bluuebunny/crossref_metadata_2025_split huggingface dataset:
SNP‐array reveals genome‐wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar)
Authors: Bourret Vincent , Kent Matthew P. , Primmer Craig R. , Vasemägi Anti , Karlsson Sten , Hindar Kjetil , McGinnity Philip , Verspoor Eric , Bernatchez Louis , Lien Sigbjørn 
Published: September 2012

AbstractAtlantic salmon (Salmo salar) is one of the most extensively studied fish species in the world due to its significance in aquaculture, fisheries and ongoing conservation efforts to protect declining populations. Yet, limited genomic resources have hampered our understanding of genetic architecture in the species and the genetic basis of adaptation to the wide range of natural and artificial environments it occupies. In this study, we describe the development of a medium‐density Atlantic salmon single nucleotide polymorphism (SNP) array based on expressed sequence tags (ESTs) and genomic sequencing. The array was used in the most extensive assessment of population genetic structure performed to date in this species. A total of 6176 informative SNPs were successfully genotyped in 38 anadromous and freshwater wild populations distributed across the species natural range. Principal component analysis clearly differentiated European and North American populations, and within Europe, three major regional genetic groups were identified for the first time in a single analysis. We assessed the potential for the array to disentangle neutral and putative adaptive divergence of SNP allele frequencies across populations and among regional groups. In Europe, secondary contact zones were identified between major clusters where endogenous and exogenous barriers could be associated, rendering the interpretation of environmental influence on potentially adaptive divergence equivocal. A small number of markers highly divergent in allele frequencies (outliers) were observed between (multiple) freshwater and anadromous populations, between northern and southern latitudes, and when comparing Baltic populations to all others. We also discuss the potential future applications of the SNP array for conservation, management and aquaculture.
Genomic scan for single nucleotide polymorphisms reveals patterns of divergence and gene flow between ecologically divergent species
Authors: Stölting Kai N. , Nipper Rick , Lindtke Dorothea , Caseys Celine , Waeber Stephan , Castiglione Stefano , Lexer Christian 
Published: September 2012

AbstractRecent advances in population genomics have triggered great interest in the genomic landscape of divergence in taxa with ‘porous’ species boundaries. One important obstable of previous studies of this topic was the low genomic coverage achieved. This issue can now be overcome by the use of ‘next generation’ or short‐read DNA‐sequencing approaches capable of assaying many thousands of single nucleotide polymorphisms (SNPs) in divergent species. We have scanned the ‘porous’ genomes of Populus alba and Populus tremula, two ecologically divergent hybridizing forest trees, using >38 000 SNPs assayed by restriction site associated DNA (RAD) sequencing. Windowed analyses indicate great variation in genetic divergence (e.g. the proportion of fixed SNPs) between species, and these results are unlikely to be strongly biased by genomic features of the Populus trichocarpa reference genome used for SNP calling. Divergence estimates were significantly autocorrelated (P < 0.01; Moran's I up to 0.6) along 11 of 19 chromosomes. Many of these autocorrelations involved low divergence blocks, thus suggesting that allele sharing was caused by recurrent gene flow rather than shared ancestral polymorphism. A conspicuous low divergence block of three megabases was detected on chromosome XIX, recently put forward as an incipient sex chromosome in Populus, and was largely congruent with introgression of mapped microsatellites in two natural hybrid zones (N > 400). Our results help explain the origin of the ‘genomic mosaic’ seen in these taxa with ‘porous’ genomes and suggest rampant introgression or extensive among‐species conservation of an incipient plant sex chromosome. RAD sequencing holds great promise for detecting patterns of divergence and gene flow in highly divergent hybridizing species.
NaxD is a deacetylase required for lipid A modification and Francisella pathogenesis
Authors: Llewellyn Anna C. , Zhao Jinshi , Song Feng , Parvathareddy Jyothi , Xu Qian , Napier Brooke A. , Laroui Hamed , Merlin Didier , Bina James E. , Cotter Peggy A. , Miller Mark A. , Raetz Christian R. H. , Weiss David S. 
Published: September 2012

SummaryModification of specific Gram‐negative bacterial cell envelope components, such as capsule, O‐antigen and lipid A, are often essential for the successful establishment of infection. Francisella species express lipid A molecules with unique characteristics involved in circumventing host defences, which significantly contribute to their virulence. In this study, we show that NaxD, a member of the highly conserved YdjC superfamily, is a deacetylase required for an important modification of the outer membrane component lipid A in Francisella. Mass spectrometry analysis revealed that NaxD is essential for the modification of a lipid A phosphate with galactosamine in Francisella novicida, a model organism for the study of highly virulent Francisella tularensis. Significantly, enzymatic assays confirmed that this protein is necessary for deacetylation of its substrate. In addition, NaxD was involved in resistance to the antimicrobial peptide polymyxin B and critical for replication in macrophages and in vivo virulence. Importantly, this protein is also required for lipid A modification in F. tularensis as well as Bordetella bronchiseptica. Since NaxD homologues are conserved among many Gram‐negative pathogens, this work has broad implications for our understanding of host subversion mechanisms of other virulent bacteria.
Pseudomonas aeruginosa lipopolysaccharide inhibits Candida albicans hyphae formation and alters gene expression during biofilm development
Authors: Bandara H.M.H.N. , K Cheung B.P. , Watt R.M. , Jin L.J. , Samaranayake L.P. 
Published: September 2012

SummaryElucidation of bacterial and fungal interactions in multispecies biofilms will have major impacts on understanding the pathophysiology of infections. The objectives of this study were to (i) evaluate the effect of Pseudomonas aeruginosa lipopolysaccharide (LPS) on Candida albicans hyphal development and transcriptional regulation, (ii) investigate protein expression during biofilm formation, and (iii) propose likely molecular mechanisms for these interactions. The effect of LPS on C. albicans biofilms was assessed by XTT‐reduction and growth curve assays, light microscopy, scanning electron microscopy (SEM), and confocal laser scanning microscopy (CLSM). Changes in candidal hypha‐specific genes (HSGs) and transcription factor EFG1 expression were assessed by real‐time polymerase chain reaction and two‐dimensional gel electrophoresis, respectively. Proteome changes were examined by mass spectrometry. Both metabolic activities and growth rates of LPS‐treated C. albicans biofilms were significantly lower (P < 0.05). There were higher proportions of budding yeasts in test biofilms compared with the controls. SEM and CLSM further confirmed these data. Significantly upregulated HSGs (at 48 h) and EFG1 (up to 48 h) were noted in the test biofilms (P < 0.05) but cAMP levels remained unaffected. Proteomic analysis showed suppression of candidal septicolysin‐like protein, potential reductase‐flavodoxin fragment, serine hydroxymethyltransferase, hypothetical proteins Cao19.10301(ATP7), CaO19.4716(GDH1), CaO19.11135(PGK1), CaO19.9877(HNT1) by P. aeruginosa LPS. Our data imply that bacterial LPS inhibit C. albicans biofilm formation and hyphal development. The P. aeruginosa LPS likely target glycolysis‐associated mechanisms during candidal filamentation.
Safe perioperative pediatric care around the world
Authors: Ivani Giorgio , Walker Isabeau , Enright Angela 
Published: September 2012

SummaryPediatric anesthesia is no longer a small subspecialty, but an important sector where developments in the new century have brought effective and safe management to children in the perioperative period. Unfortunately, what is common daily practice in the high‐income countries with all the guidelines, checklists, instruments, and dedicated pediatric anesthesiologists is often only a dream in the low‐ and middle‐income countries where the basic anesthesia services for improving the high rate of morbidity and mortality still are lacking. Anesthesia given by nonphysicians, with no monitoring, lack of elementary supplies, poor control of infections and hemorrhage, and no water or electricity are very often the ‘usual’ conditions. The World Health Organization is working hard to offer teams, basic equipments, and teaching and what is needed to offer children of these countries the same opportunities given in the industrialized countries. Other projects such as the Lifebox Project have a similar aim. This paper outlines some of what organizations are doing around the world, with different strategies all having the same target: safe pediatric anesthesia.
Pediatric airway management: current practices and future directions
Authors: Sunder Rani A. , Haile Dawit T. , Farrell Patrick T. , Sharma Anshuman 
Published: September 2012

SummaryManagement of a pediatric airway can be a challenge, especially for the nonpediatric anesthesiologists. Structured algorithms for an unexpected difficult pediatric airway have been missing so far. A recent step wise algorithm, based on the Difficult Airway society (DAS) adult protocol, is a step in the right direction. There have been some exciting advances in development of pediatric extra‐glottic devices for maintaining ventilation, and introduction of pediatric versions of new ‘non line of sight’ laryngoscopes and optical stylets. The exact role of these devices in routine and emergent situations is still evolving. Recent advances in simulation technology has become a valuable tool in imparting psychomotor and procedural skills to trainees and allied healthcare workers. Moving toward the goal of eliminating serious adverse events during the management of routine and difficult pediatric airway, authors propose that institutions develop a dedicated Difficult Airway Service comprising of a team of experts in advanced airway management.
Identification of an additional protein involved in mannan biosynthesis
Authors: Wang Yan , Mortimer Jennifer C. , Davis Jonathan , Dupree Paul , Keegstra Kenneth 
Published: September 2012

SummaryGalactomannans comprise a β‐1,4‐mannan backbone substituted with α‐1,6‐galactosyl residues. Genes encoding the enzymes that are primarily responsible for backbone synthesis and side‐chain addition of galactomannans were previously identified and characterized. To identify additional genes involved in galactomannan biosynthesis, we previously performed deep EST profiling of fenugreek (Trigonella foenum‐graecum L.) seed endosperm, which accumulates large quantities of galactomannans as a reserve carbohydrate during seed development. One of the candidate genes encodes a protein that is likely to be a glycosyltransferase. Because this protein is involved in mannan biosynthesis, we named it ‘mannan synthesis‐related’ (MSR). Here, we report the characterization of a fenugreek MSR gene (TfMSR) and its two Arabidopsis homologs, AtMSR1 and AtMSR2. TfMSR was highly and specifically expressed in the endosperm. TfMSR, AtMSR1 and AtMSR2 proteins were all determined to be localized to the Golgi by fluorescence confocal microscopy. The level of mannosyl residues in stem glucomannans decreased by approximately 40% for Arabidopsis msr1 single T‐DNA insertion mutants and by more than 50% for msr1 msr2 double mutants, but remained unchanged for msr2 single mutants. In addition, in vitro mannan synthase activity from the stems of msr1 single and msr1 msr2 double mutants also decreased. Expression of AtMSR1 or AtMSR2 in the msr1 msr2 double mutant completely or partially restored mannosyl levels. From these results, we conclude that the MSR protein is important for mannan biosynthesis, and offer some ideas about its role.
Effects of different parameters in the fast scanning method for HIFU treatment
Authors: Qiao Shan , Shen Guofeng , Bai Jingfeng , Chen Yazhu 
Published: September 2012

Purpose:High‐intensity focused ultrasound is a promising method for the noninvasive treatment of benign and malignant tumors. This study analyzes the effects of scanning path, applied power, and geometric characteristics of the transducer on ablation using fast scanning method, a new scanning method that uses high‐intensity focused ultrasound at different blood perfusion levels.Methods:Two transducers, six scanning paths, and three focal patterns were used to examine the ablation results of the fast scanning method using power densities from 1.35 × 107 W/m3 to 4.5 × 107 W/m3 and blood perfusion rates from 2 × 10−3 ml/ml/s to 16 × 10−3 ml/ml/s. The Pennes equation was solved using the finite‐difference time‐domain method to simulate the heating procedure.Results:Based on the results of the fast‐scanning method, the different scanning paths exhibited small effect on the total treatment time supported by both simulation and least‐square fit. Similar‐sized lesions can result from the five different repeated paths, whereas a random path may lead to relative large fluctuations in ablation volume because of asymmetry of the lesions. Higher power levels increase the lesion volume and decrease the treatment time required for ablating a target area using the fast scanning method, whereas increased blood perfusion has the opposite effect on ablation volume and treatment time. A symmetric lesion can be produced through fast scanning method using a 65‐element and a 90‐element transducer. However, lesion production using the same operation scheme differs between the two transducers.Conclusions:Unlike traditional scanning methods, fast scanning method produces a planned lesion regardless of scanning path, as long as the path consists of repeated subsequences. This attribute makes fast scanning method an easy‐operation scheme that produces relatively large symmetric lesions in homogeneous tissues. Applied power is the most important factor; however, high blood perfusion levels can limit or even hinder the full ablation of the target area. Therefore, tissue perfusion and transducer type should be given special attention to ensure the success and safety of ablation treatment.
Segmentation of artifacts and anatomy in CT metal artifact reduction
Authors: Karimi Seemeen , Cosman Pamela , Wald Christoph , Martz Harry 
Published: September 2012

Purpose:Metal objects present in x‐ray computed tomography (CT) scans are accompanied by physical phenomena that render CT projections inconsistent with the linear assumption made for analytical reconstruction. The inconsistencies create artifacts in reconstructed images. Metal artifact reduction algorithms replace the inconsistent projection data passing through metals with estimates of the true underlying projection data, but when the data estimates are inaccurate, secondary artifacts are generated. The secondary artifacts may be as unacceptable as the original metal artifacts; therefore, better projection data estimation is critical. This research uses computer vision techniques to create better estimates of the underlying projection data using observations about the appearance and nature of metal artifacts.Methods:The authors developed a method of estimating underlying projection data through the use of an intermediate image, called the prior image. This method generates the prior image by segmenting regions of the originally reconstructed image, and discriminating between regions that are likely to be metal artifacts and those that are likely to represent anatomical structures. Regions identified as metal artifact are replaced with a constant soft‐tissue value, while structures such as bone or air pockets are preserved. This prior image is reprojected (forward projected), and the reprojections guide the estimation of the underlying projection data using previously published interpolation techniques. The algorithm is tested on head CT test cases containing metal implants and compared against existing methods.Results:Using the new method of prior image generation on test images, metal artifacts were eliminated or reduced and fewer secondary artifacts were present than with previous methods. The results apply even in the case of multiple metal objects, which is a challenging problem. The authors did not observe secondary artifacts that were comparable to or worse than the original metal artifacts, as sometimes occurred with the other methods. The accuracy of the prior was found to be more critical than the particular interpolation method.Conclusions:Metals produce predictable artifacts in CT images of the head. Using the new method, metal artifacts can be discriminated from anatomy, and the discrimination can be used to reduce metal artifacts.
Is RapidArc more susceptible to delivery uncertainties than dynamic IMRT?
Authors: Betzel Gregory T. , Yi Byong Yong , Niu Ying , Yu Cedric X. 
Published: September 2012

Purpose:Rotational IMRT has been adopted by many clinics for its promise to deliver treatments in a shorter amount of time than other conventional IMRT techniques. In this paper, the authors investigate whether RapidArc is more susceptible to delivery uncertainties than dynamic IMRT using fixed fields.Methods:Dosimetric effects of delivery uncertainties in dose rate, gantry angle, and MLC leaf positions were evaluated by incorporating these uncertainties into RapidArc and sliding window IMRT (SW IMRT) treatment plans for five head‐and‐neck and five prostate cases. Dose distributions and dose‐volume histograms of original and modified plans were recalculated and compared using Gamma analysis and dose indices of planned treatment volumes (PTV) and organs at risk (OAR). Results of Gamma analyses using passing criteria ranging from 1%–1 mm up to 5%–3 mm were reported.Results:Systematic shifts in MLC leaf bank positions of SW‐IMRT cases resulted in 2–4 times higher average percent differences than RapidArc cases. Uniformly distributed random variations of 2 mm for active MLC leaves had a negligible effect on all dose distributions. Sliding window cases were much more sensitive to systematic shifts in gantry angle. Dose rate variations during RapidArc must be much larger than typical machine tolerances to affect dose distributions significantly; dynamic IMRT is inherently not susceptible to such variations.Conclusions:RapidArc deliveries were found to be more tolerant to variations in gantry position and MLC leaf position than SW IMRT. This may be attributed to the fact that the average segmental field size or MLC leaf opening is much larger for RapidArc. Clinically acceptable treatments may be delivered successfully using RapidArc despite large fluctuations in dose rate and gantry position.
Communication avoiding successive band reduction
Authors: Ballard Grey , Demmel James , Knight Nicholas 
Published: September 2012

The running time of an algorithm depends on both arithmetic and communication (i.e., data movement) costs, and the relative costs of communication are growing over time. In this work, we present both theoretical and practical results for tridiagonalizing a symmetric band matrix: we present an algorithm that asymptotically reduces communication, and we show that it indeed performs well in practice.
The tridiagonalization of a symmetric band matrix is a key kernel in solving the symmetric eigenvalue problem for both full and band matrices. In order to preserve sparsity, tridiagonalization routines use annihilate-and-chase procedures that previously have suffered from poor data locality. We improve data locality by reorganizing the computation, asymptotically reducing communication costs compared to existing algorithms. Our sequential implementation demonstrates that avoiding communication improves runtime even at the expense of extra arithmetic: we observe a 2x speedup over Intel MKL while doing 43% more floating point operations.
Our parallel implementation targets shared-memory multicore platforms. It uses pipelined parallelism and a static scheduler while retaining the locality properties of the sequential algorithm. Due to lightweight synchronization and effective data reuse, we see 9.5x scaling over our serial code and up to 6x speedup over the PLASMA library, comparing parallel performance on a ten-core processor.
DOJ
Authors: Eom Yong hun , Yang Stephen , Jenista James C. , Demsky Brian 
Published: September 2012

We present Dynamic Out-of-Order Java (DOJ), a dynamic parallelization approach. In DOJ, a developer annotates code blocks as tasks to decouple these blocks from the parent execution thread. The DOJ compiler then analyzes the code to generate heap examiners that ensure the parallel execution preserves the behavior of the original sequential program. Heap examiners dynamically extract heap dependences between code blocks and determine when it is safe to execute a code block.
We have implemented DOJ and evaluated it on twelve benchmarks. We achieved an average compilation speedup of 31.15 times over OoOJava and an average execution speedup of 12.73 times over sequential versions of the benchmarks.
Lock cohorting
Authors: Dice David , Marathe Virendra J. , Shavit Nir 
Published: September 2012

Multicore machines are quickly shifting to NUMA and CC-NUMA architectures, making scalable NUMA-aware locking algorithms, ones that take into account the machines' non-uniform memory and caching hierarchy, ever more important. This paper presents lock cohorting, a general new technique for designing NUMA-aware locks that is as simple as it is powerful.
Lock cohorting allows one to transform any spin-lock algorithm, with minimal non-intrusive changes, into scalable NUMA-aware spin-locks. Our new cohorting technique allows us to easily create NUMA-aware versions of the TATAS-Backoff, CLH, MCS, and ticket locks, to name a few. Moreover, it allows us to derive a CLH-based cohort abortable lock, the first NUMA-aware queue lock to support abortability.
We empirically compared the performance of cohort locks with prior NUMA-aware and classic NUMA-oblivious locks on a synthetic micro-benchmark, a real world key-value store application memcached, as well as the libc memory allocator. Our results demonstrate that cohort locks perform as well or better than known locks when the load is low and significantly out-perform them as the load increases.
Adapting the polyhedral model as a framework for efficient speculative parallelization
Authors: Jimborean Alexandra , Clauss Philippe , Pradelle Benoît , Mastrangelo Luis , Loechner Vincent 
Published: September 2012

In this paper, we present a Thread-Level Speculation (TLS) framework whose main feature is to be able to speculatively parallelize a sequential loop nest in various ways, by re-scheduling its iterations. The transformation to be applied is selected at runtime with the goal of minimizing the number of rollbacks and maximizing performance. We perform code transformations by applying the polyhedral model that we adapted for speculative and runtime code parallelization. For this purpose, we design a parallel code pattern which is patched by our runtime system according to the profiling information collected on some execution samples. Adaptability is ensured by considering chunks of code of various sizes, that are launched successively, each of which being parallelized in a different manner, or run sequentially, depending on the currently observed behavior for accessing memory.
We show on several benchmarks that our framework yields good performance on codes which could not be handled efficiently by previously proposed TLS systems.