External Set Research Articles

Risk score stratification of cutaneous melanomas based on whole slide images using deep learning.

e21573 Background: Predictive and prognostic biomarkers represent the cornerstone of clinical oncology. Improving the prognostication of melanoma is needed to select patients for effective adjuvant therapies. Taking into account that tumor tissue contains a large amount of clinically relevant hidden information that is not fully exploited, we applied a weakly-supervised deep-learning approach on H&E-stained whole-slide image (WSI) to directly predict 5-year survival outcomes in melanoma patients. Methods: We designed a deep neural (DL) network that extracts features from no-padding patches of WSI (tiles of size 512x512 pixels) using a self-supervised learning framework as well as from the tumor region. These features are then fed along with survival information into the deep learning fusion network assigning a survival risk score to each WSI. The model was trained and validated on 195 cases of primary melanoma diagnosed between 2015 and 2017 originating from the IHP Group and the French RICMel melanoma database. Performance was evaluated using a cross-validation and cross-testing framework as well as on an external set of 238 cases from the TCGA database. Concordance index (c-index) was used as a metric to assess the performance of the proposed algorithm. Results: For the prediction of survival, the proposed pipeline yielded c-index of 0.76 and 0.66 for the IHP Group cohort and TCGA dataset respectively. Furthermore, the model is able to significantly discriminate between the 2 groups of patients, with a good and a poor prognosis in terms of overall survival (p-value < 0.001 for IHP and p-value = 0.01 for TCGA). Also, the proposed score is statistically significant when added to a multivariate cox model incorporating the classic prognosis factors (p-value < 0.005) and allows to reach a c-index of 0.81 over the discovery cohort. Conclusions: This infrequent weakly-supervised deep-learning approach to HE images analysis has the advantage of leaving the feature selection entirely to the deep network, and so discover new morphological biomarkers. By this way, it could have in the near future the potential to accelerate and improve the clinical decision-making process in the field of melanoma. Also, these findings will undoubtedly open room for substantial applications with economic and treatment delay fallouts.

Modeling and diagnosis of water quality parameters in wastewater treatment process based on improved particle swarm optimization and self-organizing neural network

The study designs a strategy to predict water quality parameters and identify faults in the activated sludge process. The proposed method combines the improved beetle antennae search (IBAS) with the dynamic particle swarm multi-objective optimization algorithm based on crowding distance (DMOPSO-CD), named DMOPSO-CD-IBAS. The fault diagnosis prediction interval of chemical oxygen demand (COD), biochemical oxygen demand (BOD5) and total suspended substance (TSS) was conducted by self-organizing fuzzy neural network with an efficient scheme for parsimonious (SOFNN-ESP). DMOPSO-CD enhances the efficiency of the beetle antenna search by adjusting inertia weights and acceleration factors, reaching the optimal state with a fitness value of 0.0961. Furthermore, the crowding distance sorting preserve the external elite set and update the global optimal values, upgrading the individual search mechanism of beetle antenna search to a group search mechanism to enhance population diversity. The proposed fault diagnosis method's effectiveness is validated through three specific faults (sensor fault of COD and BOD5, and the index of sludge expansion) during the sewage treatment process. The results of the prediction mean square error, root mean square error, and average absolute error of the proposed model were kept at about 0.011, 0.15 and 0.524, respectively, having better tracking performance and stronger robustness than SOFNN-ESP and backpropagation.

Coronary CTA-based vascular radiomics predicts atherosclerosis development proximal to LAD myocardial bridging.

Cardiac cycle morphological changes can accelerate plaque growth proximal to myocardial bridging (MB) in the left anterior descending artery (LAD). To assess coronary computed tomography angiography (CCTA)-based vascular radiomics for predicting proximal plaque development in LAD MB. Patients with repeated CCTA scans showing LAD MB without proximal plaque in index CCTA were included from Jinling Hospital as a development set. They were divided into training and internal testing in an 8:2 ratio. Patients from four other tertiary hospitals were set as external validation set. The endpoint was proximal plaque development of LAD MB in follow-up CCTA. Four vascular radiomics models were built: MB centreline (MB CL), proximal MB CL (pMB CL), MB cross-section (MB CS), and proximal MB CS (pMB CS), whose performances were evaluated using area under the receiver operating characteristic curve (AUC), integrated discrimination improvement (IDI), and net reclassification improvement (NRI). In total, 295 patients were included in the development (n = 192; median age, 54 ± 11 years; 137 men) and external validation sets (n = 103; median age, 57 ± 9 years; 57 men). The pMB CS vascular radiomics model exhibited higher AUCs in training, internal test, and external sets (AUC = 0.78, 0.75, 0.75) than the clinical and anatomical model (all P < 0.05). Integration of the pMB CS vascular radiomics model significantly raised the AUC of the clinical and anatomical model from 0.56 to 0.75 (P = 0.002), along with enhanced NRI [0.76 (0.37-1.14), P < 0.001] and IDI [0.17 (0.07-0.26), P < 0.001] in the external validation set. The CCTA-based pMB CS vascular radiomics model can predict plaque development in LAD MB.

ChemFH: an integrated tool for screening frequent false positives in chemical biology and drug discovery.

High-throughput screening rapidly tests an extensive array of chemical compounds to identify hit compounds for specific biological targets in drug discovery. However, false-positive results disrupt hit compound screening, leading to wastage of time and resources. To address this, we propose ChemFH, an integrated online platform facilitating rapid virtual evaluation of potential false positives, including colloidal aggregators, spectroscopic interference compounds, firefly luciferase inhibitors, chemical reactive compounds, promiscuous compounds, and other assay interferences. By leveraging a dataset containing 823391 compounds, we constructed high-quality prediction models using multi-task directed message-passing network (DMPNN) architectures combining uncertainty estimation, yielding an average AUC value of 0.91. Furthermore, ChemFH incorporated 1441 representative alert substructures derived from the collected data and ten commonly used frequent hitter screening rules. ChemFH was validated with an external set of 75 compounds. Subsequently, the virtual screening capability of ChemFH was successfully confirmed through its application to five virtual screening libraries. Furthermore, ChemFH underwent additional validation on two natural products and FDA-approved drugs, yielding reliable and accurate results. ChemFH is a comprehensive, reliable, and computationally efficient screening pipeline that facilitates the identification of true positive results in assays, contributing to enhanced efficiency and success rates in drug discovery. ChemFH is freely available via https://chemfh.scbdd.com/.

Machine learning-based preoperative analytics for the prediction of anastomotic leakage in colorectal surgery: a swiss pilot study

BackgroundAnastomotic leakage (AL), a severe complication following colorectal surgery, arises from defects at the anastomosis site. This study evaluates the feasibility of predicting AL using machine learning (ML) algorithms based on preoperative data.MethodsWe retrospectively analyzed data including 21 predictors from patients undergoing colorectal surgery with bowel anastomosis at four Swiss hospitals. Several ML algorithms were applied for binary classification into AL or non-AL groups, utilizing a five-fold cross-validation strategy with a 90% training and 10% validation split. Additionally, a holdout test set from an external hospital was employed to assess the models' robustness in external validation.ResultsAmong 1244 patients, 112 (9.0%) suffered from AL. The Random Forest model showed an AUC-ROC of 0.78 (SD: ± 0.01) on the internal test set, which significantly decreased to 0.60 (SD: ± 0.05) on the external holdout test set comprising 198 patients, including 7 (3.5%) with AL. Conversely, the Logistic Regression model demonstrated more consistent AUC-ROC values of 0.69 (SD: ± 0.01) on the internal set and 0.61 (SD: ± 0.05) on the external set. Accuracy measures for Random Forest were 0.82 (SD: ± 0.04) internally and 0.87 (SD: ± 0.08) externally, while Logistic Regression achieved accuracies of 0.81 (SD: ± 0.10) and 0.88 (SD: ± 0.15). F1 Scores for Random Forest moved from 0.58 (SD: ± 0.03) internally to 0.51 (SD: ± 0.03) externally, with Logistic Regression maintaining more stable scores of 0.53 (SD: ± 0.04) and 0.51 (SD: ± 0.02).ConclusionIn this pilot study, we evaluated ML-based prediction models for AL post-colorectal surgery and identified ten patient-related risk factors associated with AL. Highlighting the need for multicenter data, external validation, and larger sample sizes, our findings emphasize the potential of ML in enhancing surgical outcomes and inform future development of a web-based application for broader clinical use.

Association between A/G ratio and arterial stiffness among Chinese type 2 diabetics: A cross-sectional study

BackgroundThe android-to-gynoid fat ratio (A/G ratio), an emerging indicator of obesity independent of body mass index (BMI), has yet to be conclusively associated with arterial stiffness in type 2 diabetes mellitus (T2DM). This study aimed to construct a nomogram to estimate arterial stiffness risk in diabetics and explore the interaction effect between A/G ratio and traditional obesity indicators on arterial stiffness. Methods1313 diabetics were divided into 2 groups based on arterial stiffness identified by brachial ankle pulse wave velocity (baPWV), and demographic and clinical features were measured. The LASSO and multivariate logistics regression were used to develop the nomogram. Calibration curve, decision curve analysis (DCA) and receiver operating characteristic (ROC) were applied to assess calibration and clinical usefulness. Interaction effect analysis was performed to quantify the interactive relationship of A/G ratio and obesity indicators on arterial stiffness. Results6 independent predictors (age, gender, A/G ratio, SBP, LDL-C and HbA1C) were screened to construct a nomogram prediction model. The calibration curve demonstrated satisfactory agreement between predicted and actual probability, and the nomogram exhibited clinical beneficial at the threshold between 8 % and 95 % indicated by DCA. The area under curve (AUC) was 0.918 and 0.833 for training and external set, respectively. Further investigation revealed A/G ratio and BMI acted positively synergistically towards arterial stiffness, and in BMI-based subgroup analysis, elevated A/G ratio was a significant risk factor for arterial stiffness, especially in normal BMI. ConclusionsA/G ratio showed a substantial association with arterial stiffness, and the nomogram, incorporating age, gender, A/G ratio, SBP, LDL-C, and HbA1c, exhibited high predictive value. A/G ratio measurement in BMI-normal individuals assisted in identifying cardiovascular diseases early.

A telomere-related gene risk model for predicting prognosis and treatment response in acute myeloid leukemia

Acute myeloid leukemia (AML) is a prevalent hematological malignancy among adults. Recent studies suggest that the length of telomeres could significantly affect both the risk of developing AML and the overall survival (OS). Despite the limited focus on the prognostic value of telomere-related genes (TRGs) in AML, our study aims at addressing this gap by compiling a list of TRGs from TelNet, as well as collecting clinical information and TRGs expression data through the Gene Expression Omnibus (GEO) database. The GSE37642 dataset, sourced from GEO and based on the GPL96 platform, was divided into training and validation sets at a 6:4 ratio. Additionally, the GSE71014 dataset (based on the GPL10558 platform), GSE12417 dataset (based on the GPL96 and GPL570 platforms), and another portion of the GSE37642 dataset (based on the GPL570 platform) were designated as external testing sets. Univariate Cox regression analysis identified 96 TRGs significantly associated with OS. Subsequent Lasso-Cox stepwise regression analysis pinpointed eight TRGs (MCPH1, SLC25A6, STK19, PSAT1, KCTD15, DNMT3B, PSMD5, and TAF2) exhibiting robust predictive potential for patient survival. Both univariate and multivariate survival analyses unveiled TRG risk scores and age as independent prognostic variables. To refine the accuracy of survival prognosis, we developed both a nomogram integrating clinical parameters and a predictive risk score model based on TRGs. In subsequent investigations, associations were emphasized not solely regarding the TRG risk score and immune infiltration patterns but also concerning the response to immune-checkpoint inhibitor (ICI) therapy. In summary, the establishment of a telomere-associated genetic risk model offers a valuable tool for prognosticating AML outcomes, thereby facilitating informed treatment decisions.

Testing the fit of data and external sets via an imprecise Sargan-Hansen test

In empirical sciences such as psychology, the term cumulative science mostly refers to the integration of theories, while external (prior) information may also be used in statistical inference. This external information can be in the form of statistical moments and is subject to various types of uncertainty, e.g., because it is estimated, or because of qualitative uncertainty due to differences in study design or sampling. Before using it in statistical inference, it is therefore important to test whether the external information fits a new data set, taking into account its uncertainties. As a frequentist approach, the Sargan-Hansen test from the generalized method of moments framework is used in this paper. It tests, given a statistical model, whether data and point-wise external information are in conflict. A separability result is given that simplifies the Sargan-Hansen test statistic in most cases. The Sargan-Hansen test is then extended to the imprecise scenario with (estimated) external sets using stochastically ordered credal sets. Furthermore, an exact small sample version is derived for normally distributed variables. As a Bayesian approach, two prior-data conflict criteria are discussed as a test for the fit of external information to the data. Two simulation studies are performed to test and compare the power and type I error of the methods discussed. Different small sample scenarios are implemented, varying the moments used, the level of significance, and other aspects. The results show that both the Sargan-Hansen test and the Bayesian criteria control type I errors while having sufficient or even good power. To facilitate the use of the methods by applied scientists, easy-to-use R functions are provided in the R script in the supplementary materials.

Automated Analysis of Split Kidney Function from CT Scans Using Deep Learning and Delta Radiomics.

Background: Differential kidney function assessment is an important part of preoperative evaluation of various urological interventions. It is obtained through dedicated nuclear medical imaging and is not yet implemented through conventional Imaging. Objective: We assess if differential kidney function can be obtained through evaluation of contrast-enhanced computed tomography(CT) using a combination of deep learning and (2D and 3D) radiomic features. Methods: All patients who underwent kidney nuclear scanning at Mayo Clinic sites between 2018-2022 were collected. CT scans of the kidneys were obtained within a 3-month interval before or after the nuclear scans were extracted. Patients who underwent a urological or radiological intervention within this time frame were excluded. A segmentation model was used to segment both kidneys. 2D and 3D radiomics features were extracted and compared between the two kidneys to compute delta radiomics and assess its ability to predict differential kidney function. Performance was reported using receiver operating characteristics, sensitivity, and specificity. Results: Studies from Arizona & Rochester formed our internal dataset (n = 1,159). Studies from Florida were separately processed as an external test set to validate generalizability. We obtained 323 studies from our internal sites and 39 studies from external sites. The best results were obtained by a random forest model trained on 3D delta radiomics features. This model achieved an area under curve (AUC) of 0.85 and 0.81 on internal and external test sets, while specificity and sensitivity were 0.84,0.68 on the internal set, 0.70, and 0.65 on the external set. Conclusion: This proposed automated pipeline can derive important differential kidney function information from contrast-enhanced CT and reduce the need for dedicated nuclear scans for early-stage differential kidney functional assessment. Clinical Impact: We establish a machine learning methodology for assessing differential kidney function from routine CT without the need for expensive and radioactive nuclear medicine scans.

Machine learning insights into predicting biogas separation in metal-organic frameworks

Breakthroughs in efficient use of biogas fuel depend on successful separation of carbon dioxide/methane streams and identification of appropriate separation materials. In this work, machine learning models are trained to predict biogas separation properties of metal-organic frameworks (MOFs). Training data are obtained using grand canonical Monte Carlo simulations of experimental MOFs which have been carefully curated to ensure data quality and structural viability. The models show excellent performance in predicting gas uptake and classifying MOFs according to the trade-off between gas uptake and selectivity, with R2 values consistently above 0.9 for the validation set. We make prospective predictions on an independent external set of hypothetical MOFs, and examine these predictions in comparison to the results of grand canonical Monte Carlo calculations. The best-performing trained models correctly filter out over 90% of low-performing unseen MOFs, illustrating their applicability to other MOF datasets.

Breaking the Barriers: Machine-Learning-Based c-RASAR Approach for Accurate Blood-Brain Barrier Permeability Prediction.

The intricate nature of the blood-brain barrier (BBB) poses a significant challenge in predicting drug permeability, which is crucial for assessing central nervous system (CNS) drug efficacy and safety. This research utilizes an innovative approach, the classification read-across structure-activity relationship (c-RASAR) framework, that leverages machine learning (ML) to enhance the accuracy of BBB permeability predictions. The c-RASAR framework seamlessly integrates principles from both read-across and QSAR methodologies, underscoring the need to consider similarity-related aspects during the development of the c-RASAR model. It is crucial to note that the primary goal of this research is not to introduce yet another model for predicting BBB permeability but rather to showcase the refinement in predicting the BBB permeability of organic compounds through the introduction of a c-RASAR approach. This groundbreaking methodology aims to elevate the accuracy of assessing neuropharmacological implications and streamline the process of drug development. In this study, an ML-based c-RASAR linear discriminant analysis (LDA) model was developed using a dataset of 7807 compounds, encompassing both BBB-permeable and -nonpermeable substances sourced from the B3DB database (freely accessible from https://github.com/theochem/B3DB), for predicting BBB permeability in lead discovery for CNS drugs. The model's predictive capability was then validated using three external sets: one containing 276,518 natural products (NPs) from the LOTUS database (accessible from https://lotus.naturalproducts.net/download) for data gap filling, another comprising 13,002 drug-like/drug compounds from the DrugBank database (available from https://go.drugbank.com/), and a third set of 56 FDA-approved drugs to assess the model's reliability. Further diversifying the predictive arsenal, various other ML-based c-RASAR models were also developed for comparison purposes. The proposed c-RASAR framework emerged as a powerful tool for predicting BBB permeability. This research not only advances the understanding of molecular determinants influencing CNS drug permeability but also provides a versatile computational platform for the rapid assessment of diverse compounds, facilitating informed decision-making in drug development and design.

ECG-surv: A deep learning-based model to predict time to 1-year mortality from 12-lead electrocardiogram

Electrocardiogram (ECG) abnormalities have demonstrated potential as prognostic indicators of patient survival. However, the traditional statistical approach is constrained by structured data input, limiting its ability to fully leverage the predictive value of ECG data in prognostic modeling. This study aims to introduce and evaluate a deep-learning model to simultaneously handle censored data and unstructured ECG data for survival analysis. We herein introduce a novel deep neural network called ECG-surv, which includes a feature extraction neural network and a time-to-event analysis neural network. The proposed model is specifically designed to predict the time to 1-year mortality by extracting and analyzing unique features from 12-lead ECG data. ECG-surv was evaluated using both an independent test set and an external set, which were collected using different ECG devices. The performance of ECG-surv surpassed that of the Cox proportional model, which included demographics and ECG waveform parameters, in predicting 1-year all-cause mortality, with a significantly higher concordance index (C-index) in ECG-surv than in the Cox model using both the independent test set (0.860 [95% CI: 0.859- 0.861] vs. 0.796 [95% CI: 0.791- 0.800]) and the external test set (0.813 [95% CI: 0.807- 0.814] vs. 0.764 [95% CI: 0.755- 0.770]). ECG-surv also demonstrated exceptional predictive ability for cardiovascular death (C-index of 0.891 [95% CI: 0.890- 0.893]), outperforming the Framingham risk Cox model (C-index of 0.734 [95% CI: 0.715-0.752]). ECG-surv effectively utilized unstructured ECG data in a survival analysis. It outperformed traditional statistical approaches in predicting 1-year all-cause mortality and cardiovascular death, which makes it a valuable tool for predicting patient survival.

Development and validation of a risk scoring system to identify patients with lupus nephritis in electronic health record data

ObjectiveAccurate identification of lupus nephritis (LN) cases is essential for patient management, research and public health initiatives. However, LN diagnosis codes in electronic health records (EHRs) are underused, hindering efficient...

Metabolic phenotyping with computed tomography deep learning for metabolic syndrome, osteoporosis and sarcopenia predicts mortality in adults.

Computed tomography (CT) body compositions reflect age-related metabolic derangements. We aimed to develop a multi-outcome deep learning model using CT multi-level body composition parameters to detect metabolic syndrome (MS), osteoporosis and sarcopenia by identifying metabolic clusters simultaneously. We also investigated the prognostic value of metabolic phenotyping by CT model for long-term mortality. The derivation set (n=516; 75% train set, 25% internal test set) was constructed using age- and sex-stratified random sampling from two community-based cohorts. Data from participants in the individual health assessment programme (n=380) were used as the external test set 1. Semi-automatic quantification of body compositions at multiple levels of abdominal CT scans was performed to train a multi-layer perceptron (MLP)-based multi-label classification model. External test set 2 to test the prognostic value of the model output for mortality was built using data from individuals who underwent abdominal CT in a tertiary-level institution (n=10141). The mean ages of the derivation and external sets were 62.8 and 59.7years, respectively, without difference in sex distribution (women 50%) or body mass index (BMI; 23.9kg/m2). Skeletal muscle density (SMD) and bone density (BD) showed a more linear decrement across age than skeletal muscle area. Alternatively, an increase in visceral fat area (VFA) was observed in both men and women. Hierarchical clustering based on multi-level CT body composition parameters revealed three distinctive phenotype clusters: normal, MS and osteosarcopenia clusters. The L3 CT-parameter-based model, with or without clinical variables (age, sex and BMI), outperformed clinical model predictions of all outcomes (area under the receiver operating characteristic curve: MS, 0.76 vs. 0.55; osteoporosis, 0.90 vs. 0.79; sarcopenia, 0.85 vs. 0.81 in external test set 1; P<0.05 for all). VFA contributed the most to the MS predictions, whereas SMD, BD and subcutaneous fat area were features of high importance for detecting osteoporosis and sarcopenia. In external test set 2 (mean age 63.5years, women 79%; median follow-up 4.9years), a total of 907 individuals (8.9%) died during follow-up. Among model-predicted metabolic phenotypes, sarcopenia alone (adjusted hazard ratio [aHR] 1.55), MS+sarcopenia (aHR 1.65), osteoporosis+sarcopenia (aHR 1.83) and all three combined (aHR 1.87) remained robust predictors of mortality after adjustment for age, sex and comorbidities. A CT body composition-based MLP model detected MS, osteoporosis and sarcopenia simultaneously in community-dwelling and hospitalized adults. Metabolic phenotypes predicted by the CT MLP model were associated with long-term mortality, independent of covariates.

A multi-step attack identification and correlation method based on multi-information fusion

With the continuous development of Internet technology, network security issues are becoming more and more complex. In order to obtain or damage user information, attackers usually need to use multiple attack steps to attack different network nodes to achieve the final goal. Currently, traditional intrusion detection mainly focuses on classifying attacks on a single piece of traffic information, and lacks the use of correlation and timing information between multi-step attack traffic to carry out multi-step attack identification and correlation research. To this end, we introduce an edge-based graph attention network to aggregate the neighbor information of flows and use a long short-term memory neural network to obtain time series information. By considering neighbor traffic and time information during the classification process, we are able to achieve accurate classification in multi-step attack scenarios. Then, based on the classification results, the sum of the number of attacks and the number of attacks is counted for each host node. Then standardize the statistical counts of internal network host nodes and external network host nodes and set thresholds to exclude low-risk nodes. Finally, a time-based depth-first traversal algorithm is used to obtain the key attack chain. However, this method may face some challenges, such as high computational complexity, the ability to handle large-scale data, and the generalization ability of the model. Experimental results show that the method we proposed is significantly better than the traditional method in terms of accuracy and recall rate for multi-step attacks, and it can effectively correlate attack steps and obtain multiple key attack chains.

ProTox 3.0: a webserver for the prediction of toxicity of chemicals.

Interaction with chemicals, present in drugs, food, environments, and consumer goods, is an integral part of our everyday life. However, depending on the amount and duration, such interactions can also result in adverse effects. With the increase in computational methods, the in silico methods can offer significant benefits to both regulatory needs and requirements for risk assessments and the pharmaceutical industry to assess the safety profile of a chemical. Here, we present ProTox3.0, which incorporates molecular similarity and machine-learning models for the prediction of 61 toxicity endpoints such as acute toxicity, organ toxicity, clinical toxicity, molecular-initiating events (MOE), adverse outcomes (Tox21) pathways, several other toxicological endpoints and toxicity off-targets. All the ProTox 3.0 models are validated on independent external sets and have shown strong performance. ProTox envisages itself as a complete, freely available computational platform for in silico toxicity prediction for toxicologists, regulatory agencies, computational chemists, and medicinal chemists. The ProTox 3.0 webserver is free and open to all users, and there is no login requirement and can be accessed via https://tox.charite.de. The web server takes a 2D chemical structure as input and reports the toxicological profile of the compound for each endpoint with a confidence score and overall toxicity radar plot and network plot.

Prediction of tumor origin in cancers of unknown primary origin with cytology-based deep learning.

Cancer of unknown primary (CUP) site poses diagnostic challenges due to its elusive nature. Many cases of CUP manifest as pleural and peritoneal serous effusions. Leveraging cytological images from 57,220 cases at four tertiary hospitals, we developed a deep-learning method for tumor origin differentiation using cytological histology (TORCH) that can identify malignancy and predict tumor origin in both hydrothorax and ascites. We examined its performance on three internal (n = 12,799) and two external (n = 14,538) testing sets. In both internal and external testing sets, TORCH achieved area under the receiver operating curve values ranging from 0.953 to 0.991 for cancer diagnosis and 0.953 to 0.979 for tumor origin localization. TORCH accurately predicted primary tumor origins, with a top-1 accuracy of 82.6% and top-3 accuracy of 98.9%. Compared with results derived from pathologists, TORCH showed better prediction efficacy (1.677 versus 1.265, P < 0.001), enhancing junior pathologists' diagnostic scores significantly (1.326 versus 1.101, P < 0.001). Patients with CUP whose initial treatment protocol was concordant with TORCH-predicted origins had better overall survival than those who were administrated discordant treatment (27 versus 17 months, P = 0.006). Our study underscores the potential of TORCH as a valuable ancillary tool in clinical practice, although further validation in randomized trials is warranted.

The rat acute oral toxicity of trifluoromethyl compounds (TFMs): a computational toxicology study combining the 2D-QSTR, read-across and consensus modeling methods.

All areas of the modern society are affected by fluorine chemistry. In particular, fluorine plays an important role in medical, pharmaceutical and agrochemical sciences. Amongst various fluoro-organic compounds, trifluoromethyl (CF3) group is valuable in applications such as pharmaceuticals, agrochemicals and industrial chemicals. In the present study, following the strict OECD modelling principles, a quantitative structure-toxicity relationship (QSTR) modelling for the rat acute oral toxicity of trifluoromethyl compounds (TFMs) was established by genetic algorithm-multiple linear regression (GA-MLR) approach. All developed models were evaluated by various state-of-the-art validation metrics and the OECD principles. The best QSTR model included nine easily interpretable 2D molecular descriptors with clear physical and chemical significance. The mechanistic interpretation showed that the atom-type electro-topological state indices, molecular connectivity, ionization potential, lipophilicity and some autocorrelation coefficients are the main factors contributing to the acute oral toxicity of TFMs against rats. To validate that the selected 2D descriptors can effectively characterize the toxicity, we performed the chemical read-across analysis. We also compared the best QSTR model with public OPERA tool to demonstrate the reliability of the predictions. To further improve the prediction range of the QSTR model, we performed the consensus modelling. Finally, the optimum QSTR model was utilized to predict a true external set containing many untested/unknown TFMs for the first time. Overall, the developed model contributes to a more comprehensive safety assessment approach for novel CF3-containing pharmaceuticals or chemicals, reducing unnecessary chemical synthesis whilst saving the development cost of new drugs.

Study on energy capture characteristics of piezoelectric stack energy harvester for railway track

Railway traffic plays a pivotal role within the current transportation system, with ensuring its safety being of paramount importance. Real-time monitoring of train track health through sensor technology has emerged as a significant approach for achieving this objective. However, a persistent challenge lies in providing cost-effective and stable power to sensors in remote areas. This paper proposes the utilization of a novel piezoelectric stack energy harvester in railway systems to address this issue. The substantial and consistent vibration energy produced by railway operations makes it an ideal source for energy harvesting, unaffected by environmental conditions. Through simulation analysis and experimental verification, this study explores the impact of load size, load frequency, and external resistance on the energy harvesting efficiency of the proposed piezoelectric stack energy harvester. The results indicate that the output power of the energy harvester increases with the load size. Furthermore, the frequency significantly influences the energy capture efficiency when below 8 Hz, with minimal impact on frequencies above 8 Hz. Interestingly, the load dramatically affects the energy capture efficiency, even at higher frequencies. With the external resistance set to 250 kΩ, the harvester achieves a maximum output power of 42.76 mW.

Evaluation of the prognostic performance of different cutoff values of lymph node ratio staging system for stage III colorectal cancer.

This study attempted to compare the prognostic performance of lymph node ratio (LNR) staging system with different cutoff values relative to American Joint Committee on Cancer (AJCC) pN staging system in stage III colorectal cancer (CRC). Overall, 45,069 patients from the SEER dataset and 69 patients from the Second Affiliated Hospital of Nanjing Medical University (the External set) who underwent surgical resection of the primary tumor and were diagnosed with stage III CRC by postoperative pathology were included. Patients were divided into three subgroups based on the LNR cutoff used in previous studies, Kaplan-Meier curves were plotted, and log-rank test was used to compare the differences among groups in terms of cancer-specific survival (CSS). Cox regression model was applied for survival analysis. To evaluate the discriminatory power of different lymph node staging systems, Harrell's C statistic(C-index) and Akaike's Information Criterion (AIC) were applied. A set of optimal cutoff values (0.11; 0.36; 0.66) of LNR staging system with the most considerable discriminatory power to the prognosis in patients with stage III CRC (SEER set: C-index = 0.714; AIC = 58,942.46, External set: C-index = 0.809; AIC = 164.36) were obtained, and both were superior to the AJCC pN staging system (SEER set: C-index = 0.708; AIC = 59,071.20, External set: C-index = 0.788; AIC = 167.06). For evaluating the prognostic efficacy of patients with stage III colorectal cancer, the cutoff value (0.11; 0.36; 0.66) of LNR staging system had the best discrimination and prognostic ability, which was superior to LNR staging system under other cutoff values and AJCC pN staging system.