bluuebunny/crossref_metadata_2025 huggingface dataset:
Scanning magnetron-sputtered TiN coating as diffusion barrier for silicon devices
Authors: Lingwal Vijendra , Panwar N. S.
Published: April 2005

Scanning magnetron-sputtered titanium nitride (TiN) films were deposited onto silicon substrates under varying nitrogen and argon pressures. Golden TiN films with (220) orientation were deposited at different substrate bias voltages (0to−120V). Auger electron spectroscopy measurements show N∕Ti ratio between 1.18 and 1.07, and oxygen content between 11% and 5% in the as-deposited TiN film samples. Dependence of the stress and grain size on substrate bias voltage and dependence of resistivity on bias voltage and annealing temperature have been studied for the deposited TiN films. Resistivity was found minimum for the TiN samples deposited at −40V bias, which decreases from 320to132μΩcm on annealing, up to 750°C. Copper was sputter deposited on the as-grown TiN films deposited at −40V bias. The Cu∕TiN∕Si samples were annealed at different temperatures. Resistivity, x-ray diffraction, scanning electron microscopy, and energy dispersive x-ray analysis results of the Cu∕TiN∕Si structure are consistent with each other, and show that scanning magnetron sputtering deposited TiN film is a good diffusion barrier for copper metallization of the silicon devices, up to 750°C.
Topological criteria for amorphization based on a thermodynamic approach
Authors: Senkov O. N. , Miracle D. B. , Mullens H. M.
Published: April 2005

The effects of composition, atomic radii, atomic size ratios, and elastic constants of the constitutive elements on the glass-forming ability of metallic glasses have been identified using a thermodynamic model. This model is based on the comparison of the Gibbs free energy and entropy between a nonequilibrium crystalline solid solution and the undercooled liquid. According to this model, the glass-forming ability (reduced glass transition temperature, Tg∕Tm) of an alloy should increase with (a) an increase in the atom size and/or shear modulus of the solvent; (b) an increase in the bulk modulus of a solute; and (c) a decrease in the melting temperature of the alloy. At constant values for other parameters, the glass-forming ability is maximum at a certain concentration and relative atomic size of a solute. Recently, these topological criteria have been successfully used to produce a number of Ca-based bulk metallic glasses.
Growth and hydrogen uptake of Mg–Y thin films
Authors: Chacon C. , Johansson E. , Hjörvarsson B. , Zlotea C. , Andersson Y.
Published: April 2005

Wedged Mg–Y films with compositions ranging from pure Mg to Mg0.83Y0.17 were grown by dc-magnetron sputtering and hydrogenated. Mg1−xYx forms a substitutional alloy, ranging from 0 to at least 17at.% in thin films. The c lattice parameter of the film containing 17at.% of yttrium is determined to be approximatively 1% larger than in pure Mg. Upon exposure to 1bar of hydrogen at 300K, the samples switch from shiny metals to colorless semiconductor. Different characteristic hydrogen depth distributions are found for different Y concentrations. At low yttrium contents, a large concentration gradient is observed, with the highest hydrogen concentration close to the Pd∕Mg1−xYx interface. For yttrium concentrations larger than 7at.%, the obtained hydrogen distribution is almost independent of depth. The optical band gap is determined to be 3.6eV, for all the Y concentrations. The optical transmission is found to decrease for increasing Y content, which is associated with an incomplete hydride formation in the films.
Electronic structures of wide-band-gap (SiC)1−x(AlN)x quaternary semiconductors
Authors: Tang Y.-H. , Tsai M.-H.
Published: April 2005

Due to small lattice mismatch and large-band-gap difference between SiC and AlN, the light-emitting devices fabricated from (SiC)1−x(AlN)x quaternary semiconductors may be tuned over a wide wavelength range. To understand the feasibility of this application, first-principles calculations have been done to study their electronic structures. It is found that there is a transition of the band gap from indirect to direct when x is greater than about 0.20. The band gap is also found to bow down as a function of x. The calculated results suggest that the direct band gap of (SiC)1−x(AlN)x can be tuned over a wide range from 2.97to6.28eV. Thus, (SiC)1−x(AlN)x is potentially useful for optoelectronic applications.
Synchronization in power-law networks
Authors: Kocarev Ljupco , Amato Paolo
Published: April 2005

We consider realistic power-law graphs, for which the power-law holds only for a certain range of degrees. We show that synchronizability of such networks depends on the expected average and expected maximum degree. In particular, we find that networks with realistic power-law graphs are less synchronizable than classical random networks. Finally, we consider hybrid graphs, which consist of two parts: a global graph and a local graph. We show that hybrid networks, for which the number of global edges is proportional to the number of total edges, almost surely synchronize.
Stochastic multiresonance in the coupled relaxation oscillators
Authors: Volkov E. I. , Ullner E. , Kurths J.
Published: April 2005

We study the noise-dependent dynamics in a chain of four very stiff excitable oscillators of the FitzHugh–Nagumo type locally coupled by inhibitor diffusion. We could demonstrate frequency- and noise-selective signal acceptance which is based on several noise-supported stochastic attractors that arise owing to slow variable diffusion between identical excitable elements. The attractors have different average periods distinct from that of an isolated oscillator and various phase relations between the elements. We explain the correspondence between the noise-supported stochastic attractors and the observed resonance peaks in the curves for the linear response versus signal frequency.
Stabilization of thermogravitational flows by magnetic field and surface tension
Authors: Henry D. , Kaddeche S. , BenHadid H.
Published: April 2005

The influence of a vertical magnetic field and of surface tension on the stability of thermogravitational convection in an infinite layer subject to a horizontal temperature gradient is investigated through a linear stability analysis. Magnetic field is found to strongly stabilize the flow, as well as surface tension if thermocapillary effects contribute to increase the velocity at the upper surface of the layer. This strong stabilization is mainly connected to the modifications of the basic flow profile. A simple model based on the existence of an inflexion point in the velocity profile is proposed which qualitatively depicts these results.
The directed-assembly of CdS interconnects between targeted points in a circuit
Authors: Ozturk Birol , Talukdar Ishan , Flanders Bret N.
Published: April 2005

We demonstrate the one-step dielectrophoretic assembly and interfacing of individual interconnects from populations of 3.7 nm CdS nanoparticles between targeted points in a circuit. We further show that the nanoparticles fuse into bulk CdS during the fabrication process. This finding is significant because it establishes a critical step towards the fabrication of structurally continuous semiconducting interconnects from nanoscopic building blocks.
Position- and size-controlled fabrication of iron silicide nanorods by electron-beam-induced deposition using an ultrahigh-vacuum transmission electron microscope
Authors: Tanaka M. , Chu F. , Shimojo M. , Takeguchi M. , Mitsuishi K. , Furuya K.
Published: April 2005

We have fabricated arrays of nanorods of cubic iron silicide from iron pentacarbonyl gas source on Si(111) substrates by electron-beam-induced deposition at elevated temperature in an ultrahigh-vacuum transmission electron microscope. The nanorods are aligned along one of the Si⟨110⟩ directions. Their length could be controlled by changing the irradiation time. It was revealed that the vicinity of the substrate surface influences the growth direction and location of the nanorods.
Phase control through anisotropic strain in Nd0.5Sr0.5MnO3 thin films
Authors: Nakamura Masao , Ogimoto Yasushi , Tamaru Hiroharu , Izumi Makoto , Miyano Kenjiro
Published: April 2005

Strain effect in charge- and orbital-ordered state has been investigated for Nd0.5Sr0.5MnO3 thin films deposited on (100), (110), and (111)-oriented substrates of SrTiO3. Films on (001) and (111) substrates have a monotonous temperature dependence for magnetic and transport properties showing no first-order phase transition. On the other hand, films on (110) substrate show a clear ferromagnetic-antiferromagnetic and metal-insulator transition around 170K similar to that in a bulk single crystal, which is a manifestation of the charge and orbital order. Precise control of the hole concentration was also demonstrated around half doping.
Assessment of internal quality attributes of mandarin fruit. 2. NIR calibration model robustness
Authors: Guthrie J. A. , Reid D. J. , Walsh K. B.
Published: April 2005

The robustness of multivariate calibration models, based on near infrared spectroscopy, for the assessment of total soluble solids (TSS) and dry matter (DM) of intact mandarin fruit (Citrus reticulata cv. Imperial) was assessed. TSS calibration model performance was validated in terms of prediction of populations of fruit not in the original population (different harvest days from a single tree, different harvest localities, different harvest seasons). Of these, calibration performance was most affected by validation across seasons (signal to noise statistic on root mean squared error of prediction of 3.8, compared with 20 and 13 for locality and harvest day, respectively). Procedures for sample selection from the validation population for addition to the calibration population (‘model updating’) were considered for both TSS and DM models. Random selection from the validation group worked as well as more sophisticated selection procedures, with approximately 20 samples required. Models that were developed using samples at a range of temperatures were robust in validation for TSS and DM.
Raft lipids as common components of human extracellular amyloid fibrils
Authors: Gellermann Gerald P. , Appel Thomas R. , Tannert Astrid , Radestock Anja , Hortschansky Peter , Schroeckh Volker , Leisner Christian , Lütkepohl Tim , Shtrasburg Shmuel , Röcken Christoph , Pras Mordechai , Linke Reinhold P. , Diekmann Stephan , Fändrich Marcus
Published: April 2005

Amyloid fibrils are fibrillar polypeptide aggregates from several degenerative human conditions, including Alzheimer's and Creutzfeldt-Jakob diseases. Analysis of amyloid fibrils derived from various human diseases (AA, ATTR, Aβ2M, ALλ, and ALκ amyloidosis) shows that these are associated with a common lipid component that has a conserved chemical composition and that is specifically rich in cholesterol and sphingolipids, the major components of cellular lipid rafts. This pattern is not notably affected by the purification procedure, and no tight lipid interactions can be detected when preformed fibrils are mixed with lipids. By contrast, the early and prefibrillar aggregates formed in an AA amyloid-producing cell system interact with the raft marker ganglioside-1, and amyloid formation is impaired by addition of cholesterol-reducing agents. These data suggest the existence of common cellular mechanisms in the generation of different types of clinical amyloid deposits.
Solving the protein sequence metric problem
Authors: Atchley William R. , Zhao Jieping , Fernandes Andrew D. , Drüke Tanja
Published: April 2005

Biological sequences are composed of long strings of alphabetic letters rather than arrays of numerical values. Lack of a natural underlying metric for comparing such alphabetic data significantly inhibits sophisticated statistical analyses of sequences, modeling structural and functional aspects of proteins, and related problems. Herein, we use multivariate statistical analyses on almost 500 amino acid attributes to produce a small set of highly interpretable numeric patterns of amino acid variability. These high-dimensional attribute data are summarized by five multidimensional patterns of attribute covariation that reflect polarity, secondary structure, molecular volume, codon diversity, and electrostatic charge. Numerical scores for each amino acid then transform amino acid sequences for statistical analyses. Relationships between transformed data and amino acid substitution matrices show significant associations for polarity and codon diversity scores. Transformed alphabetic data are used in analysis of variance and discriminant analysis to study DNA binding in the basic helix-loop-helix proteins. The transformed scores offer a general solution for analyzing a wide variety of sequence analysis problems.
Sequence signatures and the probabilistic identification of proteins in the Myc-Max-Mad network
Authors: Atchley William R. , Fernandes Andrew D.
Published: April 2005

Accurate identification of specific groups of proteins by their amino acid sequence is an important goal in genome research. Here we combine information theory with fuzzy logic search procedures to identify sequence signatures or predictive motifs for members of the Myc-Max-Mad transcription factor network. Myc is a well known oncoprotein, and this family is involved in cell proliferation, apoptosis, and differentiation. We describe a small set of amino acid sites from the N-terminal portion of the basic helix-loop-helix (bHLH) domain that provide very accurate sequence signatures for the Myc-Max-Mad transcription factor network and three of its member proteins. A predictive motif involving 28 contiguous bHLH sequence elements found 337 network proteins in the GenBank NR database with no mismatches or misidentifications. This motif also identifies at least one previously unknown fungal protein with strong affinity to the Myc-Max-Mad network. Another motif found 96% of known Myc protein sequences with only a single mismatch, including sequences from genomes previously not thought to contain Myc proteins. The predictive motif for Myc is very similar to the ancestral sequence for the Myc group estimated from phylogenetic analyses. Based on available crystal structure studies, this motif is discussed in terms of its functional consequences. Our results provide insight into evolutionary diversification of DNA binding and dimerization in a well characterized family of regulatory proteins and provide a method of identifying signature motifs in protein families.
Rapid electrostatic evolution at the binding site for cytochrome c on cytochrome c oxidase in anthropoid primates
Authors: Schmidt Timothy R. , Wildman Derek E. , Uddin Monica , Opazo Juan C. , Goodman Morris , Grossman Lawrence I.
Published: April 2005

Cytochrome
c
(CYC) oxidase (COX), a multisubunit enzyme that functions in mitochondrial aerobic energy production, catalyzes the transfer of electrons from CYC to oxygen and participates in creating the electrochemical gradient used for ATP synthesis. Modeling three-dimensional structural data on COX and CYC reveals that 57 of the >1,500 COX residues can be implicated in binding CYC. Because of the functional importance of the transfer of electrons to oxygen, it might be expected that natural selection would drastically constrain amino acid replacement rates of CYC and COX. Instead, in anthropoid primates, although not in other mammals, CYC and COX show markedly accelerated amino acid replacement rates, with the COX acceleration being much greater at the positions that bind CYC than at those that do not. Specifically, in the anthropoid lineage descending from the last common ancestor of haplorhines (tarsiers and anthropoids) to that of anthropoids (New World monkeys and catarrhines) and that of catarrhines (Old World monkeys and apes, including humans), a minimum of 27 of the 57 COX amino acid residues that bind CYC were replaced, most frequently from electrostatically charged to noncharged residues. Of the COX charge-bearing residues involved in binding CYC, half (11 of 22) have been replaced with uncharged residues. CYC residues that interact with COX residues also frequently changed, but only two of the CYC changes altered charge. We suggest that reducing the electrostatic interaction between COX and CYC was part of the adaptive evolution underlying the emergence of anthropoid primates.
Varicella-zoster virus infection of human dorsal root ganglia
in vivo
Authors: Zerboni Leigh , Ku Chia-Chi , Jones Carol D. , Zehnder James L. , Arvin Ann M.
Published: April 2005

Varicella-zoster virus (VZV) causes varicella and establishes latency in sensory ganglia. VZV reactivation results in herpes zoster. We developed a model using human dorsal root ganglion (DRG) xenografts in severe combined immunodeficient (SCID) mice to investigate VZV infection of differentiated neurons and satellite cells
in vivo
. DRG engrafted under the kidney capsule and contained neurons and satellite cells within a typical DRG architecture. VZV clinical isolates infected the neurons within DRG. At 14 days postinfection, VZ virions were detected by electron microscopy in neuronal cell nuclei and cytoplasm but not in satellite cells. The VZV genome copy number was 7.1 × 10
7
to 8.0 × 10
8
copies per 10
5
cells, and infectious virus was recovered. This initial phase of viral replication was followed within 4-8 weeks by a transition to VZV latency, characterized by the absence of infectious virus release, the cessation of virion assembly, and a reduction in VZV genome copies to 3.7 × 10
5
to 4.7 × 10
6
per 10
5
cells. VZV persistence in DRG was achieved without any requirement for VZV-specific adaptive immunity and was associated with continued transcription of the ORF63 regulatory gene. The live attenuated varicella vaccine virus exhibited the same pattern of short-term replication, persistence of viral DNA, and prominent ORF63 transcription as the clinical isolates. VZV-infected T cells transferred virus from the circulation into DRG, suggesting that VZV lymphotropism facilitates its neurotropism. DRG xenografts may be useful for investigating neuropathogenic mechanisms of other human viruses.
Developmental plasticity and the origin of species differences
Authors: West-Eberhard Mary Jane
Published: April 2005

Speciation is the origin of reproductive isolation and divergence between populations, according to the “biological species concept” of Mayr. Studies of reproductive isolation have dominated research on speciation, leaving the origin of species differences relatively poorly understood. Here, I argue that the origin of species differences, and of novel phenotypes in general, involves the reorganization of ancestral phenotypes (developmental recombination) followed by the genetic accommodation of change. Because selection acts on phenotypes, not directly on genotypes or genes, novel traits can originate by environmental induction as well as mutation, then undergo selection and genetic accommodation fueled by standing genetic variation or by subsequent mutation and genetic recombination. Insofar as phenotypic novelties arise from adaptive developmental plasticity, they are not “random” variants, because their initial form reflects adaptive responses with an evolutionary history, even though they are initiated by mutations or novel environmental factors that are random with respect to (future) adaptation. Change in trait frequency involves genetic accommodation of the threshold or liability for expression of a novel trait, a process that follows rather than directs phenotypic change. Contrary to common belief, environmentally initiated novelties may have greater evolutionary potential than mutationally induced ones. Thus, genes are probably more often followers than leaders in evolutionary change. Species differences can originate before reproductive isolation and contribute to the process of speciation itself. Therefore, the genetics of speciation can profit from studies of changes in gene expression as well as changes in gene frequency and genetic isolation.
Decoding the genomic tree of life
Authors: Simonson Anne B. , Servin Jacqueline A. , Skophammer Ryan G. , Herbold Craig W. , Rivera Maria C. , Lake James A.
Published: April 2005

Genomes hold within them the record of the evolution of life on Earth. But genome fusions and horizontal gene transfer (HGT) seem to have obscured sufficiently the gene sequence record such that it is difficult to reconstruct the phylogenetic tree of life. HGT among prokaryotes is not random, however. Some genes (informational genes) are more difficult to transfer than others (operational genes). Furthermore, environmental, metabolic, and genetic differences among organisms restrict HGT, so that prokaryotes preferentially share genes with other prokaryotes having properties in common, including genome size, genome G+C composition, carbon utilization, oxygen utilization/sensitivity, and temperature optima, further complicating attempts to reconstruct the tree of life. A new method of phylogenetic reconstruction based on gene presence and absence, called conditioned reconstruction, has improved our prospects for reconstructing prokaryotic evolution. It is also able to detect past genome fusions, such as the fusion that appears to have created the first eukaryote. This genome fusion between a deep branching eubacterium, possibly an ancestor of the cyanobacterium and a proteobacterium, with an archaeal eocyte (crenarchaea), appears to be the result of an early symbiosis. Given new tools and new genes from relevant organisms, it should soon be possible to test current and future fusion theories for the origin of eukaryotes and to discover the general outlines of the prokaryotic tree of life.
Examining bacterial species under the specter of gene transfer and exchange
Authors: Ochman Howard , Lerat Emmanuelle , Daubin Vincent
Published: April 2005

Even in lieu of a dependable species concept for asexual organisms, the classification of bacteria into discrete taxonomic units is considered to be obstructed by the potential for lateral gene transfer (LGT) among lineages at virtually all phylogenetic levels. In most bacterial genomes, large proportions of genes are introduced by LGT, as indicated by their compositional features and/or phylogenetic distributions, and there is also clear evidence of LGT between very distantly related organisms. By adopting a whole-genome approach, which examined the history of every gene in numerous bacterial genomes, we show that LGT does not hamper phylogenetic reconstruction at many of the shallower taxonomic levels. Despite the high levels of gene acquisition, the only taxonomic group for which appreciable amounts of homologous recombination were detected was within bacterial species. Taken as a whole, the results derived from the analysis of complete gene inventories support several of the current means to recognize and define bacterial species.
A multidimensional approach for detecting species patterns in Malagasy vertebrates
Authors: Yoder Anne D. , Olson Link E. , Hanley Carol , Heckman Kellie L. , Rasoloarison Rodin , Russell Amy L. , Ranivo Julie , Soarimalala Voahangy , Karanth K. Praveen , Raselimanana Achille P. , Goodman Steven M.
Published: April 2005

The biodiversity of Madagascar is extraordinarily distinctive, diverse, and endangered. It is therefore urgent that steps be taken to document, describe, interpret, and protect this exceptional biota. As a collaborative group of field and laboratory biologists, we employ a suite of methodological and analytical tools to investigate the vertebrate portion of Madagascar's fauna. Given that species are the fundamental unit of evolution, where micro- and macroevolutionary forces converge to generate biological diversity, a thorough understanding of species distribution and abundance is critical for understanding the evolutionary, ecological, and biogeographic forces that have shaped Malagasy vertebrate diversity. We illustrate the means by which we apply Mayr's “three basic tasks” of the systematist [Mayr, E. (1942)
Systematics and the Origin of Species from the Viewpoint of a Zoologist
(Harvard Univ. Press, Cambridge, MA)] to identify, classify, and study the organisms that together constitute Madagascar's vertebrate community. Using field inventory methods, specimen-based studies, and morphological and molecular analyses, we formulate hypotheses of species identity that then serve as the foundation for subsequent studies of biology and history. Our experience, as well as that of other investigators, has shown that much of the vertebrate species diversity in Madagascar is “cryptic” for both biological and practical reasons. Beyond issues of cryptic biological diversity, the resolution of species identity in Madagascar has been hampered because of a lack of vouchered comparative material at the population level. Through our activities, we are attempting to remedy these limitations while simultaneously enhancing research capacity in Madagascar.
Mayr, Dobzhansky, and Bush and the complexities of sympatric speciation inRhagoletis
Authors: Feder Jeffrey L. , Xie Xianfa , Rull Juan , Velez Sebastian , Forbes Andrew , Leung Brian , Dambroski Hattie , Filchak Kenneth E. , Aluja Martin
Published: April 2005

TheRhagoletis pomonellasibling species complex is a model for sympatric speciation by means of host plant shifting. However, genetic variation aiding the sympatric radiation of the group in the United States may have geographic roots. Inversions on chromosomes 1-3 affecting diapause traits adapting flies to differences in host fruiting phenology appear to exist in the United States because of a series of secondary introgression events from Mexico. Here, we investigate whether these inverted regions of the genome may have subsequently evolved to become more recalcitrant to introgression relative to collinear regions, consistent with new models for chromosomal speciation. As predicted by the models, gene trees for six nuclear loci mapping to chromosomes other than 1-3 tended to have shallower node depths separating Mexican and U.S. haplotypes relative to an outgroup sequence than nine genes residing on chromosomes 1-3. We discuss the implications of secondary contact and differential introgression with respect to sympatric host race formation and speciation inRhagoletis, reconciling some of the seemingly dichotomous views of Mayr, Dobzhansky, and Bush concerning modes of divergence.
Evolutionary origin of cAMP-based chemoattraction in the social amoebae
Authors: Alvarez-Curto Elisa , Rozen Daniel E. , Ritchie Allyson V. , Fouquet Celine , Baldauf Sandra L. , Schaap Pauline
Published: April 2005

Phenotypic novelties can arise if integrated developmental pathways are expressed at new developmental stages and then recruited to serve new functions. We analyze the origin of a novel developmental trait of Dictyostelid amoebae: the evolution of cAMP as a developmental chemoattractant. We show that cAMP's role of attracting starving amoebae arose through recruitment of a pathway that originally evolved to coordinate fruiting body morphogenesis. Orthologues of the high-affinity cAMP receptor (cAR), cAR1, were identified in a selection of species that span the Dictyostelid phylogeny. The cAR1 orthologue from the basal species
Dictyostelium minutum
restored aggregation and development when expressed in an aggregation-defective mutant of the derived species
Dictyostelium discoideum
that lacks high-affinity cARs, thus demonstrating that the
D. minutum
cAR is a fully functional cAR. cAR1 orthologues from basal species are expressed during fruiting body formation, and only this process, and not aggregation, was disrupted by abrogation of cAR1 function. This is in contrast to derived species, where cAR1 is also expressed during aggregation and critically regulates this process. Our data show that coordination of fruiting body formation is the ancestral function of extracellular cAMP signaling, whereas its derived role in aggregation evolved by recruitment of a preexisting pathway to an earlier stage of development. This most likely occurred by addition of distal cis-regulatory regions to existing cAMP signaling genes.
Distinct role of lymphocyte function-associated antigen-1 in mediating effective cytolytic activity by cytotoxic T lymphocytes
Authors: Anikeeva Nadia , Somersalo Kristina , Sims Tasha N. , Thomas V. Kaye , Dustin Michael L. , Sykulev Yuri
Published: April 2005

Lymphocyte function-associated antigen-1 (LFA-1) interaction with intercellular adhesion molecules (ICAMs) facilitates T cell antigen receptor (TCR)-mediated killing. To dissect TCR and LFA-1 contributions, we evaluated cytolytic activity and granule release by cytotoxic T lymphocytes (CTL) as well as intracellular granule redistribution and morphology of CTL stimulated with natural TCR ligand in the presence or absence of LFA-1 engagement. Although other adhesion mechanisms, e.g., CD2-CD58 interaction, could substitute for LFA-1 to trigger CTL degranulation, productive LFA-1 ligation was indispensable for effective target cell lysis by the released granules. LFA-1-mediated adhesion to glass-supported bilayers containing intercellular adhesion molecule-1 was characterized by a much larger junction area, marked by LFA-1 segregation, and a more compact cell shape compared with those observed for CD2-mediated adhesion to bilayers containing CD58. A larger contact induced by intercellular adhesion molecule 1 determined a unique positioning of granules near the interface. These data provide evidence that LFA-1 delivers a distinct signal essential for directing released cytolytic granules to the surface of antigen-bearing target cells to mediate the effective destruction of these cells by CTL.
The 3′ end of the heavy chain constant region locus enhances germline transcription and switch recombination of the four γ genes
Authors: Dunnick Wesley A. , Shi Jian , Graves Kevin A. , Collins John T.
Published: April 2005

The switch in immunoglobulin (Ig) heavy chain class is preceded by germline transcription and then mediated by a DNA recombination event. To study germline transcription and class switch recombination we used transgenic mice with a 230-kilobase bacterial artificial chromosome that included a rearranged VDJ gene and the entire heavy chain constant region locus. In addition to several lines with intact transgenes, we identified two lines in which the heavy chain locus transgene lacked Cα and everything 3′ of it, including the regulatory elements HS3a, HS1-2, HS3b, and HS4. B cells from both lines with the truncated transgenes make abundant transgenic (Tg) VDJCμ transcripts and IgM protein. Deletion of the 3′ end of the locus results in dramatically reduced expression of both germline transcripts and switched VDJCH transcripts of the γ3, γ2b, γ2a, and ε genes. In addition, the transgenes lacking the 3′ end of the locus express reduced amounts of γ1 germline transcripts and 2–3% of the amount of Tg IgG1 in tissue culture compared with intact transgenes. Finally, switch recombination to γ1 is undetectable in the transgenes lacking the 3′ elements, as measured by digestion circularization–polymerase chain reaction or by the expression of VDJCγ1 transcripts.
Monism on the One Hand, Pluralism on the Other
Authors: Slater Matthew H.
Published: April 2005

In this paper, I consider ways of responding to critiques of natural kinds monism recently suggested from the pluralist camp. Even if monism is determined to be untenable in certain domains (say, about species), it might well be tenable in others. Chemistry is suggested to be such a monist-friendly domain. Suggestions of trouble for chemical kinds can be defused by attending to the difference between monism as a metaphysical thesis and as a claim about classification systems. Finally, I consider enantiomers as a test case for the monism/pluralism debate. The question of whether enantiomers differ in kind does not appear easily answerable. I suggest that this legislates for pluralism in chemistry.
Enumerative Induction and Lawlikeness
Authors: Spohn Wolfgang
Published: April 2005

The paper is based on ranking theory, a theory of degrees of disbelief (and hence belief). On this basis, it explains enumerative induction, the confirmation of a law by its positive instances, which may, indeed, take various schemes. It gives a ranking theoretic explication of a possible law or a nomological hypothesis. It proves, then, that such schemes of enumerative induction uniquely correspond to mixtures of such nomological hypotheses. Thus, it shows both that de Finetti's probabilistic representation theorems may be transformed into an account of confirmation of possible laws and that enumerative induction is equivalent to such an account. The paper concludes with some remarks about the apriority of lawfulness, or the uniformity of nature.
Follow the Leader: Local Interactions with Influence Neighborhoods
Authors: Vanderschraaf Peter , Alexander J. McKenzie
Published: April 2005

We introduce a dynamic model for evolutionary games played on a network where strategy changes are correlated according to degree of influence between players. Unlike the notion of stochastic stability (Foster and Young, 1990), which assumes mutations are stochastically independent and identically distributed, our framework allows for the possibility that agents correlate their strategies with the strategies of those they trust, or those who have influence over them. We show that the dynamical properties of evolutionary games, where suchinfluence neighborhoodsappear, differ dramatically from those where all mutations are stochastically independent, and establish some elementary convergence results relevant for the evolution of social institutions.
The Bible in History
Authors: Kling David W.
Published: April 2005

This book examines the dynamic interplay between scripture and society. Kling traces the story of how specific biblical texts have at different times emerged to be the inspiration of movements that have changed the course of history. He selects eight specific texts (sometimes a single verse, other times a selection of verses or chapters, even books) and demonstrates how each shaped the direction of Christian history. These texts include the story of the rich young ruler (Matthew 19: 16–22) as an inspiration for Anthony and the beginnings of monasticism; the “Petrine text” (Matthew 16:18) as the basis for the papacy; the centrality of the Song of Songs in medieval Christendom, particularly as interpreted through the mystical leanings of Bernard of Clairvaux; Romans 1:17 and its influence upon Martin Luther and the Protestant Reformation; Jesus’ teachings in the Sermon on the Mount, embraced by Anabaptists as a call to radical discipleship, including pacifism; the varied applications of the exodus motif and Moses figures in African-American history, from slavery to Martin Luther King to liberation theology; the Book of Acts with its references to the outpouring of the Spirit and speaking in tongues as the basis for the rise of modern Pentecostalism; and Galatians 3:28, which has been adopted by feminists as a rallying cry for women’s ordination. Kling’s study demonstrates that scripture has functioned in a dialectical interplay of influences; texts have shaped history and history has shaped the interpretation of texts. Specifically, texts have functioned in at least five ways: (1) as transforming agents to another way of thinking and acting, believing and behaving; (2) as recreated meaning, undergoing multiple interpretations and applications; (3) as comprehending sources, drawing other biblical texts into their thematic orbit; (4) as hermeneutical keys unlocking the essential meaning in or resolving tensions within scripture; and (5) as secondary justifications, legitimizing after the fact to support existing historical realities.
“Let Him Kiss Me with the Kisses of His Mouth!”
Authors: Kling David W.
Published: April 2005

This chapter focuses on the history of interpretation of the Song of Songs, with a particular attention given to Bernard of Clairvaux’s Sermons on the Song of Songs. It also considers the important contribution of Origen in the history of biblical interpretation, as well as contemporary interpretations (e.g., feminist) of this poetic book in Hebrew Scripture.
“The Righteous Will Live by Faith”
Authors: Kling David W.
Published: April 2005

This chapter focuses on Martin Luther and his search for a gracious God. It surveys Luther’s life as a prelude to his theological and biblical studies which culminated in a new understanding of his place before God as he wrestled with the meaning of Romans 1:17. It concludes with a discussion of the history of interpretation of this text and its understanding among contemporary commentators.
“Love Your Enemies”
Authors: Kling David W.
Published: April 2005

This chapter focuses on the emergence of the Anabaptist peace tradition in the sixteenth century and its various expressions extending into the present. It considers the importance of the person of Jesus and his teachings (particularly the Sermon on the Mount) as the ethical rationale for their pacifism.
God and Other Spirits
Authors: Wiebe Phillip
Published: April 2005

This book advances three central propositions: (a) Claims about what is real, including a transcendent reality, if it exists, cannot be achieved by short, snappy proofs, but by the hard work of examining phenomena closely, conjecturing about how they might explained, and critically scrutinizing the explanations that are suggested by the phenomena; (b) The methodology that is needed in a critical scrutiny of religion is neither deductive nor inductive argumentation, both of which have been prominent in philosophy of religion, but abductive argumentation, in which unobservable objects are tentatively postulated to exist, in an effort to determine how well they explain otherwise inexplicable phenomena; and (c) The phenomena that ought to be made central to the study of religion are the varied experiences that people have reported and continue to report, especially those that suggest to educated and articulate adults that an order of reality might exist that transcends the known natural one. Empirical grounds for advancing the existence of spirits are examined in several chapters, such as the phenomena of (alleged) demonic possession and exorcism, as well as other phenomena in biblical history and in contemporary life that suggest the existence of holy beings. These phenomena are used to reconstruct the theory of spirits in a critical realist way, according to which the postulated entities are contextually defined by the causal roles these entities are deemed to play. The abductive argumentation to unobservable objects that is advocated is perhaps best known from atomism, but it has also been vital to evolutionary theory, genetic theory, psychoanalysis, and to other well known fields of scientific inquiry. Various objections are examined against the thesis of the book, including the view that the concepts of religion are mythopoeic, the claim that naturalism as it is presently known is adequate to explain all phenomena, and the position that Christian theism is incoherent. The plausibility of contextual realism is defended according to which separate domains of critical inquiry have epistemic independence from one another, so that ontological reduction is neither routinely imposed on religious claims nor deemed to be impossible. The competing claims that theism is properly basic and that probabilistic argument affords the best approach toward theism are resisted. The author calls for “naturalizing epistemology” of religion, following W. V. O. Quine, which requires paying more attention than classical empiricism has given to the circumstances in which educated and articulate adults adopt beliefs, including beliefs that accommodate God and other spirits.
Naturalizing Supernaturalism
Authors: Wiebe Phillip
Published: April 2005

This chapter considers competitor views concerning the existence of God, including: (a) the claim of Alvin Plantinga that God is “properly basic” and is not subject to having evidence adduced for or against the claim; (b) the claim of Richard Swinburne that the most appropriate argument for the existence of God is one that is probabilistic, with various kinds of evidence all advancing the probability that God exists. These and some other views are set aside in order to argue that epistemic claims concerning the existence of a transcendent domain need to be “naturalized,” by identifying the most impressive phenomena that both induce rational non-believers to abandon conventional naturalistic views and embrace some form of “supernaturalism,” as well as continue to provide data for which a transcendent reality appears to provide the most convincing explanation.
Introduction
Authors: Goldschmidt Henry
Published: April 2005

The introduction to the collection offers a theoretical overview of the relationships among race, nation, and religion as categories of collective identity formation. It argues, in brief, that these categories are always already inextricably linked and cannot be studied in isolation from each other—that they are, in fact, co-constituted categories, wholly dependent on each other for their social existence and symbolic meanings. It then explores some of the implications of this argument for our understanding of racial, national, and religious identities in the Americas and elsewhere. It focuses, above all, on a critique of the presumed secularity of racial and national identities and thus casts doubt on the popular equation of modernity and secularization.
Race and Religion on the Periphery
Authors: Murphree Daniel
Published: April 2005

This chapter evaluates the process by which Spanish missionaries racialized Native Americans in the colonial Floridas between 1566 and 1763. During this period, Europeans involved in Christianizing natives expanded an idiom of description initiated by earlier Spanish explorers in reaction to ongoing failures relating to conquest and settlement. Missionaries and other colonists used these descriptions to fashion a unique European Floridian identity in the region premised on distinction from indigenous peoples. The related processes of racialization and identity formation influenced intercultural relationships in the region into the modern era.
The Jew in the Haitian Imagination
Authors: McAlister Elizabeth
Published: April 2005

This essay explores the contemporary legacies of colonial religious discourses, by examining how participants in Haiti’s annual Rara festival—a Lenten carnival and public performance of Haitian Vodou—at once inherit and transform the anti-Jewish sentiments of the clergy in colonial Saint Domingue. Through an active identification with the Jews who “killed Jesus,” disenfranchised Haitians reinvent the European demonization of Jews and Africans, deconstructing colonial religious categories from within, in order to craft rituals of resistance to their country’s predominantly Catholic and mulatto elites.
“Marked in Body, Mind, and Spirit”
Authors: Chang Derek
Published: April 2005

This essay discusses the work of the American Baptist Home Mission Society with African-Americans and Chinese immigrants in the late nineteenth century. It explores the tensions between hierarchy and inclusion in the efforts of White evangelists to incorporate racialized minorities into the Baptist Church and the body politic, as well as the tensions that ultimately arose between White missionary discourses and the proselytes’ own alternative visions of race, nation, and religion. It thus demonstrates the complex role of religion in the U.S. process of nation building.
Catholics, Creoles, and the Redefinition of Race in New Orleans
Authors: Bennett James B.
Published: April 2005

This essay traces the role of Catholicism in the shifting racial identity of Creoles of color in New Orleans in the late nineteenth and early twentieth centuries. The implementation of racially segregated Catholic parishes in New Orleans played an important role in changing the way white New Orleanians classified Creoles of color, who were once considered a distinct racial category but came to be described as simply “black.” At the same time, resistance to separate parishes demonstrated both the difficulty of instituting segregation and the creative ways that Creoles preserved a distinct identity even within a society divided along a black-white binary.
Beyond the Binary
Authors: Sigler Danielle Brune
Published: April 2005

This essay examines the construction of alternate racial identities within American religious organizations. It focuses on Father Divine and Daddy Grace, men generally considered “black” by U.S. society, who strove to create multi-racial congregations. Within his Peace Mission, Divine and his followers eschewed any type of racial designation. Grace turned to the United House of Prayer for All People to help assert his own alternate identity as a “white” man from Portugal and to create a place of worship literally for “all people” regardless of race, nationality, or ethnicity.
Legislating “Civilization” in Postrevolutionary Haiti
Authors: Ramsey Kate
Published: April 2005

This article examines the nineteenth century Haitian state’s penal prohibition of “le vaudoux” as a form of “sortilege” or spell. It studies how, in the face of unremitting white Western hostility and racist malign, successive post-revolutionary Haitian governments relied on juridical law both as a sign of political modernity and as a space for the repudiation of the so-called primitive in Haiti. The article focuses on two significant episodes of enforcement of these laws following the return of the Roman Catholic Church to Haiti in 1860. At this point, popular ritual practice fell, in effect, under a second punitive regime, even as the newly arrived foreign clergy also pressed the Haitian state for stricter enforcement of the laws already in place. I argue, however, that the application of what were frequently consolidated after 1860 as “les lois divines et humaines” against “le vaudoux” proved, repeatedly, to be impossible for both state and Church. The disparity between how this word was constructed through penal and ecclesiastical laws versus how it was popularly understood became the key point on which both the state’s and the Church’s campaigns against popular ritual invariably foundered.
The Civilization of White Men
Authors: Snow Jennifer
Published: April 2005

This essay examines a landmark 1922 case in which the United States Supreme Court denied a Sikh immigrant’s application for citizenship under the 1790 statute restricting naturalization to “free white men.” Despite his undisputed “Aryan blood,” the Supreme Court decreed that Bhagat Singh Thind could not become an American citizen because because his “Hindoo” religion was inconsistent with “the civilization of white men.”
Projecting Blackness
Authors: Weisenfeld Judith
Published: April 2005

This chapter discusses approaches to the co-construction of religion and race in Hollywood films focusing on the case of Metro-Goldwyn-Mayer’s 1929 film Hallelujah. Directed by King Vidor, the film extended popular culture and literary traditions of naturalizing and sanctioning American racial hierarchies through the presentation of an aesthetic of primitive black religion. The chapter examines the production history and reception of the film with attention to discourses about race, religion, and representation, as well as about the relationship between African-American religious practices and civil rights more broadly.