164 research outputs found
Two-Dimensional Topology of the 2dF Galaxy Redshift Survey
We study the topology of the publicly available data released by the 2dFGRS.
The 2dFGRS data contains over 100,000 galaxy redshifts with a magnitude limit
of b_J=19.45 and is the largest such survey to date. The data lie over a wide
range of right ascension (75 degree strips) but only within a narrow range of
declination (10 degree and 15 degree strips). This allows measurements of the
two-dimensional genus to be made.
The NGP displays a slight meatball shift topology, whereas the SGP displays a
bubble like topology. The current SGP data also have a slightly higher genus
amplitude. In both cases, a slight excess of overdense regions are found over
underdense regions. We assess the significance of these features using mock
catalogs drawn from the Virgo Consortium's Hubble Volume LCDM z=0 simulation.
We find that differences between the NGP and SGP genus curves are only
significant at the 1 sigma level. The average genus curve of the 2dFGRS agrees
well with that extracted from the LCDM mock catalogs.
We compare the amplitude of the 2dFGRS genus curve to the amplitude of a
Gaussian random field with the same power spectrum as the 2dFGRS and find,
contradictory to results for the 3D genus of other samples, that the amplitude
of the GRF genus curve is slightly lower than that of the 2dFGRS. This could be
due to a a feature in the current data set or the 2D genus may not be as
sensitive as the 3D genus to non-linear clustering due to the averaging over
the thickness of the slice in 2D. (Abridged)Comment: Submitted to ApJ A version with Figure 1 in higher resolution can be
obtained from http://www.physics.drexel.edu/~hoyle
Abrogation of Stem Loop Binding Protein (Slbp) function leads to a failure of cells to transition from proliferation to differentiation, retinal coloboma and midline axon guidance deficits
Through forward genetic screening for mutations affecting visual system development, we identified prominent coloboma and cell-autonomous retinal neuron differentiation, lamination and retinal axon projection defects in eisspalte (ele) mutant zebrafish. Additional axonal deficits were present, most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp, which encodes a conserved RNA stem-loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when, and locations where, post-mitotic cells have differentiated in wild-type siblings. Indeed, RNAseq analysis showed down-regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated, for instance, in axon guidance, that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise, or promote transitions in, cell state and require the correct function of Slbp-dependent histone and chromatin regulatory genes
A Three-Dimensional Atlas of the Honeybee Neck
Three-dimensional digital atlases are rapidly becoming indispensible in modern biology. We used serial sectioning combined with manual registration and segmentation of images to develop a comprehensive and detailed three-dimensional atlas of the honeybee head-neck system. This interactive atlas includes skeletal structures of the head and prothorax, the neck musculature, and the nervous system. The scope and resolution of the model exceeds atlases previously developed on similar sized animals, and the interactive nature of the model provides a far more accessible means of interpreting and comprehending insect anatomy and neuroanatomy
Can the Universe Create Itself?
The question of first-cause has troubled philosophers and cosmologists alike.
Now that it is apparent that our universe began in a Big Bang explosion, the
question of what happened before the Big Bang arises. Inflation seems like a
very promising answer, but as Borde and Vilenkin have shown, the inflationary
state preceding the Big Bang must have had a beginning also. Ultimately, the
difficult question seems to be how to make something out of nothing. This paper
explores the idea that this is the wrong question --- that that is not how the
Universe got here. Instead, we explore the idea of whether there is anything in
the laws of physics that would prevent the Universe from creating itself.
Because spacetimes can be curved and multiply connected, general relativity
allows for the possibility of closed timelike curves (CTCs). Thus, tracing
backwards in time through the original inflationary state we may eventually
encounter a region of CTCs giving no first-cause. This region of CTCs, may well
be over by now (being bounded toward the future by a Cauchy horizon). We
illustrate that such models --- with CTCs --- are not necessarily inconsistent
by demonstrating self-consistent vacuums for Misner space and a multiply
connected de Sitter space in which the renormalized energy-momentum tensor does
not diverge as one approaches the Cauchy horizon and solves Einstein's
equations. We show such a Universe can be classically stable and
self-consistent if and only if the potentials are retarded, giving a natural
explanation of the arrow of time. Some specific scenarios (out of many possible
ones) for this type of model are described. For example: an inflationary
universe gives rise to baby universes, one of which turns out to be itself.
Interestingly, the laws of physics may allow the Universe to be its own mother.Comment: 48 pages, 8 figure
Origin and evolution of the light nuclides
After a short historical (and highly subjective) introduction to the field, I
discuss our current understanding of the origin and evolution of the light
nuclides D, He-3, He-4, Li-6, Li-7, Be-9, B-10 and B-11. Despite considerable
observational and theoretical progress, important uncertainties still persist
for each and every one of those nuclides. The present-day abundance of D in the
local interstellar medium is currently uncertain, making it difficult to infer
the recent chemical evolution of the solar neighborhood. To account for the
observed quasi-constancy of He-3 abundance from the Big Bang to our days, the
stellar production of that nuclide must be negligible; however, the scarce
observations of its abundance in planetary nebulae seem to contradict this
idea. The observed Be and B evolution as primaries suggests that the source
composition of cosmic rays has remained quasi-constant since the early days of
the Galaxy, a suggestion with far reaching implications for the origin of
cosmic rays; however, the main idea proposed to account for that constancy,
namely that superbubbles are at the source of cosmic rays, encounters some
serious difficulties. The best explanation for the mismatch between primordial
Li and the observed "Spite-plateau" in halo stars appears to be depletion of Li
in stellar envelopes, by some yet poorly understood mechanism. But this
explanation impacts on the level of the recently discovered early ``Li-6
plateau'', which (if confirmed), seriously challenges current ideas of cosmic
ray nucleosynthesis.Comment: 18 pages, 9 figs. Invited Review in "Symposium on the Composition of
Matter", honoring Johannes Geiss on the occasion of his 80th birthday
(Grindelwald, Switzerland, Sept. 2006), to be published in Space Science
Series of ISS
Abrogation of Stem Loop Binding Protein (Slbp) function leads to a failure of cells to transition from proliferation to differentiation, retinal coloboma and midline axon guidance deficits
Through forward genetic screening for mutations affecting visual system development, we identified prominent coloboma and cell-autonomous retinal neuron differentiation, lamination and retinal axon projection defects in eisspalte (ele) mutant zebrafish. Additional axonal deficits were present, most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp, which encodes a conserved RNA stem-loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when, and locations where, post-mitotic cells have differentiated in wild-type siblings. Indeed, RNAseq analysis showed down-regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated, for instance, in axon guidance, that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise, or promote transitions in, cell state and require the correct function of Slbp-dependent histone and chromatin regulatory genes
Gravitating discs around black holes
Fluid discs and tori around black holes are discussed within different
approaches and with the emphasis on the role of disc gravity. First reviewed
are the prospects of investigating the gravitational field of a black
hole--disc system by analytical solutions of stationary, axially symmetric
Einstein's equations. Then, more detailed considerations are focused to middle
and outer parts of extended disc-like configurations where relativistic effects
are small and the Newtonian description is adequate.
Within general relativity, only a static case has been analysed in detail.
Results are often very inspiring, however, simplifying assumptions must be
imposed: ad hoc profiles of the disc density are commonly assumed and the
effects of frame-dragging and completely lacking. Astrophysical discs (e.g.
accretion discs in active galactic nuclei) typically extend far beyond the
relativistic domain and are fairly diluted. However, self-gravity is still
essential for their structure and evolution, as well as for their radiation
emission and the impact on the environment around. For example, a nuclear star
cluster in a galactic centre may bear various imprints of mutual star--disc
interactions, which can be recognised in observational properties, such as the
relation between the central mass and stellar velocity dispersion.Comment: Accepted for publication in CQG; high-resolution figures will be
available from http://www.iop.org/EJ/journal/CQ
Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context
Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts
Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas
This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing
molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin
Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas
Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN
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