bluuebunny/crossref_metadata_2025 huggingface dataset:
Electronic structure and magnetic properties of solids
Authors: Savrasov Sergej Y. , Toropova Antonina , Katsnelson Mikhail I. , Lichtenstein Alexander I. , Antropov Vladimir , Kotliar Gabriel
Published: May 2005

We review basic computational techniques for simulations of various magnetic properties of solids. Several applications to compute magnetic anisotropy energy, spin wave spectra, magnetic susceptibilities and temperature dependent magnetisations for a number of real systems are presented for illustrative purposes.
Calculation of lattice energies of organic crystals: the PIXEL integration method in comparison with more traditional methods
Authors: Gavezzotti Angelo
Published: May 2005

The lattice energies of 47 crystal structures of organic compounds spanning a wide range of chemical functionalities are calculated using simple atom-atom potential energy functions, using coulombic terms with point-charge parameters, and using the PIXEL formulation, which is based on integral sums over the molecular electron density to obtain coulombic, polarization, dispersion and repulsion lattice energies. Comparisons among the different formulations, and the sensitivity and significance of the results against convenience, ease of application and number of parameters, are discussed. Improvements in the treatment of overlap repulsion in PIXEL are described, as well as a scheme for the minimization of the crystal lattice energy, based on the Symplex algorithm, which although computationally demanding, is shown to be feasible even with comparatively modest computing resources. The reproduction of experimental heats of sublimation is only marginally better with the PIXEL method, which however has great advantages in its being generally applicable in principle throughout the periodic table, at the expense of a minimal number of parameters, and in the fact that it sees the intermolecular interaction as the effect of the whole molecular electron density, in a physically more justifiable approach. This latter view in turn suggests a transition from a consideration of atom-atom bonds to a consideration of molecule-molecule bonding, opening a new view of packing factors in molecular crystals.
CPMD: Car-Parrinello molecular dynamics
Authors: Hutter Jürg , Iannuzzi Marcella
Published: May 2005

We present the ab initio molecular dynamics code CPMD. This plane wave/pseudopotential based Kohn-Sham density functional code with a rich set of features is successfully applied to calculate static and dynamic properties for a wide range of molecules and materials. Its flexibility and high performance on many computer platforms make it an optimal tool for the study of liquids, surfaces, crystals as well as biomolecules.
A brief introduction to the ABINIT software package
Authors: Gonze Xavier
Published: May 2005

A brief introduction to the ABINIT software package is given. Available under a free software license, it allows to compute directly a large set of properties useful for solid state studies, including structural and elastic properties, prediction of phase (meta)stability or instability, specific heat and free energy, spectroscopic and vibrational properties. These are described, and corresponding applications are presented. The emphasis is also laid on its ease of use and extensive documentation, allowing newcomers to quickly step in.
First principles methods using CASTEP
Authors: Clark Stewart J. , Segall Matthew D. , Pickard Chris J. , Hasnip Phil J. , Probert Matt I. J. , Refson Keith , Payne Mike C.
Published: May 2005

The CASTEP code for first principles electronic structure calculations will be described. A brief, non-technical overview will be given and some of the features and capabilities highlighted. Some features which are unique to CASTEP will be described and near-future development plans outlined.
CRYSTAL: a computational tool for the ab initio study of the electronic properties of crystals
Authors: Dovesi Roberto , Orlando Roberto , Civalleri Bartolomeo , Roetti Carla , Saunders Victor R. , Zicovich-Wilson Claudio M.
Published: May 2005

CRYSTAL [1] computes the electronic structure and properties of periodic systems (crystals, surfaces, polymers) within Hartree-Fock [2], Density Functional and various hybrid approximations.

CRYSTAL was developed during nearly 30 years (since 1976) [3] by researchers of the Theoretical Chemistry Group in Torino (Italy), and the Computational Materials Science group in CLRC (Daresbury, UK), with important contributions from visiting researchers, as documented by the main authors list and the bibliography.

The basic features of the program CRYSTAL are presented, with two examples of application in the field of crystallography [4, 5].
GDIS: a visualization program for molecular and periodic systems
Authors: Fleming Sean , Rohl Andrew
Published: May 2005

GDIS is a freely available chemical visualization program for displaying molecules, periodic structures, and crystal morphologies. A key feature of the package is the mechanism for constructing and manipulating arbitrary crystal surfaces. This enables GDIS to offer a powerful tool set for computing surface and interfacial properties and predicting crystal morphologies. Also included are modules for computing powder diffraction patterns, generating molecular surfaces, and analyzing dynamics trajectories. Further, the program may be used as a graphical interface to simplify the construction of input files for the command line codes: GULP, GAMESS(US), and SIESTA.
Distribution of Porphyromonas gingivalis fimA Genotypes in Japanese Children and Adolescents
Authors: Tamura Kiyoko , Nakano Kazuhiko , Nomura Ryota , Miyake Sonoko , Nakagawa Ichiro , Amano Atsuo , Ooshima Takashi
Published: May 2005

Background:Porphyromonas gingivalis is considered to be one of the most important pathogens in periodontal disease and its fimA genes have been classified into six variants (types I through V and Ib). A majority of the P. gingivalis organisms isolated from periodontitis patients are type II, followed by type IV, while type I is prevalent in healthy adults.

Methods: A total of 650 saliva samples were taken from 464 children (3 to 18 years of age), who visited Osaka University Dental Hospital. Genomic DNA was extracted from each sample and analyzed using a polymerase chain reaction (PCR) method with P. gingivalis‐specific primers, followed by an additional PCR assay to determine the fimA genotypes for P. gingivalis‐ positive subjects.

Results: Fifteen (3.23%) of the subjects were P. gingivalis‐positive and none of those samples showed a positive reaction to the type II fimA‐specific primers, while four, one, and two subjects were shown to be positive for the type I, Ib, and III genotypes, respectively. In addition, the type IV genotype was detected in three subjects in the older age group.

Conclusions: Our findings suggest that a limited number of children harbor P. gingivalis, and that the distribution of type II and IV fimA genotypes is extremely low. Further, some adolescents were found to possess the type IV fimA genotype which has been shown to be possibly related to adult periodontitis, in contrast to types I, III, and V. J Periodontol 2005;76:674‐679.
Coronally Advanced Flap: The Post‐Surgical Position of the Gingival Margin Is an Important Factor for Achieving Complete Root Coverage
Authors: Pini Prato Giovan Paolo , Baldi Carlo , Nieri Michele , Franseschi Debora , Cortellini Pierpaolo , Clauser Carlo , Rotundo Roberto , Muzzi Leonardo
Published: May 2005

Background: An assessment of the factors affecting the clinical outcome of root coverage procedures may be useful in clinical decision making. The aim of this study is to investigate whether the post‐surgical location of gingival margin relative to the cemento‐enamel junction (CEJ) can influence the recession reduction (RecRed) and complete root coverage (CRC) following coronally advanced flap procedure (CAF).

Methods: Sixty patients, aged between 22 and 57 years, 15 males and 45 females, each showing maxillary buccal recessions (≥2 mm) identified as Miller's Class I were consecutively enrolled. All the defects were treated by CAF procedure from 2000 to 2003 by a single operator with more than 20 years of clinical experience. Age, gender, smoking habits, and type of tooth of each patient were recorded. In addition, the following clinical data were measured or computed: recession depth, width of keratinized tissue, probing depth, distance between incisal margin (IM) and CEJ, dental hypersensitivity, clinical attachment level, distance between IM and gingival margin (IMGM), distance between IM and mucogingival junction (IMMG), and the location of gingival margin relative to the CEJ following CAF procedure (GM1). A multiple linear regression, and a logistic linear regression analyses were performed.

Results: The recession depth at baseline (RecT0) and the location of the gingival margin after suturing (GM1) are positively correlated to recession reduction. Complete root coverage appeared to be influenced by GM1: the more coronal the level of the gingival margin after suturing (GM1), the greater the probability of CRC.

Conclusion: The location of the gingival margin relative to the cemento‐enamel junction following CAF procedure seems to affect CRC. J Periodontol 2005;76:713‐722.
Cigarette Smoking and Apoptosis
Authors: Imirzalioĝlu P. , Uckan S. , Alaaddinoĝlu E.E. , Haberal A. , Uckan D.
Published: May 2005

Background: Epithelial cell hyperplasia and significant increase in thickness of the overlying orthokeratin layer are characteristic findings noted in the oral cavity of subjects who smoke. Increased proliferation of epithelial cells or defective apoptosis may play a role in the development of epithelial hyperplasia. Thus we analyzed soluble Fas and nuclear matrix protein (NMP) levels in the saliva of smokers (N = 13) and non‐smokers (N = 14) to assess apoptosis.

Methods: Ten ml of unstimulated saliva samples was obtained from 14 non‐smoker and 13 smoker subjects with the spitting method. These samples were analyzed by using an immunoassay kit to detect soluble human APO‐1/Fas and cell death detection enzyme‐linked immunosorbent assay (ELISA) kit based on nuclear matrix protein 41/7 qualification.

Results: The mean soluble Fas levels were 153.8 ± 290 pg/ml and 315.4 ± 490 pg/ml and NMP levels were 21.81 ± 10.70 U/ml and 30.31 ± 19.86 U/ml, respectively, in smokers and nonsmokers. The difference between NMP levels of smoker and non‐smoker groups was statistically significant (P = 0.05).

Conclusion: The results of the present study suggest that smoking may induce anti‐apoptotic mechanism in the oral cavity. J Periodontol 2005;76:737‐739.
Prostaglandin E2 Is a Main Mediator in Receptor Activator of Nuclear Factor‐κB Ligand‐Dependent Osteoclastogenesis Induced by Porphyromonas gingivalis, Treponema denticola, and Treponema socranskii
Authors: Choi Bong‐Kyu , Moon Sun‐Young , Cha Jeong‐Heon , Kim Kih‐Wan , Yoo Yun‐Jung
Published: May 2005

Background: Periodontitis is an inflammatory disease that often leads to destruction of alveolar bone; a number of bacteria in subgingival plaque are associated with bone destruction in periodontitis. To understand the mechanism of how periodontopathogens induce osteoclastogenesis, we determined which mediators are involved in the osteoclastogenesis.

Methods: We investigated effects of sonicates from three periodontopathic bacteria, Porphyromonas gingivalis, Treponema denticola, and Treponema socranskii, on osteoclast formation in a co‐culture system of mouse calvaria‐derived osteoblasts and bone marrow cells. The osteoclast formation was determined by tartrate resistant acid phosphatase (TRAP) staining. The expression of the receptor activator of nuclear factor‐κ B ligand (RANKL), prostaglandin E2 (PGE2) and osteoprotegerin (OPG) in mouse calvaria‐derived osteoblasts was determined by immunoassay.

Results: Each bacterial sonicate induced the osteoclast formation in the co‐culture system. These bacterial sonicates increased the expression of RANKL and PGE2, and decreased the expression of OPG in osteoblasts. The addition of OPG, an inhibitor of RANKL, in the co‐culture completely suppressed the osteoclastogenesis that was stimulated by each bacterial sonicate. Indomethacin, which is an inhibitor of PGE2 synthesis, reduced more than 88% of the osteoclast formation induced by each bacterial sonicate. Indomethacin inhibited more than 80% of RANKL expression in osteoblasts induced by T. denticola and T. socranskii, and 59% by P. gingivalis. Indomethacin completely recovered the depression of OPG expression in osteoblasts by T. denticola and T. socranskii to the level of the untreated osteoblasts. Indomethacin recovered the reduction of OPG expression by P. gingivalis to 67%.

Conclusion: These findings suggest that the osteoclastogenesis by P. gingivalis, T. denticola, and T. socranskii is mediated by a RANKL‐dependent pathway and that PGE2 is a main factor in the pathway by the enhancing of RANKL expression and the depression of osteoprotegerin, a RANKL inhibitor. J Periodontol 2005;76:813‐820.
Treatment Options Following Single‐Rooted Tooth Removal: A Literature Review and Proposed Hierarchy of Treatment Selection
Authors: Fugazzotto Paul A.
Published: May 2005

Background: Alveolar bone changes following tooth extraction have been well documented and have given rise to a number of treatment approaches. Included in these approaches are placement of various grafting materials, immediate implant placement, and a combination of both.

Methods: A review of all pertinent literature discussing regenerative therapy at the time of tooth extraction or immediate implant placement with or without concomitant regenerative therapy was carried out.

Results: A clinically‐based hierarchy of treatment selection following extraction of single rooted teeth is proposed, based upon the available literature and clinical experience. The role of patient phenotype is considered.

Conclusion: Utilization of the proposed hierarchy of treatment selection affords a logical framework within which to predictably treat a variety of patients. J Periodontol 2005;76:821‐831.
A New Incision Design for Mandibular Symphysis Bone‐Grafting Procedures
Authors: Schuler Ralf , Verardi Simone
Published: May 2005

Background: Traditional methods of procuring mandibular symphysis bone grafts may leave soft tissue scarring, and cause paresthesia and lip droop.

Methods: Nineteen patients selected for treatment were given general health, periodontal, and radiographic evaluations. Patients had inadequate bone volume for dental implant placement or required preprosthetic ridge augmentation procedures. Prior to surgery, bone sounding was performed to determine tissue thickness. All patients had a minimum of 4 mm of keratinized gingiva. Under local anesthesia, incisions were initiated within the keratinized gingiva. Full‐thickness mucoperiosteal flaps were elevated, and small burs were used to obtain bone blocks from the mandibular symphysis. A bone‐scraping device was used to obtain strips of cortical bone. A combination of sling and interrupted sutures was used for wound closure.

Results: All patients healed uneventfully without wound dehiscence, paresthesia, or lip droop. Sufficient bone was obtained for ridge or sinus augmentation with eventual implant placement.

Conclusions: A new incision design is presented. This flap design is carried out within keratinized gingiva. Limiting the flap design to keratinized tissue facilitates flap closure and avoids wound dehiscence. J Periodontol 2005;76:845‐849.
Measurement and Modeling of Temporal Variations in Hydrocarbon Vapor Behavior in a Layered Soil Profile
Authors: Davis G. B. , Rayner J. L. , Trefry M. G. , Fisher S. J. , Patterson B. M.
Published: May 2005

Fine‐scale measurement of gasoline vapors, major gases (O2, CO2, N2, and CH4), residual nonaqueous phase liquid (NAPL) gasoline, and soil physical properties has allowed detailed assessment of the role of soil layering and seasonal variability on hydrocarbon vapor fate and biodegradation. In this study we conducted coring and static depth profile monitoring at the end of summer and end of winter for a layered sandy vadose zone in Perth, Western Australia. Transient on‐line monitoring of vapors and O2 was also performed with in situ multilevel volatile organic compound (VOC) and O2 probes. For high soil moisture contents at the end of winter, vapors were shown to accumulate beneath a compacted, cemented layer approximately 0.3 m below the ground surface, and O2 penetrated only to depths of 0.4 m below ground. At the end of summer, when soil moisture was lower, O2 penetrated to depths of up to 1.5 m, and hydrocarbon vapors remained at or below this depth. Regardless of seasonal changes, sharp separations were seen between the depth of O2 penetration from the ground surface and the depth of penetration of the vapors upward from the hydrocarbon‐contaminated zone. Modeling of steady‐state O2 profiles indicated that a number of simple O2 consumption models might apply, including point‐sink, distributed zero‐order, or distributed first‐order models, each leading to different biodegradation rates. Combining independent data with modeling helped determine the most appropriate model, and hence estimates of O2 consumption and hydrocarbon biodegradation. Also, reliable estimates of the biodegradation rate could only be calculated after consideration of the layered features.
Intercomparison of Flow and Transport Models Applied to Vertical Drainage in Cropped Lysimeters
Authors: Herbst M. , Fialkiewicz W. , Chen T. , Pütz T. , Thiéry D. , Mouvet C. , Vachaud G. , Vereecken H.
Published: May 2005

Models predicting flow and transport in the vadose zone differ in their conceptual approach, their complexity, and their mathematical formulation. Four models (MARTHE, TRACE, ANSWERS, and MACRO), which differ significantly in their model concepts and complexity, were applied to a common data set to evaluate and compare the different model approaches. Five free‐draining lysimeters, cropped with winter wheat, barley, and oat were used to monitor actual evapotranspiration, soil moisture, and drainage for 627 d. One of the five lysimeters was also treated with methabenzthiazuron (MBT), and soil residues as well as leaching were experimentally determined. In Europe, MBT has been commonly used as a herbicide for almost 30 years. Generally, the use of given model inputs is recommended, apart from plant parameters, which need calibration. The use of validation criteria revealed proper simulation of water flow for the four models. After calibration, the Richards' equation–based models MARTHE, TRACE, and MACRO performed better for water flow predictions than the capacity‐based ANSWERS. A small amount of preferential flow, which is not included in the model structures of MARTHE, TRACE, and ANSWERS, did not influence the simulation of water flow significantly. But preferential flow was associated with the leaching of 0.0059% of the applied mass of MBT, causing relevant concentrations in the leachate. Leaching could be described well with MACRO after calibration. The difficulty of estimating parameters for modeling macropore transport is seen as an obstacle to common application.
Unsaturated Flow Through Spherical Inclusions with Contrasting Sorptive Numbers
Authors: Furman Alex , Warrick A. W.
Published: May 2005

The analytic element method (AEM) is used to model unsaturated flow through a spherical inclusion of contrasting hydraulic properties. The steady state Richards' equation is combined with the Gardner model for unsaturated hydraulic conductivity to form the Helmholtz equation. The later is solved by means of the AEM. The background and inclusion materials are assumed to have different saturated hydraulic conductivities and different sorptive numbers; hence, the conditions are more general than treatments of spherical inclusions. Continuity of the interfacial head boundary condition leads to a nonlinear system of equations, whose solution requires an iterative solution. Analysis includes the effect of the hydraulic properties and of the background flux and evaluation of computational efficiency for contrasting hydraulic properties. To examine water contents, a methodology is presented for matching Gardner and van Genuchten parameters. The new solution is more realistic than the previous solution for a spherical inclusion with a sorptive number the same as the background but is computationally more tedious.
Experimental Observations and Numerical Modeling of Coupled Microbial and Transport Processes in Variably Saturated Sand
Authors: Rockhold M. L. , Yarwood R. R. , Niemet M. R. , Bottomley P. J. , Selker J. S.
Published: May 2005

An experimental and numerical investigation was conducted to study interactions between microbial dynamics and transport processes in variably saturated porous media. Experiments were conducted with constant, surface‐applied water fluxes in duplicate, variably saturated, sand‐filled columns that were uniformly inoculated with the bacterium Pseudomonas fluorescens HK44. The permeability of the sand in the columns was reduced by a factor of 45 during 1 wk of growth on glucose. Pressure heads increased (became less negative) at all measured depths, but significant increases in the apparent volumetric water contents were observed in only the upper 5 cm of the columns, corresponding to the areas with the highest concentrations of attached bacteria. A numerical model was used to simulate the experiments. The model accounted for the processes of water flow, solute and bacterial transport, cell growth and accumulation, glucose and O2 consumption, and gas diffusion and exchange. Observed changes in water content and pressure head were reproduced approximately using fluid‐media scaling to account for an apparent surface‐tension lowering effect. Reasonable correspondence was obtained between observed and simulated effluent data and final attached biomass concentration distributions using first‐order reversible cell attachment and detachment kinetics. The attachment rate coefficients were based on particle‐filtration theory and time‐dependent detachment rate coefficients. The results of this study illustrate the potential importance of using fully coupled multifluid flow and multicomponent reactive transport equations to model coupled biogeochemical and transport processes in soils.
Using TDR and Inverse Modeling to Characterize Solute Transport in a Layered Agricultural Volcanic Soil
Authors: Ritter A. , Muñoz‐Carpena R. , Regalado C. M. , Javaux M. , Vanclooster M.
Published: May 2005

Volcanic soils exhibit particular physical‐chemical properties (i.e., strong and stable natural aggregation and high content of variable‐charge minerals) that may influence solute transport. To determine if such techniques like TDR and inverse modeling are useful for analyzing solute transport in volcanic soils, we studied the governing transport processes by means of a miscible displacement experiment of Br− in a large undisturbed soil monolith. Bromide resident concentrations at several depths were monitored successfully with TDR technology, while parameters for the convective–dispersive (CDE) and mobile–immobile (MIM) transport models were estimated by inverse modeling. For the relatively high soil moisture conditions, typical of high frequency‐irrigation systems that we considered, Br− was found to move slowly by convection–dispersion. Simulations with the CDE and MIM transport models yielded very similar results. Although Br− is generally assumed to behave as a tracer, we found that this anion in our experiment was subject to adsorption at the bottom part of the monolith. This may be explained by the variable‐charge nature of the minerals (Fe and Al oxihydroxides) present in this volcanic soil, which exhibited anion exchange when the pH of the soil solution decreased below the zero point of charge.
A Genetic Algorithm for Predicting Pore Geometry Based on Air Permeability Measurements
Authors: Unsal E. , Dane J. H. , Dozier G. V.
Published: May 2005

Pore size distributions of porous media are of interest to soil scientists, geologists, and engineers with a variety of backgrounds. If known, pore size distributions can be used to determine fluid retention and permeability relationships. In this study, we propose a methodology to predict pore size distributions from air permeability measurements combined with a numerical model representing a porous medium. The model is an extension of the capillary model, which was modified so that the capillaries are composed of sections with different diameters. An optimization scheme that makes use of the measured air permeability values was developed to predict the best possible pore size distribution and pore arrangement. A genetic algorithm, a popular evolutionary computational methodology, was chosen for the optimization process. During our numerical study, we observed that it is not only the pore size distribution that is important, but also how the pores are distributed, in other words, the pore geometry.
Selenium content of Finnish oats in 1997-1999: effect of cultivars and cultivation techniques
Authors: EUROLA M. , HIETANIEMI V. , KONTTURI M.
Published: May 2005

Se-supplemented fertilization is the main factor affecting the selenium (Se) contents of cereals in Finland. Soil and climatic conditions determine the activity of selenate added to soils and bioavailability to plants. In the present study the Se contents and its variation in Finnish oats, the differences between oat cultivars and cultivation techniques were examined. The selenium (Se) contents of oats (Avena sativa L.) in Finland were examined during 1997-1999 in 3 types of trial: official variety, organic cultivation variety and organic vs. conventional cultivation trials. Farm samples were also examined. The mean Se contents of oats in official variety trials were 0.110, 0.120 and 0.160 mg kg-1 dry weight (dw) range 0.016-0.460 mg kg-1dw in 1997-1999, respectively. The mean Se contents in farm samples were 0.050 and 0.130 mg kg-1dw in 1998 and 1999, ranging between < 0.010 and 0.330 mg kg-1 dw. Considerable regional and seasonal variations existed. The Se contents of oats were significantly higher in 1999 probably due to the combined effect of not increased fertilizer level (from 6 to 10 mg Se kg-1 fertilizer) and very low precipitation in 1999. The Se contents of oats were significantly lower in organic cultivation, due to the absence of Se-supplemented fertilization. Significant (P < 0.001) cultivar differences were detected in official variety trials. The cultivars Veli and Leila showed higher levels of Se.;
Dehulling capacity and storability of naked oat
Authors: KIRKKARI A-M. , PELTONEN-SAINIO P. , LEHTINEN P.
Published: May 2005

Harvested naked oat is not completely hulless. Hull content of various cultivars ranged between one and six percent. Genotype and environment control expression of nakedness. Using different threshing settings at different grain moisture contents, it was investigated whether grain moisture at threshing and combine harvester settings affected hull content and its relationship to germination capacity. Naked groats were stored at room temperature and analysed for protein content and fatty acid composition to determine storability. Grain moisture content at threshing had contrary effects on hull content and degree of hull retention in different years. Small grains tended to retain hulls more tightly during threshing. Grain filling capacity appears to be the dominant factor determining degree of nakedness rather than stage of maturity. The postulated protective nature of hulls was confirmed only for cultivar Lisbeth. Highly viable samples of grain of cv. Lisbeth, threshed at normal settings, contained a higher percentage of hulls than those with low germination capacity, while for cv. Bullion, a protective effect of the hulls was not evident. Grain moisture content at threshing did not affect protein content of naked cultivars, but some differences in fatty acid composition were recorded. Changes in lipid composition and volatile oxidation products during storage of groats were relatively moderate, indicating no major problems related to storage when naked oat was dried well.;
Alterations in growth and canopy architecture among dwarf, semidwarf and tall oat lines grown under northern conditions
Authors: MÄKELÄ P. , MUURINEN S. , PELTONEN-SAINIO P.
Published: May 2005

The Finnish growing season is particularly short, with an intensive growth period, unfavourable rainfall distribution and frequently occurring fluctuations in climate that affect crop growth and yield formation. A three-year study was conducted in the field to determine the contribution of alterations in canopy structure, tillering and stem elongation among dwarf (D), semidwarf (SD) and tall (T) oat (Avena sativa L.) lines to yield formation. Yield components, leaf characteristics and straw traits were measured from six oat lines (D lines Pal and Grane, SD lines Hja 76416 and Salo, and T lines Veli and Jalostettu maatiainen) separately on the main shoot and tillers. Results indicated that long leaf area duration and high leaf area index were associated with increased grain yield probably due to more persistent and active assimilation. Also, higher number of leaves increased the grain yield. Higher peduncle, straw and node weights associating with increased grain yield may result from more abundant assimilate reserves; however, the longer the straw and peduncle, the lower the grain yield, which may result from increased lodging of SD and T lines. The traits contributing most to the grain yield varied greatly from year to year. It is concluded that no single dominant trait determined grain yield, since yield is a product of several different traits. SD lines seemed to be most promising for further breeding programs on the basis of their growth pattern and yielding ability.;
Germination: a means to improve the functionality of oat
Authors: KAUKOVIRTA-NORJA A. , WIHELMSON A. , POUTANEN K.
Published: May 2005

The biochemical and physiological reactions of germination have long been utilised to produce barley malt for brewing and other purposes. Also some oat malt has been produced as raw-material of ale and stout production. The main goals of malting have been the degradation of grain storage components to soften the kernel structure, synthesis of amylolytic enzymes and production of nutrients for brewing yeast. Also flavour and colour attributes have been important. During the recent years interest has arisen also in the secondary metabolites produced during germination, which can have valuable health promoting properties and act as bioactive or functional compounds in foods. By using a tailored germination/malting process a desired combination of valuable properties may be obtained in germinating grains or seeds. All this requires knowledge and know-how of the germination process and the biochemistry behind it. This paper reviews the scientific knowledge about germination/malting of oat with special emphasis on changes in grain characteristics.;
Anther culture properties of oat x wild red oat progenies and a search for RAPD markers associated with anther culture ability
Authors: KIVIHARJU E. , LAURILA J. , LEHTONEN M.
Published: May 2005

A study was carried out to improve anther culture ability of the non-responsive cultivated oat, Avena sativa L. cv. Puhti by introgressing favourable alleles from the responsive wild red oat, Avena sterilis L. acc. CAV 2648. Anther culture ability of these parental lines and F2 progenies of their cross and two backcrosses was tested. Genotype effects were significant on all anther culture traits measured. The number of anther culture derived embryo-like structures was highest in acc. CAV 2648, and the number of green regenerants from the Puhti × CAV 2648 progeny. Anther culture response was greatly reduced in backcross progeny and was least in cv. Puhti. Random amplified polymorphic DNA (RAPD) was used to test for marker associations with oat anther culture traits in a population of 38 F2 progenies. Two RAPD markers were putatively associated with improved production of green regenerants (one derived from acc. CAV 2648 and the other from cv. Puhti). One marker putatively associated with decreased albino plant regeneration (derived from acc. CAV 2648). These markers might be useful for selecting alleles for better anther culture ability among progeny of planned crosses. In addition, three markers, derived from acc. CAV 2648, were putatively associated with decreased anther culture response rates.;
Characterising strengths, weaknesses, opportunities and threats in producing naked oat as a novel crop for northern growing conditions
Authors: PELTONEN-SAINIO P. , KIRKKARI A-M. , JAUHIAINEN L.
Published: May 2005

Naked oat (Avena sativa ssp. nuda L.) is the highest quality small-grain cereal that can be grown at the northernmost margin of cereal production. It remains an under-utilised crop and it contributes less than 0.1% to the total oat area in Finland. In general, limited interest in growing naked oat more extensively is attributed to its weaknesses, which ironically result from nakedness that improves the quality of the crop. This paper reviews the available literature and assesses the balance of the arguments for and against naked oats. Results from the study were transformed into quantitative variables and analysed for strengths, weaknesses, opportunities and threats (SWOT) using an analytical hierarchical process. As the importance of different SWOT-factors depends largely on targeted end-use of yield, separate analyses were done for use of naked oats as on-farm feed and as an input for the feed and food industry. If we aim at increasing area under naked oat in Finland, the most feasible starting point would be on-farm feed. In this case, strengths (high nutritional quality and energy content) outweighed weaknesses (sensitivity to grain damage) and threats (problems in germination). Increasing naked oat production in this respect is likely to encourage solving the remaining problems that deter industry. Threats (availability) regarding the feed industry and weaknesses (incomplete expression of nakedness) in the food industry out-weighed strengths (high nutritional quality and storability) and opportunities (potential niches).;
On diversity effects of alternative agricultural policy reforms in Finland: an agricultural sector modelling approach
Authors: MIETTINEN A. , LEHTONEN H. , HIETALA-KOIVU R.
Published: May 2005

The European Union has decided to reform its agricultural policy and decouple Common Agricultural Policy support partially from production. The aim of this study is to predict the diversity effects of agricultural policy reforms in which direct aid payments are disconnected from production, and compare the outcomes with the effects of a policy in which Common Agricultural Policy support is coupled to production. The study employs a dynamic regional sector model of Finnish agriculture. The sector model predicts regional agricultural land use, numbers of livestock, stocking densities, pesticide application areas, and nutrient balances. Diversity of agricultural land use is measured by Shannons diversity index. The results indicate that if agricultural support is independent from production, the amount of fallow land will increase considerably in the future. This will decrease the diversity of agricultural land use at landscape level, but may not be harmful at species level since green fallow has some positive effects, especially on the densities and abundance of farmland birds. Instead, the decrease in bovine animals is likely to run down biological diversity, since it simplifies crop rotation and diminishes grazing.;
Continuous plug‐flow bioreactor: Experimental testing with Pseudomonas putida culture grown on benzoate
Authors: Voloshin Yury , Lawal Adeniyi , Panikov Nicolai S.
Published: May 2005

The goals of this work were to test the feasibility of a continuous plug‐flow (PF) bioreactor and to compare the growth in the PF bioreactor to that in a batch bioreactor. A culture of Pseudomonas putida was pumped through a tube made of Teflon with varying residence times. The culture was aerated by pumping of air simultaneously with liquid medium to provide air bubbles along the tubular culture. When the residence time in the PF bioreactor was greater than the time needed to reach the stationary phase in batch mode, the maximum biomass density reached in PF mode was the same as the maximum density reached in the batch bioreactor, and benzoate (the only carbon and energy source) was completely consumed. The drawbacks for practical application of PF were found to be fluctuations of cell concentration in the outflow cultural liquid due to cell aggregation, significant cell adhesion to the inner wall of Teflon tubing, and inadequate aeration. © 2005 Wiley Periodicals, Inc.
Virus detection using filament‐coupled antibodies
Authors: Stone Gregory P. , Mernaugh Ray , Haselton Frederick R.
Published: May 2005

Two attractive features of ELISA are the specificity of antibody–antigen recognition and the sensitivity achieved by enzymatic amplification. This report describes the development of a non‐enzymatic molecular recognition platform adaptable to point‐of‐care clinical settings and field detection of biohazardous materials. This filament‐antibody recognition assay (FARA) is based on circumferential bands of antibody probes coupled to a 120 μm diameter polyester filament. One advantage of this design is that automated processing is achieved by sequential positioning of filament‐coupled probes through a series of 25–60 μL liquid filled microcapillary chambers. This approach was evaluated by testing for the presence of M13KO7 bacterial virus using anti‐M13KO7 IgG1 monoclonal antibody coupled to a filament. Filament motion first positioned the antibodies within a microcapillary tube containing a solution of M13KO7 virus before moving the probes through subsequent chambers, where the filament‐coupled probes were washed, exposed to a fluorescently labeled anti‐M13K07 antibody, and washed again. Filament fluorescence was then measured using a flatbed microarray scanner. The presence of virus in solution produced a characteristic increase in filament fluorescence only in regions containing coupled antibody probes. Even without the enzymatic amplification of a typical ELISA, the presence of 8.3 × 108 virus particles produced a 30‐fold increase in fluorescence over an immobilized negative control antibody. In an ELISA comparison study, the filament‐based approach had a similar lower limit of sensitivity of ∼1.7 × 107 virus particles. This platform may prove attractive for point‐of‐care settings, the detection of biohazardous materials, or other applications where sensitive, rapid, and automated molecular recognition is desired. © 2005 Wiley Periodicals, Inc.
Controlling protein transport in ultrafiltration using small charged ligands
Authors: Rao Suma , Zydney Andrew L.
Published: May 2005

Previous studies have demonstrated that protein transport during ultrafiltration can be strongly influenced by solution pH and ionic strength. The objective of this study was to examine the possibility of controlling protein transmission using a small, highly charged ligand that selectively binds to the protein of interest. Experiments were performed using bovine serum albumin and the dye Cibacron Blue. Protein sieving data were obtained with essentially neutral and negatively charged versions of a composite regenerated cellulose membrane to examine the effects of electrostatic interactions. The addition of only 1 g/L of Cibacron Blue to an 8 g/L BSA solution reduced the BSA sieving coefficient through the negatively‐charged membrane by more than two orders of magnitude, with this effect being largely eliminated at high salt and with the neutral membrane. Protein sieving data were in good agreement with model calculations based on the partitioning of a charged sphere in a charged pore accounting for the change in net protein charge due to ligand binding and the increase in solution ionic strength due to the free ligand in solution. © 2005 Wiley Periodicals, Inc.
Zoledronic acid down‐regulates adhesion molecules of bone marrow stromal cells in multiple myeloma
Authors: Corso Alessandro , Ferretti Eleonora , Lunghi Monia , Zappasodi Patrizia , Mangiacavalli Silvia , De Amici Mara , Rusconi Chiara , Varettoni Marzia , Lazzarino Mario
Published: May 2005

BACKGROUND

Myeloma plasma cells interact with the bone marrow microenvironment which, in turn, supports their growth and protects them from apoptosis. In vitro studies have demonstrated the antitumor potential of zoledronic acid (ZOL) on myeloma cell lines, but few data are available on its effects on bone marrow stromal cells (BMSCs). The aim of the current study was to evaluate the antiproliferative and apoptotic effect of ZOL on BMSCs, as well as its effect on the expression of adhesion molecules.

METHODS

BMSCs, obtained from bone marrow mononucleated cells of 8 patients with multiple myeloma, were treated with increasing concentrations of ZOL for 3 days. Cytotoxic effect was analyzed by 3‐(4‐5‐dimethylthiazol‐2‐yl)‐2,5 diphenyltetrazolium bromide; thiazolyl blue (MTT) assay whereas the induction of apoptosis was evaluated by flow cytometric detection of fluorescein isothiocyanate‐labeled annexin V, terminal deoxynucleotidyl transferase‐mediated dUTP nick‐end labeling assay, and nuclear changes. Moreover, expression of CD106, CD56, CD50, CD49d, CD44, and CD40 was analyzed by flow cytometry. Data were evaluated by the Friedman test.

RESULTS

After 3 days of exposure at concentrations of 10−4 to 10−5 M, ZOL induced a decrease in proliferation (P < 0.0001) and an increase in apoptosis (P < 0.002). Analysis of culture supernatants showed that myeloma BMSCs expressed interleukin (IL)‐6, negligible levels of tumor necrosis factor‐alpha, and no IL‐1β. In vitro exposure to the lowest concentrations of ZOL decreased IL‐6 production by BMSCs. Among the adhesion molecules, CD106, CD54, CD49d, and CD40, which were strongly expressed at baseline, showed a statistically significant reduction compared with controls after exposure to ZOL.

CONCLUSIONS

ZOL interfered with myeloma BMSCs by reducing proliferation, increasing apoptosis, and modifying the pattern of expression of adhesion molecules, especially those involved in plasma cell binding. These effects on BMSCs might explain the antitumor activity of ZOL. Cancer 2005;. © 2005 American Cancer Society.
Chondrosarcoma of the scapula
Authors: Pant Rajeev , Yasko Alan W. , Lewis Valerae O. , Raymond Kevin , Lin Patrick P.
Published: May 2005

BACKGROUND

Chondrosarcoma is the second most common primary sarcoma of bone. It often develops within flat bones, such as the pelvis, ribs, and scapula. In the current study, the authors reviewed the surgical experience and long‐term oncologic outcomes of patients with chondrosarcoma arising in the scapula.

METHODS

The medical records of 29 consecutive patients with chondrosarcoma of the scapula were reviewed. The patients were treated between 1954 and 1994. All patients had localized disease at the time of presentation. The tumors were classified histologically as Grade 1 (10 patients), Grade 2 (10 patients), Grade 3 (7 patients), dedifferentiated (1 patient), and mesenchymal (1 patient) (using the criteria of Evans et al.). The mean maximal dimension of the tumors was 11 cm. Twenty‐five patients underwent limb‐sparing surgical resection and 4 patients underwent forequarter amputations. The median follow‐up was 13 years (range, 1–35 years).

RESULTS

At last follow‐up, 22 patients (76%) were free of disease and 7 patients (24%) had died of their disease. Local recurrence occurred in 4 patients at 7 months, 16 months, 40 months, and 43 months, respectively. The local recurrence‐free survival rate was 86% at 5 years, 10 years, and 20 years. Disease‐specific survival was 83% at 5 years, 74% at 10 years, and 74% at 20 years. Patients who had low‐grade chondrosarcomas had better survival compared with patients who had high‐grade chondrosarcomas (P = 0.07).

CONCLUSIONS

Patients who had localized chondrosarcoma of the scapula had a favorable long‐term outcome, most likely due to the unique anatomic features that improved the likelihood of achieving wide surgical margins with limb‐sparing surgery, despite the frequent presentation of locally advanced disease. Cancer 2005. © 2005 American Cancer Society.
Reclassification of patients with pT3 and pT4 renal cell carcinoma improves prognostic accuracy
Authors: Thompson R. Houston , Cheville John C. , Lohse Christine M. , Webster W. Scott , Zincke Horst , Kwon Eugene D. , Frank Igor , Blute Michael L. , Leibovich Bradley C.
Published: May 2005

BACKGROUND

The significance of adrenal invasion and tumor thrombus in renal cell carcinoma (RCC) has been debated recently. The authors evaluated the associations of direct adrenal invasion, perinephric fat invasion, and tumor thrombus level with outcome to determine whether reclassification would improve the prognostic accuracy of the current primary tumor classification.

METHODS

The authors studied 697 patients treated with nephrectomy for pT3 and pT4 RCC between 1970 and 2000. Associations with outcome were evaluated using Cox proportional hazards regression and prognostic accuracy was measured using the c index.

RESULTS

Among patients with pT3 RCC, direct adrenal invasion was significantly associated with death from RCC (risk ratio, 2.11; P = 0.004). No significant difference in survival was found between patients with pT4 RCC and pT3 tumors with direct adrenal invasion (P = 0.490). Among patients with pT3b RCC, those with level I–III tumor thrombus were significantly more likely to die of RCC compared with patients harboring level 0 tumor thrombus (risk ratio, 1.62; P < 0.001). In addition, patients with fat invasion were more likely to die of RCC compared with pT3 patients without fat invasion (risk ratio, 1.87; P < 0.001). Therefore, patients with pT3 RCC were reclassified into 4 prognostic groups, and this reclassification significantly improved prediction of death from RCC compared with the current classification (c indices of 0.61 vs. 0.55, respectively).

CONCLUSIONS

Direct adrenal invasion from RCC should be reclassified as pT4. In addition, the proposed reclassification for patients with pT3 RCC improved prognostic accuracy. Cancer 2005;. © 2005 American Cancer Society.