bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trace-based derivation of a scalable lock-free stack algorithm
Authors: Groves Lindsay , Colvin Robert 
Published: October 2008

Abstract
We show how a sophisticated, lock-free concurrent stack implementation can be derived from an abstract specification in a series of verifiable steps. The algorithm is based on the scalable stack algorithm of Hendler et al. (Proceedings of the sixteenth annual ACM symposium on parallel algorithms, 27–30 June 2004, Barcelona, Spain, pp 206–215), which allows push and pop operations to be paired off and eliminated without affecting the central stack, thus reducing contention on the stack, and allowing multiple pairs of push and pop operations to be performed in parallel. Our algorithm uses a simpler data structure than Hendler, Shavit and Yerushalmi’s, and avoids an ABA problem. We first derive a simple lock-free stack algorithm using a linked-list implementation, and discuss issues related to memory management and the ABA problem. We then add an abstract model of the elimination process, from which we derive our elimination algorithm. This allows the basic algorithmic ideas to be separated from implementation details, and provides a basis for explaining and comparing different variants of the algorithm. We show that the elimination stack algorithm is linearisable by showing that any execution of the implementation can be transformed into an equivalent execution of an abstract model of a linearisable stack. Each step in the derivation is either a data refinement which preserves the level of atomicity, an operational refinement which may alter the level of atomicity, or a refactoring step which alters the structure of the system resulting from the preceding derivation. We verify our refinements using an extension of Lipton’s reduction method, allowing concurrent and non-concurrent aspects to be considered separately.
Gene expression profiling of human hibernating myocardium: Increased expression of B‐type natriuretic peptide and proenkephalin in hypocontractile vs normally‐contracting regions of the heart
Authors: Prasad Sanjay K. , Clerk Angela , Cullingford Timothy E. , Chen Alexander W.Y. , Kemp Timothy J. , Cannell Timothy M. , Cowie Martin R. , Petrou Mario 
Published: October 2008

AbstractA greater understanding of the molecular basis of hibernating myocardium may assist in identifying those patients who would most benefit from revascularization. Paired heart biopsies were taken from hypocontractile and normally‐contracting myocardium (identified by cardiovascular magnetic resonance) from 6 patients with chronic stable angina scheduled for bypass grafting. Gene expression profiles of hypocontractile and normally‐contracting samples were compared using Affymetrix microarrays. The data for patients with confirmed hibernating myocardium were analysed separately and a different, though overlapping, set (up to 380) of genes was identified which may constitute a molecular fingerprint for hibernating myocardium. The expression of B‐type natriuretic peptide (BNP) was increased in hypocontractile relative to normally‐contracting myocardium. The expression of BNP correlated most closely with the expression of proenkephalin and follistatin 3, which may constitute additional heart failure markers. Our data illustrate differential gene expression in hypocontractile and/hibernating myocardium relative to normally‐contracting myocardium within individual human hearts. Changes in expression of these genes, including increased relative expression of natriuretic and other factors, may constitute a molecular signature for hypocontractile and/or hibernating myocardium.
A microstep control approach for a millimeter-sized omni-directional mobile microrobot actuated by 3-mm-electromagnetic micromotors
Authors: Li Jianghao , Li Zhenbo , Chen Jiapin 
Published: October 2008

SUMMARYThis paper presents a novel microstep control approach for improving the positioning precision of a millimeter-sized omni-directional mobile microrobot. The microrobot that is designed for microassembly in a microfactory is driven by three electromagnetic micromotors. The structures of both the microrobot and the micromotor are described in the paper. The torque vectors synthesis method (TVSM) is developed and the torque self-balance principle (TSBP) is employed to realize the microstep control. The control circuit that needs a complex digital logic is devised with a complex programmable logic device (CPLD). The experiments using a hard disk and the real microrobot demonstrated the validity and performance of TVSM and TSBP. And the angular step precision of the microrobot is increased by three times compared to the normal control.
Transactional events
Authors: DONNELLY KEVIN , FLUET MATTHEW 
Published: October 2008

AbstractConcurrent programs require high-level abstractions in order to manage complexity and enable compositional reasoning. In this paper, we introduce a novel concurrency abstraction, dubbedtransactional events, which combines first-class synchronous message passing events with all-or-nothing transactions. This combination enables simple solutions to interesting problems in concurrent programming. For example, guarded synchronous receive can be implemented as an abstract transactional event, whereas in other languages it requires a non-abstract, non-modular protocol. As another example, three-way rendezvous can be implemented as an abstract transactional event, which is impossible using first-class events alone. Both solutions are easy to code and easy to reason about.The expressive power of transactional events arises from a sequencing combinator whose semantics enforces an all-or-nothing transactional property – either both of the constituent events synchronize in sequence or neither of them synchronizes. This sequencing combinator, along with a non-deterministic choice combinator, gives transactional events the compositional structure of a monad-with-plus. We provide a formal semantics for transactional events and give a detailed account of an implementation.
Du syriaque au latin par l'intermédiaire de l'arabe: leKunnāšde Yūḥannā ibn Sarābiyūn
Authors: Troupeau Gérard 
Published: October 2008

This treatise of medicine by Yühannā ibn Sarābiyūn, written in Syriac in the 8th century, translated into Arabic in the 10th century and then into Latin in the 12th century, is a typical example of the transmission of Hippocratic medicine from the Arabic East to the Latin West in the Middle Ages. However, while the complete Latin translation of Gerard of Cremona has reached us, we have only fragments of the Arabic text, dispersed in five manuscripts preserved in four European libraries.In the first part we shall try to establish the biographical information about the author and the four translators of his treatise from Syriac to Arabic. In the second part we shall study the Arabic fragments of the Paris manuscript and the two Escorial manuscripts, first by examining their language, and then by comparing them to the Latin translation.
fMRI activation during a language task in adolescents with ASD
Authors: KNAUS TRACEY A. , SILVER ANDREW M. , LINDGREN KRISTEN A. , HADJIKHANI NOUCHINE , TAGER-FLUSBERG HELEN 
Published: October 2008

AbstractAutism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by language and communication impairments, social impairments, and repetitive behaviors or restricted interests. Previous studies of semantic functions have found differences in semantic processing and differences in the activation of the language network in adults with ASD compared to controls. The goal of this study is to examine semantic functions in adolescents with ASD compared to typically developing adolescents. We utilized fMRI with a reading version of a response-naming task to investigate activation in 12 right-handed adolescent boys with ASD and 12 typically developing boys. Both groups performed the task at ceiling levels. Boys with ASD had significantly stronger activation than controls in Broca's area, which was less left lateralized in ASD individuals. Controls had a significant correlation between frontal and temporal language area activation in the left hemisphere, whereas ASD adolescents did not. Direct group comparisons revealed additional regions activated in the ASD group relative to the control group. These results suggest differences in semantic organization, approaches to the semantic task, or efficiency in semantic processing in ASD adolescents relative to typically developing adolescents. (JINS, 2008,14, 967–979.)
Subjective memory complaints and concurrent memory performance in older patients of primary care providers
Authors: SNITZ BETH E. , MORROW LISA A. , RODRIGUEZ ERIC G. , HUBER KIMBERLY A. , SAXTON JUDITH A. 
Published: October 2008

AbstractSubjective memory complaints (SMCs) are known to be inconsistently related to current memory impairment in older adults but this association has not been well investigated in primary care provider (PCP) settings. To characterize the complexity of the relationship between SMCs and objective memory in older outpatients of PCPs, we collected neuropsychological, subjective memory, depression and medical chart data from outpatients aged 65 and older, without documented dementia diagnoses, in eleven PCP offices in and around the Pittsburgh metropolitan area. Results indicated that self-estimates of current memory ability were most strongly associated with objective memory performance; in contrast, perception of worsening memory over the past year showed no association; and specific memory-related activities were only weakly associated. Women were more likely than men to show inconsistency between SMCs and objective memory performance. Only two of the 11 most significantly memory-impaired participants endorsed SMCs and only four had PCP chart documentation of memory problems. Eliciting SMCs in non-demented older adults can be of clinical value in a PCP setting, but significant limitations of patient self-report in more memory-impaired patients underscore the need to develop brief, objective indicators of memory impairment for PCP office use when there is suspicion of decline. (JINS, 2008,14, 1004–1013.)
Neurocognitive predictors of social and communicative developmental trajectories in preschoolers with autism spectrum disorders
Authors: MUNSON JEFFREY , FAJA SUSAN , MELTZOFF ANDREW , ABBOTT ROBERT , DAWSON GERALDINE 
Published: October 2008

AbstractCurrently, the heterogeneity in the developmental trajectories of autism spectrum disorders (ASD) is poorly understood. Preschool children with ASD participating in a longitudinal study received a battery of neurocognitive tasks that measured the learning of reward associations (Lrn-Rew), spatial working memory (SpatWM), and imitation from memory and novelty preference (Mem/Nov), as well as a measure of nonverbal problem-solving ability (NVDQ). Growth curve analyses via HLM were used to predict the variability in growth rates between age 4 to age 6.5 in Vineland Socialization and Communication scores. Individual differences in both Lrn-Rew and Mem/Nov were significantly related to Socialization and Communication growth rates above and beyond NVDQ, whereas SpatWM was not. Thus, specific aspects of neurocognitive functioning appear to be important predictors of developmental variability during the preschool years in children with ASD. We speculate that these findings support the combined role of ventromedial prefrontal and medial temporal lobe systems in the early pathogenesis of ASD and may be useful in predicting developmental trajectory. The benefits and challenges of assessing specific neurocognitive functions in children with autism is discussed with regard to general cognitive/developmental ability and the behavioral requirements of most assessment settings. (JINS, 2008, 14, 956–966.)
Shotgun metaproteomics of the human distal gut microbiota
Authors: Verberkmoes Nathan C , Russell Alison L , Shah Manesh , Godzik Adam , Rosenquist Magnus , Halfvarson Jonas , Lefsrud Mark G , Apajalahti Juha , Tysk Curt , Hettich Robert L , Jansson Janet K 
Published: October 2008

Abstract
The human gut contains a dense, complex and diverse microbial community, comprising the gut microbiome. Metagenomics has recently revealed the composition of genes in the gut microbiome, but provides no direct information about which genes are expressed or functioning. Therefore, our goal was to develop a novel approach to directly identify microbial proteins in fecal samples to gain information about the genes expressed and about key microbial functions in the human gut. We used a non-targeted, shotgun mass spectrometry-based whole community proteomics, or metaproteomics, approach for the first deep proteome measurements of thousands of proteins in human fecal samples, thus demonstrating this approach on the most complex sample type to date. The resulting metaproteomes had a skewed distribution relative to the metagenome, with more proteins for translation, energy production and carbohydrate metabolism when compared to what was earlier predicted from metagenomics. Human proteins, including antimicrobial peptides, were also identified, providing a non-targeted glimpse of the host response to the microbiota. Several unknown proteins represented previously undescribed microbial pathways or host immune responses, revealing a novel complex interplay between the human host and its associated microbes.
Genomic comparison ofBradyrhizobium japonicumstrains with different symbiotic nitrogen-fixing capabilities and other Bradyrhizobiaceae members
Authors: Itakura Manabu , Saeki Kazuhiko , Omori Hirofumi , Yokoyama Tadashi , Kaneko Takakazu , Tabata Satoshi , Ohwada Takuji , Tajima Shigeyuki , Uchiumi Toshiki , Honnma Keina , Fujita Konosuke , Iwata Hiroyoshi , Saeki Yuichi , Hara Yoshino , Ikeda Seishi , Eda Shima , Mitsui Hisayuki , Minamisawa Kiwamu 
Published: October 2008

AbstractComparative genomic hybridization (CGH) was performed with nine strains of Bradyrhizobium japonicum (a symbiotic nitrogen-fixing bacterium associated with soybean) and eight other members of the Bradyrhizobiaceae by DNA macroarray of B. japonicum USDA110. CGH clearly discriminated genomic variations in B. japonicum strains, but similar CGH patterns were observed in other members of the Bradyrhizobiaceae. The most variable regions were 14 genomic islands (4–97 kb) and low G+C regions on the USDA110 genome, some of which were missing in several strains of B. japonicum and other members of the Bradyrhizobiaceae. The CGH profiles of B. japonicum were classified into three genome types: 110, 122 and 6. Analysis of DNA sequences around the boundary regions showed that at least seven genomic islands were missing in genome type 122 as compared with type 110. Phylogenetic analysis for internal transcribed sequences revealed that strains belonging to genome types 110 and 122 formed separate clades. Thus genomic islands were horizontally inserted into the ancestor genome of type 110 after divergence of the type 110 and 122 strains. To search for functional relationships of variable genomic islands, we conducted linear models of the correlation between the existence of genomic regions and the parameters associated with symbiotic nitrogen fixation in soybean. Variable genomic regions including genomic islands were associated with the enhancement of symbiotic nitrogen fixation in B. japonicum USDA110.
Conditional random pattern algorithm for LOH inference and segmentation
Authors: Wu Ling-Yun , Zhou Xiaobo , Li Fuhai , Yang Xiaorong , Chang Chung-Che , Wong Stephen T. C. 
Published: October 2008

Abstract
Motivation: Loss of heterozygosity (LOH) is one of the most important mechanisms in the tumor evolution. LOH can be detected from the genotypes of the tumor samples with or without paired normal samples. In paired sample cases, LOH detection for informative single nucleotide polymorphisms (SNPs) is straightforward if there is no genotyping error. But genotyping errors are always unavoidable, and there are about 70% non-informative SNPs whose LOH status can only be inferred from the neighboring informative SNPs.
Results: This article presents a novel LOH inference and segmentation algorithm based on the conditional random pattern (CRP) model. The new model explicitly considers the distance between two neighboring SNPs, as well as the genotyping error rate and the heterozygous rate. This new method is tested on the simulated and real data of the Affymetrix Human Mapping 500K SNP arrays. The experimental results show that the CRP method outperforms the conventional methods based on the hidden Markov model (HMM).
Availability: Software is available upon request.
Contact: xzhou@tmhs.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Challenges facing a network of representative marine protected areas in the Mediterranean: prioritizing the protection of underrepresented habitats
Authors: Abdulla Ameer , Gomei Marina , Hyrenbach David , Notarbartolo-di-Sciara Giuseppe , Agardy Tundi 
Published: October 2008

AbstractAbdulla, A., Gomei, M., Hyrenbach, D., Notarbartolo-di-Sciara, G., and Agardy, T. 2009. Challenges facing a network of representative marine protected areas in the Mediterranean: prioritizing the protection of underrepresented habitats. – ICES Journal of Marine Science, 66: 22–28. The high endemism of the Mediterranean Sea provides strong motivation to develop a comprehensive plan for the conservation of its biodiversity and the management of its marine resources. Increasingly, this ecosystem-level approach calls for a comprehensive network of marine protected areas (MPAs) representative of the richness and diversity of this shared basin. Today, Mediterranean MPAs do not represent the diverse geography and habitats in the region. Despite a recent declaration on trawling restrictions in deep waters (>1000 m), there are no true deep-sea Mediterranean MPAs. All but one (98.9%) of the 94 marine areas currently under some type of protection or management are coastal. Moreover, 69 (73.4%) are located along the basin's northern shore, highlighting the lack of MPAs in the south and east coasts. Yet, these underrepresented regions and habitats are ecologically distinctive by virtue of their particular oceanographic and biogeographic conditions. We identify several obstacles to Mediterranean MPA implementation and discuss how they can be overcome through strategic MPA network planning, contending that regional disparities in governance, institutional structures, wealth distribution, social capital, and availability of ecological data are responsible for discrepancies in the establishment and effectiveness of MPAs in this region.
Arabidopsis CLP1-SIMILAR PROTEIN3, an Ortholog of Human Polyadenylation Factor CLP1, Functions in Gametophyte, Embryo, and Postembryonic Development
Authors: Xing Denghui , Zhao Hongwei , Li Qingshun Quinn 
Published: October 2008

AbstractPolyadenylation factor CLP1 is essential for mRNA 3′-end processing in yeast and mammals. The Arabidopsis (Arabidopsis thaliana) CLP1-SIMILAR PROTEIN3 (CLPS3) is an ortholog of human hCLP1. CLPS3 was previously found to be a subunit in the affinity-purified PCFS4-TAP (tandem affinity purification) complex involved in the alternative polyadenylation of FCA and flowering time control in Arabidopsis. In this article, we further explored the components in the affinity-purified CLPS3-TAP complex, from which Arabidopsis cleavage and polyadenylation specificity factor (CPSF) subunits AtCPSF100 and AtCPSF160 were found. This result implies that CLPS3 may bridge CPSF to the PCFS4 complex. Characterization of the CLPS3 mutant revealed that CLPS3 was essential for embryo development and important for female gametophyte transmission. Overexpression of CLPS3-TAP fusion caused a range of postembryonic development abnormalities, including early flowering time, altered phyllotaxy, and abnormal numbers and shapes of flower organs. These phenotypes are associated with the altered gene expression levels of FCA, WUS, and CUC1. The decreased ratio of FCA-β to FCA-γ in the overexpression plants suggests that CLPS3 favored the usage of FCA regular poly(A) site over the alternative site. These observations indicate that Arabidopsis CLPS3 might be involved in the processing of pre-mRNAs encoded by a distinct subset of genes that are important in plant development.
Seroprevalence of Turkey Coronavirus in North American Turkeys Determined by a Newly Developed Enzyme-Linked Immunosorbent Assay Based on Recombinant Antigen
Authors: Gomaa Maged H. , Yoo Dongwan , Ojkic Davor , Barta John R. 
Published: October 2008

ABSTRACTTurkey coronavirus (TCoV) causes diarrhea in young turkey poults, but little is known about its prevalence in the field. To address this, the complete nucleocapsid gene was cloned and expressed inEscherichia coli. Expressed nucleocapsid gene produced two distinct proteins (52 and 43 kDa); their specificity was confirmed by Western blotting using two different monoclonal antibodies. Recombinant N protein was purified and used as an antigen to develop an enzyme-linked immunosorbent assay (ELISA) for the serological detection of TCoV that was then validated using experimentally derived turkey serum. The N-based ELISA showed (97%) sensitivity and (93%) specificity for TCoV, which was significantly higher than an infectious bronchitis coronavirus-based commercial test for TCoV. To assess the utility of this recombinant ELISA, 360 serum samples from turkey farms in Ontario, Canada, and 81 serum samples from farms in Arkansas were tested for TCoV-specific antibodies. A high seroprevalence of TCoV was found in turkeys from the Ontario farms with 73.9% of breeders and 60.0% of meat turkeys testing seropositive using the N-based ELISA. Similarly, a high field prevalence was found in the turkeys from Arkansas, for which 64.2% of the serum samples tested seropositive.
Carriage of Methicillin-Resistant Staphylococci and Their SCC
mec
Types in a Long-Term-Care Facility
Authors: Ibrahem Salha , Salmenlinna Saara , Virolainen Anni , Kerttula Anne-Marie , Lyytikäinen Outi , Jägerroos Henrik , Broas Markku , Vuopio-Varkila Jaana 
Published: October 2008

ABSTRACT

Following an outbreak caused by staphylococcal cassette chromosome
mec
(SCC
mec
) type V methicillin (meticillin)-resistant
Staphylococcus aureus
(MRSA), a point-prevalence survey of the nasal carriage of staphylococci was conducted in a long-term-care facility in northern Finland in 2004. The focus was directed at methicillin-resistant coagulase-negative staphylococci (MR-CNS) and their SCC
mec
elements. A nasal swab was taken from 76 of the 80 residents 6 months after the onset of the outbreak. Staphylococcal isolates were identified by conventional methods and the GenoType
Staphylococcus
test, and their SCC
mec
elements were analyzed. Of the 76 individuals, 24 (32%) carried
S. aureus
and 67 (88%) CNS in their nostrils. Of the CNS carriers, 41 (61%) had at least one
mecA
-positive MR-CNS, and two individuals (3%) had both MRSA and methicillin-resistant
Staphylococcus epidermidis
(MRSE). Among the 61 MR-CNS isolates identified, 49 (80%) were MRSE. The distribution of the SCC
mec
types was diverse: 20 (33%) were of type IV, 11 (18%) of type V, 4 (6%) of type I or IA, 3 (4%) of type II, and 23 (38%) of new types (with six different combinations of
ccr
and other
mec
genes or only
mecA
). Both of the individuals with MRSA and MRSE shared SCC
mec
type V among their isolates. Nasal MR-CNS carriage was common among the residents of this long-term-care facility. A variety of SCC
mec
types, including many new types, were identified among the MR-CNS strains. The horizontal transfer of SCC
mec
elements is speculated based on the sharing of SCC
mec
type V between MRSA and MRSE.