1,048 research outputs found
Building nonparametric -body force fields using Gaussian process regression
Constructing a classical potential suited to simulate a given atomic system
is a remarkably difficult task. This chapter presents a framework under which
this problem can be tackled, based on the Bayesian construction of
nonparametric force fields of a given order using Gaussian process (GP) priors.
The formalism of GP regression is first reviewed, particularly in relation to
its application in learning local atomic energies and forces. For accurate
regression it is fundamental to incorporate prior knowledge into the GP kernel
function. To this end, this chapter details how properties of smoothness,
invariance and interaction order of a force field can be encoded into
corresponding kernel properties. A range of kernels is then proposed,
possessing all the required properties and an adjustable parameter
governing the interaction order modelled. The order best suited to describe
a given system can be found automatically within the Bayesian framework by
maximisation of the marginal likelihood. The procedure is first tested on a toy
model of known interaction and later applied to two real materials described at
the DFT level of accuracy. The models automatically selected for the two
materials were found to be in agreement with physical intuition. More in
general, it was found that lower order (simpler) models should be chosen when
the data are not sufficient to resolve more complex interactions. Low GPs
can be further sped up by orders of magnitude by constructing the corresponding
tabulated force field, here named "MFF".Comment: 31 pages, 11 figures, book chapte
Glomerular filtration rate in patients with atrial fibrillation and 1-year outcomes
We assessed 1-year outcomes in patients with atrial fibrillation enrolled in the EurObservational Research Programme AF General Pilot Registry (EORP-AF), in relation to kidney function, as assessed by glomerular filtration rate (eGFR). In a cohort of 2398 patients (median age 69 years; 61% male), eGFR (ml/min/1.73 m(2)) calculated using the CKD-EPI formula was ≥80 in 35.1%, 50-79 in 47.2%, 30-49 in 13.9% and <30 in 3.7% of patients. In a logistic regression analysis, eGFR category was an independent predictor of stroke/TIA or death, with elevated odds ratios associated with severe to mild renal impairment, ie. eGFR < 30 ml/min/1.73 m(2) [OR 3.641, 95% CI 1.572-8.433, p < 0.0001], 30-49 ml/min/1.73 m(2) [OR 3.303, 95% CI 1.740-6.270, p = 0.0026] or 50-79 ml/min/1.73 m2 [OR 2.094, 95% CI 1.194-3.672, p = 0.0003]. The discriminant capability for the risk of death was tested among various eGFR calculation algorithms: the best was the Cockcroft-Gault equation adjusted for BSA, followed by Cockcroft-Gault equation, and CKD-EPI equation, while the worst was the MDRD equation. In conclusion in this prospective observational registry, renal function was a major determinant of adverse outcomes at 1 year, and even mild or moderate renal impairments were associated with an increased risk of stroke/TIA/death
Ownership-dependent mating tactics of minor males of the beetle Librodor japonicus (Nitidulidae) with intra-sexual dimorphism of mandibles
Intra-sexual dimorphism is found in the weapons of many male beetles. Different behavioral tactics to access females between major and minor males, which adopt fighting and alternative tactics, respectively, are thought to maintain the male dimorphism. In these species major males have enlarged weapons that they use in fights with rival males. Minor males also have small weapons in some of these species, and it is unclear why these males possess weapons. We examined the hypothesis that minor males might adopt a fighting tactic when their status was relatively high in comparison with that of other males (e.g., ownership of a territory). We observed the behavioral tactics of major and minor males of the beetle Librodor japonicus, whose males have a dimorphism of their mandibles. Major males fought for resources, whereas minor males adopted two status-dependent tactics, fighting and sneaking, to access females, depending on their ownership of a sap site. We suggest that ownership status-dependent mating tactics in minor males may maintain the intra-sexual dimorphism in this beetle.</p
Glomerular filtration rate in patients with atrial fibrillation and 1-year outcomes
We assessed 1-year outcomes in patients with atrial fibrillation enrolled in the EurObservational Research Programme AF General Pilot Registry (EORP-AF), in relation to kidney function, as assessed by glomerular filtration rate (eGFR). In a cohort of 2398 patients (median age 69 years; 61% male), eGFR (ml/min/1.73\u2009m(2)) calculated using the CKD-EPI formula was 6580 in 35.1%, 50-79 in 47.2%, 30-49 in 13.9% and <30 in 3.7% of patients. In a logistic regression analysis, eGFR category was an independent predictor of stroke/TIA or death, with elevated odds ratios associated with severe to mild renal impairment, ie. eGFR\u2009<\u200930\u2009ml/min/1.73\u2009m(2) [OR 3.641, 95% CI 1.572-8.433, p\u2009<\u20090.0001], 30-49\u2009ml/min/1.73\u2009m(2) [OR 3.303, 95% CI 1.740-6.270, p\u2009=\u20090.0026] or 50-79\u2009ml/min/1.73\u2009m2 [OR 2.094, 95% CI 1.194-3.672, p\u2009=\u20090.0003]. The discriminant capability for the risk of death was tested among various eGFR calculation algorithms: the best was the Cockcroft-Gault equation adjusted for BSA, followed by Cockcroft-Gault equation, and CKD-EPI equation, while the worst was the MDRD equation. In conclusion in this prospective observational registry, renal function was a major determinant of adverse outcomes at 1 year, and even mild or moderate renal impairments were associated with an increased risk of stroke/TIA/death
Machine-learning of atomic-scale properties based on physical principles
We briefly summarize the kernel regression approach, as used recently in
materials modelling, to fitting functions, particularly potential energy
surfaces, and highlight how the linear algebra framework can be used to both
predict and train from linear functionals of the potential energy, such as the
total energy and atomic forces. We then give a detailed account of the Smooth
Overlap of Atomic Positions (SOAP) representation and kernel, showing how it
arises from an abstract representation of smooth atomic densities, and how it
is related to several popular density-based representations of atomic
structure. We also discuss recent generalisations that allow fine control of
correlations between different atomic species, prediction and fitting of
tensorial properties, and also how to construct structural kernels---applicable
to comparing entire molecules or periodic systems---that go beyond an additive
combination of local environments
Entropic Tension in Crowded Membranes
Unlike their model membrane counterparts, biological membranes are richly
decorated with a heterogeneous assembly of membrane proteins. These proteins
are so tightly packed that their excluded area interactions can alter the free
energy landscape controlling the conformational transitions suffered by such
proteins. For membrane channels, this effect can alter the critical membrane
tension at which they undergo a transition from a closed to an open state, and
therefore influence protein function \emph{in vivo}. Despite their obvious
importance, crowding phenomena in membranes are much less well studied than in
the cytoplasm.
Using statistical mechanics results for hard disk liquids, we show that
crowding induces an entropic tension in the membrane, which influences
transitions that alter the projected area and circumference of a membrane
protein. As a specific case study in this effect, we consider the impact of
crowding on the gating properties of bacterial mechanosensitive membrane
channels, which are thought to confer osmoprotection when these cells are
subjected to osmotic shock. We find that crowding can alter the gating energies
by more than in physiological conditions, a substantial fraction of
the total gating energies in some cases.
Given the ubiquity of membrane crowding, the nonspecific nature of excluded
volume interactions, and the fact that the function of many membrane proteins
involve significant conformational changes, this specific case study highlights
a general aspect in the function of membrane proteins.Comment: 20 pages (inclduing supporting information), 4 figures, to appear in
PLoS Comp. Bio
Multiple reassortment events in the evolutionary history of H1N1 influenza A virus since 1918
The H1N1 subtype of influenza A virus has caused substantial morbidity and mortality in humans, first documented in the global pandemic of 1918 and continuing to the present day. Despite this disease burden, the evolutionary history of the A/H1N1 virus is not well understood, particularly whether there is a virological basis for several notable epidemics of unusual severity in the 1940s and 1950s. Using a data set of 71 representative complete genome sequences sampled between 1918 and 2006, we show that segmental reassortment has played an important role in the genomic evolution of A/H1N1 since 1918. Specifically, we demonstrate that an A/H1N1 isolate from the 1947 epidemic acquired novel PB2 and HA genes through intra-subtype reassortment, which may explain the abrupt antigenic evolution of this virus. Similarly, the 1951 influenza epidemic may also have been associated with reassortant A/H1N1 viruses. Intra-subtype reassortment therefore appears to be a more important process in the evolution and epidemiology of H1N1 influenza A virus than previously realized
New uses of the Migraine Screen Questionnaire (MS-Q): validation in the Primary Care setting and ability to detect hidden migraine. MS-Q in Primary Care
<p>Abstract</p> <p>Background</p> <p>PC plays an important role in early diagnosis of health disorders, particularly migraine, due to the financial impact of this disease for the society and its impact on patients' quality of life. The aim of the study was to validate the self-administered MS-Q questionnaire for detection of hidden migraine in the field of primary care (PC), and to explore its use in this setting.</p> <p>Methods</p> <p>Cross-sectional, observational, and multicentre study in subjects above 18 years of age patients attending PC centers (regardless of the reason for consultation). A MS-Q score ≥ 4 was considered possible migraine. Level of agreement with IHS criteria clinical diagnosis (kappa coefficient), and instrument's validity properties: sensitivity, specificity, positive (PPV) and negative (NPV) predictive values were determined. The ability of the instrument to identify possible new cases of migraine was calculated, as well as the ratio of hidden disease compared to the ratio obtained by IHS criteria.</p> <p>Results</p> <p>A total of 9,670 patients were included [48.9 ± 17.2 years (mean ± SD); 61.9% women], from 410 PC centers representative of the whole national territory. The clinical prevalence of migraine according to the IHS criteria was 24.7%, and 20.4% according to MS-Q: Kappa index of agreement 0.82 (p < 0.05). MS-Q sensitivity was 0.82 (95% CI, 0.81 - 0.84), specificity 0.97 (95% CI, 0.98 - 0.99), PPV 0.95 (95% CI, 0.94 - 0.96), and NPV 0.94 (95% CI, 0.93 - 0.95). No statistically significant differences were found in the percentages of patients with <it>de novo </it>and hidden migraine identified by MS-Q and by IHS criteria: 5.7% vs. 6.1% and 26.6% vs. 24.1%, respectively.</p> <p>Conclusions</p> <p>The results of the present study confirm the usefulness of the MS-Q questionnaire for the early detection and assessment of migraine in PC settings, and its ability to detect hidden migraine.</p
How can humans understand their automated cars? HMI principles, problems and solutions
As long as vehicles do not provide full automation, the design and function of the Human Machine Interface (HMI) is crucial for ensuring that the human “driver” and the vehicle-based automated systems collaborate in a safe manner. When the driver is decoupled from active control, the design of the HMI becomes even more critical. Without mutual understanding, the two agents (human and vehicle) will fail to accurately comprehend each other’s intentions and actions. This paper proposes a set of design principles for in-vehicle HMI and reviews some current HMI designs in the light of those principles. We argue that in many respects, the current designs fall short of best practice and have the potential to confuse the driver. This can lead to a mismatch between the operation of the automation in the light of the current external situation and the driver’s awareness of how well the automation is currently handling that situation. A model to illustrate how the various principles are interrelated is proposed. Finally, recommendations are made on how, building on each principle, HMI design solutions can be adopted to address these challenges
Rapid global ocean-atmosphere response to Southern Ocean freshening during the last glacial.
Contrasting Greenland and Antarctic temperatures during the last glacial period (115,000 to 11,650 years ago) are thought to have been driven by imbalances in the rates of formation of North Atlantic and Antarctic Deep Water (the 'bipolar seesaw'). Here we exploit a bidecadally resolved 14C data set obtained from New Zealand kauri (Agathis australis) to undertake high-precision alignment of key climate data sets spanning iceberg-rafted debris event Heinrich 3 and Greenland Interstadial (GI) 5.1 in the North Atlantic (~30,400 to 28,400 years ago). We observe no divergence between the kauri and Atlantic marine sediment 14C data sets, implying limited changes in deep water formation. However, a Southern Ocean (Atlantic-sector) iceberg rafted debris event appears to have occurred synchronously with GI-5.1 warming and decreased precipitation over the western equatorial Pacific and Atlantic. An ensemble of transient meltwater simulations shows that Antarctic-sourced salinity anomalies can generate climate changes that are propagated globally via an atmospheric Rossby wave train.A challenge for testing mechanisms of past climate change is the precise correlation of palaeoclimate records. Here, through climate modelling and the alignment of terrestrial, ice and marine 14C and 10Be records, the authors show that Southern Ocean freshwater hosing can trigger global change
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