bluuebunny/crossref_metadata_2025 huggingface dataset:
Database of Structural Motifs in Proteins
Authors: Guruprasad Kunchur , Prasad Maheshuni S. , Kumar Gundu R.
Published: July 2002

Summary: The database of structural motifs in proteins (DSMP) contains data relevant to helices, β-turns, γ-turns, β-hairpins, ψ-loops, β-α-β motifs, β-sheets, β-strands and disulphide bridges extracted from all proteins in the Protein Data Bank primarily using the PROMOTIF program and implemented as a web-based network service using the SRS. The data corresponding to the structural motifs includes; sequence, position in polypeptide chain, geometry, type, unique code, keywords and resolution of crystal structure. This data is available for a representative data set of 1028 protein chains and also for all 10 213 proteins in the Protein Data Bank. The three-dimensional coordinates for all structural motifs (except sheet and disulphide bridge) are also available for the representative data set. Using features in SRS, DSMP can be queried to extract information from one or more structural motifs that may be useful for sequence-structure analysis, prediction, modelling or design.

Availability: http://www.cdfd.org.in/dsmp.html

Contact: guru@www.cdfd.org.in
The 10% Flat Tax: Tithing and the Definition of Income
Authors: Dahl Gordon B. , Ransom Michael R
Published: July 2002

Developing a fair and widely accepted income definition presents one of the greatest challenges to tax reform. To arrive at a definition separate from the federal tax code, we surveyed 1200 Latter‐day Saints about their practice of tithing. Tithing is similar to a flat tax with no deductions, where individuals voluntarily contribute 10% of self‐defined income to the church. The results of our survey indicate that most respondents operate on a cash realization basis, which excludes savings and does not allow any deductions. Respondents' income concepts generally do not coincide with current tax laws or economists' views of comprehensive income.
Tramtrack69 interacts with the dMi‐2 subunit of the Drosophila NuRD chromatin remodelling complex
Authors: Murawsky Chris M , Brehm Alexander , Badenhorst Paul , Lowe Nicholas , Becker Peter B , Travers Andrew A
Published: July 2002

dMi‐2, the ATPase subunit of the Drosophila nucleosome remodelling and histone deacetylation (dNuRD) complex, was identified in a two‐hybrid screen as an interacting partner of the transcriptional repressor, Tramtrack69 (Ttk69). A short region of Ttk69 is sufficient to mediate this interaction. Ttk69, but not the Ttk88 isoform, co‐purifies with the dNuRD complex isolated from embryo extracts. dMi‐2 and Ttk69 co‐immunoprecipitate from embryonic extracts, indicating that they can associate in vivo. Both dMi‐2 and Ttk69 co‐localize at a number of discrete sites on polytene chromosomes, showing that they bind common target loci. We also demonstrate that dMi‐2 and Ttk interact genetically, indicating a functional interaction in vivo. We propose that Ttk69 represses some target genes by remodelling chromatin structure through the recruitment of the dNuRD complex.
Porcine Toxicology Studies of SCH 58500, an Adenoviral Vector for the p53 Gene
Authors: Morrissey Richard E. , Horvath Christopher , Snyder Eileen A. , Patrick James , Collins Nathaniel , Evans Ellen , MacDonald James S.
Published: July 2002

Adenoviral vectors are being actively investigated for their potential utility in gene therapy. SCH 58500, a replication-deficient adenoviral vector, carries the normal p53 tumor suppressor gene, which is frequently mutated or absent in several human cancers. To assess the potential toxicity associated with adenoviral use, Yorkshire pigs were dosed by intravenous, intrahepatic, or local routes (subcutaneous and intradermal) to support a variety of potential clinical indications. Porcine cells were shown to support replication of wild-type human adenovirus. The nonlethal and asymptomatic dose in pigs following dosing via the intrahepatic route was greater than 3 × 108 plaque-forming units (pfu)/kg (2.2 × 1011 particles/kg), but less than 2.1 × 109 pfu/kg (1.5 × 1012 particles/kg). By the intravenous route it was 1 × 108 pfu/kg, and by the ip route it was greater than or equal to 3 × 108 pfu/kg. In a multicycle intraperitoneal study in pigs, the high dose of 3 × 108 pfu/kg caused an increased antibody and/or an inflammatory response. By the intravenous route, plaque-forming units were present in most pigs at 5 min postdose, but only in a few at 10 min postdose. No expression was found in gonadal tissue approximately 3 weeks after a single intravenous injection of 3 × 108 pfu/kg. At high intrahepatic doses (about 1.5 × 1012 particles/kg), acute cardiovascular and hemodynamic effects were found, which in subsequent studies were also present at high doses by intravenous administration. Based on these findings, careful evaluation of hemodynamic parameters in patients receiving systemic doses of SCH 58500 is warranted.
Induction of cancer cell apoptosis by α‐tocopheryl succinate: molecular pathways and structural requirements
Authors: NEUZIL JIRÍ , WEBER TOBIAS , SCHRÖDER ANDREAS , LU MIN , OSTERMANN GEORG , GELLERT NINA , MAYNE GEORGE C. , OLEJNICKA BEATA , NÈGRE‐SALVAYRE ANNE , STÍCHA MARTIN , COFFEY ROBERT J. , WEBER CHRISTIAN
Published: July 2002

The vitamin E analog α‐tocopheryl succinate (α‐TOS) can induce apoptosis. We show that the proapoptotic activity of α‐TOS in hematopoietic and cancer cell lines involves inhibition of protein kinase C (PKC), since phorbol myristyl acetate prevented α‐TOS‐triggered apoptosis. More selective effectors indicated that α‐TOS reduced PKCα isotype activity by increasing protein phosphatase 2A (PP2A) activity. The role of PKCα inhibition in α‐TOS‐induced apoptosis was confirmed using antisense oligonucleotides or PKCα overexpression. Gain‐ or loss‐of‐function bcl‐2 mutants implied modulation of bcl‐2 activity by PKC/ PP2A as a mitochondrial target of α‐TOS‐induced proapoptotic signals. Structural analogs revealed that α‐tocopheryl and succinyl moieties are both required for maximizing these effects. In mice with colon cancer xenografts, α‐TOS suppressed tumor growth by 80%. This epitomizes cancer cell killing by a pharmacologically relevant compound without known side effects.—Neuzil, J., Weber, T., Schröder, A., Lu, M., Ostermann, G., Gellert, N., Mayne, G. C., Olejnicka, B., Nègre‐Salvayre, A., Stícha, M., Coffey, R. J., Weber, C. Induction of cancer cell apoptosis by α‐tocopheryl succinate: molecular pathways and structural requirements. FASEB J. 15, 403‐415 (2001)
Levels of genetic polymorphism: marker loci versus quantitative traits
Authors: Butlin R. K. , Tregenza T.
Published: July 2002

Species are the units used to measure ecological diversity and alleles are the units of genetic diversity. Genetic variation within and among species has been documented most extensively using allozyme electrophoresis. This reveals wide differences in genetic variability within, and genetic distances among, species, demonstrating that species are not equivalent units of diversity. The extent to which the pattern observed for allozymes can be used to infer patterns of genetic variation in quantitative traits depends on the forces generating and maintaining variability. Allozyme variation is probably not strictly neutral but, nevertheless, heterozygosity is expected to be influenced by population size and genetic distance will be affected by time since divergence. The same is true for quantitative traits influenced by many genes and under weak stabilizing selection. However, the limited data available suggest that allozyme variability is a poor predictor of genetic variation in quantitative traits within populations. It is a better predictor of general phenotypic divergence and of postzygotic isolation between populations or species, but is only weakly correlated with prezygotic isolation. Studies of grasshopper and planthopper mating signal variation and assortative mating illustrate how these characters evolve independently of general genetic and morphological variation. The role of such traits in prezygotic isolation, and hence speciation, means that they will contribute significantly to the diversity of levels of genetic variation within and among species.
Are there multiple pathways in the pathogenesis of Huntington'sdisease?
Authors: Aronin Neil , Kim Manho , Laforet Genevieve , DiFiglia Marian
Published: July 2002

Studies of huntingtin localization in human post–mortem brain offer insights and a framework for basic experiments in the pathogenesis of Huntington'sdisease. In neurons of cortex and striatum, we identified changes in the cytoplasmic localization of huntingtin including a marked perinuclear accumulation of huntingtin and formation of multivesicular bodies, changes conceivably pointing to an altered handling of huntingtin in neurons. In Huntington'sdisease, huntingtin also accumulates in aberrant subcellular compartments such as nuclear and neuritic aggregates co–localized with ubiquitin. The site of protein aggregation is polyglutamine–dependent, both in juvenile–onset patients having more aggregates in the nucleus and in adult–onset patients presenting more neuritic aggregates. Studies
in vitro
reveal that the genesis of these aggregates and cell death are tied to cleavage of mutant huntingtin. However, we found that the aggregation of mutant huntingtin can be dissociated from the extent of cell death. Thus properties of mutant huntingtin more subtle than its aggregation, such as its proteolysis and protein interactions that affect vesicle trafficking and nuclear transport, might suffice to cause neurodegeneration in the striatum and cortex. We propose that mutant huntingtin engages multiple pathogenic pathways leading to neuronal death.
Statistical limitations in functional neuroimaging II. Signal detection and statistical inference
Authors: Petersson Karl Magnus , Nichols Thomas E. , Poline Jean-Baptiste , Holmes Andrew P.
Published: July 2002

The field of functional neuroimaging (FNI) methodology has developed into a mature but evolving area of knowledge and its applications have been extensive. A general problem in the analysis of FNI data is finding a signal embedded in noise. This is sometimes called signal detection. Signal detection theory focuses in general on issues relating to the optimization of conditions for separating the signal from noise. When methods from probability theory and mathematical statistics are directly applied in this procedure it is also called statistical inference. In this paper we briefly discuss some aspects of signal detection theory relevant to FNI and, in addition, some common approaches to statistical inference used in FNI. Low–pass filtering in relation to functional–anatomical variability and some effects of filtering on signal detection of interest to FNI are discussed. Also, some general aspects of hypothesis testing and statistical inference are discussed. This includes the need for characterizing the signal in data when the null hypothesis is rejected, the problem of multiple comparisons that is central to FNI data analysis, omnibus tests and some issues related to statistical power in the context of FNI. In turn, random field, scale space, non–parametric and Monte Carlo approaches are reviewed, representing the most common approaches to statistical inference used in FNI. Complementary to these issues an overview and discussion of non–inferential descriptive methods, common statistical models and the problem of model selection is given in a companion paper. In general, model selection is an important prelude to subsequent statistical inference. The emphasis in both papers is on the assumptions and inherent limitations of the methods presented. Most of the methods described here generally serve their purposes well when the inherent assumptions and limitations are taken into account. Significant differences in results between different methods are most apparent in extreme parameter ranges, for example at low effective degrees of freedom or at small spatial autocorrelation. In such situations or in situations when assumptions and approximations are seriously violated it is of central importance to choose the most suitable method in order to obtain valid results.
The clinical and functional measurement of cortical (in)activity in the visual brain, with special reference to the two subdivisions (V4 and V4α) of the human colour centre
Authors: Zeki S. , Bartels A.
Published: July 2002

We argue below that, at least in studying the visual brain, the old and simple methods of detailed clinical assessment and perimetric measurement still yield important insights into the organization of the visual brain as a whole, as well as the organization of the individual areas within it. To demonstrate our point, we rely especially on the motion and colour systems, emphasizing in particular how clinical observations predicted an important feature of the organization of the colour centre in the human brain. With the use of data from functional magnetic resonance imaging analysed by statistical parametric mapping and independent component analysis, we show that the colour centre is composed of two subdivisions, V4 and V4α, the two together constituting the V4 complex of the human brain. These two subdivisions are intimately linked anatomically and act cooperatively. The new evidence about the architecture of the colour centre might help to explain why the syndrome, cerebral achromatopsia, produced by lesions in it is so variable.
Unanswered questions in ecology
Authors: May Robert
Published: July 2002

This is very much a personal view of what I think are some of the most important unanswered questions in ecology. That is, these are the questions that I expect will be high on the research agenda over the coming century. The list is organized hierarchically, beginning with questions at the level of individual populations, and progressing through interacting populations to entire communities or ecosystems. I will try to guess both at possible advances in basic knowledge and at potential applications. The only thing that is certain about this view of the future is that much of it will surely turn out to be wrong, and many of the most interesting future developments will be quite unforeseen.
The relationship between the position of the retinal area centralis and feeding behaviour in juvenile black bream
Acanthopagrus butcheri
(Sparidae: Teleostei)
Authors: Shand Julia , Chin Stephanie M. , Harman Alison M. , Collin Shaun P.
Published: July 2002

The topography of the neurons in the retinal ganglion cell layer of juvenile black bream
Acanthopagrus butcheri
changes during development. The region of high cell density, the area centralis (AC), relocates from a temporal (central) to a dorsal (peripheral) position within the dorso-temporal retinal quadrant. Toascertain whether the differences in the position of the AC during development are related to feeding behaviour, we monitored fishes that were given a choice of food. A range of feeding behaviour patterns was recorded in individual fishes. The smallest fishes (8-15mm standard length (SL)) took live food from the water column. Following weaning onto pellets, fishes exhibited a preference for taking food from either the substrate or the surface (but not both).When greater than 20 mm SL, a number of individuals then divided their time between surface and substrate feeding before all fishes became exclusive benthic feeders at a stage between 50 and 80 mm SL. Three individual fishes, for which behaviour patterns were categorized, were killed and the topography of the retinal ganglion cell layer analysed. A range of positions for the AC was found with the smallest fish (12mm SL) possessing a region of high cell density in the temporal retina. In a larger fish (70 mm SL), feeding from both the substrate and the surface, the AC was found in an intermediate dorso-temporal position. The AC of a fish (51mm SL) preferentially taking food from the substrate was located in a dorsal position.
Adaptive sex allocation in birds: the complexities of linking theory and practice
Authors: Komdeur J. , Pen I.
Published: July 2002

We review some recent theoretical and empirical developments in the study of sex allocation in birds. The advent of reliable molecular sexing techniques has led to a sharp increase in the number of studies that report biased offspring sex ratios in birds. However, compelling evidence for adaptive sex allocation in birds is still very scant. We argue that there are two reasons for this: (i) standard sex allocation models, very helpful in understanding sex allocation of invertebrates, do not sufficiently take the complexities of bird life histories and physiology into account. Recent theoretical work might bring us a step closer to more realistic models; (ii) experimental field and laboratory studies on sex allocation in birds are scarce. Recent experimental work both in the laboratory and in the field shows that this is a promising approach.
Evolutionary transitions in parental care and live bearing in vertebrates
Authors: Reynolds J. D. , Goodwin N. B. , Freckleton R. P.
Published: July 2002

We provide the first review of phylogenetic transitions in parental care and live bearing for a wide variety of vertebrates. This includes new analyses of both numbers of transitions and transition probabilities. These reveal numerous transitions by shorebirds and anurans toward uniparental care by either sex. Whereas most or all of the shorebird transitions were from biparental care, nearly all of the anuran transitions have been from no care, reflecting the prevalence of each form of care in basal lineages in each group. Teleost (bony) fishes are similar to anurans in displaying numerous transitions toward uniparental contributions by each sex. Whereas cichlid fishes have often evolved from biparental care to female care, other teleosts have usually switched from no care to male care. Taxa that have evolved exclusive male care without courtship–role reversal are characterized by male territoriality and low costs of care per brood. Males may therefore benefit from care through female preference of parental ability in these species. Primates show a high frequency of transitions from female care to biparental care, reflecting the prevalence of female care in basal lineages. In the numerous taxa that display live bearing by females, including teleosts, elasmobranchs, squamate reptiles and invertebrates, we find that live bearing has always evolved from a lack of care. Although the transition counts and probabilities will undoubtedly be refined as phylogenetic information and methodologies improve, the overall biases in these taxa should help to place adaptive hypotheses for the evolution of care into a stronger setting for understanding directions of change.
The fractal nature of nature: power laws, ecological complexity and biodiversity
Authors: Brown James H. , Gupta Vijay K. , Li Bai-Lian , Milne Bruce T. , Restrepo Carla , West Geoffrey B.
Published: July 2002

Underlying the diversity of life and the complexity of ecology is order that reflects the operation of fundamental physical and biological processes. Power laws describe empirical scaling relationships that are emergent quantitative features of biodiversity. These features are patterns of structure or dynamics that are self–similar or fractal–like over many orders of magnitude. Power laws allow extrapolation and prediction over a wide range of scales. Some appear to be universal, occurring in virtually all taxa of organisms and types of environments. They offer clues to underlying mechanisms that powerfully constrain biodiversity. We describe recent progress and future prospects for understanding the mechanisms that generate these power laws, and for explaining the diversity of species and complexity of ecosystems in terms of fundamental principles of physical and biological science.
Composition of the editing complex ofTrypanosoma brucei
Authors: Stuart K. , Panigrahi A. K. , Schnaufer A. , Drozdz M. , Clayton C. , Salavati R.
Published: July 2002

The RNA editing that produces most functional mRNAs in trypanosomes is catalysed by a multiprotein complex. This complex catalyses the endoribonucleolytic cleavage, uridylate addition and removal, and RNA ligation steps of the editing process. Enzymatic andin vitroediting analyses reveal that each catalytic step contributes to the specificity of the editing and, together with the interaction between gRNA and the mRNA, results in precisely edited mRNAs. Tandem mass spectrometric analysis was used to identify the genes for several components of biochemically purified editing complexes. Their identity and presence in the editing complex were confirmed using immunochemical analyses utilizing mAbs specific to the editing complex components. The genes for two RNA ligases were identified. Genetic studies show that some, but not all, of the components of the complex are essential for editing. The TbMP52 RNA ligase is essential for editing while the TbMP48 RNA ligase is not. Editing was found to be essential in bloodstream form trypanosomes. This is surprising because mutants devoid of genes encoding RNAs that become edited survive as bloodstream forms but encouraging since editing complex components may be targets for chemotherapy.
Bayesian natural selection and the evolution of perceptual systems
Authors: Geisler Wilson S. , Diehl Randy L.
Published: July 2002

In recent years, there has been much interest in characterizing statistical properties of natural stimuli in order to better understand the design of perceptual systems. A fruitful approach has been to compare the processing of natural stimuli in real perceptual systems with that of ideal observers derived within the framework of Bayesian statistical decision theory. While this form of optimization theory has provided a deeper understanding of the information contained in natural stimuli as well as of the computational principles employed in perceptual systems, it does not directly consider the process of natural selection, which is ultimately responsible for design. Here we propose a formal framework for analysing how the statistics of natural stimuli and the process of natural selection interact to determine the design of perceptual systems. The framework consists of two complementary components. The first is a maximum fitness ideal observer, a standard Bayesian ideal observer with a utility function appropriate for natural selection. The second component is a formal version of natural selection based upon Bayesian statistical decision theory. Maximum fitness ideal observers and Bayesian natural selection are demonstrated in several examples. We suggest that the Bayesian approach is appropriate not only for the study of perceptual systems but also for the study of many other systems in biology.
Degradation of p53 by adenovirus E4orf6 and E1B55K proteins occurs via a novel mechanism involving a Cullin-containing complex
Authors: Querido Emmanuelle , Blanchette Paola , Yan Qin , Kamura Takumi , Morrison Megan , Boivin Dominique , Kaelin William G. , Conaway Ronald C. , Conaway Joan Weliky , Branton Philip E.
Published: July 2002

Although MDM2 plays a major role in regulating the stability of the p53 tumor suppressor protein, other poorly understood MDM2-independent pathways also exist. Human adenoviruses have evolved strategies to regulate p53 function and stability to permit efficient viral replication. One mechanism involves adenovirus E1B55K and E4orf6 proteins, which collaborate to target p53 for degradation. To determine the mechanism of this process, a multiprotein E4orf6-associated complex was purified and shown to contain a novel Cullin-containing E3 ubiquitin ligase that is (1) composed of Cullin family member Cul5, Elongins B and C, and the RING-H2 finger protein Rbx1(ROC1); (2) remarkably similar to the von Hippel-Lindau tumor suppressor and SCF (Skp1–Cul1/Cdc53–F-box) E3 ubiquitin ligase complexes; and (3) capable of stimulating ubiquitination of p53 in vitro in the presence of E1/E2 ubiquitin-activating and -conjugating enzymes. Cullins are activated by NEDD8 modification; therefore, to determine whether Cullin complexes are required for adenovirus-induced p53 degradation, studies were conducted in ts41 Chinese hamster ovary cells that are temperature sensitive for the NEDD8 pathway. E4orf6/E1B55K failed to induce the degradation of p53 at the nonpermissive temperature. Thus, our results identify a novel role for the Cullin-based machinery in regulation of p53.
Opposing effects of Ctk1 kinase and Fcp1 phosphatase at Ser 2 of the RNA polymerase II C-terminal domain
Authors: Cho Eun-Jung , Kobor Michael S. , Kim Minkyu , Greenblatt Jack , Buratowski Stephen
Published: July 2002

The C-terminal domain (CTD) of the RNA polymerase II (Pol II) largest subunit is hyperphosphorylated during transcription. Using an in vivo cross-linking/chromatin immunoprecipitation assay, we found previously that different phosphorylated forms of RNA Pol II predominate at different stages of transcription. At promoters, the Pol II CTD is phosphorylated at Ser 5 by the basal transcription factor TFIIH. However, in coding regions, the CTD is predominantly phosphorylated at Ser 2. Here we show that the elongation-associated phosphorylation of Ser 2 is dependent upon the Ctk1 kinase, a putative yeast homolog of Cdk9/P-TEFb. Furthermore, mutations in the Fcp1 CTD phosphatase lead to increased levels of Ser 2 phosphorylation. Both Ctk1 and Fcp1 cross-link to promoter and coding regions, suggesting that they associate with the elongating polymerase. Both Ctk1 and Fcp1 have been implicated in regulation of transcription elongation. Our results suggest that this regulation may occur by modulating levels of Ser 2 phosphorylation, which in turn, may regulate the association of elongation factors with the polymerase.
Inverse treatment planning for Gamma Knife radiosurgery
Authors: Shepard D. M. , Ferris M. C. , Ove R. , Ma L.
Published: July 2002

An inverse treatment planning system for Gamma Knife radiosurgery has been developed using nonlinear programming techniques. The system optimizes the shot sizes, locations, and weights for Gamma Knife treatments. In the patient's prescription, the user can specify both the maximum number of shots of radiation and a minimum isodose line that must surround the entire treatment volume. After satisfying all of the constraints included in the prescription, the system maximizes the conformity of the dose distribution. This automated approach to treatment planning has been applied retrospectively to a series of patient cases, and each optimized plan has been compared to the corresponding manual plan produced by an experienced user. The results demonstrate that this tool can often improve the tumor dose homogeneity while using fewer shots than were included in the original plan. Therefore, inverse treatment planning should improve both the quality and the efficiency of Gamma Knife treatments.
A two‐source model for electron beams: Calculation of relative output factors
Authors: Chen J. Z. , VanDyk J. , Lewis C. , Battista J. J.
Published: July 2002

A two‐source model for the calculation of relative output factors (ROF) for clinical applications of electron beams has been developed. The model consists of (1) an effective extended source above the final field‐defining aperture (cutout) plane and (2) a source due to scattering from the aperture. Calculations are based on Fermi–Eyges theory and a pencil beam algorithm with parameters determined independently for each major scattering component. The model predicts a modified inverse square law for determining the dose rate for the electron beams. It also generalizes the “square‐root method” and “one‐dimensional method” that are often used clinically for ROF calculations. A computer program based on the model has been developed to calculate ROF for irregular fields. The predictions of ROF values have been compared with measurements on a Varian CLINAC 2100C/D accelerator for different cutout size, energies, applicators, and SSDs for square fields, rectangular fields, circular fields, and irregular fields. The agreement between prediction and measurement of the ROF for these wide range of conditions is generally within 1% for energies from 6 to 20 MeV. This two‐source model can be used for clinical applications and it requires a minimal set of measured input data.
Laser trapping of microscopic particles for undergraduate experiments
Authors: Pastel Robert , Struthers Allan , Ringle Ryan , Rogers Jeremy , Rohde Charles , Geiser Peter
Published: July 2002

We present detailed instructions for constructing and operating an optical trap using a hollow core fiber and two-laser beams. The trap is stable, confining 100-nm to 10-μm particles of a variety of materials for hours of leisurely observation. The trap operates at room temperature and atmospheric pressure, costs less than $1400, and requires no machining. The hollow fiber provides automatic relative beam alignment and shields trapped particles from the ambient convective flow. An experiment and analysis of the Mie scattering from the trapped particle is outlined. A list of other interesting experiments based on the trap is provided.
From rapidity to vibracy (logarithmic frequency)
Authors: Wilkins Daniel , Williams Deborah
Published: July 2002

Logarithmic parameters have been been found useful for describing the translational and gravitational states of some systems. These parameters are additive, and may serve to push unwanted singularities off to infinity. The best known of these is rapidity, a speedlike parameter used in special relativity. Another is the so-called “linear time” of Misner and Lévy-Leblond, which applies to general relativistic cosmology. We point out that these two parameters are both logarithmic measures of frequency shift and represent a quantity we call “vibracy.” Majernik’s trigonometric variant of rapidity is found to be an aberration angle.
An electrical measurement of the speed of light
Authors: Clark George W.
Published: July 2002

A pedagogical experiment is described for a determination of the speed of light by measurements of the dimensions and resonance frequency of an LRC circuit. The only calibrated devices employed are instruments for measuring frequency and length. An accuracy of approximately 1% is achieved.
“Franklin’s Bells” and charge transport as an undergraduate lab
Authors: Krotkov R. V. , Tuominen M. T. , Breuer M. L.
Published: July 2002

“Franklin’s Bells” is a popular lecture demonstration in electricity but seems to have been overlooked as a quantitative undergraduate lab experiment. In our version, a charged ball oscillates back and forth between the plates of a capacitor. This paper has two purposes: one is to discuss some of the wide variety of experiments and calculations which this system affords, the other is to present an analysis of a particular situation in which the ball excites resonant modes of the plates. This excitation gives rise to unexpected steps in the graph of shuttle frequency versus the potential difference between the plates. The apparatus required to show the demonstration is available in most physics departments. Similarly, a quantitative experiment for an introductory undergraduate lab does not require any unusual equipment, nor particularly high voltages. (In our experiment, the highest voltage used was 600 V; this can probably be reduced by scaling down the apparatus.) The physical situation may be analyzed at many different levels, suitable for students in the freshman to senior years, and ranging from a qualitative understanding of the demonstration to computer calculations of chaotic dynamics. The apparatus may be a simple one appropriate to the introductory level, or, at an “Advanced Lab” level, a sophisticated one, with computer-controlled measurements and analysis of various parameters. It is surprising that such a rich system has been neglected in the traditional curriculum.
Eikonal equation from continuum mechanics and analogy between equilibrium of a string and geometrical light rays
Authors: Bellver-Cebreros Consuelo , Rodriguez-Danta Marcelo
Published: July 2002

This work of didactic character on geometrical optics consists of two parts, whose main link is the use of methods associated with continuum physics. First, the formalism of continuum physics is applied in order to derive the eikonal equation from the study of propagation of discontinuities in electromagnetic fields in such a way that the eikonal equation is an exact derivation from Maxwell equations. The results obtained are well known from the works of Luneburg [Mathematical Theory of Optics (California U.P., Berkeley, 1964)], although the method used is new and efficient and provides a good occasion to use the continuum physics beyond its standard applications. Second, from the identity between the differential equation of light rays and the equilibrium equation of a flexible and inextensible string subjected to a conservative force, the analogy between both physical models is inferred. To illustrate this analogy, two applications in the realms of mechanics and optics are shown. The obtained results in statics have been reinterpreted from the dynamical scheme.
Resource letter CPPPT-1: Critical point phenomena and phase transitions
Authors: Tobochnik Jan
Published: July 2002

This Resource Letter provides a guide to the literature on critical point phenomena and phase transitions. Journal articles and books are cited for the following topics: continuous phase transitions, critical points, model systems with special attention to the Ising model and the Kosterlitz–Thouless transition, mean-field theory, computer simulation methods, scaling, universality, and the renormalization group.
A simple interference scanner
Authors: Hinrichsen P. F.
Published: July 2002

An inexpensive device for measuring interference and diffraction patterns, based on a linear potentiometer for position determination, is described. The linearity, resolution, and reproducibility are discussed.
Response to “Comment on ‘Nonlocal character of quantum theory,’ ” by Abner Shimony and Howard Stein [Am. J. Phys. 69 (8), 848–853 (2001)]
Authors: Stapp Henry P.
Published: July 2002

The question raised by Shimony and Stein is examined and used to explain in more detail a key point of my proof that any theory that conforms to certain general ideas of orthodox relativistic quantum field theory must permit transfers of information over space-like intervals. It is also explained why this result is not a problem for relativistic quantum theory, but, on the contrary, opens the door to a satisfactory realistic relativistic quantum theory based on the ideas of Tomonaga, Schwinger, and von Neumann.
Electric and magnetic forces and energies for a parallel-plate capacitor and a flattened, slip-joint solenoid
Authors: Boyer Timothy H.
Published: July 2002

A current-carrying solenoid can be imagined as fitted with slip-joints and flattened into a shape comparable to a parallel-plate capacitor. In this shape it is easy to calculate forces, the work done, and energy changes that are analogous to those for a capacitor with constant charge or constant voltage.
Contemporary electronics: A focussed concept laboratory
Authors: Panitz J. A.
Published: July 2002

Contemporary Electronics is an advanced undergraduate lecture and laboratory introduction to analog and digital electronics. Fundamentals of analog measurements, analog data collection, and digital data collection are included in this one-semester course. Laboratory exercises introduce diodes, transistors, operational amplifiers, and their use in simple circuits. Focus and continuity are provided by the construction of a printed circuit board nanoammeter. The nanoammeter is used to measure the tunneling current generated by a commercial field emission electron microscope. An introduction to LABVIEW programming allows each student to create a “virtual instrument” for data collection and analysis. An analysis of the tunneling data using Fowler–Nordheim theory is the focus of a midterm and a final exam.
A comparison between the Doppler and cosmological redshifts
Authors: Bedran Maria Luiza
Published: July 2002

We compare the Doppler effect of special relativity with the cosmological redshift of general relativity in order to clarify the difference between them. Some basic concepts of observational cosmology, such as the definitions of distance and cosmological parameters, are also presented.
Illustrations of the Becchi–Rouet–Stora–Tyutin invariance by means of simple toy models
Authors: Bes D. R. , Civitarese O.
Published: July 2002

Among the available quantization methods for gauge field theories, the Becchi–Rouet–Stora–Tyutin (BRST) procedure has emerged as the simplest one for non-Abelian field theories, and thus the one that is systematically used in such cases. Our aim is to provide the reader with an accessible introduction to this modern and elegant treatment of constrained systems through its application to two simple mechanical models: a particle moving on a ring, and a particle on the surface of a sphere. If the description of these models is made from a moving frame of reference, they constitute simple analogs of gauge field theories. Notwithstanding their simplicity, these two applications display the main features of the BRST method, dealing with Abelian and non-Abelian symmetries, respectively. They also illustrate the solution of many-body problems in which broken symmetries are restored by means of collective coordinates describing the motion of the moving frame. Both the Hamiltonian and the Lagrangian formulations are presented, the latter using the antifield formalism.
An experiment to measure Mie and Rayleigh total scattering cross sections
Authors: Cox A. J. , DeWeerd Alan J. , Linden Jennifer
Published: July 2002

We present an undergraduate-level experiment using a conventional absorption spectrophotometer to measure the wavelength dependence of light scattering from small dielectric spheres suspended in water. The experiment yielded total scattering cross-section values throughout the visible region that were in good agreement with theoretical values predicted by the Rayleigh and Mie theories.
A thermodynamic derivative means an experiment
Authors: Styer Daniel F.
Published: July 2002

All too often, courses in thermodynamics and statistical mechanics barrage their students with numerous equations that are left unexamined and uninvestigated. This note explains how to pause, examine a thermodynamic equation, and render it more meaningful. Three techniques are discussed: (1) design two experiments that would measure the quantities on either side of the equality; (2) examine special cases; (3) consider the consequences if the equality failed to hold.
A simple demonstration of a metastable state
Authors: Menon Narayanan
Published: July 2002

A system whose macroscopic properties appear to be unchanging in time may not be in a state of minimum free energy. A common example of such a metastable state is a supercooled liquid. Liquid sodium acetate is a system in which the passage of a supercooled liquid into its stable, crystalline form is readily demonstrated.
Blue skies and effective interactions
Authors: Holstein Barry R.
Published: July 2002

This paper shows how the basic physics of Rayleigh scattering, responsible for the blueness of the sky, can be extracted using the techniques of effective interactions, which have become widespread in contemporary particle and nuclear physics.
On electromagnetic conservation laws
Authors: Goedecke G. H.
Published: July 2002

Subdivision of any charge-current source into N separately conserved sources results in N(N+1)/2 separate conservation laws for each of the interesting electromagnetic quantities, energy, momentum, and angular momentum. The subdivision may be done arbitrarily, so N is also arbitrary. These separate conservation laws are derived and applied to several examples, including the Fourier series representation of any time-dependent source, the derivation of the optical theorem in scattering, the energy balance for a resistor carrying a steady current, and the force on one charged capacitor plate due to the other. A general result is that the Lorentz force exerted by any static source on itself is zero. Other applications are also discussed.
Extended charge in motion: Why is the Hamiltonian of a magnetic dipole −m⋅B?
Authors: Arsenović D. , Božić M.
Published: July 2002

The interaction potential energy of a rigid moving mass and charge distribution (magnetic and electrical dipole in motion) in an electromagnetic field is expressed in terms of the center of mass coordinate, the rotation dyadic of a mass distribution, and magnetic and electric dipole moments.
Discreteness effects on soliton dynamics: A simple experiment
Authors: Laroche Claude , Dauxois Thierry , Peyrard Michel
Published: July 2002

We present a simple laboratory experiment to illustrate some aspects of the soliton theory in discrete lattices with a system that models the dynamics of dislocations in a crystal or the properties of adsorbed atomic layers. The apparatus not only shows the role of the Peierls–Nabarro potential but also illustrates the hierarchy of depinning transitions and the importance of the collective motion in mass transport.
Application of a finite-element model to low-frequency sound insulation in dwellings
Authors: Maluski Sophie P. S. , Gibbs Barry M.
Published: July 2002

The sound transmission between adjacent rooms has been modeled using a finite-element method. Predicted sound-level difference gave good agreement with experimental data using a full-scale and a quarter-scale model. Results show that the sound insulation characteristics of a party wall at low frequencies strongly depend on the modal characteristics of the sound field of both rooms and of the partition. The effect of three edge conditions of the separating wall on the sound-level difference at low frequencies was examined: simply supported, clamped, and a combination of clamped and simply supported. It is demonstrated that a clamped partition provides greater sound-level difference at low frequencies than a simply supported. It also is confirmed that the sound-pressure level difference is lower in equal room than in unequal room configurations.
Acoustic waveform inversion with application to seasonal snow covers
Authors: Albert Donald G.
Published: July 2002

The amplitude and waveform shape of atmospheric acoustic pulses propagating horizontally over a seasonal snow cover are profoundly changed by the air forced into the snow pores as the pulses move over the surface. This interaction greatly reduces the pulse amplitude and elongates the waveform compared to propagation above other ground surfaces. To investigate variations in snow-cover effects, acoustic pulses were recorded while propagating horizontally over 11 different naturally occurring snow covers during two winters. Two inversion procedures were developed to automatically match the observed waveforms by varying the snow-cover parameters in theoretical calculations. A simple frequency-domain technique to match the dominant frequency of the measured waveform suffered from multiple solutions and poor waveform matching, while a time-domain minimization method gave unique solutions and excellent waveform agreement. Results show that the effective flow resistivity and depth of the snow are the parameters controlling waveform shape, with the pore shape factor ratio of secondary importance. Inversion estimates gave flow resistivities ranging from 11 to 29 kN s m−4, except for two late-season cases where values of 60 and 140 were determined (compared to 345 for the vegetation-covered site in the summer). Acoustically determined snow depths agreed with the measured values in all but one case, when the depth to a snow layer interface instead of the total snow depth was determined. Except for newly fallen snow, the pore shape factor ratio values clustered near two values that appear to correspond to wet (1.0) or dry (0.8) snow.
Influence of emotion and focus location on prosody in matched statements and questions
Authors: Pell Marc D.
Published: July 2002

Preliminary data were collected on how emotional qualities of the voice (sad, happy, angry) influence the acoustic underpinnings of neutral sentences varying in location of intra-sentential focus (initial, final, no) and utterance “modality” (statement, question). Short (six syllable) and long (ten syllable) utterances exhibiting varying combinations of emotion, focus, and modality characteristics were analyzed for eight elderly speakers following administration of a controlled elicitation paradigm (story completion) and a speaker evaluation procedure. Duration and fundamental frequency (f0) parameters of recordings were scrutinized for “keyword” vowels within each token and for whole utterances. Results generally re-affirmed past accounts of how duration and f0 are encoded on key content words to mark linguistic focus in affectively neutral statements and questions for English. Acoustic data on three “global” parameters of the stimuli (speech rate, mean f0, f0 range) were also largely supportive of previous descriptions of how happy, sad, angry, and neutral utterances are differentiated in the speech signal. Important interactions between emotional and linguistic properties of the utterances emerged which were predominantly (although not exclusively) tied to the modulation of f0; speakers were notably constrained in conditions which required them to manipulate f0 parameters to express emotional and nonemotional intentions conjointly. Sentence length also had a meaningful impact on some of the measures gathered.
Forward- and simultaneous-masked thresholds in bandlimited maskers in subjects with normal hearing and cochlear hearing loss
Authors: Dubno Judy R. , Ahlstrom Jayne B.
Published: July 2002

Forward- and simultaneous-masked thresholds were measured at 0.5 and 2.0 kHz in bandpass maskers as a function of masker bandwidth and in a broadband masker with the goal of estimating psychophysical suppression. Suppression was operationally defined in two ways: (1) as a change in forward-masked threshold as a function of masker bandwidth, and (2) as a change in effective masker level with increased masker bandwidth, taking into account the nonlinear growth of forward masking. Subjects were younger adults with normal hearing and older adults with cochlear hearing loss. Thresholds decreased as a function of masker bandwidth in forward masking, which was attributed to effects of suppression; thresholds remained constant or increased slightly with increasing masker bandwidth in simultaneous masking. For subjects with normal hearing, slightly larger estimates of suppression were obtained at 2.0 kHz rather than at 0.5 kHz. For hearing-impaired subjects, suppression was reduced in regions of hearing loss. The magnitude of suppression was strongly correlated with the absolute threshold at the signal frequency, but did not vary with thresholds at frequencies remote from the signal. The results suggest that measuring forward-masked thresholds in bandlimited and broadband maskers may be an efficient psychophysical method for estimating suppression.