bluuebunny/crossref_metadata_2025 huggingface dataset:
Hyperbaric Oxygen Therapy for Radionecrosis of the Jaw: A Randomized, Placebo-Controlled, Double-Blind Trial From the ORN96 Study Group
Authors: Annane Djillali , Depondt Joël , Aubert Philippe , Villart Maryvonne , Géhanno Pierre , Gajdos Philippe , Chevret Sylvie
Published: November 2004

Purpose

To determine the efficacy and safety of hyperbaric oxygen therapy (HBO) for overt mandibular osteoradionecrosis.

Patients and Methods

This prospective, multicenter, randomized, double-blind, placebo-controlled trial was conducted at 12 university hospitals. Ambulatory adults with overt osteoradionecrosis of the mandible were assigned to receive 30 HBO exposures preoperatively at 2.4 absolute atmosphere for 90 minutes or a placebo, and 10 additional HBO dives postoperatively or a placebo. The main outcome measure was 1-year recovery rate from osteoradionecrosis. Secondary end points included time to treatment failure, time to pain relief, 1-year mortality rate, and treatment safety.

Results

At the time of the second interim analysis, based on the triangular test, the study was stopped for potentially worse outcomes in the HBO arm. A total of 68 patients were enrolled and analyzed. At 1 year, six (19%) of 31 patients had recovered in the HBO arm and 12 (32%) of 37 in the placebo arm (relative risk = 0.60; 95% CI, 0.25 to 1.41; P = .23). Time to treatment failure (hazard ratio = 1.33; 95% CI, 0.68 to 2.60; P = .41) and time to pain relief (hazard ratio = 1.00; 95% CI, 0.52 to 1.89; P = .99) were similar between the two treatment arms.

Conclusion

Patients with overt mandibular osteoradionecrosis did not benefit from hyperbaric oxygenation.
Mammalian GRIP domain proteins differ in their membrane binding properties and are recruited to distinct domains of the TGN
Authors: Derby Merran C. , van Vliet Catherine , Brown Darren , Luke Michael R. , Lu Lei , Hong Wanjin , Stow Jennifer L. , Gleeson Paul A.
Published: November 2004

The four mammalian golgins, p230/golgin-245, golgin-97, GCC88 and GCC185 are targeted to trans-Golgi network (TGN) membranes by their C-terminal GRIP domain in a G-protein-dependent process. The Arf-like GTPase, Arl1, has been shown to mediate TGN recruitment of p230/golgin245 and golgin-97 by interaction with their GRIP domains; however, it is not known whether all the TGN golgins bind to Arl1 and whether they are all recruited to the same or different TGN domains. Here we demonstrate differences in membrane binding properties and TGN domain recruitment of the mammalian GRIP domain proteins. Overexpression of full-length GCC185 resulted in the appearance of small punctate structures dispersed in the cytoplasm of transfected cells that were identified as membrane tubular structures by immunoelectron microscopy. The cytoplasmic GCC185-labelled structures were enriched for membrane binding determinants of GCC185 GRIP, whereas the three other mammalian GRIP family members did not colocalize with the GCC185-labelled structures. These GCC185-labelled structures included the TGN resident protein α2,6 sialyltransferase and excluded the recycling TGN protein, TGN46. The Golgi stack was unaffected by overexpression of GCC185. Overexpression of both full-length GCC185 and GCC88 showed distinct and nonoverlapping structures. We also show that the GRIP domains of GCC185 and GCC88 differ in membrane binding properties from each other and, in contrast to p230/golgin-245 and golgin-97, do not interact with Arl1 in vivo. Collectively these results show that GCC88, GCC185 and p230/golgin245 are recruited to functionally distinct domains of the TGN and are likely to be important for the maintenance of TGN subdomain structure, a critical feature for mediating protein sorting and membrane transport.
DNA replication licensing in somatic and germ cells
Authors: Eward Kathryn Leigh , Obermann Ellen C. , Shreeram S. , Loddo Marco , Fanshawe Thomas , Williams Craig , Jung Hyo-Il , Prevost A. Toby , Blow J. Julian , Stoeber Kai , Williams Gareth H.
Published: November 2004

The DNA replication (or origin) licensing system ensures precise duplication of the genome in each cell cycle and is a powerful regulator of cell proliferation in metazoa. Studies in yeast, Drosophila melanogaster and Xenopus laevis have characterised the molecular machinery that constitutes the licensing system, but it remains to be determined how this important evolutionary conserved pathway is regulated in Homo sapiens. We have investigated regulation of the origin licensing factors Cdc6, Cdt1, Mcm2 and Geminin in human somatic and germ cells. Cdc6 and Cdt1 play an essential role in DNA replication initiation by loading the Mcm2-7 complex, which is required for unwinding the DNA helix, onto chromosomal origins. Geminin is a repressor of origin licensing that blocks Mcm2-7 loading onto origins. Our studies demonstrate that Cdc6, Cdt1 and Mcm2 play a central role in coordinating growth during the proliferation-differentiation switch in somatic self-renewing systems and that Cdc6 expression is rate-limiting for acquisition of replication competence in primary oocytes. In striking contrast, we show that proliferation control during male gametogenesis is not linked to Cdc6 or Mcm2, but appears to be coordinated by the negative regulator Geminin with Cdt1 becoming rate-limiting in late prophase. Our data demonstrate a striking sexual dimorphism in the mechanisms repressing origin licensing and preventing untimely DNA synthesis during meiosis I, implicating a pivotal role for Geminin in maintaining integrity of the male germline genome.
GSK-3β inhibition/β-catenin stabilization in ventral midbrain precursors increases differentiation into dopamine neurons
Authors: Castelo-Branco Gonçalo , Rawal Nina , Arenas Ernest
Published: November 2004

Wnts are important regulators of dopamine (DA) neuron differentiation in the developing ventral mesencephalon and could thus serve as potential tools in the treatment of Parkinson's disease. In this study, we investigate whether established intracellular Wnt signalling components could modulate the development of DA neurons. Two chemical inhibitors of glycogen synthase kinase (GSK)-3β, indirubin-3-monoxime and kenpaullone, were found to increase neuronal differentiation in ventral mesencephalon precursor cultures. In addition, the GSK-3β-specific inhibitor kenpaullone increased the size of the DA neuron population through conversion of precursors expressing the orphan nuclear receptor-related factor 1 into tyrosine hydroxylase positive neurons, thereby mimicking an effect of Wnts. We show that GSK-3β inhibitors stabilized β-catenin and that overexpression of β-catenin in ventral mesencephalic precursors resulted in increased DA differentiation. The three- to fivefold increase in DA differentiation of precursor cells by GSK-3β inhibitors suggests that such compounds could be used to improve stem/precursor cell therapy approaches in Parkinson's disease.
Migration and retraction of endothelial and epithelial cells require PHI-1, a specific protein-phosphatase-1 inhibitor protein
Authors: Tountas Nikolaos A. , Brautigan David L.
Published: November 2004

Cell migration and retraction are interrelated activities that are crucial for a range of physiological processes such as wound healing and vascular permeability. Immunostaining of brain sections for the specific inhibitor of type-1 protein Ser/Thr phosphatase called PHI-1 showed high expression levels in smooth muscle and especially in vascular endothelial cells. During migration of cultured human lung microvascular endothelial cells, endogenous PHI-1 was concentrated to the trailing edge of the cells. Knockdown of PHI-1 using small interfering RNAs reduced by 45% the rate of HeLa cell migration in a wound-healing assay. These cells exhibited an extremely elongated phenotype relative to controls and time-lapse movies revealed a defect in retraction of the trailing edge. Both HeLa and human vascular endothelial cells depleted of PHI-1 showed increased surface areas relative to controls during cell spreading in a replating assay. Analysis of sequential microscopic images demonstrated this was due to a significant decrease in the number of retraction events, whereas protrusive action was unaffected. The Ser/Thr phosphorylation of several signaling, cytoskeletal and focal-adhesion proteins was unchanged in PHI-1-depleted cells, so the target of PHI-1 inhibited protein-phosphatase 1 remains unidentified. Nonetheless, the results show that PHI-1 participates in regulatory events at the trailing edge of migrating cells and modulates retraction of endothelial and epithelial cells.
Stress concentration factors for an eccentric circular hole in a finite-width strip or in a semi-infinite plate in tension
Authors: Wang Q. Z
Published: November 2004

An explicit expression for the largest stress concentration factor (SCF) for an eccentric circular hole in a finite-width strip under remote uniform tension is formulated by approximate stress analysis and asymptotic matching with two exact limit SCF values, which are given by Kirsch and Koiter for very small and large ratios of hole radius to strip half width respectively. The explicit expression of the largest SCF for the tension semi-infinite plate with a circular hole near the free straight boundary is obtained as a special case of the first problem. The accuracy of the proposed expressions is measured by (a) comparison with data of the SCF handbook and (b) comparison with the results from finite element analysis. Corrections for the values given by Jeffery and confirmation of Koiter's exact limit value when the circular hole is very near the free straight boundary are also obtained.
Limit load solutions for thin-walled cylinders with circumferential cracks under combined internal pressure, axial tension and bending
Authors: Lei Y , Budden P. J
Published: November 2004

Limit load solutions for thin-walled cylinders with circumferential cracks under combined axial tension, bending and pressure are developed, considering the effect of pressure-induced hoop stress via the Mises yield criterion. The new solutions cover thin-walled cylinders with constant-depth or semi-elliptical surface cracks and through-wall cracks. The predictions of the new Mises-based limit load equation agree very well with elastic-perfectly plastic finite element results. However, net-section collapse equations, which ignore the hoop stress in the cylinder, tend to over-estimate the limit load when internal pressure is dominant. The solution for constant-depth cracks without crack closure is proposed for inclusion in fitness-for-purpose assessment procedures for constant-depth or semi-elliptical surface cracks and through-wall cracks.
Relationship between orthographic‐motor integration and computer use for the production of creative and well‐structured written text
Authors: Christensen Carol A.
Published: November 2004

Background: Orthographic‐motor integration refers to the way in which orthographic knowledge is integrated with fine‐motor demands of handwriting. A strong relationship has shown to exist between orthographic‐motor integration and students' ability to produce creative and well‐structured written text (De La Paz & Graham, 1995). This relationship is thought to be due to the cognitive load resulting from lack of automaticity in orthographic‐motor integration so that writers do not have sufficient resources to accomplish the more demanding aspects of writing. Interventions to improve children's orthographic‐motor integration result in improved written text (Jones & Christensen, 1999).

Aim: This study first extended findings related to handwritten text to the relationship between typing and the length and quality of computer‐based written text. Second, it examined the efficacy of an intervention to develop proficiency in typing skills on the length and quality of students' written language.

Sample: Participants in the first study were 276 Grade 8 and 9 students. In the second study 35 students in Grades 8 and 9 who exhibited very low levels of proficiency in typing were the participants.

Methods: In Study 1, orthographic‐motor integration related to typing as well as handwriting was assessed for all students. They were asked to complete a piece of handwritten and computer‐based text. Students in the intervention study completed the same measures as Study 1, at pre‐ and post‐test. During the intervention half the students completed a daily typed journal and half completed a program designed to facilitate their typing skills.

Results: There was a significant relationship between orthographic‐motor integration — handwriting and the length and quality of handwritten text, and a stronger relationship between orthographic‐motor integration — typing and length and quality of computer‐based text. Both intervention groups in the second study showed significant differences in writing skills from pre‐ to post‐test. However, the typing skills group showed significantly better scores on typing and quality of typewritten text than the journal group at post‐test. The impact of the intervention was specific to typewritten text. There was no difference in length or quality of handwritten text.

Conclusion: It is suggested that developing proficiency in orthographic‐motor integration related to typing allows writers to employ their cognitive resources more flexibly when working on a computer, so that they can devote attention to higher‐order processes involved in ideation, syntactic and semantic monitoring and pragmatic awareness.
The British Journal of Psychology centenary: A preliminary content survey and its problems
Authors: Richards Graham
Published: November 2004

The preliminary findings are reported of a review of the contents of the British Journal of Psychology 1904–2003 undertaken to mark the journal's centenary. This identifies (a) the top 11 categories of paper published and their patterns of distribution, (b) an apparent change in the nature of papers published after 1983, (c) the overall pattern of category‐introduction, showing a dramatic change in 1965 and (d) a provisional typology of the principal patterns of distribution over time. Major conceptual and practical problems arising in the categorization of papers, and their implications, are discussed. Some reflections are offered on the possible value of research of this kind and on the nature of the journal itself.
Evidence for executive deficits among users of MDMA (Ecstasy)
Authors: Fisk John E. , Montgomery Catharine , Murphy Philip , Wareing Michelle
Published: November 2004

Random letter generation and computation span are tasks known to load on executive, prefrontal resources. Previous research suggests that Ecstasy users are impaired on random letter generation. The current study, employing a larger sample (44 current Ecstasy users, and 59 non‐Ecstasy users), together with more effective statistical controls for other drug use, failed to replicate previous findings. Ecstasy users were unimpaired on all measures of random generation performance. A significant difference was obtained on the computation span measure, with Ecstasy users scoring significantly lower than non‐Ecstasy users. This difference remained statistically significant following control for various indicators of the use of other drugs including cannabis. The results are discussed in terms of the potential effects that Ecstasy might have on different component executive processes.
Personality and coping: A context for examining celebrity worship and mental health
Authors: Maltby John , Day Liza , McCutcheon Lynn E. , Gillett Raphael , Houran James , Ashe Diane D.
Published: November 2004

The adaptational‐continuum model of personality and coping suggests a useful context for research areas that emphasize both personality and coping. The present paper used Ferguson's (2001) model integrating personality and coping factors to further conceptualize findings around celebrity worship. Three hundred and seventy‐two respondents completed measures of celebrity worship, personality, coping style, general health, stress, positive and negative affect and life satisfaction. Celebrity worship for intense‐personal reasons is associated with poorer mental heath and this relationship can be understood within the dimensions of neuroticism and a coping style that suggests disengagement. Such findings suggest the utility of examining the relationship between celebrity worship and mental health within both personality and coping variables, which have practical implications for understanding and addressing mental health problems that may occur as the result of engaging in celebrity worship for intense‐personal reasons.
Circuitry for Associative Plasticity in the Amygdala Involves Endocannabinoid Signaling
Authors: Azad Shahnaz C. , Monory Krisztina , Marsicano Giovanni , Cravatt Benjamin F. , Lutz Beat , Zieglgänsberger Walter , Rammes Gerhard
Published: November 2004

Endocannabinoids are crucial for the extinction of aversive memories, a process that considerably involves the amygdala. Here, we show that low-frequency stimulation of afferents in the lateral amygdala with 100 pulses at 1 Hz releases endocannabinoids postsynaptically from neurons of the basolateral amygdala of micein vitroand thereby induces a long-term depression of inhibitory GABAergic synaptic transmission (LTDi) via a presynaptic mechanism. Lowering inhibitory synaptic transmission significantly increases the amplitude of excitatory synaptic currents in principal neurons of the central nucleus, which is the main output site of the amygdala. LTDi involves a selective mGluR1 (metabotropic glutamate receptor 1)-mediated calcium-independent mechanism and the activation of the adenylyl cyclase-protein kinase A pathway. LTDi is abolished by the cannabinoid type 1 (CB1) receptor antagonist SR141716A and cannot be evoked in CB1 receptor-deficient animals. LTDi is significantly enhanced in mice lacking the anandamide-degrading enzyme fatty acid amide hydrolase. The present findings show for the first time that mGluR activation induces a retrograde endocannabinoid signaling via activation of the adenylyl cyclase-protein kinase A pathway and the release of anandamide. Furthermore, the results indicate that anandamide decreases the activity of inhibitory interneurons in the amygdala. This disinhibition increases the activity of common output neurons and could provide a prerequisite for extinction by formation of new memory.
Spiral Waves in Disinhibited Mammalian Neocortex
Authors: Huang Xiaoying , Troy William C. , Yang Qian , Ma Hongtao , Laing Carlo R. , Schiff Steven J. , Wu Jian-Young
Published: November 2004

Spiral waves are a basic feature of excitable systems. Although such waves have been observed in a variety of biological systems, they have not been observed in the mammalian cortex during neuronal activity. Here, we report stable rotating spiral waves in rat neocortical slices visualized by voltage-sensitive dye imaging. Tissue from the occipital cortex (visual) was sectioned parallel to cortical lamina to preserve horizontal connections in layers III-V (500-μm-thick, ∼4 × 6 mm2). In such tangential slices, excitation waves propagated in two dimensions during cholinergic oscillations. Spiral waves occurred spontaneously and alternated with plane, ring, and irregular waves. The rotation rate of the spirals was ∼10 turns per second, and the rotation was linked to the oscillations in a one-cycle- one-rotation manner. A small (<128 μm) phase singularity occurred at the center of the spirals, about which were observed oscillations of widely distributed phases. The phase singularity drifted slowly across the tissue (∼1 mm/10 turns). We introduced a computational model of a cortical layer that predicted and replicated many of the features of our experimental findings. We speculate that rotating spiral waves may provide a spatial framework to organize cortical oscillations.
Modulation of an Afterhyperpolarization by the Substantia Nigra Induces Pauses in the Tonic Firing of Striatal Cholinergic Interneurons
Authors: Reynolds John N. J. , Hyland Brian I. , Wickens Jeff R.
Published: November 2004

Striatal cholinergic interneurons, also known as tonically active neurons (TANs), acquire a pause in firing during learning of stimulus-reward associations. This pause response to a sensory stimulus emerges after repeated pairing with a reward. The conditioned pause is dependent on dopamine from the substantia nigra, but its underlying cellular mechanism is unknown. Usingin vivointracellular recording, we found that both subthreshold and suprathreshold depolarizations in cholinergic interneurons induced a prolonged after-hyperpolarization (AHP) associated with a pause in their tonic firing. The AHP duration was dependent on the level of depolarization, whether elicited by intracellular current injection or by activation of excitatory inputs from the cortex. High-frequency stimulation of the substantia nigra induced potentiation of the cortically evoked excitation and increased the prolonged AHP after the stimulus. These findings from anesthetized animals suggest that a substantia nigra-induced AHP produces stimulus-associated firing pauses in cholinergic interneurons. This mechanism may underlie the acquisition of the pause response in TANs recorded from behaving animals during learning.
Caspase-7 Expanded Function and Intrinsic Expression Level Underlies Strain-Specific Brain Phenotype ofCaspase-3-Null Mice
Authors: Houde Caroline , Banks Kathleen G. , Coulombe Nathalie , Rasper Dita , Grimm Erich , Roy Sophie , Simpson Elizabeth M. , Nicholson Donald W.
Published: November 2004

Caspase-3-deficient mice of the 129S1/SvImJ (129) strain show severe brain development defects resulting in brain overgrowth and perinatal lethality, whereas on the C57BL/6J (B6) background, these mice develop normally. We therefore sought to identify the strain-dependent ameliorating gene. We biochemically isolated caspase-7 from B6-caspase-3-null (Casp3-/-) tissues as being the enzyme with caspase-3-like properties and capability of performing a caspase-3 surrogate function, apoptotic DNA fragmentation. Moreover, we show that, in contrast to the human enzymes, mouse caspase-7 is as efficient as caspase-3 at cleaving and thus inactivating ICAD (inhibitor of caspase-activated DNase), the inhibitor of apoptotic DNA fragmentation. Low levels of caspase-7 expression and activation correlate with lack of DNA fragmentation in 129-Casp3-/-apoptotic precursor neurons, whereas B6-Casp3-/-cells, which can fragment their DNA, show higher levels of caspase-7 expression and activation. The amount of caspase-7 activation in apoptotic precursor neurons is independent of the presence of caspase-3. Together, our findings demonstrate for the first time a strong correlation between caspase-7 activity, normal brain development, and apoptotic DNA fragmentation inCasp3-/-mice.
Deletion of N-Type Calcium Channels Alters Ethanol Reward and Reduces Ethanol Consumption in Mice
Authors: Newton Philip M. , Orr Christine J. , Wallace Melisa J. , Kim Chanki , Shin Hee-Sup , Messing Robert O.
Published: November 2004

N-type calcium channels are modulated by acute and chronic ethanol exposurein vitroat concentrations known to affect humans, but it is not known whether N-type channels are important for behavioral responses to ethanolin vivo. Here, we show that in mice lacking functional N-type calcium channels, voluntary ethanol consumption is reduced and place preference is developed only at a low dose of ethanol. The hypnotic effects of ethanol are also substantially diminished, whereas ethanol-induced ataxia is mildly increased. These results demonstrate that N-type calcium channels modulate acute responses to ethanol and are important mediators of ethanol reward and preference.
On the Effect of Fluctuating Recombination Rates on the Decorrelation of Gene Histories in the Human Genome
Authors: Eriksson A , Mehlig B
Published: November 2004

We show how to incorporate fluctuations of the recombination rate along the chromosome into standard gene-genealogical models for the decorrelation of gene histories. This enables us to determine how small-scale fluctuations (Poissonian hot-spot model) and large-scale variations (Konget al. 2002) of the recombination rate influence this decorrelation. We find that the empirically determined large-scale variations of the recombination rate give rise to a significantly slower decay of correlations compared to the standard, unstructured gene-genealogical model assuming constant recombination rate. A model with long-range recombination-rate variations and with demographic structure (divergent population) is found to be consistent with the empirically observed slow decorrelation of gene histories. Conversely, we show that small-scale recombination-rate fluctuations do not alter the large-scale decorrelation of gene histories.
Distribution of Activator (Ac) Throughout the Maize Genome for Use in Regional MutagenesisSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AY559172, AY559173, AY559174, AY559175, AY559176, AY559177, AY559178, AY559179, AY559180, AY559181, AY559182, AY559183, AY559184, AY559185, AY559186, AY559187, AY559188, AY559189, AY559190, AY559191, AY559192, AY559193, AY559194, AY559195, AY559196, AY559197, AY559198, AY559199, AY559200, AY559201, AY559202, AY559203, AY559204, AY559205, AY559206, AY559207, AY559208, AY559209, AY559210, AY559211, AY559212, AY559213, AY559214, AY559215, AY559216, AY559217, AY559218, AY559219, AY559220, AY559221, AY559223, AY559224, AY559225, AY559226, AY559227, AY559228, AY559229, AY559230, AY559231, AY559232, AY559233, AY559234, and AY618471, AY618472, AY618473, AY618474, AY618475, AY618476, AY618477, AY618478, AY618479.
Authors: Kolkman Judith M , Conrad Liza J , Farmer Phyllis R , Hardeman Kristine , Ahern Kevin R , Lewis Paul E , Sawers Ruairidh J H , Lebejko Sara , Chomet Paul , Brutnell Thomas P
Published: November 2004

A collection of Activator (Ac)-containing, near-isogenic W22 inbred lines has been generated for use in regional mutagenesis experiments. Each line is homozygous for a single, precisely positioned Ac element and the Ds reporter, r1-sc:m3. Through classical and molecular genetic techniques, 158 transposed Ac elements (tr-Acs) were distributed throughout the maize genome and 41 were precisely placed on the linkage map utilizing multiple recombinant inbred populations. Several PCR techniques were utilized to amplify DNA fragments flanking tr-Ac insertions up to 8 kb in length. Sequencing and database searches of flanking DNA revealed that the majority of insertions are in hypomethylated, low- or single-copy sequences, indicating an insertion site preference for genic sequences in the genome. However, a number of Ac transposition events were to highly repetitive sequences in the genome. We present evidence that suggests Ac expression is regulated by genomic context resulting in subtle variations in Ac-mediated excision patterns. These tr-Ac lines can be utilized to isolate genes with unknown function, to conduct fine-scale genetic mapping experiments, and to generate novel allelic diversity in applied breeding programs.
Drosophila Su(Hw) Insulator Can Stimulate Transcription of a Weakened yellow Promoter Over a Distance
Authors: Golovnin Anton , Melnick Elena , Mazur Alexander , Georgiev Pavel
Published: November 2004

The insulator element from the gypsy transposon is a DNA sequence that blocks activation of a promoter by a transcriptional enhancer when placed between them. The insulator contains reiterated binding sites for the Suppressor of Hairy-wing [Su(Hw)] zinc-finger protein. A protein encoded by another gene, modifier of mdg4 [mod(mdg4)], is also required for the enhancer-blocking activity of the Su(Hw) insulator. Here we present evidence that the Su(Hw) insulator activates a weakened yellow promoter at a distance. Deletion of the upstream promoter region (UPR), located close by the TATA box, significantly reduces yellow expression. The Su(Hw) insulator placed at different positions relative to the yellow promoter partially compensates for loss of the UPR. Su(Hw) is able to stimulate yellow expression even if it is located at a 5-kb distance from the promoter. The stimulatory activity depends on the number of Su(Hw)-binding sites. Mutational analysis demonstrates that only the DNA-binding domain and adjacent regions of the Su(Hw) protein are required for stimulation of yellow transcription.
The Relative Roles in Vivo of Saccharomyces cerevisiae Pol η, Pol ζ, Rev1 Protein and Pol32 in the Bypass and Mutation Induction of an Abasic Site, T-T (6-4) Photoadduct and T-T cis-syn Cyclobutane Dimer
Authors: Gibbs Peter E M , McDonald John , Woodgate Roger , Lawrence Christopher W
Published: November 2004

We have investigated the relative roles in vivo of Saccharomyces cerevisiae DNA polymerase η, DNA polymerase ζ, Rev1 protein, and the DNA polymerase δ subunit, Pol32, in the bypass of an abasic site, T-T (6-4) photoadduct and T-T cis-syn cyclobutane dimer, by transforming strains deleted for RAD30, REV3, REV1, or POL32 with duplex plasmids carrying one of these DNA lesions located within a 28-nucleotide single-stranded region. DNA polymerase η was found to be involved only rarely in the bypass of the T-T (6-4) photoadduct or the abasic sites in the sequence context used, although, as expected, it was solely responsible for the bypass of the T-T dimer. We argue that DNA polymerase ζ, rather than DNA polymerase δ as previously suggested, is responsible for insertion in bypass events other than those in which polymerase η performs this function. However, DNA polymerase δ is involved indirectly in mutagenesis, since the strain lacking its Pol32 subunit, known to be deficient in mutagenesis, shows as little bypass of the T-T (6-4) photoadduct or the abasic sites as those deficient in Pol ζ or Rev1. In contrast, bypass of the T-T dimer in the pol32Δ strain occurs at the wild-type frequency.
Catalytic Promiscuity in Biocatalysis: Using Old Enzymes to Form New Bonds and Follow New Pathways
Authors: Bornscheuer Uwe T. , Kazlauskas Romas J.
Published: November 2004

Biocatalysis has expanded rapidly in the last decades with the discoveries of highly stereoselective enzymes with broad substrate specificity. A new frontier for biocatalysis is broad reaction specificity, where enzymes catalyze alternate reactions. Although often underappreciated, catalytic promiscuity has a natural role in evolution and occasionally in the biosynthesis of secondary metabolites. Examples of catalytic promiscuity with current or potential applications in synthesis are reviewed here. Combined with protein engineering, the catalytic promiscuity of enzymes may broadly extend their usefulness in organic synthesis.
On optimal regularity of free boundary problems and a conjecture of De Giorgi
Authors: Koch Herbert , Leoni Giovanni , Morini Massimiliano
Published: November 2004

We present a general theory to study optimal regularity for a large class of nonlinear elliptic systems satisfying general boundary conditions and in the presence of a geometric transmission condition on the free boundary. As an application we give a full positive answer to a conjecture of De Giorgi on the analyticity of local minimizers of the Mumford‐Shah functional. © 2004 Wiley Periodicals, Inc.
ATP‐induced structural change of dephosphocoenzyme A kinase from Thermus thermophilus HB8
Authors: Seto Azusa , Murayama Kazutaka , Toyama Mitsutoshi , Ebihara Akio , Nakagawa Noriko , Kuramitsu Seiki , Shirouzu Mikako , Yokoyama Shigeyuki
Published: November 2004

Dephosphocoenzyme A kinase (DCK) catalyzes phosphorylation in the final step of coenzyme A (CoA) biosynthesis. In this phosphorylation process, domain movements play a very important role. To reveal the structural changes induced by ligand binding, we determined the crystal structure of DCK from Thermus thermophilus HB8 by the multiwavelength anomalous dispersion method at 2.8 Å. The crystal structure includes three independent protein molecules in the asymmetric unit: One is a liganded form and the others are unliganded. The topology shows a canonical nucleotide‐binding protein possessing the P‐loop motif. A structure homology search by DALI revealed the similarity of the DCKs from T. thermophilus HB8, Haemophilus influenzae, and Escherichia coli. Structural comparisons between the liganded and unliganded forms of DCK from T. thermophilus HB8 indicated domain movements induced by adenosine triphosphate (ATP) binding. For the domain movements, proline residues confer flexibility at the domain linkages. In particular, Pro91 plays an important role in moving the CoA domain. Proteins 2005. © 2004 Wiley‐Liss, Inc.
Anchor profiles of HLA‐specific peptides: Analysis by a novel affinity scoring method and experimental validation
Authors: Desmet Johan , Meersseman Geert , Boutonnet Nathalie , Pletinckx Jurgen , De Clercq Krista , Debulpaep Maja , Braeckman Tessa , Lasters Ignace
Published: November 2004

The study of intermolecular interactions is a fundamental research subject in biology. Here we report on the development of a quantitative structure‐based affinity scoring method for peptide–protein complexes, named PepScope. The method operates on the basis of a highly specific force field function (CHARMM) that is applied to all‐atom structural representations of peptide–receptor complexes. Peptide side‐chain contributions to total affinity are scored after detailed rotameric sampling followed by controlled energy refinement. A de novo approach to estimate dehydration energies was developed, based on the simulation of individual amino acids in a solvent box filled with explicit water molecules. Transferability of the method was demonstrated by its application to the hydrophobic HLA‐A2 and ‐A24 receptors, the polar HLA‐A1, and the sterically ruled HLA‐B7 receptor. A combined theoretical and experimental study on 39 anchor substitutions in FxSKQYMTx/HLA‐A2 and ‐A24 complexes indicated a prediction accuracy of about two thirds of a log‐unit in Kd. Analysis of free energy contributions identified a great role of desolvation and conformational strain effects in establishing a given specificity profile. Interestingly, the method rightly predicted that most anchor profiles are less specific than so far assumed. This suggests that many potential T‐cell epitopes could be missed with current prediction methods. The results presented in this work may therefore significantly affect T‐cell epitope discovery programs applied in the field of peptide vaccine development. Proteins 2005. © 2004 Wiley‐Liss, Inc.
Silicon‐based light emitting diode material studied under high pressure
Authors: Prins A. D. , Ishibashi Y. , Sasahara S. , Nakahara J. , Lourenco M. A. , Gwilliam R. M. , Kobayashi T. , Nagata A. , Homewood K. P.
Published: November 2004

The influence of pressure up to around 30 kbar on the photoluminescence (PL) of material from a silicon light‐emitting diode (LED) that operates efficiently at room temperature is reported for the first time. The observed PL peak at 1140 nm shifts to lower energy at a rate of –1.4 ± 0.1 meV/kbar. The value of this shift agrees with earlier absorption measurements on the indirect band‐gap of silicon, confirming that the emission is closely related to this transition. This peak shows an increase in intensity from low to room temperature and peak position temperature results are compared to other sources. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Dual apoptotic effect of Xrel3 c‐Rel/NF‐κB homolog in human cervical cancer cells
Authors: Shehata Marlene , Shehata Marian , Shehata Fady , Pater Alan
Published: November 2004

Cervical cancer is one of the most common cancers affecting a woman's reproductive organs. Despite its frequency and recurrence, the death rate has been declining over the past 40 years, due to early detection and treatment. In a previous report [Shehata Marlene, Shehata Marian, Shehata Fady, Pater Alan. Apoptosis effects of Xrel3 c‐Rel/Nuclear factor‐kappa B homolog in human cervical cancer cells. Cell Biology International, in press], we studied the role of the NF‐κB gene family in HeLa human cervical cancer cells, using the Xrel3 c‐Rel homologue of Xenopus laevis. These results showed that the expression of Xrel3/c‐Rel slowed cell growth, consistent with an upregulated expression of the cell cycle inhibitor p21 and the activated poly(ADP‐ribose) polymerase (PARP) apoptosis effector. However, in this report, we examined more apoptotic and anti‐apoptotic factors acting upstream and downstream in apoptosis pathways after cisplatin treatment of HeLa cervical cancer cells. After 1 μM cisplatin treatment, Xrel3 had an anti‐apoptotic effect, based on significantly lower levels of apoptotic proteins, including caspase‐8, caspase‐3 and p21. Anti‐apoptotic BAG‐1 isoforms were upregulated. After 5 μM cisplatin treatment, expression of HeLa Xrel3 had an apoptotic effect, based on significantly increased expression of the cell cycle inhibitor p21 and apoptotic proteins, including cleaved PARP, caspase‐8, and caspase‐3. However, anti‐apoptotic Bcl‐2 and Bcl‐XL were elevated and the cell cycle regulator cyclin D1 was slightly upregulated with both 1 and 5 μM cisplatin treatment. The HPV E6 oncoprotein showed no significant changes. These results support previous conclusions on the potential anti‐apoptotic effects of c‐Rel/NF‐κB in mild stress environments, as opposed to the apoptotic effects associated with high stress conditions [Lake BB, Ford R, Kao KR. Xrel3 is required for head development in Xenopus laevis. Development 2001; 128(2), 263–73.]. Thus, c‐Rel/NF‐κB may potentially be of clinical significance in chemotherapy.
Efficient service location design in government services
Authors: Narasimhan Ram , Talluri Srinivas , Sarkis Joseph , Ross Anthony
Published: November 2004

This paper presents a decision support system for efficient service location design for an agency in the State of Michigan. We consider a total of 169 branch offices of the agency located in 79 counties that process a variety of transactions and provide services including automobile registrations, issuance of driver licenses, recreational vehicle registration, and personal identification registry. The proposed methodology and decision support system incorporate a number of factors such as branch office efficiencies based on multiple measures, budget restrictions, capacity limitations for processing transactions, and demand requirements in designing an efficient service system. Our approach employs data envelopment analysis (DEA) and mixed‐integer programming (MIP) models. A series of experiments are conducted with the proposed model by varying the levels of system‐wide efficiency, resource reallocation, and budget in generating a set of decisions that executive management of the agency can implement. In addition, we investigate service channel management issues that the agency is currently facing in providing the services by web, phone, facsimile, and mail in addition to branch offices. We discuss how the branch closures influence channel management decisions.
The effects of internal versus external integration practices on time‐based performance and overall firm performance
Authors: Droge Cornelia , Jayaram Jayanth , Vickery Shawnee K.
Published: November 2004

This paper examines the effects of integration practices on time‐based performance and on overall firm performance (financial and market share). Integration practices are grouped into two categories: (1) external strategic design integration, which reaches across firm boundaries to involve suppliers and customers and (2) internal design‐process integration, which comprises more tactically oriented, integration practices that match design requirements and process capabilities. First, regression results show that both internal and external integration are related to time‐based performance, which in turn is related to firm performance. Thus, two indirect routes to firm performance are identified. Second, hierarchical regression reveals that integration directly affects firm performance even after time‐based performance is accounted for. Finally, we found that the interaction of internal and external integration is significantly related to both market share and financial performance (after controlling for all other effects). This latter result suggests that the joint use of external and internal integration practices has a synergistic effect on firm performance.
‘The Hand That Stirs the Pot Can Also Run the Country’: electing women to parliament in Namibia
Authors: Bauer Gretchen
Published: November 2004

In early 2004, 29% of Namibian Members of Parliament were women, putting Namibia fourth in continental Africa and seventeenth worldwide in terms of women's representation in a national legislature. This article sets out to determine how such a high percentage of women has been elected to the National Assembly in Namibia since independence. It suggests that electoral gains have been achieved through a combination of factors: the use of a closed list proportional representation electoral system and voluntary quotas on the part of political parties at the national level, sustained pressure over the past three to five years from a nascent women's movement influenced by the global women's movement, and the active participation of women inside and outside the country in a protracted and violent struggle for independence that was only attained in 1990. The first two factors confirm past experience and accumulated knowledge on the significance of choice of electoral system and use of quotas, and the importance of women's organisations to elected women's legislative agendas and success. The last factor deviates from experience, and from a literature that suggests that women's active participation in political struggles has not always translated into tangible gains for women.
Cotonou's Klondike: African traders and second-hand car markets in Bénin
Authors: Beuving J. Joost
Published: November 2004

This article addresses the theme of entrepreneurship in Africa by focusing on second-hand car markets in Cotonou, Bénin. At first glance this booming business seems to confirm neo-liberal and institutional models of entrepreneurship, in which entrepreneurial behaviour constitutes rational calculation in a situation of economic opportunity. The universe in which African car traders operate, however, is characterised by significant capital scarcity, dramatic losses and widespread bankruptcies. The article argues that viewing entrepreneurs as economic calculators is not the proper way to understand the Cotonou car trade. Based on case analysis of a Béninese car trader, it shows that the outcome of car trading in Cotonou is determined by the manipulation of social contacts, characterised by self-interest and distrust among business partners. Analogous to the Klondike gold rush, it appears that the car trader's engagement with the trade is to a large extent motivated by the dream of making a fortune. Thus, even though entrepreneurial failure is widespread among African car traders, most of them remain convinced that car trading can yield significant profits.
Three-Dimensional Imaging ofToxoplasma gondii–Host Cell Interactions within the Parasitophorous Vacuole
Authors: Schatten Heide , Ris Hans
Published: November 2004

The protozoan parasiteToxoplasma gondiiis a representative of apicomplexan parasites that invades host cells through an unconventional motility mechanism. During host cell invasion it forms a specialized membrane-surrounded compartment that is called the parasitophorous vacuole. The interactions between the host cell and parasite membranes are complex and recent studies have revealed in more detail that both the host cell and the parasite membrane contribute to the formation of the parasitophorous vacuole. By using our a new specimen preparation technique that allows three-dimensional imaging of thick-sectioned internal cell structures with high-resolution, low-voltage field emission scanning electron microscopy, we were able to visualize continuous structural interactions of the host cell membrane with the parasite within the parasitophorous vacuole. Fibrous and tubular material extends from the host cell membrane and is connected to parasite membrane components. Shorter protrusions are also elaborated from the parasite. Several of these shorter fine protrusions connect to the fibrous material of the host cell membrane. The elaborate network may be used for modifications of the parasitophorous vacuole membrane that will allow utilization of nutrients from the host cell by the parisite while it is being protected from host cell attacks. The structural interactions between parasite and host cells undergo time-dependent changes, and a fission pore is the most prominent structure left connecting the parasite with the host cell. The fission pore is anchored in the host cell by thick structural components of unknown nature. The new information gained with this technique includes structural details of fibrous and tubular material that is continuous between the parasite and host cell and can be imaged in three dimensions. We present this technique as a tool to investigate more fully the complex structural interactions of the host cell and the parasite residing in the parasitophorous vacuole.
Trichomonads under Microscopy
Authors: Benchimol Marlene
Published: November 2004

Trichomonads are flagellate protists, and among themTrichomonas vaginalisandTritrichomonas foetusare the most studied because they are parasites of the urogenital tract of humans and cattle, respectively. Microscopy provides new insights into the cell biology and morphology of these parasites, and thus allows better understanding of the main aspects of their physiology. Here, we review the ultrastructure ofT. foetusandT. vaginalis, stressing the participation of the axostyle in the process of cell division and showing that the pseudocyst may be a new form in the trichomonad cell cycle and not simply a degenerative form. Other organelles, such as the Golgi and hydrogenosomes, are also reviewed. The virus present in trichomonads is discussed.
Three-Dimensional Ultrastructure of the Ring Stage ofPlasmodium falciparum: Evidence for Export Pathways
Authors: Bannister Lawrence Howard , Hopkins John Mervyn , Margos Gabriele , Dluzewski Anton Richard , Mitchell Graham Howard
Published: November 2004

The three-dimensional structure of thePlasmodium falciparumring stage has been explored by reconstruction from serial sections and stereoscopic examination of tilted sections. The ring-like light microscopic appearance is related to the shape and contents of the biconcave discoidal parasite at this stage, its thick perimeter containing most of the ribosomes and its thin center containing smooth membrane organelles. The shapes of rings vary between flat and curved cuplike forms. The rough endoplasmic reticulum is a branched network continuous with the nuclear envelope. Evidence for a simple Golgi complex is seen in the presence on the outer nuclear envelope of a locus of coated vesicle budding associated with a single membranous cisterna or cluster of smooth vesicles. In middle and late stage rings this complex migrates along an extension of the nuclear envelope continuous with the rough endoplasmic reticulum. Evidence is also presented for a mechanism of exporting membrane from the parasite into the parasitophorous vacuole membrane and beyond into the red blood cell, by means of double-membraned vesicle-based exocytosis.