4,619 research outputs found
Geometric and Statistical Properties of the Mean-Field HP Model, the LS Model and Real Protein Sequences
Lattice models, for their coarse-grained nature, are best suited for the
study of the ``designability problem'', the phenomenon in which most of the
about 16,000 proteins of known structure have their native conformations
concentrated in a relatively small number of about 500 topological classes of
conformations. Here it is shown that on a lattice the most highly designable
simulated protein structures are those that have the largest number of
surface-core switchbacks. A combination of physical, mathematical and
biological reasons that causes the phenomenon is given. By comparing the most
foldable model peptides with protein sequences in the Protein Data Bank, it is
shown that whereas different models may yield similar designabilities,
predicted foldable peptides will simulate natural proteins only when the model
incorporates the correct physics and biology, in this case if the main folding
force arises from the differing hydrophobicity of the residues, but does not
originate, say, from the steric hindrance effect caused by the differing sizes
of the residues.Comment: 12 pages, 10 figure
Linear, Deterministic, and Order-Invariant Initialization Methods for the K-Means Clustering Algorithm
Over the past five decades, k-means has become the clustering algorithm of
choice in many application domains primarily due to its simplicity, time/space
efficiency, and invariance to the ordering of the data points. Unfortunately,
the algorithm's sensitivity to the initial selection of the cluster centers
remains to be its most serious drawback. Numerous initialization methods have
been proposed to address this drawback. Many of these methods, however, have
time complexity superlinear in the number of data points, which makes them
impractical for large data sets. On the other hand, linear methods are often
random and/or sensitive to the ordering of the data points. These methods are
generally unreliable in that the quality of their results is unpredictable.
Therefore, it is common practice to perform multiple runs of such methods and
take the output of the run that produces the best results. Such a practice,
however, greatly increases the computational requirements of the otherwise
highly efficient k-means algorithm. In this chapter, we investigate the
empirical performance of six linear, deterministic (non-random), and
order-invariant k-means initialization methods on a large and diverse
collection of data sets from the UCI Machine Learning Repository. The results
demonstrate that two relatively unknown hierarchical initialization methods due
to Su and Dy outperform the remaining four methods with respect to two
objective effectiveness criteria. In addition, a recent method due to Erisoglu
et al. performs surprisingly poorly.Comment: 21 pages, 2 figures, 5 tables, Partitional Clustering Algorithms
(Springer, 2014). arXiv admin note: substantial text overlap with
arXiv:1304.7465, arXiv:1209.196
Stereotactic body radiotherapy for hepatocellular carcinoma: meta-analysis and International Stereotactic Radiosurgery Society practice guidelines
PURPOSE
This systematic review and meta-analysis reports on outcomes and hepatic toxicity rates following stereotactic body radiotherapy (SBRT) for liver confined hepatocellular carcinoma (HCC), and presents consensus guidelines regarding appropriate patient management.
METHODS AND MATERIALS
Using the Preferred Reporting Items for Systemic Review and Meta-analyses guidelines, a systematic review was performed from articles reporting outcomes at ≥5 years published prior to October 2022 from the Embase, MEDLINE, Cochrane, and Scopus databases using the key words terms ("Stereotactic body radiotherapy" OR "SBRT" OR "SABR" OR "Stereotactic ablative radiotherapy") AND ("Hepatocellular carcinoma" OR "HCC"). An aggregated data (AD) meta-analysis was conducted to assess overall survival (OS) and local control (LC) using weighted random effects models. In addition, an individual patient data (IPD) analysis incorporating data from 6 institutions was conducted as its own subgroup analyses.
RESULTS
Seventeen observational studies, comprising 1889 HCC patients treated with ≤9 SBRT fractions, between 2003 and 2019, were included in the AD meta-analysis. The 3- and 5- year OS rates after SBRT were 57% (95% confidence interval [CI], 47-66%) and 40% (95% CI, 29-51%). The 3- and 5- year LC rates after SBRT were 84% (95% CI, 77-90%) and 82% (95% CI, 74-88%), respectively. Tumor size was the only prognostic factor for LC. Tumor size and region were significantly associated with OS. Five-year LC and OS rates of 79% (95% CI, 0.74-0.84) and 25% (95% CI, 0.20-0.30), respectively, were observed in the IPD analyses. Factors prognostic for improved OS were tumor size <3 cm, eastern region, Child-Pugh score ≤B7, and the Barcelona Clinic Liver Cancer stage of 0 and A. The incidence of severe hepatic toxicity varied according to the criteria applied.
CONCLUSIONS
SBRT is an effective treatment modality for HCC patients with mature follow up. Clinical practice guidelines were developed on behalf of the XXXX
Comparison of primary care experiences among adults in general outpatient clinics and private general practice clinics in Hong Kong
Abstract. Background. The main goal of Hong Kong's publicly-funded general outpatient clinics (GOPCs) is to provide primary medical services for the financially vulnerable. The objective of the current study was to compare the primary care experiences of GOPC users and the users of care provided by private general practitioners (GPs) in Hong Kong via a territory-wide telephone survey. Methods. One thousand adults in Hong Kong aged 18 and above were interviewed by a telephone survey. The modified Chinese translated Primary Care Assessment Tool was used to collect data on respondents' primary care experience. Results. Our results indicated that services provided by GOPC were more often used by female, older, poorer, chronically-ill and less educated population. GOPC participants were also more likely to have visited a specialist or used specialist services (69.7% vs. 52.0%; p < 0.001), although this difference in utilization of specialist services disappeared after adjusting for age (55.7% vs. 52.0%, p = 0.198). Analyses were also performed to asses the relationship between healthcare settings (GOPCs versus private GPs) and primary care quality. Private GP patients achieved higher overall PCAT scores largely due to better accessibility (Mean: 6.88 vs. 8.41, p < 0.001) and person-focused care (Mean: 8.37 vs. 11.69, p < 0.001). Conclusions. Our results showed that patients primarily receiving care from private GPs in Hong Kong reported better primary care experiences than those primarily receiving care from GOPCs. This was largely due to the greater accessibility and better interpersonal relationships offered by the private GPs. As most patients use both GOPCs and private GPs, their overall primary care experiences may not be as different as the findings of this study imply. © 2010 Wong et al; licensee BioMed Central Ltd.link_to_subscribed_fulltex
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Measurement of B(B-->X_s {\gamma}), the B-->X_s {\gamma} photon energy spectrum, and the direct CP asymmetry in B-->X_{s+d} {\gamma} decays
The photon spectrum in B --> X_s {\gamma} decay, where X_s is any strange
hadronic state, is studied using a data sample of (382.8\pm 4.2) \times 10^6
e^+ e^- --> \Upsilon(4S) --> BBbar events collected by the BABAR experiment at
the PEP-II collider. The spectrum is used to measure the branching fraction B(B
--> X_s \gamma) = (3.21 \pm 0.15 \pm 0.29 \pm 0.08)\times 10^{-4} and the
first, second, and third moments = 2.267 \pm 0.019 \pm 0.032 \pm
0.003 GeV,, )^2> = 0.0484 \pm 0.0053 \pm 0.0077 \pm
0.0005 GeV^2, and )^3> = -0.0048 \pm 0.0011 \pm 0.0011
\pm 0.0004 GeV^3, for the range E_\gamma > 1.8 GeV, where E_{\gamma} is the
photon energy in the B-meson rest frame. Results are also presented for
narrower E_{\gamma} ranges. In addition, the direct CP asymmetry A_{CP}(B -->
X_{s+d} \gamma) is measured to be 0.057 \pm 0.063. The spectrum itself is also
unfolded to the B-meson rest frame; that is the frame in which theoretical
predictions for its shape are made.Comment: 37 pages, 19 postscript figures, submitted to Phys. Rev. D. No
analysis or results have changed from previous version. Some changes to
improve clarity based on interactions with Phys. Rev. D referees, including
one new Figure (Fig. 13), and some minor wording/punctuation/spelling
mistakes fixe
A Study of Time-Dependent CP-Violating Asymmetries and Flavor Oscillations in Neutral B Decays at the Upsilon(4S)
We present a measurement of time-dependent CP-violating asymmetries in
neutral B meson decays collected with the BABAR detector at the PEP-II
asymmetric-energy B Factory at the Stanford Linear Accelerator Center. The data
sample consists of 29.7 recorded at the
resonance and 3.9 off-resonance. One of the neutral B mesons,
which are produced in pairs at the , is fully reconstructed in
the CP decay modes , , , () and , or in flavor-eigenstate
modes involving and (). The flavor of the other neutral B meson is tagged at the time of
its decay, mainly with the charge of identified leptons and kaons. The proper
time elapsed between the decays is determined by measuring the distance between
the decay vertices. A maximum-likelihood fit to this flavor eigenstate sample
finds . The value of the asymmetry amplitude is determined from
a simultaneous maximum-likelihood fit to the time-difference distribution of
the flavor-eigenstate sample and about 642 tagged decays in the
CP-eigenstate modes. We find , demonstrating that CP violation exists in the neutral B meson
system. (abridged)Comment: 58 pages, 35 figures, submitted to Physical Review
Measurement of ISR-FSR interference in the processes e+ e- --> mu+ mu- gamma and e+ e- --> pi+ pi- gamma
Charge asymmetry in processes e+ e- --> mu+ mu- gamma and e+ e- --> pi+ pi-
gamma is measured using 232 fb-1 of data collected with the BABAR detector at
center-of-mass energies near 10.58 GeV. An observable is introduced and shown
to be very robust against detector asymmetries while keeping a large
sensitivity to the physical charge asymmetry that results from the interference
between initial and final state radiation. The asymmetry is determined as
afunction of the invariant mass of the final-state tracks from production
threshold to a few GeV/c2. It is compared to the expectation from QED for e+ e-
--> mu+ mu- gamma and from theoretical models for e+ e- --> pi+ pi- gamma. A
clear interference pattern is observed in e+ e- --> pi+ pi- gamma, particularly
in the vicinity of the f_2(1270) resonance. The inferred rate of lowest order
FSR production is consistent with the QED expectation for e+ e- --> mu+ mu-
gamma, and is negligibly small for e+ e- --> pi+ pi- gamma.Comment: 32 pages,29 figures, to be submitted to Phys. Rev.
Single hadron response measurement and calorimeter jet energy scale uncertainty with the ATLAS detector at the LHC
The uncertainty on the calorimeter energy response to jets of particles is
derived for the ATLAS experiment at the Large Hadron Collider (LHC). First, the
calorimeter response to single isolated charged hadrons is measured and
compared to the Monte Carlo simulation using proton-proton collisions at
centre-of-mass energies of sqrt(s) = 900 GeV and 7 TeV collected during 2009
and 2010. Then, using the decay of K_s and Lambda particles, the calorimeter
response to specific types of particles (positively and negatively charged
pions, protons, and anti-protons) is measured and compared to the Monte Carlo
predictions. Finally, the jet energy scale uncertainty is determined by
propagating the response uncertainty for single charged and neutral particles
to jets. The response uncertainty is 2-5% for central isolated hadrons and 1-3%
for the final calorimeter jet energy scale.Comment: 24 pages plus author list (36 pages total), 23 figures, 1 table,
submitted to European Physical Journal
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Precise Measurement of the e+ e- --> pi+ pi- (gamma) Cross Section with the Initial-State Radiation Method at BABAR
A precise measurement of the cross section of the process
from threshold to an energy of 3GeV is obtained
with the initial-state radiation (ISR) method using 232fb of data
collected with the BaBar detector at center-of-mass energies near
10.6GeV. The ISR luminosity is determined from a study of the leptonic process
, which is found to agree with the
next-to-leading-order QED prediction to within 1.1%. The cross section for the
process is obtained with a systematic uncertainty
of 0.5% in the dominant resonance region. The leading-order hadronic
contribution to the muon magnetic anomaly calculated using the measured
cross section from threshold to 1.8GeV is .Comment: 58 pages, 56 figures, to be submitted to Phys. Rev.
Branching fraction and form-factor shape measurements of exclusive charmless semileptonic B decays, and determination of |V_{ub}|
We report the results of a study of the exclusive charmless semileptonic
decays, B^0 --> pi^- l^+ nu, B^+ --> pi^0 l^+ nu, B^+ --> omega l^+ nu, B^+ -->
eta l^+ nu and B^+ --> eta^' l^+ nu, (l = e or mu) undertaken with
approximately 462x10^6 B\bar{B} pairs collected at the Upsilon(4S) resonance
with the BABAR detector. The analysis uses events in which the signal B decays
are reconstructed with a loose neutrino reconstruction technique. We obtain
partial branching fractions in several bins of q^2, the square of the momentum
transferred to the lepton-neutrino pair, for B^0 --> pi^- l^+ nu, B^+ --> pi^0
l^+ nu, B^+ --> omega l^+ nu and B^+ --> eta l^+ nu. From these distributions,
we extract the form-factor shapes f_+(q^2) and the total branching fractions
BF(B^0 --> pi^- l^+ nu) = (1.45 +/- 0.04_{stat} +/- 0.06_{syst})x10^-4
(combined pi^- and pi^0 decay channels assuming isospin symmetry), BF(B^+ -->
omega l^+ nu) = (1.19 +/- 0.16_{stat} +/- 0.09_{syst})x10^-4 and BF(B^+ --> eta
l^+ nu) = (0.38 +/- 0.05_{stat} +/- 0.05_{syst})x10^-4. We also measure BF(B^+
--> eta^' l^+ nu) = (0.24 +/- 0.08_{stat} +/- 0.03_{syst})x10^-4. We obtain
values for the magnitude of the CKM matrix element V_{ub} by direct comparison
with three different QCD calculations in restricted q^2 ranges of B --> pi l^+
nu decays. From a simultaneous fit to the experimental data over the full q^2
range and the FNAL/MILC lattice QCD predictions, we obtain |V_{ub}| = (3.25 +/-
0.31)x10^-3, where the error is the combined experimental and theoretical
uncertainty.Comment: 35 pages, 14 figures, submitted to PR
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