A summary of water-quality and salt marsh monitoring, Humboldt Bay, California

This report summarizes data-collection activities associated with the U.S. Geological Survey Humboldt Bay Water-Quality and Salt Marsh Monitoring Project. This work was undertaken to gain a comprehensive understanding ofwater-quality conditions, salt marsh accretion processes, marsh-edge erosion, and soil-carbon storage in Humboldt Bay, California. Multiparameter sondes recorded water temperature, specific conductance, and turbidity at a 15-minute timestep at two U.S. Geological Survey water-quality stations: Mad River Slough near Arcata, California (U.S. Geological Survey station 405219124085601) and (2) Hookton Slough near Loleta, California (U.S. Geological Survey station 404038124131801). At each station, discrete water samples were collected to develop surrogate regression models that were used to compute a continuous time seriesof suspended-sediment concentration from continuously measured turbidity. Data loggers recorded water depth at a 6-minute timestep in the primary tidal channels (Mad River Slough and Hookton Slough) in two adjacent marshes (Mad River marsh and Hookton marsh). The marsh monitoring network included five study marshes. Three marshes (Mad River, Manila, and Jacoby) are in the northern embayment of Humboldt Bay and two marshes (White and Hookton) are in the southern embayment. Surface deposition and elevation change were measured using deep rod surface elevation tables and feldspar marker horizons. Sediment characteristics and soil-carbon storage were measured using a total of 10 shallow cores, distributed across 5 study marshes, collected using an Eijkelkamp peat sampler. Rates of marsh edge erosion (2010–19) were quantified in four marshes (Mad River, Manila, Jacoby, and White) by estimating changes in the areal extent of the vegetated marsh plain using repeat aerial imagery and light detection and ranging (LiDAR)-derived elevation data. During the monitoring period (2016–19), the mean suspended-sediment concentration computed for Hookton Slough (50±20 milligrams per liter [mg/L]) was higher than Mad River Slough (18±7 mg/L). Uncertainty in mean suspended-sediment concentration values is reported using a 90-percent confidence interval. Across the five study marshes, elevation change (+1.8±0.6 millimeters per year[mm/yr]) and surface deposition (+2.5±0.5 mm/yr) were lower than published values of local sea-level rise (4.9±0.8 mm/yr), and mean carbon density was 0.029±0.005 grams of carbon per cubic centimeter. From 2010 to 2019, marsh edge erosion and soil carbon loss were greatest in low-elevation marshes with the marsh edge characterized by a gentle transition from mudflat to vegetated marsh (herein, ramped edge morphology) and larger wind-wave exposure. Jacoby Creek marsh experienced the greatest edge erosion. In total, marsh edge erosion was responsible for 62.3 metric tons of estuarine soil carbon storage loss across four study marshes. Salt marshes are an important component of coastal carbon, which is frequently referred to as “blue carbon.” The monitoring data presented in this report provide fundamental information needed to manage blue carbon stocks, assess marsh vulnerability, inform sea-level rise adaptation planning, and build coastal resiliency to climate change

Cell-free Embryonic Stem Cell Extract-mediated Derivation of Multi-potent Stem Cells from NIH3T3 Fibroblasts for Functional and Anatomical Ischemic Tissue Repair

The oocyte-independent generation of multipotent stem cells is one of the goals in regenerative medicine. We report that upon exposure to mouse ES cell (ESC) extracts, reversibly permeabilized NIH3T3 cells undergo de-differentiation followed by stimulus-induced re-differentiation into multiple lineage cell types. Genome-wide expression profiling revealed significant differences between NIH3T3 and ESC-extract treated NIH3T3 cells including re-activation of ESC specific transcripts. Epigenetically, ESC extracts induced CpG de-methylation of Oct4 promoter, hyper-acetylation of histones 3 and 4 and decreased lysine 9 (K-9) dimethylation of histone 3. In mouse models of surgically-induced hind limb ischemia (HLI) or acute myocardial infarction (AMI) transplantation of reprogrammed NIH3T3 cells significantly improved post-injury physiological functions and showed antomical evidence of engraftment and trans-differentiation into skeletal muscle, endothelial cell and cardiomyocytes. These data provide evidence for the generation of functional multi-potent stem like cells from terminally differentiated somatic cells without the introduction of trans-genes or ESC fusion

Spontaneous Clearance Of Vertically Acquired Hepatitis C Infection: Implications For Testing And Treatment

BACKGROUND: Current guidelines recommend that infants born to women with hepatitis C (HCV) viremia are screened for HCV antibody at age 18 months, and if positive, referred for RNA testing at 3 years to confirm chronic infection. This policy is based in part on analyses suggesting 25%-40% of vertically acquired HCV infections clear spontaneously within 4-5 years. METHODS: Data on 179 infants with HCV RNA and/or anti-HCV evidence of vertically acquired infection in three prospective European cohorts were investigated. Ages at clearance of infection were estimated taking account of interval censoring and delayed entry. We also investigated clearance in initially HCV RNA negative infants in whom RNA was not detectable until after 6 weeks. RESULTS: Clearance rates are initially high then decline slowly. Apparently, many infections clear before they can be confirmed. An estimated 65.9% (50.1-81.6) of confirmed infections cleared by 5 years, at a median 12.4 (7.1-18.9) months. If treatment began at age 6 months, 18 months or 3 years, at least 59.0% (42.0-76.9), 39.7% (17.9-65.9), and 20.9% (4.6-44.8) of those treated would clear without treatment. In seven (6.6%) confirmed infections, RNA was not detectable until after 6 weeks, and in 2 (1.9%) not until after 6 months. However, all such cases subsequently cleared. CONCLUSIONS: Most confirmed infection clears by age 3 years. Treatment before age 3, if it was available, would avoid loss to follow-up, but would result in substantial over-treatment

Overall vertical transmission of HCV, transmission net of clearance, and timing of transmission

Background: It is widely accepted that the risk of HCV vertical transmission (VT) is 5-6% in mono-infected women, and that 25-40% of HCV infection clears spontaneously within 5 years. However, there is no consensus on how VT rates should be estimated, and there is a lack of information on VT rates “net” of clearance. // Methods: We re-analysed data on 1749 children in 3 prospective cohorts to obtain coherent estimates of overall VT rate and VT rates “net” of clearance at different ages. Clearance rates were used to impute the proportion of uninfected children who had been infected and then cleared before testing negative. The proportion of transmission early in utero, late in utero and at delivery was estimated from data on the proportion of HCV RNA positive within three days of birth, and differences between elective caesarean and non-elective caesarean deliveries. // Findings: Overall VT rates were 7.2% (95% credible interval 5.6-8.9) in mothers who were HIV negative and 12.1% (8.6-16.8) in HIV-co-infected women. The corresponding rates net of clearance at 5 years were 2.4% (1.1-4.1) and 4.1% (1.7-7.3). We estimated that 24.8% (12.1-40.8) of infections occur early in utero, 66.0% (42.5-83.3) later in utero, and 9.3% (0.5-30.6) during delivery. // Conclusion: Overall VT rates are about 24% higher than previously assumed, but the risk of infection persisting beyond age 5 years is about 38% lower. The results can inform design of trials of to prevent or treat pediatric HCV infection, and strategies to manage children exposed in utero

Single slice vs. volumetric MR assessment of visceral adipose tissue: reliability and validity among the overweight and obese.

To access publisher's full text version of this article. Please click on the hyperlink in Additional Links field.Visceral adipose tissue (VAT) is associated with abnormal cardiovascular and metabolic profiles. Total VAT volume of the abdominal compartment by magnetic resonance imaging (MRI) is the gold-standard measurement for VAT but is costly and time consuming. Prior studies suggest VAT area on a single slice MR image may serve as a surrogate for total VAT volume but it is unknown if this relationship is maintained in overweight and obese men and women. Untreated sleep apnea subjects enrolled into the Icelandic Sleep Apnea Cohort (ISAC) underwent abdominal MRI. VAT area and subcutaneous adipose tissue (SAT) area at the L2-L3 and L4-L5 interspaces and total VAT and SAT volumes were determined by manual examination using image analysis software; 539 men and 129 women with mean ages of 54.1 and 58.8 years and mean BMI of 32.2 kg/m(2) and 33.7 kg/m(2), respectively, were studied. Mean total VAT volume was 40% smaller and mean total SAT was 25% larger among females compared with males. The correlation with VAT volume was significantly larger for L2-L3 VAT area (r = 0.96) compared to L4-L5 VAT area (r = 0.83). The difference in correlation coefficients was statistically significant (nonparametric bootstrap P < 0.001 with 95% confidence interval (CI) for the difference from 0.11 to 0.15. VAT area at L2-L3 was also significantly better correlated with VAT volume than traditional anthropometric variables. Linear regression analyses demonstrated that L2-L3 area alone was sufficient for predicting total VAT volume and that the nature of the linear association was maintained across all levels of obesity and in both genders.NIH HL070267 HL09430

Potential effects of sea-level rise on plant productivity: species-specific responses in northeast Pacific tidal marshes

Coastal wetland plants are adapted to varying degrees of inundation. However, functional relationships between inundation and productivity are poorly characterized for most species. Determining species-specific tolerances to inundation is necessary to evaluate sea-level rise (SLR) effects on future marsh plant community composition, quantify organic matter inputs to marsh accretion, and inform predictive modeling of tidal wetland persistence. In 2 macrotidal estuaries in the northeast Pacific we grew 5 common species in experimental mesocosms across a gradient of tidal elevations to assess effects on growth. We also tested whether species abundance distributions along elevation gradients in adjacent marshes matched productivity profiles in the mesocosms. We found parabolic relationships between inundation and total plant biomass and shoot counts in Spartina foliosa and Bolboschoenus maritimus in California, USA, and in Carex lyngbyei in Oregon, USA, with maximum total plant biomass occurring at 38, 28, and 15% time submerged, respectively. However, biomass of Salicornia pacifica and Juncus balticus declined monotonically with increasing inundation. Inundation effects on the ratio of belowground to aboveground biomass varied inconsistently among species. In comparisons of field distributions with mesocosm results, B. maritimus, C. lyngbyei and J. balticus were abundant in marshes at or above elevations corresponding with their maximum productivity; however, S. foliosa and S. pacifica were frequently abundant at lower elevations corresponding with sub-optimal productivity. Our findings show species-level differences in how marsh plant growth may respond to future SLR and highlight the sensitivity of high marsh species such as S. pacifica and J. balticus to increases in flooding.Keywords: Root-to-shoot ratio, Zonation, Plant biomass, Tidal wetlands, Marsh organ

Stress gradients structure spatial variability in coastal tidal marsh plant composition and diversity in a major Pacific coast estuary

Understanding the drivers of variability in plant diversity from local to landscape spatial scales is a challenge in ecological systems. Environmental gradients exist at several spatial scales and can be nested hierarchically, influencing patterns of plant diversity in complex ways. As plant community dynamics influence ecosystem function, understanding the drivers of plant community variability across space is paramount for predicting potential shifts in ecosystem function from global change. Determining the scales at which stress gradients influence vegetation composition is crucial to inform management and restoration of tidal marshes for specific functions. Here, we analyzed vegetation community composition in 51 tidal marshes from the San Francisco Bay Estuary, California, USA. We used model-based compositional analysis and rank abundance curves to quantify environmental (elevation/tidal frame position, distance to channel, and channel salinity) and species trait (species form, wetland indicator status, and native status) influences on plant community variability at the marsh site and estuary scales. While environmental impacts on plant diversity varied by species and their relationships to each other, overall impacts increased in strength from marsh to estuary scales. Relative species abundance was important in structuring these tidal marsh communities even with the limited species pools dominated by a few species. Rank abundance curves revealed different community structures by region with higher species evenness at plots higher in the tidal frame and adjacent to freshwater channels. By identifying interactions (species–species, species–environment, and environment–trait) at multiple scales (local, landscape), we begin to understand how variability measurements could be interpreted for conservation and land management decisions

The Host Galaxy of FRB 20171020A Revisited

The putative host galaxy of FRB 20171020A was first identified as ESO 601-G036 in 2018, but as no repeat bursts have been detected, direct confirmation of the host remains elusive. In light of recent developments in the field, we re-examine this host and determine a new association confidence level of 98%. At 37 Mpc, this makes ESO 601-G036 the third closest FRB host galaxy to be identified to date and the closest to host an apparently non-repeating FRB (with an estimated repetition rate limit of < 0.011 bursts per day above 10 erg). Due to its close distance, we are able to perform detailed multi-wavelength analysis on the ESO 601-G036 system. Follow-up observations confirm ESO 601-G036 to be a typical star-forming galaxy with HI and stellar masses of log(M_HI/M_sol) ~ 9.2 and log(M_*/M_sol) = 8.64, and a star formation rate of SFR = 0.09 +/- 0.01 M_sol/yr. We detect, for the first time, a diffuse gaseous tail (log(M_HI/M_sol) ~ 8.3) extending to the south-west that suggests recent interactions, likely with the confirmed nearby companion ESO 601-G037. ESO 601-G037 is a stellar shred located to the south of ESO 601-G036 that has an arc-like morphology, is about an order of magnitude less massive, and has a lower gas metallicity that is indicative of a younger stellar population. The properties of the ESO 601-G036 system indicate an ongoing minor merger event, which is affecting the overall gaseous component of the system and the stars within ESO 601-G037. Such activity is consistent with current FRB progenitor models involving magnetars and the signs of recent interactions in other nearby FRB host galaxies.Comment: 16 pages, 9 figures, accepted for publication in PAS

Spontaneous Clearance Of Vertically Acquired Hepatitis C Infection: Implications For Testing And Treatment.

BACKGROUND: Current guidelines recommend that infants born to women with hepatitis C (HCV) viremia are screened for HCV antibody at age 18 months, and if positive, referred for RNA testing at 3 years to confirm chronic infection. This policy is based in part on analyses suggesting 25%-40% of vertically acquired HCV infections clear spontaneously within 4-5 years. METHODS: Data on 179 infants with HCV RNA and/or anti-HCV evidence of vertically acquired infection in three prospective European cohorts were investigated. Ages at clearance of infection were estimated taking account of interval censoring and delayed entry. We also investigated clearance in initially HCV RNA negative infants in whom RNA was not detectable until after 6 weeks. RESULTS: Clearance rates are initially high then decline slowly. Apparently, many infections clear before they can be confirmed. An estimated 65.9% (50.1-81.6) of confirmed infections cleared by 5 years, at a median 12.4 (7.1-18.9) months. If treatment began at age 6 months, 18 months or 3 years, at least 59.0% (42.0-76.9), 39.7% (17.9-65.9), and 20.9% (4.6-44.8) of those treated would clear without treatment. In seven (6.6%) confirmed infections, RNA was not detectable until after 6 weeks, and in 2 (1.9%) not until after 6 months. However, all such cases subsequently cleared. CONCLUSIONS: Most confirmed infection clears by age 3 years. Treatment before age 3, if it was available, would avoid loss to follow-up, but would result in substantial over-treatment