Parameterization of single-scattering albedo (SSA) and absorption Ångström exponent (AAE) with EC/OC for aerosol emissions from biomass burning

Single-scattering albedo (SSA) and absorption Ångström exponent (AAE) are two critical parameters in determining the impact of absorbing aerosol on the Earth\u27s radiative balance. Aerosol emitted by biomass burning represent a significant fraction of absorbing aerosol globally, but it remains difficult to accurately predict SSA and AAE for biomass burning aerosol. Black carbon (BC), brown carbon (BrC), and non-absorbing coatings all make substantial contributions to the absorption coefficient of biomass burning aerosol. SSA and AAE cannot be directly predicted based on fuel type because they depend strongly on burn conditions. It has been suggested that SSA can be effectively parameterized via the modified combustion efficiency (MCE) of a biomass burning event and that this would be useful because emission factors for CO and CO2, from which MCE can be calculated, are available for a large number of fuels. Here we demonstrate, with data from the FLAME-4 experiment, that for a wide variety of globally relevant biomass fuels, over a range of combustion conditions, parameterizations of SSA and AAE based on the elemental carbon (EC) to organic carbon (OC) mass ratio are quantitatively superior to parameterizations based on MCE. We show that the EC/OC ratio and the ratio of EC/(EC + OC) both have significantly better correlations with SSA than MCE. Furthermore, the relationship of EC/(EC + OC) with SSA is linear. These improved parameterizations are significant because, similar to MCE, emission factors for EC (or black carbon) and OC are available for a wide range of biomass fuels. Fitting SSA with MCE yields correlation coefficients (Pearson\u27s r) of ∼0.65 at the visible wavelengths of 405, 532, and 660 nm while fitting SSA with EC/OC or EC/(EC + OC) yields a Pearson\u27s r of 0.94-0.97 at these same wavelengths. The strong correlation coefficient at 405 nm (r = 0.97) suggests that parameterizations based on EC/OC or EC/(EC + OC) have good predictive capabilities even for fuels in which brown carbon absorption is significant. Notably, these parameterizations are effective for emissions from Indonesian peat, which have very little black carbon but significant brown carbon (SSA = 0.990 ± 0.001 at 532 and 660 nm, SSA = 0.937 ± 0.011 at 405 nm). Finally, we demonstrate that our parameterization based on EC/(EC + OC) accurately predicts SSA during the first few hours of plume aging with data from Yokelson et al. (2009) gathered during a biomass burning event in the Yucatán Peninsula of Mexico

Genetic Variation in an Individual Human Exome

There is much interest in characterizing the variation in a human individual, because this may elucidate what contributes significantly to a person's phenotype, thereby enabling personalized genomics. We focus here on the variants in a person's ‘exome,’ which is the set of exons in a genome, because the exome is believed to harbor much of the functional variation. We provide an analysis of the ∼12,500 variants that affect the protein coding portion of an individual's genome. We identified ∼10,400 nonsynonymous single nucleotide polymorphisms (nsSNPs) in this individual, of which ∼15–20% are rare in the human population. We predict ∼1,500 nsSNPs affect protein function and these tend be heterozygous, rare, or novel. Of the ∼700 coding indels, approximately half tend to have lengths that are a multiple of three, which causes insertions/deletions of amino acids in the corresponding protein, rather than introducing frameshifts. Coding indels also occur frequently at the termini of genes, so even if an indel causes a frameshift, an alternative start or stop site in the gene can still be used to make a functional protein. In summary, we reduced the set of ∼12,500 nonsilent coding variants by ∼8-fold to a set of variants that are most likely to have major effects on their proteins' functions. This is our first glimpse of an individual's exome and a snapshot of the current state of personalized genomics. The majority of coding variants in this individual are common and appear to be functionally neutral. Our results also indicate that some variants can be used to improve the current NCBI human reference genome. As more genomes are sequenced, many rare variants and non-SNP variants will be discovered. We present an approach to analyze the coding variation in humans by proposing multiple bioinformatic methods to hone in on possible functional variation

Relative importance of black carbon, brown carbon, and absorption enhancement from clear coatings in biomass burning emissions

A wide range of globally significant biomass fuels were burned during the fourth Fire Lab at Missoula Experiment (FLAME-4). A multi-channel photoacoustic absorption spectrometer (PAS) measured dry absorption at 405, 532, and 660 nm and thermally denuded (250 °C) absorption at 405 and 660 nm. Absorption coefficients were broken into contributions from black carbon (BC), brown carbon (BrC), and lensing following three different methodologies, with one extreme being a method that assumes the thermal denuder effectively removes organics and the other extreme being a method based on the assumption that black carbon (BC) has an Ångström exponent of unity. The methodologies employed provide ranges of potential importance of BrC to absorption but, on average, there was a difference of a factor of 2 in the ratio of the fraction of absorption attributable to BrC estimated by the two methods. BrC absorption at shorter visible wavelengths is of equal or greater importance to that of BC, with maximum contributions of up to 92 % of total aerosol absorption at 405 nm and up to 58 % of total absorption at 532 nm. Lensing is estimated to contribute a maximum of 30 % of total absorption, but typically contributes much less than this. Absorption enhancements and the estimated fraction of absorption from BrC show good correlation with the elemental-carbon-to-organic-carbon ratio (EC/OC) of emitted aerosols and weaker correlation with the modified combustion efficiency (MCE). Previous studies have shown that BrC grows darker (larger imaginary refractive index) as the ratio of black to organic aerosol (OA) mass increases. This study is consistent with those findings but also demonstrates that the fraction of total absorption attributable to BrC shows the opposite trend: increasing as the organic fraction of aerosol emissions increases and the EC/OC ratio decreases

Coupling Field and Laboratory Measurements to Estimate the Emission Factors of Identified and Unidentified Trace Gases for Prescribed Fires

An extensive program of experiments focused on biomass burning emissions began with a laboratory phase in which vegetative fuels commonly consumed in prescribed fires were collected in the southeastern and southwestern US and burned in a series of 71 fires at the US Forest Service Fire Sciences Laboratory in Missoula, Montana. The particulate matter (PM2.5) emissions were measured by gravimetric filter sampling with subsequent analysis for elemental carbon (EC), organic carbon (OC), and 38 elements. The trace gas emissions were measured by an open-path Fourier transform infrared (OP-FTIR) spectrometer, proton-transfer-reaction mass spectrometry (PTRMS), proton-transfer ion-trap mass spectrometry (PIT-MS), negative-ion proton-transfer chemical-ionization mass spectrometry (NI-PT-CIMS), and gas chromatography with MS detection (GC-MS). 204 trace gas species (mostly non-methane organic compounds (NMOC)) were identified and quantified with the above instruments. Many of the 182 species quantified by the GC-MS have rarely, if ever, been measured in smoke before. An additional 153 significant peaks in the unit mass resolution mass spectra were quantified, but either could not be identified or most of the signal at that molecular mass was unaccounted for by identifiable species. In a second, field phase of this program, airborne and ground-based measurements were made of the emissions from prescribed fires that were mostly located in the same land management units where the fuels for the lab fires were collected. A broad variety, but smaller number of species (21 trace gas species and PM2.5) was measured on 14 fires in chaparral and oak savanna in the southwestern US, as well as pine forest understory in the southeastern US and Sierra Nevada mountains of California. The field measurements of emission factors (EF) are useful both for modeling and to examine the representativeness of our lab fire EF. The lab EF/field EF ratio for the pine understory fuels was not statistically different from one, on average. However, our lab EF for smoldering compounds emitted from the semiarid shrubland fuels should likely be increased by a factor of similar to 2.7 to better represent field fires. Based on the lab/field comparison, we present emission factors for 357 pyrogenic species (including unidentified species) for 4 broad fuel types: pine understory, semiarid shrublands, coniferous canopy, and organic soil. To our knowledge this is the most comprehensive measurement of biomass burning emissions to date and it should enable improved representation of smoke composition in atmospheric models. The results support a recent estimate of global NMOC emissions from biomass burning that is much higher than widely used estimates and they provide important insights into the nature of smoke. 31-72% of the mass of gas-phase NMOC species was attributed to species that we could not identify. These unidentified species are not represented in most models, but some provision should be made for the fact that they will react in the atmosphere. In addition, the total mass of gas-phase NMOC divided by the mass of co-emitted PM2.5 averaged about three (range similar to 2.0-8.7). About 35-64% of the NMOC were likely semivolatile or of intermediate volatility. Thus, the gas-phase NMOC represent a large reservoir of potential precursors for secondary formation of ozone and organic aerosol. For the single lab fire in organic soil about 28% of the emitted carbon was present as gas-phase NMOC and similar to 72% of the mass of these NMOC was unidentified, highlighting the need to learn more about the emissions from smoldering organic soils. The mass ratio of total NMOC to NOx as NO ranged from 11 to 267, indicating that NOx-limited O-3 production would be common in evolving biomass burning plumes. The fuel consumption per unit area was 7.0 +/- 2.3 Mg ha(-1) and 7.7 +/- 3.7 Mg ha(-1) for pine-understory and semiarid shrubland prescribed fires, respectively

Affected Experiencers

Numerous languages permit an NP that is not selected by the verb to be added to a clause, with several different possible interpretations. We divide such non-selected arguments into possessor, benefactive, attitude holder, and affected experiencer categories, on the basis of syntactic and semantic differences between them. We propose a formal analysis of the affected experiencer construction. In our account, a syntactic head Aff(ect) introduces the experiencer argument, and adds a conventional implicature to the effect that any event of the type denoted by its syntactic sister is the source of the experiencer’s psychological experience. Hence, our proposal involves two tiers of meaning: the at-issue meaning of the sentence, and some not-at-issue meaning (an implicature). A syntactic head can introduce material on both tiers. Additionally, we allow two parameters of variation: (i) the height of the attachment of Aff, and (ii) how much of the semantics is at-issue and how much is an implicature. We show that these two parameters account for the attested variation across our sample of languages, as well as the significant commonalities among them. Our analysis also accounts for significant differences between affected experiencers and the other types of non-selected arguments, and we also note a generalization to the effect that purely not-at-issue non-selected arguments can only be weak or clitic pronouns

The Diploid Genome Sequence of an Individual Human

Presented here is a genome sequence of an individual human. It was produced from ∼32 million random DNA fragments, sequenced by Sanger dideoxy technology and assembled into 4,528 scaffolds, comprising 2,810 million bases (Mb) of contiguous sequence with approximately 7.5-fold coverage for any given region. We developed a modified version of the Celera assembler to facilitate the identification and comparison of alternate alleles within this individual diploid genome. Comparison of this genome and the National Center for Biotechnology Information human reference assembly revealed more than 4.1 million DNA variants, encompassing 12.3 Mb. These variants (of which 1,288,319 were novel) included 3,213,401 single nucleotide polymorphisms (SNPs), 53,823 block substitutions (2–206 bp), 292,102 heterozygous insertion/deletion events (indels)(1–571 bp), 559,473 homozygous indels (1–82,711 bp), 90 inversions, as well as numerous segmental duplications and copy number variation regions. Non-SNP DNA variation accounts for 22% of all events identified in the donor, however they involve 74% of all variant bases. This suggests an important role for non-SNP genetic alterations in defining the diploid genome structure. Moreover, 44% of genes were heterozygous for one or more variants. Using a novel haplotype assembly strategy, we were able to span 1.5 Gb of genome sequence in segments >200 kb, providing further precision to the diploid nature of the genome. These data depict a definitive molecular portrait of a diploid human genome that provides a starting point for future genome comparisons and enables an era of individualized genomic information

Darwin Core: An Evolving Community-Developed Biodiversity Data Standard

Biodiversity data derive from myriad sources stored in various formats on many distinct hardware and software platforms. An essential step towards understanding global patterns of biodiversity is to provide a standardized view of these heterogeneous data sources to improve interoperability. Fundamental to this advance are definitions of common terms. This paper describes the evolution and development of Darwin Core, a data standard for publishing and integrating biodiversity information. We focus on the categories of terms that define the standard, differences between simple and relational Darwin Core, how the standard has been implemented, and the community processes that are essential for maintenance and growth of the standard. We present case-study extensions of the Darwin Core into new research communities, including metagenomics and genetic resources. We close by showing how Darwin Core records are integrated to create new knowledge products documenting species distributions and changes due to environmental perturbations

Integrating ecology and evolutionary theory. A game changer for biodiversity conservation?

Currently, one of the central arguments in favour of biodiversity conservation is that it is essential for the maintenance of ecosystem services, that is, the benefits that people receive from ecosystems. However, the relationship between ecosystem services and biodiversity is contested and needs clarification. The goal of this chapter is to spell out the interaction and reciprocal influences between conservation science, evolutionary biology, and ecology, in order to understand whether a stronger integration of evolutionary and ecological studies might help clarify the interaction between biodiversity and ecosystem functioning as well as influence biodiversity conservation practices. To this end, the eco-evolutionary feedback theory proposed by David Post and Eric Palkovacs is analysed, arguing that it helps operationalise niche construction theory and develop a more sophisticated understanding of the relationship between ecosystem functioning and biodiversity. Finally, it is proposed that by deepening the integration of ecological and evolutionary factors in our understanding of ecosystem functioning, the eco-evolutionary feedback theory is supportive of an “evolutionary-enlightened management” of biodiversity within the ecosystem services approach.info:eu-repo/semantics/publishedVersio

Locating Pleistocene Refugia: Comparing Phylogeographic and Ecological Niche Model Predictions

Ecological niche models (ENMs) provide a means of characterizing the spatial distribution of suitable conditions for species, and have recently been applied to the challenge of locating potential distributional areas at the Last Glacial Maximum (LGM) when unfavorable climate conditions led to range contractions and fragmentation. Here, we compare and contrast ENM-based reconstructions of LGM refugial locations with those resulting from the more traditional molecular genetic and phylogeographic predictions. We examined 20 North American terrestrial vertebrate species from different regions and with different range sizes for which refugia have been identified based on phylogeographic analyses, using ENM tools to make parallel predictions. We then assessed the correspondence between the two approaches based on spatial overlap and areal extent of the predicted refugia. In 14 of the 20 species, the predictions from ENM and predictions based on phylogeographic studies were significantly spatially correlated, suggesting that the two approaches to development of refugial maps are converging on a similar result. Our results confirm that ENM scenario exploration can provide a useful complement to molecular studies, offering a less subjective, spatially explicit hypothesis of past geographic patterns of distribution