bluuebunny/crossref_metadata_2025 huggingface dataset:
Ti
O
2
–
Cd
Se
nanowire arrays showing visible-range light absorption
Authors: Lee Jung-Chul , Sung Yun-Mo , Kim Tae Geun , Choi Heon-Jin
Published: September 2007

High-density single crystalline TiO2 nanowires (∼50nm diameter) were grown on Ti substrates by chemical vapor deposition, and they were overcoated with the solution containing CdSe nanocrystals (∼5nm diameter) and heat treated at 600°C to form TiO2 hetersotructured nanowire arrays. The TiO2 nanowire arrays showed uniformly distributed CdSe nanocrystals and high crystallinity of rutile and wurtzite from the TiO2 and the CdSe, respectively. Owing to the heterostructure of TiO2, they demonstrate almost full visible-range light absorption, and thus enhanced photocatalytic activity by the charge separation via electron and hole transfers between the CdSe and the TiO2.
Nonmagnetic cloak with minimized scattering
Authors: Cai Wenshan , Chettiar Uday K. , Kildishev Alexander V. , Shalaev Vladimir M. , Milton Graeme W.
Published: September 2007

In an electromagnetic cloak based on a transformation approach, reduced sets of material properties are generally favored due to their easier implementation in reality, although a seemingly inevitable drawback of undesired scattering exists in such cloaks. Here, the authors suggest the use of high-order transformations to create smooth moduli at the outer boundary of the cloak, therefore completely eliminating the detrimental scattering within the limit of geometric optics. The authors apply this scheme to a nonmagnetic cylindrical cloak and demonstrate that the scattered field is reduced substantially in a cloak with optimal quadratic transformation as compared to its linear counterpart.
High performance thin film transistors with cosputtered amorphous indium gallium zinc oxide channel
Authors: Jeong Jae Kyeong , Jeong Jong Han , Yang Hui Won , Park Jin-Seong , Mo Yeon-Gon , Kim Hye Dong
Published: September 2007

The authors report the fabrication of high performance thin film transistors (TFTs) with an amorphous indium gallium zinc oxide (a-IGZO) channel, which was deposited by cosputtering using a dual IGZO and indium zinc oxide (IZO) target. The effect of the indium content on the device performance of the a-IGZO TFTs was investigated. At a relatively low IZO power of 400W, the field-effect mobility (μFE) and subthreshold gate swing (S) of the a-IGZO TFTs were dramatically improved to 19.3cm2∕Vs and 0.35V/decade, respectively, compared to those (11.2cm2∕Vs and 1.11V/decade) for the TFTs with the a-IGZO channel (reference sample) prepared using only the IGZO target. The enhancement in the subthreshold IDS-VGS characteristics at an IZO power of 400W compared to those of the reference sample was attributed to the reduction of the interface trap density rather than the reduction of the bulk defects of the a-IGZO channel.
Absence of defect state creation in nanocrystalline silicon thin film transistors deduced from constant current stress measurements
Authors: Esmaeili-Rad Mohammad R. , Sazonov Andrei , Nathan Arokia
Published: September 2007

The authors discuss time and temperature dependences of the shift in threshold voltage (ΔVT) of nanocrystalline silicon (nc-Si) thin film transistors (TFTs) stressed at constant drain currents. In contrast to the behavior of the hydrogenated amorphous silicon (a-Si:H) counterpart, a weak temperature dependence of ΔVT was observed. The results follow the charge trapping model and the predicted stretched-exponential time dependence that saturates at prolonged stress times. In addition, ΔVT does not fit into the thermalization energy concept that was developed based on the defect state creation model for a-Si:H TFTs. The results indicate absence of defect state creation in nc-Si TFTs.
Thickness and stoichiometry dependence of the thermal conductivity of GeSbTe films
Authors: Reifenberg John P. , Panzer Matthew A. , Kim SangBum , Gibby Aaron M. , Zhang Yuan , Wong Simon , Wong H.-S. Philip , Pop Eric , Goodson Kenneth E.
Published: September 2007

Thermal conduction in GeSbTe films strongly influences the writing energy and time for phase change memory (PCM) technology. This study measures the thermal conductivity of Ge2Sb2Te5 between 25 and 340°C for layers with thicknesses near 60, 120, and 350nm. A strong thickness dependence of the thermal conductivity is attributed to a combination of thermal boundary resistance (TBR) and microstructural imperfections. Stoichiometric variations significantly alter the phase transition temperatures but do not strongly impact the thermal conductivity at a given temperature. This work makes progress on extracting the TBR for Ge2Sb2Te5 films, which is a critical unknown parameter for PCM simulations.
Suppression of short channel effect in organic thin film transistors
Authors: Tukagoshi K. , Fujimori F. , Minari T. , Miyadera T. , Hamano T. , Aoyagi Y.
Published: September 2007

Short-channel effect in organic thin film transistors with top-contact configuration is effectively suppressed to enhance the performance. The space charge limited current, which prevents the appearance of output saturation behavior, is sufficiently suppressed by reducing the thickness of both the pentacene film and the gate insulator. Molecular doping of the pentacene thin film in the contact reduces the contact resistance and allows a greater increase in field-effect mobility with decreasing channel length. These structural optimizations realize a submicrometer-channel transistor with clear saturation characteristics and low-voltage operation.
Surface Charge Modification of Nano-Sized Silica Colloid
Authors: Pham Khoa N. , Fullston Damian , Sagoe-Crentsil Kwesi
Published: September 2007

The surface of commercial 30-nm colloidal silica particles were modified by reaction with functional silanes. The high specific surface area and reactivity of the particles, due to their small size, makes the process susceptible to irreversible aggregation not found previously with larger particles. The present study compares surface charge results from amino silanes with one or three alkoxy groups. Measurements of the zeta potential as a function of pH, and gelation kinetics shed light on the mechanism of surface charge changes from the modification. Instability in suspensions before and after the surface modification is also studied using a new data analysis technique from simple light-scattering equipment. Experimental results show very stable particles are obtained by amino silane surface modification. Factors affecting susceptibility of small particles to irreversible aggregation caused by a non-aqueous solvent or high concentration of a trialkoxy silane, including the large number of reactive silanol groups in the surface gel layer of the particles, are discussed.
Interaction of signal-recognition particle 54 GTPase domain and signal-recognition particle RNA in the free signal-recognition particle
Authors: Hainzl Tobias , Huang Shenghua , Sauer-Eriksson A. Elisabeth
Published: September 2007

The signal-recognition particle (SRP) is a ubiquitous protein–RNA complex that targets proteins to cellular membranes for insertion or secretion. A key player in SRP-mediated protein targeting is the evolutionarily conserved core consisting of the SRP RNA and the multidomain protein SRP54. Communication between the SRP54 domains is critical for SRP function, where signal sequence binding at the M domain directs receptor binding at the GTPase domain (NG domain). These SRP activities are linked to domain rearrangements, for which the role of SRP RNA is not clear. In free SRP, a direct interaction of the GTPase domain with SRP RNA has been proposed but has never been structurally verified. In this study, we present the crystal structure at 2.5-Å resolution of the SRP54–SRP19–SRP RNA complex of
Methanococcus jannaschii
SRP. The structure reveals an RNA-bound conformation of the SRP54 GTPase domain, in which the domain is spatially well separated from the signal peptide binding site. The association of both the N and G domains with SRP RNA in free SRP provides further structural evidence for the pivotal role of SRP RNA in the regulation of the SRP54 activity.
Dual-specificity splice sites function alternatively as 5′ and 3′ splice sites
Authors: Zhang Chaolin , Hastings Michelle L. , Krainer Adrian R. , Zhang Michael Q.
Published: September 2007

As a result of large-scale sequencing projects and recent splicing-microarray studies, estimates of mammalian genes expressing multiple transcripts continue to increase. This expansion of transcript information makes it possible to better characterize alternative splicing events and gain insights into splicing mechanisms and regulation. Here, we describe a class of splice sites that we call dual-specificity splice sites, which we identified through genome-wide, high-quality alignment of mRNA/EST and genome sequences and experimentally verified by RT-PCR. These splice sites can be alternatively recognized as either 5′ or 3′ splice sites, and the dual splicing is conceptually similar to a pair of mutually exclusive exons separated by a zero-length intron. The dual-splice-site sequences are essentially a composite of canonical 5′ and 3′ splice-site consensus sequences, with a CAG|GURAG core. The relative use of a dual site as a 5′ or 3′ splice site can be accurately predicted by assuming competition for specific binding between spliceosomal components involved in recognition of 5′ and 3′ splice sites, respectively. Dual-specificity splice sites exist in human and mouse, and possibly in other vertebrate species, although most sites are not conserved, suggesting that their origin is recent. We discuss the implications of this unusual splicing pattern for the diverse mechanisms of exon recognition and for gene evolution.
High-density lipoprotein protects macrophages from oxidized low-density lipoprotein-induced apoptosis by promoting efflux of 7-ketocholesterol via ABCG1
Authors: Terasaka Naoki , Wang Nan , Yvan-Charvet Laurent , Tall Alan R.
Published: September 2007

Oxidized sterols consumed in the diet or formed on low-density lipoprotein (LDL) are toxic to endothelial cells and macrophages and are thought to have a central role in promoting atherogenesis. The ATP-binding cassette transporter ABCG1 was recently shown to promote efflux of cholesterol from macrophages to high-denisty lipoprotein (HDL). We show that HDL protects macrophages from apoptosis induced by loading with free cholesterol or oxidized LDL. The protective effect of HDL was reduced in
Abcg1
−/−
macrophages, especially after loading with oxidized LDL. Similarly, HDL exerted a protective effect against apoptosis induced by 7-ketocholesterol, the major oxysterol present in oxidized LDL and atherosclerotic lesions, in
Abcg1
+/+
, but not in
Abcg1
−/−
macrophages. In transfected 293 cells, efflux of 7-ketocholesterol and related oxysterols was completely dependent on expression of ABCG1 and the presence of HDL in media. In contrast, ABCA1 and apoA-1 did not stimulate the efflux of 7-ketocholesterol into media. HDL stimulated the efflux of 7-ketocholesterol from
Abcg1
+/+
, but not from
Abcg1
−/−
macrophages. In
Abcg1
−/−
mice fed a high-cholesterol diet, plasma levels of 7-ketocholesterol were reduced, whereas their macrophages accumulated 7-ketocholesterol. These findings indicate a specific role for ABCG1 in promoting efflux of 7-ketocholesterol and related oxysterols from macrophages onto HDL and in protecting these cells from oxysterol-induced cytotoxicity.
Targeting the absence: Homozygous DNA deletions as immutable signposts for cancer therapy
Authors: Varshavsky Alexander
Published: September 2007

Many cancers harbor homozygous DNA deletions (HDs). In contrast to other attributes of cancer cells, their HDs are immutable features that cannot change during tumor progression or therapy. I describe an approach, termed deletion-specific targeting (DST), that employs HDs (not their effects on RNA/protein circuits, but deletions themselves) as the targets of cancer therapy. The DST strategy brings together both existing and new methodologies, including the ubiquitin fusion technique, the split-ubiquitin assay, zinc-finger DNA-recognizing proteins and split restriction nucleases. The DST strategy also employs a feedback mechanism that receives input from a circuit operating as a Boolean OR gate and involves the activation of split nucleases, which destroy DST vector in normal (nontarget) cells. The logic of DST makes possible an incremental and essentially unlimited increase in the selectivity of therapy. If DST strategy can be implemented in a clinical setting, it may prove to be curative and substantially free of side effects.
The Rho GTPase-activating proteins RGA-3 and RGA-4 are required to set the initial size of PAR domains in
Caenorhabditis elegans
one-cell embryos
Authors: Schonegg Stephanie , Constantinescu Alexandru T. , Hoege Carsten , Hyman Anthony A.
Published: September 2007

Caenorhabditis elegans
embryos establish cortical domains of PAR proteins of reproducible size before asymmetric cell division. The ways in which the size of these domains is set remain unknown. Here we identify the GTPase-activating proteins (GAPs) RGA-3 and RGA-4, which regulate the activity of the small GTPase RHO-1.
rga-3/4(RNAi)
embryos have a hypercontractile cortex, and the initial relative size of their anterior and posterior PAR domains is altered. Thus, RHO-1 activity appears to control the level of cortical contractility and concomitantly the size of cortical domains. These data support the idea that in
C. elegans
embryos the initial size of the PAR domains is set by regulating the contractile activity of the acto-myosin cytoskeleton through the activity of RHO-1. RGA-3/4 have functions different from CYK-4, the other known GAP required for the first cell division, showing that different GAPs cooperate to control the activity of the acto-myosin cytoskeleton in the first cell division of
C. elegans
embryos.
Effects of simian immunodeficiency virus on the circadian rhythms of body temperature and gross locomotor activity
Authors: Huitron-Resendiz Salvador , Marcondes Maria Cecilia G. , Flynn Claudia T. , Lanigan Caroline M. S. , Fox Howard S.
Published: September 2007

In monkeys infected with simian immunodeficiency virus (SIV), changes in body temperature and locomotor activity occur after the acute retroviral syndrome stage of the disease. However, alterations to the circadian rhythm of these factors in SIV-infected monkeys have not been reported. To determine whether the circadian rhythm of body temperature and locomotor activity are disrupted during SIV infection, we analyzed the temperature and activity patterns of SIV-infected monkeys through different stages of the disease, progressing to SIV encephalitis by using the cosinor model for circadian oscillation. We found that SIV infection resulted in significant impairments of the amplitude and mean of the circadian rhythm of body temperature and activity and in the acrophase of the circadian rhythm for temperature. These alterations were not related to changes observed in the acute febrile response induced after viral inoculation. In animals killed once marked circadian anomalies were evident, microglia infiltration and macrophage accumulation in the hypothalamus were observed. Together, these results clearly demonstrate that SIV infection compromises aspects of circadian regulation in monkeys, with important implications for physiological functions, including cognition, in HIV-infected individuals.
Epidermal terminal differentiation depends on B lymphocyte-induced maturation protein-1
Authors: Magnúsdóttir Erna , Kalachikov Sergey , Mizukoshi Koji , Savitsky David , Ishida-Yamamoto Akemi , Panteleyev Andrey A. , Calame Kathryn
Published: September 2007

The cornified layer is a compacted lattice of lipid-embedded corneocytes that provides an organism's barrier to the external environment. Cornification is the final differentiative step for epidermal keratinocytes and involves dramatic cell condensation before death. Using conditional gene deletion in mice, we identified the transcriptional repressor Blimp-1 (B lymphocyte-induced maturation protein-1) as an important regulator of keratinocyte transition from the granular to the cornified layer. More than 250 genes are misregulated in conditional knockout epidermis, including those encoding transcription factors, signal transduction components, proteinases, and enzymes involved in lipid metabolism. Steady-state mRNA and ChIP analyses of a subset of these genes provide evidence that
nfat5
,
fos
,
prdm1
, and
dusp16
are novel direct targets of Blimp-1. Identifying
nfat5
as a target of Blimp-1 repression indicates that cornification involves suppression of normal osmotic regulation in granular cells. Consistently, conditional knockout mice have delayed barrier formation as embryos, enlarged granular layer cells and corneocytes, and a morphologically abnormal cornified layer. These studies provide insight into cornification, identifying transcriptional regulatory circuitry and indicating the importance of blocking osmotic homeostasis.
Functionally specialized junctions between endothelial cells of lymphatic vessels
Authors: Baluk Peter , Fuxe Jonas , Hashizume Hiroya , Romano Talia , Lashnits Erin , Butz Stefan , Vestweber Dietmar , Corada Monica , Molendini Cinzia , Dejana Elisabetta , McDonald Donald M.
Published: September 2007

Recirculation of fluid and cells through lymphatic vessels plays a key role in normal tissue homeostasis, inflammatory diseases, and cancer. Despite recent advances in understanding lymphatic function (Alitalo, K., T. Tammela, and T.V. Petrova. 2005. Nature. 438:946–953), the cellular features responsible for entry of fluid and cells into lymphatics are incompletely understood. We report the presence of novel junctions between endothelial cells of initial lymphatics at likely sites of fluid entry. Overlapping flaps at borders of oak leaf–shaped endothelial cells of initial lymphatics lacked junctions at the tip but were anchored on the sides by discontinuous button-like junctions (buttons) that differed from conventional, continuous, zipper-like junctions (zippers) in collecting lymphatics and blood vessels. However, both buttons and zippers were composed of vascular endothelial cadherin (VE-cadherin) and tight junction–associated proteins, including occludin, claudin-5, zonula occludens–1, junctional adhesion molecule–A, and endothelial cell–selective adhesion molecule. In C57BL/6 mice, VE-cadherin was required for maintenance of junctional integrity, but platelet/endothelial cell adhesion molecule–1 was not. Growing tips of lymphatic sprouts had zippers, not buttons, suggesting that buttons are specialized junctions rather than immature ones. Our findings suggest that fluid enters throughout initial lymphatics via openings between buttons, which open and close without disrupting junctional integrity, but most leukocytes enter the proximal half of initial lymphatics.
Neurofascin as a novel target for autoantibody-mediated axonal injury
Authors: Mathey Emily K. , Derfuss Tobias , Storch Maria K. , Williams Kieran R. , Hales Kimberly , Woolley David R. , Al-Hayani Abdulmonem , Davies Stephen N. , Rasband Matthew N. , Olsson Tomas , Moldenhauer Anja , Velhin Sviataslau , Hohlfeld Reinhard , Meinl Edgar , Linington Christopher
Published: September 2007

Axonal injury is considered the major cause of disability in patients with multiple sclerosis (MS), but the underlying effector mechanisms are poorly understood. Starting with a proteomics-based approach, we identified neurofascin-specific autoantibodies in patients with MS. These autoantibodies recognize the native form of the extracellular domains of both neurofascin 186 (NF186), a neuronal protein concentrated in myelinated fibers at nodes of Ranvier, and NF155, the oligodendrocyte-specific isoform of neurofascin. Our in vitro studies with hippocampal slice cultures indicate that neurofascin antibodies inhibit axonal conduction in a complement-dependent manner. To evaluate whether circulating antineurofascin antibodies mediate a pathogenic effect in vivo, we cotransferred these antibodies with myelin oligodendrocyte glycoprotein–specific encephalitogenic T cells to mimic the inflammatory pathology of MS and breach the blood–brain barrier. In this animal model, antibodies to neurofascin selectively targeted nodes of Ranvier, resulting in deposition of complement, axonal injury, and disease exacerbation. Collectively, these results identify a novel mechanism of immune-mediated axonal injury that can contribute to axonal pathology in MS.
Metric conformal structures and hyperbolic dimension
Authors: Mineyev Igor
Published: September 2007

For any hyperbolic complex

X
X

and

a
∈
X

a\in X

we construct a visual metric 

d
ˇ

=

d
ˇ

a

\check {d}=\check {d}_a

on

∂
X

\partial X

that makes the

Isom
⁡
(
X
)

\operatorname {Isom}(X)

-action on

∂
X

\partial X

bi-Lipschitz, Möbius, symmetric and conformal.

We define a stereographic projection of 

d
ˇ

a

\check {d}_a

and show that it is a metric conformally equivalent to 

d
ˇ

a

\check {d}_a

.

We also introduce a notion of hyperbolic dimension for hyperbolic spaces with group actions. Problems related to hyperbolic dimension are discussed.
Clustal W and Clustal X version 2.0
Authors: Larkin M.A. , Blackshields G. , Brown N.P. , Chenna R. , McGettigan P.A. , McWilliam H. , Valentin F. , Wallace I.M. , Wilm A. , Lopez R. , Thompson J.D. , Gibson T.J. , Higgins D.G.
Published: September 2007

Summary: The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems.

Availability: The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/

Contact:  clustalw@ucd.ie
Construction of a reference gene association network from multiple profiling data: application to data analysis
Authors: Ucar Duygu , Neuhaus Isaac , Ross-MacDonald Petra , Tilford Charles , Parthasarathy Srinivasan , Siemers Nathan , Ji Rui-Ru
Published: September 2007

Motivation: Gene expression profiling is an important tool for gaining insight into biology. Novel strategies are required to analyze the growing archives of microarray data and extract useful information from them. One area of interest is in the construction of gene association networks from collections of profiling data. Various approaches have been proposed to construct gene networks using profiling data, and these networks have been used in functional inference as well as in data visualization. Here, we investigated a non-parametric approach to translate profiling data into a gene network. We explored the characteristics and utility of the resulting network and investigated the use of network information in analysis of variance models and hypothesis testing.

Results: Our work is composed of two parts: gene network construction and partitioning and hypothesis testing using sub-networks as groups. In the first part, multiple independently collected microarray datasets from the Gene Expression Omnibus data repository were analyzed to identify probe pairs that are positively co-regulated across the samples. A co-expression network was constructed based on a reciprocal ranking criteria and a false discovery rate analysis. We named this network Reference Gene Association (RGA) network. Then, the network was partitioned into densely connected sub-networks of probes using a multilevel graph partitioning algorithm. In the second part, we proposed a new, MANOVA-based approach that can take individual probe expression values as input and perform hypothesis testing at the sub-network level. We applied this MANOVA methodology to two published studies and our analysis indicated that the methodology is both effective and sensitive for identifying transcriptional sub-networks or pathways that are perturbed across treatments.

Contact:  Nathan.Siemers@bms.com or Ruiru.Ji@bms.com
2D NMR metabonomic analysis: a novel method for automated peak alignment
Authors: Zheng Ming , Lu Peng , Liu Yanzhou , Pease Joseph , Usuka Jonathan , Liao Guochun , Peltz Gary
Published: September 2007

Motivation: Comparative metabolic profiling by nuclear magnetic resonance (NMR) is showing increasing promise for identifying inter-individual differences to drug response. Two dimensional (2D) 1H13C NMR can reduce spectral overlap, a common problem of 1D 1H NMR. However, the peak alignment tools for 1D NMR spectra are not well suited for 2D NMR. An automated and statistically robust method for aligning 2D NMR peaks is required to enable comparative metabonomic analysis using 2D NMR.

Results: A novel statistical method was developed to align NMR peaks that represent the same chemical groups across multiple 2D NMR spectra. The degree of local pattern match among peaks in different spectra is assessed using a similarity measure, and a heuristic algorithm maximizes the similarity measure for peaks across the whole spectrum. This peak alignment method was used to align peaks in 2D NMR spectra of endogenous metabolites in liver extracts obtained from four inbred mouse strains in the study of acetaminophen-induced liver toxicity. This automated alignment method was validated by manual examination of the top 50 peaks as ranked by signal intensity. Manual inspection of 1872 peaks in 39 different spectra demonstrated that the automated algorithm correctly aligned 1810 (96.7%) peaks.

Availability: Algorithm is available upon request.

Contact:  guochun.liao@roche.com
A genotype calling algorithm for the Illumina BeadArray platform
Authors: Teo Yik Y. , Inouye Michael , Small Kerrin S. , Gwilliam Rhian , Deloukas Panagiotis , Kwiatkowski Dominic P. , Clark Taane G.
Published: September 2007

Motivation: Large-scale genotyping relies on the use of unsupervised automated calling algorithms to assign genotypes to hybridization data. A number of such calling algorithms have been recently established for the Affymetrix GeneChip genotyping technology. Here, we present a fast and accurate genotype calling algorithm for the Illumina BeadArray genotyping platforms. As the technology moves towards assaying millions of genetic polymorphisms simultaneously, there is a need for an integrated and easy-to-use software for calling genotypes.

Results: We have introduced a model-based genotype calling algorithm which does not rely on having prior training data or require computationally intensive procedures. The algorithm can assign genotypes to hybridization data from thousands of individuals simultaneously and pools information across multiple individuals to improve the calling. The method can accommodate variations in hybridization intensities which result in dramatic shifts of the position of the genotype clouds by identifying the optimal coordinates to initialize the algorithm. By incorporating the process of perturbation analysis, we can obtain a quality metric measuring the stability of the assigned genotype calls. We show that this quality metric can be used to identify SNPs with low call rates and accuracy.

Availability: The C++ executable for the algorithm described here is available by request from the authors.

Contact:  teo@well.ox.ac.uk or tgc@well.ox.ac.uk
A mixed-age classed ‘pelycosaur’ aggregation from South Africa: earliest evidence of parental care in amniotes?
Authors: Botha-Brink Jennifer , Modesto Sean P
Published: September 2007

Living species of mammals, crocodiles and most species of birds exhibit parental care, but evidence of this behaviour is extremely rare in the fossil record. Here, we present a new specimen of varanopid ‘pelycosaur’ from the Middle Permian of South Africa. The specimen is an aggregation, consisting of five articulated individuals preserved in undisturbed, close, lifelike, dorsal-up, subparallel positions, indicating burial in ‘life position’. Two size classes are represented. One is 50% larger than the others, is well ossified, has fused neurocentral sutures and is distinguished by a coat of dermal ossifications that covers the neck and shoulder regions. We regard this individual to be an adult. The remaining four skeletons are considered to be juveniles as they are approximately the same size, are poorly ossified, have open neurocentral sutures and lack dermal ossifications. Aggregates of juvenile amniotes are usually siblings. Extant analogues of adult and juvenile groupings suggest that the adult is one of the parents, leading us to regard the aggregation as a family group. The Late Middle Permian age of the varanopid family predates the previously known oldest fossil evidence of parental care in terrestrial vertebrates by 140 Myr.
Resolving a zoological mystery: the kouprey is a real species
Authors: Hassanin Alexandre , Ropiquet Anne
Published: September 2007

The kouprey is a rare and enigmatic forest ox discovered by scientists in Cambodia only in 1937. Numerous morphological hypotheses have been proposed for the origin of the kouprey: that it is a species closely related to banteng and gaur, two other wild oxen of southeast Asia; a morphologically divergent species placed in a separate genus, named
Novibos
; a wild species linked to aurochs and domestic cattle; a vicariant population of banteng; a feral cattle; or a hybrid of banteng with either zebu cattle, gaur or water buffalo.

In a recent paper, which gained a lot of media coverage, Galbreath
et al
. analysed mitochondrial DNA sequences and concluded that the kouprey never existed as a wild, natural species, and that it was a feral hybrid between banteng and zebu cattle.

Here we analyse eight DNA markers—three mitochondrial regions and five nuclear fragments—representing an alignment of 4582 nucleotides for the holotype of the kouprey and all related species. Our results demonstrate that the kouprey is a real and naturally occurring species, and show that Cambodian populations of banteng acquired a mitochondrial genome of kouprey by natural introgressive hybridization during the Pleistocene epoch.
Prehistoric inter-archipelago trading of Polynesian tree snails leaves a conservation legacy
Authors: Lee Taehwan , Burch John B , Coote Trevor , Fontaine Benoît , Gargominy Olivier , Pearce-Kelly Paul , Foighil Diarmaid Ó
Published: September 2007

Inter-archipelago exchange networks were an important aspect of prehistoric Polynesian societies. We report here a novel genetic characterization of a prehistoric exchange network involving an endemic Pacific island tree snail,Partula hyalina. It occurs in the Society (Tahiti only), Austral and Southern Cook Islands. Our genetic data, based on museum, captive and wild-caught samples, establish Tahiti as the source island. The source lineage is polymorphic in shell coloration and contains a second nominal species, the dark-shelledPartula clara, in addition to the white-shelledP. hyalina. Prehistoric inter-island introductions were non-random: they involved white-shelled snails only and were exclusively inter-archipelago in scope. Partulid shells were commonly used in regional Polynesian jewellery, and we propose that the white-shelledP. hyalina, originally restricted to Tahiti, had aesthetic value throughout these archipelagoes. Demand within the Society Islands could be best met by trading dead shells, but a low rate of inter-archipelago exchange may have prompted the establishment of multiple founder populations in the Australs and Southern Cooks. The alien carnivorous land snailEuglandina roseahas recently devastated populations of all 61 endemic species of Society Island partulid snails. Southern Cooks and AustralsP. hyalinanow represent the only unscathed wild populations remaining of this once spectacular land snail radiation.
Q-cgi: new techniques to assess variation in perception applied to facial attractiveness
Authors: Michael Burt D , Kentridge Robert W , Good James M.M , Perrett David I , Tiddeman Bernard P , Boothroyd Lynda G
Published: September 2007

We present novel methods for assessing variation in the perception of subjective cues based on a fusion of Q-methodology with computer graphics techniques. Participants first Q-sort face stimuli based upon a subjective quality; a randomization-based statistic is then calculated to test whether groups of participants differ in their perception. Computer graphics are then used to extract and illustrate the differences in the manner which participants sorted so that the differences can be quantified. As a demonstration, the technique is applied to investigate the effects of prospective relationship duration and of sexual restrictiveness on the characteristics which participants find attractive in photographs of opposite-sex faces. Results show that in a naturally varying set of faces, female participants prefer facial cues related to masculinity for short-term relationships, whereas characteristics related to positive personality attributes are preferred for long-term relationships. For short-term relationships, male participants appear to prefer more feminine, youthful faces. Preferences of individuals with less restricted sexual strategy paralleled short-term preferences in that more feminine female faces and more masculine male faces were preferred.
The fiddler crabUca mjoebergiuses colour vision in mate choice
Authors: Detto Tanya
Published: September 2007

Although the role of colour in mate choice is well known, few tests of colour vision have been based on mating behaviour. Females of the fiddler crabUca mjoebergihave recently been shown to use claw coloration to recognize conspecific males. In this study I demonstrate that the females use colour vision for this task; preferentially approaching yellow claws over grey claws regardless of their intensity while failing to discriminate between yellow claws differing in intensity. This is one of only a handful of studies confirming the involvement of colour vision in mate choice and the first conclusive evidence in fiddler crabs.
Mixed valence complexes involving MM quadruple bonds (M=Mo or W)
Authors: Chisholm Malcolm H
Published: September 2007

The MM quadruple bond of configuration MM σ
2
π
4
δ
2
is redox active and in many ways ideally suited for studies of mixed valency when two or more such centres are linked by a bridging ligand. In this account, the mechanism of electronic coupling is examined for complexes of the type [L
3
M
2
bridgeM
2
L
3
]
0/+
where L, a pivalate; bridge, a dicarboxylate or related ligand and M, Mo or W. The represented examples allow us to probe electronic factors close to the class II/III border and readily distinguish between electron and hole transfer in the superexchange mechanism. The potential for mixed valence organic radical anions mediated by the M
2
centre is also raised and one specific example of class III behaviour is described.
Traces of ancient range shifts in a mountain plant group (Androsace halleri complex, Primulaceae)
Authors: DIXON CHRISTOPHER J. , SCHÖNSWETTER PETER , SCHNEEWEISS GERALD M.
Published: September 2007

Phylogeographical studies frequently detect range shifts, both expansions (including long‐distance dispersal) and contractions (including vicariance), in the studied taxa. These processes are usually inferred from the patterns and distribution of genetic variation, with the potential pitfall that different historical processes may result in similar genetic patterns. Using a combination of DNA sequence data from the plastid genome, AFLP fingerprinting, and rigorous phylogenetic and coalescence‐based hypothesis testing, we show that Androsace halleri (currently distributed disjunctly in the northwestern Iberian Cordillera Cantábrica, the eastern Pyrenees, and the French Massif Central and Vosges), or its ancestor, was once more widely distributed in the Pyrenees. While there, it hybridized with Androsace laggeri and Androsace pyrenaica, both of which are currently allopatric with A. halleri. The common ancestor of A. halleri and the north Iberian local endemic Androsace rioxana probably existed in the north Iberian mountain ranges with subsequent range expansion (to the French mountain ranges of the Massif Central and the Vosges) and allopatric speciation (A. rioxana, A. halleri in the eastern Pyrenees, A. halleri elsewhere). We have thus been able to use the reticulate evolution in this species group to help elucidate its phylogeographical history, including evidence of range contraction.
The effect of mosapride citrate on proximal and distal colonic motor function in the guinea‐pigin vitro
Authors: Kim H. S. , Choi E. J. , Park H.
Published: September 2007

Abstract Mosapride citrate (mosapride), a substituted benzamide, is a selective 5‐HT4receptor agonist, and is known to have prokinetic properties on the stomach. However, it is unclear whether mosapride also has a prokinetic effect on the colon. We previously found that mosapride significantly shortened colonic transit time in the guinea‐pig, an animal with a distribution of colonic 5‐HT4receptors similar to that of a human. So, we aimed to separately evaluate the effect of mosapride on proximal and distal colonic motor function in the guinea‐pig. Proximal (approximately 8 cm from the ileocolic junction) and distal colon (approximately 8 cm from the anus) were removed. Both ends of the colon were connected to a chamber containing a Krebs‐Henseleit solution. To measure colonic transit time, artificial faeces were inserted into the oral side of the lumen and moved towards the anal side by intraluminal perfusion via a peristaltic pump. A total of 6 cm of transit was observed and time was measured in 2 cm increments. A tissue bath study, using electrical stimulation, was performed to estimate the contractile activity of the circular musculature of the colon. Immunohistochemical staining for 5‐HT4receptors was performed in the myenteric plexus and circular muscle in both proximal and distal colon, and the stained area was measured using a microscope and computer software. Mosapride enhanced contraction at 10−9to 10−7 mol L−1, coinciding with rapid transit both in proximal and distal colon. This pattern was more prominent in proximal colon. At the high dose (10−6 mol L−1) mosapride had little or no effect on colonic contraction. This stimulatory effect was attenuated by GR113808, atropine and tetrodotoxin. In the myenteric plexus, the density of 5‐HT4receptors was significantly greater in the proximal colon than in the distal colon, but in circular muscle the density was greater in the distal colon. Thus, mosapride accelerates transit through increased contraction in the proximal colon more than distal colon. The different distribution of neuronal and muscular 5‐HT4receptors may support these findings. Therefore, mosapride may be a useful alternative to tegaserod and cisapride for constipation.
Hypersensitivity for capsaicin in patients with functional dyspepsia
Authors: Hammer J. , Führer M. , Pipal L. , Matiasek J.
Published: September 2007

Abstract The pathophysiology of functional dyspepsia is poorly understood, thus diagnostic and therapeutic options for this disease are limited. We assessed the relevance of a simple test for chemical hypersensitivity by applying an oral capsaicin load. After a preliminary dose‐finding study, 61 healthy controls and 54 functional dyspepsia patients swallowed a capsule containing 0.75 mg capsaicin. A graded questionnaire evaluated severity of symptoms before and after capsule ingestion; an aggregate symptom score was calculated by adding all symptom scores. Controls developed moderate symptoms (symptom score: 6.0 ± 4.1; median: 5.0). The 75% quartile (9.0) was considered the upper limit of normal. Functional dyspepsia patients had significantly higher symptom scores (10.0 ± 6.5) than controls. About 54% of functional dyspepsia patients tested positive; clinically this group was not different from the group testing negative besides being on average younger and suffering more from bloating. In additional 13 patients with functional dyspepsia who tested positive (symptom score: 15.8 ± 0.9), symptom response to placebo capsules (1.9 ± 0.6) was similar to controls. In reliability testing, the Cronbach α‐value of the capsaicin test was 0.86. The capsaicin test is a simple and non‐invasive method to detect a subgroup of functional dyspepsia with chemical hypersensitivity.
Development of in situ melanoma after allogeneic bone marrow transplantation in Griscelli syndrome type II
Authors: Köse Osman , Kürekçi Ahmet Emin , Safali Mükerrem , Akin Rıdvan , Köseoğlu Vedat , Tezcan İlhan
Published: September 2007

Abstract:  GS is an uncommon autosomal recessive disorder characterized by pigmentary dilution of the skin and hair and in most patients by abnormal regulation of the immune system. Childhood melanoma is rare in the pediatric population. The best prognosis is achieved with early diagnosis and definitive surgical excision of melanoma. We report a case of a patient with GS type II and melanoma who was successfully treated by allogeneic bone marrow transplantation and surgical excision of the melanoma.
Joining the Gang and Becoming aBroder: The Violence of Ethnography in Contemporary Nicaragua
Authors: RODGERS DENNIS
Published: September 2007

The fact that anthropologists ‘construct’ the field in which they conduct their ethnographic research has long been recognised, but less considered are the ways in which the field can ‘construct’ both the anthropologist and fieldwork practices. In many ways, this process is a natural corollary of the fact that researchers must always adapt and sensitise themselves to the realities of their field locations, and more importantly, the inherently dialogical nature of ethnographic research. At the same time, this ‘construction’ can potentially have more singular ramifications, particularly when fieldwork is carried out in situations characterised by chronic violence. In such circumstances, the ethnographic process almost inevitably exposes the anthropologist to violence, but can also become intrinsically imbued with violence, to the extent that it can make sense to talk of the ‘violence’ of ethnography. This article illustrates this idea through a consideration of the author’s doctoral fieldwork experiences in Managua, Nicaragua, including his ritual initiation into an urban youth gang, and considers some of the ethical and practical ramifications of this experience.
Learning at the Edges: Participatory Action Research and Child Maltreatment in Post‐War Guatemala
Authors: SCHRADER McMILLAN ANITA
Published: September 2007

This article focuses on the effect of Participatory Action Research (PAR) on changing parents’ disciplinary practices and galvanising community organisation in Guatemala City. The article analyses PAR with reference to Carr and Kemmis’s threefold typology. The project involved a transition from a technical model, in which participant actors investigate a subject proposed by the lead researcher, through a practical stage, in which participants and lead researcher interact on an equal basis, to participant‐led action that has a critical intent.
Mapping the Labyrinth from Within: The Political Economy of Nicaraguan Youth Policy Concerning Violence
Authors: GÓMEZ JOSÉ LUIS ROCHA
Published: September 2007

This article explores some of the methodological dimensions relating to the study of the two main Nicaraguan governmental organisations that deal with youth violence: the National Police and the Office of the Special Ombudsman for Children and Adolescents. It details how they were mapped institutionally and how their dysfunctions, contradictions and interactions were identified, including the ways in which the problem of political interference emerged and manifested itself through the coexistence of incongruent interest groups, discourses and practices in both organisations. The analytical process is explained and there is a detailed discussion of how the author obtained access to information.
Tears, Trauma and Suicide: Everyday Violence among Street Youth in Puebla, Mexico1
Authors: JONES GARETH A. , HERRERA ELSA , THOMAS DE BENÍTEZ SARAH
Published: September 2007

Despite considerable ethnographic research with young people in street situations and a growing interest in violence, little attention has been paid to suicide. The occurrence of suicide is a dramatic event that reveals weaknesses in support systems established by governments and civil society organisations, as well as perceived failings of friends. While an interest in suicide usually considers cause, in this paper we explore effect. How does the death of a member of a tightly knit group of street youth affect others and what does the suicide tell us about their identification with death more generally? Research for the paper was part of an in‐depth study of identities among street youth in Mexico.
Using ‘Participatory’ Methods with Young People in Contexts of Violence: Reflections from Guatemala
Authors: WINTON AILSA
Published: September 2007

This article is based on research carried out with young people in Guatemala City, in communities with a high incidence of youth gang violence. The demands of working with a traditionally ‘disempowered’ social group, youth, and in situations of violence, provide a timely opportunity for methodological reflection. The central objective is to discuss the means through which perceptions and experiences of gang violence were reported during the research. It deals in particular with the relative benefits of Participatory Appraisal methods in research with young people in situations of violence. Empirical material from Guatemala is used to reflect on the particular ways in which violence is variously revealed and explained. It also comments on the ways in which violence, in turn, impacted upon the conduct of the research itself.
‘(Young) Men With Big Guns’: Reflexive Encounters with Violence and Youth in El Salvador
Authors: HUME MO
Published: September 2007

The phenomenon of youth gangs has emerged as one of the most visible and feared expressions of violence in El Salvador in recent years. This article explores the process of researching violence associated with gangs from a feminist perspective, focusing on the challenges presented by conducting research in a context where popular perceptions of violence often reflect wider hegemonic social discourses concerning gender and youth, and where there exists a gap between actual violence and its representation. The article addresses the tensions that can emerge between the research process and popular conceptualisations of violence through an exploration of issues of researcher identity, subjectivity and constructions of ‘other’. It documents a research process that came to be shaped – theoretically and practically – by both individual and collective representations of violence, and shows how youth violence and youth gangs, in particular, concretely come to provide a central epistemological axis for societal fears and insecurities.