This repository contains data, manual picks, catalogs and codes to reproduce the results and figures shown in the scientific paper "Harnessing secondary phases for rapid magnitude estimation with DAS offshore Chile and its implications for Early Warning".

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Pleural mesothelioma (PM) is an aggressive cancer with a dismal prognosis. Co-targeting of immune checkpoint inhibitors (ICI) CTLA-4 and PD-1, the new standard of care for PM, is still clinically unsatisfying, regardless of PM histotype. Moreover, no predictive biomarkers of ICI efficacy are available in PM. We performed multi-omics analysis of pre-ICI therapy lesions from 91 PM patients enrolled in the multicenter NIBIT-EPI-MESO study and identified four clinically meaningful PM subsets with progressively increasing global DNA methylation profiles from demethylated (DEM), LOW, intermediate (INT), and CpG island methylator phenotype (CIMP). This tumor methylome classification predicted both response and survival to ICI therapy. Indeed, the LOW subset was enriched in responder patients, who also had the longest median Overall Survival (mOS) and the highest 3-year OS rate, and showed a T- and B cell-rich immune microenvironment. The LOW subtype was also the most predictive variable of ICI therapy outcome, irrespective of the PM subtype, in a multivariate model, including gender, age, tumor mutational burden, and an interferon-gamma gene expression signature. Conversely, the CIMP subtype was enriched in non-responder patients who had the shortest mOS and OS rate, along with a depleted tumor immune microenvironment. We also developed a publicly available, methylation-based, decision-making probabilistic classification tool to predict the outcome to ICI treatment of PM patients. The NIBIT-EPI-MESO study included PM patients enrolled in NCT01655888, NCT02588131, and NIBIT MESO-2 Study Protocol Number 22973, as well as patients treated in routine clinical practice.

Pleural mesothelioma (PM) is an aggressive cancer with a dismal prognosis. Co-targeting of immune checkpoint inhibitors (ICI) CTLA-4 and PD-1, the new standard of care for PM, is still clinically unsatisfying, regardless of PM histotype. Moreover, no predictive biomarkers of ICI efficacy are available in PM. We performed multi-omics analysis of pre-ICI therapy lesions from 91 PM patients enrolled in the multicenter NIBIT-EPI-MESO study and identified four clinically meaningful PM subsets with progressively increasing global DNA methylation profiles from demethylated (DEM), LOW, intermediate (INT), and CpG island methylator phenotype (CIMP). This tumor methylome classification predicted both response and survival to ICI therapy. Indeed, the LOW subset was enriched in responder patients, who also had the longest median Overall Survival (mOS) and the highest 3-year OS rate, and showed a T- and B cell-rich immune microenvironment. The LOW subtype was also the most predictive variable of ICI therapy outcome, irrespective of the PM subtype, in a multivariate model, including gender, age, tumor mutational burden, and an interferon-gamma gene expression signature. Conversely, the CIMP subtype was enriched in non-responder patients who had the shortest mOS and OS rate, along with a depleted tumor immune microenvironment. We also developed a publicly available, methylation-based, decision-making probabilistic classification tool to predict the outcome to ICI treatment of PM patients. The NIBIT-EPI-MESO study included PM patients enrolled in NCT01655888, NCT02588131, and NIBIT MESO-2 Study Protocol Number 22973, as well as patients treated in routine clinical practice.

Cross_Correlation_Functions_Nagano.zip : Compress folder with (1) the daily noise cross-correlation functions ZZ (in MSEED format) of the station pairs used in the paper (folder name : "Station_Pair_Cross_Correlation"); (2) the daily auto-correlation functions ZZ, EE, and NN (in H5 format) of the stations used in the paper (folder name : "Auto_Correlation"); (3) the daily single station cross-correlation functions ZZ, EE, and NN (in H5 format) of the stations used in the paper (folder name : "Single_Station_Cross_Correlation").

Cross_Correlation_Functions_Nagano.zip : Compress folder with (1) the daily noise cross-correlation functions ZZ (in MSEED format) of the station pairs used in the paper (folder name : "Station_Pair_Cross_Correlation"); (2) the daily auto-correlation functions ZZ, EE, and NN (in H5 format) of the stations used in the paper (folder name : "Auto_Correlation"); (3) the daily single station cross-correlation functions ZZ, EE, and NN (in H5 format) of the stations used in the paper (folder name : "Single_Station_Cross_Correlation").

The evolution of stomatal morphology is a defining trait among plant lineages. Grasses (Poaceae) have distinctive dumbbell-shaped stomata that enhance water-use efficiency compared to the more common kidney-shaped stomata. In the closely related sedges (Cyperaceae), both kidney-shaped and dumbbell-like stomata can be found. Dumbbell-like stomata in sedges share morphological features with grasses, suggesting potential conservation of developmental pathways. To investigate the evolution of dumbbell and dumbbell-like stomata, we analyzed genomic and transcriptomic data from 29 sedge species and 5 grass species. Using their predicted proteomes, we identified orthologues involved in stomatal development and reconstructed their phylogenetic histories. Among the 16 gene families analyzed, EPFL9, YODA, SCR, and SHR were expanded in grasses but not in sedges. POLAR, SPCH, and ABI were expanded in both lineages, seven families were conserved in both, BASL was lost in both, and, in the SCRM/ICE family, SCRM was lost while ICE was duplicated in sedges. Gene family expansion in grasses occurred primarily in genes involved in early stages of stomatal development, while gene families non-duplicated or independently expanded act in later stages. The non-duplicated or independently expanded genes shared by sedges and grasses contribute to development of the two lateral subsidiary cells as well as the guard cells, suggesting shared regulatory networks underlying the stomata morphology typical of the order Poales. Our study provides a crucial guide to further test functional proteins underlying paracytic dumbbell-like stomata development.

This replication package contains the questionnaire and the collected responses of the study "AI in GUI-Based Testing: A Survey of Techniques, Tools, and Perceived Benefits and Limitations".