Identifying analogues for data-limited volcanoes using hierarchical clustering and expert knowledge: a case study of Melimoyu (Chile)

Determining the eruption frequency-Magnitude (f-M) relationship for data-limited volcanoes is challenging since it requires a comprehensive eruption record of the past eruptive activity. This is the case for Melimoyu, a long-dormant and data-limited volcano in the Southern Volcanic Zone (SVZ) in Chile with only two confirmed Holocene eruptions (VEI 5). To supplement the eruption records, we identified analogue volcanoes for Melimoyu (i.e., volcanoes that behave similarly and are identified through shared characteristics) using a quantitative and objective approach. Firstly, we compiled a global database containing 181 variables describing the eruptive history, tectonic setting, rock composition, and morphology of 1,428 volcanoes. This database was filtered primarily based on data availability into an input dataset comprising 37 numerical variables for 438 subduction zone volcanoes. Then, we applied Agglomerative Nesting, a bottom-up hierarchical clustering algorithm on three datasets derived from the input dataset: 1) raw data, 2) output from a Principal Component Analysis, and 3) weighted data tuned to minimise the dispersion in the absolute probability per VEI. Lastly, we identified the best set of analogues by analysing the dispersion in the absolute probability per VEI and applying a set of criteria deemed important by the local geological service, SERNAGEOMIN, and VB. Our analysis shows that the raw data generate a low dispersion and the highest number of analogues (n = 20). More than half of these analogues are in the SVZ, suggesting that the tectonic setting plays a key role in the clustering analysis. The eruption f-M relationship modelled from the analogue’s eruption data shows that if Melimoyu has an eruption, there is a 49% probability (50th percentile) of it being VEI≥4. Meanwhile, the annual absolute probability of a VEI≤1, VEI 2, VEI 3, VEI 4, and VEI≥5 eruption at Melimoyu is 4.82 × 10−4, 1.2 × 10−3, 1.45 × 10−4, 9.77 × 10−4, and 8.3 × 10−4 (50th percentile), respectively. Our work shows the importance of using numerical variables to capture the variability across volcanoes and combining quantitative approaches with expert knowledge to assess the suitability of potential analogues. Additionally, this approach allows identifying groups of analogues and can be easily applied to other cases using numerical variables from the global database. Future work will use the analogues to populate an event tree and define eruption source parameters for modelling volcanic hazards at Melimoyu

Review article: Natural hazard risk assessments at the global scale

Since 1990, natural hazards have led to over 1.6 million fatalities globally, and economic losses are estimated at an average of around $260–310 billion per year. The scientific and policy community recognise the need to reduce these risks. As a result, the last decade has seen a rapid development of global models for assessing risk from natural hazards at the global scale. In this paper, we review the scientific literature on natural hazard risk assessments at the global scale, and specifically examine whether and how they have examined future projections of hazard, exposure, and/or vulnerability. In doing so, we examine similarities and differences between the approaches taken across the different hazards, and identify potential ways in which different hazard communities can learn from each other. For example, we show that global risk studies focusing on hydrological, climatological, and meteorological hazards, have included future projections and disaster risk reduction measures (in the case of floods), whilst these are missing in global studies related to geological hazards. The methods used for projecting future exposure in the former could be applied to the geological studies. On the other hand, studies of earthquake and tsunami risk are now using stochastic modelling approaches to allow for a fully probabilistic assessment of risk, which could benefit the modelling of risk from other hazards. Finally, we discuss opportunities for learning from methods and approaches being developed and applied to assess natural hazard risks at more continental or regional scales. Through this paper, we hope to encourage dialogue on knowledge sharing between scientists and communities working on different hazards and at different spatial scales

Natural hazard risk assessments at the global scale

Since 1990, natural hazards have led to over 1.6 million fatalities globally, and economic losses are estimated at an average of around USD 260–310 billion per year. The scientific and policy communities recognise the need to reduce these risks. As a result, the last decade has seen a rapid development of global models for assessing risk from natural hazards at the global scale. In this paper, we review the scientific literature on natural hazard risk assessments at the global scale, and we specifically examine whether and how they have examined future projections of hazard, exposure, and/or vulnerability. In doing so, we examine similarities and differences between the approaches taken across the different hazards, and we identify potential ways in which different hazard communities can learn from each other. For example, there are a number of global risk studies focusing on hydrological, climatological, and meteorological hazards that have included future projections and disaster risk reduction measures (in the case of floods), whereas fewer exist in the peer-reviewed literature for global studies related to geological hazards. On the other hand, studies of earthquake and tsunami risk are now using stochastic modelling approaches to allow for a fully probabilistic assessment of risk, which could benefit the modelling of risk from other hazards. Finally, we discuss opportunities for learning from methods and approaches being developed and applied to assess natural hazard risks at more continental or regional scales. Through this paper, we hope to encourage further dialogue on knowledge sharing between disciplines and communities working on different hazards and risk and at different spatial scales

Reconstructing eruptions at a data limited volcano: A case study at Gede (West Java)

Understanding past eruption dynamics at a volcano is crucial for forecasting the range of possible future eruptions and their associated hazards and risk. In this work we use numerical models to recreate the footprints of pyroclastic density currents (PDCs) and tephra fall from three eruptions at Gede volcano, Indonesia, with the aim of gaining further insight into these past eruptions and identifying suitable eruption source parameters for future hazard and risk assessment. Gede has the largest number of people living within 100 km of any volcano worldwide, and has exhibited recent unrest activity, yet little is known about its eruptive history. For PDCs, we used Titan2D to recreate geological deposits dated at 1.2 and c. 1 kyrs BP. An objective and quantitative multi-criteria method was developed to evaluate the fit of 342 model simulations with field observations. In recreating the field deposits we were able to identify the best fitting values to reconstruct these eruptions. We found that the 1.2 kyrs BP geological deposits could be reproduced with Titan2D using either a dome-collapse or a column-collapse as the triggering mechanism, although a relatively low basal friction angle of 6° would suggest that the PDCs were highly mobile. For the 1 kyrs BP PDC, a column-collapse mechanism and a higher basal friction angle were required to fit the geological deposits. In agreement with previous studies, we found that Titan2D simulations were most sensitive to the basal friction angle parameter. We used Tephra2 to recreate historic observations of tephra dispersed to Jakarta and Gunung Patuha during the last known magmatic eruption of Gede in 1948. In the absence of observable field deposits, or detailed information from the published literature, we stochastically sampled eruption source parameters from wide ranges informed by analogous volcanic systems, allowing us to constrain the eruption dynamics capable of dispersing tephra to the most populous city in Indonesia, Jakarta. Our modelling suggests that the deposition of tephra fall in Jakarta during the November 1948 eruption was a very low probability event, with a < 1% chance of occurrence. Through this work, we show how the reconstruction of past eruptions with numerical models can improve our understanding of past eruption dynamics, when faced with epistemic uncertainty. At Gede volcano, this provides a crucial step towards the reduction of risk to nearby populations through volcanic hazard assessment

The Kalanchoe genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism

Crassulacean acid metabolism (CAM) is a water-use efficient adaptation of photosynthesis that has evolved independently many times in diverse lineages of flowering plants. We hypothesize that convergent evolution of protein sequence and temporal gene expression underpins the independent emergences of CAM from C3 photosynthesis. To test this hypothesis, we generate a de novo genome assembly and genome-wide transcript expression data for Kalanchoë fedtschenkoi, an obligate CAM species within the core eudicots with a relatively small genome (~260 Mb). Our comparative analyses identify signatures of convergence in protein sequence and re-scheduling of diel transcript expression of genes involved in nocturnal CO2 fixation, stomatal movement, heat tolerance, circadian clock, and carbohydrate metabolism in K. fedtschenkoi and other CAM species in comparison with non-CAM species. These findings provide new insights into molecular convergence and building blocks of CAM and will facilitate CAM-into-C3 photosynthesis engineering to enhance water-use efficiency in crops

Facilitating the development of controlled vocabularies for metabolomics technologies with text mining

BACKGROUND: Many bioinformatics applications rely on controlled vocabularies or ontologies to consistently interpret and seamlessly integrate information scattered across public resources. Experimental data sets from metabolomics studies need to be integrated with one another, but also with data produced by other types of omics studies in the spirit of systems biology, hence the pressing need for vocabularies and ontologies in metabolomics. However, it is time-consuming and non trivial to construct these resources manually. RESULTS: We describe a methodology for rapid development of controlled vocabularies, a study originally motivated by the needs for vocabularies describing metabolomics technologies. We present case studies involving two controlled vocabularies (for nuclear magnetic resonance spectroscopy and gas chromatography) whose development is currently underway as part of the Metabolomics Standards Initiative. The initial vocabularies were compiled manually, providing a total of 243 and 152 terms. A total of 5,699 and 2,612 new terms were acquired automatically from the literature. The analysis of the results showed that full-text articles (especially the Materials and Methods sections) are the major source of technology-specific terms as opposed to paper abstracts. CONCLUSIONS: We suggest a text mining method for efficient corpus-based term acquisition as a way of rapidly expanding a set of controlled vocabularies with the terms used in the scientific literature. We adopted an integrative approach, combining relatively generic software and data resources for time- and cost-effective development of a text mining tool for expansion of controlled vocabularies across various domains, as a practical alternative to both manual term collection and tailor-made named entity recognition methods

Mendelian randomization analysis of C-reactive protein on colorectal cancer risk

Background: Chronic inflammation is a risk factor for colorectal cancer (CRC). Circulating C-reactive protein (CRP) is also moderately associated with CRC risk. However, observational studies are susceptible to unmeasured confounding or reverse causality. Using genetic risk variants as instrumental variables, we investigated the causal relationship between genetically elevated CRP concentration and CRC risk, using a Mendelian randomization approach. Methods: Individual-level data from 30 480 CRC cases and 22 844 controls from 33 participating studies in three international consortia were used: the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO), the Colorectal Transdisciplinary Study (CORECT) and the Colon Cancer Family Registry (CCFR). As instrumental variables, we included 19 single nucleotide polymorphisms (SNPs) previously associated with CRP concentration. The SNP-CRC associations were estimated using a logistic regression model adjusted for age, sex, principal components and genotyping phases. An inverse-variance weighted method was applied to estimate the causal effect of CRP on CRC risk. Results: Among the 19 CRP-associated SNPs, rs1260326 and rs6734238 were significantly associated with CRC risk (P = 7.5 × 10-4, and P = 0.003, respectively). A genetically predicted one-unit increase in the log-transformed CRP concentrations (mg/l) was not associated with increased risk of CRC [odds ratio (OR) = 1.04; 95% confidence interval (CI): 0.97, 1.12; P = 0.256). No evidence of association was observed in subgroup analyses stratified by other risk factors. Conclusions: In spite of adequate statistical power to detect moderate association, we found genetically elevated CRP concentration was not associated with increased risk of CRC among individuals of European ancestry. Our findings suggested that circulating CRP is unlikely to be a causal factor in CRC development

Cumulative Burden of Colorectal Cancer-Associated Genetic Variants Is More Strongly Associated With Early-Onset vs Late-Onset Cancer.

BACKGROUND & AIMS: Early-onset colorectal cancer (CRC, in persons younger than 50 years old) is increasing in incidence; yet, in the absence of a family history of CRC, this population lacks harmonized recommendations for prevention. We aimed to determine whether a polygenic risk score (PRS) developed from 95 CRC-associated common genetic risk variants was associated with risk for early-onset CRC. METHODS: We studied risk for CRC associated with a weighted PRS in 12,197 participants younger than 50 years old vs 95,865 participants 50 years or older. PRS was calculated based on single nucleotide polymorphisms associated with CRC in a large-scale genome-wide association study as of January 2019. Participants were pooled from 3 large consortia that provided clinical and genotyping data: the Colon Cancer Family Registry, the Colorectal Transdisciplinary Study, and the Genetics and Epidemiology of Colorectal Cancer Consortium and were all of genetically defined European descent. Findings were replicated in an independent cohort of 72,573 participants. RESULTS: Overall associations with CRC per standard deviation of PRS were significant for early-onset cancer, and were stronger compared with late-onset cancer (P for interaction = .01); when we compared the highest PRS quartile with the lowest, risk increased 3.7-fold for early-onset CRC (95% CI 3.28-4.24) vs 2.9-fold for late-onset CRC (95% CI 2.80-3.04). This association was strongest for participants without a first-degree family history of CRC (P for interaction = 5.61 × 10-5). When we compared the highest with the lowest quartiles in this group, risk increased 4.3-fold for early-onset CRC (95% CI 3.61-5.01) vs 2.9-fold for late-onset CRC (95% CI 2.70-3.00). Sensitivity analyses were consistent with these findings. CONCLUSIONS: In an analysis of associations with CRC per standard deviation of PRS, we found the cumulative burden of CRC-associated common genetic variants to associate with early-onset cancer, and to be more strongly associated with early-onset than late-onset cancer, particularly in the absence of CRC family history. Analyses of PRS, along with environmental and lifestyle risk factors, might identify younger individuals who would benefit from preventive measures

Discovery of common and rare genetic risk variants for colorectal cancer.

To further dissect the genetic architecture of colorectal cancer (CRC), we performed whole-genome sequencing of 1,439 cases and 720 controls, imputed discovered sequence variants and Haplotype Reference Consortium panel variants into genome-wide association study data, and tested for association in 34,869 cases and 29,051 controls. Findings were followed up in an additional 23,262 cases and 38,296 controls. We discovered a strongly protective 0.3% frequency variant signal at CHD1. In a combined meta-analysis of 125,478 individuals, we identified 40 new independent signals at P < 5 × 10-8, bringing the number of known independent signals for CRC to ~100. New signals implicate lower-frequency variants, Krüppel-like factors, Hedgehog signaling, Hippo-YAP signaling, long noncoding RNAs and somatic drivers, and support a role for immune function. Heritability analyses suggest that CRC risk is highly polygenic, and larger, more comprehensive studies enabling rare variant analysis will improve understanding of biology underlying this risk and influence personalized screening strategies and drug development.Goncalo R Abecasis has received compensation from 23andMe and Helix. He is currently an employee of Regeneron Pharmaceuticals. Heather Hampel performs collaborative research with Ambry Genetics, InVitae Genetics, and Myriad Genetic Laboratories, Inc., is on the scientific advisory board for InVitae Genetics and Genome Medical, and has stock in Genome Medical. Rachel Pearlman has participated in collaborative funded research with Myriad Genetics Laboratories and Invitae Genetics but has no financial competitive interest