bluuebunny/crossref_metadata_2025_split huggingface dataset:
The generation of feeding currents by flagellar motions
Authors: Higdon J. J. L. 
Published: April 2006

The use of flagella by sessile organisms to generate feeding currents is analysed. The organism consists of a spherical cell body (radius A) to which a smooth flagellum (radius a, length L) is attached radially. The cell body is a height H above the plane substrate to which it is rigidly attached via a stalk. The organism propagates plane sinusoidal waves (amplitude α, wavenumber k) from base to tip. The flagellum is represented by distributions of stokeslets and dipoles along its centre-line. The cell body and substrate are modelled by employing an approximate form of the Green's function for the sphere in the half space. The error terms in the model are O(a/L) and O(A2/H2). The analysis and method of solution are adapted from Higdon (1979).The mean flow rate and power consumption are calculated for a wide range of parameters. Optimal motions are determined with the criterion of minimizing the power required to achieve a given flow rate. The optimum wave has maximum slope in the range 2 < αk < 2·5 (compared to the optimum value αk = 1 for swimming). The optimum number of waves Nλ increases linearly with flagellar length for L/A > 10 and is approximately constant, Nλ = 1, for shorter flagella. The optimum flagellar length is in the range 5 < L/A < 10. There is no optimum flagellar radius a/A. For optimal efficiency, the height H should be greater than or equal to the length of the flagellum.The optimum values of the parameters are compared to the values for the choano-flagellates described by Lapage (1925) and Sleigh (1964). Excellent agreement is found between the predicted optima and the observed values. The calculated velocity field closely resembles the flow described by Sleigh and Lapage.
Algebraic disturbances in stratified shear flows
Authors: Chimonas G. 
Published: April 2006

Algebraic disturbances, a non-modal component of the linear perturbation fields, are shown to be an essential feature of stratified shear flows. We find that they must be included even in situations where the modes form a complete set, for such completeness does not extend to the space of these ill-behaved functions.If the Richardson number Ri is less than ¼ anywhere in the flow, the algebraic disturbances are very generally instabilities of the system, growing without limit as time t → ∞.Both of these results are in direct contradiction with the currently accepted viewpoint. We examine the previous research in this field to locate the source of this discrepancy.The algebraic instabilities are not form preserving, and display extreme distortion as they evolve. In the asymptotic limit they appear as quasi-horizontal flow fields, with a vertical ‘wavelength’ that tends to zero. As such, they must be expected to induce secondary shear instabilities and cascade into motions of smaller (horizontal) scale.
Linear stability of Poiseuille flow in a circular pipe
Authors: Salwen Harold , Cotton Fredrick W. , Grosch Chester E. 
Published: April 2006

Correction of an error in the matrix elements used by Salwen & Grosch (1972) has brought the results of the matrix-eigenvalue calculation of the linear stability of Hagen–Poiseuille flow into complete agreement with the numerical integration results of Lessen, Sadler & Liu (1968) for azimuthal index n = 1. The n = 0 results were unaffected by the error and the effect of the error for n > 1 is smaller than for n = 1. The new calculations confirm the conclusion that the flow is stable to infinitesimal disturbances.Further calculations have led to the discovery of a degeneracy at Reynolds number R = 61·452 ± 0·003 and wavenumber α = 0·9874 ± 0·0001, where the second and third eigenmodes have equal complex wave speeds. The variation of wave speed for these two modes has been studied in the vicinity of the degeneracy and shows similarities to the behaviour near the degeneracies found by Cotton and Salwen (see Cotton 1977) for rotating Hagen-Poiseuille flow. Finally, new results are given for n = 10 and 30; the n = 1 results are extended to R = 106; and new results are presented for the variation of the wave speed with αR at high Reynolds number. The high-R results confirm both Burridge & Drazin's (1969) slow-mode approximation and more recent fast-mode results of Burridge.
Mean flows driven by weak eddies in rotating systems
Authors: Mcewan A. D. , Thompson R. O. R. Y. , Plumb R. A. 
Published: April 2006

General relations are derived for the forcing of a mean zonal flow in a damped rotating barotropic system through the action of weak eddies. In particular it is found that if the eddies are forced at localized latitudes the induced motion away from these latitudes is likely to be counter to the rotation (i.e. ‘easterly’). Over the forcing latitude the mean motion is always westerly except when the forcing provides a sink of relative momentum. In the case when the background field is deformed topographically to generate eddies the divergence of the Reynolds stress is balanced at lowest order by a dynamic pressure drag, and the mean motion takes the direction of propagation of the forcing.The relations are applied to a linearized Rossby wave field in a viscous fluid driven by a moving system of boundary sources and sinks or hills and hollows. The results are compared with laboratory experiments. All major predictions are confirmed qualitatively, but the discrepancies in detail indicate the influence of nonlinear effects other than those incorporated in the theory.
A strong interaction theory for the creeping motion of a sphere between plane parallel boundaries. Part 2. Parallel motion
Authors: Ganatos Peter , Pfeffer Robert , Weinbaum Sheldon 
Published: April 2006

Exact solutions are presented for the three-dimensional creeping motion of a sphere of arbitrary size and position between two plane parallel walls for the following conditions: (a) pure translation parallel to two stationary walls, (b) pure rotation about an axis parallel to the walls, (c) Couette flow past a rigidly held sphere induced by the motion of one of the boundaries and (d) two-dimensional Poiseuille flow past a rigidly held sphere in a channel. The combined analytic and numerical solution procedure is the first application for bounded flow of the three-dimensional boundary collocation theory developed in Ganatos, Pfeffer & Weinbaum (1978). The accuracy of the solution technique is tested by detailed comparison with the exact bipolar co-ordinate solutions of Goldman, Cox & Brenner (1967a, b) for the drag and torque on a sphere translating parallel to a single plane wall, rotating adjacent to the wall or in the presence of a shear field. In all cases, the converged collocation solutions are in perfect agreement with the exact solutions for all spacings tested. The new collocation solutions have also been used to test the accuracy of existing solutions for the motion of a sphere parallel to two walls using the method of reflexions technique. The first-order reflexion theory of Ho & Leal (1974) provides reasonable agreement with the present results for the drag when the sphere is five or more radii from both walls. At closer spacings first-order reflexion theory is highly inaccurate and predicts an erroneous direction for the torque on the sphere for a wide range of sphere positions. Comparison with the classical higher-order method of reflexions solutions of Faxen (1923) reveals that the convergence of the multiple reflexion series solution is poor when the sphere centre is less than two radii from either boundary.Solutions have also been obtained for the fluid velocity field. These solutions show that, for certain wall spacings and particle positions, a separated region of closed streamlines forms adjacent to the sphere which reverses the direction of the torque acting on a translating sphere.
The steady flow due to a rotating sphere at low and moderate Reynolds numbers
Authors: Dennis S. C. R. , Singh S. N. , Ingham D. B. 
Published: April 2006

The problem of determining the steady axially symmetrical motion induced by a sphere rotating with constant angular velocity about a diameter in an incompressible viscous fluid which is at rest at large distances from it is considered. The basic independent variables are the polar co-ordinates (r, θ) in a plane through the axis of rotation and with origin at the centre of the sphere. The equations of motion are reduced to three sets of nonlinear second-order ordinary differential equations in the radial variable by expanding the flow variables as series of orthogonal Gegenbauer functions with argument μ = cosθ. Numerical solutions of the finite set of equations obtained by truncating the series after a given number of terms are obtained. The calculations are carried out for Reynolds numbers in the range R = 1 to R = 100, and the results are compared with various other theoretical results and with experimental observations.The torque exerted by the fluid on the sphere is found to be in good agreement with theory at low Reynolds numbers and appears to tend towards the results of steady boundary-layer theory for increasing Reynolds number. There is excellent agreement with experimental results over the range considered. A region of inflow to the sphere near the poles is balanced by a region of outflow near the equator and as the Reynolds number increases the inflow region increases and the region of outflow becomes narrower. The radial velocity increases with Reynolds number at the equator, indicating the formation of a radial jet over the narrowing region of outflow. There is no evidence of any separation of the flow from the surface of the sphere near the equator over the range of Reynolds numbers considered.
Mutations in the MicroRNA Complementarity Site of the INCURVATA4 Gene Perturb Meristem Function and Adaxialize Lateral Organs in Arabidopsis
Authors: Ochando Isabel , Jover-Gil Sara , Ripoll Juan José , Candela Héctor , Vera Antonio , Ponce María Rosa , Martínez-Laborda Antonio , Micol José Luis 
Published: April 2006

Abstract
Here, we describe how the semidominant, gain-of-function icu4-1 and icu4-2 alleles of the INCURVATA4 (ICU4) gene alter leaf phyllotaxis and cell organization in the root apical meristem, reduce root length, and cause xylem overgrowth in the stem. The ICU4 gene was positionally cloned and found to encode the ATHB15 transcription factor, a class III homeodomain/leucine zipper family member, recently named CORONA. The icu4-1 and icu4-2 alleles bear the same point mutation that affects the microRNA complementarity site of ICU4 and is identical to those of several semidominant alleles of the class III homeodomain/leucine zipper family members PHABULOSA and PHAVOLUTA. The icu4-1 and icu4-2 mutations significantly increase leaf transcript levels of the ICU4 gene. The null hst-1 allele of the HASTY gene, which encodes a nucleocytoplasmic transporter, synergistically interacts with icu4-1, the double mutant displaying partial adaxialization of rosette leaves and carpels. Our results suggest that the ICU4 gene has an adaxializing function and that it is down-regulated by microRNAs that require the HASTY protein for their biogenesis.
Systematic Analysis of Arabidopsis Organelles and a Protein Localization Database for Facilitating Fluorescent Tagging of Full-Length Arabidopsis Proteins
Authors: Li Shijun , Ehrhardt David W. , Rhee Seung Y. 
Published: April 2006

Abstract
Cells are organized into a complex network of subcellular compartments that are specialized for various biological functions. Subcellular location is an important attribute of protein function. To facilitate systematic elucidation of protein subcellular location, we analyzed experimentally verified protein localization data of 1,300 Arabidopsis (Arabidopsis thaliana) proteins. The 1,300 experimentally verified proteins are distributed among 40 different compartments, with most of the proteins localized to four compartments: mitochondria (36%), nucleus (28%), plastid (17%), and cytosol (13.3%). About 19% of the proteins are found in multiple compartments, in which a high proportion (36.4%) is localized to both cytosol and nucleus. Characterization of the overrepresented Gene Ontology molecular functions and biological processes suggests that the Golgi apparatus and peroxisome may play more diverse functions but are involved in more specialized processes than other compartments. To support systematic empirical determination of protein subcellular localization using a technology called fluorescent tagging of full-length proteins, we developed a database and Web application to provide preselected green fluorescent protein insertion position and primer sequences for all Arabidopsis proteins to study their subcellular localization and to store experimentally verified protein localization images, videos, and their annotations of proteins generated using the fluorescent tagging of full-length proteins technology. The database can be searched, browsed, and downloaded using a Web browser at http://aztec.stanford.edu/gfp/. The software can also be downloaded from the same Web site for local installation.
Subcellular Localization and Membrane Topology of the Melon Ethylene Receptor CmERS1
Authors: Ma Biao , Cui Min-Long , Sun Hyeon-Jin , Takada Keita , Mori Hitoshi , Kamada Hiroshi , Ezura Hiroshi 
Published: April 2006

Abstract
Ethylene receptors are multispanning membrane proteins that negatively regulate ethylene responses via the formation of a signaling complex with downstream elements. To better understand their biochemical functions, we investigated the membrane topology and subcellular localization of CmERS1, a melon (Cucumis melo) ethylene receptor that has three putative transmembrane domains at the N terminus. Analyses using membrane fractionation and green fluorescent protein imaging approaches indicate that CmERS1 is predominantly associated with the endoplasmic reticulum (ER) membrane. Detergent treatments of melon microsomes showed that the receptor protein is integrally bound to the ER membrane. A protease protection assay and N-glycosylation analysis were used to determine membrane topology. The results indicate that CmERS1 spans the membrane three times, with its N terminus facing the luminal space and the large C-terminal portion lying on the cytosolic side of the ER membrane. This orientation provides a platform for interaction with the cytosolic signaling elements. The three N-terminal transmembrane segments were found to function as topogenic sequences to determine the final topology. High conservation of these topogenic sequences in all ethylene receptor homologs identified thus far suggests that these proteins may share the same membrane topology.
Functional Analysis of anArabidopsisTranscription Factor, DREB2A, Involved in Drought-Responsive Gene Expression
Authors: Sakuma Yoh , Maruyama Kyonoshin , Osakabe Yuriko , Qin Feng , Seki Motoaki , Shinozaki Kazuo , Yamaguchi-Shinozaki Kazuko 
Published: April 2006

AbstractTranscription factors DREB1A/CBF3 and DREB2A specifically interact with cis-acting dehydration-responsive element/C-repeat (DRE/CRT) involved in cold and drought stress–responsive gene expression in Arabidopsis thaliana. Intact DREB2A expression does not activate downstream genes under normal growth conditions, suggesting that DREB2A requires posttranslational modification for activation, but the activation mechanism has not been clarified. DREB2A domain analysis using Arabidopsis protoplasts identified a transcriptional activation domain between residues 254 and 335, and deletion of a region between residues 136 and 165 transforms DREB2A to a constitutive active form. Overexpression of constitutive active DREB2A resulted in significant drought stress tolerance but only slight freezing tolerance in transgenic Arabidopsis plants. Microarray and RNA gel blot analyses revealed that DREB2A regulates expression of many water stress–inducible genes. However, some genes downstream of DREB2A are not downstream of DREB1A, which also recognizes DRE/CRT but functions in cold stress–responsive gene expression. Synthetic green fluorescent protein gave a strong signal in the nucleus under unstressed control conditions when fused to constitutive active DREB2A but only a weak signal when fused to full-length DREB2A. The region between DREB2A residues 136 and 165 plays a role in the stability of this protein in the nucleus, which is important for protein activation.
The Molecular Basis of Temperature Compensation in the Arabidopsis Circadian Clock
Authors: Gould Peter D. , Locke James C.W. , Larue Camille , Southern Megan M. , Davis Seth J. , Hanano Shigeru , Moyle Richard , Milich Raechel , Putterill Joanna , Millar Andrew J. , Hall Anthony 
Published: April 2006

Abstract
Circadian clocks maintain robust and accurate timing over a broad range of physiological temperatures, a characteristic termed temperature compensation. In Arabidopsis thaliana, ambient temperature affects the rhythmic accumulation of transcripts encoding the clock components TIMING OF CAB EXPRESSION1 (TOC1), GIGANTEA (GI), and the partially redundant genes CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY). The amplitude and peak levels increase for TOC1 and GI RNA rhythms as the temperature increases (from 17 to 27°C), whereas they decrease for LHY. However, as temperatures decrease (from 17 to 12°C), CCA1 and LHY RNA rhythms increase in amplitude and peak expression level. At 27°C, a dynamic balance between GI and LHY allows temperature compensation in wild-type plants, but circadian function is impaired in lhy and gi mutant plants. However, at 12°C, CCA1 has more effect on the buffering mechanism than LHY, as the cca1 and gi mutations impair circadian rhythms more than lhy at the lower temperature. At 17°C, GI is apparently dispensable for free-running circadian rhythms, although partial GI function can affect circadian period. Numerical simulations using the interlocking-loop model show that balancing LHY/CCA1 function against GI and other evening-expressed genes can largely account for temperature compensation in wild-type plants and the temperature-specific phenotypes of gi mutants.
Independent Ancient Polyploidy Events in the Sister Families Brassicaceae and Cleomaceae
Authors: Schranz M. Eric , Mitchell-Olds Thomas 
Published: April 2006

AbstractRecent studies have elucidated the ancient polyploid history of the Arabidopsis thaliana (Brassicaceae) genome. The studies concur that there was at least one polyploidy event occurring some 14.5 to 86 million years ago (Mya), possibly near the divergence of the Brassicaceae from its sister family, Cleomaceae. Using a comparative genomics approach, we asked whether this polyploidy event was unique to members of the Brassicaceae, shared with the Cleomaceae, or an independent polyploidy event in each lineage. We isolated and sequenced three genomic regions from diploid Cleome spinosa (Cleomaceae) that are each homoeologous to a duplicated region shared between At3 and At5, centered on the paralogs of SEPALLATA (SEP) and CONSTANS (CO). Phylogenetic reconstructions and analysis of synonymous substitution rates support the hypothesis that a genomic triplication in Cleome occurred independently of and more recently than the duplication event in the Brassicaceae. There is a strong correlation in the copy number (single versus duplicate) of individual genes, suggesting functionally consistent influences operating on gene copy number in these two independently evolving lineages. However, the amount of gene loss in Cleome is greater than in Arabidopsis. The genome of C. spinosa is only 1.9 times the size of A. thaliana, enabling comparative genome analysis of separate but related polyploidy events.
Factors Associated with High Milk Test Day Somatic Cell Counts in Large Dairy Herds in Brandenburg. II. Milking Practices
Authors: Köster G. , Tenhagen B.‐A. , Scheibe N. , Heuwieser W. 
Published: April 2006

SummaryThe objective of this study was to examine the influences of different milking practices on cow udder health in 80 large dairy herds (range 100–1100 cows) in Brandenburg, Germany. Milking practices were evaluated during one complete milking using a standardized data capture form. The somatic cell count (SCC) of all lactating cows on each farm was determined monthly by the local milk recording association ‘Landeskontrollverband Brandenburg’. Factor analysis was used to investigate the relationship between the different aspects of the milking practices. The components extracted by the factor analysis were examined for their influence on the SCC of the current month (CMSCC) and the year before the visit (YASCC) using univariate analysis of variance. Three components were extracted from the milking practices. ‘Reasonable use of water’ was significantly related to CMSCC (P = 0.019) and YASCC (P = 0.003). It included information on the use of a hose to clean udders before milking, cleaning of the floor between groups and use of water to clean teats. ‘Attention of the milkers’ was also significantly associated with CMSCC (P = 0.012) and YASCC (P = 0.014). It included information on the accuracy of mastitis detection by foremilk screening and the regular use of post‐milking teat and cluster disinfection. The component ‘preparation routines’ (method of udder cleaning and forestripping) did not significantly influence CMSCC and YASCC. These results indicate that excessive use of water in the parlour during milking time is harmful to udder health and that the consistency of procedures in the milking parlour presents significant room for improvement in large dairy herds in Brandenburg.
Dispute Settlement under the UN Convention on the Law of the Sea: Survey for 2004
Authors: Churchill Robin 
Published: April 2006

AbstractThis is the first of a projected series of annual surveys reviewing dispute settlement under the UN Convention on the Law of the Sea generally, rather than focusing purely on the International Tribunal for the Law of the Sea. The main developments during 2004 were the referral of two maritime boundary disputes in the Caribbean area to arbitration under Annex VII and a prompt release of vessel judgment by the ITLOS in the Juno Trader case.
The Slow Swim From Extinction: Saving Turtles in the South Pacific
Authors: Gillespie Alexander 
Published: April 2006

AbstractThe purpose of this paper is to set out the essential requirements for a successful regional agreement for sea turtles in the South Pacific. To achieve this, the current Regional Marine Turtle Conservation Programme (RMTCP) which runs under the auspice of the South Pacific Regional Environmental Programme (SPREP) will be juxtaposed against the "best practice" in this area, as evinced by current development in international environmental law and a number of other regional agreements which focus exclusively on sea turtles.
Submission of Brazil and Article 76 of The Law of the Sea Convention (LOSC) 1982
Authors: Egede Edwin 
Published: April 2006

AbstractBrazil on 17 May 2004 became the second State to make its submission to the Commission on the Limits of the Continental Shelf (CLCS) as required by Article 76 of the Law of the Sea Convention (LOSC). The Brazilian submission assumes particular significance as the first submission to the CLCS by a developing State member of the Group of 77. This article seeks to examine the Brazilian submission vis-à-vis the provisions of Article 76 of LOSC.