bluuebunny/crossref_metadata_2025 huggingface dataset:
The epidermal growth factor receptor gene sequence is highly conserved in primary gastric cancers
Authors: Mimori Koshi , Nagahara Hisashi , Sudo Tomoya , Ishii Hideshi , Yamashita Keishi , Barnard Graham F. , Mori Masaki
Published: December 2005

Background and Objectives

Recent studies have disclosed the presence of somatic mutations in the epidermal growth factor receptor (EGFR) gene in non‐small cell lung cancers (NSCLC), and susceptibility to the EGFR tyrosine kinase inhibitor (gefitinib) was determined by the presence of mutations in the kinase domain of this gene. We thus predicted a clinical benefit of gefitinib against the 12% of primary colorectal cancers exhibiting a mutation reflective of this potential distinctive susceptibility.

Patients and Methods

The mutation status of the kinase domain in EGFR in different primary cancers has important clinical consequences, because the presence of a mutation is recognized as a reliable indicator for the effectiveness of gefitinib administration. In the current study, we investigated the presence of somatic mutations in exons 18–21 coding the ATP‐binding domain in five gastric cancer cell lines and 39 primary gastric cancers and their corresponding normal tissues.

Results and Conclusions

The kinase domain of EGFR is highly conserved in whole gastric cancer cell lines and cases, therefore treatment with gefitinib is unfortunately not recommended for such malignancy. J. Surg. Oncol. 2006;93:44–46. © 2005 Wiley‐Liss, Inc.
Immunoglobulin VH genes in thymic MALT lymphoma are biased toward a restricted repertoire and are frequently unmutated
Authors: Yoshida Megumi , Okabe Mitsukuni , Eimoto Tadaaki , Shimizu Shinichiro , Ueda‐Otsuka Kayo , Okamoto Masataka , Ishii Genichiro , Ueda Ryuzo , Chan John K C , Nakamura Shigeo , Inagaki Hiroshi
Published: December 2005

Thymic MALT lymphoma shows certain distinctive features among MALT lymphomas, such as expression of IgA isotype, consistent lack of API2–MALT1 gene fusion, and very strong association with autoimmune disease, especially Sjogren's syndrome. To help clarify the nature of the clonal lymphoid infiltrates, we analysed the usage and somatic hypermutation of the Ig heavy chain variable region (VH) genes in nine different cases. The VH rearrangement was potentially functional in all cases and was restricted to the VH3 family. VH usage was biased toward VH3‐30 (five cases) and VH3‐23 (three cases) segments, which have both been frequently expressed by autoimmune B cells. Somatic hypermutation was absent in five cases. Fewer than the expected replacement mutations were found in the framework regions in two cases, indicating a negative antigen selection pressure. Ongoing mutation was absent in all cases. D segment usage was varied, whereas JH segment usage was restricted to JH4. The observed patterns of VH usage and mutations suggested that specific antigens may play a pathologically relevant role in the genesis or progression of thymic MALT lymphoma. Copyright © 2005 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Cytokine gene expression profile distinguishes CD4+/CD57+ T cells of the nodular lymphocyte predominance type of Hodgkin's lymphoma from their tonsillar counterparts
Authors: Atayar Çiǧdem , Poppema Sibrand , Visser Lydia , van den Berg Anke
Published: December 2005

Little is known about the cytokine profile of nodular lymphocyte predominance Hodgkin's lymphoma (NLPHL) and the significance of the characteristic rosetting CD4+/CD57+ T cells. We analysed the T lymphocyte populations isolated from lymph node suspensions from five patients with NLPHL, two with follicular hyperplasia and progressive transformation of germinal centres (PTGC), three with classical Hodgkin's lymphoma (CHL) and five with hyperplasia of the tonsil. We sorted the T cells based on expression of CD3, CD4 and CD57 by flow cytometry and evaluated the cytokine mRNA profiles of the T cells with quantitative RT‐PCR. NLPHL cases were as rich in T cells as the CHL cases, but all NLPHL cases had a much higher frequency of CD4+/CD57+ T cells. In contrast to the CD4+/CD57+ T cells from tonsils, IL2 and IL4 mRNAs were consistently absent from the CD4+/CD57+ T cells of NLPHL. Even after stimulation, no IL4 transcripts could be detected in the CD4+/CD57+ T cells of NLPHL. On the other hand, IFNγ transcripts were elevated in NLPHL and PTGC T cell subsets as compared to tonsillar T cell subsets. IL13 mRNA was exclusively produced by the T cells of CHL cases, indicating that IL13 may be a key cytokine in CHL. In conclusion, elevated levels of CD4+/CD57+ T cells are characteristic of NLPHL and these T cells display a distinct cytokine mRNA profile. Copyright © 2005 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Knock‐down of hepatitis B virus X protein reduces the tumorigenicity of hepatocellular carcinoma cells
Authors: Chan David Wai , Oi‐lin Ng Irene
Published: December 2005

Hepatitis B virus (HBV) infection is a major cause of hepatocellular carcinoma (HCC) in Southeast Asia and Hong Kong. Among the four proteins that are encoded by the HBV genome, HBV X (HBx) is the most potentially oncogenic factor. It is known that HBx plays an important role in hepatocarcinogenesis, but the exact functions and molecular mechanisms of HBx in HCC are not well understood. In this study, we constructed expression vectors for small hairpin RNAs (shRNA) against HBx and investigated their regulatory effects in PLC/PRF/5 HCC cells, which constitutively produce HBx. Our data show that this tool of RNA interference (RNAi) could successfully reduce the HBx mRNA and protein levels by 50–95%. RNAi targeting HBx in PLC/PRF/5 cells demonstrated significant reduction in cell proliferation, cell growth, anchorage‐independent growth in soft agar, and tumour development in nude mice. In addition, depletion of HBx expression increased cell sensitivity to TNFα‐mediated and serum‐free‐induced apoptosis, and reduced the expression levels of C‐myc and Bcl‐XL. These findings suggest that HBx plays an important role in tumorigenicity and anti‐apoptotic mechanisms in HCC. Copyright © 2005 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Lack of genetic and epigenetic changes in meningiomas without NF2 loss
Authors: van Tilborg Angela AG , Morolli Bruno , Giphart‐Gassler Micheline , de Vries Annie , van Geenen Daniëlle AN , Lurkin Irene , Kros Johan M , Zwarthoff Ellen C
Published: December 2005

Approximately 60% of sporadic meningiomas are caused by inactivation of the NF2 tumour suppressor gene. The causative gene for the remaining meningiomas is unknown. Previous studies have shown that these tumours have no recurrent karyotypic abnormalities. They differ from their NF2‐related counterparts in that they are more often of the meningothelial subtype and are located preferentially in the anterior skull base. To gain more insight into the aetiology of these tumours, we studied genetic and epigenetic alterations in 25 meningiomas without NF2 involvement. We first established a genome‐wide allelotype using 3 microsatellite markers per chromosome arm. Loss of heterozygosity (LOH) was detected at a low frequency and no indication for the location of putative tumour suppressor genes could be established. We next screened the subtelomeric regions by using 2–3 polymorphic markers close to each telomere. Again no evidence for LOH of a particular chromosome arm was obtained, and no LOH was found in the genomic regions containing the NF2‐related ERM family members ezrin and radixin, DAL‐1, protein 4.1R, and TSLC1. Mutations in the X‐chromosome based family member, moesin, were analysed by SSCP and were not detected. Microsatellite instability was studied using 6 commonly used markers but none of these was altered in any meningioma. Methylation was detected in 5 of 16 genes (NF2, p14ARF, CDH1, BRCA1, RB1) previously shown to be silenced in a variety of tumour types. However, methylation percentages for these genes were generally higher in a group of NF2‐related meningiomas, with the exception of the BRCA1 gene. The NF2 gene was methylated in only 1 of 21 tumours. In conclusion, meningiomas with an intact NF2 gene have a normal karyotype and no obvious genetic or epigenetic aberrations, suggesting that the gene(s) involved in the pathogenesis of these tumours are altered by smaller events than can be detected with the techniques used in our study. Copyright © 2005 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Hydrogen bonding increases packing density in the protein interior
Authors: Schell David , Tsai Jerry , Scholtz J. Martin , Pace C. Nick
Published: December 2005

The contribution of hydrogen bonds and the burial of polar groups to protein stability is a controversial subject. Theoretical studies suggest that burying polar groups in the protein interior makes an unfavorable contribution to the stability, but experimental studies show that burying polar groups, especially those that are hydrogen bonded, contributes favorably to protein stability. Understanding the factors that are not properly accounted for by the theoretical models would improve the models so that they more accurately describe experimental results. It has been suggested that hydrogen bonds may contribute to protein stability, in part, by increasing packing density in the protein interior, and thereby increasing the contribution of van der Waals interactions to protein stability. To investigate the influence of hydrogen bonds on packing density, we analyzed 687 crystal structures and determined the volume of buried polar groups as a function of their extent of hydrogen bonding. Our findings show that peptide groups and polar side chains that form hydrogen bonds occupy a smaller volume than the same groups when they do not form hydrogen bonds. For example, peptide groups in which both polar groups are hydrogen bonded occupy a volume, on average, 5.2 Å3 less than a peptide group that is not hydrogen bonded. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Quantitative determination of piritramide in human plasma and urine by off‐ and on‐line solid‐phase extraction liquid chromatography coupled to tandem mass spectrometry
Authors: Kahlich Rainer , Gleiter Christoph H. , Laufer Stefan , Kammerer Bernd
Published: December 2005

A method for the liquid chromatography/tandem mass spectrometric (LC/MS/MS) quantification of piritramide, a synthetic opioid, in plasma after conventional off‐line solid‐phase extraction (SPE) and in urine by on‐line SPE‐LC/MS/MS in positive electrospray mode was developed and validated. Applicability of the on‐line approach for plasma samples was also tested. Deuterated piritramide served as internal standard. For the off‐line SPE plasma method mixed cation‐exchange SPE cartridges and a 150 × 2 mm C18 column with isocratic elution were used. For the on‐line SPE method, a Waters Oasis HLB extraction column and the same C18 analytical column in a column‐switching set‐up with gradient elution were utilized. All assays were linear within a range of 0.5–100 ng/mL with a limit of detection of 0.05 ng/mL. The intra‐ and interday coefficients of variance ranged from 1.3 to 6.1% for plasma and 0.5 to 6.4% for urine, respectively. The extraction recovery for the off‐line plasma assay was between 90.7 and 100.0%. Influence of matrix effects, and freeze/thaw and long‐term stability were validated for both approaches; influence of urine pH additionally for quantification in urine. Copyright © 2005 John Wiley & Sons, Ltd.
13C/12C isotope labelling to study leaf carbon respiration and allocation in twigs of field‐grown beech trees
Authors: Nogués Salvador , Damesin Claire , Tcherkez Guillaume , Maunoury Florence , Cornic Gabriel , Ghashghaie Jaleh
Published: December 2005

In situ 13C/12C isotopic labelling was conducted in field‐grown beech (Fagus sylvatica) twigs to study carbon respiration and allocation. This was achieved with a portable gas‐exchange open system coupled to an external chamber. This method allowed us to subject leafy twigs to CO2 with a constant carbon isotope composition (δ13C of −51.2‰) in an open system in the field. The labelling was done during the whole light period at two different dates (in June 2002 and October 2003). The δ13C values of respiratory metabolites and CO2 that is subsequently respired during the night were measured. It was found that night‐respired CO2 is not completely labelled (only ca. 58% and 27% of new carbon is found in respired CO2 immediately after the labelling in June 2002 and October 2003, respectively) and the labelling level progressively disappeared during the next day. It is concluded that the carbon respired by beech leaves after illumination was supplied by a mixture of carbon sources in which current carbohydrates were not the only contributors. In addition, as has been found in herbaceous plants, isotopic data before labelling showed that carbon isotope discrimination favoring the 13C isotope occurred during the night respiration of beech leaves. Copyright © 2005 John Wiley & Sons, Ltd.
Systematic identification of N‐acetylheparosan oligosaccharides by tandem mass spectrometric fragmentation
Authors: Minamisawa Toshikazu , Suzuki Kiyoshi , Hirabayashi Jun
Published: December 2005

Recently, a useful procedure for the preparation of both even‐ and odd‐numbered series of N‐acetylheparosan (NAH) oligosaccharides was established. The present report describes findings when these NAH oligosaccharides were subjected to comparative mass spectrometry (MS)/MS fragmentation analysis by matrix‐assisted laser desorption/ionization (MALDI)‐LIFT‐time‐of‐flight (TOF)/TOF‐MS/MS, and electrospray ionization (ESI) collision‐induced dissociation (CID) MS/MS. The resultant fragment ions were systematically assigned to elucidate fragmentation characteristics. In the MALDI‐LIFT‐MS/MS experiments, all the NAH oligosaccharides underwent unique glycosidic cleavages that included B‐Y ion cleavages (nomenclature system of Domon and Costello, Glycoconjugate J. 1988; 5: 397) at the C‐1 side, and C‐Z ion cleavages at the C‐4 side, with respect to glucuronic acid (GlcA). In addition, 0,2A and/or 0,2X cross‐ring cleavages were observed for relatively small oligosaccharides. The former observation clearly reflects the occurrence of a GlcA‐N‐acetylglucosamine (GlcNAc) alternating structure of NAH, while the latter feature implies the occurrence of the ‐β‐1‐4‐glucuronide linkage. Extensive glycosidic cleavages were also observed in the ESI‐CID‐MS/MS fragmentation, though cleavage specificity was less evident than in the case of MALDI‐LIFT‐TOF/TOF‐MS/MS. The information obtained in this study should be valuable for understanding both biosynthetic and degradation processes of NAH and its derivatives including heparin and heparan sulfate, as well as artificially modified NAH oligosaccharides. Copyright © 2005 John Wiley & Sons, Ltd.
Investigation of disulfonamide ligands derived from o‐phenylenediamine and their Pb(II) complexes by electrospray ionization mass spectrometry
Authors: Zhang Weihua , Cai Yong , Kavallieratos Konstantinos
Published: December 2005

An electrospray ionization mass spectrometry (ESI‐MS) method, in both positive and negative ion modes, was developed for characterization of disulfonamide ligands derived from o‐phenylenediamine and their Pb(II) complexes. For the ligands, negative ion mode ESI‐MS in methanolic solutions gave simple and easily interpretable mass spectra. However, the spectra of Pb complexes were not readily interpretable under the same conditions. Protonated ligands and their Pb(II) complexes were observed in methanolic solutions by ESI‐MS in positive ion mode. The formation of Na+, K+, or NH adducts was also observed, complicating the mass spectra and decreasing the signal intensity. In order to optimize the detection of the ligands and the Pb complexes, a method was developed by adding NaOAc in the solutions. The presence of 0.2 mM NaOAc simplified the mass spectra of the ligands and the Pb complexes, and significantly increased sensitivity in both negative and positive ion modes. This modification makes ESI‐MS in both modes suitable for characterization of sulfonamide ligands and their Pb complexes, thus providing a potentially powerful tool for evaluating formation of metal complexes and screening combinatorial ligand libraries. Copyright © 2005 John Wiley & Sons, Ltd.
Multilevel logistic regression modelling with correlated random effects: application to the Smoking Cessation for Youth study
Authors: Wang Kui , Lee Andy H. , Hamilton Greg , Yau Kelvin K. W.
Published: December 2005

A multilevel logistic regression model is presented for the analysis of clustered and repeated binary response data. At the subject level, serial dependence is expected between repeated measures recorded on the same individual. At the cluster level, correlations of observations within the same subgroup are present due to the inherent hierarchical setting. Two random components are therefore incorporated explicitly within the linear predictor to account for the simultaneous heterogeneity and autoregressive structure. Application to analyse a set of longitudinal data from an adolescent smoking cessation intervention that motivated this study is illustrated. Copyright © 2005 John Wiley & Sons, Ltd.
Robust estimation in mixed linear models with non‐monotone missingness
Authors: Yun Sungcheol , Lee Youngjo
Published: December 2005

We introduce a model to account for abrupt changes among repeated measures with non‐monotone missingness. Development of likelihood inferences for such models is hard because it involves intractable integration to obtain the marginal likelihood. We use hierarchical likelihood to overcome such difficulty. Abrupt changes among repeated measures can be well described by introducing random effects in the dispersion. A simulation study shows that the resulting estimator is efficient, robust against misspecification of fatness of tails. For illustration we use a schizophrenic behaviour data presented by Rubin and Wu. Copyright © 2005 John Wiley & Sons, Ltd.
C‐terminal truncation modulates both nucleation and extension phases of τ fibrillization
Authors: Yin Haishan , Kuret Jeff
Published: December 2005

Proteolytic post‐translational modification has been proposed as an early stage event in the aggregation of τ protein and formation of neurofibrillary lesions in Alzheimer's disease. Caspases and other proteases cleave τ in vivo at discrete locations including Asp421 and Glu391. Both cleavage products are prone to aggregation relative to wild‐type, full‐length τ protein. To determine the mechanism underlying this effect, the fibrillization of τ truncated after Asp421 and Glu391 residues was characterized in a full‐length four‐repeat τ background using quantitative electron microscopy methods under homogeneous nucleation conditions. Both C‐terminal truncations decreased critical concentration relative to full‐length τ, resulting in more filament mass at reaction plateau. Moreover, truncation directly augmented the efficiency of the nucleation reaction. The results suggest the mechanism through which C‐terminal proteolysis can modulate τ filament accumulation depending on whether it precedes or follows nucleation.
FCH/Cdc15 domain determines distinct subcellular localization of NOSTRIN
Authors: Icking Ann , Schilling Kirstin , Wiesenthal Anja , Opitz Nils , Müller-Esterl Werner
Published: December 2005

NOSTRIN, an NO synthase binding protein, belongs to the PCH family of proteins, exposing a typical domain structure. While its SH3 domain and the C‐terminal coiled‐coil region cc2 have been studied earlier, the function of the N‐terminal half comprising a Cdc15 domain with an FCH (Fes/CIP homology) region followed by a coiled‐coil stretch cc1 is unknown. Here, we show that the FCH region is necessary and sufficient for membrane association of NOSTRIN, whereas the Cdc15 domain further specifies subcellular distribution of the protein. Thus, the FCH region and the Cdc15 domain fulfill complementary functions in subcellular targeting of NOSTRIN.
Expression of yeast transcriptional activator MSN1 promotes accumulation of chromium and sulfur by enhancing sulfate transporter level in plants
Authors: Kim Young Jin , Kim Jong Hoon , Lee Chang Eun , Mok Young Geun , Choi Jong Soon , Shin Hyoung Sun , Hwang Seongbin
Published: December 2005

MSN1 is a putative yeast transcriptional activator involved in chromium (Cr) accumulation. Here we show that overexpression of MSN1 enhances Cr and sulfur accumulation and Cr tolerance in transgenic tobacco. In addition, we found that expression ofNtST1(Nicotiana tabacumsulfate transporter 1) was elevated in MSN1‐ expressing transgenic tobacco, suggesting that chromate and sulfate are taken up via the sulfate transporter in plants. Supporting this, expression of NtST1 increased levels of Cr and S inSaccharomyces cerevisiae. Our findings suggest that yeast transcriptional activators can be used for developing effective metal remediators, and for improving the nutritional status of plants.
Constitutive activity of a UV cone opsin
Authors: Kono Masahiro
Published: December 2005

Vertebrate visual pigment proteins contain a conserved carboxylic acid residue in the third transmembrane helix. In rhodopsin, Glu113 serves as a counterion to the positively charged protonated Schiff base formed by 11‐cis retinal attached to Lys296. Activation involves breaking of this ion pair. In UV cone pigments, the retinyl Schiff base is unprotonated, and hence such a salt bridge is not present; yet the pigment is inactive in the dark. Mutation of Glu108, which corresponds to rhodopsin's Glu113, to Gln yields a pigment that remains inactive in the dark. The apoproteins of both the wild‐type and mutant, however, are constitutively active with the mutant being of significantly higher activity. Thus, one important role for preserving the negatively charged glutamate in the third helix of UV pigments is to maintain a less active opsin in a manner similar to rhodopsin. Ligand binding itself in the absence of a salt bridge is sufficient for deactivation.
Activation of pannexin 1 channels by ATP through P2Y receptors and by cytoplasmic calcium
Authors: Locovei Silviu , Wang Junjie , Dahl Gerhard
Published: December 2005

The ability for long‐range communication through intercellular calcium waves is inherent to cells of many tissues. A dual propagation mode for these waves includes passage of IP3 through gap junctions as well as an extracellular pathway involving ATP. The wave can be regenerative and include ATP‐induced ATP release via an unknown mechanism. Here, we show that pannexin 1 channels can be activated by extracellular ATP acting through purinergic receptors of the P2Y group as well as by cytoplasmic calcium. Based on its properties, including ATP permeability, pannexin 1 may be involved in both initiation and propagation of calcium waves.
Structural insight into binding of Staphylococcus aureus to human fibronectin
Authors: Pilka Ewa S. , Werner Joern M. , Schwarz-Linek Ulrich , Pickford Andrew R. , Meenan Nicola A.G. , Campbell Iain D. , Potts Jennifer R.
Published: December 2005

Staphylococcus aureus possesses cell‐wall attached proteins that bind the human protein fibronectin (Fn). An intermodule interface between the 4F1 and 5F1 modules in the N‐terminal domain of Fn is maintained on bacterial peptide binding but there is a small change in the intermodule orientation and alignment of β‐strands that are predicted to bind the peptide. The module pair is elongated, as in the unbound state. Combined with evidence that residues in both 4F1 and 5F1 are directly involved in peptide binding, this observation supports the hypothesis that, when bound to intact Fn, the bacterial protein adopts an unusual, highly extended conformation.
NF‐κB activation is required for cisplatin‐induced apoptosis in head and neck squamous carcinoma cells
Authors: Kim Seong Bum , Kim Jong Soo , Lee Ji Hye , Yoon Won Joon , Lee Dong Seuk , Ko Myoung Seok , Kwon Byung Suk , Choi Dae Hwa , Cho Hong Rae , Lee Byung Ju , Chung Dae Kyun , Lee Hyeon Woo , Park Jeong Woo
Published: December 2005

This study demonstrates a requirement for NF‐κB activation in cis‐diamminedichloroplatinum (cisplatin)‐induced apoptosis in human head and neck squamous cell carcinoma (HNSCC) cell lines. This conclusion was supported by the following observations: cisplatin induced IκBα degradation and NF‐κB‐dependent transcriptional activation prior to cell death; pyrrolidine dithiocarbamate (PDTC), a chemical inhibitor of NF‐κB activation, prevented apoptosis; lactacystin, an inhibitor of IκBα degradation, also prevented apoptosis; and finally, the expression of a super‐repressor mutant IκBα blocked apoptosis. The expression of tumor necrosis factor α (TNFα) was promoted by cisplatin treatment and was suppressed by PDTC treatment. In addition, a neutralizing antibody against TNFα protected cells from cisplatin‐induced apoptosis. These findings suggest that NF‐κB activation is required for cisplatin‐induced apoptosis and TNFα may play an important role in NF‐κB‐mediated apoptosis in cisplatin‐treated HNSCC cell lines.
NUMERICAL TRANSFORM INVERSION USING GAUSSIAN QUADRATURE
Authors: den Iseger Peter
Published: December 2005

Numerical inversion of Laplace transforms is a powerful tool in computational probability. It greatly enhances the applicability of stochastic models in many fields. In this article we present a simple Laplace transform inversion algorithm that can compute the desired function values for a much larger class of Laplace transforms than the ones that can be inverted with the known methods in the literature. The algorithm can invert Laplace transforms of functions with discontinuities and singularities, even if we do not know the location of these discontinuities and singularities a priori. The algorithm only needs numerical values of the Laplace transform, is extremely fast, and the results are of almost machine precision. We also present a two-dimensional variant of the Laplace transform inversion algorithm. We illustrate the accuracy and robustness of the algorithms with various numerical examples.
Yes or no? How young French children combine gestures and speech to agree and refuse
Authors: GUIDETTI MICHÈLE
Published: December 2005

The aim of the study presented here was to examine variations in the forms and functions of agreement and refusal messages – which can be solely gestural, solely verbal, or combined gestural and verbal – by thirty children aged 1;4, 2;0, and 3;0 (ten in each age group) observed at home during an interaction with their mother. The results showed that even though verbal forms were the predominant ones as a whole, gestural forms were carried over into the linguistic period, and for the youngest children, constituted the sole means of agreeing and refusing. They also showed that the most frequently expressed function was assertion.
Asymmetries in the acquisition of word-initial and word-final consonant clusters
Authors: KIRK CECILIA , DEMUTH KATHERINE
Published: December 2005

Previous work on the acquisition of consonant clusters points to a tendency for word-final clusters to be acquired before word-initial clusters (Templin, 1957; Lleó & Prinz, 1996; Levelt, Schiller & Levelt, 2000). This paper evaluates possible structural, morphological, frequency-based, and articulatory explanations for this asymmetry using a picture identification task with 12 English-speaking two-year-olds. The results show that word-final stop+/s/ clusters and nasal+/z/ clusters were produced much more accurately than word-initial /s/+stop clusters and /s/+nasal clusters. Neither structural nor frequency factors are able to account for these findings. Further analysis of longitudinal spontaneous production data from 2 children aged 1;1–2;6 provides little support for the role of morphology in explaining these results. We argue that an articulatory account best explains the asymmetries in the production of word-initial and word-final clusters.
Editorial
Authors: LIEVEN ELENA
Published: December 2005

Since this is the last issue which I shall edit for the Journal, I would like to express my thanks to authors, reviewers and members of the Editorial Board, to Patrick McCartan and Gwenda Edwards at CUP and to Clive Jenkins, the copyeditor, for their efforts over the past nine years. Very special thanks go to the team of Associate Editors, past and present, the book reviews editor, the statistics consultant and Jo Lewis, the editorial assistant, who has worked with me for almost the entire period of my editorship. Their commitment to the Journal and our discipline and their hard work has made the job not only possible but also enjoyable.
Magnitude and inferred impacts of the seahorse trade in Latin America
Authors: BAUM JULIA K. , VINCENT AMANDA C.J.
Published: December 2005

Seahorses (genus Hippocampus) are traded globally for use in traditional medicines, souvenirs and as aquarium fishes. Indications that the trade was expanding geographically in response to increasing demand in consuming nations prompted this first study of the seahorse trade in Latin America. In 2000, over 400 people related to the seahorse trade in Mexico, Central America, Ecuador and Peru were interviewed. Customs data and other trade records from these and five additional countries or regions trading seahorses from Latin America were obtained. Dried seahorses were exported by almost every surveyed country at some point in the 1990s, with Ecuador, Peru and Mexico exporting hundreds of kg per year over multiple years, and the latter two nations both exporting tonnes of seahorses at least twice. The live seahorse trade was confined to Costa Rica, Mexico, Panama and Brazil; the last dominating this trade and exporting several thousand seahorses annually. Substantial declines in seahorse abundance, attributed primarily to incidental catches in shrimp trawl fisheries, were reported consistently by respondents in many regions. These data contributed to an Appendix II listing on the Convention on International Trade in Endangered Species of Wild Fauna and Flora of all seahorses, thereby requiring that the trade be monitored and controlled. Additional conservation measures are needed to address fishing pressure on seahorse populations.
Taxonomies - Gateway or Dead End?
Authors: Sturdy Derek
Published: December 2005

The objective of any taxonomy deployment must be to ensure that real benefits are delivered to the organisation. But the experience of the last few years has illustrated the risk that law firm taxonomy projects do not deliver real benefits, but instead consume substantial time and effort for little tangible benefit. The classic symptom is that lawyers still continue to use the Googlestyle simple search box, with all its attendant issues, in preference to keyword searching for internal materials; and the taxonomy is ignored in practice by those whom it was supposed to benefit.
Correction of seafloor magnetotelluric data for topographic effects during inversion
Authors: Baba Kiyoshi , Chave Alan D.
Published: December 2005

The large contrast in electrical conductivity between seawater and the underlying seafloor accumulates boundary electric charges which can severely distort observed electric and magnetic fields. For marine magnetotelluric (MT) studies, correcting this topographic effect is critical to obtaining accurate conductivity models for the mantle. Previously, correction for topography was based on the thin sheet approximation which breaks down at periods under ∼1000 s in the deep ocean. This paper introduces an analysis method for seafloor MT data which combines removal of three‐dimensional (3‐D) topographic effects with inversion of the data for 2‐D structure. The observed MT impedance is first corrected to a flat‐lying seafloor datum using the observed bathymetry without invoking the thin sheet approximation. The corrected MT response is then inverted in a flat seafloor model space. Because of coupling between topographic effects and deeper structure, the correction and inversion steps are iterated until changes in each become small. The procedure is verified using synthetic and real data. Tests for synthetic 3‐D topography over a half‐space show that the method closely recovers the true half‐space model after a few iterations. The procedure is also applied to real data collected in the Mantle Electromagnetic and Tomography (MELT) experiment on the East Pacific Rise at 17°S.
Seismological signature of chemical differentiation of Earth's upper mantle
Authors: Matsukage Kyoko N. , Nishihara Yu , Karato Shun‐ichiro
Published: December 2005

Chemical differentiation from pyrolite to harzburgite due to partial melting and melt extraction process causes the chemical heterogeneity in Earth's upper mantle that can be detected by seismological observations. The variation in major element chemistry in natural samples reflects complicated processes that include not only partial melting but also other various magmatic processes. On the basis of a comparison of chemical and mineralogical compositions of natural peridotites with those from melting experiment, density and seismic velocities of various peridotites are calculated for the range of pressure and temperature in the upper mantle using the latest data on mineral thermoelasticity. We conclude that the seismic velocities of shallow oceanic peridotites is characterized by a single parameter such as Mg # (molar ratio Mg/(Mg + Fe)), whereas the characterization of the deep continental peridotites requires two parameters, Mg # and Opx # (volume fraction of orthopyroxene). In agreement with previous studies, we find that in spinel stability field, the seismic velocities have positive correlation with Mg # from pyrolite to residual harzburgite, while in garnet stability field, seismic velocities of residual harzburgite are indistinguishable from those of pyrolite. The seismic velocities of the deep continental peridotites are lower than those of pyrolite and residual harzburgite because of the high concentration of orthopyroxene with low seismic velocities and have large pressure dependence. A jump of seismic velocity will occur at 300 km in orthopyroxene‐rich continental harzburgite due to the orthorhombic to high‐pressure monoclinic phase transition in (Mg, Fe)SiO3 pyroxene. This phase transition may correspond to the X discontinuity.
On laboratory simulation and the temperature dependence of the evaporation rate of brine on Mars
Authors: Sears Derek W. G. , Chittenden Julie D.
Published: December 2005

We have determined the evaporation rate of brine under simulated martian conditions at temperatures from 0°C to −26.0°C as part of our efforts to better understand the stability of water on Mars. Correcting for the effect of water build‐up in the atmosphere and the lower gravity on Mars relative to Earth we observed a factor of almost 30 decrease in evaporation, from 0.88 mm/h at ∼0°C to 0.04 mm/h at −25.0°C. The results are in excellent agreement with the predictions of Ingersoll's (1970) theoretical treatment, lending support to the theory and our procedures. Thus brine formation will increase the stability of water on Mars not only by extending the liquid temperature range, but also by considerably decreasing the evaporation rate.
Are multiproxy climate reconstructions robust?
Authors: Bürger Gerd , Cubasch Ulrich
Published: December 2005

64 climate reconstructions, based on regression of temperature fields on multi‐proxies and mutually distinguished by at least one of six standard criteria, cover an entire spread of millennial histories. No single criterion is accountable for the spread, which appears to depend on a complicated interplay of the criteria. The uncertainty is traced back to the fact that regression is applied here in an extrapolative manner, with millennial proxy variations exceeding the standard calibration scale by a factor of 5 and more. Even if linearity still holds for that larger domain the model error propagates in a way that is proportional to both the estimation error and the proxy variations, and is thus extrapolated accordingly. This is particularly critical for the parameter‐loaded multiproxy methods. Without a model error estimate and without techniques to keep it small, it is not clear how these methods can be salvaged to become robust.
Different optical properties of high cloud in GMS and MODIS observations
Authors: Choi Yong‐Sang , Ho Chang‐Hoi , Sui Chung‐Hsiung
Published: December 2005

The optical properties of high cloud are compared between two satellite retrievals taken from the Geostationary Meteorological Satellite‐5 (GMS) and the Moderate‐resolution Imaging Spectroradiometer (MODIS) in the tropical western Pacific (TWP) for the years 1998–2001. The MODIS high‐cloud amount determined by 1.38‐μm reflectances (>1.1%) is approximately twice that of GMS determined by 11‐μm brightness temperatures (<260 K). The optical depths associated with the retrieved high clouds are calculated using a radiative transfer model. The minimum detectable value of optical depths by the MODIS and GMS measurements is around 0.1 and 2.0, respectively. Variations of MODIS and GMS high clouds with respect to the mean sea surface temperatures (SSTs) in the TWP are examined next. There exist large discrepancies in the change rates in high clouds with increasing SST between GMS and MODIS in the available data for the years 2000 and 2001.
Reconstructing climate variability from Greenland ice sheet accumulation: An ERA40 study
Authors: Hutterli M. A. , Raible C. C. , Stocker T. F.
Published: December 2005

Re‐analysis data covering the period 1958–2001 are used to investigate the relationship between regional, inter‐annual snow accumulation variability over the Greenland Ice Sheet (GrIS) and large scale circulation patterns, cyclone frequency, and strength. Four regions of the GrIS have been identified that are highly independent with respect to accumulation variability. Accumulation indices of three of these regions are associated with distinct large‐scale circulation patterns: Central‐western GrIS reveals an inverse relationship with a NAO‐like pattern, the south‐west a positive correlation with a high pressure bridge from central North Atlantic to Scandinavia, and the south‐eastern GrIS a positive correlation with a high‐pressure anomaly over the Greenland Sea. These large‐scale patterns also impact European climate in different ways. Accumulation variability in north‐eastern GrIS, however, is dominated by cyclones originating from the Greenland Sea. Thus, Greenland ice core accumulation records offer the potential to reconstruct various large‐scale circulation patterns and regional storm activity.
Upper crustal structure and axial topography at intermediate spreading ridges: Seismic constraints from the southern Juan de Fuca Ridge
Authors: Canales J. Pablo , Detrick Robert S. , Carbotte Suzanne M. , Kent Graham M. , Diebold John B. , Harding Alistair , Babcock Jeffrey , Nedimović Mladen R. , van Ark Emily
Published: December 2005

We use multichannel seismic reflection data to image the upper crustal structure of 0–620 ka crust along the southern Juan de Fuca Ridge. The study area comprises two segments spreading at intermediate rate with an axial high morphology with narrow (Cleft) and wide (Vance) axial summit grabens (ASG). Along most of the axis of both segments we image the top of an axial magma chamber (AMC). The AMC along Cleft deepens from south to north, from 2.0 km beneath the RIDGE Cleft Observatory and hydrothermal vents near the southern end of the segment to 2.3 km at the northern end near the site of the 1980s eruptive event. Along the Vance segment, the AMC also deepens from south to north, from 2.4 to 2.7 km. Seismic layer 2A, interpreted as the basaltic extrusive layer, is 250–300 m thick at the ridge axis along the Cleft segment and 300–350 m thick along the axis of the Vance segment. However, off‐axis layer 2A is similar in both segments (500–600 m), indicating ∼90% and ∼60% off‐axis thickening at the Cleft and Vance segments, respectively. Half of the thickening occurs sharply at the walls of the ASG, with the remaining thickening occurring within 3–4 km of the ASG. Along the full length of both segments, layer 2A is thinner within the ASG, compared to the ridge flanks. Previous studies argued that the ASG is a cyclic feature formed by alternating periods of magmatism and tectonic extension. Our observations agree with the evolving nature of the ASG. However, we suggest that its evolution is related to large changes in axial morphology produced by small fluctuations in magma supply. Thus the ASG, rather than being formed by excess volcanism, is a rifted flexural axial high. The changes in axial morphology affect the distribution of lava flows along the ridge flanks, as indicated by the pattern of layer 2A thickness. The fluctuations in magma supply may occur at all spreading rates, but its effects on crustal structure and axial morphology are most pronounced along intermediate spreading rate ridges.
Geological modeling of the new CHAMP magnetic anomaly maps using a geographical information system technique
Authors: Hemant K. , Maus S.
Published: December 2005

Reliable global crustal field anomaly maps produced from magnetic measurements of the CHAMP satellite mission now allow for quantitative geological studies of crustal structure and composition. We have developed a GIS based forward modeling technique to model these anomaly maps. On the basis of the geologic and tectonic maps of the world, laboratory susceptibility values of the occurring rock types, and the seismic thickness of the crust, a vertically integrated susceptibility grid is generated in the GIS system. In addition, a remanent magnetization grid is computed for the oceanic crust using a digital isochron map of the ocean floor and rotation models of the paleoplates. Combining the global VIS and remanent magnetization grids, the vertical magnetic field anomaly is computed at satellite altitude and compared with the corresponding CHAMP magnetic anomaly map. Over the oceans, induced and remanent magnetization explains well the prominent observed anomalies over the Cretaceous quiet zones. We also find a good agreement between predicted and observed anomalies over the continents. Remaining discrepancies between the predicted and observed anomalies can be used to adjust poorly known boundaries and the composition of the buried Precambrian provinces, until the recomputed anomalies fit the observed anomalies. The feasibility of this approach is demonstrated on Greenland, the West African Craton, Bangui in central Africa, and the Kolyma‐Omolon Block in Siberia. We conclude that quantitative information on the lateral extent, the composition and the thickness of the lower crust within a Precambrian province can thus be inferred from the new satellite magnetic anomaly maps.
The Younger Dryas: From whence the fresh water?
Authors: Moore T. C.
Published: December 2005

Oxygen isotopic records of meltwater outflow and records of sea level change do not support the idea that fresh waters derived solely from the melting of Northern Hemisphere ice sheets was likely to have stabilized the upper layers of the North Atlantic Ocean and prevented deep convection during the Younger Dryas. Yet there are paleoceanographic indicators that point to a pause in the formation of North Atlantic Deep Water during the Younger Dryas. This apparent conflict in evidence may be resolved by the existence of large, relatively thick, tabular icebergs that spilled out of the Arctic and into the Norwegian‐Greenland Sea and North Atlantic. The melting of large icebergs would have no impact on sea level but combined with meltwater runoff would provide enough fresh water to “cap” the North Atlantic. The timing of the start and the end of the Younger Dryas, however, may not have been directly related to freshwater supply.
The crystal structure of CREG, a secreted glycoprotein involved in cellular growth and differentiation
Authors: Sacher Michael , Di Bacco Alessandra , Lunin Vladimir V. , Ye Zheng , Wagner John , Gill Grace , Cygler Miroslaw
Published: December 2005

The cellular repressor of E1A-stimulated genes (CREG) is a secreted glycoprotein that inhibits proliferation and enhances differentiation of human embryonal carcinoma cells. CREG binds to the cation-independent mannose 6-phosphate (M6P)/insulin-like growth factor II (IGF2) receptor (IGF2R) (M6P/IGF2R), and this receptor has been shown to be required for CREG-induced growth suppression. To better understand CREG function in cellular growth and differentiation, we solved the 3D crystal structure of this protein to 1.9-Å resolution. CREG forms a tight homodimeric complex, and CREG monomers display a β-barrel fold. The three potential glycosylation sites on CREG map to a confined patch opposite the dimer interface. Thus, dimerization of glycosylated CREG likely presents a bivalent ligand for the M6P/IGF2R. Closely related structural homologs of CREG are FMN-binding split-barrel fold proteins that bind flavin mononucleotide. Our structure shows that the putative flavin mononucleotide-binding pocket in CREG is sterically blocked by a loop and several key bulky residues. A mutant of CREG lacking a part of this loop maintained overall structure and dimerization, as well as M6P/IGF2R binding, but lost the growth suppression activity of WT CREG. Thus, analysis of a structure-based mutant of CREG revealed that binding to M6P/IGF2R, while necessary, is not sufficient for CREG-induced growth suppression. These findings indicate that CREG utilizes a known fold.
Targeted ablation of plectin isoform 1 uncovers role of cytolinker proteins in leukocyte recruitment
Authors: Abrahamsberg Christina , Fuchs Peter , Osmanagic-Myers Selma , Fischer Irmgard , Propst Friedrich , Elbe-Bürger Adelheid , Wiche Gerhard
Published: December 2005

Plectin, a typical cytolinker protein, is essential for skin and skeletal muscle integrity. It stabilizes cells mechanically, regulates cytoskeleton dynamics, and serves as a scaffolding platform for signaling molecules. A variety of isoforms expressed in different tissues and cell types account for this versatility. To uncover the role of plectin 1, the major isoform expressed in tissues of mesenchymal origin, against the background of all other variants, we raised plectin isoform 1-specific antibodies and generated isoform-deficient mice. In contrast to plectin-null mice (lacking all plectin isoforms), which die shortly after birth because of severe skin blistering, plectin isoform 1-deficient mice were viable at birth, had a normal lifespan, and did not display the skin blistering phenotype. However, dermal fibroblasts isolated from plectin 1-deficient mice exhibited abnormalities in their actin cytoskeleton and impaired migration potential. Similarly, plectin 1-deficient T cells isolated from nymph nodes showed diminished chemotactic migration
in vitro
. Most strikingly,
in vivo
we found that leukocyte infiltration during wound healing was reduced in the mutant mice. These data show a specific role of a cytolinker protein in immune cell motility. Single isoform-deficient mice thus represent a powerful tool to unravel highly specific functions of plectin variants.