bluuebunny/crossref_metadata_2025 huggingface dataset:
The haptenation theory of vitiligo and melanoma rejection: a close‐up
Authors: Westerhof Wiete , Manini Paola , Napolitano Alessandra , d’Ischia Marco
Published: January 2011

Abstract: The ‘Haptenation theory’ concerns the multicausal pathogenesis of vitiligo ending ultimately in the (partial) disappearance of melanocytes from the skin and/or hairs. The melanocyte specificity is attributed to the tyrosinase‐catalysed production of haptogenicortho‐quinones that covalently bind to tyrosinase or other melanosomal proteins to generate neo‐antigens. These latter, in turn, trigger an immunological cascade resulting in a melanocyte‐specific delayed‐type hypersensitivity reaction that eliminates melanocytes and produces the characteristic depigmentation. This causal chain of events is critically discussed with special reference to factors modifying the process and the possible influence of various biochemical changes, such as raised levels of catecholamines and epidermal hydrogen peroxide, which have been reported to be associated with the onset of vitiligo. This all adds up to the typical vitiligo reaction pattern or syndrome, which demands a treatment strategy involving most of the already known therapies. Similar pathogenetic mechanisms might be engaged in the enhancement of cellular immunity (vaccination) against melanoma.
Filaggrin knockdown and Toll‐like receptor 3 (TLR3) stimulation enhanced the production of thymic stromal lymphopoietin (TSLP) from epidermal layers
Authors: Lee Kyung Ho , Cho Kyung‐Ah , Kim Ji‐Yoon , Kim Jin‐Young , Baek Ji‐Hae , Woo So‐Youn , Kim Jin‐Woo
Published: January 2011

Abstract:  Keratinocytes constitute the first‐line barrier against exogenous antigens and contain Toll‐like receptors (TLRs), which function as pattern‐recognition molecules to activate antimicrobial innate immune responses. In an effort to ascertain whether or not filaggrin (filament‐aggregating protein) expression affected the TLR‐mediated responses of keratinocytes, we transfected filaggrin siRNA into HaCaT human keratinocyte cells and determined that thymic stromal lymphopoietin (TSLP) and IL‐6 secretion were increased by poly(I:C) stimulus. Additionally, TSLP expression is increased in filaggrin knockdown as well as TLR3 stimulation in reconstituted human epidermal layers. Therefore, the findings of this study show that reduced filaggrin levels may influence innate immune responses via TLR stimuli and may contribute to the pathogenesis of inflammatory skin disease via TSLP expression.
Tight junction proteins and the epidermis
Authors: O’Neill Catherine A. , Garrod David
Published: January 2011

Abstract:  Epithelia are found at the interfaces between body compartments where they act as selective permeability barriers that maintain the unique composition of the compartments on either side. Epithelial barrier function is dependent on tight junctions (TJs), which seal the intercellular or paracellular spaces but may permit selective permeability. In simple epithelia (one cell thick), the function of TJs is relatively well understood. By contrast, our understanding of TJ structure and function in stratified epithelia (e.g. the epidermis) is limited. This article briefly discusses what is known about TJs and their components in simple epithelia and speculates about their roles in the epidermis.
New developments in fluorescence diagnostics
Authors: Hegyi Juraj , Hegyi Vladimir , Ruzicka Thomas , Arenberger Petr , Berking Carola
Published: January 2011

In the last decade, significant advances have been achieved in the direct viewing of the skin. Non‐invasive analysis of various skin diseases in vivo has become possible by special skin display devices, allowing the physician to view the structure and properties of the skin in greater detail than can be achieved by simple visual examination. We review the last 100 years of fluorescence imaging development from clinical observation to advanced spectral imaging, addressing the role of fluorescence diagnostics (FD) in modern dermatology as well as the detection of autofluorescence.
2‐Amino‐nonyl‐6‐methoxyl‐tetralin muriate activity againstCandida albicansaugments endogenous reactive oxygen species production – a microarray analysis study
Authors: Liang Rong Mei , Yong Xiao Lan , Jiang Yun Ping , Tan Yong Hong , Dai Bao Di , Wang Shi Hua , Hu Ting Ting , Chen Xi , Li Nan , Dong Zhao Hui , Huang Xiao Chun , Chen Jun , Cao Yong Bing , Jiang Yuan Ying
Published: January 2011

Candidainfections have become an increasingly significant problem, mainly because of the widespread nature ofCandidaand drug resistance. There is an urgent need to develop new classes of drugs for the treatment of opportunisticCandidainfections, especially in medically complex patients. Previous studies have confirmed that 2‐amino‐nonyl‐6‐methoxyl‐tetralin muriate (10b) possesses powerful antifungal activityin vitroagainstCandia albicans. To clarify the underlying action mechanism, an oligonucleotide microarray study was performed inC. albicansSC5314 without and with 10b treatment. The analytical results showed that energy metabolism‐related genes, including glycolysis‐related genes (PFK1, CDC19andHXK2), fermentation‐related genes (PDC11,ALD5andADH1) and respiratory electron transport chain‐related genes (CBP3, COR1andQCR8), were downregulated significantly. Functional analysis revealed that 10b treatment increased the generation of endogenous reactive oxygen species, and decreased mitochondrial membrane potential, ubiquinone–cytochrome creductase (complex III) activity and intracellular ATP levels inC. albicansSC5314. Also, addition of the antioxidant ascorbic acid reduced the antifungal activity of 10b significantly. These results suggest that mitochondrial aerobic respiration shift and endogenous reactive oxygen species augmentation might contribute to the antifungal activity of 10b againstC. albicans. This information may prove to be useful for the development of new strategies to treatCandidainfections.
Factor‐inhibiting hypoxia‐inducible factor (FIH) catalyses the post‐translational hydroxylation of histidinyl residues within ankyrin repeat domains
Authors: Yang Ming , Chowdhury Rasheduzzaman , Ge Wei , Hamed Refaat B. , McDonough Michael A. , Claridge Timothy D. W. , Kessler Benedikt M. , Cockman Matthew E. , Ratcliffe Peter J. , Schofield Christopher J.
Published: January 2011

Factor‐inhibiting hypoxia‐inducible factor (FIH) is an Fe(II)/2‐oxoglutarate‐dependent dioxygenase that acts as a negative regulator of the hypoxia‐inducible factor (HIF) by catalysing β‐hydroxylation of an asparaginyl residue in its C‐terminal transcriptional activation domain (CAD). In addition to the hypoxia‐inducible factor C‐terminal transcriptional activation domain (HIF‐CAD), FIH also catalyses asparaginyl hydroxylation of many ankyrin repeat domain‐containing proteins, revealing a broad sequence selectivity. However, there are few reports on the selectivity of FIH for the hydroxylation of specific residues. Here, we report that histidinyl residues within the ankyrin repeat domain of tankyrase‐2 can be hydroxylated by FIH. NMR and crystallographic analyses show that the histidinyl hydroxylation occurs at the β‐position. The results further expand the scope of FIH‐catalysed hydroxylations.

Database
 The coordinates for the structure have been deposited in the Protein Data Bank in Europe (PDBe; http://www.ebi.ac.uk/pdbe) under accession code 2y0i

Structured digital abstract

FIH
and TNKS‐1 hydroxylate by enzymatic study (View Interaction 1, 2)

FIH
and Tankyrase‐2 bind by x‐ray crystallography (View interaction)

FIH
and Tankyrase‐2 hydroxylate by enzymatic study (View Interaction 1, 2, 3)

FIH
and TRPV4 hydroxylate by enzymatic study (View interaction)

GABPB2
and FIH hydroxylate by enzymatic study (View interaction)
Permanent Genetic Resources added to Molecular Ecology Resources Database 1 October 2010–30 November 2010
Authors:   Molecular Ecology Resources Primer Development Consortium, AGOSTINI CECILIA , AGUDELO P. A. , BÂ K. , BARBER P. A. , BISOL PAOLO MARIA , BROUAT C. , BURGESS TREENA I. , CALVES I. , CARRILLO AVILA MAURICIO , CHOW S. , CORDES LISA , DA SILVA D. , DALECKY A. , DE MEESTER L. , DOADRIO IGNACIO , DOBIGNY G. , DUPLANTIER J. M. , EVISON SOPHIE E. F. , FORD REBECCA , FRESNEAU DOMINIQUE , GALETTI PEDRO M. , GAUTHIER P. , GELDOF S. , GRANJON L. , GUÉRIN F. , HARDY GILES E. , HERNANDEZ ESCOBAR CARLOS , HIMA K. , HU JUAN , HUANG LUQI , HUMEAU L. , JANSEN B. , JAQUEMET S. , JIANG ZHI‐QIANG , JUNG SUNG‐JU , KIM BONG‐SEOK , KIM CHEOL‐HEE , KIM JONG‐OH , LAI CHOAY‐HOONG , LAROCHE J. , LAVERGNE E. , LAWTON‐RAUH A. , LE CORRE M. , LEACH M. M. , LEE JEHEE , LEO AUDREY E. , LICHTENZVEIG JUDITH , LIN LIN , LINDE CELESTE C. , LIU SHU‐FANG , MARINO ILARIA A. M. , McKEOWN NIALL J. , NOHARA K. , OH MYUNG‐JOO , OKAMOTO H. , OLIVER RICHARD , OLIVERA ANGEL MARTHA , ORNELAS‐GARCÍA CLAUDIA PATRICIA , ORSINI L. , OSTOS ALFONSO HENRY , OTHMAN A. S. , PAPETTI CHIARA , PATARNELLO TOMASO , PEDRAZA‐LARA CARLOS , PILLER KYLE R. , POTEAUX CHANTAL , REQUIER J.‐B. , ROZIANA M. K. , SEMBA Y. , SEMBENE M. , SHAH RAMISAH M. , SHAHRIL A. R. , SHAO AIJUAN , SHAW PAUL W. , SONG LIANGKE , SOUZA FERREIRA RONARA , SU YONG‐QUAN , SUZUKI N. , TATARD C. , TAYLOR KATHERINE M. , TAYLOR PAUL W. J. , THIAM M. , VALBUENA RUBEN , WANG HE , YANG BYUNG‐GYOO , YUAN QINGJUN , ZAJONZ U. , ZANE LORENZO , ZHU LING , ZHUANG ZHI‐MENG , ZULAIHA A. R.
Published: January 2011

This article documents the addition of 277 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Ascochyta rabiei, Cambarellus chapalanus, Chionodraco hamatus, Coptis omeiensis, Cynoscion nebulosus, Daphnia magna, Gerbillus nigeriae, Isurus oxyrinchus, Lates calcarifer, Metacarcinus magister, Oplegnathus fasciatus, Pachycondyla verenae, Phaethon lepturus, Pimelodus grosskopfii, Rotylenchulus reniformis, Scomberomorus niphonius, Sepia esculenta, Terapon jarbua, Teratosphaeria cryptica and Thunnus obesus. These loci were cross‐tested on the following species: Austropotamobius italicus, Cambarellus montezumae, Cambarellus puer, Cambarellus shufeldtii, Cambarellus texanus, Chionodraco myersi, Chionodraco rastrospinosus, Coptis chinensis, Coptis chinensis var. brevisepala, Coptis deltoidea, Coptis teeta, Orconectes virilis, Pacifastacus leniusculus, Pimelodus bochii, Procambarus clarkii, Pseudopimelodus bufonius, Rhamdia quelen, Sepia andreana, Sepiella maindroni, Thunnus alalunga, Thunnus albacares, Thunnus maccoyii, Thunnus orientalis, Thunnus thynnus and Thunnus tonggol.
Damping of Heat Exchanger Tubes in Liquids: Review and Design Guidelines
Authors: Pettigrew M. J. , Rogers R. J. , Axisa F.
Published: January 2011

This paper addresses the question of damping of multispan heat exchanger tubes with liquids (mostly water) on the shell side. The different energy dissipation mechanisms that contribute to damping are investigated. The available experimental data from the literature and from our own measurements are reviewed and analyzed. Three important energy dissipation mechanisms emerge. These are viscous damping between the tube and liquid, squeeze-film damping in the clearance between the tube, and support and friction damping at the support. Viscous damping only accounts for approximately 25% of the total damping of a typical tube. Thus, about 75% of the damping energy is dissipated at the support. Squeeze-film damping appears to be the most important energy dissipation mechanism. Squeeze-film damping is related to the support width and is inversely proportional to the tube frequency. Damping is formulated in terms of tube and tube-support parameters. Semi-empirical formulations for damping of heat exchanger tubes in liquids are recommended for design purposes.
Theoretical Determination of Modal Damping Ratio of Sloshing Using a Variational Method
Authors: Utsumi M.
Published: January 2011

This paper investigates a variational method for theoretically determining the first damping ratio of sloshing in cylindrical and arbitrary axisymmetric tanks. In this method, a virtual work expression for the viscous terms in the Navier–Stokes equations is transformed into the first-mode damping term, thereby extending Hamilton’s principle for nonviscous sloshing to a variational principle of viscous sloshing. By applying the Galerkin method to the variational principle, a computationally efficient analysis is conducted. For arbitrary axisymmetric tanks, a method for reducing the influence of the change in the fluid velocity boundary condition on the damping estimation is investigated. The proposed method provides theoretical foundations for past empirical results for cylindrical and spherical tanks.
Effect of Transitions in the Water Table and Soil Moisture Content on the Cathodic Protection of Buried Pipelines
Authors: King Fraser , Given Russell , Worthingham Robert G. , Van Boven Greg
Published: January 2011

Buried pipelines can be subject to transitional environments due to changes in soil type or moisture content. Changes in the height of the water table, for example, will affect not only the availability of water but also the access of oxygen to the pipe surface. Transitions between different soil types will also result in different exposure conditions for different parts of the pipe. These variations can affect the distribution of potential on the pipe surface and the ability of the CP system to provide adequate protection. A combination of laboratory-scale soil box tests and field measurements on operating pipelines has been used to study the effect of varying moisture content and water level on the level of cathodic protection and on pipe-depth environmental conditions. In both laboratory tests and field trials, the degree of protection was found to depend on the availability of cathodic reactants (O2 and/or H2O). Ingress of O2 results in a positive shift in potential as more current is required to electrochemically reduce the oxidant and the pipe is less easily polarized. Under some circumstances, the ingress of water has the same effect. Although more aerobic conditions lead to more positive potentials, the pipe is not necessarily less well protected. In many dry and/or high resistivity soils, the pipe surface may well be passive because of the high interfacial pH and/or high O2 concentration.
Materials Databases and Knowledge Management for Advanced Nuclear Technologies
Authors: Hoffelner Wolfgang
Published: January 2011

International collaborations like the generation IV initiative have the aim to create the technical basis for design and operation of advanced nuclear plants. Materials data shall be created in joint international materials projects. Data will be aggregated in databases like the “Generation IV Materials Handbook.” Mechanical data, and microstructural information and information concerning materials production shall be included. This information will be used to create or amend code rules, to provide a basis for life-time analysis, damage assessments, and for safety analyses. Such considerations need not only raw materials data but also tools for data analysis and evaluation. Multiscale modeling, establishing constitutive equations, development of advanced life-time prediction methods, quantitative correlation of mechanical properties with microstructure, quantification of environmental effects, tools for nondestructive evaluation, and condition based monitoring are important analysis techniques needed for safe design and operation of advanced plants. These needs led the author to ask the question if current databases could not be enlarged by data evaluation and methods tools, which could even end some day in the availability of web-based design codes and safety analyses. The database could also be used as a web-based discussion and development space. It could become then a powerful tool for knowledge management. This paper will discuss this concept based on some examples.
A Bacterial Protein Targets the BAHD1 Chromatin Complex to Stimulate Type III Interferon Response
Authors: Lebreton Alice , Lakisic Goran , Job Viviana , Fritsch Lauriane , Tham To Nam , Camejo Ana , Matteï Pierre-Jean , Regnault Béatrice , Nahori Marie-Anne , Cabanes Didier , Gautreau Alexis , Ait-Si-Ali Slimane , Dessen Andréa , Cossart Pascale , Bierne Hélène
Published: January 2011

A virulence factor secreted by
Listeria monocytogenes
induces expression of interferon-stimulated genes
Development of a forest structural complexity index based on multispectral airborne remote sensing and topographic dataThis article is one of a selection of papers from Extending Forest Inventory and Monitoring over Space and Time.
Authors: Pasher Jon , King Douglas J.
Published: January 2011

This paper presents development of a multivariate forest structural complexity index based on relationships between field-based structural variables and geospatial data. Remote sensing has been widely used to model individual forest structural attributes at many scales. As opposed to, or in addition to, individual structural parameters such as leaf area index or tree height, overall structural complexity information can enhance forest inventories and provide a variety of information to forest managers, including identifying damage and disturbance as well as indicators of habitat or biodiversity. In this study, a multivariate modelling technique, redundancy analysis, was implemented to derive a model incorporating both horizontal and vertical structural attributes as predicted by an ensemble of high-resolution multispectral airborne imagery and topographic variables. The first redundancy analysis axis of the final model explained 35% of the total variance of the field variables and was used as the complexity index. With a root mean squared error of 19.9%, the model was capable of differentiating four to five relative levels of complexity. This paper presents the forest ecological and modelling aspects of the research. A related paper presents the remote sensing aspects, including application of the model to map predicted structural complexity, map validation, and testing of the method at multiple scales.
Penalized regression techniques for prediction: a case study for predicting tree mortality using remotely sensed vegetation indicesThis article is one of a selection of papers from Extending Forest Inventory and Monitoring over Space and Time.
Authors: Lazaridis David C. , Verbesselt Jan , Robinson Andrew P.
Published: January 2011

Constructing models can be complicated when the available fitting data are highly correlated and of high dimension. However, the complications depend on whether the goal is prediction instead of estimation. We focus on predicting tree mortality (measured as the number of dead trees) from change metrics derived from moderate-resolution imaging spectroradiometer satellite images. The high dimensionality and multicollinearity inherent in such data are of particular concern. Standard regression techniques perform poorly for such data, so we examine shrinkage regression techniques such as ridge regression, the LASSO, and partial least squares, which yield more robust predictions. We also suggest efficient strategies that can be used to select optimal models such as 0.632+ bootstrap and generalized cross validation. The techniques are compared using simulations. The techniques are then used to predict insect-induced tree mortality severity for a Pinus radiata D. Don plantation in southern New South Wales, Australia, and their prediction performances are compared. We find that shrinkage regression techniques outperform the standard methods, with ridge regression and the LASSO performing particularly well.
Congruence between parental reproductive investment and success determined by DNA-based pedigree reconstruction in conifer seed orchards
Authors: Funda Tomas , Liewlaksaneeyanawin Cherdsak , Fundova Irena , Lai Ben S.K. , Walsh Chris , Van Niejenhuis Annette , Cook Cathy , Graham Hilary , Woods Jack , El-Kassaby Yousry A.
Published: January 2011

Seed orchards’ parental reproductive success is often assessed through surveys of seed- and pollen-cone production (reproductive investment). Although the reliability of this approach has been questioned, its speed and ease made it the method of choice for providing approximate estimates for the genetic quality and quantity of seed orchard crops. In this study, reproductive investment data from various female and male phenotypic assessment methods from three seed orchards (lodgepole pine ( Pinus contorta Dougl. ex. Loud. var. latifolia Engelm.), Douglas-fir ( Pseudotsuga menziesii (Mirb.) Franco), and western larch ( Larix occidentalis Nutt.)) were compared with reproductive success estimates based on DNA fingerprinting and parentage analyses. The use of reproductive investment as a proxy to reproductive success on estimating seed crop’s volume genetic worth and diversity (measured by effective number of parents) was evaluated. Regression analyses indicated that the phenotypic assessment methods reflect the true parental reproductive success and that estimates of seed- and pollen-cone volume production appear to be the most appropriate indicators of female and male reproductive success, respectively. Although the best combination of female–male survey methods produced inflated effective number of parents estimates, the genetic worth estimates were similar to those based on DNA, highlighting their robustness to fertility variation assessment.
Stand development following precommercial thinning and fertilization treatments in a western redcedar (Thuja plicata) dominated forest
Authors: Harrington Constance A. , Devine Warren D.
Published: January 2011

Western redcedar (Thuja plicata Donn ex D. Don.) is an important North American tree species, but little information is available on its long-term responses to silvicultural treatments. Stand responses (mortality, ingrowth, basal area and volume growth, and distributions of trees by diameter and height classes) were followed for 25 years after thinning and fertilization treatments (alone and in combination) were applied to a naturally regenerated, low site quality western redcedar stand on the Olympic Peninsula in western Washington, USA. Mortality was low overall, but the densest stands experienced competition-related mortality. Thinning resulted in additional stem recruitment; after 25 years, the number of ingrowth trees exceeded the number of trees in the cohort left after thinning. Fertilization (with nitrogen and phosphorus) flattened size distributions and skewed them to larger size classes. Thinning plus fertilization resulted in the largest individual trees and the most large trees, but also many trees in a wide range of diameter classes. The recruitment of a second cohort did not result in a two-storied stand. Fertilization without thinning resulted in the greatest stand basal area and volume, as well as trees with fewer live lower branches.
Model-assisted estimation of biomass in a LiDAR sample survey in Hedmark County, NorwayThis article is one of a selection of papers from Extending Forest Inventory and Monitoring over Space and Time.
Authors: Gregoire Timothy G. , Ståhl Göran , Næsset Erik , Gobakken Terje , Nelson Ross , Holm Sören
Published: January 2011

Inasmuch as LiDAR is becoming an increasingly prominent tool for forest inventory, it is timely to develop a framework to understand the statistical properties of LiDAR-based estimates. A model-assisted approach to estimation and inference when using LiDAR as a tool to inventory aboveground forest biomass is presented. An empirical example is also presented, yet the article’s focus is largely methodological. The sampling plan in the example is viewed as a two-stage design, with slightly different primary sampling units between the profiling and scanning laser surveys. A regression estimator is presented that uses biomass data from the Norwegian National Forest Inventory as the response variable and laser-derived variables as covariates. A major thrust of this article is the presentation of the variance of the estimators of total biomass and biomass per hectare as well as variance estimators.
Economic modeling of woody biomass utilization for bioenergy and its application in central Appalachia, USA
Authors: Wu Jinzhuo , Wang Jingxin , McNeel Joseph
Published: January 2011

A mixed integer programming model was developed to estimate the delivered cost of woody biomass, including the costs associated with stumpage, bundling (if any), extraction, storage, loading and hauling, and chipping–grinding under different woody biomass handling systems. The model was designed to optimize a woody biomass based biofuel facility’s location with the objective of minimizing the total annual delivered cost of woody biomass under resource and operational constraints. The model was applied in the central Appalachian region within the state of West Virginia. Results showed that the optimal plant location would be at Addison or Grantsville in West Virginia, depending on the system used when daily demand is 900 tonnes of dry woody biomass. For that base-case scenario, the average delivered cost ranged from $2.30·GJ–1to $3.02·GJ–1across the systems. Extensive sensitivity analysis was performed under different scenarios, including biomass availability and purchase–stumpage price, demand, extraction distance, and fuel pricing. The delivered cost was mostly affected by woody biomass demand. Skidding distance had the least impact on the delivered cost. The results would be useful in facilitating the research and economic development of woody biomass utilization for bioenergy in the region.
Root morphological plasticity and biomass production of two Chinese fir clones with high phosphorus efficiency under low phosphorus stress
Authors: Wu Pengfei , Ma Xiangqing , Tigabu Mulualem , Wang Chen , Liu Aiqin , Odén Per Christer
Published: January 2011

Available P is the major growth-limiting factor in southern China where Chinese fir ( Cunninghamia lanceolata (Lamb.) Hook.) plantations are increasingly established. Planting P-efficient clones is a viable option to enhance productivity of Chinese fir plantations. Two Chinese fir clones with high P efficiency (M1 and M4) were chosen as the research materials and their adaptive responses to low P stress were examined. The increment in root morphological traits and biomass production of these clones was measured by a sand culture experiment with a heterogeneous P supply. For both clones, P starvation resulted in significantly higher root surface area and root volume but not root length. For clone M4, the mean root diameter was also larger under P deficiency than under normal P supply. Interestingly, the root morphological traits varied substantially within the same root system where the starved roots had higher values for all morphological traits than the nonstarved ones. Phosphorus starvation did not affect shoot and root biomass or the root to shoot ratio, but the whole-plant biomass increment was large under P deficiency for clone M4. In conclusion, the adaptation to low P stress in these clones is attributed to increased P acquisition and utilization efficiencies.
Site index of Sitka spruce (Picea sitchensis) in relation to different measures of site quality in Ireland
Authors: Farrelly Niall , Ní Dhubháin Áine , Nieuwenhuis Maarten
Published: January 2011

To examine the relationships between Sitka spruce (Picea sitchensis (Bong.) Carr.) site index and site quality variables, we sampled 201 Sitka spruce stands covering the entire range of sites supporting the growth of the species in Ireland. Site index varied significantly with climate and climate surrogate variables, some site quality variables, soil physical and chemical properties, edatopes (combinations of soil nutrient and moisture regimes), rotation types, provenance, and fertilizer regimes. We developed a series of models to predict site index using climate, site, soil physical and chemical properties, edaphic variables, and management factors as predictor variables. Soil nutrient regime (SNR) exhibited the strongest relationship of all variables examined in the study, explaining 51% of the variation in site index, with site index increasing with increasing SNR. We found that edaphic variables of soil moisture regime and SNR produced the best prediction of site index. The species showed the best development on fresh to very moist sites, with rich to very rich soil nutrient regimes. We also developed a composite model explaining 62% of the variation in site index and an elevation zone model (>300 m) explaining 74% of the variation in site index.
Dothistroma needle blight and pitch canker: the current and future potential distribution of two important diseases of Pinus species
Authors: Watt Michael S. , Ganley Rebecca J. , Kriticos Darren J. , Manning Lucy K.
Published: January 2011

Globally, pitch canker and Dothistroma needle blight are two of the most important diseases of pine species caused, respectively, by the pathogens Fusarium circinatum Nirenberg & O’Donnell and Dothistroma spp. ( Dothistroma septosporum (Dorog.) Morelet and Dothistroma pini Hulbary). The potential distributions of these two diseases under current global climate have previously been modelled and contrast strongly with each other. In this study, we used the process-based niche model CLIMEX to estimate the potential distribution of both diseases in the 2080s under six scenarios that include three contrasting global climate models, each with moderate and high CO2 emissions. For both diseases, under the future climate scenarios, there was a global reduction in the potentially suitable area. Among the three global climate models, this reduction ranged from 11% to 22% for Dothistroma needle blight and from 39% to 58% for pitch canker. The projected potential ranges of both diseases were significantly reduced for Africa, South America, and Australia. In Asia and North America, substantial reductions in potential area were generally projected for pitch canker, while little change to moderate levels of expansion were projected for Dothistroma needle blight. For Europe and New Zealand, expansion of suitable climate was projected under all climate change scenarios for both diseases.
The effect of tree dimension on the diversity of bark microhabitat structures and bark use in Douglas-fir (Pseudotsuga menziesii var. menziesii)
Authors: Michel Alexa K. , Winter Susanne , Linde Andreas
Published: January 2011

The focus of this study was to investigate the role of tree dimension and associated bark structures for high structural complexity and high natural biodiversity in forest ecosystems. Two-hundred and ninety-one Douglas-fir (Pseudotsuga menziesii var. menziesii (Mirbel) Franco) trees in two regions of the US Pacific Northwest were investigated for the relationship between tree diameter and bark thickness (measured as bark fissure depth) and the relationships of both to bark microhabitats and signs of bark use. Our results emphasize the habitat function of tree bark of large-diameter Douglas-fir trees. Many bark microhabitat types and their total abundance significantly increased with increasing tree diameter and bark thickness. These were bark pockets with and without decaying substrate, bowls in the bark, and signs of bark use, e.g., small holes from woodpecker drillings and large insects, large bark excavations from woodpeckers, spider funnel webs, natural cavities at the stem base without decay, and the occurrence of herb vegetation at the tree base. In forest monitoring, tree diameter may be a good indicator of the number of bark microhabitats and of bark thickness because it is strongly related to both of these variables. However, because of the high variability of bark thickness in large-diameter trees, we suggest monitoring bark fissure depth if an ecological evaluation of Douglas-fir forests is needed.
Long-term effects of nitrogen fertilization on soil chemistry in three Scots pine stands in Sweden
Authors: Ring Eva , Jacobson Staffan , Högbom Lars
Published: January 2011

Adding nitrogen to coniferous forests on mineral soils will increase stem-wood growth in most boreal forests. The addition of nitrogen affects soils and waters as well. This investigation was conducted to evaluate the long-term effects of nitrogen fertilization at different intensities on soil chemistry in nitrogen-limited ecosystems. The study was performed at three experimental sites that were originally established around 1980 in Scots pine ( Pinus sylvestris L.) stands. Fertilization regimes with applications ranging from conceivable commercial rates to very intensive rates (3× 150 kg N·ha–1 up to 12× 150 kg N·ha–1) had been applied. Samples were collected from the FH horizon at all sites and 0–20 cm in the mineral soil at two sites and analyzed for pH and major nutrients. The carbon to nitrogen ratio in the FH horizon decreased with increasing total nitrogen application, while the concentrations and contents of nitrogen and exchangeable magnesium and phosphorus increased. The concentration and contents of exchangeable potassium decreased in both the FH horizon and the mineral soil. In general, larger effects on soil chemistry were observed with increasing fertilization intensity.
An exotic insect and pathogen disease complex reduces aboveground tree biomass in temperate forests of eastern North America
Authors: Busby Posy E. , Canham Charles D.
Published: January 2011

Forests store a large portion of global carbon in tree and soil biomass. However, our understanding of the factors that may reduce rates of forest carbon accumulation is incomplete. This study examines the impact of an exotic insect and fungal pathogen disease on aboveground tree biomass in forests of eastern North America. We determine how beech bark disease (BBD) — a pervasive but nonextirpating disease — influences the growth and survival of its host tree, Fagus grandifolia Ehrh., and the effects of changes in the demography of this late-successional dominant tree species on total stand-level aboveground tree biomass. Our analyses use US Forest Service Forest Inventory and Analysis data from eastern states located along a gradient in the time since introduction of BBD. In Maine, where BBD has been present for >50 years, we observed reduced growth and survival of the host tree and reduced overall stand-level aboveground tree biomass compared with states where BBD arrived more recently. Additionally, there is a negative relationship between host tree abundance and overall stand-level aboveground tree biomass. Where beech is most abundant, BBD results in substantial declines in aboveground tree biomass (e.g., 11% in Maine); where beech is less abundant, we expect more modest declines (1%–4%).
Reply to comment by Gracz on “Wetland drying and succession across the Kenai Peninsula Lowlands, south-central Alaska”Appears in the Can. J. For. Res. 35: 1931–1941.
Authors: Klein Eric S. , Berg Edward E. , Dial Roman
Published: January 2011

Gracz (2011, Can. J. For. Res. 41: 425–428) proposes that the Good Friday earthquake of 1964 caused falling lake levels and drying wetlands on Alaska’s Northern Kenai Lowlands (NKL). His hypothesis states that the earthquake increased hydraulic conductivity by fracturing a leaky confining layer, accelerating drainage of surface water into regional aquifers. We counter that a single model of draining does not apply across the heterogeneity of geomorphology and soils on the NKL. In particular, the NKL’s glacial history precludes uniform application of a subsurface hydrologic model for lake draining and the nature of peat-based wetlands precludes its application to wetland drying. Instead, small, yet cumulative, climatic reductions in moisture surplus explain both observed lake level declines and vegetation changes. Moreover, and unlike a climatic hypothesis, a seismic hypothesis fails to explain lake drying elsewhere in Alaska. Although it is likely that the earthquake influenced some hydrologic features in the NKL, it is unlikely that a single hydrologic model based on a simple mechanical cause, e.g., downward drainage, adequately explains the changes observed across the whole NKL. Conversely, we maintain that the uniformity of the vegetation response seen across different landscapes, including wetlands, forests, and alpine areas, throughout the state of Alaska strongly supports a climatic hypothesis.
Fire severity as a determinant factor of the decomposition rate of fire-killed black spruce in the northern boreal forest
Authors: Boulanger Yan , Sirois Luc , Hébert Christian
Published: January 2011

Several attributes might influence the decomposition process of fire-killed trees. Here, we tested various tree- and plot-level variables on the decomposition rate of fire-killed black spruce ( Picea mariana (Mill.) BSP) in the northern boreal forest. Data were collected from 474 individuals burned 17 years prior to sampling. Mean decomposition rate was relatively slow (k = 0.013) and was lowest for severely burned snags (k = 0.001) and highest for lightly burned logs (k = 0.027–0.036). Vertical position and fire severity were the most important variables influencing the decomposition rates, while plot-level variables were marginally significant. Both predictors strongly influenced the moisture content of fire-killed trees. Logs with greater contact with the ground and lightly burned trees had higher moisture content and faster decomposition rates. Very severely burned trees had lower moisture content because of faster bark shedding. This hampered the decomposition process by slowing the snag falling rate. Higher decomposition rates in lightly burned trees may result from greater colonization by early xylophagous species. By having a considerable impact on the decomposition of woody debris, fire severity may strongly influence many post-fire biological processes related to the woody necromass as well as carbon emission from burned stands.
PSYSTEMS WITH ACTIVE MEMBRANES WORKING IN POLYNOMIAL SPACE
Authors: PORRECA ANTONIO E. , LEPORATI ALBERTO , MAURI GIANCARLO , ZANDRON CLAUDIO
Published: January 2011

We prove that recognizer P systems with active membranes using polynomial space characterize the complexity class PSPACE. This result holds for both confluent and nonconfluent systems, and independently of the use of membrane division rules.
ON THE POWER OF FAMILIES OF RECOGNIZER SPIKING NEURALPSYSTEMS
Authors: SOSÍK PETR , RODRÍGUEZ-PATÓN ALFONSO , CIENCIALA LUDĚK
Published: January 2011

The paper summarizes recent knowledge about computational power of spiking neural P systems and presents a sequence of new more general results. The concepts of recognizer SN P systems and of uniform families of SN P systems provide a formal framework for this study. We establish the relation of computational power of spiking neural P systems with various limitations to standard complexity classes like P , NP, PSPACE and P /poly.
SMALL UNIVERSAL TVDH AND TEST TUBE SYSTEMS
Authors: ALHAZOV ARTIOM , KOGLER MARIAN , MARGENSTERN MAURICE , ROGOZHIN YURII , VERLAN SERGEY
Published: January 2011

We consider the problem of construction of small universal devices based on splicing. Our descriptional complexity measure will be the number of rules present in the system. We present two universal time-varying distributed H systems: of degree 2 with 15 rules and of degree 1 with 17 rules, and also three universal splicing test tube systems with 3 or 2 test tubes and 10 rules.
FUNCTIONS DEFINED BY REACTION SYSTEMS
Authors: EHRENFEUCHT ANDRZEJ , MAIN MICHAEL , ROZENBERG GRZEGORZ
Published: January 2011

Reaction systems are a formal model of interactions between biochemical reactions. They consist of sets of reactions, where each reaction is classified by its set of reactants (needed for the reaction to take place), its set of inhibitors (each of which prevents the reaction from taking place), and its set of products (produced when the reaction takes place) – the set of reactants and inhibitors form the resources of the reaction. Each reaction system defines a (transition) function on its set of states. (States here are subsets of an a priori given set of biochemical entities.) In this paper we investigate properties of functions defined by reaction systems. In particular, we investigate how the power of defining functions depends on available resources, and we demonstrate that with small resources one can define functions exhibiting complex behavior.
ORTHOGONAL SHUFFLE ON TRAJECTORIES
Authors: DALEY MARK , KARI LILA , SEKI SHINNOSUKE , SOSÌK PETR
Published: January 2011

A language L is called the orthogonal shuffle of the language L1 with the language L2, along the trajectory set T if every word in L is uniquely obtained as the shuffle between a word in L1, a word in L2 along a trajectory word in T. In this paper we investigate properties of the orthogonal shuffle on trajectories, as well as several types of language equations using this language operation. As a corollary, we obtain several properties of orthogonal catenation, orthogonal literal shuffle and orthogonal insertion.
Molecular Dynamics Simulation on Longitudinal Optical Phonon Mode Decay and Heat Transport in a Silicon Nano-Structure Covered with Oxide Films
Authors: Zushi Tomofumi , Kamakura Yoshinari , Taniguchi Kenji , Ohdomari Iwao , Watanabe Takanobu
Published: January 2011

A series of molecular dynamics (MD) simulations have been conducted to investigate the heat transport in terms of the phonon dynamics in nanoscale silicon (Si). This work is motivated by a concern over the stagnation of heat at the drain region of nanoscopic transistors, owing to this, a large amount of optical phonons with a low group velocity are emitted from hot electrons, which are ballistically transferred through channel region. The point of this work is the explicit inclusion of the SiO2 film in the MD simulation of the Si lattice. The calculation results show that longitudinal optical (LO) phonons decay faster as Si lattice thickness decreases and turn into acoustic phonons. In contrast, thermal diffusion rate decreases with Si lattice thickness. Both the decay rate of LO phonons and thermal diffusion rate are not governed by oxide thickness. These results imply that the phonon scattering at the SiO2/Si interface is enhanced by thinning the Si layer. In nanoscopic devices, a thin Si layer is effective in diminishing the optical phonons with a low group velocity, but it hinders the subsequent heat transport.
Local Transport Property of GaN Cluster as a Model of Nanowire
Authors: Senami Masato , Ikeda Yuji , Tachibana Akitomo
Published: January 2011

The validity of our local conductivity density analysis method is shown by using a GaN cluster model, which attempts to mimic a GaN nanowire. Conductive properties of this model are investigated by our novel quantity, a local conductive density tensor. For the analysis of nano-materials, such as nanowires, this local quantity is very useful. To use this, electronic current is required to be represented as quantum states. We have developed our new code for this purpose. Conductive states are included as plain waves in the code. We confirm that the local conductivity realizes some reasonable conductive properties, e.g., the conductive path between the nearest atoms. In addition, the rotational behavior of conductivity is found, which appears as complex eigenvalues of a conductivity tensor. This behavior can only be studied by the analysis using the tensor.
Counter-Electrode-Free Thin Cu Film Deposition Based on Ballistic Electron Injection into CuSO4 Solution from Nanosilicon Emitter
Authors: Ohta Toshiyuki , Gelloz Bernard , Koshida Nobuyoshi
Published: January 2011

It is shown that a nanocrystalline silicon (nc-Si) ballistic electron emitter acts as an active electrode in a metal–salt solution (such as CuSO4 solution). The nc-Si emitter is composed of a thin Au film (10 nm thick), anodized polycrystalline layer (1 µm thick), and single-crystalline n+-Si substrate. In accordance with the results of an analysis by cyclic-voltammogram measurements under the standard three-electrode configuration, the electron injection effect into the solution is clearly observed at a potential within the electrochemical window where no electrolytic reactions appear. When the nc-Si emitter is driven alone in a CuSO4 solution without using any counter electrodes, a polycrystalline thin Cu film is uniformly formed on the emitting surface. This is presumably due to the preferential reduction of Cu2+ ions at the interface by injected energetic electrons. The observed deposition mode is different from both the conventional electroplating and electroless plating. This technique is an alternative low-temperature wet process that will be applicable to the deposition of various thin metal films.
Interface-Controlled Self-Align Source/Drain Ge p-Channel Metal–Oxide–Semiconductor Field-Effect Transistors Fabricated Using Thermally Oxidized GeO2Interfacial Layers
Authors: Nakakita Yosuke , Nakakne Ryosho , Sasada Takashi , Takenaka Mitsuru , Takagi Shinichi
Published: January 2011

We have successfully fabricated high hole mobility Ge p-channel metal–oxide–semiconductor field-effect transistors (p-MOSFETs) with GeO2/Ge formed by direct thermal oxidation, which can yield a significantly low interface trap density (Dit). Al2O3films are employed as capping layers for protecting the GeO2/Ge MOS interfaces during the MOSFET fabrication processes. The source/drain (S/D) regions are formed by boron ion implantation in a self-align way with Al gate metal. The good MOS interface properties are found to be maintained even after the activation annealing at temperatures sufficient for obtaining the excellent junction properties. The fabricated MOSFETs exhibit high source and drain on/off current ratios of 105–104and a high peak hole mobility of 575 cm2V-1s-1at maximum, both of which are attributable to the excellent GeO2/Ge MOS interface properties. The effects of the substrate impurity concentration and the thickness of GeO2on the hole mobility are examined. It is found from the results for different substrate impurity concentrations that the universal curve between hole mobility and the effective fieldEeffholds for η= 1/3. We also investigate the impact of the oxidation temperature dependence on hole mobility in order to examine the scattering mechanism limiting the mobility of GeO2/Ge interfaces through the modulation of the MOS interfaces by changing oxidation temperature. It is found that the mobility in low-temperature and low-surface carrier density (Ns) regions is well corrected withDitevaluated from S factors in MOSFETs. In addition, it is revealed from transmission electron microscopy analyses that the interface roughness between GeO2and Ge is reduced with increasing oxidation temperature. From these experimental results, the higher mobility of GeO2/Ge p-MOSFET at higher oxidation temperatures can be explained by the reduction in the density of Coulomb scattering centers and surface roughness at elevated Ge oxidation temperatures.
Characterization of SiGe Layer during Ge Condensation Process by X-ray Diffraction Methods
Authors: Shimura Takayoshi , Inoue Tomoyuki , Shimokawa Daisuke , Hosoi Takuji , Imai Yasuhiko , Sakata Osami , Kimura Shigeru , Watanabe Heiji
Published: January 2011

We fabricated a Ge-on-insulator (GOI) structure by the Ge condensation method and characterized the SiGe layer during the condensation process by X-ray reciprocal space mapping and synchrotron microbeam X-ray diffraction. The crystalline quality of the SiGe layer degraded during the initial 1 h of oxidation at 1050 °C and it also rapidly degraded during 1 h of oxidation at 900 °C immediately before the formation of GOI structures. The slight degradation was caused by annealing in Ar, indicating that the degradation during the initial 1-h condensation is accelerated by Ge atoms being ejected from the oxidized interface.