Devil in the details: how can we avoid potential pitfalls of CATS regression when our data do not follow a Poisson distribution?

Background Community assembly by trait selection (CATS) allows for the detection of environmental filtering and estimation of the relative role of local and regional (meta-community-level) effects on community composition from trait and abundance data without using environmental data. It has been shown that Poisson regression of abundances against trait data results in the same parameter estimates. Abundance data do not necessarily follow a Poisson distribution, and in these cases, other generalized linear models should be fitted to obtain unbiased parameter estimates. Aims This paper discusses how the original algorithm for calculating the relative role of local and regional effects has to be modified if Poisson model is not appropriate. Results It can be shown that the use of the logarithm of regional relative abundances as an offset is appropriate only if a log-link function is applied. Otherwise, the link function should be applied to the product of local total abundance and regional relative abundances. Since this product may be outside the domain of the link function, the use of log-link is recommended, even if it is not the canonical link. An algorithm is also suggested for calculating the offset when data are zero-inflated. The relative role of local and regional effects is measured by Kullback-Leibler R2. The formula for this measure presented by Shipley (2014) is valid only if the abundances follow a Poisson distribution. Otherwise, slightly different formulas have to be applied. Beyond theoretical considerations, the proposed refinements are illustrated by numerical examples. CATS regression could be a useful tool for community ecologists, but it has to be slightly modified when abundance data do not follow a Poisson distribution. This paper gives detailed instructions on the necessary refinement.

Development and evaluation of a new compact mechanism for aromatic oxidation in atmospheric models

Aromatic hydrocarbons, including benzene, toluene, and xylenes, play an important role in atmospheric chemistry, but the associated chemical mechanisms are complex and uncertain. Sparing representation of this chemistry in models is needed for computational tractability. Here, we develop a new compact mechanism for aromatic chemistry (GC13) that captures current knowledge from laboratory and computational studies with only 17 unique species and 44 reactions. We compare GC13 to six other currently used mechanisms of varying complexity in box model simulations of environmental chamber data and diurnal boundary layer chemistry, and show that GC13 provides results consistent with or better than more complex mechanisms for oxygenated products (alcohols, carbonyls, dicarbonyls), ozone, and hydrogen oxide (HOx≡OH+HO2) radicals. Specifically, GC13 features increased radical recycling and increased ozone destruction from phenoxy–phenylperoxy radical cycling relative to other mechanisms. We implement GC13 into the GEOS-Chem global chemical transport model and find higher glyoxal yields and net ozone loss from aromatic chemistry compared with other mechanisms. Aromatic oxidation in the model contributes 23 %, 5 %, and 8 % of global glyoxal, methylglyoxal, and formic acid production, respectively, and has mixed effects on formaldehyde. It drives small decreases in global tropospheric OH (−2.2 %), NOx (≡NO+NO2; −3.7 %), and ozone (−0.8 %), but a large increase in NO3 (+22 %) from phenoxy–phenylperoxy radical cycling. Regional effects in polluted environments can be substantially larger, especially from the photolysis of carbonyls produced by aromatic oxidation, which drives large wintertime increases in OH and ozone concentrations.

Deep-Water Circulation over the Last Two Glacial Cycles Reconstructed from Authigenic Neodymium Isotopes in the Equatorial Indian Ocean (Core HI1808-GPC04)

We reconstructed the past deep-water character of the equatorial Indian Ocean using the isotope ratio of neodymium (εNd) in the Fe–Mn coating of mixed-species foraminifera. When compared with previous εNd records at the same site (ODP 758) and at another site to the west (SK 129), the three datasets were consistent and showed glacial-interglacial variations, even though the other two records were extracted from different media (cleaned foraminifera and bulk sediment leach). This confirms that while the foraminiferal coating is the preferred medium for reconstructing past bottom water εNd records, for carbonate-dominated lithologies, weak acid extraction of bulk sediment is also a viable option offering high-resolution capabilities. When the lithology includes volcanic particles or high organics, the extraction protocol may need to be adjusted to guard against detrital contamination or a slight correction may need to be applied. During glacials, the deep waters bathing the equatorial Indian Ocean had a larger AABW component and during interglacials a larger NADW component. Our HI1808-GPC04 record supplements the ODP 758 record in the interval with prominent AABW signal (MIS 6/5 transition and MIS 7) and reveals regional effects in some non-radiogenic intervals. The smaller differences between the HI1808-GPC04/ODP 758 and SK 129 records seem to reflect regional Nd input from river systems and non-radiogenic Nd from the boundaries.

Safety Performance of Rural Curved Corner Intersections with Regional Effects

This study evaluates the intersection of rural roads where a curved roadway segment connects the major flow of through traffic from orthogonal directions. A system of up to three intersections in combination can be represented singly by the situation modeled in this paper as a curved corner intersection site. This paper evaluates the application of random intercept negative binomial (NB) regression modeling to produce safety performance functions, and compares the outcome with NB models using fixed regional effects. At curved corner intersections, installing a combined/merged intersection approach near the midpoint of the curve is a potential countermeasure that by comparison with three-leg configurations experienced 20% fewer intersection crashes. A larger radius of curvature along the curved segment at these types of intersections is also very favorable for safety performance. Each 100 ft increase in the radius of a three-leg or four-leg curved corner intersection is estimated to reduce total non-animal crash occurrence by 5% and 7%, respectively. This study can help safety engineers to prioritize the improvement of rural un-signalized intersections.

Structural variants are a major source of gene expression differences in humans and often affect multiple nearby genes

Structural variants (SVs) are an important source of human genome diversity but their functional effects are not well understood. We mapped 61,668 SVs in 613 individuals with deep genome sequencing data from the GTEx project and measured their effects on gene expression. We estimate that common SVs are causal at 2.66% of eQTLs, which is a 10.5-fold enrichment relative to their abundance in the genome and consistent with prior work using smaller sample sizes. Duplications and deletions were the most impactful variant types, whereas the contribution of mobile element insertions was small (0.12% of eQTLs, 1.9-fold enriched). Multi-tissue analysis of expression effects revealed that gene-altering SVs show significantly more constitutive effects than other variant types, with 62.09% of coding SV-eQTLs active in all tissues with known eQTL activity compared to 23.08% of coding SNV- and indel-eQTLs, while noncoding SVs, SNVs and indels show broadly similar patterns. We also identified 539 rare SVs associated with nearby gene expression outliers. Of these, 62.34% are noncoding SVs that show strong effects on gene expression yet modest enrichment at known regulatory elements, demonstrating that rare noncoding SVs are a major source of gene expression differences but remain difficult to predict from current annotations. Both common and rare noncoding SVs often show strong regional effects on the expression of multiple genes: SV-eQTLs affect an average of 1.82 nearby genes compared to 1.09 genes affected by SNV- and indel-eQTLs, and 21.34% of rare expression-altering SVs show strong effects on 2-9 different genes. We also observe significant effects on rare gene expression changes extending 1 Mb from the SV. This provides a mechanism by which individual noncoding SVs may have strong or pleiotropic effects on phenotypic variation and disease.

Sequencing refractory regions in bird genomes are hotspots for accelerated protein evolution

Background Approximately 1000 protein encoding genes common for vertebrates are still unannotated in avian genomes. Are these genes evolutionary lost or are they not yet found for technical reasons? Using genome landscapes as a tool to visualize large-scale regional effects of genome evolution, we reexamined this question. Results On basis of gene annotation in non-avian vertebrate genomes, we established a list of 15,135 common vertebrate genes. Of these, 1026 were not found in any of eight examined bird genomes. Visualizing regional genome effects by our sliding window approach showed that the majority of these "missing" genes can be clustered to 14 regions of the human reference genome. In these clusters, an additional 1517 genes (often gene fragments) were underrepresented in bird genomes. The clusters of “missing” genes coincided with regions of very high GC content, particularly in avian genomes, making them “hidden” because of incomplete sequencing. Moreover, proteins encoded by genes in these sequencing refractory regions showed signs of accelerated protein evolution. As a proof of principle for this idea we experimentally characterized the mRNA and protein products of four "hidden" bird genes that are crucial for energy homeostasis in skeletal muscle: ALDOA, ENO3, PYGM and SLC2A4. Conclusions A least part of the “missing” genes in bird genomes can be attributed to an artifact caused by the difficulty to sequence regions with extreme GC% (“hidden” genes). Biologically, these “hidden” genes are of interest as they encode proteins that evolve more rapidly than the genome wide average. Finally we show that four of these “hidden” genes encode key proteins for energy metabolism in flight muscle.

Regional Effects of Perceived Risks of Harm on Cigarette Smoking among U.S. High School Seniors: Evidence from Monitoring the Future

Overall, there has been an increasing trend in the perceived risk of harm from smoking among U.S. high school seniors. However, these perceptions of risk have been falling in recent years. This study uses regional-level panel data from the Monitoring the Future survey and a fixed effects model to estimate the effect of perceived risk on three regional measurements of smoking behavior: consumption, lifetime prevalence, and daily smoking prevalence. Elasticity measurements at regional levels show that an increase in perceived risk decreases these regional measurements of smoking behavior. Moreover, the results show that, at regional levels, these measurements of smoking behavior are more responsive to changes in the perceived risk associated with smoking than to changes in the price of cigarettes.

Regional effect on the molecular clock rate of protein evolution in Eutherian and Metatherian genomes

Background Different types of proteins diverge at vastly different rates. Moreover, the same type of protein has been observed to evolve with different rates in different phylogenetic lineages. In the present study we measured the rates of protein evolution in Eutheria (placental mammals) and Metatheria (marsupials) on a genome-wide basis and we propose that the gene position in the genome landscape has an important influence on the rate of protein divergence. Results We analyzed a protein-encoding gene set (n = 15,727) common to 16 mammals (12 Eutheria and 4 Metatheria). Using sliding windows that averaged regional effects of protein divergence we constructed landscapes in which strong and lineage-specific regional effects were seen on the molecular clock rate of protein divergence. Within each lineage, the relatively high rates were preferentially found in subtelomeric chromosomal regions. Such regions were observed to contain important and well-studied loci for fetal growth, uterine function and the generation of diversity in the adaptive repertoire of immunoglobulins. Conclusions A genome landscape approach visualizes lineage-specific regional differences between Eutherian and Metatherian rates of protein evolution. This phenomenon of chromosomal position is a new element that explains at least part of the lineage-specific effects and differences between proteins on the molecular clock rates.

Development and evaluation of a new compact mechanism for aromatic oxidation in atmospheric models

Aromatic hydrocarbons (mainly benzene, toluene, and xylenes) play an important role in atmospheric chemistry but the associated chemical mechanisms are complex and uncertain. Spare representation of this chemistry in models is needed for computational tractability. Here we develop a new compact mechanism for aromatic chemistry (GC13) that captures current knowledge from laboratory and computational studies with only 17 unique species and 44 reactions. We compare GC13 to six other currently used mechanisms of varying complexity in box model simulations of environmental chamber data and diurnal boundary layer chemistry, and show that GC13 provides results consistent with or better than more complex mechanisms for oxygenated products (alcohols, carbonyls, dicarbonyls), ozone, and hydrogen oxide (HOx ≡ OH + HO2) radicals. GC13 features in particular increased radical recycling and increased ozone destruction from phenoxy-phenylperoxy radical cycling relative to other mechanisms. We implement GC13 into the GEOS-Chem global chemical transport model and find higher glyoxal yields and net ozone loss from aromatic chemistry compared to other mechanisms. Aromatic oxidation in the model contributes 23 %, 5 %, and 8 % of global glyoxal, methylglyoxal, and formic acid production respectively, and has mixed effects on formaldehyde. It drives small decreases in global tropospheric OH (−2.2 %), NOx (≡ NO + NO2; −3.7 %) and ozone (−0.8 %), but a large increase in NO3 (+22 %) from phenoxy-phenylperoxy radical cycling. Regional effects in polluted environments can be substantially larger, especially from photolysis of carbonyls produced by aromatic oxidation, which drives large wintertime increases in OH and ozone concentrations.