Crystallographic phase identifier of a convolutional self-attention neural network (CPICANN) on powder diffraction patterns

Spectroscopic data, particularly diffraction data, are essential for materials characterization due to their comprehensive crystallographic information. The current crystallographic phase identification, however, is very time consuming. To address this challenge, we have developed a real-time crystallographic phase identifier based on a convolutional self-attention neural network (CPICANN). Trained on 692 190 simulated powder X-ray diffraction (XRD) patterns from 23 073 distinct inorganic crystallographic information files, CPICANN demonstrates superior phase-identification power. Single-phase identification on simulated XRD patterns yields 98.5 and 87.5% accuracies with and without elemental information, respectively, outperforming JADE software (68.2 and 38.7%, respectively). Bi-phase identification on simulated XRD patterns achieves 84.2 and 51.5% accuracies, respectively. In experimental settings, CPICANN achieves an 80% identification accuracy, surpassing JADE software (61%). Integration of CPICANN into XRD refinement software will significantly advance the cutting-edge technology in XRD materials characterization.

Multivariate Modeling for Spatio-Temporal Radon Flux Predictions

Nowadays, various fields in environmental sciences require the availability of appropriate techniques to exploit the information given by multivariate spatial or spatio-temporal observations. In particular, radon flux data which are of high interest to monitor greenhouse gas emissions and to assess human exposure to indoor radon are determined by the deposit of uranium and radio (precursor elements). Furthermore, they are also affected by various atmospheric variables, such as humidity, temperature, precipitation and evapotranspiration. To this aim, a significant role can be recognized to the tools of multivariate geostatistics which supports the modeling and prediction of variables under study. In this paper, the spatio-temporal distribution of radon flux densities over the Veneto Region (Italy) and its estimation at unsampled points in space and time are discussed. In particular, the spatio-temporal linear coregionalization model is identified on the basis of the joint diagonalization of the empirical covariance matrices evaluated at different spatio-temporal lags and is used to produce predicted radon flux maps for different months. Probability maps, that the radon flux density in the upcoming months is greater than three historical statistics, are then built. This might be of interest especially in summer months when the risk of radon exhalation is higher. Moreover, a comparison with respect to alternative models in the univariate and multivariate context is provided.

Bronchial epithelial cell transcriptional responses to inhaled corticosteroids dictate severe asthmatic outcomes

BACKGROUND

Inhaled corticosteroids (CSs) are the backbone of asthma treatment, improving quality of life, exacerbation rates, and mortality. Although effective for most, a subset of patients with asthma experience CS-resistant disease despite receiving high-dose medication.

OBJECTIVE

We sought to investigate the transcriptomic response of bronchial epithelial cells (BECs) to inhaled CSs.

METHODS

Independent component analysis was performed on datasets, detailing the transcriptional response of BECs to CS treatment. The expression of these CS-response components was examined in 2 patient cohorts and investigated in relation to clinical parameters. Supervised learning was used to predict BEC CS responses using peripheral blood gene expression.

RESULTS

We identified a signature of CS response that was closely correlated with CS use in patients with asthma. Participants could be separated on the basis of CS-response genes into groups with high and low signature expression. Patients with low expression of CS-response genes, particularly those with a severe asthma diagnosis, showed worse lung function and quality of life. These individuals demonstrated enrichment for T-lymphocyte infiltration in endobronchial brushings. Supervised machine learning identified a 7-gene signature from peripheral blood that reliably identified patients with poor CS-response expression in BECs.

CONCLUSIONS

Loss of CS transcriptional responses within bronchial epithelium was related to impaired lung function and poor quality of life, particularly in patients with severe asthma. These individuals were identified using minimally invasive blood sampling, suggesting these findings may enable earlier triage to alternative treatments.

Blind recovery of sources for multivariate space-time random fields

With advances in modern worlds technology, huge datasets that show dependencies in space as well as in time occur frequently in practice. As an example, several monitoring stations at different geographical locations track hourly concentration measurements of a number of air pollutants for several years. Such a dataset contains thousands of multivariate observations, thus, proper statistical analysis needs to account for dependencies in space and time between and among the different monitored variables. To simplify the consequent multivariate spatio-temporal statistical analysis it might be of interest to detect linear transformations of the original observations that result in straightforward interpretative, spatio-temporally uncorrelated processes that are also highly likely to have a real physical meaning. Blind source separation (BSS) represents a statistical methodology which has the aim to recover so-called latent processes, that exactly meet the former requirements. BSS was already successfully used in sole temporal and sole spatial applications with great success, but, it was not yet introduced for the spatio-temporal case. In this contribution, a reasonable and innovative generalization of BSS for multivariate space-time random fields (stBSS), under second-order stationarity, is proposed, together with two space-time extensions of the well-known algorithms for multiple unknown signals extraction (stAMUSE) and the second-order blind identification (stSOBI) which solve the formulated problem. Furthermore, symmetry and separability properties of the model are elaborated and connections to the space-time linear model of coregionalization and to the classical principal component analysis are drawn. Finally, the usefulness of the new methods is shown in a thorough simulation study and on a real environmental application.

ERP Analysis Using a Multi-Channel Matching Pursuit Algorithm

In this study, we propose a new algorithm for analysing event-related components observed in EEG signals in psychological experiments. We investigate its capabilities and limitations. The algorithm is based on multivariate matching pursuit and clustering. It is aimed to find patterns in EEG signals which are similar across different experimental conditions, but it allows for variations in amplitude and slight variability in topography. The method proved to yield expected results in numerical simulations. For the real data coming from an emotional categorisation task experiment, we obtained two indications. First, the method can be used as a specific filter that reduces the variability of components, as defined classically, within each experimental condition. Second, equivalent dipoles fitted to items of the activity clusters identified by the algorithm localise in compact brain areas related to the task performed by the subjects across experimental conditions. Thus this activity may be studied as candidates for hypothetical latent components. The proposed algorithm is a promising new tool in ERP studies, which deserves further experimental evaluations.

A review of second-order blind identification methods

Second-order source separation (SOS) is a data analysis tool which can be used for revealing hidden structures in multivariate time series data or as a tool for dimension reduction. Such methods are nowadays increasingly important as more and more high-dimensional multivariate time series data are measured in numerous fields of applied science. Dimension reduction is crucial, as modeling such high-dimensional data with multivariate time series models is often impractical as the number of parameters describing dependencies between the component time series is usually too high. SOS methods have their roots in the signal processing literature, where they were first used to separate source signals from an observed signal mixture. The SOS model assumes that the observed time series (signals) is a linear mixture of latent time series (sources) with uncorrelated components. The methods make use of the second-order statistics-hence the name "second-order source separation." In this review, we discuss the classical SOS methods and their extensions to more complex settings. An example illustrates how SOS can be performed. This article is categorized under:Statistical Models > Time Series ModelsStatistical and Graphical Methods of Data Analysis > Dimension ReductionData: Types and Structure > Time Series, Stochastic Processes, and Functional Data.

Computational advances for spatio-temporal multivariate environmental models

In multivariate Geostatistics, the linear coregionalization model (LCM) has been widely used over the last decades, in order to describe the spatial dependence which characterizes two or more variables of interest. However, in spatio-temporal multiple modeling, the identification of the main elements of a space–time linear coregionalization model (ST-LCM), as well as of the latent structures underlying the analyzed phenomenon, represents a tough task. In this paper, some computational advances which support the selection of an ST-LCM are described, gathering all the necessary steps which allow the analyst to easily and properly detect the basic space–time components for the phenomenon under study. The implemented algorithm is applied on space–time air quality data measured in Scotland in 2017.

Fast tensorial JADE

We propose a novel method for tensorial-independent component analysis. Our approach is based on TJADE and k-JADE, two recently proposed generalizations of the classical JADE algorithm. Our novel method achieves the consistency and the limiting distribution of TJADE under mild assumptions and at the same time offers notable improvement in computational speed. Detailed mathematical proofs of the statistical properties of our method are given and, as a special case, a conjecture on the properties of k-JADE is resolved. Simulations and timing comparisons demonstrate remarkable gain in speed. Moreover, the desired efficiency is obtained approximately for finite samples. The method is applied successfully to large-scale video data, for which neither TJADE nor k-JADE is feasible. Finally, an experimental procedure is proposed to select the values of a set of tuning parameters. Supplementary material including the R-code for running the examples and the proofs of the theoretical results is available online.

Sampling Properties of color Independent Component Analysis

Independent Component Analysis (ICA) offers an effective data-driven approach for blind source extraction encountered in many signal and image processing problems. Although many ICA methods have been developed, they have received relatively little attention in the statistics literature, especially in terms of rigorous theoretical investigation for statistical inference. The current paper aims at narrowing this gap and investigates the statistical sampling properties of the colorICA (cICA) method. The cICA incorporates the correlation structure within sources through parametric time series models in the frequency domain and outperforms several existing ICA alternatives numerically. We establish the consistency and asymptotic normality of the cICA estimates, which then enables statistical inference based on the estimates. These asymptotic properties are further validated using simulation studies.

IL-33 Signaling Alters Regulatory T Cell Diversity in Support of Tumor Development

Regulatory T cells (T_regs) can impair anti-tumor immune responses and are associated with poor prognosis in multiple cancer types. T_regs in human tumors span diverse transcriptional states distinct from those of peripheral T_regs, but their contribution to tumor development remains unknown. Here, we use single-cell RNA sequencing (RNA-seq) to longitudinally profile dynamic shifts in the distribution of T_regs in a genetically engineered mouse model of lung adenocarcinoma. In this model, interferon-responsive T_regs are more prevalent early in tumor development, whereas a specialized effector phenotype characterized by enhanced expression of the interleukin-33 receptor ST2 is predominant in advanced disease. T_reg-specific deletion of ST2 alters the evolution of effector T_reg diversity, increases infiltration of CD8⁺ T cells into tumors, and decreases tumor burden. Our study shows that ST2 plays a critical role in T_reg-mediated immunosuppression in cancer, highlighting potential paths for therapeutic intervention.

Rapid Multi-Sensor Feature Fusion Based on Non-Stationary Kernel JADE for the Small-Amplitude Hunting Monitoring of High-Speed Trains

Joint Approximate Diagonalization of Eigen-matrices (JADE) cannot deal with non-stationary data. Therefore, in this paper, a method called Non-stationary Kernel JADE (NKJADE) is proposed, which can extract non-stationary features and fuse multi-sensor features precisely and rapidly. In this method, the non-stationarity of the data is considered and the data from multi-sensor are used to fuse the features efficiently. The method is compared with EEMD-SVD-LTSA and EEMD-JADE using the bearing fault data of CWRU, and the validity of the method is verified. Considering that the vibration signals of high-speed trains are typically non-stationary, it is necessary to utilize a rapid feature fusion method to identify the evolutionary trends of hunting motions quickly before the phenomenon is fully manifested. In this paper, the proposed method is applied to identify the evolutionary trend of hunting motions quickly and accurately. Results verify that the accuracy of this method is much higher than that of the EEMD-JADE and EEMD-SVD-LTSA methods. This method can also be used to fuse multi-sensor features of non-stationary data rapidly.

Blind Source Separation for Compositional Time Series

Many geological phenomena are regularly measured over time to follow developments and changes. For many of these phenomena, the absolute values are not of interest, but rather the relative information, which means that the data are compositional time series. Thus, the serial nature and the compositional geometry should be considered when analyzing the data. Multivariate time series are already challenging, especially if they are higher dimensional, and latent variable models are a popular way to deal with this kind of data. Blind source separation techniques are well-established latent factor models for time series, with many variants covering quite different time series models. Here, several such methods and their assumptions are reviewed, and it is shown how they can be applied to high-dimensional compositional time series. Also, a novel blind source separation method is suggested which is quite flexible regarding the assumptions of the latent time series. The methodology is illustrated using simulations and in an application to light absorbance data from water samples taken from a small stream in Lower Austria.

Extracting Conditionally Heteroskedastic Components using Independent Component Analysis

In the independent component model, the multivariate data are assumed to be a mixture of mutually independent latent components. The independent component analysis (ICA) then aims at estimating these latent components. In this article, we study an ICA method which combines the use of linear and quadratic autocorrelations to enable efficient estimation of various kinds of stationary time series. Statistical properties of the estimator are studied by finding its limiting distribution under general conditions, and the asymptotic variances are derived in the case of ARMA-GARCH model. We use the asymptotic results and a finite sample simulation study to compare different choices of a weight coefficient. As it is often of interest to identify all those components which exhibit stochastic volatility features we suggest a test statistic for this problem. We also show that a slightly modified version of the principal volatility component analysis can be seen as an ICA method. Finally, we apply the estimators in analysing a data set which consists of time series of exchange rates of seven currencies to US dollar. Supporting information including proofs of the theorems is available online.

Spatial blind source separation

Recently a blind source separation model was suggested for spatial data, along with an estimator based on the simultaneous diagonalization of two scatter matrices. The asymptotic properties of this estimator are derived here, and a new estimator based on the joint diagonalization of more than two scatter matrices is proposed. The asymptotic properties and merits of the novel estimator are verified in simulation studies. A real-data example illustrates application of the method.

CRISPR-mediated modeling and functional validation of candidate tumor suppressor genes in small cell lung cancer

Small cell lung cancer (SCLC) is a highly aggressive subtype of lung cancer that remains among the most lethal of solid tumor malignancies. Recent genomic sequencing studies have identified many recurrently mutated genes in human SCLC tumors. However, the functional roles of most of these genes remain to be validated. Here, we have adapted the CRISPR-Cas9 system to a well-established murine model of SCLC to rapidly model loss-of-function mutations in candidate genes identified from SCLC sequencing studies. We show that loss of the gene p107 significantly accelerates tumor progression. Notably, compared with loss of the closely related gene p130, loss of p107 results in fewer but larger tumors as well as earlier metastatic spread. In addition, we observe differences in proliferation and apoptosis as well as altered distribution of initiated tumors in the lung, resulting from loss of p107 or p130 Collectively, these data demonstrate the feasibility of using the CRISPR-Cas9 system to model loss of candidate tumor suppressor genes in SCLC, and we anticipate that this approach will facilitate efforts to investigate mechanisms driving tumor progression in this deadly disease.

Quantitative proteomics identify Tenascin-C as a promoter of lung cancer progression and contributor to a signature prognostic of patient survival

The extracellular microenvironment is an integral component of normal and diseased tissues that is poorly understood owing to its complexity. To investigate the contribution of the microenvironment to lung fibrosis and adenocarcinoma progression, two pathologies characterized by excessive stromal expansion, we used mouse models to characterize the extracellular matrix (ECM) composition of normal lung, fibrotic lung, lung tumors, and metastases. Using quantitative proteomics, we identified and assayed the abundance of 113 ECM proteins, which revealed robust ECM protein signatures unique to fibrosis, primary tumors, or metastases. These analyses indicated significantly increased abundance of several S100 proteins, including Fibronectin and Tenascin-C (Tnc), in primary lung tumors and associated lymph node metastases compared with normal tissue. We further showed that Tnc expression is repressed by the transcription factor Nkx2-1, a well-established suppressor of metastatic progression. We found that increasing the levels of Tnc, via CRISPR-mediated transcriptional activation of the endogenous gene, enhanced the metastatic dissemination of lung adenocarcinoma cells. Interrogation of human cancer gene expression data revealed that high TNC expression correlates with worse prognosis for lung adenocarcinoma, and that a three-gene expression signature comprising TNC, S100A10, and S100A11 is a robust predictor of patient survival independent of age, sex, smoking history, and mutational load. Our findings suggest that the poorly understood ECM composition of the fibrotic and tumor microenvironment is an underexplored source of diagnostic markers and potential therapeutic targets for cancer patients.

DDK Promotes Tumor Chemoresistance and Survival via Multiple Pathways

DBF4-dependent kinase (DDK) is a two-subunit kinase required for initiating DNA replication at individual origins and is composed of CDC7 kinase and its regulatory subunit DBF4. Both subunits are highly expressed in many diverse tumor cell lines and primary tumors, and this is correlated with poor prognosis. Inhibiting DDK causes apoptosis of tumor cells, but not normal cells, through a largely unknown mechanism. Firstly, to understand why DDK is often overexpressed in tumors, we identified gene expression signatures that correlate with DDK high- and DDK low-expressing lung adenocarcinomas. We found that increased DDK expression is highly correlated with inactivation of RB1-E2F and p53 tumor suppressor pathways. Both CDC7 and DBF4 promoters bind E2F, suggesting that increased E2F activity in RB1 mutant cancers promotes increased DDK expression. Surprisingly, increased DDK expression levels are also correlated with both increased chemoresistance and genome-wide mutation frequencies. Our data further suggest that high DDK levels directly promote elevated mutation frequencies. Secondly, we performed an RNAi screen to investigate how DDK inhibition causes apoptosis of tumor cells. We identified 23 kinases and phosphatases required for apoptosis when DDK is inhibited. These hits include checkpoint genes, G2/M cell cycle regulators, and known tumor suppressors leading to the hypothesis that inhibiting mitotic progression can protect against DDKi-induced apoptosis. Characterization of one novel hit, the LATS2 tumor suppressor, suggests that it promotes apoptosis independently of the upstream MST1/2 kinases in the Hippo signaling pathway.