Actomyosin-based Self-organization of cell internalization during C. elegans gastrulation

Background: Gastrulation is a key transition in embryogenesis; it requires self-organized cellular coordination, which has to be both robust to allow efficient development and plastic to provide adaptability. Despite the conservation of gastrulation as a key event in Metazoan embryogenesis, the morphogenetic mechanisms of self-organization (how global order or coordination can arise from local interactions) are poorly understood. Results: We report a modular structure of cell internalization in Caenorhabditis elegans gastrulation that reveals mechanisms of self-organization. Cells that internalize during gastrulation show apical contractile flows, which are correlated with centripetal extensions from surrounding cells. These extensions converge to seal over the internalizing cells in the form of rosettes. This process represents a distinct mode of monolayer remodeling, with gradual extrusion of the internalizing cells and simultaneous tissue closure without an actin purse-string. We further report that this self-organizing module can adapt to severe topological alterations, providing evidence of scalability and plasticity of actomyosin-based patterning. Finally, we show that globally, the surface cell layer undergoes coplanar division to thin out and spread over the internalizing mass, which resembles epiboly. Conclusions: The combination of coplanar division-based spreading and recurrent local modules for piecemeal internalization constitutes a system-level solution of gradual volume rearrangement under spatial constraint. Our results suggest that the mode of C. elegans gastrulation can be unified with the general notions of monolayer remodeling and with distinct cellular mechanisms of actomyosin-based morphogenesis

Reentrance of Bose-Einstein condensation in spinor atomic gases in magnetic field

We calculate the Bose-Einstein condensation (BEC) temperature of spin-1 atomic bosons in external magnetic field, taking into account the influence of the quadratic Zeeman effect. In case that the quadratic Zeeman coefficient is positive, the BEC temperature exhibits a nontrivial dependance on the magnetic field and a magnetic-field-induced reentrant phenomenon of BEC is observed. This phenomenon could be well understood by the competition between the linear and quadratic Zeeman effects. Reentrance of BEC in a trapped spinor Bose gas is also discussed.Comment: 6 pages, 6 figure

AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis

BACKGROUND: The invariant lineage of the nematode Caenorhabditis elegans has potential as a powerful tool for the description of mutant phenotypes and gene expression patterns. We previously described procedures for the imaging and automatic extraction of the cell lineage from C. elegans embryos. That method uses time-lapse confocal imaging of a strain expressing histone-GFP fusions and a software package, StarryNite, processes the thousands of images and produces output files that describe the location and lineage relationship of each nucleus at each time point. RESULTS: We have developed a companion software package, AceTree, which links the images and the annotations using tree representations of the lineage. This facilitates curation and editing of the lineage. AceTree also contains powerful visualization and interpretive tools, such as space filling models and tree-based expression patterning, that can be used to extract biological significance from the data. CONCLUSION: By pairing a fast lineaging program written in C with a user interface program written in Java we have produced a powerful software suite for exploring embryonic development

Optical Klystron Enhancement to SASE X-ray FELs

The optical klystron enhancement to self-amplified spontaneous emission (SASE) free electron lasers (FELs) is studied in theory and in simulations. In contrast to a seeded FEL, the optical klystron gain in a SASE FEL is not sensitive to any phase mismatch between the radiation and the microbunched electron beam. The FEL performance with the addition of four optical klystrons located at the undulator long breaks in the Linac Coherent Light Source (LCLS) shows significant improvement if the uncorrelated energy spread at the undulator entrance can be controlled to a very small level. In addition, FEL saturation at shorter x-ray wavelengths (around 1.0 \AA) within the LCLS undulator length becomes possible. We also discuss the application of the optical klystron in a compact x-ray FEL design that employs relatively low electron beam energy together with a short-period undulator.Comment: 17 pages, 8 figures, submitted to Phys. Rev. ST Accel. Beam

Impact of the Wiggler Coherent Synchrotron Radiation Impedance on the Beam Instability

Coherent Synchrotron Radiation (CSR) can play an important role by not only increasing the energy spread and emittance of a beam, but also leading to a potential instability. Previous studies of the CSR induced longitudinal instability were carried out for the CSR impedance due to dipole magnets. However, many storage rings include long wigglers where a large fraction of the synchrotron radiation is emitted. This includes high-luminosity factories such as DAPHNE, PEP-II, KEK-B, and CESR-C as well as the damping rings of future linear colliders. In this paper, the instability due to the CSR impedance from a wiggler is studied assuming a large wiggler parameter $K$. The primary consideration is a low frequency microwave-like instability, which arises near the pipe cut-off frequency. Detailed results are presented on the growth rate and threshold for the damping rings of several linear collider designs. Finally, the optimization of the relative fraction of damping due to the wiggler systems is discussed for the damping rings.Comment: 10 pages, 7 figure

Statin use and high-dose statin use after ischemic stroke in the UK: a retrospective cohort study.

Background: Trial evidence supports statin use after ischemic stroke and recent American, European and British guidelines recommend high-intensity statins for this indication. Limited data are available describing current statin use among these patients in unselected settings. We conducted a cohort study to examine secular trends and factors associated with statin use and dose following ischemic stroke. Methods: A retrospective cohort study of patients with first ischemic stroke between 2000 and 2014 was conducted using the Clinical Practice Research Datalink (CPRD). Proportions of statin users and high-intensity statin users within 2 years after stroke were estimated for each calendar year. We used Cox regression models to explore potential factors associated with statin use and Poisson regression models to calculate risk ratios for the use of a high-intensity statin. Results: A total of 80,442 patients with first stroke were analyzed. The proportion using statins within 2 years after stroke increased from 25% in 2000 to 70% in 2006 and remained at about 75% through 2014. Among post-stroke statin users, high-intensity use accounted for approximately 15% between 2004 and 2011 and then increased to almost 35% in 2014. Older patients (aged ≥75 years), younger patients (<45 years), patients with no prior statin treatment, dementia, underweight, or absence of cardiovascular factors (coronary heart disease, smoking, obesity, diabetes, hypertension, or transient ischemic attack) were less likely to use statins and less likely to receive a high-intensity statin. Conclusion: There has been an increase over time in both statin use and dose, but many patients with ischemic stroke continue to be under-treated. Clinical trials and policy interventions to improve appropriate post-stroke statin use should focus on younger and older patients, patients with no pre-stroke statin treatment, and patients without additional cardiovascular risk factors

Non-perturbative dynamics of hot non-Abelian gauge fields: beyond leading log approximation

Many aspects of high-temperature gauge theories, such as the electroweak baryon number violation rate, color conductivity, and the hard gluon damping rate, have previously been understood only at leading logarithmic order (that is, neglecting effects suppressed only by an inverse logarithm of the gauge coupling). We discuss how to systematically go beyond leading logarithmic order in the analysis of physical quantities. Specifically, we extend to next-to-leading-log order (NLLO) the simple leading-log effective theory due to Bodeker that describes non-perturbative color physics in hot non-Abelian plasmas. A suitable scaling analysis is used to show that no new operators enter the effective theory at next-to-leading-log order. However, a NLLO calculation of the color conductivity is required, and we report the resulting value. Our NLLO result for the color conductivity can be trivially combined with previous numerical work by G. Moore to yield a NLLO result for the hot electroweak baryon number violation rate.Comment: 20 pages, 1 figur

Continuity of transcriptomes among colorectal cancer subtypes based on meta-analysis

Background: Previous approaches to defining subtypes of colorectal carcinoma (CRC) and other cancers based on transcriptomes have assumed the existence of discrete subtypes. We analyze gene expression patterns of colorectal tumors from a large number of patients to test this assumption and propose an approach to identify potentially a continuum of subtypes that are present across independent studies and cohorts. Results: We examine the assumption of discrete CRC subtypes by integrating 18 published gene expression datasets and \u3e3700 patients, and contrary to previous reports, find no evidence to support the existence of discrete transcriptional subtypes. Using a meta-analysis approach to identify co-expression patterns present in multiple datasets, we identify and define robust, continuously varying subtype scores to represent CRC transcriptomes. The subtype scores are consistent with established subtypes (including microsatellite instability and previously proposed discrete transcriptome subtypes), but better represent overall transcriptional activity than do discrete subtypes. The scores are also better predictors of tumor location, stage, grade, and times of disease-free survival than discrete subtypes. Gene set enrichment analysis reveals that the subtype scores characterize T-cell function, inflammation response, and cyclin-dependent kinase regulation of DNA replication. Conclusions: We find no evidence to support discrete subtypes of the CRC transcriptome and instead propose two validated scores to better characterize a continuity of CRC transcriptomes

High Accordance in Prognosis Prediction of Colorectal Cancer across Independent Datasets by Multi-Gene Module Expression Profiles

A considerable portion of patients with colorectal cancer have a high risk of disease recurrence after surgery. These patients can be identified by analyzing the expression profiles of signature genes in tumors. But there is no consensus on which genes should be used and the performance of specific set of signature genes varies greatly with different datasets, impeding their implementation in the routine clinical application. Instead of using individual genes, here we identified functional multi-gene modules with significant expression changes between recurrent and recurrence-free tumors, used them as the signatures for predicting colorectal cancer recurrence in multiple datasets that were collected independently and profiled on different microarray platforms. The multi-gene modules we identified have a significant enrichment of known genes and biological processes relevant to cancer development, including genes from the chemokine pathway. Most strikingly, they recruited a significant enrichment of somatic mutations found in colorectal cancer. These results confirmed the functional relevance of these modules for colorectal cancer development. Further, these functional modules from different datasets overlapped significantly. Finally, we demonstrated that, leveraging above information of these modules, our module based classifier avoided arbitrary fitting the classifier function and screening the signatures using the training data, and achieved more consistency in prognosis prediction across three independent datasets, which holds even using very small training sets of tumors