bluuebunny/crossref_metadata_2025 huggingface dataset:
Still no evidence of new variant Chlamydia trachomatis in England and Wales
Authors: Alexander Sarah , Coelho da Silva Filomeno , Alhadi Fathiya , Ison Catherine
Published: January 2011

Background: New variant Chlamydia trachomatis (nvCT) remains an important public health concern and in 2008 four cases of nvCT were reported in Scotland. The present study set out to determine whether nvCT was present in England and Wales. Methods: 1054 clinical specimens, which had been confirmed as chlamydia positive (using an nvCT unaffected platform) at nine different diagnostic laboratories throughout England and Wales, were examined for the presence of the 377 bp nvCT deletion. Results: 92% (968/1054) of specimens examined were confirmed as wild-type C. trachomatis. The remaining 86 specimens were found to be untypeable, which was probably due to low levels of DNA. No nvCT specimens were identified. Conclusions: There is currently no evidence that nvCT is present in England and Wales; however, laboratories using nvCT-affected platform should remain vigilant.
A note on the harmonic measure doubling condition
Authors: Broch Ole , Hag Kari , Junge Steffen
Published: January 2011

We present a detailed and self-contained proof of the harmonic measure doubling characterization of bounded quasidisks due to Jerison and Kenig.
WIST: toolkit for rapid, customized LIMS development
Authors: Huang Y. Wayne , Arkin Adam P. , Chandonia John-Marc
Published: January 2011

Summary: Workflow Information Storage Toolkit (WIST) is a set of application programming interfaces and web applications that allow for the rapid development of customized laboratory information management systems (LIMS). WIST provides common LIMS input components, and allows them to be arranged and configured using a flexible language that specifies each component's visual and semantic characteristics. WIST includes a complete set of web applications for adding, editing and viewing data, as well as a powerful setup tool that can build new LIMS modules by analyzing existing database schema.

Availability and implementation: WIST is implemented in Perl and may be obtained from http://vimss.sf.net under the BSD license.

Contact:  jmchandonia@lbl.gov

Supplementary information:  Supplementary data are available at Bioinformatics online.
Computational refinement of post-translational modifications predicted from tandem mass spectrometry
Authors: Chung Clement , Liu Jian , Emili Andrew , Frey Brendan J.
Published: January 2011

Motivation: A post-translational modification (PTM) is a chemical modification of a protein that occurs naturally. Many of these modifications, such as phosphorylation, are known to play pivotal roles in the regulation of protein function. Henceforth, PTM perturbations have been linked to diverse diseases like Parkinson's, Alzheimer's, diabetes and cancer. To discover PTMs on a genome-wide scale, there is a recent surge of interest in analyzing tandem mass spectrometry data, and several unrestrictive (so-called ‘blind’) PTM search methods have been reported. However, these approaches are subject to noise in mass measurements and in the predicted modification site (amino acid position) within peptides, which can result in false PTM assignments.

Results: To address these issues, we devised a machine learning algorithm, PTMClust, that can be applied to the output of blind PTM search methods to improve prediction quality, by suppressing noise in the data and clustering peptides with the same underlying modification to form PTM groups. We show that our technique outperforms two standard clustering algorithms on a simulated dataset. Additionally, we show that our algorithm significantly improves sensitivity and specificity when applied to the output of three different blind PTM search engines, SIMS, InsPecT and MODmap. Additionally, PTMClust markedly outperforms another PTM refinement algorithm, PTMFinder. We demonstrate that our technique is able to reduce false PTM assignments, improve overall detection coverage and facilitate novel PTM discovery, including terminus modifications. We applied our technique to a large-scale yeast MS/MS proteome profiling dataset and found numerous known and novel PTMs. Accurately identifying modifications in protein sequences is a critical first step for PTM profiling, and thus our approach may benefit routine proteomic analysis.

Availability: Our algorithm is implemented in Matlab and is freely available for academic use. The software is available online from http://genes.toronto.edu.

Supplementary Information:  Supplementary data are available at Bioinformatics online.

Contact:  frey@psi.utoronto.ca
HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens
Authors: Wang Xin , Terfve Camille , Rose John C. , Markowetz Florian
Published: January 2011

Motivation: High-throughput screens (HTS) by RNAi or small molecules are among the most promising tools in functional genomics. They enable researchers to observe detailed reactions to experimental perturbations on a genome-wide scale. While there is a core set of computational approaches used in many publications to analyze these data, a specialized software combining them and making them easily accessible has so far been missing.

Results: Here we describe HTSanalyzeR, a flexible software to build integrated analysis pipelines for HTS data that contains over-representation analysis, gene set enrichment analysis, comparative gene set analysis and rich sub-network identification. HTSanalyzeR interfaces with commonly used pre-processing packages for HTS data and presents its results as HTML pages and network plots.

Availability: Our software is written in the R language and freely available via the Bioconductor project at http://www.bioconductor.org.

Contact:  florian.markowetz@cancer.org.uk
Automated validation of genetic variants from large databases: ensuring that variant references refer to the same genomic locations
Authors: Tong Mark Y. , Cassa Christopher A. , Kohane Isaac S.
Published: January 2011

Summary: Accurate annotations of genomic variants are necessary to achieve full-genome clinical interpretations that are scientifically sound and medically relevant. Many disease associations, especially those reported before the completion of the HGP, are limited in applicability because of potential inconsistencies with our current standards for genomic coordinates, nomenclature and gene structure. In an effort to validate and link variants from the medical genetics literature to an unambiguous reference for each variant, we developed a software pipeline and reviewed 68 641 single amino acid mutations from Online Mendelian Inheritance in Man (OMIM), Human Gene Mutation Database (HGMD) and dbSNP. The frequency of unresolved mutation annotations varied widely among the databases, ranging from 4 to 23%. A taxonomy of primary causes for unresolved mutations was produced.

Availability: This program is freely available from the web site (http://safegene.hms.harvard.edu/aa2nt/).

Contact:  mt153@hms.harvard.edu; mark_tong2009@yahoo.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Characterization of the RcsC Sensor Kinase from Erwinia amylovora and Other Enterobacteria
Authors: Wang Dongping , Korban Schuyler S. , Pusey P. Lawrence , Zhao Youfu
Published: January 2011

RcsC is a hybrid sensor kinase which contains a sensor domain, a histidine kinase domain, and a receiver domain. We have previously demonstrated that, although the Erwinia amylovora rcsC mutant produces more amylovoran than the wild-type (WT) strain in vitro, the mutant remains nonpathogenic on both immature pear fruit and apple plants. In this study, we have comparatively characterized the Erwinia RcsC and its homologs from various enterobacteria. Results demonstrate that expression of the Erwinia rcsC gene suppresses amylovoran production in various amylovoran overproducing WT and mutant strains, thus suggesting the presence of a net phosphatase activity of Erwinia RcsC. Findings have also demonstrated that rcsC homologs from other enterobacteria could not rescue amylovoran production of the Erwinia rcsC mutant in vitro. However, virulence of the Erwinia rcsC mutant is partially restored by rcsC homologs from Pantoea stewartii, Yersinia pestis, and Salmonella enterica but not from Escherichia coli on apple shoots. Domain-swapping experiments have indicated that replacement of the E. coli RcsC sensor domain by those of Erwinia and Yersinia spp. partially restores virulence of the Erwinia rcsC mutant, whereas chimeric constructs containing the sensor domain of E. coli RcsC could not rescue virulence of the Erwinia rcsC mutant on apple. Interestingly, only chimeric constructs containing the histidine kinase and receiver domains of Erwinia RcsC are fully capable of rescuing amylovoran production. These results suggest that the sensor domain of RcsC may be important in regulating bacterial virulence, whereas the activity of the histidine kinase and receiver domains of Erwinia RcsC may be essential for amylovoran production in vitro.
Bone marrow stromal cells inhibit mast cell function via a COX2‐dependent mechanism
Authors: Brown J. M. , Nemeth K. , Kushnir‐Sukhov N. M. , Metcalfe D. D. , Mezey E.
Published: January 2011

Cite this as: J. M. Brown, K. Nemeth, N. M. Kushnir‐Sukhov, D. D. Metcalfe and E. Mezey, Clinical & Experimental Allergy, 2011 (41) 526–534.

Background
Mast cells (MCs) have a central role in the induction of allergic inflammation, such as seen in asthma, and contribute to the severity of certain autoimmune diseases, such as rheumatoid arthritis. The MC thus represents an important inflammatory cell, and one which has resisted therapeutic attempts to alter its role in disease.

Objective
Because bone marrow‐derived stromal cells (BMSC, also known as mesenchymal stem cells or MSCs) have been reported to alter allergic inflammation in vivo, we chose to study the interaction between mouse BMSC and mouse bone marrow‐derived MCs.

Methods
MC degranulation, cytokine production and chemotaxis were evaluated in vitro following co‐culture with BMSCs either in cell contact or a transwell. In addition, MC degranulation was assessed in vivo following administration of BMSCs in a model of passive cutaneous anaphylaxis and a peritoneal degranulation assay. Mechanisms of MC suppression by BMSCs were determined through use of inhibitors or antibodies to COX1, COX2, nitric oxide, indoleamine 2, 3‐dioxygenase, EP1–4 receptors, TGF‐β and IL‐10. Lastly, we utilized either BMSCs or MCs deficient in COX1, COX2 or EP1‐4 receptors to confirm the mechanisms of inhibition of MC function by BMSCs.

Results
We discovered that BMSCs will effectively suppress specific MC functions in vitro as well as in vivo. When MCs are cocultured with BMSCs to allow cell‐to‐cell contact, BMSCs suppressed MC degranulation, pro‐inflammatory cytokine production, chemokinesis and chemotaxis. Similarly, MC degranulation within mouse skin or the peritoneal cavity was suppressed following in vivo administration of BMSCs. Further, we found that these inhibitory effects were dependent on up‐regulation of COX2 in BMSCs; and were facilitated through the activation of EP4 receptors on MCs.

Conclusion and Clinical Relevance
These observations support the concept that BMSCs have the ability to suppress MC activation and therefore could be the basis for a novel cell based therapeutic approach in the treatment of MC driven inflammatory diseases.
Differential expression profiles between α‐dystroglycan and integrin β1 in ameloblastoma: two possible perlecan signalling pathways for cellular growth and differentiation
Authors: Ida‐Yonemochi Hiroko , Ahsan Md Shahidul , Saku Takashi
Published: January 2011

Ida‐Yonemochi H, Ahsan M S & Saku T (2011) Histopathology58, 234–245 Differential expression profiles between α‐dystroglycan and integrin β1 in ameloblastoma: two possible perlecan signalling pathways for cellular growth and differentiation

Aims:  Intercellular deposition of perlecan, an extracellular matrix molecule, results in characteristic stellate reticulum‐like structures in ameloblastomas. The aims of this study were to elucidate which types of perlecan receptors function within any particular type of tissue architecture of ameloblastoma.

Methods and results:  Protein and gene expression profiles for α‐dystroglycan and integrin β1 were examined comparatively with those of their ligands in ameloblastoma using surgical specimens and cells in primary culture. In the follicular‐type tumour cell foci, α‐dystroglycan was localized uniformly over the stellate reticulum‐like cells, while integrin β1 was restricted mainly to peripheral cells facing the stroma with the interface of the basement membrane, which was also rich in perlecan. In the plexiform‐type, mRNA and protein signals for α‐dystroglycan were enhanced in the periphery of tumour cell foci, especially in their invading fronts. Integrin β1 was also immunolocalized in the basal cell zone, which was considered to be the proliferation centre of ameloblastoma cells. Furthermore, biosynthesis of α‐dystroglycan and integrin β1 by ameloblastoma cells was confirmed in vitro using immunofluorescence and reverse transcriptase–polymerase chain reaction.

Conclusions:  Ameloblastoma cells proliferate and are differentiated by capturing perlecan differentially with α‐dystroglycan and integrin β1, respectively.
Evaluation of the dimensional changes of mineral trioxide aggregate sealer
Authors: Camilleri J. , Mallia B.
Published: January 2011

Camilleri J, Mallia B. Evaluation of the dimensional changes of mineral trioxide aggregate sealer. International Endodontic Journal, 44, 416–424, 2011.

Aim  To evaluate the setting time, early age restrained dimensional stability, fluid uptake, microstructure and porosity of a root canal sealer based on mineral trioxide aggregate (MTAS).

Methodology  The MTAS, mineral trioxide aggregate (MTA) and a commercially available sealer pulp canal sealer (PCS) were investigated. The setting time of the materials was determined according to ISO 6876; 2002. The dimensional change in the vertical direction was measured over a period of 7 days from setting time using a linear variable differential transducer. The test samples were restrained in lateral directions by the metal mould. The fluid uptake of the cements was evaluated in Hank’s balanced salt solution (HBSS), and their porosity was investigated using light optical microscopy.

Results  The addition of a water‐soluble polymer to MTA reduced its setting time but PCS displayed the shortest setting time (P < 0.05). The dimensional stability of the materials was not affected by the test environmental conditions (P > 0.05). PCS exhibited a much higher degree of shrinkage than MTA (P = 0.997, 0.640, 0.449, 0.191) and MTAS (P = 0.952, 0.523, 0.380, 0.149) at 3 h and 1, 3, 7 days, respectively, when allowed to set at 100% humidity. An increase in weight and expansion was recorded for MTA when immersed in HBSS. Microscope investigation of test specimens revealed the highest degree of porosity in MTA followed by MTAS and PCS.

Conclusions  The novel sealer based on MTA demonstrated adequate setting time and was dimensionally stable. It has the potential to be used as root canal sealer cement in clinical practice.
Preliminary study of the inflammatory response to subcutaneous implantation of three root canal sealers
Authors: Silva‐Herzog D. , Ramírez T. , Mora J. , Pozos A. J. , Silva L. A. B. , Silva R. A. B. , Nelson‐Filho P.
Published: January 2011

Silva‐Herzog D, Ramírez T, Mora J, Pozos AJ, Silva LAB, Silva RAB, Nelson‐Filho P. Preliminary study of the inflammatory response to subcutaneous implantation of three root canal sealers. International Endodontic Journal, 44, 440–446, 2011.

Aim  To evaluate the kinetics of the inflammatory tissue response to three root canal sealers using a physicochemical method for quantification of the enhanced vascular permeability and histopathological analysis.

Methodology  Twenty‐eight male Wistar rats randomly assigned to four groups according to the evaluation periods (1, 3, 7 and 14 days) were used to assess the vascular permeability and histopathological reaction to RoekoSeal, AH Plus and Sealapex (new formulation) sealers, using saline and Chloropercha as negative and positive controls, respectively. Seven rats were sacrificed per period. The biocompatibility of the sealers was evaluated spectrophotometrically and histopathologically.

Results  At day 14, Sealapex produced significantly more inflammatory exudate than AH Plus and RoekoSeal (P < 0.05); however, there was no significant difference between AH Plus and RoekoSeal (P > 0.05). Sealapex (new formulation) was the most irritating sealer, producing severe inflammation with the presence of multinucleated giant cells. RoekoSeal was the most biocompatible sealer, producing the least amount of inflammatory exudate.

Conclusions  RoekoSeal root canal sealer was biocompatible when implanted in connective tissue.
Effect of gossypol on blood serum parameters and small intestinal morphology of male broilers
Authors: Özdoğan M. , Wellmann K. , Paksuz E.
Published: January 2011

Summary In the present study, the effect of varied gossypol (GOSS) amounts was investigated on blood parameters, the digesta pH, villus height, villus width, and crypta depth, width of duodenum, jejunum and ileum. A total of one hundred eight Ross 308 male broilers were fed with four diet groups as follows: no gossypol (control), gossypol rate 62 mg/kg (GOSS 62), gossypol rate 124 mg/kg (GOSS 124) and gossypol rate 186 mg/kg (GOSS 186). The effect of used gossypol amounts on blood parameters was not found to be statistically significant. Increases in digesta pH values of jejunum and ileum with GOSS 186 diet group were found to be statistically significant. The results also indicated that, except duodenum villus height, there was no statistical difference effect of GOSS on epithelial cell thickness, villus height, villus width, crypta depth and crypta width of the duodenum, jejunum and ileum. There have been no clearly negative effects of higher gossypol amounts up to 186 mg/kg diets on these parameters.
Impact of early code‐skill and oral‐comprehension training on reading achievement in first grade
Authors: Bianco Maryse , Pellenq Catherine , Lambert Eric , Bressoux Pascal , Lima Laurent , Doyen Anne‐Lise
Published: January 2011

In a 3‐year longitudinal study, we examined the relationships between oral language development, early training and reading acquisition on word‐identification and reading‐comprehension tests administered to a sample of 687 French children. Hierarchical linear models showed that both phonological awareness and oral comprehension at the age of 4 years were relevant to reading acquisition 2 years later. These two broad skills explained separate parts of the variance on both outcome measures, while revealing opposite effects: phonological skills explained more variance for alphabetic reading skills and oral comprehension explained more variance for reading comprehension. We also assessed the effects of two preschool training programmes focusing on either phonological awareness or comprehension skills. The results showed that phonological awareness training had a positive effect on alphabetic scores, and comprehension training had a positive effect on reading comprehension. These results provide insight into early oral instruction and contribute to the theoretical debate about the linguistic predictors of literacy acquisition.
KIERKEGAARD'S ANTHROPOLOGY OF THE SELF: ETHICO‐RELIGIOUS AND SOCIAL DIMENSIONS OF SELFHOOD
Authors: SOUSA DOMINGOS
Published: January 2011

It is sometimes argued that the concept of the self is the unifying thread that ties together the rich diversity of philosophical and theological themes in Kierkegaard's works.1 In his conception of the self he provides us with a coherent and unified view of human existence. For Kierkegaard the self is not a static entity but a dynamic and unfolding reality, something I must strive to become. One is not a self but becomes a self as an ethico‐religious task to be actualized. The purpose of this paper is to outline Kierkegaard's anthropology of the self with particular emphasis on the ethical and religious dimensions of selfhood. I will first elucidate the structure and dynamic character of the self, and then will examine the dialectical development of the self in the ethical and religious stages of existence. Finally I will address the widespread criticism of Kierkegaard's conception of the self as being radically individualistic and asocial.
Comparison of volatile compounds in yoghurts made from cows’, buffaloes’, ewes’ and goats’ milks
Authors: ERKAYA TUBA , ŞENGÜL MUSTAFA
Published: January 2011

The composition of the volatile fraction of yoghurts made from cows’, buffaloes’, ewes’ and goats’ milks was investigated during the 28 days of storage at 4 °C using solid‐phase microextraction technique (SPME) and gas chromatography coupled to mass spectrometry analysis (GC/MS). A total of 34 volatile compounds were identified in yoghurts during their storage at 4 °C, including aldehydes, ketones, alcohols, esters, acids, terpenes, hydrocarbons and sulphur compounds. In this study, acetaldehyde, diacetyl and acetoin, considered as the major compounds of yoghurt, were detected in all yoghurts.
A survey of the quality of extended shelf life (ESL) milk in relation to HTST and UHT milk
Authors: LORENZEN PETER CHR , CLAWIN‐RÄDECKER INGRID , EINHOFF KURT , HAMMER PHILIPP , HARTMANN RAINER , HOFFMANN WOLFGANG , MARTIN DIERK , MOLKENTIN JOACHIM , WALTE HANS G , DEVRESE MICHAEL
Published: January 2011

Thirty milk samples [high‐temperature short‐time (HTST) milk, extended shelf life (ESL) milk (directly heated, indirectly heated, microfiltered), ultra‐high temperature milk] from 17 German dairies were analysed. Total viable counts of directly or indirectly heated ESL milk were significantly lower than those in microfiltered ESL and HTST milk. Evaluation of indigenous enzyme activity revealed sufficient heat treatments in all milk samples. The manufacturing processes were differentiated by estimating furosine and acid soluble whey proteins. Sensory examinations revealed a preference for HTST heated and microfiltered ESL milk. However, a significant discrimination of drinking milk types was not possible. Vitamin losses were not detected, and concentrations of vitamins in different types of milk were comparable.
The effect of concentration of chymosin on the yield and sensory properties of camel cheese and on its microbiological quality
Authors: BENKERROUM NOREDDINE , DEHHAOUI MOHAMMED , EL FAYQ ABDELMALEK , TLAIHA RACHIDA
Published: January 2011

The transformation of camel milk into soft cheese by using chymosin and yoghurt starter culture (Streptococcus thermophilus and Lactobacillus bulgaricus) was investigated. The cheese yield and sensory properties were related to the concentration of chymosin. A yield of 16.74 g/100 mL of milk was obtained with a chymosin concentration of 1.7 mL/L of milk. The cheeses obtained with concentrations ranging between 1.0 mL and 2.9 mL of chymosin/L of milk scored highly regarding their sensory properties and had an acceptable microbiological quality. This study demonstrated that cheesemaking from camel milk can be made successfully providing that the appropriate chymosin concentration is used; and that 1.7 mL of chymosin/L of milk was optimal.
One-Dimensional Nanostructure Arrays for Dye-Sensitized Solar Cells
Authors: Charoensirithavorn Patcharee , Sagawa Takashi , Hayase Shuzi , Yoshikawa Susumu
Published: January 2011

This article reports the fabrication of ordered arrays of ZnO nanorods and TiO2 nanotubules by using a simple solution-based method and the application of these arrays as the working electrodes in dye-sensitized solar cells (DSCs) with an aim of offering superior electron transport conduits than in the conventional nanocrystalline nanoparticle films. The faster charge transport and lower recombination properties of one-dimensional (1D) nanostructure array electrodes as compared with those of the nanoparticle one observed and proved that such arrays of 1D nanostructure are the more promising electrode for DSCs in the future.
Effect of Cameralike Aperture in Quest for Maintaining Quasi-Constant Radiation Inside a Solar Reactor
Authors: Ozalp Nesrin , Toyama Anthony , Devanuri Jayakrishna , Rowshan Reza , Al-Hamidi Yasser
Published: January 2011

Solar reactors can convert intermittent solar radiation into storable chemical energy in the form of fuels that are transportable. In order to use solar energy as a source of high temperature process heat in a solar reactor, incident radiation needs to be concentrated over a small surface area, the inlet of which is called the aperture. The image of the incoming solar radiation over the aperture can be approximated by a Gaussian distribution where the solar radiation inside the reactor varies by the peak value and aperture size. Due to the transient nature of solar energy, there is a critical need for proper control to maximize system efficiency under field conditions. The objective of this paper is to present numerically proven advantages of having a camera-like variable aperture, one that is sensitive to natural variations in solar flux, and having the ability to shrink or enlarge accordingly in order to maintain quasi-constant radiation inside the reactor. Since the internal temperature has a major impact on reactant to product conversion efficiency, by maintaining the temperature constant, process efficiency is kept high. By maintaining the internal temperature despite transient operating conditions, the system can maintain peak performance through a wider insolation range than fixed aperture systems. Our numerical results from optical, thermodynamic, and flow dynamic simulations led us to develop a computational two dimensional heat transfer distribution model inside the reactor in order to validate our optical results. The combined simulation results show that correctly varying the aperture diameter with respect to transient incoming solar flux densities facilitates the maintenance of quasi-constant temperature distributions inside the reactor.
Protocol-Based Multi-Agent Systems: Examining the Effect of Diversity, Dynamism, and Cooperation in Heuristic Optimization Approaches
Authors: Landry Lindsay Hanna , Cagan Jonathan
Published: January 2011

Many heuristic optimization approaches have been developed to combat the ever-increasing complexity of engineering problems. In general, these approaches can be classified based on the diversity of the search strategies used, the amount of change in these search strategies during the optimization process, and the level of cooperation between these strategies. A review of the literature indicates that approaches that are simultaneously very diverse, highly dynamic, and cooperative are rare but have immense potential for finding high quality final solutions. In this work, a taxonomy of heuristic optimization approaches is introduced and used to motivate a new approach called protocol-based multi-agent systems. This approach is found to produce final solutions of much higher quality when its implementation includes the use of multiple search protocols, the adaptation of these protocols during the optimization, and the cooperation between these protocols than when these characteristics are absent.
Grinding Micromechanisms of a Sintered Friction Material
Authors: Bassoli E. , Atzeni E. , Iuliano L.
Published: January 2011

New brake-pad materials are inhomogeneous compounds with a variety of metallic and ceramic phases, whose interaction with the tool during the grinding operation is not fully understood. Yet, ground surface quality strongly influences the bedding-in phase. This research surveys how grinding operation affects the pad surface. The purpose is pursued by adopting an investigation protocol merging macroscopic outcomes with the study of chip-removal mechanisms and of the ground surface morphology in the microscale. A specific set of grinding tests is carried out on the friction material under different kinematic conditions. Macroscopic indicators of the process performances are measured and modeled. At a closer look, the ground surface shows a complex morphology that cannot be completely described by roughness values, but depends on how the various phases are distributed in the material and how they are affected by the tool during abrasion. A multiscale inspection procedure is proposed to assess the performances of a machining operation on complex materials, where the descriptive power of standard technological tests becomes inadequate.
Investigation of the child with an acute metabolic disorder
Authors: Cook P , Walker V
Published: January 2011

Inherited biochemical defects may present with acute life-threatening illness with a high mortality and morbidity. Some are treatable and have a good outcome with early appropriate intervention. However, because of their rarity, diagnosis is often delayed; they are not considered or investigated appropriately. This is especially likely in those presenting in previously healthy adults. The collection of acute samples is crucial. There are numerous disorders, and front-line tests must cast a wide net. A small core of emergency tests generally indicates which metabolic pathway is defective and provides a working diagnosis and basis for treatment. Later confirmation and identification of the precise defect are essential for long-term management and for genetic counselling and prenatal diagnosis of future pregnancies. An escalating number of specialist tests and mutation analyses are undertaken by metabolic laboratories worldwide, but they are not widely available, are expensive, and must be requested selectively. Guidelines are presented here for the front-line investigation of acutely ill children with hypoglycaemia, metabolic acidosis, encephalopathy and intractable seizures, and for a dying child with a suspected, undiagnosed, inherited metabolic defect. With modification, these are also applicable to adults with a metabolic defect. In order to guide further investigation, selected disorders are described briefly along with their diagnostic work-up. Information about sample collection and processing is provided.
KRASmutation analysis in genomic DNA isolated from formalin-fixed paraffin-embedded ovarian tissue: evaluation of a strip-based reverse-hybridisation assay
Authors: Kriegshäuser Gernot , Auner Veronika , Schuster Eva , Holzer Barbara , Oberkanins Christian , Horvat Reinhard , Speiser Paul , Zeillinger Robert
Published: January 2011

Aims

To evaluate a reverse-hybridisation assay (strip assay) designed for the sensitive detection of 10 mutations in codons 12 and 13 of theKRASgene. The strip assay relies on mutant-enriched PCR followed by reverse-hybridisation of biotinylated amplification products to oligonucleotide probes immobilised as an array of parallel lines on nitrocellulose test strips.

Methods

The strip assay was used to analyse genomic DNA isolated from 120 formalin-fixed paraffin-embedded (FFPE) ovarian tissue samples. The samples were analysed in parallel using a biochip-based protocol (biochip assay) covering the same mutation spectrum, and results were compared with respect to sensitivity, specificity and operational input.

Results

The strip assay identified 19 (16%) of 120 FFPE samples to carry aKRASmutation; results were in agreement with those obtained by biochip hybridisation. Both assays had an analytical sensitivity of 1% when performed on FFPE-extracted DNA with approximately the same operational input needed for post-PCR processing. In contrast to the biochip assay, strip assay hybridisation may be automated to a large extent.

Conclusions

The strip assay is an accurate and sensitive tool for the low to medium throughput detection ofKRASmutation in genomic DNA isolated from FFPE tissue.
Axillary fine needle aspiration cytology for pre-operative staging of patients with screen-detected invasive breast carcinoma
Authors: Hayes Brian D , Feeley Linda , Quinn Cecily M , Kennedy M M , O'Doherty Ann , Flanagan Fidelma , O'Connell Anna Marie
Published: January 2011

Introduction

Fine needle aspiration cytology (FNAC) of radiologically abnormal axillary lymph nodes in patients with breast cancer can identify patients suitable for primary axillary clearance (AC) rather than sentinel node biopsy, enabling surgical axillary staging by a single operation. This study assessed the accuracy of FNAC in predicting positive axillary lymph nodes.

Methods

161 patients with screen-detected invasive carcinoma and who had pre-operative FNAC of a radiologically abnormal axillary lymph node were identified from two screening units, The axillary FNAC reports were correlated with sentinel node biopsy and AC reports, and sensitivity, specificity, positive (PPV) and negative (NPV) predictive values were calculated.

Results

FNAC had a moderate sensitivity (66.3%) and NPV (71.8%), and a high specificity (98.7%) and PPV (98.3%). Most patients (86%) had a single axillary operation. The sensitivity was highest in grade 3 (81.8%) and ductal type (77.8%) tumours. The sensitivity was lower in tumours of special type (34.8%), grade 1 tumours (50%) and those without lymphovascular invasion (LVI) (55.9%). The NPV was highest in pT1 (86.7%) and in grade 1 (84.5%) tumours, and lowest (44%) in tumours with LVI. The PPV was 100% in grade 1 and 3 tumours, stage pT2 and pT3 tumours and those without LVI, and was high (>96%) in all other groups. In lymph-node-positive patients, the mean number of lymph nodes involved was higher in the case of a positive (6.4) than negative FNAC (4.4).

Conclusions

FNAC of ultrasonically abnormal axillary lymph nodes achieved surgical staging by a single operation in most patients with screen-detected invasive breast carcinoma, with moderate sensitivity and high specificity.
Inappropriate calibration and optimisation of pan-keratin (pan-CK) and low molecular weight keratin (LMWCK) immunohistochemistry tests: Canadian Immunohistochemistry Quality Control (CIQC) experience
Authors: Copete Maria , Garratt John , Gilks Blake , Pilavdzic Dragana , Berendt Richard , Bigras Gilbert , Mitchell Sarah , Lining Leslie Ann , Cheung Carol , Torlakovic Emina E
Published: January 2011

Aims

Pan-cytokeratin (pan-CK) and low molecular weight cytokeratin (LMWCK) tests are the most common immunohistochemistry (IHC) tests used to support evidence of epithelial differentiation. Canadian Immunohistochemistry Quality Control (CIQC), a new provider of proficiency testing for Canadian clinical IHC laboratories, has evaluated the performance of Canadian IHC laboratories in two proficiency testing challenges for both pan-CK and LMWCK.

Methods

CIQC has designed a 70-sample tissue microarray (TMA) for challenge 1 and a 30-sample TMA for challenge 2. There were 13 participants in challenge 1, and 62 in challenge 2. All results were evaluated and scored by CIQC assessors and compared with reference laboratory results.

Results

Participating laboratories often produced false-negative results that ranged from 20% to 80%. False-positive results were also detected. About half of participating clinical laboratories have inappropriately calibrated IHC tests for pan-CK and LMWCK, which are the most commonly used markers for demonstration of epithelial differentiation. The great majority of laboratories were not aware of the problem with calibration of pan-CK and LMWCK tests because of inappropriate selection of external positive controls and samples for optimisation of these tests. Benign liver and kidney are the most important tissues to include as positive controls for both pan-CK and LMWCK.

Conclusions

Participation in external quality assurance is important for peer comparison and proper calibration of IHC tests, which is also helpful for appropriate selection of positive control material and material for optimisation of the tests.
SPATIAL RICCI SCALAR DARK ENERGY MODEL
Authors: YANG RONG-JIA , ZHU ZONG-HONG , WU FENGQUAN
Published: January 2011

Inspired by the holographic principle, we suggest that the density of dark energy is proportional to the spatial Ricci scalar curvature (SRDE). Such a model is phenomenologically viable. The best fit values of its parameters at 68% confidence level are found to be Ωm 0= 0.259±0.016 and α = 0.261±0.0122, constrained from the Union+CFA3 sample of 397 SNIa and the BAO measurement. We find that the equation of state of SRDE crosses -1 at z ≃ -0.14. The present value of the deceleration parameter q(z) for SRDE is found to be qz = 0~-0.85. The phase transition from deceleration to acceleration of the Universe for SRDE occurs at the redshift zq = 0~0.4. After studying the perturbation of each component of the Universe, we show that the matter power spectra and cosmic microwave background temperature anisotropy are slightly affected by SRDE, compared with ΛCDM.
KILLING VECTORS IN HIGHER-DIMENSIONAL SPACETIMES WITH CONSTANT SCALAR CURVATURE INVARIANTS
Authors: MCNUTT DAVID , PELAVAS NICOS , COLEY ALAN
Published: January 2011

We study the existence of a non-spacelike isometry, ζ, in higher-dimensional Kundt spacetimes with constant scalar curvature invariants (CSI). We present the particular forms for the null or timelike Killing vectors and a set of constraints for the metric functions in each case. Within the class of N-dimensional CSI Kundt spacetimes, admitting a non-spacelike isometry, we determine which of these can admit a covariantly constant null vector that also satisfy ζ[a;b] = 0.
Environmental bisimulations for higher-order languages
Authors: Sangiorgi Davide , Kobayashi Naoki , Sumii Eijiro
Published: January 2011

Developing a theory of bisimulation in higher-order languages can be hard. Particularly challenging can be: (1) the proof of congruence, as well as enhancements of the bisimulation proof method with “up-to context” techniques, and (2) obtaining definitions and results that scale to languages with different features.

To meet these challenges, we present
environment{} bisimulations
, a form of bisimulation for higher-order languages, and its basic theory. We consider four representative calculi: pure λ-calculi (call-by-name and call-by-value), call-by-value λ-calculus with higher-order store, and then Higher-Order π-calculus. In each case: we present the basic properties of environment bisimilarity, including congruence; we show that it coincides with contextual equivalence; we develop some up-to techniques, including up-to context, as examples of possible enhancements of the associated bisimulation method.

Unlike previous approaches (such as applicative bisimulations, logical relations, Sumii-Pierce-Koutavas-Wand), our method does not require induction/indices on evaluation derivation/steps (which may complicate the proofs of congruence, transitivity, and the combination with up-to techniques), or sophisticated methods such as Howe's for proving congruence. It also scales from the pure λ-calculi to the richer calculi with simple congruence proofs.
The third information interaction in context symposium (IIiX'10)
Authors: Kelly Diane , Belkin Nicholas J.
Published: January 2011

The 3rd Information Interaction in Context Symposium (IIiX'10) was held at Rutgers University in New Brunswick, NJ, USA on 18-21 August, 2010. This report provides an overview of the purpose and program of the conference, as well as information about how to access the Proceedings.
Modeling representation uncertainty in concept-based multimedia retrieval
Authors: Aly Robin
Published: January 2011

Representing multimedia documents by means of concepts labels attached to parts of these documents has great potential for improving retrieval performance. The reason is that concepts are independent from how users refer to them and from the modality in which they occur. For example, a Flower and une Fleur refers to the same concept and a singing bird can appear in an image or an audio recording. The question whether a concept occurs in a multimedia document is answered by a concept detector. However, as building concept detectors is difficult the current detection performance is low which causes the retrieval engine to be uncertain about the actual document representation.

This thesis proposes the Uncertain Document Representation Ranking (URR) Framework which deals with this uncertainty by transferring the principles of the Portfolio Selection Theory in finance where the future win of a share is uncertain to the concept-based retrieval problem. Similarly to the distribution of future wins, the retrieval framework considers multiple possible concept-based document representations for each document resulting in multiple possible scores, which is the main scientific contribution of this thesis. Given an existing retrieval function for a certain representation, documents are ranked by the expected score plus an expression of the score's variance.

From the general URR framework, we derive ranking models for shot and video segment retrieval. The shot retrieval and the video segment model re-use the probability of relevance and a language modeling ranking function respectively, basing themselves on decades of text retrieval research. We show in experiments that the models significantly improve performance over several strong baselines in five TRECVid collections.

Furthermore, current performance of concept-based multimedia retrieval is low. A major reason for this is the performance of the concept detectors on which the simulation is based. Therefore, we predict the influence of improved concept detectors on general concept-based retrieval performance using Monte Carlo simulations. We find that more effort is needed to improve concept detectors, but it is realistic for concept-based retrieval to reach performance suitable for large-scale, real-life applications in the future.

Available at http://doc.utwente.nl/72019/ (or http://robin.aly.de, with errata).
Reliability analysis of deduplicated and erasure-coded storage
Authors: Li Xiaozhou , Lillibridge Mark , Uysal Mustafa
Published: January 2011

Space efficiency and data reliability are two primary concerns for modern storage systems. Chunk-based deduplication, which breaks up data objects into single-instance chunks that can be shared across objects, is an effective method for saving storage space. However, deduplication affects data reliability because an object's constituent chunks are often spread across a large number of disks, potentially decreasing the object's reliability. Therefore, an important problem in deduplicated storage is how to achieve space efficiency yet maintain each object's original reliability. In this paper, we present initial results on the reliability analysis of HP-KVS, a deduplicated key-value store that allows each object to specify its own reliability level and that uses software erasure coding for data reliability. The combination of deduplication and erasure coding gives rise to several interesting research problems. We show how to compare the reliability of erasure codes with different parameters and how to analyze the reliability of a big data object given its constituent parts' reliabilities. We also present a method for system designers to determine under what conditions deduplication will save space for erasure-coded data.
In-degree dynamics of large-scale P2P systems
Authors: Yao Zhongmei , Cline Daren B.H. , Loguinov Dmitri
Published: January 2011

This paper builds a complete modeling framework for understanding user churn and in-degree dynamics in unstructured P2P systems in which each user can be viewed as a stationary alternating renewal process. While the classical Poisson result on the superposition of
n
stationary renewal processes for
n
→∞ requires that each point process become sparser as
n
increases, it is often difficult to rigorously show this condition in practice. In this paper, we first prove that despite user heterogeneity and non-Poisson arrival dynamics, a superposition of edge-arrival processes to a live user under uniform selection converges to a Poisson process when system size becomes sufficiently large. Using this finding, we then obtain closed-form results on the transient behavior of in-degree, paving novel ways for a variety of additional analysis of decentralized P2P systems.
A regression approach to infer electricity consumption of legacy telecom equipment
Authors: Phillips Steven , Woodward Sheryl L. , Feuer Mark D. , Magill Peter D.
Published: January 2011

Communications technology has great potential for helping other industries reduce their greenhouse gas emissions. Nevertheless, given the relentless growth of demand for communications services, telecommunications providers will need to transition to more energy-efficient technology in order to limit their own environmental footprint. Here we focus on priority-setting for the transition process. We introduce a method for statistically inferring the electricity consumption of different components of the installed base of telecommunications equipment, while avoiding the high cost of performing direct measurements. Our method relies only on databases of installed equipment in central offices, together with aggregate electricity consumption per office. It takes advantage of inter-office variation in installed equipment to partition per-office electricity consumption by major equipment type. When applied to a collection of 3,918 central offices of a major U.S. telecommunications provider, our approach reveals the (previously unknown) network-wide energy consumption of each major type of equipment. In particular, we find that electricity consumption is dominated by Class-5 telephone switches, which account for 43% of aggregate consumption, and which should therefore be a primary target of central office electricity conservation efforts.
An Interview with Dr. Henry Jenkins
Authors: Gualtieri Lisa
Published: January 2011

Esteemed professor, media and popular culture authority, writer, and self proclaimed Aca/Fan, Dr. Henry Jenkins reflects on digital and media literacy. From Twitter to the perceptions and misconceptions about new media, Jenkins offers a thought provoking take on learning.
Learning minimal abstractions
Authors: Liang Percy , Tripp Omer , Naik Mayur
Published: January 2011

Static analyses are generally parametrized by an abstraction which is chosen from a family of abstractions. We are interested in flexible families of abstractions with many parameters, as these families can allow one to increase precision in ways tailored to the client without sacrificing scalability. For example, we consider k-limited points-to analyses where each call site and allocation site in a program can have a different k value. We then ask a natural question in this paper: What is the minimal (coarsest) abstraction in a given family which is able to prove a set of queries? In addressing this question, we make the following two contributions: (i) We introduce two machine learning algorithms for efficiently finding a minimal abstraction; and (ii) for a static race detector backed by a k-limited points-to analysis, we show empirically that minimal abstractions are actually quite coarse: It suffices to provide context/object sensitivity to a very small fraction (0.4-2.3%) of the sites to yield equally precise results as providing context/object sensitivity uniformly to all sites.