bluuebunny/crossref_metadata_2025 huggingface dataset:
Computer Modeling of High Resolution Electron Microscope Images Using
65,536 Beams
Authors: Krakow William
Published: January 2003

A system of computer programs which calculates both diffraction patterns
and images of generalized objects using the kinematical scattering
approximation has now been extended to include multislice dynamical theory.
Calculations of this type have been obtained by other authors for
interstitial defects where several approximations were necessary to save
computational time such as considering the defect strain field to be
confined to one slice or reducing the number of beams and sample thickness
(e.g. 3999 beams at 7 min./slice).
Automated Analysis of SEM X-Ray Spectral Images: A Powerful
New Microanalysis Tool
Authors: Kotula Paul G. , Keenan Michael R. , Michael Joseph R.
Published: January 2003

Spectral imaging in the scanning electron microscope (SEM)
equipped with an energy-dispersive X-ray (EDX) analyzer has
the potential to be a powerful tool for chemical phase
identification, but the large data sets have, in the past, proved
too large to efficiently analyze. In the present work, we describe
the application of a new automated, unbiased, multivariate
statistical analysis technique to very large X-ray spectral
image data sets. The method, based in part on principal components
analysis, returns physically accurate (all positive) component
spectra and images in a few minutes on a standard personal
computer. The efficacy of the technique for microanalysis is
illustrated by the analysis of complex multi-phase materials,
particulates, a diffusion couple, and a single-pixel-detection
problem.
Apoptosis Process in Mouse Leydig Cells during Postnatal
Development
Authors: Faria Maria José Salles , Simões Zilá Luz Paulino , Lunardi Laurelucia Orive , Hartfelder Klaus
Published: January 2003

The development of Leydig cells in mammals has been widely
described as a biphasic pattern with two temporally mature Leydig
cell populations, fetal stage followed by the adult generation
beginning at puberty. In the present study, mouse Leydig cells
were examined for apoptosis during postnatal testis development
using electron microscopy and in situ DNA fragmentation
by terminal deoxynucleotidyl transferase staining (TdT). Both
the morphological study and the DNA fragmentation analysis showed
that cellular death by apoptosis did not occur in Leydig cells
during the neonatal, prepubertal, puberty, and adult periods.
From these results, we suggest that the remaining fetal Leydig
cells in the neonatal testis are associated with the involution
or degeneration processes. In contrast, in the prepubertal and
puberty stages, fragmentation of apoptotic DNA was detected
in germ cells present in some seminiferous tubules.
Corrosion Casting in the Reproduction of the Microsurface Topography of Fibrillar Collagen
Authors: Sims P. A. , Albrecht R. M.
Published: January 2003

We have used a two-step casting procedure to create replicas of fibrillar collagen. A negative replica
or mold is first created using either Mercox casting resin or a prepolymerized methacrylate resin that was
originally described by Murakami. In the second step, a positive replica is made from the first using a solution
of polystyrene or polyurethane to coat the methacrylate cast. The resulting replica is removed from the
methacrylate cast. Results indicate the highest level of spatial resolution is obtained using a modified Murakami
resin for the negative cast and polystyrene for the positive replica. The 29-nm-wide repeat banding structure
present on collagen fibrils could be clearly identified in both the methacrylate cast and in the polystyrene
positive replica of the methacrylate cast. Thus high-resolution replicas can be obtained. Such replicas may be
useful to imprint inplantable devices with biologically relevant textures to improve tissue integration or for the
development of textured surfaces for the in vitro expansion of cultured cells.
Plasma Cleaning and Its Applications for Electron Microscopy
Authors: Isabell Thomas C. , Fischione Paul E. , O'Keefe Catherine , Guruz Murat U. , Dravid Vinayak P.
Published: January 2003

The effectiveness of applying a high-frequency, low-energy, reactive gas plasma for the removal of hydrocarbon contamination from specimens and components for electron microscopy has been investigated with a variety of analytical techniques. Transmission electron microscopy (TEM) analysis of specimens that have been plasma cleaned shows an elimination of the carbonaceous contamination from the specimen. With extended cleaning times the removal of existing carbon contamination debris due to previously conducted
microanalysis is shown. Following plasma cleaning, specimens may be examined in the electron microscope for several hours without exhibiting evidence of recontamination. The effectiveness of plasma cleaning is not limited to applications for TEM specimens. Scanning electron microscopy (SEM) specimens that have been plasma cleaned likewise show an elimination of carbonaceous contamination. Furthermore, other electron microscopy parts and accessories, such as aperture strips, specimen clamping rings, and Wehnelts, among
others, can benefit from plasma cleaning.
Edge Sharpening for Unbiased Edge Detection in Field Emission Scanning Electron Microscope Images
Authors: Raj P. Markondeya , Dunn Stanley M. , Cannon W. Roger
Published: January 2003

We report here a specific type of edge strength anisotropy observed in field emission scanning electron microscope (FESEM) images. The images show weaker edge gradients in the scanning direction and hence these edges frequently go undetected. Direct application of edge detection algorithms to images with nondistinct edges, such as powder particles, show strong bias to edges perpendicular to the scanning direction. Edge orientation polarograms obtained from these images always show strong fictitious particle orientation in the scanning direction. In this work, we discuss an edge-sharpening algorithm that corrects for this bias and results in relatively more accurate and consistent edge orientation information.
No Place for Particles in Relativistic Quantum Theories?
Authors: Halvorson Hans , Clifton Rob
Published: January 2003

David Malament (1996) has recently argued that there can be no relativistic quantum theory of (localizable) particles. We consider and rebut several objections that have been made against the soundness of Malament's argument. We then consider some further objections that might be made against the generality of Malament's conclusion, and we supply three no-go theorems to counter these objections. Finally, we dispel potential worries about the counterintuitive nature of these results by showing that relativistic quantum field theory itself explains the appearance of “particle detections.”
Bayesian Networks and the Problem of Unreliable Instruments
Authors: Bovens Luc , Hartmann Stephan
Published: January 2003

We appeal to the theory of Bayesian Networks to model different strategies for obtaining confirmation for a hypothesis from experimental test results provided by less than fully reliable instruments. In particular, we consider (i) repeated measurements of a single test consequence of the hypothesis, (ii) measurements of multiple test consequences of the hypothesis, (iii) theoretical support for the reliability of the instrument, and (iv) calibration procedures. We evaluate these strategies on their relative merits under idealized conditions and show some surprising repercussions on the variety-of-evidence thesis and the Duhem-Quine thesis.
The Entropy Theory of Counterfactuals
Authors: Kutach Douglas N.
Published: January 2003

I assess the thesis that counterfactual asymmetries are explained by an asymmetry of the global entropy at the temporal boundaries of the universe, by developing a method of evaluating counterfactuals that includes, as a background assumption, the low entropy of the early universe. The resulting theory attempts to vindicate the common practice of holding the past mostly fixed under counterfactual supposition while at the same time allowing the counterfactual's antecedent to obtain by a natural physical development. Although the theory has some success in evaluating a wide variety of ordinary counterfactuals, it fails as an explanation of counterfactual asymmetry.
Reconsidering Kant, Friedman, Logical Positivism, and the Exact Sciences
Authors: DiSalle Robert
Published: January 2003

This essay considers the nature of conceptual frameworks in science, and suggests a reconsideration of the role played by philosophy in radical conceptual change. On Kuhn's view of conceptual conflict, the scientist's appeal to philosophical principles is an obvious symptom of incommensurability; philosophical preferences are merely “subjective factors” that play a part in the “necessarily circular” arguments that scientists offer for their own conceptual commitments. Recent work by Friedman has persuasively challenged this view, revealing the roles that philosophical concerns have played in preparing the way for conceptual change, creating an enlarged conceptual space in which alternatives to the prevailing framework become intelligible and can be rationally discussed. If we shift our focus from philosophical themes or preferences to the process of philosophical analysis, however, we can see philosophy in a different and much more significant historic role: not merely as an external source of general heuristic principles and new conceptual possibilities, but, at least in the most important revolutionary developments, as an objective tool of scientific inquiry. I suggest that this approach offers some insight into the philosophical significance of Newton's and Einstein's revolutionary work in physics, and of the interpretation of their work by (respectively) Kant and the logical positivists. It also offers insight into the connections between modern philosophy of science and some traditional philosophical concerns about the nature of a priori knowledge.
Probability Kinematics and Commutativity
Authors: Wagner Carl G.
Published: January 2003

The so-called “non-commutativity” of probability kinematics has caused much unjustified concern. When identical learning is properly represented, namely, by identical Bayes factors rather than identical posterior probabilities, then sequential probability-kinematical revisions behave just as they should. Our analysis is based on a variant of Field's reformulation of probability kinematics, divested of its (inessential) physicalist gloss.
What Experiment Did We Just Do? Counterfactual Error Statistics and Uncertainties about the Reference Class
Authors: Staley Kent W.
Published: January 2003

Experimenters sometimes insist that it is unwise to examine data before determining how to analyze them, as it creates the potential for biased results. I explore the rationale behind this methodological guideline from the standpoint of an error statistical theory of evidence, and I discuss a method of evaluating evidence in some contexts when this predesignation rule has been violated. I illustrate the problem of potential bias, and the method by which it may be addressed, with an example from the search for the top quark. A point in favor of the error statistical theory is its ability, demonstrated here, to explicate such methodological problems and suggest solutions, within the framework of an objective theory of evidence.
Scientific Inference and the Pursuit of Fame: A Contractarian Approach
Authors: Zamora Bonilla Jesús P.
Published: January 2003

Methodological norms are seen as rules defining a competitive game, and it is argued that rational recognition-seeking scientists can reach a collective agreement about which specific norms serve better their individual interests, especially if the choice is made ‘under a veil of ignorance’, i.e., before knowing what theory will be proposed by each scientist. Norms for theory assessment are distinguished from norms for theory choice (or inference rules), and it is argued that pursuit of recognition only affects this second type of rule. An inference rule similar to ‘eliminative induction’ is defended on the basis of such a possible agreement. According to this contractarian approach, both the explanation and the justification of scientific norms only need to refer to the preferences of individual scientists, without assuming the existence of ‘collective’ points of view.
Tears, Tantrums, and Bared Teeth: The Emotional Economy of Three Conservative Prime Ministers, 1951–1963
Authors: Francis Martin
Published: January 2003

At a cabinet meeting on November 4, 1956, Anthony Eden came face to face with the unravelling of his ill-starred premiership. As two leading cabinet colleagues, Lord Butler and Lord Salisbury, insisted that British military operations in Egypt would have to be ended, the prime minister found it impossible to repress any longer his overwrought and excitable temperament. According to the journalist James Margach, “Eden was emotionally overcome. He broke down in tears and cried: ‘You are all deserting me.’ He was in total collapse, weeping unashamedly. Then he went upstairs to compose himself.” Within two months Eden had resigned. His successor, Harold Macmillan, deliberately set out to create a very different emotional environment around him. In place of Eden's petulant volatility came an emphasis on self-control and steady nerves. In the words of David Maxwell Fyfe, who served under both premiers, Eden's “chronic restlessness” gave way to “a central calmness” under Macmillan. The new prime minister adopted an air of nonchalance and indifference, and according to one of his aides, “anyone who got excited got short shrift.” The contrasting public styles of Eden and Macmillan is a commonplace in the political history of the 1950s and has been credited with facilitating the recovery in Conservative electoral fortunes in the aftermath of the Suez debacle. However, Eden's breakdown and Macmillan's apparent “unflappability” can also be identified as sites on which to explore how dominant codes of masculine emotional culture were manifested in the world of politics.
Who Was Who? Race and Jews in Turn-of-the-Century Britain
Authors: Cohen Deborah
Published: January 2003

Race—as a category—has commonly been understood as a response to difference. In the first instance, race offered a means of ordering unfamiliar peoples, whether encountered in the empire or at home. In the European historiography, the notion of “biological” race, defined by an inherited set of characteristics passed through the blood, possesses a particular genealogy: its roots can be found in the eighteenth century, its fullest articulation came in the late nineteenth century, and its twentieth-century decline was hastened by the Holocaust.

This article sets out a different, if not completely incompatible, thesis. It takes the case of British Jews to argue that racial categories could arise as a response to the apparent similarities, as well as the perceived differences, between Jews and other Britons. Put differently, in the late nineteenth century, Jews came increasingly to be identified as a race precisely because they were difficult to differentiate from their fellow citizens. Class proved a critical determinant. Jews became ever more invisible as they scaled the social ladder. “East End” Jews—poor and newly immigrated—might be readily detectable, but their middle- and upper-middle-class “West End” counterparts confounded observers. Notions of race, I will argue, emerged in part as a consequence of assimilation, delimiting difference in a nation where formal legal barriers to Jewish integration had been eliminated and social obstacles largely overcome.

Race was a staple term of the late nineteenth century. It proliferated throughout the language of the time.
Wars in the Wards: The Social Construction of Medical Work in First World War Britain
Authors: Watson Janet S. K.
Published: January 2003

When the Imperial War Museum was founded in early 1917, the subcommittee in charge of collections related to “Women's Work” solicited contributions from Dr. Flora Murray of the Military Hospital at Endell Street in London. Murray and Dr. Louisa Garrett Anderson had formed the Women's Hospital Corps and, with the French Red Cross, opened hospitals in Paris and Wimereux in the early stages of the war. After successful cooperation with British military and medical authorities overseas, they were asked to open the Endell Street facility, the only hospital operating under the auspices of the War Office to be staffed entirely by women. Murray refused to cooperate with the museum committee “because she wished her hospital to be considered purely professionally as a military hospital and not as women's war work.”

This was not just rhetoric of women's equality from someone who described herself as “one of Mrs. Pankhurst's lot,” but reflected the new emphasis on professionalism that had developed in the preceding fifty years. The First World War provided new opportunities for work in a variety of fields more or less closely related to the perpetuation and advancement of the armed conflict; scholars have recently focused in particular on working-class women in industry and paramilitary organizations. Though opportunities for educated women increased throughout civil society, my focus here is on work that was perceived as explicitly on behalf of the war effort, with a special concentration on three populations of women working in hospitals: doctors, trained nurses, and volunteers.
Dewey on Naturalism, Realism and Science
Authors: Godfrey-Smith Peter
Published: January 2003

An interpretation of John Dewey's views about realism, science, and naturalistic philosophy is presented. Dewey should be seen as an unorthodox realist, with respect to both general metaphysical debates about realism and with respect to debates about the aims and achievements of science.
What Do Brain Data Really Show?
Authors: Hardcastle Valerie Gray , Stewart C. Matthew
Published: January 2003

There is a bias in neuroscience toward localizing and modularizing brain functions. Single cell recording, imaging studies, and the study of neurological deficits all feed into the Gallian view that different brain areas do different things and the things being done are confined to particular processing streams. At the same time, there is a growing sentiment that brains probably don't work like that after all; it is better to conceive of them as fundamentally distributed units, multi-tasking at every level. This sentiment, however, is much less congenial to the tried-and-true experimental protocols available today and to theorizing about the brain in general. This essay examines the tension between current experimental methods and large-scale views of the brain. We argue that this disconnection between experiment and what really are guiding theoretical metaphors seriously impedes progress in neuroscience.
The Subtleties of Entanglement and its Role in Quantum Information Theory
Authors: Clifton Rob
Published: January 2003

My aim in this paper is a modest one. I do not have any particular thesis to advance about the nature of entanglement, nor can I claim novelty for any of the material I shall discuss. My aim is simply to raise some questions about entanglement that spring naturally from certain developments in quantum information theory and are, I believe, worthy of serious consideration by philosophers of science. The main topics I discuss are different manifestations of quantum nonlocality, entanglement-assisted communication, and entanglement thermodynamics.
50 Years of Successful Predictive Modeling Should Be Enough: Lessons for Philosophy of Science
Authors: Bishop Michael A. , Trout J. D.
Published: January 2003

Our aim in this paper is to bring the woefully neglected literature on predictive modeling to bear on some central questions in the philosophy of science. The lesson of this literature is straightforward: For a very wide range of prediction problems, statistical prediction rules (SPRs), often rules that are very easy to implement, make predictions than are as reliable as, and typically more reliable than, human experts. We will argue that the success of SPRs forces us to reconsider our views about what is involved in understanding, explanation, good reasoning, and about how we ought to do philosophy of science.
Gauge Matters
Authors: Earman John
Published: January 2003

The constrained Hamiltonian formalism is recommended as a means for getting a grip on the concepts of gauge and gauge transformation. This formalism makes it clear how the gauge concept is relevant to understanding Newtonian and classical relativistic theories as well as the theories of elementary particle physics; it provides an explication of the vague notions of “local” and “global” gauge transformations; it explains how and why a fibre bundle structure emerges for theories which do not wear their bundle structure on their sleeves; it illuminates the connections of the gauge concept to issues of determinism and what counts as a genuine “observable”; and it calls attention to problems which arise in attempting to quantize gauge theories. Some of the limitations and problematic aspects of the formalism are also discussed.
Gauge Principles, Gauge Arguments and the Logic of Nature
Authors: Martin Christopher A.
Published: January 2003

I consider the question of how literally one can construe the “gauge argument,” which is the canonical means of understanding the putatively central import of local gauge symmetry principles for fundamental physics. As I argue, the gauge argument must be afforded (at best) a heuristic reading. Claims to the effect that the argument reflects a deep “logic of nature” must, for numerous reasons I discuss, be taken with a grain of salt.
Linnaean Ranks: Vestiges of a Bygone Era
Authors: Ereshefsky Marc
Published: January 2003

We tend to think that there are different types of biological taxa: some taxa are species, others are genera, while others are families. Linnaeus gave us his ranks in 1731. Biological theory has changed since Linnaeus's time. Nevertheless, the vast majority of biologists still assign Linnaean ranks to taxa, even though that practice is at odds with evolutionary theory and even though it causes a number of practical problems. The Linnaean ranks should be abandoned and alternative methods for displaying the hierarchical relations of taxa should be adopted.
Strategies for Discovering Mechanisms: Schema Instantiation, Modular Subassembly, Forward/Backward Chaining
Authors: Darden Lindley
Published: January 2003

Discovery proceeds in stages of construction, evaluation, and revision. Each of these stages is constrained by what is known or conjectured about what is being discovered. A new characterization of mechanism aids in specifying what is to be discovered when a mechanism is sought. Guidance in discovering mechanisms may be provided by the reasoning strategies of schema instantiation, modular subassembly, and forward/backward chaining. Examples are found in mechanisms in molecular biology, biochemistry, immunology, and evolutionary biology.
Signals, Evolution and the Explanatory Power of Transient Information
Authors: Skyrms Brian
Published: January 2003

Pre-play signals that cost nothing are sometimes thought to be of no significance in interactions which are not games of pure common interest. We investigate the effect of pre-play signals in an evolutionary setting for Assurance, or Stag Hunt, games and for a Bargaining game. The evolutionary game with signals is found to have dramatically different dynamics from the same game without signals. Signals change stability properties of equilibria in the base game, create new polymorphic equilibria, and change the basins of attraction of equilibria in the base game. Signals carry information at equilibrium in the case of the new polymorphic equilibria, but transient information is the basis for large changes in the magnitude of basins of attraction of equilibria in the base game. These phenomena exemplify new and important differences between evolutionary game theory and game theory based on rational choice.
How Molecules Matter to Mental Computation
Authors: Thagard Paul
Published: January 2003

Almost all computational models of the mind and brain ignore details about neurotransmitters, hormones, and other molecules. The neglect of neurochemistry in cognitive science would be appropriate if the computational properties of brains relevant to explaining mental functioning were in fact electrical rather than chemical. But there is considerable evidence that chemical complexity really does matter to brain computation, including the role of proteins in intracellular computation, the operations of synapses and neurotransmitters, and the effects of neuromodulators such as hormones. Neurochemical computation has implications for understanding emotions, cognition, and artificial intelligence.
Methodological and Epistemic Differences between Historical Science and Experimental Science
Authors: Cleland Carol E.
Published: January 2003

Experimental research is commonly held up as the paradigm of “good” science. Although experiment plays many roles in science, its classical role is testing hypotheses in controlled laboratory settings. Historical science (which includes work in geology, biology, and astronomy, as well as paleontology and archaeology) is sometimes held to be inferior on the grounds that its hypothesis cannot be tested by controlled laboratory experiments. Using contemporary examples from diverse scientific disciplines, this paper explores differences in practice between historical and experimental research vis-à-vis the testing of hypotheses. It rejects the claim that historical research is epistemically inferior. For as I argue, scientists engage in two very different patterns of evidential reasoning and, although there is overlap, one pattern predominates in historical research and the other pattern predominates in classical experimental research. I show that these different patterns of reasoning are grounded in an objective and remarkably pervasive time asymmetry of nature.
Testing Multiple Realizability: A Discussion of Bechtel and Mundale
Authors: Kim Sungsu
Published: January 2003

Bechtel and Mundale (1999) argue that multiple realizability is not plausible. They point out that neuroscientists assume that psychological traits are realized similarly in homologous brain structures and contend that a biological aspect of the brain that is relevant to neuropsychological state individuation provides evidence against multiple realizability. I argue that Bechtel and Mundale adduce the wrong sort of evidence against multiple realizability. Homologous traits do not provide relevant evidence. It is homoplasious traits of brains that can provide evidence for or against multiple realizability.
Putting the Irrelevance Back Into the Problem of Irrelevant Conjunction
Authors: Fitelson Branden
Published: January 2003

Naive deductive accounts of confirmation have the undesirable consequence that if E confirms H, then E also confirms the conjunction H & X, for any X—even if X is utterly irrelevant to H (and E). Bayesian accounts of confirmation also have this property (in the case of deductive evidence). Several Bayesians have attempted to soften the impact of this fact by arguing that—according to Bayesian accounts of confirmation— E will confirm the conjunction H & X less strongly than E confirms H (again, in the case of deductive evidence). I argue that existing Bayesian “resolutions” of this problem are inadequate in several important respects. In the end, I suggest a new-and-improved Bayesian account (and understanding) of the problem of irrelevant conjunction.
Common-Causes are Not Common Common-Causes
Authors: Hofer-Szabó Gábor , Rédei Miklós , Szabó László E.
Published: January 2003

A condition is formulated in terms of the probabilities of two pairs of correlated events in a classical probability space which is necessary for the two correlations to have a single (Reichenbachian) common-cause and it is shown that there exists pairs of correlated events, probabilities of which violate the necessary condition. It is concluded that different correlations do not in general have a common common-cause. It is also shown that this conclusion remains valid even if one weakens slightly Reichenbach's definition of common-cause. The significance of the difference between common-causes and common common-causes is emphasized from the perspective of Reichenbach's Common Cause Principle.
Asymmetry in Party Influence: Reply
Authors: Krehbiel Keith
Published: January 2003

Groseclose and Snyder's revised method (2003) for assessing relative party influence deserves high praise for its creativity and explicitness. Two limitations should also be noted, however. First, the method seems likely to overstate majority-party influence. Second, even if taken at face value, the finding of asymmetric party influence is weak when compared with a baseline model.
Using Ecological Inference Point Estimates as Dependent Variables in Second-Stage Linear Regressions
Authors: Herron Michael C. , Shotts Kenneth W.
Published: January 2003

The practice of using point estimates produced by the King ecological inference technique as dependent variables in second-stage linear regressions leads to second-stage results that, in general, are inconsistent. This conclusion holds even when all assumptions behind King's ecological technique are satisfied. Second-stage inconsistency is a consequence of the fact that King-based point estimates of disaggregated quantities contain errors correlated with the true quantities the estimates measure. Our findings on second-stage inconsistency, as well as a fix that we propose, follow from econometric theory in conjunction with an analysis of simulated and real ecological data sets.
Cross-Contamination in EI-R: Reply
Authors: Herron Michael C. , Shotts Kenneth W.
Published: January 2003

We address in Herron and Shotts (2003; hereinafter HS) an increasingly common statistical practice called EI-R, in which point estimates generated by the King (1997) ecological inference technique are used as dependent variables in second-stage linear regressions. Although HS argue that EI-R slope estimates are inconsistent and suffer from attenuation bias, this characterization of EI-R is excessively conservative. Indeed, we show here that EI-R estimates can suffer from sign reversals, attenuation bias, and augmentation bias, that inference based on these estimates can be misleading, and that EI-R is unfixable and should not be used.
The Coefficient of Party Influence
Authors: Krehbiel Keith
Published: January 2003

In a 2000 article in American Journal of Political Science, James Snyder and Tim Groseclose develop and apply an innovative method for detecting and estimating the frequency and magnitude of party influence in congressional roll call voting. This paper presents a framework for assessing the coefficient that the authors interpret as “party influence.” The analysis reveals that, and shows why, the coefficient manifests two troublesome characteristics. The coefficient cannot discriminate between disparate types of party influence because the mapping between types of partison influence and signs of the coefficient is not one-to-one. Similarly, the coefficient has a responsiveness problem because a marginal increase in one party's influence can cause the estimate of the coefficient to increase, decrease, or remain constant. Because the literature on parties in Congress emphasizes majority-party strength, the inability of the coefficient to isolate party-specific effects is a serious drawback in the ongoing hunt for genuine party discipline.
Simultaneous light and small-angle neutron scattering on aggregating concentrated colloidal suspensions
Authors: Romer Sara , Urban Claus , Lobaskin Vladimir , Scheffold Frank , Stradner Anna , Kohlbrecher Joachim , Schurtenberger Peter
Published: January 2003

A new sample environment has been developed in order to perform light and small-angle neutron scattering (SANS) simultaneously on colloidal systems. The combination of SANS and diffusing wave spectroscopy (DWS) is of particular use in the high-concentration regime. DWS provides information on the local dynamic properties of the individual particles, whereas SANS gives access to the structural properties on similar length scales. The combination of both methods thus allows one to obtain structural and dynamic information over a very large range of length and time scales. Using this new setup, the onset of aggregation and the sol–gel transition in concentrated destabilized polystyrene sphere suspensions have been investigated. At the gel point, a dramatic change of the particle dynamics from diffusion to a subdiffusive arrested motion is observed. However, while the DWS measurements indicate that dramatic changes in the local dynamics occur over a long period, the SANS pattern quickly reaches its final appearance. The SANS experiments thus indicate that a fluid-like structure is arrested in the course of the gel formation. The data are found to be in good qualitative agreement with computer simulations.
Improved dihedral-angle restraints for protein structure refinement
Authors: Priestle John P.
Published: January 2003

Because of the relatively low-resolution diffraction of typical protein crystals, structure refinement is usually carried out employing stereochemical restraints to increase the effective number of observations. Well defined values for bond lengths and angles are available from small-molecule crystal structures. Such values do not exist for dihedral angles because of the concern that the strong crystal contacts in small-molecule crystal structures could distort the dihedral angles. This paper examines the dihedral-angle distributions in ultra-high-resolution protein structures (1.2 Å or better) as a means of analysing the population frequencies of dihedral angles in proteins and compares these with the stereochemical restraints currently used in one of the more widely used molecular-dynamics refinement packages,X-PLOR, and its successor,CNS. Discrepancies between the restraints used in these programs and what is actually seen in high-resolution protein structures are examined and an improved set of dihedral-angle restraint parameters are derived from these inspections.
Assessment of the X-ray diffraction–absorption method for quantitative analysis of largely amorphous pharmaceutical composites
Authors: Bergese P. , Colombo I. , Gervasoni D. , Depero Laura E.
Published: January 2003

Determination of the residual weight fraction of a crystalline drug in a largely amorphous pharmaceutical composite is still a challenging question. None of the quantitative X-ray diffraction (QXRD) methods found in the literature is suitable for these inclusion systems. The composite's diffraction patterns present a structured amorphous halo (arising from the amorphous matrix and drug molecular clusters) in which the crystalline drug peaks rise up. Moreover, the matrix traps a non-negligible quantity of water (which cannot be directly detected by X-ray diffraction) and the crystal structure of the drug may be unknown. In this work, a development of the QXRD analysis based on the diffraction–absorption technique is presented. The method is standardless, avoids the interpretation of the amorphous halo and the knowledge of the crystal structures of the phases, and takes into account the absorbed water. Results are in excellent agreement with those obtained by differential scanning calorimetry (DSC). The general features of the technique open its application to other classes of largely amorphous composite materials, like glass systems generated in the stabilization/solidification of toxic waste.
Modelling X-ray diffraction by lamellar structures composed of electrically charged layers
Authors: Plançon A.
Published: January 2003

The stacking parameters and nature of a mixed-layer mineral (m.l.m.) are generally determined by modelling its X-ray diffraction pattern. For m.l.m.'s containing electrically charged layers it has been assumed, until now, that they can be described by stacking of electrically neutral units that associate the charged layer itself and a compensating interlayer charge. Some consequences of this hypothesis are difficult to justify,e.g.quite different charges to compensate the same types of interlayers, or, on the contrary, the same charge to compensate quite different types of interlayers. A new model is proposed, allowing a description of any lamellar structure containing electrically charged layers. The mathematical formalism for the diffracted intensities of such a model is developed.
A heating stage up to 1173 K for X-ray diffraction studies in the whole orientation space
Authors: Resel R. , Tamas E. , Sonderegger B. , Hofbauer P. , Keckes J.
Published: January 2003

A multi-purpose heating attachment designed primarily for X-ray four-circle diffractometers but applicable also for classical powder diffraction is presented. When working in reflection geometry, the air-cooled heating stage allows diffraction studies to be performed on plate-like samples up to 1173 K in the whole orientation space. This paper gives a detailed description of the assembly and important technical specifications for the performance of experiments. The heating characteristics of the heating stage, the displacement of the sample from the goniometer centre as a result of thermal expansion and the influence of the protecting dome on the diffraction experiment are presented. The simple technical construction, the low weight, the small size and good heating performance make this equipment a general purpose heating attachment for X-ray diffraction experiments in reflection geometry.
Structural characterization of thin films of the SrBi2Nb2O9ferroelectric Aurivillius phase epitaxially grown on (110)SrTiO3
Authors: Duclère J.-R. , Guilloux-Viry M. , Perrin A.
Published: January 2003

Aurivillius-phase SrBi2Nb2O9(SBN) films grown by pulsed-laser deposition on (110)SrTiO3are nearly (116) oriented as shown by their X-ray diffraction θ–2θ scans. A specific artifact, leading possibly to an erroneous deduction of a (115) and (116) mixture of orientations, has been highlighted. The films present a quite small mosaicity (ω-scan full width at half-maximum = 0.2–0.5°). Sharp electron channeling patterns (ECPs) with the expected twofold symmetry are the signature of film epitaxy. These ECPs often display the superimposition of two individual patterns, rotated by 180° with respect to each other: two families of oriented SBN crystallites, rotated in the same way, coexist in the films. Indeed, from symmetry considerations at the film–substrate interface, these two families area prioriequiprobable. Similarly, two peaks, 180° shifted, are observed for the 00 10 reflection φ scans and fully confirm this model. However, their relative intensity, which gives access to the quantitative distribution of the two families, shows that in many cases the two families do not present the same relative weight, in good correlation with the qualitative ECP observations, indicating a subtle asymmetrization at the nucleation or growth stage. The in-plane orientation is defined as: [\bar{1}10]F|| [001]Sand nearly [33\bar{1}]For [\bar{3}\bar{3}1]F|| [\bar{1}10]S(generating the two families). The film–substrate interfacial relationship is discussed, taking into account the possible facetting of the substrate surface and the occurrence of the (11\bar{7}) SBN plane as twin boundary.
How root-mean-square distance (r.m.s.d.) values depend on the resolution of protein structures that are compared
Authors: Carugo Oliviero
Published: January 2003

The most popular estimator of structural similarity is the root-mean-square distance (r.m.s.d.) between equivalent atoms, computed after optimal superposition of the two structures that are compared. It is known that r.m.s.d. values do not depend only on conformational differences but also on other features, for example the dimensions of the structures that are compared. An open question is how they might depend on the accuracy of the experimentally determined protein structures. Given that the accuracy of the protein crystal structures is generally estimated through the crystallographic resolution, it is important to know the dependence of the r.m.s.d. on the crystallographic resolution of the two structures that are compared. 14458 protein structure pairs of identical sequence were compared and the resulting r.m.s.d. values were normalized to 100-residue length to avoid the bias introduced by the dependence of the r.m.s.d. values on the protein-pair dimensions. On average, smaller r.m.s.d. values are associated with protein structure pairs at better resolution and the r.m.s.d. values tend to increase if the two proteins that are compared have been refined at different resolutions. For crystallographic resolutions ranging between 1.6 and 2.9 Å, both relationships appear to be linear: r.m.s.d. = −0.73 + 0.48 resolution and delta_r.m.s.d. = 0.20 + 0.30 delta_resolution (`delta' indicating difference). Although the linearity of these relationships is not expected to hold outside the 1.6–2.9 Å resolution range, they are useful in making the r.m.s.d. values more reliable.
A new approach to the solution of the Takagi–Taupin equations for X-ray optics: application to a thermally deformed crystal monochromator
Authors: Mocella V. , Lee W.-K. , Tajiri G. , Mills D. , Ferrero C. , Epelboin Y.
Published: January 2003

A new computational approach to the Takagi–Taupin equations for the analysis of X-ray optics is presented and applied to heat-loaded synchrotron monochromators. The new numerical approach is based on the assumption that the incoming wave is completely incoherent (incoherent point source). The simulation avoids any kind of simplification: it takes into account the thermal deformation of the crystals calculated by the finite-element method, the transverse beam direction and the beam spatial distribution. As an application example, the theoretical rocking curves for low-energy low-order and high-energy high-order reflections are compared with results of measurements carried out at the Advanced Photon Source (APS) on a cryogenically cooled double-crystal monochromator. The good agreement shows that the adopted approach succeeds in simulating very closely the actual experimental setup while exhibiting satisfactorily short execution times.
Computer programANIZCfor the calculation of diffraction contrast factors of dislocations in elastically anisotropic cubic, hexagonal and trigonal crystals
Authors: Borbély András , Dragomir-Cernatescu Juliana , Ribárik Gábor , Ungár Tamás
Published: January 2003

The computer programANIZChas been developed using the Pascal programming language for the calculation of diffraction contrast factors of dislocations in elastically anisotropic cubic, hexagonal and trigonal crystals. The contrast factor is obtained numerically by integrating the angular part of the distortion tensor in the slip plane. The distortion tensor is calculated by solving the sextic equation provided by the mechanical equilibrium of a single dislocation in an infinite anisotropic medium. The contrast factors can be used for the interpretation of strain anisotropy as obtained from peak profile measurements made on either single crystals, textured polycrystals or powders.
MLMF: least-squares approximation of likelihood-based refinement criteria
Authors: Afonine Pavel , Lunin Vladimir Y. , Urzhumtsev Alexandre
Published: January 2003

A quadratic approximation of the maximum-likelihood criterion is defined by a target value for every calculated structure-factor magnitude and the corresponding weight. These values can be estimated using the experimental structure-factor magnitudes and general information about the model imperfection. The programMLMFprovides a user with these weights and target values. The obtained quadratic approximation allows one to carry out a kind of maximum-likelihood refinement by means of any least-squares refinement suite.
Regulation of Expression of the
Borrelia burgdorferi
β
3
-Chain Integrin Ligand, P66, in Ticks and in Culture
Authors: Cugini Carla , Medrano Melisa , Schwan Tom G. , Coburn Jenifer
Published: January 2003

Borrelia burgdorferi
is maintained in an infection cycle between mammalian and arthropod hosts. Appropriate gene expression by
B. burgdorferi
at different stages of this cycle is probably essential for transmission and establishment of infection. The
B. burgdorferi
β
3
integrin ligand P66 is expressed by the bacteria in mammals, laboratory culture, and engorged but not unfed ticks. No in vitro culture conditions in which P66 expression reflected that in the unfed tick were found, suggesting that there are aspects of
B. burgdorferi
-tick interaction that remain unexplored.
Modulation of J774.1 Macrophage
l-
Arginine Metabolism by Intracellular
Mycobacterium bovis
BCG
Authors: Peteroy-Kelly Marcy A. , Venketaraman Vishwanath , Talaue Meliza , Seth Anjali , Connell Nancy D.
Published: January 2003

Using a
Mycobacterium bovis
BCG mutant (AS1) lacking a
Bacillus subtilis
l
-arginine transporter homolog, we demonstrate here that the interaction between intracellular mycobacteria and the macrophage with respect to
l-
arginine transport and metabolism is quite complex. Intracellular AS1 stimulates macrophage
l-
arginine transport and accumulates 2.5-fold more
3
H label derived from
l-
arginine than does the wild type. These studies suggest that the accumulation of
3
H label reflects the acquisition of metabolites of
l-
arginine produced by the macrophage.
Pathogenic Potential of Environmental
Vibrio cholerae
Strains Carrying Genetic Variants of the Toxin-Coregulated Pilus Pathogenicity Island
Authors: Faruque Shah M. , Kamruzzaman M. , Meraj Ismail M. , Chowdhury Nityananda , Nair G. Balakrish , Sack R. Bradley , Colwell Rita R. , Sack David A.
Published: January 2003

The major virulence factors of toxigenic
Vibrio cholerae
are cholera toxin (CT), which is encoded by a lysogenic bacteriophage (CTXΦ), and toxin-coregulated pilus (TCP), an essential colonization factor which is also the receptor for CTXΦ. The genes for the biosynthesis of TCP are part of a larger genetic element known as the TCP pathogenicity island. To assess their pathogenic potential, we analyzed environmental strains of
V. cholerae
carrying genetic variants of the TCP pathogenicity island for colonization of infant mice, susceptibility to CTXΦ, and diarrheagenicity in adult rabbits. Analysis of 14 environmental strains, including 3 strains carrying a new allele of the
tcpA
gene, 9 strains carrying a new allele of the
toxT
gene, and 2 strains carrying conventional
tcpA
and
toxT
genes, showed that all strains colonized infant mice with various efficiencies in competition with a control El Tor biotype strain of
V. cholerae
O1. Five of the 14 strains were susceptible to CTXΦ, and these transductants produced CT and caused diarrhea in adult rabbits. These results suggested that the new alleles of the
tcpA
and
toxT
genes found in environmental strains of
V. cholerae
encode biologically active gene products. Detection of functional homologs of the TCP island genes in environmental strains may have implications for understanding the origin and evolution of virulence genes of
V. cholerae
.