bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of a tightly controlled promoter of the halophilic archaeon Haloferax volcanii and its use in the analysis of the essential cct1 gene
Authors: Large Andrew , Stamme Claudia , Lange Christian , Duan Zhenhong , Allers Thorsten , Soppa Jörg , Lund Peter A. 
Published: October 2007

SummaryA system where archaeal gene expression could be controlled by simple manipulation of growth conditions would enable the construction of conditional lethal mutants in essential genes, and permit the controlled overproduction of proteins in their native host. As tools for the genetic manipulation of Haloferax volcanii are well developed, we set out to identify promoters with a wide dynamic range of expression in this organism. Tryptophan is the most costly amino acid for the cell to make, so we reasoned that tryptophan‐regulated promoters might be good candidates. Microarray analysis of H. volcanii gene expression in the presence and absence of tryptophan identified a tryptophanase gene (tna) that showed strong induction in the presence of tryptophan. qRT‐PCR revealed a very fast response and an up to 100‐fold induction after tryptophan addition. This result has been confirmed using three independent reporter genes (cct1, pyrE2 and bgaH). Vectors containing this promoter will be very useful for investigating gene function in H. volcanii and potentially in other halophilic archaea. To demonstrate this, we used the promoter to follow the consequences of depletion of the essential chaperonin protein CCT1, and to determine the ability of heterologous CCT proteins to function in H. volcanii.
Individual chitin synthase enzymes synthesize microfibrils of differing structure at specific locations in the Candida albicans cell wall
Authors: Lenardon Megan D. , Whitton Rhian K. , Munro Carol A. , Marshall Deborah , Gow Neil A. R. 
Published: October 2007

SummaryThe shape and integrity of fungal cells is dependent on the skeletal polysaccharides in their cell walls of which β(1,3)‐glucan and chitin are of principle importance. The human pathogenic fungus Candida albicans has four genes, CHS1, CHS2, CHS3 and CHS8, which encode chitin synthase isoenzymes with different biochemical properties and physiological functions. Analysis of the morphology of chitin in cell wall ghosts revealed two distinct forms of chitin microfibrils: short microcrystalline rodlets that comprised the bulk of the cell wall; and a network of longer interlaced microfibrils in the bud scars and primary septa. Analysis of chitin ghosts of chs mutant strains by shadow‐cast transmission electron microscopy showed that the long‐chitin microfibrils were absent in chs8 mutants and the short‐chitin rodlets were absent in chs3 mutants. The inferred site of chitin microfibril synthesis of these Chs enzymes was corroborated by their localization determined in Chsp–YFP‐expressing strains. These results suggest that Chs8p synthesizes the long‐chitin microfibrils, and Chs3p synthesizes the short‐chitin rodlets at the same cellular location. Therefore the architecture of the chitin skeleton of C. albicans is shaped by the action of more than one chitin synthase at the site of cell wall synthesis.
A small non‐coding RNA of the invasion gene island (SPI‐1) represses outer membrane protein synthesis from the Salmonella core genome
Authors: Pfeiffer Verena , Sittka Alexandra , Tomer Raju , Tedin Karsten , Brinkmann Volker , Vogel Jörg 
Published: October 2007

SummaryThe Salmonella pathogenicity island (SPI‐1) encodes ∼35 proteins involved in assembly of a type III secretion system (T3SS) which endows Salmonella with the ability to invade eukaryotic cells. We have discovered a novel SPI‐1 gene, invR, which expresses an abundant small non‐coding RNA (sRNA). The invR gene, which we identified in a global search for new Salmonella sRNA genes, is activated by the major SPI‐1 transcription factor, HilD, under conditions that favour host cell invasion. The RNA chaperone, Hfq, is essential for the in vivo stability of the ∼80 nt InvR RNA. Hfq binds InvR with high affinity in vitro, and InvR co‐immunoprecipitates with FLAG epitope‐tagged Hfq in Salmonella extracts. Surprisingly, deletion/overexpression of invR revealed no phenotype in SPI‐1 regulation. In contrast, we find that InvR represses the synthesis of the abundant OmpD porin encoded by the Salmonella core genome. As invR is conserved in the early branching Salmonella bongori, we speculate that porin repression by InvR may have aided successful establishment of the SPI‐1 T3SS after horizontal acquisition in the Salmonella lineage. This study identifies the first regulatory RNA of an enterobacterial pathogenicity island, and new roles for Hfq and HilD in SPI‐1 gene expression.
Fine mapping study in Scandinavian families suggests association between coeliac disease and haplotypes in chromosome region 5q32
Authors: Adamovic S. , Amundsen S. S. , Lie B. A. , Hellqvist Å. , Gudjónsdóttir A. H. , Ek J. , Nilsson S. , Wahlström J. , Ascher H. , Sollid L. M. , Naluai Å. T. 
Published: October 2007

AbstractThe previous genome‐wide scan in Scandinavian families supported earlier evidence for linkage of a region on chromosome 5 (5q31–33) to coeliac disease. This study deals with further genetic mapping of an 18 cM region, spanning from marker GAh18A (131.87 Mb) to D5S640 (149.96 Mb). Linkage and association analyses were performed in a two‐step approach. First, seven microsatellites were added. Strong evidence for linkage was obtained with a Zlr score of 3.96, Pnc = 4 × 10−5 at marker D5S436. The strongest association was with a haplotype consisting of the markers D5S2033 and D5S2490 (Pnc < 0.001). In the second step, we added 17 microsatellites and 69 single nucleotide polymorphisms (SNPs) to the analysis. These markers were located close to or within candidate genes across the region of approximately 7 Mb beneath the linkage peak marked by D5S2017 and D5S812. A substantial increase of the linkage signal with a maximum Zlr score of 4.6 at marker rs1972644 (Pnc = 2 × 10−6) was obtained and several SNPs showed association. Seven SNPs that individually showed the strongest association were genotyped in a second independent family sample set (225 trios). In the trio family sample as well as in the multiplex family sample, the strongest association was found with SNPs within the region flanked by the associated microsatellites D5S2033 and D5S2490 at 5q32.
SNP mapping and candidate gene sequencing in the class I region of the HLA complex: searching for multiple sclerosis susceptibility genes in Tasmanians
Authors: Burfoot R. K. , Jensen C. J. , Field J. , Stankovich J. , Varney M. D. , Johnson L. J. , Butzkueven H. , Booth D. , Bahlo M. , Tait B. D. , Taylor B. V. , Speed T. P. , Heard R. , Stewart G. J. , Foote S. J. , Kilpatrick T. J. , Rubio J. P. 
Published: October 2007

AbstractThis study is an extension to previously published work that has linked variation in the human leukocyte antigen (HLA) class I region with susceptibility to multiple sclerosis (MS) in Australians from the Island State of Tasmania. Single nucleotide polymorphism (SNP) mapping was performed on an 865‐kb candidate region (D6S1683–D6S265) in 166 Tasmanian MS families, and seven candidate genes [ubiquitin D (UBD), olfactory receptor 2H3 (OR2H3), gamma‐aminobutyric acid B receptor 1 (GABBR1), myelin oligodendrocyte glycoprotein (MOG), HLA‐F, HLA complex group 4 (HCG4) and HLA‐G] were resequenced. SNPs tagging the extended MS susceptibility haplotype were genotyped in an independent sample of 356 Australian MS trios and SNPs in the MOG gene were significantly over‐transmitted to MS cases. We identified significant effects on MS susceptibility of HLA‐A*2 (OR: 0.51; P = 0.05) and A*3 (OR: 2.85; P = 0.005), and two coding polymorphisms in the MOG gene (V145I: P = 0.01, OR: 2.2; V142L: P = 0.04, OR: 0.45) after full conditioning on HLA‐DRB1. We have therefore identified plausible candidates for the causal MS susceptibility allele, and although not conclusive at this stage, our data provide suggestive evidence for multiple class I MS susceptibility genes.
HLA‐DPB1 polymorphism in Blang and Puyi ethnic groups of Southwest China inferred from sequence‐based typing
Authors: Wang B. , Hu W. , Wang J. , Li S. , Yu H. , Tang W. , Tan S. , Shou W. , Zhang J. , Xiao C. 
Published: October 2007

AbstractIn the present study, DNA typing for HLA‐DPB1 was performed using polymerase chain reaction (PCR)–sequence‐based typing method in two isolated Chinese populations: the Blangs (n = 94) in Shuangjiang County and the Puyis (n = 76) in Luoping County from Yunnan province of Southwest China. These two populations exhibited certain similarity in their allelic distributions of the HLA‐DPB1 gene. A total of 11 and 12 alleles at the DPB1 locus were found in the Blang and Puyi groups, respectively. In the Blang group, the most frequent alleles were DPB1*0501 (51.0%) and DPB1*1301 (17.0%). DPB1*030101 was also common with a frequency of 6.4%. In the Puyi group, the most frequent allele was also DPB1*0501 with a frequency of 47.5%, followed by DPB1*1301 (21.1%). Two alleles DPB1*2101 and DPB1*0202 followed, with frequencies ranging between 5% and 8%. The alleles DPB1*4101, DPB1*3301, DPB1*6801 and DPB1*8401 were found for the first time in Chinese populations. A dendrogram constructed by neighbor‐joining method showed that the Blang and Puyi ethnic minorities, which had the closest relationship belonged to the southern Chinese.
Monocular deprivation enhances the nuclear signalling of extracellular signal‐regulated kinase in the developing visual cortex
Authors: Takamura Hironori , Ichisaka Satoshi , Hayashi Chihiro , Maki Hirotoshi , Hata Yoshio 
Published: October 2007

AbstractMonocular deprivation (MD) of vision leads to a loss of cortical response to the deprived eye in the early postnatal period (ocular dominance plasticity). The activity of several signal molecules, including extracellular signal‐regulated kinase (ERK), has been reported as playing a crucial role in the ocular dominance plasticity. Although pharmacological inhibition of ERK disturbed the ocular dominance plasticity, it remains to be elucidated how the ERK activity is modulated by MD. We herein report the effects of MD on ERK activation in the visual cortex of young and adult rats. Phosphorylated ERK (pERK)‐immunopositive cells are mainly distributed in layers II/III of the visual cortex. Following MD, we found a significant decrease in the density of pERK‐immunopositive cells in the cortex receiving deprived‐eye inputs in both young and adult animals. The amount of pERK protein also decreased in the input‐deprived cortex as revealed by Western blotting. Regarding the subcellular localization of pERK, we found a significant increase in the pERK‐immunopositive nucleus following MD in young animals. In these animals, the amount of pERK protein in the nuclear fraction of cortical tissue was significantly increased. No up‐regulation of the nuclear pERK was observed in adults or following binocular deprivation. These findings suggest that ERK activation may therefore be regulated by different mechanisms between young and adult animals, and MD during the developing period may thus specifically up‐regulate the nuclear signalling of ERK.
Temporal profile of circadian clock gene expression in a transplanted suprachiasmatic nucleus and peripheral tissues
Authors: Sujino Mitsugu , Nagano Mamoru , Fujioka Atsuko , Shigeyoshi Yasufumi , Inouye Shin‐Ichi T. 
Published: October 2007

AbstractThe mammalian hypothalamic suprachiasmatic nucleus (SCN) is the master oscillator that regulates the circadian rhythms of the peripheral oscillators. Previous studies have demonstrated that the transplantation of embryonic SCN tissues into SCN‐lesioned arrhythmic mice restores the behavioral circadian rhythms of these animals. In our present study, we examined the clock gene expression profiles in a transplanted SCN and peripheral tissues, and also analysed the circadian rhythm of the locomotor activity in SCN‐grafted mice. These experiments were undertaken to elucidate whether the transplanted SCN generates a dynamic circadian oscillation and maintains the phase relationships that can be detected in intact mice. The grafted SCN indeed showed dynamic circadian expression rhythms of clock genes such as mPeriod1 (mPer1) and mPeriod2 (mPer2). Furthermore, the phase differences between the expression rhythms of these genes in the grafted SCN and the locomotor activity rhythms of the transplanted animals were found to be very similar to those in intact animals. Moreover, in the liver, kidney and skeletal muscles of the transplanted animals, the phase angles between the circadian rhythm of the grafted SCN and that of the peripheral tissues were maintained as in intact animals. However, in the SCN‐grafted animals, the amplitudes of the mPer1 and mPer2 rhythms were attenuated in the peripheral tissues. Our current findings therefore indicate that a transplanted SCN has the capacity to generate a dynamic intrinsic circadian oscillation, and can also lock the normal phase angles among the SCN, locomotor activity and peripheral oscillators in a similar manner as in intact control animals.
Ovarian and oviductal morphology of a brood parasitic bird,Molothrus bonariensis(Passeriformes, Icteridae)
Authors: Rueda‐Cediel Pamela , Kattan Gustavo , Ramírez‐Pinilla Martha Patricia 
Published: October 2007

AbstractBrood parasitic birds such as cowbirds (Molothrusspp., Icteridae) lay their eggs in the nests of other species, abandoning them to be incubated and raised by the hosts. Lack of investment in parental care results in high annual fecundities of female parasitic birds. Brood parasites lay eggs in series or clutches, separated by gaps or non‐laying intervals of a few days, but they may continuously lay for prolonged periods. In tropical latitudes, the fecundity of female shiny cowbirds (Molothrus bonariensis) has been estimated to be 120 eggs per year in a six‐month breeding season, a fecundity that is paralleled only by domestic fowl. However, no detailed morphological descriptions of the reproductive tracts of brood parasites are available. We studied the reproductive tract of female shiny cowbirds in northeastern Colombia, searching for morphological features that might be related to this high fecundity. The reproductive tracts of female shiny cowbird showed no departures from the standard morphology or follicular dynamics known for birds with different postural patterns and fecundities, suggesting that high fecundity in cowbirds does not require a specialized reproductive tract. Instead, explanations must be sought at physiological levels.
A General Multi‐step Algorithm for Voxel Traversing Along a Line
Authors: Liu Y. K. , Song H. Y. , Žalik B. 
Published: October 2007

ABSTRACT Traversing voxels along a three dimensional (3D) line is one of the most fundamental algorithms for voxel‐based applications. This paper presents a new 6‐connectivity integer algorithm for this task. The proposed algorithm accepts voxels having different sizes in x, y and z directions. To explain the idea of the proposed approach, a 2D algorithm is firstly considered and then extended in 3D. This algorithm is a multi‐step as up to three voxels may be added in one iteration. It accepts both integer and floating‐point input. The new algorithm was compared to other popular voxel traversing algorithms. Counting the number of arithmetic operations showed that the proposed algorithm requires the least amount of operations per traversed voxel. A comparison of spent CPU time using either integer or floating‐point arithmetic confirms that the proposed algorithm is the most efficient. This algorithm is simple, and in compact form which also makes it attractive for hardware implementation.
A Sketch‐Based User Interface for Reconstructing Architectural Drawings
Authors: Lee Sangwon , Feng David , Grimm Cindy , Gooch Bruce 
Published: October 2007

Abstract We present a framework for interactive sketching that allows users to create three‐dimensional (3D) architectural models quickly and easily from a source drawing. The sketching process has four steps. (1) The user calibrates a viewing camera by specifying the origin and vanishing points of the drawing. (2) The user outlines surface polygons in the drawing. (3) A 3D reconstruction algorithm uses perceptual constraints to determine the closest visual fit for the polygon. (4) The user can then adjust aesthetic controls to produce several stylistic effects in the scene: a smooth transition between day and night rendering, a horizon knockout effect and entourage figures. The major advantage of our approach lies in the combination of perception‐based techniques, which allow us to minimize unnecessary interactions, and a hinging‐angle scheme, which shows significant improvement in numerical stability over previous optimization‐based 3D reconstruction algorithms. We also demonstrate how our reconstruction algorithm can be extended to work with perspective images, a feature unavailable in previous approaches.
Object‐Space Visibility Ordering for Point‐Based and Volume Rendering
Authors: Hofsetz C. , Max N. , Bastos R. 
Published: October 2007

Abstract This paper presents a method to accelerate algorithms that need a correct and complete visibility ordering of their data for rendering. The technique works by pre‐sorting primitives in object‐space using three lists (one for each axis: X, Y and Z), and then combining the lists using graphics hardware by rendering each list to a texture and merging the textures in the end. We validate our algorithm by applying it to the splatting technique using several types of rendering, including point‐based rendering and volume rendering. We also detail our hardware implementation for volume rendering using point sprites.
A Comparison of Methods for Generating Poisson Disk Distributions
Authors: Lagae Ares , Dutré Philip 
Published: October 2007

Abstract Poisson disk distributions have many applications in the field of computer graphics. Besides sampling, Poisson disk distributions are used in object distribution, non‐photorealistic rendering and procedural texturing. Over the years, a large number of methods for generating Poisson disk distributions have been proposed, making it difficult to choose the right method for a given application. In this paper, we present a detailed comparison of most techniques for generating Poisson disk distributions. The methods we study include dart throwing, relaxation dart throwing, Lloyd's relaxation, Shade's Poisson disk tiles, tiled blue noise samples, fast hierarchical importance sampling with blue noise properties, edge‐based Poisson disk tiles, template Poisson disk tiles, corner‐based Poisson disk tiles and recursive Wang tiles for real‐time blue noise. Analysing all of these methods within a single framework is one of the major contributions of this work.
Manipulating, Deforming and Animating Sampled Object Representations
Authors: Chen M. , Correa C. , Islam S. , Jones M. W. , Shen P.‐Y. , Silver D. , Walton S. J. , Willis P. J. 
Published: October 2007

Abstract A sampled object representation (SOR) defines a graphical model using data obtained from a sampling process, which takes a collection of samples at discrete positions in space in order to capture certain geometrical and physical properties of one or more objects of interest. Examples of SORs include images, videos, volume datasets and point datasets. Unlike many commonly used data representations in computer graphics, SORs lack in geometrical, topological and semantic information, which is much needed for controlling deformation and animation. Hence it poses a significant scientific and technical challenge to develop deformation and animation methods that operate upon SORs. Such methods can enable computer graphics and computer animation to benefit enormously from the advances of digital imaging technology. In this state of the art report, we survey a wide range of techniques that have been developed for manipulating, deforming and animating SORs. We consider a collection of elementary operations for manipulating SORs, which can serve as building blocks of deformation and animation techniques. We examine a collection of techniques that are designed to transform the geometry shape of deformable objects in sampled representations and pay particular attention to their deployment in surgical simulation. We review a collection of techniques for animating digital characters in SORs, focusing on recent developments in volume animation.
Anthropometry of fetal vasculature in the chorionic plate
Authors: Gordon Z. , Elad D. , Almog R. , Hazan Y. , Jaffa A. J. , Eytan O. 
Published: October 2007

AbstractNormal fetal development is dependent on adequate placental blood perfusion. The functional role of the placenta takes place mainly in the capillary system; however, ultrasound imaging of fetal blood flow is commonly performed on the umbilical artery, or on its first branches over the chorionic plate. The objective of this study was to evaluate the structural organization of the feto‐placental vasculature of the chorionic plate. Casting of the placental vasculature was performed on 15 full‐term placentas using a dental polymer mixed with colored ink. Observations of the cast models revealed that the branching architecture of the chorionic vessel is a combination of dichotomous and monopodial patterns, where the first two to three generations are always of a dichotomous nature. Analysis of the daughter‐to‐mother diameter ratios in the chorionic vessels provided a maximum in the range of 0.6–0.8 for the dichotomous branches, whereas in monopodial branches it was in the range of 0.1–0.3. Similar to previous studies, this study reveals that the vasculature architecture is mostly monopodial for the marginal cord insertion and mostly dichotomous for the central insertion. The more marginal the umbilical cord insertion is on the chorionic plate, the more monopodial branching patterns are created to compensate the dichotomous pattern deficiency to perfuse peripheral placental territories.
Nurse‐initiated defibrillation? Reality or rhetoric
Authors: Dwyer Trudy , Williams Leonie M , Mummery Kerry 
Published: October 2007

AbstractEvidence indicates that hospital nurse‐initiated defibrillation improves survival following cardiac arrest. Accordingly, hospitals are changing their policies to permit nurses to initiate defibrillation. However, if nurse‐initiated defibrillation is to be successful implemented, nurses’ beliefs about this practice need to be understood. Therefore, the aim of this study was to explore the attitudes of rural nurses towards defibrillation to assist in the development of nurse‐initiated defibrillation programmes. This cross‐sectional study examined the defibrillation beliefs of registered nurses in rural areas. A proportionally stratified sample of registered nurses (n = 436) were drawn from 51 rural acute care hospitals in Australia. Most (n = 224; 52%) of the participants were not permitted to initiate defibrillation. A one‐way between‐groups multivariate analysis of variance showed that nurses who were permitted to initiate defibrillation held stronger positive beliefs towards defibrillation than nurses not permitted (10 410) = 13·88,p < 0·001. Nurses not permitted were more concerned about the challenge of learning rhythms, incurring litigation and harming the patient or themselves. If it is accepted that defibrillation will become an essential part of all nurses’ roles, these beliefs should be explored and integrated into educational programmes as inappropriate beliefs about defibrillation may impede implementation and skills development.