Circular Figures Research Articles

The Wnt/β-catenin/TCF/Sp5/Zic4 Gene Network That Regulates Head Organizer Activity in Hydra Is Differentially Regulated in Epidermis and Gastrodermis.

Hydra head formation depends on an organizing center in which Wnt/β-catenin signaling, that plays an inductive role, positively regulates Sp5 and Zic4, with Sp5 limiting Wnt3/β-catenin expression and Zic4 triggering tentacle formation. Using transgenic lines in which the HySp5 promoter drives eGFP expression in either the epidermis or gastrodermis, we show that Sp5 promoter activity is differentially regulated in each epithelial layer. In intact animals, epidermal HySp5:GFP activity is strong apically and weak along the body column, while in the gastrodermis, it is maximal in the tentacle ring region and maintained at a high level along the upper body column. During apical regeneration, HySp5:GFP is activated early in the gastrodermis and later in the epidermis. Alsterpaullone treatment induces a shift in apical HySp5:GFP expression towards the body column where it forms transient circular figures in the epidermis. Upon β-catenin(RNAi), HySp5:GFP activity is down-regulated in the epidermis while bud-like structures expressing HySp5:GFP in the gastrodermis develop. Sp5(RNAi) reveals a negative Sp5 autoregulation in the epidermis, but not in the gastrodermis. These differential regulations in the epidermis and gastrodermis highlight the distinct architectures of the Wnt/β-catenin/TCF/Sp5/Zic4 network in the hypostome, tentacle base and body column of intact animals, as well as in the buds and apical and basal regenerating tips.

Huddes Specilla circularia (1656), vertaald in het Nederlands

This small treatise by Hudde discusses “circular lenses, or how one can construct all kinds of optical instruments by circular figures only, both microscopes and telescopes, so that they produce the same effect as elliptical or hyperbolic figures, or at least as close as possible”.

Circular Sedimentary Figures of Anthropic Origin in a Sediment Stability Context

ABSTRACT Garlan, T.; Mathias, X.; Brenon E.; Favretto-Cristini, N.; Deschamps, A.; Beucler, E., Guyomard P., and Morio, O., 2018. Circular sedimentary figures of anthropic origin in a sediment stability context. In: Shim, J.-S.; Chun, I., and Lim, H.S. (eds.), Proceedings from the International Coastal Symposium (ICS) 2018 (Busan, Republic of Korea). Journal of Coastal Research, Special Issue No. 85, pp. 411–415. Coconut Creek (Florida), ISSN 0749-0208. The French POSA project studies the seismic energy released by bomb and mine blasting. This project is based on seismological and acoustical measurements recording during blasting actions in order to study seismic wave propagation nucleated by controlled sources (location and explosive energy). These measurements are compared to numerical modeling of the acoustic and seismic wave propagation based on the most faithful 3D representation of the seabed sediments and underlying rocks. This project first focused on the 3D environment representation based on spe...

CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline

BackgroundThe benefit of increasing genomic sequence data to the scientific community depends on easy-to-use, scalable bioinformatics support. CloVR-Comparative combines commonly used bioinformatics tools into an intuitive, automated, and cloud-enabled analysis pipeline for comparative microbial genomics.ResultsCloVR-Comparative runs on annotated complete or draft genome sequences that are uploaded by the user or selected via a taxonomic tree-based user interface and downloaded from NCBI. CloVR-Comparative runs reference-free multiple whole-genome alignments to determine unique, shared and core coding sequences (CDSs) and single nucleotide polymorphisms (SNPs). Output includes short summary reports and detailed text-based results files, graphical visualizations (phylogenetic trees, circular figures), and a database file linked to the Sybil comparative genome browser. Data up- and download, pipeline configuration and monitoring, and access to Sybil are managed through CloVR-Comparative web interface. CloVR-Comparative and Sybil are distributed as part of the CloVR virtual appliance, which runs on local computers or the Amazon EC2 cloud. Representative datasets (e.g. 40 draft and complete Escherichia coli genomes) are processed in <36 h on a local desktop or at a cost of <$20 on EC2.ConclusionsCloVR-Comparative allows anybody with Internet access to run comparative genomics projects, while eliminating the need for on-site computational resources and expertise.

SOFIA: An R Package for Enhancing Genetic Visualization With Circos

Visualization of data from any stage of genetic and genomic research is one of the most useful approaches for detecting potential errors, ensuring accuracy and reproducibility, and presentation of the resulting data. Currently software such as Circos, ClicO FS, and RCircos, among others, provide tools for plotting a variety of genetic data types in a concise manner for data exploration and presentation. However, each of the programs has 1 or more disadvantages that limit their usability in data exploration or construction of publication quality figures, such as inflexibility in formatting and configuration, reduced image quality, lack of potential for automation, or requirements of high-level computational expertise. Therefore, we developed the R package SOFIA, which leverages the capabilities of Circos by manipulating data, preparing configuration files, and running the Perl-native Circos directly from the R environment with minimal user intervention. The advantages of integrating both R and Circos into SOFIA are numerous. R is a very powerful and user-friendly programming language widely used among the genetic and genomic research community, while Circos has proven to be a novel software for arranging genomic data to create aesthetical publication quality circular figures. Producing Circos figures in R with SOFIA is simple, requires minimal coding experience, even for complex figures that incorporate high-dimensional genetic information, and allows simultaneous analysis and visual exploration of genomic and genetic data in a single programming environment.

Os limites do lugar no ocidente: breve revisão das circunscrições topológicas

Nessa revisão é discutido como as representações topológicas - aquelas que dizem o que são os lugares e espaços - são utilizadas para fins políticos, econômicos e ecológicos, a partir dos seus discursos de verdade e legitimidade de conceitos de mundo. Foram analisadas as circunscrições do lugar no Ocidente, considerando os indivíduos e suas localizações, em formas de agregar e segregar. As representações aqui consideradas se caracterizaram por meio de figuras circulares em linhas intransitivas e sedimentadas a partir de hierarquias e estamentos. Tais divisões apontam para o que convencionou-se denominar, na modernidade, de grupos sociais, linhagens, castas, etc. Além dos aspectos circunscritivo, desagregativo e excludente do outro, há um forte caráter de afastamento negativo do meio ambiente em relação ao lugar constituído idealista e politicamente: a cidade, os espaços urbanos ideais. Há um forte caráter de afastamento negativo do meio ambiente em relação ao lugar devido a formação das cidades, consideradas como os espaços urbanos ideais.&#x0D;

Contextualiser l’imagerie préhistorique : les figures circulaires et la figure « a bandoliera » des monolithes chalcolithiques centre-alpins

Pour être interprétées, les iconographies préhistoriques doivent être réinsérées dans leur contexte archéologique et culturel. À partir d’une contextualisation à différentes échelles, le présent article propose une relecture de deux images gravées sur les statues-menhirs centre-alpines du IIIe millénaire av. n. è., à savoir les figures circulaires et «a bandoliera » . Les premières sont gravées au sommet des statues-menhirs masculines et ont jusqu’alors été interprétées comme des figurations du soleil. Cette interprétation se base sur le présupposé selon lequel un même ensemble de caractéristiques formelles, un cercle radié notamment, possède une signification universelle, c’est-à-dire indépendante de son contexte de création. Or, plusieurs indices issus à la fois de l’iconographie elle-même et du contexte archéologique des Alpes centrales permettent d’envisager une lecture différente. La première objection que nous opposons à l’interprétation couramment admise est l’extrême variabilité morphologique de ces figures circulaires qui s’accorde mal avec une représentation conventionnelle du soleil. De plus, il s’agit bien de cercles et non de disques au contraire de ce qu’une représentation du soleil requiert en divers contextes culturels. Plus encore, la comparaison de ce que nous interprétons comme des individus de pierre, à partir notamment du contexte social et idéologique qui caractérise les Alpes centrales du IIIe millénaire, et en dépit de leur relative abstraction, aux autres corpus de statues-menhirs alpines suggère une seconde objection. Ces prétendues figures solaires sont absentes des autres secteurs géographiques alpins qui connaissent pourtant un phénomène idéologique semblable aux Alpes centrales. Le sommet des statues-menhirs accueille dans ces régions des figurations de colliers. Finalement, s’agissant de corps de pierre érigés sur des sites cérémoniels où des manipulations d’ossements humains sont attestées, l’interprétation des statues-menhirs requiert de prêter attention aux données funéraires qui permettent alors d’envisager une valorisation sociale importante des cultures de l’apparence dans les groupes chalcolithiques centre-alpins. En effet, sur les sites de tradition dite Civate les ornements corporels, et plus encore les éléments de colliers, prédominent parmi les objets déposés avec les défunts et en constituent la caractéristique essentielle. La contextualisation de l’iconographie permet ainsi la constitution d’un solide faisceau de données en faveur d’une relecture de ces figures. Nous proposons de reconnaître dans les cercles gravés au sommet des statues-menhirs masculines, des éléments de la culture matérielle des groupes chalcolithiques centre-alpins, des ornements corporels, et plus précisément de colliers. La lecture d’une seconde image ambiguë, la figure «a bandoliera » , est ici également révisée. Couramment interprétée comme la représentation en plan d’un enclos mégalithique, par comparaison à des structures d’habitat issues de contextes forts éloignés des Alpes centrales, cette image est associée aux figurations qualifiées de «topographiques » . Pourtant, une telle lecture constitue une réelle erreur méthodologique dans la mesure où elle extrait l’image non-seulement de son support (un corps de pierre) mais également de son contexte culturel. Aucun enclos mégalithique n’a jamais été découvert dans les Alpes centrales. Par conséquent, et en fonction du faisceau de données établi au sujet des figures circulaires, nous proposons de reconnaître dans la figure «a bandoliera » , systématiquement gravée sur deux faces contigües, un ornement corporel propre à l’équipement masculin et porté sur l’épaule. Ainsi, l’interprétation de l’imagerie gravée et plus particulièrement de certaines figures ambiguës, se doit de prendre en considération la nature des blocs érigés et le contexte archéologique. Cette contextualisation à différentes échelles permet d’envisager de nouvelles interprétations de ces images qui apparaissent dès lors comme l’indice d’une valorisation sociale des cultures de l’apparence au sein des groupes humains chalcolithiques.

Circleator: flexible circular visualization of genome-associated data with BioPerl and SVG

Summary: Circleator is a Perl application that generates circular figures of genome-associated data. It leverages BioPerl to support standard annotation and sequence file formats and produces publication-quality SVG output. It is designed to be both flexible and easy to use. It includes a library of circular track types and predefined configuration files for common use-cases, including. (i) visualizing gene annotation and DNA sequence data from a GenBank flat file, (ii) displaying patterns of gene conservation in related microbial strains, (iii) showing Single Nucleotide Polymorphisms (SNPs) and indels relative to a reference genome and gene set and (iv) viewing RNA-Seq plots.Availability and implementation: Circleator is freely available under the Artistic License 2.0 from http://jonathancrabtree.github.io/Circleator/ and is integrated with the CloVR cloud-based sequence analysis Virtual Machine (VM), which can be downloaded from http://clovr.org or run on Amazon EC2.Contact: jcrabtree@som.umaryland.eduSupplementary information: Supplementary data are available at Bioinformatics online.

The Elizabethan Cipher in Shakespeare’s Lucrece

The Elizabethan Cipher in Shakespeare’s Lucrece Miriam Jacobson I. Ciphers and the Rape of Lucrece The prologue to Henry V (1600) contains perhaps the most famous Shakespearean use of the word cipher, the Elizabethan word for zero, but The Rape of Lucrece (1594) predates both the performance and publication of Henry V by six years and contains not one but three different uses of cipher.1 All three occur at crucial dramatic moments in the poem, when Tarquin contemplates violating Lucrece, when Lucrece imagines the rape writing itself on her body, and when Lucrece confronts her inability to have forseen the rape by examining a painted wall hanging of the Trojan war. In The Rape of Lucrece, the cipher is inextricably linked with rape. Rape—both imagined and real—impresses ciphers upon and around Tarquin’s and Lucrece’s bodies; rape publishes streams of Os in its wake.2 But Tarquin’s tyrannical attempt to silence Lucrece backfires: the knowledge of the rape surfaces repeatedly throughout the text in circular and cryptic ciphers, configuring Lucrece’s body as a succession of Os and as a secret text constantly revealing [End Page 336] itself. The many senses of cipher in the poem—to embody absence, to suggest a mercantile economy, to multiply, to signify cryptically, and to generate meaning—combine with imagery of circular figures to demonstrate that rape, like murder, “will out,” in this case profusely and productively. Moreover, by making Lucrece the author and publisher of this plethora of ciphers, the poem dissolves the tawdry Renaissance commonplace that compares a woman’s body and genitalia to a nothing or an empty O: this woman’s body is productive, generative, and will not stop until its story of violation is told.3 Unlike Ophelia’s voiceless body that represents, according to Elaine Showalter, “the cipher of female sexuality to be deciphered by feminist interpretation,” Lucrece’s body and speech decipher themselves.4 Current critical analyses of The Rape of Lucrece tend to emphasize the poem’s investment in metaphors of reading, writing, and rhetoric.5 What I will argue instead is that the poem’s use of material textuality to tell the story of rape is tied up with its interest in the polysemic figure of the cipher. The poem uses the cipher graphically and metaphorically to configure economically, write, print, and publish the story of Lucrece’s rape. The cipher’s Eastern origins have been occluded by its use in a “Roman” poem, but the very presence of this Eastern import is what allows for The Rape of Lucrece to imagine rape as a force that repeatedly writes Os onto violated bodies and texts, in effect, as a kind of violent printing press.6 Before turning [End Page 337] to The Rape of Lucrece, I will first establish the generative economics of the Elizabethan cipher through its etymology and examine in detail an early modern association of the cipher with rape in the mythological figure of Zephyrus. II. Etymology A curious letter can be found in the final pages of Champfleury, Geofroy Tory’s 1529 illustrated treatise on the graphic proportion of the Roman alphabet. Tory concludes his book with a series of ornamental typefaces and foreign alphabets. The final letter of Tory’s Arabic alphabet is not an Arabic letter at all but a quasi-circular figure (more of an oval) that Tory labels nulla in the accompanying text.7 It appears opposite, in the bottom left hand corner of figure 1. Reading this alphabet in the Arabic order as Tory advises, right to left, top to bottom, places the ovoid figure at the alphabet’s end. The letter might represent the Arabic letter hâ’, third from the end in modern Arabic. However, nulla is one of the Latin words for nothing, which suggests that the circular symbol also represents the Renaissance symbol for zero. Tory grounds his argument about the proportion of Roman lettering on the perfection of the circular letter “O,” but nowhere in his text does a comparison between the letter “O” and the number zero arise. The only evidence of zero’s presence and its resemblance to “O” lies hidden in the back...

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Freeze-fracture study of the dynamics of Toxoplasma gondii parasitophorous vacuole development

Toxoplasma gondii resides in a nonfusogenic parasitophorous vacuole (PV), which provides a safe environment for parasite survival and replication. In this work, we used the freeze-fracture technique to analyze the PV during different times of T. gondii infection in an epithelial cell line. After a short time of interaction with host cell, T. gondii PV membrane already showed a significant quantity of intramembranous particles (IMPs)—293 IMPs/μm 2. The IMP density evaluated did not vary until 6 h of interaction. As the PV area enlarged with the progression of infection, the density of these particles increased, reaching a stable quantity in the order of 1100 particles/μm 2. The IMPs were heterogeneous in size and were found distributed without any special pattern throughout the time of infection studied. The membrane lining the PV presented circular figures, which resembled vesicle fusion areas or attachments of the membranous tubular network, regions free from particles and small depressions, demonstrating to be a dynamic structure. IMPs were found in tubulo-vesicular structures present in the intravacuolar matrix, although rarely observed in elements of the intravacuolar network.

Visual search for a circular region perceived as a figure versus as a hole: Evidence of the importance of part structure

To study contour curvature polarity, we compared strictly convex regions (circular figures) with strictly concave regions (circular holes). We tested for an asymmetry between visual searches for concavities and those for convexities. We found that providing a preview of the background benefited search for concavities (holes) more than it did search for convexities (figures) and that for convex figures, nearer targets were responded to more quickly. Importantly, however, we failed to find any support for the hypothesis that concave targets are inherently more salient. We conclude that previous findings in the literature, which have been taken to indicate preferential processing of concavities, due to their increased salience, are more likely the result of an early computation of part structure based on concavities.

Effects of Phyto-Oestrogens on Veal Calf Prostate Histology

In veal calf production plant-based proteins are frequently included in milk replacer fed to the animals. Since soy products, which are mostly used, are known for their high levels of phyto-oestrogens, the effects of these feeds on the veal calf prostate were examined. Goal was to determine whether these compounds could interfere with histological screening for oestrogenic growth promoters. In a feeding experiment, four groups of veal calves fed plant-based protein-supplemented milk replacer (PBM), containing 5% soy concentrate, 5% soy isolate, 5% wheat gluten and 2% potato protein, for 4 weeks were compared to animals fed dairy-based control feed (DBM); animals treated with estradiol benzoate, diethylstilbestrol and ethinylestradiol served as positive controls. Daidzein and genistein levels measured in feed and urine showed high levels of genistein and daidzein in the soy isolate and soy concentrate supplemented feeds. Genistein and daidzein were also found in the urine of the animals that were fed these feeds. Haematoxylin-eosin-stained prostate sections of PBM-fed animals showed slight hyperplasia and some dilated tubules as compared to the DBM-fed group, but no metaplasia, which is used for screening for oestrogenic hormones. The positive controls showed extensive squamous metaplasia. Immunohistochemical staining for cytokeratin 5 (using RCK 103 monoclonal antibody) in basal cells showed a normal staining pattern of basal cells in the DBM-fed calves and extensive basal cell proliferation and squamous metaplasia in the oestrogen-treated positive control animals. PBM-fed calves showed no increase of basal cell staining but showed elongations of the basal cells in most animals, sometimes resulting in circular figures. It is concluded that the feeds examined in this study did not interfere with histological screening for oestrogens in male veal calves.

Mutations in aurora prevent centrosome separation leading to the formation of monopolar spindles

We show that female sterile mutations of aurora (aur) are allelic to mutations in the lethal complementation group ck10. This lies in a cytogenetic interval, 87A7-A9, that contains eight transcription units. A 250 by region upstream of both aur and a divergent transcription unit corresponds to the site of a specific chromatin structure (scs′) previously proposed to be a barrier to insulate enhancers of the major hsp70 gene at 87A7. Syncytial embryos derived from aur mothers display closely paired centrosomes at inappropriate mitotic stages and develop interconnected spindles in which the poles are shared. Amorphic alleles result in pupal lethality and in mitotic arrest in which condensed chromosomes are arranged on circular monopolar spindles. The size of the single centrosomal body in these circular figures suggests that loss of function of the serine-threonine protein kinase encoded by aur leads to a failure of the centrosomes to separate and form a bipolar spindle.

Visualization of DNA within mitochondria by osmium-ammine staining of mouse duodenal crypt cells.

Previous investigators have examined mitochondrial DNA (mtDNA) in the electron microscope (EM) after extraction from mitochondria and rotary shadowing. We have observed mtDNA in situ by the osmiumammine procedure for specific staining of DNA in the EM. The procedure was modified to improve the regularity of the staining and then applied to the rapidly dividing cells present in mouse duodenal crypts. In the stained sections of these cells, 25% of the mitochondria exhibited discrete reactive filaments. The filaments, whether observed directly or in stereopairs, appeared either irregular or arranged into distinct patterns, some of which were similar to those previously described after rotary shadowing of duplicating mtDNA: namely, simple and double circular figures, displacement loops and supercoiled forms. The filaments could be traced in serial sections of the same mitochondria and, therefore, were not artifacts. Moreover, their disappearance after DNase digestion demonstrated that they were composed of DNA. It is concluded that mtDNA can be visualized by the modified osmium-ammine technique and may show patterns that can be interpreted as phases in its replication.

Functional monopolar spindles caused by mutation in mgr, a cell division gene of Drosophila melanogaster.

Mutation in the gene merry-go-round (mgr) of Drosophila causes a variety of phenotypic traits in somatic and germinal tissues, such as polyploid cells, metaphasic arrest, postmeiotic cysts with 16 nuclei, and spermatids with four times the normal chromosome content. The most characteristic phenotype is the appearance of mitotic and meiotic figures where all chromosomes are arranged in a circle. Treatment with anti-mitotic drugs and the phenotype of double mutants mgr asp (asp being a mutation altering the spindle) show that these circular figures need a functional spindle for their formation. These abnormal figures are caused by monopolar spindles similar to those observed after different treatments in several organisms. All mutant traits indicate that mgr performs a function necessary for the correct behaviour of centrosomes, thus opening this organelle to genetic analysis.

Myelin figures in blood cells, lysosomes, and lipidoses.

Formation of myelin figures (MF) was demonstrated in cells of the hematopoietic system, in lysosomes from leukocytes, and in Niemann-Pick’s cells. Thioflavin-T and phosphin were used as fluorochromes in the fluorescent staining method. The MF appear as shiny green, fluorescent spots, circular figures, or as elongated chains. Under polarized light, the MF are seen as maltese crosses. Large heterogenous forms of MF were seen in neutrophilic polymorphonuclears and only small MF were observed in the other blood cells. Small and round MF were seen in concentrated lysosomes. In leukemic cells, the MF did not differ from the MF seen in normal young cells. Niemann-Pick’s cells exhibited an abundance of large MF which were not observed in Gaucher cells. It is postulated that the MF originate from phospholipids of lysosomes and cell membranes.

NON-RANDOM DISTRIBUTION OF CHROMOSOMES IN METAPHASE FIGURES FROM CULTURED HUMAN LEUCOCYTES. I. THE PERIPHERAL LOCATION OF THE Y CHROMOSOME.

Flattened metaphase figures were obtained by squashing or air-drying cells from human leucocyte cultures that had been treated with colchicine and hypotonic sodium citrate prior to fixation. In such metaphase figures the Y chromosome was at the periphery of the figure more often than chance expectation and more often than the chromosome pairs 1, 2, or 16 or the chromosome groups 13–15, 17–18, 19–20, or 21–22. The Y chromosome was further from the center of circular metaphase figures than the mean value of all the chromosomes or the chromosome pairs 1, 2, or 3 or the chromosome groups 4–5, 6–12+X, 19–20 or 21–22.

燻紙上の液滴破裂

(i) If we employ the smoked paper, to make a record of rain drops (experimentally: water or liquid drops), we will observe remarkable circular figures. (fig. 1, Pl. 3 fig. 1).(ii) S: soot, a: diameter, C: central spot (diameter: d), (Pl. 3 fig. 2), C': diameter of rain drops? v: volume, t: temperature, h: height of fall (experimentally). These values were measured. (fig. 2_??_fig. 7).(iii) Assuming the form of the drops is ellipsoid of revolution. (fig. 8). 2/A was calculated. (fig. 9).(iv) A few of these figures leaves a tortoise-shell pattern on the smoked paper. (fig. 11, Pl. 3 fig. 3, 4, 5).(v) a, c[=1/2(b-a)] and n (nos. of radial lines) were measured. (fig. 12_??_14).(vi) This tortoise-shell pattern is formed as shown ihfig. 17. (?). (vii) The figures on the it clined smoked paper (inclination=α) were studied. (fig. 18_??_23, Pl. 3 fig. 6, 7).(viii) θ (fig. 18, Pl. 3 fig. 7) is formed with the splashed small water drops.