bluuebunny/crossref_metadata_2025 huggingface dataset:
Fine and Hyperfine Structures and Isotope Shifts in the Arc Spectrum of Mercury. Part II. Empirical interpretation
Authors: S Gerstenkorn  , J J Labarthe  , J Vergès
Published: January 2007

An empirical study of the mercury atom is reported. For the odd 6snp (n = 6-8), 6p' and 6s5f configurations, the levels are studied by the parametrical method with configuration interaction. Hyperfine structure and isotope shift parameters are determined for these configurations, taking into account second order hyperfine interaction effects. For the even 6snd (n = 6-8) configurations and the 199 and 201 isotopes an empirical study is made by diagonalizing the total (fine + hyperfine) hamiltonian, neglecting configuration interaction. The 6sns (n = 7-10) configurations are also considered. We discuss the electronic a
6s
factor and propose the value: a
6s
= 1.351 cm-1 for 199Hg.
Trace Element Analysis in Thick Organic Specimens by Photon Excited X-ray Fluorescence
Authors: Gunnar Alenius  , Heinrich Riedl  , Anders Rindby  , Eva Selin  , Paulis Standzenieks
Published: January 2007

Photon excited X-ray fluorescence has been used for quantitative trace element analysis in thick organic specimens. The evaluation of matrix effects has been facilitated by use of a PDP-11 computer which can be connected on line to the data collecting system. The handling of blood serum samples is discussed.
Electron Hopping and Temperature Dependent Oxidation States of Iron in Ilvaite Studied by Mössbauer Effect
Authors: I U Heilmann  , N B Olsen  , J Staun Olsen
Published: January 2007

The Mössbauer spectrum of ilvaite was measured between 115 K and 898 K, and the energy dispersive X-ray powder pattern was measured between 300 K and 1 123 K. Below 500 K the Mössbauer spectrum varies strongly with temperature while the X-ray spectrum remains unchanged. The results are interpreted by electron exchange between nearly identical Fe-sites in ilvaite.
Precise Measurements of the Elastic n-d Differential Cross Section at Low Energy
Authors: L Amtén  , L Gönczi  , A Johansson  , L Nilsson  , B Sundqvist
Published: January 2007

A recoil technique to measure the n-d/n-p differential cross section ratio is discussed. The method has been used to obtain an n-d cross section of 231.2±1.9 mb/sr at 180° and E
n.lab=8.05 MeV. The error is a quadratic combination of uncertainties from a large number of sources including counting statistics. The present lack of knowledge of the reference n-p differential cross section contributes approximately a further uncertainty of 1.5 mb/sr. A Monte Carlo program was used to calculate the average scattering angle and a correction factor to transfer the experimental numbers to an n-d cross section at 180°.
Rediscovering secondary structures as network motifs—an unsupervised learning approach
Authors: Raveh Barak , Rahat Ofer , Basri Ronen , Schreiber Gideon
Published: January 2007

Motivation: Secondary structures are key descriptors of a protein fold and its topology. In recent years, they facilitated intensive computational tasks for finding structural homologues, fold prediction and protein design. Their popularity stems from an appealing regularity in patterns of geometry and chemistry. However, the definition of secondary structures is of subjective nature. An unsupervised de-novo discovery of these structures would shed light on their nature, and improve the way we use these structures in algorithms of structural bioinformatics.

Methods: We developed a new method for unsupervised partitioning of undirected graphs, based on patterns of small recurring network motifs. Our input was the network of all H-bonds and covalent interactions of protein backbones. This method can be also used for other biological and non-biological networks.

Results: In a fully unsupervised manner, and without assuming any explicit prior knowledge, we were able to rediscover the existence of conventional α-helices, parallel β-sheets, anti-parallel sheets and loops, as well as various non-conventional hybrid structures. The relation between connectivity and crystallographic temperature factors establishes the existence of novel secondary structures.

Contact:  barak.raveh@weizmann.ac.il; gideon.schreiber@weizmann.ac.il
Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family
Authors: Najmanovich Rafael J. , Allali-Hassani Abdellah , Morris Richard J. , Dombrovsky Ludmila , Pan Patricia W. , Vedadi Masoud , Plotnikov Alexander N. , Edwards Aled , Arrowsmith Cheryl , Thornton Janet M.
Published: January 2007

Motivation: In the present work we combine computational analysis and experimental data to explore the extent to which binding site similarities between members of the human cytosolic sulfotransferase family correlate with small-molecule binding profiles. Conversely, from a small-molecule point of view, we explore the extent to which structural similarities between small molecules correlate to protein binding profiles.

Results: The comparison of binding site structural similarities and small-molecule binding profiles shows that proteins with similar small-molecule binding profiles tend to have a higher degree of binding site similarity but the latter is not sufficient to predict small-molecule binding patterns, highlighting the difficulty of predicting small-molecule binding patterns from sequence or structure. Likewise, from a small-molecule perspective, small molecules with similar protein binding profiles tend to be topologically similar but topological similarity is not sufficient to predict their protein binding patterns. These observations have important consequences for function prediction and drug design.

Contact:  rafael.najmanovich@ebi.ac.uk
Vorolign—fast structural alignment using Voronoi contacts
Authors: Birzele Fabian , Gewehr Jan E. , Csaba Gergely , Zimmer Ralf
Published: January 2007

Summary: Vorolign, a fast and flexible structural alignment method for two or more protein structures is introduced. The method aligns protein structures using double dynamic programming and measures the similarity of two residues based on the evolutionary conservation of their corresponding Voronoi-contacts in the protein structure. This similarity function allows aligning protein structures even in cases where structural flexibilities exist. Multiple structural alignments are generated from a set of pairwise alignments using a consistency-based, progressive multiple alignment strategy.

Results: The performance of Vorolign is evaluated for different applications of protein structure comparison, including automatic family detection as well as pairwise and multiple structure alignment. Vorolign accurately detects the correct family, superfamily or fold of a protein with respect to the SCOP classification on a set of difficult target structures. A scan against a database of >4000 proteins takes on average 1 min per target. The performance of Vorolign in calculating pairwise and multiple alignments is found to be comparable with other pairwise and multiple protein structure alignment methods.

Availability: Vorolign is freely available for academic users as a web server at

Contact:  fabian.birzele@ifi.lmu.de

Supplementary information: Datasets used throughout the article are available at
Identification of conserved protein complexes based on a model of protein network evolution
Authors: Hirsh Eitan , Sharan Roded
Published: January 2007

Motivation: Data on protein–protein interactions (PPIs) are increasing exponentially. To date, large-scale protein interaction networks are available for human and most model species. The arising challenge is to organize these networks into models of cellular machinery. As in other biological domains, a comparative approach provides a powerful basis for addressing this challenge.

Results: We develop a probabilistic model for protein complexes that are conserved across two species. The model describes the evolution of conserved protein complexes from an ancestral species by protein interaction attachment and detachment and gene duplication events. We apply our model to search for conserved protein complexes within the PPI networks of yeast and fly, which are the largest networks in public databases. We detect 150 conserved complexes that match well-known complexes in yeast and are coherent in their functional annotations both in yeast and in fly. In comparison with two previous approaches, our model yields higher specificity and sensitivity levels in protein complex detection.

Availability: The program is available upon request.

Contact:  roded@tau.ac.il
A comparative genome approach to marker ordering
Authors: Faraut T. , de Givry S. , Chabrier P. , Derrien T. , Galibert F. , Hitte C. , Schiex T.
Published: January 2007

Motivation: Genome maps are fundamental to the study of an organism and essential in the process of genome sequencing which in turn provides the ultimate map of the genome. The increased number of genomes being sequenced offers new opportunities for the mapping of closely related organisms. We propose here an algorithmic formalization of a genome comparison approach to marker ordering.

Results: In order to integrate a comparative mapping approach in the algorithmic process of map construction and selection, we propose to extend the usual statistical model describing the experimental data, here radiation hybrids (RH) data, in a statistical framework that models additionally the evolutionary relationships between a proposed map and a reference map: an existing map of the corresponding orthologous genes or markers in a closely related organism. This has concretely the effect of exploiting, in the process of map selection, the information of marker adjacencies in the related genome when the information provided by the experimental data is not conclusive for the purpose of ordering. In order to compute efficiently the map, we proceed to a reduction of the maximum likelihood estimation to the Traveling Salesman Problem. Experiments on simulated RH datasets as well as on a real RH dataset from the canine RH project show that maps produced using the likelihood defined by the new model are significantly better than maps built using the traditional RH model.

Availability: The comparative mapping approach is available in the last version of de Givry,S. et al. [(2004) Bioinformatics, 21, 1703–1704, ], a free (the LKH part is free for academic use only) mapping software in C++, including LKH (Helsgaun,K. (2000) Eur. J. Oper. Res., 126, 106–130, ) for maximum likelihood computation.

Contact:  thomas.faraut@toulouse.inra.fr
Difference detection in LC-MS data for protein biomarker discovery
Authors: Listgarten Jennifer , Neal Radford M. , Roweis Sam T. , Wong Peter , Emili Andrew
Published: January 2007

Motivation: There is a pressing need for improved proteomic screening methods allowing for earlier diagnosis of disease, systematic monitoring of physiological responses and the uncovering of fundamental mechanisms of drug action. The combined platform of LC-MS (Liquid-Chromatography-Mass-Spectrometry) has shown promise in moving toward a solution in these areas. In this paper we present atechnique for discovering differences in protein signal between two classes of samples of LC-MS serum proteomic data without use of tandem mass spectrometry, gels or labeling. This method works on data from a lower-precision MS instrument, the type routinely used by and available to the community at large today. We test our technique on a controlled (spike-in) but realistic (serum biomarker discovery) experiment which is therefore verifiable. We also develop a new method for helping to assess the difficulty of a given spike-in problem. Lastly, we show that the problem of class prediction, sometimes mistaken as a solution to biomarker discovery, is actually a much simpler problem.

Results: Using precision–recall curves with experimentally extracted ground truth, we show that (1) our technique has good performance using seven replicates from each class, (2) performance degrades with decreasing number of replicates, (3) the signal that we are teasing out is not trivially available (i.e. the differences are not so large that the task is easy). Lastly, we easily obtain perfect classification results for data in which the problem of extracting differences does not produce absolutely perfect results. This emphasizes the different nature of the two problems and also their relative difficulties.

Availability: Our data are publicly available as a benchmark for further studies of this nature at

Supplementary Information:  

Contact:  jenn@cs.toronto.edu
Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases
Authors: Alekseyenko Alexander V. , Lee Christopher J.
Published: January 2007

Motivation: The exponential growth of sequence databases poses a major challenge to bioinformatics tools for querying alignment and annotation databases. There is a pressing need for methods for finding overlapping sequence intervals that are highly scalable to database size, query interval size, result size and construction/updating of the interval database.

Results: We have developed a new interval database representation, the Nested Containment List (NCList), whose query time is O(n + log N), where N is the database size and n is the size of the result set. In all cases tested, this query algorithm is 5–500-fold faster than other indexing methods tested in this study, such as MySQL multi-column indexing, MySQL binning and R-Tree indexing. We provide performance comparisons both in simulated datasets and real-world genome alignment databases, across a wide range of database sizes and query interval widths. We also present an in-place NCList construction algorithm that yields database construction times that are ∼100-fold faster than other methods available. The NCList data structure appears to provide a useful foundation for highly scalable interval database applications.

Availability: NCList data structure is part of Pygr, a bioinformatics graph database library, available at http://sourceforge.net/projects/pygr

Contact: leec@chem.ucla.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Bat echolocation calls: adaptation and convergent evolution
Authors: Jones Gareth , Holderied Marc W
Published: January 2007

Bat echolocation calls provide remarkable examples of ‘good design’ through evolution by natural selection. Theory developed from acoustics and sonar engineering permits a strong predictive basis for understanding echolocation performance. Call features, such as frequency, bandwidth, duration and pulse interval are all related to ecological niche. Recent technological breakthroughs have aided our understanding of adaptive aspects of call design in free-living bats. Stereo videogrammetry, laser scanning of habitat features and acoustic flight path tracking permit reconstruction of the flight paths of echolocating bats relative to obstacles and prey in nature. These methods show that echolocation calls are among the most intense airborne vocalizations produced by animals. Acoustic tracking has clarified how and why bats vary call structure in relation to flight speed. Bats using broadband echolocation calls adjust call design in a range-dependent manner so that nearby obstacles are localized accurately. Recent phylogenetic analyses based on gene sequences show that particular types of echolocation signals have evolved independently in several lineages of bats. Call design is often influenced more by perceptual challenges imposed by the environment than by phylogeny, and provides excellent examples of convergent evolution. Now that whole genome sequences of bats are imminent, understanding the functional genomics of echolocation will become a major challenge.
‘Nasty neighbours’ rather than ‘dear enemies’ in a social carnivore
Authors: Müller Corsin A , Manser Marta B
Published: January 2007

Territorial animals typically respond less aggressively to neighbours than to strangers. This ‘dear enemy effect’ has been explained by differing familiarity or by different threat levels posed by neighbours and strangers. In most species, both the familiarity and the threat-level hypotheses predict a stronger response to strangers than to neighbours. In contrast, the threat-level hypothesis predicts a stronger response to neighbours than to strangers in species with intense competition between neighbours and with residents outnumbering strangers, as commonly found in social mammals such as the banded mongoose (
Mungos mungo
). The familiarity hypothesis predicts reduced aggression towards neighbours also in these species. We exposed free-living banded mongoose groups to translocated scent marks of neighbouring groups and strangers. Groups vocalized more and inspected more samples in response to olfactory cues of the neighbours than to the strangers. Our results support the threat-level hypothesis and contradict the familiarity hypothesis. We suggest that increased aggression towards neighbours is more common in social species with intense competition between neighbours, as opposed to reduced aggression towards neighbours typical for most solitary species.
Genetic isolation through time: allochronic differentiation of a phenologically atypical population of the pine processionary moth
Authors: Santos Helena , Rousselet Jérôme , Magnoux Emmanuelle , Paiva Maria-Rosa , Branco Manuela , Kerdelhué Carole
Published: January 2007

Allochronic speciation refers to a mode of sympatric speciation in which the differentiation of populations is primarily due to a phenological shift without habitat or host change. However, it has been so far rarely documented. The present paper reports on a plausible case of allochronic differentiation between sympatric populations of the pine processionary moth (PPM),Thaumetopoea pityocampa. The PPM is a Mediterranean insect with winter larval development. A phenologically atypical population with early adult activity and summer larval development was detected 10 years ago in Portugal. Mitochondrial and nuclear sequences strongly suggest that the ‘summer’ individuals are closely related to the sympatric winter population, while microsatellite data show a reduction in allelic richness, a distortion of allelic frequencies and significant genetic differentiation. Moreover, monitoring of adult flights suggests that reproductive activity does not overlap between the summer and winter populations. We postulate that the summer population appeared after a sudden phenological shift of some individuals of the sympatric winter population, leading to a founder effect and complete reproductive isolation. Given that the individuals showing this new phenology are subject to different selection pressures, the observed allochronic differentiation may rapidly lead to deeper divergence.
What are we learning from simulating wall turbulence?
Authors: Jiménez Javier , Moser Robert D
Published: January 2007

The study of turbulence near walls has experienced a renaissance in the last decade, largely owing to the availability of high-quality numerical simulations. The viscous and buffer layers over smooth walls are essentially independent of the outer flow, and there is a family of numerically exact nonlinear structures that account for about half of the energy production and dissipation. The rest can be modelled by their unsteady bursting. Many characteristics of the wall layer, such as the dimensions of the dominant structures, are well predicted by those models, which were essentially completed in the 1990s after the increase in computer power made the kinematic simulations of the late 1980s cheap enough to undertake dynamic experiments.

Today, we are at the early stages of simulating the logarithmic (or overlap) layer, and a number of details regarding its global properties are becoming clear. For instance, a finite Reynolds number correction to the logarithmic law has been validated in turbulent channels. This has allowed upper and lower limits of the overlap region to be clarified, with both upper and lower bounds occurring at much larger distances from the wall than commonly assumed. A kinematic picture of the various cascades present in this part of the flow is also beginning to emerge. Dynamical understanding can be expected in the next decade.
A physical model of the turbulent boundary layer consonant with mean momentum balance structure
Authors: Klewicki Joe , Fife Paul , Wei Tie , McMurtry Pat
Published: January 2007

Recent studies by the present authors have empirically and analytically explored the properties and scaling behaviours of the Reynolds averaged momentum equation as applied to wall-bounded flows. The results from these efforts have yielded new perspectives regarding mean flow structure and dynamics, and thus provide a context for describing flow physics. A physical model of the turbulent boundary layer is constructed such that it is consonant with the dynamical structure of the mean momentum balance, while embracing independent experimental results relating, for example, to the statistical properties of the vorticity field and the coherent motions known to exist. For comparison, the prevalent, well-established, physical model of the boundary layer is briefly reviewed. The differences and similarities between the present and the established models are clarified and their implications discussed.
The near-neutral atmospheric surface layer: turbulence and non-stationarity
Authors: Metzger M , McKeon B.J , Holmes H
Published: January 2007

The neutrally stable atmospheric surface layer is used as a physical model of a very high Reynolds number, canonical turbulent boundary layer. Challenges and limitations with this model are addressed in detail, including the inherent thermal stratification, surface roughness and non-stationarity of the atmosphere. Concurrent hot-wire and sonic anemometry data acquired in Utah's western desert provide insight to Reynolds number trends in the axial velocity statistics and spectra.
A model biological neural network: the cephalopod vestibular system
Authors: Williamson Roddy , Chrachri Abdul
Published: January 2007

Artificial neural networks (ANNs) have become increasingly sophisticated and are widely used for the extraction of patterns or meaning from complicated or imprecise datasets. At the same time, our knowledge of the biological systems that inspired these ANNs has also progressed and a range of model systems are emerging where there is detailed information not only on the architecture and components of the system but also on their ontogeny, plasticity and the adaptive characteristics of their interconnections. We describe here a biological neural network contained in the cephalopod statocysts; the statocysts are analogous to the vertebrae vestibular system and provide the animal with sensory information on its orientation and movements in space. The statocyst network comprises only a small number of cells, made up of just three classes of neurons but, in combination with the large efferent innervation from the brain, forms an ‘active’ sense organs that uses feedback and feed-forward mechanisms to alter and dynamically modulate the activity within cells and how the various components are interconnected. The neurons are fully accessible to physiological investigation and the system provides an excellent model for describing the mechanisms underlying the operation of a sophisticated neural network.
CONFIDENCE INTERVALS FOR POLICY REFORMS IN BEHAVIOURAL TAX MICROSIMULATION MODELLING
Authors: Creedy John , Kalb Guyonne , Kew Hsein
Published: January 2007

This paper addresses the need for a measure of the uncertainty that is associated with the results calculated using tax policy behavioural microsimulation models. Deriving the analytical measure would be extremely complicated. Therefore, a simulated approach is proposed, which approximates the sampling distribution of aggregate measures based on the sampling distribution of the estimated labour supply parameters. This approach, which is very computer intensive, is compared with a more time‐efficient approach where the functional form of the sampling distribution is assumed to be normal. The results show that in many instances the results from the two approaches are quite similar. The exception is when aggregate measures for minor types of payments, involving relatively small groups of the population, are examined.
Comparison of Single‐Point and Multipoint Grinding Damage in Glass
Authors: KIRCHNER HENRY P.
Published: January 2007

Glass plates were damaged by single‐point and multipoint grinding at various set depths and wheel speeds to evaluate the usefulness of single‐point grinding to simulate the mechanisms of damage penetration and material removal during multipoint grinding. The observed damage was much more severe in single‐point than in multipoint grinding. In both single‐point and multipoint grinding, the vertical load (Pv) dependence of the crack depth (c) Pv∞c1.2. In glass, the effect of the residual stresses in reducing the remaining strengths of the damaged bars was less than that observed for other ceramics previously investigated, mainly because much of the irreversibly deformed zone was removed by crushing. The advantages and disadvantages of using single‐point grinding to simulate multipoint grinding are discussed.
Genome‐wide array‐based comparative genomic hybridization analysis of pancreatic adenocarcinoma: Identification of genetic indicators that predict patient outcome
Authors: Loukopoulos Panayiotis , Shibata Tatsuhiro , Katoh Hiroto , Kokubu Akiko , Sakamoto Michiie , Yamazaki Ken , Kosuge Tomoo , Kanai Yae , Hosoda Fumie , Imoto Issei , Ohki Misao , Inazawa Jyoji , Hirohashi Setsuo
Published: January 2007

We analyzed the subchromosomal numerical aberrations of 44 surgically resected pancreatic adenocarcinomas by array‐based comparative genomic hybridization. The aberration profile ranged widely between cases, suggesting the presence of multiple or complementary mechanisms of evolution in pancreatic cancer, and was associated with lymph node metastasis and venous or serosal invasion. A large number of small loci, previously uncharacterized in pancreatic cancer, showed non‐random loss or gain. Frequent losses at 1p36, 4p16, 7q36, 9q34, 11p15, 11q13, 14q32‐33, 16p13, 17p11‐13, 17q11‐25, 18q21‐tel, 19p13, 21q22 and 22q11‐12, and gains at 1q25, 2p16, 2q21‐37, 3q25, 5p14, 5q11‐13, 7q21, 7p22, 8p22, 8q21‐23, 10q21, 12p13, 13q22, 15q13‐22 and 18q11 were identified. Sixteen loci were amplified recurrently. We identified novel chromosomal alterations that were significantly associated with a range of malignant phenotypes. Gain of LUNX, HCK, E2F1 and DNMT3b at 20q11, loss of p73 at 1p36 and gain of PPM1D at 17q23 independently predicted patient outcome. Expression profiling of amplified genes identified Smurf1 and TRRAP at 7q22.1, BCAS1 at 20q13.2‐3, and VCL at 10q22.1 as potential novel oncogenes. Our results contribute to a complete description of genomic structural aberrations and the identification of potential therapeutic targets and genetic indicators that predict patient outcome in pancreatic adenocarcinoma. (Cancer Sci 2007; 98: 392–400)
Depression of T cell‐mediated immunity reduces sulfadimethoxine‐induced capsular inflammation and inhibits associated development of invasive thyroid follicular cell carcinomas in rats
Authors: Imai Toshio , Hasumura Mai , Cho Young‐Man , Onose Jun‐ichi , Hirose Masao
Published: January 2007

We previously demonstrated that thyroid capsular inflammation induced by continuous treatment with the antithyroidal agent sulfadimethoxine is associated with development of invasive follicular cell carcinomas in rats initiated with N‐bis(2‐hydroxypropyl)nitrosamine (DHPN). The inflammatory changes are characterized by large numbers of macrophages and lymphocytes as well as fibroblasts and we hypothesized that it might be enhanced by interplay between macrophages and T cells. To clarify this hypothesis, a comparative study was conducted between athymic nude (rnu/rnu) rats and euthymic (rnu/+) littermates initiated with DHPN (2800 mg/kg, s.c.) followed by sulfadimethoxine treatment in drinking water (0.1%) for 10 weeks. In rnu/+rats, marked capsular thickening with inflammation was induced along with invasive follicular cell carcinomas (2.8 ± 1.3/rat). In rnu/rnu rats, limited fibrous capsular thickening was noted with or without minimal inflammatory change, and the multiplicity of invasive carcinomas was significantly lower (1.1 ± 1.0/rat, P < 0.01). Inducible nitric oxide synthase expression in the inflamed lesions was detected in three of 10 rnu/+rats but in none of the rnu/rnu animals. The results thus suggest that development of invasive carcinomas is enhanced by capsular inflammation mediated by T cells, and inducible nitric oxide synthase induction may play a role in tumor progression. (Cancer Sci 2007; 98: 294–298)
Local interferon‐α gene therapy elicits systemic immunity in a syngeneic pancreatic cancer model in hamster
Authors: Hara Hidehiko , Kobayashi Akihiko , Yoshida Kimiko , Ohashi Masaki , Ohnami Shumpei , Uchida Eiji , Higashihara Eiji , Yoshida Teruhiko , Aoki Kazunori
Published: January 2007

The interferon (IFN) protein is a cytokine with pleiotropic biological functions that include induction of apoptosis, inhibition of angiogenesis and immunomodulation. We previously examined the two antitumor mechanisms, taking advantage of the fact that IFN‐α did not show cross‐species activity in its in vivo effect. In a nude mouse subcutaneous xenograft model using human pancreatic cancer cells, the expression of human IFN‐α effectively induced cell death of human pancreatic cancer cells, whereas mouse IFN‐α augmented antitumor immunity by stimulation of natural killer cells. Here, we extended our investigation to a syngeneic pancreatic cancer model, so that the integrated antitumor activity of local IFN‐α gene therapy, including the antiproliferative, proapoptotic, antiangiogeneic and immunomodulatory effects, can be evaluated rigorously. When a recombinant hamster IFN‐α adenovirus was injected into syngeneic subcutaneous tumors of hamster pancreatic cancer (PGHAM‐1) cells in Syrian hamster, tumor growth was significantly suppressed due to cell death and T cell‐ and natural killer cell‐mediated antitumor immunity. Moreover, in this case, tumor regression was observed not only for the injected subcutaneous tumors but also for the untreated tumors both in the peritoneal cavity and at distant sites. No significant systemic toxicity was observed in the treated hamsters. Moreover, the subcutaneous rechallenge of PGHAM‐1 cells was rejected in three of four cured hamsters from the initial tumor challenge. This study further demonstrated that local IFN‐α gene therapy is a promising therapeutic strategy for pancreatic cancer, due to its multiple mechanisms of antitumor activity and its lack of significant toxicity. (Cancer Sci 2007; 98: 455–463))
Significance of error‐avoiding mechanisms for oxidative DNA damage in carcinogenesis
Authors: Tsuzuki Teruhisa , Nakatsu Yoshimichi , Nakabeppu Yusaku
Published: January 2007

Reactive oxygen species (ROS) are produced through normal cellular metabolism, and their formation is further enhanced by exposure to ionizing radiation and various chemicals. ROS attack DNA, and the resulting oxidative DNA damage is considered to contribute to aging, carcinogenesis and neurodegeneration. Among various types of oxidative DNA damage, 8‐oxo‐7,8‐dihydroguanine (8‐oxoguanine or 8‐oxoG) is the most abundant, and plays significant roles in mutagenesis because of its ability to pair with adenine as well as cytosine. Enzymatic activities that may be responsible for preventing 8‐oxoG‐evoked mutations were identified in mammalian cells. We have focused on the following three enzymes: MTH1, OGG1 and MUTYH. MTH1 is a mammalian ortholog of Escherichia coli MutT, which hydrolyzes 8‐oxo‐dGTP to its monophosphate form in nucleotide pools, thereby preventing incorporation of the mutagenic substrate into DNA. OGG1, a functional counterpart of E. coli MutM, has an 8‐oxoG DNA glycosylase activity. MUTYH, a mammalian ortholog of E. coli MutY, excises an adenine paired with 8‐oxoG. These three enzymes are thought to prevent mutagenesis caused by 8‐oxoG in mammals. To analyze the functions of mammalian MTH1 (Mth1), OGG1 (Ogg1) and MUTYH (Mutyh) in vivo, we established mutant mice for these three enzymes by targeted mutagenesis, and investigated spontaneous tumorigenesis as well as mutagenesis. Here we discuss our recent investigation of mutagenesis and carcinogenesis in these mutant mice. (Cancer Sci 2007; 98: 465–470)
Perceived freedom in leisure and physical co‐ordination ability: impact on out‐of‐school activity participation and life satisfaction
Authors: Poulsen A. A. , Ziviani J. M. , Cuskelly M.
Published: January 2007

Background  Perceived freedom in leisure (PFL) is explored as a potential mechanism mediating relationships between physical co‐ordination ability and both global life satisfaction and leisure‐time physical activity participation for boys with differing levels of physical co‐ordination ability. Understanding psychological mechanisms contributing to low rates of participation in physical activities for boys with developmental co‐ordination disorder (DCD) is a clinical and research priority with potential to inform clinical interventions and preventive health initiatives.

Method  Sixty boys aged 10–13 years with DCD and 113 boys without DCD completed self‐report measures of PFL and life satisfaction. Seven‐day leisure‐time activity diaries and 12‐month retrospective recall questionnaires were completed by parents.

Results  Lower self‐appraisals of PFL and overall life satisfaction were found for boys with DCD compared with boys without DCD. PFL mediated relationships between physical ability and both life satisfaction and team sport participation.

Conclusion  Perceived freedom in leisure, comprising self‐appraisals of leisure needs satisfaction and competence, depth of involvement and perceived control over leisure outcomes, was a significant mechanism influencing leisure‐time participation and life satisfaction for boys. The implications for effective intervention and preventive health programmes are discussed.
Corrosive poisoning mimicking cicatricial pemphigoid: Munchausen by proxy
Authors: Tamay Z. , Akcay A. , Kilic G. , Peykerli G. , Devecioglu E. , Ones U. , Guler N.
Published: January 2007

Background  Munchausen by proxy (MBP) is a severe form of abuse in which a caregiver simulates or fabricates illness in another person, primarily the elderly and children, which can even result in death.

Case  We report two siblings who were victims of MBP, one of whom died. A very rare diagnosis, cicatricial pemphigoid was suspected in the 2‐year‐old girl who was first abused. She was hospitalized twice, for 3 and 4 months, respectively. Her second hospitalization ended with her death. MBP was diagnosed after the second sibling's admission with similar atypical signs and symptoms. It was realized that a household‐cleaning product, sodium hydroxide, was administered repeatedly by oral route to the children by their own mother.

Conclusions  Physicians must consider the diagnosis of MBP whenever they are confronted with unusual, persistent or recurrent signs and symptoms in a child.
Performance on the Movement Assessment Battery for Children by Australian 3‐ to 5‐year‐old children
Authors: Livesey D. , Coleman R. , Piek J.
Published: January 2007

Background  The Movement Assessment Battery for Children (Movement ABC) was developed as a means of identifying those at risk of motor impairment. This test has been widely adopted as a means of assessing Australian children, but no attempt has been made to test the validity of its normative data for Australian samples. This study examines the 4‐ and 5‐year‐old Australian data in comparison with the Movement ABC age norms. Additionally, a 3‐year‐old sample was tested to determine if the test is suitable for discriminating motor performance in this age group.

Methods  Representative samples of 3‐, 4‐ and 5‐year‐old children from two Australian cities (Sydney and Perth) were tested on the Movement ABC band‐one tests and the results compared with 4‐ and 5‐year norms.

Results  There was significant age‐related change in performance across the Australian samples with significant gender effects on some tasks. The Australian 4‐year‐old children performed better than the American sample on most tests, but this difference had disappeared by 5 years.

Conclusion  The results indicate that the Movement ABC is a useful tool in discriminating among pre‐school Australian children as young as 3 years of age. The differences between Australian and American children indicate that further studies comparing other age groups are warranted, but the differences did not appear to be sufficiently large to have clinical significance.
Expression of c‐kit and Sca‐1 and their relationship with multidrug resistance protein 1 in mouse bone marrow mononuclear cells
Authors: Kyle‐Cezar Fernanda , Echevarria‐Lima Juliana , Goldenberg Regina Coeli dos Santos , Rumjanek Vivian M.
Published: January 2007

P‐glycoprotein (Pgp) and multidrug resistance protein 1 (MRP1) are members of the ATP‐binding cassette (ABC) family of transporter proteins. Both molecules are membrane‐associated, energy‐dependent efflux pumps with different substrate selectivity and they may play a role in the activation, differentiation and function of haematopoietic cells. Mouse haematopoietic cells are characterized by the expression of the cell surface molecules c‐kit and Sca‐1. Herein, the presence and activities of Pgp and MRP1 in mouse bone marrow mononuclear cells (BMMC) and their relationship with the proteins c‐kit and Sca‐1 were evaluated. Pgp and MRP activities were measured based on the extrusion of rhodamine 123 (for Pgp) and Fluo‐3 (for MRP). Cell populations were assessed by cytometry using anti‐c‐kit and anti‐Sca1 antibodies. Pgp activity was present in 5% of BMMC while 50% of BMMC cells showed MRP activity. These findings agreed with the proportion of cells expressing the MRP1 surface molecule (51·3 ± 4·17%). About 14% of BMMC were positive for c‐kit and/or Sca‐1 (9·3% c‐kit– Sca‐1+, 4·2% c‐kit+ Sca‐1– and 0·9% c‐kit+ Sca‐1+). Among these subpopulations only c‐kit– Sca‐1+ cells presented Pgp activity (21·36%). On the other hand, MRP activity was present in all three subpopulations. Most cells (82·5%) of the c‐kit+ Sca‐1– subpopulation presented MRP1 activity compared to only 54·1% of c‐kit+ Sca‐1+ and 38·8% of c‐kit– Sca‐1+. This study demonstrates the expression and activity of MRP1 in BMMC. While only a small proportion of precursor cells had Pgp activity, MRP1 activity was present among different subpopulations of precursor cells. Further studies are necessary to establish the role of these transporters in haematopoietic cells.
Fracture resistance of the buccal cuSPS of root filled maxillary premolar teeth restored with various techniques
Authors: Siso Ş. H. , Hürmüzlü F. , Turgut M. , Altundaşar E. , Serper A. , Er K.
Published: January 2007

Aim  To compare the cusp fracture resistance of teeth restored with composite resins and two post systems.

Methodology  Eighty extracted single‐rooted human maxillary premolars were randomly assigned to eight groups (n = 10). Group 1 (control) did not receive any preparation. From groups 2 to 8, the teeth were root filled and mesio‐occluso‐distal (MOD) cavities were prepared. Group 2 remained unrestored. Group 3 was restored with packable resin composite using a single‐step adhesive. Group 4 was restored with packable resin composite using a single‐step adhesive and a thin layer of flowable resin composite. Group 5 was restored with packable resin composite using a total‐etch two‐step adhesive. Group 6 was restored with ormocer resin composite using a total‐etch two‐step adhesive. Group 7 was restored with an endodontic glass fibre post and hybrid resin composite using a total‐etch two‐step adhesive. Group 8 was restored with an endodontic zirconium post and hybrid resin composite using a total‐etch two‐step adhesive. The teeth were then mounted in a universal testing machine, the buccal cusp loaded (30°) until fracture, and the data analysed statistically.

Results  Group 1 had the greatest fracture resistance, and group 2 the poorest. Groups 5–8 had significantly greater (P < 0.05) fracture resistance than groups 3 and 4. No significant differences were found between groups 3 and 4, or amongst groups 5–8 (P > 0.05).

Conclusions  For root filled maxillary premolars with MOD cavities, adhesive resin composite restorations, with and without glass and zirconium posts, increased the fracture resistance of the buccal cuSPS. A total‐etch two‐step adhesive increased significantly fracture resistance more than a one‐step adhesive. For the one‐step adhesive, an additional layer of flowable resin composite did not enhance fracture resistance.
Imaging of root canal fillings: a comparison of subjective image quality between limited cone‐beam CT, storage phosphor and film radiography
Authors: Soğur E. , Baksı B. G. , Gröndahl H.‐G.
Published: January 2007

Aim  To compare the subjective quality of limited cone‐beam computed tomography (LCBCT), storage phosphor plate (SPP) and F‐speed film images for the evaluation of length and homogeneity of root fillings.

Methodology  Root canals of 17 extracted permanent mandibular incisor teeth were filled. With the teeth placed in their jaws, images were obtained with Accu‐I‐Tomo LCBCT, Digora® Optime image plate system and F‐speed film using exposure parameters yielding ‘clinically’ acceptable density and contrast. Three radiologists and three endodontists independently rated the quality of all images in respect to homogeneity and the length of root fillings using a 3‐graded scale. Evaluations were undertaken in two sessions. In the first, the coronal LCBCT images were not included. In the second, both coronal and sagittal LCBCT images were rated along with F‐speed film and SPP images. Results were compared using the Friedman test (P < 0.05). Pair‐wise comparisons of systems were completed using the Wilxocon signed‐ranks test (P < 0.05). Kappa was used to measure interobserver agreement.

Results  Digora images were rated superior, consecutively followed by F‐speed films and LCBCT images, for the evaluation of both homogeneity and length of root fillings in both the evaluation sessions (P < 0.05). Kappa ranged from slight to moderate for the length evaluation of root fillings and from poor to fair for the evaluation of homogeneity of root fillings.

Conclusion  Image quality of storage phosphor images was subjectively as good as conventional film images and superior to LCBCT images for the evaluation of both homogeneity and length of root fillings in single‐rooted teeth.
Long‐term follow‐up of a complicated crown fracture treated by partial pulpotomy
Authors: Sonmez I.S. , Sonmez H.
Published: January 2007

Aim  To present the 7‐year follow‐up of a permanent incisor with complicated crown fracture, treated by partial pulpotomy.

Summary  A healthy permanent right central maxillary incisor with complicated crown fracture was treated by partial pulpotomy and reviewed clinically and radiographically for 7 years. At each recall, there was no spontaneous pain; the pulp showed signs of vitality and no periapical radiolucency developed.

Key learning points

• Partial pulpotomy may be a successful permanent treatment in cases of complicated crown fracture.
Clinical evaluation of root filled teeth restored with or without post‐and‐core systems in a specialist practice setting
Authors: Salvi G. E. , Siegrist Guldener B. E. , Amstad T. , Joss A. , Lang N. P.
Published: January 2007

Aim  To assess survival rates and complications of root‐filled teeth restored with or without post‐and‐core systems over a mean observation period of ≥4 years.

Methodology  A total of 325 single‐ and multirooted teeth in 183 subjects treated in a private practice were root filled and restored with either a cast post‐and‐core or with a prefabricated titanium post and composite core. Root‐filled teeth without post‐retained restorations served as controls. The restored teeth served as abutments for single unit metal‐ceramic or composite crowns or fixed bridges. Teeth supporting cantilever bridges, overdentures or telescopic crowns were excluded.

Results  Seventeen teeth in 17 subjects were lost to follow‐up (17/325: 5.2%). The mean observation period was 5.2 ± 1.8 (SD) years for restorations with titanium posts, 6.2 ± 2.0 (SD) years for cast post‐and‐cores and 4.4 ± 1.7 (SD) years for teeth without posts. Overall, 54% of build‐ups included the incorporation of a titanium post and 26.5% the cementation of a cast post‐and‐core. The remaining 19.5% of the teeth were restored without intraradicular retention. The adjusted 5‐year tooth survival rate amounted to 92.5% for teeth restored with titanium posts, to 97.1% for teeth restored with cast post‐and‐cores and to 94.3% for teeth without post restorations, respectively. The most frequent complications included root fracture (6.2%), recurrent caries (1.9%), post‐treatment periradicular disease (1.6%) and loss of retention (1.3%).

Conclusion  Provided that high‐quality root canal treatment and restorative protocols are implemented, high survival and low complication rates of single‐ and multirooted root‐filled teeth used as abutments for fixed restorations can be expected after a mean observation period of ≥4 years.
Predictive factors for an increased risk of sperm aneuploidies in oligo‐astheno‐teratozoospermic males
Authors: Faure A. K. , Aknin‐Seifer I. , Frérot G. , Pelletier R. , De Robertis C. , Cans C. , Levy R. , Jimenez C. , Lejeune H. , Terrier N. , Bergues U. , Hennebicq S. , Rousseaux S.
Published: January 2007

Patients with severe spermatogenesis impairment can now successfully father a child thanks to the use of intracytoplasmic sperm injection (ICSI). In oligozoospermic patients, many studies have reported significantly higher sperm aneuploidy rates and therefore an increased risk of transmitting a chromosomal abnormality via the injection of abnormal spermatozoa. However, the frequency of aneuploidy is highly variable between patients. The aim of the present work was to identify clinical and biological factors, which, together with non‐obstructive oligozoospermia, could be predictive of elevated sperm aneuploidies. The sperm aneuploidy rates for chromosomes X, Y, 13, 18 and 21 were assessed in 31 infertile men with well‐characterized spermatogenesis impairment, and in a population of control men with proven fertility. The frequency of sperm aneuploidy was compared between several patient subgroups according to their clinical and biological factors. Nearly half of the oligozoospermic males (15/31) had a significantly increased disomy rate for at least one of the five chromosomes compared with that observed in the control population (mean disomy rates + 1.96 standard deviation). Factors significantly associated with higher numbers of aneuploid sperm were cigarette smoking, an elevated follicle‐stimulating hormone level, a sperm concentration less than 1 m/mL, and a severe teratozoospermia. Hence, several factors predictive of an increased risk of sperm aneuploidy rates were identified in ICSI male candidates with a non‐obstructive oligozoospermia.