642 research outputs found
Revisiting the anomalous bending elasticity of sharply bent DNA
Several recent experiments suggest that sharply bent DNA has a surprisingly
high bending flexibility, but the cause of this flexibility is poorly
understood. Although excitation of flexible defects can explain these results,
whether such excitation can occur with the level of DNA bending in these
experiments remains unclear. Intriguingly, the DNA contained preexisting nicks
in most of these experiments but whether nicks might play a role in flexibility
has never been considered in the interpretation of experimental results. Here,
using full-atom molecular dynamics simulations, we show that nicks promote DNA
basepair disruption at the nicked sites, which drastically reduces DNA bending
energy. In addition, lower temperatures suppress the nick-dependent basepair
disruption. In the absence of nicks, basepair disruption can also occur but
requires a higher level of DNA bending. Therefore, basepair disruption inside
B-form DNA can be suppressed if the DNA contains preexisting nicks. Overall,
our results suggest that the reported mechanical anomaly of sharply bent DNA is
likely dependent on preexisting nicks, therefore the intrinsic mechanisms of
sharply bent nick-free DNA remain an open question.Comment: 39 pages, 11 figures, 1 supporting materia
Molecular vibration in cold collision theory
Cold collisions of ground state oxygen molecules with Helium have been
investigated in a wide range of cold collision energies (from 1 K up to 10
K) treating the oxygen molecule first as a rigid rotor and then introducing the
vibrational degree of freedom. The comparison between the two models shows that
at low energies the rigid rotor approximation is very accurate and able to
describe all the dynamical features of the system. The comparison between the
two models has also been extended to cases where the interaction potential He -
O is made artificially stronger. In this case vibration can perturb rate
constants, but fine-tuning the rigid rotor potential can alleviate the
discrepancies between the two models.Comment: 11 pages, 3 figure
The relationship between anogenital distance and fertility, and genome-wide associations for anogenital distance in Irish Holstein-Friesian cows
peer-reviewedThe evaluation of anogenital distance (AGD), the distance from the center of the anus to base of the clitoris, as a potential fertility trait for genetic selection in dairy cows has generated recent interest. The objectives of this cross-sectional observational study were to (1) characterize the distribution and variability of AGD, (2) determine factors associated with AGD, (3) estimate heritability for AGD, (4) identify single nucleotide polymorphisms (SNP) associated with phenotypic variation of AGD, and (5) validate the relationship between categories of AGD and fertility in Irish Holstein-Friesian cows. Anogenital distance was measured using digital calipers in 1,180 Holstein cows (mean ± standard deviation: 225 ± 79 d in milk) from 10 dairy herds located in Munster, Ireland. In addition, age (yr), weight (kg), height at hip (cm), and body condition score (BCS) at the time of AGD measurement were determined in a subset of 281 cows. Genotype information available from 908 cows was subsequently imputed to the Illumina Bovine High Density BeadChip (Illumina Inc., San Diego, CA) for genome-wide association analysis of phenotypic variation in AGD. Overall, AGD had a normal distribution and high variability (mean ± standard deviation; 119.2 ± 11.6 mm). Anogenital distance was weakly but positively associated with cow age, hip height, and body weight, and negatively associated with BCS; the phenotypic variation in AGD that was explainable by these variables was small (coefficient of determination; R2 = 0.09, 0.06, 0.10, and 0.02, respectively). The estimated heritability for AGD was 0.37 (standard error of mean ± 0.08). Six SNP of suggestive significance were identified on Bos taurus autosomes 6, 15, 20, and 26; however, none of these SNP was related to previously identified candidate genes for fertility. Cows were categorized into quartiles (Q1; 86 to 111 mm; n = 311, Q2; 112 to 120 mm; n = 330; Q3; 121 to 127 mm; n = 265, and Q4; 128 to 160 mm; n = 274) based on AGD and the association with reproductive outcomes examined (21-d submission rate, pregnancy to first AI, pregnancy rate within 21, 42 and 84-d after the farm mating start date, and number of times bred). None of the reproductive variables differed significantly between AGD categories. In summary, despite identification of high variability and moderate heritability for AGD in Irish Holstein-Friesian cows, reproductive outcomes did not differ between categories of AGD. This latter result differs from our previous finding of an inverse relationship between AGD and pregnancy outcomes in first- and second-parity Canadian Holstein cows, emphasizing the need to test and validate this new phenotype in diverse cow populations
A mutli-technique search for the most primitive CO chondrites
As part of a study to identify the most primitive COs and to look for weakly altered CMs amongst the COs, we have conducted a multi-technique study of 16 Antarctic meteorites that had been classified as primitive COs. For this study, we have determined: (1) the bulk H, C and N abundances and isotopes, (2) bulk O isotopic compositions, (3) bulk modal mineralogies, and (4) for some selected samples the abundances and compositions of their insoluble organic matter (IOM). Two of the 16 meteorites do appear to be CMs â BUC 10943 seems to be a fairly typical CM, while MIL 090073 has probably been heated. Of the COs, DOM 08006 appears to be the most primitive CO identified to date and is quite distinct from the other members of its pairing group. The other COs fall into two groups that are less primitive than DOM 08006 and ALH 77307, the previously most primitive CO. The first group is composed of members of the DOM 08004 pairing group, except DOM 08006. The second group is composed of meteorites belonging to the MIL 03377 and MIL 07099 pairing groups. These two pairing groups should probably be combined. There is a dichotomy in the bulk O isotopes between the primitive (all Antarctic finds) and the more metamorphosed COs (mostly falls). This dichotomy can only partly be explained by the terrestrial weathering experienced by the primitive Antarctic samples. It seems that the more equilibrated samples interacted to a greater extent with 16O-poor material, probably water, than the more primitive meteorites
Extreme Ultra-Violet Spectroscopy of the Lower Solar Atmosphere During Solar Flares
The extreme ultraviolet portion of the solar spectrum contains a wealth of
diagnostic tools for probing the lower solar atmosphere in response to an
injection of energy, particularly during the impulsive phase of solar flares.
These include temperature and density sensitive line ratios, Doppler shifted
emission lines and nonthermal broadening, abundance measurements, differential
emission measure profiles, and continuum temperatures and energetics, among
others. In this paper I shall review some of the advances made in recent years
using these techniques, focusing primarily on studies that have utilized data
from Hinode/EIS and SDO/EVE, while also providing some historical background
and a summary of future spectroscopic instrumentation.Comment: 34 pages, 8 figures. Submitted to Solar Physics as part of the
Topical Issue on Solar and Stellar Flare
Structure Formation, Melting, and the Optical Properties of Gold/DNA Nanocomposites: Effects of Relaxation Time
We present a model for structure formation, melting, and optical properties
of gold/DNA nanocomposites. These composites consist of a collection of gold
nanoparticles (of radius 50 nm or less) which are bound together by links made
up of DNA strands. In our structural model, the nanocomposite forms from a
series of Monte Carlo steps, each involving reaction-limited cluster-cluster
aggregation (RLCA) followed by dehybridization of the DNA links. These links
form with a probability which depends on temperature and particle
radius . The final structure depends on the number of monomers (i. e. gold
nanoparticles) , , and the relaxation time. At low temperature, the
model results in an RLCA cluster. But after a long enough relaxation time, the
nanocomposite reduces to a compact, non-fractal cluster. We calculate the
optical properties of the resulting aggregates using the Discrete Dipole
Approximation. Despite the restructuring, the melting transition (as seen in
the extinction coefficient at wavelength 520 nm) remains sharp, and the melting
temperature increases with increasing as found in our previous
percolation model. However, restructuring increases the corresponding link
fraction at melting to a value well above the percolation threshold. Our
calculated extinction cross section agrees qualitatively with experiments on
gold/DNA composites. It also shows a characteristic ``rebound effect,''
resulting from incomplete relaxation, which has also been seen in some
experiments. We discuss briefly how our results relate to a possible sol-gel
transition in these aggregates.Comment: 12 pages, 10 figure
Sex dependent risk factors for mortality after myocardial infarction : individual patient data meta-analysis
Background. Although a number of risk factors are known to predict mortality within the first years after myocardial infarction, little is known about interactions between risk factors, whereas these could contribute to accurate differentiation of patients with higher and lower risk for mortality. This study explored the effect of interactions of risk factors on all-cause mortality in patients with myocardial infarction based on individual patient data meta-analysis. Methods. Prospective data for 10,512 patients hospitalized for myocardial infarction were derived from 16 observational studies (MINDMAPS). Baseline measures included a broad set of risk factors for mortality such as age, sex, heart failure, diabetes, depression, and smoking. All two-way and three-way interactions of these risk factors were included in Lasso regression analyses to predict time-to-event related all-cause mortality. The effect of selected interactions was investigated with multilevel Cox regression models. Results. Lasso regression selected five two-way interactions, of which four included sex. The addition of these interactions to multilevel Cox models suggested differential risk patterns for males and females. Younger women (ag
Evaluation of delayed timing of artificial insemination with sex-sorted sperm on pregnancy per artificial insemination in seasonal-calving, pasture-based lactating dairy cows
peer-reviewedThe objective was to use ovulation synchronization with timed artificial insemination (TAI) to evaluate the effect of timing of artificial insemination (AI) with frozen sex-sorted sperm on fertility performance in pasture-based compact calving herds. Ejaculates from 3 Holstein-Friesian bulls were split and processed to provide frozen sex-sorted sperm (SS) at 4 Ă 106 sperm per straw, and frozen conventional sperm at 15 Ă 106 sperm per straw (CONV). A modified Progesterone-Ovsynch protocol was used for estrous synchronization, with TAI occurring 16 h after the second GnRH injection for cows assigned to CONV, and either 16 h (SS-16) or 22 h (SS-22) for cows assigned to SS. Pregnancy diagnosis was conducted by transrectal ultrasound scanning of the uterus 35 to 40 d after TAI (n = 2,175 records available for analysis). Generalized linear mixed models were used to examine the effects of treatment on pregnancy per artificial insemination (P/AI). Fixed effects included treatment (n = 3), bull (n = 3), treatment by bull interaction, parity (n = 4), days-in-milk category (n = 3), and treatment by days-in-milk category, with herd (n = 24) included as a random effect. Pregnancy per AI was greater for CONV compared with both SS-16 and SS-22 (61.1%, 49.0%, and 51.3%, respectively), and the SS treatments did not differ from each other (relative P/AI for SS-16 and SS-22 vs. CONV were 80.2% and 84.0%, respectively). There were significant bull and treatment by bull interaction effects. Additional analysis was undertaken using a model that included herd as a fixed effect. This analysis identified marked herd-to-herd variation (within-herd relative P/AI for the combined SS treatments vs. CONV ranged from 48â121%). The tertile of herds with the best performance achieved a mean relative P/AI of 100% (range = 91â121%), indicating that P/AI equivalent to CONV is achievable with SS. Conversely, the tertile of herds with the poorest performance achieved a mean relative P/AI of 67% (range = 48â77%). We found that SS resulted in poorer overall P/AI compared with CONV sperm regardless of timing of AI. Marked variation existed between herds; however, one-third of herds achieved P/AI results equal to CONV. Identification of factors responsible for the large herd-to-herd variation in P/AI with SS, and development of strategies to reduce this variation, warrant further research
Networking and the development of professionals: Beginning teachers building social capital
Beginning teachers need support when starting their teaching career. Networking can help teachers develop social capital which supports their development as professionals on their career journey. This paper presents case studies of three secondary school trainee teachers during an English year-long initial teacher education programme. The relationships supporting trainees were characterised differently: for practice development as opposed to enhancing a sense of belonging to the profession. Whether supportive relationships developed depended not only on the trainees but also on others. The paper encourages those involved in teacher education to promote social-capital building as supportive of the development of teachers as professionals
Measurement of the polarisation of W bosons produced with large transverse momentum in pp collisions at sqrt(s) = 7 TeV with the ATLAS experiment
This paper describes an analysis of the angular distribution of W->enu and
W->munu decays, using data from pp collisions at sqrt(s) = 7 TeV recorded with
the ATLAS detector at the LHC in 2010, corresponding to an integrated
luminosity of about 35 pb^-1. Using the decay lepton transverse momentum and
the missing transverse energy, the W decay angular distribution projected onto
the transverse plane is obtained and analysed in terms of helicity fractions
f0, fL and fR over two ranges of W transverse momentum (ptw): 35 < ptw < 50 GeV
and ptw > 50 GeV. Good agreement is found with theoretical predictions. For ptw
> 50 GeV, the values of f0 and fL-fR, averaged over charge and lepton flavour,
are measured to be : f0 = 0.127 +/- 0.030 +/- 0.108 and fL-fR = 0.252 +/- 0.017
+/- 0.030, where the first uncertainties are statistical, and the second
include all systematic effects.Comment: 19 pages plus author list (34 pages total), 9 figures, 11 tables,
revised author list, matches European Journal of Physics C versio
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