A Compact Beam Stop for a Rare Kaon Decay Experiment

We describe the development and testing of a novel beam stop for use in a rare kaon decay experiment at the Brookhaven AGS. The beam stop is located inside a dipole spectrometer magnet in close proximity to straw drift chambers and intercepts a high-intensity neutral hadron beam. The design process, involving both Monte Carlo simulations and beam tests of alternative beam-stop shielding arrangements, had the goal of minimizing the leakage of particles from the beam stop and the resulting hit rates in detectors, while preserving maximum acceptance for events of interest. The beam tests consisted of measurements of rates in drift chambers, scintilation counter hodoscopes, a gas threshold Cherenkov counter, and a lead glass array. Measurements were also made with a set of specialized detectors which were sensitive to low-energy neutrons, photons, and charged particles. Comparisons are made between these measurements and a detailed Monte Carlo simulation.Comment: 39 pages, 14 figures, submitted to Nuclear Instruments and Method

A straw drift chamber spectrometer for studies of rare kaon decays

We describe the design, construction, readout, tests, and performance of planar drift chambers, based on 5 mm diameter copperized Mylar and Kapton straws, used in an experimental search for rare kaon decays. The experiment took place in the high-intensity neutral beam at the Alternating Gradient Synchrotron of Brookhaven National Laboratory, using a neutral beam stop, two analyzing dipoles, and redundant particle identification to remove backgrounds

Macrophyte abundance in Waquoit Bay : effects of land-derived nitrogen loads on seasonal and multi-year biomass patterns

Author Posting. © The Author(s), 2008. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Estuaries and Coasts 31 (2008): 532-541, doi:10.1007/s12237-008-9039-6.Anthropogenic inputs of nutrients to coastal waters have rapidly restructured coastal ecosystems. To examine the response of macrophyte communities to land-derived nitrogen loading, we measured macrophyte biomass monthly for six years in three estuaries subject to different nitrogen loads owing to different land uses on the watersheds. The set of estuaries sampled had nitrogen loads over the broad range of 12 to 601 kg N ha-1 y-1. Macrophyte biomass increased as nitrogen loads increased, but the response of individual taxa varied. Specifically, biomass of Cladophora vagabunda and Gracilaria tikvahiae increased significantly as nitrogen loads increased. The biomass of other macroalgal taxa tended to decrease with increasing load, and the relative proportion of these taxa to total macrophyte biomass also decreased. The seagrass, Zostera marina, disappeared from the higher loaded estuaries, but remained abundant in the estuary with the lowest load. Seasonal changes in macroalgal standing stock were also affected by nitrogen load, with larger fluctuations in biomass across the year and higher minimum biomass of macroalgae in the higher loaded estuaries. There were no significant changes in macrophyte biomass over the six years of this study, but there was a slight trend of increasing macroalgal biomass in the latter years. Macroalgal biomass was not related to irradiance or temperature, but Z. marina biomass was highest during the summer months when light and temperatures peak. Irradiance might, however, be a secondary limiting factor controlling macroalgal biomass in the higher loaded estuaries by restricting the depth of the macroalgal canopy. The relationship between the bloom-forming macroalgal species, C. vagabunda and G. tikvahiae, and nitrogen loads suggested a strong connection between development on watersheds and macroalgal blooms and loss of seagrasses. The influence of watershed land uses largely overwhelmed seasonal and inter-annual differences in standing stock of macrophytes in these temperate estuaries.This research was supported by the National Oceanic and Atmospheric Administration (NOAA), Cooperative Institute for Coastal and Estuarine Environmental Technologies (CICEET-UNH#99-304, NOAA NA87OR512), NOAA National Estuarine Research Reserve Graduate Research Fellowship NERRS GRF, #NA77OR0228), and an Environmental Protection Agency (EPA) STAR Fellowship for Graduate Environmental Study (U-915335-01-0) awarded to J. Hauxwell. S. Fox was supported by a NOAA NERRS GRF (#NA03NOS4200132) and an EPA STAR Graduate Research Fellowship. We also thank the Quebec-Labrador Foundation Atlantic Center for the Environment's Sounds Conservancy Program and the Boston University Ablon/Bay Committee for their awarding research funds

Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements

As an accompanying manuscript to the release of the honey bee genome, we report the entire sequence of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) ribosomal RNA (rRNA)-encoding gene sequences (rDNA) and related internally and externally transcribed spacer regions of Apis mellifera (Insecta: Hymenoptera: Apocrita). Additionally, we predict secondary structures for the mature rRNA molecules based on comparative sequence analyses with other arthropod taxa and reference to recently published crystal structures of the ribosome. In general, the structures of honey bee rRNAs are in agreement with previously predicted rRNA models from other arthropods in core regions of the rRNA, with little additional expansion in non-conserved regions. Our multiple sequence alignments are made available on several public databases and provide a preliminary establishment of a global structural model of all rRNAs from the insects. Additionally, we provide conserved stretches of sequences flanking the rDNA cistrons that comprise the externally transcribed spacer regions (ETS) and part of the intergenic spacer region (IGS), including several repetitive motifs. Finally, we report the occurrence of retrotransposition in the nuclear large subunit rDNA, as R2 elements are present in the usual insertion points found in other arthropods. Interestingly, functional R1 elements usually present in the genomes of insects were not detected in the honey bee rRNA genes. The reverse transcriptase products of the R2 elements are deduced from their putative open reading frames and structurally aligned with those from another hymenopteran insect, the jewel wasp Nasonia (Pteromalidae). Stretches of conserved amino acids shared between Apis and Nasonia are illustrated and serve as potential sites for primer design, as target amplicons within these R2 elements may serve as novel phylogenetic markers for Hymenoptera. Given the impending completion of the sequencing of the Nasonia genome, we expect our report eventually to shed light on the evolution of the hymenopteran genome within higher insects, particularly regarding the relative maintenance of conserved rDNA genes, related variable spacer regions and retrotransposable elements

Cytotoxicity and DNA damage in the neutrophils of patients with sickle cell anaemia treated with hydroxyurea

Hydroxyurea (HU) is the most important advance in the treatment of sickle cell anaemia (SCA) for preventing complications and improving quality of life for patients. However, some aspects of treatment with HU remain unclear, including their effect on and potential toxicity to other blood cells such as neutrophils. This study used the measurement of Lactate Dehydrogenase (LDH) and Methyl ThiazolTetrazolium (MTT) and the comet assay to investigate the cytotoxicity and damage index (DI) of the DNA in the neutrophils of patients with SCA using HU.In the LDH and MTT assays, a cytoprotective effect was observed in the group of patients treated, as well as an absence of toxicity. When compared to patients without the treatment, the SS group (n=20, 13 women and 07 men, aged 18-69 years), and the group of healthy individuals (AA) used as a control group (n=52, 28 women and 24 men, aged 19-60 years), The SSHU group (n=21, 11 women and 10 men, aged 19-63 years) showed a significant reduction (p20 months), demonstrating that despite the cytoprotective effects in terms of cell viability, the use of HU can induce DNA damage in neutrophils

An epigenome-wide association study of posttraumatic stress disorder in US veterans implicates several new DNA methylation loci

Background Previous studies using candidate gene and genome-wide approaches have identified epigenetic changes in DNA methylation (DNAm) associated with posttraumatic stress disorder (PTSD). Methods In this study, we performed an EWAS of PTSD in a cohort of Veterans (n = 378 lifetime PTSD cases and 135 controls) from the Translational Research Center for TBI and Stress Disorders (TRACTS) cohort assessed using the Illumina EPIC Methylation BeadChip which assesses DNAm at more than 850,000 sites throughout the genome. Our model included covariates for ancestry, cell heterogeneity, sex, age, and a smoking score based on DNAm at 39 smoking-associated CpGs. We also examined in EPIC-based DNAm data generated from pre-frontal cortex (PFC) tissue from the National PTSD Brain Bank (n = 72). Results The analysis of blood samples yielded one genome-wide significant association with PTSD at cg19534438 in the gene G0S2 (p = 1.19 x 10(-7), p(adj) = 0.048). This association was replicated in an independent PGC-PTSD-EWAS consortium meta-analysis of military cohorts (p = 0.0024). We also observed association with the smoking-related locus cg05575921 in AHRR despite inclusion of a methylation-based smoking score covariate (p = 9.16 x 10(-6)), which replicates a previously observed PGC-PTSD-EWAS association (Smith et al. 2019), and yields evidence consistent with a smoking-independent effect. The top 100 EWAS loci were then examined in the PFC data. One of the blood-based PTSD loci, cg04130728 in CHST11, which was in the top 10 loci in blood, but which was not genome-wide significant, was significantly associated with PTSD in brain tissue (in blood p = 1.19 x 10(-5), p(adj) = 0.60, in brain, p = 0.00032 with the same direction of effect). Gene set enrichment analysis of the top 500 EWAS loci yielded several significant overlapping GO terms involved in pathogen response, including "Response to lipopolysaccharide" (p = 6.97 x 10(-6), p(adj) = 0.042). Conclusions The cross replication observed in independent cohorts is evidence that DNA methylation in peripheral tissue can yield consistent and replicable PTSD associations, and our results also suggest that that some PTSD associations observed in peripheral tissue may mirror associations in the brain.Stress-related psychiatric disorders across the life spa