Bioinformatics. 2024 Jul 29:btae481. doi: 10.1093/bioinformatics/btae481. Online ahead of print.

ABSTRACT

MOTIVATION: CRISPR/Cas9 technology has been revolutionizing the field of gene editing. Guide RNAs (gRNAs) enable Cas9 proteins to target specific genomic loci for editing. However, editing efficiency varies between gRNAs and so computational methods were developed to predict editing efficiency for any gRNA of interest. High-throughput datasets of Cas9 editing efficiencies were produced to train machine-learning models to predict editing efficiency. However, these high-throughput datasets have a low correlation with functional and endogenous datasets, which are too small to train accurate machine-learning models on.

RESULTS: We developed DeepCRISTL, a deep-learning model to predict the editing efficiency in a specific cellular context. DeepCRISTL takes advantage of high-throughput datasets to learn general patterns of gRNA editing efficiency, and then fine-tunes the model on functional or endogenous data to fit a specific cellular context. We tested two state-of-the-art models trained on high-throughput datasets for editing efficiency prediction, our newly improved DeepHF and CRISPRon, combined with various transfer-learning approaches. The combination of CRISPRon and fine-tuning all model weights was the overall best performer. DeepCRISTL outperformed state-of-the-art methods in predicting editing efficiency in a specific cellular context on functional and endogenous datasets. Using saliency maps, we identified and compared the important features learned by DeepCRISTL across cellular contexts. We believe DeepCRISTL will improve prediction performance in many other CRISPR/Cas9 editing contexts by leveraging transfer learning to utilize both high-throughput datasets and smaller and more biologically relevant datasets.

AVAILABILITY: DeepCRISTL is available via github.com/OrensteinLab/DeepCRISTL.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:39073893 | DOI:10.1093/bioinformatics/btae481

JMIR AI. 2024 Jul 29;3:e50800. doi: 10.2196/50800.

ABSTRACT

BACKGROUND: Clinical trials are vital for developing new therapies but can also delay drug development. Efficient trial data management, optimized trial protocol, and accurate patient identification are critical for reducing trial timelines. Natural language processing (NLP) has the potential to achieve these objectives.

OBJECTIVE: This study aims to assess the feasibility of using data-driven approaches to optimize clinical trial protocol design and identify eligible patients. This involves creating a comprehensive eligibility criteria knowledge base integrated within electronic health records using deep learning-based NLP techniques.

METHODS: We obtained data of 3281 industry-sponsored phase 2 or 3 interventional clinical trials recruiting patients with non-small cell lung cancer, prostate cancer, breast cancer, multiple myeloma, ulcerative colitis, and Crohn disease from ClinicalTrials.gov, spanning the period between 2013 and 2020. A customized bidirectional long short-term memory- and conditional random field-based NLP pipeline was used to extract all eligibility criteria attributes and convert hypernym concepts into computable hyponyms along with their corresponding values. To illustrate the simulation of clinical trial design for optimization purposes, we selected a subset of patients with non-small cell lung cancer (n=2775), curated from the Mount Sinai Health System, as a pilot study.

RESULTS: We manually annotated the clinical trial eligibility corpus (485/3281, 14.78% trials) and constructed an eligibility criteria-specific ontology. Our customized NLP pipeline, developed based on the eligibility criteria-specific ontology that we created through manual annotation, achieved high precision (0.91, range 0.67-1.00) and recall (0.79, range 0.50-1) scores, as well as a high F1-score (0.83, range 0.67-1), enabling the efficient extraction of granular criteria entities and relevant attributes from 3281 clinical trials. A standardized eligibility criteria knowledge base, compatible with electronic health records, was developed by transforming hypernym concepts into machine-interpretable hyponyms along with their corresponding values. In addition, an interface prototype demonstrated the practicality of leveraging real-world data for optimizing clinical trial protocols and identifying eligible patients.

CONCLUSIONS: Our customized NLP pipeline successfully generated a standardized eligibility criteria knowledge base by transforming hypernym criteria into machine-readable hyponyms along with their corresponding values. A prototype interface integrating real-world patient information allows us to assess the impact of each eligibility criterion on the number of patients eligible for the trial. Leveraging NLP and real-world data in a data-driven approach holds promise for streamlining the overall clinical trial process, optimizing processes, and improving efficiency in patient identification.

PMID:39073872 | DOI:10.2196/50800

J Chem Theory Comput. 2024 Jul 29. doi: 10.1021/acs.jctc.4c00141. Online ahead of print.

ABSTRACT

Molecular docking (MD) is a crucial task in drug design, which predicts the position, orientation, and conformation of the ligand when it is bound to a target protein. It can be interpreted as a combinatorial optimization problem, where quantum annealing (QA) has shown a promising advantage for solving combinatorial optimization. In this work, we propose a novel quantum molecular docking (QMD) approach based on a QA-inspired algorithm. We construct two binary encoding methods to efficiently discretize the degrees of freedom with an exponentially reduced number of bits and propose a smoothing filter to rescale the rugged objective function. We propose a new quantum-inspired algorithm, hopscotch simulated bifurcation (hSB), showing great advantages in optimizing over extremely rugged energy landscapes. This hSB can be applied to any formulation of an objective function under binary variables. An adaptive local continuous search is also introduced for further optimization of the discretized solution from hSB. Concerning the stability of docking, we propose a perturbation detection method to help rank the candidate poses. We demonstrate our approach on a typical data set. QMD has shown advantages over the search-based Autodock Vina and the deep-learning DIFFDOCK in both redocking and self-docking scenarios. These results indicate that quantum-inspired algorithms can be applied to solve practical problems in drug discovery even before quantum hardware become mature.

PMID:39073856 | DOI:10.1021/acs.jctc.4c00141

Environ Sci Pollut Res Int. 2024 Jul 29. doi: 10.1007/s11356-024-34462-9. Online ahead of print.

ABSTRACT

Predicting pollutant leakage and diffusion processes is crucial for ensuring people's safety. While the deep learning method offers high simulation efficiency and superior generalization, there is currently a lack of research on predicting pollutant leakage and diffusion flow field using deep learning. Therefore, it is necessary to conduct further studies in this area. This paper introduces a two-level network method to model the flow characteristics of pollutant diffusion. The proposed method in this study demonstrates a significant enhancement in flow field prediction accuracy compared to traditional deep learning methods. Moreover, it improves computational efficiency by over 800 times compared to traditional computational fluid dynamics (CFD) methods. Unlike conventional CFD methods that require grid expansion to calculate all operation conditions, the deep learning method is not confined by grid limitations. While deep learning methods may not entirely replace CFD methods, they can serve as a valuable supplementary tool, expanding the versatility of CFD methods. The findings of this research establish a robust foundation for incorporating deep learning methods in addressing pollutant leakage and diffusion challenges.

PMID:39073715 | DOI:10.1007/s11356-024-34462-9

World J Urol. 2024 Jul 29;42(1):455. doi: 10.1007/s00345-024-05146-3.

ABSTRACT

PURPOSE: Large language models (LLMs) are a form of artificial intelligence (AI) that uses deep learning techniques to understand, summarize and generate content. The potential benefits of LLMs in healthcare is predicted to be immense. The objective of this study was to examine the quality of patient information leaflets (PILs) produced by 3 LLMs on urological topics.

METHODS: Prompts were created to generate PILs from 3 LLMs: ChatGPT-4, PaLM 2 (Google Bard) and Llama 2 (Meta) across four urology topics (circumcision, nephrectomy, overactive bladder syndrome, and transurethral resection of the prostate). PILs were evaluated using a quality assessment checklist. PIL readability was assessed by the Average Reading Level Consensus Calculator.

RESULTS: PILs generated by PaLM 2 had the highest overall average quality score (3.58), followed by Llama 2 (3.34) and ChatGPT-4 (3.08). PaLM 2 generated PILs were of the highest quality in all topics except TURP and was the only LLM to include images. Medical inaccuracies were present in all generated content including instances of significant error. Readability analysis identified PaLM 2 generated PILs as the simplest (age 14-15 average reading level). Llama 2 PILs were the most difficult (age 16-17 average).

CONCLUSION: While LLMs can generate PILs that may help reduce healthcare professional workload, generated content requires clinician input for accuracy and inclusion of health literacy aids, such as images. LLM-generated PILs were above the average reading level for adults, necessitating improvement in LLM algorithms and/or prompt design. How satisfied patients are to LLM-generated PILs remains to be evaluated.

PMID:39073590 | DOI:10.1007/s00345-024-05146-3

Europace. 2024 Jul 29:euae201. doi: 10.1093/europace/euae201. Online ahead of print.

ABSTRACT

Atrial fibrillation (AF) prediction and screening are of important clinical interest because of the potential to prevent serious adverse events. Devices capable of detecting short episodes of arrhythmia are now widely available. Although it has recently been suggested that some high-risk patients with AF detected on implantable devices may benefit from anticoagulation, long-term management remains challenging in lower-risk patients and in those with AF detected on monitors or wearable devices as the development of clinically meaningful arrhythmia burden in this group remains unknown. Identification and prediction of clinically relevant AF is therefore of unprecedented importance to the cardiologic community. Family history and underlying genetic markers are important risk factors for AF. Recent studies suggest a good predictive ability of polygenic risk scores, with a possible additive value to clinical AF prediction scores. Artificial intelligence, enabled by the exponentially increasing computing power and digital datasets, has gained traction in the past decade and is of increasing interest in AF prediction using a single or multiple lead sinus rhythm ECG. Integrating these novel approaches could help predict AF substrate severity, thereby potentially improving the effectiveness of AF screening, and personalizing the management of patients presenting with conditions such as embolic stroke of undetermined source and subclinical AF. This review presents current evidence surrounding deep learning and polygenic risk scores in the prediction of incident AF and provides a futuristic outlook on possible ways of implementing these modalities into clinical practice, while considering current limitations and required areas of improvement.

PMID:39073570 | DOI:10.1093/europace/euae201

Surg Endosc. 2024 Jul 29. doi: 10.1007/s00464-024-10939-z. Online ahead of print.

ABSTRACT

BACKGROUND: Artificial intelligence (AI) has the potential to enhance surgical practice by predicting anatomical structures within the surgical field, thereby supporting surgeons' experiences and cognitive skills. Preserving and utilising nerves as critical guiding structures is paramount in rectal cancer surgery. Hence, we developed a deep learning model based on U-Net to automatically segment nerves.

METHODS: The model performance was evaluated using 60 randomly selected frames, and the Dice and Intersection over Union (IoU) scores were quantitatively assessed by comparing them with ground truth data. Additionally, a questionnaire was administered to five colorectal surgeons to gauge the extent of underdetection, overdetection, and the practical utility of the model in rectal cancer surgery. Furthermore, we conducted an educational assessment of non-colorectal surgeons, trainees, physicians, and medical students. We evaluated their ability to recognise nerves in mesorectal dissection scenes, scored them on a 12-point scale, and examined the score changes before and after exposure to the AI analysis videos.

RESULTS: The mean Dice and IoU scores for the 60 test frames were 0.442 (range 0.0465-0.639) and 0.292 (range 0.0238-0.469), respectively. The colorectal surgeons revealed an under-detection score of 0.80 (± 0.47), an over-detection score of 0.58 (± 0.41), and a usefulness evaluation score of 3.38 (± 0.43). The nerve recognition scores of non-colorectal surgeons, rotating residents, and medical students significantly improved by simply watching the AI nerve recognition videos for 1 min. Notably, medical students showed a more substantial increase in nerve recognition scores when exposed to AI nerve analysis videos than when exposed to traditional lectures on nerves.

CONCLUSIONS: In laparoscopic and robot-assisted rectal cancer surgeries, the AI-based nerve recognition model achieved satisfactory recognition levels for expert surgeons and demonstrated effectiveness in educating junior surgeons and medical students on nerve recognition.

PMID:39073558 | DOI:10.1007/s00464-024-10939-z

Orthopedics. 2024 Jul 31:1-8. doi: 10.3928/01477447-20240718-02. Online ahead of print.

ABSTRACT

BACKGROUND: This study focused on using deep learning neural networks to classify the severity of osteoarthritis in the knee. A continuous regression score of osteoarthritis severity has yet to be explored using artificial intelligence machine learning, which could offer a more nuanced assessment of osteoarthritis.

MATERIALS AND METHODS: This study used 8260 radiographic images from The Osteoarthritis Initiative to develop and assess four neural network models (VGG16, EfficientNetV2 small, ResNet34, and DenseNet196). Each model generated a regressor score of the osteoarthritis severity based on Kellgren-Lawrence grading scale criteria. Primary performance outcomes assessed were area under the curve (AUC), accuracy, and mean absolute error (MAE) for each model. Secondary outcomes evaluated were precision, recall, and F-1 score.

RESULTS: The EfficientNet model architecture yielded the strongest AUC (0.83), accuracy (71%), and MAE (0.42) compared with VGG16 (AUC: 0.74; accuracy: 57%; MAE: 0.54), ResNet34 (AUC: 0.76; accuracy: 60%; MAE: 0.53), and DenseNet196 (AUC: 0.78; accuracy: 62%; MAE: 0.49).

CONCLUSION: Convolutional neural networks offer an automated and accurate way to quickly assess and diagnose knee radiographs for osteoarthritis. The regression score models evaluated in this study demonstrated superior AUC, accuracy, and MAE compared with standard convolutional neural network models. The EfficientNet model exhibited the best overall performance, including the highest AUC (0.83) noted in the literature. The artificial intelligence-generated regressor exhibits a finer progression of knee osteoarthritis by quantifying severity of various hallmark features. Potential applications for this technology include its use as a screening tool in determining patient suitability for orthopedic referral. [Orthopedics. 202x;4x(x):xx-xx.].

PMID:39073041 | DOI:10.3928/01477447-20240718-02

J Appl Clin Med Phys. 2024 Jul 27:e14462. doi: 10.1002/acm2.14462. Online ahead of print.

ABSTRACT

PURPOSE: Anatomical and other changes during radiotherapy will cause inaccuracy of dose distributions, therefore the expectation for online adaptive radiation therapy (ART) is high in effectively reducing uncertainties due to intra-variation. However, ART requires extensive time and effort. This study investigated an adaptive assessment workflow based on fractional cone-beam computed tomography (CBCT) images.

METHODS: Image registration, synthetic CT (sCT) generation, auto-segmentation, and dose calculation were implemented and integrated into ArcherQA Adaptive Check. The rigid registration was based on ITK open source. The deformable image registration (DIR) method was based on a 3D multistage registration network, and the sCT generation method was performed based on a 2D cycle-consistent adversarial network (CycleGAN). The auto-segmentation of organs at risk (OARs) on sCT images was finished by a deep learning-based auto-segmentation software, DeepViewer. The contours of targets were obtained by the structure-guided registration. Finally, the dose calculation was based on a GPU-based Monte Carlo (MC) dose code, ArcherQA.

RESULTS: The dice similarity coefficient (DSCs) were over 0.86 for target volumes and over 0.79 for OARs. The gamma pass rate of ArcherQA versus Eclipse treatment planning system was more than 99% at the 2%/2 mm criterion with a low-dose threshold of 10%. The time for the whole process was less than 3 min. The dosimetric results of ArcherQA Adaptive Check were consistent with the Ethos scheduled plan, which can effectively identify the fractions that need the implementation of the Ethos adaptive plan.

CONCLUSION: This study integrated AI-based technologies and GPU-based MC technology to evaluate the dose distributions using fractional CBCT images, demonstrating remarkably high efficiency and precision to support future ART processes.

PMID:39072895 | DOI:10.1002/acm2.14462

Med Phys. 2024 Jul 27. doi: 10.1002/mp.17330. Online ahead of print.

ABSTRACT

BACKGROUND: While there are established international consensuses on the delineation of pelvic lymph node regions (LNRs), significant inter- and intra-observer variabilities persist. Contouring these clinical target volumes for irradiation in pelvic malignancies is both time-consuming and labor-intensive.

PURPOSE: The purpose of this study was to develop a deep learning model of pelvic LNRs delineation for patients with pelvic cancers.

METHODS: Planning computed tomography (CT) studies of 160 patients with pelvic primary malignancies (including rectal, prostate, and cervical cancer) were retrospectively collected and divided into training set (n = 120) and testing set (n = 40). Six pelvic LNRs, including abdominal presacral, pelvic presacral, internal iliac nodes, external iliac nodes, obturator nodes, and inguinal nodes were delineated by two radiation oncologists as ground truth (Gt) contours. The cascaded multi-heads U-net (CMU-net) was constructed based on the Gt contours from training cohort, which was subsequently verified in the testing cohort. The automatic delineation of six LNRs (Auto) was evaluated using dice similarity coefficient (DSC), average surface distance (ASD), 95th percentile Hausdorff distance (HD95), and a 7-point scale score.

RESULTS: In the testing set, the DSC of six pelvic LNRs by CMU-net model varied from 0.851 to 0.942, ASD from 0.381 to 1.037 mm, and HD95 from 2.025 to 3.697 mm. No significant differences were founded in these three parameters between postoperative and preoperative cases. 95.9% and 96.2% of auto delineations by CMU-net model got a score of 1-3 by two expert radiation oncologists, respectively, meaning only minor edits needed.

CONCLUSIONS: The CMU-net was successfully developed for automated delineation of pelvic LNRs for pelvic malignancies radiotherapy with improved contouring efficiency and highly consistent, which might justify its implementation in radiotherapy work flow.

PMID:39072765 | DOI:10.1002/mp.17330

Front Endocrinol (Lausanne). 2024 Jul 12;15:1323452. doi: 10.3389/fendo.2024.1323452. eCollection 2024.

ABSTRACT

OBJECTIVE: The objective of this study was to develop a deep learning-and-radiomics-based ultrasound nomogram for the evaluation of axillary lymph node (ALN) metastasis risk in breast cancer patients ≥ 75 years.

METHODS: The study enrolled breast cancer patients ≥ 75 years who underwent either sentinel lymph node biopsy or ALN dissection at Fudan University Shanghai Cancer Center. DenseNet-201 was employed as the base model, and it was trained using the Adam optimizer and cross-entropy loss function to extract deep learning (DL) features from ultrasound images. Additionally, radiomics features were extracted from ultrasound images utilizing the Pyradiomics tool, and a Rad-Score (RS) was calculated employing the Lasso regression algorithm. A stepwise multivariable logistic regression analysis was conducted in the training set to establish a prediction model for lymph node metastasis, which was subsequently validated in the validation set. Evaluation metrics included area under the curve (AUC), accuracy, sensitivity, specificity, positive predictive value, negative predictive value, and F1-score. The calibration of the model's performance and its clinical prediction accuracy were assessed using calibration curves and decision curves respectively. Furthermore, integrated discrimination improvement and net reclassification improvement were utilized to quantify enhancements in RS.

RESULTS: Histological grade, axillary ultrasound, and RS were identified as independent risk factors for predicting lymph node metastasis. The integration of the RS into the clinical prediction model significantly improved its predictive performance, with an AUC of 0.937 in the training set, surpassing both the clinical model and the RS model alone. In the validation set, the integrated model also outperformed other models with AUCs of 0.906, 0.744, and 0.890 for the integrated model, clinical model, and RS model respectively. Experimental results demonstrated that this study's integrated prediction model could enhance both accuracy and generalizability.

CONCLUSION: The DL and radiomics-based model exhibited remarkable accuracy and reliability in predicting ALN status among breast cancer patients ≥ 75 years, thereby contributing to the enhancement of personalized treatment strategies' efficacy and improvement of patients' quality of life.

PMID:39072273 | PMC:PMC11272464 | DOI:10.3389/fendo.2024.1323452

Front Physiol. 2024 Jul 12;15:1429161. doi: 10.3389/fphys.2024.1429161. eCollection 2024.

ABSTRACT

Cardiovascular diseases remain one of the main threats to human health, significantly affecting the quality and life expectancy. Effective and prompt recognition of these diseases is crucial. This research aims to develop an effective novel hybrid method for automatically detecting dangerous arrhythmias based on cardiac patients' short electrocardiogram (ECG) fragments. This study suggests using a continuous wavelet transform (CWT) to convert ECG signals into images (scalograms) and examining the task of categorizing short 2-s segments of ECG signals into four groups of dangerous arrhythmias that are shockable, including ventricular flutter (C1), ventricular fibrillation (C2), ventricular tachycardia torsade de pointes (C3), and high-rate ventricular tachycardia (C4). We propose developing a novel hybrid neural network with a deep learning architecture to classify dangerous arrhythmias. This work utilizes actual electrocardiogram (ECG) data obtained from the PhysioNet database, alongside artificially generated ECG data produced by the Synthetic Minority Over-sampling Technique (SMOTE) approach, to address the issue of imbalanced class distribution for obtaining an accuracy-trained model. Experimental results demonstrate that the proposed approach achieves high accuracy, sensitivity, specificity, precision, and an F1-score of 97.75%, 97.75%, 99.25%, 97.75%, and 97.75%, respectively, in classifying all the four shockable classes of arrhythmias and are superior to traditional methods. Our work possesses significant clinical value in real-life scenarios since it has the potential to significantly enhance the diagnosis and treatment of life-threatening arrhythmias in individuals with cardiac disease. Furthermore, our model also has demonstrated adaptability and generality for two other datasets.

PMID:39072217 | PMC:PMC11272599 | DOI:10.3389/fphys.2024.1429161

ACS Omega. 2024 Jul 8;9(29):31694-31702. doi: 10.1021/acsomega.4c02393. eCollection 2024 Jul 23.

ABSTRACT

Ionic liquids (ILs), known for their distinct and tunable properties, offer a broad spectrum of potential applications across various fields, including chemistry, materials science, and energy storage. However, practical applications of ILs are often limited by their unfavorable physicochemical properties. Experimental screening becomes impractical due to the vast number of potential IL combinations. Therefore, the development of a robust and efficient model for predicting the IL properties is imperative. As the defining feature, it is of practice significance to establish an accurate yet efficient model to predict the normal melting point of IL (T m), which may facilitate the discovery and design of novel ILs for specific applications. In this study, we presented a pseudo-Siamese convolution neural network (pSCNN) inspired by SCNN and focused on the T m. Utilizing a data set of 3098 ILs, we systematically assess various deep learning models (ANN, pSCNN, and Transformer-CNF), along with molecular descriptors (ECFP fingerprint and Mordred properties), for their performance in predicting the T m of ILs. Remarkably, among the investigated modeling schemes, the pSCNN, coupled with filtered Mordred descriptors, demonstrates superior performance, yielding mean absolute error (MAE) and root-mean-square error (RMSE) values of 24.36 and 31.56 °C, respectively. Feature analysis further highlights the effectiveness of the pSCNN model. Moreover, the pSCNN method, with a pair of inputs, can be extended beyond ionic liquid melting point prediction.

PMID:39072063 | PMC:PMC11270577 | DOI:10.1021/acsomega.4c02393

medRxiv [Preprint]. 2024 Jul 18:2024.07.18.24310644. doi: 10.1101/2024.07.18.24310644.

ABSTRACT

OBJECTIVE: Transcranial focused ultrasound (tFUS) is an emerging neuromodulation approach that has been demonstrated in animals but is difficult to translate to humans because of acoustic attenuation and scattering in the skull. Optimal dose delivery requires subject-specific skull porosity estimates which has traditionally been done using CT. We propose a deep learning (DL) estimation of skull porosity from T1-weighted MRI images which removes the need for radiation-inducing CT scans.

APPROACH: We evaluate the impact of different DL approaches, including network architecture, input size and dimensionality, multichannel inputs, data augmentation, and loss functions. We also propose back-propagation in the mask (BIM), a method whereby only voxels inside the skull mask contribute to training. We evaluate the robustness of the best model to input image noise and MRI acquisition parameters and propagate porosity estimation errors in thousands of beam propagation scenarios.

MAIN RESULTS: Our best performing model is a cGAN with a ResNet-9 generator with 3D 64×64×64 inputs trained with L1 and L2 losses. The model achieved a mean absolute error of 6.9% in the test set, compared to 9.5% with the pseudo-CT of Izquierdo et al. (38% improvement) and 9.4% with the generic pixel-to-pixel image translation cGAN pix2pix (36% improvement). Acoustic dose distributions in the thalamus were more accurate with our approach than with the pseudo-CT approach of both Burgos et al. and Izquierdo et al, resulting in near-optimal treatment planning and dose estimation at all frequencies compared to CT (reference).

SIGNIFICANCE: Our DL approach porosity estimates with ∼7% error, is robust to input image noise and MRI acquisition parameters (sequence, coils, field strength) and yields near-optimal treatment planning and dose estimates for both central (thalamus) and lateral brain targets (amygdala) in the 200-1000 kHz frequency range.

PMID:39072036 | PMC:PMC11275664 | DOI:10.1101/2024.07.18.24310644

medRxiv [Preprint]. 2024 Jul 21:2024.07.19.24310619. doi: 10.1101/2024.07.19.24310619.

ABSTRACT

BACKGROUND: Visual scoring of tubular damage has limitations in capturing the full spectrum of structural changes and prognostic potential. We investigate if computationally quantified tubular features can enhance prognostication and reveal spatial relationships with interstitial fibrosis.

METHODS: Deep-learning and image-processing-based segmentations were employed in N=254/266 PAS-WSIs from the NEPTUNE/CureGN datasets (135/153 focal segmental glomerulosclerosis and 119/113 minimal change disease) for: cortex, tubular lumen (TL), epithelium (TE), nuclei (TN), and basement membrane (TBM). N=104 pathomic features were extracted from these segmented tubular substructures and summarized at the patient level using summary statistics. The tubular features were quantified across the biopsy and in manually segmented regions of mature interstitial fibrosis and tubular atrophy (IFTA), pre-IFTA and non-IFTA in the NEPTUNE dataset. Minimum Redundancy Maximum Relevance was used in the NEPTUNE dataset to select features most associated with disease progression and proteinuria remission. Ridge-penalized Cox models evaluated their predictive discrimination compared to clinical/demographic data and visual-assessment. Models were evaluated in the CureGN dataset.

RESULTS: N=9 features were predictive of disease progression and/or proteinuria remission. Models with tubular features had high prognostic accuracy in both NEPTUNE and CureGN datasets and increased prognostic accuracy for both outcomes (5.6%-7.7% and 1.6%-4.6% increase for disease progression and proteinuria remission, respectively) compared to conventional parameters alone in the NEPTUNE dataset. TBM thickness/area and TE simplification progressively increased from non- to pre- and mature IFTA.

CONCLUSIONS: Previously under-recognized, quantifiable, and clinically relevant tubular features in the kidney parenchyma can enhance understanding of mechanisms of disease progression and risk stratification.

PMID:39072032 | PMC:PMC11275675 | DOI:10.1101/2024.07.19.24310619

Data Brief. 2024 Jun 26;55:110672. doi: 10.1016/j.dib.2024.110672. eCollection 2024 Aug.

ABSTRACT

The existence of diverse traditional machine learning and deep learning models designed for various multimodal music information retrieval (MIR) applications, such as multimodal music sentiment analysis, genre classification, recommender systems, and emotion recognition, renders the machine learning and deep learning models indispensable for the MIR tasks. However, solving these tasks in a data-driven manner depends on the availability of high-quality benchmark datasets. Hence, the necessity for datasets tailored for multimodal music information retrieval applications is paramount. While a handful of multimodal datasets exist for distinct music information retrieval applications, they are not available in low-resourced languages, like Sotho-Tswana languages. In response to this gap, we introduce a novel multimodal music information retrieval dataset for various music information retrieval applications. This dataset centres on Sotho-Tswana musical videos, encompassing both textual, visual, and audio modalities specific to Sotho-Tswana musical content. The musical videos were downloaded from YouTube, but Python programs were written to process the musical videos and extract relevant spectral-based acoustic features, using different Python libraries. Annotation of the dataset was done manually by native speakers of Sotho-Tswana languages, who understand the culture and traditions of the Sotho-Tswana people. It is distinctive as, to our knowledge, no such dataset has been established until now.

PMID:39071970 | PMC:PMC11282976 | DOI:10.1016/j.dib.2024.110672

Data Brief. 2024 Jun 22;55:110665. doi: 10.1016/j.dib.2024.110665. eCollection 2024 Aug.

ABSTRACT

Tennis is a popular sport, and integrating modern technological advancements can greatly enhance player training. Human pose estimation has seen substantial developments recently, driven by progress in deep learning. The dataset described in this paper was compiled from videos of researchers' friend playing tennis. These videos were retrieved frame by frame to categorize various tennis movements, and human skeleton joints were annotated using COCO-Annotator to generate labelled JSON files. By combining these JSON files with the classified image set, we constructed the dataset for this paper. This dataset enables the training and validation of four tennis postures, forehand shot, backhand shot, ready position, and serves, using deep learning models (such as OpenPose). The researchers believe that this dataset will be a valuable asset to the tennis community and human pose estimation field, fostering innovation and excellence in the sport.

PMID:39071962 | PMC:PMC11282921 | DOI:10.1016/j.dib.2024.110665

Appl Sci (Basel). 2024 Jan;14(2):769. doi: 10.3390/app14020769. Epub 2024 Jan 16.

ABSTRACT

A computational neuromuscular control system that generates lung pressure and three intrinsic laryngeal muscle activations (cricothyroid, thyroarytenoid, and lateral cricoarytenoid) to control the vocal source was developed. In the current study, LeTalker, a biophysical computational model of the vocal system was used as the physical plant. In the LeTalker, a three-mass vocal fold model was used to simulate self-sustained vocal fold oscillation. A constant/ǝ/vowel was used for the vocal tract shape. The trachea was modeled after MRI measurements. The neuromuscular control system generates control parameters to achieve four acoustic targets (fundamental frequency, sound pressure level, normalized spectral centroid, and signal-to-noise ratio) and four somatosensory targets (vocal fold length, and longitudinal fiber stress in the three vocal fold layers). The deep-learning-based control system comprises one acoustic feedforward controller and two feedback (acoustic and somatosensory) controllers. Fifty thousand steady speech signals were generated using the LeTalker for training the control system. The results demonstrated that the control system was able to generate the lung pressure and the three muscle activations such that the four acoustic and four somatosensory targets were reached with high accuracy. After training, the motor command corrections from the feedback controllers were minimal compared to the feedforward controller except for thyroarytenoid muscle activation.

PMID:39071945 | PMC:PMC11281313 | DOI:10.3390/app14020769

iScience. 2024 Jun 24;27(7):110368. doi: 10.1016/j.isci.2024.110368. eCollection 2024 Jul 19.

ABSTRACT

Deconvolution algorithms mostly rely on single-cell RNA-sequencing (scRNA-seq) data applied onto bulk RNA-sequencing (bulk RNA-seq) to estimate tissues' cell-type composition, with performance accuracy validated on deposited databases. Adipose tissues' cellular composition is highly variable, and adipocytes can only be captured by single-nucleus RNA-sequencing (snRNA-seq). Here we report the development of sNucConv, a Scaden deep-learning-based deconvolution tool, trained using 5 hSAT and 7 hVAT snRNA-seq-based data corrected by (i) snRNA-seq/bulk RNA-seq highly correlated genes and (ii) individual cell-type regression models. Applying sNucConv on our bulk RNA-seq data resulted in cell-type proportion estimation of 15 and 13 cell types, with accuracy of R = 0.93 (range: 0.76-0.97) and R = 0.95 (range: 0.92-0.98) for hVAT and hSAT, respectively. This performance level was further validated on an independent set of samples (5 hSAT; 5 hVAT). The resulting model was depot specific, reflecting depot differences in gene expression patterns. Jointly, sNucConv provides proof-of-concept for producing validated deconvolution models for tissues un-amenable to scRNA-seq.

PMID:39071890 | PMC:PMC11277759 | DOI:10.1016/j.isci.2024.110368

Arthroplast Today. 2024 Jun 27;27:101396. doi: 10.1016/j.artd.2024.101396. eCollection 2024 Jun.

ABSTRACT

Hip and knee arthroplasty are high-volume procedures undergoing rapid growth. The large volume of procedures generates a vast amount of data available for next-generation analytics. Techniques in the field of artificial intelligence (AI) can assist in large-scale pattern recognition and lead to clinical insights. AI methodologies have become more prevalent in orthopaedic research. This review will first describe an overview of AI in the medical field, followed by a description of the 3 arthroplasty research areas in which AI is commonly used (risk modeling, automated radiographic measurements, arthroplasty registry construction). Finally, we will discuss the next frontier of AI research focusing on model deployment and uncertainty quantification.

PMID:39071822 | PMC:PMC11282426 | DOI:10.1016/j.artd.2024.101396