2,833 research outputs found
Consensus Protein Design without Phylogenetic Bias
Consensus design is an appealing strategy for the stabilization of proteins. It exploits amino acid conservation in sets of homologous proteins to identify likely beneficial mutations. Nevertheless, its success depends on the phylogenetic diversity of the sequence set available. Here, we show that randomization of a single protein represents a reliable alternative source of sequence diversity that is essentially free of phylogenetic bias. A small number of functional protein sequences selected from binary-patterned libraries suffice as input for the consensus design of active enzymes that are easier to produce and substantially more stable than individual members of the starting data set. Although catalytic activity correlates less consistently with sequence conservation in these extensively randomized proteins, less extreme mutagenesis strategies might be adopted in practice to augment stability while maintaining function
Flexible Lipid Bilayers in Implicit Solvent
A minimalist simulation model for lipid bilayers is presented. Each lipid is
represented by a flexible chain of beads in implicit solvent. The hydrophobic
effect is mimicked through an intermolecular pair potential localized at the
``water''/hydrocarbon tail interface. This potential guarantees realistic
interfacial tensions for lipids in a bilayer geometry. Lipids self assemble
into bilayer structures that display fluidity and elastic properties consistent
with experimental model membrane systems. Varying molecular flexibility allows
for tuning of elastic moduli and area/molecule over a range of values seen in
experimental systems.Comment: 5 pages, 5 figure
Influence of Anthropogenic Subsidies on Movements of Common Ravens
Anthropogenic subsidies can benefit populations of generalist predators such as common ravens (ravens; Corvus corax), which in turn may depress populations of many types of species at lower-trophic levels, including desert tortoises (Gopherus agassizii) or greater sage-grouse (Centrocercus urophasianus). Management of subsidized ravens often has targeted local breeding populations that are presumed to affect species of concern and ignored âurbanâ populations of ravens. However, little is known about how ravens move, especially in response to the presence of anthropogenic subsidies. Therefore, subsidized ravens from distant populations that are not managed may influence local prey. To better understand this issue, we deployed global positioning system â global system for mobile communications transmitters to track movements of 19 ravens from September to December 2020 relative to 2 land cover types that provide subsidies: developed areas and cultivated crops. On average, ravens moved 41.5 km (±30.5) per day, although daily movement distances ranged from 0.13â206.1 km. Raven movement among cover types during the non-breeding season varied widely, with 100% of individuals each using land cover types that provide subsidy and other types at least once in the season. On 100% of days ravens used areas that did not provide subsidy, on 86.7% of days they used developed areas, and on 20.5% of days they used cultivated crops. Although on some days a raven would stay exclusively in areas that did not provide subsidy, there were no days in which a single raven ever stayed exclusively in developed or cultivated crops. Ravens moved shorter distances on days when they used subsidies more frequently. Further, time spent in developed areas and cultivated crops increased when ravens roosted closer to them, although this effect was greater for developed areas than for cultivated crops. Individual ravens were not associated exclusively with either of the subsidy-providing landscapes we considered, but instead all birds used both subsidized and other landscapes. Our research suggests that management of ravens during the non-breeding season and possibly during the breeding season, intended to reduce risk of predation on desert tortoises, will be most effective if conducted on a broad scale because of distances the birds travel and the lack of separation between putative âurbanâ and ânaturalâ populations of ravens
CfAIR2: Near Infrared Light Curves of 94 Type Ia Supernovae
CfAIR2 is a large homogeneously reduced set of near-infrared (NIR) light
curves for Type Ia supernovae (SN Ia) obtained with the 1.3m Peters Automated
InfraRed Imaging TELescope (PAIRITEL). This data set includes 4607 measurements
of 94 SN Ia and 4 additional SN Iax observed from 2005-2011 at the Fred
Lawrence Whipple Observatory on Mount Hopkins, Arizona. CfAIR2 includes JHKs
photometric measurements for 88 normal and 6 spectroscopically peculiar SN Ia
in the nearby universe, with a median redshift of z~0.021 for the normal SN Ia.
CfAIR2 data span the range from -13 days to +127 days from B-band maximum. More
than half of the light curves begin before the time of maximum and the coverage
typically contains ~13-18 epochs of observation, depending on the filter. We
present extensive tests that verify the fidelity of the CfAIR2 data pipeline,
including comparison to the excellent data of the Carnegie Supernova Project.
CfAIR2 contributes to a firm local anchor for supernova cosmology studies in
the NIR. Because SN Ia are more nearly standard candles in the NIR and are less
vulnerable to the vexing problems of extinction by dust, CfAIR2 will help the
supernova cosmology community develop more precise and accurate extragalactic
distance probes to improve our knowledge of cosmological parameters, including
dark energy and its potential time variation.Comment: 31 pages, 15 figures, 10 tables. Accepted to ApJS. v2 modified to
more closely match journal versio
Aesthetics and literature : a problematic relation?
The paper argues that there is a proper place for literature within aesthetics but that care must be taken in identifying just what the relation is. In characterising aesthetic pleasure associated with literature it is all too easy to fall into reductive accounts, for example, of literature as merely "fine writing". Belleslettrist or formalistic accounts of literature are rejected, as are two other kinds of reduction, to pure meaning properties and to a kind of narrative realism. The idea is developed that literature-both poetry and prose fiction-invites its own distinctive kind of aesthetic appreciation which far from being at odds with critical practice, in fact chimes well with it
âI Felt Like a Superheroâ: The Experience of Responding to Drug Overdose Among Individuals Trained in Overdose Prevention
BACKGROUND: Overdose prevention programs (OPPs) train people who inject drugs and other community members to prevent, recognise and respond to opioid overdose. However, little is known about the experience of taking up the role of an overdose responder for the participants.
METHODS: We present findings from qualitative interviews with 30 participants from two OPPs in Los Angeles, CA, USA from 2010 to 2011 who had responded to at least one overdose since being trained in overdose prevention and response.
RESULTS: Being trained by an OPP and responding to overdoses had both positive and negative effects for trained responders . Positive effects include an increased sense of control and confidence, feelings of heroism and pride, and a recognition and appreciation of one\u27s expertise. Negative effects include a sense of burden, regret, fear, and anger, which sometimes led to cutting social ties, but might also be mitigated by the increased empowerment associated with the positive effects.
CONCLUSION: Findings suggest that becoming an overdose responder can involve taking up a new social role that has positive effects, but also confers some stress that may require additional support. OPPs should provide flexible opportunities for social support to individuals making the transition to this new and critical social role. Equipping individuals with the skills, technology, and support they need to respond to drug overdose has the potential to confer both individual and community-wide benefits
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Impacts of elevated atmospheric COâ on nutrient content of important food crops.
One of the many ways that climate change may affect human health is by altering the nutrient content of food crops. However, previous attempts to study the effects of increased atmospheric CO2 on crop nutrition have been limited by small sample sizes and/or artificial growing conditions. Here we present data from a meta-analysis of the nutritional contents of the edible portions of 41 cultivars of six major crop species grown using free-air CO2 enrichment (FACE) technology to expose crops to ambient and elevated CO2 concentrations in otherwise normal field cultivation conditions. This data, collected across three continents, represents over ten times more data on the nutrient content of crops grown in FACE experiments than was previously available. We expect it to be deeply useful to future studies, such as efforts to understand the impacts of elevated atmospheric CO2 on crop macro- and micronutrient concentrations, or attempts to alleviate harmful effects of these changes for the billions of people who depend on these crops for essential nutrients
Type IIb Supernova SN 2011dh: Spectra and Photometry from the Ultraviolet to the Near-Infrared
We report spectroscopic and photometric observations of the Type IIb SN
2011dh obtained between 4 and 34 days after the estimated date of explosion
(May 31.5 UT). The data cover a wide wavelength range from 2,000 Angstroms in
the UV to 2.4 microns in the NIR. Optical spectra provide line profiles and
velocity measurements of HI, HeI, CaII and FeII that trace the composition and
kinematics of the SN. NIR spectra show that helium is present in the atmosphere
as early as 11 days after the explosion. A UV spectrum obtained with the STIS
reveals that the UV flux for SN 2011dh is low compared to other SN IIb. The HI
and HeI velocities in SN 2011dh are separated by about 4,000 km/s at all
phases. We estimate that the H-shell of SN 2011dh is about 8 times less massive
than the shell of SN 1993J and about 3 times more massive than the shell of SN
2008ax. Light curves (LC) for twelve passbands are presented. The maximum
bolometric luminosity of erg s occurred
about 22 days after the explosion. NIR emission provides more than 30% of the
total bolometric flux at the beginning of our observations and increases to
nearly 50% of the total by day 34. The UV produces 16% of the total flux on day
4, 5% on day 9 and 1% on day 34. We compare the bolometric light curves of SN
2011dh, SN 2008ax and SN 1993J. The LC are very different for the first twelve
days after the explosions but all three SN IIb display similar peak
luminosities, times of peak, decline rates and colors after maximum. This
suggests that the progenitors of these SN IIb may have had similar compositions
and masses but they exploded inside hydrogen shells that that have a wide range
of masses. The detailed observations presented here will help evaluate
theoretical models for this supernova and lead to a better understanding of SN
IIb.Comment: 23 pages, 14 figures, 9 tables, accepted by Ap
GRB 021211 as a Faint Analogue of GRB 990123: Exploring the Similarities and Differences in their Optical Afterglows
We present B, V, Rc, J, H, and Ks photometry of the optical afterglow of the
gamma-ray burst GRB 021211 taken at the Magellan, MMT, and WIYN observatories
between 0.7 and 50 days after the burst. We find an intrinsic spectral slope at
optical and near-infrared wavelengths of 0.69 +/- 0.14 at 0.87 days. The
optical decay during the first day is almost identical to that of GRB 990123
except that GRB 021211's optical afterglow was intrinsically approximately 38
times fainter, and the transition from the reverse shock to the forward shock
may have occurred earlier than it did for GRB 990123. We find no evidence for a
jet break or the cooling break passing through optical frequencies during the
first day after the burst. There is weak evidence for a break in the J-band
decay between 0.89 and 1.87 days which may be due to a jet. The optical and
infrared data are consistent with a relativistic fireball where the shocked
electrons are in the slow cooling regime and the electron index is 2.3 +/- 0.1.
The forward shock appears to have been expanding in a homogeneous ambient
medium during the first day after the burst. Our analysis suggests that the jet
of GRB 021211 may have a small opening angle and that the total gamma-ray
energy is likely to be much less than the canonical value of 1.33E+51 erg. If
this is the case then it is possible that most of the energy of the burst is in
another form such as a frozen magnetic field, supernova ejecta, or a second jet
component. The host galaxy of GRB 021211 is subluminous and has a star
formation rate of at least one Solar mass per year.Comment: 24 pages, 4 figures, LaTex using AASTeX v5.2, to the Nov 2004
Astronomical Journal. Some minor changes have been made to the paper in
accordance with the referee's repor
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