bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conserved structural motifs in the central pair complex of eukaryotic flagella
Authors: Carbajal‐González Blanca I. , Heuser Thomas , Fu Xiaofeng , Lin Jianfeng , Smith Brandon W. , Mitchell David R. , Nicastro Daniela 
Published: December 2012

AbstractCilia and flagella are conserved hair‐like appendages of eukaryotic cells that function as sensing and motility generating organelles. Motility is driven by thousands of axonemal dyneins that require precise regulation. One essential motility regulator is the central pair complex (CPC) and many CPC defects cause paralysis of cilia/flagella. Several human diseases, such as immotile cilia syndrome, show CPC abnormalities, but little is known about the detailed three‐dimensional (3D) structure and function of the CPC. The CPC is located in the center of typical [9+2] cilia/flagella and is composed of two singlet microtubules (MTs), each with a set of associated projections that extend toward the surrounding nine doublet MTs. Using cryo‐electron tomography coupled with subtomogram averaging, we visualized and compared the 3D structures of the CPC in both the green alga Chlamydomonas and the sea urchin Strongylocentrotus at the highest resolution published to date. Despite the evolutionary distance between these species, their CPCs exhibit remarkable structural conservation. We identified several new projections, including those that form the elusive sheath, and show that the bridge has a more complex architecture than previously thought. Organism‐specific differences include the presence of MT inner proteins in Chlamydomonas, but not Strongylocentrotus, and different overall outlines of the highly connected projection network, which forms a round‐shaped cylinder in algae, but is more oval in sea urchin. These differences could be adaptations to the mechanical requirements of the rotating CPC in Chlamydomonas, compared to the Strongylocentrotus CPC which has a fixed orientation. © 2012 Wiley Periodicals, Inc
Population‐based 10‐year oncologic outcomes after low‐dose‐rate brachytherapy for low‐risk and intermediate‐risk prostate cancer
Authors: Morris W. James , Keyes Mira , Spadinger Ingrid , Kwan Winkle , Liu Mitchell , McKenzie Michael , Pai Howard , Pickles Tom , Tyldesley Scott 
Published: December 2012

AbstractBACKGROUND.The objective of this study was to report the rates of disease‐free survival (DFS), cause‐specific survival (CSS), and overall survival after low‐dose‐rate (LDR) prostate brachytherapy (PB).METHODS.Data from 1006 consecutive patients with prostate cancer who received LDR‐PB and underwent implantation on or before October 23, 2003 were extracted from a prospective database on November 11, 2011. The selected patients had low‐risk (58%) or intermediate‐risk (42%) disease according to National Comprehensive Cancer Network criteria. The Phoenix threshold was used to define biochemical relapse. Sixty‐five percent of patients received 3 months of neoadjuvant androgen‐deprivation therapy (ADT) and 3 months of concomitant ADT. Univariate and multivariate analyses are reported in relation to patient, tumor, and treatment variables.RESULTS.The median follow‐up was 7.5 years. By using Fine and Gray competing risks analysis, the 5‐year and 10‐year actuarial DFS rates were 96.7% (95% confidence interval, 95.2%‐97.7%) and 94.1% (95% confidence interval, 92%‐95.6%), respectively. When applied to the whole cohort, none of the usual prognostic variables, including dose metrics, were correlated with DFS. However, in both univariate and multivariate models, increasing dose was the only covariate that correlated with improved DFS for the subset of men (N = 348) who did not receive ADT (P = .043). The actuarial 10‐year CSS rate was 99.1% (95% confidence interval, 97.3%‐99.7%). The overall survival rate was 93.8% at 5 years (95% confidence interval, 92%‐95.1%) and 83.5% at 10 years (95% confidence interval, 79.8%‐86.6%). Only age at implantation (P = .0001) was correlated with overall survival in multivariate analysis.CONCLUSIONS.In a consecutive cohort of 1006 men with National Comprehensive Cancer Network low‐risk and intermediate‐risk prostate cancer, the actuarial rate of recurrent disease after LDR‐PB was approximately 3% at 5 years and 6% at 10 years. Cancer 2013. © 2012 American Cancer Society.
Monte Carlo simulation of PET images for injection dose optimization
Authors: Boldyš Jiří , Dvořák Jiří , Skopalová Magdaléna , Bělohlávek Otakar 
Published: December 2012

SUMMARYWhen a patient is examined by positron emission tomography (PET), radiotracer dose amount (activity) has to be determined. However, the rules for activity correction according to patients’ weight used nowadays do not correspond with practical experience. Very high image quality is achieved for slim patients, whereas noisy images are produced for obese patients. There is opportunity to modify the correction rule with the aim to equalize image quality within the broad spectrum of patients and to diminish radiation risk to slim patients, with special importance for children.We have built a model of a particular PET scanner and approximated human trunk, which is our region of interest, by a cylindrical model with segments of liver, outer adipose tissue, and the rest. We have performed Monte Carlo simulations of PET imaging using the GATE simulation package. Under reasonably simplifying assumptions and for special parameters, we have developed curves that recommend amount of injected activity based on body parameters to give PET images of constant quality, the quality being expressed in terms of noise equivalent counts. The dependence qualitatively differs from the rules used in clinical practice nowadays, and the results indicate potential for improvement. Copyright © 2012 John Wiley & Sons, Ltd.
Patient‐specific modelling of bone and bone‐implant systems: the challenges
Authors: Pankaj Pankaj 
Published: December 2012

SUMMARYIn the past three decades, finite element (FE) modelling has provided considerable understanding to the area of musculoskeletal biomechanics. However, most of this understanding has been generated using generic, standardised or idealised models. Patient‐specific modelling (PSM) is almost never used for making clinical decisions. Imaging technologies have made it possible to create patient‐specific geometries and FE meshes for modelling. While these have brought us closer to PSM, several challenges associated with the definition of material properties, loads, boundary conditions and interaction between components still need to be overcome. This study reviews the current status of PSM with respect to defining material behaviour and prescribing boundary conditions and interactions. With regard to the constitutive modelling of bone, it is seen that imaging is being increasingly used to define elastic properties (isotropic as well as anisotropic). However, the post‐elastic and time‐dependent behaviour, important for several modelling situations, is mostly obtained from in vitro experiments. Strain‐based plasticity, not commonly available in FE codes, appears to have the potential of reducing an element of patient‐specificity in modelling the yielding behaviour of bone. PSM of real boundary conditions that include muscles and ligaments continues to remain a challenge; many clinically relevant questions can be, however, answered without their inclusion. Simulation techniques to undertake PSM of interactions between bone and uncemented implants are available. Interference fit employed in both joint replacement fracture treatments induces considerable preload whose inclusion in models is important for the prediction of interface behaviour. Copyright © 2012 John Wiley & Sons, Ltd.
Implementation and performance analysis of efficient index structures for DNA search algorithms in parallel platforms
Authors: Sebastião Nuno , Encarnação Gustavo , Roma Nuno 
Published: December 2012

SummaryBecause of the large datasets that are usually involved in deoxyribonucleic acid (DNA) sequence alignment, the use of optimal local alignment algorithms (e.g., Smith–Waterman) is often unfeasible in practical applications. As such, more efficient solutions that rely on indexed search procedures are often preferred to significantly reduce the time to obtain such alignments. Some data structures that are usually adopted to build such indexes are suffix trees, suffix arrays, and the hash tables of q‐mers.This paper presents a comparative analysis of highly optimized parallel implementations of index‐based search algorithms using these three distinct data structures, considering two different parallel platforms: a homogeneous multi‐core central processing unit (CPU) and a NVidia Fermi graphics processing unit (GPU). Contrasting to what happens with CPU implementations, the obtained experimental results reveal that GPU implementations clearly favor the suffix arrays, because of the achieved performance in terms of memory accesses. Furthermore, the results also reveal that both the suffix trees and suffix arrays outperform the hash tables of q‐mers when dealing with the largest datasets.When compared with a quad‐core CPU, the results demonstrate the possibility to achieve speedups as high as 65 with the GPU when considering a suffix‐array index, thus making it an adequate choice for high‐performance bioinfomatics applications.Copyright © 2012 John Wiley & Sons, Ltd.
Protein dynamics: Complex by itself
Authors: Palese Luigi Leonardo 
Published: December 2012

AbstractBiological functions are intimately rooted in biopolymer dynamics. It is commonly accepted that proteins can be considered as complex systems, but the origin of such complexity is still not fully understood. Moreover, it is still not really clear if proteins are true complex systems or complicated ones. Here, molecular dynamics simulations on a two helix bundle protein have been performed, and protein trajectories have been analyzed by using correlation functions in the frequency domain. We show that even a simple protein exhibits the hallmarks of complex systems. Moreover, the molecular bases of this complex behavior are possessed completely by the protein itself, because such complexity emerges without considering the solvent explicitly. © 2012 Wiley Periodicals, Inc. Complexity, 2012
The extended leukocyte differential count using the Cytodiff flow cytometric system reveals that higher CD16+ cytotoxic NK+T lymphocyte levels predict superior survival outcomes in patients with metastatic carcinoma
Authors: Park Borae G. , Park Chan‐Jeoung , Yoon Chan‐Hee , Jang Seongsoo , Chi Hyun‐Sook , Ryu Min‐Hee , Kim Sang‐We 
Published: December 2012

AbstractThe recently developed Cytodiff flow cytometric system (Beckman Coulter, Miami, FL) enables leukocyte analysis using a single immunophenotyping panel tube composed of six markers and five colors and that can detect 16 leukocyte subpopulations. We performed a preliminary investigation of whether changes in any of 16 leukocyte differentials were associated with survival and treatment outcomes in patients with metastatic carcinoma or not.We measured 16 leukocyte differential counts using the Cytodiff flow cytometric system in peripheral blood samples from 40 patients with metastatic malignancy (27 stomach cancer and 13 lung cancer) before chemotherapy and at 15 day intervals after chemotherapy for 2 months.A higher percentage of CD16+ cytotoxic NK+T lymphocytes was found to be the only significant prognostic factor among by Cox regression analysis and a higher percentage of CD16+ cytotoxic NK+T lymphocytes (>5.0%) showed significantly longer survival outcomes by Kaplan–Meier analysis (P = 0.003).The Cytodiff system enables 16 leukocyte subpopulations in a one tube assay and also can operate with only small amounts of sample, although it cannot differentiate NK cells from T lymphocytes. Hence, the monitoring of all leukocyte subpopulations using Cytodiff flow cytometry may be a helpful prognostic tool for patients with metastatic carcinoma. © 2012 International Clinical Cytometry Society
Plant quality and local adaptation undermine relocation in a bog specialist butterfly
Authors: Turlure Camille , Radchuk Viktoriia , Baguette Michel , Meijrink Mark , van den Burg Arnold , De Vries Michiel Wallis , van Duinen Gert‐Jan 
Published: December 2012

AbstractThe butterflyBoloria aquilonarisis a specialist of oligotrophic ecosystems. Population viability analysis predicted the species to be stable inBelgium and to collapse in theNetherlands with reduced host plant quality expected to drive species decline in the latter. We tested this hypothesis by rearingB. aquilonariscaterpillars fromBelgian andDutch sites on host plants (the cranberry,Vaccinium oxycoccos). Dutch plant quality was lower thanBelgian one conferring lower caterpillar growth rate and survival. Reintroduction and/or supplementation may be necessary to ensure the viability of the species in theNetherlands, but some traits may have been selected solely inDutch caterpillars to cope with gradual changes in host plant quality. To test this hypothesis, the performance ofBelgian andDutch caterpillars fed with plants from both countries were compared.Dutch caterpillars performed well on both plant qualities, whereasBelgian caterpillars could not switch to lower quality plants. This can be considered as an environmentally induced plastic response of caterpillars and/or a local adaptation to plant quality, which precludes the use ofBelgian individuals as a unique solution for strengtheningDutch populations. More generally, these results stress that the relevance of local adaptation in selecting source populations for relocation may be as important as restoring habitat quality.
Patterns of sexual dimorphism in Mexican alligator lizards, Barisia imbricata
Authors: Dashevsky Daniel , Meik Jesse M. , Mociño‐Deloya Estrella , Setser Kirk , Schaack Sarah 
Published: December 2012

AbstractWe compare morphological characteristics of male and female Barisia imbricata, Mexican alligator lizards, and find that mass, head length, coloration, incidence of scars from conspecifics, tail loss, and frequency of bearing the color/pattern of the opposite sex are all sexually dimorphic traits. Overall size (measured as snout–vent length), on the other hand, is not different between the two sexes. We use data on bite scar frequency and fecundity to evaluate competing hypotheses regarding the selective forces driving these patterns. We contend that sexual selection, acting through male‐male competition, may favor larger mass and head size in males, whereas large females are likely favored by natural selection for greater fecundity. In addition, the frequency of opposite‐sex patterning in males versus females may indicate that the costs of agonistic interactions among males are severe enough to allow for an alternative mating strategy. Finally, we discuss how sexual and natural selective forces may interact to drive or mask the evolution of sexually dimorphic traits.
The application of COSI‐Corr to determine dune system dynamics in the southern Namib Desert using ASTER data
Authors: Scheidt Stephen P. , Lancaster Nick 
Published: December 2012

ABSTRACTThe Coregistration of Optically Sensed Images and Correlation (COSI‐Corr) algorithm was used to estimate dune migration and sand flux rates from a series of remotely‐sensed optical image pairs. Several areas of barchan and transverse dunes transport sand along definite pathways, feeding the southern part of the Namib Sand Sea from beaches and deflationary basins in the Sperrgebiet. We give a detailed description of the pre‐ and post‐processing routines used for our COSI‐Corr analysis, and we evaluate the sub‐pixel dune migration results at the dune and dune‐field scales. The best set of parameters for the application of the algorithm was systematically derived, resulting in methodological refinements of the cross‐correlation windows. The Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) sensor aboard the Terra satellite provided the remote sensing imagery. Few comparisons have been made between dune migration measurements using COSI‐Corr and other types of change detection analysis, and few dune fields have served as test cases for COSI‐Corr. We suggest that analysis and interpretation of COSI‐Corr output from ASTER data is more valuable if combined with other image analysis techniques, such as manual digitization of dunes in a geographic information system (GIS), processing of write memory function insertion (WMFI) imagery and multispectral image (MSI) analysis of composition. The dune migrations estimated from COSI‐Corr results were validated using GIS and WMFI, and later MSI analysis added an important regional, contextual framework of sand transport pathways. The synthesis of these works lends more confidence to understanding the Namib dune system's dynamics and provides a basis for future comparisons to other dune fields. Copyright © 2013 John Wiley & Sons, Ltd.
Towards petascale spectral simulations for transition analysis in wall bounded flow
Authors: Montagnier Julien , Cadiou Anne , Buffat Marc , Penven Lionel Le 
Published: December 2012

SUMMARYAn efficient parallel spectral method for direct numerical simulations of transitional and turbulent flows is described in this paper. The parallelization is classically based on a bidimensional domain decomposition, but has been specifically developed for a solenoidal Fourier–Chebyshev spectral approximation where in one Fourier direction, the number of modes is very large compared with the two other directions. The approach therefore differs from classical libraries developed for cubic Fourier boxes. The strategy uses message‐passing interface (MPI) for message‐passing among nodes and is fairly portable. One of the originalities of this paper is the use of an efficient hybrid programming with MPI for internodes communications and a coarse grain parallelism using OpenMP for core shared‐memory computation, instead of the classical hybrid programming with MPI and a fine granularity parallelism at the loop level with OpenMP directives. This hybrid parallelism has been tested on the recent generation of high‐performance parallel supercomputers involving a few tens of cores per node. Performances are evaluated on different low‐frequency and high‐frequency processors massively parallel platforms. We demonstrate that spectral methods, which are known to be inherently ill‐fitted for the new generation of high‐performance distributed‐memory computers, can be implemented efficiently using this hybrid programming with good scalability and a very fast wall‐clock time per iteration. New numerical experiments are therefore now accessible on petascale computers, while keeping the attractive features of spectral methods such as accuracy, exponential convergence, computational efficiency and conservative properties. This is illustrated by a direct numerical simulation of the transition of the boundary layers developing from the entrance section of a plane channel and interacting to merge into a fully turbulent flow. Copyright © 2012 John Wiley & Sons, Ltd.
Implementation of slip boundary conditions in the finite volume method: new techniques
Authors: Ferrás L.L. , Nóbrega J.M. , Pinho F.T. 
Published: December 2012

SUMMARYTwo different techniques for the implementation of the linear and nonlinear slip boundary conditions into a finite volume method based numerical code are presented. For the linear Navier slip boundary condition, an implicit implementation in the system of equations is carried out for which there is no need for any relaxation, especially when handling high slip coefficients. For three different nonlinear slip boundary conditions, two different methods are devised, one based on solving a transcendental equation for the boundary and the other on the linearization of the slip law. For assessment purposes, comparison is made between these new methods and the usual iterative process. With these new methods, the convergence difficulties, typical of the iterative procedure, are eliminated, and for some of the test cases, the convergence rate even increased with the slip velocity. The details of these implementations are given first for a simple geometry using orthogonal meshes and Cartesian coordinates followed by their generalization to non‐Cartesian coordinates and nonorthogonal meshes. The developed code was tested in the benchmark slip‐stick and 4:1 contraction flows, evidencing the robustness of the proposed procedures. Copyright © 2013 John Wiley & Sons, Ltd.
SNP Prioritization Using a Bayesian Probability of Association
Authors: Thompson John R. , Gögele Martin , Weichenberger Christian X. , Modenese Mirko , Attia John , Barrett Jennifer H. , Boehnke Michael , De Grandi Alessandro , Domingues Francisco S. , Hicks Andrew A. , Marroni Fabio , Pattaro Cristian , Ruggeri Fabrizio , Borsani Giuseppe , Casari Giorgio , Parmigiani Giovanni , Pastore Andrea , Pfeufer Arne , Schwienbacher Christine , Taliun Daniel , Consortium CKDGen , Fox Caroline S. , Pramstaller Peter P. , Minelli Cosetta 
Published: December 2012

ABSTRACTPrioritization is the process whereby a set of possible candidate genes or SNPs is ranked so that the most promising can be taken forward into further studies. In a genome‐wide association study, prioritization is usually based on the P‐values alone, but researchers sometimes take account of external annotation information about the SNPs such as whether the SNP lies close to a good candidate gene. Using external information in this way is inherently subjective and is often not formalized, making the analysis difficult to reproduce. Building on previous work that has identified 14 important types of external information, we present an approximate Bayesian analysis that produces an estimate of the probability of association. The calculation combines four sources of information: the genome‐wide data, SNP information derived from bioinformatics databases, empirical SNP weights, and the researchers’ subjective prior opinions. The calculation is fast enough that it can be applied to millions of SNPS and although it does rely on subjective judgments, those judgments are made explicit so that the final SNP selection can be reproduced. We show that the resulting probability of association is intuitively more appealing than the P‐value because it is easier to interpret and it makes allowance for the power of the study. We illustrate the use of the probability of association for SNP prioritization by applying it to a meta‐analysis of kidney function genome‐wide association studies and demonstrate that SNP selection performs better using the probability of association compared with P‐values alone.
GENERAL BUDGET SUPPORT: HAS IT BENEFITED THE HEALTH SECTOR?
Authors: Fernandes Antunes Adelio , Xu Ke , James Chris D. , Saksena Priyanka , Van de Maele Nathalie , Carrin Guy , Evans David B. 
Published: December 2012

ABSTRACTThere has been recent controversy about whether aid directed specifically to health has caused recipient governments to reallocate their own funds to non‐health areas. At the same time, general budget support (GBS) has been increasing. GBS allows governments to set their own priorities, but little is known about how these additional resources are subsequently used. This paper uses cross‐country panel data to assess the impact of GBS programmes on health spending in low‐income and middle‐income countries, using dynamic panel techniques to estimate unbiased coefficients in the presence of serial correlation. We found no clear evidence that GBS had any impact, positive or negative, on government health spending derived from domestic sources. GBS also had no observed impact on total government health spending from all sources (external as well as domestic). In contrast, health‐specific aid was associated with a decline in health expenditures from domestic sources, but there was not a full substitution effect. That is, despite this observed fungibility, health‐specific aid still increases total government health spending from all sources. Finally, increases in total government expenditure led to substantial increases in domestic government health expenditures. Copyright © 2012 John Wiley & Sons, Ltd.