bluuebunny/crossref_metadata_2025 huggingface dataset:
Daily river water temperature forecast model with a k‐nearest neighbour approach
Authors: St‐Hilaire André , Ouarda Taha B. M. J. , Bargaoui Zoubeida , Daigle Anik , Bilodeau Laurent
Published: August 2011

Water temperature is a key abiotic variable that modulates both water chemistry and aquatic life in rivers and streams. For this reason, numerous water temperature models have been developed in recent years. In this paper, a k‐nearest neighbour model (KNN) is proposed and validated to simulate and eventually produce a one‐day forecast of mean water temperature on the Moisie River, a watercourse with an important salmon population in eastern Canada. Numerous KNN model configurations were compared by selecting different attributes and testing different weight combinations for neighbours. It was found that the best model uses attributes that include water temperature from the two previous days and an indicator of seasonality (day of the year) to select nearest neighbours. Three neighbours were used to calculate the estimated temperature, and the weighting combination that yielded the best results was an equal weight on all three nearest neighbours. This nonparametric model provided lower Root Mean Square Errors (RMSE = 1·57 °C), Higher Nash coefficient (NTD = 0·93) and lower Relative Bias (RB = − 1·5%) than a nonlinear regression model (RMSE = 2·45 °C, NTD = 0·83, RB = − 3%). The k‐nearest neighbour model appears to be a promising tool to simulate of forecast water temperature where long time series are available. Copyright © 2011 John Wiley & Sons, Ltd.
ASSET PRICE MISALIGNMENTS AND MONETARY POLICY
Authors: Bask Mikael
Published: August 2011

We augment the standard New Keynesian Model for monetary policy design with stock prices in the economy and stock traders who use a mix of fundamental and technical analyses. In contrast with most of previous literature, we argue that the central bank should augment the interest rate rule with a term for stock price misalignments because a determinate and stable rational expectations equilibrium in the economy are then easier to achieve. This equilibrium is stable under least squares learning as well. Another finding is that inertia in monetary policy does not promote macroeconomic stability when technical analysis plays a major role in stock trading. Even worse, if the central bank in its policy only indirectly responds to stock price misalignments via its effect on the inflation rate, a combination of strong inertia in monetary policy and a significant role for technical analysis in stock trading will lead to macroeconomic instability. Copyright © 2011 John Wiley & Sons, Ltd.
Functional cGMP‐gated channels in cerebellar granule cells
Authors: Lopez‐Jimenez Mª Elena , González Jose C. , Lizasoain Ignacio , Sánchez‐Prieto José , Hernández‐Guijo Jesús M. , Torres Magdalena
Published: August 2011

Cyclic nucleotide‐gated channels (CNGCs) are important transducers of external signals in sensory processes. These channels are ubiquitously expressed in a variety of neurons, and are necessary to transduce signals for growth cone guidance and plasticity. Here, we demonstrate that the CNGC subunits (CNGA1 and CNGB1, presumably the 1b isoform) are expressed in rat cerebellar granule cells and that they combine to form functional channels. The expression of the mRNAs that encode these proteins is maximal after 7 days in cell culture, when the channels are expressed at synapses and co‐localize with the synaptic marker synapsin I. These ligand‐gated channels are functional and can be blocked by Mg2+ or L‐cis‐diltiazem. Moreover, channel opening in response to increases in intracellular cGMP results in Ca2+ entry into the cell. Chronic blockade (96 h) of these channels with L‐cis‐diltiazem significantly decreases the number of functional boutons, as determined by their capacity to load and unload the styryl dye FM1‐43 when stimulated. Moreover, the unloading kinetics is modified from a biphasic to a monophasic profile in a subset of synaptic boutons. These channels are also expressed in early developmental stages, both in the soma and in emerging processes, and CNGA1 can be detected in growth cones. Pharmacological blockade of these channels with L‐cis‐diltiazem causes an overall change in growth cone morphology, impairing the formation of lamellipodia between filopodia and increasing the number of filopodia. J. Cell. Physiol. 227: 2252–2263, 2012. © 2011 Wiley Periodicals, Inc.
In vitro assessment of laser efficiency for caries prevention in pits and fissures
Authors: Correa‐Afonso Alessandra M. , Ciconne‐Nogueira Juliane C. , Pécora Jesus D. , Palma‐Dibb Regina G.
Published: August 2011

This study aimed to assess the in vitro efficacy of the lasers Er:YAG, Nd:YAG, and CO2 operating in the low energy mode for caries prevention in pits and fissures. Forty‐five caries‐free enamel occlusal sections were randomly divided into three groups: G1 − Er:YAG (80 mJ/2Hz); G2 − Nd:YAG Laser (1W and 10 Hz); and G3 − CO2 Laser (0.4 W and 20 Hz). After surface treatment, the samples were submitted to challenge with acid consisting of a 10‐day immersion in demineralizing (6 h) and remineralizing solution (18 h). Next, enamel demineralization was quantitatively evaluated by subsurface microhardness test and polarized‐light microscopy (PLM, mm2) and qualitatively assessed by scanning electron microscopy. The Wilcoxon test was used for comparison of each group with its own control. ANOVA (α = 5%) was employed for comparison among groups, and Fisher's LSD multiple comparison test was applied, to check the difference in means. Concerning the microhardness analyses, statistical difference between control, and experimental areas was only detected for the CO2 group. Experimental values were higher than the controls. As for PLM analyses, smaller demineralized areas were measured for G2 (Nd:YAG) and G3 (CO2) compared with the control areas. In conclusion, the present findings suggest that the CO2 laser should be selected in order to increase the enamel resistance to acid in pits and fissures. Microsc. Res. Tech. 2011. © 2011 Wiley Periodicals, Inc.
Fixed‐point and stratified analysis of the fine structure and composition of five gallstones with Fourier transform infrared (FT‐IR) specular reflection spectroscopy
Authors: Suo Tao , Peng Pinwei , Feng Min , Liu Houbao , Ai Zhilong , Tong Saixiong , Yang Xiaoyong , Qin Xinyu
Published: August 2011

By investigating the identities, amounts, and distributions of the major components of human gallstones, the formation mechanism of calculi may be elucidated. Using FT‐IR specular reflection spectroscopy, the compositions of five common types of gallstones, including cholesterol calculus, bile pigment calculus, cholesterol‐bilirubin calculus, mixed calculus, and black stones, were positionally, qualitatively, and quantitatively analyzed. Several organic and inorganic substances were found in human gallstones, including cholesterol, calcium bilirubinate, calcium carbonate, calcium phosphate, and calcium stearate. Among them, cholesterol and calcium bilirubinate were the main components. The amounts of these substances varied in different types of gallstone. The distributions of cholesterol and calcium salts (with the exception of calcium bilirubinate) were also closely associated with location. In the various calculi, the amounts of cholesterol and calcium bilirubinate in the cores, the layered structures outside the cores, and the outer shells were higher than those of other substances. The identities of the major components of calculi were similar in different types of gallstones, but their amounts and distributions were significantly different. The analytical method used in this study, which was able to accurately determine the location, quality, and quantity of the major components of gallstones, would be an effective tool to study the formation mechanism of calculi. Microsc. Res. Tech., 2011. © 2011 Wiley Periodicals, Inc.
Overview of the transcriptome profiles identified in hagfish, shark, and bichir: current issues arising from some nonmodel vertebrate taxa
Authors: Takechi Masaki , Takeuchi Masaki , Ota Kinya G. , Nishimura Osamu , Mochii Makoto , Itomi Kazu , Adachi Noritaka , Takahashi Maiko , Fujimoto Satoko , Tarui Hiroshi , Okabe Masataka , Aizawa Shinichi , Kuratani Shigeru
Published: August 2011

Because of their crucial phylogenetic positions, hagfishes, sharks, and bichirs are recognized as key taxa in our understanding of vertebrate evolution. The expression patterns of the regulatory genes involved in developmental patterning have been analyzed in the context of evolutionary developmental studies. However, in a survey of public sequence databases, we found that the large‐scale sequence data for these taxa are still limited. To address this deficit, we used conventional Sanger DNA sequencing and a next‐generation sequencing technology based on 454 GS FLX sequencing to obtain expressed sequence tags (ESTs) of the Japanese inshore hagfish (Eptatretus burgeri; 161,482 ESTs), cloudy catshark (Scyliorhinus torazame; 165,819 ESTs), and gray bichir (Polypterus senegalus; 34,336 ESTs). We deposited the ESTs in a newly constructed database, designated the “Vertebrate TimeCapsule.” The ESTs include sequences from genes that can be effectively used in evolutionary developmental studies; for instance, several encode cartilaginous extracellular matrix proteins, which are central to an understanding of the ways in which evolutionary processes affected the skeletal elements, whereas others encode regulatory genes involved in craniofacial development and early embryogenesis. Here, we discuss how hagfishes, sharks, and bichirs contribute to our understanding of vertebrate evolution, we review the current status of the publicly available sequence data for these three taxa, and we introduce our EST projects and newly developed database.J. Exp. Zool. (Mol. Dev. Evol.) 316:526–546, 2011. © 2011 Wiley Periodicals, Inc.
A GSM analysis of E‐plane waveguide junctions filled with piecewise homogeneous dielectric
Authors: Chumachenko Vitaliy , Vashchenko Vadym
Published: August 2011

A specific generalized scattering matrix (GSM) approach to the analysis of a piecewise homogeneous E‐plane waveguide junction with plane interfaces is presented. The object is cascaded into homogeneously filled regions, whose GSMs are found in solving two uncoupled scalar problems related to longitudinal section electric and magnetic modes, and interfaces responsible for interaction of the said modes. The GSMs of irregular constituents are determined with the help of triangular blocks. Scattering parameters of the last ones are obtained by means of the domain‐product technique. The approach was successfully verified via test problems and was applied to the analysis of scattering of the TE10 mode by an E‐plane slant interface between two dielectric media. Copyright © 2011 John Wiley & Sons, Ltd.
Localization of vascular endothelial growth factor during the early stages of osteochondral regeneration using a bioabsorbable synthetic polymer scaffold
Authors: Sakata Ryosuke , Kokubu Takeshi , Nagura Issei , Toyokawa Narikazu , Inui Atsuyuki , Fujioka Hiroyuki , Kurosaka Masahiro
Published: August 2011

Vascular endothelial growth factor (VEGF) plays a critical role in chondrogenic differentiation in the growth plate of the epiphysis. This function is necessary for chondrocyte survival in cartilage development. We investigated the localization of VEGF in the osteochondral regeneration process using a bioabsorbable polymer scaffold. Osteochondral defects (5 mm in diameter and 5 mm in depth) were made on the femoral condyle of forty‐eight skeletally mature female Japanese white rabbits. In total, twenty‐four defects were filled with poly(DL‐lactide‐co‐glycolide) scaffolds and the others were left untreated. The regeneration process was investigated macroscopically, histologically, immunohistochemically, and by gene expression analysis. In the early stages of osteochondral regeneration, bone ingrowth was observed in the deep zone of the scaffold with continuous VEGF expression; cartilage regeneration was observed in the superficial zone of the scaffold with decreased VEGF expression. In contrast, when the defect was left untreated, VEGF localization was observed throughout the entire defect area, and cartilage regeneration at the articular surface was delayed. We conclude that decrease in localization of VEGF at the articular surface in the postoperative early stage is closely related to the progression of cartilage regeneration in osteochondral defects. © 2011 Orthopaedic Research Society Published by Wiley Periodicals, Inc. J Orthop Res 30:252–259, 2012
Comparison of gene expression patterns in articular cartilage and dedifferentiated articular chondrocytes
Authors: Cheng Tiffany , Maddox Nicole C. , Wong Andrew W. , Rahnama Ruyan , Kuo Alfred C.
Published: August 2011

During monolayer culture, articular chondrocytes dedifferentiate into fibroblast‐like cells. The mechanisms underlying this process are poorly understood. We sought to further characterize dedifferentiation by identifying an extended panel of genes that distinguish articular cartilage from dedifferentiated chondrocytes. Thirty‐nine candidate marker‐genes were identified from previous studies on articular‐cartilage gene‐expression. Real‐time PCR was used to evaluate the mRNA levels for these candidates in calf articular cartilage and dedifferentiated articular chondrocytes. Twenty‐two of the candidate marker genes exhibited at least a two‐fold difference in gene expression in the two cell types. Twelve of these genes had at least a ten‐fold difference in gene expression. Tenascin C (TNC), type I collagen (COL1A1), and hypoxia‐inducible factor 1 alpha (HIF1α) showed the highest relative expression levels in dedifferentiated chonodrocytes. Type II collagen (COL2A1), type XI collagen (COL11A2), and superficial zone protein (SZP) showed the highest relative expression levels in articular cartilage. In contrast to previous findings, fibromodulin mRNA, and protein levels were higher in dedifferentiated chondrocytes. Compared to smaller subsets of markers, this panel of 12 highly differentially expressed genes may more precisely distinguish articular cartilage from dedifferentiated chondrocytes. Since many of the genes up‐regulated in dedifferentiated chondrocytes are also expressed during cartilage development, dedifferentiated chondrocytes may possess features of cartilage precursor cells. © 2011 Orthopaedic Research Society Published by Wiley Periodicals, Inc. J Orthop Res 30:234–245, 2012
Unreliable knowledge about economic impacts of large carnivores on bovine calves
Authors: Hebblewhite Mark
Published: August 2011

Sommers et al. (2010) reported that recolonizing predators increased bovine calf mortality rates in the Upper Green River Cattle Allotment in western Wyoming. However, Sommers et al. (2010) failed to consider multiple competing hypotheses explaining calf loss rates, increasing the likelihood that their results are actually spurious. I reanalyzed their data using a multiple competing hypotheses framework that considered effects of livestock density, summer precipitation, bias in reporting rates, and whether mortality by different predator species was compensatory. I found support for a confounded web of factors influencing calf losses. Calf losses increased with livestock density (which increased during the study), but also during drier summers and with increasing rancher reporting rates. Although both wolves (Canis lupus) and grizzly bears (Ursus arctos) did increase calf losses, the presence of just grizzly bears alone did not significantly increase calf losses. Unconditional estimates of the effects of wolves and grizzly bears on calf losses were only 2.0% (95% CI 0.53–3.81), compared to 3.6% reported by Sommers et al. (2010). Most importantly, however, I report bias in favor of livestock producers in the authors' assumptions that cast further doubt on the rigor of their results. In conclusion, I recommend managers not consider the spurious predator compensation factors reported by Sommers et al. (2010) to be reliable. © 2011 The Wildlife Society.
An experimental assessment of shotgun discharge on aluminum legband retention
Authors: Alisauskas Ray T. , Zimmerman Guthrie S.
Published: August 2011

Although metal legbands have been an important scientific tool, their use for estimation of harvest and survival relies on samples of dead birds harvested by hunters using shotguns. We hypothesized that the force of steel pellets discharged from a shotgun, within the range of conditions normally experienced by goose hunters, was sufficient to reduce probability of band retention. We conducted 8 experimental trials to estimate retention per round fired at aluminum bands normally applied to arctic‐nesting geese in relation to effects of 1) target range (20 m vs. 40 m), 2) steel pellet size (4.57 mm [BB] vs. 3.81 mm [number 2]), 3) cartridge size (76.2 mm [3 in.] vs. 69.9 mm [2.75 in.]), and 4) number of rounds fired (up to 25). There was nearly complete band retention (0.999/round) at 40 m regardless of shot size or shell size used. Retention per round fired at 20 m declined to between 0.984 and 0.987 for number 2 shot and between 0.968 and 0.974 for BB shot. Our conclusions apply to unworn bands, so we recommend further simulations to assess how retention may change with age of bands as they erode or corrode on free‐ranging geese. Bias in estimates associated with loss of older bands from shotgun discharge could be adjusted if bias is estimated as done in this article. © 2011 The Wildlife Society.
The Influence of a Potential Diffusion Control on the Outcome of Modular Polymer–Polymer Click Conjugations
Authors: Preuss Corinna M. , Barner‐Kowollik Christopher
Published: August 2011

The only reliable factors for assessing if a polymer–polymer click conjugation is successful are an assessment of the number average $\overline {M} _{{\rm n}} $ of the resulting molecular weight distribution (MWD) and the shape of the number, respectively, concentration distribution as was demonstrated earlier. The present contribution explores if a potential chain length dependence (CLD) of the conjugation reaction—caused by a potential diffusion control—can affect the outcome of the polymer–polymer click ligation process. The CLD of the click rate coefficient, $k_{{\rm click}}^{{\rm i},{\rm j}} $, was implemented via a geometric mean approximation for chain length dependent termination, employing α‐values from 1.0 to 0.2. The number averages $\overline {M} _{{\rm n}} $ and weight averages $\overline {M} _{{\rm w}} $ (and thus the PDIs) of the initial distributions were varied widely to explore under which conditions CLD effects have the largest impact. The present study clearly demonstrates that—if diffusion effects and thus a CLD of $k_{{\rm click}}^{{\rm i},{\rm j}} $—play a role in polymer–polymer ligation, the MWDs generated through conjugation display a marked conversion dependence, i.e., $M_{{\rm n}}^{{\rm click}} (x)$, with the maximum $M_{{\rm n}}^{{\rm click}} $ being reached at quantitative conversions. While the $\overline {M} _{{\rm n}} $ reached at quantitative conversions coincides with the $\overline {M} _{{\rm n}} $ obtained under CL‐independent conditions, the final $\overline {M} _{{\rm w}} $ of both the CLD and non‐CLD differs significantly. While the present theoretical study cannot replace the actual experiment, it unambiguously demonstrates that polymer–polymer click conjugations can be influenced by CLD effects. Given the larger α‐values for smaller chain length, broad distributions in the range up to approximately 3 000 Da are especially affected.

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The Impact of Band Broadening on Molar‐Mass Determination of Narrow‐Distribution Polymer by Size‐Exclusion Chromatography
Authors: Wolpers Arne , Russell Gregory T. , Vana Philipp
Published: August 2011

A systematic study of the effects of band broadening (BB) in size‐exclusion chromatography (SEC) on Poisson molar‐mass distributions (MMDs) is carried out. Such distributions apply for polymer standards used for SEC calibration, and they are a good model for the MMD from any quasi‐living polymerization, including reversible‐deactivation radical polymerization (RDRP). BB is simulated using the exponentially modified Gaussian model, which is shown to work excellently for actual polymer standards. A series of simulations with this model revealed how BB parameter values affect number‐average degree of polymerization and polydispersity index from SEC. It is shown that the skewness parameter is particularly important in these considerations. Many of the obtained trends echo ones from RDRP, suggesting that BB has been making a hitherto unsuspected – indeed uninvestigated – contribution to deviations from ideal behavior in such systems.

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Expression level of miR‐34a rather than P53 gene status correlates with mutability in related human lymphoblast cell lines
Authors: Chen Xinrong , Yan Jian , Chen Tao
Published: August 2011

The P53 gene is a tumor suppressor gene and can prevent mutation and tumor induction though apoptosis and DNA repair when it is activated by genotoxic stress. miR‐34a expression is regulated by the P53 gene and might be required for cell response to DNA damage. TK6 cells are human lymphoblast cells with normal P53 function while WTK1 and NH32 cells derived from the same progenitor as TK6 cells are P53‐deficient. Previous mutation research showed an unexpected result that NH32 cells were much less mutable than WTK1 cells, although the P53 gene in both the cell lines is not functional. To explore the possible mechanisms involved in the different mutability of the cell lines and relationship between P53 and miR‐34a, we investigated the expression levels of miR‐34a in the cells. The basal and X‐ray‐induced expression levels of miR‐34a in TK6 and NH32 cells were much higher than those in WTK1 cells. The miR‐34a was also able to be up‐regulated to respond to X‐ray exposure without a functional P53 gene in both of the NH32 and WTK1 cells. In addition, the expression levels of miR‐34a in these three cell lines are inversely correlated well with their mutability: higher levels of miR‐34a correspond with less mutable cells. These results suggest that alteration of miR‐34a expression is at least partially independent of P53 regulation and its expression levels are closely related to cells' mutability regardless of P53 status. 2011 Wiley Periodicals, Inc.
A Dynamic Assessment Method for Urban Eco‐environmental Quality Evaluation
Authors: Kou Gang , Wu Wenshuai , Zhao Yiyi , Peng Yi , Yaw Nti Emmanuel , Shi Yong
Published: August 2011

With the rapid development of urbanization, urban environmental problems become a big challenge for urban socio‐economic development planning. In this paper, a new Dynamic Assessment method, which integrates technique for order preference by similarity to ideal solution, Entropy weight for time series data analysis, Grey relational analysis and Clustering, is proposed for urban eco‐environmental quality assessment of the Yangtze River Delta and Pearl River Delta in China. A sensitivity analysis is also conducted to identify the influence of weight or value changes of factors. The urban eco‐environmental quality ranking by the proposed method is consistent with the Chinese city competitiveness rankings in 2009 by the Chinese Academy of Social Sciences. It is much easier and more efficient to obtain the urban eco‐environmental quality ranking by the proposed method than by field studies and surveys. Copyright © 2011 John Wiley & Sons, Ltd.
Protein modification by acrolein: Relevance to pathological conditions and inhibition by aldehyde sequestering agents
Authors: Aldini Giancarlo , Orioli Marica , Carini Marina
Published: August 2011

Acrolein (ACR) is a toxic and highly reactive α,β‐unsaturated aldehyde widely distributed in the environment as a common pollutant and generated endogenously mainly by lipoxidation reactions. Its biological effects are due to its ability to react with the nucleophilic sites of proteins, to form covalently modified biomolecules which are thought to be involved as pathogenic factors in the onset and progression of many pathological conditions such as cardiovascular and neurodegenerative diseases. Functional impairment of structural proteins and enzymes by covalent modification (crosslinking) and triggering of key cell signalling systems are now well‐recognized signs of cell and tissue damage induced by reactive carbonyl species (RCS). In this review, we mainly focus on the in vitro and in vivo evidence demonstrating the ability of ACR to covalently modify protein structures, in order to gain a deeper insight into the dysregulation of cellular and metabolic pathways caused by such modifications. In addition, by considering RCS and RCS‐modified proteins as drug targets, this survey will provide an overview on the newly developed molecules specifically tested for direct or indirect ACR scavenging, and the more significant studies performed in the last years attesting the efficacy of compounds already recognized as promising aldehyde‐sequestering agents.
Calculation methods for ventricular diffusion‐weighted imaging thermometry: phantom and volunteer studies
Authors: Sakai Koji , Yamada Kei , Sugimoto Naozo
Published: August 2011

A method for the measurement of temperature in the lateral ventricle using diffusion‐weighted imaging (DWI) has been proposed recently. This method uses predetermined arbitrary thresholds, but a more objective method of calculation would be useful. We therefore compared four different calculation methods, two of which were newly created and did not require predetermined thresholds. A rectangular polyethylene terephthalate bottle (8 × 10 × 28 cm3) was filled with heated water (35.0–38.8 °C) and used as a water phantom. The DWI data of 23 healthy subjects (aged 26–75 years; mean ± standard deviation, 50.13 ± 19.1 years) were used for this study. The temperature was calculated using the following equation: T(°C) = 2256.74/ln(4.39221/D) − 273.15, where D is the diffusion coefficient. The mean ventricular temperature was calculated by four methods: two thresholding methods and two histogram curve‐fitting methods. As a reference, we used the temperature measured at the tympanic membrane, which is known to be approximately 1 °C lower than the brain temperature. The averaged differences in temperature between mercury thermometry and classical predetermined thresholding methods for the water phantom were 0.10 ± 0.42 and 0.05 ± 0.41 °C, respectively. The histogram curve‐fitting methods, however, yielded temperatures a little lower (averaged differences of −0.24 ± 0.32 and −0.14 ± 0.31 °C, respectively) than mercury thermometry. There was very little difference in temperature between tympanic thermometry and classical predetermined thresholding methods (+0.01 and −0.07 °C, respectively). In humans, however, the histogram curve‐fitting methods yielded temperatures approximately 1 °C higher (+1.04 °C and +1.36 °C, respectively), suggesting that temperatures measured in this way more closely approximate the true brain temperature. The histogram curve‐fitting methods were more objective and better matched the estimated brain temperature than did classical predetermined thresholding methods, although the standard deviation was wider in the former methods. Copyright © 2011 John Wiley & Sons, Ltd.
Reload cost trees and network design
Authors: Gamvros Ioannis , Gouveia Luis , Raghavan S.
Published: August 2011

In this article, we consider the notion of “reload costs” in network design. Reload costs occur naturally in many different settings including telecommunication networks using diverse technologies. However, reload costs have not been studied extensively in the literature. Given that reload costs occur naturally in many settings, we are motivated by the desire to develop “good” models for network design problems involving reload costs. In this article, and as a first step in this direction, we propose and discuss the reload cost spanning tree problem (RCSTP). We show that the RCSTP is NP‐complete. We discuss several ways of modeling network design problems with reload costs. These involve models that expand the original graph significantly—to a directed line graph and a colored graph—to model reload costs. We show that the different modeling approaches lead to models with the same linear programming bound. We then discuss several variations of reload cost spanning tree and network design problems, and discuss both their complexity and models for these variations. To assess the effectiveness of the proposed models to solve RCSTP instances, we present results taken from instances with up to 50 nodes, 300 edges, and nine technologies for several variations of the problem. © 2011 Wiley Periodicals, Inc. NETWORKS, 2011
An adaptive approach to denoising tandem mass spectra
Authors: Lin Wenjun , Wu Fang‐Xiang , Shi Jinhong , Ding Jiarui , Zhang Wenjun
Published: August 2011

In our recent work on denoising, a linear combination of five features was used to adjust the peak intensities in tandem mass spectra. Although the method showed a promise, the coefficients (weights) of the linear combination were fixed and determined empirically. In this paper, we proposed an adaptive approach for estimating these weights. The proposed approach: (i) calculates the score for each peak in a data set with the previous empirically determined weights, (ii) selects the training data set based on the scores of peaks, (iii) applies the linear discriminant analysis to the training data set and takes the solution of linear discriminant analysis as the new weights, (iv) calculates the score again with the new weights, (v) repeats (ii)–(iv) until the weights have no significant change. After getting the final weights, the proposed approach follows the previous methods. The proposed approach was applied to two tandem mass spectra data sets: ISB (with low resolution) and TOV‐Q (with high resolution) to evaluate its performance. The results show that about 66% of peaks (likely noise peaks) can be removed and that the number of peptides identified by MASCOT increases by 14 and 23.4% for ISB and TOV‐Q data set, respectively, compared to the previous work.
Interactions of obstructive sleep‐disordered breathing with recurrent wheezing or asthma and their effects on sleep quality
Authors: Malakasioti Georgia , Gourgoulianis Konstantinos , Chrousos George , Kaditis Athanasios
Published: August 2011

Snoring is the most characteristic symptom of obstructive sleep‐disordered breathing (SDB) and recurrent wheezing is the most common clinical manifestation of asthma. The purpose of the present review is to outline the impact of SDB and recurrent wheezing/asthma on sleep quality and to summarize the epidemiologic and pathophysiologic evidence supporting an association between the two disorders. Enlarged tonsils and adenoid or obesity predispose to obstructive sleep apneas and hypopneas which are accompanied by arousals, restless sleep, and frequently daytime sleepiness, inattention, hyperactivity, and academic difficulties. Subjects with history of wheezing are also at risk for sleep disturbance and daytime cognitive dysfunction.

Asthmatic children have more frequent snoring, apneas, and hypopneas during sleep than non‐asthmatic subjects and tonsillar hypertrophy mediates at least in part this epidemiologic association. In addition, preliminary evidence indicates that treatment of sleep apnea with adenotonsillectomy results in improved control of coexisting asthma. Elevated concentrations of leukotrienes and oxidative stress markers have been detected in the exhaled breath condensate of children with asthma and probably contribute to bronchoconstriction. Moreover, sleep apneic children have increased expression of leukotrienes and leukotriene receptors in adenotonsillar tissue. Viral respiratory infections may induce inflammation and oxidative stress in the asthmatic airway enhancing not only bronchospasm, but also biosynthesis of leukotrienes within pharyngeal lymphoid tissues, which promote adenotonsillar enlargement and sleep apnea.

In conclusion, taking under consideration the epidemiologic association between obstructive SDB and asthma, when one of the two disorders is diagnosed, the possibility of the other disease being present should be entertained. Pediatr. Pulmonol. 2011; 46:1047–1054. © 2011 Wiley Periodicals, Inc.
The H6D variant of NAG‐1/GDF15 inhibits prostate xenograft growth in vivo
Authors: Wang Xingya , Chrysovergis Kali , Bienstock Rachelle J. , Shim Minsub , Eling Thomas E.
Published: August 2011

BACKGROUND

Non‐steroidal anti‐inflammatory drug‐activated gene (NAG‐1), a divergent member of the transforming growth factor‐beta superfamily, has been implicated in many cellular processes, including inflammation, early bone formation, apoptosis, and tumorigenesis. Recent clinical studies suggests that a C to G single nucleotide polymorphism at position 6 (histidine to aspartic acid substitution, or H6D) of the NAG‐1 protein is associated with lower human prostate cancer incidence. The objective of the current study is to investigate the activity of NAG‐1 H6D variant in prostate cancer tumorigenesis in vivo.

METHODS

Human prostate cancer DU145 cells expressing the H6D NAG‐1 or wild‐type (WT) NAG‐1 were injected subcutaneously into nude mice and tumor growth was monitored. Serum and tumor samples were collected for subsequent analysis.

RESULTS

The H6D variant was more potent than the WT NAG‐1 and inhibited tumor growth significantly compared to control mice. Mice with tumors expressing the WT NAG‐1 have greater reduced both body weight and abdominal fat than mice with H6D variant tumors suggesting different activities of the WT NAG‐1 and the H6D NAG‐1. A significant reduction in adiponectin, leptin, and IGF‐1 serum levels was observed in the tumor‐bearing mice with a more profound reduction observed with expression of H6D variant. Cyclin D1 expression was suppressed in the tumors with a dramatic reduction observed in the tumor expressing the H6D variant.

CONCLUSION

Our data suggest that the H6D variant of NAG‐1 inhibits prostate tumorigenesis by suppressing IGF‐1 and cyclin D1 expression but likely additional mechanisms are operative. Prostate 72:677–689, 2012. © 2011 Wiley Periodicals, Inc.
Structure–activity relationships of a peptidic antagonist of Id1 studied by biosensor method, circular dichroism spectroscopy, and bioassay
Authors: Yang Shih‐Ying , Chen Yeh , Yang Chia‐Xin , Yang De‐Len , Kuo Sheng‐Chu , Huang Li‐Jiau , Lung Feng‐Di T.
Published: August 2011

Id1 proteins, inhibitors of differentiation or DNA binding, act as dominant negative antagonists of the bHLH family of transcription factors, which play an important role in cellular development, proliferation, and differentiation. The mechanism of Id proteins is to antagonize bHLH proteins by forming high‐affinity heterodimers with other bHLH proteins, thereby preventing them from binding to DNA and inhibiting transcription of differentiation‐associated genes. Our goal is to study the SARs of a peptidic antagonist of Id1, peptide 3C, which exhibits high affinity for Id1 and inhibitory effect on the proliferation of cancer cells. A series of N‐terminal‐ and C‐terminal‐deleted analogs of peptide 3C were designed, synthesized, and characterized. Affinity of each peptide for Id1 or Id1‐HLH domain was determined by SPR‐based biosensor. The secondary structure of each peptide was studied by CD spectroscopy. Biological effect of each peptide in breast cancer cell (MCF‐7) was analyzed by the MTT cell viability assay. Results demonstrated that peptide 3C and peptide 3C‐CtD4 exhibited higher affinity for Id1‐HLH and the equilibrium dissociation constants (KD) were 3.16 and 2.77 µM, respectively. CD results indicated that the percentage of α‐helix (%) in the secondary structure of deleted peptides were different, ranging from 7.93 to 10.45%. Although MTT results showed that treatment of MCF‐7 with these peptides did not cause antiproliferative effects in cancer cells, SPR results demonstrated that the high‐affinity peptides 3C and 3C‐CtD4 are promising for further modifications to enhance their affinity for Id1‐HLH and antiproliferative effects in cancer cells and for the development of peptidic antagonists as anticancer agents. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.
Studies on the antileishmanial properties of the antimicrobial peptides temporin A, B and 1Sa
Authors: Chadbourne Frances L. , Raleigh Catriona , Ali Hayder Z. , Denny Paul W. , Cobb Steven L.
Published: August 2011

Given the paucity and toxicity of available drugs for leishmaniasis, coupled with the advent of drug resistance, the discovery of new therapies for this neglected tropical disease is recognised as being of the utmost urgency. As such antimicrobial peptides (AMPs) have been proposed as promising compounds against the causative Leishmania species, insect vector‐borne protozoan parasites. Here the AMP temporins A, B and 1Sa have been synthesised and screened for activity against Leishmania mexicana insect stage promastigotes and mammalian stage amastigotes, a significant cause of human cutaneous disease. In contrast to previous studies with other species the activity of these AMPs against L. mexicana amastigotes was low. This suggests that amastigotes from different Leishmania species display varying susceptibility to peptides from the temporin family, perhaps indicating differences in their surface structure, the proposed target of these AMPs. In contrast, insect stage L. mexicana promastigotes were sensitive to two of the screened temporins which clearly demonstrates the importance of screening AMPs against both forms of the parasite. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.
A statistical downscaling to identify the large‐scale circulation patterns associated with heavy precipitation events over southern France
Authors: Nuissier O. , Joly B. , Joly A. , Ducrocq V. , Arbogast P.
Published: August 2011

This study assesses the potential for a detection algorithm to identify discriminating analysis‐based statistical predictors of a few relevant parameters that can be used to capture heavy precipitation events (HPEs), or, at least, their associated large‐scale circulation (LSC) patterns in a climate scenario. HPEs are defined from a sample combining ‘large‐scale’ fields from the ECMWF ERA‐40 reanalysis with local observations from the Météo‐France rain‐gauge network. In a first step, LSC patterns considered as significantly favouring HPE over southern France are identified and described with the greatest robustness possible. For that purpose, an objective automatic clustering of the unfiltered 500 hPa geopotential height field is performed. Four clusters are obtained. Among them, the most discriminating for heavy precipitation is characterised by a synoptic‐scale deep upper‐level low northwest of the area of interest, inducing a southerly flow over the western Mediterranean Sea and southern France. In a second step, other lower‐scale parameters are used to refine the characteristics of the clusters. It has been found that the low‐level moisture transport is a relevant low‐level ingredient to regionally characterise heavy precipitation. Indeed, ‘Cévennes’ cases are related to more south to southeasterly flows over the Gulf of Lion, whereas ‘Languedoc‐Roussillon’ events occurred preferentially within a more pronounced easterly wind component with two streams of low‐level moisture transport. Moreover, in‐depth examination of the low‐level features reveals that HPEs tend to occur when the wind blows in a specific direction and for the greatest low‐level moisture flux over the Gulf of Lion. Finally, the predictive skill of a detection tool for HPEs over southern France, with only synoptic‐scale favourable parameters as predictors, is discussed. It is shown that this tool allows selection of HPE situations in more than 70% of cases. Copyright © 2011 Royal Meteorological Society
The orographic impact on patterns of embedded convection during the August 2005 Alpine flood
Authors: Langhans W. , Gohm A. , Zängl G.
Published: August 2011

Convective precipitation structures during an Alpine heavy precipitation event in August 2005 are investigated utilising a mesoscale non‐hydrostatic numerical model and observational data. The focus is on the mechanisms of convective initiation during the very beginning of the event, when organised cellular updraughts enhanced the precipitation over the southern German Alpine foreland. A set of sensitivity experiments with systematically modified topography is conducted in order to investigate the role of single topographic obstacles in initiating and arranging convection.

A reference simulation proves to be capable of qualitatively reproducing the development of two distinct, flow‐parallel aligned, non‐stationary, convective precipitation bands, which are observed by radar and surface measurements. The simulations reveal the presence of two low‐level convergence lines that provide a primary mechanism for both initiating and aligning convective cells during the analysed period. Mountains embedded in the Alpine foreland are not decisive for triggering and aligning the convective cells in this case, since the primary mechanism provides a consistent forcing for the convective precipitation bands. However, the experiments demonstrate a dependence of the alignment and intensity of one of the precipitation bands upon the position of the pre‐existing convergence line relative to a flow‐parallel aligned mountain ridge. Enhancement (weakening) of the existing banded structure and convective intensity is achieved if the convergence line is located upstream (downstream) of the ridge with respect to a cross‐ridge low‐level inflow. The ‘weakening’ mode is characterised by a subsiding cross‐ridge inflow into the convergence line that stabilises the atmosphere and therefore inhibits the formation of a continuous convective precipitation band. Copyright © 2011 Royal Meteorological Society
New results on robust output regulation of nonlinear systems with a nonlinear exosystem
Authors: Yang Xi , Huang Jie
Published: August 2011

The global robust output regulation problem for nonlinear plants subject to nonlinear exosystems has been a challenging problem and has not been well addressed. The main difficulty lies in finding a suitable internal model. The existing internal model for handling the nonlinear exosystem is not zero input globally asymptotically stable, and can only guarantee a local solution for the output regulation problem. In this paper, we first propose a new class of internal models, which is guaranteed to exist under the generalized immersion condition. An advantage of this internal model is that it is zero input globally asymptotically stable. This fact will greatly facilitate the global stabilization of the augmented system associated with the given plant and the internal model. Then we will further utilize this class of internal models to solve the global robust output regulation problem for output feedback systems with a nonlinear exosystem. Copyright © 2011 John Wiley & Sons, Ltd.
DISTRIBUTION AND HABITAT USE OF THE MISSOURI RIVER AND LOWER YELLOWSTONE RIVER BENTHIC FISHES FROM 1996 TO 1998: A BASELINE FOR FISH COMMUNITY RECOVERY
Authors: Wildhaber M. L. , Gladish D. W. , Arab A.
Published: August 2011

Past and present Missouri River management practices have resulted in native fishes being identified as in jeopardy. In 1995, the Missouri River Benthic Fishes Study was initiated to provide improved information on Missouri River fish populations and how alterations might affect them. The study produced a baseline against which to evaluate future changes in Missouri River operating criteria. The objective was to evaluate population structure and habitat use of benthic fishes along the entire mainstem Missouri River, exclusive of reservoirs. Here we use the data from this study to provide a recent‐past baseline for on‐going Missouri River fish population monitoring programmes along with a more powerful method for analysing data containing large percentages of zero values. This is carried out by describing the distribution and habitat use of 21 species of Missouri River benthic fishes based on catch‐per‐unit area data from multiple gears. We employ a Bayesian zero‐inflated Poisson model expanded to include continuous measures of habitat quality (i.e. substrate composition, depth, velocity, temperature, turbidity and conductivity). Along with presenting the method, we provide a relatively complete picture of the Missouri River benthic fish community and the relationship between their relative population numbers and habitat conditions. We demonstrate that our single model provides all the information that is often obtained by a myriad of analytical techniques. An important advantage of the present approach is reliable inference for patterns of relative abundance using multiple gears without using gear efficiencies. Copyright © 2011 John Wiley & Sons, Ltd.
Bayesian inference on joint models of HIV dynamics for time‐to‐event and longitudinal data with skewness and covariate measurement errors
Authors: Huang Yangxin , Dagne Getachew , Wu Lang
Published: August 2011

Normality (symmetry) of the model random errors is a routine assumption for mixed‐effects models in many longitudinal studies, but it may be unrealistically obscuring important features of subject variations. Covariates are usually introduced in the models to partially explain inter‐subject variations, but some covariates such as CD4 cell count may be often measured with substantial errors. This paper formulates a class of models in general forms that considers model errors to have skew‐normal distributions for a joint behavior of longitudinal dynamic processes and time‐to‐event process of interest. For estimating model parameters, we propose a Bayesian approach to jointly model three components (response, covariate, and time‐to‐event processes) linked through the random effects that characterize the underlying individual‐specific longitudinal processes. We discuss in detail special cases of the model class, which are offered to jointly model HIV dynamic response in the presence of CD4 covariate process with measurement errors and time to decrease in CD4/CD8 ratio, to provide a tool to assess antiretroviral treatment and to monitor disease progression. We illustrate the proposed methods using the data from a clinical trial study of HIV treatment. The findings from this research suggest that the joint models with a skew‐normal distribution may provide more reliable and robust results if the data exhibit skewness, and particularly the results may be important for HIV/AIDS studies in providing quantitative guidance to better understand the virologic responses to antiretroviral treatment. Copyright © 2011 John Wiley & Sons, Ltd.
Atomically Thin Mica Flakes and Their Application as Ultrathin Insulating Substrates for Graphene
Authors: Castellanos‐Gomez Andres , Wojtaszek Magdalena , Tombros Nikolaos , Agraït Nicolás , van Wees Bart J. , Rubio‐Bollinger Gabino
Published: August 2011

By mechanical exfoliation, it is possible to deposit atomically thin mica flakes down to single‐monolayer thickness on SiO2/Si wafers. The optical contrast of these mica flakes on top of a SiO2/Si substrate depends on their thickness, the illumination wavelength, and the SiO2 substrate thickness, and can be quantitatively accounted for by a Fresnel‐law‐based model. The preparation of atomically thin insulating crystalline sheets will enable the fabrication of ultrathin, defect‐free insulating substrates, dielectric barriers, or planar electron‐tunneling junctions. Additionally, it is shown that few‐layer graphene flakes can be deposited on top of a previously transferred mica flake. Our transfer method relies on viscoelastic stamps, as used for soft lithography. A Raman spectroscopy study shows that such an all‐dry deposition technique yields cleaner and higher‐quality flakes than conventional wet‐transfer procedures based on lithographic resists.