This paper quantifies the potential influence of sediment compaction on the magnitude of nineteenth and twentieth century sea-level rise, as reconstructed from salt marsh sediments. We firstly ...develop a database of the physical and compression properties of low energy intertidal and salt marsh sediments. Key compression parameters are controlled by organic content (loss on ignition), though compressibility is modulated by local-scale processes, notably the potential for desiccation of sediments. Using this database and standard geotechnical theory, we use a numerical modelling approach to generate and subsequently ‘decompact’ a range of idealised intertidal stratigraphies. We find that compression can significantly contribute to reconstructed accelerations in recent sea level, notably in transgressive stratigraphies. The magnitude of this effect can be sufficient to add between 0.1 and 0.4mmyr−1 of local sea-level rise, depending on the thickness of the stratigraphic column. In contrast, records from shallow (<0.5m) uniform-lithology stratigraphies, or shallow near-surface salt marsh deposits in regressive successions, experience negligible compaction. Spatial variations in compression could be interpreted as ‘sea-level fingerprints’ that might, in turn, be wrongly attributed to oceanic or cryospheric processes. However, consideration of existing sea-level records suggests that this is not the case and that compaction cannot be invoked as the sole cause of recent accelerations in sea level inferred from salt marsh sediments.
► Organic content and past desiccation control compressibility in salt marsh sediments. ► Compression cannot cause sharp, high-magnitude inflections in reconstructed sea level. ► Modelled compression contributions to reconstructed sea level are in the range of 0.0–0.4mmyr−1. ► Modelled transgressive successions are most prone to compression. ► Modelled uniform and regressive stratigraphies experience negligible compression.
Part 1 of this study investigated evidence of biomass burning in global ice records, and here we continue to test the hypothesis that an impact event at the Younger Dryas boundary (YDB) caused an ...anomalously intense episode of biomass burning at ̃12.8 ka on a multicontinental scale (North and South America, Europe, and Asia). Quantitative analyses of charcoal and soot records from 152 lakes, marine cores, and terrestrial sequences reveal a major peak in biomass burning at the Younger Dryas (YD) onset that appears to be the highest during the latest Quaternary. For the Cretaceous-Tertiary boundary (K-Pg) impact event, concentrations of soot were previously utilized to estimate the global amount of biomass burned, and similar measurements suggest that wildfires at the YD onset rapidly consumed ̃10 million km² of Earth’s surface, or ̃9% of Earth’s biomass, considerably more than for the K-Pg impact. Bayesian analyses and age regressions demonstrate that ages for YDB peaks in charcoal and soot across four continents are synchronous with the ages of an abundance peak in platinum in the Greenland Ice Sheet Project 2 (GISP2) ice core and of the YDB impact event (12,835–12,735 cal BP). Thus, existing evidence indicates that the YDB impact event caused an anomalously large episode of biomass burning, resulting in extensive atmospheric soot/dust loading that triggered an “impact winter.” This, in turn, triggered abrupt YD cooling and other climate changes, reinforced by climatic feedback mechanisms, including Arctic sea ice expansion, rerouting of North American continental runoff, and subsequent ocean circulation changes.
Using neutron reflectivity, self‐stratification in a model P3HT/PCBM blend is observed. The as‐spun and solvent‐annealed films show a depletion of PCBM near the top surface and enrichment of PCBM at ...the substrate (see figure). Depletion of PCBM at the cathode interface in a photovoltaic device could act as a barrier to efficient electron extraction. On thermal annealing, the PCBM depleted region is eliminated; an effect that partially explains the improvement of P3HT/PCBM devices on thermal annealing.
The Arauco Peninsula (37°-38°S) in south-central Chile has been proposed as a possible barrier to the along-strike propagation of megathrust ruptures, separating historical earthquakes to the south ...(1960 AD 1837, 1737, and 1575) and north (2010 AD, 1835, 1751, 1657, and 1570) of the peninsula. However, the 2010 (Mw 8.8) earthquake propagated into the Arauco Peninsula, re-rupturing part of the megathrust that had ruptured only 50 years earlier during the largest subduction zone earthquake in the instrumental record (Mw 9.5). To better understand long-term slip variability in the Arauco Peninsula region, we analyzed four coastal sedimentary sections from two sites (Tirúa, 38.3°S and Quidico, 38.1°S) located within the overlap of the 2010 and 1960 ruptures to reconstruct a ∼600-year record of coseismic land-level change and tsunami inundation. Stratigraphic, lithologic, and diatom results show variable coseismic land-level change coincident with tsunami inundation of the Tirúa and Quidico marshes that is consistent with regional historical accounts of coseismic subsidence during earthquakes along the Valdivia portion of the subduction zone (1960 AD and 1575) and coseismic uplift during earthquakes along the Maule portion of the subduction zone (2010 AD, 1835, 1751). In addition, we document variable coseismic land-level change associated with three new prehistoric earthquakes and accompanying tsunamis in 1470–1570 AD, 1425–1455, and 270–410. The mixed record of coseismic subsidence and uplift that we document illustrates the variability of down-dip and lateral slip distribution at the overlap of the 2010 and 1960 ruptures, showing that ruptures have repeatedly propagated into, but not through the Arauco Peninsula and suggesting the area has persisted as a long-term impediment to slip through at least seven of the last megathrust earthquakes (∼600 years).
•Diatom-based paleogeodetic methods are used to reconstruct coseismic land-level change.•Evidence of variable coseismic slip documented where the AD 2010 and 1960 ruptures overlap.•Mixed record of uplift and subsidence illustrates down-dip and lateral slip variability.•The Arauco Peninsula has been a persistent impediment to slip over multiple earthquake cycles.
Stomatal conductance (
) in terrestrial vegetation regulates the uptake of atmospheric carbon dioxide for photosynthesis and water loss through transpiration, closely linking the biosphere and ...atmosphere and influencing climate. Yet, the range and pattern of
in plants from natural ecosystems across broad geographic, climatic, and taxonomic ranges remains poorly quantified. Furthermore, attempts to characterize
on such scales have predominantly relied upon meta-analyses compiling data from many different studies. This approach may be inherently problematic as it combines data collected using unstandardized protocols, sometimes over decadal time spans, and from different habitat groups. Using a standardized protocol, we measured leaf-level
using porometry in 218 C
woody angiosperm species in natural ecosystems representing seven bioclimatic zones. The resulting dataset of 4273
measurements, which we call STraits (Stomatal Traits), was used to determine patterns in maximum
(
) across bioclimatic zones and whether there was similarity in the mean
of C3 woody angiosperms across ecosystem types. We also tested for differential
in two broadly defined habitat groups - open-canopy and understory-subcanopy - within and across bioclimatic zones. We found strong convergence in mean
of C3 woody angiosperms in the understory-subcanopy habitats across six bioclimatic zones, but not in open-canopy habitats. Mean
in open-canopy habitats (266 ± 100 mmol m
s
) was significantly higher than in understory-subcanopy habitats (233 ± 86 mmol m
s
). There was also a central tendency in the overall dataset to operate toward a
of ∼250 mmol m
s
. We suggest that the observed convergence in mean
of C3 woody angiosperms in the understory-subcanopy is due to a buffering of
against macroclimate effects which will lead to differential response of C3 woody angiosperm vegetation in these two habitats to future global change. Therefore, it will be important for future studies of
to categorize vegetation according to habitat group.
Introduction
Suicide is criminalized in more than 100 countries around the world. A dearth of research exists into the effect of suicide legislation on suicide rates and available statistics are ...mixed.
Materials and methods
This study investigates 10,353 suicide deaths in Ireland that took place between 1970 and 2000. Irish 1970–2000 annual suicide data were obtained from the Central Statistics Office and modelled via a negative binomial regression approach. We examined the effect of suicide legislation on different age groups and on both sexes. We used Bonferroni correction for multiple modelling. Statistical analysis was performed using the R statistical package version 3.1.2. The coefficient for the effect of suicide act on overall suicide deaths was −9.094 (95 % confidence interval (CI) −34.086 to 15.899), statistically non-significant (
p
= 0.476). The coefficient for the effect suicide act on undetermined deaths was statistically significant (
p
< 0.001) and was estimated to be −644.4 (95 % CI −818.6 to −469.9).
Conclusion
The results of our study indicate that legalization of suicide is not associated with a significant increase in subsequent suicide deaths. However, undetermined death verdict rates have significantly dropped following legalization of suicide.
The Bayesian additive regression trees (BART) model is an ensemble method extensively and successfully used in regression tasks due to its consistently strong predictive performance and its ability ...to quantify uncertainty. BART combines “weak” tree models through a set of shrinkage priors, whereby each tree explains a small portion of the variability in the data. However, the lack of smoothness and the absence of an explicit covariance structure over the observations in standard BART can yield poor performance in cases where such assumptions would be necessary. The Gaussian processes Bayesian additive regression trees (GP-BART) model is an extension of BART which addresses this limitation by assuming Gaussian process (GP) priors for the predictions of each terminal node among all trees. The model's effectiveness is demonstrated through applications to simulated and real-world data, surpassing the performance of traditional modelling approaches in various scenarios.
Identification of gene expression profiles that differentiate experimental groups is critical for discovery and analysis of key molecular pathways and also for selection of robust diagnostic or ...prognostic biomarkers. While integration of differential expression statistics has been used to refine gene set enrichment analyses, such approaches are typically limited to single gene lists resulting from simple two-group comparisons or time-series analyses. In contrast, functional class scoring and machine learning approaches provide powerful alternative methods to leverage molecular measurements for pathway analyses, and to compare continuous and multi-level categorical factors.
We introduce GOexpress, a software package for scoring and summarising the capacity of gene ontology features to simultaneously classify samples from multiple experimental groups. GOexpress integrates normalised gene expression data (e.g., from microarray and RNA-seq experiments) and phenotypic information of individual samples with gene ontology annotations to derive a ranking of genes and gene ontology terms using a supervised learning approach. The default random forest algorithm allows interactions between all experimental factors, and competitive scoring of expressed genes to evaluate their relative importance in classifying predefined groups of samples.
GOexpress enables rapid identification and visualisation of ontology-related gene panels that robustly classify groups of samples and supports both categorical (e.g., infection status, treatment) and continuous (e.g., time-series, drug concentrations) experimental factors. The use of standard Bioconductor extension packages and publicly available gene ontology annotations facilitates straightforward integration of GOexpress within existing computational biology pipelines.
Copy number variants (CNVs) are a form of genomic variation that changes the structure of the genome through deletion or duplication of stretches of DNA. The objective of the present study was to ...characterize CNVs in a large multibreed population of beef and dairy bulls. The CNVs were called on the autosomes of 5,551 cattle from 22 different beef and dairy breeds, using 2 freely available software suites, QuantiSNP and PennCNV. All CNVs were classified into either deletions or duplications. The median concordance between PennCNV and QuantiSNP, per animal, was 18.5% for deletions and 0% for duplications. The low concordance rate between PennCNV and QuantiSNP indicated that neither algorithm, by itself, could identify all CNVs in the population. In total, PennCNV and QuantiSNP collectively identified 747,129 deletions and 432,523 duplications; 80.2% of all duplications and 69.1% of all deletions were present only once in the population. Only 0.154% of all CNVs identified were present in more than 50 animals in the population. The distribution of the percentage of the autosomes that were composed of deletions, per animal, was positively skewed, as was the distribution for the percentage of the autosomes that were composed of duplications, per animal. The first quartile, median, and third quartile of the distribution of the percentage of the autosomes that were composed of deletions were 0.019%, 0.037%, and 0.201%, respectively. The first quartile, median, and third quartile of the distribution of the percentage of the autosomes that were composed of duplications were 0.013%, 0.028%, and 0.076%, respectively. The distributions of the number of deletions and duplications per animal were both positively skewed. The interquartile range for the number of deletions per animal in the population was between 16 and 117, whereas for duplications it was between 8 and 23. Per animal, there tended to be twice as many deletions as duplications. The distribution of the length of deletions was positively skewed, as was the distribution of the length of duplications. The interquartile range for the length of deletions in the population was between 25 and 101 kb, and for duplications the interquartile range was between 46 and 235 kb. Per animal, duplications tended to be twice as long as deletions. This study provides a description of the characteristics and distribution of CNVs in a large multibreed population of beef and dairy cattle.
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