bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association between clinical characteristics and risk‐reduction interventions in women who underwent BRCA1 and BRCA2 testing
Authors: Uyei Anne , Peterson Susan K. , Erlichman Julie , Broglio Kristine , Yekell Sandra , Schmeler Kathkeen , Lu Karen , Meric‐Bernstam Funda , Amos Chris , Strong Louise , Arun Banu 
Published: November 2006

AbstractBACKGROUND.Women who are at increased risk for breast and ovarian cancers, especially BRCA1 and BRCA2 mutation carriers, face a myriad of risk‐reduction options, including increased surveillance, chemoprevention, prophylactic oophorectomy, and prophylactic mastectomy. However, little is known about which clinical, demographic, or cancer‐related factors are associated with risk‐reduction interventions.METHODS.The authors conducted a retrospective review of records for 554 women who had undergone testing at The University of Texas M. D. Anderson Cancer Center between 2000 and 2006 for deleterious BRCA1 and BRCA2 gene mutations. Data were collected on the risk‐reduction interventions these women adopted after they underwent genetic testing. These data were tested for associations with demographic and clinical characteristics.RESULTS.Among the 554 women who underwent genetic testing for BRCA mutation, 78 were found to have a deleterious mutation in the BRCA1 gene, and 54 had a mutation in the BRCA 2 gene. Of the 554 women, 85 underwent prophylactic mastectomy, 30 prophylactic oophorectomy, and 52 both surgeries; 387 women opted for surveillance. Women who had BRCA mutations, a history of breast cancer or ductal carcinoma in situ (DCIS), or previous breast biopsies were more likely to have prophylactic surgery. Women with a family history of ovarian cancer were more likely to undergo prophylactic oophorectomy. Women with a personal history of ovarian cancer or advanced breast cancer were more likely to undergo surveillance only. Women with breast cancer who had had a total mastectomy as part of their prior breast cancer treatment underwent prophylactic mastectomy more frequently than women who either had breast‐conserving surgery or no history of breast cancer. In multivariate analysis, only positive BRCA mutation carrier status was associated with having had prophylactic surgery. In addition, breast cancer history was significantly associated with prophylactic mastectomy.CONCLUSIONS.Women who were BRCA carriers, women who had a history of breast cancer, DCIS, or breast biopsy, or had a family history of ovarian cancer were more likely to have undergone surgery for cancer risk reduction. Women with ovarian cancer or advanced breast cancer were more likely to have undergone surveillance. Cancer 2006. © 2006 American Cancer Society.
Metastatic disease of screen‐detected prostate cancer
Authors: Roemeling Stijn , Kranse Ries , Vis André N. , Gosselaar Claartje , van der Kwast Theo H. , Schröder Fritz H. 
Published: November 2006

AbstractBACKGROUND.Screening for prostate cancer has not only led to a stage migration, but also to a higher incidence of the disease. A decrease in mortality has occurred in several countries during the same time period. Risk stratification of screen‐detected cancers at diagnosis has become more important for the anticipation and interpretation of changing incidence/mortality ratios.METHODS.From 1993 to 1998, 633 men were diagnosed with nonmetastatic prostate cancer in the prevalence screen of the Rotterdam section of the European Randomized study of Screening for Prostate Cancer (ERSPC). The characteristics at diagnosis of men who developed metastatic disease were compared with men without evidence of metastases during follow‐up.RESULTS.During the median follow‐up of 7.5 years, 41 men developed metastatic disease. After 10 years the metastasis‐free survival rate was 89.6%, the overall survival 64.7%. In a Cox‐model 2logPSA (prostate‐specific antigen), biopsy Gleason score and the number of biopsy cores with prostate cancer were independent predictors for the development of metastases; the latter only predicted metastases that presented within 60 months of follow‐up.CONCLUSIONS.The metastasis‐free survival of men with prostate cancer detected in a prevalence screening was very high. Whether this was related to the beneficial effects of screening or to overdiagnosis due to screening (or both) remains unclear. The prognostic factors known for clinically diagnosed disease also hold for screen‐detected disease. Cancer 2006. © 2006 American Cancer Society.
Immunohistochemical localization of CNTFRα in adult mouse retina and optic nerve following intraorbital nerve crush: Evidence for the axonal loss of a trophic factor receptor after injury
Authors: Miotke Jill A. , MacLennan A. John , Meyer Ronald L. 
Published: November 2006

AbstractCiliary neurotrophic factor (CNTF) is important for the survival and outgrowth of retinal ganglion cells (RGCs) in vitro. However, in vivo adult RGCs fail to regenerate and subsequently die following axotomy, even though there are high levels of CNTF in the optic nerve. To address this discrepancy, we used immunohistochemistry to analyze the expression of CNTF receptor α (CNTFRα) in mouse retina and optic nerve following intraorbital nerve crush. In normal mice, RGC perikarya and axons were intensely labeled for CNTFRα. At 24 hours after crush, the immunoreactivity normally seen on axons in the nerve was lost near the lesion. This loss radiated from the crush site with time. At 2 days postlesion, labeled axons were not detected in the proximal nerve, and at 2 weeks were barely detectable in the retina. In the distal nerve, loss of axonal staining progressed to the optic chiasm by 7 days and remained undetectable at 2 weeks. Interfascicular glia in the normal optic nerve were faintly labeled, but by 24 hours after crush they became intensely labeled near the lesion. Double labeling showed these to be both astrocytes and oligodendrocytes. At 7 days postlesion, darkly labeled glia were seen throughout the optic nerve, but at 14 days labeling returned to normal. It is suggested that the loss of CNTFRα from axons renders RGCs unresponsive to CNTF, thereby contributing to regenerative failure and death, while its appearance on glia may promote glial scarring. J. Comp. Neurol. 500:384–400, 2007. © 2006 Wiley‐Liss, Inc.
The folate metabolic enzyme ALDH1L1 is restricted to the midline of the early CNS, suggesting a role in human neural tube defects
Authors: Anthony Todd E. , Heintz Nathaniel 
Published: November 2006

AbstractFolate supplementation prevents up to 70% of human neural tube defects (NTDs), although the precise cellular and metabolic sites of action remain undefined. One possibility is that folate modulates the function of metabolic enzymes expressed in cellular populations involved in neural tube closure. Here we show that the folate metabolic enzyme ALDH1L1 is cell‐specifically expressed in PAX3‐negative radial glia at the midline of the neural tube during early murine embryogenesis. Midline restriction is not a general property of this branch of folate metabolism, as MTHFD1 displays broad and apparently ubiquitous expression throughout the neural tube. Consistent with previous work showing antiproliferative effects in vitro, ALDH1L1 upregulation during central nervous system (CNS) development correlates with reduced proliferation and most midline ALDH1L1+ cells are quiescent. These data provide the first evidence for localized differences in folate metabolism within the early neural tube and suggest that folate might modulate proliferation via effects on midline Aldh1l1+ cells. To begin addressing its role in neurulation, we analyzed a microdeletion mouse strain lacking Aldh1l1 and observed neither increased failure of neural tube closure nor detectable proliferation defects. Although these results indicate that loss‐of‐function Aldh1l1 mutations do not impair these processes in mice, the specific midline expression of ALDH1L1 and its ability to dominantly suppress proliferation in a folate responsive manner may suggest that mutations contributing to disease are gain‐of‐function, rather than loss‐of‐function. Moreover, a role for loss‐of‐function mutations in human NTDs remains possible, as Mthfr null mice do not develop NTDs even though MTHFR mutations increase human NTD risk. J. Comp. Neurol. 500:368–383, 2007. © 2006 Wiley‐Liss, Inc.
MyCoG.NET: a multi‐language CoG toolkit
Authors: Paventhan A. , Takeda Kenji , Cox Simon J. , Nicole Denis A. 
Published: November 2006

AbstractGrid application developers utilize Commodity Grid (CoG) toolkits to access Globus Grid services. Existing CoG toolkits are language‐specific and have, for example, been developed for Java, Python and the Matlab scripting environment. In this paper we describe MyCoG.NET, a CoG toolkit supporting multi‐language programmability under the Microsoft .NET framework. MyCoG.NET provides a set of classes and APIs to access Globus Grid services from languages supported by the .NET Common Language Runtime. We demonstrate its programmability using FORTRAN, C++, C# and Java, and discuss its performance over LAN and WAN infrastructures. We present a Grid application, in the field of experimental aerodynamics, as a case study to show how MyCoG.NET can be exploited. We demonstrate how scientists and engineers can create and use domain‐specific workflow activity sets for rapid application development using Windows Workflow Foundation. We also show how users can easily extend and customize these activities. Copyright © 2006 John Wiley & Sons, Ltd.
Towards an autonomic approach for edge computing
Authors: Desertot Mikael , Escoffier Clement , Donsez Didier 
Published: November 2006

AbstractNowadays, one of the biggest challenges for companies is to cope with the high cost of their information technologies infrastructure. Edge computing is a new computing paradigm designed to allocate on‐demand computing and storage resources. Those resources are Web cache servers scattered over the ISP backbones. We argue that this paradigm could be applied for on‐demand full application hosting, helping to reduce costs. In this paper, we present a J2EE (Java Enterprise Edition) dynamic server able to deploy/host J2EE applications on demand and its autonomic manager. For this, we reengineer and experiment with JOnAS, an open‐source J2EE static server. Two management policies of the autonomic manager were stressed by a simulation of a worldwide ISP network. Copyright © 2006 John Wiley & Sons, Ltd.
Benchmarking the iPSC/2 hypercube multiprocessor
Authors: Bomans Luc , Roose Dirk 
Published: November 2006

AbstractIn this paper the performance of the Intel iPSC/2 hypercube multiprocessor is analyzed. Computation and communication performance for a number of benchmarks are presented. We derive some fundamental performance parameters of the machine. Further, we investigate the difference between several communication schemes. Using the results of our measurements we can highlight some features and peculiarities in the iPSC/2 hardware and software. Where possible we make a comparison with the iPSC/1 and Ncube hypercubes.
The performance of a distributed combat simulation with the time warp operating system
Authors: Wieland Frederick , Hawley Lawrence , Feinberg Abe , Loreto Mike Di , Blume Leo , Ruffles Joseph , Reiher Peter , Beckman Brian , Hontalas Philip , Bellenot Steven , Jefferson David 
Published: November 2006

AbstractThis paper analyzes the performance of a discrete‐event combat simulation executed on a parallel processor under control of the Time Warp Operating System. Time Warp is in a class of distributed simulation methods called Optimistic methods which have proven to be useful over a wide range of simulations. The combat simulation used for this performance study, called STB88, is a division‐corps model incorporating a number of different types of computations. The speed‐up for three versions of this model on the Caltech/JPL Mark III Hypercube and the BBN Butterfly parallel processors was measured relative to an efficient sequential execution of the same model on the same hardware. The results indicate that STB88 version 1 achieves a speed‐up of 28.6 on 60 Mark III processors, while STB88 version 2 achieves a speed‐up of 36.8 on 100 Butterfly processors. Version 3 of STB88 achieved a speed‐up of 38.5 on 128 Mark III processors. The versions differed only in their interface to Time Warp. On the Butterfly, the sequential execution completed in 2 hours, while the 100 processor execution completed in 3.2 minutes.
Translating from PARLOG to occam2: A methodology
Authors: Scott Robert B. , Trehan Rajiv 
Published: November 2006

AbstractWe describe a novel methodology for translating some PARLOG programs to occam2. Our methodology directs the translation based on a process level description generated from the PARLOG program. The translation of several example PARLOG programs is included. These examples feature: dynamic creation of processes; the one‐to‐many communication capabilities of PARLOG; and use of unbounded, asynchronous communication. The examples are then used to consider the translation of a previously developed programming application from the field of Artificial Intelligence, namely a PARLOGchart parser.We see two main interests in such a methodology: firstly, as a means of obtaining high‐performance execution of PARLOG programs–PARLOG programs translated to occam2 can be executed on the high‐performance Transputer device; secondly, PARLOG may have a use as a declarative specification language for the development of occam2 programs.
What price regularity?
Authors: Prior Dominic M. N. , Norman Michael G. , Radcliffe Nicholas J. , Clarke Lyndon J. 
Published: November 2006

AbstractWe review various properties of irregular graphs and suggest that they may provide useful maps for connecting processors together in distributed‐memory MIMD machines. In particular, for many applications the performance of a system in an irregular configuration can be expected to exceed by far that of systems in standard configurations such as hypercubes and tori, which are poor over many performance measures. Techniques are discussed which allow the construction of near‐optimal or optimal graphs with respect to various measures of goodness, including diameter, mean interprocessor distance and worst through‐routing load. We conclude that where regularity is not important, irregular graphs will almost always outperform standard, regular ones.
Declarative languages and program transformation for programming parallel systems: A case study
Authors: Darlington John , Reeve Mike , Wright Sue 
Published: November 2006

AbstractThere are many problems associated with current methodologies employed for the development and maintenance of efficient computer systems. This has lead to an interest in both declarative programming languages and parallel computer architectures. These two areas can be combined to produce effective systems by the use of new program development philosophies. In particular, the mathematical basis and inherent parallelism of declarative languages enable formal techniques to be adopted for the development of programs tailored towards parallel machines. This paper provides an overview of one such methodology developed at Imperial College (IC) and presents a case study that illustrates its operation, using the IC Programming/Transformation Environment, and quantifies its benefits using performance prediction equations together with the results of experiments carried out on the ALICE parallel machine.
Exception handling for a communicating‐sequential‐processes‐based extension of C++
Authors: Adamo Jean‐Marc 
Published: November 2006

AbstractAn exception handling system for a language defined as a CSP/OCCAM‐based extension of C++ is presented. This language is part of a project we are developing which aims at constructing a high level programming environment for transputer‐based multiprocessors. In this proposal, the replacement model of Yemini and Berry (1985) is considered, parallelism and exception handling are closely combined, making process pre‐emption available but raising problems of atomicity and non‐determinism. These problems are discussed, a solution is suggested and an efficient implementation we have carried out is presented.
Implementation of Apply on a transputer array
Authors: Wang Han , Dew Peter M. , Webb Jon A. 
Published: November 2006

AbstractApply is a machine‐independent, low‐level image processing language for expressing local window operations. It has two main advantages: (1) it significantly reduces the programming effort, and (2) it can be mapped onto a wide range of parallel computers. In this paper we report our recent experience on implementing Apply on a Meiko Computing Surface (transputer array machine) using a farmer/gather model. The performance of the Meiko implementation on a number of edge detection algorithms including the popular Canny operator is analysed. Results suggest that the performance of Apply generated code represents peak performance and it is likely to be as efficient as hand‐written code.
Execution time support for adaptive scientific algorithms on distributed memory machines
Authors: Berryman Harry , Saltz Joel , Scroggs Jeffrey 
Published: November 2006

AbstractWe consider optimizations that are required for efficient execution of code segments that consist of loops over distributed data structures. The PARTI execution time primitives are designed to perform these optimizations and can be used to Implement a wide range of scientific algorithms on distributed memory machines.These primitives allow the user to control array mappings in a way that gives an appearance of shared memory. Computations can be based on a global index set. Primitives are used to perform gather and scatter operations on distributed arrays. Communications patterns are derived at run time, and the appropriate send and receive messages are automatically generated.
The parallel computation of eigenvalues and eigenvectors of large Hermitian matrices using the AMT DAP 510
Authors: Weston J. S. , Clint M. , Bleakney C. W. 
Published: November 2006

AbstractThe solution of the algebraic eigenvalue problem is an important component of many applications in science and engineering. With the advent of novel architecture machines, much research effort is now being expended in the search for parallel algorithms for the computation of eigensystems which can gainfully exploit the processing power which these machines provide. Among important recent work References 1‐4 address the real symmetric eigenproblem in both its dense and sparse forms, Reference 5 treats the unsymmetric eigenproblem, and Reference 6 investigates the solution of the generalized eigenproblem. In this paper two algorithms for the parallel computation of the eigensolution of Hermitian matrices on an array processor are presented. These algorithms are based on the Parallel Orthogonal Transformation algorithm (POT) for the solution of real symmetric matrices[7,8]. POT was developed to exploit the SIMD parallelism supported by array processors such as the AMT DAP 510. The new algorithms use the highly efficient implementation strategies devised for use in POT. The implementations of the algorithms permit the computation of the eigensolution of matrices whose order exceeds the mesh size of the array processor used. A comparison of the efficiency of the two algorithms for the solution of a variety of matrices is given.
A network multi‐processor for experiments in parallelism
Authors: Marsland T. A. , Breitkreutz T. , Sutphen S. 
Published: November 2006

AbstractAlthough both shared memory and loosely coupled parallel computing systems are now common, many still do not offer an easy way to design, implement, and test parallel algorithms. Our system provides software tools that make possible a variety of connection structures between processes. These structures are said to form a 'Network Multi‐Processor', which is implemented on a local area network of heterogeneous UNIX‐based timesharing computers, plus a set of processor boards dedicated to an application so that accurate timing measurements can be made. We explain how these tools have been used both to aid parallel algorithm development and to explore the properties of different computer interconnection methods.
Evaluating the basic performance of the Intel iPSC/860 parallel computer
Authors: Berrendorf Rudolf , Helin Jukka 
Published: November 2006

AbstractWe evaluate the basic performance of the Intel iPSC/860 computer, which can have up to 128 Intel i860‐based nodes connected together with a hypercube network topology. After giving a brief overview of the system, the properties and bottlenecks of the hardware architecture and software environment are discussed. Basic memory, scalar and vector performance of a single node is evaluated, and the communication performance and the overlap of computation and communication are analysed.
The MPE toolkit for supporting distributed applications
Authors: Barak Amnon , Guday Shai , Laor Roy 
Published: November 2006

AbstractThis paper presents a toolkit for supporting the execution of coarse‐grain, parallel (distributed) applications under the MOSIX multicomputer operating system. These tools use standard UNIX System V process control and message‐passing facilities, as well as the dynamic process migration mechanisms of MOSIX. The MPE tools can be used to modify sequential applications that were originally written for execution in a uniprocessor environment, to run efficiently in a distributed environment, consisting of several loosely coupled independent computers that communicate by messages. After presenting the MPE tools, the paper gives examples of several sequential algorithms that have been modified for execution in such a distributed multicomputer, as well as the resulting execution speed‐ups that were obtained.
An experiment in concurrent software evaluation
Authors: Perrott R. H. , Ramasubbu A. 
Published: November 2006

AbstractThis paper considers a method for evaluating the concurrent programming language available on a multiprocessor system – in particular, a shared‐memory multiprocessor system. The method is based on the consideration of well‐known algorithms which have been used as a means of demonstrating the expressive power of new concurrent language constructs. The algorithms considered are the Readers and Writers Problem and the Drinking Philosophers Problem. Both algorithms are coded using features that are widely regarded as being state‐of‐the‐art for shared‐memory systems and are then recoded in the language available on an actual multiprocessor system in order to carry out a comparison and evaluation. Several observations and conclusions are drawn.
Allocating data to multicomputer nodes by physical optimization algorithms for loosely synchronous computations
Authors: Mansour Nashat , Fox Geoffrey C. 
Published: November 2006

AbstractThree optimization methods derived from natural sciences are considered for allocating data to multicomputer nodes. These are simulated annealing, genetic algorithms and neural networks. A number of design choices and the addition of preprocessing and postprocessing steps lead to versions of the algorithms which differ in solution qualities and execution times. In this paper the performances of these versions are critically evaluated and compared for test cases with different features. The performance criteria are solution quality, execution time, robustness, bias and parallelizability. Experimental results show that the physical algorithms produce better solutions than those of recursive bisection methods and that they have diverse properties. Hence, different algorithms would be suitable for different applications. For example, the annealing and genetic algorithms produce better solutions and do not show a bias towards particular problem structures, but they are slower than the neural network algorithms. Preprocessing graph contraction is one of the additional steps suggested for the physical methods. It produces a significant reduction in execution time, which is necessary for their applicability to large problems.