bluuebunny/crossref_metadata_2025 huggingface dataset:
Improving the geometry and quality of a micro-hole fuel injection nozzle by means of hydroerosive grinding
Authors: Diver C , Atkinson J , Befrui B , Helml H J , Li L
Published: April 2007

Hydroerosive grinding of small orifice components often creates a feature known, for the purposes of this paper, as a keyhole. The keyhole is created by undesirable erosion close to the entry of a hole, which results in an asymmetrical geometrical form and poor quality. This paper details how the keyhole problem can be eliminated and applied to diesel fuel injection nozzle manufacture.

The hydroerosive grinding process consists of a low viscosity fluid, similar to the viscosity of diesel fuel, containing abrasive particles such as silicon carbide and boron carbide. A fuel injection nozzle tends to have five to seven injection holes ranging in diameter from 100 μm to 200 μm. This fluid is passed through the injection holes in a fuel injection nozzle to calibrate the nozzle flowrate, improve surface finish, pre-age the nozzle radius and micro-deburr the hole edge at the fuel inlet, and to improve the flow efficiency of the hole. The paper addresses problems associated with hydroerosive grinding, such as the keyhole feature and asymmetrical holes, and describes a solution to eliminate the keyhole effect and to increase the flowrate of the nozzle without resulting in poor hole geometry. The paper contains a study on the process development, understanding of the two-phase flow characteristics, and practical implementation of the technique.
A hybrid method for feature recognition in computer-aided design models
Authors: Dimov S S , Brousseau E B , Setchi R
Published: April 2007

Automatic feature recognition (AFR) techniques applied to three-dimensional (3D) solid models are an important tool for achieving a true integration of computer-aided design (CAD) and computer-aided manufacturing (CAM) processes. In particular, AFR systems allow the identification in CAD models of high-level geometrical entities: features that are semantically significant for manufacturing operations. However, the recognition performances of most of the existing AFR systems are limited to the requirements of specific manufacturing applications. This paper presents a new hybrid method that facilitates the deployment of AFR systems in different application domains. In particular, the method includes two main processing stages: learning and feature recognition. During the learning stage, knowledge acquisition techniques are applied for generating feature-recognition rules and feature hints automatically from training data. Then, these hints and rule bases are utilized in the feature-recognition stage to analyse boundary representation (B-Rep) part models and identify their feature-based internal structure. The proposed AFR method is implemented within a prototype feature-recognition system and its capabilities are verified on two benchmarking parts.
Tool condition monitoring in end milling using a torque-based sensorized toolholder
Authors: Dini G , Tognazzi F
Published: April 2007

The automation of metal-cutting processes needs robust sensing systems and monitoring methods, able to detect the tool condition on-line. In milling operations, powerful tool-monitoring solutions are based on cutting force measurement, performed by using sensorized toolholders. This paper deals with a particular application of this method, consisting of acquiring the cutting torque signal in end milling by means of a commercial low-cost rotating dynamometer, usually applied in other machining operations. The dynamometer is directly integrated into a toolholder body, properly modified in order to obtain the needed specifications. The proposed solution is not invasive and, therefore, avoids a strong reduction in mechanical properties of the tool and the toolholder set. Preliminary cutting tests were performed in order to detect if the acquired signal can be successfully used to recognize on-line the status of the cutting tool. On-line threshold-based monitoring strategies were also proposed, and significant indicators were considered for tool condition monitoring in milling.
Statistical modelling and optimization of surface roughness in the selective laser sintering process
Authors: Bacchewar P B , Singhal S K , Pandey P M
Published: April 2007

Selective laser sintering (SLS) is a layered manufacturing process that builds prototypes by selective sintering of materials in powder form, like thermoplastic polymer powder (Polyamide 2200), using a CO2 laser. Prototypes made by SLS are widely used in product development as they can be used for product testing. SLS prototypes, therefore, should have a very good surface finish for functional performance as well as aesthetics. However, prototypes made by the SLS process have comparatively high surface roughness due to the stair stepping effect. Surface roughness of the prototypes also depends on the various process parameters. This paper attempts to study the effect of process parameters, namely build orientation, laser power, layer thickness, beam speed, and hatch spacing, on surface roughness. Central rotatable composite design (CCD) of experiments was used to plan the experiments. Analysis of variance (ANOVA) was used to study the significance of process variables on surface roughness. In the case of upward-facing surfaces, build orientation and layer thickness have been found to be significant parameters. In downward-facing surfaces, other than build orientation and layer thickness, laser power has also been found to be significant. Empirical models have been developed for estimating the surface roughness of the parts. A trust-region-based optimization method (standard module of MATLAB) has been employed to obtain a set of process parameters for obtaining the best surface finish. A confirmation experiment has been carried out at an optimum set of parameters and predicted results were found to be in good agreement with experimental findings. A case study of a standard part ‘Truncheon’ is also presented.
Austenitic-ferritic transition joint cracking under thermal fatigue loading
Authors: Petridis P P , Tsoukalas V D
Published: April 2007

The use of transition joints is connected with problems caused owing to differences between austenitic-ferritic thermal expansion coefficient, moderate oxidation resistance of the low-alloy ferritic steel, metallurgical deterioration caused by elevated temperature service, and decarburization. Additional factors that come out of pure operational conditions and stochastic parameters deteriorate the problem, which in some cases results in crack formation. The problem can be enhanced when crystallographic transitions occur at high temperatures. The focus of this paper is the study of failure in austenitic-ferritic transition joints in connection with simultaneous cell transition when the ferritic material temperature goes beyond the critical eutectoid temperature of the respective ferritic steel.
Predicting the life of steel rails
Authors: Garnham J E , Franklin F J , Fletcher D I , Kapoor A , Davis C L
Published: April 2007

A model of plastic strain accumulation, wear, and rolling contact fatigue (RCF) crack initiation in rail steel has been developed. Local to the contact zone, material is subject to severe cyclic stresses taking it beyond yield and leading to incremental accumulation of plastic deformation (ratcheting). This model is based on a ratcheting law derived from twin-disc, rolling-sliding contact experiments and can simulate thousands of ratcheting cycles with corresponding strain hardening.

The model is being further refined to account for detailed microstructural changes. Sections of worn and fatigued rail, removed from service, have been metallurgically analysed. To obtain further data on rail-steel deformation and RCF crack initiation, twin-disc tests have been performed using discs cut from across a railhead and wheel rim. Two heat treatments were applied to some rail discs to investigate the effect of pro-eutectoid ferrite phase distributions and volume fractions. Tests were run to failure (defined by an eddy current crack-detection system) and to percentages of fatigue lives. Micro- and nano-hardness tests, and microstructural observations, have been used to suggest a micromechanism of fatigue crack initiation for the model. Application of this model will contribute to reduced maintenance costs and an improved understanding of RCF development.
The railway as a socio-technical system: Human factors at the heart of successful rail engineering
Authors: Wilson J R , Farrington-Darby T , Cox G , Bye R , Hockey G R J
Published: April 2007

High-quality engineering and operations management are key to meeting all the requirements of a successful railway-quality of service, reliable and safe performance, and maximum possible use of capacity. However, the railway is a socio-technical system and therefore has human factors at its core, which requires a strong integrated ergonomics contribution. Moreover, this contribution must be at a systems level rather than providing point solutions to particular equipment, interface, workplace, or job problems. This paper draws from the first two human factors projects in the EPSRC Rail Research UK programme, interpreting them for an engineering audience. The paper first emphasizes and gives examples of the need for a systems ergonomics contribution to engineering an improved railway. Then the available literature is summarized in a structured fashion. Finally, a short summary is provided of the research which has started to develop a distributed cognition model of work on the railways, especially across functional groups of signalling, control, and train driving.
Low frequency motions and motion sickness on a tilting train
Authors: Donohew B E , Griffin M J
Published: April 2007

Tilting trains have been developed to reduce rail transport times by allowing greater train speeds without increased discomfort from increased lateral acceleration. It is reported that passengers on tilting trains experience motion sickness, but there have been few published studies of motions of tilting trains and the associated sickness. This paper presents the motion and motion sickness on an experimental tilting train during two trials: the first involved 200 subjects on five return journeys, the second involved 445 subjects and 14 return journeys. For each journey, lateral and vertical translational accelerations and roll velocities were measured in the passenger car-body. Simultaneously, subjects assessed their motion sickness at periodic intervals using an illness rating scale. The characteristics of the translational acceleration and roll velocity were investigated for each journey and the covariant relationships between the low frequency motions were explored. Illness ratings were found to be correlated with the vertical acceleration and roll velocity. A single motion variable is considered insufficient to predict motion sickness on tilting trains.
Effects of non-Newtonian rheology on the film-height history between non-parallel sliding-squeezing surfaces
Authors: Lin J-R , Teng M-Y , Ho M-H
Published: April 2007

The effects of flow rheology of non-Newtonian fluids on the time-dependent film-thickness history between non-parallel sliding-squeezing surfaces are studied. On the basis of the power-law fluid model, the hydrodynamic film pressure is obtained from the non-Newtonian dynamic Reynolds-type equation by considering the transient squeezing-action effect. The hydrodynamic film force is then applied to derive the non-linear motion equation of the squeezing part. Using the non-linear transient method, the film-height trajectory of the squeezing part is presented. The results of the present study provide a reference for engineer applications in machine tools, the matched gears, the rolling elements, and the piston-cylinder systems when viscosity-pressure dependence, viscosity-temperature variation, and elastic deformations of the contacting surfaces are neglected.
Surface roughness effect on the torque-tension relationship in threaded fasteners
Authors: Nassar S. A. , Sun T. S.
Published: April 2007

An experimental study is presented in order to investigate the effect of surface roughness on the torque-tension relationship in threaded fasteners. Three levels of surface roughness are considered for the fastener underhead and the joint surface; namely, low, medium, and high levels of surface roughness. The study is conducted for two joint materials, two fastener classes, and for coarse and fine threads. In this study, the torque-tension data are expressed in terms of the value of the nut factor as well as its scatter. The effect of the number of tightening on surface roughness and on the torque-tension relationship is investigated as well. The surface roughness is measured before tightening, and after each loosening using a WYKO optical profiling system. An M12 fastener is used in this study. Both fine and coarse threads and fastener material Classes 8.8 and 10.9 for M12 fasteners are used in this study. The torque-tension data is analysed for both steel and aluminium joints. The safety and reliability of bolted assemblies are mainly determined by the level and the stability of the clamp load provided by the initial tightening of the threaded fastener. The value of initial clamp load, which is achieved by a specific level of tightening torque, is highly sensitive to the friction torque components. This study provides an insight into the reliability of the existing engineering practices for estimating the clamp load level from the tightening torque. Hence, the findings of the study would help enhance the reliability and the safety of bolted assemblies, especially in critical applications.
Thermal elastohydrodynamic lubrication characteristics of couple stress fluids in rolling/sliding line contacts
Authors: Saini P. K. , Kumar P , Tandon P
Published: April 2007

A mathematical model is developed to analyse the effect of polymer additives on thermal elastohydrodynamic lubrication (EHL) behaviour under heavily-loaded rolling/sliding line contacts. The lubricant is assumed to be couple stress fluid and a non-dimensional couple stress parameter represents the molecular length of the additives. The Reynolds and mean temperature equations for the couple stress fluid (CSF) are derived using the rheological relationship presented by Stokes. The thermal EHL characteristics computed for polymer modified oils are found to have a strong dependence on the couple stress parameter. Polymer additives are shown to cause a significant increase in fluid-film thickness along with a noteworthy reduction in the coefficient of friction without any rise in fluid pressure. In addition, the polymer additives are found to cause a minimization of the thermal reduction in the fluid-film thickness as a well as decrease in fluid temperature, particularly under low speed-high load conditions, where fluid films are quite thin. These improvements are desirable in situations involving continuously varying slide to roll ratios, e.g. in gears.
Multi-body modelling and analysis into the non-linear behaviour of modern motorcycles
Authors: Meijaard J P , Popov A A
Published: April 2007

The stationary and periodic motion of a motorcycle under typical and extreme running conditions on a straight road and during cornering is investigated. The motorcycle model consists of six rigid bodies: a rear frame, a steering head with handlebar and the suspended part of the front fork, the unsuspended part of the front fork, a rear swing arm, and two wheels. The tyre force model deals effectively with large camber angles and combined longitudinal and lateral slips plus normal spin rate. The equations of motion are generated in a symbolic form by the multi-body dynamics program AutoSim. For analysing solutions of the equations of motion, the numerical continuation program AUTO 97 is employed.

Bifurcation diagrams for a motorcycle running straight ahead or in a circle are presented and discussed. The motorcycle can have three basic modes of instability: capsize, wobble, and weave mode. The results indicate that aerodynamic drag has a tendency to make the wobble mode more damped and the weave mode less damped. The emerging bifurcating periodic solutions are mostly of the subcritical kind for the weave and of the supercritical kind for the wobble.
Combined bounce, pitch, and roll dynamics of vehicles negotiating single speed bump events
Authors: Azman M , King P D , Rahnejat H
Published: April 2007

This paper investigates vehicle dynamic response for the increasingly common manoeuvre over single speed bumps, which is a non-trivial complex motion. One major aim of the study is to investigate the effect of the anti-roll bar upon vehicle body dynamics, while negotiating such traffic calming features. Numerical predictions are made with an intermediate vehicle model, whose results conform well to the actual vehicle tests. These results seem to suggest that events caused by truncated speed bumps can have implications for design of anti-roll bars from a ride comfort viewpoint, over and above the usual requirements dictated by safe vehicle handling.
Standard multi-body system software in the vehicle development process
Authors: Fischer E
Published: April 2007

In the developmental processes of a complex product, such as a passenger car, simulation software tools are used today to such an extent that the notion of a ‘virtual development process’ is justified, paralleling the hardware-based development process. In conjunction with several other software tools, a multi-body software system (MBS) can be an integral part of the virtual process, covering the area of suspension analysis and vehicle dynamics, provided it is tailored to the specific needs of the product, the software users, and the industrial organization. This article describes these needs by showing the context in which MBS is used, its interface with other tools, and the expectations of the users and concludes with an assessment of the current state.
A framework for the characterization of the transient handling responses of non-linear vehicles
Authors: Mavros G , Rahnejat H , King P D
Published: April 2007

The paper attempts to provide an integrated framework for the objective assessment of the transient handling responses of non-linear vehicles. The ultimate aim of the proposed framework is the characterization of such responses as neutral or under/over-steering. A new methodology is employed, which has previously been applied for the classification of the transient response of linear vehicles. The success of the proposed method is judged based on its robustness, the consistency of the results, and their practical implications. Furthermore, the results are compared with the findings of traditional approaches for the characterization of the steady-state and transient handling behaviour. The corresponding discussion reveals the agreement between the approaches, but also highlights the slightly different definition of the neutrally steering vehicle, as perceived by the proposed method.
Quantitative reliability and availability analysis for design evaluation of generic pod propulsion systems
Authors: Aksu S , Aksu S. K. , Turan O
Published: April 2007

Application of pod propulsion on a variety of vessels such as cruise ships, ropax, and tanker vessels has increased significantly over the last two decades owing to the benefits offered by pods. Despite the clear benefits, operators are still reluctant to have this innovation on board because of unknown overall reliability. Many of the published research efforts in the area of pod propulsion have been concentrated on hydrodynamics and manoeuvring aspects with little in the area of quantitative pod reliability assessment.

In this paper, the applicability and appropriateness of various quantitative fault tree solution techniques (exact and approximate) for the reliability assessment of a generic pod propulsion system are investigated. Also, the paper demonstrates that the proposed quantitative reliability assessment methodology can be used to make design changes by identifying critical components in system functionality and modifying the system with improvements, where needed.
Enhanced Hydrogen Adsorption/Desorption Characteristic of Ta2O5-coated Pt Electrode Prepared by Electrodeposition of Ta and the Subsequent Calcination
Authors: Sata Shunsuke , Okajima Takeyoshi , Kitamura Fusao , Kaneda Kazuhiro , Ohsaka Takeo
Published: April 2007

Ta2O5-coated Pt electrodes prepared by electrodeposition of Ta and the subsequent calcination were found to possess a remarkably enhanced adsorption/desorption characteristic of hydrogen atoms in sulfuric acid solutions compared with bare Pt electrodes. This enhancement can be explained by a spillover–reverse spillover of hydrogen atoms adsorbed at Pt sites over the Ta2O5 surface.
Effect of Solvent on the Lipase-catalyzed Synthesis of Poly(octanedioladipate-co-octanediolmalate)
Authors: Yao Dahu , Li Guangji , Zong Minhua
Published: April 2007

Terpolymer of 1,8-octanediol, adipic acid, and l-malic acid was synthesized via a lipase-catalyzed direct polycondensation in different organic solvents. The results of GPC show that an organic solvent possessing low polarity is a better organic medium for the lipase-catalyzed polymerization. The 1H NMR spectra of the obtained copolymer samples indicate that hydroxy groups of l-malic acid do not take part in the polymerization reaction.
Upregulation of Vascular Endothelial Growth Factor Receptors Flt-1 and Flk-1 Following Acute Spinal Cord Contusion in Rats
Authors: Choi Jeong-Sun , Kim Ha-Young , Cha Jung-Ho , Choi Jae-Youn , In Park Sang , Jeong Chang Hyun , Jeun Sin-Soo , Lee Mun-Yong
Published: April 2007

To investigate the possible role of vascular endothelial growth factor (VEGF) in the injured spinal cord, we analyzed the distribution and time course of the two tyrosine kinase receptors for VEGF, Flt-1 and Flk-1, in the rat spinal cord following contusion injury using a weight-drop impactor. The semi-quantitative RT-PCR analysis of Flt-1 and Flk-1 in the spinal cord showed slight upregulation of these receptors following spinal cord injury. Although mRNAs for Flt-1 and Flk-1 were constitutively expressed in neurons, vascular endothelial cells, and some astrocytes in laminectomy control rats, their upregulation was induced in association with microglia/macrophages and reactive astrocytes in the vicinity of the lesion within 1 day in rats with a contusion injury and persisted for at least 14 days. The spatiotemporal expression of Flt-1 in the contused spinal cord mirrored that of Flk-1 expression. In the early phase of spinal cord injury, upregulation of Flt-1 and Flk-1 mRNA occurred in microglia/macrophages that infiltrated the lesion. In addition, the expression of both receptors increased progressively in reactive astrocytes within the vicinity of the lesion, predominately in the white matter, and almost all reactive astrocytes coexpressed Flt-1 or Flk-1 and nestin. These results suggest that VEGF may be involved in the inflammatory response and the astroglial reaction to contusion injuries of the spinal cord via specific VEGF receptors. (J Histochem Cytochem 55: 821–830, 2007)
Proteome Analysis of Microdissected Formalin-fixed and Paraffin-embedded Tissue Specimens
Authors: Guo Tong , Wang Weijie , Rudnick Paul A. , Song Tao , Li Jie , Zhuang Zhengping , Weil Robert J. , DeVoe Don L. , Lee Cheng S. , Balgley Brian M.
Published: April 2007

Targeted proteomics research, based on the enrichment of disease-relevant proteins from isolated cell populations selected from high-quality tissue specimens, offers great potential for the identification of diagnostic, prognostic, and predictive biological markers for use in the clinical setting and during preclinical testing and clinical trials, as well as for the discovery and validation of new protein drug targets. Formalin-fixed and paraffin-embedded (FFPE) tissue collections, with attached clinical and outcome information, are invaluable resources for conducting retrospective protein biomarker investigations and performing translational studies of cancer and other diseases. Combined capillary isoelectric focusing/nano-reversed-phase liquid chromatography separations equipped with nano-electrospray ionization-tandem mass spectrometry are employed for the studies of proteins extracted from microdissected FFPE glioblastoma tissues using a heat-induced antigen retrieval (AR) technique. A total of 14,478 distinct peptides are identified, leading to the identification of 2733 non-redundant SwissProt protein entries. Eighty-three percent of identified FFPE tissue proteins overlap with those obtained from the pellet fraction of fresh-frozen tissue of the same patient. This large degree of protein overlapping is attributed to the application of detergent-based protein extraction in both the cell pellet preparation protocol and the AR technique.
Evaluation of a New Pooling Strategy Based on Leukocyte Count for Rapid Quantification of Allele Frequencies
Authors: Rossmann Heidi , Büchler Elena , Wenzel Jürgen J , Neukirch Carolin , du Prel Jean-Baptist , Lackner Karl J
Published: April 2007

Background: Allele frequencies of single-nucleotide polymorphisms (SNPs) can be quantified from DNA pools. The conventional preparation of DNA pools requires DNA isolation and quantification for each blood sample. We hypothesized that pooling of whole blood samples according to their leukocyte count, which determines DNA content, would be as reliable as the conventional pooling method but much less tedious to perform.

Methods: We collected 100 whole blood samples and measured the leukocyte count. Samples were frozen until further use. After thawing, pools were generated by combining aliquots containing an equal number of leukocytes. In parallel, DNA was extracted from another aliquot, DNA concentration was measured, and DNA concentration-based pools were assembled. All original samples were genotyped directly using 4 different SNP assays to obtain the exact allele frequencies in the pool. In addition, samples of known genotypes were mixed according to the DNA concentration or the leukocyte count to generate artificial samples of known allele frequencies. We analyzed pools and mixes in triplicate by pyrosequencing and calculated allelic frequencies.

Results: Leukocyte and DNA pooling provided equally accurate and precise SNP frequencies comparable to published data.

Conclusion: DNA and leukocyte pooling are both suitable strategies to determine allele frequencies in frozen samples. The leukocyte pooling approach is much less tedious, quicker, and less expensive. It should be always considered if leukocyte counts are available.
Biomass and leaf dynamics of Cymodocea nodosa in the Ria Formosa lagoon, South Portugal
Authors: Cunha Alexandra H. , Duarte Carlos M.
Published: April 2007

We describe shoot density, aboveground and belowground biomass, form and leaf production per shoot over a one-year cycle for Cymodocea nodosa meadows in the Ria Formosa lagoon (South Portugal). Habitat conditions in Ria Formosa allow the development of lush meadows (up to 1752 shoots m-2), supporting high shoot biomass (up to 945 g DW m-2), high leaf productivity (up to 14 g DW m-2 d-1) and large shoots (up to 113 cm leaf length) despite being located at the northern limit of the distributional range in the Atlantic Ocean. Biomass in the meadows examined is higher than other Atlantic sites with C. nodosa, and comparable to the most productive seagrass meadows yet reported. Shoot morphometry and biomass distribution were variable within Ria Formosa, with the stands growing in muddy sediments having a lower ratio of belowground/aboveground biomass than those in sandy sites. C. nodosa had a clear unimodal growth cycle, reaching maximum leaf development in summer. Mean leaf length and number of leaves per shoot, the rate of appearance of new leaves and the rate of leaf fall, average leaf growth and leaf turnover rates (P/B) were minimal in February and March, and maximal in July and September. The high production of the meadows examined may be related to the high nutrient availability in Ria Formosa, evidenced by the high leaf nutrient content (3.4% of DW and 0.38% of DW for nitrogen and phosphorus, respectively).
Mortality of shoots of Posidonia oceanica following meadow invasion by the red alga Lophocladia lallemandii
Authors: Ballesteros Enric , Cebrian Emma , Alcoverro Teresa
Published: April 2007

Lophocladia lallemandii, an Indo-Pacific alga that is currently invading several Mediterranean areas, is especially aggressive when colonizing meadows of Posidonia oceanica in Formentera (Balearic Islands). L. lallemandii settles on rhizomes and old leaves situated mainly at meadow edges and in low density Posidonia patches, growing rapidly, producing disc-like holdfasts along the thalli that allow formation of a mat of the red algal filaments intermingled with P. oceanica leaves. This mat can get so thick and dense that new leaves become confined inside the web of red algal filaments. The seagrass leaves display chlorosis and sometimes die. Invasion by L. lallemandii significantly reduces seagrass shoot size, leaf biomass, and percentage of living shoots. A lower content of sucrose in shoots from invaded plots points to a reduction of photosynthetic activity. However, other causes such as enhanced sediment trapping, organic and nutrient enrichment inside the algal carpet, and increased oxygen consumption may jointly or individually contribute to observed seagrass shoot demise.
Check-list of seaweeds recorded in the last 20 years in Venice lagoon, and a comparison with the previous records
Authors: Sfriso Adriano , Curiel Daniele
Published: April 2007

We present a check-list of the seaweeds for Venice lagoon, based on literature and recent records. At present the total number of taxa is 277, including 71 Chlorophyceae s.l. (25.6%), 148 Rhodophyceae (53.4%), 56 Phaeophyceae (20.2%) and 2 Chrysophyceae (0.7%). Using present day taxonomy, the number of taxa is about double that in previous lists. Since 1983, there have been 92 (ca. 33%) new records for Venice littoral zone. Of these, 19 (ca. 21%) are first records for the Mediterranean Sea, and many are alien taxa that seriously compete with the growth of indigenous species. The number of taxa that have disappeared from the lagoon, or have not been found in the recent years, is 96.
Concentrations of iodide and total iodine in edible seaweeds harvested on the Galician coast (Northwest Spain)
Authors: Moreda-Piñeiro Antonio , Bermejo-Barrera Adela , Bermejo-Barrera Pilar
Published: April 2007

We developed a rapid and feasible method to determine total iodine and iodide in edible seaweeds by an inexpensive analytical technique, catalytic spectrophotometry. Seaweed samples were solubilized by applying a microwave-assisted alkaline digestion with tetramethylammonium hydroxide (TMAH). The percentage of iodide was measured directly in the alkaline digests by observing the catalytic effect of iodide on the oxidation of As(III) by Ce(IV) in H2SO4/HCl medium. In order to determine total iodine, a microwave-assisted sodium tetrahydroborate (NaBH4) reduction was optimized. After this treatment, all iodine species present in the alkaline digests were reduced to iodide. Microwave-assisted alkaline digestion was performed using 7.5 ml of TMAH and irradiating samples at 670 W for two 5.5 min steps. Microwave-assisted NaBH4 reduction was carried out using 2.5 ml of the alkaline digest, 3.0 ml of a 10% (m/v) NaBH4 solution and 2.0 ml of 5.0 M hydrochloric acid, at a microwave power of 360 W for 3.5 min. The linear calibration ranges were 0.30–20.0 and 0.43–20.0 μg l-1 for iodide determination and total iodine determination, respectively. The limit of detection was 9.2 μg g-1 for iodide and 54.0 μg g-1 for total iodine. Repeatability of the overall procedures, expressed as RSD for eleven determinations, was 10.4% (microwave-assisted alkaline digestion followed by microwave-assisted NaBH4 reduction for the determination of total iodine). Accuracy of the method was assessed by analyzing the NIES-09 (Sargasso) certified reference material. Edible seaweed analysis has shown that most of the iodine is present as iodide in brown seaweed samples (90% of the total iodine), while red seaweeds have iodide percentages lower than 30% and green seaweeds lower than 80%.
Temporal Dynamics and Linkage Disequilibrium in NaturalCaenorhabditis elegansPopulations
Authors: Barrière Antoine , Félix Marie-Anne
Published: April 2007

Caenorhabditis elegans is a major laboratory model system yet a newcomer to the field of population genetics, and relatively little is known of its biology in the wild. Recent studies of natural populations at a single time point revealed strong spatial population structure and suggested that these populations may be very dynamic. We have therefore studied several natural C. elegans populations over time and genotyped them at polymorphic microsatellite loci. While some populations appear to be genetically stable over the course of observation, others seem to go extinct, with full replacement of multilocus genotypes upon regrowth. The frequency of heterozygotes indicates that outcrossing occurs at a mean frequency of 1.7% and is variable between populations. However, in genetically stable populations, linkage disequilibrium between different chromosomes can be maintained over several years at a level much higher than expected from the heterozygote frequency. C. elegans seems to follow metapopulation dynamics, and the maintenance of linkage disequilibrium despite a low yet significant level of outcrossing suggests that selection may act against the progeny of outcrossings.
An Exact Nonparametric Method for Inferring Mosaic Structure in Sequence Triplets
Authors: Boni Maciej F , Posada David , Feldman Marcus W
Published: April 2007

Statistical tests for detecting mosaic structure or recombination among nucleotide sequences usually rely on identifying a pattern or a signal that would be unlikely to appear under clonal reproduction. Dozens of such tests have been described, but many are hampered by long running times, confounding of selection and recombination, and/or inability to isolate the mosaic-producing event. We introduce a test that is exact, nonparametric, rapidly computable, free of the infinite-sites assumption, able to distinguish between recombination and variation in mutation/fixation rates, and able to identify the breakpoints and sequences involved in the mosaic-producing event. Our test considers three sequences at a time: two parent sequences that may have recombined, with one or two breakpoints, to form the third sequence (the child sequence). Excess similarity of the child sequence to a candidate recombinant of the parents is a sign of recombination; we take the maximum value of this excess similarity as our test statistic Δm,n,b. We present a method for rapidly calculating the distribution of Δm,n,b and demonstrate that it has comparable power to and a much improved running time over previous methods, especially in detecting recombination in large data sets.
Genetic Improvement of Traits Affected by Interactions Among Individuals: Sib Selection Schemes
Authors: Ellen Esther D , Muir William M , Teuscher Friedrich , Bijma Piter
Published: April 2007

Livestock populations are usually kept in groups. As a consequence, social interactions among individuals affect productivity, health, and welfare. Current selection methods (individual selection), however, ignore those interactions and yield suboptimal or in some cases even negative responses. In principle, selection between groups instead of individuals offers a solution, but has rarely been adopted in practice for two reasons. First, the relationship between group selection theory and common animal breeding concepts, such as the accuracy of selection, is unclear. Second, application of group selection requires keeping selection candidates in groups, which is often undesirable in practice. This work has two objectives. First, we derive expressions for the accuracy of individual and group selection, which provides a measurement of quality for those methods. Second, we investigate the opportunity to improve traits affected by interactions by using information on relatives kept in family groups, while keeping selection candidates individually. The accuracy of selection based on relatives is shown to be an analogy of the classical expression for traits not affected by interactions. Our results show that selection based on relatives offers good opportunities for effective genetic improvement of traits affected by interactions.
The Biologically Relevant Targets and Binding Affinity Requirements for the Function of the Yeast Actin-Binding Protein 1 Src-Homology 3 Domain Vary With Genetic Context
Authors: Haynes Jennifer , Garcia Bianca , Stollar Elliott J , Rath Arianna , Andrews Brenda J , Davidson Alan R
Published: April 2007

Many protein–protein interaction domains bind to multiple targets. However, little is known about how the interactions of a single domain with many proteins are controlled and modulated under varying cellular conditions. In this study, we investigated the in vivo effects of Abp1p SH3 domain mutants that incrementally reduce target-binding affinity in four different yeast mutant backgrounds in which Abp1p activity is essential for growth. Although the severity of the phenotypic defects observed generally increased as binding affinity was reduced, some genetic backgrounds (prk1Δ and sla1Δ) tolerated large affinity reductions while others (sac6Δ and sla2Δ) were much more sensitive to these reductions. To elucidate the mechanisms behind these observations, we determined that Ark1p is the most important Abp1p SH3 domain interactor in prk1Δ cells, but that interactions with multiple targets, including Ark1p and Scp1p, are required in the sac6Δ background. We establish that the Abp1p SH3 domain makes different, functionally important interactions under different genetic conditions, and these changes in function are reflected by changes in the binding affinity requirement of the domain. These data provide the first evidence of biological relevance for any Abp1p SH3 domain-mediated interaction. We also find that considerable reductions in binding affinity are tolerated by the cell with little effect on growth rate, even when the actin cytoskeletal morphology is significantly perturbed.
toutvelu, a Regulator of Heparan Sulfate Proteoglycan Biosynthesis, Controls Guidance Cues for Germ-Cell Migration
Authors: Deshpande Girish , Sethi Nilay , Schedl Paul
Published: April 2007

The primitive embryonic gonad in Drosophila melanogaster is composed of germ cells and somatic gonadal precursor cells (SGPs). The assembly of a functional gonad involves a complex series of germ-cell migration events, which are thought to be guided by attractive and repulsive cues. Here, we demonstrate a novel role for toutvelu (ttv), a regulator of heparan sulfate proteoglycan biosynthesis during this process. Germline clonal analysis suggests that maternal deposition of ttv is required for proper germ-cell migration. Conversely, ectopic expression of ttv in early embryos results in severe germ-cell migration defects and inappropriate spreading of Hh protein. Moreover, overexpression of ttv in only the receiving cells, rather than in the sending cells, leads to phenotypic consequences. Finally, supporting the claim that the signaling molecule Hedgehog (Hh) may function as a chemoattractant to guide germ cells, errant germ cells are found localized near pockets containing high concentrations of Hh protein.
Divergent Regulatory OsMADS2 Functions Control Size, Shape and Differentiation of the Highly Derived Rice Floret Second-Whorl Organ
Authors: Yadav Shri Ram , Prasad Kalika , Vijayraghavan Usha
Published: April 2007

Functional diversification of duplicated genes can contribute to the emergence of new organ morphologies. Model eudicot plants like Arabidopsis thaliana and Antirrhinum majus have a single PI/GLO gene that together with AP3/DEF regulate petal and stamen formation. Lodicules of grass flowers are morphologically distinct reduced organs occupying the position of petals in other flowers. They serve a distinct function in partial and transient flower opening to allow stamen emergence and cross-pollination. Grasses have duplicated PI/GLO-like genes and in rice (Oryza sativa) one these genes, OsMADS2, controls lodicule formation without affecting stamen development. In this study, we investigate the mechanistic roles played by OsMADS2. We ascribe a function for OsMADS2 in controlling cell division and differentiation along the proximal–distal axis. OsMADS2 is required to trigger parenchymatous and lodicule-specific vascular development while maintaining a small organ size. Our data implicate the developmentally late spatially restricted accumulation of OsMADS2 transcripts in the differentiating lodicule to control growth of these regions. The global architecture of transcripts regulated by OsMADS2 gives insights into the regulation of cell division and vascular differentiation that together can form this highly modified grass organ with important functions in floret opening and stamen emergence independent of the paralogous gene OsMADS4.
The Centromeric Retrotransposons of Rice Are Transcribed and Differentially Processed by RNA Interference
Authors: Neumann Pavel , Yan Huihuang , Jiang Jiming
Published: April 2007

Retrotransposons consist of significant portions of many complex eukaryotic genomes and are often enriched in heterochromatin. The centromeric retrotransposon (CR) family in grass species is colonized in the centromeres and highly conserved among species that have been diverged for >50 MY. These unique characteristics have inspired scientists to speculate about the roles of CR elements in organization and function of centromeric chromatin. Here we report that the CRR (CR of rice) elements in rice are highly enriched in chromatin associated with H3K9me2, a hallmark for heterochromatin. CRR elements were transcribed in root, leaf, and panicle tissues, suggesting a constitutive transcription of this retrotransposon family. However, the overall transcription level was low and the CRR transcripts appeared to be derived from relatively few loci. The majority of the CRR transcripts had chimerical structures and contained only partial CRR sequences. We detected small RNAs (smRNAs) cognate to nonautonomous CRR1 (noaCRR1) and CRR1, but not CRR2 elements. This result was also confirmed by in silico analysis of rice smRNA sequences. These results suggest that different CRR subfamilies may play different roles in the RNAi-mediated pathway for formation and maintenance of centromeric heterochromatin.
Suppression of the Schizosaccharomyces pombe
cut12.1 Cell-Cycle Defect by Mutations in cdc25 and Genes Involved in Transcriptional and Translational Control
Authors: Tallada Victor A , Bridge Alan J , Emery Patrick A , Hagan Iain M
Published: April 2007

Cdc25 phosphatase primes entry to mitosis by removing the inhibitory phosphate that is transferred to mitosis promoting factor (MPF) by Wee1 related kinases. A positive feedback loop then boosts Cdc25 and represses Wee1 activities to drive full-scale MPF activation and commitment to mitosis. Dominant mutations in the Schizosaccharomyces pombe spindle pole body (SPB) component Cut12 enable cdc25.22 mutants to overcome a G2 arrest at 36° and enter mitosis. The recessive temperature-sensitive cut12.1 mutation results in the formation of monopolar spindles in which the spindle pole marker Sad1 is enriched on the nonfunctional SPB at 36°. We identified mutations at five loci that suppressed the lethality of the recessive cut12.1 mutation at 36° and conferred lethality at 20°. Three of the five mutations led to the formation of monopolar spindles at restrictive temperatures, affected cell size at commitment to mitosis, and generated multiple Sad1 foci at nuclear periphery. The five loci, tfb2.rt1, tfb5.rt5, pla1.rt3, rpl4301.rt4, and rot2.1, and multicopy suppressors, including tfb1+ and dbp10+, are involved in transcription, translation, or RNA processing, prompting us to establish that elevating Cdc25 levels with the dominant cdc25.d1 allele, suppressed cut12.1. Thus, rot mutants provide a further link between protein production and cell-cycle progression.
Interphase Chromosome Arrangement in Arabidopsis thaliana Is Similar in Differentiated and Meristematic Tissues and Shows a Transient Mirror Symmetry After Nuclear Division
Authors: Berr Alexandre , Schubert Ingo
Published: April 2007

Whole-mount fluorescence in situ hybridization (FISH) was applied to Arabidopsis thaliana seedlings to determine the three-dimensional (3D) interphase chromosome territory (CT) arrangement and heterochromatin location within the positional context of entire tissues or in particular cell types of morphologically well-preserved seedlings. The interphase chromosome arrangement was found to be similar between all inspected meristematic and differentiated root and shoot cells, indicating a lack of a gross reorganization during differentiation. The predominantly random CT arrangement (except for a more frequent association of the homologous chromosomes bearing a nucleolus organizer) and the peripheric location of centromeric heterochromatin were as previously observed for flow-sorted nuclei, but centromeres tend to fuse more often in nonendoreduplicating cells and NORs in differentiated cells. After mitosis, sister nuclei revealed a symmetric arrangement of homologous CTs waning with the progress of the cell cycle or in the course of differentiation. Thus, the interphase chromosome arrangement in A. thaliana nuclei seems to be constrained mainly by morphological features such as nuclear shape, presence or absence of a nucleolus organizer on chromosomes, nucleolar volume, and/or endopolyploidy level.
Factors Influencing the Hooking Mortality of Walleyes Caught by Recreational Anglers on Mille Lacs, Minnesota
Authors: Reeves Keith A. , Bruesewitz Richard E.
Published: April 2007

Recent implementation of size-based regulations in recreational fisheries for walleye Sander vitreus have led to more released walleyes and presumably to more losses of released fish. We conducted this study to estimate hooking mortality in Mille Lacs, Minnesota, and to determine factors that influence the survival of released walleyes. Volunteers and Minnesota Department of Natural Resources employees sampled walleyes with common angling methods in 2003 and 2004 on Mille Lacs (n = 1,246). Simple hooking mortality rates ranged from 0% (95% confidence interval = 0–1.8%; n = 204) in May, when lake water temperatures were less than 20°C, to 12.2% (9.2–15.9%; n = 392) in the July–August period, when lake water temperatures were at least 20°C. We used logistic regression within generalized linear or additive models to determine influential variables. Hooking mortality was most associated with water temperature, bleeding, fish length, hook location, and fish floating upon release. Mortality increased as the water warmed above 18°C and was higher for fish that bled at temperatures less than 24°C but similar for both bleeding and nonbleeding fishes at temperatures of 24°C or more. Fish hooked in the throat or stomach died at higher rates than fish hooked in the jaw, inner mouth, or gills and those that were externally foul-hooked, especially when they were smaller. Although fish of medium length (300–600 mm) were more likely to be deep hooked, they died less frequently than walleyes of other lengths. Cutting the line did not significantly improve survival in deeply hooked fish. Mortality was similar between live bait jigs and live bait regular hooks. Most observed hooking mortality was caused by damage to major internal organs. Hooking mortality is minimized when anglers fish in cool water, use active fishing methods, and catch medium-length walleyes.