bluuebunny/crossref_metadata_2025 huggingface dataset:
Improved detection of motifs with preferential location in promoters
Authors: Bernard Virginie , Lecharny Alain , Brunaud Véronique
Published: October 2010

Many transcription factor binding sites (TFBSs) involved in gene expression regulation are preferentially located relative to the transcription start site. This property is exploited in in silico prediction approaches, one of which involves studying the local overrepresentation of motifs using a sliding window to scan promoters with considerable accuracy. Nevertheless, the consequences of the choice of the sliding window size have never before been analysed. We propose an automatic adaptation of this size to each motif distribution profile. This approach allows a better characterization of the topological constraints of the motifs and the lists of genes containing them. Moreover, our approach allowed us to highlight a nonconstant frequency of occurrence of spurious motifs that could be counter-selected close to their functional area. Therefore, to improve the accuracy of in silico prediction of TFBSs and the sensitivity of the promoter cartography, we propose, in addition to automatic adaptation of window size, consideration of the nonconstant frequency of motifs in promoters.
Complex prokaryotic genome structure: rapid evolution of chromosome II
Authors: Bavishi Anish , Abhishek Ankur , Lin Lin , Choudhary Madhusudan
Published: October 2010

Although many bacteria with two chromosomes have been sequenced, the roles of such complex genome structuring are still unclear. To uncover levels of chromosome I (CI) and chromosome II (CII) sequence divergence, Mauve 2.2.0 was used to align the CI- and CII-specific sequences of bacteria with complex genome structuring in two sets of comparisons: the first set was conducted among the CI and CII of bacterial strains of the same species, while the second set was conducted among the CI and CII of species in Alphaproteobacteria that possess two chromosomes. The analyses revealed a rapid evolution of CII-specific DNA sequences compared with CI-specific sequences in a majority of organisms. In addition, levels of protein divergence between CI-specific and CII-specific genes were determined using phylogenetic analyses and confirmed the DNA alignment findings. Analysis of synonymous and nonsynonymous substitutions revealed that the structural and functional constraints on CI and CII genes are not significantly different. Also, horizontal gene transfer estimates in selected organisms demonstrated that CII in many species has acquired higher levels of horizontally transferred segments than CI. In summary, rapid evolution of CII may perform particular roles for organisms such as aiding in adapting to specialized niches.
Genetic diversity and population structure analysis of the tropical pasture grassBrachiaria humidicolabased on microsatellites, cytogenetics, morphological traits, and geographical origin
Authors: Jungmann L. , Vigna B. B.Z. , Boldrini K. R. , Sousa A. C.B. , do Valle C. B. , Resende R. M.S. , Pagliarini M. S. , Zucchi M. I. , de Souza A. P.
Published: October 2010

Brachiaria humidicola (Rendle) Schweick. is a warm-season grass commonly used as forage in the tropics. Accessions of this species were collected in eastern Africa and massively introduced into South America in the 1980s. Several of these accessions form a germplasm collection at the Brazilian Agricultural Research Corporation. However, apomixis, ploidy, and limited knowledge of the genetic basis of this germplasm collection have constrained breeding activities. The objectives of this work were to identify genetic variability in the Brazilian B. humidicola germplasm collection using microsatellite markers and to compare the results with information on the following: (1) collection sites of the accessions; (2) reproductive mode and ploidy levels; and (3) genetic diversity revealed by morphological traits. The evaluated germplasm population is highly structured into four major groups. The sole sexual accession did not group with any of the clusters. Genetic dissimilarities did not correlate with either geographic distances or genetic distances inferred from morphological descriptors. Additionally, the genetic structure identified in this collection did not correspond to differences in ploidy level. Alleles exclusive to either sexual or apomictic accessions were identified, suggesting that further evaluation of the association of these loci with apospory should be carried out.
Value analysis system development for water treatment plant maintenance method selection
Authors: Seo Jong-Won , Jung Pyung-Ki , Lee Min-Jae
Published: October 2010

Even though the life span of a water treatment facility is relatively long, the decision-making process related to method selection for repair and reinforcement is generally influenced by an engineer's experience. These decisions should be made systematically after considering facility use, damage features, technical features, reconstruction costs, maintenance costs, and others. The purpose of this study is to provide a value analysis system for the effective selection of repairing and (or) reinforcing methods for water treatment plant concrete structures. Analysis of the concrete structure's damage type and maintenance records allowed the development of a value analysis system for more effective and systematic decision making. Performance evaluation criteria were established using a survey of field professionals as the decision basis. Weight for each performance criterion was determined by using the field personnel survey and the analytic hierarchy process (AHP) methodology. The rank rating standard for each performance evaluation criterion was established for each maintenance method type. Finally, an automated system was developed that can give guidance on repair and reinforcement method selection by applying proposed performance indices that are related to the maintenance method selection and the value analysis of the different methods.
Experimental seismic behavior of a five-storey double-midply wood shear wall in a full scale building
Authors: Pei Shiling , van de Lindt John W. , Ni Chun , Pryor Steven E.
Published: October 2010

In July 2009, a full-scale six-storey platform wood frame apartment building was subjected to a series of earthquakes at the world’s largest shake table in Miki, Japan. Two double-midply shear wall stacks were installed in the building from the first storey through to the fifth storey. A continuous anchor tie-down system (ATS) was used to prevent overturning and allow the shear walls to develop their full lateral load capacities. This paper focuses on the behavior of the stacked double-midply shear wall in a full-scale midrise building during a series of triaxial shakes scaled for the city of Los Angeles, California. The stacked midply shear wall achieved a maximum interstorey deformation of 40.4 mm (equivalent to 1.64% drift). The uplift forces measured at the bottom storey of the stacked wall exceeded 760 kN, indicating the need for substantial tie-down systems for this type of wall when utilized in a midrise platform wood frame building.
Effects of water–air mixtures on hydraulic transients
Authors: Pozos Oscar , Sanchez Alejandro , Rodal Eduardo A. , Fairuzov Yuri V.
Published: October 2010

The purpose of this study is to investigate pressurized pipelines and the potential effects on pressure transients of air entrained at the downstream end of large entrapped air pockets followed by a hydraulic jump in pressurized pipelines. The homogeneous two-phase flow model is used to simulate the transient response of the bubbly mixture after a pump shutdown. The results show that pressure transients are significantly reduced with increasing air-pocket volumes and bubbly flow air content. Experimental investigations were carried out to analyze the impact of different air-pocket volumes located at high points of pressurized pipelines. A case study of an existing pumping system was considered to exemplify the impact of the bubbly flow air content on hydraulic transients.
New installation scheme for viscoelastic dampers using cables
Authors: Choi Hyunhoon , Kim Jinkoo
Published: October 2010

Passive energy dissipation devices, such as, viscous, viscoelastic, and friction devices are generally installed in buildings using diagonal or chevron braces. To increase the effective damping force and to reduce the damper volume, various magnifying system of the damper displacement, such as, toggle brace system and scissor-jack-damper configuration have been developed with increase in installation cost. In this study, new installation scheme for passive dampers was proposed using cables installed in such a way that relative displacement equal to storey displacement occurs between the cable and the structure when the structure is subjected to lateral load. The cables can be installed continuously or discretely between base and top storey of the structure. To verify the validity of the proposed method nonlinear dynamic analysis of model structures with viscoelastic dampers installed using the proposed configuration scheme was carried out using three earthquake records and two sinusoidal forces. According to the analysis, the proposed method resulted in significant reduction in the size of dampers compared with the conventional installation methods.
Influence of aggregate size on the mechanical and transport properties of concretes and concrete-equivalent mortars
Authors: Özbay Erdoğan
Published: October 2010

In this study, the influence of the aggregate size on the mechanical and transport properties of concrete and concrete-equivalent mortars is investigated. A concrete mixture was proportioned having a water–cement ratio of 0.45 and a cement content of 450 kg/m3 with a maximum aggregate size of 22.4 mm. Then, keeping the total aggregate surface area constant, three mixtures were proportioned with the same water–cement ratio, but the maximum aggregate size decreased to 16, 8, and 4 mm using the concrete-equivalent mortar method. Mechanical properties including compressive strength, splitting tensile strength and transport properties including rapid chloride permeability, water sorptivity, water absorption, and water permeability tests were performed at 7 and 28 d. Test results revealed that decreasing the maximum aggregate size increased the water permeability, rapid chloride permeability, water absorption, and sorptivity values, but decreased the compressive and split tensile strengths of concrete and concrete-equivalent mortars.
Strengthening of a concrete masonry wall subject to lateral load with sprayed glass-fibre-reinforced polymer
Authors: Haddad M. A. , Shaheen E. , Parsekian G. A. , Tilleman D. , Shrive N. G.
Published: October 2010

Unreinforced hollow concrete masonry walls could be used to construct basements if strengthened to resist the lateral load. Two face-shell-bedded concrete masonry walls were constructed, 3 m high by 6 m long. As a simple strengthening technique, one wall was sprayed with glass-fibre-reinforced polymer (GFRP) on one side to a nominal average thickness of 5 mm. The walls were subjected to distributed point loading simulating increasing pressure from top to bottom of the wall. Support conditions were applied to simulate the walls being part of a basement. The plain wall failed with a failure line cracking pattern at a lateral load of 44 kN. The sprayed wall failed in a much more brittle fashion when the load reached 330 kN. The GFRP suffered a mode III tear at the bottom course. The results indicate that spraying a plain masonry wall with GFRP increases its ability to resist lateral load considerably, and that the process could be improved in terms of both the thickness of the layer and the area of wall covered to achieve a specific target. The two walls were analyzed using the yield-line, fracture-line, and failure-line methods. The failure-line method was improved by accounting for the stiffness orthotropy of masonry and gave the most accurate prediction of these plastic design methods. A finite element model of the masonry provided the most accurate prediction of capacity.
Pavement surface friction and noise: integration into the pavement management system
Authors: Ahammed M. Alauddin , Tighe Susan L.
Published: October 2010

Pavement surface friction is an essential attribute of highway safety. The desired surface friction should also accommodate the seasonal and long-term variations. The available surface friction depends mainly on microtexture and macrotexture on pavement surfaces. An increased surface texture for increased and durable friction may increase the roadway noise, which is also a growing problem. Traditional sound barriers, constructed to reduce noise exposure, are very expensive. As the pavement surface characteristics play a key role in roadway noise generation, it provides a window for noise reduction by altering the pavement surface. The challenge, however, is to provide a smooth, quiet, long-lasting, and economic pavement with adequate and durable surface friction. This paper addresses this challenge and provides a realistic guideline. The correlation of tire–road noise and surface friction is examined using data collected from five different asphalt pavements. Frameworks for desired minimum surface friction and maximum roadway noise are provided. A modified value-engineering approach is proposed to accommodate the construction and maintenance costs, longevity, smoothness, safety, and noise in the selection of pavement surfaces.
Flexural behaviour of concrete beams strengthened with near surface mounted fibre reinforced polymer bars
Authors: Soliman Shehab M. , El-Salakawy Ehab , Benmokrane Brahim
Published: October 2010

Fibre reinforced polymer (FRP) composite materials have been used as internal and external reinforcement for concrete structures. Flexural strengthening of concrete elements using near surface mounted (NSM)–FRP materials are a promising technology. This research is designed to investigate the behaviour of reinforced concrete beams strengthened in flexure with NSM–FRP bars. A total of 20 reinforced concrete beams were tested. Different parameters including internal steel reinforcement ratio, type of NSM–FRP bars, FRP bar diameter, bonded length, and groove size were investigated in this research. Test results showed that the use of NSM–FRP bars is effective in increasing the flexural capacity of concrete beams. In addition, a nonlinear 3D finite element (FE) analysis was used to numerically simulate the behaviour of the test beams. Comparisons between the FE predictions and experimental results showed very good agreement in terms of the load−deflection and load−strain relationships, ultimate capacities, and modes of failure for the tested beams.
Higher expression of ferritin protectsChlamydia trachomatisinfected HeLa 229 cells from reactive oxygen species mediated cell death
Authors: Vardhan Harsh , Bhengraj Apurb Rashmi , Jha Rajneesh , Srivastava Pragya , Jha Hem Chandra , Mittal Aruna
Published: October 2010

Apoptosis plays an important role in modulating the pathogenesis of a variety of infectious diseases. Chlamydial infection protects cells against different forms of apoptosis: extrinsic, intrinsic, and granzyme B mediated. Redox reactions are central to the life and death decision of cells and pathogens and an intimate relationship exists between oxidative stress and iron metabolism. The link between redox status and ferritin was largely unexplored in chlamydia-infected cells. In the present study, we showed that Chlamydia trachomatis (CT) infection induced FHC protein in HeLa cells. FHC induction by CT-infected cells stably expressing FHC blunted ROS production compared with mock infected cells, and the infected cells were relatively resistant to apoptosis induced by H2O2. We also demonstrated that endogenous FHC overexpression correlates well with the stabilization of the mitochondrial membrane potential in CT-infected cells. Increased expression of FHC is independent of iron supplementation (FAC) and depletion (DFO) in CT-infected cells. These data suggest that FHC up-regulation is an acute response of HeLa cells against CT infection and that FHC exerts anti-apoptotic activity against oxidative stress.
Target excitation dependence of degree of multifractality and critical exponent in ultrarelativistic nuclear collision
Authors: Ghosh Dipak , Deb Argha , Saha Ruma , Das Rupa
Published: October 2010

The target excitation dependence of the degree of multifractality and critical exponent of pions produced for the 16O-AgBr interaction at 60 AGeV has been investigated. To study target excitation dependence, the data for the produced pions were distributed into three sets, depending on the number of grey tracks (ng). The different sets correspond to the different degrees of target excitation. The probability G-moments were used for the analysis in pseudorapidity space. The analysis reveals that the produced particle density distribution possesses multifractal structure for all degrees of target excitation (0 ≤ ng ≤ 3, 4 ≤ ng ≤ 7, and ng ≥ 8). The distribution Levy index and the phase transition critical exponent are calculated. The study indicates the non-thermal phase transition, but it does not show evidence for the second-order phase transition.
Unsteady flow of a generalized Oldroyd-B fluid due to an infinite plate subject to a time-dependent shear stress
Authors: Vieru D. , Fetecau Corina , Fetecau C.
Published: October 2010

The unsteady flow of an incompressible generalized Oldroyd-B fluid induced by an infinite plate subject to a time-dependent shear-stress is studied by means of the Fourier cosine and Laplace transforms. The solutions that have been obtained, written under integral and series form in terms of the generalized Ga,b,c(·,t) functions, are presented as a sum of the Newtonian solutions and the corresponding non-Newtonian contributions. They satisfy all imposed initial and boundary conditions, and for λ and λr → 0 reduce to the Newtonian solutions. Furthermore, the similar solutions for generalized Maxwell fluids as well as those for ordinary fluids are also obtained as limiting cases of general solutions. Finally, to reveal some relevant physical aspects of the obtained results, the diagrams of the velocity field v(y, t) have been depicted against y for different values of t and of the material and fractional parameters.
Falling and rising in a fluid with both linear and quadratic drag
Authors: Mohazzabi Pirooz
Published: October 2010

The falling and rising of objects of arbitrary shapes in incompressible Newtonian fluids with a drag force of the form k1v + k2v2 are investigated. Exact analytical expressions for the velocity and displacement as a function of time are derived and discussed.
Rheological properties of fine-grained sediment: the roles of texture and mineralogy
Authors: Jeong Sueng Won , Locat Jacques , Leroueil Serge , Malet Jean-Philippe
Published: October 2010

Rheological properties of fine-grained sediments depending on index properties and salinity were examined. To characterize flow behaviors as a function of soil type, groups were made for convenience: (i) low-activity clays (group 1), (ii) high-activity clays (group 2), and (iii) silt-rich soils (especially for iron tailings; group 3). Low-activity and high-activity clays have characteristics of pseudoplastic (shear thinning) fluids, and exhibit a decrease in viscosity with increasing shear rate. However, in terms of the change in soil structure due to particle–particle interactions, illitic and montmorillonitic clays have opposite responses to salinity. As most of our data were obtained on low-activity clays — mostly illitic mixtures — we implemented a test program to ascertain the influence of montmorillonite on flow behavior. Using the Bingham model, a simple relationship is presented in terms of the possible critical limits of rheological transitions from clay- to silt- to sand-rich soils.
Preferential flow in geosynthetic clay liners exhumed from final covers with composite barriers
Authors: Scalia Joseph , Benson Craig H.
Published: October 2010

Geosynthetic clay liners (GCLs) were exhumed from final covers with composite barriers (geomembrane over GCL) at two municipal solid waste landfills in the USA. Preferential flow and high hydraulic conductivity (>2 × 10−9 m/s) was observed in eight of the 18 GCL samples collected from both sites. At one site, manganese oxide precipitate was concomitant with bundles of needle-punched fibers that conducted preferential flow. Nearly complete replacement of Na by Ca on the bentonite surface occurred in all GCL samples. GCLs with and without preferential flow could not be differentiated by physical and chemical properties commonly used to differentiate GCLs with high and low hydraulic conductivities (exhumed water content, swell index, mole fraction monovalent cations, soluble cation concentrations). The relative abundance of soluble cations in the pore water of GCLs exhibiting preferential flow was comparable to the relative abundance in the subgrade pore water, whereas the pore water in GCLs with distributed flow was more sodic than the pore water in the subgrade. Hydration experiments indicated that bentonite in GCLs initially hydrates in a zone surrounding bundles of needle-punching fibers. Cation exchange during this hydration process may create zones of higher hydraulic conductivity surrounding the fiber bundle, permitting preferential flow.
Numerical simulations of stone column installation
Authors: Castro Jorge , Karstunen Minna
Published: October 2010

This paper describes the results of numerical simulations investigating the installation effects of stone columns in a natural soft clay. The geometry of the problem is simplified to axial symmetry, considering the installation of one column only. Stone column installation is modelled as an undrained expansion of a cylindrical cavity. The excess pore pressures generated in this process are subsequently assumed to dissipate towards the permeable column. The process is simulated using a finite element code that allows for large displacements. The properties of the soft clay correspond to Bothkennar clay, modelled using S-CLAY1 and S-CLAY1S, which are Cam clay–type models that account for anisotropy and destructuration. Stone column installation alters the surrounding soil. The expansion of the cavity generates excess pore pressures, increases the horizontal stresses of the soil, and most importantly modifies the soil structure. The numerical simulations performed allow quantitative assessment of the post-installation value of the lateral earth pressure coefficient and the changes in soil structure caused by column installation. These effects and their influence on stone column design are discussed.
Frequency of virulence genes and antibiotic resistances inEnterococcusspp. isolates from wastewater and feces of domesticated mammals and birds, and wildlife
Authors: Lanthier Martin , Scott Andrew , Lapen David R. , Zhang Yun , Topp Edward
Published: October 2010

Enterococci are gastrointestinal tract residents and also an important cause of nosocomial infections. To understand which species, virulence determinants, and antibiotic resistances are prevalent in enterococci shed by various hosts groups, a total of 1460 strains isolated from 144 fecal samples obtained from wastewater, domesticated mammals and birds, and wildlife were characterized. Identification of isolates to the species level showed that Enterococcus faecalis was dominant in domesticated mammals and birds and wildlife feces, whereas Enterococcus faecium was dominant among wastewater isolates, and that no single Enterococcus species could be associated with a specific host group. The frequency of 12 virulence determinants was evaluated among isolates, but no single virulence determinant could be associated with a specific host group. Resistance to 12 antibiotics was evaluated among isolates, and it was shown that the highest frequency of resistance at breakpoint concentration was found in domesticated mammals and birds (P ≤ 0.05 for 4 antibiotics). Our results suggests that (1) species identification and virulence typing of Enterococcus spp. isolates are not useful for the identification of the host groups responsible for fecal contamination of water by microbial source tracking and that (2) antibiotic use for clinical, veterinary, or animal husbandry practices is promoting resistance.
Occurrence and dominance of yeast species in naturally fermented milk from the Tibetan Plateau of China
Authors: Bai Mei , Qing Manjun , Guo Zhuang , Zhang Yong , Chen Xia , Bao Qiuhua , Zhang Heping , Sun Tian-song
Published: October 2010

To determine which yeasts are present in the naturally fermented milks of China, 69 samples made by the nomads of Tibet were collected from the Tibetan Plateau in China. From these samples, 225 strains of yeast were isolated and identified using conventional microbiological analysis and gene sequencing analysis of the D1/D2 domain of the large subunit (26S) ribosomal DNA. The results showed that the total concentration of yeasts in these samples ranged from 5.01 to 8.97 log10 colony-forming units (CFU)/mL (6.91 ± 1.02 log10 CFU/mL; mean ± SD). The number of cultivable yeasts was higher in the samples from Qinghai (7.55 ± 0.75 log10 CFU/mL) than those from Tibet (6.21 ± 0.79 log10 CFU/mL, P < 0.05). Moreover, there were 15 phylotypes in these 69 samples. Among these phylotypes, Kluyveromyces marxianus (49.3%, frequency percentage), Saccharomyces cerevisiae (62.3%), and Pichia fermentans (46.4%) appeared frequently and can be considered the most common culturable species in naturally fermented milk products. Traditional fermented Mongolian cow milk featured a wide diversity of yeast species, including Issatchenkia orientalis , Kazachstania unisporus , Rhodotorula mucilaginosa , Candida pararugosa , Torulaspora delbrueckii , Geotrichum sp., Kazachstania unisporus , Geotrichum fragrans , Debaryomyces hansenii , Yarrowia lipolytica , Trichosporon gracile , and Pichia membranifaciens . This study provides new data on yeast composition in naturally fermented milk and shows the yeast biodiversity of fermented milk products from the Tibetan Plateau of China.
Responses of Staphylococcus aureus exposed to HCl and organic acid stress
Authors: Rode Tone Mari , Møretrø Trond , Langsrud Solveig , Langsrud Øyvind , Vogt Gjermund , Holck Askild
Published: October 2010

Staphylococcus aureus is an important food poisoning bacterium. In food preservation, acidification is a well-known method. Permeant weak organic acids, like lactic and acetic acids, are known to be more effective against bacteria than inorganic strong acids (e.g., HCl). Growth experiments and metabolic and transcriptional analyses were used to determine the responses of a food pathogenic S. aureus strain exposed to lactic acid, acetic acid, and HCl at pH 4.5. Lactic and acetic acid stress induced a slower transcriptional response and large variations in growth patterns compared with the responses induced by HCl. In cultures acidified with lactic acid, the pH of the medium gradually increased to 7.5 during growth, while no such increase was observed for bacteria exposed to acetic acid or HCl. Staphylococcus aureus increased the pH in the medium mainly through accumulation of ammonium and the removal of acid groups, resulting in increased production of diacetyl (2,3-butanedione) and pyrazines. The results showed flexible and versatile responses of S. aureus to different types of acid stress. As measured by growth inhibition, permeant organic acid stress introduced severe stress compared with the stress caused by HCl. Cells exposed to lactic acid showed specific mechanisms of action in addition to sharing many of the mechanisms induced by HCl stress.
Presence of antibiotic-resistant commensal bacteria in samples from agricultural, city, and national park environments evaluated by standard culture and real-time PCR methods
Authors: Yang Hua , Byelashov Oleksandr A. , Geornaras Ifigenia , Goodridge Lawrence D. , Nightingale Kendra K. , Belk Keith E. , Smith Gary C. , Sofos John N.
Published: October 2010

This study examined the presence of antibiotic-resistant commensal bacteria among cattle operations representing areas heavily affected by agriculture, city locations representing areas affected by urban activities and indirectly affected by agriculture, and a national park representing an area not affected by agriculture. A total of 288 soil, fecal floor, and water samples were collected from cattle operations, from the city of Fort Collins, and from Rocky Mountain National Park (RMNP) in Colorado. In addition, a total of 42 new and unused feed, unused bedding, compost, and manure samples were obtained from the cattle operations. Total, tetracycline-resistant, and ceftiofur-resistant bacterial populations were enumerated by both standard culture plating and real-time PCR methods. Only wastewater samples from the cattle operations demonstrated both higher tetracycline-resistant bacterial counts (enumerated by the culture plating method) and tetracycline resistance gene copies (quantified by real-time PCR) compared to water samples collected from non-farm environments. The ceftiofur resistance gene, blaCMY-2, was not detectable in any of the samples, while the tetracycline resistance genes examined in this study, tet(B), tet(C), tet(W), and tet(O), were detected in all types of tested samples, except soil samples from RMNP. Tetracycline resistance gene pools quantified from the tet(O) and tet(W) genes were bigger than those from the tet(B) and tet(C) genes in fecal and water samples. Although only limited resistance genes, instead of a full set, were selected for real-time PCR quantification in this study, our results point to the need for further studies to determine natural and urban impacts on antibiotic resistance.
Plasticity of growth and biomass production of an intraspecific Populus alba family grown at three sites across Europe during three growing seasons
Authors: Marron Nicolas , Ricciotti Luca , Bastien Catherine , Beritognolo Isacco , Gaudet Muriel , Paolucci Isabella , Fabbrini Francesco , Salani Francesco , Dillen Sophie Y. , Ceulemans Reinhart , Pinel Matthieu P.C. , Taylor Gail , Scarascia-Mugnozza Giuseppe , Sabatti Maurizio
Published: October 2010

White poplar ( Populus alba L.) is a native species in Europe, but its growth potential is largely unknown. The general objectives of our study were to determine the impact of contrasted environments across Europe and the influence of parental characteristics on the growth potential of an intraspecific F1white poplar family originating from a cross between parents native from the south and the north of Italy. The growth of the family was monitored at three sites located in the north of Italy, in central France, and in the southern United Kingdom. The family showed a highly superior productivity in Italy. A pronounced plasticity among sites was found for the male parent only. Indeed, for this parent, the highest growth was observed in northern Italy, its area of origin. A positive heterosis was observed mainly in France and in the United Kingdom. Broad-sense heritability values were moderate in most cases. However, the growth of the family was in some cases superior to the one of several other interspecific hybrid families growing under the same conditions, underlying the poorly known growth potential of such intraspecific hybrids for biomass production under European conditions.
Impact du feu sur la structure et la composition floristique d’un peuplement forestier de Côte d’Ivoire et interaction avec les traitements sylvicoles
Authors: Yedmel Memel S. Ch. , Kadio Adjumane A. , Hardy Olivier J. , Kouame N’Guessan François , Barbier Nicolas S.
Published: October 2010

La dynamique structurale et floristique des forêts tropicales humides en réponse aux perturbations reste très méconnue, en dépit des problématiques actuelles de stockage de carbone et de conservation de la biodiversité. Le dispositif de la Téné (Côte d’Ivoire) est un peuplement forestier suivi depuis 1978, afin d’étudier à long terme la dynamique des espèces à potentiel commercial. En 1983, il a été accidentellement parcouru par le feu, et plus de 65 % de la surface totale a été atteinte. L’objectif de cette étude est d’évaluer l’impact des modalités sylvicoles combinées au passage du feu sur la structure et la composition floristique du peuplement. Les variations structurales et floristiques ont été testées respectivement à l’aide d’un simple modèle d’ANCOVA et d’une ordination. Les résultats obtenus montrent que l’impact du feu, en termes de surface brûlée, de structure et de composition floristique, a été significativement accru par les perturbations induites par les traitements sylvicoles. Les modalités sylvicoles supposées bénéfiques à l’accroissement des espèces à potentiel commercial peuvent accroître la susceptibilité aux feux et entraîner à long terme des effets majeurs sur la structure et la composition floristique du peuplement.
Challenging growth–survival trade-off: a key for Acer negundo invasion in European floodplains?
Authors: Saccone Patrick , Brun Jean-Jacques , Michalet Richard
Published: October 2010

We compared the performances of juvenile Acer negundo with those of native species to assess how this species has invaded intermediate habitats along European riparian successional gradients. In the middle Rhône floodplain (France), we measured survival and growth of transplants of the invasive and of three native tree species from contrasted successional status within forests and in experimental gaps and at three positions along a riparian gradient: (i) a highly disturbed Salix – Populus stand, (ii) a moderately disturbed stand dominated by the invasive Acer , and (iii) a mature Fraxinus community. Acer’s growth in the gaps was as high as that of the two native early-successional species, Salix and Populus, and higher than that of the native late-successional Fraxinus. In contrast, Acer survived as well in the shadiest understory conditions of the Fraxinus community as did Fraxinus and better than the two early-successional species. Inconsistent with the resource trade-off of succession theory, Acer showed both a high survival in the shade and a high growth in full light. This particular suite of traits shared with other invasive and native Acer species could be an example of adaptive plasticity that certainly represents an advantage to give it a competitive advantage over native species.
Effects of two Ca fertilizer types on sugar maple vitality
Authors: Moore Jean-David , Ouimet Rock
Published: October 2010

Over the last decades, continuous signs of sugar maple ( Acer saccharum Marsh.) dieback in stands of northeastern North America have promoted the experimentation of corrective measures to restore sugar maple vitality. To verify the hypothesis that K–Mg antagonism may have limited the full response of sugar maple to dolomitic lime application in a previous experiment (CaMg(CO3)2, 12% Mg), two Ca fertilizers (CaCO3 and CaSO4·2H2O), having negligible Mg content, were applied at rates of 1, 2, and 4 t Ca·ha–1 on sugar maple trees adjacent to the limed area. After 3 years, most of the foliar nutrient concentrations of treated trees were improved, particularly Ca, for both Ca fertilizers, in line with published ranges for healthy sugar maple trees, except for Mg. Moreover, no persistent nutrient antagonism was observed. The crown dieback rate of treated sugar maple was ≤5.8% after 3 years, while it reached 12% for the controls. Also, relative basal area growth showed that both Ca sources can improve growth rate. Growth response following Ca treatments was, however, lower than for the former lime experiment after the same period of time. In this context, our results suggest that Mg nutrition could be more important for sugar maple in this ecosystem than initially thought.
Natural and logging disturbances in the temperate rain forests of the Central Coast, British Columbia
Authors: Pearson Audrey F.
Published: October 2010

Natural disturbances frame the spatial and temporal processes of ecosystems and are the foundation for ecosystem-based management. In the coastal temperate rain forests of British Columbia, landscape patterns of natural disturbances and their contrasts with logging are not well documented. Stand-replacing disturbances over the past 140 years were investigated for the Central Coast (1.5 million ha) at regional and local scales using a combination of aerial photograph interpretation and forest management GIS databases. At the regional scale, stand-replacing natural disturbances affected 3.1% of the forested area. The extent of natural disturbances was not strongly affected by the scale of analysis. In contrast, spatial pattern and scale were essential for discerning the full impact of logging. At the regional scale, logging affected 5.4% of the forested area. Within watersheds, however, logging occurred primarily in valley bottoms (81% ± 4%) with 59% ± 10% of valley bottom areas logged, 10 times the area of natural disturbances. Watershed size strongly affected riparian zones, with active floodplains comprising 53% ± 5% of valley bottom area in large (>20 000 ha) watersheds. In physiographically diverse landscapes, geomorphic features (such as watersheds, valley bottoms, and fluvial landforms) are crucial for determining disturbance processes and effects of logging at ecologically relevant scales.
Linear mixed-effects models for estimating biomass and fuel loads in shrublands
Authors: Pearce H.G. , Anderson W.R. , Fogarty L.G. , Todoroki C.L. , Anderson S.A.J.
Published: October 2010

Shrubland biomass is important for fire management programmes and for carbon estimates. Aboveground biomass and the combustible portion of biomass, the fuel load, in the past have been measured using destructive techniques. These techniques are detailed, highly labour intensive, and costly; hence, an alternative approach was sought. The new approach used linear mixed-effects models to estimate biomass and fuel loads from easily measured field variables: shrub overstorey height and cover, and understorey height and cover. Site was regarded as a random effect. Sampling sites were located throughout New Zealand and included a range of shrubland vegetation types: manuka ( Leptospermum scoparium J.R. Forst. et G. Forst.) and kanuka ( Kunzea ericoides (A. Rich.) J. Thomps.) scrub and heath, pakihi (mixed low heath, fern, and rushes), and gorse ( Ulex europaeus L.). The approach was extended and confidence intervals were constructed for the regression models. Statistical analysis showed that understorey height and overstorey cover were significant (at the 5% level) in some cases. Overstorey height was highly significant in all cases (p < 0.0001), allowing development of models useful to the operational user. The models allow rapid estimation of average fuel loads or biomass on new sites, and double sampling theory can be applied to calculate the error in the resultant biomass estimate.
Regional changes of Pinus pinaster site index in Spain using a climate-based dominant height model
Authors: Bravo-Oviedo Andrés , Gallardo-Andrés Clemente , del Río Miren , Montero Gregorio
Published: October 2010

This study compares two site index estimations for Mediterranean maritime pine ( Pinus pinaster Ait.) stands in the Iberian Peninsula. The first prediction was performed under the assumption of constant climate conditions, whereas the second one used foreseen climate according to an energy-use increment and high population growth (IPCC’s A2 emission scenario). We used an existing climate-based dominant height model that incorporates temperature, seasonal precipitation in winter and autumn, and drought length as driver variables for dominant height growth. Climate attributes were retrieved from eight regional climate models nested in the same atmospheric–ocean global circulation model. Forest stand data from 188 experimental plots in four natural regions were used to compare regional climate change trends. Results indicated a climate-related diminishing trend of site index values, although some regional differences were evident. In the northern stands, the negative effects were not observed, and in some cases, forest productivity increased on low site index classes. Conversely, in the southernmost stands, there is a significant decrease in the site index across all productivity classes. Western and eastern stands also showed a decreasing trend but to a lesser extent. Our results confirm the vulnerability of stands to warmer and drier climate conditions in the southern Mediterranean region in relation to wood productivity.
Long fire cycle in northern boreal Pinus forests in Finnish Lapland
Authors: Wallenius T. H. , Kauhanen H. , Herva H. , Pennanen J.
Published: October 2010

Knowledge of past forest fire regimes is important for developing management plans for conservation areas and for predicting the probable effects of forest management and climate change on the structure and dynamics of forests. In this study, fire scars on living and dead trees were systematically sampled on 256 study plots in three landscapes in northeastern Finland dominated by Scots pine ( Pinus sylvestris L.). A total of 1030 disks or partial cross sections from different trees, including scars from 98 distinct forest fires, were dendrochronologically dated with an accuracy of 1 year or better. The extraordinarily well-preserved old Pinus snags and stumps allowed us to reconstruct annual tree-ring and fire chronologies beginning from the year AD 653. The fire cycles in the studied landscapes were exceptionally long for a boreal region dominated by Pinus, on average 350 years during the last millennium. This demonstrates that the fire regimes of poorly studied remote regions cannot be extrapolated from fire regimes of sites examined in more detail. Based on statistics on lightning-ignition densities, we suggest that most of the fires detected in this study were ignited by humans. The reconstructed past fire cycles were probably shortened by human influence.
Allometric models for predicting the aboveground biomass of Canada yew (Taxus canadensis Marsh.) from visual and digital cover estimates
Authors: Quint Thomas C. , Dech Jeffery P.
Published: October 2010

The objectives of this study were to evaluate visual and digital estimates of percent cover as source data and to develop cover-based allometric models for the prediction of aboveground biomass of Canada yew ( Taxus canadensis Marsh.). Cover was determined from visual assessment and digital images captured over 25 plots (1 m2) at a model training site near Timmins, Ontario. Linear and power functions were fit to the cover–biomass data to develop models of foliage, stem, and total aboveground biomass. Both sources of cover data produced models that explained between 70% and 85% of the variance in the training data, with root mean square error estimates ranging from 27 g·m–2 (foliage) to 85 g·m–2 (total). Models based on visual cover data performed consistently better and were tested on independent data. Stem and total biomass were underestimated in the model testing data set; however, prediction statistics indicated that the linear and power forms of foliage biomass models were validated by the testing data. Final models of foliage biomass were developed from the entire data set, with mean absolute errors of 18.3 and 18.7 g·m–2 for the linear and power forms, respectively. Additional variables (e.g., plant height, age) may be required to provide general predictions of the woody biomass of Canada yew.
Extracellular glutamate alters mature osteoclast and osteoblast functions
Authors: Seidlitz Eric P. , Sharma Mohit K. , Singh Gurmit
Published: October 2010

Glutamatergic intercellular communication is involved in many aspects of metabolic homeostasis in normal bone. In bone metastasis, the balance between bone formation and degradation is disrupted. Although the responsible mechanisms are not clear, we have previously identified that cancer cell lines used in bone tumour models secrete glutamate, suggesting that tumour-derived glutamate may disrupt sensitive signalling systems in bone. This study examines the role of glutamate in mature osteoclastic bone resorption, osteoblast differentiation, and bone nodule formation. Glutamate was found to have no effect on the survival or activity of mature osteoclasts, although glutamate transporter inhibition and receptor blockade increased the number of bone resorption pits. Furthermore, transporter inhibition increased the area of resorbed bone while significantly decreasing the number of osteoclasts. Alkaline phosphatase activity and extracellular matrix mineralization were used as measurements of osteoblast differentiation. Glutamate significantly increased osteoblast differentiation and mineralization, but transport inhibitors had no effect. These studies support earlier findings suggesting that glutamate may be more important for osteoclastogenesis than for osteoclast proliferation or functions. Since glutamate is capable of changing the differentiation and activities of both osteoclast and osteoblast cell types in bone, it is reasonable to postulate that tumour-derived glutamate may impact bone homeostasis in bone metastasis.
Habitat selection at multiple spatial scales in Northern Map Turtles (Graptemys geographica)
Authors: Carrière M.-A. , Blouin-Demers G.
Published: October 2010

Understanding habitat use of declining species is essential for their management and successful recovery. We examined habitat selection at multiple spatial scales by Northern Map Turtles ( Graptemys geographica (Le Sueur, 1817)), a species at risk, in the St. Lawrence Islands National Park, Ontario, Canada. At the scale of the home range, Map Turtles generally avoided deep water (>2 m) and selected home ranges in waters <1 m deep. Importantly, turtles used home ranges with significantly more natural than developed shoreline. At the scale of the location, adult females used deep water more often and males preferred areas with surface cover. Management efforts should implement regulations concerning further shoreline development.
Morphometrics of the eyes and orbits of the nocturnal Swallow-tailed Gull (Creagrus furcatus)
Authors: Iwaniuk Andrew N. , Heesy Christopher P. , Hall Margaret I.
Published: October 2010

The Swallow-tailed Gull ( Creagrus furcatus (Neboux, 1846)) is known for its nocturnal feeding habits and apparently large eyes. Despite frequent observations of its large eyes, detailed measurements of its eyes and orbits are wanting. Here, we provide a detailed analysis of the size and shape of the eye and orbits of this unique species in relation to a range of other gull species. Although the C. furcatus does have a slightly enlarged cornea and optical axis, neither the transverse orbit diameter nor the shape of its eye differs significantly from other larids. In addition, we found no significant difference between C. furcatus and other gulls in terms of its orbit dimensions and orbit orientation. We therefore conclude that C. furcatus does not possess a transversely enlarged eye, but rather a slightly larger cornea and longer eye. Our results do not, however, preclude the presence of other changes in the visual system, such as retinal morphology or neurophysiology, that could be adaptive for nocturnal feeding.