Jacoby Creek Site Inventory Assessment and Management Recommendations for Parcel 502-052-022

Jacoby Creek is a 16.6 mi2 watershed that discharges into Humboldt Bay in Humboldt County, California. Legacy use of this watershed consisted of unmanaged logging and diking to create pastureland for agriculture until the 1970’s. Currently, 187 acres of the Jacoby Creek watershed is owned by the Jacoby Creek Land Trust (JCLT). JCLT focuses on creating a space for recreation and conservation within the Jacoby Creek watershed. The parcel (parcel 502-052-022) was assessed to identify social trails, invasive species, tree density, and upland understory vegetation to provide restoration recommendations. Non-native invasive species, such as Hedera helix (English ivy) and Rubus armeniacus (Himalayan Blackberry), without proper management have the potential to grow and outcompete native flora. A system of social trails were found, most of which lead to less accessible routes. It is recommended that JCLT discourage the use of social trails by covering trail entrances and with online notices and other forms of outreach. A tree density assessment was conducted on the previously logged, second growth forest, showing it is of high density. A variable density thinning treatment is recommended to allow for healthier trees similar to old growth redwood forest conditions

Recent Duplication and Functional Divergence in Parasitic Nematode Levamisole-Sensitive Acetylcholine Receptors

Helminth parasites rely on fast-synaptic transmission in their neuromusculature to experience the outside world and respond to it. Acetylcholine plays a pivotal role in this and its receptors are targeted by a wide variety of both natural and synthetic compounds used in human health and for the control of parasitic disease. The model, Caenorhabditis elegans is characterized by a large number of acetylcholine receptor subunit genes, a feature shared across the nematodes. This dynamic family is characterized by both gene duplication and loss between species. The pentameric levamisole-sensitive acetylcholine receptor has been characterized from C. elegans, comprised of five different subunits. More recently, cognate receptors have been reconstituted from multiple parasitic nematodes that are found to vary in subunit composition. In order to understand the implications of receptor composition change and the origins of potentially novel drug targets, we investigated a specific example of subunit duplication based on analysis of genome data for 25 species from the 50 helminth genome initiative. We found multiple independent duplications of the unc-29, acetylcholine receptor subunit, where codon substitution rate analysis identified positive, directional selection acting on amino acid positions associated with subunit assembly. Characterization of four gene copies from a model parasitic nematode, Haemonchus contortus, demonstrated that each copy has acquired unique functional characteristics based on phenotype rescue of transgenic C. elegans and electrophysiology of receptors reconstituted in Xenopus oocytes. We found evidence that a specific incompatibility has evolved for two subunits co-expressed in muscle. We demonstrated that functional divergence of acetylcholine receptors, driven by directional selection, can occur more rapidly than previously thought and may be mediated by alteration of receptor assembly. This phenomenon is common among the clade V parasitic nematodes and this work provides a foundation for understanding the broader context of changing anthelmintic drug targets across the parasitic nematodes

GAS in Protoplanetary Systems (GASPS). I. First results

Context. Circumstellar discs are ubiquitous around young stars, but rapidly dissipate their gas and dust on timescales of a few Myr. The Herschel Space Observatory allows for the study of the warm disc atmosphere, using far-infrared spectroscopy to measure gas content and excitation conditions, and far-IR photometry to constrain the dust distribution. Aims. We aim to detect and characterize the gas content of circumstellar discs in four targets as part of the Herschel science demonstration phase. Methods. We carried out sensitive medium resolution spectroscopy and high sensitivity photometry at λ ∼60–190 μm using the Photodetector Array Camera and Spectrometer instrument on the Herschel Space Observatory. Results. We detect [OI] 63 μm emission from the young stars HD 169142, TW Hydrae, and RECX 15, but not HD 181327. No other lines, including [CII] 158 and [OI] 145, are significantly detected. All four stars are detected in photometry at 70 and 160 μm. Extensive models are presented in associated papers

The Herschel view of GAS in Protoplanetary Systems (GASPS). First comparisons with a large grid of models

The Herschel GASPS key program is a survey of the gas phase of protoplanetary discs, targeting 240 objects which cover a large range of ages, spectral types, and disc properties. To interpret this large quantity of data and initiate self-consistent analyses of the gas and dust properties of protoplanetary discs, we have combined the capabilities of the radiative transfer code MCFOST with the gas thermal balance and chemistry code ProDiMo to compute a grid of ≈300 000 disc models (DENT). We present a comparison of the first Herschel/GASPS line and continuum data with the predictions from the DENT grid of models. Our objective is to test some of the main trends already identified in the DENT grid, as well as to define better empirical diagnostics to estimate the total gas mass of protoplanetary discs. Photospheric UV radiation appears to be the dominant gas-heating mechanism for Herbig stars, whereas UV excess and/or X-rays emission dominates for T Tauri stars. The DENT grid reveals the complexity in the analysis of far-IR lines and the difficulty to invert these observations into physical quantities. The combination of Herschel line observations with continuum data and/or with rotational lines in the (sub-)millimetre regime, in particular CO lines, is required for a detailed characterisation of the physical and chemical properties of circumstellar discs

Gas Lines from the 5-Myr old Optically Thin Disk around HD141569A

At the distance of 99-116 pc, HD141569A is one of the nearest HerbigAe stars that is surrounded by a tenuous disk, probably in transition between a massive primordial disk and a debris disk. We observed the fine-structure lines of OI at 63 and 145 micron and the CII line at 157 micron with the PACS instrument onboard the Herschel Space Telescope as part of the open-time large programme GASPS. We complemented the atomic line observations with archival Spitzer spectroscopic and photometric continuum data, a ground-based VLT-VISIR image at 8.6 micron, and 12CO fundamental ro-vibrational and pure rotational J=3-2 observations. We simultaneously modeled the continuum emission and the line fluxes with the Monte Carlo radiative transfer code MCFOST and the thermo-chemical code ProDiMo to derive the disk gas- and dust properties assuming no dust settling. The models suggest that the oxygen lines are emitted from the inner disk around HD141569A, whereas the [CII] line emission is more extended. The CO submillimeter flux is emitted mostly by the outer disk. Simultaneous modeling of the photometric and line data using a realistic disk structure suggests a dust mass derived from grains with a radius smaller than 1 mm of 2.1E-7 MSun and from grains with a radius of up to 1 cm of 4.9E-6 MSun. We constrained the polycyclic aromatic hydrocarbons (PAH) mass to be between 2E-11 and 1..4E-10 MSun assuming circumcircumcoronene (C150H30) as the representative PAH. The associated PAH abundance relative to hydrogen is lower than those found in the interstellar medium (3E-7) by two to three orders of magnitude. The disk around HD141569A is less massive in gas (2.5 to 4.9E-4 MSun or 67 to 164 MEarth) and has a flat opening angle (\u3c10%). [abridged

Gas in the protoplanetary disc of HD 169142: Herschel\u27s view

In an effort to simultaneously study the gas and dust components of the disc surrounding the young Herbig Ae star HD 169142, we present far-IR observations obtained with the PACS instrument onboard the Herschel Space Observatory. This work is part of the open time key program GASPS, which is aimed at studying the evolution of protoplanetary discs. To constrain the gas properties in the outer disc, we observed the star at several key gas-lines, including [OI] 63.2 and 145.5 mum, [CII] 157.7 mum, CO 72.8 and 90.2 mum, and o-H2O 78.7 and 179.5 mum. We only detect the [OI] 63.2 mum line in our spectra, and derive upper limits for the other lines. We complement our data set with PACS photometry and 12/13CO data obtained with the Submillimeter Array. Furthermore, we derive accurate stellar parameters from optical spectra and UV to mm photometry. We model the dust continuum with the 3D radiative transfer code MCFOST and use this model as an input to analyse the gas lines with the thermo-chemical code ProDiMo. Our dataset is consistent with a simple model in which the gas and dust are well-mixed in a disc with a continuous structure between 20 and 200 AU, but this is not a unique solution. Our modelling effort allows us to constrain the gas-to-dust mass ratio as well as the relative abundance of the PAHs in the disc by simultaneously fitting the lines of several species that originate in different regions. Our results are inconsistent with a gas-poor disc with a large UV excess; a gas mass of 5.0 ± 2.0 × 10-3 M&sun; is still present in this disc, in agreement with earlier CO observations. Herschel is an ESA space observatory with science instruments provided by European-led Principal Investigator consortia and with important participation from NASA

Herschel-PACS observation of the 10 Myr old T Tauri disk TW Hya. Constraining the disk gas mass

Planets are formed in disks around young stars. With an age of ~10 Myr, TW Hya is one of the nearest T Tauri stars that is still surrounded by a relatively massive disk. In addition a large number of molecules has been found in the TW Hya disk, making TW Hya the perfect test case in a large survey of disks with Herschel–PACS to directly study their gaseous component. We aim to constrain the gas and dust mass of the circumstellar disk around TW Hya. We observed the fine-structure lines of [O i] and [C ii] as part of the open-time large program GASPS. We complement this with continuum data and ground-based 12 CO 3–2 and 13CO 3–2 observations. We simultaneously model the continuum and the line fluxes with the 3D Monte-Carlo code MCFOST and the thermo-chemical code ProDiMo to derive the gas and dust masses. We detect the [O i] line at 63 μm. The other lines that were observed, [O i] at 145 μm and [C ii] at 157 μm, are not detected. No extended emission has been found. Preliminary modeling of the photometric and line data assuming [ 12CO] /[ 13CO] = 69 suggests a dust mass for grains with radius ~1.9 × 10-4 (total solid mass of 3 × 10-3 ) and a gas mass of (0.5–5) × 10-3 . The gas-to-dust mass may be lower than the standard interstellar value of 100

Long-Term Exposure to Primary Traffic Pollutants and Lung Function in Children: Cross-Sectional Study and Meta-Analysis.

BACKGROUND: There is widespread concern about the possible health effects of traffic-related air pollution. Nitrogen dioxide (NO2) is a convenient marker of primary pollution. We investigated the associations between lung function and current residential exposure to a range of air pollutants (particularly NO2, NO, NOx and particulate matter) in London children. Moreover, we placed the results for NO2 in context with a meta-analysis of published estimates of the association. METHODS AND FINDINGS: Associations between primary traffic pollutants and lung function were investigated in 4884 children aged 9-10 years who participated in the Child Heart and Health Study in England (CHASE). A systematic literature search identified 13 studies eligible for inclusion in a meta-analysis. We combined results from the meta-analysis with the distribution of the values of FEV1 in CHASE to estimate the prevalence of children with abnormal lung function (FEV1<80% of predicted value) expected under different scenarios of NO2 exposure. In CHASE, there were non-significant inverse associations between all pollutants except ozone and both FEV1 and FVC. In the meta-analysis, a 10 μg/m3 increase in NO2 was associated with an 8 ml lower FEV1 (95% CI: -14 to -1 ml; p: 0.016). The observed effect was not modified by a reported asthma diagnosis. On the basis of these results, a 10 μg/m3 increase in NO2 level would translate into a 7% (95% CI: 4% to 12%) increase of the prevalence of children with abnormal lung function. CONCLUSIONS: Exposure to traffic pollution may cause a small overall reduction in lung function and increase the prevalence of children with clinically relevant declines in lung function

International validation of the EORTC QLQ-PRT20 module for assessment of quality of life symptoms relating to radiation proctitis: A phase IV study

Background: Although patients experience radiation proctitis post radiotherapy no internationally tested instruments exist to measure these symptoms. This Phase IV study tested the scale structure, reliability and validity and cross-cultural applicability of the EORTC proctitis module (QLQ-PRT23) in patients who were receiving pelvic radiotherapy. Methods: Patients (n = 358) from six countries completed the EORTC QLQ-C30, QLQ-PRT23 and EORTC Quality of Life Group debriefing questions. Clinicians completed the EORTC Radiation Therapy Oncology Group scale. Questionnaires were completed at four time-points. The module’s scale structure was examined and validated using standard psychometric analysis techniques. Results: Three items were dropped from the module (QLQ-PRT23→QLQ-PRT20). Factor analysis identified five factors in the module: bowel control; bloating and gas; emotional function/lifestyle; pain; and leakage. Inter-item correlations were within r = 0.3–0.7. Test-Retest reliability was high. All multi-item scales discriminated between patients showing symptoms and those without symptomology. The module discriminated symptoms from the clinician completed scoring and for age, gender and comorbidities. Conclusion: The EORTC QLQ-PRT20 is designed to be used in addition to the EORTC QLQ-C30 to measure quality of life in patients who receive pelvic radiotherapy. The EORTC QLQ-PRT20 is quick to complete, acceptable to patients, has good content validity and high reliability. Trial registration: Australian and New Zealand Clinical Trials Registry (ANZCTR) ACTRN1260900097222

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice