bluuebunny/crossref_metadata_2025_split huggingface dataset:
Length-based assessment of sustainability benchmarks for coral reef fishes in Puerto Rico
Authors: AULT JERALD S. , SMITH STEVEN G. , LUO JIANGANG , MONACO MARK E. , APPELDOORN RICHARD S. 
Published: November 2008

SUMMARYThe sustainability of multispecies coral reef fisheries is a key conservation concern given their economic and ecological importance. Empirical estimation and numerical model analyses were conducted to evaluate exploitation status via resource reference points (or sustainability benchmarks) for coral reef fishes of the snapper-grouper complex in Puerto Rico. Mean size (L, in length) of animals in the exploited part of the population was estimated from fishery-dependent and fishery-independent size composition data and used as an indicator variable of exploitation rates. In application, fishing mortality rates estimated fromLof various data sources were comparable. Of the 25 reef fish species assessed, 16 were below 30% spawning potential ratio (SPR), six were above 30% SPR, and three could not be reliably determined owing to low sample sizes. These findings indicate that a majority of snapper-grouper species in Puerto Rico are currently fished at unsustainable levels.
Primate color vision: A comparative perspective
Authors: JACOBS GERALD H. 
Published: November 2008

AbstractThirty years ago virtually everything known about primate color vision derived from psychophysical studies of normal and color-defective humans and from physiological investigations of the visual system of the macaque monkey, the most popular of human surrogates for this purpose. The years since have witnessed much progress toward the goal of understanding this remarkable feature of primate vision. Among many advances, investigations focused on naturally occurring variations in color vision in a wide range of nonhuman primate species have proven to be particularly valuable. Results from such studies have been central to our expanding understanding of the interrelationships between opsin genes, cone photopigments, neural organization, and color vision. This work is also yielding valuable insights into the evolution of color vision.
The fronting of the back upgliding vowels in Charleston, South Carolina
Authors: Baranowski Maciej 
Published: November 2008

AbstractIn a radical reorganization of its sound system, Charleston has lost most of the distinctive features of the traditional dialect, including monophthongal and ingliding /ey/ (face) and /ow/ (goat). The traditionally back nucleus of /ow/ is now further to the front in Charleston than it is in most other dialects of American English. The fronting is led by the highest-status social group and appears not to conform to the generalization of the curvilinear principle, whereby an intermediately located social group leads linguistic change from below. It is argued that the fronting is not internally motivated, but rather it is being introduced into the dialect as a systematic borrowing. It is a change from above and as such does not bear on the curvilinear principle.
Reversing “drift”: Innovation and diffusion in the London diphthong system
Authors: Kerswill Paul , Torgersen Eivind Nessa , Fox Susan 
Published: November 2008

AbstractThis study contributes to innovation and diffusion models by examining phonetic changes in London English. It evaluates Sapir's notion of “drift,” which involves “natural,” unconscious change, in relation to these changes. Investigating parallel developments in two related varieties of English enables drift to be tested in terms of the effect of extralinguistic factors. The diphthongs ofprice,mouth,face, andgoatin both London and New Zealand English are characterized by “Diphthong Shift,” a process that continued unabated in New Zealand. A new, large data set of London speech shows Diphthong Shift reversal, providing counterevidence for drift. We discuss Diphthong Shift and its “reversal” in relation to innovation, diffusion, leveling, and supralocalization, arguing that sociolinguistic factors and dialect contact override natural Diphthong Shift. Studying dialect change in a metropolis, with its large and linguistically innovative minority ethnic population, is of the utmost importance in understanding the dynamics of change.
Structural variation in Old English root clauses
Authors: Pintzuk Susan , Haeberli Eric 
Published: November 2008

AbstractA standard observation concerning basic constituent order in Old English (OE) is that the position of finite verbs varies by clause type. In root clauses, the finite verb tends to occur toward the beginning of the clause, and we frequently find Verb Second (V2) order. In contrast, in subordinate clauses, finite verbs generally occur toward the end of the clause, and these clauses are frequently verb-final. We challenge the traditional assumption that verb-final orders and, hence, the occurrence of the finite verb in a head-final structural position are rare in OE root clauses. We present new data demonstrating that the frequency of head-final structure in OE root clauses is much higher than previously acknowledged. We then explore some of the implications of this finding for the general structural analysis of OE.
Extracellular HspBP1 and Hsp72 synergistically activate epidermal growth factor receptor
Authors: Evdonin Anton , Kinev Alexander , Tsupkina Natalia , Guerriero Vince , Raynes Deborah A. , Medvedeva Natalia 
Published: November 2008

Background information. Heat‐inducible Hsp72 is the founding member of the Hsp70 (heat shock proteins of 70 kDa) family of molecular chaperones. It is localized primarily in cytoplasm and nucleus but is also found extracellularly. The source of e‐Hsp72 (extracellular Hsp72) is not precisely identified and may not be the same in every situation. A number of studies demonstrated that e‐Hsp72 plays an important role in cell survival, tumour rejection and immune response. However, currently little is known about regulation of e‐Hsp72 function. In cells, Hsp72 is controlled by co‐chaperones. An abundant co‐chaperone, HspBP1 (Hsp72‐binding protein 1) was found extracellularly in the serum. In the present study we analysed the secretion and function of e‐HspBP1 (extracellular HspBP1).Results. A431 human squamous carcinoma cells accumulated Hsp72 and HspBP1 in chromogranin A‐positive granules following heat stress or in the presence of U73122, an inhibitor of phospholipase C. Following these treatments, A431 cells also increased the secretion of both proteins into the culture medium. The secreted e‐Hsp72 and e‐HspBP1 were co‐immunoprecipitated from the conditioned medium. Purified recombinant HspBP1 augmented e‐Hsp72‐mediated phosphorylation of EGFR (epidermal growth factor receptor) and its down‐stream targets, ERK1 (extracellular signal‐regulated kinase 1) and ERK2 in a concentration‐dependent manner. Finally, a HspBP1 N‐terminal domain deletion mutant and boiled recombinant HspBP1 did not affect the e‐Hsp72‐mediated activity.Conclusions. Heat stress and PLC (phospholipase C) inhibition result in the enhanced secretion of both Hsp72 and HspBP1. In an extracellular environment, the two chaperones interact both physically and functionally, leading to the activation of th EGFR—ERK1/2 signalling pathway. However, the magnitude of EGFR activation depends on the e‐HspBP1/e‐Hsp72 ratio in the medium. Extracellular chaperone‐mediated activation of EGFR can provide a survival advantage to cells under heat shock and other stresses.
Multicultural Considerations in Assessing and Treating Hispanic Americans who Stutter
Authors: Tellis Glen 
Published: November 2008

Abstract
The purpose of this paper is to provide speech-language pathologists with information that addresses multicultural perceptions about stuttering and suggestions for the assessment and treatment of stuttering in Hispanic Americans. The psychometric properties of the Stuttering Inventory for Hispanic Americans are discussed. Results indicate that this scale is reliable and valid. Overall, Hispanic Americans had positive perceptions about stuttering. Suggestions for evaluation and treatment of stuttering are provided.
Client Variables Related to Relapse: A Case Study
Authors: Montgomery Catherine 
Published: November 2008

Abstract
The process of changing an aspect on one’s self that has been such an integral part of life is challenging, to say the least. Even though we believe we want this change, we sometimes unknowingly create obstacles for ourselves, generally due to fears of what life changes are to come as a result. What follows is a story of one client, his honest self exploration of his fears about becoming more fluent and the ultimate outcome.
Working with People Who Stutter of Diverse Cultural Backgrounds: Some Ideas to Consider
Authors: Daniels Derek E. 
Published: November 2008

Abstract
As the United States continues to undergo changing demographics, speech-language pathologists will find themselves working more with clients who stutter of diverse cultural backgrounds. The purpose of this article is to outline key principles for addressing cultural issues with clients who stutter. Sociocultural theory is introduced as a conceptual framework to guide assessment and therapeutic decision-making processes. Next, key principles are presented to assist clinicians in understanding a client’s cultural context, and using this as a frame of reference for treatment. Finally, a case example is presented to illustrate the ways in which a clinician can approach treatment in the specific cultural context of the client.
Cross-hybridization modeling on Affymetrix exon arrays
Authors: Kapur Karen , Jiang Hui , Xing Yi , Wong Wing Hung 
Published: November 2008

Abstract
Motivation: Microarray designs have become increasingly probe-rich, enabling targeting of specific features, such as individual exons or single nucleotide polymorphisms. These arrays have the potential to achieve quantitative high-throughput estimates of transcript abundances, but currently these estimates are affected by biases due to cross-hybridization, in which probes hybridize to off-target transcripts.
Results: To study cross-hybridization, we map Affymetrix exon array probes to a set of annotated mRNA transcripts, allowing a small number of mismatches or insertion/deletions between the two sequences. Based on a systematic study of the degree to which probes with a given match type to a transcript are affected by cross-hybridization, we developed a strategy to correct for cross-hybridization biases of gene-level expression estimates. Comparison with Solexa ultra high-throughput sequencing data demonstrates that correction for cross-hybridization leads to a significant improve-ment of gene expression estimates.
Availability: We provide mappings between human and mouse exon array probes and off-target transcripts and provide software extending the GeneBASE program for generating gene-level expression estimates including the cross-hybridization correction http://biogibbs.stanford.edu/~kkapur/GeneBase/.
Contact: whwong@stanford.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops
Authors: Milne Iain , Lindner Dominik , Bayer Micha , Husmeier Dirk , McGuire Gráinne , Marshall David F. , Wright Frank 
Published: November 2008

Abstract
Summary: TOPALi v2 simplifies and automates the use of several methods for the evolutionary analysis of multiple sequence alignments. Jobs are submitted from a Java graphical user interface as TOPALi web services to either run remotely on high-performance computing clusters or locally (with multiple cores supported). Methods available include model selection and phylogenetic tree estimation using the Bayesian inference and maximum likelihood (ML) approaches, in addition to recombination detection methods. The optimal substitution model can be selected for protein or nucleic acid (standard, or protein-coding using a codon position model) data using accurate statistical criteria derived from ML co-estimation of the tree and the substitution model. Phylogenetic software available includes PhyML, RAxML and MrBayes.
Availability: Freely downloadable from http://www.topali.org for Windows, Mac OS X, Linux and Solaris.
Contact: iain.milne@scri.ac.uk
TheArabidopsisGRAS Protein SCL14 Interacts with Class II TGA Transcription Factors and Is Essential for the Activation of Stress-Inducible Promoters
Authors: Fode Benjamin , Siemsen Tanja , Thurow Corinna , Weigel Ralf , Gatz Christiane 
Published: November 2008

AbstractThe plant signaling molecule salicylic acid (SA) and/or xenobiotic chemicals like the auxin mimic 2,4-D induce transcriptional activation of defense- and stress-related genes that contain activation sequence-1 (as-1)–like cis-elements in their promoters. as-1–like sequences are recognized by basic/leucine zipper transcription factors of the TGA family. Expression of genes related to the SA-dependent defense program systemic acquired resistance requires the TGA-interacting protein NPR1. However, a number of as-1–containing promoters can be activated independently from NPR1. Here, we report the identification of Arabidopsis thaliana SCARECROW-like 14 (SCL14), a member of the GRAS family of regulatory proteins, as a TGA-interacting protein that is required for the activation of TGA-dependent but NPR1-independent SA- and 2,4-D–inducible promoters. Chromatin immunoprecipitation experiments revealed that class II TGA factors TGA2, TGA5, and/or TGA6 are needed to recruit SCL14 to promoters of selected SCL14 target genes identified by whole-genome transcript profiling experiments. The coding regions and the expression profiles of the SCL14-dependent genes imply that they might be involved in the detoxification of xenobiotics and possibly endogenous harmful metabolites. Consistently, plants ectopically expressing SCL14 showed increased tolerance to toxic doses of the chemicals isonicotinic acid and 2,4,6-triiodobenzoic acid, whereas the scl14 and the tga2 tga5 tga6 mutants were more susceptible. Hence, the TGA/SCL14 complex seems to be involved in the activation of a general broad-spectrum detoxification network upon challenge of plants with xenobiotics.
Morphology and sedimentary systems in the Central Bransfield Basin, Antarctic Peninsula: sedimentary dynamics from shelf to basin
Authors: García Marga , Ercilla Gemma , Alonso Belén 
Published: November 2008

ABSTRACTA detailed regional characterization of the physiography, morphology and sedimentary systems of the Central Bransfield Basin (CBB) was carried out using swath bathymetry and high‐ and very high‐resolution seismic profiles. The basin margins show continental shelves with numerous glacial troughs, and continental slopes where relatively wide and flat slope platforms represent the middle domain in an atypical physiographic scenario in glaciated margins. Although the CBB is tectonically active, most of the morphologic features are sedimentary in origin, and can be classified into four sedimentary systems: (1) glacial‐glaciomarine, composed of erosional surfaces, glacial troughs, furrows and draping sheets; (2) slope‐basin, formed by trough mouth fans, slope aprons, the Gebra‐Magia instability complex and turbidity systems; (3) seabed fluid outflow system composed of pockmark fields; and (4) contourite, composed of drifts and moats. The sedimentary systems show a clear zonation from shelf to basin and their dynamics reflects the complex interplay among glacial, glaciomarine, marine and oceanographic processes involved in the entire shelf‐to‐basin sediment distribution. The CBB morphology is primarily controlled by glacial/interglacial cyclicity and physiography and to a lesser extent by tectonics and oceanography. These factors have affected the South Shetland Islands (SSI) and Antarctic Peninsula (AP) margins differently, creating a relatively starved SSI margin and a more constructional AP margin. They have also created two entire sediment‐dispersal domains: the shelf‐to‐slope, which records the glaciation history of the CBB; and the lower slope‐to‐basin, which records the imprint of local factors. This study provides a ‘source‐to‐sink’ sedimentary scheme for glaciated margins, which may be applied to the basin research in other margins, based on the characterization of sedimentary systems, their boundaries and the linkages among them. This approach proves to be adequate for the identification of global and local factors governing the CBB and may therefore be applied to other study areas.
Adolescent smoking and health‐related behaviours: interrelations in a Greek school‐based sample
Authors: Giannakopoulos G. , Panagiotakos D. , Mihas C. , Tountas Y. 
Published: November 2008

AbstractBackground  Although several studies have reported findings concerning the interrelationship between smoking and specific health behaviours, little research has investigated how smoking behaviour may be associated with a cluster of health‐related behaviours. The present study was an effort to extend previous research through assessing smoking status, patterns of physical and sedentary activity, as well as eating behaviours and diet quality, in order to gain some insight regarding the relationship between cigarette smoking and a cluster of health behaviours in a Greek sample of adolescents.Methods  A sample of 2008 students (1021 male and 987 female, 12–17 years of age, 7th–12th grade) was selected from all schools of a representative Athens suburb in Greece. All children completed a questionnaire that was developed for the purposes of the study which retrieved information about age, sex, school class, individual and family smoking status, dietary habits and physical activity. Various statistical tests were performed.Results  Age, playtime, consumption of soft drinks and foods from school canteens were positively associated with smoking status while the consumption of fruit juice, dairy products for breakfast and the frequency of breakfasts were inversely associated the aforementioned dependent variable.Conclusions  This study supports the interrelationships between multiple lifestyle behaviours and tobacco use in adolescents. Future research is needed in order to elaborate on the nature of these relations, especially for those at higher risk.
Children's specific fears
Authors: Meltzer H. , Vostanis P. , Dogra N. , Doos L. , Ford T. , Goodman R. 
Published: November 2008

AbstractBackground  Most children experience some degree of fear during their development. Specific fears are considered as an appropriate response provided that they are proportionate to the intensity of the perceived threat. Our aim is to present the prevalence of specific fears among children in the Great Britain, their socio‐demographic correlates, in particular their association with ethnicity.Methods  Data on the child's experience of specific fears were obtained from parents of a national representative sample of 5‐ to 16‐year‐olds using the Development and Well‐Being Assessment. Biographic, socio‐demographic and socioeconomic characteristics of the child and the family were included in the questionnaire.Results  About one‐third of children were assessed by their parents as having at least one of 12 specific fears. The most commonly reported fears were animals (11.6%), blood/injections (10.8%) and the dark (6.3%). Just less than 1% of all children were assessed according to International Classification of Diseases research diagnostic criteria as having a specific phobia. Biographic, socio‐demographic and socioeconomic factors were independently associated with a greater likelihood of a child having particular fears. The most marked associations were fears of the dark, loud noises, imagined supernatural beings in younger children and fear of animals among girls and all non‐white groups.Conclusions  Although fears are only labelled as phobias when they impair functioning and interfere with life, they can cause personal distress to children and also can interfere with their daily activities. Children's fears differ in nature across different ethnic groups. Culturally mediated beliefs, values and traditions may play a role in their expression.
Non-response to infliximab may be due to innate neutralizing anti-tumour necrosis factor-α antibodies
Authors: Ebert E C , Das K M , Mehta V , Rezac C 
Published: November 2008

SummaryInfliximab is a chimeric anti-tumour necrosis factor (TNF)-α antibody that is therapeutic in many patients with inflammatory bowel disease. What causes certain patients not to respond is unknown. The question posed is whether innate anti-TNF-α antibodies play any role in the response to infliximab. Blood was drawn prior to the initial dose of infliximab. Serum anti-TNF-α antibodies were quantitated by enzyme-linked immunosorbent assay (ELISA). Affinity-purified anti-TNF-α antibodies were isolated from serum immunoglobulin G using TNF-α-coated beads. The ability of these antibodies to induce apoptosis of macrophages was measured by annexin and propidium iodide staining. Changes in TNF receptor type 2 (TNFR2) expression and release were determined by immunofluorescence and ELISA respectively. TNF-α-neutralization was assessed by the reversal of the lytic actions of TNF-α on WEHI cells. The amounts of innate anti-TNF-α antibodies in the serum from infliximab responders versus non-responders were the same. Apoptosis of monocytes increased with infliximab and by several of the purified anti-TNF-α antibodies, but these findings did not vary with the patients' responses to infliximab. Effects of the anti-TNF-α antibodies on the expression of TNFR2 on monocytes and their release of soluble TNFR2 did not vary with the patients' responses to infliximab. However, the neutralizing capacity of these antibodies differed, with responders having antibodies that reduced only 47 ± 4% of the TNF-α activity while those from non-responders reduced 70 ± 5% of the TNF-α activity (P &lt; 0·01). Non-responders have innate anti-TNF-α antibodies with greater neutralizing activity than antibodies from responders. Any TNF-α-mediated disease process would be neutralized by intrinsic antibodies, so that the disease is likely to be driven by non-TNF-α-mediated events.
Expression of a B‐cell‐restricted isoform of CD45 is associated with maturity in rat serosal and connective‐tissue mast cells
Authors: Yu Chunping , Moghaddami Mahin , Mayrhofer Graham 
Published: November 2008

SummaryA number of technical limitations make differential staining with dyes such as Alcian blue and Safranin O unsatisfactory as the primary method for assessing the maturity of connective tissue mast cells in rodents. We demonstrated for the first time that in the steady state, most serosal mast cells in normal rats express a high‐molecular‐weight isoform of CD45 that reacts with monoclonal antibody OX33 (OX33+) and has been reported previously only on B cells. However, a small proportion did not express this isoform (OX33−) and this subset predominated during the early stages of mast cell regeneration in the peritoneal cavity. Furthermore, there was a progressive increase in the proportion of donor‐derived OX33+ cells after intraperitoneal adoptive transfer of purified OX33− mast cells to CD45 congenic recipients. These results indicate that serosal mast cells up‐regulate expression of the OX33‐reactive CD45 isoform(s) as they mature. Interestingly, acquisition of OX33‐reactive CD45 did not correlate temporally with sulphation of glycosaminglycan in the mast cell granules. Expression of this isoform was used also to assess the maturity of connective tissue mast cells during mastocytosis in synovium associated with T‐cell‐mediated experimental polyarthritis. Together, our results demonstrate that OX33‐reactive CD45 is a marker that can be used to assess the maturity of serosal and connective tissue mast cells during normal homeostasis and during pathological processes. The significance of differential expression of CD45 isoforms may be to regulate the sensitivity of maturing mast cells to the actions of growth factors and activating stimuli.