bluuebunny/crossref_metadata_2025 huggingface dataset:
HIV Coreceptor Downregulation as Antiviral Principle: SDF-1α–dependent Internalization of the Chemokine Receptor CXCR4 Contributes to Inhibition of HIV Replication
Authors: Amara Ali , Gall Sylvie Le , Schwartz Olivier , Salamero Jean , Montes Monica , Loetscher Pius , Baggiolini Marco , Virelizier Jean-Louis , Arenzana-Seisdedos Fernando
Published: July 2002

Ligation of CCR5 by the CC chemokines RANTES, MIP-1α or MIP-1β, and of CXCR4 by the CXC chemokine SDF-1α, profoundly inhibits the replication of HIV strains that use these coreceptors for entry into CD4+ T lymphocytes. The mechanism of entry inhibition is not known. We found a rapid and extensive downregulation of CXCR4 by SDF-1α and of CCR5 by RANTES or the antagonist RANTES(9-68). Confocal laser scanning microscopy showed that CCR5 and CXCR4, after binding to their ligands, are internalized into vesicles that qualify as early endosomes as indicated by colocalization with transferrin receptors. Internalization was not affected by treatment with Bordetella pertussis toxin, showing that it is independent of signaling via Gi-proteins. Removal of SDF-1α led to rapid, but incomplete surface reexpression of CXCR4, a process that was not inhibited by cycloheximide, suggesting that the coreceptor is recycling from the internalization pool. Deletion of the COOH-terminal, cytoplasmic domain of CXCR4 did not affect HIV entry, but prevented SDF-1α–induced receptor downregulation and decreased the potency of SDF-1α as inhibitor of HIV replication. Our results indicate that the ability of the coreceptor to internalize is not required for HIV entry, but contributes to the HIV suppressive effect of CXC and CC chemokines.
In Vivo Microbial Stimulation Induces Rapid CD40 Ligand–independent Production of Interleukin 12 by Dendritic Cells and their Redistribution to T Cell Areas
Authors: Sousa Caetano Reis e , Hieny Sara , Scharton-Kersten Tanya , Jankovic Dragana , Charest Hugues , Germain Ronald N. , Sher Alan
Published: July 2002

The early induction of interleukin (IL)-12 is a critical event in determining the development of both innate resistance and adaptive immunity to many intracellular pathogens. Previous in vitro studies have suggested that the macrophage (MΦ) is a major source of the initial IL-12 produced upon microbial stimulation and that this response promotes the differentiation of protective T helper cell 1 (Th1) CD4+ lymphocytes from precursors that are primed on antigen-bearing dendritic cells (DC). Here, we demonstrate by immunolocalization experiments and flow cytometric analysis that, contrary to expectation, DC and not MΦ are the initial cells to synthesize IL-12 in the spleens of mice exposed in vivo to an extract of Toxoplasma gondii or to lipopolysaccharide, two well characterized microbial stimulants of the cytokine. Importantly, this production of IL-12 occurs very rapidly and is independent of interferon γ priming or of signals from T cells, such as CD40 ligand. IL-12 production by splenic DC is accompanied by an increase in number of DCs, as well as a redistribution to the T cell areas and the acquisition of markers characteristic of interdigitating dendritic cells. The capacity of splenic DC but not MΦ to synthesize de novo high levels of IL-12 within hours of exposure to microbial products in vivo, as well as the ability of the same stimuli to induce migration of DC to the T cell areas, argues that DC function simultaneously as both antigen-presenting cells and IL-12 producing accessory cells in the initiation of cell-mediated immunity to intracellular pathogens. This model avoids the need to invoke a three-cell interaction for Th1 differentiation and points to the DC as both a sentinel for innate recognition and the dictator of class selection in the subsequent adaptive response.
Immunization with a Lymphocytic Choriomeningitis Virus Peptide Mixed with Heat Shock Protein 70 Results in Protective Antiviral Immunity and Specific Cytotoxic T Lymphocytes
Authors: Ciupitu Anne-Marie T. , Petersson Max , O'Donnell Carey L. , Williams Kevin , Jindal Satish , Kiessling Rolf , Welsh Raymond M.
Published: July 2002

Heat shock proteins (hsp's) isolated from murine cancer cells can elicit protective immunity and specific cytotoxic T lymphocytes (CTLs) by channeling tumor-derived peptides bound to hsp's to the major histocompatibility class I antigen presentation pathway. Here we have investigated if hsp70 can be used in a novel peptide vaccine for the induction of protective antiviral immunity and memory CTLs. A CTL epitope from the well-defined lymphocytic choriomeningitis virus (LCMV) system was mixed with recombinant hsp70 in vitro under conditions that optimize peptide binding to hsp70. Mice were immunized with the hsp70–peptide mixture and challenged with LCMV. Virus titers were reduced 10–100-fold in these mice compared to control mice. Immunization with the hsp70–peptide mixture resulted in the development of CTL memory cells that could be reactivated during LCMV infection, and that in a 51Cr-release assay could lyse cells pulsed with the same peptide, but not cells pulsed with another LCMV peptide. These results show that hsp70 can be used with CTL epitopes to induce efficient protective antiviral immunity and the generation of peptide-specific CTLs. The results also demonstrate the usefulness of hsp70 as an alternative to adjuvants and DNA vectors for the delivery of CTL epitopes to antigen-presenting cells.
Natural Killer (NK) Cell–mediated Cytotoxicity: Differential Use of  TRAIL and Fas Ligand by Immature and Mature Primary Human NK Cells
Authors: Zamai Loris , Ahmad Manzoor , Bennett Ian M. , Azzoni Livio , Alnemri Emad S. , Perussia Bice
Published: July 2002

Mature natural killer (NK) cells use Ca2+-dependent granule exocytosis and release of cytotoxic proteins, Fas ligand (FasL), and membrane-bound or secreted cytokines (tumor necrosis factor [TNF]-α) to induce target cell death. Fas belongs to the TNF receptor family of molecules, containing a conserved intracytoplasmic “death domain” that indirectly activates the caspase enzymatic cascade and ultimately apoptotic mechanisms in numerous cell types. Two additional members of this family, DR4 and DR5, transduce apoptotic signals upon binding soluble TNF-related apoptosis-inducing ligand (TRAIL) that, like FasL, belongs to the growing TNF family of molecules. Here, we report that TRAIL produced or expressed by different populations of primary human NK cells is functional, and represents a marker of differentiation or activation of these, and possibly other, cytotoxic leukocytes. During differentiation NK cells, sequentially and differentially, use distinct members of the TNF family or granule exocytosis to mediate target cell death. Phenotypically immature CD161+/CD56− NK cells mediate TRAIL-dependent but not FasL- or granule release–dependent cytotoxicity, whereas mature CD56+ NK cells mediate the latter two.
Identification of MAGE-3 Epitopes Presented by HLA-DR Molecules to CD4+ T Lymphocytes
Authors: Chaux Pascal , Vantomme Valérie , Stroobant Vincent , Thielemans Kris , Corthals Jurgen , Luiten Rosalie , Eggermont Alexander M.M. , Boon Thierry , van der Bruggen Pierre
Published: July 2002

MAGE-type genes are expressed by many tumors of different histological types and not by normal cells, except for male germline cells, which do not express major histocompatibility complex (MHC) molecules. Therefore, the antigens encoded by MAGE-type genes are strictly tumor specific and common to many tumors. We describe here the identification of the first MAGE-encoded epitopes presented by histocompatibility leukocyte antigen (HLA) class II molecules to CD4+ T lymphocytes. Monocyte-derived dendritic cells were loaded with a MAGE-3 recombinant protein and used to stimulate autologous CD4+ T cells. We isolated CD4+ T cell clones that recognized two different MAGE-3 epitopes, MAGE-3114–127 and MAGE-3121–134, both presented by the HLA-DR13 molecule, which is expressed in 20% of Caucasians. The second epitope is also encoded by MAGE-1, -2, and -6. Our procedure should be applicable to other proteins for the identification of new tumor-specific antigens presented by HLA class II molecules. The knowledge of such antigens will be useful for evaluation of the immune response of cancer patients immunized with proteins or with recombinant viruses carrying entire genes coding for tumor antigens. The use of antigenic peptides presented by class II in addition to peptides presented by class I may also improve the efficacy of therapeutic antitumor vaccination.
The Intestinal T Cell Response to α-Gliadin in Adult Celiac Disease Is Focused on a Single Deamidated Glutamine Targeted by Tissue Transglutaminase
Authors: Arentz-Hansen Helene , Körner Roman , Molberg Øyvind , Quarsten Hanne , Vader Willemijn , Kooy Yvonne M.C. , Lundin Knut E.A. , Koning Frits , Roepstorff Peter , Sollid Ludvig M. , McAdam Stephen N.
Published: July 2002

The great majority of patients that are intolerant of wheat gluten protein due to celiac disease (CD) are human histocompatibility leukocyte antigen (HLA)-DQ2+, and the remaining few normally express HLA-DQ8. These two class II molecules are chiefly responsible for the presentation of gluten peptides to the gluten-specific T cells that are found only in the gut of CD patients but not of controls. Interestingly, tissue transglutaminase (tTG)-mediated deamidation of gliadin plays an important role in recognition of this food antigen by intestinal T cells. Here we have used recombinant antigens to demonstrate that the intestinal T cell response to α-gliadin in adult CD is focused on two immunodominant, DQ2-restricted peptides that overlap by a seven-residue fragment of gliadin. We show that tTG converts a glutamine residue within this fragment into glutamic acid and that this process is critical for T cell recognition. Gluten-specific T cell lines from 16 different adult patients all responded to one or both of these deamidated peptides, indicating that these epitopes are highly relevant to disease pathology. Binding studies showed that the deamidated peptides displayed an increased affinity for DQ2, a molecule known to preferentially bind peptides containing negatively charged residues. Interestingly, the modified glutamine is accommodated in different pockets of DQ2 for the different epitopes. These results suggest modifications of anchor residues that lead to an improved affinity for major histocompatibility complex (MHC), and altered conformation of the peptide–MHC complex may be a critical factor leading to T cell responses to gliadin and the oral intolerance of gluten found in CD.
Identification of Ny-Eso-1 Epitopes Presented by Human Histocompatibility Antigen (Hla)-Drb4*0101–0103 and Recognized by Cd4+T Lymphocytes of Patients with Ny-Eso-1–Expressing Melanoma
Authors: Jäger Elke , Jäger Dirk , Karbach Julia , Chen Yao-Tseng , Ritter Gerd , Nagata Yasuhiro , Gnjatic Sacha , Stockert Elisabeth , Arand Michael , Old Lloyd J. , Knuth Alexander
Published: July 2002

NY-ESO-1 is a member of the cancer-testis family of tumor antigens that elicits strong humoral and cellular immune responses in patients with NY-ESO-1–expressing cancers. Since CD4+ T lymphocytes play a critical role in generating antigen-specific cytotoxic T lymphocyte and antibody responses, we searched for NY-ESO-1 epitopes presented by histocompatibility leukocyte antigen (HLA) class II molecules. Autologous monocyte-derived dendritic cells of cancer patients were incubated with recombinant NY-ESO-1 protein and used in enzyme-linked immunospot (ELISPOT) assays to detect NY-ESO-1–specific CD4+ T lymphocyte responses. To identify possible epitopes presented by distinct HLA class II alleles, overlapping 18-mer peptides derived from NY-ESO-1 were synthetized and tested for recognition by CD4+ T lymphocytes in autologous settings. We identified three NY-ESO-1–derived peptides presented by DRB4*0101–0103 and recognized by CD4+ T lymphocytes of two melanoma patients sharing these HLA class II alleles. Specificity of recognition was confirmed by proliferation assays. The characterization of HLA class II–restricted epitopes will be useful for the assessment of spontaneous and vaccine-induced immune responses of cancer patients against defined tumor antigens. Further, the therapeutic efficacy of active immunization using antigenic HLA class I–restricted peptides may be improved by adding HLA class II–presented epitopes.
Intrinsic Constraint on Plasmablast Growth and Extrinsic Limits of Plasma Cell Survival
Authors: Sze Daniel M.-Y. , Toellner Kai-Michael , de Vinuesa Carola García , Taylor Dale R. , MacLennan Ian C.M.
Published: July 2002

B cells recruited into splenic antibody responses grow exponentially, either in extrafollicular foci as plasmablasts, or in follicles where they form germinal centers. Both responses yield plasma cells. Although many splenic plasma cells survive <3 d, some live much longer. This study shows that early plasma cell death relates to a finite capacity of the spleen to sustain plasma cells rather than a life span endowed by the cell's origin or the quality of antibody it produces. Antibody responses were compared where the peak numbers of plasma cells in spleen sections varied between 100 and 5,000 cells/mm2. In each response, plasmablast clones divided some five times, with the peak numbers of plasma cells produced relating directly to the number of B cells recruited into the response. The spleen seems to have the capacity to sustain between 20 and 100 plasma cells/mm2. When this number is exceeded, there is a loss of excess cells. Immunoglobulin variable region gene sequencing, and 5-bromo-2′-deoxyuridine pulse–chase studies indicate that long-lived splenic plasma cells are a mixture of cells derived from the extrafollicular and germinal center responses and cells derived from virgin and memory B cells. Only a proportion has switched immunoglobulin class.
Ionic Regulatory Properties of Brain and Kidney Splice Variants of the Ncx1 Na+–Ca2+ Exchanger
Authors: Dyck Chris , Omelchenko Alexander , Elias Chadwick L. , Quednau Beate D. , Philipson Kenneth D. , Hnatowich Mark , Hryshko Larry V.
Published: July 2002

Ion transport and regulation of Na+–Ca2+ exchange were examined for two alternatively spliced isoforms of the canine cardiac Na+–Ca2+ exchanger, NCX1.1, to assess the role(s) of the mutually exclusive A and B exons. The exchangers examined, NCX1.3 and NCX1.4, are commonly referred to as the kidney and brain splice variants and differ only in the expression of the BD or AD exons, respectively. Outward Na+–Ca2+ exchange activity was assessed in giant, excised membrane patches from Xenopus laevis oocytes expressing the cloned exchangers, and the characteristics of Na+i- (i.e., I1) and Ca2+i- (i.e., I2) dependent regulation of exchange currents were examined using a variety of experimental protocols. No remarkable differences were observed in the current–voltage relationships of NCX1.3 and NCX1.4, whereas these isoforms differed appreciably in terms of their I1 and I2 regulatory properties. Sodium-dependent inactivation of NCX1.3 was considerably more pronounced than that of NCX1.4 and resulted in nearly complete inhibition of steady state currents. This novel feature could be abolished by proteolysis with α-chymotrypsin. It appears that expression of the B exon in NCX1.3 imparts a substantially more stable I1 inactive state of the exchanger than does the A exon of NCX1.4. With respect to I2 regulation, significant differences were also found between NCX1.3 and NCX1.4. While both exchangers were stimulated by low concentrations of regulatory Ca2+i, NCX1.3 showed a prominent decrease at higher concentrations (>1 μM). This does not appear to be due solely to competition between Ca2+i and Na+i at the transport site, as the Ca2+i affinities of inward currents were nearly identical between the two exchangers. Furthermore, regulatory Ca2+i had only modest effects on Na+i-dependent inactivation of NCX1.3, whereas I1 inactivation of NCX1.4 could be completely eliminated by Ca2+i. Our results establish an important role for the mutually exclusive A and B exons of NCX1 in modulating the characteristics of ionic regulation and provide insight into how alternative splicing tailors the regulatory properties of Na+–Ca2+ exchange to fulfill tissue-specific requirements of Ca2+ homeostasis.
Biotechnology in the Netherlands: controversy or consensus?
Authors: Gutteling Jan M.
Published: July 2002

This paper addresses the issue of public perception of modern biotechnology in the Netherlands. Contrary to expectations, data from the 1999 Eurobarometer on biotechnology indicate that the position of the Dutch public in general is rather ambiguous, which is in contrast to many of its neighboring countries. The issue is described in terms of differences between the Netherlands and other European countries on political-economic, social-cultural, or media coverage indicators. On many indicators, the Dutch population differs from that of other European countries, and the Dutch opinion-leading media present a rather balanced perspective on modern biotechnology.
The efficient computation of Fourier transforms on the symmetric group
Authors: Maslen David
Published: July 2002

This paper introduces new techniques for the efficient computation of Fourier transforms on symmetric groups and their homogeneous spaces. We replace the matrix multiplications in Clausen’s algorithm with sums indexed by combinatorial objects that generalize Young tableaux, and write the result in a form similar to Horner’s rule. The algorithm we obtain computes the Fourier transform of a function on

S
n

S_n

in no more than

3
4

n
(
n
−
1
)

|

S
n

|

\frac {3}{4} n(n-1) |S_n|

multiplications and the same number of additions. Analysis of our algorithm leads to several combinatorial problems that generalize path counting. We prove corresponding results for inverse transforms and transforms on homogeneous spaces.
Evidence That Ternary Complex (eIF2-GTP-tRNAiMet)–Deficient Preinitiation Complexes Are Core Constituents of Mammalian Stress Granules
Authors: Kedersha Nancy , Chen Samantha , Gilks Natalie , Li Wei , Miller Ira J. , Stahl Joachim , Anderson Paul
Published: July 2002

Environmental stress-induced phosphorylation of eIF2α inhibits protein translation by reducing the availability of eIF2-GTP-tRNAiMet, the ternary complex that joins initiator tRNAMetto the 43S preinitiation complex. The resulting untranslated mRNA is dynamically routed to discrete cytoplasmic foci known as stress granules (SGs), a process requiring the related RNA-binding proteins TIA-1 and TIAR. SGs appear to be in equilibrium with polysomes, but the nature of this relationship is obscure. We now show that most components of the 48S preinitiation complex (i.e., small, but not large, ribosomal subunits, eIF3, eIF4E, eIF4G) are coordinately recruited to SGs in arsenite-stressed cells. In contrast, eIF2 is not a component of newly assembled SGs. Cells expressing a phosphomimetic mutant (S51D) of eIF2α assemble SGs of similar composition, confirming that the recruitment of these factors is a direct consequence of blocked translational initiation and not due to other effects of arsenite. Surprisingly, phospho-eIF2α is recruited to SGs that are disassembling in cells recovering from arsenite-induced stress. We discuss these results in the context of a translational checkpoint model wherein TIA and eIF2 are functional antagonists of translational initiation, and in which lack of ternary complex drives SG assembly.
A Bayesian framework for the analysis of microarray expression

data: regularized t -test and statistical inferences of

gene changes
Authors: Baldi Pierre , Long Anthony D.
Published: July 2002

Motivation: DNA microarrays are now capable of providing genome-wide patterns of gene expression across many different conditions. The first level of analysis of these patterns requires determining whether observed differences in expression are significant or not. Current methods are unsatisfactory due to the lack of a systematic framework that can accommodate noise, variability, and low replication often typical of microarray data.

Results: We develop a Bayesian probabilistic framework for microarray data analysis. At the simplest level, we model log-expression values by independent normal distributions, parameterized by corresponding means and variances with hierarchical prior distributions. We derive point estimates for both parameters and hyperparameters, and regularized expressions for the variance of each gene by combining the empirical variance with a local background variance associated with neighboring genes. An additional hyperparameter, inversely related to the number of empirical observations, determines the strength of the background variance. Simulations show that these point estimates, combined with a t -test, provide a systematic inference approach that compares favorably with simple t -test or fold methods, and partly compensate for the lack of replication.

Availability: The approach is implemented in software called Cyber-T accessible through a Web interface at www.genomics.uci.edu/software.html. The code is available as Open Source and is written in the freely available statistical language R.

Contact: pfbaldi@ics.uci.edu; tdlong@uci.edu

* To whom correspondence should be addressed.

3 Also at Department of Biological Chemistry, College of Medicine, University of California, Irvine.
Inter‐chromosomal recombination of Mll and Af9 genes mediated by cre‐loxP in mouse development
Authors: Collins Emma C , Pannell Richard , Simpson Elizabeth M , Forster Alan , Rabbitts Terence H
Published: July 2002

Chromosomal translocations are crucial events in the aetiology of many leukaemias, lymphomas and sarcomas, resulting in enforced oncogene expression or the creation of novel fusion genes. The study of the biological outcome of such events ideally requires recapitulation of the tissue specificity and timing of the chromosomal translocation itself. We have used the Cre‐loxP system of phage P1 to induce de novo Mll–Af9 chromosomal recombination during mouse development. loxP sites were introduced into the Mll and Af9 genes on chromosomes 9 and 4, respectively, and mice carrying these alleles were crossed with mice expressing Cre recombinase. A resulting Mll–Af9 fusion gene was detected whose transcription and splicing were verified. Thus, programmed inter‐chromosomal recombination can be achieved in mice. This approach should allow the design of mouse models of tumorigenesis with greater biological relevance than those available at present.
A Public Health Response to Emerging Technology: Expansion of the Massachusetts Newborn Screening Program
Authors: Atkinson Kathleen , Zuckerman Barry , Sharfstein Joshua M. , Levin Donna , Blatt Robin J.R. , Koh Howard K.
Published: July 2002

The development of a new technology, called tandem mass spectrometry (tandem MS), has challenged governments worldwide to consider expanding universal newborn screening for rare metabolic disorders. In 1997 the Massachusetts Department of Public Health developed a public process to meet this challenge. After addressing significant medical, legal, ethical, and logistical issues raised by tandem MS, Massachusetts incorporated one new disorder into the mandatory newborn screen and developed an optional pilot program for 20 additional disorders. The Massachusetts experience has wide relevance for other nations and states. As screening protocols are contemplated for entire populations—for newborns and others—it will remain essential that the public participate in an open process of reviewing the justification for and logistics of screening.
Risk Factors for Lyme Disease in Chester County, Pennsylvania
Authors: Smith Gary , Wileyto E. Paul , Hopkins Robert B. , Cherry Bryan R. , Maher John P.
Published: July 2002

Objective.

To identify factors associated with increased or decreased risk of infection for Lyme disease in Chester County, Pennyslvania.

Methods.

The authors designed an unmatched case-control study involving 294 incident cases reported to the Chester County Health Department in 1998 and 449 controls selected by random digit dialing. All case and control participants were interviewed by telephone.

Results.

Age is a risk factor for Lyme disease for groups aged 10–19 years old and 50 years or older. Sex was not a risk factor. Incidence of Lyme disease in a rural setting was three times the incidence in an urban setting. Increased risk also was associated with living in single family homes, homes with yards or attached land, woods on the land, signs of tick hosts seen on the land, and homes within 100 feet of woodland. Gardening for more than four hours per week was also a risk factor, but most other outdoor activities were not. Twice as many participants took protective measures against tick bites before outdoor employment than those who merely ventured into the yard or land associated with the home. Only checking for ticks during outdoor activity and the use of repellents prior to outdoor activities outside the yard were unequivocally associated with a reduced risk of Lyme disease.

Conclusions.

It is important to increase public awareness about the risk of acquiring Lyme disease from ticks in the immediate environment of the home.
Cross–modal links in spatial attention
Authors: Driver Jon , Spence Charles
Published: July 2002

A great deal is now known about the effects of spatial attention within individual sensory modalities, especially for vision and audition. However, there has been little previous study of possible crossmodal links in attention. Here, we review recent findings from our own experiments on this topic, which reveal extensive spatial links between the modalities. An irrelevant but salient event presented within touch, audition, or vision, can attract covert spatial attention in the other modalities (with the one exception that visual events do not attract auditory attention when saccades are prevented). By shifting receptors in one modality relative to another, the spatial coordinates of these crossmodal interactions can be examined. For instance, when a hand is placed in a new position, stimulation of it now draws visual attention to a correspondingly different location, although some aspects of attention do not spatially remap in this way. Crossmodal links are also evident in voluntary shifts of attention. When a person strongly expects a target in one modality (e.g. audition) to appear in a particular location, their judgements improve at that location not only for the expected modality but also for other modalities (e.g. vision), even if events in the latter modality are somewhat more likely elsewhere. Finally, some of our experiments suggest that information from different sensory modalities may be integrated preattentively, to produce the multimodal internal spatial representations in which attention can be directed. Such preattentive crossmodal integration can, in some cases, produce helpful illusions that increase the efficiency of selective attention in complex scenes.
Knowledge management of the neuroscientific literature: the data model and underlying strategy of the NeuroScholar system
Authors: Burns Gully A. P. C.
Published: July 2002

This paper describes the underlying strategy and system's design of a knowledge management system for the neuroscientific literature called ‘NeuroScholar’. The problem that the system is designed to address is to delineate fully the neural circuitry involved in a specific behaviour. The use of this system provides experimental neuroscientists with a new method of building computational models (‘knowledge models’) of the contents of the published literature. These models may provide input for analysis (conceptual or computational), or be used as constraint sets for conventional neural modelling work. The underlying problems inherent in this approach, the general framework for the proposed solution, the practical issues concerning usage of the system and a detailed, technical account of the system are described. The author uses a widely used software specification language (the Universal Modelling Language) to describe the design of the system and present examples from published work concerned with classical eyeblink conditioning in the rabbit.
C. elegans condensin promotes mitotic chromosome architecture, centromere organization, and sister chromatid segregation during mitosis and meiosis
Authors: Hagstrom Kirsten A. , Holmes Victor F. , Cozzarelli Nicholas R. , Meyer Barbara J.
Published: July 2002

Chromosome segregation and X-chromosome gene regulation inCaenorhabditis elegans share the component MIX-1, a mitotic protein that also represses X-linked genes during dosage compensation. MIX-1 achieves its dual roles through interactions with different protein partners. To repress gene expression, MIX-1 acts in an X-chromosome complex that resembles the mitotic condensin complex yet lacks chromosome segregation function. Here we show that MIX-1 interacts with a mitotic condensin subunit, SMC-4, to achieve chromosome segregation. The SMC-4/MIX-1 complex positively supercoils DNA in vitro and is required for mitotic chromosome structure and segregation in vivo. Thus, C. elegans has two condensin complexes, one conserved for mitosis and another specialized for gene regulation. SMC-4 and MIX-1 colocalize with centromere proteins on condensed mitotic chromosomes and are required for the restricted orientation of centromeres toward spindle poles. This cell cycle-dependent localization requires AIR-2/AuroraB kinase. Depletion of SMC-4/MIX-1 causes aberrant mitotic chromosome structure and segregation, but not dramatic decondensation at metaphase. Moreover, SMC-4/MIX-1 depletion disrupts sister chromatid segregation during meiosis II but not homologous chromosome segregation during meiosis I, although both processes require chromosome condensation. These results imply that condensin is not simply required for compaction, but plays a more complex role in chromosome architecture that is essential for mitotic and meiotic sister chromatid segregation.
Understanding the Adaptation of Halobacterium Species NRC-1 to Its Extreme Environment through Computational Analysis of Its Genome Sequence
Authors: Kennedy Sean P. , Ng Wailap Victor , Salzberg Steven L. , Hood Leroy , DasSarma Shiladitya
Published: July 2002

The genome of the halophilic archaeon Halobacterium sp. NRC-1 and predicted proteome have been analyzed by computational methods and reveal characteristics relevant to life in an extreme environment distinguished by hypersalinity and high solar radiation: (1) The proteome is highly acidic, with a median pI of 4.9 and mostly lacking basic proteins. This characteristic correlates with high surface negative charge, determined through homology modeling, as the major adaptive mechanism of halophilic proteins to function in nearly saturating salinity. (2) Codon usage displays the expected GC bias in the wobble position and is consistent with a highly acidic proteome. (3) Distinct genomic domains of NRC-1 with bacterial character are apparent by whole proteome BLAST analysis, including two gene clusters coding for a bacterial-type aerobic respiratory chain. This result indicates that the capacity of halophiles for aerobic respiration may have been acquired through lateral gene transfer. (4) Two regions of the large chromosome were found with relatively lower GC composition and overrepresentation of IS elements, similar to the minichromosomes. These IS-element-rich regions of the genome may serve to exchange DNA between the three replicons and promote genome evolution. (5) GC-skew analysis showed evidence for the existence of two replication origins in the large chromosome. This finding and the occurrence of multiple chromosomes indicate a dynamic genome organization with eukaryotic character.
The role of a β‐bulge in the folding of the β‐hairpin structure in ubiquitin
Authors: Chen Pei‐Yeh , Gopalacushina B.G. , Yang Chien‐Chih , Chan Sunney I. , Evans Philip A.
Published: July 2002

It is known that the peptide corresponding to the N‐terminal β‐hairpin of ubiquitin, U(1–17), can populate the monomeric β‐hairpin conformation in aqueous solution. In this study, we show that the Gly‐10 that forms the bulge of the β‐turn in this hairpin is very important to the stability of the hairpin. The deletion of this residue to desG10(1–16) unfolds the structure of the peptide in water. Even under denaturing conditions, this bulge appears to be important in maintaining the residual structure of ubiquitin, which involves tertiary interactions within the sequence 1 to 34 in the denatured state. We surmise that this residual structure functions as one of the nucleation centers in the folding process and is important in stabilizing the transition state. In accordance with this idea, deleting Gly‐10 slows down the refolding and unfolding rate by about one half.
Influence of Glu‐376 → Gln mutation on enthalpy and heat capacity changes for the binding of slightly altered ligands to medium chain acyl‐CoA dehydrogenase
Authors: Peterson Karen M. , Gopalan K.V. , Nandy Andreas , Srivastava D.K.
Published: July 2002

We showed that the α‐CH2 → NH substitution in octanoyl‐CoA alters the ground and transition state energies for the binding of the CoA ligands to medium‐chain acyl‐CoA dehydrogenase (MCAD), and such an effect is caused by a small electrostatic difference between the ligands. To ascertain the extent that the electrostatic contribution of the ligand structure and/or the enzyme site environment modulates the thermodynamics of the enzyme–ligand interaction, we undertook comparative microcalorimetric studies for the binding of 2‐azaoctanoyl‐CoA (α‐CH2 → NH substituted octanoyl‐CoA) and octenoyl‐CoA to the wild‐type and Glu‐376 → Gln mutant enzymes. The experimental data revealed that both enthalpy (ΔH°) and heat capacity changes (ΔCp°) for the binding of 2‐azaoctanoyl‐CoA (ΔH°298 = −21.7 ± 0.8 kcal/mole, ΔCp° = −0.627 ± 0.04 kcal/mole/K) to the wild‐type MCAD were more negative than those obtained for the binding of octenoyl‐CoA (ΔH°298 = −17.2 ± 1.6 kcal/mole, ΔCp° = −0.526 ± 0.03 kcal/mole/K). Of these, the decrease in the magnitude of ΔCp° for the binding of 2‐azaoctanoyl‐CoA (vis‐à‐vis octenoyl‐CoA) to the enzyme was unexpected, because the former ligand could be envisaged to be more polar than the latter. To our further surprise, the ligand‐dependent discrimination in the above parameters was completely abolished on Glu‐376 → Gln mutation of the enzyme. Both ΔH° and ΔCp° values for the binding of 2‐azaoctanoyl‐CoA (ΔH°298 = −13.3 ± 0.6 kcal/mole, ΔCp° = −0.511 ± 0.03 kcal/mole/K) to the E376Q mutant enzyme were found to be correspondingly identical to those obtained for the binding of octenoyl‐CoA (ΔH°298 = −13.2 ± 0.6 kcal/mole, ΔCp° = −0.520 ± 0.02 kcal/mole/K). However, in neither case could the experimentally determined ΔCp° values be predicted on the basis of the changes in the water accessible surface areas of the enzyme and ligand species. Arguments are presented that the origin of the above thermodynamic differences lies in solvent reorganization and water‐mediated electrostatic interaction between ligands and enzyme site groups, and such interactions are intrinsic to the molecular basis of the enzyme–ligand complementarity.
Analysis of the dose‐surface histogram and dose‐wall histogram for the rectum and bladder
Authors: Li Shidong , Boyer Arthur , Lu Yong , Chen George T. Y.
Published: July 2002

Dose distribution throughout a hollow organ is represented by either a dose‐surface histogram (DSH) or a dose‐wall histogram (DWH). A spherical shell model for the bladder and a cylindrical shell model for the rectum were introduced for quantifying the difference between the DWH and DSH. The difference was given by subtraction of the percent volume of the wall from the percent area of the surface for any specific dose level. Taking the dose‐grid size and contour‐delineation uncertainties into account, the DSH and DWH calculation errors were estimated by simplified formulas. The DSHs and DWHs for the rectum and bladder in patients undergoing four‐field‐prostate treatment and gynecological intracavitary brachytherapy were computed with a refined numerical algorithm. Results of the analytic models and the numerical calculations demonstrated that the difference between the DWH and DSH was small (about 5%) for a fully filled bladder or rectum but large (about 10%) for an empty rectum or a contracted bladder. The error of DSH was about 3%, which is much smaller than that of DWH.
A dual source photon beam model used in convolution/superposition dose calculations for clinical megavoltage x‐ray beams
Authors: Liu H. Helen , Mackie T. Rock , McCullough Edwin C.
Published: July 2002

A realistic model of photon beams generated by clinical linear accelerators has been incorporated in a convolution/superposition method to compute dose distributions in photon treatment fields. In this beam model, a primary photon source represents photons directly from the target, and an extra‐focal photon source represents scattered photons from the primary collimator and the flattening filter. Monte Carlo simulation was used to study clinical linear accelerators producing photon beams. From the output of the Monte Carlo simulation, the fluence and spectral distributions of each photon component, as well as the geometrical characteristics of each photon source with respect to its distance to the isocenter and its source distribution, were analyzed. These quantities were used to reproduce realistic photon distributions in treatment fields, and thus to compute dose distributions using the convolution method. Our results showed that compared to the primary photon fluence, the extra‐focal photon fluence from the primary collimator and the flattening filter was 11%–16% at the isocenter, among which 70% was contributed by the flattening filter. The variation of extra‐focal photons in different treatment fields was predicted accurately by accounting for the finite size of the extra‐focal source. Compared to measurements, dose distributions in photon treatment fields, including those of asymmetric jaw settings and at different SSDs were calculated accurately, particularly in the penumbral region, by using the convolution method with the new dual source photon beam model.
Calibration of photon and electron beams with an extrapolation chamber
Authors: Zankowski Corey E. , Podgorsak Ervin B.
Published: July 2002

A variable air‐volume, parallel‐plate extrapolation chamber forming an integral part of a Solid Water phantom was built to determine the absorbed dose in Solid Water directly. The sensitive air‐volume of the extrapolation chamber is controlled through the movement of the chamber piston by means of a micrometer mounted to the phantom body. The relative displacement of the piston is monitored by a calibrated mechanical distance travel indicator with a precision on the order of 0.002 mm. Irradiations were carried out with cobalt‐60 gamma rays, x‐ray beams ranging from 4 to 18 MV, and electron beams between 6 and 22 MeV. The absorbed dose at a given depth in Solid Water is proportional to the ionization gradient measured in the Bragg–Gray cavity region with an extrapolation chamber embedded in the Solid Water phantom. The discrepancies between the doses determined in Solid Water with our uncalibrated extrapolation chamber and doses obtained with a calibrated standard thimble ionization chamber are at most 1% for photon and electron beams at all megavoltage clinical energies. Uncalibrated extrapolation chambers thus offer a simple and practical alternative to other techniques used in output measurements of megavoltage photon and electron machines.
A tilt and roll device for automated correction of rotational setup errors
Authors: Hornick David C. , Litzenberg Dale W. , Lam Kwok L. , Balter James M. , Hetrick Joel , Ten Haken Randall K.
Published: July 2002

A tilt and roll device has been developed to add two additional degrees of freedom to an existing treatment table. This device allows computer‐controlled rotational motion about the inferior–superior and left–right patient axes. The tilt and roll device comprises three supports between the tabletop and base. An automotive type universal joint welded to the end of a steel pipe supports the center of the table. Two computer‐controlled linear electric actuators utilizing high accuracy stepping motors support the foot of table and control the tilt and roll of the tabletop. The current system meets or exceeds all pre‐design specifications for precision, weight capacity, rigidity, and range of motion.
American Association of Physicists in Medicine Radiation Therapy Committee Task Group 53: Quality assurance for clinical radiotherapy treatment planning
Authors: Fraass Benedick , Doppke Karen , Hunt Margie , Kutcher Gerald , Starkschall George , Stern Robin , Van Dyke Jake
Published: July 2002

In recent years, the sophistication and complexity of clinical treatment planning and treatment planning systems has increased significantly, particularly including three‐dimensional (3D) treatment planning systems, and the use of conformal treatment planning and delivery techniques. This has led to the need for a comprehensive set of quality assurance (QA) guidelines that can be applied to clinical treatment planning. This document is the report of Task Group 53 of the Radiation Therapy Committee of the American Association of Physicists in Medicine. The purpose of this report is to guide and assist the clinical medical physicist in developing and implementing a comprehensive but viable program of quality assurance for modern radiotherapy treatment planning. The scope of the QA needs for treatment planning is quite broad, encompassing image‐based definition of patient anatomy, 3D beam descriptions for complex beams including multileaf collimator apertures, 3D dose calculation algorithms, and complex plan evaluation tools including dose volume histograms. The Task Group recommends an organizational framework for the task of creating a QA program which is individualized to the needs of each institution and addresses the issues of acceptance testing, commissioning the planning system and planning process, routine quality assurance, and ongoing QA of the planning process. This report, while not prescribing specific QA tests, provides the framework and guidance to allow radiation oncology physicists to design comprehensive and practical treatment planning QA programs for their clinics.
Sensitivity studies of beam directionality, beam size, and neutron spectrum for a fission converter‐based epithermal neutron beam for boron neutron capture therapy
Authors: Sakamoto S. , Kiger W. S. , Harling O. K.
Published: July 2002

Sensitivity studies of epithermal neutron beam performance in boron neutron capture therapy are presented for realistic neutron beams with varying filter/moderator and collimator/delimiter designs to examine the relative importance of neutron beam spectrum, directionality, and size. Figures of merit for in‐air and in‐phantom beam performance are calculated via the Monte Carlo technique for different well‐optimized designs of a fission converter‐based epithermal neutron beam with head phantoms as the irradiation target. It is shown that increasing a measure of beam directionality, does not always lead to corresponding monotonic improvements in beam performance. Due to the relatively low significance, for most configurations, of its effect on in‐phantom performance and the large intensity losses required to produce beams with very high beam directionality should not be considered an important figure of merit in epithermal neutron beam design except in terms of its consequences on patient positioning and collateral dose. Hardening the epithermal beam spectrum, while maintaining the specific fast neutron dose well below the inherent hydrogen capture dose, improves beam penetration and advantage depth and, as a desirable by‐product, significantly increases beam intensity. Beam figures of merit are shown to be strongly dependent on beam size relative to target size. Beam designs with specific fast neutron doses of and beam sizes equal to or larger than the size of the head target produced the deepest useful penetration, highest therapeutic ratios, and highest intensities.
Intensity‐modulation radiotherapy using independent collimators: An algorithm study
Authors: Dai Jian‐Rong , Hu Yi‐Min
Published: July 2002

The purpose of this work is to investigate algorithms for the delivery of intensity‐modulated fields using independent collimators (IC). Two heuristic algorithms are proposed to calculate jaw‐setting sequences for arbitrary 2D intensity distributions. The first algorithm is based on searching the whole intensity matrix to find the largest nonzero rectangular area as a segment while the second algorithm is to find a nonzero rectangular area as a segment which makes the complexity of the remaining intensity matrix minimum. After a sequence is obtained, the delivery order of all its segments is optimized with the technique of simulated annealing to minimize the total jaw‐moving time. To evaluate these two algorithms, randomly generated intensity matrices and three clinical cases of different complexity have been tested, and the results have been compared with one algorithm proposed for MLC technique. It is shown that the efficiency of IC technique becomes increasingly lower than that of MLC technique, and the relative efficiency of two algorithms proposed here is related to machine dose rate and jaw speed. Assuming the prescribed dose is 200 cGY per fraction, machine dose rate is 250 MU/min, and jaw speed is 1.5 cm/s, the treatment can be delivered within about 20 min for all three cases with the first algorithm. The second algorithm requires longer delivery time under such assumptions. The delivery time can be further reduced through increasing machine dose rate and jaw speed, and developing more efficient algorithms. The use of IC for intensity‐modulation radiotherapy has some potential advantages over other techniques.
European methodology for testing the airborne sound insulation characteristics of noise barriers in situ: Experimental verification and comparison with laboratory data
Authors: Garai Massimo , Guidorzi Paolo
Published: July 2002

In the frame of the 1994–1997 Standard, Measurement and Testing program, the European Commission funded a research project, named Adrienne, to define new test methods for measuring the intrinsic characteristics of road traffic noise reducing devices in situ. The research team produced innovative methods for testing the sound reflection/absorption and the airborne sound insulation characteristics of noise barriers. These methods are now under consideration at CEN (European Committee for Standardization), to become European standards. The present work reports a detailed verification of the test method for airborne sound insulation over a selection of 17 noise barriers, representative of the Italian and European production. The samples were tested both outdoors, using the new Adrienne method, and in laboratory, following the European standard EN 1793-2. In both cases the single number rating for airborne sound insulation recommended by the European standard was calculated. The new method proved to be easy to use and reliable for all kinds of barriers. It has been found sensitive to quality of mounting, presence of seals, and other details typical of outdoor installations. The comparison between field and laboratory results shows a good correlation, while existing differences can be explained with the different sound fields and mounting conditions between the outdoor and laboratory tests. It is concluded that the Adrienne method is adequate for its intended use.