bluuebunny/crossref_metadata_2025 huggingface dataset:
Music training, engagement with sequence, and the development of the natural number concept in young learners
Authors: Gardiner Martin F.
Published: December 2008

Studies by Gardiner and colleagues connecting musical pitch and arithmetic learning support Rips et al.'s proposal that natural number concepts are constructed on a base of innate abilities. Our evidence suggests that innate ability concerning sequence (“Basic Sequencing Capability” or BSC) is fundamental. Mathematical engagement relating number to BSC does not develop automatically, but, rather, should be encouraged through teaching.
The role of the brain in the metaphorical mathematical cognition
Authors: Lakoff George
Published: December 2008

Rips et al. appear to discuss, and then dismiss with counterexamples, the brain-based theory of mathematical cognition given in Lakoff and Núñez (2000). Instead, they present another theory of their own that they correctly dismiss. Our theory is based on neural learning. Rips et al. misrepresent our theory as being directly about real-world experience and mappings directly from that experience.
Why cardinalities are the “natural” natural numbers
Authors: Le Corre Mathieu
Published: December 2008

According to Rips et al., numerical cognition develops out of two independent sets of cognitive primitives – one that supports enumeration, and one that supports arithmetic and the concepts of natural numbers. I argue against this proposal because it incorrectly predicts that natural number concepts could develop without prior knowledge of enumeration.
The development of modeling or the modeling of development?
Authors: Rakison David H. , Lupyan Gary
Published: December 2008

We agree with many theoretical points presented by Rogers & McClelland (R&M), especially the role of domain-general learning of coherent covariation. Nonetheless, we argue that in failing to be informed by key aspects of development, including the role of labels on categorization and the emergence of constraints on learning, their model fails to capture important features of the ontogeny of knowledge.
Action or inaction? Food and nutrition in Australian local governments
Authors: Yeatman Heather
Published: December 2008

Objective

To determine the current level of activity of Australian local governments in twenty-nine food and nutrition action areas and whether the level of activity had changed between 1995 and 2007.

Design

A cross-sectional study utilising a postal survey was undertaken of all local governments in Australia. The same instrument and protocol were used in 1995 and 2007.

Setting

Australian local governments.

Results

Local governments in Australia continue to be engaged in food and nutrition activities. This involvement has constricted in range in the last 12 years but higher levels of engagement are reported for several areas. The levels of involvement of local governments in the different states varied significantly, with Victoria reporting higher levels of involvement in several areas, particularly in food and nutrition activities related to community services. Local governments in New South Wales and Western Australia reported significantly lower levels of involvement in food and nutrition activities. Several factors may have contributed to these differences, including availability of resources and support, mandatory requirements by state governments, different attitudes of General Managers and staff and availability of funds for special projects.

Conclusions

If Australian local governments are to be recognised and supported for their involvements in food and nutrition activities, more in-depth research is required to elucidate the factors that act as barriers or facilitate their on-going involvement in this important area. Support for local governments in rural areas to become or remain engaged in food matters should receive special consideration.
Do contrails significantly reduce daily temperature range?
Authors: Hong Gang , Yang Ping , Minnis Patrick , Hu Yong X. , North Gerald
Published: December 2008

One of the most visible anthropogenic phenomena in the atmosphere is the occurrence of contrails. The direct effects of contrails on surface temperature are investigated on the basis of the data sets for the cloud cover and surface temperature over the conterminous United States for the period 1971–2001. It is shown that the increase of the average daily temperature range (DTR) over the United States during the three‐day grounding period of 11–14 September 2001 cannot be attributed to the absence of contrails, a subject was debated in several previous studies. The present analysis suggests that the DTR is attributed to the change of low cloudiness.
Structural changes of filled ice Ic structure for hydrogen hydrate under high pressure
Authors: Machida Shin-ichi , Hirai Hisako , Kawamura Taro , Yamamoto Yoshitaka , Yagi Takehiko
Published: December 2008

High-pressure experiments of hydrogen hydrate, filled ice Ic structure, were performed using a diamond-anvil cell in the pressure range of 0.1–80.3 GPa at room temperature. In situ x-ray diffractometry (XRD) revealed that structural changes took place at approximately 35–40 and 55–60 GPa, and that the high-pressure phase of hydrogen hydrate survived up to at least 80.3 GPa. Raman spectroscopy showed that the changes in vibrational mode for the hydrogen molecules in hydrogen hydrate occurred at around 40 and 60 GPa, and these results were consistent with those of the XRD. At about 40 GPa, the intermolecular distance of host water molecules consisting the framework attained the critical distance of symmetrization of the hydrogen bond for water molecules, which suggested that symmetrization of the hydrogen bond occurred at around 40 GPa. The symmetrization might introduce some structural change in the filled ice Ic structure. In addition, the existence of the high-pressure phase above 55–60 GPa implies that a denser structure than that of filled ice Ic may exist in hydrogen hydrate.
Barrier layer mechanism engineering in calcium copper titanate thin film capacitors through microstructure control
Authors: Paisley E. A. , Losego M. D. , Aygun S. M. , Craft H. S. , Maria J.-P.
Published: December 2008

A peak permittivity greater than 10 000 has been achieved for calcium copper titanate (CCT) thin films by engineering a thin film microstructure that maximizes space charge contributions to polarizability. This permittivity is an order of magnitude greater than previous polycrystalline thin film efforts. This unique microstructure control is accomplished using a chemical solution deposition process flow that produces highly dense parallel layers ∼100 nm in thickness. We observe a thickness dependent permittivity where the entire film thickness constitutes the conducting region of a barrier layer capacitor despite the presence of multiple grain boundaries within that thickness. The model predictions are in good agreement with experimental data and are consistent with existing literature reports. These trends in permittivity with dielectric thickness raise new questions regarding the nature of barrier layers in CCT—and specifically, these results suggest that grain boundaries may not always participate as high resistance interlayers.
Theory of conduction in ultrafast metal-insulator varistors
Authors: Weimer Michael A. , Weimer Alan W. , Park Wounjhang
Published: December 2008

This paper investigates the fundamental operation of and mechanism of conduction occurring within metal-insulator varistors (MIVs). MIVs based on micron-sized spherical metal particles coated with nanometer-thick Al2O3, SiO2, and BN films are investigated and discussed. MIV functionality is found to be dependent on the non-Ohmic operation of the thin electrically insulating films separating adjacent conductive metal particles within the high-density varistor particle matrix. Several experimental results suggest that the breakdown and conduction behavior are strongly dominated by Fowler–Nordheim tunneling and can be accurately modeled by a simple tunneling expression. The exceptional electrical properties exhibited by MIVs suggest a strong potential for use in the suppression of fast rise-time transients.
Efficient evaluation of analytic Fukui functions
Authors: Flores-Moreno Roberto , Melin Junia , Ortiz J. V. , Merino Gabriel
Published: December 2008

An efficient method for the analytic evaluation of Fukui functions is proposed. Working equations are derived and numerical results are used to validate the method on medium size set of molecules. In addition to the obvious advantages of analytic differentiation, the proposed method is efficient enough to be considered a practical alternative to the finite difference formulation used routinely. The reliability of the approximations used here is demonstrated and discussed. Problems found in other methods for prediction of electrophilic centers are corrected automatically when using the new method.
Critical thickness of high structural quality SrTiO3 films grown on orthorhombic (101) DyScO3
Authors: Biegalski M. D. , Fong D. D. , Eastman J. A. , Fuoss P. H. , Streiffer S. K. , Heeg T. , Schubert J. , Tian W. , Nelson C. T. , Pan X. Q. , Hawley M. E. , Bernhagen M. , Reiche P. , Uecker R. , Trolier-McKinstry S. , Schlom D. G.
Published: December 2008

Strained epitaxial SrTiO3 films were grown on orthorhombic (101) DyScO3 substrates by reactive molecular-beam epitaxy. The epitaxy of this substrate/film combination is cube on cube with a pseudocubic out-of-plane (001) orientation. The strain state and structural perfection of films with thicknesses ranging from 50 to 1000 Å were examined using x-ray scattering. The critical thickness at which misfit dislocations was introduced was between 350 and 500 Å. These films have the narrowest rocking curves (full width at half maximum) ever reported for any heteroepitaxial oxide film (0.0018°). Only a modest amount of relaxation is seen in films exceeding the critical thicknesses even after postdeposition annealing at 700 °C in 1 atm of oxygen. The dependence of strain relaxation on crystallographic direction is attributed to the anisotropy of the substrate. These SrTiO3 films show structural quality more typical of semiconductors such as GaAs and silicon than perovskite materials; their structural relaxation behavior also shows similarity to that of compound semiconductor films.
Transmission electron microscopic study of the long period modulated phase in the morphotropic phase-boundary region of (1−x)NaNbO3–xCaTiO3 for x=0.16
Authors: Tripathi Saurabh , Lalla N. P. , Pandey Dhananjai
Published: December 2008

The recently reported structure of the long period modulated phase of (1−x)NaNbO3–xCaTiO3, with x=0.16, has been revisited using transmission electron microscopic studies. It is shown that the dominant phase in the morphotropic phase boundary region of this mixed system is incommensurately modulated in the [001] direction with an approximate unit cell size of 2ap×2ap×24ap, where ap is the pseudoperovskite cell parameter.
Recording performance improvement for perpendicular recording head with shielded sloped pole design
Authors: Gubbins Mark , Cazacu Alexandru , Kolbo Paul , Nolan Tom , Lamberton Robert , Johnston Alan
Published: December 2008

A sloped write pole design is assessed for perpendicular magnetic recording at high areal densities. Modeling shows that there is a significant increase in magnetic field from the sloped pole design over the conventional pole design at a fixed write width. Spin stand measurements were carried out in order to investigate the recording benefits of the sloped pole design. Writing improvements from this writer were best observed at high media coercivity.
Near-infrared emission properties and energy transfer of Tm3+-doped and Tm3+/Dy3+-codoped chalcohalide glasses
Authors: Tang Gao , Liu Cunming , Yang Zhiyong , Luo Lan , Chen Wei
Published: December 2008

Near-infrared emission properties of Tm3+ in GeSe2–Ga2Se3–CsI glasses were investigated. The increase in emission intensity ratio I1.47 μm/I1.22 μm and the large increase in the lifetime of the Tm3+:H34 level from 189 to 2480 μs can be obtained as CsI concentration changes from 20% to 40%. These improved emission properties result from the appearance of I-containing structural units, which have low phonon energy and are located near the Tm3+ ions, dominating the multiphonon relaxation and cross relaxation. Radiative parameters of Tm3+ were calculated based on the Judd–Ofelt analysis. The potential use of Tm3+-doped GeSe2–Ga2Se3–CsI glasses for S-band fiber amplifiers was discussed. Additionally, the intensity and lifetime of 1.2, 1.3, and 1.47 μm infrared fluorescence on Tm3+/Dy3+-codoped GeSe2–Ga2Se3–CsI glasses were studied, and the energy transfer mechanisms were discussed.
Real-time acoustic emission testing based on wavelet transform for the failure process of thermal barrier coatings
Authors: Yang L. , Zhou Y. C. , Mao W. G. , Lu C.
Published: December 2008

The fracture type differentiation, quantification, and source identification are desirable and yet intractable in the acoustic emission (AE) testing of a complex coating system. In this letter, a technique combining wavelet transform and conventional AE parameter analysis was developed to study the tensile failure process of thermal barrier coatings in real time. It is demonstrated that the failure of thermal barrier coatings originates from surface vertical cracking and follows interface cracking, and that the AE count increases with tensile load following a power law. The cracking source identified from AE signals agrees well with that observed by optical microscopy. This technique provides a powerful tool for the study of failure processes of a wide range of coatings and thin films.
A flexible organic pentacene nonvolatile memory based on high-κ dielectric layers
Authors: Chang Ming-Feng , Lee Po-Tsung , McAlister S. P. , Chin Albert
Published: December 2008

We report a pentacene thin film transistor nonvolatile memory fabricated on a flexible polyimide substrate. This device shows a low program/erase voltage of 12 V, a speed of 1/100 ms, an initial memory window of 2.4 V, and a 0.78 V memory window after 48 h. This has been achieved by using a high-κ dielectric as charge trapping, blocking, and tunneling gate insulator layers.
Performance comparison of Pb(Zr0.52Ti0.48)O3-only and Pb(Zr0.52Ti0.48)O3-on-silicon resonators
Authors: Chandrahalim Hengky , Bhave Sunil A. , Polcawich Ronald , Pulskamp Jeff , Judy Daniel , Kaul Roger , Dubey Madan
Published: December 2008

This paper provides a quantitative comparison and explores the design space of lead zirconium titanate (PZT)–only and PZT-on-silicon length-extensional mode resonators for incorporation into radio frequency microelectromechanical system filters and oscillators. We experimentally measured the correlation of motional impedance (RX) and quality factor (Q) with the resonators’ silicon layer thickness (tSi). For identical lateral dimensions and PZT-layer thicknesses (tPZT), the PZT-on-silicon resonator has higher resonant frequency (fC), higher Q (5100 versus 140), lower RX (51 Ω versus 205 Ω), and better linearity [third-order input intercept point (IIP3) of +43.7 dBm versus +23.3 dBm]. In contrast, the PZT-only resonator demonstrated much wider frequency tuning range (5.1% versus 0.2%).
Optical methodology for detecting histologically unapparent nanoscale consequences of genetic alterations in biological cells
Authors: Subramanian Hariharan , Pradhan Prabhakar , Liu Yang , Capoglu Ilker R. , Li Xu , Rogers Jeremy D. , Heifetz Alexander , Kunte Dhananjay , Roy Hemant K. , Taflove Allen , Backman Vadim
Published: December 2008

Recently, there has been a major thrust to understand biological processes at the nanoscale. Optical microscopy has been exceedingly useful in imaging cell microarchitecture. Characterization of cell organization at the nanoscale, however, has been stymied by the lack of practical means of cell analysis at these small scales. To address this need, we developed a microscopic spectroscopy technique, single-cell partial-wave spectroscopy (PWS), which provides insights into the statistical properties of the nanoscale architecture of biological cells beyond what conventional microscopy reveals. Coupled with the mesoscopic light transport theory, PWS quantifies the disorder strength of intracellular architecture. As an illustration of the potential of the technique, in the experiments with cell lines and an animal model of colon carcinogenesis we show that increase in the degree of disorder in cell nanoarchitecture parallels genetic events in the early stages of carcinogenesis in otherwise microscopically/histologically normal-appearing cells. These data indicate that this advance in single-cell optics represented by PWS may have significant biomedical applications.
A cytokine-neutralizing antibody as a structural mimetic of 2 receptor interactions
Authors: Grütter Christian , Wilkinson Trevor , Turner Richard , Podichetty Sadhana , Finch Donna , McCourt Matthew , Loning Scott , Jermutus Lutz , Grütter Markus G.
Published: December 2008

TGF-β isoforms are key modulators of a broad range of biological pathways and increasingly are exploited as therapeutic targets. Here, we describe the crystal structures of a pan-TGF-β neutralizing antibody, GC-1008, alone and in complex with TGF-β3. The antibody is currently in clinical evaluation for idiopathic pulmonary fibrosis, melanoma, and renal cell cancer. GC-1008 recognizes an asymmetric binding interface across the TGF-β homodimer with high affinity. Whereas both cognate receptors, TGF-β-receptor types I and II, are required to recognize all 3 TGF-β isoforms, GC-1008 has been engineered to bind with high affinity to TGF-β1, 2, and 3 via a single interaction surface. Comparison with existing structures and models of TGF-β interaction with its receptors suggests that the antibody binds to a similar epitope to the 2 receptors together and is therefore a structurally different but functionally identical mimic of the binding mode of both receptors.
Thermodynamics and kinetics of protein folding under confinement
Authors: Mittal Jeetain , Best Robert B.
Published: December 2008

Understanding the effects of confinement on protein stability and folding kinetics is important for describing protein folding in the cellular environment. We have investigated the effects of confinement on two structurally distinct proteins as a function of the dimension
d
c
and characteristic size
R
of the confining boundary. We find that the stabilization of the folded state relative to bulk conditions is quantitatively described by
R

−γ
c

, where the exponent γ
c
is ≈5/3 independent of the dimension of confinement
d
c
(cylindrical, planar, or spherical). Moreover, we find that the logarithm of the folding rates also scale as
R

−γ
c

, with deviations only being seen for very small confining geometries, where folding is downhill; for both stability and kinetics, the dominant effect is the change in the free energy of the unfolded state. A secondary effect on the kinetics is a slight destabilization of the transition state by confinement, although the contacts present in the confined transition state are essentially identical to the bulk case. We investigate the effect of confinement on the position-dependent diffusion coefficients
D
(
Q
) for dynamics along the reaction coordinate
Q
(fraction of native contacts). The diffusion coefficients only change in the unfolded state basin, where they are increased because of compaction.
RNA interference and retinoblastoma-related genes are required for repression of endogenous siRNA targets in
Caenorhabditis elegans
Authors: Grishok Alla , Hoersch Sebastian , Sharp Phillip A.
Published: December 2008

In
Caenorhabditis elegans
, a vast number of endogenous short RNAs corresponding to thousands of genes have been discovered recently. This finding suggests that these short interfering RNAs (siRNAs) may contribute to regulation of many developmental and other signaling pathways in addition to silencing viruses and transposons. Here, we present a microarray analysis of gene expression in RNA interference (RNAi)-related mutants
rde-4
,
zfp-1
, and
alg-1
and the retinoblastoma (Rb) mutant
lin-35
. We found that a component of Dicer complex RDE-4 and a chromatin-related zinc finger protein ZFP-1, not implicated in endogenous RNAi, regulate overlapping sets of genes. Notably, genes a) up-regulated in the
rde-4
and
zfp-1
mutants and b) up-regulated in the
lin-35
(Rb) mutant, but not the down-regulated genes are highly represented in the set of genes with corresponding endogenous siRNAs (endo-siRNAs). Our study suggests that endogenous siRNAs cooperate with chromatin factors, either
C. elegans
ortholog of acute lymphoblastic leukemia-1 (ALL-1)-fused gene from chromosome 10 (AF10), ZFP-1, or tumor suppressor Rb, to regulate overlapping sets of genes and predicts a large role for RNAi-based chromatin silencing in control of gene expression in
C. elegans
.
Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma
Authors: Chiu Rossa W. K. , Chan K. C. Allen , Gao Yuan , Lau Virginia Y. M. , Zheng Wenli , Leung Tak Y. , Foo Chris H. F. , Xie Bin , Tsui Nancy B. Y. , Lun Fiona M. F. , Zee Benny C. Y. , Lau Tze K. , Cantor Charles R. , Lo Y. M. Dennis
Published: December 2008

Chromosomal aneuploidy is the major reason why couples opt for prenatal diagnosis. Current methods for definitive diagnosis rely on invasive procedures, such as chorionic villus sampling and amniocentesis, and are associated with a risk of fetal miscarriage. Fetal DNA has been found in maternal plasma but exists as a minor fraction among a high background of maternal DNA. Hence, quantitative perturbations caused by an aneuploid chromosome in the fetal genome to the overall representation of sequences from that chromosome in maternal plasma would be small. Even with highly precise single molecule counting methods such as digital PCR, a large number of DNA molecules and hence maternal plasma volume would need to be analyzed to achieve the necessary analytical precision. Here we reasoned that instead of using approaches that target specific gene loci, the use of a locus-independent method would greatly increase the number of target molecules from the aneuploid chromosome that could be analyzed within the same fixed volume of plasma. Hence, we used massively parallel genomic sequencing to quantify maternal plasma DNA sequences for the noninvasive prenatal detection of fetal trisomy 21. Twenty-eight first and second trimester maternal plasma samples were tested. All 14 trisomy 21 fetuses and 14 euploid fetuses were correctly identified. Massively parallel plasma DNA sequencing represents a new approach that is potentially applicable to all pregnancies for the noninvasive prenatal diagnosis of fetal chromosomal aneuploidies.
The defect in T-cell regulation in NOD mice is an effect on the T-cell effectors
Authors: D'Alise Anna Morena , Auyeung Vincent , Feuerer Markus , Nishio Junko , Fontenot Jason , Benoist Christophe , Mathis Diane
Published: December 2008

FoxP3
+
regulatory T cells (Tregs) protect against autoimmunity, type 1 diabetes (T1D) in particular, prompting the hypothesis that a deficiency in Tregs is a critical determinant of diabetes susceptibility in NOD mice. However, tests of this hypothesis have yielded contradictory results. We confirmed that NOD mice, compared with reference strains, do not have a primary deficit in Treg numbers in the lymphoid organs, whether in prediabetic mice of any age or in animals with recent-onset diabetes. NOD Tregs did show a defect in standard
in vitro
T cell suppression assays, particularly at low suppressor/effector ratios. Gene expression profiling revealed the vast majority of transcripts constituting the “Treg signature” to be normally distributed in NOD Tregs versus CD4
+
T conventional (Tconv) cells, although there were a few differences affecting one or the other population. According to results from criss-cross experiments, the functional inefficacy was not rooted in NOD Tregs, which suppressed as well as their C57BL/6 (B6) counterparts, but rather in NOD Tconv, which were less prone to suppression than were B6 Tconv cells. They also responded more effectively to anti-CD3/28 monoclonal antibody (mAb) stimulation
in vitro
or to a natural pancreatic antigen
in vivo
. This difference was independent of autoimmune inflammation, did not map to the
idd3
region, and was not due to the overproduction of interleukin-21 in NOD mice. That the immune dysregulation in this T1D model is rooted in the ability of effector T cells to be regulated, rather than in Tregs themselves, has implications for proposed therapeutic interventions.
Nuclear retention of ICP0 in cells exposed to HDAC inhibitor or transfected with DNA before infection with herpes simplex virus 1
Authors: Kalamvoki Maria , Roizman Bernard
Published: December 2008

The α (immediate early) protein ICP0 of herpes simplex virus 1 enhances the expression of genes introduced by infection or transfection. Early in infection it performs two key functions: It blocks the silencing of the viral DNA by cellular proteins and it blocks the IFN stimulated host response to infection. Between 5 and 9 h after infection, ICP0 is translocated to the cytoplasm but remains dynamically associated with proteasomes. In this report we show that in permissive cells that are poor expressors of transfected genes (HEp-2, U2OS, etc.), ICP0 is retained in the nucleus if the cells had been transfected with DNA and then infected. The retention is DNA dose- and size-dependent but not DNA type-dependent. Retention of ICP0 is also a consequence of infection with wild-type virus concomitant with exposure of cells to sodium butyrate. ICP0 is not retained in transfected/infected cells that efficiently express transfected genes (HEK293, rabbit skin cells). The retention of ICP0 in the nucleus is concordant with failure to degrade PML and disperse ND10 structures, and delays in the transition to post α genes expression, translocation of components of the CoREST/REST/HDAC1 complex and histone relocation in the infected cell. The data suggest that (
i
) retention of ICP0 is linked to its function to remodel acetylated DNA but not DNA in heterochromatin. This function is independent of response elements embedded in the DNA and (
ii
) transfection-resistant cells do take up DNA but process it differently than cells that readily express transfected genes.
Linking parent input and child receptivity to symbolic gestures
Authors: Namy Laura L. , Vallas Rebecca , Knight-Schwarz Jennifer
Published: December 2008

This study explored the relation between parents’ production of gestures and symbolic play during free play and children’s production and comprehension of symbolic gestures. Thirty-one 16- to 22-month-olds and their parents participated in a free play session. Children also participated in a forced-choice novel gesture-learning task. Parents’ pretend play with objects in hand was predictive of children’s gesture production during play and gesture vocabulary according to parental report. No relationship was found between parent gesture and child performance on the forced-choice gesture-learning task, although children’s performance was negatively correlated with their verbal vocabulary size. These data suggest a strong link between parental input and the children’s use of gestures as symbols, although not a direct link from parent gesture to child gesture. The data also suggest that children’s overall expectations that gestures can be symbols is unaffected by parental input, and highlight the possibility that children play a role in transforming the symbolic play behaviors that they observe into communicative signals.
Gesture and melody in Indian vocal music
Authors: Rahaim Matt
Published: December 2008

The gestures that accompany improvisation in Indian vocal music, like the gestures that accompany speech, are closely co-ordinated with vocalization. Though linked to what is being sung, these movements are not determined by vocal action; nor are they taught explicitly, deliberately rehearsed, or tied to specific meanings. Students tend to gesture recognizably like their teachers, producing lineage-based gesture dialects, but the gestural repertoire of every vocalist is nonetheless idiosyncratic. This paper aims to trace a brief history of song gesture in India, and to show some of the links between gesture and vocalization. It also adapts Katharine Young’s theory of the “family body” to the transmission of gesture dialects through teaching lineages. Gesture and sound are taken to be parallel channels for the expression of melody.
A study on intergranular strain evolution in nanostructured Ni–Fe alloys
Authors: Li Hongqi , Choo Hahn , Saleh Tarik , Lienert Ulrich , Liaw Peter K. , Ebrahimi Fereshteh , Ren Yang
Published: December 2008

The investigation of the lattice strain development in three Ni–Fe alloys suggests that the lattice strain evolution behaviour depends on the deformation mechanism. When the plastic deformation is governed by the dislocation, the lattice strain exhibited pronounced nonlinear behaviour around the elastic limit. When the grain boundary sliding dominates the deformation, there is no obvious shift in the lattice strain evolution as soon as plastic deformation occurs.
NRSF2 load frame: design, control, and testing
Authors: An Ke , Bailey William B. , Craig Stewart O. , Choo Hahn , Hubbard Camden R. , Erdman Donald L.
Published: December 2008

A neutron diffraction load frame has been constructed for the Second Generation Neutron Residual Stress Mapping Facility (NRSF2) at the High Flux Isotope Reactor, Oak Ridge National Laboratory. The load frame is designed to study micromechanical behaviour of materials under applied tensile or compressive loads and to characterize specimens with stress risers (e.g., cracks) while under load, in combination with the existing mapping capabilities at NRSF2.
Investigation of residual stress in a bent Ti-clad Cu bus-bar by neutron diffraction and finite element modelling
Authors: Xu F. , Fredette J.C. , Holt R.A. , Rogge R.B. , Pickard D. , Tuck L.
Published: December 2008

Titanium-clad copper bus-bars are used to provide corrosion resistance in high temperature electrolytic cells. When cold-formed, such components will have a complex residual stress pattern. We report the investigation of residual stress in a high conductivity Cu bus-bar clad with Grade-2 Ti by neutron diffraction and finite element modelling. Straight bars were co-extruded, air-cooled and cold-stretched. The bars were cold-bent into an inverted ‘top-hat’ shape with four 90° bends. Residual stresses were investigated at the apex of a 90° bend. Three sets of measurements were performed in each of the measurement directions (transverse, normal and axial, relative to the straight bar): one set along the centre line in Cu; one set along the edge in Cu and one set along the edge in Ti. Residual stresses were then calculated in the three directions assuming both materials are elastically isotropic. The cooling, stretching and bending processes were simulated with an explicit finite element program, while the springback was modelled with dynamic relaxation. The neutron diffraction and finite element modelling results show reasonable agreement. Both materials exhibit unbalanced profiles relating to the combination of higher yield stress in the Ti cladding, and larger cross section of the copper bar.
Coordination of Cytokinesis and Cell Separation by Endosomal Targeting of a Cdc42-specific Guanine Nucleotide Exchange Factor inUstilago maydis
Authors: Schink Kay Oliver , Bölker Michael
Published: December 2008

The small GTPase Cdc42 is a key regulator of cell polarity and cytoskeletal organization in most eukaryotic cells. In Ustilago maydis, Cdc42 and the guanine nucleotide exchange factor (GEF) Don1 regulate cytokinesis and cell separation. Don1 belongs to the FGD1 family of Cdc42-specific GEFs that are characterized by a C-terminal lipid-binding FYVE domain. Although the FGD1/frabin family of Rho-GEFs is evolutionary conserved from fungi to mammals the role of the FYVE domain for its biological function is unknown. Here, we show that the FYVE domain is specific for phosphatidylinositol-3-phosphate (PtdIns(3)P) and targets Don1 to endosomal vesicles. During cytokinesis asymmetric accumulation of Don1-containing vesicles occurs at the site of septation. We could show that FYVE-dependent localization is critical for the function of Don1 at normal expression levels but can be compensated for by overexpression of Don1 lacking a functional FYVE domain. Our results demonstrate that endosomal compartmentalization of a Cdc42-specific exchange factor is involved in the coordination of cytokinesis and cell separation.
Sec6p Anchors the Assembled Exocyst Complex at Sites of Secretion
Authors: Songer Jennifer A. , Munson Mary
Published: December 2008

The exocyst is an essential protein complex required for targeting and fusion of secretory vesicles to sites of exocytosis at the plasma membrane. To study the function of the exocyst complex, we performed a structure-based mutational analysis of the Saccharomyces cerevisiae exocyst subunit Sec6p. Two “patches” of highly conserved residues are present on the surface of Sec6p; mutation of either patch does not compromise protein stability. Nevertheless, replacement of SEC6 with the patch mutants results in severe temperature-sensitive growth and secretion defects. At nonpermissive conditions, although trafficking of secretory vesicles to the plasma membrane is unimpaired, none of the exocyst subunits are polarized. This is consistent with data from other exocyst temperature-sensitive mutants, which disrupt the integrity of the complex. Surprisingly, however, these patch mutations result in mislocalized exocyst complexes that remain intact. Our results indicate that assembly and polarization of the exocyst are functionally separable events, and that Sec6p is required to anchor exocyst complexes at sites of secretion.
ARCS-Motif: discovering correlated motifs from unaligned biological sequences
Authors: Zhang Shijie , Su Wei , Yang Jiong
Published: December 2008

Motivation: The goal of motif discovery is to detect novel, unknown, and important signals from biology sequences. In most models, the importance of a motif is equal to the sum of the similarity of every single position. In 2006, Song et al. introduced Aggregated Related Column Score (ARCS) measure which includes correlation information to the evaluation of motif importance. The paper showed that the ARCS measure is superior to other measures. Due to the complicated nature of the ARCS motif model, we cannot directly apply existing sequential motif discovery methods to find motifs with high ARCS values.

Results: This article presents a novel mining algorithm, ARCSMotif, to discover related sequential motifs in biological sequences. ARCS-Motif is applied to 400 PROSITE datasets and compared with five alternative methods (CONSENSUS, Gibbs sampler, MEME, SPLASH and DIALIGN-TX). ARCS-Motif outperforms all the methods in accuracy, and most of the methods in efficiency. Although SPLASH has better efficiency than ARCS-Motif, ARCS-Motif has much better accuracy than SPLASH. On average, ARCS-Motif is able to produce the motifs which are at least 10% better than the best of the alternative methods. Among the 400 PROSITE datasets, ARCS-Motif produces the best motifs for more than 200 families. Other than SPLASH, the execution time of ARCS-Motif is less than a third of that of the fastest alternative method and its execution time grows at the slowest rate with respect to the number of sequences and the average sequence among all methods.

Availability: Software: http://beijing.case.edu/ARCS_Motif/ARCS_Motif; Results: http://beijing.case.edu/ARCS_Motif

Contact:  jiong.yang@case.edu
PASTAA: identifying transcription factors associated with sets of co-regulated genes
Authors: Roider Helge G. , Manke Thomas , O'Keeffe Sean , Vingron Martin , Haas Stefan A.
Published: December 2008

Motivation: A major challenge in regulatory genomics is the identification of associations between functional categories of genes (e.g. tissues, metabolic pathways) and their regulating transcription factors (TFs). While, for a limited number of categories, the regulating TFs are already known, still for many functional categories the responsible factors remain to be elucidated.

Results: We put forward a novel method (PASTAA) for detecting transcriptions factors associated with functional categories, which utilizes the prediction of binding affinities of a TF to promoters. This binding strength information is compared to the likelihood of membership of the corresponding genes in the functional category under study. Coherence between the two ranked datasets is seen as an indicator of association between a TF and the category. PASTAA is applied primarily to the determination of TFs driving tissue-specific expression. We show that PASTAA is capable of recovering many TFs acting tissue specifically and, in addition, provides novel associations so far not detected by alternative methods. The application of PASTAA to detect TFs involved in the regulation of tissue-specific gene expression revealed a remarkable number of experimentally supported associations. The validated success for various datasets implies that PASTAA can directly be applied for the detection of TFs associated with newly derived gene sets.

Availability: The PASTAA source code as well as a corresponding web interface is freely available at http://trap.molgen.mpg.de

Contact:  roider@molgen.mpg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Better bioinformatics through usability analysis
Authors: Bolchini Davide , Finkelstein Anthony , Perrone Vito , Nagl Sylvia
Published: December 2008

Motivation: Improving the usability of bioinformatics resources enables researchers to find, interact with, share, compare and manipulate important information more effectively and efficiently. It thus enables researchers to gain improved insights into biological processes with the potential, ultimately, of yielding new scientific results. Usability ‘barriers’ can pose significant obstacles to a satisfactory user experience and force researchers to spend unnecessary time and effort to complete their tasks. The number of online biological databases available is growing and there is an expanding community of diverse users. In this context there is an increasing need to ensure the highest standards of usability.

Results: Using ‘state-of-the-art’ usability evaluation methods, we have identified and characterized a sample of usability issues potentially relevant to web bioinformatics resources, in general. These specifically concern the design of the navigation and search mechanisms available to the user. The usability issues we have discovered in our substantial case studies are undermining the ability of users to find the information they need in their daily research activities. In addition to characterizing these issues, specific recommendations for improvements are proposed leveraging proven practices from web and usability engineering. The methods and approach we exemplify can be readily adopted by the developers of bioinformatics resources.

Contact:  dbolchin@iupui.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Glycan family analysis for deducing N-glycan topology from single MS
Authors: Goldberg David , Bern Marshall , North Simon J. , Haslam Stuart M. , Dell Anne
Published: December 2008

Motivation: In the past few years, mass spectrometry (MS) has emerged as the premier tool for identification and quantification of biological molecules such as peptides and glycans. There are two basic strategies: single-MS, which uses a single round of mass analysis, and MS/MS (or higher order MSn), which adds one or more additional rounds of mass analysis, interspersed with fragmentation steps. Single-MS offers higher throughput, broader mass coverage and more direct quantitation, but generally much weaker identification. Single-MS, however, does work fairly well for the case of N-glycan identification, which are more constrained than other biological polymers. We previously demonstrated single-MS identification of N-glycans to the level of ‘cartoons’ (monosaccharide composition and topology) by a system that incorporates an expert's detailed knowledge of the biological sample. In this article, we explore the possibility of ab initio single-MS N-glycan identification, with the goal of extending single-MS, or primarily-single-MS, identification to non-expert users, novel conditions and unstudied tissues.

Results: We propose and test three cartoon-assignment algorithms that make inferences informed by biological knowledge about glycan synthesis. To test the algorithms, we used 71 single-MS spectra from a variety of tissues and organisms, containing more than 2800 manually annotated peaks. The most successful of the algorithms computes the most richly connected subgraph within a ‘cartoon graph’. This algorithm uniquely assigns the correct cartoon to more than half of the peaks in 41 out of the 71 spectra.

Contact:  goldberg@parc.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
SIMoNe: Statistical Inference for MOdular NEtworks
Authors: Chiquet Julien , Smith Alexander , Grasseau Gilles , Matias Catherine , Ambroise Christophe
Published: December 2008

Summary: The R package SIMoNe (Statistical Inference for MOdular NEtworks) enables inference of gene-regulatory networks based on partial correlation coefficients from microarray experiments. Modelling gene expression data with a Gaussian graphical model (hereafter GGM), the algorithm estimates non-zero entries of the concentration matrix, in a sparse and possibly high-dimensional setting. Its originality lies in the fact that it searches for a latent modular structure to drive the inference procedure through adaptive penalization of the concentration matrix.

Availability: Under the GNU General Public Licence at http://cran.r-project.org/web/packages/simone/

Contact:  julien.chiquet@genopole.cnrs.fr
Eating Disorders
Authors: Simon Chantal
Published: December 2008

Although classification of eating disorders is relatively recent, cases of female anorexia have been recorded since the eleventh century. Then, the intentional self-starvation of women was thought to result from religious yearnings resulting in these women being termed ‘fasting saints’. Freud recorded a case of bulimia nervosa in a female patient in the nineteenth century. There are currently three recognized eating disorders: anorexia nervosa, bulimia nervosa and binge eating disorder. Many more people have disordered eating patterns that show features of these conditions but do not meet the criteria for diagnosis.
Self-Harm in Adolescence
Authors: Shiner Alice
Published: December 2008

Self-harm is a common yet frequently concealed activity among adolescents. GP trainees are likely to encounter young people who self-harm, not only in primary care, but also during placements in Accident and Emergency or general medicine. The type of self-harm seen in each situation is likely to vary and the approach to it may need to change accordingly. However, some themes remain constant and as self-harm is a prevalent phenomenon among adolescents, it is an area with which GPs should be familiar.
Crammer's Corner
Authors: Riley Ben
Published: December 2008

This issue of Crammer's Corner considers how to quickly evaluate the quality of an educational resource being used to support GP training.
Disorders of Puberty
Authors: Kirk Jeremy , Bandhakavi Meenakshi , Simon Chantal
Published: December 2008

Puberty is defined as the time when the onset of sexual maturity occurs and the reproductive organs become functional, and it is therefore the time when a child becomes an adult capable of reproduction. Although the terms puberty and adolescence are commonly used interchangeably, the term puberty tends to be used for the physical, and adolescence for the psychological and social changes.
Peroxisomal ATP Import Is Essential for Seedling Development inArabidopsis thaliana
Authors: Linka Nicole , Theodoulou Frederica L. , Haslam Richard P. , Linka Marc , Napier Jonathan A. , Neuhaus H. Ekkehard , Weber Andreas P.M.
Published: December 2008

Several recent proteomic studies of plant peroxisomes indicate that the peroxisomal matrix harbors multiple ATP-dependent enzymes and chaperones. However, it is unknown whether plant peroxisomes are able to produce ATP by substrate-level phosphorylation or whether external ATP fuels the energy-dependent reactions within peroxisomes. The existence of transport proteins that supply plant peroxisomes with energy for fatty acid oxidation and other ATP-dependent processes has not previously been demonstrated. Here, we describe two Arabidopsis thaliana genes that encode peroxisomal adenine nucleotide carriers, PNC1 and PNC2. Both proteins, when fused to enhanced yellow fluorescent protein, are targeted to peroxisomes. Complementation of a yeast mutant deficient in peroxisomal ATP import and in vitro transport assays using recombinant transporter proteins revealed that PNC1 and PNC2 catalyze the counterexchange of ATP with ADP or AMP. Transgenic Arabidopsis lines repressing both PNC genes were generated using ethanol-inducible RNA interference. A detailed analysis of these plants showed that an impaired peroxisomal ATP import inhibits fatty acid breakdown during early seedling growth and other β-oxidation reactions, such as auxin biosynthesis. We show conclusively that PNC1 and PNC2 are essential for supplying peroxisomes with ATP, indicating that no other ATP generating systems exist inside plant peroxisomes.
Effects of the eye fluke Diplostomum spathaceum on the energetics and feeding of Arctic charr Salvelinus alpinus
Authors: Voutilainen A. , Figueiredo K. , Huuskonen H.
Published: December 2008

In the present study, effects of the trematode eye fluke Diplostomum spathaceum infection and parasite‐induced cataract on energetic costs and feeding of hatchery‐bred one‐summer‐old Lake Saimaa Arctic charr Salvelinus alpinus were examined. The energetic effects (measured as oxygen uptake) of acute eye fluke infection on S. alpinus were negligible, but in the chronic infections mean oxygen consumption of infected fish was significantly higher than that of controls. Feeding capability of S. alpinus was studied in aquarium experiments, and uninfected healthy‐eyed fish reacted to zooplankton more rapidly and caught zooplankton with better success compared to individuals with cataracts in the same school. The results suggested that to compensate energetic costs and impaired feeding capability caused by eye fluke, cataract‐bearing fish spend more time foraging, which may result in increased predation risk.
Effect of Ligula intestinalis on the reproductive capacity of Rastrineobola argentea in Lake Victoria
Authors: Cowx I. G. , Rollins D. , Tumwebaze R.
Published: December 2008

This study examined the potential effect of the cestode Ligula intestinalis on the reproduction of the indigenous cyprinid Rastrineobola argentea in Lake Victoria. Ligula intestinalis had a marked effect on the breeding cycle of R. argentea. The proportion of the infected population in advanced stages of maturation prior to spawning was considerably reduced compared with uninfected fish. Infection by L. intestinalis significantly reduced the fecundity of individual fish, particularly in the 45–60 mm size range; the component of the population that makes the greatest contribution to reproductive output. The reduction in reproductive output of the R. argentea population could potentially affect replenishment of stocks in this important fishery.