Clinical and Translational Research on Technologies for Diagnosis and Treatment

A special issue of Bioengineering (ISSN 2306-5354). This special issue belongs to the section "Biomedical Engineering and Biomaterials".

Deadline for manuscript submissions: 30 June 2024 | Viewed by 10261

Special Issue Editor


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Guest Editor
Medical Physics Program, University of Nevada, Las Vegas, NV, USA
Interests: combining biological- and imaging- biomarkers for early detection of cancers and cancer interventions; nanotechnology and its application in imaging and therapeutics; bioinformatics and AI for cancer biology and clinical applications
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Special Issue Information

Dear Colleagues,

The purpose of this Special Issue is to publish latest scientific discoveries and/or engineering developments in imaging, data science, biological technologies and relevant clinical and translational methods or tools that address contemporary problems in understanding the fundamental biology, pathology, risk assessment, diagnosis, treatment, and/or monitoring disease status for cancer or other diseases.

The Special Issue will be accepting contributions (both original articles and reviews) mainly focus on the following topics (but not limited to):

  • Imaging applications in clinical trials, clinical and translational research, and/or patient care;
  • The integration of modern computational or integrative informatics methods (e.g., machine learning/vision, deep learning, neural networks, machine intelligence, integrated bioinformatics, predictive analytics, etc.) into preclinical and clinical methods to enhance/optimize utility to detection, diagnosis, workflow, or treatment monitoring;
  • Development, integration and validation of new molecular diagnosis, imaging systems, technologies, methods, assays, or devices, related component technologies, image processing methods, and development of informatics tools;
  • Multi-modal imaging for diagnosis and patient care;
  • Multi-modal image-guided cancer or other diseases’ intervention;
  • Combined biological and imaging biomarkers for diagnosis and treatment;
  • Quantification methods;
  • Affordable and point of care systems, methods, tools, or devices for low resource settings, or underserved populations;
  • Knowledge-based systems;
  • Analytical and clinical validation using clinical samples, and correlation studies

Dr. Yu Kuang
Guest Editor

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Bioengineering is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • radiation oncology
  • early cancer detection
  • medical imaging
  • point of care
  • combined biological and imaging biomarkers
  • image-guided intervention
  • medical devices

Published Papers (7 papers)

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Research

9 pages, 1205 KiB  
Article
Profile of a Multivariate Observation under Destructive Sampling—A Monte Carlo Approach to a Case of Spina Bifida
by Tianyuan Guan, Rigwed Tatu, Koffi Wima, Marc Oria, Jose L. Peiro, Chia-Ying Lin and Marepalli. B. Rao
Bioengineering 2024, 11(3), 249; https://doi.org/10.3390/bioengineering11030249 - 3 Mar 2024
Viewed by 874
Abstract
A biodegradable hybrid polymer patch was invented at the University of Cincinnati to cover gaps on the skin over the spinal column of a growing fetus, characterized by the medical condition spina bifida. The inserted patch faces amniotic fluid (AF) on one side [...] Read more.
A biodegradable hybrid polymer patch was invented at the University of Cincinnati to cover gaps on the skin over the spinal column of a growing fetus, characterized by the medical condition spina bifida. The inserted patch faces amniotic fluid (AF) on one side and cerebrospinal fluid on the other side. The goal is to provide a profile of the roughness of a patch over time at 0, 4, 8, 12, and 16 weeks with a 95% confidence band. The patch is soaked in a test tube filled with either amniotic fluid (AF) or phosphate-buffered saline (PBS) in the lab. If roughness is measured at any time point for a patch, the patch is destroyed. Thus, it is impossible to measure roughness at all weeks of interest for any patch. It is important to assess the roughness of a patch because the rougher the patch is, the faster the skin grows under the patch. We use a model-based approach with Monte Carlo simulations to estimate the profile over time with a 95% confidence band. The roughness profiles are similar with both liquids. The profile can be used as a template for future experiments on the composition of patches. Full article
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16 pages, 6531 KiB  
Article
A Disulfidptosis-Related Gene Signature Associated with Prognosis and Immune Cell Infiltration in Osteosarcoma
by Pengyu Chen and Jingnan Shen
Bioengineering 2023, 10(10), 1121; https://doi.org/10.3390/bioengineering10101121 - 25 Sep 2023
Cited by 2 | Viewed by 1275
Abstract
Osteosarcoma (OS) stands as a leading aggressive bone malignancy that primarily affects children and adolescents worldwide. A recently identified form of programmed cell death, termed Disulfidptosis, may have implications for cancer progression. Yet, its role in OS remains elusive. To elucidate this, we [...] Read more.
Osteosarcoma (OS) stands as a leading aggressive bone malignancy that primarily affects children and adolescents worldwide. A recently identified form of programmed cell death, termed Disulfidptosis, may have implications for cancer progression. Yet, its role in OS remains elusive. To elucidate this, we undertook a thorough examination of Disulfidptosis-related genes (DRGs) within OS. This involved parsing expression data, clinical attributes, and survival metrics from the TARGET and GEO databases. Our analysis unveiled a pronounced association between the expression of specific DRGs, particularly MYH9 and LRPPRC, and OS outcome. Subsequent to this, we crafted a risk model and a nomogram, both honed for precise prognostication of OS prognosis. Intriguingly, risks associated with DRGs strongly resonated with immune cell infiltration levels, myriad immune checkpoints, genes tethered to immunotherapy, and sensitivities to systematic treatments. To conclude, our study posits that DRGs, especially MYH9 and LRPPRC, hold potential as pivotal architects of the tumor immune milieu in OS. Moreover, they may offer predictive insights into treatment responses and serve as reliable prognostic markers for those diagnosed with OS. Full article
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11 pages, 4264 KiB  
Article
Non-Contrasted CT Radiomics for SAH Prognosis Prediction
by Dezhi Shan, Junjie Wang, Peng Qi, Jun Lu and Daming Wang
Bioengineering 2023, 10(8), 967; https://doi.org/10.3390/bioengineering10080967 - 16 Aug 2023
Viewed by 1209
Abstract
Subarachnoid hemorrhage (SAH) denotes a serious type of hemorrhagic stroke that often leads to a poor prognosis and poses a significant socioeconomic burden. Timely assessment of the prognosis of SAH patients is of paramount clinical importance for medical decision making. Currently, clinical prognosis [...] Read more.
Subarachnoid hemorrhage (SAH) denotes a serious type of hemorrhagic stroke that often leads to a poor prognosis and poses a significant socioeconomic burden. Timely assessment of the prognosis of SAH patients is of paramount clinical importance for medical decision making. Currently, clinical prognosis evaluation heavily relies on patients’ clinical information, which suffers from limited accuracy. Non-contrast computed tomography (NCCT) is the primary diagnostic tool for SAH. Radiomics, an emerging technology, involves extracting quantitative radiomics features from medical images to serve as diagnostic markers. However, there is a scarcity of studies exploring the prognostic prediction of SAH using NCCT radiomics features. The objective of this study is to utilize machine learning (ML) algorithms that leverage NCCT radiomics features for the prognostic prediction of SAH. Retrospectively, we collected NCCT and clinical data of SAH patients treated at Beijing Hospital between May 2012 and November 2022. The modified Rankin Scale (mRS) was utilized to assess the prognosis of patients with SAH at the 3-month mark after the SAH event. Based on follow-up data, patients were classified into two groups: good outcome (mRS ≤ 2) and poor outcome (mRS > 2) groups. The region of interest in NCCT images was delineated using 3D Slicer software, and radiomic features were extracted. The most stable and significant radiomic features were identified using the intraclass correlation coefficient, t-test, and least absolute shrinkage and selection operator (LASSO) regression. The data were randomly divided into training and testing cohorts in a 7:3 ratio. Various ML algorithms were utilized to construct predictive models, encompassing logistic regression (LR), support vector machine (SVM), random forest (RF), light gradient boosting machine (LGBM), adaptive boosting (AdaBoost), extreme gradient boosting (XGBoost), and multi-layer perceptron (MLP). Seven prediction models based on radiomic features related to the outcome of SAH patients were constructed using the training cohort. Internal validation was performed using five-fold cross-validation in the entire training cohort. The receiver operating characteristic curve, accuracy, precision, recall, and f-1 score evaluation metrics were employed to assess the performance of the classifier in the overall dataset. Furthermore, decision curve analysis was conducted to evaluate model effectiveness. The study included 105 SAH patients. A comprehensive set of 1316 radiomics characteristics were initially derived, from which 13 distinct features were chosen for the construction of the ML model. Significant differences in age were observed between patients with good and poor outcomes. Among the seven constructed models, model_SVM exhibited optimal outcomes during a five-fold cross-validation assessment, with an average area under the curve (AUC) of 0.98 (standard deviation: 0.01) and 0.88 (standard deviation: 0.08) on the training and testing cohorts, respectively. In the overall dataset, model_SVM achieved an accuracy, precision, recall, f-1 score, and AUC of 0.88, 0.84, 0.87, 0.84, and 0.82, respectively, in the testing cohort. Radiomics features associated with the outcome of SAH patients were successfully obtained, and seven ML models were constructed. Model_SVM exhibited the best predictive performance. The radiomics model has the potential to provide guidance for SAH prognosis prediction and treatment guidance. Full article
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11 pages, 676 KiB  
Article
“Could Patient Age and Gender, along with Mass Size, Be Predictive Factors for Benign Kidney Tumors?”: A Retrospective Analysis of 307 Consecutive Single Renal Masses Treated with Partial or Radical Nephrectomy
by Raffaele Baio, Giovanni Molisso, Christian Caruana, Umberto Di Mauro, Olivier Intilla, Umberto Pane, Costantino D’Angelo, Antonio Campitelli, Francesca Pentimalli and Roberto Sanseverino
Bioengineering 2023, 10(7), 794; https://doi.org/10.3390/bioengineering10070794 - 3 Jul 2023
Cited by 1 | Viewed by 1168
Abstract
Due to the increased use of common and non-invasive abdominal imaging techniques over the last few decades, the diagnosis of about 60% of renal tumors is incidental. Contrast-enhancing renal nodules on computed tomography are diagnosed as malignant tumors, which are often removed surgically [...] Read more.
Due to the increased use of common and non-invasive abdominal imaging techniques over the last few decades, the diagnosis of about 60% of renal tumors is incidental. Contrast-enhancing renal nodules on computed tomography are diagnosed as malignant tumors, which are often removed surgically without first performing a biopsy. Most kidney nodules are renal cell carcinoma (RCC) after surgical treatment, but a non-negligible rate of these nodules may be benign on final pathology; as a result, patients undergo unnecessary surgery with an associated significant morbidity. Our study aimed to identify a subgroup of patients with higher odds of harboring benign tumors, who would hence benefit from further diagnostic examinations (such as renal biopsy) or active surveillance. We performed a retrospective review of the medical data, including pathology results, of patients undergoing surgery for solid renal masses that were suspected to be RCCs (for a total sample of 307 patients). Owing to the widespread use of common and non-invasive imaging techniques, the incidental diagnosis of kidney tumors has become increasingly common. Considering that a non-negligible rate of these tumors is found to be benign after surgery at pathological examination, it is crucial to identify features that can correctly diagnose a mass as benign or not. According to our study results, female sex and tumor size ≤ 3 cm were independent predictors of benign disease. Contrary to that demonstrated by other authors, increasing patient age was also positively linked to a greater risk of malign pathology. Full article
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16 pages, 4897 KiB  
Article
Kidney Segmentation from Dynamic Contrast-Enhanced Magnetic Resonance Imaging Integrating Deep Convolutional Neural Networks and Level Set Methods
by Moumen T. El-Melegy, Rasha M. Kamel, Mohamed Abou El-Ghar, Norah Saleh Alghamdi and Ayman El-Baz
Bioengineering 2023, 10(7), 755; https://doi.org/10.3390/bioengineering10070755 - 24 Jun 2023
Cited by 2 | Viewed by 1171
Abstract
The dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) technique has taken on a significant and increasing role in diagnostic procedures and treatments for patients who suffer from chronic kidney disease. Careful segmentation of kidneys from DCE-MRI scans is an essential early step towards the [...] Read more.
The dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) technique has taken on a significant and increasing role in diagnostic procedures and treatments for patients who suffer from chronic kidney disease. Careful segmentation of kidneys from DCE-MRI scans is an essential early step towards the evaluation of kidney function. Recently, deep convolutional neural networks have increased in popularity in medical image segmentation. To this end, in this paper, we propose a new and fully automated two-phase approach that integrates convolutional neural networks and level set methods to delimit kidneys in DCE-MRI scans. We first develop two convolutional neural networks that rely on the U-Net structure (UNT) to predict a kidney probability map for DCE-MRI scans. Then, to leverage the segmentation performance, the pixel-wise kidney probability map predicted from the deep model is exploited with the shape prior information in a level set method to guide the contour evolution towards the target kidney. Real DCE-MRI datasets of 45 subjects are used for training, validating, and testing the proposed approach. The valuation results demonstrate the high performance of the two-phase approach, achieving a Dice similarity coefficient of 0.95 ± 0.02 and intersection over union of 0.91 ± 0.03, and 1.54 ± 1.6 considering a 95% Hausdorff distance. Our intensive experiments confirm the potential and effectiveness of that approach over both UNT models and numerous recent level set-based methods. Full article
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19 pages, 4357 KiB  
Article
Radiomics for the Prediction of Pathological Complete Response to Neoadjuvant Chemoradiation in Locally Advanced Rectal Cancer: A Prospective Observational Trial
by Liming Shi, Yang Zhang, Jiamiao Hu, Weiwen Zhou, Xi Hu, Taoran Cui, Ning J. Yue, Xiaonan Sun and Ke Nie
Bioengineering 2023, 10(6), 634; https://doi.org/10.3390/bioengineering10060634 - 24 May 2023
Cited by 5 | Viewed by 1539
Abstract
(1) Background: An increasing amount of research has supported the role of radiomics for predicting pathological complete response (pCR) to neoadjuvant chemoradiation treatment (nCRT) in order to provide better management of locally advanced rectal cancer (LARC) patients. However, the lack of validation from [...] Read more.
(1) Background: An increasing amount of research has supported the role of radiomics for predicting pathological complete response (pCR) to neoadjuvant chemoradiation treatment (nCRT) in order to provide better management of locally advanced rectal cancer (LARC) patients. However, the lack of validation from prospective trials has hindered the clinical adoption of such studies. The purpose of this study is to validate a radiomics model for pCR assessment in a prospective trial to provide informative insight into radiomics validation. (2) Methods: This study involved a retrospective cohort of 147 consecutive patients for the development/validation of a radiomics model, and a prospective cohort of 77 patients from two institutions to test its generalization. The model was constructed using T2-weighted, diffusion-weighted, and dynamic contrast-enhanced MRI to understand the associations with pCR. The consistency of physicians’ evaluations and agreement on pathological complete response prediction were also evaluated, with and without the aid of the radiomics model. (3) Results: The radiomics model outperformed both physicians’ visual assessments in the prospective test cohort, with an area under the curve (AUC) of 0.84 (95% confidence interval of 0.70–0.94). With the aid of the radiomics model, a junior physician could achieve comparable performance as a senior oncologist. (4) Conclusion: We have built and validated a radiomics model with pretreatment MRI for pCR prediction of LARC patients undergoing nCRT. Full article
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16 pages, 4092 KiB  
Article
Spatial Distribution of Inhibitory Innervations of Excitatory Pyramidal Cells by Major Interneuron Subtypes in the Auditory Cortex
by Wen Zhong, Wenhong Zheng and Xuying Ji
Bioengineering 2023, 10(5), 547; https://doi.org/10.3390/bioengineering10050547 - 1 May 2023
Viewed by 2081
Abstract
Mental disorders, characterized by the National Institute of Mental Health as disruptions in neural circuitry, currently account for 13% of the global incidence of such disorders. An increasing number of studies suggest that imbalances between excitatory and inhibitory neurons in neural networks may [...] Read more.
Mental disorders, characterized by the National Institute of Mental Health as disruptions in neural circuitry, currently account for 13% of the global incidence of such disorders. An increasing number of studies suggest that imbalances between excitatory and inhibitory neurons in neural networks may be a crucial mechanism underlying mental disorders. However, the spatial distribution of inhibitory interneurons in the auditory cortex (ACx) and their relationship with excitatory pyramidal cells (PCs) remain elusive. In this study, we employed a combination of optogenetics, transgenic mice, and patch-clamp recording on brain slices to investigate the microcircuit characteristics of different interneurons (PV, SOM, and VIP) and the spatial pattern of inhibitory inhibition across layers 2/3 to 6 in the ACx. Our findings revealed that PV interneurons provide the strongest and most localized inhibition with no cross-layer innervation or layer specificity. Conversely, SOM and VIP interneurons weakly regulate PC activity over a broader range, exhibiting distinct spatial inhibitory preferences. Specifically, SOM inhibitions are preferentially found in deep infragranular layers, while VIP inhibitions predominantly occur in upper supragranular layers. PV inhibitions are evenly distributed across all layers. These results suggest that the input from inhibitory interneurons to PCs manifests in unique ways, ensuring that both strong and weak inhibitory inputs are evenly dispersed throughout the ACx, thereby maintaining a dynamic excitation–inhibition balance. Our findings contribute to understanding the spatial inhibitory characteristics of PCs and inhibitory interneurons in the ACx at the circuit level, which holds significant clinical implications for identifying and targeting abnormal circuits in auditory system diseases. Full article
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