Affirmative action and effort choice: An experimental investigation (WIDER Working Paper 2016/54)

We study the effect of affirmative action on effort in an experiment conducted in high schools in socioeconomically disadvantaged areas in Queensland, Australia. All participating schools have a large representation of indigenous Australians, a population group that is frequently targeted by affirmative action. Our participants perform a simple real-effort task in a competitive setting. Those ranked in the top third receive a high piece-rate payment and all the others receive a low payment. We introduce affirmative action by providing the lowest (bottom third) performers with a positive handicap increasing their chances to achieve the high payment target. Our findings show that the policy increases effort of those that it aims to favour, without discouraging effort of those who are indirectly penalized by affirmative action

Elliptic flow from partially thermalized heavy-ion collisions

We study to what extent the measured elliptic flow at RHIC constrains viscous deviations from ideal hydrodynamics. We solve a toy model where only transverse momenta are thermalized while the system undergoes longitudinal free-streaming. We show that RHIC data exclude such a model and thus require fast 3-dimensional thermalization.Comment: 4 pages (incl. 2 postscript figures); uses espcrc1.sty (included in submission). Talk given at Quark Matter 2002, Nantes, June 18-24, 2002, to appear in the proceedings in Nucl. Phys.

Impact of the electron density and temperature gradient on drift-wave turbulence in the Large Plasma Device

In this paper we present an experimental study of edge turbulence in the Large Plasma Device at UCLA. We utilize a scan of discharge power and prefill pressure (neutral density) to show experimentally that turbulent density fluctuations decrease with decreasing density gradient, as predicted for resistive drift-wave turbulence (RDWT). As expected for RDWT, we observe that the cross-phase between the density and potential fluctuations is close to 0. Moreover, the addition of an electron temperature gradient leads to a reduction in the amplitude of the density fluctuations, as expected for RDWT. However, counter to theoretical expectations, we find that the potential fluctuations do not follow the same trends as the density fluctuations for changes either in density gradients or the addition of a temperature gradient. The disconnect between the density and potential fluctuations is connected to changes in the parallel flows as a result of differences in the prefill pressure, i.e. neutral density. Further analysis of the density and potential fluctuation spectra show that the electron temperature gradient reduces the low frequency fluctuations up to 10kHz role= presentation style= box-sizing: border-box; margin: 0px; padding: 0px; border: 0px; font-family: inherit; font-variant-caps: inherit; font-stretch: inherit; line-height: normal; vertical-align: baseline; display: inline; word-spacing: normal; word-wrap: normal; white-space: nowrap; float: none; direction: ltr; max-width: none; max-height: none; min-width: 0px; min-height: 0px; position: relative; \u3e10kHz10kHzand the introduction of a temperature gradient leads to an unexpected ∼π role= presentation style= box-sizing: border-box; margin: 0px; padding: 0px; border: 0px; font-family: inherit; font-variant-caps: inherit; font-stretch: inherit; line-height: normal; vertical-align: baseline; display: inline; word-spacing: normal; word-wrap: normal; white-space: nowrap; float: none; direction: ltr; max-width: none; max-height: none; min-width: 0px; min-height: 0px; position: relative; \u3e∼∼πshift of the density–potential cross-phase at ∼10kHz role= presentation style= box-sizing: border-box; margin: 0px; padding: 0px; border: 0px; font-family: inherit; font-variant-caps: inherit; font-stretch: inherit; line-height: normal; vertical-align: baseline; display: inline; word-spacing: normal; word-wrap: normal; white-space: nowrap; float: none; direction: ltr; max-width: none; max-height: none; min-width: 0px; min-height: 0px; position: relative; \u3e∼10kHz∼10kHz, while maintaining the typical resistive drift-wave cross-phase at lower frequencies. These experiments partly confirm existing knowledge on resistive drift-wave turbulence, but also introduce new observations that indicate a need for dedicated nonlinear three-dimensional turbulence simulations that include neutrals

Chesapeake Bay benthic community restoration goals

Benthic macroinvertebrate assemblages have been an integral part of the Chesapeake Bay monitoring program since its inception due to their ecological importance and their value as biological indicators. The condition of benthic assemblages reflects an integration of temporally variable environmental conditions and the effects of multiple types of environmental stresses. As such, benthic assemblages provide a useful complement to more temporally variable chemical and water quality monitoring measures. While assessments using benthic monitoring data have been useful for characterizing changes in environmental conditions at individual sites over time, and for relating the condition of sites to pollution loadings and sources, the full potential of these assessments for addressing larger management questions, such as What is the overall condition of the Bay? or How does the condition of various tributaries compare? has not yet been realized. Regional-scale assessments of ecological status and trends using benthic assemblages are limited by the fact that benthic assemblages are strongly influenced by naturally varying habitat elements, such as salinity, sediment type, and depth. Such natural variability confounds interpretation of differences in the benthic community differences as simple responses to anthropogenic environmental perturbations. An additional limitation is that different sampling methodologies used in various programs often constrain the extent to which the benthic data can be integrated for a unified assessment. The objective of this project was to develop a practical and conceptually sound framework for assessing benthic environmental conditions in Chesapeake Bay that would address the general constraints and limitations just described. This was accomplished by standardizing benthic data from several different monitoring programs to allow their integration into a single, coherent data base. From that data base a set of measures (Chesapeake Bay Benthic Restoration Goals) was developed to describe characteristics of benthic assemblages expected at sites having little evidence of environmental stress or disturbance. Using these goals, benthic data from any part of the Bay could be compared to determine whether conditions at that site met, were above, or were below expectations defined for reference sites in similar habitats

Population Genetic Study of the Brain-Derived Neurotrophic Factor (BDNF) Gene

Genetic variants in the brain-derived neurotrophic factor (BDNF) gene, predominantly the functional Val66Met polymorphism, have been associated with risk of bipolar disorder and other psychiatric disorders. However, not all studies support these findings, and overall the evidence for the association of BDNF with disease risk is weak. As differences in population genetic structure between patient samples could cause discrepant or spurious association results, we investigated this possibility by carrying out population genetic analyses of the BDNF genomic region. Substantial variation was detected in BDNF coding region single-nucleotide polymorphism (SNP) allele and haplotype frequencies between 58 global populations, with the derived Met allele of Val66Met ranging in frequency from 0 to 72% across populations. FST analyses to assess diversity in the HapMap populations determined that the Val66Met FST value was at the 99.8th percentile among all SNPs in the genome. As the BDNF population genetic differences may be due to local selection, we performed the long-range haplotype test for selection using 68 SNPs spanning the BDNF genomic region in 12 European-derived pedigrees. Evidence for positive selection was found for a high-frequency Val-carrying haplotype, with a relative extended haplotype homozygosity value above the 99th percentile compared with HapMap data $(P=4.6 \times 10^{−4})$. In conclusion, we observed considerable BDNF allele and haplotype diversity among global populations and evidence for positive selection at the BDNF locus. These phenomena can have a profound impact on the detection of disease susceptibility genes and must be considered in gene association studies of BDNF.Organismic and Evolutionary BiologyOther Research Uni

Combining genomics and epidemiology to track mumps virus transmission in the United States.

Unusually large outbreaks of mumps across the United States in 2016 and 2017 raised questions about the extent of mumps circulation and the relationship between these and prior outbreaks. We paired epidemiological data from public health investigations with analysis of mumps virus whole genome sequences from 201 infected individuals, focusing on Massachusetts university communities. Our analysis suggests continuous, undetected circulation of mumps locally and nationally, including multiple independent introductions into Massachusetts and into individual communities. Despite the presence of these multiple mumps virus lineages, the genomic data show that one lineage has dominated in the US since at least 2006. Widespread transmission was surprising given high vaccination rates, but we found no genetic evidence that variants arising during this outbreak contributed to vaccine escape. Viral genomic data allowed us to reconstruct mumps transmission links not evident from epidemiological data or standard single-gene surveillance efforts and also revealed connections between apparently unrelated mumps outbreaks

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay

Although studies have identified hundreds of loci associated with human traits and diseases, pinpointing causal alleles remains difficult, particularly for non-coding variants. To address this challenge, we adapted the massively parallel reporter assay (MPRA) to identify variants that directly modulate gene expression. We applied it to 32,373 variants from 3,642 cis-expression quantitative trait loci and control regions. Detection by MPRA was strongly correlated with measures of regulatory function. We demonstrate MPRA’s capabilities for pinpointing causal alleles, using it to identify 842 variants showing differential expression between alleles, including 53 well-annotated variants associated with diseases and traits. We investigated one in detail, a risk allele for ankylosing spondylitis, and provide direct evidence of a non-coding variant that alters expression of the prostaglandin EP4 receptor. These results create a resource of concrete leads and illustrate the promise of this approach for comprehensively interrogating how non-coding polymorphism shapes human biology.National Institutes of Health (U.S.) (grant DP2OD006514)National Institutes of Health (U.S.) (grant K99HG0081)National Institutes of Health (U.S.) (grant R01HG006785

A Composite of Multiple Signals Distinguishes Causal Variants in Regions of Positive Selection

The human genome contains hundreds of regions whose patterns of genetic variation indicate recent positive natural selection, yet for most the underlying gene and the advantageous mutation remain unknown. We developed a method, composite of multiple signals (CMS), that combines tests for multiple signals of selection and increases resolution by up to 100-fold. By applying CMS to candidate regions from the International Haplotype Map, we localized population-specific selective signals to 55 kilobases (median), identifying known and novel causal variants. CMS can not just identify individual loci but implicates precise variants selected by evolution.Organismic and Evolutionary BiologyOther Research Uni

The Case for Selection at CCR5-Δ32

The C-C chemokine receptor 5, 32 base-pair deletion (CCR5-Δ32) allele confers strong resistance to infection by the AIDS virus HIV. Previous studies have suggested that CCR5-Δ32 arose within the past 1,000 y and rose to its present high frequency (5%–14%) in Europe as a result of strong positive selection, perhaps by such selective agents as the bubonic plague or smallpox during the Middle Ages. This hypothesis was based on several lines of evidence, including the absence of the allele outside of Europe and long-range linkage disequilibrium at the locus. We reevaluated this evidence with the benefit of much denser genetic maps and extensive control data. We find that the pattern of genetic variation at CCR5-Δ32 does not stand out as exceptional relative to other loci across the genome. Moreover using newer genetic maps, we estimated that the CCR5-Δ32 allele is likely to have arisen more than 5,000 y ago. While such results can not rule out the possibility that some selection may have occurred at C-C chemokine receptor 5 (CCR5), they imply that the pattern of genetic variation seen atCCR5-Δ32 is consistent with neutral evolution. More broadly, the results have general implications for the design of future studies to detect the signs of positive selection in the human genome

Reporter Assays for Ebola Virus Nucleoprotein Oligomerization, Virion-Like Particle Budding, and Minigenome Activity Reveal the Importance of Nucleoprotein Amino Acid Position 111

For highly pathogenic viruses, reporter assays that can be rapidly performed are critically needed to identify potentially functional mutations for further study under maximal containment (e.g., biosafety level 4 [BSL-4]). The Ebola virus nucleoprotein (NP) plays multiple essential roles during the viral life cycle, yet few tools exist to study the protein under BSL-2 or equivalent containment. Therefore, we adapted reporter assays to measure NP oligomerization and virion-like particle (VLP) production in live cells and further measured transcription and replication using established minigenome assays. As a proof-of-concept, we examined the NP-R111C substitution, which emerged during the 20132016 Western African Ebola virus disease epidemic and rose to high frequency. NP-R111C slightly increased NP oligomerization and VLP budding but slightly decreased transcription and replication. By contrast, a synthetic charge-reversal mutant, NP-R111E, greatly increased oligomerization but abrogated transcription and replication. These results are intriguing in light of recent structures of NP oligomers, which reveal that the neighboring residue, K110, forms a salt bridge with E349 on adjacent NP molecules. By developing and utilizing multiple reporter assays, we find that the NP-111 position mediates a complex interplay between NP\u27s roles in protein structure, virion budding, and transcription and replication