bluuebunny/crossref_metadata_2025_split huggingface dataset:
Creating optimal code for GPU‐accelerated CT reconstruction using ant colony optimization
Authors: Papenhausen Eric , Zheng Ziyi , Mueller Klaus 
Published: March 2013

Purpose:CT reconstruction algorithms implemented on the GPU are highly sensitive to their implementation details and the hardware they run on. Fine‐tuning an implementation for optimal performance can be a time consuming task and require many updates when the hardware changes. There are some techniques that do automatic fine‐tuning of GPU code. These techniques, however, are relatively narrow in their fine‐tuning and are often based on heuristics which can be inaccurate. The goal of this paper is to present a framework that will automate the process of code optimization with maximum flexibility and produce a final result that is efficient and readable to the user.Methods:The authors propose a method that is able to tune high level implementation details by using the ant colony optimization algorithm to find the optimal implementation in a relatively short amount of time. Our framework does this by taking as input, a file that describes a graph, such that a path through this graph represents a potential implementation. They then use the ant colony optimization algorithm to find the optimal path through this graph based on the execution time and the quality of the image.Results:Two experimental studies are carried out. Using the presented framework, they optimize the performance of a GPU accelerated FDK backprojection implementation and a GPU accelerated separable footprint backprojection implementation. The authors demonstrate that the resulting optimal implementation can be different depending on the hardware specifications. They then compare the results of the framework produced with the results produced by manual optimization.Conclusions:The framework they present is a useful tool for increasing programmer productivity and reducing the overhead of leveraging hardware specific resources. By performing an intelligent search, our framework produces a more efficient image reconstruction implementation in a shorter amount of time.
Patchwork reconstruction with resolution modeling for digital breast tomosynthesis
Authors: Michielsen Koen , Van Slambrouck Katrien , Jerebko Anna , Nuyts Johan 
Published: March 2013

Purpose:Digital breast tomosynthesis is a relatively new diagnostic x‐ray modality that allows high resolution breast imaging while suppressing interference from overlapping anatomical structures. However, proper visualization of microcalcifications remains a challenge. For the subset of systems considered by the authors, the main cause of deterioration is movement of the x‐ray source during exposures. They propose a modified grouped coordinate ascent algorithm that includes a specific acquisition model to compensate for this deterioration.Methods:A resolution model based on the movement of the x‐ray source during image acquisition is created and combined with a grouped coordinate ascent algorithm. Choosing planes parallel to the detector surface as the groups enables efficient implementation of the position dependent resolution model. In the current implementation, the resolution model is approximated by a Gaussian smoothing kernel. The effect of the resolution model on the iterative reconstruction is evaluated by measuring contrast to noise ratio (CNR) of spherical microcalcifications in a homogeneous background. After this, the new reconstruction method is compared to the optimized filtered backprojection method for the considered system, by performing two observer studies: the first study simulates clusters of spherical microcalcifications in a power law background for a free search task; the second study simu‐lates smooth or irregular microcalcifications in the same type of backgrounds for a classification task.Results:Including the resolution model in the iterative reconstruction methods increases the CNR of microcalcifications. The first observer study shows a significant improvement in detection of microcalcifications (p = 0.029), while the second study shows that performance on a classification task remains the same (p = 0.935) compared to the filtered backprojection method.Conclusions:The new method shows higher CNR and improved visualization of microcalcifications in an observer experiment on synthetic data. Further study of the negative results of the classification task showed performance variations throughout the volume linked to the changing noise structure introduced by the combination of the resolution model and the smoothing prior.
Temporal resolution and motion artifacts in single‐source and dual‐source cardiac CT
Authors: Schöndube Harald , Allmendinger Thomas , Stierstorfer Karl , Bruder Herbert , Flohr Thomas 
Published: March 2013

Purpose:The temporal resolution of a given image in cardiac computed tomography (CT) has so far mostly been determined from the amount of CT data employed for the reconstruction of that image. The purpose of this paper is to examine the applicability of such measures to the newly introduced modality of dual‐source CT as well as to methods aiming to provide improved temporal resolution by means of an advanced image reconstruction algorithm.Methods:To provide a solid base for the examinations described in this paper, an extensive review of temporal resolution in conventional single‐source CT is given first. Two different measures for assessing temporal resolution with respect to the amount of data involved are introduced, namely, either taking the full width at half maximum of the respective data weighting function (FWHM‐TR) or the total width of the weighting function (total TR) as a base of the assessment. Image reconstruction using both a direct fan‐beam filtered backprojection with Parker weighting as well as using a parallel‐beam rebinning step are considered. The theory of assessing temporal resolution by means of the data involved is then extended to dual‐source CT. Finally, three different advanced iterative reconstruction methods that all use the same input data are compared with respect to the resulting motion artifact level. For brevity and simplicity, the examinations are limited to two‐dimensional data acquisition and reconstruction. However, all results and conclusions presented in this paper are also directly applicable to both circular and helical cone‐beam CT.Results:While the concept of total TR can directly be applied to dual‐source CT, the definition of the FWHM of a weighting function needs to be slightly extended to be applicable to this modality. The three different advanced iterative reconstruction methods examined in this paper result in significantly different images with respect to their motion artifact level, despite exactly the same amount of data being used in the reconstruction process.Conclusions:The concept of assessing temporal resolution by means of the data employed for reconstruction can nicely be extended from single‐source to dual‐source CT. However, for advanced (possibly nonlinear iterative) reconstruction algorithms the examined approach fails to deliver accurate results. New methods and measures to assess the temporal resolution of CT images need to be developed to be able to accurately compare the performance of such algorithms.
Draft Genome Sequence of
Rhizopus chinensis
CCTCCM201021, Used for Brewing Traditional Chinese Alcoholic Beverages
Authors: Wang Dong , Wu Rong , Xu Yan , Li Ming 
Published: March 2013

ABSTRACT

The filamentous fungus genus
Rhizopus
has traditionally been used for brewing alcoholic beverages and fermented foods in China. The 45,666,236-bp draft genome sequence of
R. chinensis
CCTCCM201021, isolated from the leaven Daqu, was determined, annotated, and analyzed. Analysis of the sequence might provide insight into the properties of this fungus and lead to its further development for industrial applications.
Complete Genome Sequence of Escherichia coli O157:H7 Bacteriophage phiJLA23 Isolated in Mexico
Authors: Amarillas Luis , Chaidez Cristobal , Lugo Yadira , León-Félix Josefina 
Published: March 2013

ABSTRACT

The bacteriophage phiJLA23 was isolated from an animal feces sample and lytic activity was demonstrated against the
Escherichia coli
O157:H7 strain. We report the complete nucleotide sequence of bacteriophage phiJLA23, information which may be useful for determining whether this phage is a candidate for biocontrol or another biotechnological application.
Whole-Genome Sequencing and Comparative Analysis of Yersinia pestis, the Causative Agent of a Plague Outbreak in Northern Peru
Authors: Cáceres O. , Montenegro J. , Padilla C. , Tarazona D. , Bailón H. , García P. , Céspedes M. , Valencia P. , Guio H. 
Published: March 2013

ABSTRACT

The plague is a zoonotic disease caused by the bacterium
Yersinia pestis
. Here, we report the complete genome sequence of the
Y. pestis
strain INS, which was isolated from swollen lymph gland aspirate (bubo aspirate) of an infected patient from a pneumonic outbreak in 2010 in northern Peru.
Influenza Viruses with Rearranged Genomes as Live-Attenuated Vaccines
Authors: Pena Lindomar , Sutton Troy , Chockalingam Ashok , Kumar Sachin , Angel Matthew , Shao Hongxia , Chen Hongjun , Li Weizhong , Perez Daniel R. 
Published: March 2013

ABSTRACT

H5N1 and H9N2 avian influenza virus subtypes top the World Health Organization's list for the greatest pandemic potential. Inactivated H5N1 vaccines induce limited immune responses and, in the case of live-attenuated influenza virus vaccines (LAIV), there are safety concerns regarding the possibility of reassortment between the H5 gene segment and circulating influenza viruses. In order to overcome these drawbacks, we rearranged the genome of an avian H9N2 influenza virus and expressed the entire H5 hemagglutinin open reading frame (ORF) from the segment 8 viral RNA. These vectors had reduced polymerase activities as well as viral replication
in vitro
and excellent safety profiles
in vivo
. Immunization with the dual H9-H5 influenza virus resulted in protection against lethal H5N1 challenge in mice and ferrets, and also against a potentially pandemic H9 virus. Our studies demonstrate that rearranging the influenza virus genome has great potential for the development of improved vaccines against influenza virus as well as other pathogens.
Mother-Offspring Transmission and Age-Dependent Accumulation of Simian Foamy Virus in Wild Chimpanzees
Authors: Blasse Anja , Calvignac-Spencer Sébastien , Merkel Kevin , Goffe Adeelia S. , Boesch Christophe , Mundry Roger , Leendertz Fabian H. 
Published: March 2013

ABSTRACT

Simian foamy viruses (SFVs) are thought to infect virtually any adult nonhuman primate (NHP). While many data have accumulated about patterns of codivergence with their hosts and cross-species transmission events, little is known about the modalities of SFV transmission within NHP species, especially in the wild. Here we provide a detailed investigation of the dynamics of SFV circulation in a wild community of Western chimpanzees (
Pan troglodytes verus
). We demonstrate that mother-offspring (vertical) SFV transmission is common and hypothesize that it accounts for a number of primary infections. We also show that multiple infections with several chimpanzee-specific SFV strains (i.e., superinfection) commonly happen in adult chimpanzees, which might point to adult-specific aggressive behaviors as a lifelong source of SFV infection. Our data give evidence for complex SFV dynamics in wild chimpanzees, even at a single community scale, and show that linking wild NHP social interactions and their microorganisms' dynamics is feasible.
Human Cytomegalovirus pp71 Stimulates Major Histocompatibility Complex Class I Presentation of IE1-Derived Peptides at Immediate Early Times of Infection
Authors: Hesse Julia , Reyda Sabine , Tenzer Stefan , Besold Katrin , Reuter Nina , Krauter Steffi , Büscher Nicole , Stamminger Thomas , Plachter Bodo 
Published: March 2013

ABSTRACT
Suppression of major histocompatibility complex (MHC) class I-mediated presentation of human cytomegalovirus (HCMV) peptides is an important mechanism to avoid CD8 T lymphocyte recognition and killing of infected cells. Of particular interest is how MHC class I presentation of essential regulatory immediate early (IE) proteins of HCMV can be effectively compromised at times when known viral immunoevasins are not abundantly expressed. The tegument protein pp71 had been suggested to be involved in MHC class I downregulation. Intriguingly, this polypeptide is also critically engaged in the initial derepression of the major IE gene locus, leading to enhanced expression of IE proteins IE1-pp72 and IE2-pp86. Using a set of viral mutants, we addressed the role of pp71 in MHC class I presentation of IE1-pp72-derived peptides. We show that the amount of “incoming” pp71 positively correlates with IE1-pp72 protein levels and with the presentation of IE1-derived peptides. This indicates that the amount of the IE1 protein, induced by pp71, rather than a putative immunoevasive function of the tegument protein, determines MHC class I antigen presentation of IE1-derived peptides. This process proved to be independent of the presence of pp65, which had been reported to interfere with IE1 presentation. It may thus be beneficial for the success of HCMV replication to limit the level of pp71 delivered from infecting particles in order to avoid critical levels of MHC class I presentation of IE protein-derived peptides.
Identification of a Genetic Locus on Chromosome 11 That Regulates Leukocyte Infiltration in Mouse Carotid Artery
Authors: Smolock Elaine M. , Machleder Dietrich E. , Korshunov Vyacheslav A. , Berk Bradford C. 
Published: March 2013

Objective—
We demonstrated that inflammatory cells and intima–media thickening are increased in carotids exposed to low-blood flow in the SJL/J (SJL) strain compared with other mouse strains. We hypothesized that the extent of inflammation associated with intima–media thickening is a genetically regulated trait.

Approach and Results—

We performed a whole genome approach to measure leukocyte infiltration in the carotid intima as a quantitative trait in a genetic cross between C3HeB/FeJ (C3H/F) and SJL mice. Immunostaining for CD45
+
(a pan-specific leukocyte marker) was performed on carotids from C3H/F, SJL, F1, and N2 progeny to measure leukocyte infiltration. We identified a nearly significant quantitative trait locus for CD45
+
on chromosome (chr) 11 (17 cM, LOD=2.3; significance was considered at threshold
P
=0.05). Interval mapping showed that the CD45
+
locus on chr 11 accounted for 8% of the variation in the logarithm of odds backcross. Importantly, the CD45
+
locus colocalized with the intima-modifier 2 (
Im
2) locus, which controls 17% of intima variation. We created 2
Im
2 congenic lines of mice (C3H/F.SJL.11.1 and C3H/F.SJL.11.2) to better understand the regulation of intima–media thickening by the chr 11 locus. The C3H/F.SJL.11.1 congenic mouse showed ≈30% of the SJL trait, confirming that CD45
+
cell infiltration contributed to the intima trait.

Conclusions—

We discovered a novel locus on chr 11 that controls leukocyte infiltration in the carotid. Importantly, this locus overlaps with our previously published
Im
2 locus on chr 11. Our study reveals a potential mechanistic relationship between leukocyte infiltration and intima–media thickening in response to decreased blood flow.
Temperature Profiles and Lapse Rate Climatology in Altostratus and Nimbostratus Clouds Derived from GPS RO Data
Authors: Yang S. , Zou X. 
Published: March 2013

Abstract
Constellation Observing System for Meteorology, Ionosphere and Climate (COSMIC) radio occultation (RO) refractivity profiles in altostratus and nimbostratus clouds from 2007 to 2010 are first identified based on collocated CloudSat data. Vertical temperature profiles in these clouds are then retrieved from cloudy refractivity profiles. Contributions of cloud liquid water content and ice water content are also included in the retrieval algorithm. The temperature profiles and their lapse rates are compared with those from a standard GPS RO wet retrieval without including cloud effects. On average, the temperatures from cloudy retrieval are about 0.5–1.0 K warmer than the GPS RO wet retrieval, except for the altitudes near the nimbostratus base. The differences of temperature between the two methods are largest in summer and smallest in winter. The lapse rate in altostratus clouds is around 6.5°–7.5°C km−1 and does not vary greatly with height. On the contrary, the lapse rate increases significantly with height in nimbostratus clouds, from about 2.5°–3.5°C km−1 near the cloud base to about 5.0°–6.0°C km−1 at cloud center and 6.5°–7.5°C km−1 below the cloud top. Seasonal variability of lapse rate derived from the cloudy retrieval is larger than that derived from the wet retrieval. The lapse rate within clouds is smaller in summer and larger in winter. The mean lapse rate decreases with temperature in all seasons.
Evaluating Low-Cloud Simulation from an Upgraded Multiscale Modeling Framework Model. Part III: Tropical and Subtropical Cloud Transitions over the Northern Pacific
Authors: Cheng Anning , Xu Kuan-Man 
Published: March 2013

Abstract
An analysis of simulated cloud regime transitions along a transect from the subtropical California coast to the tropics for the northern summer season (June–August) is presented in this study. The Community Atmosphere Model, version 5 (CAM5), superparameterized CAM (SPCAM), and an upgraded SPCAM with intermediately prognostic higher-order closure (SPCAM-IPHOC) are used to perform global simulations by imposing climatological sea surface temperature and sea ice distributions. The seasonal-mean properties are compared with recent observations of clouds, radiation, and precipitation and with multimodel intercomparison results. There are qualitative agreements in the characteristics of cloud regimes along the transect among the three models. CAM5 simulates precipitation and shortwave radiative fluxes well but the stratocumulus-to-cumulus transition occurs too close to the coast of California. SPCAM-IPHOC simulates longwave radiative fluxes and precipitable water well, but with systematic biases in shortwave radiative fluxes. The broad, stronger ascending band in SPCAM is related to the large biases in the convective region but the characteristics of the stratocumulus region are still more realistic and the transition occurs slightly farther away from the coast than in CAM5. Even though SPCAM-IPHOC produces the most realistic seasonal-mean transition, it underestimates the mean gradient in low-cloud cover (LCC) across the mean transition location because of an overestimate of LCC in the transition and convective regions that shifts the transition locations farther from the coast. Analysis of two decoupling measures shows consistency in the mean location and the histogram of decoupling locations with those of LCC transition. CAM5, however, lacks such a consistency, suggesting a need for further refinement of its boundary layer cloud parameterization.
A Modeling Study of Irrigation Effects on Surface Fluxes and Land–Air–Cloud Interactions in the Southern Great Plains
Authors: Qian Yun , Huang Maoyi , Yang Ben , Berg Larry K. 
Published: March 2013

AbstractIn this study, the authors incorporate an operational-like irrigation scheme into the Noah land surface model as part of the Weather Research and Forecasting Model (WRF). A series of simulations, with and without irrigation, is conducted over the Southern Great Plains (SGP) for an extremely dry (2006) and wet (2007) year. The results show that including irrigation reduces model bias in soil moisture and surface latent heat (LH) and sensible heat (SH) fluxes, especially during a dry year. Irrigation adds additional water to the surface, leading to changes in the planetary boundary layer. The increase in soil moisture leads to increases in the surface evapotranspiration and near-surface specific humidity but decreases in the SH and surface temperature. Those changes are local and occur during daytime. There is an irrigation-induced decrease in both the lifting condensation level (ZLCL) and mixed-layer depth. The decrease in ZLCL is larger than the decrease in mixed-layer depth, suggesting an increasing probability of shallow clouds. The simulated changes in precipitation induced by irrigation are highly variable in space, and the average precipitation over the SGP region only slightly increases. A high correlation is found among soil moisture, SH, and ZLCL. Larger values of soil moisture in the irrigated simulation due to irrigation in late spring and summer persist into the early fall, suggesting that irrigation-induced soil memory could last a few weeks to months. The results demonstrate the importance of irrigation parameterization for climate studies and improve the process-level understanding on the role of human activity in modulating land–air–cloud interactions.
Estimation of the Effect of Eddies on Coastal El Niño Flows Using Along-Track Satellite Altimeter Data
Authors: Giunipero Emma M. , Clarke Allan J. 
Published: March 2013

Abstract
Previous work has shown that the El Niño sea level signal leaks through the gappy western equatorial Pacific to the coasts of western and southern Australia. South of about 22°S, in the region of the Leeuwin Current, the amplitude of this El Niño signal falls. Using coastal sea level measurements and along-track altimetry data from the Ocean Topography Experiment (TOPEX)/Poseidon, Jason-1, and OSTM/Jason-2 satellites, this study finds that the interannual divergence of the eddy momentum flux D′ is correlated with the southward along-shelf sea level amplitude decay, consistent with the eddies removing energy from the large-scale sea level signal. The quantity D′ is also correlated with the interannual flow with a surprisingly short dissipation time scale of only 2 days, much shorter than the interannual time scale.
A similar analysis off the western coast of South America, site of the originally named “El Niño” current, was carried out. Interannual sea level decay along the shelf edge is observed, and the interannual southward flow along the shelf edge is found to be highly positively correlated with the along-shelf sea level decay with a dissipation time scale of a few days. Dynamics similar to the Australian case likely apply.
Infants at Risk: Perinatal and Neonatal Factors
Authors: Lipsitt Lewis P. 
Published: March 2013

Studies have been reviewed to indicate that (a) prematurity and other perinatal hazards impose congenital constraints upon the behavior of the young infant, (b) experimental deficits within the earliest days and weeks of life can compound the risk, (c) infants who succumb to crib death (sudden infant death syndrome) have demonstrably more risk factors present in their prenatal and neonatal histories than matched controls, and (d) premature and other high-risk infants can benefit from early stimulation and learning experiences. Present indications are that the interdisciplinary field of infant behavior and development has just recently warmed to its urgent task of more completely documenting the full capabilities of infants, both normal and those at risk, and exploring the interactions of biological and experiential factors. The significance of infancy lies in its importance as a training period for the exercise of sensory capacities and congenital reflexes. The mutual dependence of experience and neurostructural development suggests that infancy is a period of critical learning experiences, from which the young child who traverses the period successfully will emerge capable of defending himself or herself against threats, and able to maximize the pleasures of sensation and of attachment to others.