Leave-one-out Cross-validation Research Articles

Coomans plot classification of lard in the ink blends and ink extracts from printed packaging films using lard Fourier transform infrared spectral profile and multivariate analysis

Lard in blends of commercial gravure ink (ranging from 0.5 to 20%) and ink extracts from eleven commercially printed packaging films for foodstuffs was characterized using Fourier transform infrared (FTIR) spectroscopy. The FTIR spectral bands at 4000 ‒ 650 cm-1 associated with the lard fingerprint were acquired and used to classify the lard and its blends using partial least squares (PLS) regression and discriminant analysis (DA). Commercial gravure inks (also used for preparing calibration curve samples), blends of lard ranging from 0.5 to 20% in gravure inks, and commercially printed food packaging films were tested. Linear correlation of predicted and actual values of lard were determined using PLS calibration and validation models. They produced a high coefficient of determination (R2 ) of 0.943, a low root mean square error of calibration (RMSEC) of 1.674, as well as a high R2 = 0.999 and a low root mean square error of prediction (RMSEP) of 1.233, respectively. The PLS calibration was verified employing a leave-oneout cross-validation, while DA was used to classify a series of lard standard, lard-added ink, and commercial food packaging films. The Coomans plot classification of the lardadded ink and commercial food packaging films illustrated that the food packaging samples were plotted in the right and left hemispheres in the lard-added ink class. This result also demonstrated that FTIR coupled with chemometric PLS predicted the lard content in the printing inks with high overall accuracy, as indicated by a low mean difference (MD) value of 0.577 and a low standard deviation of difference (SDD) value of 0.599. The DA allowed the ink packaging samples that potentially contained lard to be distinguished from those without lard. Sample 7 (commercially printed food packaging ink) exhibits the highest possibility of containing lard.

PreDBP-PLMs: Prediction of DNA-binding proteins based on pre-trained protein language models and convolutional neural networks

The recognition of DNA-binding proteins (DBPs) is the crucial step to understanding their roles in various biological processes such as genetic regulation, gene expression, cell cycle control, DNA repair, and replication within cells. However, conventional experimental methods for identifying DBPs are usually time-consuming and expensive. Therefore, there is an urgent need to develop rapid and efficient computational methods for the prediction of DBPs. In this study, we proposed a novel predictor named PreDBP-PLMs to further improve the identification accuracy of DBPs by fusing the pre-trained protein language model (PLM) ProtT5 embedding with evolutionary features as input to the classic convolutional neural network (CNN) model. Firstly, the ProtT5 embedding was combined with different evolutionary features derived from the position-specific scoring matrix (PSSM) to represent protein sequences. Then, the optimal feature combination was selected and input to the CNN classifier for the prediction of DBPs. Finally, the 5-fold cross-validation (CV), the leave-one-out CV (LOOCV), and the independent set test were adopted to examine the performance of PreDBP-PLMs on the benchmark datasets. Compared to the existing state-of-the-art predictors, PreDBP-PLMs exhibits an accuracy improvement of 0.5% and 5.2% on the PDB186 and PDB2272 datasets, respectively. It demonstrated that the proposed method could serve as a useful tool for the recognition of DBPs.

Rapid quantitative analysis of multiple rare earth elements in NdFeB alloys based on laser-induced breakdown spectroscopy (LIBS) and random forest (RF)

NdFeB material has excellent comprehensive magnetic properties, which plays a crucial role in the field of rare earth magnetic materials, and is one of the important basic materials to support modern high-tech industries. In the production of NdFeB alloys, the control of rare earth elements (REEs) is directly related to the quality and resource utilization efficiency of NdFeB materials. Therefore, the prediction of REEs content in NdFeB alloys is of great research significance and application value for the quality control of products, the enhancement of production efficiency and reduction of energy consumption by the rare earth material industry. In this study, a combination of laser-induced breakdown spectroscopy (LIBS) and random forest (RF) was used to investigate the quantitative analysis of four REEs (Nd, Pr, Tb and Dy) in NdFeB alloys. Firstly, the original LIBS spectra were screened by principal component analysis-mahalanobis distance (PCA-MD). Then, the effects of different data processing methods on the screened LIBS spectra were explored, and next, the feature variables were extracted from the preprocessed spectral data by the variable importance measurement (VIM). In order to further verify the prediction performance of the model, the prediction results of the RF models based on the different methods were compared. Finally, a PCA-VIM-RF calibration model was established on the basis of the optimized spectra, selected feature variables and parameters. Leave-one-out cross validation (LOOCV) was used to optimize the parameters of PCA-MD method, spectral preprocessing method and variable importance thresholds during the construction of the calibration model. The results show that the PCA-VIM-RF model has better prediction performance than the RF calibration model based on the raw spectra. For the PCA-VIM-RF calibration method of Nd, Pr, Tb and Dy elements, the values of R2CV are 0.9991, 0.9998, 0.9986, and 0.9984, respectively, the values of RMSECV are 0.06296%, 0.02788%, 0.04647% and 0.05252%, respectively. The values of R2P are 0.9508, 0.9975, 0.9691 and 0.9457, respectively, and the values of RMSEP are 0.6082%, 0.09205%, 0.5776% and 0.2631%, respectively.The above results indicate that LIBS combined with PCA-VIM-RF algorithm is a promising method for rapid quantitative analysis of REEs in NdFeB alloys without complicated sample preparation, which can provide some new ideas or strategies for the future research, development and quality control of rare earth materials.

Discrimination of maize transgenic and non-transgenic varieties by laser induced spectroscopy (LIBS) and machine learning algorithms

BackgroundIn the last decades, the production and consumption of genetically modified agricultural products have increased markedly due to the worldwide population growth and rising demand for food and feed. Consequently, genetically modified crops have been extensively produced and consumed, which required identifying and discriminating transgenic and non-transgenic products. ResultsLaser-induced breakdown spectroscopy (LIBS) combined with chemometric methods was applied to identify and discriminate two varieties of conventional (not-genetically modified, NGM) maize from four varieties of transgenic maize (genetically modified, GM). The LIBS spectra acquired under reduced pressure (100 Torr) conditions over two ranges, i.e., 175–330 nm and 275–770 nm, were subjected to Standard Normal Variation (SNV) and multivariate methods such as Principal Component Analysis (PCA) to reduce data matrices dimensionality and spectral noise. The supervised machine learning algorithms k-nearest neighbor (k-NN) and support vector machine (SVM) have been applied to discriminate among NGM and GM maize reserving 25 % of data for external validation. The training data were employed for hyperparameter optimization of classifiers using the Leave-One-Out Cross-Validation (LOOCV) method. Considering all six maize varieties simultaneously, the highest training accuracy achieved was 90.56 %, with an external validation accuracy of 88.33 %. In an alternative approach based on pairwise combinations of one GM variety against one NGM variety, the best outcome achieved was 100 % LOOCV and external validation accuracy. ConclusionsThese results showed that LIBS supported by appropriate chemometric methods represents an alternative screening technique for identifying and discriminating transgenic from non-transgenic maize.

Human movement detection and classification capabilities using passive Wi-Fi based radar

Human detection and classification via Wi-Fi transmission have received a lot of attention in recent years as crucial facilitators in security and human-computer interaction (HCI). The passive Wi-Fi radar (PWR) system used by previous researchers applied cross-ambiguity function (CAF) and CLEAN algorithms to process the detected signals. This paper explores the feasibility and viability of a PWR system in detecting and classifying human movements without utilizing CAF and CLEAN algorithms. The movements are performed by four participants but with comparable body sizes and heights. Three daily human movements are investigated namely walking, bending, and sitting, with each participant performing each movement 24 times, providing a total of 96 samples per activity. The system is evaluated based on the consistency of the signal pattern in a frequency domain and the percentage accuracy is assessed using an artificial neural network (ANN) classifier and trained using a leave-one-out cross-validation (LOOCV) method. The frequency domain results reveal that the signals are consistent, with no noticeable variations or changes in the voltage intensity or shape of the main lobe. The classification of the movements shows that the classifier has an overall accuracy of 97.6%.

Geospatial analysis for environmental noise mapping: A land use regression approach in a metropolitan city

Environmental noise can lead to adverse health outcomes. Understanding the spatial variability of environmental noise is crucial for mitigating potential health risks and developing influential urban strategies for reducing noise levels. This study aimed to measure noise levels and develop a land use regression (LUR) model to determine the spatial variability of environmental noise in Shiraz, Iran. A grid-based technique was used to establish 191 noise measurement sites (summer) across the city to generate the LUR model based on two noise metrics: Lden and Lnight. Leave-one-out cross-validation (LOOCV) and 38 additional measurement sites (winter) were used for the LUR model assessment. The mean values of Lden and Lnight during summer were 68.20 (±8.05) and 58.95 (±9.55), respectively, while during winter, the corresponding values were 69.46 (±5.46) and 58.81 (±6.79). The LUR models explained 67% and 65% of the spatial variability in Lden and Lnight, respectively. LOOCV analysis demonstrated R2 values of 0.64 and 0.61. Moreover, findings indicated mean absolute error (MAE) values of 3.96 dB(A) for Lden and 4.74 dB(A) for Lnight. Validation based on an additional set of 38 measurement sites revealed R2 values of 0.62 for both Lden and Lnight, with MAE of 2.78 and 3.31, respectively. In addition, the adjusted R2 values were 0.54 and 0.53. The results indicated no significant temporal variations between summer and winter. The results revealed that road-related variables significantly influenced noise levels. Moreover, the results indicated that Lden and Lnight levels were higher than the World Health Organization recommendations for exposure to road traffic noise. The results of our study showed that the LUR modeling approach based on geographical predictors is an effective tool for assessing changes in ambient noise levels in other cities in Iran and around the globe.

Modelo estadístico de la descontaminación de aguas residuales que contienen Carbendazim mediante foto-Fenton

Homogeneous photo-Fenton photocatalysis is one of the most widely used advanced oxidation processes in treating wastewater containing pesticides, where optimizing the catalyst dosage and oxidizing agent, with the response being mineralization in terms of total organic carbon (TOC) or removal of the specific contaminant, is the goal of any experimental design. Experimental development in treatment processes necessitates executing a significant number of experimental conditions that require the use of reagents, energy, and execution time. Therefore, modeling such phenomena emerges as an alternative to these limitations in wastewater treatment. In this research, the influence of factors FeSO4 and H2O2, each at three levels, on the mineralization of a synthetic solution of the insecticide Carbendazim (50 mg/L) in terms of TOC was evaluated using a multiple linear regression model optimized by response surface methodology. The main results established that the best model fit considers the interaction between FeSO4 and H2O2 (X1*X2) and the quadratic terms of each (X21,X22) with p-values < 0.05. The validation of the model using the Leave-One-Out Cross Validation (LOOCV) technique, as well as accuracy and precision through residual analysis and ordinary least squares assumptions, confirms the validity of the conclusions derived from it.

Comparison of machine learning and deep learning models for the assessment of rondo wine grape quality with a hyperspectral camera

Hyperspectral images provide rich spectral/spatial data and have shown remarkable performance in precision viticulture. Standardized data-processing methods are necessary to reduce the dimensionality and to identify powerful wavelengths. Toward this goal, we evaluated and compared the performance and novel-wavelength-identification ability of five renowned machine learning models: the linear models Ridge and LASSO, a 1D + 2D convolutional neural network (1D +2D CNN) non-linear model, a gradient boosting decision tree (GBDT) using XGBoost as an ensemble model, and an explainable boosting machine (EBM) followed by support vector regression (SVR) as a hybrid model. The model evaluations were conducted using leave-one-out cross-validation (LOOCV) as we sought to clarify the best-fitted machine learning model. Our results demonstrated that Ridge, LASSO, showed better performance with relatively high accuracy but were weak as a wavelength identifier. GDBT-XGBoost showed considerable prediction power and wavelength identification. EBM-SVM emerged as the most powerful model, demonstrating exceptional stability and clear wavelength classification even for destructive measurements under varying environmental stresses across Rondo's growth stages. The combined approach of 1D + 2D CNN algorithms was advantageous to handle the dynamic shapes of spectral curve and horizontal shift of the wavelengths obtained from outdoor data acquisition, and notably, it showed the highest accuracy to predict the brix and pH of wine grapes for both indoor and outdoor sensings. But the combined effects of 1D and 2D CNN algorithms were difficult to clarify the importance of spectral features for the brix and pH prediction. The integrated machine learning models with dimensionality reduction, and proper image acquisition can increase the model's accuracy. The common absorption peaks were observed in the near-infrared region of 700 nm and 900 nm. Those wavelengths should be considered for the development of low-cost sensing platforms with fewer bands. Wavelengths over 900 nm are also important to develop outdoor sensing platforms.

Utility of CT Radiomics and Delta Radiomics for Survival Evaluation in Locally Advanced Nasopharyngeal Carcinoma with Concurrent Chemoradiotherapy.

A high incidence rate of nasopharyngeal carcinoma (NPC) has been observed in Southeast Asia compared to other parts of the world. Radiomics is a computational tool to predict outcomes and may be used as a prognostic biomarker for advanced NPC treated with concurrent chemoradiotherapy. Recently, radiomic analysis of the peripheral tumor microenvironment (TME), which is the region surrounding the gross tumor volume (GTV), has shown prognostic usefulness. In this study, not only was gross tumor volume (GTVt) analyzed but also tumor peripheral regions (GTVp) were explored in terms of the TME concept. Both radiomic features and delta radiomic features were analyzed using CT images acquired in a routine radiotherapy process. A total of 50 patients with NPC stages III, IVA, and IVB were enrolled between September 2004 and February 2014. Survival models were built using Cox regression with clinical factors (i.e., gender, age, overall stage, T stage, N stage, and treatment dose) and radiomic features. Radiomic features were extracted from GTVt and GTVp. GTVp was created surrounding GTVt for TME consideration. Furthermore, delta radiomics, which is the longitudinal change in quantitative radiomic features, was utilized for analysis. Finally, C-index values were computed using leave-one-out cross-validation (LOOCV) to evaluate the performances of all prognosis models. Models were built for three different clinical outcomes, including overall survival (OS), local recurrence-free survival (LRFS), and progression-free survival (PFS). The range of the C-index in clinical factor models was (0.622, 0.729). All radiomics models, including delta radiomics models, were in the range of (0.718, 0.872). Among delta radiomics models, GTVt and GTVp were in the range of (0.833, 0.872) and (0.799, 0.834), respectively. Radiomic analysis on the proximal region surrounding the gross tumor volume of advanced NPC patients for survival outcome evaluation was investigated, and preliminary positive results were obtained. Radiomic models and delta radiomic models demonstrated performance that was either superior to or comparable with that of conventional clinical models.

Machine learning based technique to predict the water adulterant in milk using portable near infrared spectroscopy

Milk adulteration is a significant problem globally, as it is the most widely consumed and essential food product. Due to this, monitoring milk quality is necessary for sustaining human health. A Machine Learning (ML) based non-destructive system was developed to identify water adulteration in milk using Near Infrared (NIR) Spectroscopy. A database was created by mixing water in milk in varying proportions (0–40 %) and capturing spectra using compact TI DLP NIR scan Nano spectroscopy in the 900–1700 nm range. The captured spectra were pre-processed with the Savitzky-Golay (SG) filter, Multiplicative Scatter Correction (MSC), and Standard Normal Variate (SNV) method. The most informative wavelength points were selected using the wavelength/feature selection technique, and the dimensions of these wavelengths were reduced using Principal Component Analysis (PCA). Various ML models were employed to predict the water concentration in milk. Both classification and regression methods were applied to check the system's performance. In the regression analysis, the k-Nearest Neighbour (KNN) achieved the best R2, Root Mean Square Error (RMSE), Standard Error of Prediction (SEP), Mean Absolute Error (MAE), Ratio of Performance to Deviation (RPD), Leave One Out Cross-Validation (LOOCV)-R2, and LOOCV-RMSE of 0.999, 0.399 mL ( % v/v), 0.096 mL ( % v/v), 0.227 mL ( % v/v), 33.005, 0.999, and 0.353 mL ( % v/v), respectively, while for classification analysis, the Random Forest (RF) achieved 100 % accuracy and Matthew's Correlation Coefficient (MCC). The impact of the proposed portable system, which has the potential to reshape practices and set new standards for food quality assurance, transformative, and offers solutions to critical challenges in the dairy industry.

Utilizing CNN to predict homogeneous thermo-mechanical properties of conductive layers for reliability numerical analysis in electronics

This study explores the application of Convolutional Neural Networks (CNN) in predicting the partitioned homogeneous properties (PHPs) of electronic product wiring structures, aiming to enhance the efficiency of reliability analysis through Finite Element Analysis (FEA). A systematic and novel method was developed to generate the input partitioned wiring diagram image sets that foster model generalization and universality. The performance of the CNN-based approach was assessed through regression analysis by employing a leave-one-out cross-validation (LOOCV) approach across three PCBs. Additionally, the predicted PHPs of one of the PCBs were applied in product-level FEA to validate their reliability, further demonstrating the practical applicability of the CNN-based method. The results demonstrate that a well-trained CNN model can accurately predict the properties of previously unencountered wiring structures, thereby facilitating direct application in product-level reliability FEA and improving the efficiency of reliability assessment. Furthermore, efficiency evaluation revealed that the CNN-based method offers significant advantages in terms of time and cost economy compared to the mesoscopic FEA method in determining, highlighting its potential for broader application in electronic product reliability analysis. The findings provide preliminary insights and propose strategies to enhance the applicability of CNN methods in this domain, ultimately aiming to improve the efficiency and reduce costs in reliability assessments, thereby streamlining the overall product development process.

Design and validation of a diagnostic suspicion checklist to differentiate epileptic from psychogenic nonepileptic seizures (PNES-DSC)

ObjectivePsychogenic non-epileptic seizures (PNES) are complex clinical manifestations and misdiagnosis as status epilepticus remains high, entailing deleterious consequences for patients. Video-electroencephalography (vEEG) remains the gold-standard method for diagnosing PNES. However, time and economic constraints limit access to vEEG, and clinicians lack fast and reliable screening tools to assist in the differential diagnosis with epileptic seizures (ES). This study aimed to design and validate the PNES-DSC, a clinically based PNES diagnostic suspicion checklist with adequate sensitivity (Se) and specificity (Sp) to discriminate PNES from ES. MethodsA cross-sectional study with 125 patients (n = 104 drug-resistant epilepsy; n = 21 PNES) admitted for a vEEG protocolised study of seizures. A preliminary PNES-DSC (16-item) was designed and used by expert raters blinded to the definitive diagnosis to evaluate the seizure video recordings for each patient. Cohen's kappa coefficient, leave-one-out cross-validation (LOOCV) and balance accuracy (BAC) comprised the main validation analysis. ResultsThe final PNES-DSC is a 6-item checklist that requires only two to be present to confirm the suspicion of PNES. The LOOCV showed 71.4% BAC (Se = 45.2%; Sp = 97.6%) when the expert rater watched one seizure video recording and 83.4% BAC (Se = 69.6%; Sp = 97.2%) when the expert rater watched two seizure video recordings. ConclusionThe PNES-DSC is a straightforward checklist with adequate psychometric properties. With an integrative approach and appropriate patient history, the PNES-DSC can assist clinicians in expediting the final diagnosis of PNES when vEEG is limited. The PNES-DSC can also be used in the absence of patients, allowing clinicians to assess seizure recordings from smartphones.

Design and validation of novel maize grain cleaning loss detection system based on classification models of particle time-domain signals

Quantitative evaluation of grain cleaning loss is a central concern in maize intelligent direct harvesting. This study integrates particle time-domain signals with machine learning models to develop a novel grain cleaning loss detection system and create modular embedded companion software. Specifically, collisional time-domain signals of grains and impurities with varying mass gradients are captured, and abnormal data are eliminated utilizing the Mahalanobis Distance (MD) algorithm. Signal classification models incorporating diverse preprocessing methods are trained using Naive Bayes (NB) and Support Vector Machine (SVM) algorithms. Model performance is evaluated through internal leave-one-out-cross-validation (LOOCV) and external validation sets. The best classification model is integrated into the grain loss detection software, and bench tests verify real-time cleaning loss rates for detection systems. Results demonstrate that the SVM model with Savitzky-Golay (S-G) smoothing + Second-Order Derivative (SOD) preprocessing achieves the highest predictive accuracy, with 97.44 % and 96.15 % in training and validation sets, respectively. When the feeding rate of maize mixtures is 5 kg/s, absolute grain loss rates for three measurements are 1.62 %, 1.72 % and 1.86 %, respectively. Compared to traditional loss detection systems with multifunctional circuits, the novel loss detection system enhances the average accuracy of grain loss rate by 6.54, 6.82 and 8.93 percentage points. Hence, the proposed method and apparatus can be applied to detect grain cleaning loss quantitatively.

Hologram quantitative structure-activity relationship on the gas chromatographic retention index of plant essential oil constituents

The gas chromatography retention index (RI) is an important parameter for the identification of different types of compounds in the field of chromatographic analysis; however, the experimental collection of RI values is a extremely cumbersome process. Thus, there is an urgent need for the establishment of a simple, efficient, and accurate model for the prediction of the RI values of compounds. In this study, first, the experimental RI values for 60 plant essential oil constituents were obtained. Next, a model describing the hologram quantitative structure-activity relationship (HQSAR) between the structural properties of the essential oil constituents and their RI values was investigated and constructed. The optimal HQSAR model was established by setting the model parameters "fragment size", "fragment distinction", "hologram length" and "principal components" to "1-4", "C, Ch", "199", and "4", respectively. Finally, the predictive ability of the model was verified using external test set validation and leave-one-out cross-validation (LOO-CV). The experimental results were as follows, the root mean square error of prediction (RMSEP), predictive determination coefficient ([Formula: see text]), concordance correlation coefficient (CCC), and mean relative error (MRE) for external test set validation were 40.45, 0.984, 0.968, and 2.20%, respectively. Meanwhile, the root mean square error of cross validation (RMSECV) and MRE for LOO-CV were 72.56 and 4.17%, respectively. These findings demonstrate that the established HQSAR model has a good predictive ability and can accurately predict the RI values of plant essential oil constituents. In addition, the molecular contribution maps of the HQSAR model revealed that the RI values of aromatic compounds increase when hydroxyl groups are connected to their alkyl chains. Aliphatic compounds feature long chain alkyl groups, which can lead to an increase in RI values. The above phenomena highlight the promising application prospects of HQSAR for studying the RI values of plant essential oil constituents. Therefore, this study provides a reliable theoretical basis for predicting the RI values of other essential oil constituents.

Comprehensive analysis of the interaction of antigen presentation during anti-tumour immunity and establishment of AIDPS systems in ovarian cancer.

There are hundreds of prognostic models for ovarian cancer. These genes are based on different gene classes, and there are many ways to construct the models. Therefore, this paper aims to build the most stable prognostic evaluation system known to date through 101 machine learning strategies. We combined 101 algorithm combinations with 10 machine learning algorithms to create antigen presentation-associated genetic markers (AIDPS) with outstanding precision and steady performance. The inclusive set of algorithms comprises the elastic network (Enet), Ridge, stepwise Cox, Lasso, generalized enhanced regression model (GBM), random survival forest (RSF), supervised principal component (SuperPC), Cox partial least squares regression (plsRcox), survival support vector machine (Survival-SVM). Then, in the train cohort, the prediction model was fitted using a leave-one cross-validation (LOOCV) technique, which involved 101 different possible combinations of prognostic genes. Seven validation data sets (GSE26193, GSE26712, GSE30161, GSE63885, GSE9891, GSE140082 and ICGC_OV_AU) were compared and analysed, and the C-index was calculated. Finally, we collected 32 published ovarian cancer prognostic models (including mRNA and lncRNA). All data sets and prognostic models were subjected to a univariate Cox regression analysis, and the C-index was calculated to demonstrate that the antigen presentation process should be the core criterion for evaluating ovarian cancer prognosis. In a univariate Cox regression analysis, 22 prognostic genes were identified based on the expression profiles of 283 genes involved in antigen presentation and the intersection of genes (p < 0.05). AIDPS were developed by our machine learning-based integration method, which was applied to these 22 genes. One hundred and one prediction models are fitted using the LOOCV framework, and the C-index is calculated for each model across all validation sets. Interestingly, RSF + Lasso was the best model overall since it had the greatest average C-index and the highest C-index of any combination of models tested on the validated data sets. In comparing external cohorts, we found that the C-index correlated AIDPS method using the RSF + Lasso method in 101 prediction models was in contrast to other features. Notably, AIDPS outperformed the vast majority of models across all data sets. Antigen-presenting anti-tumour immune pathways can be used as a representative gene set of ovarian cancer to track the prognosis of patients with cancer. The antigen-presenting model obtained by the RSF + Lasso method has the best C-INDEX, which plays a key role in developing antigen-presenting targeted drugs in ovarian cancer and improving the treatment outcome of patients.

Abstract 2986: Germline signatures predicting toxicity and response to CTLA4 inhibitors

Abstract Background: Because germline microRNA-based variants predict toxicity risk to anti-PD-1/PDL-1 treatment, and CTLA4 inhibitors are often used in combination with them, we wanted to see if we could also predict toxicity and/or response to anti-CTLA4 therapy. Methods: The study included 69 patients from 3 institutions treated with anti-CTLA4 therapy alone. Patients were 23-89 years old with median age of 62. “Toxicity” was defined as grade 3 or higher toxicity and “Response” as a complete response, partial response, or stable disease. A panel of previously tested variants (n=139), age, sex and cycles of anti-CTLA4 were used to predict endpoints of interest. To balance model dimensionality we pre-screened variants and included them if they were marginally associated with our outcomes of interest via Fisher’s Exact Test or Jonckheere-Terpstra Test at a p-value threshold of &amp;lt; 0.2. We fit Elastic Net (EN), Random Forest (RF), and Boosted Tree (BT) models with up-sampling to predict outcomes of interest. Leave-one-out cross validation (LOOCV) was used to evaluate model performance, and the model with the highest LOOCV AUC (between all EN, RF, and BT) was chosen as the final model and re-fit using all observations. We also performed a stratified gene ontology (GO) analysis to assess biological differences between variants involved in the signatures. Our GO analysis compared gene clusters across groupings with an adjusted p-value cutoff of 0.05 against a universal genomic background. Results: 15 patients had toxicity and 21 patients had a response, with 27/139 and 25/139 variants marginally associated with these endpoints, respectively. Our toxicity model had a LOOCV AUC of 0.811 with the top variables being age, TNNT2_rs3729843, REV3L_rs465646, miR34b_c_rs4938723, and XRCC3_rs861539. Our response model had an LOOCV AUC of 0.716 with top variants being IL2RA_rs2476491, REV3L_rs465646, and IL10RB_rs2834167. Including anti-CTLA4 cycles improved the prediction accuracy for Response with an AUC 0.764. GO analysis revealed 117 pathways enriched in both the Toxicity and Response signatures, which were predominantly involved in pri-miRNA transcriptional regulation. Top GO terms in the Response signature (333 unique) were related to apoptosis and cell death. Top GO terms in the Toxicity signature (425 unique) were related to DNA replication and cellular signaling and response, including the interleukin-35-mediated signaling pathway. Conclusion: We identified germline signatures predicting toxicity and response following anti-CTLA4 therapy. These signatures differed from each other as well as from a previously identified signature of toxicity to anti-PD1/PDL-1 therapy, and GO analysis identified plausible underlying signaling pathways. Our findings continue to validate the potential of these variants to predict meaningful endpoints in cancer therapy, and thus further research in larger and more diverse cohorts is warranted. Citation Format: Joanne B. Weidhaas, Kristen McGreevy, Nicholas Marco, Nora Sundahl, Christopher R. Cabanski, Christine Spencer, Piet Ost, Donatello Telesca. Germline signatures predicting toxicity and response to CTLA4 inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2986.

Honey differentiation with FTIR-ATR spectroscopy – Comparison with physicochemical parameters of a Polish honey sample set

The varietal discrimination of honey is important because its bioactive properties, as well as specific characteristics, depend on the botanical origin. The present study aimed to verify the discriminatory power of Fourier-transform infrared spectroscopy (FT-IR) for differentiating Polish honeys and compare the results with the discrimination power of a model built on the basis of selected physicochemical parameters. For this purpose, buckwheat, rape, acacia, heather, goldenrod, and coniferous honeydew honeys were collected from trustworthy apiaries in different regions of Poland. The samples were further authenticated using pollen analysis and tested by means of FT-IR and the attenuated total reflection (ATR) technique. Basic psychochemical parameters were also assessed. The obtained data were analyzed by means of principal component analysis (PCA) and linear discriminant analysis (LDA). The obtained models were validated with a leave-one-out cross-validation (LOOCV) procedure. PCA analysis confirmed the usefulness of the ATR FT-IR method as a honey differentiation tool. The LDA for the FT-IR model allowed to correctly classify 26 out of 32 samples (81.3% accuracy), which was only slightly lower than for data the model based on the physiochemical characteristics (27 out of 32 samples and 84.4% accuracy), revealing a certain potential of FT-IR as fast evaluation method.

Abstract 4920: A nanopore sequencing approach characterizes cell-free DNA methylation-fragmentomics profiles indicative of breast cancer in a large cohort

Abstract The detection of breast cancer from cell-free DNA (cfDNA) offers a new approach with the potential to benefit individual screening and early detection. However, identifying breast cancer from cfDNA remains a major challenge when one uses conventional short-read sequencing. Methylation and DNA fragmentation characteristics provide highly informative biomarkers for detecting and monitoring cancer. To characterize these genomic features from cfDNA, we developed an approach using single molecule Nanopore sequencing. Single cfDNA molecules are sequenced intact with the methylation and fragment size directly extrapolated from Nanopore data. Moreover, our approach requires small amounts of cfDNA to discern specific genomic features from individual molecules. Thus, the use of Nanopore sequencing provides both methylation and fragment size as directly measured from native cfDNA without the use of any chemical processing or other molecular manipulation. We studied an extended breast cancer cohort with in total 1080 of samples, consisting of 440 untreated breast cancer patients and 640 healthy controls. Nanopore sequencing analysis of these cfDNA samples identified a range of 1 to 4 million CpG sites from 1 ml of plasma. Leveraging the cohort, we developed an ensemble classifier for breast cancer detection based on cfDNA methylation and fragmentation. The classifier leveraged a leave-one-out cross-validation (LOOCV) to generate predicted probability. We created nucleosome-specific methylation scores as the input features to the classifier, which scores quantified the similarity of each sample's methylation profile to a training set on a selected set of CpG sites associated with cancers. Furthermore, we also identified DNA fragmentation features, revealing distinct mono-nucleosome and di-nucleosome patterns that distinguish cancers from healthy controls. Aggregating the DNA nucleosome-specific scores and fragmentation features, we built an ensemble LOOCV random forest model. We applied the model to the breast cancer cohort and achieved a detection specificity of 74%, a sensitivity of 71%, and an overall accuracy of approximately 73%. The area under the receiver operating characteristic curve (AUROC) reached 80%. We validated the classifier with two external independent cohorts. Validation cohort 1 demonstrated as a specificity of 85%, a sensitivity of 80%, and overall accuracy of 83% with AUROC of 90%. Validation cohort 2 without controls demonstrated that the classifier achieved a sensitivity of 94%. Both validation sets confirm that our model can achieve excellent performance for early breast cancer detection. In summary, our findings demonstrate that nanopore sequencing provides cfDNA methylation and fragment profiling that enables breast cancer detection. This approach holds the potential to improve cancer diagnosis and treatment outcomes. Citation Format: Xiangqi Bai, Billy T. Lau, Alison Almada, Sue Grimes, Tianqi Chen, Hojoon Lee, Hanlee P. Ji. A nanopore sequencing approach characterizes cell-free DNA methylation-fragmentomics profiles indicative of breast cancer in a large cohort [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4920.

Optimizing echo state networks for continuous gesture recognition in mobile devices: A comparative study

Continuous gesture recognition can be used to enhance human-computer interaction. This can be accomplished by capturing human movement with the use of the Inertial Measurement Units in smartphones and using machine learning algorithms to predict the intended gestures. Echo State Networks (ESNs) consist of a fixed internal reservoir that is able to generate rich and diverse nonlinear dynamics in response to input signals that capture temporal dependencies within the signal. This makes ESNs well-suited for time series prediction tasks, such as continuous gesture recognition. However, their application has not been rigorously explored, with regard to gesture recognition. In this study, we sought to enhance the efficacy of ESN models in continuous gesture recognition by exploring diverse model structures, fine-tuning hyperparameters, and experimenting with various training approaches. We used three different training schemes that used the Leave-one-out Cross-validation (LOOCV) protocol to investigate the performance in real-world scenarios with different levels of data availability: Leaving out data from one user to use for testing (F1-score: 0.89), leaving out a fraction of data from all users to use in testing (F1-score: 0.96), and training and testing using LOOCV on a single user (F1-score: 0.99). The obtained results outperformed the Long Short-Term Memory (LSTM) performance from past research (F1-score: 0.87) while maintaining a low training time of approximately 13 seconds compared to 63 seconds for the LSTM model. Additionally, we further explored the performance of the ESN models through behaviour space analysis using memory capacity, Kernel Rank, and Generalization Rank. Our results demonstrate that ESNs can be optimized to achieve high performance on gesture recognition in mobile devices on multiple levels of data availability. These findings highlight the practical ability of ESNs to enhance human-computer interaction.

Qingxiangxing Baijiu sensory quality grade classification by 1H NMR and GC combined with multivariate statistical analysis

The traditional uniform artificial sensory evaluation makes it difficult to standardize the classification of different sensory quality grades of Baijiu. In this study, a total of 92 authentic Qingxiangxing Baijiu samples with 3 sensory quality grades were carefully collected. Gas chromatography (GC) was used to determine 46 main flavor components and proton nuclear magnetic resonance (1H NMR) spectroscopy was employed to obtain hydrogen atom characteristic information of organic compounds. The principal component analysis (PCA), k-nearest neighbor (KNN) and linear discriminant analysis (LDA) models were conducted and fully validated by internal leave-one-out cross validation (LOOCV) and external repeated double random cross validation (RDRCV). The sensory quality grades of Qingxiangxing Baijiu were effectively classified by using GC and 1H NMR techniques coupled with PCA/KNN analysis with the averaged accuracy higher than 80%. In addition, synthetic minority oversampling technique (SMOTE) algorithm was successfully used to address the model overfitting problem caused by an unbalanced sample composition. This study demonstrated that 1H NMR and GC combined with multivariate statistical analysis were effective for sensory quality classification of Qingxiangxing Baijiu.