bluuebunny/crossref_metadata_2025_split huggingface dataset:
Growth cones contain a dynamic population of neurofilament subunits
Authors: Chan Walter K.‐H. , Yabe Jason T. , Pimenta Aurea F. , Ortiz Daniela , Shea Thomas B. 
Published: February 2003

AbstractNeurofilaments (NFs) are classically considered to transport in a primarily anterograde direction along axons, and to undergo bulk degradation within the synapse or growth cone (GC). We compared overall NF protein distribution with that of newly expressed NF subunits within NB2a/d1 cells by transfection with a construct encoding green fluorescent protein (GFP) conjugated NF‐M subunits. GCs lacked phosphorylated NF epitopes, and steady‐state levels of non‐phosphosphorylated NF subunits within GC were markedly reduced compared to those of neurite shaft as indicated by conventional immunofluorescence. However, GCs contained significant levels of GFP‐tagged subunits in the form of punctate or short filamentous structures that in some cases exceeded that visualized along the shaft itself, suggesting that GCs contained a relatively higher concentration of newly synthesized subunits. GFP‐tagged NF subunits within GCs co‐localized with non‐phosphorylated NF immunoreactivity. GFP‐tagged subunits were observed within GC filopodia in which steady‐state levels of NF subunits were too low to be detected by conventional immunofluorescence. Selective localization of fluorescein versus rhodamine fluorescene was observed within GCs following expression of NF‐M conjugated to DsRed1‐E5, which shifts from fluorescein to rhodamine fluorescence within hours after expression; axonal shafts contained a more even distribution of fluorescein and rhodamine fluorescence, further indicating that GCs contained relatively higher levels of the most‐recently expressed subunits. GFP‐tagged structures were rapidly extracted from GCs under conditions that preserved axonal structures. These short filamentous and punctate structures underwent rapid bi‐directional movement within GCs. Movement of GFP‐tagged structures within GCs ceased following application of nocodazole, cytochalasin B, and the kinase inhibitor olomoucine, indicating that their motility was dependent upon microtubules and actin and, moreover, was due to active transport rather than simple diffusion. Treatment with the protease inhibitor calpeptin increased overall NF subunits, but increased those within the GC to a greater extent than those along the shaft, indicating that subunits in the GC undergo more rapid turnover than do those within the shaft. Some GCs contained coiled aggregates of GFP‐tagged NFs that appeared to be contiguous with axonal NFs. NFs extended from these aggregates into the advancing GC as axonal neurites elongated. These data are consistent with the presence of a population of dynamic NF subunits within GCs that is apparently capable of participating in regional filament formation during axonal elongation, and support the notion that NF polymerization and transport need not necessarily occur in a uniform proximal‐distal manner. Cell Motil. Cytoskeleton 54:195–207, 2003. © 2003 Wiley‐Liss, Inc.
Role of the two type II myosins, Myo2 and Myp2, in cytokinetic actomyosin ring formation and function in fission yeast
Authors: Mulvihill Daniel P. , Hyams Jeremy S. 
Published: February 2003

AbstractThe formation and contraction of a cytokinetic actomyosin ring (CAR) is essential for the execution of cytokinesis in fission yeast. Unlike most organisms in which its composition has been investigated, the fission yeast CAR contains two type II myosins encoded by the genes myo2+ and myp2+. myo2+ is an essential gene whilst myp2+ is dispensable under normal growth conditions. Myo2 is hence the major contractile protein of the CAR whilst Myp2 plays a more subtle and, as yet, incompletely documented role. Using a fission yeast strain in which the chromosomal copy of the myo2+ gene is fused to the gene encoding green fluorescent protein (GFP), we analysed CAR formation and function in the presence and absence of Myp2. No change in the rate of CAR contraction was observed when Myp2 was absent although the CAR persisted longer in the contracted state and was occasionally observed to split into two discrete rings. This was also observed in myp2Δ cells following actin depolymerisation with latrunculin. CAR contraction in the absence of Myp2 was completely abolished in the presence of elevated levels of chloride ions. Thus, Myp2 appears to contribute to the stability of the CAR, in particular at a late stage of CAR contraction, and to be a component of the signalling pathway that regulates cytokinesis in response to elevated levels of chloride. To determine whether the presence of two type II myosins was a feature of cytokinesis in other fungi that divide by septation, we searched the genomes of two filamentous fungi, Aspergillus fumigatus and Neurospora crassa, for myosin genes. As in fission yeast, both A. fumigatus and N. crassa contained myosins of classes I, II, and V. Unlike fission yeast, both contained a single type II myosin gene that, on the basis of its tail structure, was more reminiscent of Myp2 than Myo2. The significance of these observations to our understanding of septum to formation and cleavage is discussed. Cell Motil. Cytoskeleton 54:208–216, 2003. © 2003 Wiley‐Liss, Inc.
Dynamics of the endoplasmic reticulum during early development of Drosophila melanogaster
Authors: Bobinnec Yves , Marcaillou Christiane , Morin Xavier , Debec Alain 
Published: February 2003

AbstractIn this study, we analyze for the first time endoplasmic reticulum (ER) dynamics and organization during oogenesis and embryonic divisions of Drosophila melanogaster using a Protein Disulfide Isomerase (PDI) GFP chimera protein. An accumulation of ER material into the oocyte takes place during the early steps of oogenesis. The compact organization of ER structures undergoes a transition to an expanded reticular network at fertilization. At the syncytial stage, this network connects to the nuclear envelope as each nucleus divides. Time‐lapse confocal microscopy on PDI transgenic embryos allowed us to characterize a rapid redistribution of the ER during the mitotic phases. The ER network is massively recruited to the spindle poles in prophase. During metaphase most of the ER remains concentrated at the spindle poles and shortly thereafter forms several layers of membranes along the ruptured nuclear envelope. Later, during telophase an accumulation of ER material occurs at the spindle equator. We also analyzed the subcellular organization of the ER network at the ultrastructural level, allowing us to corroborate the results from confocal microscopy studies. This dynamic redistribution of ER suggests an unexpected regulatory function for this organelle during mitosis. Cell Motil. Cytoskeleton 54:217–225, 2003. © 2003 Wiley‐Liss, Inc.
Dynamic properties of APC‐decorated microtubules in living cells
Authors: Dayanandan Rejith , Butler Rachel , Gordon‐Weeks Phillip R. , Matus Andrew , Kaech Stefanie , Lovestone Simon , Anderton Brian H. , Gallo Jean‐Marc 
Published: February 2003

AbstractThe adenomatous polyposis coli (APC) tumour suppressor protein is a component of the Wnt signalling pathway in which it plays a major role in controlling nuclear accumulation of β‐catenin and hence in the modulation of β‐catenin‐regulated gene transcription. APC also associates with microtubules at the ends of cytoplasmic extensions in epithelial cells, a distribution that can be reproduced in COS cells ectopically expressing APC. To examine the effect of APC on microtubule properties, we monitored directly the behaviour of APC and of APC‐decorated microtubules by time‐lapse imaging of cytoplasmic extensions in live COS cells expressing APC tagged with a green fluorescent protein. On the proximal part of microtubules, APC was visualised as particulate material moving unidirectionally towards the plus end of microtubules. The distal parts of microtubules were uniformly decorated by APC and were animated by a motile behaviour in the form of aperiodic bending. This behaviour is likely to be the consequence of compression forces acting on microtubules encountering obstacles while elongating. The majority of APC‐decorated microtubules in transfected COS cells was sensitive to depolymerisation by nocodazole, but they contained detyrosinated and acetylated α‐tubulin, suggesting a reduction in the rate of subunit exchange at their growing end. Taken together, these results demonstrate that microtubule domains uniformly decorated by APC display dynamic and motile properties that may be significant for the postulated role of APC in targeting microtubules to specialised membrane sites. Cell Motil. Cytoskeleton 54:237–247, 2003. © 2003 Wiley‐Liss, Inc.
Smad3 mediates the TGF‐β‐induced contraction of type I collagen gels by mouse embryo fibroblasts
Authors: Liu Xiangde , Wen Fu‐Qiang , Kobayashi Tetsu , Abe Shinji , Fang Qiuhong , Piek Ester , Bottinger Erwin P. , Roberts Anita B. , Rennard Stephen I. 
Published: February 2003

AbstractTGF‐β signals through TGF‐β receptors and Smad proteins. TGF‐β also augments fibroblast‐mediated collagen gel contraction, an in vitro model of connective tissue remodeling. To investigate the importance of Smad2 or Smad3 in this augmentation process, embryo‐derived fibroblasts from mice lacking expression of Smad2 or Smad3 genes were cast into native type I collagen gels. Fibroblast‐populated gels were then released into 0.2% FCS‐DMEM alone or with recombinant human TGF‐β1, β2, β3, or recombinant rat PDGF‐BB. Gel contraction was determined using an image analyzer. All three isoforms of TGF‐β significantly augmented contraction of collagen gels mediated by fibroblasts with genotypes of Smad2 knockout (S2KO), Smad2 wildtype (S2WT), and Smad3 wildtype (S3WT), but not Smad3 knockout (S3KO) mice. PDGF‐BB augmented collagen gel contraction by all fibroblast types. These results suggest that expression of Smad3 but not Smad2 may be critical in TGF‐β augmentation of fibroblast‐mediated collagen gel contraction. Thus, the Smad3 gene could be a target for blocking contraction of fibrotic tissue induced by TGF‐β. Cell Motil. Cytoskeleton 54:248–253, 2003. © 2003 Wiley‐Liss, Inc.
ALP and MLP distribution during myofibrillogenesis in cultured cardiomyocytes
Authors: Henderson James R. , Pomiès Pascal , Auffray Charles , Beckerle Mary C. 
Published: February 2003

AbstractThe Z‐line is a multifunctional macromolecular complex that anchors sarcomeric actin filaments, mediates interactions with intermediate filaments and costameres, and recruits signaling molecules. Antiparallel α‐actinin homodimers, present at Z‐lines, cross‐link overlapping actin filaments and also bind other cytoskeletal and signaling elements. Two LIM domain containing proteins, α‐actinin associated LIM protein (ALP) and muscle LIM protein (MLP), interact with α‐actinin, distribute in vivo to Z‐lines or costameres, respectively, and, when absent, are associated with heart disease. Here we describe the behavior of ALP and MLP during myofibrillogenesis in cultured embryonic chick cardiomyocytes. As myofibrils develop, ALP and MLP are observed in distinct distribution patterns in the cell. ALP is coincident with α‐actinin from the first stage of myofibrillogenesis and co‐distributes with α‐actinin to Z‐lines and intercalated discs in mature myofibrils. Interestingly, we also demonstrate using ALP‐GFP transfection experiments and an in vitro binding assay that the ALP‐α‐actinin binding interaction is not required to target ALP to the Z‐line. In contrast, MLP localization is not co‐incident with that of α‐actinin until late stages of myofibrillogenesis; however, it is present in premyofibrils and nascent myofibrils prior to the incorporation of other costameric components such as vinculin, vimentin, or desmin. Our observations support the view that ALP function is required specifically at actin anchorage sites. The subcellular distribution pattern of MLP during myofibrillogenesis suggests that it functions during differentiation prior to the establishment of costameres. Cell Motil. Cytoskeleton 54:254–265, 2003. © 2003 Wiley‐Liss, Inc.
Identification and characterisation of a novel human isoform of Arp2/3 complex subunit p16‐ARC/ARPC5. T.H. Millard, B. Behrendt, S. Launay, K. Fütterer, L.M. Machesky, Cell Motil.Cytoskeleton (2003) 54(1):81–90.
Authors: Millard Thomas H. , Behrendt Barbara , Launay Sophie , Fütterer Klaus , Machesky Laura M. 
Published: February 2003

AbstractThe original article to which this Erratum refers was published in Cell Motility and the Cytoskeleton 54(1) 81–90Figure 1 was incorrectly printed in the article. The missing portions of the sequence are herein reprinted with the accompanying legend.In the legend accompanying Figure 7, the residues referred to as "blue" appear in purple in the figure.
Framework for testing multi‐threaded Java programs
Authors: Edelstein Orit , Farchi Eitan , Goldin Evgeny , Nir Yarden , Ratsaby Gil , Ur Shmuel 
Published: February 2003

AbstractFinding bugs due to race conditions in multi‐threaded programs is difficult, mainly because there are many possible interleavings, any of which may contain a fault. In this work we present a methodology for testing multi‐threaded programs which has minimal impact on the user and is likely to find interleaving bugs. Our method reruns existing tests in order to detect synchronization faults. We find that a single test executed a number of times in a controlled environment may be as effective in finding synchronization faults as many different tests. A great deal of resources are saved since tests are very expensive to write and maintain. We observe that simply rerunning tests, without ensuring in some way that the interleaving will change, yields almost no benefits. We implement the methodology in our test generation tool—ConTest. ConTest combines the replay algorithm, which is essential for debugging, with our interleaving test generation heuristics. ConTest also contains an instrumentation engine, a coverage analyzer, and a race detector (not finished yet) that enhance bug detection capabilities. The greatest advantage of ConTest, besides finding bugs of course, is its minimal effect on the user. When ConTest is combined into the test harness, the user may not even be aware that ConTest is being used. Copyright © 2003 John Wiley & Sons, Ltd.
High‐performance Java codes for computational fluid dynamics
Authors: Riley Christopher J. , Chatterjee Siddhartha , Biswas Rupak 
Published: February 2003

AbstractThe computational science community is reluctant to write large‐scale computationally‐intensive applications in Java due to concerns over Java's poor performance, despite the claimed software engineering advantages of its object‐oriented features. Naive Java implementations of numerical algorithms can perform poorly compared to corresponding Fortran or C implementations. To achieve high performance, Java applications must be designed with good performance as a primary goal. This paper presents the object‐oriented design and implementation of two real‐world applications from the field of computational fluid dynamics (CFD): a finite‐volume fluid flow solver (LAURA, from NASA Langley Research Center) and an unstructured mesh adaptation algorithm (2D_TAG, from NASA Ames Research Center). This work builds on our previous experience with the design of high‐performance numerical libraries in Java. We examine the performance of the applications using the currently available Java infrastructure and show that the Java version of the flow solver LAURA performs almost within a factor of 2 of the original procedural version. Our Java version of the mesh adaptation algorithm 2D_TAG performs within a factor of 1.5 of its original procedural version on certain platforms. Our results demonstrate that object‐oriented software design principles are not necessarily inimical to high performance. Copyright © 2003 John Wiley & Sons, Ltd.
Benchmarking Java against C and Fortran for scientific applications
Authors: Bull J. M. , Smith L. A. , Ball C. , Pottage L. , Freeman R. 
Published: February 2003

AbstractIncreasing interest is being shown in the use of Java for scientific applications. The Java Grande benchmark suite was designed with such applications primarily in mind. The perceived lack of performance of Java still deters many potential users, despite recent advances in just‐in‐time and adaptive compilers. There are, however, few benchmark results available comparing Java to more traditional languages such as C and Fortran. To address this issue, a subset of the Java Grande benchmarks has been re‐written in C and Fortran allowing direct performance comparisons between the three languages. The performance of a range of Java execution environments, C and Fortran compilers have been tested across a number of platforms using the suite. These demonstrate that on some platforms (notable Intel Pentium) the performance gap is now quite small. Copyright © 2003 John Wiley & Sons, Ltd.
Spar: a set of extensions to Java for scientific computation
Authors: van Reeuwijk C. , Kuijlman F. , Sips H. J. 
Published: February 2003

AbstractWe present a set of language extensions that improve the expressiveness and performance of Java for scientific computation. The language extensions allow the manipulation of multi‐dimensional arrays to be expressed more naturally, and to be implemented more efficiently. Furthermore, data‐parallel programming is supported, allowing efficient parallelization of a large class of operations on arrays. We also provide language extensions to construct specialized array representations, such as symmetric, block, and sparse matrices. These extensions are: tuples, parameterized types, array subscript overloading, and the inline modifier. These extensions are not only useful in the construction of special array representations, but are also useful in their own right. Finally, we add complex numbers as a primitive type to the language. We evaluate our language extensions using performance results. We also compare relevant code fragments of our extended language with standard Java implementations and language extensions proposed by others. Copyright © 2003 John Wiley & Sons, Ltd.
Run‐time optimizations for a Java DSM implementation
Authors: Veldema R. , Hofman R. F. H. , Bhoedjang R. A. F. , Bal H. E. 
Published: February 2003

AbstractJackal is a fine‐grained distributed shared memory implementation of the Java programming language. Jackal implements Java's memory model and allows multithreaded Java programs to run unmodified on distributed‐memory systems.This paper focuses on Jackal's run‐time system, which implements a multiple‐writer, home‐based consistency protocol. Protocol actions are triggered by software access checks that Jackal's compiler inserts before object and array references. To reduce access‐check overhead, the compiler exploits source‐level information and performs extensive static analysis to optimize, lift, and remove access checks. We describe optimizations for Jackal's run‐time system, which mainly consists of discovering opportunities to dispense with flushing of cached data. We give performance results for different run‐time optimizations, and compare their impact with the impact of one compiler optimization. We find that our run‐time optimizations are necessary for good Jackal performance, but only in conjunction with the Jackal compiler optimizations described by Veldema et al. As a yardstick, we compare the performance of Java applications run on Jackal with the performance of equivalent applications that use a fast implementation of Java's Remote Method Invocation instead of shared memory. Copyright © 2003 John Wiley & Sons, Ltd.
CartaBlanca—a pure‐Java, component‐based systems simulation tool for coupled nonlinear physics on unstructured grids—an update
Authors: VanderHeyden W. B. , Dendy E. D. , Padial‐Collins N. T. 
Published: February 2003

AbstractThis paper describes a component‐based nonlinear physical system simulation prototyping package written entirely in Java using object‐oriented design. The package provides scientists and engineers with a ‘developer‐friendly’ software environment for large‐scale computational algorithm and physical model development. The software design centers on the Jacobian‐free Newton–Krylov solution method surrounding a finite‐volume treatment of conservation equations. This enables a clean component‐like implementation. We first provide motivation for the development of the software and then discuss software structure. The discussion includes a description of the use of Java's built‐in thread facility that enables parallel, shared‐memory computations on a wide variety of unstructured grids with triangular, quadrilateral, tetrahedral and hexahedral elements. We also discuss the use of Java's inheritance mechanism in the construction of a hierarchy of physics systems objects and linear and nonlinear solver objects that simplify development and foster software re‐use. We provide a brief review of the Jacobian‐free Newton–Krylov nonlinear system solution method and discuss how it fits into our design. Following this, we show results from example calculations and then discuss plans including the extension of the software to distributed‐memory computer systems. Copyright © 2003 John Wiley & Sons, Ltd.
Providing soft real‐time quality of service guarantees for Java threads
Authors: Pang James C. , Shoja Gholamali C. , Manning Eric G. 
Published: February 2003

AbstractThe Java platform has many characteristics that make it very desirable for integrated continuous media processing. Unfortunately, it lacks the necessary CPU resource management facilities to support quality of service (QoS) guarantees for soft real‐time multimedia tasks. In this paper, we present our new Java Virtual Machine, Q‐JVM, which brings CPU resource management to the Java platform. Q‐JVM is based on Sun's JVM version 1.1.5. It implements an enhanced version of the MTR‐LS algorithm in its thread scheduler. Combined with admission control that could be implemented in an application‐level resource manager, it is able to support QoS parameters such as fairness, bandwidth partitioning and delay bound guarantees, as well as the cumulative service guarantee. Our test results show that Q‐JVM is backward compatible with the standard JVM from Sun, has low scheduling overhead, and is able to provide QoS guarantees as specified. Copyright © 2003 John Wiley & Sons, Ltd.
CCJ: object‐based message passing and collective communication in Java
Authors: Nelisse Arnold , Maassen Jason , Kielmann Thilo , Bal Henri E. 
Published: February 2003

AbstractCCJ is a communication library that adds MPI‐like message passing and collective operations to Java. Rather than trying to adhere to the precise MPI syntax, CCJ aims at a clean integration of communication into Java's object‐oriented framework. For example, CCJ uses thread groups to support Java's multithreading model and it allows any data structure (not just arrays) to be communicated. CCJ is implemented entirely in Java, on top of RMI, so it can be used with any Java virtual machine. The paper discusses three parallel Java applications that use collective communication. It compares the performance (on top of a Myrinet cluster) of CCJ, RMI and mpiJava versions of these applications and also compares their code complexity. A detailed performance comparison between CCJ and mpiJava is given using the Java Grande Forum MPJ benchmark suite. The results show that neither CCJ's object‐oriented design nor its implementation on top of RMI impose a performance penalty on applications compared to their mpiJava counterparts. The source of CCJ is available from our Web site http://www.cs.vu.nl/manta. Copyright © 2003 John Wiley & Sons, Ltd.