Sipping Fuel and Saving Lives: Increasing Fuel Economy without Sacrificing Safety

Demonstrates how new fuel-efficiency technologies make it possible, and advisable, to significantly increase the fuel economy of motor vehicles without compromising their safety

The Case for a Muon Collider Higgs Factory

We propose the construction of a compact Muon Collider Higgs Factory. Such a machine can produce up to \sim 14,000 at 8\times 10^{31} cm^-2 sec^-1 clean Higgs events per year, enabling the most precise possible measurement of the mass, width and Higgs-Yukawa coupling constants.Comment: Supporting letter for the document: "Muon Collider Higgs Factory for Smowmass 2013", A White Paper submitted to the 2013 U.S. Community Summer Study of the Division of Particles and Fields of the American Physical Society, Y. Alexahin, et. al, FERMILAB-CONF-13-245-T (July, 2013

Fin whale (Balaenoptera physalus) mitogenomics: A cautionary tale of defining sub-species from mitochondrial sequence monophyly

The advent of massive parallel sequencing technologies has resulted in an increase of studies based upon complete mitochondrial genome DNA sequences that revisit the taxonomic status within and among species. Spatially distinct monophyly in such mitogenomic genealogies, i.e., the sharing of a recent common ancestor among con-specific samples collected in the same region has been viewed as evidence for subspecies. Several recent studies in cetaceans have employed this criterion to suggest subsequent intraspecific taxonomic revisions. We reason that employing intra-specific, spatially distinct monophyly at non-recombining, clonally inherited genomes is an unsatisfactory criterion for defining subspecies based upon theoretical (genetic drift) and practical (sampling effort) arguments. This point was illustrated by a re-analysis of a global mitogenomic assessment of fin whales, Balaenoptera physalus spp., published by Archer et al. (2013), which proposed to further subdivide the Northern Hemisphere fin whale subspecies, B. p. physalus. The proposed revision was based upon the detection of spatially distinct monophyly among North Atlantic and North Pacific fin whales in a genealogy based upon complete mitochondrial genome DNA sequences. The extended analysis conducted in this study (1676 mitochondrial control region, 162 complete mitochondrial genome DNA sequences and 20 microsatellite loci genotyped in 380 samples) revealed that the apparent monophyly among North Atlantic fin whales reported by Archer et al. (2013) to be due to low sample sizes. In conclusion, defining sub-species from monophyly (i.e., the absence of para- or polyphyly) can lead to erroneous conclusions due to relatively 'trivial' aspects, such as sampling. Basic population genetic processes (i.e., genetic drift and migration) also affect the time to the most recent common ancestor and hence the probability that individuals in a sample are monophyletic

Fin whale (Balaenoptera physalus) mitogenomics: A cautionary tale of defining sub-species from mitochondrial sequence monophyly

© The Authors, 2019. This article is distributed under the terms of the Creative Commons Attribution-Noncommercial-Share Alike 4.0 International License. The definitive version was published in Molecular Phylogenetics and Evolution (2019), doi:10.1016/j.ympev.2019.02.003.The advent of massive parallel sequencing technologies has resulted in an increase of studies based upon complete mitochondrial genome DNA sequences that revisit the taxonomic status within and among species. Spatially distinct monophyly in such mitogenomic genealogies, i.e., the sharing of a recent common ancestor among con-specific samples collected in the same region has been viewed as evidence for subspecies. Several recent studies in cetaceans have employed this criterion to suggest subsequent intraspecific taxonomic revisions. We reason that employing intra-specific, spatially distinct monophyly at non-recombining, clonally inherited genomes is an unsatisfactory criterion for defining subspecies based upon theoretical (genetic drift) and practical (sampling effort) arguments. This point was illustrated by a re-analysis of a global mitogenomic assessment of fin whales, Balaenoptera physalus spp., published by Archer et al. (2013), which proposed to further subdivide the Northern Hemisphere fin whale subspecies, B. p. physalus. The proposed revision was based upon the detection of spatially distinct monophyly among North Atlantic and North Pacific fin whales in a genealogy based upon complete mitochondrial genome DNA sequences. The extended analysis conducted in this study (1,676 mitochondrial control region, 162 complete mitochondrial genome DNA sequences and 20 microsatellite loci genotyped in 358 samples) revealed that the apparent monophyly among North Atlantic fin whales reported by Archer et al. (2013) to be due to low sample sizes. In conclusion, defining sub-species from monophyly (i.e., the absence of para- or polyphyly) can lead to erroneous conclusions due to relatively “trivial” aspects, such as sampling. Basic population genetic processes (i.e., genetic drift and migration) also affect the time to the most recent common ancestor and hence the probability that individuals in a sample are monophyletic.We are grateful to Hanne Jørgensen, Anna Sellas, Mary Beth Rew and Christina Færch-Jensen for technical assistance. We thank Drs. P. E. Rosel and K. D. Mullin (U.S. National Marine Fisheries Service Southeast Fisheries Science Center) and members of the U.S. Northeast and Southeast Region Marine Mammal Stranding Network and its response teams, including the International Fund for Animal Welfare, the Marine Mammal Stranding Center, Mystic Aquarium, the Riverhead Foundation for Marine Research and Preservation (K. Durham) and the Marine Mammal Stranding Program of the University of North Carolina Wilmington for access to fin whale samples from the western North Atlantic. We thank Gisli Vikingsson for providing samples. We are indebted to Dr. Eduardo Secchi for facilitating data sharing. Data collection in the Southern Ocean was conducted under research projects Baleias (CNPq grants 557064/2009-0 and 408096/2013-6), INTERBIOTA (CNPq 407889/2013-2) and INCT-APA (CNPq 574018/2008-5), of the Brazilian Antarctic Program and a contribution by the research consortium ‘Ecology and Conservation of Marine Megafauna – EcoMega-CNPq’. MAS was supported through a FCT Investigator contract funded by POPH, QREN European Social Fund, and Portuguese Ministry for Science and Education. Data collection in the Azores was funded by TRACE-PTDC/MAR/74071/2006 and MAPCET-M2.1.2/F/012/2011 [FEDER, COMPETE, QREN European Social Fund, and Proconvergencia Açores/EU Program]. Fin whale illustration herein is used with the permission of Frédérique Lucas. We acknowledge the Center for Information Technology of the University of Groningen for IT support and access to the Peregrine high performance-computing cluster

The genetic architecture of helminth-specific immune responses in a wild population of Soay sheep (Ovis aries)

Much of our knowledge of the drivers of immune variation, and how these responses vary over time, comes from humans, domesticated livestock or laboratory organisms. While the genetic basis of variation in immune responses have been investigated in these systems, there is a poor understanding of how genetic variation influences immunity in natural, untreated populations living in complex environments. Here, we examine the genetic architecture of variation in immune traits in the Soay sheep of St Kilda, an unmanaged population of sheep infected with strongyle gastrointestinal nematodes. We assayed IgA, IgE and IgG antibodies against the prevalent nematode Teladorsagia circumcincta in the blood plasma of > 3,000 sheep collected over 26 years. Antibody levels were significantly heritable (h2 = 0.21 to 0.57) and highly stable over an individual’s lifespan. IgA levels were strongly associated with a region on chromosome 24 explaining 21.1% and 24.5% of heritable variation in lambs and adults, respectively. This region was adjacent to two candidate loci, Class II Major Histocompatibility Complex Transactivator (CIITA) and C-Type Lectin Domain Containing 16A (CLEC16A). Lamb IgA levels were also associated with the immunoglobulin heavy constant loci (IGH) complex, and adult IgE levels and lamb IgA and IgG levels were associated with the major histocompatibility complex (MHC). This study provides evidence of high heritability of a complex immunological trait under natural conditions and provides the first evidence from a genome-wide study that large effect genes located outside the MHC region exist for immune traits in the wild

Assessment of DRI’s Two-Stage Logistic Regression Model Used to Simultaneously Estimate the Relationship between Vehicle Mass or Size Reduction and U.S. Fatality Risk, Crashworthiness/Compatibility, and Crash Avoidance:

This report summarizes an effort to replicate the results from a 2-stage regression model developed by Dynamic Research Inc. (DRI) to simultaneously estimate the effect of mass or footprint reduction on the two components of societal fatality risk per vehicle miles of travel, crashes per VMT (crash frequency) and fatality risk once a crash has occurred (crashworthiness/ compatibility). Lawrence Berkeley National Laboratory (LBNL) was not able to exactly replicate the results from DRI’s simultaneous 2-stage regression model. This may be because of discrepancies in how DRI and LBNL classified the state police-reported crash data into crash types. LBNL’s analysis of four alternate regression models suggests that the results from DRI’s method are sensitive to changes in what data are used in the analysis, or even the particular vehicles included in the decimation sample; in some cases the sign of the estimated relationship from DRI’s results changes under an alternate LBNL regression. However, for the most part LBNL’s alternate regressions confirm the general results from DRI’s simultaneous model, and LBNL’s analysis in its Phase 2 report: that mass reduction is associated with an increase in crash frequency (crashes per VMT), but a decrease in fatality risk once a crash has occurred, across all vehicle types. Similar results were obtained after using stopped rather than non-culpable vehicles as the induced exposure records, and replacing footprint with wheelbase and track width

Sensitivity of Light-Duty Vehicle Crash Frequency per Vehicle Mile of Travel to Additional Vehicle and Driver Variables:

This report examines the sensitivity of the estimated effect of mass reduction on crash frequency in the National Highway Traffic Safety Administration (NHTSA) baseline regression model to including several additional vehicle and driver characteristics. The additional variables include handling and braking capability by vehicle model, from three Consumer Reports road tests; initial vehicle purchase price and vehicle manufacturer; average household income and “bad driver” rating by vehicle model; and whether the driver was using alcohol or drugs, or was properly restrained. The three Consumer Reports road tests are associated with an unexpected increase in crash frequency, in both all crashes and single vehicle crashes with a stationary object. For this reason they were not included in the sensitivity regression models. As expected, vehicle initial purchase price, median household income, and whether the driver was wearing a seat belt are associated with statistically significant decreases in crash frequency, while whether the driver was using alcohol or drugs is associated with a statistically significant increase in crash frequency. A poor average driving record by vehicle model is associated with an expected increase in crash frequency in cars, but unexpected decreases in crash frequency in light trucks and crossover utility vehicles (CUVs)/minivans. Including these variables, either individually or including all in the same regression model, does not change the general results of the baseline NHTSA regression model: that mass reduction is associated with an increase in crash frequency in all three types of vehicles, while footprint reduction is associated with an increase in crash frequency in cars and light trucks, but with a decrease in crash frequency in CUVs/minivans. The variable with the biggest effect is initial vehicle purchase price, which dramatically reduces the estimated increase in crash frequency in heavier-than-average cars and light trucks, and all CUVs/minivans. These results suggest that other, more subtle, differences in vehicles and their drivers account for the unexpected finding that lighter vehicles have higher crash frequencies than heavier vehicles, for all three types of vehicles

Effect of Accounting for Crash Severity on the Relationship between Mass Reduction and Crash Frequency and Risk per Crash:

Previous analyses have indicated that mass reduction is associated with an increase in crash frequency (crashes per VMT), but a decrease in fatality or casualty risk once a crash has occurred, across all types of light-duty vehicles. These results are counter-intuitive: one would expect that lighter, and perhaps smaller, vehicles have better handling and shorter braking distances, and thus should be able to avoid crashes that heavier vehicles cannot. And one would expect that heavier vehicles would have lower risk once a crash has occurred than lighter vehicles. However, these trends occur under several alternative regression model specifications. This report tests whether these results continue to hold after accounting for crash severity, by excluding crashes that result in relatively minor damage to the vehicle(s) involved in the crash. Excluding non-severe crashes from the initial LBNL Phase 2 and simultaneous two-stage regression models for the most part has little effect on the unexpected relationships observed in the baseline regression models. This finding suggests that other subtle differences in vehicles and/or their drivers, or perhaps biases in the data reported in state crash databases, are causing the unexpected results from the regression models