The early medieval origin of Perth, Scotland

The radiocarbon results (and Bayesian modeling) of 15 samples of carbonized food residues removed from the external surface of rim sherds of cooking pots indicate that shellyware pottery first appeared in Perth, Scotland, around cal AD 9101020 (95% probability) and that it had disappeared by cal AD 10201140 (95% probability). Previously, it had been suggested that this pottery could not date to before AD 1150. These data, together with 14C analyses carried out on leather artifacts and a sample of wattle from a ditch lining, also demonstrate that there was occupation in Perth about 100 yr or more prior to the granting of royal burgh status to Perth in the 1120s

Effects of Whole Drilling Mud and Selected Components on the Shell Movements of the Bay Scallop, Argopecten irradians

The shell movements of bay scallops (Argopecten irradlans) were electronically monitored before and after different amounts of whole drilling mud, barite, lignosulfonate, and calcium carbonate were added to their tanks. Movements were compared with those made by scallops exposed to seawater for the same duration using six response measures. For whole drilling mud, a graded dose-response relationship existed for two response measures: change In the number of major Rapid Valve Closures (RVCs) and change In the cumulative magnitude of all RVCs. Ejection of pseudofeces Is frequently associated with RVCs. Scallops tested simultaneously with barite, lignosulfonate, and calcium carbonate showed Irregular but similar dose-response relationships for these two response measures. Three other measures (changes In gape width, RVC magnitude, and number of all RVCs) were not reliable Indicators of responsiveness for any materials. None of the materials caused significant changes In the number of swimming attempts, but only one-third of the animals ever attempted to swim. Scallops exposed to seawater showed no significant change for any response measure

Evolutionary prisoner's dilemma games with optional participation

Competition among cooperators, defectors, and loners is studied in an evolutionary prisoner's dilemma game with optional participation. Loners are risk averse i.e. unwilling to participate and rather rely on small but fixed earnings. This results in a rock-scissors-paper type cyclic dominance of the three strategies. The players are located either on square lattices or random regular graphs with the same connectivity. Occasionally, every player reassesses its strategy by sampling the payoffs in its neighborhood. The loner strategy efficiently prevents successful spreading of selfish, defective behavior and avoids deadlocks in states of mutual defection. On square lattices, Monte Carlo simulations reveal self-organizing patterns driven by the cyclic dominance, whereas on random regular graphs different types of oscillatory behavior are observed: the temptation to defect determines whether damped, periodic or increasing oscillations occur. These results are compared to predictions by pair approximation. Although pair approximation is incapable of distinguishing the two scenarios because of the equal connectivity, the average frequencies as well as the oscillations on random regular graphs are well reproduced.Comment: 6 pages, 7 figure

An evaluation of the cost/benefits of concrete biodecontamination

Two candidate technologies for decontamination of extensive areas of radioactively contaminated concrete, a biological technology and electro-hydraulic scabbling, that had been rated as highly useful in an earlier study were assessed more precisely. These technologies were compared to a base technology, scarification. The evaluation method was an adaptation of the Multi-Attribute Utility Technique (MAUT), a formal quantitative approach for analyzing decisions with regard to multiple objectives. The advantages of the biodecontamination technology were confirmed by this more precise quantitative analysis

Comparison of DTPA and resin extractable soil Zn to plant Zn uptake

Extraction of soil zinc with routine chemical extractants does not always reflect differences in Zn availability as detected by plant uptake. This study was undertaken to explore and compare the use of an ion exchange resin and diethylenetriaminepentaacetic acid (DTPA) for extracting soil Zn as related to plant Zn uptake. Beans were grown in 1989 following differential cropping with corn and beans or fallow in 1988 on a Portneuf silt loam near Kimberly, Idaho. Two Zn fertilizer treatments were imposed across previous cropping treatments. A batch method for determining resin extractable soil Zn was established. Both plant Zn concentration and Zn uptake by beans in 1989 were significantly higher in Zn fertilized than unfertilized treatments regardless of previous crop; and higher in plots previously cropped with corn than beans or fallow, regardless of Zn treatment. DTPA and resin extractable soil Zn were significantly higher in Zn fertilized plots compared to unfertilized plots but did not differ between previous cropping treatments. Resin and DTPA extractable soil Zn concentrations were positively correlated. Resin extracted soil Zn correlated better with plant Zn concentration and Zn uptake throughout the growing season than DTPA extracted soil Zn, particularly in plots that had been fallowed or previously cropped with corn. Resin may be extracting labile soil Zn not extracted with DTPA and, therefore, be better simulating plant uptake. Both extraction methods correlated better with Zn uptake when evaluated within cropping treatments, emphasizing the need to consider previous crop when calibrating soil tests

Rifting along the northern Gondwana margin and the evolution of the Rheic Ocean: A Devonian age for the El Castillo volcanic rocks (Salamanca, Central Iberian Zone)

Exposures of volcanic rocks (El Castillo) in the Central Iberian Zone near Salamanca, Spain, are representative of Paleozoic volcanic activity along the northern Gondwanan passive margin. Alkaline basalts and mafic volcaniclastic rocks of this sequence are structurally preserved in the core of the Variscan–Tamames Syncline. On the basis of the occurrence of graptolite fossils in immediately underlying strata, the El Castillo volcanics traditionally have been regarded as Lower Silurian in age. In contrast, most Paleozoic volcanic units in western Iberia are rift- elated mafic to felsic rocks emplaced during the Late Cambrian–Early Ordovician, and are attributed to the opening of the Rheic Ocean. We present new zircon U–Pb TIMS data from a mafic volcaniclastic rock within the El Castillo unit. These data yield a near-concordant, upper intercept age of 394.7±1.4 Ma that is interpreted to reflect a Middle Devonian (Emsian–Eifelian) age for the magmatism, demonstrating that the El Castillo volcanic rocks are separated from underlying lower Silurian strata by an unconformity. TheU–Pb age is coeval with a widespread extensional event in Iberia preserved in the form of a generalized paraconformity surface described in most of the Iberian Variscan realm. However, in the inner part of the Gondwanan platform, the Cantabrian Zone underwent a major, coeval increase in subsidence and the generation of sedimentary troughs. From this perspective, the eruption age reported here probably represents a discrete phase of incipient rifting along the southern flank of the Rheic Ocean. Paleogeographic reconstructions indicate that this rifting event was coeval with widespread orogeny and ridge subduction along the conjugate northern flank of the Rheic Ocean, the so called Acadian “orogeny”. We speculate that ridge subduction resulted in geodynamic coupling of the northern and southern flanks of the Rheic Ocean, and that the extension along the southern flank of the Rheic Ocean is a manifestation of slab pull along the northern flank. This scenario provides a uniform explanation for many features that form at ca. 395 Ma along the Gondwanan margin and has implications for the origin of the coeval oceanic Devonian mafic rocks currently exposed in the Variscan suture of NW Iberia

Factors affecting zinc uptake in cropping systems

Zinc availabilities can change with different cropping management practices. The objective of this study was to identify some of the causative factors associated with previous crops contributing to Zn uptake differences in a subsequent crop. Field studies over 3 yr evaluated the Zn availability after four precropping treatments: bean (Phaseolus vulgaris L.), corn (Zea mays L.), wheat (Triticum aestivum L.), and fallow, across two Zn fertilization rates (with and without 11 kg Zn ha-1 as ZnSO4), using the 'Viva' bean as a test crop. Soil samples taken before and after the test crop were analyzed for extractable P, Zn, Cu, Mn, and Fe, and organic matter. Soil respiration during the test crop was periodically estimated the last cropping year. Whole plant samples estimated nutrient concentration and uptake. Soil Zn extracted by diethylenetriaminepentaacetic acid (DTPA) was increased by Zn fertilization but not affected by precropping treatments. Zinc uptake by bean was significantly higher after precropping with corn and lower after fallow regardless of Zn fertilization. Uptake differences were most pronounced during early plant growth. Phosphorus and Cu uptake varied with treatment in a similar pattern as Zn uptake, and were positively correlated with each other. Zinc uptake was also positively correlated with soil organic matter and negatively correlated with soil P. Soil respiration rate was significantly lower after the fallow treatment compared with other precropping treatments. Vesicular-arbuscular mycorrhiza (VAM) colonization in the test crop roots was higher after corn and lower after fallow regardless of soil Zn concentrations. Colonization was positively correlated with Zn, P, and Cu uptake during early plant growth. The VAM colonization, soil respiration, and DTPA-extractable Zn were selected by a stepwise regression procedure as the important variables affecting Zn uptake during early plant growth. These results emphasize the importance of the soil's biological activities on Zn availability and may help explain some field observations where chemical soil tests appear to fail

Race and Ancestry in Immune Response to Breast Cancer

Martini and colleagues performed genetic ancestry estimation on a unique international triple-negative breast cancer (TNBC) study enriched for participants with African ancestry. They identified gene signatures indicative of ancestry in race-associated TNBC and found ancestry-associated immunologic differences that may contribute to racial disparities in breast cancer

DeCompress: Tissue compartment deconvolution of targeted mRNA expression panels using compressed sensing

Targeted mRNA expression panels, measuring up to 800 genes, are used in academic and clinical settings due to low cost and high sensitivity for archived samples. Most samples assayed on targeted panels originate from bulk tissue comprised of many cell types, and cell-type heterogeneity confounds biological signals. Reference-free methods are used when cell-type-specific expression references are unavailable, but limited feature spaces render implementation challenging in targeted panels. Here, we present DeCompress, a semi-reference-free deconvolution method for targeted panels. DeCompress leverages a reference RNA-seq or microarray dataset from similar tissue to expand the feature space of targeted panels using compressed sensing. Ensemble reference-free deconvolution is performed on this artificially expanded dataset to estimate cell-type proportions and gene signatures. In simulated mixtures, four public cell line mixtures, and a targeted panel (1199 samples; 406 genes) from the Carolina Breast Cancer Study, DeCompress recapitulates cell-type proportions with less error than reference-free methods and finds biologically relevant compartments. We integrate compartment estimates into cis-eQTL mapping in breast cancer, identifying a tumor-specific cis-eQTL for CCR3 (C-C Motif Chemokine Receptor 3) at a risk locus. DeCompress improves upon reference-free methods without requiring expression profiles from pure cell populations, with applications in genomic analyses and clinical settings