJECTIVE

To compare the diagnostic performance of an autonomous diagnostic artificial intelligence (AI) system for the diagnosis of derivable diabetic retinopathy (RDR) with manual classification.

MATERIALS AND METHODS

Patients with type 1 and type 2 diabetes participated in a diabetic retinopathy (DR) screening program between 2011-2012. 2 images of each eye were collected. Unidentifiable retinal images were obtained, one centered on the disc and one on the fovea. The exams were classified with the autonomous AI system and manually by anonymous ophthalmologists. The results of the AI system and manual classification were compared in terms of sensitivity and specificity for the diagnosis of both (RDR) and diabetic retinopathy with decreased vision (VTDR).

RESULTS

10,257 retinal inages of 5,630 eyes of 2,680 subjects were included. According to the manual classification, the prevalence of RDR was 4.14% and that of VTDR 2.57%. The AI system recorded 100% (95% CI: 97-100%) sensitivity and 81.82% (95% CI: 80 -83%) specificity for RDR, and 100% (95% CI: 95-100%) of sensitivity and 94.64% (95% CI: 94-95%) of specificity for VTDR.

CONCLUSIONS

Compared to the manual classification, the autonomous diagnostic AI system registered a high sensitivity (100%) and specificity (82%) in the diagnosis of RDR and macular edema in people with diabetes. Due to its immediate diagnosis, the autonomous diagnostic AI system can increase the accessibility of RDR screening in primary care settings.

Artificial intelligence in retina

Major advances in diagnostic technologies are offering unprecedented insight into the condition of the retina and beyond ocular disease. Digital images providing millions of morphological datasets can fast and non-invasively be analyzed in a comprehensive manner using artificial intelligence (AI). Methods based on machine learning (ML) and particularly deep learning (DL) are able to identify, localize and quantify pathological features in almost every macular and retinal disease. Convolutional neural networks thereby mimic the path of the human brain for object recognition through learning of pathological features from training sets, supervised ML, or even extrapolation from patterns recognized independently, unsupervised ML. The methods of AI-based retinal analyses are diverse and differ widely in their applicability, interpretability and reliability in different datasets and diseases. Fully automated AI-based systems have recently been approved for screening of diabetic retinopathy (DR). The overall potential of ML/DL includes screening, diagnostic grading as well as guidance of therapy with automated detection of disease activity, recurrences, quantification of therapeutic effects and identification of relevant targets for novel therapeutic approaches. Prediction and prognostic conclusions further expand the potential benefit of AI in retina which will enable personalized health care as well as large scale management and will empower the ophthalmologist to provide high quality diagnosis/therapy and successfully deal with the complexity of 21st century ophthalmology.

Pilot Study of an Open-source Image Analysis Software for Automated Screening of Conventional Cervical Smears

Introduction

The Pap stained cervical smear is a screening tool for cervical cancer. Commercial systems are used for automated screening of liquid based cervical smears. However, there is no image analysis software used for conventional cervical smears. The aim of this study was to develop and test the diagnostic accuracy of a software for analysis of conventional smears.

Materials and Methods

The software was developed using Python programming language and open source libraries. It was standardized with images from Bethesda Interobserver Reproducibility Project. One hundred and thirty images from smears which were reported Negative for Intraepithelial Lesion or Malignancy (NILM), and 45 images where some abnormality has been reported, were collected from the archives of the hospital. The software was then tested on the images.

Results

The software was able to segregate images based on overall nuclear: cytoplasmic ratio, coefficient of variation (CV) in nuclear size, nuclear membrane irregularity, and clustering. 68.88% of abnormal images were flagged by the software, as well as 19.23% of NILM images. The major difficulties faced were segmentation of overlapping cell clusters and separation of neutrophils.

Conclusion

The software shows potential as a screening tool for conventional cervical smears; however, further refinement in technique is required.

Integrating a FISH imaging system into the cytology laboratory

We have implemented an interactive imaging system for the interpretation of UroVysion fluorescence in situ hybridization (FISH) to improve throughput, productivity, quality control and diagnostic accuracy. We describe the Duet imaging system, our experiences with implementation, and outline the financial investment, space requirements, information technology needs, validation, and training of cytotechnologists needed to integrate such a system into a cytology laboratory. Before purchasing the imaging system, we evaluated and validated the instrument at our facility. Implementation required slide preparation changes, IT modifications, development of training programs, and revision of job descriptions for cytotechnologists. A darkened room was built to house the automated scanning station and microscope, as well as two imaging stations. IT changes included generation of storage for archival images on the LAN, addition of external hard drives for back-up, and changes to cable connections for communication between remote locations. Training programs for cytotechnologists, and pathologists/fellows/residents were developed, and cytotechnologists were integrated into multiple steps of the process. The imaging system has resulted in increased productivity for pathologists, concomitant with an expanded role of cytotechnologists in multiple critical steps, including FISH, scan setup, reclassification, and initial interpretation.