Cathelicidin AS-12W Derived from the Alligator sinensis and Its Antimicrobial Activity Against Drug-Resistant Gram-Negative Bacteria In Vitro and In Vivo.

Antimicrobial peptides (AMPs) have the potential to treat multidrug-resistant bacterial infections. Cathelicidins are a class of cationic antimicrobial peptides that are found in nearly all vertebrates. Herein, we determined the mature peptide region of Alligator sinensis cathelicidin by comparing its cathelicidin peptide sequence with those of other reptiles and designed nine peptide mutants based on the Alligator sinensis cathelicidin mature peptide. According to the antibacterial activity and cytotoxicity screening, the peptide AS-12W demonstrated broad-spectrum antibacterial activity and exhibited low erythrocyte hemolytic activity. In particular, AS-12W exhibited strong antibacterial activity and rapid bactericidal activity against carbapenem-resistant Pseudomonas aeruginosa in vitro. Additionally, AS-12W effectively removed carbapenem-resistant P. aeruginosa from blood and organs in vivo, leading to improved survival rates in septic mice. Furthermore, AS-12W exhibited good stability and tolerance to harsh conditions such as high heat, high salt, strong acid, and strong alkali, and it also displayed high stability toward trypsin and simulated gastric fluid (SGF). Moreover, AS-12W showed significant anti-inflammatory effects in vitro by inhibiting the production of proinflammatory factors induced by lipopolysaccharide (LPS). Due to its antibacterial mechanism against Escherichia coli, we found that this peptide could neutralize the negative charge on the surface of the bacteria and disrupt the integrity of the bacterial cell membrane. In addition, AS-12W has the ability to bind to the genomic DNA of bacteria and stimulate the production of reactive oxygen species (ROS) within bacteria, which is believed to be the reason for the good antibacterial activity of AS-12W. These results demonstrated that AS-12W exhibits remarkable antibacterial activity, particularly against carbapenem-resistant P. aeruginosa. Therefore, it is a potential candidate for antibacterial drug development.

Efficient Generation of Pretraining Samples for Developing a Deep Learning Brain Injury Model via Transfer Learning.

The large amount of training samples required to develop a deep learning brain injury model demands enormous computational resources. Here, we study how a transformer neural network (TNN) of high accuracy can be used to efficiently generate pretraining samples for a convolutional neural network (CNN) brain injury model to reduce computational cost. The samples use synthetic impacts emulating real-world events or augmented impacts generated from limited measured impacts. First, we verify that the TNN remains highly accurate for the two impact types (N = 100 each; [Formula: see text] of 0.948-0.967 with root mean squared error, RMSE, ~ 0.01, for voxelized peak strains). The TNN-estimated samples (1000-5000 for each data type) are then used to pretrain a CNN, which is further finetuned using directly simulated training samples (250-5000). An independent measured impact dataset considered of complete capture of impact event is used to assess estimation accuracy (N = 191). We find that pretraining can significantly improve CNN accuracy via transfer learning compared to a baseline CNN without pretraining. It is most effective when the finetuning dataset is relatively small (e.g., 2000-4000 pretraining synthetic or augmented samples improves success rate from 0.72 to 0.81 with 500 finetuning samples). When finetuning samples reach 3000 or more, no obvious improvement occurs from pretraining. These results support using the TNN to rapidly generate pretraining samples to facilitate a more efficient training strategy for future deep learning brain models, by limiting the number of costly direct simulations from an alternative baseline model. This study could contribute to a wider adoption of deep learning brain injury models for large-scale predictive modeling and ultimately, enhancing safety protocols and protective equipment.

A Morphologically Individualized Deep Learning Brain Injury Model.

The brain injury modeling community has recommended improving model subject specificity and simulation efficiency. Here, we extend an instantaneous (< 1 sec) convolutional neural network (CNN) brain model based on the anisotropic Worcester Head Injury Model (WHIM) V1.0 to account for strain differences due to individual morphological variations. Linear scaling factors relative to the generic WHIM along the three anatomical axes are used as additional CNN inputs. To generate training samples, the WHIM is randomly scaled to pair with augmented head impacts randomly generated from real-world data for simulation. An estimation of voxelized peak maximum principal strain of the whole-brain is said to be successful when the linear regression slope and Pearson's correlation coefficient relative to directly simulated do not deviate from 1.0 (when identical) by more than 0.1. Despite a modest training dataset (N = 1363 vs. ∼5.7 k previously), the individualized CNN achieves a success rate of 86.2% in cross-validation for scaled model responses, and 92.1% for independent generic model testing for impacts considered as complete capture of kinematic events. Using 11 scaled subject-specific models (with scaling factors determined from pre-established regression models based on head dimensions and sex and age information, and notably, without neuroimages), the morphologically individualized CNN remains accurate for impacts that also yield successful estimations for the generic WHIM. The individualized CNN instantly estimates subject-specific and spatially detailed peak strains of the entire brain and thus, supersedes others that report a scalar peak strain value incapable of informing the location of occurrence. This tool could be especially useful for youths and females due to their anticipated greater morphological differences relative to the generic model, even without the need for individual neuroimages. It has potential for a wide range of applications for injury mitigation purposes and the design of head protective gears. The voxelized strains also allow for convenient data sharing and promote collaboration among research groups.

Approximating subject-specific brain injury models via scaling based on head-brain morphological relationships.

Most human head/brain models represent a generic adult male head/brain. They may suffer in accuracy when investigating traumatic brain injury (TBI) on a subject-specific basis. Subject-specific models can be developed from neuroimages; however, neuroimages are not typically available in practice. In this study, we establish simple and elegant regression models between brain outer surface morphology and head dimensions measured from neuroimages along with age and sex information (N = 191; 141 males and 50 females with age ranging 14-25 years). The regression models are then used to approximate subject-specific brain models by scaling a generic counterpart, without using neuroimages. Model geometrical accuracy is assessed using adjusted [Formula: see text] and absolute percentage error (e.g., 0.720 and 3.09 ± 2.38%, respectively, for brain volume when incorporating tragion-to-top). For a subset of 11 subjects (from smallest to largest in brain volume), impact-induced brain strains are compared with those from "morphed models" derived from neuroimage-based mesh warping. We find that regional peak strains from the scaled subject-specific models are comparable to those of the morphed counterparts but could be considerably different from those of the generic model (e.g., linear regression slope of 1.01-1.03 for gray and white matter regions versus 1.16-1.19, or up to ~ 20% overestimation for the smallest brain studied). These results highlight the importance of incorporating brain morphological variations in impact simulation and demonstrate the feasibility of approximating subject-specific brain models without neuroimages using age, sex, and easily measurable head dimensions. The scaled models may improve subject specificity for future TBI investigations.

Real-time dynamic simulation for highly accurate spatiotemporal brain deformation from impact.

Real-time dynamic simulation remains a significant challenge for spatiotemporal data of high dimension and resolution. In this study, we establish a transformer neural network (TNN) originally developed for natural language processing and a separate convolutional neural network (CNN) to estimate five-dimensional (5D) spatiotemporal brain-skull relative displacement resulting from impact (isotropic spatial resolution of 4 mm with temporal resolution of 1 ms). Sequential training is applied to train (N = 5184 samples) the two neural networks for estimating the complete 5D displacement across a temporal duration of 60 ms. We find that TNN slightly but consistently outperforms CNN in accuracy for both displacement and the resulting voxel-wise four-dimensional (4D) maximum principal strain (e.g., root mean squared error (RMSE) of ~1.0% vs. ~1.6%, with coefficient of determination, R 2 >0.99 vs. >0.98, respectively, and normalized RMSE (NRMSE) at peak displacement of 2%-3%, based on an independent testing dataset; N = 314). Their accuracies are similar for a range of real-world impacts drawn from various published sources (dummy, helmet, football, soccer, and car crash; average RMSE/NRMSE of ~0.3 mm/~4%-5% and average R 2 of ~0.98 at peak displacement). Sequential training is effective for allowing instantaneous estimation of 5D displacement with high accuracy, although TNN poses a heavier computational burden in training. This work enables efficient characterization of the intrinsically dynamic brain strain in impact critical for downstream multiscale axonal injury model simulation. This is also the first application of TNN in biomechanics, which offers important insight into how real-time dynamic simulations can be achieved across diverse engineering fields.

Effective Head Impact Kinematics to Preserve Brain Strain.

Conventional kinematics-based brain injury metrics often approximate peak maximum principal strain (MPS) of the whole brain but ignore the anatomical location of occurrence. In this study, we develop effective impact kinematics consisting of peak rotational velocity and the associated rotational axis to preserve not only peak MPS but also spatially detailed MPS. A pre-computed brain response atlas (pcBRA) serves as a common reference. A training dataset (N = 3069) is used to develop a convolutional neural network (CNN) to automate impact simplification. When preserving peak MPS alone, the CNN-estimated effective peak rotational velocity achieves a coefficient of determination ([Formula: see text]) of ~ 0.96 relative to the directly identified counterpart, far outperforming nominal peak velocity from the resultant profiles ([Formula: see text] of ~ 0.34). Impacts from a subset of data (N = 1900) are also successfully matched with pcBRA idealized impacts based on elementwise MPS, where their regression slope and Pearson correlation coefficient do not deviate from 1.0 (when identical) by more than 0.1. The CNN-estimated effective peak rotation velocity and rotational axis are sufficiently accurate for ~ 73.5% of the impacts. This is not possible for the nominal peak velocity or any other conventional injury metric. The performance may be further improved by expanding the pcBRA to include deceleration and focusing on region-wise strains. This study establishes a new avenue to reduce an arbitrary head impact into an idealized but actual "impact mode" characterized by triplets of basic kinematic variables. They retain specific physical interpretations of head impact and may be an advancement over state-of-the-art kinematics-based scalar metrics for more effective impact comparison in the future.

A level-wise spine registration framework to account for large pose changes.

PURPOSES: Accurate and efficient spine registration is crucial to success of spine image guidance. However, changes in spine pose cause intervertebral motion that can lead to significant registration errors. In this study, we develop a geometrical rectification technique via nonlinear principal component analysis (NLPCA) to achieve level-wise vertebral registration that is robust to large changes in spine pose. METHODS: We used explanted porcine spines and live pigs to develop and test our technique. Each sample was scanned with preoperative CT (pCT) in an initial pose and rescanned with intraoperative stereovision (iSV) in a different surgical posture. Patient registration rectified arbitrary spinal postures in pCT and iSV into a common, neutral pose through a parameterized moving-frame approach. Topologically encoded depth projection 2D images were then generated to establish invertible point-to-pixel correspondences. Level-wise point correspondences between pCT and iSV vertebral surfaces were generated via 2D image registration. Finally, closed-form vertebral level-wise rigid registration was obtained by directly mapping 3D surface point pairs. Implanted mini-screws were used as fiducial markers to measure registration accuracy. RESULTS: In seven explanted porcine spines and two live animal surgeries (maximum in-spine pose change of 87.5 mm and 32.7 degrees averaged from all spines), average target registration errors (TRE) of 1.70 ± 0.15 mm and 1.85 ± 0.16 mm were achieved, respectively. The automated spine rectification took 3-5 min, followed by an additional 30 secs for depth image projection and level-wise registration. CONCLUSIONS: Accuracy and efficiency of the proposed level-wise spine registration support its application in human open spine surgeries. The registration framework, itself, may also be applicable to other intraoperative imaging modalities such as ultrasound and MRI, which may expand utility of the approach in spine registration in general.

Instantaneous Brain Strain Estimation for Automotive Head Impacts via Deep Learning.

Efficient brain strain estimation is critical for routine application of a head injury model. Lately, a convolutional neural network (CNN) has been successfully developed to estimate spatially detailed brain strains instantly and accurately in contact sports. Here, we extend its application to automotive head impacts, where impact profiles are typically more complex with longer durations. Head impact kinematics (N=458) from two public databases were used to generate augmented impacts (N=2694). They were simulated using the anisotropic Worcester Head Injury Model (WHIM) V1.0, which provided baseline elementwise peak maximum principal strain (MPS). For each augmented impact, rotational velocity (vrot) and the corresponding rotational acceleration (arot) profiles were concatenated as static images to serve as CNN input. Three training strategies were evaluated: 1) "baseline", using random initial weights; 2) "transfer learning", using weight transfer from a previous CNN model trained on head impacts drawn from contact sports; and 3) "combined training", combining previous training data from contact sports (N=5661) for training. The combined training achieved the best performances. For peak MPS, the CNN achieved a coefficient of determination (R2) of 0.932 and root mean squared error (RMSE) of 0.031 for the real-world testing dataset. It also achieved a success rate of 60.5% and 94.8% for elementwise MPS, where the linear regression slope, k, and correlation coefficient, r, between estimated and simulated MPS did not deviate from 1.0 (when identical) by more than 0.1 and 0.2, respectively. Cumulative strain damage measure (CSDM) from the CNN estimation was also highly accurate compared to those from direct simulation across a range of thresholds (R2 of 0.899-0.943 with RMSE of 0.054-0.069). Finally, the CNN achieved an average k and r of 0.98±0.12 and 0.90±0.07, respectively, for six reconstructed car crash impacts drawn from two other sources independent of the training dataset. Importantly, the CNN is able to efficiently estimate elementwise MPS with sufficient accuracy while conventional kinematic injury metrics cannot. Therefore, the CNN has the potential to supersede current kinematic injury metrics that can only approximate a global peak MPS or CSDM. The CNN technique developed here may offer enhanced utility in the design and development of head protective countermeasures, including in the automotive industry. This is the first study aimed at instantly estimating spatially detailed brain strains for automotive head impacts, which employs >8.8 thousand impact simulations generated from ~1.5 years of nonstop computations on a high-performance computing platform.

Instantaneous Whole-Brain Strain Estimation in Dynamic Head Impact.

Head injury models are notoriously time consuming and resource demanding in simulations, which prevents routine application. Here, we extend a convolutional neural network (CNN) to instantly estimate element-wise distribution of peak maximum principal strain (MPS) of the entire brain (>36 k speedup accomplished on a low-end computing platform). To achieve this, head impact rotational velocity and acceleration temporal profiles are combined into two-dimensional images to serve as CNN input for training and prediction of MPS. Compared with the directly simulated counterparts, the CNN-estimated responses (magnitude and distribution) are sufficiently accurate for 92.1% of the cases via 10-fold cross-validation using impacts drawn from the real world (n = 5661; range of peak rotational velocity in augmented data extended to 2-40 rad/sec). The success rate further improves to 97.1% for "in-range" impacts (n = 4298). When using the same CNN architecture to train (n = 3064) and test on an independent, reconstructed National Football League (NFL) impact dataset (n = 53; 20 concussions and 33 non-injuries), 51 out of 53, or 96.2% of the cases, are sufficiently accurate. The estimated responses also achieve virtually identical concussion prediction performances relative to the directly simulated counterparts, and they often outperform peak MPS of the whole brain (e.g., accuracy of 0.83 vs. 0.77 via leave-one-out cross-validation). These findings support the use of CNN for accurate and efficient estimation of spatially detailed brain strains across the vast majority of head impacts in contact sports. Our technique may hold the potential to transform traumatic brain injury (TBI) research and the design and testing standards of head protective gears by facilitating the transition from acceleration-based approximation to strain-based design and analysis. This would have broad implications in the TBI biomechanics field to accelerate new scientific discoveries. The pre-trained CNN is freely available online at https://github.com/Jilab-biomechanics/CNN-brain-strains.

A network-based response feature matrix as a brain injury metric.

Conventional brain injury metrics are scalars that treat the whole head/brain as a single unit but do not characterize the distribution of brain responses. Here, we establish a network-based "response feature matrix" to characterize the magnitude and distribution of impact-induced brain strains. The network nodes and edges encode injury risks to the gray matter regions and their white matter interconnections, respectively. The utility of the metric is illustrated in injury prediction using three independent, real-world datasets: two reconstructed impact datasets from the National Football League (NFL) and Virginia Tech, respectively, and measured concussive and non-injury impacts from Stanford University. Injury predictions with leave-one-out cross-validation are conducted using the two reconstructed datasets separately, and then by combining all datasets into one. Using support vector machine, the network-based injury predictor consistently outperforms four baseline scalar metrics including peak maximum principal strain of the whole brain (MPS), peak linear/rotational acceleration, and peak rotational velocity across all five selected performance measures (e.g., maximized accuracy of 0.887 vs. 0.774 and 0.849 for MPS and rotational acceleration with corresponding positive predictive values of 0.938, 0.772, and 0.800, respectively, using the reconstructed NFL dataset). With sufficient training data, real-world injury prediction is similar to leave-one-out in-sample evaluation, suggesting the potential advantage of the network-based injury metric over conventional scalar metrics. The network-based response feature matrix significantly extends scalar metrics by sampling the brain strains more completely, which may serve as a useful framework potentially allowing for other applications such as characterizing injury patterns or facilitating targeted multi-scale modeling in the future.

Convolutional neural network for efficient estimation of regional brain strains.

Head injury models are important tools to study concussion biomechanics but are impractical for real-world use because they are too slow. Here, we develop a convolutional neural network (CNN) to estimate regional brain strains instantly and accurately by conceptualizing head rotational velocity profiles as two-dimensional images for input. We use two impact datasets with augmentation to investigate the CNN prediction performances with a variety of training-testing configurations. Three strain measures are considered, including maximum principal strain (MPS) of the whole brain, MPS of the corpus callosum, and fiber strain of the corpus callosum. The CNN is further tested using an independent impact dataset (N = 314) measured in American football. Based on 2592 training samples, it achieves a testing R2 of 0.916 and root mean squared error (RMSE) of 0.014 for MPS of the whole brain. Combining all impact-strain response data available (N = 3069), the CNN achieves an R2 of 0.966 and RMSE of 0.013 in a 10-fold cross-validation. This technique may enable a clinical diagnostic capability to a sophisticated head injury model, such as facilitating head impact sensors in concussion detection via a mobile device. In addition, it may transform current acceleration-based injury studies into focusing on regional brain strains. The trained CNN is publicly available along with associated code and examples at https://github.com/Jilab-biomechanics/CNN-brain-strains. They will be updated as needed in the future.

Concussion classification via deep learning using whole-brain white matter fiber strains.

Developing an accurate and reliable injury predictor is central to the biomechanical studies of traumatic brain injury. State-of-the-art efforts continue to rely on empirical, scalar metrics based on kinematics or model-estimated tissue responses explicitly pre-defined in a specific brain region of interest. They could suffer from loss of information. A single training dataset has also been used to evaluate performance but without cross-validation. In this study, we developed a deep learning approach for concussion classification using implicit features of the entire voxel-wise white matter fiber strains. Using reconstructed American National Football League (NFL) injury cases, leave-one-out cross-validation was employed to objectively compare injury prediction performances against two baseline machine learning classifiers (support vector machine (SVM) and random forest (RF)) and four scalar metrics via univariate logistic regression (Brain Injury Criterion (BrIC), cumulative strain damage measure of the whole brain (CSDM-WB) and the corpus callosum (CSDM-CC), and peak fiber strain in the CC). Feature-based machine learning classifiers including deep learning, SVM, and RF consistently outperformed all scalar injury metrics across all performance categories (e.g., leave-one-out accuracy of 0.828-0.862 vs. 0.690-0.776, and .632+ error of 0.148-0.176 vs. 0.207-0.292). Further, deep learning achieved the best cross-validation accuracy, sensitivity, AUC, and .632+ error. These findings demonstrate the superior performances of deep learning in concussion prediction and suggest its promise for future applications in biomechanical investigations of traumatic brain injury.