155 research outputs found
Towards Reliable Automatic Protein Structure Alignment
A variety of methods have been proposed for structure similarity calculation,
which are called structure alignment or superposition. One major shortcoming in
current structure alignment algorithms is in their inherent design, which is
based on local structure similarity. In this work, we propose a method to
incorporate global information in obtaining optimal alignments and
superpositions. Our method, when applied to optimizing the TM-score and the GDT
score, produces significantly better results than current state-of-the-art
protein structure alignment tools. Specifically, if the highest TM-score found
by TMalign is lower than (0.6) and the highest TM-score found by one of the
tested methods is higher than (0.5), there is a probability of (42%) that
TMalign failed to find TM-scores higher than (0.5), while the same probability
is reduced to (2%) if our method is used. This could significantly improve the
accuracy of fold detection if the cutoff TM-score of (0.5) is used.
In addition, existing structure alignment algorithms focus on structure
similarity alone and simply ignore other important similarities, such as
sequence similarity. Our approach has the capacity to incorporate multiple
similarities into the scoring function. Results show that sequence similarity
aids in finding high quality protein structure alignments that are more
consistent with eye-examined alignments in HOMSTRAD. Even when structure
similarity itself fails to find alignments with any consistency with
eye-examined alignments, our method remains capable of finding alignments
highly similar to, or even identical to, eye-examined alignments.Comment: Peer-reviewed and presented as part of the 13th Workshop on
Algorithms in Bioinformatics (WABI2013
Discrete molecular dynamics simulations of peptide aggregation
We study the aggregation of peptides using the discrete molecular dynamics
simulations. At temperatures above the alpha-helix melting temperature of a
single peptide, the model peptides aggregate into a multi-layer parallel
beta-sheet structure. This structure has an inter-strand distance of 0.48 nm
and an inter-sheet distance of 1.0 nm, which agree with experimental
observations. In this model, the hydrogen bond interactions give rise to the
inter-strand spacing in beta-sheets, while the Go interactions among side
chains make beta-strands parallel to each other and allow beta-sheets to pack
into layers. The aggregates also contain free edges which may allow for further
aggregation of model peptides to form elongated fibrils.Comment: 15 pages, 8 figure
Atom focusing by far-detuned and resonant standing wave fields: Thin lens regime
The focusing of atoms interacting with both far-detuned and resonant standing
wave fields in the thin lens regime is considered. The thin lens approximation
is discussed quantitatively from a quantum perspective. Exact quantum
expressions for the Fourier components of the density (that include all
spherical aberration) are used to study the focusing numerically. The following
lens parameters and density profiles are calculated as functions of the pulsed
field area : the position of the focal plane, peak atomic density,
atomic density pattern at the focus, focal spot size, depth of focus, and
background density. The lens parameters are compared to asymptotic, analytical
results derived from a scalar diffraction theory for which spherical aberration
is small but non-negligible (). Within the diffraction theory
analytical expressions show that the focused atoms in the far detuned case have
an approximately constant background density
while the peak density behaves as , the focal distance or
time as , the focal spot size as
, and the depth of focus as .
Focusing by the resonant standing wave field leads to a new effect, a Rabi-
like oscillation of the atom density. For the far-detuned lens, chromatic
aberration is studied with the exact Fourier results. Similarly, the
degradation of the focus that results from angular divergence in beams or
thermal velocity distributions in traps is studied quantitatively with the
exact Fourier method and understood analytically using the asymptotic results.
Overall, we show that strong thin lens focusing is possible with modest laser
powers and with currently achievable atomic beam characteristics.Comment: 21 pages, 11 figure
Grover search with pairs of trapped ions
The desired interference required for quantum computing may be modified by
the wave function oscillations for the implementation of quantum
algorithms[Phys.Rev.Lett.84(2000)1615]. To diminish such detrimental effect, we
propose a scheme with trapped ion-pairs being qubits and apply the scheme to
the Grover search. It can be found that our scheme can not only carry out a
full Grover search, but also meet the requirement for the scalable hot-ion
quantum computing. Moreover, the ion-pair qubits in our scheme are more robust
against the decoherence and the dissipation caused by the environment than
single-particle qubits proposed before.Comment: RevTe
Quasiparticle Density-Matrix Representation of Nonlinear TDDFT Response Functions
The time-dependent density functional (TDDFT) equations may be written either
for the Kohn-Sham orbitals in Hilbert space or for the single electron density
matrix in Liouville space. A collective-oscillator, quasiparticle,
representation of the density response of many-electron systems which
explicitly reveals the relevant electronic coherence sizes is developed using
the Liouville space representation of adiabatic TDDFT. Closed expressions for
the nonlinear density-density response are derived, eliminating the need to
solve nonlinear integral equations, as required in the Hilbert space
formulation of the response.Comment: 24 page
Manufacturing flow line systems: a review of models and analytical results
The most important models and results of the manufacturing flow line literature are described. These include the major classes of models (asynchronous, synchronous, and continuous); the major features (blocking, processing times, failures and repairs); the major properties (conservation of flow, flow rate-idle time, reversibility, and others); and the relationships among different models. Exact and approximate methods for obtaining quantitative measures of performance are also reviewed. The exact methods are appropriate for small systems. The approximate methods, which are the only means available for large systems, are generally based on decomposition, and make use of the exact methods for small systems. Extensions are briefly discussed. Directions for future research are suggested.National Science Foundation (U.S.) (Grant DDM-8914277
Tracking development assistance for health and for COVID-19 : a review of development assistance, government, out-of-pocket, and other private spending on health for 204 countries and territories, 1990-2050
Background The rapid spread of COVID-19 renewed the focus on how health systems across the globe are financed, especially during public health emergencies. Development assistance is an important source of health financing in many low-income countries, yet little is known about how much of this funding was disbursed for COVID-19. We aimed to put development assistance for health for COVID-19 in the context of broader trends in global health financing, and to estimate total health spending from 1995 to 2050 and development assistance for COVID-19 in 2020. Methods We estimated domestic health spending and development assistance for health to generate total health-sector spending estimates for 204 countries and territories. We leveraged data from the WHO Global Health Expenditure Database to produce estimates of domestic health spending. To generate estimates for development assistance for health, we relied on project-level disbursement data from the major international development agencies' online databases and annual financial statements and reports for information on income sources. To adjust our estimates for 2020 to include disbursements related to COVID-19, we extracted project data on commitments and disbursements from a broader set of databases (because not all of the data sources used to estimate the historical series extend to 2020), including the UN Office of Humanitarian Assistance Financial Tracking Service and the International Aid Transparency Initiative. We reported all the historic and future spending estimates in inflation-adjusted 2020 US per capita, purchasing-power parity-adjusted US8. 8 trillion (95% uncertainty interval [UI] 8.7-8.8) or 40.4 billion (0.5%, 95% UI 0.5-0.5) was development assistance for health provided to low-income and middle-income countries, which made up 24.6% (UI 24.0-25.1) of total spending in low-income countries. We estimate that 13.7 billion was targeted toward the COVID-19 health response. 1.4 billion was repurposed from existing health projects. 2.4 billion (17.9%) was for supply chain and logistics. Only 1519 (1448-1591) per person in 2050, although spending across countries is expected to remain varied. Interpretation Global health spending is expected to continue to grow, but remain unequally distributed between countries. We estimate that development organisations substantially increased the amount of development assistance for health provided in 2020. Continued efforts are needed to raise sufficient resources to mitigate the pandemic for the most vulnerable, and to help curtail the pandemic for all. Copyright (C) 2021 The Author(s). Published by Elsevier Ltd.Peer reviewe
Mapping local patterns of childhood overweight and wasting in low- and middle-income countries between 2000 and 2017
A double burden of malnutrition occurs when individuals, household members or communities experience both undernutrition and overweight. Here, we show geospatial estimates of overweight and wasting prevalence among children under 5 years of age in 105 low- and middle-income countries (LMICs) from 2000 to 2017 and aggregate these to policy-relevant administrative units. Wasting decreased overall across LMICs between 2000 and 2017, from 8.4 (62.3 (55.1�70.8) million) to 6.4 (58.3 (47.6�70.7) million), but is predicted to remain above the World Health Organization�s Global Nutrition Target of <5 in over half of LMICs by 2025. Prevalence of overweight increased from 5.2 (30 (22.8�38.5) million) in 2000 to 6.0 (55.5 (44.8�67.9) million) children aged under 5 years in 2017. Areas most affected by double burden of malnutrition were located in Indonesia, Thailand, southeastern China, Botswana, Cameroon and central Nigeria. Our estimates provide a new perspective to researchers, policy makers and public health agencies in their efforts to address this global childhood syndemic. © 2020, The Author(s)
Global, regional, and national age-sex-specific mortality and life expectancy, 1950–2017: a systematic analysis for the Global Burden of Disease Study 2017
BACKGROUND:
Assessments of age-specific mortality and life expectancy have been done by the UN Population Division, Department of Economics and Social Affairs (UNPOP), the United States Census Bureau, WHO, and as part of previous iterations of the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD). Previous iterations of the GBD used population estimates from UNPOP, which were not derived in a way that was internally consistent with the estimates of the numbers of deaths in the GBD. The present iteration of the GBD, GBD 2017, improves on previous assessments and provides timely estimates of the mortality experience of populations globally.
METHODS:
The GBD uses all available data to produce estimates of mortality rates between 1950 and 2017 for 23 age groups, both sexes, and 918 locations, including 195 countries and territories and subnational locations for 16 countries. Data used include vital registration systems, sample registration systems, household surveys (complete birth histories, summary birth histories, sibling histories), censuses (summary birth histories, household deaths), and Demographic Surveillance Sites. In total, this analysis used 8259 data sources. Estimates of the probability of death between birth and the age of 5 years and between ages 15 and 60 years are generated and then input into a model life table system to produce complete life tables for all locations and years. Fatal discontinuities and mortality due to HIV/AIDS are analysed separately and then incorporated into the estimation. We analyse the relationship between age-specific mortality and development status using the Socio-demographic Index, a composite measure based on fertility under the age of 25 years, education, and income. There are four main methodological improvements in GBD 2017 compared with GBD 2016: 622 additional data sources have been incorporated; new estimates of population, generated by the GBD study, are used; statistical methods used in different components of the analysis have been further standardised and improved; and the analysis has been extended backwards in time by two decades to start in 1950.
FINDINGS:
Globally, 18·7% (95% uncertainty interval 18·4–19·0) of deaths were registered in 1950 and that proportion has been steadily increasing since, with 58·8% (58·2–59·3) of all deaths being registered in 2015. At the global level, between 1950 and 2017, life expectancy increased from 48·1 years (46·5–49·6) to 70·5 years (70·1–70·8) for men and from 52·9 years (51·7–54·0) to 75·6 years (75·3–75·9) for women. Despite this overall progress, there remains substantial variation in life expectancy at birth in 2017, which ranges from 49·1 years (46·5–51·7) for men in the Central African Republic to 87·6 years (86·9–88·1) among women in Singapore. The greatest progress across age groups was for children younger than 5 years; under-5 mortality dropped from 216·0 deaths (196·3–238·1) per 1000 livebirths in 1950 to 38·9 deaths (35·6–42·83) per 1000 livebirths in 2017, with huge reductions across countries. Nevertheless, there were still 5·4 million (5·2–5·6) deaths among children younger than 5 years in the world in 2017. Progress has been less pronounced and more variable for adults, especially for adult males, who had stagnant or increasing mortality rates in several countries. The gap between male and female life expectancy between 1950 and 2017, while relatively stable at the global level, shows distinctive patterns across super-regions and has consistently been the largest in central Europe, eastern Europe, and central Asia, and smallest in south Asia. Performance was also variable across countries and time in observed mortality rates compared with those expected on the basis of development.
INTERPRETATION:
This analysis of age-sex-specific mortality shows that there are remarkably complex patterns in population mortality across countries. The findings of this study highlight global successes, such as the large decline in under-5 mortality, which reflects significant local, national, and global commitment and investment over several decades. However, they also bring attention to mortality patterns that are a cause for concern, particularly among adult men and, to a lesser extent, women, whose mortality rates have stagnated in many countries over the time period of this study, and in some cases are increasing
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