Specification versus data fitting: SEM prediction and the Q‐class estimator

We propose a new class of limited information estimators built upon an explicit trade‐off between data fitting and a priori model specification. The estimators offer the researcher a continuum of estimators that range from an extreme emphasis on data fitting and robust reduced‐form estimation to the other extreme of exact model specification and efficient estimation. The approach used to generate the estimators illustrates why ULS often outperforms 2SLS‐PRRF even in the context of a correctly specified model, provides a new interpretation of 2SLS, and integrates Wonnacott and Wonnacott's (1970) least weighted variance estimators with other techniques. We apply the new class of estimators to Klein's Model I and generate forecasts. We find for this example that an emphasis on specification (as opposed to data fitting) produces better out‐of‐sample predictions. Copyright © 1999 John Wiley & Sons, Ltd.     

Unusual selection on the KIR3DL1/S1 natural killer cell receptor in Africans

Interactions of killer cell immunoglobulin-like receptors (KIRs) with major histocompatibility complex (MHC) class I ligands diversify natural killer cell responses to infection. By analyzing sequence variation in diverse human populations, we show that the KIR3DL1/S1 locus encodes two lineages of polymorphic inhibitory KIR3DL1 allotypes that recognize Bw4 epitopes of protein">HLA-A and HLA-B and one lineage of conserved activating KIR3DS1 allotypes, also implicated in Bw4 recognition. Balancing selection has maintained these three lineages for over 3 million years. Variation was selected at D1 and D2 domain residues that contact HLA class I and at two sites on D0, the domain that enhances the binding of KIR3D to HLA class I. HLA-B variants that gained Bw4 through interallelic microconversion are also products of selection. A worldwide comparison uncovers unusual KIR3DL1/S1 evolution in modern sub-Saharan Africans. Balancing selection is weak and confined to D0, KIR3DS1 is rare and KIR3DL1 allotypes with similar binding sites predominate. Natural killer cells express the dominant KIR3DL1 at a high frequency and with high surface density, providing strong responses to cells perturbed in Bw4 expression.     

Physiogenomic resources for rat models of heart, lung and blood disorders

Cardiovascular disorders are influenced by genetic and environmental factors. The TIGR rodent expression web-based resource (TREX) contains over 2,200 microarray hybridizations, involving over 800 animals from 18 different rat strains. These strains comprise genetically diverse parental animals and a panel of chromosomal substitution strains derived by introgressing individual chromosomes from normotensive Brown Norway (BN/NHsdMcwi) rats into the background of Dahl salt sensitive (SS/JrHsdMcwi) rats. The profiles document gene-expression changes in both genders, four tissues (heart, lung, liver, kidney) and two environmental conditions (normoxia, hypoxia). This translates into almost 400 high-quality direct comparisons (not including replicates) and over 100,000 pairwise comparisons. As each individual chromosomal substitution strain represents on average less than a 5% change from the parental genome, consomic strains provide a useful mechanism to dissect complex traits and identify causative genes. We performed a variety of data-mining manipulations on the profiles and used complementary physiological data from the PhysGen resource to demonstrate how TREX can be used by the cardiovascular community for hypothesis generation.     

Holocene vegetation and historic grazing impacts at Capitol Reef National Park reconstructed using packrat middens

Mid- to late-Holocene vegetation change from a remote high-desert site was reconstructed using plant macrofossils and pollen from 9 packrat middens ranging from 0 to 5400 yr in age. Presettlement middens consistently contained abundant macrofossils of plant species palatable to large herbivores that are now absent or reduced, such as winterfat ( Ceratoides lanata ) and ricegrass ( Stipa hymenoides ). Macrofossils and pollen of pinyon pine ( Pinus edulis ), sagebrush ( Artemisia spp.), and roundleaf buffaloberry ( Shepherdia rotundifolia ) were recently reduced to their lowest levels for the 5400-yr record. Conversely, species typical of overgrazed range, such as snakeweed ( Gutierrezia sarothrae ), viscid rabbitbrush ( Chrysothamnus visidiflorus ), and Russian thistle ( Salsola sp.), were not recorded prior to the historic introduction of grazing animals. Pollens of Utah juniper ( Juniperus osteosperma ) also increased during the last 200 yr. These records demonstrate that the most sever vegetation changes of the last 5400 yr occurred during the past 200 yr. The nature and timing of these changes suggest that they were primarily caused by the 19th-century open-land sheep and cattle ranching. The reduction of pinyon and sagebrush concurrent with other grazing impacts suggests that effects of cattle grazing at modern stocking levels may be a poor analog for the effects of intense sheep grazing during drought.