4,241 research outputs found
Inexact Newton Dogleg Methods
The dogleg method is a classical trust-region technique for globalizing Newton\u27s method. While it is widely used in optimization, including large-scale optimization via truncated-Newton approaches, its implementation in general inexact Newton methods for systems of nonlinear equations can be problematic. In this paper, we first outline a very general dogleg method suitable for the general inexact Newton context and provide a global convergence analysis for it. We then discuss certain issues that may arise with the standard dogleg implementational strategy and propose modified strategies that address them. Newton-Krylov methods have provided important motivation for this work, and we conclude with a report on numerical experiments involving a Newton-GMRES dogleg method applied to benchmark CFD problems
Transcriptional regulation of protein complexes in yeast
BACKGROUND: Multiprotein complexes play an essential role in many cellular processes. But our knowledge of the mechanism of their formation, regulation and lifetimes is very limited. We investigated transcriptional regulation of protein complexes in yeast using two approaches. First, known regulons, manually curated or identified by genome-wide screens, were mapped onto the components of multiprotein complexes. The complexes comprised manually curated ones and those characterized by high-throughput analyses. Second, putative regulatory sequence motifs were identified in the upstream regions of the genes involved in individual complexes and regulons were predicted on the basis of these motifs. RESULTS: Only a very small fraction of the analyzed complexes (5-6%) have subsets of their components mapping onto known regulons. Likewise, regulatory motifs are detected in only about 8-15% of the complexes, and in those, about half of the components are on average part of predicted regulons. In the manually curated complexes, the so-called 'permanent' assemblies have a larger fraction of their components belonging to putative regulons than 'transient' complexes. For the noisier set of complexes identified by high-throughput screens, valuable insights are obtained into the function and regulation of individual genes. CONCLUSIONS: A small fraction of the known multiprotein complexes in yeast seems to have at least a subset of their components co-regulated on the transcriptional level. Preliminary analysis of the regulatory motifs for these components suggests that the corresponding genes are likely to be co-regulated either together or in smaller subgroups, indicating that transcriptionally regulated modules might exist within complexes
Certainty Closure: Reliable Constraint Reasoning with Incomplete or Erroneous Data
Constraint Programming (CP) has proved an effective paradigm to model and
solve difficult combinatorial satisfaction and optimisation problems from
disparate domains. Many such problems arising from the commercial world are
permeated by data uncertainty. Existing CP approaches that accommodate
uncertainty are less suited to uncertainty arising due to incomplete and
erroneous data, because they do not build reliable models and solutions
guaranteed to address the user's genuine problem as she perceives it. Other
fields such as reliable computation offer combinations of models and associated
methods to handle these types of uncertain data, but lack an expressive
framework characterising the resolution methodology independently of the model.
We present a unifying framework that extends the CP formalism in both model
and solutions, to tackle ill-defined combinatorial problems with incomplete or
erroneous data. The certainty closure framework brings together modelling and
solving methodologies from different fields into the CP paradigm to provide
reliable and efficient approches for uncertain constraint problems. We
demonstrate the applicability of the framework on a case study in network
diagnosis. We define resolution forms that give generic templates, and their
associated operational semantics, to derive practical solution methods for
reliable solutions.Comment: Revised versio
Ground-State Electromagnetic Moments of Calcium Isotopes
High-resolution bunched-beam collinear laser spectroscopy was used to measure
the optical hyperfine spectra of the Ca isotopes. The ground state
magnetic moments of Ca and quadrupole moments of Ca were
measured for the first time, and the Ca ground state spin was
determined in a model-independent way. Our results provide a critical test of
modern nuclear theories based on shell-model calculations using
phenomenological as well as microscopic interactions. The results for the
neutron-rich isotopes are in excellent agreement with predictions using
interactions derived from chiral effective field theory including three-nucleon
forces, while lighter isotopes illustrate the presence of particle-hole
excitations of the Ca core in their ground state.Comment: Accepted as a Rapid Communication in Physical Review
Electronic transport in polycrystalline graphene
Most materials in available macroscopic quantities are polycrystalline.
Graphene, a recently discovered two-dimensional form of carbon with strong
potential for replacing silicon in future electronics, is no exception. There
is growing evidence of the polycrystalline nature of graphene samples obtained
using various techniques. Grain boundaries, intrinsic topological defects of
polycrystalline materials, are expected to dramatically alter the electronic
transport in graphene. Here, we develop a theory of charge carrier transmission
through grain boundaries composed of a periodic array of dislocations in
graphene based on the momentum conservation principle. Depending on the grain
boundary structure we find two distinct transport behaviours - either high
transparency, or perfect reflection of charge carriers over remarkably large
energy ranges. First-principles quantum transport calculations are used to
verify and further investigate this striking behaviour. Our study sheds light
on the transport properties of large-area graphene samples. Furthermore,
purposeful engineering of periodic grain boundaries with tunable transport gaps
would allow for controlling charge currents without the need of introducing
bulk band gaps in otherwise semimetallic graphene. The proposed approach can be
regarded as a means towards building practical graphene electronics.Comment: accepted in Nature Material
Dipole polarizability of 120Sn and nuclear energy density functionals
The electric dipole strength distribution in 120Sn between 5 and 22 MeV has
been determined at RCNP Osaka from a polarization transfer analysis of proton
inelastic scattering at E_0 = 295 MeV and forward angles including 0{\deg}.
Combined with photoabsorption data an electric dipole polarizability
\alpha_D(120Sn) = 8.93(36) fm^3 is extracted. The dipole polarizability as
isovector observable par excellence carries direct information on the nuclear
symmetry energy and its density dependence. The correlation of the new value
with the well established \alpha_D(208Pb) serves as a test of its prediction by
nuclear energy density functionals (EDFs). Models based on modern Skyrme
interactions describe the data fairly well while most calculations based on
relativistic Hamiltonians cannot.Comment: 6 pages, 4 figure
Low-energy electric dipole response in 120Sn
The electric dipole strength in 120Sn has been extracted from proton
inelastic scattering experiments at E_p = 295 MeV and at forward angles
including 0 degree. Below neutron threshoild it differs from the results of a
120Sn(gamma,gamma') experiment and peaks at an excitation energy of 8.3 MeV.
The total strength corresponds to 2.3(2)% of the energy-weighted sum rule and
is more than three times larger than what is observed with the (gamma,gamma')
reaction. This implies a strong fragmentation of the E1 strength and/or small
ground state branching ratios of the excited 1- states.Comment: 7 pages, 6 figure
Epidemiology, patterns of care, and mortality for patients with acute respiratory distress syndrome in intensive care units in 50 countries
IMPORTANCE: Limited information exists about the epidemiology, recognition, management, and outcomes of patients with the acute respiratory distress syndrome (ARDS).
OBJECTIVES: To evaluate intensive care unit (ICU) incidence and outcome of ARDS and to assess clinician recognition, ventilation management, and use of adjuncts-for example prone positioning-in routine clinical practice for patients fulfilling the ARDS Berlin Definition.
DESIGN, SETTING, AND PARTICIPANTS:The Large Observational Study to Understand the Global Impact of Severe Acute Respiratory Failure (LUNG SAFE) was an international, multicenter, prospective cohort study of patients undergoing invasive or noninvasive ventilation, conducted during 4 consecutive weeks in the winter of 2014 in a convenience sample of 459 ICUs from 50 countries across 5 continents.
EXPOSURES:Acute respiratory distress syndrome.
MAIN OUTCOMES AND MEASURES: The primary outcome was ICU incidence of ARDS. Secondary outcomes included assessment of clinician recognition of ARDS, the application of ventilatory management, the use of adjunctive interventions in routine clinical practice, and clinical outcomes from ARDS.
RESULTS: Of 29,144 patients admitted to participating ICUs, 3022 (10.4%) fulfilled ARDS criteria. Of these, 2377 patients developed ARDS in the first 48 hours and whose respiratory failure was managed with invasive mechanical ventilation. The period prevalence of mild ARDS was 30.0% (95% CI, 28.2%-31.9%); of moderate ARDS, 46.6% (95% CI, 44.5%-48.6%); and of severe ARDS, 23.4% (95% CI, 21.7%-25.2%). ARDS represented 0.42 cases per ICU bed over 4 weeks and represented 10.4% (95% CI, 10.0%-10.7%) of ICU admissions and 23.4% of patients requiring mechanical ventilation. Clinical recognition of ARDS ranged from 51.3% (95% CI, 47.5%-55.0%) in mild to 78.5% (95% CI, 74.8%-81.8%) in severe ARDS. Less than two-thirds of patients with ARDS received a tidal volume 8 of mL/kg or less of predicted body weight. Plateau pressure was measured in 40.1% (95% CI, 38.2-42.1), whereas 82.6% (95% CI, 81.0%-84.1%) received a positive end-expository pressure (PEEP) of less than 12 cm H2O. Prone positioning was used in 16.3% (95% CI, 13.7%-19.2%) of patients with severe ARDS. Clinician recognition of ARDS was associated with higher PEEP, greater use of neuromuscular blockade, and prone positioning. Hospital mortality was 34.9% (95% CI, 31.4%-38.5%) for those with mild, 40.3% (95% CI, 37.4%-43.3%) for those with moderate, and 46.1% (95% CI, 41.9%-50.4%) for those with severe ARDS.
CONCLUSIONS AND RELEVANCE: Among ICUs in 50 countries, the period prevalence of ARDS was 10.4% of ICU admissions. This syndrome appeared to be underrecognized and undertreated and associated with a high mortality rate. These findings indicate the potential for improvement in the management of patients with ARDS
Beyond the neutron drip line: The unbound oxygen isotopes (25)O and (26)O
This is the publisher's version, and is also available electronically from http://journals.aps.org/prc/abstract/10.1103/PhysRevC.88.034313.The very neutron-rich oxygen isotopes 25O and 26O are investigated experimentally and theoretically. The unbound states are populated in an experiment performed at the R3B-LAND setup at GSI via proton-knockout reactions from 26F and 27F at relativistic energies around 442 and 414 MeV/nucleon, respectively. From the kinematically complete measurement of the decay into 24O plus one or two neutrons, the 25O ground-state energy and width are determined, and upper limits for the 26O ground-state energy and lifetime are extracted. In addition, the results provide indications for an excited state in 26O at around 4 MeV. The experimental findings are compared to theoretical shell-model calculations based on chiral two- and three-nucleon (3N) forces, including for the first time residual 3N forces, which are shown to be amplified as valence neutrons are added
MINE: Module Identification in Networks
<p>Abstract</p> <p>Background</p> <p>Graphical models of network associations are useful for both visualizing and integrating multiple types of association data. Identifying modules, or groups of functionally related gene products, is an important challenge in analyzing biological networks. However, existing tools to identify modules are insufficient when applied to dense networks of experimentally derived interaction data. To address this problem, we have developed an agglomerative clustering method that is able to identify highly modular sets of gene products within highly interconnected molecular interaction networks.</p> <p>Results</p> <p>MINE outperforms MCODE, CFinder, NEMO, SPICi, and MCL in identifying non-exclusive, high modularity clusters when applied to the <it>C. elegans </it>protein-protein interaction network. The algorithm generally achieves superior geometric accuracy and modularity for annotated functional categories. In comparison with the most closely related algorithm, MCODE, the top clusters identified by MINE are consistently of higher density and MINE is less likely to designate overlapping modules as a single unit. MINE offers a high level of granularity with a small number of adjustable parameters, enabling users to fine-tune cluster results for input networks with differing topological properties.</p> <p>Conclusions</p> <p>MINE was created in response to the challenge of discovering high quality modules of gene products within highly interconnected biological networks. The algorithm allows a high degree of flexibility and user-customisation of results with few adjustable parameters. MINE outperforms several popular clustering algorithms in identifying modules with high modularity and obtains good overall recall and precision of functional annotations in protein-protein interaction networks from both <it>S. cerevisiae </it>and <it>C. elegans</it>.</p
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