Differential responses of two nearshore infaunal assemblages to experimental petroleum additions

Empirical support is provided for the hypothesis that benthic communities found in relatively constant and predictable environments are less stable (resistant and resilient) following unusual disturbances than lower-diversity communities found in more inconstant and unpredictable environments. A less diverse benthic community (i.e., the Streblospio-Tubificoides assemblage) inhabiting an inconstant and unpredictable, shallow marsh cove was disturbed less and recovered faster from an experimental addition of No. 2 fuel oil, than the more diverse benthos (i.e., the Nucula-Mediomastus assemblage) inhabiting a relatively more constant and predictable, deeper coastal embayment. Disturbed sediment had a stimulatory effect on most populations in the marsh and an inhibitory effect on most populations in the bay. Initial amount and subsequent behavior of oil were similar in the two environments. Thus, differential responses of the two communities are attributable to intrinsic biological properties rather than differences in levels or composition of oil

Ecological condition of coastal ocean waters along the U.S. Mid-Atlantic Bight: 2006

In May 2006, the NOAA National Ocean Service (NOS), in conjunction with the EPA National Health and Environmental Effects Laboratory (NHEERL), conducted an assessment of the status of ecological condition of soft-bottom habitat and overlying waters throughout the mid-Atlantic Bight (MAB) portion of the eastern U.S. continental shelf. The study area encompassed the region from Cape Cod, MA and Nantucket Shoals in the northeast to Cape Hatteras in the south, and was defined using a one nautical mile buffer of the shoreline extended seaward to the shelf break (~100-m depth contour). A total of 50 stations were targeted for sampling using standard methods and indicators applied in prior NOAA coastal studies and EPA’s Environmental Monitoring and Assessment Program (EMAP) and National Coastal Assessment (NCA). A key feature adopted from these studies was the incorporation of a random probabilistic sampling design. Such a design provides a basis for making unbiased statistical estimates of the spatial extent of ecological condition relative to various measured indicators and corresponding thresholds of concern. Indicators included multiple measures of water quality, sediment quality, and biological condition (benthic fauna). Through coordination with the NOAA Fisheries Service/Northeast Fisheries Science Center (NFS/NEFSC), samples of summer flounder (Paralichthys dentatus) also were obtained from 30 winter 2007 bottom-trawl survey stations in overlapping portions of the study area and used for analysis of chemical-contaminant body burdens

Ecological Condition of Coastal Ocean Waters within Stellwagen Bank National Marine Sanctuary: 2008

In June 2008, the NOAA National Ocean Service (NOS), in conjunction with the EPA National Health and Environmental Effects Laboratory (NHEERL), conducted an assessment of the status of ecological condition of soft-bottom habitat and overlying waters within the boundaries of Stellwagen Bank National Marine Sanctuary (SBNMS). The sanctuary lies approximately 20 nautical miles east of Boston, MA in the southwest Gulf of Maine between Cape Ann and Cape Cod and encompassing 638 square nautical miles (2,181 km2). A total of 30 stations were targeted for sampling using standard methods and indicators applied in prior NOAA coastal studies and EPA’s Environmental Monitoring and Assessment Program (EMAP) and National Coastal Assessment (NCA). A key feature adopted from these studies was the incorporation of a random probabilistic sampling design. Such a design provides a basis for making unbiased statistical estimates of the spatial extent of ecological condition relative to various measured indicators and corresponding thresholds of concern. Indicators included multiple measures of water quality, sediment quality, and biological condition (benthic fauna, fish tissue contaminant levels). Depths ranged from 31 – 137 m throughout the study area. About 76 % of the area had sediments composed of sands ( 80 % siltclay). About 70 % of the area (represented by 21 sites) had sediment total organic carbon (TOC) concentrations 50 mg/g). Surface salinities ranged from 30.6 – 31.5 psu, with the majority of the study region (approximately 80 % of the area) having surface salinities between 30.8 and 31.4 psu. Bottom salinities varied between 32.1 and 32.5 psu, with bottom salinities at all sites having values above the range of surface salinities. Surface-water temperatures varied between 12.1 and 16.8 ºC, while near-bottom waters ranged in temperature from 4.4 – 6.2 ºC. An index of density stratification (Δσt) indicated that the waters of SBNMS were stratified at the time of sampling. Values of Δσt at 29 of the 30 sites sampled in this study (96.7 % of the study area) varied from 2.1 – 3.2, which is within the range considered to be indicative of strong vertical stratification (Δσt > 2) and typical of the western Gulf of Maine in summer. Levels of dissolved oxygen (DO) were confined to a fairly narrow range in surface (8.8 – 10.4 mg/L) and bottom (8.5 – 9.6 mg/L) waters throughout the survey area. These levels are within the range considered indicative of good water quality (> 5 mg/L) with respect to DO. None of these waters had DO at low levels (< 2 mg/L) potentially harmful to benthic fauna and fish

Immunoglobulin G immune response to SARS-CoV-2 vaccination in people living with multiple sclerosis within Multiple Sclerosis Partners Advancing Technology and Health Solutions

The impact of multiple sclerosis (MS) disease-modifying therapies (DMTs) on SARS-CoV-2 vaccination response is uncertain. Post-SARS-CoV-2 vaccination blood samples across multiple DMTs were tested for SARS-CoV-2 immunoglobulin G (IgG) response. Three hundred twenty-two people with MS were included; 91.9% received an mRNA vaccine. Post-vaccination reactive IgG rates (IgG index > 1) were 40% for anti-CD20 (32/80 patients); 41% for sphingosine 1-phosphate receptor modulators (S1PRM, 16/39); and 100% for all other classes, including the no DMT group. Anti-CD20 therapies and S1PRMs reduce IgG response to SARS-CoV-2 vaccination; IgG response is preserved with other DMTs

The effect of Dnaaf5 gene dosage on primary ciliary dyskinesia phenotypes

DNAAF5 is a dynein motor assembly factor associated with the autosomal heterogenic recessive condition of motile cilia, primary ciliary dyskinesia (PCD). The effects of allele heterozygosity on motile cilia function are unknown. We used CRISPR-Cas9 genome editing in mice to recreate a human missense variant identified in patients with mild PCD and a second, frameshift-null deletion in Dnaaf5. Litters with Dnaaf5 heteroallelic variants showed distinct missense and null gene dosage effects. Homozygosity for the null Dnaaf5 alleles was embryonic lethal. Compound heterozygous animals with the missense and null alleles showed severe disease manifesting as hydrocephalus and early lethality. However, animals homozygous for the missense mutation had improved survival, with partially preserved cilia function and motor assembly observed by ultrastructure analysis. Notably, the same variant alleles exhibited divergent cilia function across different multiciliated tissues. Proteomic analysis of isolated airway cilia from mutant mice revealed reduction in some axonemal regulatory and structural proteins not previously reported in DNAAF5 variants. Transcriptional analysis of mouse and human mutant cells showed increased expression of genes coding for axonemal proteins. These findings suggest allele-specific and tissue-specific molecular requirements for cilia motor assembly that may affect disease phenotypes and clinical trajectory in motile ciliopathies

RNA-Seq Mapping and Detection of Gene Fusions with a Suffix Array Algorithm

High-throughput RNA sequencing enables quantification of transcripts (both known and novel), exon/exon junctions and fusions of exons from different genes. Discovery of gene fusions–particularly those expressed with low abundance– is a challenge with short- and medium-length sequencing reads. To address this challenge, we implemented an RNA-Seq mapping pipeline within the LifeScope software. We introduced new features including filter and junction mapping, annotation-aided pairing rescue and accurate mapping quality values. We combined this pipeline with a Suffix Array Spliced Read (SASR) aligner to detect chimeric transcripts. Performing paired-end RNA-Seq of the breast cancer cell line MCF-7 using the SOLiD system, we called 40 gene fusions among over 120,000 splicing junctions. We validated 36 of these 40 fusions with TaqMan assays, of which 25 were expressed in MCF-7 but not the Human Brain Reference. An intra-chromosomal gene fusion involving the estrogen receptor alpha gene ESR1, and another involving the RPS6KB1 (Ribosomal protein S6 kinase beta-1) were recurrently expressed in a number of breast tumor cell lines and a clinical tumor sample

Scientific assessment of the use of sugars as cigarette tobacco ingredients: A review of published and other publicly available studies

Sugars, such as sucrose or invert sugar, have been used as tobacco ingredients in American-blend cigarettes to replenish the sugars lost during curing of the Burley component of the blended tobacco in order to maintain a balanced flavor. Chemical-analytical studies of the mainstream smoke of research cigarettes with various sugar application levels revealed that most of the smoke constituents determined did not show any sugar-related changes in yields (per mg nicotine), while ten constituents were found to either increase (formaldehyde, acrolein, 2-butanone, isoprene, benzene, toluene, benzo[k]fluoranthene) or decrease (4-aminobiphenyl, N-nitrosodimethylamine, N-nitrosonornicotine) in a statistically significant manner with increasing sugar application levels. Such constituent yields were modeled into constituent uptake distributions using simulations of nicotine uptake distributions generated on the basis of published nicotine biomonitoring data, which were multiplied by the constituent/nicotine ratios determined in the current analysis. These simulations revealed extensive overlaps for the constituent uptake distributions with and without sugar application. Moreover, the differences in smoke composition did not lead to relevant changes in the activity in in vitro or in vivo assays. The potential impact of using sugars as tobacco ingredients was further assessed in an indirect manner by comparing published data from markets with predominantly American-blend or Virginia-type (no added sugars) cigarettes. No relevant difference was found between these markets for smoking prevalence, intensity, some markers of dependence, nicotine uptake, or mortality from smoking-related lung cancer and chronic obstructive pulmonary disease. In conclusion, thorough examination of the data available suggests that the use of sugars as ingredients in cigarette tobacco does not increase the inherent risk and harm of cigarette smoking

Search for eccentric black hole coalescences during the third observing run of LIGO and Virgo

Despite the growing number of confident binary black hole coalescences observed through gravitational waves so far, the astrophysical origin of these binaries remains uncertain. Orbital eccentricity is one of the clearest tracers of binary formation channels. Identifying binary eccentricity, however, remains challenging due to the limited availability of gravitational waveforms that include effects of eccentricity. Here, we present observational results for a waveform-independent search sensitive to eccentric black hole coalescences, covering the third observing run (O3) of the LIGO and Virgo detectors. We identified no new high-significance candidates beyond those that were already identified with searches focusing on quasi-circular binaries. We determine the sensitivity of our search to high-mass (total mass M&gt;70 M⊙) binaries covering eccentricities up to 0.3 at 15 Hz orbital frequency, and use this to compare model predictions to search results. Assuming all detections are indeed quasi-circular, for our fiducial population model, we place an upper limit for the merger rate density of high-mass binaries with eccentricities 0&lt;e≤0.3 at 0.33 Gpc−3 yr−1 at 90\% confidence level

Search for gravitational-lensing signatures in the full third observing run of the LIGO-Virgo network

Gravitational lensing by massive objects along the line of sight to the source causes distortions of gravitational wave-signals; such distortions may reveal information about fundamental physics, cosmology and astrophysics. In this work, we have extended the search for lensing signatures to all binary black hole events from the third observing run of the LIGO--Virgo network. We search for repeated signals from strong lensing by 1) performing targeted searches for subthreshold signals, 2) calculating the degree of overlap amongst the intrinsic parameters and sky location of pairs of signals, 3) comparing the similarities of the spectrograms amongst pairs of signals, and 4) performing dual-signal Bayesian analysis that takes into account selection effects and astrophysical knowledge. We also search for distortions to the gravitational waveform caused by 1) frequency-independent phase shifts in strongly lensed images, and 2) frequency-dependent modulation of the amplitude and phase due to point masses. None of these searches yields significant evidence for lensing. Finally, we use the non-detection of gravitational-wave lensing to constrain the lensing rate based on the latest merger-rate estimates and the fraction of dark matter composed of compact objects