Radiomics and visual analysis for predicting success of transplantation of heterotopic glioblastoma in mice with MRI.

BACKGROUND: Quantifying tumor growth and treatment response noninvasively poses a challenge to all experimental tumor models. The aim of our study was, to assess the value of quantitative and visual examination and radiomic feature analysis of high-resolution MR images of heterotopic glioblastoma xenografts in mice to determine tumor cell proliferation (TCP). METHODS: Human glioblastoma cells were injected subcutaneously into both flanks of immunodeficient mice and followed up on a 3 T MR scanner. Volumes and signal intensities were calculated. Visual assessment of the internal tumor structure was based on a scoring system. Radiomic feature analysis was performed using MaZda software. The results were correlated with histopathology and immunochemistry. RESULTS: 21 tumors in 14 animals were analyzed. The volumes of xenografts with high TCP (H-TCP) increased, whereas those with low TCP (L-TCP) or no TCP (N-TCP) continued to decrease over time (p < 0.05). A low intensity rim (rim sign) on unenhanced T1-weighted images provided the highest diagnostic accuracy at visual analysis for assessing H-TCP (p < 0.05). Applying radiomic feature analysis, wavelet transform parameters were best for distinguishing between H-TCP and L-TCP / N-TCP (p < 0.05). CONCLUSION: Visual and radiomic feature analysis of the internal structure of heterotopically implanted glioblastomas provide reproducible and quantifiable results to predict the success of transplantation.

Prediction of Mycobacterium tuberculosis cell wall permeability using machine learning methods.

Tuberculosis (TB) caused by the bacteria Mycobacterium tuberculosis (M. tb), continues to pose a significant worldwide health threat. The advent of drug-resistant strains of the disease highlights the critical need for novel treatments. The unique cell wall of M. tb provides an extra layer of protection for the bacteria and hence only compounds that can penetrate this barrier can reach their targets within the bacterial cell wall. The creation of a reliable machine learning (ML) model to predict the mycobacterial cell wall permeability of small molecules is presented in this work and four ML algorithms, including Random Forest, Support Vector Machines (SVM), k-nearest Neighbour (k-NN) and Logistic Regression were trained on a dataset of 5368 compounds. RDKit and Mordred toolkits were used to calculate features. To determine the most effective model, various performance metrics were used such as accuracy, precision, recall, F1 score, and area under the receiver operating characteristic curve. The best-performing model was further refined with hyperparameter tuning and tenfold cross-validation. The SVM model with filtering outperformed the other machine learning models and demonstrated 80.26% and 81.13% accuracy on the test and validation datasets, respectively. The study also provided insights into the molecular descriptors that play the most important role in predicting the ability of a molecule to pass the M. tb cell wall, which could guide future compound design. The model is available at https://github.com/PGlab-NIPER/MTB_Permeability .

A spatial feature analysis of primary health care utilization in a large city in China and its implications for family doctor contract service policy.

BACKGROUND: Family doctor contract policy is now run by the State Council as an important move to promote the hierarchical medical system. Whether the family doctor contract policy achieves the initial government's goal should be measured further from the perspective of patient visits between hospitals and community health centers, which are regarded as grass medical agencies. METHODS: The spatial feature measurement method is applied with ArcGIS 10.2 software to analyze the spatial aggregation effect of patient visits to hospitals or community health centers among 20 districts of one large city in China and analyze the family doctor contract policy published in those areas to compare the influence of visit tendencies. RESULTS: From year 2016-2020, visits to hospitals were in the high-high cluster, and the density was spatially overflow, while there was no such tendency in visits to community health centers. The analysis of different family doctor contract policy implementation times in 20 districts reflects that the family doctor contract policy has a very limited effect on the promotion of the hierarchical medical system, and the innovation of the family doctor contract policy needs to be considered. CONCLUSIONS: A brief summary and potential implications. A multi-integrated medical system along with family doctor contract policy needs to be established, especially integrated in leadership and governance, financing, workforce, and service delivery between hospitals and community health centers, to promote the hierarchical medical system.

Spectral Features Analysis for Print Quality Prediction in Additive Manufacturing: An Acoustics-Based Approach.

Quality prediction in additive manufacturing (AM) processes is crucial, particularly in high-risk manufacturing sectors like aerospace, biomedicals, and automotive. Acoustic sensors have emerged as valuable tools for detecting variations in print patterns by analyzing signatures and extracting distinctive features. This study focuses on the collection, preprocessing, and analysis of acoustic data streams from a Fused Deposition Modeling (FDM) 3D-printed sample cube (10 mm × 10 mm × 5 mm). Time and frequency-domain features were extracted at 10-s intervals at varying layer thicknesses. The audio samples were preprocessed using the Harmonic-Percussive Source Separation (HPSS) method, and the analysis of time and frequency features was performed using the Librosa module. Feature importance analysis was conducted, and machine learning (ML) prediction was implemented using eight different classifier algorithms (K-Nearest Neighbors (KNN), Support Vector Machine (SVM), Gaussian Naive Bayes (GNB), Decision Trees (DT), Logistic Regression (LR), Random Forest (RF), Extreme Gradient Boosting (XGB), and Light Gradient Boosting Machine (LightGBM)) for the classification of print quality based on the labeled datasets. Three-dimensional-printed samples with varying layer thicknesses, representing two print quality levels, were used to generate audio samples. The extracted spectral features from these audio samples served as input variables for the supervised ML algorithms to predict print quality. The investigation revealed that the mean of the spectral flatness, spectral centroid, power spectral density, and RMS energy were the most critical acoustic features. Prediction metrics, including accuracy scores, F-1 scores, recall, precision, and ROC/AUC, were utilized to evaluate the models. The extreme gradient boosting algorithm stood out as the top model, attaining a prediction accuracy of 91.3%, precision of 88.8%, recall of 92.9%, F-1 score of 90.8%, and AUC of 96.3%. This research lays the foundation for acoustic based quality prediction and control of 3D printed parts using Fused Deposition Modeling and can be extended to other additive manufacturing techniques.

Classification of Sand-Binder Mixtures from the Foundry Industry Using Electrical Impedance Spectroscopy and Support Vector Machines.

Molding sand mixtures used in the foundry industry consist of various sands (quartz sands, chromite sands, etc.) and additives such as bentonite. The optimum control of the processes involved in using the mixtures and in their regeneration after the casting requires an efficient in-line monitoring method that is not available today. We are investigating whether such a method can be based on electrical impedance spectroscopy (EIS). To establish a database, we have characterized various sand mixtures by EIS in the frequency range from 0.5 kHz to 1 MHz under laboratory conditions. Attempts at classifying the different molding sand mixtures by support vector machines (SVM) show encouraging results. Already high assignment accuracies (above 90%) could even be improved with suitable feature selection (sequential feature selection). At the same time, the standard uncertainty of the SVM results is low, i.e., data assigned to a class by the presented SVMs have a high probability of being assigned correctly. The application of EIS with subsequent evaluation by machine learning (machine-learning-enhanced EIS, MLEIS) in the field of bulk material monitoring in the foundry industry appears possible.

Deep learning applications to breast cancer detection by magnetic resonance imaging: a literature review.

Deep learning analysis of radiological images has the potential to improve diagnostic accuracy of breast cancer, ultimately leading to better patient outcomes. This paper systematically reviewed the current literature on deep learning detection of breast cancer based on magnetic resonance imaging (MRI). The literature search was performed from 2015 to Dec 31, 2022, using Pubmed. Other database included Semantic Scholar, ACM Digital Library, Google search, Google Scholar, and pre-print depositories (such as Research Square). Articles that were not deep learning (such as texture analysis) were excluded. PRISMA guidelines for reporting were used. We analyzed different deep learning algorithms, methods of analysis, experimental design, MRI image types, types of ground truths, sample sizes, numbers of benign and malignant lesions, and performance in the literature. We discussed lessons learned, challenges to broad deployment in clinical practice and suggested future research directions.

NeuroPpred-Fuse: an interpretable stacking model for prediction of neuropeptides by fusing sequence information and feature selection methods.

Neuropeptides acting as signaling molecules in the nervous system of various animals play crucial roles in a wide range of physiological functions and hormone regulation behaviors. Neuropeptides offer many opportunities for the discovery of new drugs and targets for the treatment of neurological diseases. In recent years, there have been several data-driven computational predictors of various types of bioactive peptides, but the relevant work about neuropeptides is little at present. In this work, we developed an interpretable stacking model, named NeuroPpred-Fuse, for the prediction of neuropeptides through fusing a variety of sequence-derived features and feature selection methods. Specifically, we used six types of sequence-derived features to encode the peptide sequences and then combined them. In the first layer, we ensembled three base classifiers and four feature selection algorithms, which select non-redundant important features complementarily. In the second layer, the output of the first layer was merged and fed into logistic regression (LR) classifier to train the model. Moreover, we analyzed the selected features and explained the feasibility of the selected features. Experimental results show that our model achieved 90.6% accuracy and 95.8% AUC on the independent test set, outperforming the state-of-the-art models. In addition, we exhibited the distribution of selected features by these tree models and compared the results on the training set to that on the test set. These results fully showed that our model has a certain generalization ability. Therefore, we expect that our model would provide important advances in the discovery of neuropeptides as new drugs for the treatment of neurological diseases.

RFhy-m2G: Identification of RNA N2-methylguanosine modification sites based on random forest and hybrid features.

N2-methylguanosine is a post-transcriptional modification of RNA that is found in eukaryotes and archaea. The biological function of m2G modification discovered so far is to control and stabilize the three-dimensional structure of tRNA and the dynamic barrier of reverse transcription. To discover additional biological functions of m2G, it is necessary to develop time-saving and labor-saving calculation tools to identify m2G. In this paper, based on hybrid features and a random forest, a novel predictor, RFhy-m2G, was developed to identify the m2G modification sites for three species. The hybrid feature used by the predictor is used to fuse the three features of ENAC, PseDNC, and NPPS. These three features include primary sequence derivation properties, physicochemical properties, and position-specific properties. Since there are redundant features in hybrid features, MRMD2.0 is used for optimal feature selection. Through feature analysis, it is found that the optimal hybrid features obtained still contain three kinds of properties, and the hybrid features can more accurately identify m2G modification sites and improve prediction performance. Based on five-fold cross-validation and independent testing to evaluate the prediction model, the accuracies obtained were 0.9982 and 0.9417, respectively. The robustness of the predictor is demonstrated by comparisons with other predictors.

m6AmPred: Identifying RNA N6, 2'-O-dimethyladenosine (m6Am) sites based on sequence-derived information.

N6,2'-O-dimethyladenosine (m6Am) is a reversible modification widely occurred on varied RNA molecules. The biological function of m6Am is yet to be known though recent studies have revealed its influences in cellular mRNA fate. Precise identification of m6Am sites on RNA is vital for the understanding of its biological functions. We present here m6AmPred, the first web server for in silico identification of m6Am sites from the primary sequences of RNA. Built upon the eXtreme Gradient Boosting with Dart algorithm (XgbDart) and EIIP-PseEIIP encoding scheme, m6AmPred achieved promising prediction performance with the AUCs greater than 0.954 when tested by 10-fold cross-validation and independent testing datasets. To critically test and validate the performance of m6AmPred, the experimentally verified m6Am sites from two data sources were cross-validated. The m6AmPred web server is freely accessible at: https://www.xjtlu.edu.cn/biologicalsciences/m6am, and it should make a useful tool for the researchers who are interested in N6,2'-O-dimethyladenosine RNA modification.

Identification of radiomic biomarkers in a set of four skeletal muscle groups on Dixon MRI of the NAKO MR study.

In this work, we propose a processing pipeline for the extraction and identification of meaningful radiomics biomarkers in skeletal muscle tissue as displayed using Dixon-weighted MRI. Diverse and robust radiomics features can be identified that may be of aid in the accurate quantification e.g. varying degrees of sarcopenia in respective muscles of large cohorts. As such, the approach comprises the texture feature extraction from raw data based on well established approaches, such as a nnU-Net neural network and the Pyradiomics toolbox, a subsequent selection according to adequate conditions for the muscle tissue of the general population, and an importance-based ranking to further narrow the amount of meaningful features with respect to auxiliary targets. The performance was investigated with respect to the included auxiliary targets, namely age, body mass index (BMI), and fat fraction (FF). Four skeletal muscles with different fiber architecture were included: the mm. glutaei, m. psoas, as well as the extensors and adductors of the thigh. The selection allowed for a reduction from 1015 available texture features to 65 for age, 53 for BMI, and 36 for FF from the available fat/water contrast images considering all muscles jointly. Further, the dependence of the importance rankings calculated for the auxiliary targets on validation sets (in a cross-validation scheme) was investigated by boxplots. In addition, significant differences between subgroups of respective auxiliary targets as well as between both sexes were shown to be present within the ten lowest ranked features by means of Kruskal-Wallis H-tests and Mann-Whitney U-tests. The prediction performance for the selected features and the ranking scheme were verified on validation sets by a random forest based multi-class classification, with strong area under the curve (AUC) values of the receiver operator characteristic (ROC) of 73.03 ± 0.70 % and 73.63 ± 0.70 % for the water and fat images in age, 80.68 ± 0.30 % and 88.03 ± 0.89 % in BMI, as well as 98.36 ± 0.03 % and 98.52 ± 0.09 % in FF.

How effective are community-based disaster reduction strategies? Evidence from the largest-scale program so far.

Strategies of community-based disaster risk reduction have been advocated for more than 2 decades. However, we still lack in-depth quantitative assessments of the effectiveness of such strategies. Our research is based on a national experiment in this domain: the "Comprehensive Disaster Reduction Demonstration Community" project, a governmental program running in China since 2007. Information on more than 11,000 demonstration communities was collected. Combined with the local disaster information and socioeconomic conditions, the spatiotemporal characteristics of these communities over 12 years and their differences in performance by region and income group were analyzed. We performed an attribution analysis for disaster risk reduction effectiveness. This is the first time a series of quantitative evaluation methods have been applied to verify the effectiveness of a large-scale community-based disaster risk reduction project, both from the perspective of demonstrative effects and loss reduction benefits. Here, we find that the project is obviously effective from these two perspectives, and the disaster loss reduction effectiveness illustrates clear regional differences, where the regional economic level and hazard severity act as important drivers. Significant differences of urban-rural and income call for matching fortification measures, and the dynamic management of demonstration community size is required, since the loss reduction benefit converges when the penetration rate of the demonstration community reaches approximately 4% in a province. These and further results provide diverse implications for community-based disaster risk reduction policies and practices.

Detection and Quantification of Extraterrestrial Platinum Group Element Alloy Micronuggets from Archean Impactite Deposits by Low-Voltage Scanning Electron Microscopy/Energy-Dispersive X-ray Spectrometry.

Rare, heterogeneously composed platinum group element alloy micronuggets (PGNs) occur in primitive meteorites, micrometeorites, and terrestrial impactite deposits. To gain insight into the nature of these phases, we developed a workflow for the characterization of PGNs using modern scanning electron microscopy (SEM) and energy-dispersive X-ray spectrometry at a low accelerating voltage of 6 kV. Automated feature analysis-a combination of morphological image analysis and elemental analysis with stage control-allowed us to detect PGNs down to 200 nm over a relatively large analysis area of 53 mm2 with a conventional silicon drift detector (SDD). Hyperspectral imaging with a high-sensitivity, annular SDD can be performed at low beam current (∼100 pA) which improves the SEM image resolution and minimizes hydrocarbon contamination. The severe overlapping peaks of the platinum group element L and M line families at 2-3 keV and the Fe and Ni L line families at <1 keV can be resolved by peak deconvolution. Quantitative elemental analysis can be performed at a spatial resolution of <80 nm; however, the results are affected by background subtraction errors for the Fe L line family. Furthermore, the inaccuracy of the matrix correction coefficients may influence standards-based quantification with pure element reference samples.

Long-Term Coronary Artery Disease Risk Prediction with Machine Learning Models.

The heart is the most vital organ of the human body; thus, its improper functioning has a significant impact on human life. Coronary artery disease (CAD) is a disease of the coronary arteries through which the heart is nourished and oxygenated. It is due to the formation of atherosclerotic plaques on the wall of the epicardial coronary arteries, resulting in the narrowing of their lumen and the obstruction of blood flow through them. Coronary artery disease can be delayed or even prevented with lifestyle changes and medical intervention. Long-term risk prediction of coronary artery disease will be the area of interest in this work. In this specific research paper, we experimented with various machine learning (ML) models after the use or non-use of the synthetic minority oversampling technique (SMOTE), evaluating and comparing them in terms of accuracy, precision, recall and an area under the curve (AUC). The results showed that the stacking ensemble model after the SMOTE with 10-fold cross-validation prevailed over the other models, achieving an accuracy of 90.9 %, a precision of 96.7%, a recall of 87.6% and an AUC equal to 96.1%.

Explaining Accurate Predictions of Multitarget Compounds with Machine Learning Models Derived for Individual Targets.

In drug discovery, compounds with well-defined activity against multiple targets (multitarget compounds, MT-CPDs) provide the basis for polypharmacology and are thus of high interest. Typically, MT-CPDs for polypharmacology have been discovered serendipitously. Therefore, over the past decade, computational approaches have also been adapted for the design of MT-CPDs or their identification via computational screening. Such approaches continue to be under development and are far from being routine. Recently, different machine learning (ML) models have been derived to distinguish between MT-CPDs and corresponding compounds with activity against the individual targets (single-target compounds, ST-CPDs). When evaluating alternative models for predicting MT-CPDs, we discovered that MT-CPDs could also be accurately predicted with models derived for corresponding ST-CPDs; this was an unexpected finding that we further investigated using explainable ML. The analysis revealed that accurate predictions of ST-CPDs were determined by subsets of structural features of MT-CPDs required for their prediction. These findings provided a chemically intuitive rationale for the successful prediction of MT-CPDs using different ML models and uncovered general-feature subset relationships between MT- and ST-CPDs with activities against different targets.

Development of sign phonology in Kata Kolok.

Much like early speech, early signing is characterised by modifications. Sign language phonology has been analysed on the feature level since the 1980s, yet acquisition studies predominately examine handshape, location, and movement. This study is the first to analyse the acquisition of phonology in the sign language of a Balinese village with a vibrant signing community and applies the same feature analysis to adult and child data. We analyse longitudinal data of four deaf children from the Kata Kolok Child Signing Corpus. The form comparison of child productions and adult targets yields three main findings: i) handshape modifications are most frequent, echoing cross-linguistic patterns; ii) modification rates of other features differ from previous studies, possibly due to differences in methodology or KK's phonology; iii) co-occurrence of modifications within a sign suggest feature interdependencies. We argue that nuanced approaches to child signing are necessary to understand the complexity of early signing.

Focusing on the locus of the breakdown for treatment of anomia: a pilot study.

The primary goal of this study was to evaluate the treatment effects of semantic feature analysis (SFA) and phonological components analysis (PCA) on word retrieval processing in persons with aphasia (PWAs). After identifying the locus of the breakdown in lexical retrieval processing, 15 monolingual native Persian speakers with aphasia were divided into two groups. After three naming trials, participants with dominant semantic deficits received SFA, and participants with primary phonological deficits were provided with PCA three times a week for eight weeks. Both approaches improved participants' naming and performance on language tests, including spontaneous speech, repetition, comprehension, and semantic processing. However, the correct naming of treated and untreated items was higher in mild-to-moderate participants, with mostly circumlocution and semantic paraphasias in the SFA group. The same holds for mild-to-moderate participants with mostly phonemic paraphasia who received PCA therapy. Moreover, the results showed that participants' baseline naming performance and semantic abilities could be associated with the treatment outcomes. Although limited by a lack of a control group, this study provided evidence supporting the possible benefits of focusing on the locus of the breakdown for treating anomia through SFA and PCA approaches, specifically in participants with mild to moderate aphasia. However, for those with severe aphasia, the treatment choice may not be as straightforward because several variables are likely to contribute to this population's word-finding difficulties. Replication with larger, well-stratified samples, use of a within-subjects alternating treatment design and consideration of treatments' long-term effects are required to better ascertain the effects of focusing on the locus of breakdown for treatment of anomia.

A Hybrid Recommender System Based on Autoencoder and Latent Feature Analysis.

A recommender system (RS) is highly efficient in extracting valuable information from a deluge of big data. The key issue of implementing an RS lies in uncovering users' latent preferences on different items. Latent Feature Analysis (LFA) and deep neural networks (DNNs) are two of the most popular and successful approaches to addressing this issue. However, both the LFA-based and the DNNs-based models have their own distinct advantages and disadvantages. Consequently, relying solely on either the LFA or DNN-based models cannot ensure optimal recommendation performance across diverse real-world application scenarios. To address this issue, this paper proposes a novel hybrid recommendation model that combines Autoencoder and LFA techniques, termed AutoLFA. The main idea of AutoLFA is two-fold: (1) It leverages an Autoencoder and an LFA model separately to construct two distinct recommendation models, each residing in a unique metric representation space with its own set of strengths; and (2) it integrates the Autoencoder and LFA model using a customized self-adaptive weighting strategy, thereby capitalizing on the merits of both approaches. To evaluate the proposed AutoLFA model, extensive experiments on five real recommendation datasets are conducted. The results demonstrate that AutoLFA achieves significantly better recommendation performance than the seven related state-of-the-art models.

An application of slow feature analysis to the genetic sequences of coronaviruses and influenza viruses.

BACKGROUND: Mathematical approaches have been for decades used to probe the structure of DNA sequences. This has led to the development of Bioinformatics. In this exploratory work, a novel mathematical method is applied to probe the DNA structure of two related viral families: those of coronaviruses and those of influenza viruses. The coronaviruses are SARS-CoV-2, SARS-CoV-1, and MERS. The influenza viruses include H1N1-1918, H1N1-2009, H2N2-1957, and H3N2-1968. METHODS: The mathematical method used is the slow feature analysis (SFA), a rather new but promising method to delineate complex structure in DNA sequences. RESULTS: The analysis indicates that the DNA sequences exhibit an elaborate and convoluted structure akin to complex networks. We define a measure of complexity and show that each DNA sequence exhibits a certain degree of complexity within itself, while at the same time there exists complex inter-relationships between the sequences within a family and between the two families. From these relationships, we find evidence, especially for the coronavirus family, that increasing complexity in a sequence is associated with higher transmission rate but with lower mortality. CONCLUSIONS: The complexity measure defined here may hold a promise and could become a useful tool in the prediction of transmission and mortality rates in future new viral strains.

A methodological framework for AI-assisted diagnosis of active aortitis using radiomic analysis of FDG PET-CT images: Initial analysis.

BACKGROUND: The aim of this study was to explore the feasibility of assisted diagnosis of active (peri-)aortitis using radiomic imaging biomarkers derived from [18F]-Fluorodeoxyglucose Positron Emission Tomography-Computed Tomography (FDG PET-CT) images. METHODS: The aorta was manually segmented on FDG PET-CT in 50 patients with aortitis and 25 controls. Radiomic features (RF) (n = 107), including SUV (Standardized Uptake Value) metrics, were extracted from the segmented data and harmonized using the ComBat technique. Individual RFs and groups of RFs (i.e., signatures) were used as input in Machine Learning classifiers. The diagnostic utility of these classifiers was evaluated with area under the receiver operating characteristic curve (AUC) and accuracy using the clinical diagnosis as the ground truth. RESULTS: Several RFs had high accuracy, 84% to 86%, and AUC scores 0.83 to 0.97 when used individually. Radiomic signatures performed similarly, AUC 0.80 to 1.00. CONCLUSION: A methodological framework for a radiomic-based approach to support diagnosis of aortitis was outlined. Selected RFs, individually or in combination, showed similar performance to the current standard of qualitative assessment in terms of AUC for identifying active aortitis. This framework could support development of a clinical decision-making tool for a more objective and standardized assessment of aortitis.

Dual-Scale Doppler Attention for Human Identification.

This paper considers a Deep Convolutional Neural Network (DCNN) with an attention mechanism referred to as Dual-Scale Doppler Attention (DSDA) for human identification given a micro-Doppler (MD) signature induced as input. The MD signature includes unique gait characteristics by different sized body parts moving, as arms and legs move rapidly, while the torso moves slowly. Each person is identified based on his/her unique gait characteristic in the MD signature. DSDA provides attention at different time-frequency resolutions to cater to different MD components composed of both fast-varying and steady. Through this, DSDA can capture the unique gait characteristic of each person used for human identification. We demonstrate the validity of DSDA on a recently published benchmark dataset, IDRad. The empirical results show that the proposed DSDA outperforms previous methods, using a qualitative analysis interpretability on MD signatures.