bluuebunny/crossref_metadata_2025 huggingface dataset:
A scalable formal method for design and automatic checking of user interfaces
Authors: Berstel Jean , Reghizzi Stefano Crespi , Roussel Gilles , Pietro Pierluigi San
Published: August 2005

The article addresses the formal specification, design and implementation of the behavioral component of graphical user interfaces. The complex sequences of visual events and actions that constitute dialogs are specified by means of modular, communicating grammars called VEG (Visual Event Grammars), which extend traditional BNF grammars to make them more convenient to model dialogs.A VEG specification is independent of the actual layout of the GUI, but it can easily be integrated with various layout design toolkits. Moreover, a VEG specification may be verified with the model checker SPIN, in order to test consistency and correctness, to detect deadlocks and unreachable states, and also to generate test cases for validation purposes.Efficient code is automatically generated by the VEG toolkit, based on compiler technology. Realistic applications have been specified, verified and implemented, like a Notepad-style editor, a graph construction library and a large real application to medical software. It is also argued that VEG can be used to specify and test voice interfaces and multimodal dialogs. The major contribution of our work is blending together a set of features coming from GUI design, compilers, software engineering and formal verification. Even though we do not claim novelty in each of the techniques adopted for VEG, they have been united into a toolkit supporting all GUI design phases, that is, specification, design, verification and validation, linking to applications and coding.
Advanced SQL modeling in RDBMS
Authors: Witkowski Andrew , Bellamkonda Srikanth , Bozkaya Tolga , Folkert Nathan , Gupta Abhinav , Haydu John , Sheng Lei , Subramanian Sankar
Published: August 2005

Commercial relational database systems lack support for complex business modeling. ANSI SQL cannot treat relations as multidimensional arrays and define multiple, interrelated formulas over them, operations which are needed for business modeling. Relational OLAP (ROLAP) applications have to perform such tasks using joins, SQL Window Functions, complex CASE expressions, and the GROUP BY operator simulating the pivot operation. The designated place in SQL for calculations is the SELECT clause, which is extremely limiting and forces the user to generate queries with nested views, subqueries and complex joins. Furthermore, SQL query optimizers are preoccupied with determining efficient join orders and choosing optimal access methods and largely disregard optimization of multiple, interrelated formulas. Research into execution methods has thus far concentrated on efficient computation of data cubes and cube compression rather than on access structures for random, interrow calculations. This has created a gap that has been filled by spreadsheets and specialized MOLAP engines, which are good at specification of formulas for modeling but lack the formalism of the relational model, are difficult to coordinate across large user groups, exhibit scalability problems, and require replication of data between the tool and RDBMS. This article presents an SQL extension called
SQL Spreadsheet
, to provide array calculations over relations for complex modeling. We present optimizations, access structures, and execution models for processing them efficiently. Special attention is paid to compile time optimization for expensive operations like aggregation. Furthermore, ANSI SQL does not provide a good separation between data and computation and hence cannot support parameterization for SQL Spreadsheets models. We propose two parameterization methods for SQL. One parameterizes ANSI SQL view using subqueries and scalars, which allows passing data to SQL Spreadsheet. Another method presents parameterization of the SQL Spreadsheet formulas. This supports building stand-alone SQL Spreadsheet libraries. These models are then subject to the SQL Spreadsheet optimizations during model invocation time.
ABF++: fast and robust angle based flattening
Authors: Sheffer Alla , Lévy Bruno , Mogilnitsky Maxim , Bogomyakov Alexander
Published: August 2005

Conformal parameterization of mesh models has numerous applications in geometry processing. Conformality is desirable for remeshing, surface reconstruction, and many other mesh processing applications. Subject to the conformality requirement, these applications typically benefit from parameterizations with smaller stretch. The Angle Based Flattening (ABF) method, presented a few years ago, generates provably valid conformal parameterizations with low stretch. However, it is quite time-consuming and becomes error prone for large meshes due to numerical error accumulation. This work presents ABF++, a highly efficient extension of the ABF method, that overcomes these drawbacks while maintaining all the advantages of ABF. ABF++ robustly parameterizes meshes of hundreds of thousands and millions of triangles within minutes. It is based on three main components: (1) a new numerical solution technique that dramatically reduces the dimension of the linear systems solved at each iteration, speeding up the solution; (2) a new robust scheme for reconstructing the 2D coordinates from the angle space solution that avoids the numerical instabilities which hindered the ABF reconstruction scheme; and (3) an efficient hierarchical solution technique. The speedup with (1) does not come at the expense of greater distortion. The hierarchical technique (3) enables parameterization of models with millions of faces in seconds at the expense of a minor increase in parametric distortion. The parameterization computed by ABF++ are provably valid, that is they contain no flipped triangles. As a result of these extensions, the ABF++ method is extremely suitable for robustly and efficiently parameterizing models for geometry-processing applications.
Nonblocking memory management support for dynamic-sized data structures
Authors: Herlihy Maurice , Luchangco Victor , Martin Paul , Moir Mark
Published: August 2005

Conventional dynamic memory management methods interact poorly with lock-free synchronization. In this article, we introduce novel techniques that allow lock-free data structures to allocate and free memory dynamically using any thread-safe memory management library. Our mechanisms are lock-free in the sense that they do not allow a thread to be prevented from allocating or freeing memory by the failure or delay of other threads. We demonstrate the utility of these techniques by showing how to modify the lock-free FIFO queue implementation of Michael and Scott to free unneeded memory. We give experimental results that show that the overhead introduced by such modifications is moderate, and is negligible under low contention.
Sarbanes-Oxley and software projects
Authors: Armour Phillip G.
Published: August 2005

"If we managed finances in companies the way we manage software…somebody would go to prison."

---Introduction to a workshop on configuration management conducted by Corvus International in 1996
Protecting 3d graphics content
Authors: Koller David , Levoy Marc
Published: August 2005

The digital rights management problem of protecting data from theft and misuse has been addressed for many information types, including software code, digital images, and audio files. Few technological solutions are designed specifically to protect interactive 3D graphics content.Demand for ways to protect 3D graphical models is significant and growing. Contemporary 3D digitization technologies allow the efficient creation of accurate 3D models of many physical objects. For example, our Stanford Digital Michelangelo Project [3] has developed a high-resolution digital archive of 10 of Michelangelo's large statues, including the
David
(see the sidebar "Generating a Replica of Michelangelo's
David
"). These statues represent the artistic patrimony of Italy's cultural institutions, and our contract with the Italian authorities permits distribution of the 3D models only to established scholars for noncommercial use. Though everyone involved would like the models to be available for any constructive purpose, the digital 3D model of the
David
would quickly be pirated if it were distributed without protection; simulated marble replicas would be manufactured outside the provisions of the parties authorizing creation of the model.
A practical and fast iterative algorithm for ϕ-function computation using DJ graphs
Authors: Das Dibyendu , Ramakrishna U.
Published: August 2005

We present a new and practical method of computing ϕ-function for all variables in a function for Static Single Assignment (SSA) form. The new algorithm is based on computing the
Merge
set of each node in the control flow graph of a function (a node here represents a basic block and the terms will be used interchangeably). Merge set of a node
n
is the set of nodes
N
, where ϕ-functions may need to be placed if variables are defined in
n
. It is not necessary for
n
to have a definition of a variable in it. Thus, the merge set of
n
is dictated by the underlying structure of the CFG. The new method presented here precomputes the merge set of every node in the CFG using an iterative approach. Later, these merge sets are used to carry out the actual ϕ-function placement. The advantages are in examples where
dense
definitions of variables are present (i.e., original definitions of variables---user defined or otherwise, in a majority of basic blocks). Our experience with SSA in the High Level Optimizer (optimization levels +O3/+O4) shows that most examples from the Spec2000 benchmark suite require a high percentage of basic blocks to have their ϕ points computed. Previous methods of computing the same relied on the dominance frontier (
DF
) concept, first introduced by Cytron et al. The method presented in this paper gives a new effective iterative solution to the problem. Also, in cases, where the control flow graph does not change, our method does not require any additional computation for new definitions introduced as part of optimizations. We present implementation details with results from Spec2000 benchmarks. Our algorithm runs faster than the existing methods used.
Comparing conservative coalescing criteria
Authors: Hailperin Max
Published: August 2005

Graph-coloring register allocators can eliminate copy instructions from a program by coalescing the interference graph nodes corresponding to the source and destination. Briggs showed that by limiting coalescing to those situations that he dubbed “conservative,” it could be prevented from causing spilling, that is, a situation where the allocator fails to assign a register to each live range. George and Appel adopted Briggs's conservativeness criterion in general, but provided an alternative criterion (the George test) to use in those cases where one of the nodes has been “precolored,” that is, preassigned a specific register. They motivated this alternative criterion by efficiency considerations, and provided no indication of the relative power of the two criteria. Thus it remained an open question whether the efficiency had been bought at the expense of reduced coalescing. Their implementation also used a limited version of the Briggs test, in place of the original, full version, without any comment on the impact of this substitution. In this article, we also present an analogously limited version of the George test.Thus we are now confronted with four different criteria for conservative coalescing: the full and limited Briggs tests and the full and limited George tests. We present a number of theorems characterizing the relative power of these different criteria, and a number of theorems characterizing the form of safety that each achieves. For example, we show that for coalescing with precolored nodes, the full George criterion is strictly more powerful than the full Briggs criterion, while offering an equally strong safety guarantee. Thus no coalesces are lost through George and Appel's introduction of the George test, and some can be gained without sacrificing safety.We also show that George and Appel's limited version of the Briggs test is probably undesirable. Although a slightly stronger safety result applies to it than to the full Briggs test, this comes at the expense of eliminating all coalesces that can reduce spilling.
Mobile research strategies for a global market
Authors: Page Colleen
Published: August 2005

The user-centered design focus at Microsoft has evolved in parallel with emerging mobile technologies. We started with a Contextual Inquiry (CI) initiative in 1997 to gather mobile communication and information requirements in the Northwest U.S. Later, as users adopted wireless data services---Short Message Service (SMS), Wireless Application Protocol (WAP), mobile instant messenger, and email clients---the focus turned to more specific usage issues in key international markets. This article presents an overview of the evolution of the qualitative field research methods that have been used to respond to increasingly global research requirements.
1
Datalog programs and their persistency numbers
Authors: Afrati Foto , Cosmadakis Stavros , Foustoucos Eugénie
Published: August 2005

The relation between Datalog programs and homomorphism problems and between Datalog programs and bounded treewidth structures has been recognized for some time and given much attention recently. Additionally, the essential role of persistent variables (of program expansions) in solving several relevant problems has also started to be observed. It turns out that to understand the contribution of these persistent variables to the difficulty of some expressibility problems, we need to understand the interrelationship among different notions of
persistency numbers
, some of which we introduce and/or formalize in the present work.This article is a first foundational study of the various persistency numbers and their interrelationships. To prove the relations among these persistency numbers, we had to develop some nontrivial technical tools that promise to help in proving other interesting results too. More precisely, we define the
adorned dependency graph of a program
, a useful tool for visualizing sets of persistent variables, and we define automata that recognize persistent sets in expansions.We start by elaborating on finer definitions of expansions and queries, which capture aspects of homomorphism problems on bounded treewidth structures. The main results of this article are (a) a program transformation technique, based on automata-theoretic tools, which manipulates persistent variables (leading, in certain cases, to programs of fewer persistent variables); (b) a categorization of the different roles of persistent variables; this is done by defining four notions of persistency numbers which capture the propagation of persistent variables from a syntactical level to a semantical one; (c) decidability results concerning the syntactical notions of persistency numbers that we have defined; and (d) the exhibition of new classes of programs for which boundedness is undecidable.
Disjunction and modular goal-directed proof search
Authors: Stone Matthew
Published: August 2005

This article explores goal-directed proof search in first-order multimodal logic. I focus on a family of modal logics which offer the expressive power to specify modular goals and local assumptions. A modular goal must be proved from designated assumptions; conversely, a local assumption can only be used to prove a designated goal. Indefinite modal specifications can avoid combinatorial interactions among independent ambiguities by making separate goals modular and corresponding disjunctive alternatives local. Such specifications can effectively guarantee that provable goals have short proofs. The key result of this article is to establish a sound and complete goal-directed proof system that actively uses the modularity and locality of modal logic to constrain proof search. In particular, logically independent, local ambiguities will not interact in proof search. The challenge is that, in goal-directed proof, a modal prover cannot simply reason locally, in a module, because modularity is a property of formulas rather than proof problems. The result therefore requires prior proof-theoretic justifications of logic programming to be extended, strengthened, and combined with new proof-theoretic analyses of modal deduction.
Arithmetic, first-order logic, and counting quantifiers
Authors: Schweikardt Nicole
Published: August 2005

This article gives a thorough overview of what is known about first-order logic with counting quantifiers and with arithmetic predicates. As a main theorem we show that Presburger arithmetic is closed under unary counting quantifiers. Precisely, this means that for every first-order formula φ(
y
,
z
) over the signature {<,+} there is a first-order formula ψ(
x
,
z
) which expresses over the structure 〈ℕ,<,+〉 (respectively, over initial segments of this structure) that the variable
x
is interpreted exactly by the number of possible interpretations of the variable
y
for which the formula φ(
y
,
z
) is satisfied. Applying this theorem, we obtain an easy proof of Ruhl's result that reachability (and similarly, connectivity) in finite graphs is not expressible in first-order logic with unary counting quantifiers and addition. Furthermore, the above result on Presburger arithmetic helps to show the failure of a particular version of the Crane Beach conjecture.
XQBE
(
XQ
uery
B
y
E
xample)
Authors: Braga Daniele , Campi Alessandro , Ceri Stefano
Published: August 2005

The spreading of XML data in many contexts of modern computing infrastructures and systems causes a pressing need for adequate XML querying capabilities; to address this need, the W3C is proposing XQuery as the standard query language for XML, with a language paradigm and a syntactic flavor comparable to the SQL relational language. XQuery is designed for meeting the requirements of skilled database programmers; its inherent complexity makes the new language unsuited to unskilled users.In this article we present XQBE (XQuery By Example), a visual query language for expressing a large subset of XQuery in a visual form. In designing XQBE, we targeted both unskilled users and expert users wishing to speed up the construction of their queries; we have been inspired by QBE, a relational language initially proposed as an alternative to SQL, which is supported by Microsoft Access. QBE is extremely successful among users who are not computer professionals and do not understand the subtleties of query languages, as well as among professionals who can draft their queries very quickly.According to the hierarchical nature of XML, XQBE's main graphical elements are trees. One or more trees denote the documents assumed as query input, and one tree denotes the document produced by the query. Similar to QBE, trees are annotated so as to express selection predicates, joins, and the passing of information from the input trees to the output tree.This article formally defines the syntax and semantics of XQBE, provides a large set of examples, and presents a prototype implementation.
Review of "Privacy: What Developers and IT Professionals Should Know by J. C. Cannon," Addison-Wesley Professional, 2004, $49.99. ISBN: 0321224094
Authors: Chand Don
Published: August 2005

Review of "Privacy: What Developers and IT Professionals Should Know by J. C. Cannon," Addison-Wesley Professional, 2004, $49.99. ISBN: 0321224094
Toward an engineering discipline for grammarware
Authors: Klint Paul , Lämmel Ralf , Verhoef Chris
Published: August 2005

Grammarware comprises grammars and all grammar-dependent software. The termgrammaris meant here in the sense of all established grammar formalisms and grammar notations including context-free grammars, class dictionaries, and XML schemas as well as some forms of tree and graph grammars. The termgrammar-dependent softwarerefers to all software that involves grammar knowledge in an essential manner. Archetypal examples of grammar-dependent software are parsers, program converters, and XML document processors. Despite the pervasive role of grammars in software systems, the engineering aspects of grammarware are insufficiently understood. We lay out an agenda that is meant to promote research on increasing the productivity of grammarware development and on improving the quality of grammarware. To this end, we identify the problems with the current grammarware practices, the barriers that currently hamper research, and the promises of an engineering discipline for grammarware, its principles, and the research challenges that have to be addressed.
Is the thrill gone?
Authors: Arora Sanjeev , Chazelle Bernard
Published: August 2005

Computer science is nothing less than a new way of thinking; explaining it to the wider world is critical to the future of the field.
What do consumers really know about spyware?
Authors: Zhang Xiaoni
Published: August 2005

Technology has revolutionized information collection and distribution to the point where marketers have expanded and implemented new technologies to enable efficient consumer information acquisition. Such sophisticated data collection methods have raised serious concerns about consumer privacy, as some marketers have quickly discovered ways to abuse this power.
Jerome Dedicates his Vita Hilarionis
Authors: Harvey Paul
Published: August 2005

Jerome's three exercises in hagiography, his Paul, Malchus, and Hilarion, as printed in our standard editions, lack dedications. The manuscript tradition, however, reveals a special (possibly first) edition of the Hilarion explicitly dedicated to the ascetic Roman woman Asella. The present study reviews the nature of the pertinent manuscript evidence, identifies the discovery of the dedication in the early seventeenth century, and then discusses the dedication's loss from scholarly sight (and why it was lost), until its rediscovery by a graduate student at the University of Illinois in the 1930s. Finally, the literary and social contexts prompting Jerome's dedication of this particular vita to Asella are discussed.
Lessons from European Population Genetic Databases: Comparing the Law in Estonia, Iceland, Sweden and the United Kingdom
Authors: Nõmper Ants , Helgason HörÐur Helgi , Wendel Lotta , Kaye Jane , Gibbons Susan
Published: August 2005

The advent of large-scale, population genetic databases (PGDs) in several countries around the world marks a significant development in human DNA banking and genetic research. The European countries that have led the way in the development of PGDs are Iceland, Sweden, Estonia and the U.K. In legal terms, the emergence of PGDs has been far from straightforward as such projects pose a range of difficult and complex issues for the law to address. This article canvasses the current law in Iceland, Estonia, Sweden and the U.K. on four fundamental issues of principle pertaining to PGDs, in order to illustrate the difficulties that have emerged around PGDs, highlight key areas of legal concern, and shed light on possible ways forward. It compares and contrasts the differing legal positions and lawmakers' responses to date in these four European countries that have established PGDs or are seeking to do so. The four fundamental issues examined are: (1) consent, especially for secondary research purposes; (2) ownership of biological samples, data and databases; (3) the rights of certain third parties to gain access to, and to use, PGD biological samples and data; and (4) benefit sharing, including the provision of feedback and genetic counselling to participants. This analysis may offer some guidance for policymakers in other jurisdictions where PGDs have been proposed or are being established.
Serum Neuron‐specific Enolase as a Predictor of Short‐term Outcome in Children with Closed Traumatic Brain Injury
Authors: Bandyopadhyay Subhankar , Hennes Halim , Gorelick Marc H. , Wells Robert G. , Walsh‐Kelly Christine M.
Published: August 2005

Background: Closed traumatic brain injury (cTBI) is a significant cause of mortality and morbidity in children. The natural course and extent of recovery from cTBI in children are poorly understood. Neuron‐specific enolase (NSE), an enzyme detected in serum following structural damage of neuronal brain cells, appears to be a good marker for intracranial injury. However, to the best of the authors' knowledge, the usefulness of NSE as a predictor of disability in children with cTBI has not been reported. Objectives: To examine the association between posttraumatic serum NSE level and short‐term physical disability in children with cTBI. Methods: This was a retrospective analysis of a prospectively enrolled cohort of children aged 0–18 years with isolated cTBI presenting to the emergency department (ED) within 24 hours of injury, and having a cranial computed tomography (CT) scan as part of the evaluation. The NSE level was obtained at the time of ED evaluation. Physical disability was measured using the Glasgow Outcome Scale (GOS). The GOS score was assigned retrospectively for enrolled patients by a single investigator blinded to NSE level. Patient outcomes were categorized as good (GOS = 5) or poor (GOS < 5). A single radiologist reviewed all cranial CT scans. Results: Ninety eligible subjects with NSE levels were identified; 86 met the enrollment criteria. Seven subjects (8%) had poor outcome. There was a significant difference in NSE levels between the poor and good outcome groups, even within high‐risk subgroups. The area under the curve (AUC) for NSE prediction of poor vs. good outcome was 0.83. A serum NSE level of 21.2 ng/dL was 86% sensitive and 74% specific in predicting poor outcome. Conclusions: It appears that the serum NSE level can be used as a predictor of global short‐term physical disability in children following cTBI.
Obese Patients with Abdominal Pain Presenting to the Emergency Department Do Not Require More Time or Resources for Evaluation Than Nonobese Patients
Authors: Platts‐Mills Timothy F. , Burg Michael D. , Snowden Brandy
Published: August 2005

Objectives: The authors describe the evaluation of obese and nonobese adult patients with abdominal pain presenting to an emergency department (ED). The hypothesis was that more ED and hospital resources are used to evaluate and treat obese patients. Methods: A prospective observational study of obese (n= 98; body mass index ≥30 kg/m2) and nonobese (n= 176; body mass index < 30 kg/m2) adults presenting to the ED with abdominal pain was performed. ED length of stay (LOS) was the primary outcome. Secondary outcomes included use of laboratory tests, computed tomography, and ultrasonography, and rates of consultations, operations, and admissions. ED diagnoses were compared between the two groups. Results: Obese patients were older (41.9 vs. 38.3 years; p = 0.027) and more often female (69% vs. 51%; p = 0.003) than nonobese patients. There were no significant differences between obese and nonobese patients in either the primary or the secondary outcome measures. Obese patients were similar to nonobese patients in regard to LOS (457 vs. 486 minutes), laboratory studies (3.2 vs. 2.9 tests), abdominopelvic computed tomographic scans (30% vs. 31%), and abdominal ultrasounds (16% vs. 13%). Obese and nonobese patients were also similar in their rates of consultations (27% vs. 31%), operations (14% vs. 12%), and admissions (18% vs. 24%). No difference was found for LOS between obese and nonobese patients as evaluated by the Wilcoxon rank‐sum test (p = 0.81). Logistic regression analysis controlling for baseline characteristics revealed no significant differences between obese and nonobese patients for secondary outcome variables. ED diagnoses for obese and nonobese patients were similar except that genitourinary diagnoses were less common in obese patients (8% vs. 21%; p = 0.01). Conclusions: In contradiction to the hypothesis, the results suggest that LOS and ED resource use in obese patients with abdominal pain are not increased when compared with nonobese patients.
Dynein and the actin cytoskeleton control kinesin-driven cytoplasmic streaming inDrosophilaoocytes
Authors: Serbus Laura R. , Cha Byeong-Jik , Theurkauf William E. , Saxton William M.
Published: August 2005

Mass movements of cytoplasm, known as cytoplasmic streaming, occur in some large eukaryotic cells. In Drosophila oocytes there are two forms of microtubule-based streaming. Slow, poorly ordered streaming occurs during stages 8-10A, while pattern formation determinants such as oskar mRNA are being localized and anchored at specific sites on the cortex. Then fast well-ordered streaming begins during stage 10B, just before nurse cell cytoplasm is dumped into the oocyte. We report that the plus-end-directed microtubule motor kinesin-1 is required for all streaming and is constitutively capable of driving fast streaming. Khc mutations that reduce the velocity of kinesin-1 transport in vitro blocked streaming yet still supported posterior localization of oskar mRNA, suggesting that streaming is not essential for the oskar localization mechanism. Inhibitory antibodies indicated that the minus-end-directed motor dynein is required to prevent premature fast streaming, suggesting that slow streaming is the product of a novel dynein-kinesin competition. As F-actin and some associated proteins are also required to prevent premature fast streaming, our observations support a model in which the actin cytoskeleton triggers the shift from slow to fast streaming by inhibiting dynein. This allows a cooperative self-amplifying loop of plus-end-directed organelle motion and parallel microtubule orientation that drives vigorous streaming currents and thorough mixing of oocyte and nurse-cell cytoplasm.
The Arf GAPs AGAP1 and AGAP2 distinguish between the adaptor protein complexes AP-1 and AP-3
Authors: Nie Zhongzhen , Fei Jiajing , Premont Richard T. , Randazzo Paul A.
Published: August 2005

ADP ribosylation factors (Arf) regulate membrane trafficking at multiple intracellular sites by recruiting coat proteins to membranes. The site-specific regulation of Arf is thought to be mediated by regulatory proteins including the guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). Here, we test this hypothesis by comparing the site of action of the Arf GAP AGAP2 to the closely related AGAP1. AGAP1 has previously been found to associate with the adaptor protein complex AP-3 and regulate the function of AP-3 endosomes. We found that AGAP2 directly interacted with AP-1. AGAP2 colocalized with AP-1, transferrin receptor and Rab4 on endosomes. Overexpression of AGAP2 changed the intracellular distribution of AP-1 and promoted Rab4-dependent fast recycling of transferrin. Based on these results, we concluded that the closely related Arf GAPs, AGAP1 and AGAP2, distinguish between these related heterotetrameric adaptor protein complexes to specifically regulate AP-3 endosomes and AP-1 recycling endosomes.
State-of-the-Art Review: A User’s Guide to the Brave New World of Designing Simulation Experiments
Authors: Kleijnen Jack P. C. , Sanchez Susan M. , Lucas Thomas W. , Cioppa Thomas M.
Published: August 2005

Many simulation practitioners can get more from their analyses by using the statistical theory on design of experiments (DOE) developed specifically for exploring computer models. We discuss a toolkit of designs for simulators with limited DOE expertise who want to select a design and an appropriate analysis for their experiments. Furthermore, we provide a research agenda listing problems in the design of simulation experiments—as opposed to real-world experiments—that require more investigation. We consider three types of practical problems: (1) developing a basic understanding of a particular simulation model or system, (2) finding robust decisions or policies as opposed to so-called optimal solutions, and (3) comparing the merits of various decisions or policies. Our discussion emphasizes aspects that are typical for simulation, such as having many more factors than in real-world experiments, and the sequential nature of the data collection. Because the same problem type may be addressed through different design types, we discuss quality attributes of designs, such as the ease of design construction, the flexibility for analysis, and efficiency considerations. Moreover, the selection of the design type depends on the metamodel (response surface) that the analysts tentatively assume; for example, complicated metamodels require more simulation runs. We present several procedures to validate the metamodel estimated from a specific design, and we summarize a case study illustrating several of our major themes. We conclude with a discussion of areas that merit more work to achieve the potential benefits—either via new research or incorporation into standard simulation or statistical packages.
Wavenumber Calibration of Fourier Transform Spectra
Authors: Hawkins R. L. , Hoke M. L. , Shaw J. H.
Published: August 2005

Spectra with a resolution of about 0.06 cm−1 obtained by a Fourier transform spectrometer have been calibrated by the internal standard method. An accuracy of 3 × 10−3 cm−1 over intervals of several thousand wavenumbers has been obtained by measuring the lines with a precision of 2 × 10−3 cm−1 and by using a large number of standard lines.
Identification of Pentachlorobiphenyl Isomers by Application of Diffuse Reflectance Fourier Transform Infrared Spectroscopy
Authors: Nyquist R. A. , Putzig C. L. , Peterson D. P.
Published: August 2005

The IR spectra presented in this paper are useful for scientists engaged in the isolation and identification of polychlorobiphenyl isomers via spectral comparison. IR correlations presented should also be useful in the identification of other polychlorobiphenyl isomers, especially in cases where the mass spectral data for the corresponding fractions are also available.
Microcomputer Controlled Flash Photometry with Submicrosecond Resolution and Raman Spectroscopy
Authors: Meiri Zvi , Berezin Yaakov , Shemesh Avraham , Ehrenberg Benjamin
Published: August 2005

The interfacing of two spectrophotometric systems to an Apple II microcomputer is described. The first is a flash photometric setup in which light flashes are formed either with a chopper wheel, or with an acousto-optic modulator which is activated by the microcomputer. Spectroscopic transients are monitored with a time resolution as short as 250 ns, by counting photon pulses into the computer's memory in the fast direct memory access mode. The formation half-times of the M412 intermediate in the photocycle of bacteriorhodopsin were measured in H2O and in D2O using the characteristic Raman band of this species, and are 68 ± 2 and 300 ± 5 μs, respectively. A microcomputer-controlled Raman spectrometer, in which the Apple II is interfaced to a Spex monochromator and the photon counting electronics, is also described. These microcomputer-controlled configurations provide simple and inexpensive setups for data collection in flash photometry and Raman and fluorescence spectroscopy.
A Resonance Raman Method for the Rapid Detection and Identification of Algae in Water
Authors: Brahma S. K. , Hargraves P. E. , Howard W. F. , Nelson W. H.
Published: August 2005

Resonance Raman spectra are reported for aqueous suspensions of nine clones of marine plankton algae representing three classes, five genera, and seven species. Spectra are obtained easily either directly from culture or from samples concentrated by sedimentation. Spectra taken at 488 or 457.9 nm are of high quality and are sufficiently distinct to differentiate clones at the algal class level, and possibly also at the genus level. Strongest peaks occur near 1527 and 1158 cm−1 associated with ν(c = c) and ν(c – c) of carotenoid pigments, but information is contained in the entire region between 900 and 3000 cm−1 due to associated overtone and combination bands which can be assigned along with fundamental vibrations. Chlorophyll peaks also are quite pronounced. Spectra obtained using rapid flow techniques match those taken using slurries in sealed tubes if low laser power is used. The sensitivity and rapidity of the technique suggest that it may be useful in remote sensing applications.
The Determination of Trace Elements in Natural Waters Using the Stabilized Temperature Platform Furnace
Authors: Manning D. C. , Slavin W.
Published: August 2005

We have developed procedures to determine 12 trace elements, Al, As, Be, Cd, Co, Cr, Cu, Mn, Ni, Pb, Se, and V, in natural water using the stabilized temperature platform furnace. Suitable matrix modifiers were tested. Confirmation of the techniques was obtained by recovery experiments at four different concentration levels. Only simple aqueous standards were required and the method of additions was not used. A simple recovery experiment was satisfactory confirmation of freedom from chemical interferences. The detection limits in the natural waters were less than 1 μg/liter, closer to 0.1 μg/liter for most of the elements. The precision was 10 to 15%. The work did not require clean-room facilities.
Some Observations on the Resolution Enhancement of Spectral Data by the Method of Self-Deconvolution
Authors: Jones R. Norman , Shimokoshi Kazuo
Published: August 2005

The directly observable information in a digitally encoded spectrum can be selectively enhanced by deconvolution with an appropriate filter operator. This may be carried out on the frequency (wavenumber) domain spectrum or on its Fourier transform. Depending on the choice of the filter, one may achieve: (1) reduction in the random noise, (2) reduction of systematic instrumental errors, (3) enhancement of the resolution. These general deconvolution procedures are briefly reviewed in terms of this classification. Recent work at the National Research Council of Canada at Ottawa has emphasized the application to band resolution enhancement (self-deconvolution), principally with respect to Fourier transform infrared spectra. Experience in our laboratory with infrared data generated on dispersion spectrometers is described. Our results confirm those reported by Kauppinen et al. at Ottawa, but the need for caution in applying self-deconvolution in routine laboratory measurements is stressed.
A Comparison of the Kubelka-Munk, Rozenberg, and Pitts-Giovanelli Methods of Analysis of Diffuse Reflectance for Several Model Systems
Authors: Hecht Harry G.
Published: August 2005

Previous studies have shown that the Rozenberg and Pitts-Giovanelli methods are useful alternatives that may be applied to diffusely reflecting samples that fail to conform to the Kubelka-Munk theory. These studies are extended in the present work to include samples of three additional types, namely, those which incorporate the absorber in solid solution within the scattering particles, those in which the absorber is adsorbed on the surface of the scattering particles, and those consisting of a dye spotted on chromatographic papers. No single method of analysis is superior in all cases. Although the Pitts-Giovanelli method gives a much better fit in some cases, it fails to converge in others. For this reason the Kubelka-Munk and Rozenberg methods are preferred, particularly when applied to diffusers in a medium of refractive index n = 1. For such systems the Rozenberg equation reduces to a simple form that is as easy to apply as the Kubelka-Munk equation.
Characterization of and Correction for Memory Effects Produced by Pneumatic Nebulizers in Inductively Coupled Plasma Emission Spectroscopy
Authors: Dobb David E. , Jenke Dennis R.
Published: August 2005

Memory effects or sample carry over characteristics of five pneumatic nebulizers routinely used for sample introduction into plasma emission spectrometers are studied. It is observed that the primary source of the memory noted for the nebulizers studied is the dissipation rate of the fog produced by the nebulizer during introduction of the previous sample or samples. Contributions to memory from the aspiration tube, salt deposition at the nebulizer tip, and a chromatographic effect at the torch tip are minimal. In terms of operational stability, detection capability, tolerance for particulates, and low memory, a concentric nebulizer with a Pt: Ir needle, Teflon nose cone, and an extended spray director is superior to the others tested. Even under the most optimum conditions, the washout time required to reduce sample emission to 0.1% of its maximum intensity varies from 2 to 4 min, thereby greatly increasing per sample analysis time. The memory effect phenomena can be accurately modeled by a hyperbolic curve and can, therefore, be easily corrected for in routine analysis. The memory correction value, which is subtracted from a sample's net emission intensity, is calculated from the product of an empirically defined correction constant and the emission intensity of previously run samples divided by the washout time. Examples of the utilization of the correction are shown.
Structure Determination of Carbonates and Diglycol Carbonates by Gas Chromatography-Mass Spectrometry
Authors: Griff Stanley P.
Published: August 2005

The use of spectrometry and chromatography permitted the elucidation of the structures of various carbonates and diglycol carbonates as well as the predication of fragmentation pathways for these classes of compounds.
Computer Measurement of Line Strengths with Application to the Methane Spectrum
Authors: Brown Linda R. , Margolis Jack S. , Norton Robert H. , Stedry Barbara D.
Published: August 2005

Computer-aided measurement of absorption line strengths from high resolution spectra greatly improves the accuracies to which relative line strengths can be determined. This article describes a computer program written for interactive use on a Prime minicomputer to fit simultaneously absorption line positions, strengths, linewidths, and continuum parameters. Application to the methane spectrum indicates that relative line strengths have been measured with accuracies of 2% or better for single isolated absorptions. Line strengths from the Q branches of the ν4 and ν1 + ν4 bands of methane are reported and compared to calculated values given in the 1980 Air Force Geophysical Laboratory (AFGL) Compilation of Molecular Parameters.
Implicit Apodization of Interferograms in Fourier Transform Spectroscopy
Authors: Baghdadi Aslan
Published: August 2005

The removal of secondary and tertiary interferograms from the main interferogram in Fourier transform spectroscopy can lead to an implicit apodization of the specimen interferogram. This effect can result in the generation of unwanted artifacts in the specimen's transmittance or absorption spectrum. One approach for avoiding this problem is to use an apodization function on the background and reference interferograms which matches the function used on the specimen interferogram.
Near-Infrared Reflectance Analysis by Gauss-Jordan Linear Algebra
Authors: Honigs D. E. , Freelin J. M. , Hieftje G. M. , Hirschfeld T. B.
Published: August 2005

Near-infrared reflectance analysis is an analytical technique that uses the near-infrared diffuse reflectance of a sample at several discrete wavelengths to predict the concentration of one or more of the chemical species in that sample. However, because near-infrared bands from solid samples are both abundant and broad, the reflectance at a given wavelength usually contains contributions from several sample components, requiring extensive calculations on overlapped bands. In the present study, these calculations have been performed using an approach similar to that employed in multi-component spectrophotometry, but with Gauss-Jordan linear algebra serving as the computational vehicle. Using this approach, correlations for percent protein in wheat flour and percent benzene in hydrocarbons have been obtained and are evaluated. The advantages of a linear-algebra approach over the common one employing stepwise regression are explored.
Examination of the Convolution Method for Numerical Smoothing and Differentiation of Spectroscopic Data in Theory and in Practice
Authors: Gans Peter , Gill J. Bernard
Published: August 2005

General expressions have been derived for the effects of convolution on a set of experimental data, from which the noise reduction may be predicted quantitatively. From these, a new criterion is proposed for the choice of convolution function in terms of the degree, number of convolution points, and number of passes of the convolution function through the data. This criterion gives maximal noise reduction with minimal signal distortion, and is particularly applicable in resolution enhancement applications. The new criteria have been tested with experimental data.
A Critical Evaluation of the Tangential Flow Torch Microwave-Induced Plasma Detector for Gas Chromatography
Authors: Goode Scott R. , Chambers Boyce , Buddin Norman P.
Published: August 2005

The tangential-flow torch was evaluated as part of an atomic emission microwave plasma detector for gas chromatography. Emission intensities for the elements carbon, sulfur, and bromine in a variety of organic molecules were studied. Calibration plots showed good linearity, indicating that the chemical matrix has little effect on the relative degree of atomization.
Mapping Labels in the Human Developing Visual System and the Evolution of Binocular Vision
Authors: Lambot Marie-Alexandra , Depasse Fanny , Noel Jean-Christophe , Vanderhaeghen Pierre
Published: August 2005

Topographic representation of visual fields from the retina to the brain is a central feature of vision. The development of retinotopic maps has been studied extensively in model organisms and is thought to be controlled in part by molecular labels, including ephrin/Eph axon guidance molecules, displayed in complementary gradients across the retina and its targeting areas. The visual system in these organisms is primarily monocular, with each retina mapping topographically to its contralateral target. In contrast, mechanisms of retinal mapping in binocular species such as primates, characterized by the congruent, aligned mapping of both retinas onto the same brain target, remain completely unknown. Here, we show that the distribution ofephrin/Ephgenes in the human developing visual system is fundamentally different from what is known in model organisms. In the human embryonic retina, EphA receptors are displayed along two gradients, sloping down from the center of the retina to its periphery. The EphB1 receptor, which controls the ipsilateral routing of retinal axons in the mouse, is expressed throughout the human temporal retina in coordination with the changes inEphAgene expression. In the dorsal lateral geniculate nucleus, ephrin-A/EphAs are displayed along complementary retinotopic gradients. Our data point to an evolutionary model in which the coordinated divergence of the distribution of the receptors controlling retinal guidance and retinal mapping enabled the emergence of a fully binocular system. They also indicate that ephrin/Eph signaling plays a potentially major role in the development of neuronal connectivity in humans.
Bradykinin stimulates cell proliferation through an extracellular-regulated kinase 1 and 2-dependent mechanism in breast cancer cells in primary culture
Authors: Greco S , Elia M G , Muscella A , Romano S , Storelli C , Marsigliante S
Published: August 2005

We have previously reported that bradykinin (BK) represents an influential mitogenic agent in normal breast glandular tissue. We here investigated the mitogenic effects and the signalling pathways of BK in primary cultured human epithelial breast cells obtained from a tumour and from the histologically proven non-malignant tissue adjacent to the tumour. BK provoked cell proliferation, increase in cytosolic calcium, activation of protein kinase C (PKC)-α, -β, -δ, -ε and -η and phosphorylation of the extracellular-regulated kinases 1 and 2 (ERK1/2). The following compounds blocked the proliferative effects of BK: Hyp3-BK, a B2 receptor subtype inhibitor; U73122, a phospholipase C-β inhibitor; GF109203X, a protein kinase C (PKC) inhibitor; and PD98059, a mitogen-activated protein kinase kinase inhibitor. Gö6976, a Ca2+-dependent PKC inhibitor, did not have any effect. In conclusion, the mitogenic effects of BK are retained in peritumour and tumour cells; hence, it is likely that BK has an important role in cancer endorsement and progression.