The Pan-STARRS1 Database and Data Products Flewelling, H. A.; Magnier, E. A.; Chambers, K. C. ...
The Astrophysical journal. Supplement series,
11/2020, Letnik:
251, Številka:
1
Journal Article
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Abstract
This paper describes the organization of the database and the catalog data products from the Pan-STARRS1 3
π
Steradian Survey. The catalog data products are available in the form of an ...SQL-based relational database from MAST, the Mikulski Archive for Space Telescopes at STScI. The database is described in detail, including the construction of the database, the provenance of the data, the schema, and how the database tables are related. Examples of queries for a range of science goals are included.
Soil extracts usually contain large quantities of dissolved humified organic material, typically reflected by high polyphenolic content. Since polyphenols seriously confound quantification of ...extracted protein, minimising this interference is important to ensure measurements are representative. Although the Bradford colorimetric assay is used routinely in soil science for rapid quantification protein in soil-extracts, it has several limitations. We therefore investigated an alternative colorimetric technique based on the Lowry assay (frequently used to measure protein and humic substances as distinct pools in microbial biofilms). The accuracies of both the Bradford assay and a modified Lowry microplate method were compared in factorial combination. Protein was quantified in soil-extracts (extracted with citrate), including standard additions of model protein (BSA) and polyphenol (Sigma H1675-2). Using the Lowry microplate assay described, no interfering effects of citrate were detected even with concentrations up to 5 times greater than are typically used to extract soil protein. Moreover, the Bradford assay was found to be highly susceptible to two simultaneous and confounding artefacts: 1) the colour development due to added protein was greatly inhibited by polyphenol concentration, and 2) substantial colour development was caused directly by the polyphenol addition. In contrast, the Lowry method enabled distinction between colour development from protein and non-protein origin, providing a more accurate quantitative analysis. These results suggest that the modified-Lowry method is a more suitable measure of extract protein (defined by standard equivalents) because it is less confounded by the high polyphenolic content which is so typical of soil extracts.
•Bradford and Lowry techniques for measuring protein in soil extracts were compared.•We found polyphenol content affected Bradford estimations substantially more than Lowry.•Citrate (often used to extract soil protein) was not found to be problematic for the Lowry assay.•Using the Lowry microplate method, analytical response due to polyphenol and protein is ascribed.
Microglia are dependent upon colony-stimulating factor 1 receptor (CSF1R) signaling for their survival in the adult brain, with administration of the dual CSF1R/c-kit inhibitor PLX3397 leading to the ...near-complete elimination of all microglia brainwide. Here, we determined the dose-dependent effects of a specific CSF1R inhibitor (PLX5622) on microglia in both wild-type and the 3xTg-AD mouse model of Alzheimer's disease.
Wild-type mice were treated with PLX5622 for up to 21 days, and the effects on microglial numbers were assessed. 3xTg-AD mice were treated with PLX5622 for 6 or 12 weeks and effects on microglial numbers and pathology subsequently assessed.
High doses of CSF1R inhibitor eliminate most microglia from the brain, but a 75% lower-dose results in sustained elimination of ~30 of microglia in both wild-type and 3xTg-AD mice. No behavioral or cognitive deficits were found in mice either depleted of microglia or treated with lower CSF1R inhibitor concentrations. Aged 3xTg-AD mice treated for 6 or 12 weeks with lower levels of PLX5622 resulted in improved learning and memory. Aβ levels and plaque loads were not altered, but microglia in treated mice no longer associated with plaques, revealing a role for the CSF1R in the microglial reaction to plaques, as well as in mediating cognitive deficits.
We find that inhibition of CSF1R alone is sufficient to eliminate microglia and that sustained microglial elimination is concentration-dependent. Inhibition of the CSF1R at lower levels in 3xTg-AD mice prevents microglial association with plaques and improves cognition.
The Reuven Ramaty High Energy Solar Spectroscopic Imager (RHESSI) and the Nobeyama Radioheliograph (NoRH) are used to investigate coronal hard X-ray and microwave emissions in the partially ...disk-occulted solar flare of 2007 December 31. The STEREO mission provides EUV images of the flare site at different viewing angles, establishing a two-ribbon flare geometry and occultation heights of the RHESSI and NoRH observations of {approx}16 Mm and {approx}25 Mm, respectively. Despite the occultation, intense hard X-ray emission up to {approx}80 keV occurs during the impulsive phase from a coronal source that is also seen in microwaves. The hard X-ray and microwave source during the impulsive phase is located {approx}6 Mm above thermal flare loops seen later at the soft X-ray peak time, similar in location to the above-the-loop-top source in the Masuda flare. A single non-thermal electron population with a power-law distribution (with spectral index of {approx}3.7 from {approx}16 keV up to the MeV range) radiating in both bremsstrahlung and gyrosynchrotron emission can explain the observed hard X-ray and microwave spectrum, respectively. This clearly establishes the non-thermal nature of the above-the-loop-top source. The large hard X-ray intensity requires a very large number (>5 x 10{sup 35} above 16 keV for the derived upper limit of the ambient density of {approx}8 x 10{sup 9} cm{sup -3}) of suprathermal electrons to be present in this above-the-loop-top source. This is of the same order of magnitude as the number of ambient thermal electrons. We show that collisional losses of these accelerated electrons would heat all ambient electrons to superhot temperatures (tens of keV) within seconds. Hence, the standard scenario, with hard X-rays produced by a beam comprising the tail of a dominant thermal core plasma, does not work. Instead, all electrons in the above-the-loop-top source seem to be accelerated, suggesting that the above-the-loop-top source is itself the electron acceleration region.
Abstract
The expansion and potential rupture of the swim bladder due to rapid decompression, a major cause of barotrauma injury in fish that pass through turbines and pumps, is generally assumed to ...be governed by Boyle’s Law. In this study, two swim bladder expansion models are presented and tested in silico. One based on the quasi-static Boyle’s Law, and a Modified Rayleigh Plesset Model (MRPM), which includes both inertial and pressure functions and was parametrised to be representative of a fish swim bladder. The two models were tested using a range of: (1) simulated and (2) empirically derived pressure profiles. Our results highlight a range of conditions where the Boyle’s Law model (BLM) is inappropriate for predicting swim bladder size in response to pressure change and that these conditions occur in situ, indicating that this is an applied and not just theoretical issue. Specifically, these conditions include any one, or any combination, of the following factors: (1) when rate of pressure change is anything but very slow compared to the resonant frequency of the swim bladder; (2) when the nadir pressure is near or at absolute zero; and (3) when a fish experiences liquid tensions (i.e. negative absolute pressures). Under each of these conditions, the MRPM is more appropriate tool for predicting swim bladder size in response to pressure change and hence it is a better model for quantifying barotrauma in fish.
In an effort to provide a framework for the accurate identification of elasmobranchs, driven in large part by the needs of parasitological studies, a comprehensive survey of DNA sequences derived ...from the mitochondrial NADH2 gene was conducted for elasmobranchs collected from around the world. Analysis was based on sequences derived from 4283 specimens representing an estimated 574 (of ∼1221) species (305 sharks, 269 batoids), each represented by 1 to 176 specimens, in 157 (of 193 described) elasmobranch genera in 56 (of 57 described) families of elasmobranchs (only Hypnidae was not represented). A total of 1921 (44.9%) of the samples were represented by vouchers and/or images available in an online host specimen database (http://elasmobranchs.tapewormdb.uconn.edu). A representative sequence for each of the 574 species identified in this survey, as well as an additional 11 sequences for problematic complexes, has been deposited in GenBank. Neighbor-joining analysis of the data revealed a substantial amount of previously undocumented genetic diversity in elasmobranchs, suggesting 79 potentially new taxa (38 sharks, 41 batoids). Within-species p-distance variation in NADH2-percent sequence divergence ranged from 0 to 2.12 with a mean of 0.27; within-genus p-distance variation ranged from 0.03 to 27.01, with a mean of 10.16. These values are roughly consistent with estimates from prior studies based on barcode COI sequences for elasmobranchs and fishes. While biogeographic influences have likely shaped the diversification of the entire group, the traces left by older influences tend to be overprinted by newer ones. As a result, the most clearly interpretable influences are those associated with recently diverged taxa. Among closely related elasmobranchs, four regions appear to be of particular importance: (1) the Atlantic Ocean, (2) Arabian Sea, Persian Gulf, and Red Sea, (3) Southeast Asia, and (4) Australia. Each of these regions has a substantial proportion of taxa that are genetically distinct from their closest relatives in other regions. These results suggest that great care should be taken in establishing the identities of elasmobranch hosts in parasitological studies. Furthermore, it is likely that many existing host records require confirmation.
There is some limited evidence for the presence of viruses in herniated disc material including a previous case series that claimed to provide "unequivocal evidence of the presence of herpes virus ...DNA in intervertebral disc specimens of patients with lumbar disc herniation suggesting the potential role of herpes viruses as a contributing factor to the pathogenesis of degenerative disc disease". This study has not been replicated. The objective of our study was to determine if viruses were present in herniated disc fragments in participants with a prior history of back pain.
We recruited fifteen participants with a history of prior low-back pain prior to undergoing disc herniation surgery in the lumbar spine. Harvested disc samples were subject to next generation sequencing for detection of both RNA and DNA viral pathogens. Additionally, samples were analysed by a broadly reactive PCR targeting herpesviral DNA. Ethics approval was granted by the Human Research Ethics Committees of both Murdoch University, and St John of God Hospital, Western Australia.
Of the fifteen research participants, 8 were female. Mean age was 49.4 years (SD 14.5 yrs) with a range of 24-70 years. All participants had prior back pain with mean time since first ever attack being 8.8 years (SD 8.8 yrs). No samples contained significant DNA sequences relating to known human viral agents. Inconsequential retroviral sequences were commonly found and were a mixture of putative animal and human retroviral protein coding segments. All samples were negative for herpesvirus DNA when analysed by pan-herpesvirus PCR.
This study found no viral pathogens in any intervertebral disc fragments of patients who had previous back pain and underwent discectomy for disc herniation and thus it is unlikely that viruses are associated with disc herniation, however given the contradiction between key studies enhanced replication of this experiment is recommended.
An emerging paradigm in soil science suggests microbes can perform ‘N mining’ from recalcitrant soil organic matter (SOM) in conditions of low N availability. However, this requires the production of ...extracellular structures rich in N (including enzymes and structural components) and thus defies stoichiometric expectation. We set out to extract newly synthesised peptides from the extracellular matrix in soil and compare the amino acid (AA) profiles, N incorporation and AA dynamics in response to labile inputs of contrasting C/N ratio. Glycerol was added both with and without an inorganic source of N (10% 15N labelled NH4NO3) to a soil already containing a large pool of refractory SOM and incubated for 10 days. The resulting total soil peptide (TSP) and extracellular pools were compared using colorimetric methods, gas chromatography, and isotope ratio mass spectrometry. N isotope compositions showed that the extracellular polymeric substance (EPS) contained a greater proportion of products formed de novo than did TSP, with hydrophobic EPS-AAs (leucine, isoleucine, phenylalanine, hydroxyproline and tyrosine) deriving substantially more N from the inorganic source provided. Quantitative comparison between extracts showed that the EPS contained greater relative proportions of alanine, glycine, proline, phenylalanine and tyrosine. The greatest increases in EPS-peptide and EPS-polysaccharide concentrations occurred at the highest C/N ratios. All EPS-AAs responded similarly to treatment whereas the responses of TSP were more complex. The results suggest that extracellular investment of N (as EPS peptides) is a microbial survival mechanism in conditions of low N/high C which, from an evolutionary perspective, must ultimately lead to the tendency for increased N returns to the microbial biomass. A conceptual model is proposed that describes the dynamics of the extracellular matrix in response to the C/N ratio of labile inputs.
•Extracellular polymeric substances (EPS) increased with labile C availability.•EPS production efficiency decreased with C/N ratio of available substrate.•A conceptual model for the EPS response to C/N ratio of inputs is proposed.•High e-polysaccharide was coupled with improved extracellular peptide extraction.•Colorimetric analysis of protein reflected similar trends given by GC/FID.
The sequestration in soil of organic carbon (SOC) derived from atmospheric carbon dioxide (CO2) by replacing arable crops with leys, has been measured over 70 years on a sandy loam soil. The ...experiment was designed initially to test the effect of leys on the yields of arable crops. A 3‐year grazed grass with clover (grass + clover) ley in a 5‐year rotation with arable crops increased percentage organic carbon (%OC) in the top 25 cm of the soil from 0.98 to 1.23 in 28 years, but with little further increase during the next 40 years with all‐grass leys given fertilizer nitrogen (N). In this second period, OC inputs were balanced by losses, suggesting that about 1.3% OC might be near the equilibrium content for this rotation. Including 3‐year lucerne (Medicago sativa) leys had little effect on %OC over 28 years, but after changing to grass + clover leys, %OC increased to 1.24 during the next 40 years. Eight‐year leys (all grass with N or grass + clover) in 10‐year rotations with arable crops were started in the 1970s, and after three rotations %OC had increased to ca. 1.40 in 2000–2009. Over 70 years, %OC declined from 0.98 to 0.94 in an all‐arable rotation with mainly cereals and to 0.82 with more root crops. Applications of 38 t ha−1 farmyard manure (FYM) every fifth year increased %OC by 0.13% by the mid‐1960s when applications ceased. Soil treated with FYM still contained 0.10% more OC in 2000–2009. Changes in the amount of OC have been modelled with RothC‐26.3 and estimated inputs of C for selected rotations. Little of the OC input during the 70 years has been retained; most was retained in the grazed ley rotation, but 9 t ha−1 only of a total input of 189 t ha−1. In other rotations more than 98% of the total OC input was lost. Despite large losses of C, annual increases in OC of 4‰ are possible on this soil type with the inclusion of grass or grass + clover leys or the application of FYM, but only for a limited period. Such increases in SOC might help to limit increases in atmospheric CO2.
Highlights
Can leys sequester significant amounts of atmospheric CO2 in SOM and contribute to the 4‰ initiative?
Changes in the percentage and amount of OC were measured and modelled over 70 years and OC losses estimated.
Three‐year grass or grass + clover leys increased %OC, but only to an equilibrium level that was then maintained.
Despite large losses, sequestering CO2‐C at 4‰ year−1 by growing grass or grass + clover leys is possible.
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