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1.
Eur J Neurosci ; 59(11): 3074-3092, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38578844

ABSTRACT

Focal structural damage to white matter tracts can result in functional deficits in stroke patients. Traditional voxel-based lesion-symptom mapping is commonly used to localize brain structures linked to neurological deficits. Emerging evidence suggests that the impact of structural focal damage may extend beyond immediate lesion sites. In this study, we present a disconnectome mapping approach based on support vector regression (SVR) to identify brain structures and white matter pathways associated with functional deficits in stroke patients. For clinical validation, we utilized imaging data from 340 stroke patients exhibiting motor deficits. A disconnectome map was initially derived from lesions for each patient. Bootstrap sampling was then employed to balance the sample size between a minority group of patients exhibiting right or left motor deficits and those without deficits. Subsequently, SVR analysis was used to identify voxels associated with motor deficits (p < .005). Our disconnectome-based analysis significantly outperformed alternative lesion-symptom approaches in identifying major white matter pathways within the corticospinal tracts associated with upper-lower limb motor deficits. Bootstrapping significantly increased the sensitivity (80%-87%) for identifying patients with motor deficits, with a minimum lesion size of 32 and 235 mm3 for the right and left motor deficit, respectively. Overall, the lesion-based methods achieved lower sensitivities compared with those based on disconnection maps. The primary contribution of our approach lies in introducing a bootstrapped disconnectome-based mapping approach to identify lesion-derived white matter disconnections associated with functional deficits, particularly efficient in handling imbalanced data.


Subject(s)
Stroke , Humans , Stroke/diagnostic imaging , Stroke/physiopathology , Female , Male , Middle Aged , Aged , White Matter/diagnostic imaging , White Matter/pathology , Adult , Brain Mapping/methods , Brain/diagnostic imaging , Brain/pathology , Brain/physiopathology , Magnetic Resonance Imaging/methods , Pyramidal Tracts/diagnostic imaging , Pyramidal Tracts/pathology
2.
Antimicrob Agents Chemother ; 68(7): e0026524, 2024 Jul 09.
Article in English | MEDLINE | ID: mdl-38808999

ABSTRACT

In order to predict the anti-trypanosome effect of carbazole-derived compounds by quantitative structure-activity relationship, five models were established by the linear method, random forest, radial basis kernel function support vector machine, linear combination mix-kernel function support vector machine, and nonlinear combination mix-kernel function support vector machine (NLMIX-SVM). The heuristic method and optimized CatBoost were used to select two different key descriptor sets for building linear and nonlinear models, respectively. Hyperparameters in all nonlinear models were optimized by comprehensive learning particle swarm optimization with low complexity and fast convergence. Furthermore, the models' robustness and reliability underwent rigorous assessment using fivefold and leave-one-out cross-validation, y-randomization, and statistics including concordance correlation coefficient (CCC), [Formula: see text] , [Formula: see text] , and [Formula: see text] . Among all the models, the NLMIX-SVM model, which was established by support vector regression using a nonlinear combination of radial basis kernel function, sigmoid kernel function, and linear kernel function as a new kernel function, demonstrated excellent learning and generalization abilities as well as robustness: [Formula: see text] = 0.9581, mean square error (MSE) = 0.0199 for the training set and [Formula: see text] = 0.9528, MSE = 0.0174 for the test set. [Formula: see text] , [Formula: see text] , CCC, [Formula: see text] , [Formula: see text], and [Formula: see text] are 0.9539, 0.8908, 0.9752, 0.9529, 0.9528, and 0.9633, respectively. The NLMIX-SVM method proved to be a promising way in quantitative structure-activity relationship research. In addition, molecular docking experiments were conducted to analyze the properties of new derivatives, and a new potential candidate drug molecule was ultimately found. In summary, this study will provide help for the design and screening of novel anti-trypanosome drugs.


Subject(s)
Carbazoles , Quantitative Structure-Activity Relationship , Support Vector Machine , Carbazoles/pharmacology , Trypanocidal Agents/pharmacology
3.
Hum Brain Mapp ; 45(4): e26639, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38433712

ABSTRACT

Multi-target attention, that is, the ability to attend and respond to multiple visual targets presented simultaneously on the horizontal meridian across both visual fields, is essential for everyday real-world behaviour. Given the close link between the neuropsychological deficit of extinction and attentional limits in healthy subjects, investigating the anatomy that underlies extinction is uniquely capable of providing important insights concerning the anatomy critical for normal multi-target attention. Previous studies into the brain areas critical for multi-target attention and its failure in extinction patients have, however, produced heterogeneous results. In the current study, we used multivariate and Bayesian lesion analysis approaches to investigate the anatomical substrate of visual extinction in a large sample of 108 acute right hemisphere stroke patients. The use of acute stroke patient data and multivariate/Bayesian lesion analysis approaches allowed us to address limitations associated with previous studies and so obtain a more complete picture of the functional network associated with visual extinction. Our results demonstrate that the right temporo-parietal junction (TPJ) is critically associated with visual extinction. The Bayesian lesion analysis additionally implicated the right intraparietal sulcus (IPS), in line with the results of studies in neurologically healthy participants that highlighted the IPS as the area critical for multi-target attention. Our findings resolve the seemingly conflicting previous findings, and emphasise the urgent need for further research to clarify the precise cognitive role of the right TPJ in multi-target attention and its failure in extinction patients.


Subject(s)
Neuroanatomy , Stroke , Humans , Bayes Theorem , Cerebral Cortex , Stroke/diagnostic imaging , Brain/diagnostic imaging
4.
Biostatistics ; 24(2): 295-308, 2023 04 14.
Article in English | MEDLINE | ID: mdl-34494086

ABSTRACT

Support vector regression (SVR) is particularly beneficial when the outcome and predictors are nonlinearly related. However, when many covariates are available, the method's flexibility can lead to overfitting and an overall loss in predictive accuracy. To overcome this drawback, we develop a feature selection method for SVR based on a genetic algorithm that iteratively searches across potential subsets of covariates to find those that yield the best performance according to a user-defined fitness function. We evaluate the performance of our feature selection method for SVR, comparing it to alternate methods including LASSO and random forest, in a simulation study. We find that our method yields higher predictive accuracy than SVR without feature selection. Our method outperforms LASSO when the relationship between covariates and outcome is nonlinear. Random forest performs equivalently to our method in some scenarios, but more poorly when covariates are correlated. We apply our method to predict donor kidney function 1 year after transplant using data from the United Network for Organ Sharing national registry.


Subject(s)
Algorithms , Regression Analysis , Humans , Support Vector Machine
5.
Amino Acids ; 56(1): 16, 2024 Feb 15.
Article in English | MEDLINE | ID: mdl-38358574

ABSTRACT

Antimicrobial peptide (AMP) is the polypeptide, which protects the organism avoiding attack from pathogenic bacteria. Studies have shown that there were some antimicrobial peptides with molecular action mechanism involved in crossing the cell membrane without inducing severe membrane collapse, then interacting with cytoplasmic target-nucleic acid, and exerting antibacterial activity by interfacing the transmission of genetic information of pathogenic microorganisms. However, the relationship between the antibacterial activities and peptide structures was still unclear. Therefore, in the present work, a series of AMPs with a sequence of 20 amino acids was extracted from DBAASP database, then, quantitative structure-activity relationship (QSAR) methods were conducted on these peptides. In addition, novel antimicrobial peptides with  stronger antimicrobial activities were designed according to the information originated from the constructed models. Hence, the outcome of this study would lay a solid foundation for the in-silico design and exploration of novel antibacterial peptides with improved activity activities.


Subject(s)
Peptides , Quantitative Structure-Activity Relationship , Peptides/pharmacology , Antimicrobial Peptides , Amino Acids , Anti-Bacterial Agents/pharmacology
6.
Environ Sci Technol ; 58(19): 8404-8416, 2024 May 14.
Article in English | MEDLINE | ID: mdl-38698567

ABSTRACT

In densely populated urban areas, PM2.5 has a direct impact on the health and quality of residents' life. Thus, understanding the disparities of PM2.5 is crucial for ensuring urban sustainability and public health. Traditional prediction models often overlook the spillover effects within urban areas and the complexity of the data, leading to inaccurate spatial predictions of PM2.5. We propose Deep Support Vector Regression (DSVR) that models the urban areas as a graph, with grid center points as the nodes and the connections between grids as the edges. Nature and human activity features of each grid are initialized as the representation of each node. Based on the graph, DSVR uses random diffusion-based deep learning to quantify the spillover effects of PM2.5. It leverages random walk to uncover more extensive spillover relationships between nodes, thereby capturing both the local and nonlocal spillover effects of PM2.5. And then it engages in predictive learning using the feature vectors that encapsulate spillover effects, enhancing the understanding of PM2.5 disparities and connections across different regions. By applying our proposed model in the northern region of New York for predictive performance analysis, we found that DSVR consistently outperforms other models. During periods of PM2.5 surges, the R-square of DSVR reaches as high as 0.729, outperforming non-spillover models by 2.5 to 5.7 times and traditional spatial metric models by 2.2 to 4.6 times. Therefore, our proposed model holds significant importance for understanding disparities of PM2.5 air pollution in urban areas, taking the first steps toward a new method that considers both the spillover effects and nonlinear feature of data for prediction.


Subject(s)
Air Pollution , Particulate Matter , Support Vector Machine , Humans , Air Pollutants/analysis , Cities , Environmental Monitoring
7.
Cereb Cortex ; 33(5): 1941-1954, 2023 02 20.
Article in English | MEDLINE | ID: mdl-35567793

ABSTRACT

Reduced empathy and elevated alexithymia are observed in autism spectrum disorder (ASD), which has been linked to altered asymmetry in brain morphology. Here, we investigated whether trait autism, empathy, and alexithymia in the general population is associated with brain morphological asymmetry. We determined left-right asymmetry indexes for cortical thickness and cortical surface area (CSA) and applied these features to a support-vector regression model that predicted trait autism, empathy, and alexithymia. Results showed that less leftward asymmetry of CSA in the gyrus rectus (a subregion of the orbitofrontal cortex) predicted more difficulties in social functioning, as well as reduced cognitive empathy and elevated trait alexithymia. Meta-analytic decoding of the left gyrus rectus annotated functional items related to social cognition. Furthermore, the link between gyrus rectus asymmetry and social difficulties was accounted by trait alexithymia and cognitive empathy. These results suggest that gyrus rectus asymmetry could be a shared neural correlate among trait alexithymia, cognitive empathy, and social functioning in neurotypical adults. Left-right asymmetry of gyrus rectus influenced social functioning by affecting the cognitive processes of emotions in the self and others. Interventions that increase leftward asymmetry of the gyrus rectus might improve social functioning for individuals with ASD.


Subject(s)
Autism Spectrum Disorder , Empathy , Humans , Adult , Affective Symptoms/epidemiology , Affective Symptoms/psychology , Cognition , Prefrontal Cortex
8.
Environ Res ; 248: 118296, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38280525

ABSTRACT

This investigation assesses the embodied energy and carbon footprint in the manufacture of pavers using varying proportions of recycled Construction and Demolition Waste (CDW). Additionally, Thin Film Composite Polyamide fiber (TFC PA), extracted from end-of-life Reverse Osmosis (RO) membranes, is introduced as an additive to enhance the concrete's strength. Machine learning techniques, namely Artificial Neural Network (ANN), Support Vector Regression (SVR), and Response Surface Methodology (RSM), are employed to predict the mechanical properties of pavers. The study focuses on examining the energy required and embodied carbon in various mix proportions, as well as the mechanical properties-specifically compressive strength and split tensile strength of concrete with different CDW and TFC PA proportions. Findings reveal that the optimal percentage of TFC PA is 3 % for all CDW replacement proportions, resulting in low carbon content both in terms of energy and embodiment and in mechanical behavior. The implementation of ANN and SVR is conducted in MATLAB, while a Design Expert is employed to generate the experimental design for RSM. The RSM regression model demonstrates a robust correlation between variables and observed outcomes, with optimal p-values, R2 values, and f-values. The ANN model successfully captures the variability in the data. Additionally, the findings indicate a consistent superiority of the Support Vector Regression (SVR) model over both Artificial Neural Network (ANN) and Response Surface Model (RSM) models when considering diverse performance metrics such as residuals and correlation coefficients.


Subject(s)
Carbon , Construction Materials , Industrial Waste/analysis , Recycling/methods , Filtration
9.
Int J Biometeorol ; 2024 Aug 31.
Article in English | MEDLINE | ID: mdl-39215818

ABSTRACT

Crop yield prediction gains growing importance for all stakeholders in agriculture. Since the growth and development of crops are fully connected with many weather factors, it is inevitable to incorporate meteorological information into yield prediction mechanism. The changes in climate-yield relationship are more pronounced at a local level than across relatively large regions. Hence, district or sub-region-level modeling may be an appropriate approach. To obtain a location- and crop-specific model, different models with different functional forms have to be explored. This systematic review aims to discuss research papers related to statistical and machine-learning models commonly used to predict crop yield using weather factors. It was found that Artificial Neural Network (ANN) and Multiple Linear Regression were the most applied models. Support Vector Regression (SVR) model has a high success ratio as it performed well in most of the cases. The optimization options in ANN and SVR models allow us to tune models to specific patterns of association between weather conditions of a location and crop yield. ANN model can be trained using different activation functions with optimized learning rate and number of hidden layer neurons. Similarly, the SVR model can be trained with different kernel functions and various combinations of hyperparameters. Penalized regression models namely, LASSO and Elastic Net are better alternatives to simple linear regression. The nonlinear machine learning models namely, SVR and ANN were found to perform better in most of the cases which indicates there exists a nonlinear complex association between crop yield and weather factors.

10.
Sensors (Basel) ; 24(11)2024 May 24.
Article in English | MEDLINE | ID: mdl-38894185

ABSTRACT

Tool wear prediction is of great significance in industrial production. Current tool wear prediction methods mainly rely on the indirect estimation of machine learning, which focuses more on estimating the current tool wear state and lacks effective quantification of random uncertainty factors. To overcome these shortcomings, this paper proposes a novel method for predicting cutting tool wear. In the offline phase, the multiple degradation features were modeled using the Brownian motion stochastic process and a SVR model was trained for mapping the features and the tool wear values. In the online phase, the Bayesian inference was used to update the random parameters of the feature degradation model, and the future trend of the features was estimated using simulation samples. The estimation results were input into the SVR model to achieve in-advance prediction of the cutting tool wear in the form of distribution densities. An experimental tool wear dataset was used to verify the effectiveness of the proposed method. The results demonstrate that the method shows superiority in prediction accuracy and stability.

11.
Sensors (Basel) ; 24(5)2024 Feb 24.
Article in English | MEDLINE | ID: mdl-38475022

ABSTRACT

The critical challenge of estimating the Remaining Useful Life (RUL) of MoSi2 heating elements utilized in pusher kiln processes is to enhance operational efficiency and minimize downtime in industrial applications. MoSi2 heating elements are integral components in high-temperature environments, playing a pivotal role in achieving optimal thermal performance. However, prolonged exposure to extreme conditions leads to degradation, necessitating precise RUL predictions for proactive maintenance strategies. Since insufficient failure experience deals with Predictive Maintenance (PdM) in real-life scenarios, a Generative Adversarial Network (GAN) generates specific training data as failure experiences. The Remaining Useful Life (RUL) is the duration of the equipment's operation before repair or replacement, often measured in days, miles, or cycles. Machine learning models are trained using historical data encompassing various operational scenarios and degradation patterns. The RUL prediction model is determined through training, hyperparameter tuning, and comparisons based on the machine-learning model, such as Long Short-Term Memory (LSTM) or Support Vector Regression (SVR). As a result, SVR reflects the actual resistance variation, achieving the R-Square (R2) of 0.634, better than LSTM. From a safety perspective, SVR offers high prediction accuracy and sufficient time to schedule maintenance plans.

12.
Sensors (Basel) ; 24(7)2024 Apr 07.
Article in English | MEDLINE | ID: mdl-38610560

ABSTRACT

Dynamic wireless charging (DWC) has emerged as a viable approach to mitigate range anxiety by ensuring continuous and uninterrupted charging for electric vehicles in motion. DWC systems rely on the length of the transmitter, which can be categorized into long-track transmitters and segmented coil arrays. The segmented coil array, favored for its heightened efficiency and reduced electromagnetic interference, stands out as the preferred option. However, in such DWC systems, the need arises to detect the vehicle's position, specifically to activate the transmitter coils aligned with the receiver pad and de-energize uncoupled transmitter coils. This paper introduces various machine learning algorithms for precise vehicle position determination, accommodating diverse ground clearances of electric vehicles and various speeds. Through testing eight different machine learning algorithms and comparing the results, the random forest algorithm emerged as superior, displaying the lowest error in predicting the actual position.

13.
Int J Mol Sci ; 25(10)2024 May 12.
Article in English | MEDLINE | ID: mdl-38791306

ABSTRACT

Computational drug-repositioning technology is an effective tool for speeding up drug development. As biological data resources continue to grow, it becomes more important to find effective methods to identify potential therapeutic drugs for diseases. The effective use of valuable data has become a more rational and efficient approach to drug repositioning. The disease-drug correlation method (DDCM) proposed in this study is a novel approach that integrates data from multiple sources and different levels to predict potential treatments for diseases, utilizing support-vector regression (SVR). The DDCM approach resulted in potential therapeutic drugs for neoplasms and cardiovascular diseases by constructing a correlation hybrid matrix containing the respective similarities of drugs and diseases, implementing the SVR algorithm to predict the correlation scores, and undergoing a randomized perturbation and stepwise screening pipeline. Some potential therapeutic drugs were predicted by this approach. The potential therapeutic ability of these drugs has been well-validated in terms of the literature, function, drug target, and survival-essential genes. The method's feasibility was confirmed by comparing the predicted results with the classical method and conducting a co-drug analysis of the sub-branch. Our method challenges the conventional approach to studying disease-drug correlations and presents a fresh perspective for understanding the pathogenesis of diseases.


Subject(s)
Algorithms , Drug Repositioning , Drug Repositioning/methods , Humans , Support Vector Machine , Computational Biology/methods , Neoplasms/drug therapy , Cardiovascular Diseases/drug therapy
14.
J Environ Manage ; 354: 120349, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38401497

ABSTRACT

Flow obstructed by bridge piers can increase sediment transport leading to local scour. This local scour poses a risk to the stability of bridge structures, which could lead to structural failures. There are two main approaches for evaluating the scour depth (ds) of bridge piers. The first is based on understanding hydraulic phenomena and developing relationships with properties affecting scour. The second uses data-driven soft computing models that lack physical interpretations but rely on algorithms to predict outcomes. Methods are chosen by researchers based on their goals and resources. This study aims to create innovative ensemble frameworks comprising support vector machine for regression (SVMR), random forest regression (RFR), and reduced error pruning tree (REPTree) as base learners, alongside bagging regression tree (BRT) and stochastic gradient boosting (SGB) as meta learners. These ensembles were developed to analyse maximum scour depths (dsm) in clear water conditions, utilizing 35 literature's experimental data published in last 63 years. The performance of each machine learning (ML) approach was assessed using statistical performance indicators. The proposed model was also compared with top six empirical equations with strong predictive ability. Results show that among these empirical equations, the equation from Nandi and Das (2023) performs best. Performance evaluation considering training, testing, and the entire dataset, SGB (REPTree), BRT(SVMR-PUK), and SGB (REPTree) exhibited the highest performance, securing the top rank among all ML models and empirical equations. Sensitivity analysis identified sediment gradation and flow intensity as the most influential variables for predicting dsm during both training and testing phases, respectively.


Subject(s)
Metadata , Water , Algorithms , Machine Learning
15.
Environ Geochem Health ; 46(2): 31, 2024 Jan 16.
Article in English | MEDLINE | ID: mdl-38227052

ABSTRACT

Laboratory determination of trihalomethanes (THMs) is a very time-consuming task. Therefore, establishing a THMs model using easily obtainable water quality parameters would be very helpful. This study explored the modeling methods of the random forest regression (RFR) model, support vector regression (SVR) model, and Log-linear regression model to predict the concentration of total-trihalomethanes (T-THMs), bromodichloromethane (BDCM), and dibromochloromethane (DBCM), using nine water quality parameters as input variables. The models were developed and tested using a dataset of 175 samples collected from a water treatment plant. The results showed that the RFR model, with the optimal parameter combination, outperformed the Log-linear regression model in predicting the concentration of T-THMs (N25 = 82-88%, rp = 0.70-0.80), while the SVR model performed slightly better than the RFR model in predicting the concentration of BDCM (N25 = 85-98%, rp = 0.70-0.97). The RFR model exhibited superior performance compared to the other two models in predicting the concentration of T-THMs and DBCM. The study concludes that the RFR model is superior overall to the SVR model and Log-linear regression models and could be used to monitor THMs concentration in water supply systems.


Subject(s)
Water Quality , Water Supply , Linear Models , Machine Learning , Trihalomethanes
16.
J Xray Sci Technol ; 32(4): 1185-1197, 2024.
Article in English | MEDLINE | ID: mdl-38607729

ABSTRACT

PURPOSE: This study aims to propose and develop a fast, accurate, and robust prediction method of patient-specific organ doses from CT examinations using minimized computational resources. MATERIALS AND METHODS: We randomly selected the image data of 723 patients who underwent thoracic CT examinations. We performed auto-segmentation based on the selected data to generate the regions of interest (ROIs) of thoracic organs using the DeepViewer software. For each patient, radiomics features of the thoracic ROIs were extracted via the Pyradiomics package. The support vector regression (SVR) model was trained based on the radiomics features and reference organ dose obtained by Monte Carlo (MC) simulation. The root mean squared error (RMSE), mean absolute percentage error (MAPE), and coefficient of determination (R-squared) were evaluated. The robustness was verified by randomly assigning patients to the train and test sets of data and comparing regression metrics of different patient assignments. RESULTS: For the right lung, left lung, lungs, esophagus, heart, and trachea, results showed that the trained SVR model achieved the RMSEs of 2 mGy to 2.8 mGy on the test sets, 1.5 mGy to 2.5 mGy on the train sets. The calculated MAPE ranged from 0.1 to 0.18 on the test sets, and 0.08 to 0.15 on the train sets. The calculated R-squared was 0.75 to 0.89 on test sets. CONCLUSIONS: By combined utilization of the SVR algorithm and thoracic radiomics features, patient-specific thoracic organ doses could be predicted accurately, fast, and robustly in one second even using one single CPU core.


Subject(s)
Algorithms , Radiation Dosage , Support Vector Machine , Tomography, X-Ray Computed , Humans , Tomography, X-Ray Computed/methods , Male , Female , Lung/diagnostic imaging , Monte Carlo Method , Radiography, Thoracic/methods , Middle Aged , Adult , Aged
17.
Hum Brain Mapp ; 44(6): 2266-2278, 2023 04 15.
Article in English | MEDLINE | ID: mdl-36661231

ABSTRACT

Studies in patients with brain lesions play a fundamental role in unraveling the brain's functional anatomy. Lesion-symptom mapping (LSM) techniques can relate lesion location to cognitive performance. However, a limitation of current LSM approaches is that they can only evaluate one cognitive outcome at a time, without considering interdependencies between different cognitive tests. To overcome this challenge, we implemented canonical correlation analysis (CCA) as combined multivariable and multioutcome LSM approach. We performed a proof-of-concept study on 1075 patients with acute ischemic stroke to explore whether addition of CCA to a multivariable single-outcome LSM approach (support vector regression) could identify infarct locations associated with deficits in three well-defined verbal memory functions (encoding, consolidation, retrieval) based on four verbal memory subscores derived from the Seoul Verbal Learning Test (immediate recall, delayed recall, recognition, learning ability). We evaluated whether CCA could extract cognitive score patterns that matched prior knowledge of these verbal memory functions, and if these patterns could be linked to more specific infarct locations than through single-outcome LSM alone. Two of the canonical modes identified with CCA showed distinct cognitive patterns that matched prior knowledge on encoding and consolidation. In addition, CCA revealed that each canonical mode was linked to a distinct infarct pattern, while with multivariable single-outcome LSM individual verbal memory subscores were associated with largely overlapping patterns. In conclusion, our findings demonstrate that CCA can complement single-outcome LSM techniques to help disentangle cognitive functions and their neuroanatomical correlates.


Subject(s)
Cognition Disorders , Ischemic Stroke , Stroke , Humans , Stroke/complications , Stroke/diagnostic imaging , Stroke/pathology , Ischemic Stroke/complications , Cognition Disorders/complications , Cognition , Infarction/complications , Neuropsychological Tests , Brain Mapping/methods
18.
Brief Bioinform ; 22(6)2021 11 05.
Article in English | MEDLINE | ID: mdl-33963831

ABSTRACT

Nowadays, advances in high-throughput sequencing benefit the increasing application of genomic prediction (GP) in breeding programs. In this research, we designed a Cosine kernel-based KRR named KCRR to perform GP. This paper assessed the prediction accuracies of 12 traits with various heritability and genetic architectures from four populations using the genomic best linear unbiased prediction (GBLUP), BayesB, support vector regression (SVR), and KCRR. On the whole, KCRR performed stably for all traits of multiple species, indicating that the hypothesis of KCRR had the potential to be adapted to a wide range of genetic architectures. Moreover, we defined a modified genomic similarity matrix named Cosine similarity matrix (CS matrix). The results indicated that the accuracies between GBLUP_kinship and GBLUP_CS almost unanimously for all traits, but the computing efficiency has increased by an average of 20 times. Our research will be a significant promising strategy in future GP.


Subject(s)
Genomics , Genotype , Models, Genetic
19.
Int J Neuropsychopharmacol ; 26(3): 207-216, 2023 03 22.
Article in English | MEDLINE | ID: mdl-36545813

ABSTRACT

BACKGROUND: Brain age is a popular brain-based biomarker that offers a powerful strategy for using neuroscience in clinical practice. We investigated the brain-predicted age difference (PAD) in patients with schizophrenia (SCZ), first-episode schizophrenia spectrum disorders (FE-SSDs), and treatment-resistant schizophrenia (TRS) using structural magnetic resonance imaging data. The association between brain-PAD and clinical parameters was also assessed. METHODS: We developed brain age prediction models for the association between 77 average structural brain measures and age in a training sample of controls (HCs) using ridge regression, support vector regression, and relevance vector regression. The trained models in the controls were applied to the test samples of the controls and 3 patient groups to obtain brain-based age estimates. The correlations were tested between the brain PAD and clinical measures in the patient groups. RESULTS: Model performance indicated that, regardless of the type of regression metric, the best model was support vector regression and the worst model was relevance vector regression for the training HCs. Accelerated brain aging was identified in patients with SCZ, FE-SSDs, and TRS compared with the HCs. A significant difference in brain PAD was observed between FE-SSDs and TRS using the ridge regression algorithm. Symptom severity, the Social and Occupational Functioning Assessment Scale, chlorpromazine equivalents, and cognitive function were correlated with the brain PAD in the patient groups. CONCLUSIONS: These findings suggest additional progressive neuronal changes in the brain after SCZ onset. Therefore, pharmacological or psychosocial interventions targeting brain health should be developed and provided during the early course of SCZ.


Subject(s)
Schizophrenia , Humans , Schizophrenia/diagnostic imaging , Schizophrenia/drug therapy , Schizophrenia, Treatment-Resistant , Brain , Aging/physiology , Magnetic Resonance Imaging/methods
20.
Cereb Cortex ; 32(8): 1593-1607, 2022 04 05.
Article in English | MEDLINE | ID: mdl-34541601

ABSTRACT

Temporal correlation analysis of spontaneous brain activity (e.g., Pearson "functional connectivity," FC) has provided insights into the functional organization of the human brain. However, bivariate analysis techniques such as this are often susceptible to confounding physiological processes (e.g., sleep, Mayer-waves, breathing, motion), which makes it difficult to accurately map connectivity in health and disease as these physiological processes affect FC. In contrast, a multivariate approach to imputing individual neural networks from spontaneous neuroimaging data could be influential to our conceptual understanding of FC and provide performance advantages. Therefore, we analyzed neural calcium imaging data from Thy1-GCaMP6f mice while either awake, asleep, anesthetized, during low and high bouts of motion, or before and after photothrombotic stroke. A linear support vector regression approach was used to determine the optimal weights for integrating the signals from the remaining pixels to accurately predict neural activity in a region of interest (ROI). The resultant weight maps for each ROI were interpreted as multivariate functional connectivity (MFC), resembled anatomical connectivity, and demonstrated a sparser set of strong focused positive connections than traditional FC. While global variations in data have large effects on standard correlation FC analysis, the MFC mapping methods were mostly impervious. Lastly, MFC analysis provided a more powerful connectivity deficit detection following stroke compared to traditional FC.


Subject(s)
Brain Mapping , Stroke , Animals , Brain/diagnostic imaging , Brain/physiology , Brain Mapping/methods , Magnetic Resonance Imaging/methods , Mice , Neural Pathways/diagnostic imaging , Neural Pathways/physiology , Stroke/diagnostic imaging , Wakefulness
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