Ancient DNA reveals the timing and persistence of organellar genetic bottlenecks over 3,000 years of sunflower domestication and improvement

Here, we report a comprehensive paleogenomic study of archaeological and ethnographic sunflower remains that provides significant new insights into the process of domestication of this important crop. DNA from both ancient and historic contexts yielded high proportions of endogenous DNA, and although archaeological DNA was found to be highly degraded, it still provided sufficient coverage to analyze genetic changes over time. Shotgun sequencing data from specimens from the Eden's Bluff archaeological site in Arkansas yielded organellar DNA sequence from specimens up to 3,100 years old. Their sequences match those of modern cultivated sunflowers and are consistent with an early domestication bottleneck in this species. Our findings also suggest that recent breeding of sunflowers has led to a loss of genetic diversity that was present only a century ago in Native American landraces. These breeding episodes also left a profound signature on the mitochondrial and plastid haplotypes in cultivars, as two types were intentionally introduced from other Helianthus species for crop improvement. These findings gained from ancient and historic sunflower specimens underscore how future in-depth gene-based analyses can advance our understanding of the pace and targets of selection during the domestication of sunflower and other crop species

New SPB stars in the field of the young open cluster NGC 2244 discovered by the MOST photometric satellite

During two weeks of nearly continuous optical photometry of the young open cluster NGC 2244 obtained by the MOST satellite, we discovered two new SPB stars, GSC 00154-00785 and GSC 00154-01871. We present frequency analyses of the MOST light curves of these stars, which reveal two oscillation frequencies (0.61 and 0.71 c/d) in GSC 00154-00785 and two (0.40 and 0.51 c/d) in GSC 00154-01871. These frequency ranges are consistent with g-modes of $\ell \leq 2$ excited in models of main-sequence or pre-main-sequence (PMS) stars of masses 4.5 - 5 $M_{\odot}$ and solar composition $(X, Z)= (0.7, 0.02)$. Published proper motion measurements and radial velocities are insufficient to establish unambiguously cluster membership for these two stars. However, the PMS models which fit best their eigenspectra have ages consistent with NGC 2244. If cluster membership can be confirmed, these would be the first known PMS SPB stars, and would open a new window on testing asteroseismically the interior structures of PMS stars.Comment: accepted for publication in MNRA

Recognizing Treelike k-Dissimilarities

A k-dissimilarity D on a finite set X, |X| >= k, is a map from the set of size k subsets of X to the real numbers. Such maps naturally arise from edge-weighted trees T with leaf-set X: Given a subset Y of X of size k, D(Y) is defined to be the total length of the smallest subtree of T with leaf-set Y . In case k = 2, it is well-known that 2-dissimilarities arising in this way can be characterized by the so-called "4-point condition". However, in case k > 2 Pachter and Speyer recently posed the following question: Given an arbitrary k-dissimilarity, how do we test whether this map comes from a tree? In this paper, we provide an answer to this question, showing that for k >= 3 a k-dissimilarity on a set X arises from a tree if and only if its restriction to every 2k-element subset of X arises from some tree, and that 2k is the least possible subset size to ensure that this is the case. As a corollary, we show that there exists a polynomial-time algorithm to determine when a k-dissimilarity arises from a tree. We also give a 6-point condition for determining when a 3-dissimilarity arises from a tree, that is similar to the aforementioned 4-point condition.Comment: 18 pages, 4 figure

Benchmarking Crimes: An Emerging Threat in Systems Security

Properly benchmarking a system is a difficult and intricate task. Unfortunately, even a seemingly innocuous benchmarking mistake can compromise the guarantees provided by a given systems security defense and also put its reproducibility and comparability at risk. This threat is particularly insidious as it is generally not a result of malice and can easily go undetected by both authors and reviewers. Moreover, as modern defenses often trade off security for performance in an attempt to find an ideal design point in the performance-security space, the damage caused by benchmarking mistakes is increasingly worrisome. To analyze the magnitude of the phenomenon, we identify a set of 22 "benchmarking crimes" that threaten the validity of systems security evaluations and perform a survey of 50 defense papers published in top venues. To ensure the validity of our results, we perform the complete survey twice, with two independent readers. We find only a very small number of disagreements between readers, showing that our assessment of benchmarking crimes is highly reproducible. We show that benchmarking crimes are widespread even in papers published at tier-1 venues. We find that tier-1 papers commit an average of five benchmarking crimes and we find only a single paper in our sample that committed no benchmarking crimes. Moreover, we find that the scale of the problem is constant over time, suggesting that the community is not yet addressing it despite the problem being now more relevant than ever. This threatens the scientific process, which relies on reproducibility and comparability to ensure that published research advances the state of the art. We hope to raise awareness of these issues and provide recommendations to improve benchmarking quality and safeguard the scientific process in our community. Computer Systems, Imagery and Medi

The BNL ASTD Field Lab - Near - Real - Time Characterization of BNL Stockpiled Soils to Accelerate Completion of the EM Chemical Holes Project

As of October 2001, approximately 7,000 yd{sup 3} of stockpiled soil remained at Brookhaven National Laboratory (BNL) after the remediation of the BNL Chemical/Animal/Glass Pits disposal area. The soils were originally contaminated with radioactive materials and heavy metals, depending on what materials had been interred in the pits, and how the pits were excavated. During the 1997 removal action, the more hazardous/radioactive materials were segregated, along with, chemical liquids and solids, animal carcasses, intact gas cylinders, and a large quantity of metal and glass debris. Nearly all of these materials have been disposed of. In order to ensure that all debris was removed and to characterize the large quantity of heterogeneous soil, BNL initiated an extended sorting, segregation, and characterization project directed at the remaining soil stockpiles. The project was co-funded by the Department of Energy Environmental Management Office (DOE EM) through the BNL Environmental Restoration program and through the DOE EM Office of Science and Technology Accelerated Site Technology Deployment (ASTD) program. The focus was to remove any non-conforming items, and to assure that mercury and radioactive contaminant levels were within acceptable limits for disposal as low-level radioactive waste. Soils with mercury concentrations above allowable levels would be separated for disposal as mixed waste. Sorting and segregation were conducted simultaneously. Large stockpiles (ranging from 150 to 1,200 yd{sup 3}) were subdivided into manageable 20 yd{sup 3} units after powered vibratory screening. The 1/2-inch screen removed almost all non-conforming items (plus some gravel). Non-conforming items were separated for further characterization. Soil that passed through the screen was also visually inspected before being moved to a 20 yd{sup 3} ''subpile.'' Eight samples from each subpile were collected after establishing a grid of four quadrants: north, east, south and west, and two layers: top and bottom. Field personnel collected eight 100-gram samples, plus quality assurance (QA) duplicates for chemical analysis, and a 1-liter jar of material for gamma spectroscopy. After analyses were completed and reviewed, the stockpiles were reconstructed for later disposal as discrete entities within a disposal site profile. A field lab was set up in a trailer close to the stockpile site, equipped with instrumentation to test for mercury, RCRA metals, and gamma spectroscopy, and a tumbler for carrying out a modified Toxicity Characteristic Leaching Procedure (TCLP) protocol. Chemical analysis included X-ray fluorescence (XRF) to screen for high (>260 ppm) total mercury concentrations, and modified TCLP tests to verify that the soils were not RCRA hazardous. The modified TCLP tests were 1/10th scale, to minimize secondary (leachate) waste and maximize tumbler capacity and sampler throughput. TCLP leachate analysis was accomplished using a Milestone Direct Mercury Analyzer (DMA80). Gamma spectroscopy provided added assurance of previously measured Am-241, Cs-137, and Co-60 contamination levels

Determinants of response to a parent questionnaire about development and behaviour in 3 year olds: European multicentre study of congenital toxoplasmosis.

Background: We aimed to determine how response to a parent-completed postal questionnaire measuring development, behaviour, impairment, and parental concerns and anxiety, varies in different European centres. Methods: Prospective cohort study of 3 year old children, with and without congenital toxoplasmosis, who were identified by prenatal or neonatal screening for toxoplasmosis in 11 centres in 7 countries. Parents were mailed a questionnaire that comprised all or part of existing validated tools. We determined the effect of characteristics of the centre and child on response, age at questionnaire completion, and response to child drawing tasks. Results: The questionnaire took 21 minutes to complete on average. 67% (714/1058) of parents responded. Few parents (60/1058) refused to participate. The strongest determinants of response were the score for organisational attributes of the study centre (such as direct involvement in follow up and access to an address register), and infection with congenital toxoplasmosis. Age at completion was associated with study centre, presence of neurological abnormalities in early infancy, and duration of prenatal treatment. Completion rates for individual questions exceeded 92% except for child completed drawings of a man (70%), which were completed more by girls, older children, and in certain centres. Conclusion: Differences in response across European centres were predominantly related to the organisation of follow up and access to correct addresses. The questionnaire was acceptable in all six countries and offers a low cost tool for assessing development, behaviour, and parental concerns and anxiety, in multinational studies

Plasmas and Controlled Nuclear Fusion

Contains research objectives and reports on four research projects.National Science Foundation (Grant GK-614)National Science Foundation (Grant GK-57