bluuebunny/crossref_metadata_2025_split huggingface dataset:
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.SummaryBackground
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 differentiationAims:  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.AbstractAim  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.AbstractAim  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.
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

AimsTo 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.MethodsThe 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.ResultsThe 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.ConclusionsThe 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

IntroductionFine 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.Methods161 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.ResultsFNAC 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).ConclusionsFNAC 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

AimsPan-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.MethodsCIQC 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.ResultsParticipating 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.ConclusionsParticipation 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.
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).
A parametric segmentation functor for fully automatic and scalable array content analysis
Authors: Cousot Patrick , Cousot Radhia , Logozzo Francesco 
Published: January 2011

We introduce FunArray, a parametric segmentation abstract domain functor for the fully automatic and scalable analysis of array content properties. The functor enables a natural, painless and efficient lifting of existing abstract domains for scalar variables to the analysis of uniform compound data-structures such as arrays and collections. The analysis automatically and semantically divides arrays into consecutive non-overlapping possibly empty segments. Segments are delimited by sets of bound expressions and abstracted uniformly. All symbolic expressions appearing in a bound set are equal in the concrete. The FunArray can be naturally combined via reduced product with any existing analysis for scalar variables. The analysis is presented as a general framework parameterized by the choices of bound expressions, segment abstractions and the reduction operator. Once the functor has been instantiated with fixed parameters, the analysis is fully automatic.
We first prototyped FunArray in Arrayal to adjust and experiment with the abstractions and the algorithms to obtain the appropriate precision/ratio cost. Then we implemented it into Clousot, an abstract interpretation-based static contract checker for .NET. We empirically validated the precision and the performance of the analysis by running it on the main libraries of .NET and on its own code. We were able to infer thousands of non-trivial invariants and verify the implementation with a modest overhead (circa 1%). To the best of our knowledge this is the first analysis of this kind applied to such a large code base, and proven to scale.
Multivariate amortized resource analysis
Authors: Hoffmann Jan , Aehlig Klaus , Hofmann Martin 
Published: January 2011

We study the problem of automatically analyzing the worst-case resource usage of procedures with several arguments. Existing automatic analyses based on amortization, or sized types bound the resource usage or result size of such a procedure by a sum of unary functions of the sizes of the arguments.

In this paper we generalize this to arbitrary multivariate polynomial functions thus allowing bounds of the form
mn
which had to be grossly overestimated by

m
2
+n
2

before. Our framework even encompasses bounds like

∗
i,j≤n
m_i m
j

where the

m
i

are the sizes of the entries of a list of length
n
.

This allows us for the first time to derive useful resource bounds for operations on matrices that are represented as lists of lists and to considerably improve bounds on other super-linear operations on lists such as longest common subsequence and removal of duplicates from lists of lists.
Furthermore, resource bounds are now closed under composition which improves accuracy of the analysis of composed programs when some or all of the components exhibit super-linear resource or size behavior.
The analysis is based on a novel multivariate amortized resource analysis. We present it in form of a type system for a simple first-order functional language with lists and trees, prove soundness, and describe automatic type inference based on linear programming.
We have experimentally validated the automatic analysis on a wide range of examples from functional programming with lists and trees. The obtained bounds were compared with actual resource consumption. All bounds were asymptotically tight, and the constants were close or even identical to the optimal ones.
The Development of Cortical Sensitivity to Visual Word Forms
Authors: Ben-Shachar Michal , Dougherty Robert F. , Deutsch Gayle K. , Wandell Brian A. 
Published: January 2011

Abstract
The ability to extract visual word forms quickly and efficiently is essential for using reading as a tool for learning. We describe the first longitudinal fMRI study to chart individual changes in cortical sensitivity to written words as reading develops. We conducted four annual measurements of brain function and reading skills in a heterogeneous group of children, initially 7–12 years old. The results show age-related increase in children's cortical sensitivity to word visibility in posterior left occipito-temporal sulcus (LOTS), nearby the anatomical location of the visual word form area. Moreover, the rate of increase in LOTS word sensitivity specifically correlates with the rate of improvement in sight word efficiency, a measure of speeded overt word reading. Other cortical regions, including V1, posterior parietal cortex, and the right homologue of LOTS, did not demonstrate such developmental changes. These results provide developmental support for the hypothesis that LOTS is part of the cortical circuitry that extracts visual word forms quickly and efficiently and highlight the importance of developing cortical sensitivity to word visibility in reading acquisition.
Baroclinic Stationary Waves in Aquaplanet Models
Authors: Zappa Giuseppe , Lucarini Valerio , Navarra Antonio 
Published: January 2011

Abstract
An aquaplanet model is used to study the nature of the highly persistent low-frequency waves that have been observed in models forced by zonally symmetric boundary conditions.
Using the Hayashi spectral analysis of the extratropical waves, the authors find that a quasi-stationary wave 5 belongs to a wave packet obeying a well-defined dispersion relation with eastward group velocity. The components of the dispersion relation with k ≥ 5 baroclinically convert eddy available potential energy into eddy kinetic energy, whereas those with k &lt; 5 are baroclinically neutral. In agreement with Green’s model of baroclinic instability, wave 5 is weakly unstable, and the inverse energy cascade, which had been previously proposed as a main forcing for this type of wave, only acts as a positive feedback on its predominantly baroclinic energetics. The quasi-stationary wave is reinforced by a phase lock to an analogous pattern in the tropical convection, which provides further amplification to the wave. It is also found that the Pedlosky bounds on the phase speed of unstable waves provide guidance in explaining the latitudinal structure of the energy conversion, which is shown to be more enhanced where the zonal westerly surface wind is weaker. The wave’s energy is then trapped in the waveguide created by the upper tropospheric jet stream. In agreement with Green’s theory, as the equator-to-pole SST difference is reduced, the stationary marginally stable component shifts toward higher wavenumbers, while wave 5 becomes neutral and westward propagating.
Some properties of the aquaplanet quasi-stationary waves are found to be in interesting agreement with a low frequency wave observed by Salby during December–February in the Southern Hemisphere so that this perspective on low frequency variability, apart from its value in terms of basic geophysical fluid dynamics, might be of specific interest for studying the earth’s atmosphere.