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ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates. Nucleic Acids Res 2020; 48:D668-D675. [PMID: 31680137 PMCID: PMC7145539 DOI: 10.1093/nar/gkz955] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/08/2019] [Accepted: 10/11/2019] [Indexed: 12/22/2022] Open
Abstract
ANISEED (https://www.aniseed.cnrs.fr) is the main model organism database for the worldwide community of scientists working on tunicates, the vertebrate sister-group. Information provided for each species includes functionally-annotated gene and transcript models with orthology relationships within tunicates, and with echinoderms, cephalochordates and vertebrates. Beyond genes the system describes other genetic elements, including repeated elements and cis-regulatory modules. Gene expression profiles for several thousand genes are formalized in both wild-type and experimentally-manipulated conditions, using formal anatomical ontologies. These data can be explored through three complementary types of browsers, each offering a different view-point. A developmental browser summarizes the information in a gene- or territory-centric manner. Advanced genomic browsers integrate the genetic features surrounding genes or gene sets within a species. A Genomicus synteny browser explores the conservation of local gene order across deuterostome. This new release covers an extended taxonomic range of 14 species, including for the first time a non-ascidian species, the appendicularian Oikopleura dioica. Functional annotations, provided for each species, were enhanced through a combination of manual curation of gene models and the development of an improved orthology detection pipeline. Finally, gene expression profiles and anatomical territories can be explored in 4D online through the newly developed Morphonet morphogenetic browser.
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Iterative and Complex Asymmetric Divisions Control Cell Volume Differences in Ciona Notochord Tapering. Curr Biol 2019; 29:3466-3477.e4. [PMID: 31607534 DOI: 10.1016/j.cub.2019.08.056] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/29/2019] [Accepted: 08/21/2019] [Indexed: 12/12/2022]
Abstract
The notochord of the invertebrate chordate Ciona forms a tapered rod at tailbud stages consisting of only 40 cylindrical cells in a single-file column. This tapered shape involves differences in notochord cell volume along the anterior-posterior axis. Here, we quantify sibling cell volume asymmetry throughout the developing notochord and find that there are distinctive patterns of unequal cleavage in all 4 bilateral pairs of A-line primary notochord founder cells and also in the B-line-derived secondary notochord founder cells. A quantitative model confirms that the observed patterns of unequal cleavage are sufficient to explain all the anterior-posterior variation in notochord cell volume. Many examples are known of cells that divide asymmetrically to give daughter cells of different size and fate. Here, by contrast, a series of subtle but iterative and finely patterned asymmetric divisions controls the shape of an entire organ. Quantitative 3D analysis of cell shape and spindle positioning allows us to infer multiple cellular mechanisms driving these unequal cleavages, including polarized displacements of the mitotic spindle, contributions from the shape of the mother cell, and late changes occurring between anaphase and abscission that potentially involve differential cortical contractility. We infer differential use of these mechanisms between different notochord blastomeres and also between different rounds of cell division. These results demonstrate a new role for asymmetric division in directly shaping a developing organ and point toward complex underlying mechanisms.
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ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets. Nucleic Acids Res 2019; 46:D718-D725. [PMID: 29149270 PMCID: PMC5753386 DOI: 10.1093/nar/gkx1108] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/09/2017] [Indexed: 12/14/2022] Open
Abstract
ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates.
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Multiple inputs into a posterior-specific regulatory network in the Ciona notochord. Dev Biol 2018; 448:136-146. [PMID: 30287118 DOI: 10.1016/j.ydbio.2018.09.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 09/04/2018] [Accepted: 09/28/2018] [Indexed: 11/28/2022]
Abstract
The gene regulatory networks underlying Ciona notochord fate specification and differentiation have been extensively investigated, but the regulatory basis for regionalized expression within the notochord is not understood. Here we identify three notochord-expressed genes, C11.331, C12.115 and C8.891, with strongly enriched expression in the secondary notochord cells at the posterior tip of the tail. C11.331 and C12.115 share a distinctive expression pattern that is highly enriched in the secondary notochord lineage but also graded within that lineage with the strongest expression at the posterior tip. Both genes show similar responses to pharmacological perturbations of Wnt and FGF signaling, consistent with an important role for Wnt and FGF ligands expressed at the tail tip. Reporter analysis indicates that the C11.331 cis-regulatory regions are extensively distributed, with multiple non-overlapping regions conferring posterior notochord-enriched expression. Fine-scale analysis of a minimal cis-regulatory module identifies discrete positive and negative elements including a strong silencer. Truncation of the silencer region leads to increased expression in the primary notochord, indicating that C11.331 expression is influenced by putative regulators of primary versus secondary notochord fate. The minimal CRM contains predicted ETS, GATA, LMX and Myb sites, all of which lead to reduced expression in secondary notochord when mutated. These results show that the posterior-enriched notochord expression of C11.331 depends on multiple inputs, including Wnt and FGF signals from the tip of the tail, multiple notochord-specific regulators, and yet-to-be identified regulators of regional identity within the notochord.
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Reciprocal and dynamic polarization of planar cell polarity core components and myosin. eLife 2015; 4:e05361. [PMID: 25866928 PMCID: PMC4417934 DOI: 10.7554/elife.05361] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 04/10/2015] [Indexed: 12/05/2022] Open
Abstract
The Ciona notochord displays planar cell polarity (PCP), with anterior localization of Prickle (Pk) and Strabismus (Stbm). We report that a myosin is polarized anteriorly in these cells and strongly colocalizes with Stbm. Disruption of the actin/myosin machinery with cytochalasin or blebbistatin disrupts polarization of Pk and Stbm, but not of myosin complexes, suggesting a PCP-independent aspect of myosin localization. Wash out of cytochalasin restored Pk polarization, but not if done in the presence of blebbistatin, suggesting an active role for myosin in core PCP protein localization. On the other hand, in the pk mutant line, aimless, myosin polarization is disrupted in approximately one third of the cells, indicating a reciprocal action of core PCP signaling on myosin localization. Our results indicate a complex relationship between the actomyosin cytoskeleton and core PCP components in which myosin is not simply a downstream target of PCP signaling, but also required for PCP protein localization. DOI:http://dx.doi.org/10.7554/eLife.05361.001 Animal cells that form flat layers of a tissue, such as the skin or the lining of internal cavities, are often orientated in the same direction. The same is true for structures such as hairs or feathers, which are attached to the skin. This phenomenon is known as ‘planar cell polarity’ (or ‘PCP’ for short). Many different organisms use similar mechanisms to establish this kind of tissue pattern. The best-studied mechanism involves the so-called ‘core PCP pathway’. Signaling proteins in this pathway coordinate the polarity of neighboring cells. Other ‘global signaling pathways’ are thought to first ensure that tissues are correctly orientated within the embryo as a whole, and to do this, the global pathways are thought to align a network of filament-like structures within the cells in a particular direction. Once correctly orientated, these filaments—known as microtubules—have been proposed to help position the components of the core PCP pathway such that they can correctly orientate the rest of the cell. Now Newman-Smith, Kourakis et al. have identified another network of filaments within cells that interacts with components of the core PCP pathway in a sea squirt called Ciona savignyi. This organism begins life as a tadpole-like larva that has a flexible rod-shaped structure, called a ‘notochord’, running along the length of its body. The cells of the notochord become polarized as they develop. When microtubules are disrupted, their planar polarity remains unaffected. However, when another network of filaments—called the actomyosin network––is chemically disrupted, the polarity of certain core PCP components is lost. The findings of Newman-Smith, Kourakis et al. reveal that the core PCP components and the actomyosin network in this sea squirt reinforce each other's polarity. This represents an alternative to the previously described models of planar polarity in which the core PCP components are thought to drive the polarization of the actomyosin network. Whether this model extends to planar cell polarity mechanisms in other organisms, such humans and other animals with backbones, remains a question for future work. DOI:http://dx.doi.org/10.7554/eLife.05361.002
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Quantitative and in toto imaging in ascidians: working toward an image-centric systems biology of chordate morphogenesis. Genesis 2015; 53:143-59. [PMID: 25262824 PMCID: PMC4378666 DOI: 10.1002/dvg.22828] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 08/20/2014] [Accepted: 09/25/2014] [Indexed: 12/16/2022]
Abstract
Developmental biology relies heavily on microscopy to image the finely controlled cell behaviors that drive embryonic development. Most embryos are large enough that a field of view with the resolution and magnification needed to resolve single cells will not span more than a small region of the embryo. Ascidian embryos, however, are sufficiently small that they can be imaged in toto with fine subcellular detail using conventional microscopes and objectives. Unlike other model organisms with particularly small embryos, ascidians have a chordate embryonic body plan that includes a notochord, hollow dorsal neural tube, heart primordium and numerous other anatomical details conserved with the vertebrates. Here we compare the size and anatomy of ascidian embryos with those of more traditional model organisms, and relate these features to the capabilities of both conventional and exotic imaging methods. We review the emergence of Ciona and related ascidian species as model organisms for a new era of image-based developmental systems biology. We conclude by discussing some important challenges in ascidian imaging and image analysis that remain to be solved.
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Stochasticity and stereotypy in the Ciona notochord. Dev Biol 2014; 397:248-56. [PMID: 25459659 DOI: 10.1016/j.ydbio.2014.11.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 10/17/2014] [Accepted: 11/13/2014] [Indexed: 12/21/2022]
Abstract
Fate mapping with single cell resolution has typically been confined to embryos with completely stereotyped development. The lineages giving rise to the 40 cells of the Ciona notochord are invariant, but the intercalation of those cells into a single-file column is not. Here we use genetic labeling methods to fate map the Ciona notochord with both high resolution and large sample sizes. We find that the ordering of notochord cells into a single column is not random, but instead shows a distinctive signature characteristic of mediolaterally-biased intercalation. We find that patterns of cell intercalation in the notochord are somewhat stochastic but far more stereotyped than previously believed. Cell behaviors vary by lineage, with the secondary notochord lineage being much more constrained than the primary lineage. Within the primary lineage, patterns of intercalation reflect the geometry of the intercalating tissue. We identify the latest point at which notochord morphogenesis is largely stereotyped, which is shortly before the onset of mediolateral intercalation and immediately after the final cell divisions in the primary lineage. These divisions are consistently oriented along the AP axis. Our results indicate that the interplay between stereotyped and stochastic cell behaviors in morphogenesis can only be assessed by fate mapping experiments that have both cellular resolution and large sample sizes.
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A one-dimensional model of PCP signaling: polarized cell behavior in the notochord of the ascidian Ciona. Dev Biol 2014; 395:120-30. [PMID: 25173874 DOI: 10.1016/j.ydbio.2014.08.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 07/25/2014] [Accepted: 08/19/2014] [Indexed: 12/12/2022]
Abstract
Despite its importance in development and physiology the planar cell polarity (PCP) pathway remains one of the most enigmatic signaling mechanisms. The notochord of the ascidian Ciona provides a unique model for investigating the PCP pathway. Interestingly, the notochord appears to be the only embryonic structure in Ciona activating the PCP pathway. Moreover, the Ciona notochord as a single-file array of forty polarized cells is a uniquely tractable system for the study of polarization dynamics and the transmission of the PCP pathway. Here, we test models for propagation of a polarizing signal, interrogating temporal, spatial and signaling requirements. A simple cell-cell relay cascading through the entire length of the notochord is not supported; instead a more complex mechanism is revealed, with interactions influencing polarity between neighboring cells, but not distant ones. Mechanisms coordinating notochord-wide polarity remain elusive, but appear to entrain general (i.e., global) polarity even while local interactions remain important. However, this global polarizer does not appear to act as a localized, spatially-restricted determinant. Coordination of polarity along the long axis of the notochord requires the PCP pathway, a role we demonstrate is temporally distinct from this pathway's earlier role in convergent extension and intercalation. We also reveal polarity in the notochord to be dynamic: a cell's polarity state can be changed and then restored, underscoring the Ciona notochord's amenability for in vivo studies of PCP.
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Role of vaginal mesh hysteropexy for the management of advanced uterovaginal prolapse. THE JOURNAL OF REPRODUCTIVE MEDICINE 2014; 59:371-378. [PMID: 25098027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
OBJECTIVE To determine the role of vaginal mesh hysteropexy in the management of advanced genital organ prolapse as assessed by subjective and objective parameters. STUDY DESIGN Retrospective case series of 77 women followed for at least 1 year after vaginal mesh hysteropexy performed for stage III or greater uterovaginal prolapse. The primary outcome was Pelvic Organ Prolapse Quantification (POP- Q) stage < II and no subjective bothersome bulge and no further interventions for prolapse. Secondary outcomes assessed were complications such as intraoperative bleeding, injuries, and postoperative complications such as mesh exposure, mesh retraction, dyspareunia, urinary incontinence, and voiding dysfunction. RESULTS Mean follow-up was 13.7 +/- 4.1 months. Our composite success score was 85.7%. The anatomic (POP-Q) success score was 90.9%. Most failures (all but 1) were stage II with cervix as leading edge. Incidence of de novo dyspareunia was 3.7% and vaginal mesh erosion was 6.5%. Most patients 68/77 (88.3%) were discharged home voiding normally. CONCLUSION Vaginal mesh hysteropexy offers good success; however, comparative studies are required to validate its true role.
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Anterior-posterior regionalized gene expression in the Ciona notochord. Dev Dyn 2013; 243:612-620. [PMID: 24288133 DOI: 10.1002/dvdy.24101] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 11/19/2013] [Accepted: 11/20/2013] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND In the simple ascidian chordate Ciona, the signaling pathways and gene regulatory networks giving rise to initial notochord induction are largely understood and the mechanisms of notochord morphogenesis are being systematically elucidated. The notochord has generally been thought of as a non-compartmentalized or regionalized organ that is not finely patterned at the level of gene expression. Quantitative imaging methods have recently shown, however, that notochord cell size, shape, and behavior vary consistently along the anterior-posterior (AP) axis. RESULTS Here we screen candidate genes by whole mount in situ hybridization for potential AP asymmetry. We identify 4 genes that show non-uniform expression in the notochord. Ezrin/radixin/moesin (ERM) is expressed more strongly in the secondary notochord lineage than the primary. CTGF is expressed stochastically in a subset of notochord cells. A novel calmodulin-like gene (BCamL) is expressed more strongly at both the anterior and posterior tips of the notochord. A TGF-β ortholog is expressed in a gradient from posterior to anterior. The asymmetries in ERM, BCamL, and TGF-β expression are evident even before the notochord cells have intercalated into a single-file column. CONCLUSIONS We conclude that the Ciona notochord is not a homogeneous tissue but instead shows distinct patterns of regionalized gene expression.
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Accumulation of the transcription factor ABA-insensitive (ABI)4 is tightly regulated post-transcriptionally. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:3971-9. [PMID: 21504878 PMCID: PMC3134352 DOI: 10.1093/jxb/err093] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 02/21/2011] [Accepted: 03/09/2011] [Indexed: 05/17/2023]
Abstract
ABA-INSENSITIVE (ABI)4 is a transcription factor implicated in response to ABA in maturing seeds, and seedling responses to ABA, salt, and sugar. Previous studies have shown that ABI4 transcripts are high in seeds and in seedlings exposed to high concentrations of glucose and, to a lesser extent, osmotic agents and ABA, but that transcript levels are very low through most of vegetative growth. This study examined ABI4 protein accumulation indirectly, using transgenic lines expressing fusions to GFP and GUS. The GFP fusions were active, but undetectable visually or immunologically. Comparison of transcript and activity levels for GUS expression showed that inclusion of the ABI4 coding sequence reduced the ratio of activity to transcript ∼40-fold when driven by the CaMV 35S promoter, and nearly 150-fold when controlled by the ABI4 promoter. At least part of this discrepancy is due to proteasomal degradation of ABI4, resulting in a half-life of 5-6 h for the ABI4-GUS fusion. Comparison of the spatial localization of transcripts and fusion proteins indicated that the protein preferentially accumulated in roots such that transcript and protein distribution had little similarity. The components mediating targeting to the proteasome or other mechanisms of spatial restriction have not yet been identified, but several domains of ABI4 appear to contribute to its instability.
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Abstract
Seed dormancy provides a mechanism for plants to delay germination until conditions are optimal for survival of the next generation. Dormancy release is regulated by a combination of environmental and endogenous signals with both synergistic and competing effects. Molecular studies of dormancy have correlated changes in transcriptomes, proteomes, and hormone levels with dormancy states ranging from deep primary or secondary dormancy to varying degrees of release. The balance of abscisic acid (ABA):gibberellin (GA) levels and sensitivity is a major, but not the sole, regulator of dormancy status. ABA promotes dormancy induction and maintenance, whereas GA promotes progression from release through germination; environmental signals regulate this balance by modifying the expression of biosynthetic and catabolic enzymes. Mediators of environmental and hormonal response include both positive and negative regulators, many of which are feedback-regulated to enhance or attenuate the response. The net result is a slightly heterogeneous response, thereby providing more temporal options for successful germination.
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The potential role of dynamic thermal analysis in breast cancer detection. INTERNATIONAL SEMINARS IN SURGICAL ONCOLOGY : ISSO 2006; 3:8. [PMID: 16584542 PMCID: PMC1450295 DOI: 10.1186/1477-7800-3-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2006] [Accepted: 04/03/2006] [Indexed: 11/16/2022]
Abstract
BACKGROUND It is presently well accepted that the breast exhibits a circadian rhythm reflective of its physiology. There is increasing evidence that rhythms associated with malignant cells proliferation are largely non-circadian. Cancer development appears to generate its own thermal signatures and the complexity of these signatures may be a reflection of its degree of development. The limitations of mammography as a screening modality especially in young women with dense breasts necessitated the development of novel and more effective screening strategies with a high sensitivity and specificity. The aim of this prospective study was to evaluate the feasibility of dynamic thermal analysis (DTA) as a potential breast cancer screening tool. METHODS 173 women undergoing mammography as part of clinical assessment of their breast symptoms were recruited prior to having a biopsy. Thermal data from the breast surface were collected every five minutes for a period of 48 hours using eight thermal sensors placed on each breast surface [First Warning System (FWS), Lifeline Biotechnologies, Florida, USA]. Thermal data were recorded by microprocessors during the test period and analysed using specially developed statistical software. Temperature points from each contra-lateral sensor are plotted against each other to form a thermal motion picture of a lesion's physiological activity. DTA interpretations [positive (abnormal thermal signature) and negative (normal thermal signature)] were compared with mammography and final histology findings. RESULTS 118 (68%) of participating patients, were found to have breast cancer on final histology. Mammography was diagnostic of malignancy (M5) in 55 (47%), indeterminate (M3, M4) in 54 (46%) and normal/benign (M1, M2) in 9 (8%) patients. DTA data was available on 160 (92.5%) participants. Using our initial algorithm, DTA was interpreted as positive in 113 patients and negative in 47 patients. Abnormal thermal signatures were found in 76 (72%) out of 105 breast cancer patients and 37 of the 55 benign cases. Then we developed a new algorithm using multiple-layer perception and SoftMax output artificial neural networks (ANN) on a subgroup (n = 38) of recorded files. The sensitivity improved to 76% (16/21) and false positives decreased to 26% (7/27) CONCLUSION DTA of the breast is a feasible, non invasive approach that seems to be sensitive for the detection of breast cancer. However, the test has a limited specificity that can be improved further using ANN. Prospective multi-centre trials are required to validate this promising modality as an adjunct to screening mammography especially in young women with dense breasts.
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Extruded soft glass photonic crystal fiber for ultrabroad supercontinuum generation. OPTICS EXPRESS 2002; 10:1520-1525. [PMID: 19461687 DOI: 10.1364/oe.10.001520] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We report the fabrication and properties of soft glass photonic crystal fibers (PCF's) for supercontinuum generation. The fibers have zero or anomalous group velocity dispersion at wavelengths around 1550 nm, and approximately an order of magnitude higher nonlinearity than attainable in comparable silica fibers. We demonstrate the generation of an ultrabroad supercontinuum spanning at least 350 nm to 2200 nm using a 1550 nm ultrafast pump source.
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Diagnosis and treatment of leptomeningeal metastases in a patient with renal carcinoma responding to 5-fluorouracil and gemcitabine. J Urol 1999; 162:155-6. [PMID: 10379761 DOI: 10.1097/00005392-199907000-00038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Reference sera for antinuclear antibodies. II. Further definition of antibody specificities in international antinuclear antibody reference sera by immunofluorescence and western blotting. ARTHRITIS AND RHEUMATISM 1997; 40:413-8. [PMID: 9082926 DOI: 10.1002/art.1780400304] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVE To define the fine specificity of the 10 reference sera used for determination of antinuclear antibodies (ANA) and ANA subsets which are available from the Arthritis Foundation (AF) and from the Centers for Disease Control and Prevention (CDC). METHODS AF/CDC sera were assessed by experienced laboratory staff, using indirect immunofluorescence and Western blotting. RESULTS The original assignment of fluorescence patterns to 4 reference sera was confirmed, and the fluorescence intensities were determined using reference fluorescent beads. On Western blots, sera AF/CDC2 (anti-SS-B/La) and AF/CDC7 (anti-SS-A/Ro) did not detect Ro antigens, sera AF/CDC9 and AF/CDC10 appeared to be monospecific anti-Scl-70 and anti-Jo-1 sera, respectively, serum AF/CDC4 (anti-U1 small nuclear RNP) recognized the 70-kd band, and serum AF/CDC5 recognized the Sm antigen with its multiple bands. Semiquantitative analyses revealed that AF/CDC5, AF/CDC2, and AF/CDC10 were strongly reactive sera, whereas AF/CDC4 and AF/CDC9 were much weaker and should be used at lower dilutions on Western blots. CONCLUSION The AF/CDC ANA reference sera, originally described as reference reagents for indirect immunofluorescence and double immunodiffusion techniques, are also useful for Western blotting. The data presented herein further support the use of these sera for reference purposes.
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Complementation of the ionizing radiation sensitivity, DNA end binding, and V(D)J recombination defects of double-strand break repair mutants by the p86 Ku autoantigen. Proc Natl Acad Sci U S A 1995; 92:890-4. [PMID: 7846073 PMCID: PMC42726 DOI: 10.1073/pnas.92.3.890] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Two ionizing radiation-sensitive (IRs) and DNA double-strand break (DSB) mutants, sxi-3 and sxi-2, were shown to be severely deficient in a DNA end binding activity, similar to a previously described activity of the Ku autoantigen, correlating with the xrs (XRCC5) mutations. Cell fusions with xrs-6, another IRs, DSB repair-deficient cell line, defined these sxi mutants in the XRCC5 group. sxi-3 cells have low expression levels of the p86Ku mRNA. Introduction of the Ku p86 gene, but not the p70 Ku gene, complemented the IRs, DNA end binding, and variable (diversity) joining [V(D)J] recombination signal and coding junction deficiencies of sxi-3. Thus, the p86 Ku gene product is essential for DSB repair and V(D)J recombination.
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Aeromedical evacuation of ophthalmic patients. INSIGHT (AMERICAN SOCIETY OF OPHTHALMIC REGISTERED NURSES) 1994; 19:20-3. [PMID: 7963899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The ophthalmic nurse practices in a wide variety of settings. One unique area of practice is in the aeromedical environment. Here, the nurse cares for a wide variety of patients. Patients might have ocular trauma or routine ocular conditions, such as cataracts, glaucoma, or macular degeneration. The opportunity to adapt learned skills and provide the same quality of care in an aircraft environment offers additional challenges to the ophthalmic nurse because of the effects of altitude physiology and stresses of flight. However, the patients' perceptions of pain and fear, due to the possibility of surgery and total blindness, are a common thread for all patients with ocular trauma and disease. Aeromedical evacuation of ophthalmic patients provides yet another challenging and rewarding role for the ophthalmic nurse.
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Surgical experience of the ophthalmic patient. INSIGHT (AMERICAN SOCIETY OF OPHTHALMIC REGISTERED NURSES) 1993; 18:16-9, 22. [PMID: 8509677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The role of the ophthalmic nurse is vital to patient continuity of care. By acquiring a multitude of skills, the ophthalmic nurse provides excellent care, is a vital part of the ophthalmology team, and decreases the stress of surgery for the patient. Understanding other mental and physical stresses affecting the patient help make surgery a more positive experience.
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Evaluation of methods for detecting human papillomavirus deoxyribonucleotide sequences in clinical specimens. J Clin Microbiol 1988; 26:236-43. [PMID: 2830308 PMCID: PMC266259 DOI: 10.1128/jcm.26.2.236-243.1988] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Specimens from 26 condylomatous lesions, 24 invasive cancer cells, and 33 cervices, without evidence of the diseases, were tested for the presence of human papillomavirus (HPV) types 6, 11, 16, and 18 by Southern blot hybridization, in situ filter hybridization, or in situ tissue hybridization methods. A total of 89% (23 of 26) of the condylomatous lesions contained HPV DNAs, as determined by one or more of the methods. The positive rates for the detection of HPV DNA in condylomas by the different methods were 82% for Southern blot hybridization, 62% for in situ filter hybridization, and 72% for in situ tissue hybridization. Among the specimens from patients with cancer, HPV DNA was found in 83% (19 of 23) by one or more of the methods. Positive rates of 89 and 70%, respectively, were obtained for cancer lesions tested by the filter in situ and Southern blot hybridization methods; however, only 30% of those lesions were positive by the in situ tissue hybridization method. Thirteen percent of the control cervices were positive for HPV DNA by one or more of the assays. With respect to all disease categories, the methods had comparable sensitivities and specificities, except for the in situ tissue hybridization method, which revealed a specificity of 72% for condylomatous lesions and 30% for invasive cancer cells.
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Abstract
In urinary epithelia, like the turtle bladder, protons are transported by a H+ translocating ATPase located in the luminal membrane. We have recently discovered that the H+ pump is stored in small vesicles that lie underneath the luminal membrane. CO2, a major regulator of H+ transport causes these vesicles to fuse with the membrane thereby inserting more H+ pumps. We have now isolated these vesicles from the turtle bladder and from beef kidney medulla. Based on inhibitor sensitivity and substrate specificity this proton translocating ATPase is different from the mitochondrial F0-F1 ATPase, yeast plasma membrane and the gastric H+,K+-ATPase. Solubilization and reconstitution of the enzyme into liposomes shows retention of transport activity and inhibitor sensitivity.
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Diagnosis and Treatment of Immunodeficiency Diseases. Clin Mol Pathol 1981. [DOI: 10.1136/jcp.34.8.941-f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Intracytoplasmic IgM in a nonsecretory myeloma. Arch Pathol Lab Med 1981; 105:165-6. [PMID: 6894084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Abstract
Using a modification of the histologic grading system of the NSABP, we observed a trend towards higher levels of estrogen (E2R) and progesterone receptor (PR) content in well (grade I) and moderately (grade II) differentiated mammary carcinomas. This relationship between receptor content and histologic grade is enhanced by considering estrogen and progesterone receptor simultaneously. The rank correlation between the quantitative levels of E2R and PR was 0.74 among histologic grade I tumors and 0.64 among histologic grade II tumors. Among the grade III carcinomas, the majority of tumors displayed either a paucity of measurable receptor or a divergence between levels of estrogen versus progesterone receptor (r = 0.19). The use of ultrastructural evaluation of features of differentiation is discussed in the evaluation of grade III tumors and in the evaluation of specific histologic types of mammary carcinoma.
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The Alaskan health aide: a successful model of family and community health. FAMILY & COMMUNITY HEALTH 1980; 3:71-84. [PMID: 10247501 DOI: 10.1097/00003727-198008000-00008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Abstract
Echocardiography was performed in a woman with long-standing scleroderma with the CRST syndrome in whom the murmur of mitral regurgitation had been present for one year. The echocardiogram showed an irregular shaggy thickening of the anterior mitral valve leaflet. At autopsy three months later, myocardial fibrosis, small coronary artery sclerosis, and nodular thickening of the mitral valve were found. To our knowledge, anterior mitral leaflet thickening in scleroderma has not been reported previously. In this patient, it was associated with a poor prognosis.
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Echocardiographic visualisation of the interatrial baffle after Mustard's operation. BRITISH HEART JOURNAL 1979; 41:359. [PMID: 426985 PMCID: PMC482042 DOI: 10.1136/hrt.41.3.359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Differentiation of epithelial foot processes and filtration slits: sequential appearance of occluding junctions, epithelial polyanion, and slit membranes in developing glomeruli. J Transl Med 1978; 39:90-100. [PMID: 682603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The visceral glomerular epithelium of immature glomeruli from newborn rats was examined in order to determine the sequence of events that occurs during differentiation of foot processes and filtration slits. Four different stages of glomerular development were defined: vesicle, S-shaped body, developing capillary loop, and maturing stages. During the vesicle stage, the precursor cells of the glomerular and tubular epithelium are joined by occluding junctions at their apices. During the S-shaped body stage, the tubular and parietal visceral glomerular epithelium differentiate, and the occluding zonulae remain along the presumptive tubule lumen and Bowman's space, respectively. With the appearance of capillary loops the parietal and tubular junctions maintain this arrangement, but the junctions of the visceral epithelium are seen at various levels along the lateral cell margins, suggesting that they migrate along the lateral cell surfaces from apex to base. Initially, broad epithelial processes cover the entire outer aspect of the developing basement membrane. After junctional migration interdigitation of epithelial processes is seen, and the processes are joined by focal occluding junctions (maculae or fasciae). With more elaborate interdigitation, fewer and fewer intercellular spaces are closed by occluding junctions, the junctions become less and less extensive, and normal slit architecture with foot processes bridged by slit membranes predominate. Colloidal iron staining (i.e., epithelial polyanion) is first detected along the lateral epithelial cell surfaces early in the capillary loop stage and becomes concentrated along their basal cell surfaces facing the basement membrane at about the same time as interdigitation is occurring. Therefore, facing the basement membrane at about the same time as interdigitation is occurring. Therefore, sialoproteins appear on the epithelial cell surfaces prior to the development of foot processes and slits. This finding is in keeping with the assumption that epithelial polyanion may be required for development and maintenance of normal foot process and slit organization. Prior to the development of extensive interdigitation, the differentiating glomerular epithelium bears a number of striking similarities to the nephrotic epithelium: foot processes are broad, reduced in number, and often joined by focal occluding junctions; slit diaphragms are reduced in number and displaced away from the basement membrane; and ladder-like structures occur in the filtration slits. The epithelial changes seen in aminonucleoside nephrosis therefore appear to represent a "dedifferentiation" to a more primitive organization, and the events that occur early in this disease process represent a rerun inreverse of events that occur during normal glomerular development.
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A prospective analysis interstitial pneumonia and opportunistic viral infection among recipients of allogeneic bone marrow grafts. J Infect Dis 1977; 136:754-67. [PMID: 21931 DOI: 10.1093/infdis/136.6.754] [Citation(s) in RCA: 234] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A prospective study of 80 bone marrow transplant recipients with acute leukemia and aplastic anemia employed serial viral cultures, determination of complement-fixing antibody to cytomegalovirus (CMV), and study of material obtained from open lung biopsy and autopsy. There were 43 episodes of interstitial pneumonia, 28 of which were fatal. About 40% of the cases were idiopathic. CMV was the most common candidate pathogen, present in 47% of affected lungs. By a median of 53 days following transplantation, 46% of the recipients were shedding CMV from some site. This event was three times more frequent among recipients who had positive titers of antibody to CMV before transplantation than among seronegative recipients. Failure to respond werologically to CMV infection markedly increased the hazard of dying of interstitial pneumonia. Graft-vs-host disease significantly increased the incidence and lethality of interstitial pneumonia. The presence of leukemia (rather than aplastic anemia) and/or certain factors in the technique of preparation for engraftment may have been significant.
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Patient flow in pediatrics. Private practive vs the pediatric clinic. AMERICAN JOURNAL OF DISEASES OF CHILDREN (1960) 1974; 127:818-21. [PMID: 4834773 DOI: 10.1001/archpedi.1974.02110250044006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Professional Etiquette. West J Med 1842; 4:465. [DOI: 10.1136/bmj.s1-4.23.465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Letter on a Breach of Etiquette at Carlisle. West J Med 1842; 4:376-7. [DOI: 10.1136/bmj.s1-4.19.376-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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