Fast and scalable inference of multi-sample cancer lineages.

Somatic variants can be used as lineage markers for the phylogenetic reconstruction of cancer evolution. Since somatic phylogenetics is complicated by sample heterogeneity, novel specialized tree-building methods are required for cancer phylogeny reconstruction. We present LICHeE (Lineage Inference for Cancer Heterogeneity and Evolution), a novel method that automates the phylogenetic inference of cancer progression from multiple somatic samples. LICHeE uses variant allele frequencies of somatic single nucleotide variants obtained by deep sequencing to reconstruct multi-sample cell lineage trees and infer the subclonal composition of the samples. LICHeE is open source and available at http://viq854.github.io/lichee

IMPACT World+: a globally regionalized life cycle impact assessment method

International audiencePurpose This paper addresses the need for a globally regionalized method for life cycle impact assessment (LCIA), integrating multiple state-of-the-art developments as well as damages on water and carbon areas of concern within a consistent LCIA framework. This method, named IMPACT World+, is the update of the IMPACT 2002+, LUCAS, and EDIP methods. This paper first presents the IMPACT World+ novelties and results and then analyzes the spatial variability for each regionalized impact category. Methods With IMPACT World+, we propose a midpoint-damage framework with four distinct complementary viewpoints to present an LCIA profile: (1) midpoint impacts, (2) damage impacts, (3) damages on human health, ecosystem quality, and resources & ecosystem service areas of protection, and (4) damages on water and carbon areas of concerns. Most of the regional impact categories have been spatially resolved and all the long-term impact categories have been subdivided between shorter-term damages (over the 100 years after the emission) and long-term damages. The IMPACT World+ method integrates developments in the following categories, all structured according to fate (or competition/scarcity), exposure, exposure response, and severity: (a) Complementary to the global warming potential (GWP100), the IPCC Global Temperature Potentials (GTP100) are used as a proxy for climate change long-term impacts at midpoint. At damage level, shorter-term damages (over the first 100 years after emission) are also differentiated from long-term damages. (b) Marine acidification impact is based on the same fate model as climate change, combined with the H + concentration affecting 50% of the exposed species. (c) For mineral resources depletion Responsible editor: Serenella Sala Electronic supplementary material The online version of this article (https://doi. impact, the material competition scarcity index is applied as a midpoint indicator. (d) Terrestrial and freshwater acidification impact assessment combines, at a resolution of 2°× 2.5°(latitude × longitude), global atmospheric source-deposition relationships with soil and water ecosystems' sensitivity. (e) Freshwater eutrophication impact is spatially assessed at a resolution grid of 0.5°× 0.5°, based on a global hydrological dataset. (f) Ecotoxicity and human toxicity impact are based on the parameterized version of USEtox for continents. We consider indoor emissions and differentiate the impacts of metals and persistent organic pollutants for the first 100 years from longer-term impacts. (g) Impacts on human health related to particulate matter formation are modeled using the USEtox regional archetypes to calculate intake fractions and epidemiologically derived exposure response factors. (h) Water consumption impacts are modeled using the consensus-based scarcity indicator AWARE as a proxy midpoint, whereas damages account for competition and adaptation capacity. (i) Impacts on ecosystem quality from land transformation and occupation are empirically characterized at the biome level. Results and discussion We analyze the magnitude of global potential damages for each impact indicator, based on an estimation of the total annual anthropogenic emissions and extractions at the global scale (i.e., Bdoing the LCA of the world^). Similarly with ReCiPe and IMPACT 2002+, IMPACT World+ finds that (a) climate change and impacts of particulate matter formation have a dominant contribution to global human health impacts whereas ionizing radiation, ozone layer depletion, and photochemical oxidant formation have a low contribution and (b) climate change and land use have a dominant contribution to global ecosystem quality impact. (c) New impact indicators introduced in IMPACT World+ and not considered in ReCiPe or IMPACT 2002+, in particular water consumption impacts on human health and the long-term impacts of marine acidification on ecosystem quality, are significant contributors to the overall global potential damage. According to the areas of concern version of IMPACT World+ applied to the total annual world emissions and extractions, damages on the water area of concern, carbon area of concern, and the remaining damages (not considered in those two areas of concern) are of the same order of magnitude, highlighting the need to consider all the impact categories. The spatial variability of human health impacts related to exposure to toxic substances and particulate matter is well reflected by using outdoor rural, outdoor urban, and indoor environment archetypes. For Bhuman toxicity cancer^impact of substances emitted to continental air, the variability between continents is of two orders of magnitude, which is substantially lower than the 13 orders of magnitude total variability across substances. For impacts of water consumption on human health, the spatial variability across extraction locations is substantially higher than the variations between different water qualities. For regionalized impact categories affecting ecosystem quality (acidification, eutrophication, and land use), the characterization factors of half of the regions (25th to 75th percentiles) are within one to two orders of magnitude and the 95th percentile within three to four orders of magnitude, which is higher than the variability between substances, highlighting the relevance of regionalizing. Conclusions IMPACT World+ provides characterization factors within a consistent impact assessment framework for all region-alized impacts at four complementary resolutions: global default, continental, country, and native (i.e., original and non-aggre-gated) resolutions. IMPACT World+ enables the practitioner to parsimoniously account for spatial variability and to identify the elementary flows to be regionalized in priority to increase the discriminating power of LCA

IMPACT World+: a globally regionalized life cycle impact assessment method

Purpose This paper addresses the need for a globally regionalized method for life cycle impact assessment (LCIA), integrating multiple state-of-the-art developments as well as damages on water and carbon areas of concern within a consistent LCIA framework. This method, named IMPACT World+, is the update of the IMPACT 2002+, LUCAS, and EDIP methods. This paper first presents the IMPACT World+ novelties and results and then analyzes the spatial variability for each regionalized impact category. Methods With IMPACT World+, we propose a midpoint-damage framework with four distinct complementary viewpoints to present an LCIA profile: (1) midpoint impacts, (2) damage impacts, (3) damages on human health, ecosystem quality, and resources & ecosystem service areas of protection, and (4) damages on water and carbon areas of concerns. Most of the regional impact categories have been spatially resolved and all the long-term impact categories have been subdivided between shorterterm damages (over the 100 years after the emission) and long-term damages. The IMPACT World+ method integrates developments in the following categories, all structured according to fate (or competition/scarcity), exposure, exposure response, and severity: (a) Complementary to the global warming potential (GWP100), the IPCC Global Temperature Potentials (GTP100) are used as a proxy for climate change long-term impacts at midpoint. At damage level, shorter-term damages (over the first 100 years after emission) are also differentiated from long-term damages. (b) Marine acidification impact is based on the same fate model as climate change, combined with the H+ concentration affecting 50% of the exposed species. (c) For mineral resources depletion impact, the material competition scarcity index is applied as a midpoint indicator. (d) Terrestrial and freshwater acidification impact assessment combines, at a resolution of 2° × 2.5° (latitude × longitude), global atmospheric source-deposition relationships with soil and water ecosystems’sensitivity. (e) Freshwater eutrophication impact is spatially assessed at a resolution grid of 0.5° × 0.5°, based on a global hydrological dataset. (f) Ecotoxicity and human toxicity impact are based on the parameterized version of USEtox for continents. We consider indoor emissions and differentiate the impacts of metals and persistent organic pollutants for the first 100 years from longer-term impacts. (g) Impacts on human health related to particulate matter formation are modeled using the USEtox regional archetypes to calculate intake fractions and epidemiologically derived exposure response factors. (h) Water consumption impacts are modeled using the consensus-based scarcity indicator AWARE as a proxy midpoint, whereas damages account for competition and adaptation capacity. (i) Impacts on ecosystem quality from land transformation and occupation are empirically characterized at the biome level. Results and discussion We analyze the magnitude of global potential damages for each impact indicator, based on an estimation of the total annual anthropogenic emissions and extractions at the global scale (i.e., Bdoing the LCA of the world^). Similarly with ReCiPe and IMPACT 2002+, IMPACT World+ finds that (a) climate change and impacts of particulate matter formation have a dominant contribution to global human health impacts whereas ionizing radiation, ozone layer depletion, and photochemical oxidant formation have a low contribution and (b) climate change and land use have a dominant contribution to global ecosystem quality impact. (c) New impact indicators introduced in IMPACT World+ and not considered in ReCiPe or IMPACT 2002+, in particular water consumption impacts on human health and the long-term impacts of marine acidification on ecosystem quality, are significant contributors to the overall global potential damage. According to the areas of concern version of IMPACT World+ applied to the total annual world emissions and extractions, damages on the water area of concern, carbon area of concern, and the remaining damages (not considered in those two areas of concern) are of the same order of magnitude, highlighting the need to consider all the impact categories. The spatial variability of human health impacts related to exposure to toxic substances and particulate matter is well reflected by using outdoor rural, outdoor urban, and indoor environment archetypes. For Bhuman toxicity cancer^ impact of substances emitted to continental air, the variability between continents is of two orders of magnitude, which is substantially lower than the 13 orders of magnitude total variability across substances. For impacts of water consumption on human health, the spatial variability across extraction locations is substantially higher than the variations between different water qualities. For regionalized impact categories affecting ecosystem quality (acidification, eutrophication, and land use), the characterization factors of half of the regions (25th to 75th percentiles) are within one to two orders of magnitude and the 95th percentile within three to four orders of magnitude, which is higher than the variability between substances, highlighting the relevance of regionalizing. Conclusions IMPACT World+ provides characterization factors within a consistent impact assessment framework for all regionalized impacts at four complementary resolutions: global default, continental, country, and native (i.e., original and non-aggregated) resolutions. IMPACT World+ enables the practitioner to parsimoniously account for spatial variability and to identify the elementary flows to be regionalized in priority to increase the discriminating power of LCA

Effect of freeze-thaw temperature cycles on the mobility and morphology of residual non-aqueous phase liguids

Uncontrolled discharges of significant volumes of non-aqueous phase liquids such as petroleum fuels and chlorinated solvents have occurred at many sites. Understanding the fate and transport of NAPLs in the subsurface is necessary for assessing the extent and environmental impacts of the contamination, and its remediation. Temperature changes that cause freeze and thawing of soil moisture can result in the alteration of the soil pore structure, which can induce changes in the distribution and morphology of liquid phases present in soil. This study focuses on the effect of freeze-thaw cycles on the volume distribution, morphology and specific surface area of the NAPLs, gasoline and perchloroethylene (PCE) present at residual saturation in porous media. The volume distribution of NAPL blobs in packed sand columns were characterized using a medical X-ray CT scanner. The results show that gasoline blobs were mobilized to a significantly greater extent than PCE blobs. The morphology of the gasoline blobs such as volume, surface area and fractal dimension were also altered more than PCE blobs as a result of freeze and thaw. The extent of mobilization and morphological changes were a function of the freezing rate

Physico–Chemical Processes Limiting CO₂ Uptake in Concrete during Accelerated Carbonation Curing

Accelerated curing of fresh concrete using CO₂ is a possible approach for value-added, high-volume usage products from waste CO₂ emitted from stationary sources. The extent of CO₂ uptake and the spatial distribution of the CaCO₃(s) precipitates formed during accelerated carbonation curing of compacted, 4-h hydrated cement mortar (fresh concrete mixture with fine aggregates) samples were investigated in this study. The maximum carbonation efficiency achieved was 20% of the theoretical uptake. Microprobe imaging was used to analyze the composition of the compacted cement mortar microstructure and showed extensive filling of pores of diameters 4 μm and smaller, with CaCO₃(s). The carbonation efficiency, however, reached 67% when an aqueous suspension of cement was carbonated in a completely mixed reactor, where interparticle pores do not exist and a higher surface area of cement particles is exposed to dissolved CO₂. The theoretical efficiency was not achieved because all reactive cement surfaces were saturated with carbonation products, as indicated by equilibrium concentrations of dissolved calcium, silica, inorganic carbon, and pH. This study shows that both deposition of CaCO₃(s), on reactive surfaces, and pore filling may regulate the extent of CO₂ uptake during accelerated carbonation curing of concrete

Learning Algorithms for Automata with Observations

We consider the problem of learning the behavior of a POMDP (Partially Observable Markov Decision Process) with deterministic actions and observations. This is a challenging problem due to the fact that the observations can only partially identify the states. Recent work by Holmes and Isbell offers an approach for inferring the hidden states from experience in deterministic POMDP environments. We propose an alternative algorithm that ensures more accurate predictions, and we show that in fact it produces the minimal predicting machine.