bluuebunny/crossref_metadata_2025 huggingface dataset:
Linguistic assimilation in two variables
Authors: Amastae Jon , Satcher David
Published: November 2008

This article examines the type of relatively rapid speech modification sometimes called “accommodation” (Trudgill, 1986). In this case, we track change on the part of speakers of Honduran Spanish newly resident among speakers of Northern Mexican Spanish. The two variables investigated are final /n/ velarization and spirantization, both of which differ in the two dialects. (Honduran Spanish velarizes final /n/, while Northern Mexican Spanish does not; Honduran Spanish conserves stops l, r, s and glides, whereas Northern Mexican Spanish produces fricatives.) It is found that, although there is change in the direction of local norms in both variables, velarization shows greater change. In addition, the degree of contact with local speakers also leads to greater change for velarization only. Reasons for the different behavior are considered.
The messy phonology of Hungarians in South Bend: A contribution to the study of near-mergers
Authors: Kontra Miklós
Published: November 2008

Standard Hungarian has a short front unrounded low vowel phoneme /ε/, but certain dialects have a mid /e/ as well. The standard /ε/ evolved from a merger of the two phonemes. A formal reading of word groups and a same/different listening test revealed that Hungarian–Americans in South Bend, Indiana, exhibit a continuum between the /ε/ dialect and the /ε/versus /e/ dialect, showing important differences between the informants' perception and production. The Hungarian–American data and metropolitan Hungarian data were compared to Labov, Karen, and Miller's (1991) findings on near-mergers. The importance of investigating perceptual and productive systems separtely is emphasized.
On resolving disagreement: Linguistic theory and variation – There's bridges
Authors: Meechan Marjory , Foley Michele
Published: November 2008

Studies of concord variation in English have found subject-verb concord to be particularly low in existential sentences such as There's bridges. Noting that these sentences are unusual because the subject NP is postverbal and is generally indefinite, we hypothesized that the unusual concord variation pattern was a result of structural differences associated with the restriction on the type of determiners preceding the postverbal NP. Using variationist methodology, we analyzed natural speech data from 31 speakers of standard Canadian English and found an overwhelming preference for singular agreement in existentials. Contrary to our predictions, this was not linked to a determiner-based structural distinction, but rather to the form of the copula (i.e., full or clitic) and the speaker's level of education. Our findings have implications for those theoretical studies of existentials that assume concord, because the effect of education suggests that this assumption reflects the bias of the higher educational level of the researchers.
A linguistic innovation of women in Cairo
Authors: Haeri Niloofar
Published: November 2008

This article investigates the sociolinguistic variable of apical palatalization in Cairene Arabic. First, I discuss its linguistic features and then its sociolinguistic distribution. The significance of palatalization as a sociolinguistic variable is its status as a stylistic resource of Cairene Arabic. Depending on the complex interaction of a number of factors, some Egyptians use features of Classical Arabic while speaking in Egyptian Arabic for stylistic purposes. Palatalization, on the other hand, is an example of a stylistic resource that belongs to Cairene Arabic proper. The roles of gender and social class in the distribution of palatalization are explored in some detail. As in a number of other speech communities, women in Cairo seem to have been the innovators of this sound change.
Contemporary Japanese attitudes toward honorifics (keigo)
Authors: Wetzel Patricia J.
Published: November 2008

This article describes results from a subjective reaction test of Japanese speakers' attitudes towardkeigo‘polite language’. Hypotheses regarding attitudes toward “correct” language were for the most part verified, whereas attitudes toward “incorrect” forms were decidedly mixed. These results provide a first step in ascertaining attitudes toward a set of forms that are said to be in a state of flux in contemporary Japan. Also impinging on interpretation of the data are questions of descriptive terminology and culture. Such issues provide additional insight into the controversy within sociolinguistics over quantitative description and normative explanation.
Changes in verb position in French negative infinitival clauses
Authors: Hirschbühler Paul , Labelle Marie
Published: November 2008

Since the 15th century, negative infinitives in French have undergone a change fromneVpastone pasV. This change takes place at different times, depending on the nature of the verb. Lexical verbs undergo the change between 1550 and 1750, modals (pouvoir, vouloir, devoir) essentially change between 1650 and 1900, and auxiliaries have been changing at a slow pace since 1650. We explore the idea that, for main verbs, the change in word order reflects a change in the position ofpas, while the change in the position of modals and auxiliaries results from the fact that these verbs start assuming a position lower in the structure. Our analysis of the historically different evolution of each type of verb is based on their lexical properties and their distinct affinities with abstract Tense.
The gradual loss of mood distinctions in Los Angeles Spanish
Authors: Silva-Corvalán Carmen
Published: November 2008

This article focuses on a change affecting Spanish in contact with English in the United States: namely, simplification and loss of Subjunctive (Sub) mood morphology. Conversational data from 17 Mexican-American bilinguals living in the eastern section of Los Angeles are analyzed qualitatively and quantitatively. The speakers represent three different immigrant groups, according to length of family stay in the United States. The variation between Indicative (Ind) and Sub usage attested in the Spanish-speaking world results from the continuing modifications which have affected the distribution of Ind and Sub forms through the diachronic development of Spanish: previously obligatory contexts for the use of Sub are now categorically Ind or allow both Sub and Ind to different degrees across social and geographic parameters. In the Spanish of Los Angeles, the internal tendencies toward a reduction of the obligatory use of the Sub are strengthened, as may be expected in a situation of language contact in which obligatory contexts for the use of a form are more resistant to change than those that allow a selection between two or more forms with closely related meanings.
Convergent explanation and alternative regularization patterns:Were/weren'tleveling in a vernacular English variety
Authors: Schilling-Estes Natalie , Wolfram Walt
Published: November 2008

Although the process of analogical leveling seems relatively straightforward and its directionality readily predictable, the existence of cross-dialectal leveling alternatives suggests that the processes that actuate and embed analogical leveling can actually be quite complex. Using the case of a vernacular variety spoken on the Outer Banks of North Carolina, we demonstrate how linguistic-systemic principles such as remorphologization, psycholinguistic principles of perceptual saliency, and sociolinguistic processes of symbolic identity converge to account for the development and maintenance of leveling toweren't(I/you/(s)he/we/ you/they weren't here) in this post-insular island community.
Consonant cluster reduction in Tejano English
Authors: Bayley Robert
Published: November 2008

This study examines the well-known process of consonant cluster reduction in the English of residents of a San Antonio, Texas,barrio. The study compares Tejano patterns of /-t, d/ deletion with the pan-English pattern summarized by Labov (1989). Results of VARBRUL analysis show that /-t, d/ deletion in Tejano English is constrained by many of the same factors as in other English dialects, including Los Angeles Chicano English. Results also suggest, however, a complex pattern of convergence and divergence. Younger Tejanos are converging toward other dialects of English with respect to the effect of the morphological class on cluster simplification. Yet there is some evidence that they are diverging from other dialects with respect to the effect of syllable stress. On this latter dimension, younger Tejanos replicate the pattern found by Santa Ana (1991) among Los Angeles Chicanos. Finally, the study compares /-t, d/ deletion in Tejano/Chicano English in San Antonio and Los Angeles and shows that, despite many similarities, Mexican American varieties exhibit regional as well as generational differences.
Variability in negation in African American Vernacular English
Authors: Weldon Tracey
Published: November 2008

For quantitative sociolinguists, one of the goals of investigating variability in African American Vernacular English (AAVE) is to understand better the nature of the grammar. Specifically, researchers have been interested in whether the variation observed in AAVE is inherent to a single system or the result of interaction between two separate systems of AAVE and Standard English (SE). Variability in negation is an area of the AAVE grammar that has received minimal attention, but one that may offer some interesting insights into the nature of the system or systems at work. This article provides a framework to describe the variability between negative auxiliaries in predicative constructions based on a quantitative analysis of data collected in Columbus, Ohio. Five variables are investigated in this study. One involves interaction between third-person singular inflection and non-inflection in present do-support constructions (NEG pres). A second involves variation between ain't and don't with the predicates got or gotta (NEG GOT(ta)). And the other three involve interaction between ain't and negative auxiliaries in present copular (NEG COP), present perfect (NEG perf), and past do-support (NEG past) constructions. The results of this study show that, with the possible exception of the (NEG pres) variation, these alternations all appear to belong to one underlying system.
A long‐term, high‐resolution record of surface water iron concentrations in the upwelling‐driven central California region
Authors: Elrod V. A. , Johnson K. S. , Fitzwater S. E. , Plant J. N.
Published: November 2008

Seven years of observations of surface water iron concentrations in the Monterey Bay region of central California reveal a consistent annual cycle dominated by the injection of high concentrations of particulate iron each spring. A companion study of the water column near the upwelling center at the north end of the bay clearly indicates a sedimentary source for the iron. Local river discharge, during winter storm events, results in the deposition of a fine‐grained sediment “fluff” layer along the shelf. The initial rapid shoaling of isotherms at the onset of upwelling in spring brings water from the fluff layer to the surface. Concentrations of iron in both surface and source waters are then quickly diminished although upwelling intensifies, bringing the highest concentration of nitrate to the surface ∼3 months later. The concentration of a number of constituents measured in bottom water samples collected during the companion study strongly suggests that the rapid decrease in surface water iron concentrations is due to the depletion of the fluff layer following initial isotherm shoaling. The decoupling of iron and nitrate supply sets up the potential for iron limitation. However, on the basis of average Fe/NO3 ratios, we conclude that the region is not often iron limited. Iron limitation was apparent only one summer at the offshore station. Summer chlorophyll concentrations are highly correlated to dissolvable (unfiltered) iron concentrations, evidence in support of the role of particulate iron in meeting the ecosystem's iron requirements.
Influence of stream‐groundwater interactions in the streambed sediments on NO3− flux to a low‐relief coastal stream
Authors: Gu Chuanhui , Hornberger George M. , Herman Janet S. , Mills Aaron L.
Published: November 2008

Water‐saturated, organic‐rich sediments immediately surrounding a stream channel can provide a protective buffer between streams and adjacent land‐based activities by removing plant nutrients from shallow groundwater flowing through them, but the hydrological factors that influence the effectiveness of nitrate removal are not well characterized. A two‐dimensional, fully distributed, variably saturated flow and transport model was evaluated for its success in using mechanisms of biological reaction in streambed sediments to quantify nitrate flux into the stream under base flow conditions. The model was used to interpret the observed hydrological dynamics during storms at Cobb Mill Creek, Virginia. During base flow conditions, relatively deep groundwater flow paths carrying water containing high nitrate concentrations discharged through the streambed sediments, and high denitrification rates were observed along with a substantial reduction in the nitrate concentration. During storm events, reduced discharge of groundwater in the face of a diminished hydraulic gradient during passage of a flood wave led to longer residence times for water in the biologically active sediments underlying the stream channel, thus providing an opportunity for enhanced denitrification to further reduce nitrate loads to the stream. We conclude that in cases of low‐relief streams with substantial hillslopes adjacent to the stream combined with transmissive sediments, storm events can actually contribute to enhanced removal of nitrate locally (at the hillslope scale) as opposed to a simple lowering of concentration due to dilution.
Direct ocean surface velocity measurements from space: Improved quantitative interpretation of Envisat ASAR observations
Authors: Johannessen J. A. , Chapron B. , Collard F. , Kudryavtsev V. , Mouche A. , Akimov D. , Dagestad K.‐F.
Published: November 2008

Previous analysis of Advanced Synthetic Aperture Radar (ASAR) signals collected by ESA's Envisat has demonstrated a very valuable source of high‐resolution information, namely, the line‐of‐sight velocity of the moving ocean surface. This velocity is estimated from a Doppler frequency shift, consistently extracted within the ASAR scenes. The Doppler shift results from the combined action of near surface wind on shorter waves, longer wave motion, wave breaking and surface current. Both kinematic and dynamic properties of the moving ocean surface roughness can therefore be derived from the ASAR observations. The observations are compared to simulations using a radar imaging model extended to include a Doppler shift module. The results are promising. Comparisons to coincident altimetry data suggest that regular account of this combined information would advance the use of SAR in quantitative studies of ocean currents.
Importance of ocean tidal load corrections for differential InSAR
Authors: DiCaprio Christopher J. , Simons Mark
Published: November 2008

Large time series of interferometric synthetic aperture radar (InSAR) measurements make it possible to detect slow tectonic motions of the Earth's surface on the order of millimeters per year. Here, we illustrate the importance of correcting InSAR data for the effects of ground displacements due to ocean tidal loads (OTL). These loads can cause displacement gradients greater than 3 cm per 100 km, which is larger than the accuracy of InSAR techniques and can be a significant percentage of the measured displacement due to slow tectonic processes. We demonstrate the importance of OTL with predicted displacements from selected regions of tectonic interest.
Surface‐based observation of aerosol indirect effect in the Mid‐Atlantic region
Authors: Nzeffe Fonya , Joseph Everette , Min Qilong
Published: November 2008

A method for assessing the aerosol indirect effect based on back trajectory analysis and cloud and aerosol properties derived from a combination of observations from the Multifilter Rotating Shadow Band Radiometer and microwave radiometer at a newly established atmospheric measurement field station in the Baltimore‐Washington corridor is reported in this article. Six months of aerosol and cloud optical depth data are segregated according to air mass history based on back trajectory analysis. Under stagnant and polluted conditions where air flow across the region is predominantly from west–southwest, aerosol optical depth is on average three to four times greater than in air masses that advect rapidly from north and east. When sorted by mean cloud liquid water path, cloud‐droplet effective radius in polluted air masses is on average 0.9 μm smaller than that observed under more pristine conditions. Analysis is presented to confirm the statistical significance of this result.
A model of the secondary radiation belt
Authors: Selesnick R. S. , Looper M. D. , Mewaldt R. A.
Published: November 2008

Products of nuclear reactions between primary radiation belt protons and constituents of the tenuous upper atmosphere form a collocated secondary radiation belt. A calculation of the time‐dependent secondary intensity provides a model specification of this environmental component for low‐ and medium‐altitude satellite orbits. It is based on an earlier model of the radiation belt protons, the novel feature being a determination of the secondary source function from nuclear reaction cross sections. All long‐lived secondary products are included, isotopes of H and He being dominant while the heavier Li to O isotopes are present at relatively low levels. Secondary protons are shown to be a minor correction to the primary radiation belt.
A COPI coat subunit interacts directly with an early‐Golgi localized Arf exchange factor
Authors: Deng Yi , Golinelli‐Cohen Marie‐Pierre , Smirnova Elena , Jackson Catherine L
Published: November 2008

Arf (ADP‐ribosylation factor) family small G proteins are crucial regulators of intracellular transport. The active GTP‐bound form of Arf interacts with a set of proteins—effectors—which mediate the downstream signalling events of Arf activation. A well‐studied class of Arf1 effectors comprises the coat complexes, such as the cis‐Golgi‐localized COPI (coat protein complex I) coat, and trans‐Golgi network‐endosomal clathrin coats. At least five different coats require Arf1‐GTP to localize to organelle membranes. How a single Arf protein recruits different coat complexes to distinct membrane sites raises the question of how specificity is achieved. Here, we propose a molecular mechanism of this specificity for the COPI coat by showing a direct and specific interaction between a COPI subunit and a cis‐Golgi localized subfamily of Arf guanine nucleotide exchange factors (GEFs) that takes place independently of Arf1 activation. In this way, a specific output on Arf1 activation can be programmed before the exchange reaction by the GEF itself.
GAS, a new glutamate‐rich protein, interacts differentially with SRCs and is involved in oestrogen receptor function
Authors: Liang Jing , Zhang Hua , Zhang Yu , Zhang Ying , Shang Yongfeng
Published: November 2008

Steroid receptor coactivators (SRCs) exert profound effects on animal development and physiology. Genetic ablation experiments indicate that various SRC proteins might have differential physiological roles; however, clear evidence of functional specificity has not yet been shown at the molecular level. Here we report the identification of a new SRC1 interacting protein, glutamate‐rich coactivator interacting with SRC1 (GAS), which contains a central glutamate‐rich region and has transactivation activity. Interestingly, GAS interacts only with SRC1, and not with glucocorticoid receptor interacting protein 1 (GRIP1) or amplified in breast cancer 1 (AIB1), the other two members of the SRC family. It interacts with oestrogen receptor‐α (ERα) and participates in both oestrogen receptor‐regulated gene transcription and oestrogen‐stimulated G1/S cell‐cycle transition. Our data thus indicate that GAS is a new transcription cofactor and that different SRCs are associated with distinct secondary cofactors.
Role of PPARγ in renoprotection in Type 2 diabetes: molecular mechanisms and therapeutic potential
Authors: Yang Jichun , Zhang Dongjuan , Li Jing , Zhang Xiaoyan , Fan Fenling , Guan Youfei
Published: November 2008

DN (diabetic nephropathy) is a chronic disease characterized by proteinuria, glomerular hypertrophy, decreased glomerular filtration and renal fibrosis with loss of renal function. DN is the leading cause of ESRD (end-stage renal disease), accounting for millions of deaths worldwide. TZDs (thiazolidinediones) are synthetic ligands of PPARγ (peroxisome-proliferator-activated receptor γ), which is involved in many important physiological processes, including adipose differentiation, lipid and glucose metabolism, energy homoeostasis, cell proliferation, inflammation, reproduction and renoprotection. A large body of research over the past decade has revealed that, in addition to their insulin-sensitizing effects, TZDs play an important role in delaying and preventing the progression of chronic kidney disease in Type 2 diabetes. Although PPARγ activation by TZDs is in general considered beneficial for the amelioration of diabetic renal complications in Type 2 diabetes, the underlying mechanism(s) remains only partially characterized. In this review, we summarize and discuss recent findings regarding the renoprotective effects of PPARγ in Type 2 diabetes and the potential underlying mechanisms.
Atorvastatin enhances interleukin-10 levels and improves cardiac function in rats after acute myocardial infarction
Authors: Stumpf Christian , Petzi Sebastian , Seybold Katrin , Wasmeier Gerald , Arnold Martin , Raaz Dorette , Yilmaz Atilla , Daniel Werner G. , Garlichs Christoph D.
Published: November 2008

LV (left ventricular) remodelling is the basic mechanism of HF (heart failure) following MI (myocardial infarction). Although there is evidence that pro-inflammatory cytokines [including TNF-α (tumour necrosis factor-α) and IL-6 (interleukin-6)] are involved in the remodelling process, only little is known about the role of anti-inflammatory cytokines, such as IL-10. As accumulating evidence has revealed that statins possess anti-inflammatory properties, the aim of the present study was to elucidate the effect of atorvastatin on the modulation of the anti-inflammatory cytokine IL-10 and its effect on LV function in rats with HF subsequent to MI. Rats with MI, induced by permanent LAD (left anterior descending) branch coronary artery ligation, were treated for 4 weeks with atorvastatin (10 mg·kg−1 of body weight·day−1 via oral gavage) starting on the first day after induction of MI. Cardiac function was assessed by echocardiography and cardiac catheterization 4 weeks after MI induction. Membrane-bound and soluble fractions of TNF-α, IL-6 and IL-10 protein, the TNF-α/IL-10 ratio, serum levels of MCP-1 (monocyte chemoattractant protein-1) as well as myocardial macrophage infiltration were analysed. Treatment with atorvastatin significantly improved post-MI LV function (fractional shortening, +120%; dP/dtmax, +147%; and LV end-diastolic pressure, −27%). Furthermore atorvastatin treatment markedly decreased the levels of TNF-α, IL-6 and MCP-1, reduced myocardial infiltration of macrophages and significantly increased myocardial and serum levels of the anti-inflammatory cytokine IL-10. Thus the balance between pro-inflammatory and anti-inflammatory cytokines was shifted in the anti-inflammatory direction, as shown by a significantly decreased TNF-α/IL-10 ratio. Atorvastatin ameliorated early LV remodelling and improved LV function in rats with HF subsequent to MI. Our study suggests that the modulation of the balance between pro- and anti-inflammatory cytokines towards the anti-inflammatory cytokine IL-10 is one salutary mechanism underlying how atorvastatin influences post-MI remodelling and thus improves LV function.
Chronic administration of ursodeoxycholic acid decreases portal pressure in rats with biliary cirrhosis
Authors: Yang Ying-Ying , Huang Yi-Tsau , Lee Kuei-Chuan , Lee Fa-Yauh , Lee Tzung-Yan , Hou Ming-Chih , Lin Han-Chieh , Lee Shou-Dong
Published: November 2008

Liver cirrhosis is characterized by increased IHR (intrahepatic resistance) and lipid peroxidation, and decreased antioxidative defence. The present study investigates the effects of administration for 1 month of the antioxidant UDCA (ursodeoxycholic acid) in BDL (bile-duct-ligated) cirrhotic rats. Splanchnic haemodynamics, IHR, hepatic levels of TBARS (thiobarbituric acid-reacting substances), GSH (glutathione), SOD (superoxide dismutase) activity, nitrite, PIIINP (N-terminal propeptide of type III procollagen) and collagen deposition, histological examination of liver, mRNA expression of PIIIP-α1 (type III procollagen) and TGF-β1 (transforming growth factor-β1), protein expression of TXS (thromboxane synthase) and iNOS (inducible NO synthase), and TXA2 (thromboxane A2) production in liver perfusates were measured. The results showed that portal pressure and IHR, hepatic levels of PIIINP, hepatic collagen deposition, mRNA expression of PIIIP-α1 and TGF-β1, protein expression of iNOS and TXS, and production of TXA2 in liver perfusates were significantly decreased in UDCA-treated BDL rats. The increased levels of hepatic GSH and SOD activity and decreased levels of TBARS and nitrite were also observed in UDCA-treated BDL rats. In UDCA-treated BDL rats, the reduction in portal pressure resulted from a decrease in IHR, which mostly acted through the suppression of hepatic TXA2 production and lipid peroxidation, and an increase in antioxidative defence, leading to the prevention of hepatic fibrosis.
Metal patterning using maskless vacuum evaporation process based on selective deposition of photochromic diarylethene
Authors: Takagi Rie , Masui Kyoko , Nakamura Shinichiro , Tsujioka Tsuyoshi
Published: November 2008

We developed an electrode/wiring patterning method that does not employ evaporation shadow masks; this method is based on selective metal deposition of photochromic diarylethene (DAE). In the selective Mg deposition based on the photoisomerization of DAE, Mg vapor atoms are deposited only on colored DAE film obtained upon UV irradiation, but not on uncolored film. We demonstrated fine metal Mg patterning with a minimum width of 3μm and the preparation of a patterned cathode. The selective metal deposition method has significant potential for preparing fine electrodes/wiring for various organic electronic devices.
Solution-processed carbon electrodes for organic field-effect transistors
Authors: Wada Hiroshi , Mori Takehiko
Published: November 2008

Bottom-contact organic transistors with carbon-paste electrodes are fabricated by means of the surface selective deposition technique, where a carbon-paste solution is deposited on the region in which the self-assembled monolayers are removed by ultraviolet light irradiation. The resulting bottom-contact pentacene transistor realizes high performance of 1.0cm2V−1s−1. The present method is applied to solution-processed polythiophene transistors as well as n-channel materials.
Single mode emitting ridge waveguide quantum cascade lasers coupled to an active ring resonator filter
Authors: Semmel Julia , Kaiser Wolfgang , Hofmann Holger , Höfling Sven , Forchel Alfred
Published: November 2008

Quantum cascade ridge waveguide lasers with coupled ring resonators have been fabricated. Coupling of an actively pumped microring resonator to a ridge waveguide device allows for filtering the numerous Fabry–Pérot modes emerging in the ridge waveguide. Due to the large free spectral range of the ring resonators mode selection is accomplished, resulting in stable single mode emission for an optimized design. Thus, side mode suppression ratios of up to 26 dB over a temperature range of 140 K are attained by on-chip coupling of a ridge waveguide device with a microsquare ring resonator. The tuning rate of the microring resonator laser is 0.40 nm/K. Output powers of several milliwatts are obtained.
Explanations for the Age, Sex, Spatial, and Temporal Structure of Czech Mortality for the Period 1987–97
Authors: Spijker Jeroen
Published: November 2008

The author disentangles the age sex, spatial, and temporal structure of mortality in the Czech Republic during the period 1987–97 for a selection of cause-of-death categories and investigates possible socioeconomic and other causes for the mortality differences uncovered. The clarification of the major effects, as well as possible interactions between them, verifies whether causes of death should be modelled separately, and which interactions should be tested in the explanatory analysis. For instance, it was considered inappropriate to incorporate district-level time-series data in the analysis when spatial mortality differences did not show significant variation between 1987 and 1997—as occurred with cancer and digestive system diseases. In this case, the exogenous variables would take on the average for the study period.
A Dynamic Graph Automata Approach to Modeling Landscape Change in the Andes and the Amazon
Authors: Sarkar Sahotra , Crews-Meyer Kelley A , Young Kenneth R , Kelley Christopher D , Moffett Alexander
Published: November 2008

A generalization of cellular automata was developed that allows flexible, dynamic updating of variable neighborhood relationships, which in turn allows the integration of interactions at widely disparate spatial and temporal scales. Cells in the landscapes were modeled as vertices of dynamic graph automata that allow temporally variable causal connectivity between spatially nonadjacent cells. A trial was carried out to represent changes in an Amazonian and a tropical Andean landscape modeled as dynamic graph automata with input from a Landsat TM-derived Level 1 classification with the following classes: for the Amazon—forest, nonforest vegetation, water, and urban or bare (soil); for the Andes—forest, scrub (shrub or grassland), agriculture, and bare or exposed ground. Explicit automata transition rules were used to simulate temporal land-cover change. These rules were derived independently from fieldwork in each area, including vegetation plots or transects and informal interviews. Such a generalization of cellular automata was useful for modeling land-use–land-cover change (LULCC), although it potentially increases the computational complexity of an already data intensive process (involving 5–8 million cells, in 1000 stochastic simulations, with each simulation encompassing 15 annual time steps). The interannual predicted LULCC, while more nuanced in the Andean site, poses a serious threat to compositional and configurational stability in both the Andes and the Amazon, with implications for landscape heterogeneity and habitat fragmentation.
Information Searching and Buying on the Internet: Travel-Related Activities?
Authors: Hjorthol Randi J
Published: November 2008

The use of the Internet for information searching and purchasing of goods and services has rapidly increased. The development of e-shopping might have an impact on travel activity, but for the present the results from different studies are still inconclusive. In this paper the interaction between information searching, e-shopping, and travel activity is examined. The analysis is based on answers from 2700 Norwegian respondents. The dataset provides detailed information about the respondents' activities and trips, and which type of goods and services they search for information about and purchase. The analysis indicates that there are different segments using the Internet for information and purchase, and that different types of goods attract different customers. The analyses of the interaction between e-shopping and travel suggest no direct relation between the two phenomena. There is no indication of substitution of travel by shopping online. The multivariate analyses show, rather, a higher mobility among frequent e-shoppers than among those buying on the Internet less often. E-shopping seems to be a complementary activity to traditional shopping, at least for the time being.
Evaluating Community Engagement through Argumentation Maps—A Public Participation GIS Case Study
Authors: Rinner Claus , Bird Michelle
Published: November 2008

Significant advances in public participation geographic information systems technology and online mapping platforms have not translated into enhanced citizen participation in democratic planning processes. This study contributes to addressing this gap by evaluating the engagement of members of an urban community in sustainable neighbourhood planning through argumentation mapping. The study provided an online public discussion forum, together with a neighbourhood map to which the participants could link their discussion contributions. On the basis of participation statistics, contents of contributions, and responses to a survey, we discuss the participants' technical and engagement experiences. The sixteen registered participants lived within or near the ‘Queen West Triangle’ in downtown Toronto, Canada. They rated themselves as experienced computer users and consequently found the participation in the online discussion forum to be easy. The contributions showed a great degree of interest and knowledge in the issues of sustainable community development. However, while the majority of participants also rated themselves as comfortable with map reading, they found the handling of the online neighbourhood map difficult and did not use the option to link their comments to the map.
Significance of nuclear hTra2‐beta1 expression in cervical cancer
Authors: GABRIEL BORIS , HAUSEN AXEL ZUR , BOUDA JIRI , BOUDOVA LUDMILA , KOPRIVOVA MIROSLAVA , HIRSCHFELD MARC , JÄGER MARKUS , STICKELER ELMAR
Published: November 2008

Objective. Human Tra2‐beta1, a member of the serine/arginine‐rich splicing factors, is involved in C/A‐dependent mRNA processing and regulation of gene expression. Since several genes involved in cervical carcinogenesis are alternatively spliced and contain C/A rich elements, we aimed to analyze hTra2‐beta1 expression and subcellular localization in tumor tissue of women with cervical cancer and to determine its clinical significance. Design. Retrospective study. Setting. Tertiary‐care academic medical center. Sample. One hundred and five patients with cervical cancer and a mean follow up time of 73.1 months. Methods. Immunohistochemistry of paraffin‐embedded tissues was performed and hTra2‐beta1 expression was correlated with clinico‐pathological variables including patient outcome. Results. Cytoplasmic hTra2‐beta1 protein expression was found in 20% of cases, while all tumors revealed nuclear immunoreactivity with strong expression in 54.3% of cases. There was a significant inverse correlation between nuclear and cytoplasmic protein expression, suggesting a potentially relevant shuttle process of hTra2‐beta1 between both cellular compartments. Patients with weak expressing hTra2‐beta1 tumors showed an improved survival with a tumor‐related death rate of 8.3% compared to 23.7% in patients with moderate and high intranuclear hTra2‐beta1 expression, respectively. Conclusions. Our data support the hypothesis of a biological relevance for hTra2‐beta1 expression in cervical cancer. The observed shuttle process of this splicing factor with higher concentrations in the nucleus should have pronounced effects on the cellular function and tumor biology of the affected tumors, leading to the worse patient outcome.
Short Article: Segregated in Perception, Integrated for Action: Immunity of Rhythmic Sensorimotor Coordination to Auditory Stream Segregation
Authors: Repp Bruno H.
Published: November 2008

Auditory stream segregation can occur when tones of different pitch (A, B) are repeated cyclically: The larger the pitch separation and the faster the tempo, the more likely perception of two separate streams is to occur. The present study assessed stream segregation in perceptual and sensorimotor tasks, using identical ABBABB … sequences. The perceptual task required detection of single phase-shifted A tones; this was expected to be facilitated by the presence of B tones unless segregation occurred. The sensorimotor task required tapping in synchrony with the A tones; here the phase correction response (PCR) to shifted A tones was expected to be inhibited by B tones unless segregation occurred. Two sequence tempi and three pitch separations (2, 10, and 48 semitones) were used with musically trained participants. Facilitation of perception occurred only at the smallest pitch separation, whereas the PCR was reduced equally at all separations. These results indicate that auditory action control is immune to perceptual stream segregation, at least in musicians. This may help musicians coordinate with diverse instruments in ensemble playing.
Sparse combinatorial inference with an application in cancer biology
Authors: Mukherjee Sach , Pelech Steven , Neve Richard M. , Kuo Wen-Lin , Ziyad Safiyyah , Spellman Paul T. , Gray Joe W. , Speed Terence P.
Published: November 2008

Motivation: Combinatorial effects, in which several variables jointly influence an output or response, play an important role in biological systems. In many settings, Boolean functions provide a natural way to describe such influences. However, biochemical data using which we may wish to characterize such influences are usually subject to much variability. Furthermore, in high-throughput biological settings Boolean relationships of interest are very often sparse, in the sense of being embedded in an overall dataset of higher dimensionality. This motivates a need for statistical methods capable of making inferences regarding Boolean functions under conditions of noise and sparsity.

Results: We put forward a statistical model for sparse, noisy Boolean functions and methods for inference under the model. We focus on the case in which the form of the underlying Boolean function, as well as the number and identity of its inputs are all unknown. We present results on synthetic data and on a study of signalling proteins in cancer biology.

Availability:  go.warwick.ac.uk/sachmukherjee/sci

Contact:  s.n.mukherjee@warwick.ac.uk
Identification of structurally conserved residues of proteins in absence of structural homologs using neural network ensemble
Authors: Pugalenthi Ganesan , Tang Ke , Suganthan P. N. , Chakrabarti Saikat
Published: November 2008

Motivation: So far various bioinformatics and machine learning techniques applied for identification of sequence and functionally conserved residues in proteins. Although few computational methods are available for the prediction of structurally conserved residues from protein structure, almost all methods require homologous structural information and structure-based alignments, which still prove to be a bottleneck in protein structure comparison studies. In this work, we developed a neural network approach for identification of structurally important residues from a single protein structure without using homologous structural information and structural alignment.

Results: A neural network ensemble (NNE) method that utilizes negative correlation learning (NCL) approach was developed for identification of structurally conserved residues (SCRs) in proteins using features that represent amino acid conservation and composition, physico-chemical properties and structural properties. The NCL-NNE method was applied to 6042 SCRs that have been extracted from 496 protein domains. This method obtained high prediction sensitivity (92.8%) and quality (Matthew's correlation coefficient is 0.852) in identification of SCRs. Further benchmarking using 60 protein domains containing 1657 SCRs that were not part of the training and testing datasets shows that the NCL-NNE can correctly predict SCRs with ∼ 90% sensitivity. These results suggest the usefulness of NCL-NNE for facilitating the identification of SCRs utilizing information derived from a single protein structure. Therefore, this method could be extremely effective in large-scale benchmarking studies where reliable structural homologs and alignments are limited.

Availability: The executable for the NCL-NNE algorithm is available at http://www3.ntu.edu.sg/home/EPNSugan/index_files/SCR.htm

Contact:  epnsugan@ntu.edu.sg; chakraba@ncbi.nlm.nih.gov.

Supplementary information:  Supplementary data are available at Bioinformatics online.
Management of Chronic Asthma in Adults
Authors: Hussain Panna
Published: November 2008

Asthma is a chronic inflammatory disease of the airways. It is characterized by recurrent episodes of dyspnoea, wheeze and cough caused by reversible airways obstruction. Three factors are responsible for the airways narrowing: bronchial muscle contraction, mucosal swelling/inflammation and increased mucous production ( Fig. 1 ). About 10–15% of the UK population have asthma and the number appears to be growing although there is some difficulty understanding why. It affects 1 in 20 adults and 1 in 10 children. Approximately 5.1 million people are currently being treated for asthma in the UK.
Online communities serving the consumer/producer: observations from the study of a fantasy world
Authors: Boulaire Christele , Graf Raoul , Guelmami Raja
Published: November 2008

Purpose

The purpose of this paper is to identify the main individual and collective strategies online communities employ to appropriate fantasy worlds and the ways in which community members use imagination within this context.

Design/methodology/approach

A qualitative study drawing on an ethnography of online communities including individual in‐person interviews with community members of the world is considered.

Findings

The predominance and the vital importance of the production/consumption of stories within these communities has been shown. The multiple benefits of this practice have been illustrated, including the pleasure of creating and playing with one's imagination. These benefits engender the surprise and enchantment of community members, who lavish other members with encouragement, congratulations and thanks.

Research limitations/implications

Because of opting for a non‐participatory ethnography, it was impossible to directly contact the members of the community to conduct interviews. Thus a convenience sample was chosen representative of the study subject and individuals outside of these communities were questioned.

Originality/value

The online community allows members to collectively and playfully participate in entertainment related to the fantasy world. It appears as an imaginary organization of the (entertainment) service provider. The members of this organization can take part in value coproduction and share the benefits of an extended entertainment service that sparks their imagination and allows them to enjoy the fruits of their creations. Given the fantasy world's power to fire the imagination of fantasy lovers, the paper demonstrates that it is important for leisure and entertainment service providers to consider adding a fantasy component to their service.
Live imaging early immune cell ontogeny and function in zebrafish Danio rerio
Authors: Hall C. J. , Flores M. V. , Crosier K. E. , Crosier P. S.
Published: November 2008

The success of a robust vertebrate inflammatory response is in part because of the migratory potential of its haematopoietic components. Once these cells converge at an inflammatory site, they interact with each other as well as non‐immune tissues and infectious agents to help manage both the scale and the duration of any ensuing response. Exactly how these blood cells, that constitute the innate and adaptive immune systems, contribute to such immune responses remain largely unknown. Traditionally, assessing these contributions relied upon histological analysis of fixed tissue sections complemented with in vitro dynamic data. Although informative, translating results from these studies into the multicellular whole‐animal setting remain difficult. Recently, non‐invasive live imaging of the immune system in animal models is providing significant insights into how immune cells function within their intact natural environment. Although the majority of these studies have been conducted within mice, another vertebrate, the zebrafish Danio rerio is being recognized as an ideal platform for non‐invasive live imaging applications. The optical transparency, rapid development, genetic tractability and highly conserved innate and adaptive immune systems of this well‐established developmental model have been exploited in a number of recent studies evaluating the immunocompetence of fluorescently tagged blood cells. In addition, similar live imaging studies are helping to dissect the ontogeny of blood‐cell development by tracking various haematopoietic precursor cells to assess their contribution to different blood lineages. This review will examine some recent advances that have helped D. rerio emerge as a live imaging platform as well as its potential to offer valuable insights into the genetics behind diseases associated with immune cell dysfunction.
Embryonic stages and eye‐specific gene expression of the local cyprinoid fish Anabarilius grahami in Fuxian Lake, China
Authors: MA L. , Pan X. F. , WEI Y. H. , LI Z. Y. , LI C. C. , YANG J. X. , MAO B. Y.
Published: November 2008

Anabarilius grahami is a cyprinoid fish endemic to Fuxian Lake, Yunnan, China. In this study, a comprehensive staging series of A. grahami was produced. The embryonic development of A. grahami was divided into six main periods: zygote period, cleavage period, blastula period, gastrula period, segmentation period and hatching period. Its embryonic development is essentially similar to that of zebrafish Danio rerio but relatively slower. The expression patterns of A. grahami sox2, pax6a, six3a and rx2 genes were also cloned and checked during eye development. The four genes showed similar expression patterns to their D. rerio homologues, suggesting the evolutionary conservation of the regulatory network of eye development.
Identification and expression characterization of pepsinogen A in orange‐spotted grouper, Epinephelus coioides
Authors: Feng S. Z. , Li W. S. , Lin H. R.
Published: November 2008

To understand the molecular mechanisms associated with digestive physiology of the stomach of orange‐spotted grouper Epinephelus coioides, a cDNA library was constructed and 331 expressed sequence tags (EST) were generated and annotated. About 37·17% of 226 identified ESTs were possibly related to digestive enzymes. Two type‐A pepsinogens differing in putative isoelectric point were identified and characterized for the first time in E. coioides. The complete cDNAs were 1312 and 1314 bp in length, and the deduced polypeptide sequences comprised 376 and 377 amino acids, respectively. Both genes consisted of eight introns of various lengths. Alignment and a phylogenetic tree based on the amino acid sequences of pepsins indicated that pepsin A1 and A2 could be classified into two different subtypes. Northern blot hybridization showed that there were two forms of transcripts for pepsinogen A1 and three for pepsinogen A2. Reverse transcription‐PCR (RT‐PCR) followed by Southern blot analysis revealed that two type‐A pepsinogen mRNAs were present in the adult stomach tissue, and pepsinogen A2 was also detectable in the mid‐intestine. Furthermore, pepsinogen A1 transcript was first detected at 29 days post‐hatching, while pepsinogen A2 was continuously expressed through hatching to adult fish. These results imply that transcriptional regulation and physiological function of the two type‐A pepsinogens may be different.