bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computer-based quantification of the mean Achilles tendon thickness in ultrasound images: effect of tendinosis
Authors: Syha R , Peters M , Birnesser H , Niess A , Hirschmueller A , Dickhuth H-H , Sandrock M 
Published: June 2007

Background:B-mode measurement of the sagital diameter of the Achilles tendon based on a manual tracing (MT) procedure is partly dependent on the subjectivity of the reader. The aim of this study is to establish a standardised automatic procedure to differentiate between normal and chronically degenerated tendons. For this comparison, the tracing results of the tendon boundaries of an automatic identification (AI) process, already established with the detection of intima–media thickness, are compared with computer-assisted MT.Methods:The detection of the tendon boundaries was performed in 115 ultrasound images including the cranial border of the calcaneal tuberosity. The measured section (starting point 4 cm away from the anterior boundary of the calcaneal tuberosity) amounted to 3 cm, and was divided into three sub-segments (1 cm each). Intra- and inter-reader/observer variability for mean and maximum Achilles tendon thickness (ATT) with AI and MT were evaluated. A normal group and a group with clinically diagnosed chronic tendon degeneration had mean and maximum ATT readings compared.Results:Using MT, the intra- and inter-reader variability was 3.0% and 6.8%, respectively, using AI the variability was 1.6% and 3.9%, respectively. Mean and maximum ATT were measured systematically lower by AI compared to MT in all regions by 0.4 mm. The AI procedure was most accurate in the second segment. The mean ATT and maximum ATT were correctly detected in 93.9% and 96.6% of the images.Conclusion:The AI procedure detected the ATT with a high level of precision in all three segments. The most robust measurement was reached in the second segment. It eliminates most of the inter-/intra-reader variability in ATT measurement using MT. We suggest this new method could be a new gold standard for quantification of chronic disorder in Achilles tendons.
ANGULAR POWER SPECTRUM IN MODULAR INVARIANT INFLATION MODEL
Authors: HAYASHI MITSUO J. , HIRAI SHIRO , TAKAMI TOMOYUKI , OKAMEI YUSUKE , TAKAGI KENJI , WATANABE TOMOKI 
Published: June 2007

We propose a scalar potential of inflation, motivated by modular invariant supergravity, and compute the angular power spectra of the adiabatic density perturbations that result from this model. The potential consists of three scalar fields, S, Y and T, together with two free parameters. By fitting the parameters to cosmological data at the fixed point T = 1, we find that the potential behaves like the single-field potential of S, which slowly rolls down along the minimized trajectory in Y. We further show that the inflation predictions corresponding to this potential provide a good fit to the recent three-year WMAP data, e.g. the spectral index ns = 0.951. The TT and TE angular power spectra obtained from our model almost completely coincide with the corresponding results obtained from the ΛCDM model. We conclude that our model is considered to be an adequate theory of inflation that explains the present data, although the theoretical basis of this model should be further explicated.
Allocating architected registers through differential encoding
Authors: Zhuang Xiaotong , Pande Santosh 
Published: June 2007

Micro-architecture designers are very cautious about expanding the number of architected and exposed registers in the instruction set because increasing the register field adds to the code size, raises the I-cache and memory pressure, and may complicate the processor pipeline. Especially for low-end processors, encoding space could be extremely limited due to area and power considerations. On the other hand, the number of architected registers exposed to the compiler could directly affect the effectiveness of compiler analysis and optimization. For high-performance computers, register pressure can be higher than the available registers in some regions. This could be due to optimizations like aggressive function inlining, software pipelining, etc. The compiler cannot effectively perform compilation and optimization if only a small number of registers are exposed through the ISA. Therefore, it is crucial that more architected registers are available at the compiler's disposal, without expanding the code size significantly.
In this article, we devise a new register encoding scheme, called differential encoding, that allows more registers to be addressed in the operand field of instructions than the direct encoding currently being used. We show that this can be implemented with very low overhead. Based upon differential encoding, we apply it in several ways such that the extra architected registers can benefit the performance. Three schemes are devised to integrate differential encoding with register allocation. We demonstrate that differential register allocation is helpful in improving the performance of both high-end and low-end processors. Moreover, we can combine it with software pipelining to provide more registers and reduce spills.
Our results show that differential encoding significantly reduces the number of spills and speeds-up program execution. For a low-end configuration, we achieve over 14% speedup while keeping code size almost unaffected. For a high-end VLIW in-order machine, it can significantly speed-up loops with high register pressure (about 80% speedup) and the overall speedup is about 15%. Moreover, our scheme can be applied in an adaptive manner, making its overhead much smaller.
An empirical study of static program slice size
Authors: Binkley David , Gold Nicolas , Harman Mark 
Published: June 2007

This article presents results from a study of all slices from 43 programs, ranging up to 136,000 lines of code in size. The study investigates the effect of five aspects that affect slice size. Three slicing algorithms are used to study two algorithmic aspects: calling-context treatment and slice granularity. The remaining three aspects affect the upstream dependencies considered by the slicer. These include collapsing structure fields, removal of dead code, and the influence of points-to analysis.
The results show that for the most precise slicer, the average slice contains just under one-third of the program. Furthermore, ignoring calling context causes a 50% increase in slice size, and while (coarse-grained) function-level slices are 33% larger than corresponding statement-level slices, they may be useful predictors of the (finer-grained) statement-level slice size. Finally, upstream analyses have an order of magnitude less influence on slice size.
Saturn
Authors: Xie Yichen , Aiken Alex 
Published: June 2007

This article presents Saturn, a general framework for building precise and scalable static error detection systems. Saturn exploits recent advances in Boolean satisfiability (SAT) solvers and is path sensitive, precise down to the bit level, and models pointers and heap data. Our approach is also highly scalable, which we achieve using two techniques. First, for each program function, several optimizations compress the size of the Boolean formulas that model the control flow and data flow and the heap locations accessed by a function. Second, summaries in the spirit of type signatures are computed for each function, allowing interprocedural analysis without a dramatic increase in the size of the Boolean constraints to be solved.
We have experimentally validated our approach by conducting two case studies involving a Linux lock checker and a memory leak checker. Results from the experiments show that our system scales well, parallelizes well, and finds more errors with fewer false positives than previous static error detection systems.
Requirements for scalable access control and security management architectures
Authors: Keromytis Angelos D. , Smith Jonathan M. 
Published: June 2007

Maximizing local autonomy by delegating functionality to end nodes when possible (the end-to-end design principle) has led to a scalable Internet. Scalability and the capacity for distributed control have unfortunately not extended well to resource access-control policies and mechanisms. Yet management of security is becoming an increasingly challenging problem in no small part due to scaling up of measures such as number of users, protocols, applications, network elements, topological constraints, and functionality expectations.
In this article, we discuss scalability challenges for traditional access-control mechanisms at the architectural level and present a set of fundamental requirements for authorization services in large-scale networks. We show why existing mechanisms fail to meet these requirements and investigate the current design options for a scalable access-control architecture.
We argue that the key design options to achieve scalability are the choice of the representation of access control policy, the distribution mechanism for policy, and the choice of the access-rights revocation scheme. Although these ideas have been considered in the past, current access-control systems in use continue to use simpler but restrictive architectural models. With this article, we hope to influence the design of future access-control systems towards more decentralized and scalable mechanisms.
Improving fairness, throughput and energy-efficiency on a chip multiprocessor through DVFS
Authors: Kondo Masaaki , Sasaki Hiroshi , Nakamura Hiroshi 
Published: June 2007

Recently, a single chip multiprocessor (CMP) is becoming an attractive architecture for improving throughput of program execution. In CMPs, multiple processor cores share several hardware resources such as cache memory and memory bus. Therefore, the resource contention significantly degrades performance of each thread and also loses fairness between threads.
In this paper, we propose a Dynamic Frequency and Voltage Scaling (DVFS) algorithm for improving total instruction throughput, fairness, and energy efficiency of CMPs. The proposed technique periodically observes the utilization ratio of shared resources and controls the frequency and the voltage of each processor core individually to balance the ratio between threads. We evaluate our technique and the evaluation results show that fairness between threads are greatly improved by the technique. Moreover, the total instruction throughput increases in many cases while reducing energy consumption.
Nucleol - a minimal list processor
Authors: Nievergelt J. , Fischer F. , Irland M. I. , Sidlo J. R. 
Published: June 2007

NUCLEOL is a low-level list processor designed as a basis in terms of which higher-level list- and string-processing languages could be implemented easily and efficiently. Hence its design aims at:
a) Simplicity
b) Complete and concise description
c) General data structures and a small, well-chosen set of primitive operations
d) A scheme for implementation which makes it easy to transfer the system from one computer to another.
The system is currently implemented as a PL/1 program.
P2P replica synchronization with vector sets
Authors: Malkhi Dahlia , Novik Lev , Purcell Chris 
Published: June 2007

This paper describes an enhanced replica synchronization mechanism built in Microsoft's WinFS replica management system.
The system reconciles autonomously-operating replicas in a completely peer-to-peer manner, without employing a central master or locking. The main challenge is for two replicas to exchange meta-information efficiently about (potentially numerous) data objects in order to discover what updates they are missing, and detect conflicts.
The paper introduces a novel bundling mechanisms called VS, that groups together multiple objects and represents their state in a single version-vector. VS provides improved storage and communication overheads over previously known optimistic replication schemes, in the following sense. Under normal, low-fault situations, it maintains and communicates as little as a single version vector in order to represent precedence ordering of the entire set of data objects. Moreover, under settings of severe communication disruptions, VS degenerates to no worse than a single vector per object. This dramatically improves the complexities described in a preliminary write-up of the WinFS replication scheme.
The VS mechanism has potentially wide applicability as a mechanism for compactly handling synchronization of arbitrarily overlapping groups of objects.
US Public Diplomacy: A Cold War Success Story?
Authors: Kelley John Robert 
Published: June 2007

AbstractThe post-'9/11' revival of interest in US public diplomacy encompasses a wide variety of opinions, all overwhelmingly critical. In view of falling global favourability towards and the foreign policy challenges of the United States during this period, the purveyors of these opinions ultimately agree that US public diplomacy efforts are flawed and ineffective. Of these critical observations, it is interesting to track a thread of logic that yearns for the restoration of public diplomacy's Cold War-era standing, which holds that the spread of liberal democracy behind the Berlin Wall owes a debt to the Voice of America and Radio Free Europe, that cultural exchanges with influential members of Soviet society helped to create the groundswell that undermined the communist regime, and that public diplomats made these outcomes possible by being equipped with the necessary tools of statecraft, as well as by wielding an important measure of influence over policy-makers. The fall of the Soviet Union merely underscores their notion that public diplomacy during the Cold War was a success. It would thus seem that the problems of today could be remedied by adopting lessons from the past. This article explores the viability of this claim by reviewing the ongoing debate on how the historical memory and lessons of Cold War-era public diplomacy may be applied to the challenges of the post-'9/11' era. Of particular importance is ascertaining the degree to which the Cold War's campaigns of information, influence and engagement could be viewed as a success. By subdividing public diplomacy's activities in these ways, greater potential exists to attribute these activities to more compelling determinations of success or failure.
Cytidine monophospho-N-acetylneuraminic acid hydroxylase (CMAH) mutations associated with the domestic cat AB blood group
Authors: Bighignoli Barbara , Niini Tirri , Grahn Robert A , Pedersen Niels C , Millon Lee V , Polli Michele , Longeri Maria , Lyons Leslie A 
Published: June 2007

AbstractBackgroundThe cat has one common blood group with two major serotypes, blood type A that is dominant to type B. A rare type AB may also be allelic and is suspected to be recessive to A and dominant to B. Cat blood type antigens are defined, N-glycolylneuraminic acid (NeuGc) is associated with type A and N-acetylneuraminic acid (NeuAc) with type B. The enzymecytidine monophospho-N-acetylneuraminic acid hydroxylase(CMAH) determines the sugar bound to the red cell by converting NeuAc to NeuGc. Thus, mutations inCMAHmay cause the A and B blood types.ResultsGenomic sequence ofCMAHfrom eight cats and the cDNA of four cats representing all blood types were analyzed to identify causative mutations. DNA variants consistent with the blood types were genotyped in over 200 cats. Five SNPs and an indel formed haplotypes that were consistent with each blood type.ConclusionMutations in type B cats likely disrupt the gene function ofCMAH, leading to a predominance of NeuAc. Type AB concordant variants were not identified, however, cDNA species suggest an alternative allele that activates a downstream start site, leading to a CMAH protein that would be altered at the 5' region. The cat AB blood group system is proposed to be designated by three alleles,A>aab>b. TheAandb CMAHalleles described herein can distinguish type A and type B cats without blood sample collections.CMAHrepresents the first blood group gene identified outside of non-human primates and humans.
Characterization of expressed sequence tags obtained by SSH during somatic embryogenesis in Cichorium intybus L
Authors: Legrand Sylvain , Hendriks Theo , Hilbert Jean-Louis , Quillet Marie-Christine 
Published: June 2007

Abstract

Background
Somatic embryogenesis (SE) is an asexual propagation pathway requiring a somatic-to-embryonic transition of differentiated somatic cells toward embryogenic cells capable of producing embryos in a process resembling zygotic embryogenesis. In chicory, genetic variability with respect to the formation of somatic embryos was detected between plants from a population of Cichorium intybus L. landrace Koospol. Though all plants from this population were self incompatible, we managed by repeated selfing to obtain a few seeds from one highly embryogenic (E) plant, K59. Among the plants grown from these seeds, one plant, C15, was found to be non-embryogenic (NE) under our SE-inducing conditions. Being closely related, we decided to exploit the difference in SE capacity between K59 and its descendant C15 to study gene expression during the early stages of SE in chicory.

Results
Cytological analysis indicated that in K59 leaf explants the first cell divisions leading to SE were observed at day 4 of culture. In contrast, in C15 explants no cell divisions were observed and SE development seemed arrested before cell reactivation. Using mRNAs isolated from leaf explants from both genotypes after 4 days of culture under SE-inducing conditions, an E and a NE cDNA-library were generated by SSH. A total of 3,348 ESTs from both libraries turned out to represent a maximum of 2,077 genes. In silico subtraction analysis sorted only 33 genes as differentially expressed in the E or NE genotype, indicating that SSH had resulted in an effective normalisation. Real-time RT-PCR was used to verify the expression levels of 48 genes represented by ESTs from either library. The results showed preferential expression of genes related to protein synthesis and cell division in the E genotype, and related to defence in the NE genotype.

Conclusion
In accordance with the cytological observations, mRNA levels in explants from K59 and C15 collected at day 4 of SE culture reflected differential gene expression that presumably are related to processes accompanying early stages of direct SE. The E and NE library obtained thus represent important tools for subsequent detailed analysis of molecular mechanisms underlying this process in chicory, and its genetic control.
Homologous high-throughput expression and purification of highly conserved E coli proteins
Authors: Ergin Asgar , Büssow Konrad , Sieper Joachim , Thiel Andreas , Duchmann Rainer , Adam Thomas 
Published: June 2007

Abstract

Background
Genetic factors and a dysregulated immune response towards commensal bacteria contribute to the pathogenesis of Inflammatory Bowel Disease (IBD). Animal models demonstrated that the normal intestinal flora is crucial for the development of intestinal inflammation. However, due to the complexity of the intestinal flora, it has been difficult to design experiments for detection of proinflammatory bacterial antigen(s) involved in the pathogenesis of the disease. Several studies indicated a potential association of E. coli with IBD. In addition, T cell clones of IBD patients were shown to cross react towards antigens from different enteric bacterial species and thus likely responded to conserved bacterial antigens. We therefore chose highly conserved E. coli proteins as candidate antigens for abnormal T cell responses in IBD and used high-throughput techniques for cloning, expression and purification under native conditions of a set of 271 conserved E. coli proteins for downstream immunologic studies.

Results
As a standardized procedure, genes were PCR amplified and cloned into the expression vector pQTEV2 in order to express proteins N-terminally fused to a seven-histidine-tag. Initial small-scale expression and purification under native conditions by metal chelate affinity chromatography indicated that the vast majority of target proteins were purified in high yields. Targets that revealed low yields after purification probably due to weak solubility were shuttled into Gateway (Invitrogen) destination vectors in order to enhance solubility by N-terminal fusion of maltose binding protein (MBP), N-utilizing substance A (NusA), or glutathione S-transferase (GST) to the target protein. In addition, recombinant proteins were treated with polymyxin B coated magnetic beads in order to remove lipopolysaccharide (LPS). Thus, 73% of the targeted proteins could be expressed and purified in large-scale to give soluble proteins in the range of 500 μg.

Conclusion
Here, we report a cost-efficient procedure to produce around 200 soluble recombinant E. coli proteins in large-scale, including removal of LPS by polymyxin B coated beads for subsequent use of the proteins in downstream immunological studies.
Androgen-regulated genes differentially modulated by the androgen receptor coactivator L-dopa decarboxylase in human prostate cancer cells
Authors: Margiotti Katia , Wafa Latif A , Cheng Helen , Novelli Giuseppe , Nelson Colleen C , Rennie Paul S 
Published: June 2007

AbstractBackgroundThe androgen receptor is a ligand-induced transcriptional factor, which plays an important role in normal development of the prostate as well as in the progression of prostate cancer to a hormone refractory state. We previously reported the identification of a novel AR coactivator protein, L-dopa decarboxylase (DDC), which can act at the cytoplasmic level to enhance AR activity. We have also shown that DDC is a neuroendocrine (NE) marker of prostate cancer and that its expression is increased after hormone-ablation therapy and progression to androgen independence. In the present study, we generated tetracycline-inducible LNCaP-DDC prostate cancer stable cells to identify DDC downstream target genes by oligonucleotide microarray analysis.ResultsComparison of induced DDC overexpressing cells versus non-induced control cell lines revealed a number of changes in the expression of androgen-regulated transcripts encoding proteins with a variety of molecular functions, including signal transduction, binding and catalytic activities. There were a total of 35 differentially expressed genes, 25 up-regulated and 10 down-regulated, in the DDC overexpressing cell line. In particular, we found a well-known androgen induced gene,TMEPAI, which wasup-regulated in DDC overexpressing cells, supporting its known co-activation function. In addition, DDC also further augmented the transcriptional repression function of AR for a subset of androgen-repressed genes. Changes in cellular gene transcription detected by microarray analysis were confirmed for selected genes by quantitative real-time RT-PCR.ConclusionTaken together, our results provide evidence for linking DDC action with AR signaling, which may be important for orchestrating molecular changes responsible for prostate cancer progression.